{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2016:G4TPCGF7VAAIU3ZNB5NPIAT763","short_pith_number":"pith:G4TPCGF7","canonical_record":{"source":{"id":"1609.00959","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2016-09-04T17:03:06Z","cross_cats_sorted":[],"title_canon_sha256":"ba38a37e85901db1ea3b8142c52e3811a5bbc22659fbd577d11658265282875e","abstract_canon_sha256":"3017140c5d0079764ac5f7ea3bede70078c241f6a56f18947850cb3c873e7313"},"schema_version":"1.0"},"canonical_sha256":"3726f118bfa8008a6f2d0f5af4027ff6d0e055c7de2b908c760474b8f57e1459","source":{"kind":"arxiv","id":"1609.00959","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1609.00959","created_at":"2026-05-18T01:06:19Z"},{"alias_kind":"arxiv_version","alias_value":"1609.00959v1","created_at":"2026-05-18T01:06:19Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1609.00959","created_at":"2026-05-18T01:06:19Z"},{"alias_kind":"pith_short_12","alias_value":"G4TPCGF7VAAI","created_at":"2026-05-18T12:30:15Z"},{"alias_kind":"pith_short_16","alias_value":"G4TPCGF7VAAIU3ZN","created_at":"2026-05-18T12:30:15Z"},{"alias_kind":"pith_short_8","alias_value":"G4TPCGF7","created_at":"2026-05-18T12:30:15Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2016:G4TPCGF7VAAIU3ZNB5NPIAT763","target":"record","payload":{"canonical_record":{"source":{"id":"1609.00959","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2016-09-04T17:03:06Z","cross_cats_sorted":[],"title_canon_sha256":"ba38a37e85901db1ea3b8142c52e3811a5bbc22659fbd577d11658265282875e","abstract_canon_sha256":"3017140c5d0079764ac5f7ea3bede70078c241f6a56f18947850cb3c873e7313"},"schema_version":"1.0"},"canonical_sha256":"3726f118bfa8008a6f2d0f5af4027ff6d0e055c7de2b908c760474b8f57e1459","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T01:06:19.478860Z","signature_b64":"l4lwNpNmueRxdbaUXBpwRdWKfdGN0bc6HXT3uqQBy3S3dm2Ib7o4qFxIPL6jx0ZRjr2dEQC4HVou0ReGLf+vDQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"3726f118bfa8008a6f2d0f5af4027ff6d0e055c7de2b908c760474b8f57e1459","last_reissued_at":"2026-05-18T01:06:19.478175Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T01:06:19.478175Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1609.00959","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T01:06:19Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5LWxUasR9MnyCYWKxjil+EiOgm2A+r5b22dDQehv1t6qHOReyLiQY2xzCjaiLOLDiMnnIQ/5wjLvkM+I7RTCBQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-31T10:18:40.266606Z"},"content_sha256":"6ad5e00060f1b6bdd0e8aa36ad64dc93c22a6aa0371311565e2bacd3cb436ecc","schema_version":"1.0","event_id":"sha256:6ad5e00060f1b6bdd0e8aa36ad64dc93c22a6aa0371311565e2bacd3cb436ecc"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2016:G4TPCGF7VAAIU3ZNB5NPIAT763","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Ciaran Evans, Daniel Stoebel, Johanna Hardin","submitted_at":"2016-09-04T17:03:06Z","abstract_excerpt":"RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct comparison of expression measures. Errors in normalization can have a significant impact on downstream analysis, such as inflated false positives in differential expression analysis. An under-emphasized feature of normalization is the assumptions upon which the methods rely and how the validity of these assumptions can have a substantial impact on the performanc"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1609.00959","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T01:06:19Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Kg4+hv6LSCKWAAGGBFW9TtBMFRcm6skmjRgQsUV7V15Srmqz9crTWe0Toez9+3WVRdiYmJ4KZHCFn5HBVnFcDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-31T10:18:40.266953Z"},"content_sha256":"e3f4ea49ee091ff0a6c9e0f47620b61d7cb7989d016f82a5001767df841ffb48","schema_version":"1.0","event_id":"sha256:e3f4ea49ee091ff0a6c9e0f47620b61d7cb7989d016f82a5001767df841ffb48"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/G4TPCGF7VAAIU3ZNB5NPIAT763/bundle.json","state_url":"https://pith.science/pith/G4TPCGF7VAAIU3ZNB5NPIAT763/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/G4TPCGF7VAAIU3ZNB5NPIAT763/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-05-31T10:18:40Z","links":{"resolver":"https://pith.science/pith/G4TPCGF7VAAIU3ZNB5NPIAT763","bundle":"https://pith.science/pith/G4TPCGF7VAAIU3ZNB5NPIAT763/bundle.json","state":"https://pith.science/pith/G4TPCGF7VAAIU3ZNB5NPIAT763/state.json","well_known_bundle":"https://pith.science/.well-known/pith/G4TPCGF7VAAIU3ZNB5NPIAT763/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2016:G4TPCGF7VAAIU3ZNB5NPIAT763","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"3017140c5d0079764ac5f7ea3bede70078c241f6a56f18947850cb3c873e7313","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2016-09-04T17:03:06Z","title_canon_sha256":"ba38a37e85901db1ea3b8142c52e3811a5bbc22659fbd577d11658265282875e"},"schema_version":"1.0","source":{"id":"1609.00959","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1609.00959","created_at":"2026-05-18T01:06:19Z"},{"alias_kind":"arxiv_version","alias_value":"1609.00959v1","created_at":"2026-05-18T01:06:19Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1609.00959","created_at":"2026-05-18T01:06:19Z"},{"alias_kind":"pith_short_12","alias_value":"G4TPCGF7VAAI","created_at":"2026-05-18T12:30:15Z"},{"alias_kind":"pith_short_16","alias_value":"G4TPCGF7VAAIU3ZN","created_at":"2026-05-18T12:30:15Z"},{"alias_kind":"pith_short_8","alias_value":"G4TPCGF7","created_at":"2026-05-18T12:30:15Z"}],"graph_snapshots":[{"event_id":"sha256:e3f4ea49ee091ff0a6c9e0f47620b61d7cb7989d016f82a5001767df841ffb48","target":"graph","created_at":"2026-05-18T01:06:19Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"paper":{"abstract_excerpt":"RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct comparison of expression measures. Errors in normalization can have a significant impact on downstream analysis, such as inflated false positives in differential expression analysis. An under-emphasized feature of normalization is the assumptions upon which the methods rely and how the validity of these assumptions can have a substantial impact on the performanc","authors_text":"Ciaran Evans, Daniel Stoebel, Johanna Hardin","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2016-09-04T17:03:06Z","title":"Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1609.00959","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:6ad5e00060f1b6bdd0e8aa36ad64dc93c22a6aa0371311565e2bacd3cb436ecc","target":"record","created_at":"2026-05-18T01:06:19Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"3017140c5d0079764ac5f7ea3bede70078c241f6a56f18947850cb3c873e7313","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2016-09-04T17:03:06Z","title_canon_sha256":"ba38a37e85901db1ea3b8142c52e3811a5bbc22659fbd577d11658265282875e"},"schema_version":"1.0","source":{"id":"1609.00959","kind":"arxiv","version":1}},"canonical_sha256":"3726f118bfa8008a6f2d0f5af4027ff6d0e055c7de2b908c760474b8f57e1459","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"3726f118bfa8008a6f2d0f5af4027ff6d0e055c7de2b908c760474b8f57e1459","first_computed_at":"2026-05-18T01:06:19.478175Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T01:06:19.478175Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"l4lwNpNmueRxdbaUXBpwRdWKfdGN0bc6HXT3uqQBy3S3dm2Ib7o4qFxIPL6jx0ZRjr2dEQC4HVou0ReGLf+vDQ==","signature_status":"signed_v1","signed_at":"2026-05-18T01:06:19.478860Z","signed_message":"canonical_sha256_bytes"},"source_id":"1609.00959","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:6ad5e00060f1b6bdd0e8aa36ad64dc93c22a6aa0371311565e2bacd3cb436ecc","sha256:e3f4ea49ee091ff0a6c9e0f47620b61d7cb7989d016f82a5001767df841ffb48"],"state_sha256":"b1657334d9ffee2271f99c47e7ae693473515315c7eac971749be6785057d6e7"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ba1hJnHHTzQCbDTengXkmSNkVlV8fc6f04dbALnNTumVHDnUIxpPKQ6I/8HD4Rr6xu21NLyDVhR3lxTrOcbmAQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-31T10:18:40.269524Z","bundle_sha256":"2bde30d6fb6a940f1c89be7be03917a6aafd2f25abad25544fc40142844511ca"}}