title: G30-MixedSamples

description: IXTCB00003_R:FEMALE; IXTCB00045_R:FEMALE; IXTCB01379_R:FEMALE; IXTCB01352_R:FEMALE; IXTCB01356_R:FEMALE

value: IXTCB00003_R:CTRL; IXTCB00045_R:CTRL; IXTCB01379_R:RA; IXTCB01352_R:RA; IXTCB01356_R:RA

value: IXTCB00003_R:CTRL; IXTCB00045_R:CTRL; IXTCB01379_R:wk0; IXTCB01352_R:wk12; IXTCB01356_R:wk12

value: IXTCB00003_R:CTRL; IXTCB00045_R:CTRL; IXTCB01379_R:GOOD; IXTCB01352_R:NON_RESP; IXTCB01356_R:GOOD

value: IXTCB00003_R:CTRL; IXTCB00045_R:CTRL; IXTCB01379_R:Etanercept; IXTCB01352_R:Certolizumab; IXTCB01356_R:Etanercept

value: IXTCB00003_R:CTRL; IXTCB00045_R:CTRL; IXTCB01379_R:Neg; IXTCB01352_R:Pos; IXTCB01356_R:Pos

value: IXTCB00003_R:CTRL; IXTCB00045_R:CTRL; IXTCB01379_R:Pos; IXTCB01352_R:Pos; IXTCB01356_R:Pos

value: IXTCB00003_R:CTRL; IXTCB00045_R:CTRL; IXTCB01379_R:High; IXTCB01352_R:High; IXTCB01356_R:Low


title: G31-MixedSamples

status: Public on Feb 23 2024

type: SRA

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

description: IXTCB00105:FEMALE; IXTCB00195:FEMALE; IXTCB01337:FEMALE; IXTCB01347:FEMALE; IXTCB01432:FEMALE

library_source: transcriptomic

data_processing:
*library strategy: Adaptive Immune Receptor Repertoire(AIRR)-seq
Illumina paired-end reads were demultiplexed and collapsed by 8 base pairs barcode and 10 base pairs UMI tag using the default MIG size threshold set by MiGEC v1.2 software. In order to assemble the full TCR/BCR sequences, the resulting UMI-collapsed fastq files were mapped to the V, D, J and C reference sequences from the International ImMunoGeneTics (IMGT) database using the MiXCR software (v3.0.14) with the clustering parameters turned off. From the two alignment algorithms that are implemented in MiXCR software which were developed for immune repertoire data based on a seed-and-vote strategy, the default Kaligner and its own built-in reference library (repseqio v1.7) were used. Sequences that were out-of-frame or contained stop codons were filtered out from the analysis. The resulting AIRR-seq data contained sequences from the seven chains that cover the receptor sequence spanning from the FR1-IMGT to FR4-IMGT region, as well as the constant region of the receptor.
Assembly: hg19
Supplementary files format and content: AIRR-seq information is provided separately for each lymphoctye receptor chain. For each sample and replicate, a tsv file containing quantitative information at the clone level (e.g., expression counts, fraction, CDR3 sequence, gene segments, etc) is provided.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral whole blood

extract_protocol:
Peripheral whole blood from venipuncture was dispensed into PAXgene™ Blood RNA Tubes (Qiagen). Whole blood samples in PAXgene™ Blood RNA Tubes were stored at -80°C until RNA extraction. RNA was extracted from PAXgene™ Blood RNA Tubes via the PreAnalytiX PAXgene™ blood RNA kit (Qiagen) and automated using the QIAcube.
Two independent next generation sequencing libraries covering all TCR (i.e., TRA, TRB, TRD and TRG) and BCR (i.e., IGH, IGL and IGK) chains were generated from each sample using iR-RepSeq+ 7-Chain service (iRepertoire, US). This technology allows the amplification of the seven receptors chains by addressing every known source of errors in AIRR-seq analyses30. In this procedure, the first set of primer pairs for each V-J combination is used, allowing the extension with tags that, in turn, enable a second set of primers to be utilized for global amplification of all seven chains. This essentially bias-free amplification was conducted in a single assay using UMI during the reverse transcription step. The introduction of UMI to distinguish between single RNA molecules during cDNA synthesis was essential to minimize the impact of PCR duplicates and sequencing errors. All necessary reagents for amplification and purification are preloaded into the cassette. Extracted RNA (1,000 ng) with an appropriate volume of RT mix and nuclease-free water were added into the cassette, which was processed by the iR-Processor. The instrument can automatically set up and carry out all amplification and purification. Briefly, RT is performed using Qiagen OneStep RT-PCR mix (Qiagen). First-strand cDNA was selected, and remnant primers were removed by SPRIselect bead selection (Beckman Coulter) followed by the second round of binding and extension with the V-gene primer mix. After binding and extension, SPRIselect beads were used to purify the first and second strand synthesis products. Library amplification was performed with a pair of primers that are specific for communal sites engineered onto the 5’ end of the C- and V- primers used in first and second-strand synthesis. The final constructed library includes Illumina dual index sequencing adapters, a 10-nucleotide UMIs, and an 8-nucleotide internal barcode associated with the C-gene primer. Amplified libraries were multiplexed and pooled for sequencing on the Illumina NovaSeq platform with a 500-cycle kit (250 paired-end reads) at Hudson Alpha Institute for Biotechnology (Huntsville, AL, USA). The output of the immune receptor sequence covers within the first framework region through the beginning of the constant region, including the CDR3 hypervariable region

tag: mixed sample_id

tag: tissue

value: Peripheral whole blood

tag: gender

value: pooled male and female

tag: age

tag: imid

value: IXTCB00105:CTRL; IXTCB00195:CTRL; IXTCB01337:RA; IXTCB01347:RA; IXTCB01432:RA

tag: week

value: IXTCB00105:CTRL; IXTCB00195:CTRL; IXTCB01337:wk12; IXTCB01347:wk12; IXTCB01432:wk0

tag: resp

value: IXTCB00105:CTRL; IXTCB00195:CTRL; IXTCB01337:NON_RESP; IXTCB01347:MOD; IXTCB01432:MOD

tag: treatment

value: IXTCB00105:CTRL; IXTCB00195:CTRL; IXTCB01337:Golimumab; IXTCB01347:Golimumab; IXTCB01432:Certolizumab

tag: acpa

value: IXTCB00105:CTRL; IXTCB00195:CTRL; IXTCB01337:Neg; IXTCB01347:Pos; IXTCB01432:Pos

tag: rf

value: IXTCB00105:CTRL; IXTCB00195:CTRL; IXTCB01337:Pos; IXTCB01347:Pos; IXTCB01432:Pos

tag: actb

value: IXTCB00105:CTRL; IXTCB00195:CTRL; IXTCB01337:High; IXTCB01347:High; IXTCB01432:High


title: Corpus_73

city: Marburg

first: Laura

last: Koebbe

address: Baldingerstraße

country: Germany

institute: University of Marburg

data_processing:
Quality control of sequencing data was performed with FastQC v0.11.7.
For adaptor trimming bbduk from the BBMap v37.44 was used.
The read alignment against GRCh38 was performed with STAR Aligner 2.5.2b.
FeatureCounts v1.5.1 was used for quantification of gene expression using the Ensembl annotation GRCh38.89 as reference.
Further QC was performed using RSeQC.
Assembly: GRCh38
Supplementary files format and content: gastric_expression_unique_counts.csv: comma-separated file with number of unique counts per gene and sample (columns = samples, rows = genes (Ensembl Ids))

molecule: polyA RNA

source_name: Corpus

extract_protocol:
Tissue samples were mechanically homogenized with ceramic beads and a Precellys tissue homogenizer. Total RNA (and genomic DNA) was extracted using the Allprep DNA/RNA Mini Kit from Qiagen.
RNA libraries for RNA-Seq were prepared using Lexogen's QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina following manufacturer's protocol.

value: Corpus


title: SKO, female, 7w (rep 3)

city: New Haven

first: Stefan

last: Somlo

state: CT

address: 333 Cedar Street

country: USA

institute: Yale University

description:
2731FM3
ribosomal pulldown mRNA

data_processing:
Raw TRAPSeq fastq files were processed using fastp tool (version 0.20.0)
Cleaned reads were aligned using STAR (version 2.7.9)
Expression quantification for aligned reads was performed using featureCounts (version 2.0.0)
an expression threshold of >6 read counts in at least 20% of samples for each sex; genes not meeting this expression threshold were eliminated from downstream analyses
The filtered read counts matrix was normalized by the transcripts per million (TPM) method
Assembly: mouse reference genome gencode version GRCm38.p6 with vM25 gene annotation
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Mus musculus

source_name: TRAPseq, SKO, female, 7w (P49)

extract_protocol:
TRAP was performed largely by the method described by PMID: 24810037 with a few mondifications
The sequencing library was prepared using the ribosomal depletion method (KAPA RNA HyperPrep Kit with RiboErase, Roche)
sequencing was run on Illumina’s NovaSeq 6000 platform using 150 bp paired end reads with read depth 100 million reads per sample

value: Kidney

tag: genotype

value: SKO, Pkd1fl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Antrum_70

source_name: Antrum

value: Antrum


title: Corpus_74


title: Corpus_72


title: SKO, female, 7w (rep 2)

description:
2656FM3
ribosomal pulldown mRNA


title: G29-MixedSamples

description: IXTCB00003:FEMALE; IXTCB00045:FEMALE; IXTCB01379:FEMALE; IXTCB01352:FEMALE; IXTCB01356:FEMALE

value: IXTCB00003:CTRL; IXTCB00045:CTRL; IXTCB01379:RA; IXTCB01352:RA; IXTCB01356:RA

value: IXTCB00003:CTRL; IXTCB00045:CTRL; IXTCB01379:wk0; IXTCB01352:wk12; IXTCB01356:wk12

value: IXTCB00003:CTRL; IXTCB00045:CTRL; IXTCB01379:GOOD; IXTCB01352:NON_RESP; IXTCB01356:GOOD

value: IXTCB00003:CTRL; IXTCB00045:CTRL; IXTCB01379:Etanercept; IXTCB01352:Certolizumab; IXTCB01356:Etanercept

value: IXTCB00003:CTRL; IXTCB00045:CTRL; IXTCB01379:Neg; IXTCB01352:Pos; IXTCB01356:Pos

value: IXTCB00003:CTRL; IXTCB00045:CTRL; IXTCB01379:Pos; IXTCB01352:Pos; IXTCB01356:Pos

value: IXTCB00003:CTRL; IXTCB00045:CTRL; IXTCB01379:High; IXTCB01352:High; IXTCB01356:Low


title: G28-MixedSamples

description: IXTCB00234_R:FEMALE; IXTCB00204_R:MALE; IXTCB01443_R:FEMALE; IXTCB01460_R:MALE; IXTCB01461_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00234_R:CTRL; IXTCB00204_R:CTRL; IXTCB01443_R:RA; IXTCB01460_R:RA; IXTCB01461_R:RA

value: IXTCB00234_R:CTRL; IXTCB00204_R:CTRL; IXTCB01443_R:wk12; IXTCB01460_R:wk0; IXTCB01461_R:wk0

value: IXTCB00234_R:CTRL; IXTCB00204_R:CTRL; IXTCB01443_R:MOD; IXTCB01460_R:MOD; IXTCB01461_R:MOD

value: IXTCB00234_R:CTRL; IXTCB00204_R:CTRL; IXTCB01443_R:Certolizumab; IXTCB01460_R:Etanercept; IXTCB01461_R:Etanercept

value: IXTCB00234_R:CTRL; IXTCB00204_R:CTRL; IXTCB01443_R:Neg; IXTCB01460_R:Pos; IXTCB01461_R:Pos

value: IXTCB00234_R:CTRL; IXTCB00204_R:CTRL; IXTCB01443_R:Pos; IXTCB01460_R:Pos; IXTCB01461_R:Pos

value: IXTCB00234_R:CTRL; IXTCB00204_R:CTRL; IXTCB01443_R:High; IXTCB01460_R:High; IXTCB01461_R:Low


title: G27-MixedSamples

description: IXTCB00234:FEMALE; IXTCB00204:MALE; IXTCB01443:FEMALE; IXTCB01460:MALE; IXTCB01461:FEMALE

value: IXTCB00234:CTRL; IXTCB00204:CTRL; IXTCB01443:RA; IXTCB01460:RA; IXTCB01461:RA

value: IXTCB00234:CTRL; IXTCB00204:CTRL; IXTCB01443:wk12; IXTCB01460:wk0; IXTCB01461:wk0

value: IXTCB00234:CTRL; IXTCB00204:CTRL; IXTCB01443:MOD; IXTCB01460:MOD; IXTCB01461:MOD

value: IXTCB00234:CTRL; IXTCB00204:CTRL; IXTCB01443:Certolizumab; IXTCB01460:Etanercept; IXTCB01461:Etanercept

value: IXTCB00234:CTRL; IXTCB00204:CTRL; IXTCB01443:Neg; IXTCB01460:Pos; IXTCB01461:Pos

value: IXTCB00234:CTRL; IXTCB00204:CTRL; IXTCB01443:Pos; IXTCB01460:Pos; IXTCB01461:Pos

value: IXTCB00234:CTRL; IXTCB00204:CTRL; IXTCB01443:High; IXTCB01460:High; IXTCB01461:Low;


title: SKO, female, 7w (rep 1)

description:
2458FM3
ribosomal pulldown mRNA

value: Kidney

value: SKO, Pkd1fl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Antrum_67

value: Antrum


title: Antrum_68


title: G26-MixedSamples

description: IXTCB00426_R:FEMALE; IXTCB00432_R:FEMALE; IXTCB01526_R:FEMALE; IXTCB01503_R:FEMALE; IXTCB01518_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00426_R:CTRL; IXTCB00432_R:CTRL; IXTCB01526_R:RA; IXTCB01503_R:RA; IXTCB01518_R:RA

value: IXTCB00426_R:CTRL; IXTCB00432_R:CTRL; IXTCB01526_R:NON_RESP; IXTCB01503_R:MOD; IXTCB01518_R:GOOD

value: IXTCB00426_R:CTRL; IXTCB00432_R:CTRL; IXTCB01526_R:Adalimumab; IXTCB01503_R:Adalimumab; IXTCB01518_R:Etanercept

value: IXTCB00426_R:CTRL; IXTCB00432_R:CTRL; IXTCB01526_R:Pos; IXTCB01503_R:Pos; IXTCB01518_R:Pos

value: IXTCB00426_R:CTRL; IXTCB00432_R:CTRL; IXTCB01526_R:High; IXTCB01503_R:High; IXTCB01518_R:Low


title: Antrum_66


title: WT, female, 7w (rep 7)

description:
2634FM2
ribosomal pulldown mRNA

source_name: TRAPseq, WT, female, 7w (P49)

value: wild type, Pkd1fl/+; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_71

value: Corpus


title: WT, female, 7w (rep 6)

description:
2799FM2
ribosomal pulldown mRNA


title: Corpus_69


title: Corpus_70


title: G24-MixedSamples

description: IXTCB00021_R:FEMALE; IXTCB00066_R:MALE; IXTCB01359_R:FEMALE; IXTCB01399_R:FEMALE; IXTCB01341_R:FEMALE

value: IXTCB00021_R:CTRL; IXTCB00066_R:CTRL; IXTCB01359_R:RA; IXTCB01399_R:RA; IXTCB01341_R:RA

value: IXTCB00021_R:CTRL; IXTCB00066_R:CTRL; IXTCB01359_R:wk0; IXTCB01399_R:wk0; IXTCB01341_R:wk12

value: IXTCB00021_R:CTRL; IXTCB00066_R:CTRL; IXTCB01359_R:NON_RESP; IXTCB01399_R:GOOD; IXTCB01341_R:MOD

value: IXTCB00021_R:CTRL; IXTCB00066_R:CTRL; IXTCB01359_R:Certolizumab; IXTCB01399_R:Etanercept; IXTCB01341_R:Etanercept

value: IXTCB00021_R:CTRL; IXTCB00066_R:CTRL; IXTCB01359_R:Pos; IXTCB01399_R:Pos; IXTCB01341_R:Pos

value: IXTCB00021_R:CTRL; IXTCB00066_R:CTRL; IXTCB01359_R:High; IXTCB01399_R:Low; IXTCB01341_R:High


title: Antrum_65


title: Antrum_64


title: WT, female, 7w (rep 4)

description:
2776FM2
ribosomal pulldown mRNA

value: Kidney


title: Antrum_69

value: Antrum


title: Corpus_67


title: WT, female, 7w (rep 3)

description:
2733FM2
ribosomal pulldown mRNA


title: G23-MixedSamples

description: IXTCB00021:FEMALE; IXTCB00066:MALE; IXTCB01359:FEMALE; IXTCB01399:FEMALE; IXTCB01341:FEMALE

value: Peripheral whole blood

value: IXTCB00021:CTRL; IXTCB00066:CTRL; IXTCB01359:RA; IXTCB01399:RA; IXTCB01341:RA

value: IXTCB00021:CTRL; IXTCB00066:CTRL; IXTCB01359:wk0; IXTCB01399:wk0; IXTCB01341:wk12

value: IXTCB00021:CTRL; IXTCB00066:CTRL; IXTCB01359:NON_RESP; IXTCB01399:GOOD; IXTCB01341:MOD

value: IXTCB00021:CTRL; IXTCB00066:CTRL; IXTCB01359:Certolizumab; IXTCB01399:Etanercept; IXTCB01341:Etanercept

value: IXTCB00021:CTRL; IXTCB00066:CTRL; IXTCB01359:Pos; IXTCB01399:Pos; IXTCB01341:Pos

value: IXTCB00021:CTRL; IXTCB00066:CTRL; IXTCB01359:High; IXTCB01399:Low; IXTCB01341:High


title: G22-MixedSamples

description: IXTCB00141_R:MALE; IXTCB00207_R:FEMALE; IXTCB01437_R:FEMALE; IXTCB01354_R:FEMALE; IXTCB01394_R:FEMALE

value: pooled male and female

value: IXTCB00141_R:CTRL; IXTCB00207_R:CTRL; IXTCB01437_R:RA; IXTCB01354_R:RA; IXTCB01394_R:RA

value: IXTCB00141_R:CTRL; IXTCB00207_R:CTRL; IXTCB01437_R:MOD; IXTCB01354_R:MOD; IXTCB01394_R:MOD

value: IXTCB00141_R:CTRL; IXTCB00207_R:CTRL; IXTCB01437_R:Golimumab; IXTCB01354_R:Etanercept; IXTCB01394_R:Etanercept

value: IXTCB00141_R:CTRL; IXTCB00207_R:CTRL; IXTCB01437_R:Pos; IXTCB01354_R:Pos; IXTCB01394_R:Pos

value: IXTCB00141_R:CTRL; IXTCB00207_R:CTRL; IXTCB01437_R:Pos; IXTCB01354_R:Neg; IXTCB01394_R:Pos

value: IXTCB00141_R:CTRL; IXTCB00207_R:CTRL; IXTCB01437_R:High; IXTCB01354_R:High; IXTCB01394_R:High


title: Antrum_62


title: WT, female, 7w (rep 2)

description:
2657FM2
ribosomal pulldown mRNA

value: wild type, Pkd1fl/+; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_66

value: Corpus


title: G21-MixedSamples

description: IXTCB00141:MALE; IXTCB00207:FEMALE; IXTCB01437:FEMALE; IXTCB01354:FEMALE; IXTCB01394:FEMALE

value: IXTCB00141:CTRL; IXTCB00207:CTRL; IXTCB01437:RA; IXTCB01354:RA; IXTCB01394:RA

value: IXTCB00141:CTRL; IXTCB00207:CTRL; IXTCB01437:MOD; IXTCB01354:MOD; IXTCB01394:MOD

value: IXTCB00141:CTRL; IXTCB00207:CTRL; IXTCB01437:Golimumab; IXTCB01354:Etanercept; IXTCB01394:Etanercept

value: IXTCB00141:CTRL; IXTCB00207:CTRL; IXTCB01437:Pos; IXTCB01354:Pos; IXTCB01394:Pos

value: IXTCB00141:CTRL; IXTCB00207:CTRL; IXTCB01437:Pos; IXTCB01354:Neg; IXTCB01394:Pos

value: IXTCB00141:CTRL; IXTCB00207:CTRL; IXTCB01437:High; IXTCB01354:High; IXTCB01394:High


title: WT, female, 7w (rep 1)

description:
2975FM2
ribosomal pulldown mRNA

value: Kidney


title: Antrum_61

value: Antrum


title: G25-MixedSamples

description: IXTCB00426:FEMALE; IXTCB00432:FEMALE; IXTCB01526:FEMALE; IXTCB01503:FEMALE; IXTCB01518:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00426:CTRL; IXTCB00432:CTRL; IXTCB01526:RA; IXTCB01503:RA; IXTCB01518:RA

value: IXTCB00426:CTRL; IXTCB00432:CTRL; IXTCB01526:NON_RESP; IXTCB01503:MOD; IXTCB01518:GOOD

value: IXTCB00426:CTRL; IXTCB00432:CTRL; IXTCB01526:Adalimumab; IXTCB01503:Adalimumab; IXTCB01518:Etanercept

value: IXTCB00426:CTRL; IXTCB00432:CTRL; IXTCB01526:Pos; IXTCB01503:Pos; IXTCB01518:Pos

value: IXTCB00426:CTRL; IXTCB00432:CTRL; IXTCB01526:High; IXTCB01503:High; IXTCB01518:Low


title: WT, female, 7w (rep 5)

description:
3312FM2
ribosomal pulldown mRNA

value: wild type, Pkd1fl/+; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: G19-MixedSamples

description: IXTCB00132:FEMALE; IXTCB00189:FEMALE; IXTCB01339:FEMALE; IXTCB01397:FEMALE; IXTCB01380:FEMALE

value: IXTCB00132:CTRL; IXTCB00189:CTRL; IXTCB01339:RA; IXTCB01397:RA; IXTCB01380:RA

value: IXTCB00132:CTRL; IXTCB00189:CTRL; IXTCB01339:wk0; IXTCB01397:wk0; IXTCB01380:wk0

value: IXTCB00132:CTRL; IXTCB00189:CTRL; IXTCB01339:MOD; IXTCB01397:MOD; IXTCB01380:MOD

value: IXTCB00132:CTRL; IXTCB00189:CTRL; IXTCB01339:Golimumab; IXTCB01397:Etanercept; IXTCB01380:Etanercept

value: IXTCB00132:CTRL; IXTCB00189:CTRL; IXTCB01339:Pos; IXTCB01397:Pos; IXTCB01380:Pos

value: IXTCB00132:CTRL; IXTCB00189:CTRL; IXTCB01339:Pos; IXTCB01397:Neg; IXTCB01380:Pos

value: IXTCB00132:CTRL; IXTCB00189:CTRL; IXTCB01339:High; IXTCB01397:High; IXTCB01380:High


title: Corpus_68

value: Corpus


title: DKO, male, 7w (rep 9)

description:
3164MM6
ribosomal pulldown mRNA

source_name: TRAPseq, DKO, male, 7w (P49)

value: Kidney

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_64


title: G18-MixedSamples

description: IXTCB00120_R:FEMALE; IXTCB00177_R:MALE; IXTCB01350_R:FEMALE; IXTCB01439_R:FEMALE; IXTCB01373_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00120_R:CTRL; IXTCB00177_R:CTRL; IXTCB01350_R:RA; IXTCB01439_R:RA; IXTCB01373_R:RA

value: IXTCB00120_R:CTRL; IXTCB00177_R:CTRL; IXTCB01350_R:wk0; IXTCB01439_R:wk12; IXTCB01373_R:wk12

value: IXTCB00120_R:CTRL; IXTCB00177_R:CTRL; IXTCB01350_R:GOOD; IXTCB01439_R:NON_RESP; IXTCB01373_R:MOD

value: IXTCB00120_R:CTRL; IXTCB00177_R:CTRL; IXTCB01350_R:Etanercept; IXTCB01439_R:Golimumab; IXTCB01373_R:Certolizumab

value: IXTCB00120_R:CTRL; IXTCB00177_R:CTRL; IXTCB01350_R:Pos; IXTCB01439_R:Pos; IXTCB01373_R:Pos

value: IXTCB00120_R:CTRL; IXTCB00177_R:CTRL; IXTCB01350_R:Pos; IXTCB01439_R:Neg; IXTCB01373_R:Pos

value: IXTCB00120_R:CTRL; IXTCB00177_R:CTRL; IXTCB01350_R:Low; IXTCB01439_R:High; IXTCB01373_R:High


title: DKO, male, 7w (rep 8)

description:
1898MM6
ribosomal pulldown mRNA


title: Antrum_63

value: Antrum


title: DMS53 Ecub Rep 2

city: Illkirch-Graffenstaden

first: Frédéric

last: Coin

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
P2683: Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422. P2988: Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None. P3057: Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Assembly: hg38
Supplementary files format and content: xlsx files containing RPKM values for each sample, and log2(FC) and adjPvals of drug-treated samples vs DMSO controls.

extract_protocol:
P3057
The RNAs of all the samples have been extracted using the Macherey-Nagel NucleoSpin RNA Plus Kit (Ref. 740984.250) and stored at -80*
P2683 : Total RNA-Seq libraries were generated from 700 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.  P2988 : RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (Illumina, San Diego, USA), according to manufacturer's instructions with minor modifications. Following polyA selection, mRNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).  P3057 : Total RNA-Seq libraries were generated from 500 ng of total RNA. Before cDNA synthesis, cytoplasmic and mitochondrial ribosomal RNA (rRNA) were removed using a biotin-streptavidin magnetic bead-based procedure with the riboPOOL kit targeting h/m/r ribosomal rRNA (siTOOLs Biotech, Planegg/Martinsried, DE) according to manufacturer's instructions. Ribodepleted RNAs were purified using Agencourt RNAClean XP (Beckman-Coulter, Villepinte, France) and eluted in 8,5 µl ELB buffer (Illumina, San Diego, USA). Purified RNAs were then processed using Illumina TruSeq Stranded Total RNA Library Prep Gold and IDT for Illumina - TruSeq RNA UD Indexes, omitting the ribodepletion step and starting directly from the fragmentation step. RNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

tag: cell line

tag: cell type

value: SCLC

value: WT

value: Ecubectedin 10xIC50, 8h


title: Corpus_65


title: DMS53 Lurbi Rep 2

value: Lurbinectedin 10xIC50, 8h


title: Antrum_60


title: Corpus_63

value: Corpus


title: G20-MixedSamples

description: IXTCB00132_R:FEMALE; IXTCB00189_R:FEMALE; IXTCB01339_R:FEMALE; IXTCB01397_R:FEMALE; IXTCB01380_R:FEMALE

value: IXTCB00132_R:CTRL; IXTCB00189_R:CTRL; IXTCB01339_R:RA; IXTCB01397_R:RA; IXTCB01380_R:RA

value: IXTCB00132_R:CTRL; IXTCB00189_R:CTRL; IXTCB01339_R:wk0; IXTCB01397_R:wk0; IXTCB01380_R:wk0

value: IXTCB00132_R:CTRL; IXTCB00189_R:CTRL; IXTCB01339_R:MOD; IXTCB01397_R:MOD; IXTCB01380_R:MOD

value: IXTCB00132_R:CTRL; IXTCB00189_R:CTRL; IXTCB01339_R:Golimumab; IXTCB01397_R:Etanercept; IXTCB01380_R:Etanercept

value: IXTCB00132_R:CTRL; IXTCB00189_R:CTRL; IXTCB01339_R:Pos; IXTCB01397_R:Pos; IXTCB01380_R:Pos

value: IXTCB00132_R:CTRL; IXTCB00189_R:CTRL; IXTCB01339_R:Pos; IXTCB01397_R:Neg; IXTCB01380_R:Pos

value: IXTCB00132_R:CTRL; IXTCB00189_R:CTRL; IXTCB01339_R:High; IXTCB01397_R:High; IXTCB01380_R:High


title: DMS53 DMSO Rep 2

value: DMSO 8h


title: DKO, male, 7w (rep 7)

description:
3253MM6
ribosomal pulldown mRNA

value: Kidney

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: DMS53 Comp Rep 1

value: CompIA 10xIC50, 8h


title: DKO, male, 7w (rep 6)

description:
1848MM6
ribosomal pulldown mRNA


title: DMS53 Comp Rep 2


title: G16-MixedSamples

description: IXTCB00243_R:FEMALE; IXTCB00153_R:FEMALE; IXTCB01370_R:FEMALE; IXTCB01408_R:FEMALE; IXTCB01436_R:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00243_R:CTRL; IXTCB00153_R:CTRL; IXTCB01370_R:RA; IXTCB01408_R:RA; IXTCB01436_R:RA

value: IXTCB00243_R:CTRL; IXTCB00153_R:CTRL; IXTCB01370_R:GOOD; IXTCB01408_R:GOOD; IXTCB01436_R:GOOD

value: IXTCB00243_R:CTRL; IXTCB00153_R:CTRL; IXTCB01370_R:Certolizumab; IXTCB01408_R:Certolizumab; IXTCB01436_R:Etanercept

value: IXTCB00243_R:CTRL; IXTCB00153_R:CTRL; IXTCB01370_R:Neg; IXTCB01408_R:Neg; IXTCB01436_R:Pos

value: IXTCB00243_R:CTRL; IXTCB00153_R:CTRL; IXTCB01370_R:Pos; IXTCB01408_R:Pos; IXTCB01436_R:Pos

value: IXTCB00243_R:CTRL; IXTCB00153_R:CTRL; IXTCB01370_R:Low; IXTCB01408_R:Low; IXTCB01436_R:Low


title: Antrum_59

value: Antrum


title: DKO, male, 7w (rep 5)

description:
3254MM6
ribosomal pulldown mRNA


title: G17-MixedSamples

description: IXTCB00120:FEMALE; IXTCB00177:MALE; IXTCB01350:FEMALE; IXTCB01439:FEMALE; IXTCB01373:FEMALE

value: IXTCB00120:CTRL; IXTCB00177:CTRL; IXTCB01350:RA; IXTCB01439:RA; IXTCB01373:RA

value: IXTCB00120:CTRL; IXTCB00177:CTRL; IXTCB01350:wk0; IXTCB01439:wk12; IXTCB01373:wk12

value: IXTCB00120:CTRL; IXTCB00177:CTRL; IXTCB01350:GOOD; IXTCB01439:NON_RESP; IXTCB01373:MOD

value: IXTCB00120:CTRL; IXTCB00177:CTRL; IXTCB01350:Etanercept; IXTCB01439:Golimumab; IXTCB01373:Certolizumab

value: IXTCB00120:CTRL; IXTCB00177:CTRL; IXTCB01350:Pos; IXTCB01439:Pos; IXTCB01373:Pos

value: IXTCB00120:CTRL; IXTCB00177:CTRL; IXTCB01350:Pos; IXTCB01439:Neg; IXTCB01373:Pos

value: IXTCB00120:CTRL; IXTCB00177:CTRL; IXTCB01350:Low; IXTCB01439:High; IXTCB01373:High


title: DMS53 Ecub Rep 1

value: SCLC

value: WT

value: Ecubectedin 10xIC50, 8h


title: Corpus_62

value: Corpus


title: Antrum_58


title: DKO, male, 7w (rep 4)

description:
2547MM6
ribosomal pulldown mRNA

value: Kidney

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: DMS53 Lurbi Rep 1

value: Lurbinectedin 10xIC50, 8h


title: DKO, male, 7w (rep 3)

description:
2535MM6
ribosomal pulldown mRNA


title: G15-MixedSamples

description: IXTCB00243:FEMALE; IXTCB00153:FEMALE; IXTCB01370:FEMALE; IXTCB01408:FEMALE; IXTCB01436:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00243:CTRL; IXTCB00153:CTRL; IXTCB01370:RA; IXTCB01408:RA; IXTCB01436:RA

value: IXTCB00243:CTRL; IXTCB00153:CTRL; IXTCB01370:GOOD; IXTCB01408:GOOD; IXTCB01436:GOOD

value: IXTCB00243:CTRL; IXTCB00153:CTRL; IXTCB01370:Certolizumab; IXTCB01408:Certolizumab; IXTCB01436:Etanercept

value: IXTCB00243:CTRL; IXTCB00153:CTRL; IXTCB01370:Neg; IXTCB01408:Neg; IXTCB01436:Pos

value: IXTCB00243:CTRL; IXTCB00153:CTRL; IXTCB01370:Pos; IXTCB01408:Pos; IXTCB01436:Pos

value: IXTCB00243:CTRL; IXTCB00153:CTRL; IXTCB01370:Low; IXTCB01408:Low; IXTCB01436:Low


title: G14-MixedSamples

description: IXTCB00360_R:FEMALE; IXTCB00333_R:FEMALE; IXTCB01456_R:FEMALE; IXTCB01470_R:FEMALE; IXTCB01486_R:FEMALE

value: IXTCB00360_R:CTRL; IXTCB00333_R:CTRL; IXTCB01456_R:RA; IXTCB01470_R:RA; IXTCB01486_R:RA

value: IXTCB00360_R:CTRL; IXTCB00333_R:CTRL; IXTCB01456_R:wk12; IXTCB01470_R:wk0; IXTCB01486_R:wk12

value: IXTCB00360_R:CTRL; IXTCB00333_R:CTRL; IXTCB01456_R:GOOD; IXTCB01470_R:GOOD; IXTCB01486_R:MOD

value: IXTCB00360_R:CTRL; IXTCB00333_R:CTRL; IXTCB01456_R:Etanercept; IXTCB01470_R:Etanercept; IXTCB01486_R:Adalimumab

value: IXTCB00360_R:CTRL; IXTCB00333_R:CTRL; IXTCB01456_R:Pos; IXTCB01470_R:Pos; IXTCB01486_R:Pos

value: IXTCB00360_R:CTRL; IXTCB00333_R:CTRL; IXTCB01456_R:Pos; IXTCB01470_R:Pos; IXTCB01486_R:Neg

value: IXTCB00360_R:CTRL; IXTCB00333_R:CTRL; IXTCB01456_R:Low; IXTCB01470_R:High; IXTCB01486_R:High


title: Corpus_61

value: Corpus


title: G12-MixedSamples

description: IXTCB00264_R:FEMALE; IXTCB00303_R:FEMALE; IXTCB01487_R:MALE; IXTCB01489_R:FEMALE; IXTCB01455_R:MALE

value: IXTCB00264_R:CTRL; IXTCB00303_R:CTRL; IXTCB01487_R:RA; IXTCB01489_R:RA; IXTCB01455_R:RA

value: IXTCB00264_R:CTRL; IXTCB00303_R:CTRL; IXTCB01487_R:wk12; IXTCB01489_R:wk0; IXTCB01455_R:wk0

value: IXTCB00264_R:CTRL; IXTCB00303_R:CTRL; IXTCB01487_R:GOOD; IXTCB01489_R:GOOD; IXTCB01455_R:GOOD

value: IXTCB00264_R:CTRL; IXTCB00303_R:CTRL; IXTCB01487_R:Certolizumab; IXTCB01489_R:Etanercept; IXTCB01455_R:Etanercept

value: IXTCB00264_R:CTRL; IXTCB00303_R:CTRL; IXTCB01487_R:Pos; IXTCB01489_R:Pos; IXTCB01455_R:Neg

value: IXTCB00264_R:CTRL; IXTCB00303_R:CTRL; IXTCB01487_R:Pos; IXTCB01489_R:Pos; IXTCB01455_R:Pos

value: IXTCB00264_R:CTRL; IXTCB00303_R:CTRL; IXTCB01487_R:Low; IXTCB01489_R:Low; IXTCB01455_R:Low


title: DMS53 DMSO Rep 1

value: SCLC

value: WT

value: DMSO 8h


title: DKO, male, 7w (rep 2)

description:
3255MM6
ribosomal pulldown mRNA

value: Kidney

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_60


title: 501mel Comp Rep 2

extract_protocol:
P2988
The RNAs of all the samples have been extracted using the Macherey-Nagel NucleoSpin RNA Plus Kit (Ref. 740984.250) and stored at -80*
P2683 : Total RNA-Seq libraries were generated from 700 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.  P2988 : RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (Illumina, San Diego, USA), according to manufacturer's instructions with minor modifications. Following polyA selection, mRNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).  P3057 : Total RNA-Seq libraries were generated from 500 ng of total RNA. Before cDNA synthesis, cytoplasmic and mitochondrial ribosomal RNA (rRNA) were removed using a biotin-streptavidin magnetic bead-based procedure with the riboPOOL kit targeting h/m/r ribosomal rRNA (siTOOLs Biotech, Planegg/Martinsried, DE) according to manufacturer's instructions. Ribodepleted RNAs were purified using Agencourt RNAClean XP (Beckman-Coulter, Villepinte, France) and eluted in 8,5 µl ELB buffer (Illumina, San Diego, USA). Purified RNAs were then processed using Illumina TruSeq Stranded Total RNA Library Prep Gold and IDT for Illumina - TruSeq RNA UD Indexes, omitting the ribodepletion step and starting directly from the fragmentation step. RNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 13 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

value: Differentiated melanoma

value: CompIA 10xIC50, 8h


title: Corpus_59


title: DKO, male, 7w (rep 1)

description:
2639MM6
ribosomal pulldown mRNA


title: 501mel Ecub Rep 2

value: Ecubectedin 10xIC50, 8h


title: G11-MixedSamples

description: IXTCB00264:FEMALE; IXTCB00303:FEMALE; IXTCB01487:MALE; IXTCB01489:FEMALE; IXTCB01455:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00264:CTRL; IXTCB00303:CTRL; IXTCB01487:RA; IXTCB01489:RA; IXTCB01455:RA

value: IXTCB00264:CTRL; IXTCB00303:CTRL; IXTCB01487:wk12; IXTCB01489:wk0; IXTCB01455:wk0

value: IXTCB00264:CTRL; IXTCB00303:CTRL; IXTCB01487:GOOD; IXTCB01489:GOOD; IXTCB01455:GOOD

value: IXTCB00264:CTRL; IXTCB00303:CTRL; IXTCB01487:Certolizumab; IXTCB01489:Etanercept; IXTCB01455:Etanercept

value: IXTCB00264:CTRL; IXTCB00303:CTRL; IXTCB01487:Pos; IXTCB01489:Pos; IXTCB01455:Neg

value: IXTCB00264:CTRL; IXTCB00303:CTRL; IXTCB01487:Pos; IXTCB01489:Pos; IXTCB01455:Pos

value: IXTCB00264:CTRL; IXTCB00303:CTRL; IXTCB01487:Low; IXTCB01489:Low; IXTCB01455:Low


title: Antrum_57

value: Antrum


title: SKO, male, 7w (rep 7)

description:
3150MM3
ribosomal pulldown mRNA

source_name: TRAPseq, SKO, male, 7w (P49)

value: SKO, Pkd1fl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: 501mel Lurbi Rep 2

value: WT

value: Lurbinectedin 10xIC50, 8h


title: G10-MixedSamples

description: IXTCB00276_R:FEMALE; IXTCB00315_R:MALE; IXTCB01507_R:FEMALE; IXTCB01464_R:MALE; IXTCB01498_R:FEMALE

value: IXTCB00276_R:CTRL; IXTCB00315_R:CTRL; IXTCB01507_R:RA; IXTCB01464_R:RA; IXTCB01498_R:RA

value: IXTCB00276_R:CTRL; IXTCB00315_R:CTRL; IXTCB01507_R:wk0; IXTCB01464_R:wk0; IXTCB01498_R:wk12

value: IXTCB00276_R:CTRL; IXTCB00315_R:CTRL; IXTCB01507_R:NON_RESP; IXTCB01464_R:NON_RESP; IXTCB01498_R:GOOD

value: IXTCB00276_R:CTRL; IXTCB00315_R:CTRL; IXTCB01507_R:Etanercept; IXTCB01464_R:Golimumab; IXTCB01498_R:Etanercept

value: IXTCB00276_R:CTRL; IXTCB00315_R:CTRL; IXTCB01507_R:Neg; IXTCB01464_R:Pos; IXTCB01498_R:Pos

value: IXTCB00276_R:CTRL; IXTCB00315_R:CTRL; IXTCB01507_R:Low; IXTCB01464_R:Low; IXTCB01498_R:Low


title: G13-MixedSamples

description: IXTCB00360:FEMALE; IXTCB00333:FEMALE; IXTCB01456:FEMALE; IXTCB01470:FEMALE; IXTCB01486:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00360:CTRL; IXTCB00333:CTRL; IXTCB01456:RA; IXTCB01470:RA; IXTCB01486:RA

value: IXTCB00360:CTRL; IXTCB00333:CTRL; IXTCB01456:wk12; IXTCB01470:wk0; IXTCB01486:wk12

value: IXTCB00360:CTRL; IXTCB00333:CTRL; IXTCB01456:GOOD; IXTCB01470:GOOD; IXTCB01486:MOD

value: IXTCB00360:CTRL; IXTCB00333:CTRL; IXTCB01456:Etanercept; IXTCB01470:Etanercept; IXTCB01486:Adalimumab

value: IXTCB00360:CTRL; IXTCB00333:CTRL; IXTCB01456:Pos; IXTCB01470:Pos; IXTCB01486:Pos

value: IXTCB00360:CTRL; IXTCB00333:CTRL; IXTCB01456:Pos; IXTCB01470:Pos; IXTCB01486:Neg

value: IXTCB00360:CTRL; IXTCB00333:CTRL; IXTCB01456:Low; IXTCB01470:High; IXTCB01486:High


title: G9-MixedSamples

description: IXTCB00276:FEMALE; IXTCB00315:MALE; IXTCB01507:FEMALE; IXTCB01464:MALE; IXTCB01498:FEMALE

value: IXTCB00276:CTRL; IXTCB00315:CTRL; IXTCB01507:RA; IXTCB01464:RA; IXTCB01498:RA

value: IXTCB00276:CTRL; IXTCB00315:CTRL; IXTCB01507:wk0; IXTCB01464:wk0; IXTCB01498:wk12

value: IXTCB00276:CTRL; IXTCB00315:CTRL; IXTCB01507:NON_RESP; IXTCB01464:NON_RESP; IXTCB01498:GOOD

value: IXTCB00276:CTRL; IXTCB00315:CTRL; IXTCB01507:Etanercept; IXTCB01464:Golimumab; IXTCB01498:Etanercept

value: IXTCB00276:CTRL; IXTCB00315:CTRL; IXTCB01507:Neg; IXTCB01464:Pos; IXTCB01498:Pos

value: IXTCB00276:CTRL; IXTCB00315:CTRL; IXTCB01507:Low; IXTCB01464:Low; IXTCB01498:Low


title: G8-MixedSamples

description: IXTCB00438_R:FEMALE; IXTCB00456_R:MALE; IXTCB01530_R:FEMALE; IXTCB01485_R:FEMALE; IXTCB01509_R:MALE

value: IXTCB00438_R:CTRL; IXTCB00456_R:CTRL; IXTCB01530_R:RA; IXTCB01485_R:RA; IXTCB01509_R:RA

value: IXTCB00438_R:CTRL; IXTCB00456_R:CTRL; IXTCB01530_R:wk0; IXTCB01485_R:wk12; IXTCB01509_R:wk12

value: IXTCB00438_R:CTRL; IXTCB00456_R:CTRL; IXTCB01530_R:NON_RESP; IXTCB01485_R:GOOD; IXTCB01509_R:GOOD

value: IXTCB00438_R:CTRL; IXTCB00456_R:CTRL; IXTCB01530_R:Adalimumab; IXTCB01485_R:Etanercept; IXTCB01509_R:Etanercept

value: IXTCB00438_R:CTRL; IXTCB00456_R:CTRL; IXTCB01530_R:Pos; IXTCB01485_R:Pos; IXTCB01509_R:Pos

value: IXTCB00438_R:CTRL; IXTCB00456_R:CTRL; IXTCB01530_R:Pos; IXTCB01485_R:Pos; IXTCB01509_R:Neg

value: IXTCB00438_R:CTRL; IXTCB00456_R:CTRL; IXTCB01530_R:Low; IXTCB01485_R:Low; IXTCB01509_R:Low


title: Corpus_58

value: Corpus


title: 501mel Comp Rep 1

value: Differentiated melanoma

value: WT

value: CompIA 10xIC50, 8h


title: 501mel DMSO Rep 2

value: DMSO 8h


title: Corpus_57


title: Antrum_56

value: Antrum


title: SKO, male, 7w (rep 5)

description:
2412MM3
ribosomal pulldown mRNA

value: Kidney

value: SKO, Pkd1fl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: SKO, male, 7w (rep 4)

description:
2462MM3
ribosomal pulldown mRNA


title: G7-MixedSamples

description: IXTCB00438:FEMALE; IXTCB00456:MALE; IXTCB01530:FEMALE; IXTCB01485:FEMALE; IXTCB01509:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00438:CTRL; IXTCB00456:CTRL; IXTCB01530:RA; IXTCB01485:RA; IXTCB01509:RA

value: IXTCB00438:CTRL; IXTCB00456:CTRL; IXTCB01530:wk0; IXTCB01485:wk12; IXTCB01509:wk12

value: IXTCB00438:CTRL; IXTCB00456:CTRL; IXTCB01530:NON_RESP; IXTCB01485:GOOD; IXTCB01509:GOOD

value: IXTCB00438:CTRL; IXTCB00456:CTRL; IXTCB01530:Adalimumab; IXTCB01485:Etanercept; IXTCB01509:Etanercept

value: IXTCB00438:CTRL; IXTCB00456:CTRL; IXTCB01530:Pos; IXTCB01485:Pos; IXTCB01509:Pos

value: IXTCB00438:CTRL; IXTCB00456:CTRL; IXTCB01530:Pos; IXTCB01485:Pos; IXTCB01509:Neg

value: IXTCB00438:CTRL; IXTCB00456:CTRL; IXTCB01530:Low; IXTCB01485:Low; IXTCB01509:Low


title: SKO, male, 7w (rep 3)

description:
2388MM3
ribosomal pulldown mRNA


title: Antrum_55


title: 501mel Lurbi Rep 1

value: Lurbinectedin 10xIC50, 8h


title: Corpus_56

value: Corpus


title: G5-MixedSamples

description: IXTCB00411:FEMALE; IXTCB00381:FEMALE; IXTCB01453:FEMALE; IXTCB01467:FEMALE; IXTCB01466:FEMALE

value: IXTCB00411:CTRL; IXTCB00381:CTRL; IXTCB01453:RA; IXTCB01467:RA; IXTCB01466:RA

value: IXTCB00411:CTRL; IXTCB00381:CTRL; IXTCB01453:wk0; IXTCB01467:wk0; IXTCB01466:wk12

value: IXTCB00411:CTRL; IXTCB00381:CTRL; IXTCB01453:GOOD; IXTCB01467:NON_RESP; IXTCB01466:MOD

value: IXTCB00411:CTRL; IXTCB00381:CTRL; IXTCB01453:Etanercept; IXTCB01467:Adalimumab; IXTCB01466:Etanercept

value: IXTCB00411:CTRL; IXTCB00381:CTRL; IXTCB01453:Pos; IXTCB01467:Pos; IXTCB01466:Neg

value: IXTCB00411:CTRL; IXTCB00381:CTRL; IXTCB01453:Pos; IXTCB01467:Pos; IXTCB01466:Pos

value: IXTCB00411:CTRL; IXTCB00381:CTRL; IXTCB01453:High; IXTCB01467:Low; IXTCB01466:High


title: G6-MixedSamples

description: IXTCB00411_R:FEMALE; IXTCB00381_R:FEMALE; IXTCB01453_R:FEMALE; IXTCB01467_R:FEMALE; IXTCB01466_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00411_R:CTRL; IXTCB00381_R:CTRL; IXTCB01453_R:RA; IXTCB01467_R:RA; IXTCB01466_R:RA

value: IXTCB00411_R:CTRL; IXTCB00381_R:CTRL; IXTCB01453_R:wk0; IXTCB01467_R:wk0; IXTCB01466_R:wk12

value: IXTCB00411_R:CTRL; IXTCB00381_R:CTRL; IXTCB01453_R:GOOD; IXTCB01467_R:NON_RESP; IXTCB01466_R:MOD

value: IXTCB00411_R:CTRL; IXTCB00381_R:CTRL; IXTCB01453_R:Etanercept; IXTCB01467_R:Adalimumab; IXTCB01466_R:Etanercept

value: IXTCB00411_R:CTRL; IXTCB00381_R:CTRL; IXTCB01453_R:Pos; IXTCB01467_R:Pos; IXTCB01466_R:Neg

value: IXTCB00411_R:CTRL; IXTCB00381_R:CTRL; IXTCB01453_R:Pos; IXTCB01467_R:Pos; IXTCB01466_R:Pos

value: IXTCB00411_R:CTRL; IXTCB00381_R:CTRL; IXTCB01453_R:High; IXTCB01467_R:Low; IXTCB01466_R:High


title: SKO, male, 7w (rep 2)

description:
2603MM3
ribosomal pulldown mRNA

value: Kidney

value: SKO, Pkd1fl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: 501mel DMSO Rep 1

value: Differentiated melanoma

value: WT

value: DMSO 8h


title: G4-MixedSamples

description: IXTCB00450_R:FEMALE; IXTCB00417_R:FEMALE; IXTCB01433_R:MALE; IXTCB01523_R:MALE; IXTCB01529_R:FEMALE

value: IXTCB00450_R:CTRL; IXTCB00417_R:CTRL; IXTCB01433_R:RA; IXTCB01523_R:RA; IXTCB01529_R:RA

value: IXTCB00450_R:CTRL; IXTCB00417_R:CTRL; IXTCB01433_R:wk0; IXTCB01523_R:wk0; IXTCB01529_R:wk12

value: IXTCB00450_R:CTRL; IXTCB00417_R:CTRL; IXTCB01433_R:MOD; IXTCB01523_R:GOOD; IXTCB01529_R:GOOD

value: IXTCB00450_R:CTRL; IXTCB00417_R:CTRL; IXTCB01433_R:Etanercept; IXTCB01523_R:Etanercept; IXTCB01529_R:Adalimumab

value: IXTCB00450_R:CTRL; IXTCB00417_R:CTRL; IXTCB01433_R:Pos; IXTCB01523_R:Pos; IXTCB01529_R:Pos

value: IXTCB00450_R:CTRL; IXTCB00417_R:CTRL; IXTCB01433_R:Pos; IXTCB01523_R:Neg; IXTCB01529_R:Pos

value: IXTCB00450_R:CTRL; IXTCB00417_R:CTRL; IXTCB01433_R:High; IXTCB01523_R:Low; IXTCB01529_R:Low


title: Antrum_54

value: Antrum


title: SKO, male, 7w (rep 1)

description:
2765MM3
ribosomal pulldown mRNA


title: Antrum_53


title: SKO, male, 7w (rep 6)

description:
3149MM3
ribosomal pulldown mRNA


title: WT, male, 7w (rep 8)

description:
2667MM2
ribosomal pulldown mRNA

source_name: TRAPseq, WT, male, 7w (P49)

value: wild type, Pkd1fl/+; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: MM029 ATAC Rep 2

description: MM029 ATAC pooled.bw

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
The adapter sequence: CTGTCTCTTATA has been trimmed with cutadapt 1.18 with option: -a CTGTCTCTTATA -A CTGTCTCTTATA -m 5 -e 0.1 and Bowtie2 parameter: -N 1 -X 1000, was used for mapping to the human genome. After the mapping, reads overlapping with ENCODE blacklist V2 were filtered. Each de-duplicated read was extended to its fragment size. Tracks were normalized with RPKM method. Peak calling was performed using Macs2 2.2.7.1 in BEDPE and narrow mode. narrowPeaks from biological triplicate samples were then merged to a single master peak set. BEDtools was used to calculate the read coverage for each peak and for each sample. Peaks were annotated using Homer software with ucsc 6.4 gene annotation. Bigwig tracks were generated using bamCoverage from deepTools 3.5.4. ATAC-Seq samples were analyzed using the ENCODE ATACseq pipeline release v2.0.2 .
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (pooled replicates)

molecule: genomic DNA

extract_protocol:
Chem-Mapping and Cut&Tag experiments were performed using the Active Motif CUT&Tag-IT assay kit (53160, 53165), following the manufacturer’s instructions. ATAC-Seq experiments were performed using the Active Motif ATAC-Seq Kit (53150), following the manufacturer’s instructions.
Libraries were sequenced on an Illumina NextSeq 2000 sequencer as paired-end 50 base reads. Image analysis and base calling were performed using RTA version 2.7.7 and BCL Convert version 3.8.4. The adapter sequence: CTGTCTCTTATA has been trimmed with cutadapt 1.18 with option: -a CTGTCTCTTATA -A CTGTCTCTTATA -m 5 -e 0.1 and Bowtie2 parameter: -N 1 -X 1000, was used for mapping to the human genome. After the mapping, reads overlapping with ENCODE blacklist V2 were filtered. Each de-duplicated read was extended to its fragment size. Tracks were normalized with RPKM method. Peak calling was performed using Macs2 2.2.7.1 in BEDPE and narrow mode. narrowPeaks from biological triplicate samples were then merged to a single master peak set. BEDtools was used to calculate the read coverage for each peak and for each sample. Peaks were annotated using Homer software with ucsc 6.4 gene annotation. Bigwig tracks were generated using bamCoverage from deepTools 3.5.4. ATAC-Seq samples were analyzed using the ENCODE ATACseq pipeline release v2.0.2 .

value: Undifferentiated melanoma


title: MM029 ATAC Rep 1

description: MM029 ATAC pooled.bw


title: G2-MixedSamples

description: IXTCB00201_R:FEMALE; IXTCB00270_R:FEMALE; IXTCB01521_R:MALE; IXTCB01438_R:FEMALE; IXTCB01501_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00201_R:CTRL; IXTCB00270_R:CTRL; IXTCB01521_R:RA; IXTCB01438_R:RA; IXTCB01501_R:RA

value: IXTCB00201_R:CTRL; IXTCB00270_R:CTRL; IXTCB01521_R:wk12; IXTCB01438_R:wk0; IXTCB01501_R:wk12

value: IXTCB00201_R:CTRL; IXTCB00270_R:CTRL; IXTCB01521_R:GOOD; IXTCB01438_R:GOOD; IXTCB01501_R:NON_RESP

value: IXTCB00201_R:CTRL; IXTCB00270_R:CTRL; IXTCB01521_R:Golimumab; IXTCB01438_R:Adalimumab; IXTCB01501_R:Etanercept

value: IXTCB00201_R:CTRL; IXTCB00270_R:CTRL; IXTCB01521_R:Neg; IXTCB01438_R:NA; IXTCB01501_R:Pos

value: IXTCB00201_R:CTRL; IXTCB00270_R:CTRL; IXTCB01521_R:Neg; IXTCB01438_R:Neg; IXTCB01501_R:Pos

value: IXTCB00201_R:CTRL; IXTCB00270_R:CTRL; IXTCB01521_R:Low; IXTCB01438_R:High; IXTCB01501_R:High


title: 501mel Ecub Rep 1

value: Differentiated melanoma

value: WT

value: Ecubectedin 10xIC50, 8h


title: WT, male, 7w (rep 7)

description:
2725MM2
ribosomal pulldown mRNA

value: Kidney


title: WT, male, 7w (rep 6)

description:
2722MM2
ribosomal pulldown mRNA


title: Corpus_55

value: Corpus


title: MM029 BRD4 Rep 2

description: MM029 BRD4 pooled.bw

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
The adapter sequence: CTGTCTCTTATA has been trimmed with cutadapt 1.18 with option: -a CTGTCTCTTATA -A CTGTCTCTTATA -m 5 -e 0.1 and Bowtie2 parameter: -N 1 -X 1000, was used for mapping to the human genome. After the mapping, reads overlapping with ENCODE blacklist V2 were filtered. Each de-duplicated read was extended to its fragment size. Tracks were normalized with RPKM method. Peak calling was performed using Macs2 2.2.7.1 in BEDPE and narrow mode. narrowPeaks from biological triplicate samples were then merged to a single master peak set. BEDtools was used to calculate the read coverage for each peak and for each sample. Peaks were annotated using Homer software with ucsc 6.4 gene annotation. Bigwig tracks were generated using bamCoverage from deepTools 3.5.4. ATAC-Seq samples were analyzed using the ENCODE ATACseq pipeline release v2.0.2 .
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (pooled replicates)
Library strategy: Cut & Tag


title: Corpus_54


title: MM029 BRD4 Rep 1

description: MM029 BRD4 pooled.bw


title: WT, male, 7w (rep 5)

description:
2647MM2
ribosomal pulldown mRNA


title: AHC_pbmc_10

city: Nanjing

first: Xiaokai

last: Fang

state: Jiangsu

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing City, Jiangsu Province

country: China

institute: Dermatology Hospital of Chinese Academy of Medical Sciences

data_processing:
quality control
reads mapping to the reference genome
quantification of gene expression level
differential expression analysis
enrichment analysis of differentially expressed genes, gene set enrichment analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: pbmc

extract_protocol:
RNA was harvested using Trizol reagent. Illumina Truseq RNA Sample Prep Kit (Cat#FC-122-1001) was used to total RNA extraction.
Total RNA was used as input material for the RNA sample preparations.Briefly, mRNA was purified from total RNA using poly-T oligo-attached magneticbeads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized usingrandom hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase HRemaining overhangs were converted into blunt ends via exonuclease/polymerase activities.After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNA fragments of preferentially370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-FidelityDNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products werepurified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer2100 system.

value: pbmc


title: AHC_pbmc_9


title: AHC_pbmc_8


title: MM029 RNAPII Rep 2

description: MM029 RNAPII pooled.bw


title: AHC_pbmc_7


title: WT, male, 7w (rep 4)

description:
2464MM2
ribosomal pulldown mRNA

value: wild type, Pkd1fl/+; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_53


title: MM029 RNAPII Rep 1

description: MM029 RNAPII pooled.bw

value: Undifferentiated melanoma


title: AHC_pbmc_6


title: Antrum_51

value: Antrum


title: WT, male, 7w (rep 3)

description:
1872MM2
ribosomal pulldown mRNA


title: G3-MixedSamples

description: IXTCB00450:FEMALE; IXTCB00417:FEMALE; IXTCB01433:MALE; IXTCB01523:MALE; IXTCB01529:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00450:CTRL; IXTCB00417:CTRL; IXTCB01433:RA; IXTCB01523:RA; IXTCB01529:RA

value: IXTCB00450:CTRL; IXTCB00417:CTRL; IXTCB01433:wk0; IXTCB01523:wk0; IXTCB01529:wk12

value: IXTCB00450:CTRL; IXTCB00417:CTRL; IXTCB01433:MOD; IXTCB01523:GOOD; IXTCB01529:GOOD

value: IXTCB00450:CTRL; IXTCB00417:CTRL; IXTCB01433:Etanercept; IXTCB01523:Etanercept; IXTCB01529:Adalimumab

value: IXTCB00450:CTRL; IXTCB00417:CTRL; IXTCB01433:Pos; IXTCB01523:Pos; IXTCB01529:Pos

value: IXTCB00450:CTRL; IXTCB00417:CTRL; IXTCB01433:Pos; IXTCB01523:Neg; IXTCB01529:Pos

value: IXTCB00450:CTRL; IXTCB00417:CTRL; IXTCB01433:High; IXTCB01523:Low; IXTCB01529:Low


title: MM029 H3K27ac Rep 2

description: MM029 H3K27ac pooled.bw

value: WT


title: AHC_pbmc_5


title: WT, male, 7w (rep 2)

description:
3405MM2
ribosomal pulldown mRNA


title: AHC_pbmc_4


title: Antrum_52


title: G1-MixedSamples

description: IXTCB00201:FEMALE; IXTCB00270:FEMALE; IXTCB01521:MALE; IXTCB01438:FEMALE; IXTCB01501:FEMALE

value: IXTCB00201:CTRL; IXTCB00270:CTRL; IXTCB01521:RA; IXTCB01438:RA; IXTCB01501:RA

value: IXTCB00201:CTRL; IXTCB00270:CTRL; IXTCB01521:wk12; IXTCB01438:wk0; IXTCB01501:wk12

value: IXTCB00201:CTRL; IXTCB00270:CTRL; IXTCB01521:GOOD; IXTCB01438:GOOD; IXTCB01501:NON_RESP

value: IXTCB00201:CTRL; IXTCB00270:CTRL; IXTCB01521:Golimumab; IXTCB01438:Adalimumab; IXTCB01501:Etanercept

value: IXTCB00201:CTRL; IXTCB00270:CTRL; IXTCB01521:Neg; IXTCB01438:NA; IXTCB01501:Pos

value: IXTCB00201:CTRL; IXTCB00270:CTRL; IXTCB01521:Neg; IXTCB01438:Neg; IXTCB01501:Pos

value: IXTCB00201:CTRL; IXTCB00270:CTRL; IXTCB01521:Low; IXTCB01438:High; IXTCB01501:High


title: MM029 Bio-Comp Rep 3

description: MM029 Bio-CompIA pooled.bw

value: Undifferentiated melanoma

value: Bio-Comp IA 10xIC50, 8h


title: AHC_pbmc_3

value: pbmc


title: MM029 Bio-Comp Rep 2

description: MM029 Bio-CompIA pooled.bw


title: Corpus_51

value: Corpus


title: BR5

city: Tokyo

first: ANHAO

last: LIU

state: Tokyo

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Periodontology

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Data (26.7M reads/13.3M pairs per sample) was processed using packages based on R.
Low-quality and adapter sequences from the paired-end reads were trimmed using Trimmomatic v0.39.
The quality of the trimmed reads was assessed using FastQC v0.11.9.
Trimmed paired-end reads were aligned to the mouse reference genome (GRCm39) using HISAT2 v2.2.1.
StringTie v2.1.7 was used to assemble transcripts and estimate abundance based on GRCm39 gene annotations.
Assembly: GRCm39
Supplementary files format and content: *.csv: Comma-separated spreadsheet files include raw counts for each sample (concluded by tissue type).

source_name: Bone tissue

extract_protocol:
RNA was harvested from maxillae samples fixed in RNAlater (Sigma) using Direct-zol-96 RNA Kits (ZYMO). 0.57 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM ll Directional RNA Library Prep Kit following manufacturer's protocols.

value: Bone tissue

tag: strain

tag: Sex

value: Male

tag: individual


title: Corpus_50


title: AHC_pbmc_2


title: Corpus_49


title: MM029 Bio-Comp Rep 1

description: MM029 Bio-CompIA pooled.bw


title: BR2


title: BR4


title: Corpus_48


title: Antrum_50

value: Antrum


title: EHC_pbmc_10


title: EHC_pbmc_9


title: BR3


title: Corpus_52


title: MM029 Bio-Lurbi Rep 3

description: MM029 Bio-Lurbi pooled.bw

value: Bio-Lurbi 10xIC50, 8h


title: MM029 H3K27ac Rep 1

description: MM029 H3K27ac pooled.bw


title: Corpus_47


title: MM029 Bio-Lurbi Rep 1

description: MM029 Bio-Lurbi pooled.bw


title: BL5

value: Ligature placement for 5 days


title: EHC_pbmc_8


title: MM029 Bio-Lurbi Rep 2

description: MM029 Bio-Lurbi pooled.bw

value: WT


title: Antrum_49


title: 501mel ATAC Rep 2

description: 501mel ATAC pooled.bw

value: Differentiated melanoma


title: BL4


title: AHC_pbmc_1


title: WT, male, 7w (rep 1)

description:
3406MM2
ribosomal pulldown mRNA

value: Kidney

value: wild type, Pkd1fl/+; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: BL3


title: EHC_pbmc_7


title: Corpus_46


title: EHC_pbmc_6


title: 501mel ATAC Rep 1

description: 501mel ATAC pooled.bw


title: Corpus_45


title: 501mel BRD4 Rep 2

description: 501mel BRD4 pooled.bw


title: PR5

source_name: Peri-root tissue (Approximately periodontal tissue)


title: 501mel BRD4 Rep 1

description: 501mel BRD4 pooled.bw


title: Corpus_44


title: EHC_pbmc_4


title: EHC_pbmc_3


title: Corpus_43


title: 501mel RNAPII Rep 2

description: 501mel RNAPII pooled.bw


title: PR4

value: Peri-root tissue (Approximately periodontal tissue)


title: PR3


title: 501mel RNAPII Rep 1

description: 501mel RNAPII pooled.bw


title: Corpus_42


title: PR2


title: Antrum_47


title: Antrum_48


title: PL5


title: EHC_pbmc_2


title: EAD_pbmc_9


title: BL2


title: 501mel H3K27ac Rep 2

description: 501mel H3K27ac pooled.bw


title: EHC_pbmc_5


title: PL4


title: EAD_pbmc_8


title: EHC_pbmc_1


title: 501mel H3K27ac Rep 1

description: 501mel H3K27ac pooled.bw


title: 501mel Bio-Comp Rep 3

description: 501mel Bio-CompIA pooled.bw


title: Corpus_41


title: PL3


title: 501mel Bio-Comp Rep 2

description: 501mel Bio-CompIA pooled.bw


title: Antrum_46


title: EAD_pbmc_7


title: Corpus_39


title: PL2


title: Corpus_40


title: EAD_pbmc_6


title: 501mel Bio-Comp Rep 1

description: 501mel Bio-CompIA pooled.bw


title: EAD_pbmc_5


title: GR5

source_name: Gingiva

value: Gingiva


title: 501mel Bio-Lurbi Rep 3

description: 501mel Bio-Lurbi pooled.bw


title: Antrum_45


title: 501mel Bio-Lurbi Rep 2

description: 501mel Bio-Lurbi pooled.bw


title: Corpus_38


title: GR4


title: 501mel Bio-Lurbi Rep 1

description: 501mel Bio-Lurbi pooled.bw


title: EAD_pbmc_4


title: GR3


title: GR2


title: EAD_pbmc_3


title: PE+IUGR_209_TGCTAT

city: Budapest

first: Tamás

middle: István

last: Orbán

address: Magyar tudósok körútja 2.

department: Enzimology Institute

country: Hungary

institute: Research Centre for Natural Sciences

data_processing:
Data analysis was performed by exceRpt pipeline (github.com/gersteinlab/exceRpt). Read Per Million (RPM) normalized readcounts were generated by exceRpt and used for differential exosomal miRNA and piRNA expression analysis in edgeR package in R, where the completed gestational weeks at sampling time were added as an additional experimental factor.
Assembly: hg38
Supplementary files format and content: comma-separated value file includes raw counts for each sample
Supplementary files format and content: comma-separated value file includes read per million normalized counts for each sample

source_name: PE+IUGR pregnancy, early gestation, exosome

extract_protocol:
Plasma samples were pre-filtered by a 0.22 μm syringe filter. Exosomes were isolated from ~200μl pre-filtered plasma samples and subsequently total RNA was extracted directly from exosomes using exoRNeasy Midi Kit (QIAGEN).
small RNA libraries were prepared from average 1 ng of exosomal total RNA samples without small RNA enrichment using Small RNA-Seq Library Prep Kit for Illumina (052UG128V0110) provided by Lexogen GmbH.

value: Plasma

tag: subject status

value: PE+IUGR pregnancy

tag: systolic blood_pressure_(mmhg)

tag: dyastolic blood_pressure

tag: pulse

tag: proteinuria

value: T

tag: gestational age_ate_delivery_(week)

tag: type of_delivery

value: C-section

tag: newborn weight_(g)

tag: estimated fetal_weight_percente

tag: newborn gender

value: Girl

tag: ethnics

value: Caucasian

tag: bmi (kg/m2)

tag: gravidity

tag: parity

tag: family history_of_preeclampsia

value: F

tag: allergy

tag: crown-rump lenght_(mm)

tag: gestational age_at_sampling_time_(week)


title: EAD_pbmc_2

tag: tissue

value: pbmc


title: Antrum_42

value: Antrum


title: GL5

tag: strain

tag: genotype

tag: treatment

tag: Sex

value: Male

tag: individual


title: Antrum_43


title: EAD_pbmc_1


title: Control_799_GGCCAA

source_name: Normal pregnancy, early gestation, exosome

tag: subject status

value: Normal pregnancy

tag: systolic blood_pressure_(mmhg)

tag: dyastolic blood_pressure

tag: pulse

tag: proteinuria

tag: gestational age_ate_delivery_(week)

tag: type of_delivery

value: Spontaneous

tag: newborn weight_(g)

value: Boy


title: GL4

value: WT

value: Ligature placement for 5 days


title: Control_214_GCAGCC

tag: estimated fetal_weight_percente

tag: newborn gender

tag: ethnics

tag: bmi (kg/m2)

tag: gravidity

tag: parity

tag: family history_of_preeclampsia

tag: allergy


title: GL3

tag: tissue

tag: strain

tag: genotype

tag: treatment

tag: Sex

tag: individual


title: Corpus_37

value: Corpus


title: Corpus_36


title: AAD_pbmc_7


title: Control_776_CGCGGA

tag: subject status

tag: systolic blood_pressure_(mmhg)

tag: dyastolic blood_pressure

tag: pulse

tag: proteinuria

tag: gestational age_ate_delivery_(week)

tag: crown-rump lenght_(mm)

tag: gestational age_at_sampling_time_(week)


title: GL2

value: Gingiva


title: AAD_pbmc_6


title: Control_207_CCGACC

value: Plasma

tag: type of_delivery

tag: newborn weight_(g)

tag: estimated fetal_weight_percente

tag: newborn gender

tag: ethnics

tag: bmi (kg/m2)

tag: gravidity

tag: parity


title: Corpus_35

tag: tissue


title: AAD_pbmc_5


title: Mini-colon  (tumorigenic)

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Mini-colon  (tumorigenic)

library_source: transcriptomic single cell

data_processing:
The reads were aligned using Cell Ranger v6.1.2 to the mouse genome (mm10) carrying artificial chromosomes for both GFP and CellTag UTR genes.
Raw count matrices were imported into R and analyzed using Seurat v4.2.0
Dead cells were discarded on the basis of the number of detected genes (less than 3,000) and the percentage of mitochondrial genes (more than 20%), leading to 2,429 cells after filtering.
The data were log-normalized and scaled, and dimensionality reduction was conducted using UMAP with 10 dimensions.
Louvain clustering yielded 17 clusters that were merged and named on the basis of canonical cell type markers.
Assembly: mm10
Supplementary files format and content: Tab-separated text files include count values, features and barcodes

source_name: Colon

extract_protocol:
After 7 days in the mini-colon and when tumors were clearly visible, we extracted the cells by digesting the hydrogel with collagenase I and TrypLE as indicated in the manuscript.
After pooling and filtering (40 μm) the cell suspensions from two mini-colons, the single-cell sequencing library was constructed using 10× Genomics Chromium 3′ reagents v3.1 according to the manufacturer’s instructions.

value: Colon

tag: cell line

value: Mini-colon AKP

tag: cell type

tag: genotype

value: AKP

tag: treatment

value: OptoCre activation


title: Antrum_44


title: 12DPA_32C_biorep3

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

data_processing:
Sequence quality was controlled with FastQC, read trimmed with cutadapt (https://doi.org/10.14806/ej.17.1.200) and mapped with STAR (Dobin et al., 2013), as described in Pirrello et al., 2018.
We used the SLYMIC 1.0 reference genome along with ERCC sequences for read mapping with STAR (Dobin et al., 2013). After mapping, paired reads were assigned to genes or ERCC spike-ins using featurecounts from the subread package (Liao et al., 2014) and SLYMIC 1.0 annotation.
Differential gene expression analyses were performed with the DESeq2 package (Love et al., 2014), after standard normalization, in R/Bioconductor as previously described (Pirrello et al., 2018). We considered as differentially expressed the genes that displayed an absolute log2 fold-change > 1 and an FDR-adjusted p-value <0.01.
Assembly: SLYMIC 1.0
Supplementary files format and content: rawCounts.tsv is a tab-separated  matrix of read counts per gene obtained from featurecounts (for each sample: number of reads mapped to each gene)

molecule: nuclear RNA

organism: Solanum lycopersicum

source_name: tomato pericarp

growth_protocol: Tomato plants Solanum lycopersicum Mill. Cv. West Virginia 106 (WVA106) were cultivated in greenhouse with photoperiod of 16h light condition at 25°C and 8h night at 20°C and a relative humidity between 70 and 75%. Individual flowers were tagged on the day of anthesis, fully opened flowers that is wilt the next day. Fruits were harvested at three stages: 6DPA,9DPA and 12DPA.

extract_protocol:
Nuclei were prepared from 20 tomato fruits pericarp at 6DPA and 10 fruits at 9DPA and 12DPA. Nuclei were sorted by FANS as described in (Bourge et al., 2018). Pericarp pieces were chopped using a razor blade in 2mL of Gif Nuclear Buffer (GNB: 45 mM MgCl2, 30 mM Sodium-Citrate and 60 mM MOPS pH 7.0, 1% PVP 10.000, 0.1% Triton X-100 and 10 mM sodium metabisulfite (S2O5Na2)) and the suspension was filtered twice through a 48 µm nylon mesh before adding DAPI (4’,6-diamidino-2-phenylindole). 100k nuclei were sorted according to their ploidy levels with a MoFlo ASTRIOS EQ (BECKMAN COULTER) and collected in a tube containing 900µL of TRIzol™ Reagent (THERMOFISHER SCIENTIFIC). Before RNA extraction, 1µL of a dilution 1:1000 of ERCC RNA Spike-In Mix (THERMOFISHER SCIENTIFIC) was added. The mix of nuclei and spike-ins were shortly vortexed and rested for 5mn at room temperature before adding 200µL of Chloroform, agitating the tubes by hand for 15sec and incubating them for 3min at room temperature. After the incubation, tubes were centrifuged for 15mn at 12000g and 4°C, and the upper aqueous phase was transferred (around 840µL) to a fresh tube and mixed with 420µL of 100% ethanol. Then, total RNA was further purified using the RNeasy Micro Kit (QIAGEN) according to the provider’s instructions. A final volume of 14µL of total RNA was obtained.
Total RNA was used for construction of libraries following the instructions from the Illumina TruSeq Stranded RNA Sample Prep Kit. After library preparation for sequencing, a Duplex-specific nuclease (DSN) treatment was done using the commercial enzyme from EVROGEN following manufacturer’s instructions. Following DSN treatment, libraries were purified with SPRI beads (BECKMAN) and paired-end sequenced (2x150bp) with a HiSeq3000 (ILLUMINA).

value: tomato pericarp

value: 32C sorted nuclei

tag: sample type

value: nuclei sorted by ploidy level

tag: developmental stage

tag: ploidy


title: Corpus_34


title: 12DPA_32C_biorep2


title: AAD_pbmc_4

value: pbmc


title: PE+IUGR_142_AGACCA

tag: subject status

value: PE+IUGR pregnancy

tag: systolic blood_pressure_(mmhg)

tag: dyastolic blood_pressure

tag: pulse

tag: proteinuria

value: T

tag: gestational age_ate_delivery_(week)

value: C-section

value: Caucasian

tag: family history_of_preeclampsia

value: F

tag: allergy

tag: crown-rump lenght_(mm)

tag: gestational age_at_sampling_time_(week)


title: AAD_pbmc_9

tag: tissue


title: Antrum_40

value: Antrum


title: PE+IUGR_283_ACTCTT

tag: type of_delivery

tag: newborn weight_(g)

tag: estimated fetal_weight_percente

tag: newborn gender

value: Girl

tag: ethnics

tag: bmi (kg/m2)

tag: gravidity

tag: parity


title: Corpus_33

value: Corpus


title: Control_257_AAGTGG

value: Plasma

tag: subject status

value: Normal pregnancy

tag: systolic blood_pressure_(mmhg)

tag: dyastolic blood_pressure


title: AAD_pbmc_2


title: 12DPA_32C_biorep1

tag: cell type

tag: genotype

tag: sample type

tag: developmental stage

tag: ploidy


title: Antrum_39

tag: tissue


title: PE+IUGR_820_CTCATA

tag: pulse

tag: proteinuria

tag: gestational age_ate_delivery_(week)

tag: type of_delivery

value: Spontaneous

tag: family history_of_preeclampsia

tag: allergy

tag: crown-rump lenght_(mm)

tag: gestational age_at_sampling_time_(week)


title: Antrum_41


title: 12DPA_16C_biorep3

value: 16C sorted nuclei


title: 12DPA_16C_biorep2


title: PE+IUGR_796_CCTGCT

tag: subject status

tag: newborn weight_(g)

tag: estimated fetal_weight_percente

tag: newborn gender

tag: ethnics

tag: bmi (kg/m2)

tag: gravidity

tag: parity


title: AAD_pbmc_8

tag: tissue


title: AAD_pbmc_1


title: 12DPA_16C_biorep1

tag: cell type

tag: genotype

tag: sample type

tag: developmental stage

tag: ploidy


title: Corpus_32


title: CAD_pbmc_10


title: Corpus_31


title: CAD_pbmc_9


title: CD3+ T cells, trained, UES-WH s012

city: Duesseldorf

first: Christopher

last: Nelke

state: NRW

address: UKD, Moorenstraße 5

institute: University Hospital Düsseldorf

description:
sample 3
In count_matrix.csv, cell IDs ending in _3 correspond to sample 3

data_processing:
CellRanger Pipeline
Assembly: Genome assemblyGRCm38
Supplementary files format and content: count matrix

source_name: brain

extract_protocol:
The ipsilateral hemisphere of brains from trained mice and untrained mice (controls) were isolated 14 days post stroke. Brain mononuclear cells were isolated from single cell suspensions by Percoll density centrifugation (37% Percoll, 20 min at 2800 x g without brake, 18°C). Cells were washed, resuspended in PBS/2mM EDTA/2% FCS and stained with fluorochrome-labelled antibodies (anti-CD45 PB (30-F11) Biolegend; anti-CD3 PE (145-2C11), BD Biosciences). After washing, single cells were sorted into 384 so-called primer plates (Single Cell Discoveries) using a BD Aria FACS Fusion (BD Biosciences).
Single cells were sorted into 384 so-called primer plates (Single Cell Discoveries) using a BD Aria FACS Fusion (BD Biosciences). The primer plates contain mineral oil and 50 nl droplet with reagents. Plates were recovered with an aluminium sealer, centrifuged for 2 min and snap frozen on dry ice. SIngle cell sequencing (SORT-Seq) was performed by SIngle Cell DIscoveries, Netherlands.

value: brain

value: CD3+ T cells

value: wildtype

tag: treatment

value: trained


title: CD3+ T cells, trained, UES-WH s014

description:
sample 5
In count_matrix.csv, cell IDs ending in _5 correspond to sample 5


title: CD3+ T cells, untrained, UES-WH s013

description:
sample 4
In count_matrix.csv, cell IDs ending in _4 correspond to sample 4

value: untrained


title: 12DPA_8C_biorep3

value: tomato pericarp

value: 8C sorted nuclei

value: nuclei sorted by ploidy level


title: 12DPA_8C_biorep2


title: CD3+ T cells, trained, UES-WH s011

description:
sample 2
In count_matrix.csv, cell IDs ending in _2 correspond to sample 2


title: Corpus_30


title: Corpus_29


title: AAD_pbmc_3

value: pbmc


title: CAD_pbmc_8


title: 12DPA_8C_biorep1


title: CD3+ T cells, untrained, UES-WH s010

description:
sample 1
In count_matrix.csv, cell IDs ending in _1 (eg, X003_1) correspond to sample 1


title: CAD_pbmc_7


title: Corpus_28


title: Antrum_38


title: 12DPA_4C_biorep3

value: 4C sorted nuclei


title: CAD_pbmc_6


title: CAD_pbmc_5


title: 12DPA_4C_biorep2


title: Corpus_27


title: CAD_pbmc_4


title: Antrum_37

value: Antrum


title: 12DPA_4C_biorep1


title: CAD_pbmc_3


title: 100dpi5

city: IOWA CITY

first: Abhishek

middle: K

last: Verma

state: IA

address: 3-730, Bowen Science Building, 51 Newton Road

department: Department of Microbiology and Immunology

institute: The University of Iowa

data_processing:
RNA from the CD11b cells were isolated using RNeasy micro kit (Qiagen)
The isolated RNA were shipped to University of Minnesota where quality check was performed followed by library preparation.
Sequencing reads were mapped to the mouse reference genome (Mus_musculus.GRCm39.109) using Hisat2.
Genes differentially expressed between Day100 and mock cells were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Mus_musculus.GRCm39.109.gtf
Supplementary files format and content: RawCounts_Pearlman006.txt

source_name: Brain

extract_protocol:
Miltenyi CD11b magnetic beads
RNA libraries were prepared for sequencing using Takara Pico Mammalian V2 (ribo-depletion) protocols

value: Brain

value: CD11b cells

value: SARS-CoV-2 infected


title: 100dpi3


title: 100dpi2


title: Antrum_36


title: 100dpi1


title: CAD_pbmc_2


title: Antrum_35


title: Mock CD11b8

value: PBS treated


title: 9DPA_32C_biorep1

value: 32C sorted nuclei


title: Mock CD11b7


title: CAD_pbmc_1


title: 9DPA_16C_biorep3

value: 16C sorted nuclei


title: Mock CD11b4


title: EHC_skin_6

source_name: skin

value: skin


title: Antrum_33


title: Mock CD11b3


title: 9DPA_16C_biorep2


title: EHC_skin_5


title: Corpus_26

source_name: Corpus

value: Corpus


title: 9DPA_16C_biorep1


title: Antrum_32

source_name: Antrum


title: EHC_skin_4


title: Genital tubercle, Tgfbr1-cKO, biol rep2

city: Oeiras

first: Anastasiia

last: Lozovska

address: Rua da Quinta Grande 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

data_processing:
Adapters were trimmed and reads with length  < 20 bp were removed using cutadapt (v1.16.5)  (3´ adapter sequence: CTGTCTCTTATACACATCT).
The trimmed reads were aligned to the mouse reference genome using Bowtie2 (v2.4.2) [parameters paired-end options (-X/–maxins 1000, --fr, --dovetail), --very-sensitive].
The aligned reads were filtered using BamTools Filter (v2.4.1) (parameters --isProperPair true, --mapQuality ≥ 30, and --reference!=chrM) and the duplicate reads were removed using Picard MarkDuplicates (v2.18.2.2) (http://broadinstitute.github.io/picard/).
The resulting BAM files were converted to BED and the reads that overlap to the blacklisted regions listed in https://www.encodeproject.org/files/ENCFF547MET/ were removed using Bedtools (v2.30.0)
The filtered BED files were used as inputs for peak calling. Peaks were called from individual replicates using MACS2 callpeak (v2.1.1) (parameters --format single-end BED, --nomodel, --extsize 200, --shift -100, --qvalue 0.05).
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig, xlsx includes the results of pairwise chromatin accessibility comparisons with EdgeR

source_name: Genital tubercle

extract_protocol:
ATAC-seq was performed as in [Corces et al., 2017] with minor alterations. E11.25 mouse embryos were dissected on ice in DMEM High Glucose medium (Biowest, L0102-500) containing 10% FBS (this will be referred to as medium in the rest of the protocol). Hindlimbs and genital tubercles were dissected out and collected on ice-cold media. Single cell suspension was prepared by treating the tissue with 500 ul of Accutase (Sigma, A6964-500ML) for 30 minutes at 37˚C with shaking at 600 rpm. Single cells were pelleted at 6000 rcf for 5 minutes at 4˚C, resuspended in 200 ul of media and counted. 50000 viable cells from each sample were used for nuclei extraction. Cells were incubated with 50 ul of ATAC resuspension buffer (10mM Tris HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 (Sigma-Aldrich, P7949), 0.01% Digitonin (Target Mol, 282T2721-1ml/10mM in DMSO) for 3 minutes on ice. Lysis was quenched by adding 1 ml of ATAC resuspension buffer without NP-40 and Digitonin. Nuclei were pelleted by centrifugation at 500 rcf for 10 minutes at 4˚C. The pellet was then resuspended in 50 ul of transposition buffer [for 50 ul: 25 ul 2x TD buffer, 2.5 ul Tn5 transposition enzyme (100 nM final) (Illumina, 15028212), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O] and incubated at 37˚C for 30 minutes with shaking at 1000 rpm. The DNA was purified with Qiagen MinElute PCR purification kit (50928004) and eluted in 20 ul of the kit’s elution buffer.
Libraries were amplified by PCR with NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, 174M0541S) for 9 cycles in 96-well Thermal cycler (Biorad) and purified with Qiagen MinElute PCR purification kit. Tagmentation efficiency was assessed on TapeStation 4200 (Agilent). Double size selection to remove primer dimers and fragments exceeding 1 kb was performed using SPRIselect beads (Beckman Coulter). Another quality control was performed with High Sensitivity DNA assay using the Fragment Analyzer (Agilent). The 4nM libraries pool was sequenced with Illumina NextSeq 2000 (100 cycles, Pair-end 50 bp). Two biological replicates were performed per tissue

value: Genital tubercle


title: 9DPA_32C_biorep3


title: 9DPA_8C_biorep3


title: Genital tubercle, Tgfbr1-cKO, biol rep1


title: 9DPA_32C_biorep2


title: EHC_skin_3


title: Antrum_34


title: Antrum_31


title: 9DPA_8C_biorep2


title: EHC_skin_1


title: Antrum_30


title: Extra Hindlimb, Tgfbr1-cKO, biol rep2

source_name: Extra hindilmb

value: Extra hindilmb


title: 9DPA_8C_biorep1


title: Extra Hindlimb, Tgfbr1-cKO, biol rep1


title: 9DPA_4C_biorep3


title: Antrum_29


title: EHC_skin_2


title: 9DPA_4C_biorep2


title: Corpus_25


title: Genital tubercle, control, biol rep1


title: EAD_lesion_7


title: Genital tubercle, control, biol rep2


title: EAD_lesion_8


title: 9DPA_4C_biorep1


title: Hindlimb, control, biol rep2

source_name: Hindlimb

value: Hindlimb


title: EAD_lesion_6


title: Corpus_23


title: EAD_lesion_5


title: Corpus_22


title: 6DPA_16C_biorep3

value: tomato pericarp


title: Hindlimb, control, biol rep1


title: EAD_lesion_4


title: Antrum_28


title: Gpx2 KD (after induction) rep2

data_processing:
Reads were aligned to the mouse genome (GRCm39) using star (version 2.7.0e).
R (version 4.1.2) was used to perform the differential expression analyses. Count values were imported and processed using edgeR.
Expression values were normalized using the trimmed mean of M values (TMM) method and lowly-expressed genes (< 1 counts per million) were filtered out.
Differentially expressed genes were identified using linear models (Limma-Voom), and P values were adjusted for multiple comparisons by applying the Benjamini-Hochberg correction method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include count values for each sample

source_name: Colon, AKP (Gpx2 KD)

extract_protocol:
Cells were collected using TrypLE Express Enzyme, lysed in RLT buffer (QIAGEN, Catalog No. 74004), and the RNA was extracted using the QIAGEN RNeasy Micro Kit (QIAGEN, Catalog No. 74004) according to the manufacturer’s instructions.
Purified RNA was quality checked using a TapeStation 4200 (Agilent), and 500 ng were used for QuantSeq 3′ mRNA-Seq library construction according to the manufacturer’s instructions (Lexogen, Catalog No. 015.96).

value: Colon

value: Gpx2 KD

value: OptoCre activation


title: 6DPA_16C_biorep1

value: nuclei sorted by ploidy level


title: Corpus_21


title: 6DPA_8C_biorep3

value: 8C sorted nuclei


title: Gpx2 KD (after induction) rep1


title: Corpus_24


title: EAD_lesion_2


title: Antrum_27

value: Antrum


title: EAD_lesion_1


title: 6DPA_16C_biorep2


title: 6DPA_8C_biorep1


title: Control (after induction) rep3

source_name: Colon, AKP (control)

value: Control


title: Control (after induction) rep2


title: Corpus_20


title: Gpx2 KD (after induction) rep3


title: Antrum_25


title: AAD_lesion_8


title: 6DPA_4C_biorep3

value: 4C sorted nuclei


title: Control (after induction) rep1


title: AAD_lesion_6


title: EAD_lesion_3


title: Corpus_19


title: 6DPA_4C_biorep1


title: 6DPA_8C_biorep2


title: 6DPA_4C_biorep2


title: Gpx2 KD (before induction) rep2

source_name: Colon, Non-induced AKP (Gpx2 KD)

value: No treatment


title: Antrum_26


title: AAD_lesion_5


title: Antrum_24


title: 6DPA_2C_biorep3

value: 2C sorted nuclei


title: AAD_lesion_4


title: Corpus_18


title: AAD_lesion_7


title: 6DPA_2C_biorep2


title: Gpx2 KD (before induction) rep1


title: AAD_lesion_3


title: Control (before induction) rep3

source_name: Colon, Non-induced AKP (control)


title: Gpx2 KD (before induction) rep3


title: Corpus_17


title: 6DPA_2C_biorep1


title: Antrum_23


title: AAD_lesion_2


title: RBE cells, sh#HSDL2 2

city: Bengbu

first: Shuoshuo

last: Ma

state: Anhui

address: NO. 287, Changhuai Road, Longzihu district, Bengbu 233000, Anhui, China;

institute: The First Affiliated Hospital of Bengbu Medical College

data_processing:
The sequencing data was filtered with SOAPnuke(v1.5.2)
After obtaining the clean reads, we used HISAT2(v2.0.4) to align the clean reads to the reference genome sequence
clean reads were compared to reference gene sequences using Bowtie2(v2.2.5)
then the expression level of gene was calculated by RSEM(v1.2.12),differential expression analysis was performed using DESeq2(v1.4.5)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files files include fpkm, tpm,read count values for each Sample

source_name: human bile duct

growth_protocol: RBE cholangiocarcinoma cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted using trizol reagent. 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA-Seq Library Preparation Protocol(DNBSEQ) following manufacturer's protocols.

treatment_protocol: routine culture

value: human bile duct

tag: cell line

value: RBE

value: cholangiocarcinoma cell

value: HSDL3 knockdown

value: routine culture


title: Corpus_16

value: Corpus


title: AAD_lesion_1

value: skin


title: Control (before induction) rep1

value: Colon


title: RBE cells, sh#HSDL2 3

value: HSDL4 knockdown


title: Corpus_15


title: CAD_lesion_7


title: DKO_10wk_2DG-treated_12

city: Charlottesville

first: Loren

last: Erickson

state: Virginia

address: 345 Crispell Drive

department: Department of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

data_processing:
RNA-seq reads were filtered and trimmed for quality scores >30 using a custom python script.
Filtered reads were aligned to Mus musculus GRCm38 using Bowtie2 (v2.2.0)
Expected counts were determined using RSEM (v1.2.12)
Assembly: GRcm38
Supplementary files format and content: tab-delimited text file containing per sample counts data

source_name: Spleen

extract_protocol:
Total RNA was isolated with the QIAGEN miRNeasy mini extraction kit and cDNA was synthesized with the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) following manufacturer's protocols.
Poly(A)-selected RNA-seq libraries were generated using the Illumina TruSeq RNA Sample preparation kit v2 following manufacturer's protocols.

treatment_protocol: 2DG (Thermo Fisher, 6 g/L) was dissolved in drinking water and was provided to mice ad libitum

value: Spleen

tag: time

value: 10 weeks

value: BXSB.Cg-Cd8atm1Mak Il15tm1Imx Yaa (Yaa DKO)

value: 2-deoxyglucose (2DG) treated


title: Antrum_22

value: Antrum


title: CAD_lesion_6


title: DKO_10wk_2DG-treated_11


title: RBE cells, sh#NC 3

value: WT


title: CAD_lesion_5


title: DKO_10wk_2DG-treated_10


title: RBE cells, sh#NC 2


title: DKO_10wk_2DG-treated_9


title: CAD_lesion_4


title: Control (before induction) rep2

value: Control

value: No treatment


title: RBE cells, sh#NC 1

value: human bile duct


title: Antrum_20


title: CAD_lesion_3


title: w1118 (wild-type), 0-12h Embryo, Rep1

city: Piscataway

first: Ruth

last: Steward

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute of Microbiology

institute: Rutgers University

data_processing:
Raw reads were trimmed using cutadapt v2.0 to remove adapter and low-quality reads.
The processed reads were mapped to the Drosophila melanogaster BDGP6 (dm6) reference genome from Ensembl release 88 using the BWA version 0.7.5-r404 for ChIP-seq.
For analysis, only unique reads with mapping quality >20 were accepted. Further, redundant reads with identical coordinates were filtered out.
Aligned reads were processed by Model-based Analysis of ChIP-seq (MACS2) using Input ChIP DNA as control. For peak calling the MACS2 ‘callpeak’ function was used (-p 1e-2 -g 1.2e+08 -B --nomodel –ext size 147 –SPMR) for each replicate vs. control input. Peaks were selected using the following criteria: p-value <10e-5, fold enrichment over control greater than 10 and a minimal number of reads higher than 50.
Bedtools (version v2.24.0) was used to identify overlapping peaks in replicates. A sliding window of 50, 100, 150, 200, 250 and 300 bp around the peak summit (base position of maximum enrichment) was used to determine best range for overlapping peaks. The number of overlapping peaks saturated around window size of 250 bp. Thus, for downstream analysis, windows size of 250 bp was used to identify overlapping peaks in replicates.
bigwig peak files were generated using “bdgcmp” function in MACS2 with option “-m logFE -p 0.00001”.
Assembly: dm6
Supplementary files format and content: bw and tab-delimited text annotation files (except input).

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: All flies were reared at 25oC and kept on standard medium.

extract_protocol:
0-12h embryos were collected, processed, and chromatin was prepared according to Yad et al. 29, except lysates were sonicated on a Covaris S2 sonication device (intensity 8, duty cycle 20%, cycle burst 200) for 30 minutes at 4˚C to reach fragments ranging from 150–500 bp and then centrifuged at 20,000g at 4˚C for 1 minute. Supernatants were collected and centrifuged again for 15 minute to remove debris. Chromatin samples were then snap frozen in dry ice and stored at -80˚C until immunoprecipitation in triplicets. All buffers contained cOmplete EDTA-free protease inhibitor cocktail (Roche).
NGS Libraries were made from eluted DNA using the NEBNext Ultra II DNA Library Prep kit (New England Biolabs) according to the manufacturer’s protocol. Briefly, 20 ng of DNA fragments were end-repaired and the blunt, phosphorylated ends were treated with Klenow DNA polymerase and dATP to yield a 3′ A base overhang for ligation of Illumina adapters. After adapter ligation, DNA was PCR amplified with indexed primer for 12 cycles. Libraries were size-selected using Ampure XP beads (Beckman Coulter) to remove adapter dimers. DNA was quantified by fluorometry with the Qubit 2.0 (Thermo Scientific) and DNA integrity was assessed with a Fragment Analyzer (Agilent). The libraries were pooled and sequenced on the NextSeq 500 platform using 75 bp single end sequencing according to manufacturer’s protocol using Reagent v.2.5 at the Waksman Institute Genomics Core.

treatment_protocol: No treatment applied.

value: Embryo

value: whole embryo

value: 0-12h embryo

value: w1118 (wild type)

tag: chip antibody


title: Corpus_14

data_processing:
Quality control of sequencing data was performed with FastQC v0.11.7.
For adaptor trimming bbduk from the BBMap v37.44 was used.
The read alignment against GRCh38 was performed with STAR Aligner 2.5.2b.
FeatureCounts v1.5.1 was used for quantification of gene expression using the Ensembl annotation GRCh38.89 as reference.
Further QC was performed using RSeQC.
Assembly: GRCh38
Supplementary files format and content: gastric_expression_unique_counts.csv: comma-separated file with number of unique counts per gene and sample (columns = samples, rows = genes (Ensembl Ids))

extract_protocol:
Tissue samples were mechanically homogenized with ceramic beads and a Precellys tissue homogenizer. Total RNA (and genomic DNA) was extracted using the Allprep DNA/RNA Mini Kit from Qiagen.
RNA libraries for RNA-Seq were prepared using Lexogen's QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina following manufacturer's protocol.

value: Corpus


title: DKO_10wk_Untreated_8

value: Untreated


title: DKO_10wk_Untreated_7


title: Corpus_13


title: Tet-GFP, 0-12h Embryo, Rep3

value: Tet-GFP

value: GFP-Trap Magnetic Agarose (Chromotek #gtma)


title: RBE cells, sh#HSDL2 1

value: RBE

value: cholangiocarcinoma cell

value: HSDL2 knockdown

value: routine culture


title: 710T-Pre (matched to DGay24-27879)

city: La Jolla

first: Theresa

last: Guo

state: California

address: 3855 Health Sciences Dr, MC 0987

institute: University of California, San Diego

description:
HPV-positive oropharyngeal cancer without recurrence, matched FFPE extraction from prior cohort
710T-Pre

data_processing:
Sequences were trimmed for adaptor sequence using Trim Galore
Trimmed reads were mapped to GRCH37/hg19 using Salmon aligner
Transcript abundance was caputured using tximport pipeline and data was compared to previously published cohort of HPV-positive oropharyngeal cancers
Batch correction was performed using DESeq2
Assembly: GRCH37/hg19
Supplementary files format and content: tab-delimited text file shows normalized transcript abundance estimates from DESeq2

source_name: HPV-positive oropharyngeal squamous cell carcinoma tumor without recurrence, FFPE

extract_protocol:
RNA was extracted from formalin fixed tissue using Qiagen AllPrep Kit
Library prep was performed using Takara SMARTer Stranded Total RNA-Seq Kit v2 using manufacturer protocols

tag: age

tag: Sex

value: M

tag: smoking history

value: Never smoker

tag: tumor stage_(ajcc_8)

value: NED, 44.8 months

tag: group

value: Tumor


title: CAD_lesion_2

value: skin


title: Antrum_19

value: Antrum


title: Antrum_18


title: DKO_10wk_Untreated_5

value: Spleen

value: 10 weeks

value: BXSB.Cg-Cd8atm1Mak Il15tm1Imx Yaa (Yaa DKO)


title: Tet-GFP, 0-12h Embryo, Rep2

value: Embryo

value: whole embryo

value: 0-12h embryo


title: DKO_10wk_Untreated_6

value: Untreated


title: 629T-Pre (matched to DGay8-30811)

description:
HPV-positive oropharyngeal cancer without recurrence, matched FFPE extraction from prior cohort
629T-Pre

value: HPV-positive oropharyngeal squamous cell carcinoma tumor without recurrence, FFPE

value: Former smoker

value: NED, 86.8 months


title: DKO_6wk_Untreated_4

value: 6 weeks


title: CAD_lesion_1


title: Antrum_17


title: Antrum_21


title: 831-Pre (matched to DGay6-24648)

description:
HPV-positive oropharyngeal cancer without recurrence, matched FFPE extraction from prior cohort
831-Pre

value: M

value: Alive at 133.3 months, second primary in oral tongue at 94 months


title: P6975_196

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
Sequence data for RNA-Seq were quality controlled using FastQC and summarized with multiQC
Trimmomatic was used to trim low-quality bases and sequencing adapters from the reads
The CHO-K1 reference genome was extended to incorporate the transgene sequences so that the transcripts of the heterologous secretome can be quantified
Reads were then quasi-mapped to the extended CHO-K1 genome and quantified with Salmon
Assembly: CHO-K1
Supplementary files format and content: CSV (comma-separated values) file with gene counts for each Sample
Supplementary files format and content: CSV (comma-separated values) file with TPMs for each Sample
Supplementary files format and content: CSV (comma-separated values) file with transgene abundance for each Sample

organism: Cricetulus griseus

source_name: Icosagen QMCF

extract_protocol:
RNA was extracted using RNeasy plus Mini Kit (Qiagen) according to manufacturer’s guidelines and the quality of the isolated RNA was evaluated by BIOanalyzer 2100 (Agilent, Santa Clara, CA) using the Agilent RNA 6000 Nano Kit.
Library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103), according to manufacturer’s protocol

value: Icosagen QMCF

value: WT


title: Antrum_16


title: DKO_6wk_Untreated_3


title: P6975_195

value: expressing CCL20


title: Patient 5 Pre treatment Tumor

description:
HPV-positive orohparyngeal cancer, chemoradiation resistant, Pretreatment
379T-Pt5-Pre

source_name: HPV-positive orohparyngeal cancer, chemoradiation resistant, Pretreatment, FFPE

value: Current smoker

value: Died of disease, 9,7 months


title: DKO_6wk_Untreated_2

value: Spleen


title: P6975_194

value: expressing ADM5


title: Antrum_15

value: Antrum


title: Patient 3 Normal tissue

description:
Matched normal adjacent tissue from Patient 3 (tumor sample 421T-WR)
421N-Pt3

source_name: Matched adjacent normal tissue, FFPE

value: Matched adjacent normal tissue, FFPE

value: Normal


title: DKO_6wk_Untreated_1

value: BXSB.Cg-Cd8atm1Mak Il15tm1Imx Yaa (Yaa DKO)

value: Untreated


title: In vivo AKP rep6

description: In vivo AKP rep6

source_name: Colon tumor

value: Colon tumor

value: In vivo AKP

value: Colon

value: AKP

value: Cdx2-Cre activation


title: Patient 3 Pre treatment Tumor

description:
HPV-positive orohparyngeal cancer, chemoradiation resistant, Pretreatment
421T-Pt3-Pre

value: HPV-positive orohparyngeal cancer, chemoradiation resistant, Pretreatment, FFPE

value: M

value: Former smoker

value: Died of disease, 4.7 months


title: Corpus_12

source_name: Corpus

value: Corpus


title: Patient 2 Post treatment Tumor

description:
HPV-positive orohparyngeal cancer, chemoradiation resistant, Post treatment
430T-Pt2-Post

source_name: HPV-positive orohparyngeal cancer, chemoradiation resistant, Post treatment, FFPE

value: Never smoker

value: Died of disease, 13.9 months


title: Tet-GFP, 0-12h Embryo, Rep1

value: Embryo

value: whole embryo

value: 0-12h embryo

value: Tet-GFP

value: GFP-Trap Magnetic Agarose (Chromotek #gtma)


title: P6975_192

value: Icosagen QMCF

value: expressing FLT3LG


title: Corpus_11


title: Antrum_13

source_name: Antrum

value: Antrum


title: P6975_191

value: expressing MYOC


title: In vivo AKP rep5

description: In vivo AKP rep5

value: Colon tumor

value: In vivo AKP

value: Colon

value: AKP

value: Cdx2-Cre activation


title: Corpus_10

value: Corpus


title: In vivo AKP rep4

description: In vivo AKP rep4


title: Patient 5 Post treatment Tumor

description:
HPV-positive orohparyngeal cancer, chemoradiation resistant, Post treatment
823T-Pt5-Post

value: HPV-positive orohparyngeal cancer, chemoradiation resistant, Post treatment, FFPE

value: M

value: Current smoker

value: Died of disease, 9,7 months


title: P6975_190

value: expressing MMP14


title: Patient 1 Normal tissue

description:
Matched normal adjacent tissue from Patient 1 (tumor sample 352T-BU)
352N-Pt1

value: Matched adjacent normal tissue, FFPE

value: Never smoker

value: Normal


title: P6975_188

value: Icosagen QMCF

value: expressing GXYLT1


title: Patient 3 Post treatment Tumor

description:
HPV-positive orohparyngeal cancer, chemoradiation resistant, Post treatment
755T-Pt3-Post

value: Former smoker

value: Died of disease, 4.7 months


title: Patient 1 Pretreatment Tumor

description:
HPV-positive orohparyngeal cancer, chemoradiation resistant, Pretreatment
352T-Pt1-Pre

value: HPV-positive orohparyngeal cancer, chemoradiation resistant, Pretreatment, FFPE

value: Died of disease, 5.6 months


title: In vivo AKP rep2

description: In vivo AKP rep2

value: Colon tumor

value: In vivo AKP

value: Colon

value: AKP


title: Antrum_14

value: Antrum


title: In vivo AKP rep1

description: In vivo AKP rep1

value: Cdx2-Cre activation


title: Corpus_9

value: Corpus


title: Antrum_12


title: P6975_187

value: expressing LRG1


title: P6975_193

value: expressing CXCL13


title: P6975_189

value: expressing FURIN_2


title: Mini-colon AKP #v rep3

description: Mini-colon AKP #v rep3

source_name: Colon

value: Mini-colon AKP

value: OptoCre activation


title: P6975_186

value: Icosagen QMCF

value: expressing IL20


title: P6975_185

value: expressing ITGBL1


title: Corpus_8


title: Mini-colon AKP #v rep2

description: Mini-colon AKP #v rep2


title: In vivo AKP rep3

description: In vivo AKP rep3


title: Mini-colon AKP #v rep1

description: Mini-colon AKP #v rep1


title: P6975_184

value: expressing MSTN


title: Antrum_10


title: Mini-colon AKP #iv rep3

description: Mini-colon AKP #iv rep3


title: P6975_183

value: expressing SFTPD


title: Mini-colon AKP #iv rep2

description: Mini-colon AKP #iv rep2


title: P6975_182

value: expressing MBL2


title: Antrum_9


title: Mini-colon AKP #iii rep3

description: Mini-colon AKP #iii rep3


title: Corpus_6


title: P6975_180

value: expressing PROCR


title: Mini-colon AKP #iii rep2

description: Mini-colon AKP #iii rep2

value: Colon


title: Mini-colon AKP #iv rep1

description: Mini-colon AKP #iv rep1

value: AKP


title: P6975_181

value: expressing GLCE


title: Antrum_8

value: Antrum


title: Corpus_7

value: Corpus


title: Antrum_7


title: P6975_179

value: expressing ANGPTL4


title: Antrum_11


title: CUT&RUN TTC549 IgG for H3K4me1 rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
library strategy: CUT&RUN
CUT&RUN analysis: CUT&RUNTools was used for CUNT&RUN data analysis including adapter trimming, alignment, duplication marking, and peak calling. DiffBind was then applied to get consensus peaks for H3K4me3 and H3K27ac
ATAC-seq anaysis: After adaptor trimming by Cutadapt, ATAC-seq reads were aligned to the human genome hg19 using Bowtie2. Peaks were called using MACS2 with q-value of 0.05. Peaks present in at least two replicates per condition were included, and peaks identified across conditions were combined into a final peak set and ATAC-seq read counts were calculated for the final peak set. Differential enriched peaks were identified using DiffBind with a FDR < 0.05
RNA-seq analysis: RNA-seq reads were aligned to the genome using STAR after adapter trimming, and quantified by featureCounts. Differential analysis were performed by DESeq2.
Assembly: hg19
Supplementary files format and content: CUT&RUN: peak file for each condition
Supplementary files format and content: ATAC-seq: peak file for each condition
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each sample

growth_protocol: JMU-RTK-2 cells were maintained in DMEM supplemented with 10% FBS and 1%Penicillin/Streptomycin. A204 and TTC-549 were maintained in RPMI supplemented with 10% FBS and 1%Penicillin/Streptomycin. This maintenance media was also the same media that DMSO, cis-ACBI1, or ACBI1 was diluted in.

extract_protocol:
For ATAC-seq, 100,000 cells were harvested and nuclei were treated with the Active Motif transposase included in the Active Motif ATAC-seq kit. All subsequent processing following the Active motif protocol. For RNA-seq, RNA was extracted from 2-3 million cells using Trizol and the Direct-zol RNA mini prep kit by Zymo Research. For CUT&RUN, 500,000 cells were bound to ConA beads and processed following the Cell Signaling CUT&RUN kit protocol.
For ATAC-seq, libraries were made using the Active Motif ATAC-seq kit, which included index primers and all PCR reagents. For RNA-seq, libraries were made at Vanderbilt University Medical Center VANTAGE core using their standard methods with ribosomal RNA depletion. For CUT&RUN, we made libraries of DNA fragments using the NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiple Oligos for Illumina.

treatment_protocol: All cells were treated with indicated amounts of DMSO, cis-ACBI1, or ACBI1 for 24 hours (ATAC-seq and RNA-seq). For CUT&RUN, no treatment was performed prior to collection.

value: rhabdoid tumor cell line

value: No treatment


title: Mini-colon AKP #iii rep1

description: Mini-colon AKP #iii rep1

value: Mini-colon AKP


title: Antrum_6

first: Laura

last: Koebbe

address: Baldingerstraße

institute: University of Marburg


title: P6975_178

value: expressing PGLYRP3


title: Mini-colon AKP #ii rep3

description: Mini-colon AKP #ii rep3

value: OptoCre activation


title: Mini-colon AKP #ii rep2

description: Mini-colon AKP #ii rep2


title: Corpus_5


title: CUT&RUN TTC549 IgG for H3K4me1 rep1


title: Antrum_5


title: P6975_176

value: Icosagen QMCF

value: expressing CCL23


title: Antrum_4


title: CUT&RUN TTC549 H3K4me1 rep3


title: Mini-colon AKP #ii rep1

description: Mini-colon AKP #ii rep1


title: CUT&RUN TTC549 H3K4me1 rep2


title: Mini-colon AKP #i rep3

description: Mini-colon AKP #i rep3


title: P6975_175

value: expressing NPTX2


title: Corpus_4


title: Mini-colon AKP #i rep2

description: Mini-colon AKP #i rep2


title: Corpus_3


title: CUT&RUN TTC549 IgG for H3K4me1 rep2


title: CUT&RUN TTC549 H3K4me1 rep1


title: P6975_174

value: expressing NHLRC3


title: Mini-colon AKP #i rep1

description: Mini-colon AKP #i rep1


title: CUT&RUN A204 IgG for H3K4me1 rep3


title: P6975_177

value: expressing FCN3


title: P6975_172

value: expressing MYL1


title: P6975_173

value: expressing SERPINA9


title: Corpus_2


title: Organoid AKP rep6

description: Organoid AKP rep6

value: Colon

value: Organoid AKP

value: AKP


title: CUT&RUN A204 IgG for H3K4me1 rep2


title: P6975_171

value: expressing HGF


title: Antrum_3

value: Antrum


title: CUT&RUN A204 IgG for H3K4me1 rep1

value: rhabdoid tumor cell line


title: Corpus_1

value: Corpus


title: Organoid AKP rep5

description: Organoid AKP rep5


title: P6975_170

value: expressing CHAD


title: CUT&RUN A204 H3K4me1 rep3

value: No treatment