title: 270002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: N1-2 (biopsy positive)


title: 250001_RNAseq

status: Public on Jan 08 2021

type: SRA

city: Columbus

first: Daniel

last: Stover

state: OH

address: Biomedical Research Tower, Room 512, 460 W. 12th Avenue

country: USA

institute: Ohio State University Comprehensive Cancer Center

library_source: transcriptomic

data_processing:
Samples with >10 million unique reads were included for further analyses
RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
Genome_build: Ensembl release 76
Supplementary_files_format_and_content: log2 normalized abundance data as a matrix table in a text file

molecule: total RNA

organism: Homo sapiens

source_name: Tumor biopsy

extract_protocol:
Pre-treatment biopsies were collected in RNAlater and total RNA was extracted.
Total RNA underwent whole transcriptome RNA sequencing (RNAseq) using RiboZero Gold rRNA depletion
All samples were sequenced on an Illumina HiSeq 3000 with single-end 50bp reads

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Every 2 weeks

value: Never

value: pCR


title: 219006_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 220001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: Former

value: RD


title: LampKD [GGACTCCT_ATAGAGAG]

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
The sample is aligned to GRCm38 transcriptome using Kallisto (v0.46.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Kallisto alignment/quantification software output including txt format with transcripts ID and abundance.

organism: Mus musculus

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al. 2014).

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: strain

value: WT C57Bl/6

tag: Sex

value: Female

tag: age

value: 12-13 weeks

tag: cell type

value: Astrocytes

tag: sg

tag: disease state

value: Induced EAE


title: 232001_RNAseq


title: 501005_RNAseq

value: Every 3 weeks

value: Current


title: 220002_RNAseq

value: N1-2 (biopsy positive)


title: 219007_RNAseq


title: SgScrmbl CGATCAGT_TCTTACGC

data_processing:
Reads were aligned against the GRCm38 mouse transcriptome using kallisto (v0.46.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: run_info.json: Alignment QC; abundance.tsv: count file compatible with Excel; abundance.h5: count table for downstream analysis, same as abundance.tsv.

source_name: SgScrmbl

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)

value: F


title: 260001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Every 2 weeks


title: Scr [CGTACTAG_ATAGAGAG]

value: sgScrmbl


title: 217017_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)


title: 217014_RNAseq

value: A

value: Former

value: pCR


title: 219005_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Never


title: Scr [AGGCAGAA_ATAGAGAG]

value: WT C57Bl/6

value: Female

value: 12-13 weeks

value: Astrocytes

value: Induced EAE


title: 217011_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Every 3 weeks

value: RD


title: 217009_RNAseq

value: C

value: Every 2 weeks


title: 217010_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 217008_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: Naive_Tomato+LAMP+TRAIL-

data_processing:
The data was demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatics (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were aligned to mouse (GRCm38) genome by bowtie.
The reads were quantified and expression of genes were calculated using the inDrop pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited tsv file consisting of UMI gene counts for cells.

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on TdTomato fluorescence, LAMP1 expression, or TRAIL expression. Post-sort, cells were suspended in 0.1% BSA in 1X PBS.
Libraries were created according to the InDrop protocol in Klein et al. Cell 2015 in the Harvard Medical School Single Cell Core according to the standard v3 protocol.

tag: background strain

tag: cell markers

value: astrocytes

value: naive


title: HUVEC HU-3

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

description: RIN: 9.6

data_processing:
Reads trimmed using Trimmomatic
Reads pseudo-aligned and counted with Salmon (ver. 1.2.1)
Normalization and comparisons performed using DESeq2
Genome_build: GRCh38 - gencode ver. 36
Supplementary_files_format_and_content: Tab-delimited text files include variance-stabilized transformed values for each sample

source_name: HUVEC- untreated

growth_protocol: HUVEC were cultured in Nunc EasYFlasks in Endothelial Cell Growth medium 2 (Promocell). Cells were collected by TrypLE express enzyme (Thermo Fisher Scientific) according to manufacturer’s instructions. Epi5 Episomal iPSC Reprogramming Kit (Thermo Fisher Scientific) was used for reprogramming in combination with Neon™ Transfection System 10µL Kit. Shortly, 105 living cells in 10µL R buffer were prepared and 1µL of content of each vial from reprogramming kit was added. Neon Transfection tube was filled with 3mL E buffer and cells with plasmid were electroporated with Pulse voltage 1400V, Pulse Width 20ms, Pulse number 2. Cells were seeded on hESC-qualified MatriGel coated cell culture treated 35mm Petri dishes in endothelial medium, which was changed daily until day 5, when it was exchanged for mTeSR. To establish cell lines, individual clones were picked mechanically and cultured on hESC-qualified MatriGel (Corning) in mTeSR 1, subsequent passaging method was EDTA dissociation to clumps with ROCKi supplementation (Y-27632 2HCl, Seleckchem). All media were supplemented with ZellShield (Minerva biolabs).

extract_protocol:
Total RNA was obtained from HUVEC cells CTL, macroH2A1.1 and macroH2A1.2 with TRIzol Reagent (ThermoFisher Scientific, Waltham, USA).
Indexed libraries were prepared from 2 mg/ea RNA with the TruSeq Total Stranded RNA Sample Prep Kit (Illumina, Cambridge, UK) according to the manufacturer's instructions. Libraries were quantified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). Libraries were prepared so that each index‐tagged sample was present in equimolar amounts with a final concentration of 2 nmol/L. l/L.

treatment_protocol: Where applicable, 1µg of plasmids expressing macroH2A1.1-6His or macroH2A1.2-6His (Addgene) (Chadwick et al.; Hum Mol Genet. 2001) were added together with the Episome construct .

tag: tissue

value: Endothelial Cells (Umbilical Vein)


title: 217012_RNAseq

value: N1-2 (biopsy positive)

value: Never

value: pCR


title: EAE_Tomato+LAMP+TRAIL+

value: induced EAE


title: HUVEC HU-2

description: RIN: 9.1


title: HUVEC HU-1

description: RIN: 9.4


title: 217006_RNAseq


title: 217005_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Former


title: 217004_RNAseq


title: EAE_Tomato+LAMP+TRAIL-


title: 217007_RNAseq


title: 216004_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Unknown


title: 216002_RNAseq


title: Not infected CR.2

city: Naples

first: Giuseppe

last: Matarese

address: Via Pansini 5

department: Dipartimento di Medicina Molecolare e Biotecnologie Mediche

institute: Università di Napoli Federico II

data_processing:
Illumina CASAVA 1.8.2 version software used for basecalling
On average 47M of reads were produced per sample (min 40.1M, max 53.5M). RNA-Seq standard bioinformatics analysis included base calling and demultiplexing; trimming (removing lower quality bases and adapters) using ERNE and Cutadapt softwares.
Alignments with STAR,  a splice junction mapper that alignes reads on UCSC mm10 reference genome/transcriptome using default parameters; transcripts count by Stringtie and quality control by using RSeqQC package.
Htseq-count was used to preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. DESeq was used to perform comparisons between expression levels of genes and transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: Spleen cells

extract_protocol:
Spleens were removed, a cell suspension was prepared and RNA was harvested using miRVANA Total RNA Isolation kit ((Ambion/RNA, Life Technologies, Carlsbad, California) and RNA preparation was treated with DNAse.
‘TruSeq Stranded Total RNA with Ribo-Zero Gold’ (Illumina, San Diego, CA) was used for library preparation following the manufacturer’s instructions, starting with 200 ng of RNA as input. Both RNA samples and final libraries were quantified by using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and quality tested by Agilent 2100 Bioanalyzer assay (Agilent technologies, Santa Clara, CA). Libraries were then processed and sequenced on single-end 1x75 mode on NextsSeq500 (Illumina, San Diego, CA) following the manufacturer’s instructions.

tag: genotype

value: wild type

value: 17 weeks

value: Spleen

tag: infection state

value: Not infected

tag: feeding

value: Caloric restricted


title: Not infected CR.3


title: 217013_RNAseq

value: Every 2 weeks

value: RD


title: 403003_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: N0 (clinically negative or biopsy negative)


title: macroH2A12_epi 2_II

description: RIN: 8.6

source_name: HUVEC- reprogrammed using Episome and macroH2A1.2 overexpressing vector

value: Endothelial Cells (Umbilical Vein)


title: Not infected CR.1


title: Naive_Tomato+LAMP+TRAIL+

value: astrocytes

value: naive


title: macroH2A12_epi 2_I

description: RIN: 9.3


title: 215005_RNAseq

value: Never


title: 214015_RNAseq

value: C

value: pCR


title: macroH2A12_epi 2_III

description: RIN: 9.4


title: macroH2A11_epi 1_1_3

description: RIN: 9

source_name: HUVEC- reprogrammed using Episome and macroH2A1.1 overexpressing vector


title: 214014_RNAseq

value: N1-2 (biopsy positive)


title: 214012_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Former


title: Not infected AL.3

value: wild type

value: 17 weeks

value: Spleen

value: Ad libitum


title: 214011_RNAseq

value: Every 2 weeks


title: Not infected AL.2

value: Not infected


title: Not infected AL.1


title: macroH2A11_epi 1_1_2

description: RIN: 9.9


title: 214010_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: RD


title: 214009_RNAseq


title: 214007_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 215008_RNAseq


title: 214006_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: macroH2A11_epi 1_1_1

description: RIN: 7.4

value: Endothelial Cells (Umbilical Vein)


title: 212008_RNAseq

value: C

value: Never

value: pCR


title: CTL 3_II

description: RIN: 9.6

source_name: HUVEC- reprogrammed using Episome


title: MTB CR.3

value: Mycobacterium tuberculosis (virulent H37rv)

value: Caloric restricted


title: MTB CR.2

value: wild type

value: 17 weeks


title: CTL 3_I

description: RIN: 10


title: 212009_RNAseq

value: N1-2 (biopsy positive)


title: MTB CR.1

value: Spleen


title: 212006_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Every 2 weeks


title: 211012_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: Current


title: 212007_RNAseq

value: N0 (clinically negative or biopsy negative)


title: CTL EPI

description: RIN: 10


title: MTB AL.3

value: Ad libitum


title: MTB AL.2


title: 211009_RNAseq

value: RD


title: 211007_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: 211006_RNAseq

value: Former


title: 211005_RNAseq

value: Never


title: 211004_RNAseq

value: pCR


title: I-3356

city: Tehran

first: kolsoum

last: InanlooRahatloo

address: velenjak

country: Iran

institute: University of social welfare and rehabilitation sciences

data_processing:
Paired-end fastq sequence reads from each sample were quality and adaptor trimmed using trimmomatic (v0.36).
The trimmed reads were subsequently aligned to the UCSC human reference genome assembly hg19 and the human transcriptome sequences (Ensembl v70) using the ultrafast aligner the Spliced Transcripts Alignment to a Reference software (STAR, v. 2.5.3) with maximum tolerated mismatches set at 10 and the outSAMstrandField intronMotif option enabled8.
The trimmed reads were also assembled to hg19 using the Tophat v2.1.1 (http://tophat.cbcb.umd.edu) with the Illumina-supplied hg19 gene-model annotation file (gtf annotation). The number of reads uniquely mapped to each gene were counted using Python-HTSeq count module (version 0.5.3p9)
Differential expression analysis was performed on the counts data using DESeq2 (version 1.1.0, http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html)10.
Cufflinks (http://cufflinks.cbcb.umd.edu) was used to estimate the gene expression level (FPKM, fragments per kilobase of exon per million fragments mapped).
Briefly, after read counts were retrieved for each gene, differential gene expression was compared using the DESeq2 package in the following four groups: 1) two patients with mutation in CCNT2 gene and all 6 controls, 2) two patients with mutation in CDK9 gene and all 6 controls, 3) two patients with mutation in TAF2 gene and all 6 controls, and 4) all 6 patients and all 6 controls. Read counts for the patients and controls were compared to determine the log2-fold change in abundance of each transcript. In some cases, raw p-values were then adjusted for multiple testing with the Benjamini-Hochberg procedure. For CCNT2 and TAF2 family, genes with p-value of 0.01 or less and for CDK9 family genes with adjusted p-value of 0.05 or less were termed as differentially expressed genes. The analysis was performed using R 2.15 and R 3.1.3.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files are in excel format and contains differentially expressed genes with p value, fold change and q value.

source_name: blood

extract_protocol:
Total RNA from blood extracted using the QIAamp RNA Blood Kit (Qiagen) according to the manufacturer’s protocol.
Ten micrograms of total RNA was used to generate index-tagged paired-end cDNA libraries. Sample preparation was performed using TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina). Briefly, rRNA and globin RNA was depleted using Globin Removal Mix (Illumina). RNA fragmentation was performed using RNA Fragmentation Reagents (Life Technologies) to obtain 200–300 bp fragments. First strand cDNA was generated using the Superscript II Reverse Transcriptase and random hexamers (Life technologies). Second strand cDNA was synthesized and 3’ ends adenylation was performed (Illumina). Illumina sequencing adapters were ligated to cDNA and PCR amplification was performed on the adapter-ligated cDNA with 2X Phusion DNA polymerase Master Mix (New England Biolabs). Samples were sequenced 100bp (2×100) paired-end on Illumina HiSeq2500

tag: mutation

tag: conditon

value: control


title: I-3352


title: 211003_RNAseq


title: ICU 4

city: Paris

first: Agnes

last: Lehuen

address: 123, bd de Port-Royal

country: France

institute: Institut Cochin

description: ICU 4 = NGS20-039_run604-606/12/molecule_info.h5

data_processing:
Reference : refdata-gex-GRCh38-2020-A, from the 10X website
cellranger count –id=$id --transcriptome=$reference --fastqs=$fastqs --sample=$samplename --localcores=40
Supplementary_files_format_and_content: output from cellranger, bundled in tar. gz zrchive

source_name: PBMC

growth_protocol: MAIT cells defined as CD3+CD4–TCRgd-CD161hiVa7.2+Tetramer MR1+ were flow-sorted. Single-cell Gel Bead-In-EMulsions (GEMs) were generated using a Chromium Controller instrument (10x Genomics)

extract_protocol: Sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kits (10x Genomics)

value: MAIT cells

tag: infection

value: SARS-CoV-2 positive


title: ICU 3

description: ICU 3=  NGS20-039_resultats_4.0.0/Patient/molecule_info.h5


title: 210007_RNAseq


title: 210011_RNAseq


title: I-38386


title: I-3341

value: patient


title: ICU 2

description: ICU 2 = NGS20-039_resultats_4.0.0/Patient-GP/molecule_info.h5


title: I-38385


title: 204015_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 211011_RNAseq

value: Every 2 weeks


title: 204008_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: 204010_RNAseq

value: N1-2 (biopsy positive)


title: 204012_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Current


title: 211010_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: RD


title: I-38380


title: ICU 1

description: ICU 1 = NGS20-039_resultats_4.0.0/9/molecule_info.h5


title: 204007_RNAseq

value: B


title: Uninfected 3

description: Uninfected 3 = NGS20-039_resultats_4.0.0/Controle/molecule_info.h5

value: negative


title: 204006_RNAseq

value: Former


title: MTB AL.1

value: wild type

value: 17 weeks

value: Spleen

value: Mycobacterium tuberculosis (virulent H37rv)

value: Ad libitum


title: I-3333

value: control


title: 204004_RNAseq

value: Every 2 weeks

value: pCR


title: 204005_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Never


title: I-3332


title: I-3347

value: patient


title: 210008_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)


title: Uninfected 1

description: Uninfected 1 = NGS20-039_run604-606/11/molecule_info.h5

value: MAIT cells


title: 204002_RNAseq

value: Current


title: 203006_RNAseq

value: B


title: 204003_RNAseq

value: Former


title: I-3321


title: 202012_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: I-38382


title: HEK293flpGR3KR_RNAseq_ML792-Dex_rep1

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
FASTX-toolkit was used to trim low quality reads and sequence duplicates were collapsed
The reads were aligned to human reference genome version hg19 by using Bowtie software version 0.12.9
Peaks were called using HOMER program version 4.9. with default parameters in findPeaks. Rabbit IgG sample from HEK293flpFRT cells or mouse IgG sample from HEK293flpGR cells was used as control.
Alignment of RNA-seq data to human reference genome version hg19 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

molecule: polyA RNA

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), ML-792 + dex, RNA

growth_protocol: HEK293flpGR cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. HEK293flpPIAS1 cells were also supplemented with 15 µg/ml of blasticidin.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using Qiagen RNeasy Mini kit.
For ChIP-seq, NEBNext Ultra II DNA Library Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: HEK293flpGR cells were seeded at 70 % confluence in 10-cm plates and allowed to grow in steroid-depleted medium (2.5 % charcoal stripped FBS in DMEM) 72 h and the cells were subsequently treated wither with vehicle (EtOH) or 100 nM of dexamethasone for 1 h prior ChIP or ATAC. For RNA-seq 6 h hormone treatment was used. SAE inhibitor treatment was 1 uM for 24 h prior extraction. HEK293flpPIAS1 cells were treated with 100 ng/ml of tetracycline for 24 h prior ChIP.

tag: cell line

value: human embryonal kidney cell line

tag: stably expressing

value: SUMOylation-defective GR (GR3KR)

tag: treatment

value: ML-792 + dexamethasone

tag: concentration

tag: time


title: Uninfected 4

description: Uninfected 4 = NGS20-039_run604-606/14-YD/molecule_info.h5

tag: cell type

value: negative


title: HEK293flpGR3KR_RNAseq_ML792-Dex_rep2


title: HEK293flpGR3KR_RNAseq_ML792-EtOH_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), ML-792 + vehicle, RNA

value: ML-792 + EtOH


title: 202004_RNAseq

value: N1-2 (biopsy positive)

value: Every 3 weeks

value: pCR


title: 201017_RNAseq

value: Every 2 weeks

value: Never


title: 201016_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: N0 (clinically negative or biopsy negative)

value: RD


title: 201015_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Current


title: Uninfected 2

description: Uninfected 2 = NGS20-039_run604-606/13-RCM/molecule_info.h5

value: MAIT cells


title: 201014_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: HEK293flpGR3KR_RNAseq_ML792-EtOH_rep1

value: human embryonal kidney cell line

value: SUMOylation-defective GR (GR3KR)


title: 201013_RNAseq


title: 201011_RNAseq


title: I-3324

value: patient


title: HEK293flpGR3KR_RNAseq_DMSO-Dex_rep1

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), dex, RNA

value: DMSO + dexamethasone


title: 201010_RNAseq

value: pCR


title: 203001_RNAseq

value: N1-2 (biopsy positive)

value: Every 2 weeks

value: Former


title: 201008_RNAseq

value: Never


title: 202003_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 201006_RNAseq

value: Every 3 weeks


title: HEK293flpGR3KR_RNAseq_DMSO-EtOH_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, RNA

value: DMSO + EtOH


title: HEK293flpGR3KR_RNAseq_DMSO-EtOH_rep1


title: 200018_RNAseq


title: 200016_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: RD


title: 200013_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: HEK293flpGR_RNAseq_ML792-Dex_rep2

source_name: Isogenic HEK293 cells, wild-type GR, ML-792 + dex, RNA

value: wild-type GR

value: ML-792 + dexamethasone


title: HEK293flpGR3KR_RNAseq_DMSO-Dex_rep2

value: human embryonal kidney cell line

value: SUMOylation-defective GR (GR3KR)


title: HEK293flpGR_RNAseq_ML792-Dex_rep1


title: 200009_RNAseq


title: 200010_RNAseq

value: A

value: Current


title: 200021_RNAseq

value: N1-2 (biopsy positive)


title: 193004_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Every 2 weeks

value: pCR


title: 200004_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Every 3 weeks

value: Never


title: HEK293flpGR_RNAseq_ML792-EtOH_rep1

source_name: Isogenic HEK293 cells, wild-type GR, ML-792 + vehicle, RNA

value: ML-792 + EtOH


title: 193002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: RD


title: HEK293flpGR_RNAseq_DMSO-Dex_rep2

source_name: Isogenic HEK293 cells, wild-type GR, dex, RNA

value: wild-type GR

value: DMSO + dexamethasone


title: 83N

type: RNA

city: Guangzhou

first: yongmei

last: cui

address: No. 58, ZhongShan Second Road

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: Gene expression without any treatment

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed

scan_protocol: Slides were scanned immediately after washing using the Agilent DNA Microarray Scanner (part number G2505C). Scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). Genes that were expressed at a low level or close to the background level were excluded from further analyses. After quantile normalization of the raw data, genes that had at least 1 out of 3 samples flagged as detected (“All Targets Value”) were chosen for further data analysis.

source_name: Fresh Lung Tissue, Normal

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Store at liquid nitrogen

extract_protocol: Total RNA was harvested from fresh LUAD tissues using TRIzol (Roche, Indianapolis, USA) and an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was analyzed using a Nanodrop 2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Fresh lung tissues, collected from patients, were washed in PBS and cut into tissue block with a size of 0.5 cm diameter. These tissue block were loaded into 2ml freezing tubes, and stored at liquid nitrogen.

tag: gender

value: female

tag: age

tag: clinical stage

tag: smoke

value: no


title: LEN-N

description: Gene expression without any treatment

value: male


title: 193003_RNAseq

source_name: Tumor biopsy

value: N1-2 (biopsy positive)


title: 200012_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: HEK293flpGR_RNAseq_DMSO-Dex_rep1

value: human embryonal kidney cell line


title: 82N

description: Gene expression without any treatment


title: 88N

description: Gene expression without any treatment

value: yes


title: 53N

description: Gene expression without any treatment


title: 77N

description: Gene expression without any treatment


title: 51N

description: Gene expression without any treatment


title: 193001_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Former

value: pCR


title: 192001_RNAseq

value: Every 2 weeks

value: Never


title: 47N

description: Gene expression without any treatment


title: 42N

description: Gene expression without any treatment


title: 41N

description: Gene expression without any treatment


title: 190004_RNAseq

value: Current


title: HEK293flpGR_RNAseq_DMSO-EtOH_rep2

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, RNA

value: DMSO + EtOH


title: 200006_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Every 3 weeks


title: 190003_RNAseq


title: Q_N

description: Gene expression without any treatment

value: no


title: 35N

description: Gene expression without any treatment

value: female


title: HEK293flpGR_RNAseq_ML792-EtOH_rep2

value: wild-type GR

value: ML-792 + EtOH


title: 190001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: N1-2 (biopsy positive)


title: 40N

description: Gene expression without any treatment

value: male

value: yes


title: 165002_RNAseq

value: N0 (clinically negative or biopsy negative)

value: pCR


title: 164005_RNAseq

value: Every 2 weeks

value: Never

value: RD


title: 164004_RNAseq


title: HEK293flpGR_RNAseq_DMSO-EtOH_rep1

value: human embryonal kidney cell line

value: DMSO + EtOH


title: HEK293flpGR3KR_GR_ML792-EtOH_rep2

library_source: genomic

molecule: genomic DNA

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), ML-792 + vehicle, GR ChIP

value: SUMOylation-defective GR (GR3KR)

tag: chip antibody

value: GR (Santa Cruz, sc-1003, lot # D1812)


title: HEK293flpGR3KR_GR_ML792-Dex_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), ML-792 + dex, GR ChIP

value: ML-792 + dexamethasone


title: 164003_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 161002_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Every 3 weeks

value: Former


title: HEK293flpGR3KR_GR_ML792-Dex_rep1


title: HEK293flpGR3KR_GR_ML792-EtOH_rep1

value: ML-792 + EtOH


title: 161003_RNAseq

value: N1-2 (biopsy positive)


title: 31N

description: Gene expression without any treatment

value: female

value: no


title: 161001_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Every 2 weeks


title: 32N

description: Gene expression without any treatment


title: HEK293flpGR3KR_GR_DMSO-Dex_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), dex, GR ChIP

value: DMSO + dexamethasone


title: HEK293flpGR3KR_GR_DMSO-Dex_rep1

value: human embryonal kidney cell line


title: 159002_RNAseq

value: A

value: Never

value: pCR


title: 159003_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: RD


title: 159001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Current


title: HEK293flpGR3KR_GR_DMSO-EtOH_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, GR ChIP

value: SUMOylation-defective GR (GR3KR)

value: DMSO + EtOH

value: GR (Santa Cruz, sc-1003, lot # D1812)


title: 156003_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: 28N

description: Gene expression without any treatment

value: female

value: no


title: 156002_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Every 2 weeks


title: 164001_RNAseq

value: N1-2 (biopsy positive)


title: 1225869N

description: Gene expression without any treatment


title: 29N

description: Gene expression without any treatment


title: 22N

description: Gene expression without any treatment

value: male


title: HEK293flpGR3KR_GR_DMSO-EtOH_rep1

value: human embryonal kidney cell line


title: HEK293flpGR_GR_ML792-Dex_rep2

source_name: Isogenic HEK293 cells, wild-type GR, ML-792 + dex, GR ChIP

value: wild-type GR

value: ML-792 + dexamethasone


title: 159004_RNAseq

value: A

value: Never

value: RD


title: 150001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: 154003_RNAseq

value: Unknown


title: 156001_RNAseq


title: 154002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: pCR


title: HEK293flpGR_GR_ML792-Dex_rep1

value: GR (Santa Cruz, sc-1003, lot # D1812)


title: 149001_RNAseq

value: Every 3 weeks

value: Current


title: 149003_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)

value: Former


title: HEK293flpGR_GR_ML792-EtOH_rep2

source_name: Isogenic HEK293 cells, wild-type GR, ML-792 + vehicle, GR ChIP

value: human embryonal kidney cell line

value: wild-type GR

value: ML-792 + EtOH


title: 148002_RNAseq

value: Every 2 weeks

value: Never


title: 1185294N

description: Gene expression without any treatment

value: female

value: no


title: 0030422980N

description: Gene expression without any treatment

value: male


title: 148001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: N1-2 (biopsy positive)


title: 147002_RNAseq

value: A

value: pCR


title: 164002_RNAseq


title: HEK293flpGR_GR_ML792-EtOH_rep1

value: GR (Santa Cruz, sc-1003, lot # D1812)


title: 00568386N

description: Gene expression without any treatment


title: 0030417215N

description: Gene expression without any treatment


title: HEK293flpGR_GR_DMSO-Dex_rep2

source_name: Isogenic HEK293 cells, wild-type GR, dex, GR ChIP

value: DMSO + dexamethasone


title: 147001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)

value: Current

value: RD


title: 0030412011N

description: Gene expression without any treatment

value: yes


title: 144001_RNAseq

value: Every 2 weeks

value: Former


title: 139002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Never


title: HEK293flpGR_GR_DMSO-Dex_rep1

value: human embryonal kidney cell line

value: wild-type GR


title: 139001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: HEK293flpGR_GR_DMSO-EtOH_rep2

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, GR ChIP

value: DMSO + EtOH


title: HEK293flpGR_GR_DMSO-EtOH_rep1

value: GR (Santa Cruz, sc-1003, lot # D1812)


title: 0030402210N

description: Gene expression without any treatment

value: female

value: no


title: 136003_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: N1-2 (biopsy positive)

value: pCR


title: 133001_RNAseq

value: Every 2 weeks

value: Current

value: RD


title: 132001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: Neo4p13-200d_Rad21

city: Oxford

first: Marina

last: Murillo-Pineda

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
All analysis were perfomed using Galaxy platform
Reads were trimmed to keep bases 11 to 75 (version tool 1.0.2) and any reads smaller than 50 bp were removed (FASTQ filter tool). Reads were aligned to the human genome build hg38 and the mouse genome build mm10 using Bowtie 2 with very sensitive end to end preset option.Unmapped reads against mm10 were aligned against hg38 and duplicates were removed.
Internal calibration done as described previously (Bonhoure et al., 2014; Hu et al., 2015; Orlando et al., 2014). The factors were corrected using the read counts corresponding to Input samples as described in (Fursova et al., 2019).
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: BamCoverages (deeptool) normalized for read number and including the appropriate scaling factor due to internal normalization.

source_name: Transformed immortalized retinal pigment epithelium cells

growth_protocol: Cells were grown at 37°C, 5% CO2 in DMEM/F-12 cell culture media. Media was supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 14.5 mM sodium bicarbonate, 100 U/ml penicillin, 100 μg/ml streptomycin and 1% non-essential amino acids.

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
Sequencing libraries were generated and barcoded for multiplexing using adaptors described by (Buenrostro et al., 2013). The average size and concentration of all libraries was analyzed using the Fragment Analyzer system (Agilent) followed by qPCR using KAPA Library Quantification Kit (Illumina). Libraries were sequenced as 75 bp single-end reads on Illumina NextSeq 500 platform.

value: SV40 large-T antigen transformed hTERT RPE-1 cells (ATCC CRL-4000)

tag: days in continuous culture

value: Rad21 (Abcam- ab992)

tag: cell cycle

value: Mitotic enriched samples:cells were treated for 24h with 2.4 μM Eg5 inhibitor III (Dimethylenastron-DMEIII –Calbiochem-)


title: 129008_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: N0 (clinically negative or biopsy negative)

value: Never


title: 0030349249N

description: Gene expression without any treatment

value: female

value: no


title: 0030348590N

description: Gene expression without any treatment


title: 129005_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: 128001_RNAseq

value: N1-2 (biopsy positive)

value: pCR


title: 129002_RNAseq

value: Every 2 weeks


title: 129001_RNAseq

value: RD


title: Neo4p13-200d_inputRC

value: Random cycling cells


title: 128002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 136004_RNAseq


title: 0030338793N_1

description: Gene expression without any treatment


title: Neo4p13-100d_Rad21

value: SV40 large-T antigen transformed hTERT RPE-1 cells (ATCC CRL-4000)

value: Rad21 (Abcam- ab992)


title: 00030378704N

description: Gene expression without any treatment


title: 124004_RNAseq


title: 124003_RNAseq


title: 23N

description: Gene expression without any treatment

value: male


title: 123002_RNAseq

value: Current


title: 0030340180N

description: Gene expression without any treatment


title: 135001_RNAseq


title: Neo4p13-100d_inputMit

value: Mitotic enriched samples:cells were treated for 24h with 2.4 μM Eg5 inhibitor III (Dimethylenastron-DMEIII –Calbiochem-)


title: Neo4p13-200d_H3K9me3

value: H3K9me3 (Abcam-ab8898)


title: 129006_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Never


title: Neo4p13-200d_inputMit


title: 123001_RNAseq

value: Former


title: 121005_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: Unknown


title: 0001227682N

description: Gene expression without any treatment

value: yes


title: Neo4p13-100d_H3K9me3


title: 121004_RNAseq

value: N1-2 (biopsy positive)

value: Every 2 weeks

value: RD


title: Neo4p13-100d_inputRC

value: Random cycling cells


title: 0001217601N

description: Gene expression without any treatment

value: no


title: 121002_RNAseq


title: 121003_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 0001215629N

description: Gene expression without any treatment

value: female


title: 117007_RNAseq

value: pCR


title: 117009_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: 117003_RNAseq

value: N0 (clinically negative or biopsy negative)


title: Neo4p13_inputMit

value: SV40 large-T antigen transformed hTERT RPE-1 cells (ATCC CRL-4000)

value: Mitotic enriched samples:cells were treated for 24h with 2.4 μM Eg5 inhibitor III (Dimethylenastron-DMEIII –Calbiochem-)


title: Neo4p13_Rad21

value: Rad21 (Abcam- ab992)


title: 114008_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: Every 3 weeks

value: Never


title: 116001_RNAseq

value: N1-2 (biopsy positive)

value: Every 2 weeks

value: Current

value: RD


title: Neo4p13_H3K9me3

value: H3K9me3 (Abcam-ab8898)

value: Random cycling cells


title: 0001201499N

description: Gene expression without any treatment

value: male

value: no


title: Neo4p13_inputRC


title: 0001215469N

description: Gene expression without any treatment

value: female


title: 114007_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: N0 (clinically negative or biopsy negative)

value: pCR


title: 114001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: S40-RPE_Rad21

value: SV40 large-T antigen transformed hTERT RPE-1 cells (ATCC CRL-4000)

value: Rad21 (Abcam- ab992)

value: Mitotic enriched samples:cells were treated for 24h with 2.4 μM Eg5 inhibitor III (Dimethylenastron-DMEIII –Calbiochem-)


title: 0001213586N

description: Gene expression without any treatment


title: 0001200370N

description: Gene expression without any treatment

value: yes


title: S40-RPE_inputMit


title: 112006_RNAseq

value: A

value: Every 2 weeks

value: Never


title: 112007_RNAseq

value: Former


title: 117005_RNAseq

value: RD


title: 0001196092N

description: Gene expression without any treatment

value: male


title: 0001189546N

description: Gene expression without any treatment


title: 113001_RNAseq

value: N1-2 (biopsy positive)


title: 0001188096N

description: Gene expression without any treatment

value: no


title: 112004_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Every 3 weeks


title: S40-RPE_H3K9me3

value: H3K9me3 (Abcam-ab8898)

value: Random cycling cells


title: 114003_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)


title: 0001224139N

description: Gene expression without any treatment


title: 110019_RNAseq

value: Current

value: pCR


title: 0001187889N

description: Gene expression without any treatment


title: 110018_RNAseq

value: A


title: 110016_RNAseq

value: Every 2 weeks


title: 110014_RNAseq

value: Never


title: 0001185076N

description: Gene expression without any treatment

value: female


title: 110008_RNAseq


title: Neo4p13_CA

data_processing:
All analysis were perfomed using Galaxy platform
Reads were aligned to the human genome build hg38 using BWA and duplicates were removed.
Genome_build: hg38
Supplementary_files_format_and_content: BamCoverages samples (deeptool) normalized for read number (rpkm) and also Bamcompare showing the coverage of the CA IP substracting the input

extract_protocol:
Lysates were clarified from native enriched chromatin digested with micrococcal nuclease and protein-DNA complexes were isolated with antibody.
For library preparation we used NEBNext Ultra II DNA library prep kit for Illumina (E7645) and NEBnext Multiplex oligos for Illumina (NEB E7335) using the manufacturer's recommendations. Libraries were size-selected using AMPure XP magnetic beads (Beckman Coulter) to exclude polynucleosomes (200bp + adaptors size) and PCR amplified before submission to 75-bp single-end sequencing on Illumina NextSeq 500 platform.

value: SV40 large-T antigen transformed hTERT RPE-1 cells (ATCC CRL-4000)

value: CENP-A clone A5 from (Ando et al., 2002) or abcam ab13939


title: Neo4p13_neg


title: 109002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Former

value: RD


title: Neo4p13_input


title: 0001166241N

description: Gene expression without any treatment

value: no


title: HEK293flpGR3KR_ATAC_dex_rep2

data_processing:
Basecalls performed using CASAVA
FASTX-toolkit was used to trim low quality reads and sequence duplicates were collapsed
The reads were aligned to human reference genome version hg19 by using Bowtie software version 0.12.9
Peaks were called using HOMER program version 4.9. with default parameters in findPeaks. Rabbit IgG sample from HEK293flpFRT cells or mouse IgG sample from HEK293flpGR cells was used as control.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), dex, ATAC

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit.
For ChIP-seq, NEBNext Ultra II DNA Library Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit

treatment_protocol: HEK293flpGR cells were seeded at 70 % confluence in 10-cm plates and allowed to grow in steroid-depleted medium (2.5 % charcoal stripped FBS in DMEM) 72 h and the cells were subsequently treated wither with vechicle (EtOH) or 100 nM of dexamethasone for 1 h prior ChIP. HEK293flpPIAS1 cells were treated with 100 ng/ml of tetracycline for 24 h prior ChIP.

value: human embryonal kidney cell line

value: SUMOylation-defective GR (GR3KR)

value: dexamethasone

value: 1 h


title: 107019_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N1-2 (biopsy positive)


title: 0001164948N

description: Gene expression without any treatment


title: 107016_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: N0 (clinically negative or biopsy negative)


title: 30N

description: Gene expression without any treatment

value: female


title: 107015_RNAseq

value: Every 2 weeks

value: pCR


title: 107017_RNAseq

value: A

value: Never


title: HEK293flpGR3KR_ATAC_dex_rep1


title: 0001164189N

description: Gene expression without any treatment


title: 107010_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Former


title: S40-RPE_inputRC

value: SV40 large-T antigen transformed hTERT RPE-1 cells (ATCC CRL-4000)

value: Random cycling cells


title: 110010_RNAseq

value: RD


title: 107008_RNAseq


title: 110015_RNAseq

value: Current


title: 107003_RNAseq


title: 0001162111N_1

description: Gene expression without any treatment

value: male

value: no


title: HEK293flpGR3KR_ATAC_EtOH_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, ATAC

value: human embryonal kidney cell line

value: SUMOylation-defective GR (GR3KR)

value: EtOH vehicle

value: 1 h


title: 0001156551N_1

description: Gene expression without any treatment


title: HEK293flpGR3KR_ATAC_EtOH_rep1


title: 190002_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Every 2 weeks


title: 0001156496N

description: Gene expression without any treatment

value: yes


title: 106012_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: Never

value: pCR


title: 106013_RNAseq


title: HEK293flpGR_ATAC_dex_rep2

source_name: Isogenic HEK293 cells, wild-type GR, dex, ATAC

value: wild-type GR

value: dexamethasone


title: HEK293flpGR_ATAC_dex_rep1


title: 106007_RNAseq

value: Former


title: 106010_RNAseq

value: N1-2 (biopsy positive)

value: Every 3 weeks

value: RD


title: Q_T

description: Gene expression without any treatment

source_name: Fresh Lung Tissue, Tumor

value: male

value: ⅣA

value: no

tag: differentiation

value: moderate


title: 106009_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: N0 (clinically negative or biopsy negative)


title: 106008_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Every 2 weeks


title: HEK293flpGR_ATAC_EtOH_rep2

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, ATAC

value: human embryonal kidney cell line

value: EtOH vehicle

value: 1 h


title: 106004_RNAseq

value: Never

value: pCR


title: LEN-T

description: Gene expression without any treatment

value: Ⅳ


title: HEK293flpGR_ATAC_EtOH_rep1

value: wild-type GR


title: 105007_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: 107007_RNAseq

value: Former


title: 105006_RNAseq

value: N1-2 (biopsy positive)


title: 105005_RNAseq


title: 105004_RNAseq


title: 105003_RNAseq


title: HEK293flpGR3KR_H3K4me2_dex_rep1

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), dex, H3K4me2 ChIP

value: SUMOylation-defective GR (GR3KR)

value: dexamethasone


title: HEK293flpGR3KR_H3K4me2_EtOH_rep1

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, H3K4me2 ChIP


title: 83T

description: Gene expression without any treatment

value: female

value: no

value: moderate


title: HEK293flpGR3KR_SUMO2_EtOH_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, SUMO-2/3 ChIP

value: SUMO-2/3 (MBL International, M114-3, lot # 25)


title: 104010_RNAseq

source_name: Tumor biopsy

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: N0 (clinically negative or biopsy negative)

value: Every 2 weeks

value: RD


title: 82T

description: Gene expression without any treatment

value: Ⅳ


title: 88T

description: Gene expression without any treatment

value: male

value: yes

value: low


title: 77T

description: Gene expression without any treatment

value: ⅣC


title: 106006_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: N1-2 (biopsy positive)

value: Never


title: 104008_RNAseq

value: pCR


title: 104009_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Former


title: 51T

description: Gene expression without any treatment

value: female

value: no

value: moderate


title: 104006_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: N0 (clinically negative or biopsy negative)

value: Every 2 weeks


title: 102004_RNAseq

value: Every 3 weeks


title: 104007_RNAseq

value: RD


title: HEK293flpGR_H3K4me2_EtOH_rep1

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, H3K4me2 ChIP

value: human embryonal kidney cell line

value: wild-type GR

value: EtOH vehicle

value: 1 h


title: 53T

description: Gene expression without any treatment

value: ⅣA


title: HEK293flpGR_SUMO2_EtOH_rep3

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, SUMO-2/3 ChIP

value: SUMO-2/3 (MBL International, M114-3, lot # 25)


title: HEK293flpGR_H3K4me2_dex_rep2

source_name: Isogenic HEK293 cells, wild-type GR, dex, H3K4me2 ChIP

value: dexamethasone


title: 102003_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Former


title: 102001_RNAseq

value: N1-2 (biopsy positive)

value: Current


title: 0001024264N

description: Gene expression without any treatment

source_name: Fresh Lung Tissue, Normal

value: male

value: no


title: 105002_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: N0 (clinically negative or biopsy negative)

value: Every 2 weeks

value: Never


title: HEK293flpGR3KR_NCOA1_dex_rep1

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), dex, NCOA1 ChIP

value: human embryonal kidney cell line

value: SUMOylation-defective GR (GR3KR)

value: NCOA1 (Bethyl, A300-343A, lot # 2)


title: HEK293flpGR3KR_NCOA1_EtOH_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, NCOA1 ChIP

value: EtOH vehicle

value: 1 h


title: HEK293flpGR3KR_NCOA1_EtOH_rep1


title: 40T

description: Gene expression without any treatment

value: Ⅳ

value: yes

value: moderate


title: HEK293flpGR3KR_NCOA1_dex_rep2

value: dexamethasone


title: 42T

description: Gene expression without any treatment

value: ⅣC


title: 47T

description: Gene expression without any treatment

value: male


title: 41T

description: Gene expression without any treatment

value: female

value: no


title: HEK293flpGR3KR_NCOR1_dex_rep2

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), dex, NCOR1 ChIP

value: NCOR1 (Bethyl, A301-145A, lot # 2)


title: 35T

description: Gene expression without any treatment


title: HEK293flpGR3KR_NCOR1_dex_rep1


title: 31T

description: Gene expression without any treatment

value: ⅢB


title: 30T

description: Gene expression without any treatment

value: ⅢA


title: HEK293flpFRT_dex_IgG_rep1

description: isogenic HEK293 control FRT cells were created by using the Flp-In System (Invitrogen)

data_processing:
Basecalls performed using CASAVA
FASTX-toolkit was used to trim low quality reads and sequence duplicates were collapsed
The reads were aligned to human reference genome version hg19 by using Bowtie software version 0.12.9
Peaks were called using HOMER program version 4.9. with default parameters in findPeaks. Rabbit IgG sample from HEK293flpFRT cells or mouse IgG sample from HEK293flpGR cells was used as control.
Genome_build: hg19
Supplementary_files_format_and_content: none

source_name: Isogenic HEK293 cells, FRT background, dex, IgG ChIP

value: Rabbit IgG (Santa Cruz, sc-2027, lot # A2412)


title: HEK293flpGR3KR_SUMO2_EtOH_rep1

value: human embryonal kidney cell line

value: SUMO-2/3 (MBL International, M114-3, lot # 24)


title: HEK293flpGR3KR_NCOR1_EtOH_rep1

source_name: Isogenic HEK293 cells, SUMOylation-defective GR (GR3KR), vehicle, NCOR1 ChIP

value: SUMOylation-defective GR (GR3KR)


title: HEK293flpPIAS1_Pol2_tet_rep2

source_name: Isogenic HEK293 cells, 3x-FLAG-PIAS1, tet, RNA polymerase II ChIP

value: tetracycline

value: 100 ng/ml

value: RNA polymerase II (Covance Incorporation, MMS-126R, lot # E12CF00481)


title: HEK293flpPIAS1_Pol2_tet_rep1


title: HEK293flpGR3KR_NCOR1_EtOH_rep2

value: EtOH vehicle

value: 1 h


title: 32T

description: Gene expression without any treatment

value: moderate


title: HEK293flpGR_NCOA1_EtOH_rep2

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, NCOA1 ChIP

value: wild-type GR

value: NCOA1 (Bethyl, A300-343A, lot # 2)


title: HEK293flpGR_NCOA1_dex_rep1

source_name: Isogenic HEK293 cells, wild-type GR, dex, NCOA1 ChIP

value: dexamethasone


title: 28T

description: Gene expression without any treatment

source_name: Fresh Lung Tissue, Tumor

value: female

value: no


title: HEK293flpGR_NCOA1_EtOH_rep1


title: 0030422980T

description: Gene expression without any treatment

value: male


title: 1185294T

description: Gene expression without any treatment

value: ⅢA


title: 00568386T

description: Gene expression without any treatment


title: 22T

description: Gene expression without any treatment


title: 29T

description: Gene expression without any treatment


title: 0030417215T

description: Gene expression without any treatment


title: HEK293flpGR_NCOR1_dex_rep1

source_name: Isogenic HEK293 cells, wild-type GR, dex, NCOR1 ChIP

value: NCOR1 (Bethyl, A301-145A, lot # 2)


title: HEK293flpGR_NCOR1_EtOH_rep2

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, NCOR1 ChIP

value: human embryonal kidney cell line


title: 1225869T

description: Gene expression without any treatment


title: 0030412011T

description: Gene expression without any treatment

value: ⅢB

value: yes


title: HEK293flpGR_NCOA1_dex_rep2


title: HEK293flpGR_NCOR1_EtOH_rep1


title: HEK293flpGR_NCOR1_dex_rep2


title: 0030402210T

description: Gene expression without any treatment

value: ⅡA


title: 0030340180T

description: Gene expression without any treatment


title: 23T

description: Gene expression without any treatment


title: cell_line

city: San Francisco

first: George

middle: Christopher

last: Hartoularos

state: CA

address: 513 Parnassus Ave S965F

department: Graduate Division

institute: University of California, San Francisco

description: Combinatorially-indexed transcriptome

data_processing:
Fastq files generated from raw Illumina base calls using bcl2fastq v2.0, demultiplexed along the second combinatorial barcode.
Reads trimmed using Trim Galore v0.6.5 with parameters: -a AAAAAAAA --three_prime_clip_R1 1
Reads aligned using STAR v2.7.0a with parameters: --outFilterMatchNminOverLread 0.3 --outSAMstrandField intronMotif
Reads quality filtered using samtools v1.10 with parameters: view -bh -q 30 -F 4
Reads UMI deduplicated and split along the first combinatorial barcode using a custom python script.
Cell by gene matrix generated using a custom python script.
Genome_build: Merged GRCm38 GRCh38 genome
Supplementary_files_format_and_content: 10X_raw_feature_bc_matrix.h5: 10x-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: 10X_mouse_down_processed.h5ad: AnnData-formatted h5 file containing a matrix with downsampled, transformed counts from mouse cells of a liver slice.
Supplementary_files_format_and_content: L10C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L30C8.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L30C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L20C1.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L20T.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: cell_line_raw_labeled.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a cell line mixture.
Supplementary_files_format_and_content: S10C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S20C2.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S20C1.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S15C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: liver_all_raw_labeled.loom: Loom file containing a matrix with raw counts and cell labels from multiple liver slices.
Supplementary_files_format_and_content: spleen_all_raw_labeled.h5ad: AnnData-formatted h5 file containing a matrix with raw counts and cell labels from multiple spleen slices.

organism:
Homo sapiens
Mus musculus

source_name: mixture of HEK293t and 3T3 cell lines

growth_protocol: MC38 cell line was cultured in complete cell culture medium (RPMI 1640 with GlutaMAX, penicillin, streptomycin, sodium pyruvate, HEPES, NEAA, and 10% fetal bovine serum).

extract_protocol:
Cell lysis and amplification.
In-situ reverse transcription on spatially barcoded microwell array. Pooling cells off array and FACS sorting for secondary indexing. Cell lysis, reverse transcription template switching and barcoded cDNA amplification. cDNA tagmentation amplification with primers containing short-read sequencing adapters (Illumina).
Combinatorial indexing for single cell barcoding. Initial barcoding step provides 2-dimensional spatial index.

treatment_protocol: MC38 tumor cells (5x10^5 cells) were injected directly into liver or spleen of a C57BL/6 mouse. 10 days post tumor inoculation, mice were sacrificed and harvested. Organs were fixed in dithiobis (succinimidyl propionate) (DSP) and cryopreserved.

tag: mouse cell line

tag: human cell line


title: HEK239flpGR_siUBC9_dex_6h_rep1

description:
UBC9_10
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol. Arrays were scanned by Illumina BeadArray Reader.

data_processing: Obtained data was normalized using VST transformation and RSN normalization used as standard approach for Illumina arrays with the R/lumi package.

label: biotin

source_name: Isogenic HEK293 cells, wild-type GR, siUBC9 treated, 72h, dex treated, 6h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmk kit for Illumina arrays.

growth_protocol: Isogenic HEK293 cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 100 µg hygromycin-B, and kept at 37 °C in a humidified 95% air/ 5% CO2.

extract_protocol: Total RNA was extracted using TriPure (Roche Diagnostics GmbH, Mannheim, Germany) according to manufacturer's instructions.

treatment_protocol: siUBC9 or siNON in 40 nM final concentration were added with Lipofectamine RNAiMAX to 6-well plates and incubated for 20 min RT. Subsequently, 300,000 isogenic HEK293 cells were seeded at each 6-well plates and allowed to grow in steroid-depleted medium (2.5% charcoal stripped FBS in DMEM) 72 h. The cells were treated with or without 100 nM of dexamethasone for 6 h prior extraction of RNA.

tag: sirna treatment

value: Dharmacon On-TARGETplus SMARTpool for human UBE2I

tag: sirna concentration

value: 40 nM

tag: time for sirna

tag: ligand treatment

tag: ligand concentration

tag: time for ligand

value: 6 h


title: HEK239flpGR_siUBC9_vehicle_6h_rep3

description:
UBC9_9
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

source_name: Isogenic HEK293 cells, wild-type GR, siUBC9 treated, 72h, vehicle treated, 6h

tag: cell line

tag: cell type

tag: stably expressing

value: EtOH vehicle


title: HEK239flpGR_siUBC9_dex_6h_rep3

description:
UBC9_12
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).


title: PN_3

city: Beijing

first: Yan-Tao

last: Ma

address: No. 5 Yiheyuan Road

institute: Peking University

description:
PE150
fpkm_all_samples.txt

data_processing:
RNA-seq reads from each sample were aligned to mouse reference genome mm10 by using TopHat22 (version 2.1.1) with default parameters.
Gene expression levels (FPKM values) were quantified by Cuffdiff3 (version2.2.1).
For differential gene expression analysis, reads count of each gene were obtained by HTSeq4 (version 0.11.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: fpkm_all_samples.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: brain

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: primary neurons


title: 0030349249T

description: Gene expression without any treatment

tag: gender

tag: age

tag: clinical stage

tag: smoke

value: high


title: HEK293flpGR_IgG_dex_rep1

source_name: Isogenic HEK293 cells, wild-type GR, dex, IgG ChIP

value: wild-type GR

tag: treatment

tag: concentration

tag: time

value: 1 h

tag: chip antibody

value: IgG (Santa Cruz Biotechnology, sc-2025, lot # H1512)


title: 0030338793T_1

description: Gene expression without any treatment

value: female

value: no

tag: differentiation

value: moderate


title: HEK239flpGR_siNON_dex_6h_rep3

description:
NON_6
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

source_name: Isogenic HEK293 cells, wild-type GR, siNON treated, 72h, dex treated, 6h

tag: sirna treatment

value: Dharmacon On-TARGETplus SMARTpool for nontargeting pool

tag: sirna concentration

tag: time for sirna

value: dexamethasone


title: PN_1

description:
PE150
fpkm_all_samples.txt


title: PN_2

description:
PE150
fpkm_all_samples.txt


title: HEK293flpPIAS1_H3K4me2_tet_rep1

description: HEK293flpPIAS1 cells were created by using the Flp-In T-REx System (Invitrogen).

data_processing:
Basecalls performed using CASAVA.
FASTX-toolkit was used to trim low-quality reads and sequence duplicates were collapsed.
The reads were aligned to human reference genome version hg19 by using Bowtie software version 0.12.9 with the command line: -e 70 -l 50 -n 1 -k 1 -m1 \ -t -p 12 -q -S --best
Peaks were called using HOMER program version 4.6 with default parameters in findPeaks. Rabbit IgG immunoprecipitated sample from HEK293flpFRT cells was used as control.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: HOMER program generated bedGraph (makeUCSCfile-command) from alignment file.

source_name: Isogenic HEK293 cells, 3x-FLAG-PIAS1, tet, H3K4me2 ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with 1 µg of antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HEK293flpGR cells were seeded at 70% confluence in 10-cm plates and allowed to grow in steroid-depleted medium (2.5% charcoal stripped FBS in DMEM) 72 h, and the cells were subsequently treated with vehicle (EtOH) or 100 nM of dexamethasone for 1 h prior to ChIP. HEK293flpPIAS1 cells were treated with 100 ng/ml of tetracycline for 24 h prior to ChIP.

value: human embryonal kidney cell line

value: tetracycline

value: 100 ng/ml


title: 00030378704T

description: Gene expression without any treatment

value: ⅡA


title: HEK239flpGR_siUBC9_vehicle_6h_rep2

description:
UBC9_8
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

value: Dharmacon On-TARGETplus SMARTpool for human UBE2I

value: 40 nM

tag: ligand treatment

tag: ligand concentration

tag: time for ligand


title: HEK293flpPIAS1_PIAS1+2_tet_rep2

source_name: Isogenic HEK293 cells, 3x-FLAG-PIAS1, tet, PIAS1+2 ChIP

tag: cell line

tag: cell type

tag: stably expressing

value: PIAS1+PIAS2 (Abcam, ab77231, lot # YI122105C)


title: 0030348590T

description: Gene expression without any treatment

tag: gender

tag: age

value: ⅡB


title: HEK293flpPIAS1_PIAS1+2_tet_rep1


title: D16_3

description:
PE150
fpkm_all_samples.txt

tag: strain

value: chemical-induced neurons at D16


title: HEK293flpPIAS1_SUMO2_tet_rep1

source_name: Isogenic HEK293 cells, 3x-FLAG-PIAS1, tet, SUMO-2/3 ChIP

tag: treatment

value: SUMO-2/3 (MBL International, M114-3, lot # 24)


title: D16_2

description:
PE150
fpkm_all_samples.txt


title: HEK293flpPIAS1_SUMO2_tet_rep2

tag: concentration


title: HEK293flpGR_Pol2_dex_rep1

description: HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

source_name: Isogenic HEK293 cells, wild-type GR, dex, RNA polymerase II ChIP

value: wild-type GR

tag: time

value: 1 h

value: RNA polymerase II (Covance Incorporation, MMS-126R, lot # E12CF00481)


title: ML300  CON [re-used]

first: Annie

last: Kathuria

address: 185 cambridge street

institute: Mass Gen Hospital

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: 2D cortical neurons_control

growth_protocol: Shi et al protocol (https://www.nature.com/articles/nprot.2012.116)

extract_protocol:
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R

tag: subject status

value: healthy control

value: Human iPSC derieved cortical neurons

value: 3 months of differention


title: D16_1

description:
PE150
fpkm_all_samples.txt


title: ML292  CON [re-used]


title: ML226  CON [re-used]


title: 0001224139T

description: Gene expression without any treatment

value: male

tag: clinical stage

tag: smoke

value: yes

tag: differentiation

value: moderate


title: HEK239flpGR_siNON_vehicle_6h_rep2

description:
NON_2
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

source_name: Isogenic HEK293 cells, wild-type GR, siNON treated, 72h, vehicle treated, 6h

value: human embryonal kidney cell line

tag: sirna treatment

value: Dharmacon On-TARGETplus SMARTpool for nontargeting pool

tag: sirna concentration

tag: time for sirna

value: EtOH vehicle

value: 6 h


title: D8_3

description:
PE150
fpkm_all_samples.txt

value: chemical-induced neurons at D8


title: HEK293flpGR_Pol2_EtOH_rep1

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, RNA polymerase II ChIP

tag: chip antibody


title: 0001227682T

description: Gene expression without any treatment

value: ⅡB


title: HEK239flpGR_siNON_vehicle_6h_rep3

description:
NON_3
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

tag: cell line

value: 40 nM

tag: ligand treatment

tag: ligand concentration

tag: time for ligand


title: 0001217601T

description: Gene expression without any treatment

tag: gender

tag: age

value: no

value: low


title: 0001215629T

description: Gene expression without any treatment

value: female


title: HEK239flpGR_siUBC9_vehicle_6h_rep1

description:
UBC9_7
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

tag: cell type

tag: stably expressing

value: wild-type GR

value: Dharmacon On-TARGETplus SMARTpool for human UBE2I


title: 0001215469T

description: Gene expression without any treatment

value: ⅡA


title: ML126  CON [re-used]

value: healthy control

value: Human iPSC derieved cortical neurons

value: 3 months of differention


title: HEK239flpGR_siNON_dex_6h_rep1

description:
NON_4
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

value: dexamethasone


title: HEK293flpGR_H3K4me2_dex_rep1

source_name: Isogenic HEK293 cells, wild-type GR, dex, H3K4me2 ChIP

value: human embryonal kidney cell line

tag: treatment

tag: concentration

tag: time

value: 1 h


title: HEK239flpGR_siNON_dex_6h_rep2

description:
NON_5
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

value: Dharmacon On-TARGETplus SMARTpool for nontargeting pool


title: 0001213586T

description: Gene expression without any treatment

source_name: Fresh Lung Tissue, Tumor

tag: clinical stage

tag: smoke

value: moderate


title: HEK239flpGR_siNON_vehicle_6h_rep1

description:
NON_1
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

tag: sirna treatment

value: EtOH vehicle

value: 6 h


title: ML135  CON [re-used]

tag: subject status


title: HEK239flpGR_siUBC9_dex_6h_rep2

description:
UBC9_11
HEK293flpGR cells were created by using the Flp-In System (Invitrogen).

tag: sirna concentration

value: 40 nM

tag: time for sirna


title: HEK293flpGR_PIAS1+2_dex_rep2

source_name: Isogenic HEK293 cells, wild-type GR, dex, PIAS1+2 ChIP

tag: cell line

tag: chip antibody

value: PIAS1+PIAS2 (Abcam, ab77231, lot # YI122105C)


title: HEK293flpGR_PIAS1+2_dex_rep1


title: 0001201499T

description: Gene expression without any treatment

value: male

value: ⅡB

value: no

tag: differentiation


title: ML56  CON [re-used]


title: D4_3

description:
PE150
fpkm_all_samples.txt

tag: strain

value: chemical-induced neurons at D4


title: D8_1

description:
PE150
fpkm_all_samples.txt

value: chemical-induced neurons at D8


title: ML51  CON [re-used]

value: healthy control


title: D4_2

description:
PE150
fpkm_all_samples.txt


title: HEK293flpGR_PIAS1+2_EtOH_rep2

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, PIAS1+2 ChIP

value: wild-type GR


title: D4_1

description:
PE150
fpkm_all_samples.txt


title: D0_3

description:
PE150
fpkm_all_samples.txt

value: astrocytes


title: ML15 CON

value: Human iPSC derieved cortical neurons

value: 3 months of differention


title: ML27 CON [re-used]


title: D0_2

description:
PE150
fpkm_all_samples.txt


title: ML233 SCZ

source_name: 2D cortical neurons_SCZ

value: schizophrenia (SCZ) patient


title: ML250 SCZ


title: cKO_rep3

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by featureCounts.
Genome_build: mm10

source_name: Dnmt1 KO_satellite cells

growth_protocol: Mice were generated using Pax7-CreERT2 and Dnmt1 flox mice.

extract_protocol:
Total RNA was extracted with Isogen (Nippon gene, Japan) and RNeasy spin column kit (Qiagen, USA). 1 µg of RNA samples with RNA integrity number (RIN) greater than 8 were used for library prepairation.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently validated for an average size of about 305-310 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit for the construction of sequencing libraries.

treatment_protocol: Seven-week-old male mice were treated with Tamoxifene or vehicle for 5 consecutive days.

tag: strain background

tag: genotype/variation

value: Dnmt1 KO

value: 7 weeks old

tag: gender

value: skeletal muscle satellite cells


title: HEK293flpGR_SUMO2_EtOH_rep1

source_name: Isogenic HEK293 cells, wild-type GR, vehicle, SUMO-2/3 ChIP

tag: cell type

value: human embryonal kidney cell line

tag: stably expressing

value: EtOH vehicle

value: 1 h

value: SUMO-2/3 (MBL International, M114-3, lot # 24)


title: HEK293flpGR_SUMO2_EtOH_rep2

tag: treatment

tag: concentration


title: ML164 SCZ

tag: age


title: CGTACTAG

data_processing:
Reads were processed using the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/)
Individual cells were tagged with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers).
Reads were trimmed at 3' end to remove poly(A) tails with length greater than 5 and at the 5' end for adapters
Reads with barcode base quality less than 10 were filtered out.
Raw reads were aligned to mouse  (GRCm38) genome by STAR (v2.4.0) with default settings
UMI counts expression matrix were generated using Dropseq Tools software (v1.13.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file consisting of UMI gene counts for cells with minimum 500 genes.

source_name: Flow cytometry sorted astrocytes based on TdTomato fluorscence

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on TdTomato fluorescence. Post-sort, cells were suspended in PBS and 16% Opti-prep.
Libraries were created according to the Drop-seq protocol in Macosko et al. Cell 2015. Following reverse transcription, exonuclease I treatment, and PCR, cDNA libraries were quantified and 600 pg of cDNA was tagmented using Nextera XT library prep kit.

value: WT C57Bl/6

tag: Sex

value: Male


title: 0001196092T

description: Gene expression without any treatment

value: male

tag: clinical stage

value: ⅠA

tag: smoke

value: yes

value: moderate


title: 0001189546T

description: Gene expression without any treatment


title: 0001188096T

description: Gene expression without any treatment

value: no


title: 0001164948T

description: Gene expression without any treatment

value: female

value: low


title: 0001187889T

description: Gene expression without any treatment

value: ⅠB


title: 0001166241T

description: Gene expression without any treatment


title: ML141 SCZ

tag: subject status

value: schizophrenia (SCZ) patient

value: Human iPSC derieved cortical neurons

value: 3 months of differention


title: HEK293flpGR_PIAS1+2_EtOH_rep1

value: human embryonal kidney cell line

value: wild-type GR

tag: time

value: PIAS1+PIAS2 (Abcam, ab77231, lot # YI122105C)


title: cKO_rep1

value: Dnmt1 KO

value: 7 weeks old

value: skeletal muscle satellite cells


title: ML67 SCZ


title: cKO_rep2

value: male


title: TAGGCATG

value: WT C57Bl/6

value: Male


title: TAGCGCTC

value: Female


title: D0_1

description:
PE150
fpkm_all_samples.txt

source_name: brain

value: astrocytes


title: 0001164189T

description: Gene expression without any treatment

value: female

value: ⅠA

value: no

value: moderate


title: 0001162111T

description: Gene expression without any treatment


title: 0001185076T

description: Gene expression without any treatment

value: ⅠB

value: high


title: Control_rep3

source_name: control_satellite cells

value: control


title: ML40 SCZ

value: schizophrenia (SCZ) patient

value: Human iPSC derieved cortical neurons

value: 3 months of differention


title: ML37 SCZ


title: Control_rep1

value: 7 weeks old


title: TAAGGCGA


title: 0001156496T

description: Gene expression without any treatment

value: yes


title: 24MUBR4KO-2

status: Public on Jan 07 2021

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: 24 months UBR4 knockout replicate 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all 16 samples

source_name: tibialis anterior muscles from male mice

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from UBR4 mKO tibialis anterior muscle at 6 and 24 months of age.
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 2000 platform.

tag: tissue

value: Tibialis anterior muscles

value: male

value: 24 months

tag: genotype

value: UBR4 knockout


title: 24MUBR4KO-4

description: 24 months UBR4 knockout replicate 4


title: ML33 SCZ


title: 24MUBR4KO-3

description: 24 months UBR4 knockout replicate 3


title: 0001156551T

description: Gene expression without any treatment

tag: differentiation

value: low


title: Control_rep2

value: skeletal muscle satellite cells


title: 0001024264T

description: Gene expression without any treatment

value: ⅠA


title: 24MWT-2

description: 24 months wild type replicate 2

tag: strain

value: wild type


title: 24MUBR4KO-1

description: 24 months UBR4 knockout replicate 1


title: 6MUBR4KO-2

description: 6 months UBR4 knockout replicate 2

value: 6 months


title: 6MUBR4KO-4

description: 6 months UBR4 knockout replicate 4


title: 24MWT-1

description: 24 months wild type replicate 1


title: 24MWT-4

description: 24 months wild type replicate 4


title: GGACTCCT

value: WT C57Bl/6

value: Female


title: 6MUBR4KO-1

description: 6 months UBR4 knockout replicate 1


title: 6MWT-3

description: 6 months wild type replicate 3


title: 6MWT-2

description: 6 months wild type replicate 2


title: 6MWT-1

description: 6 months wild type replicate 1


title: 6MWT-4

description: 6 months wild type replicate 4


title: EVD5_1

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Genome_build: mm10
Supplementary_files_format_and_content: txt files of normalized gene counts for each sample

source_name: Colon

extract_protocol:
Colon were removed, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 6 weeks


title: EVD5_2


title: WTD5_2


title: 24MWT-3

description: 24 months wild type replicate 3


title: WTD5_1


title: SCF SVF 8w C57BL/6J WT

city: Neuherberg

first: Matthias

last: Heinig

address: Ingolstädter Landstrasse

country: Germany

institute: Helmholtz-Zentrum München

data_processing:
Pre-processing of sequencing results to generate transcript matrices was performed using the 10x genomics Cell Ranger pipeline with default settings (v2.1.1) and aligning to the GRC38 genome build and genome annotation release 94 from Ensembl.
Genome_build: GRCm38
Supplementary_files_format_and_content: QC filtered cell ranger output consists of gene by barcode (cell) count matrices in sparse matrix market format (mtx) and corresponding row and column annotation in *genes.tsv and *barcode.tsv files

source_name: Subcutaneous white adipose tissue

extract_protocol:
Inguinal subcutaneous white adipose tissues were isolated from 2 and 8 week old, male WT C57BL/6 mice. SCF was minced and digested with 1mg/ml type-A collagenase (Gibco) in DMEM (Gibco) for 30 minutes at 37°C. The SVF was obtained by centrifugation and live cells were sorted using flow cytometry following dead cell exclusion using 7-AAD.
Single cell libraries were generated using the ChromiumTM Single cell 3'library and gel bead kit v2 (PN #120237) from 10x Genomics.

value: Stromal vascular fraction of subcutaneous white adipose tissue

value: post natal week 8


title: SCF SVF 2w C57BL/6J WT

value: post natal week 2


title: 6MUBR4KO-3

description: 6 months UBR4 knockout replicate 3


title: Hippocampus P347 CASTxB6 Cell 186

city: Cambridge

first: Longzhi

last: Tan

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

data_processing:
Library strategy: Dip-C
Please see 00README.md
Genome_build: mm10
Supplementary_files_format_and_content: Please see 00README.md

source_name: hippocampus

extract_protocol: [Isolation of cell nuclei] Cell nuclei were isolated based on protocols from (Krishnaswami et al., 2016; Lacar et al., 2016) with minor modifications. In particular, Tris buffer would react with formaldehyde, and was therefore substituted with equal molarity of HEPES buffer. See details below:  Cortex and hippocampus were dissected in ice-cold PBS, and placed in 2 mL nuclei isolation medium with Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT, 0.1% Triton X-100) in a 2 mL Dounce homogenizer (Sigma D8938). Note that DTT concentration was not specified in (Krishnaswami et al., 2016); here we used 1 uM from (Lacar et al., 2016).  Tissues were homogenized with 5 strokes of the loose (A) pestle, and 15 strokes of the tight (B) pestle. The homogenate was centrifuged for 8 min at 94 g, 4 C, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei isolation medium without Triton (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM HEPES pH 8.0, 1 uM DTT).  The tube was centrifuged for 8 min at 94 g, 4 C again, and the supernatant removed carefully. The pellet was re-suspended in 1 mL nuclei storage buffer (0.1665 M sucrose, 5 mM MgCl2, 10 mM HEPES pH 8.0), and filtered with 40 um. Note that sucrose concentration was not specified in (Krishnaswami et al., 2016); here we used 0.1665 M from (Lacar et al., 2016). Also note that the recipe in (Lacar et al., 2016) seems to have typos in some ingredient volumes; here we followed the final concentrations.  [Fixation of cell nuclei] Nuclei were fixed according to our Dip-C protocol (Tan et al., 2019) with minor modifications. In particular, nuclei were fixed directly in the 1 mL nuclei storage buffer (with HEPES instead of Tris buffer; see above) rather than switching to PBS; and centrifugation was performed at 1,000 g rather than 600 g. See detailed below:  Nuclei were directly in the nuclei storage buffer (1 mL) with the addition of 66.7 uL 32% PFA (EMS 15714) to a final concentration of 2%. The tube was rotated for 10 min at room temperature; and 200 uL 1% BSA in PBS was then added. The tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant removed. The pellet was resuspended in 1 mL ice-cold 1% BSA in PBS. Nuclei were counted and aliquoted to up to 0.5 million per tube. Each tube was centrifuged for 5 min at 1,000 g, 4 C, and the supernatant was removed. The pellet was stored at -80 C.  [Diploid chromatin conformation Capture (Dip-C)] A pellet of fixed cell nuclei was thawed on ice. We then proceeded directly to the step where 50 uL 0.5% SDS was added in the Dip-C protocol (Tan et al., 2019) and followed through with no modifications. Cells were sorted on a Beckman Coulter MoFlo Astrios, and amplified with homemade Nextera.

value: hippocampus


title: Hippocampus P347 CASTxB6 Cell 192


title: Hippocampus P347 CASTxB6 Cell 190


title: Hippocampus P347 CASTxB6 Cell 191


title: Hippocampus P347 CASTxB6 Cell 185


title: Hippocampus P347 CASTxB6 Cell 188


title: Hippocampus P347 CASTxB6 Cell 189


title: Hippocampus P347 CASTxB6 Cell 187


title: Hippocampus P347 CASTxB6 Cell 182


title: Hippocampus P347 CASTxB6 Cell 180


title: Hippocampus P347 CASTxB6 Cell 178


title: Hippocampus P347 CASTxB6 Cell 183


title: Hippocampus P347 CASTxB6 Cell 184


title: Hippocampus P347 CASTxB6 Cell 181


title: Hippocampus P347 CASTxB6 Cell 179


title: Hippocampus P347 CASTxB6 Cell 177


title: Hippocampus P347 CASTxB6 Cell 176


title: Hippocampus P347 CASTxB6 Cell 172


title: Hippocampus P347 CASTxB6 Cell 174


title: Hippocampus P347 CASTxB6 Cell 166


title: Hippocampus P347 CASTxB6 Cell 168


title: Hippocampus P347 CASTxB6 Cell 170


title: Hippocampus P347 CASTxB6 Cell 165


title: Hippocampus P347 CASTxB6 Cell 171


title: Hippocampus P347 CASTxB6 Cell 169


title: Hippocampus P347 CASTxB6 Cell 159


title: Hippocampus P347 CASTxB6 Cell 160


title: Hippocampus P347 CASTxB6 Cell 161


title: Hippocampus P347 CASTxB6 Cell 167


title: Hippocampus P347 CASTxB6 Cell 164


title: Hippocampus P347 CASTxB6 Cell 175


title: Hippocampus P347 CASTxB6 Cell 154


title: Hippocampus P347 CASTxB6 Cell 157


title: Hippocampus P347 CASTxB6 Cell 155


title: Hippocampus P347 CASTxB6 Cell 151


title: Hippocampus P347 CASTxB6 Cell 156


title: Hippocampus P347 CASTxB6 Cell 153


title: Hippocampus P347 CASTxB6 Cell 163


title: Hippocampus P347 CASTxB6 Cell 158


title: Hippocampus P347 CASTxB6 Cell 152


title: Hippocampus P347 CASTxB6 Cell 162


title: Hippocampus P347 CASTxB6 Cell 148


title: Hippocampus P347 CASTxB6 Cell 149


title: Hippocampus P347 CASTxB6 Cell 146


title: Hippocampus P347 CASTxB6 Cell 147


title: Hippocampus P347 CASTxB6 Cell 145


title: Hippocampus P347 CASTxB6 Cell 150


title: Hippocampus P347 CASTxB6 Cell 142


title: Hippocampus P347 CASTxB6 Cell 141


title: Hippocampus P347 CASTxB6 Cell 139


title: Hippocampus P347 CASTxB6 Cell 140


title: Hippocampus P347 CASTxB6 Cell 138


title: Hippocampus P347 CASTxB6 Cell 136


title: Hippocampus P347 CASTxB6 Cell 135


title: Hippocampus P347 CASTxB6 Cell 132


title: Hippocampus P347 CASTxB6 Cell 134


title: Hippocampus P347 CASTxB6 Cell 126


title: Hippocampus P347 CASTxB6 Cell 129


title: Hippocampus P347 CASTxB6 Cell 131


title: Hippocampus P347 CASTxB6 Cell 133


title: Hippocampus P347 CASTxB6 Cell 143


title: Hippocampus P347 CASTxB6 Cell 128


title: Hippocampus P347 CASTxB6 Cell 123


title: Hippocampus P347 CASTxB6 Cell 173


title: Hippocampus P347 CASTxB6 Cell 125


title: Hippocampus P347 CASTxB6 Cell 124


title: Hippocampus P347 CASTxB6 Cell 144


title: D8_2

description:
PE150
fpkm_all_samples.txt

value: chemical-induced neurons at D8


title: Hippocampus P347 CASTxB6 Cell 121


title: Hippocampus P347 CASTxB6 Cell 120


title: Hippocampus P347 CASTxB6 Cell 118


title: Hippocampus P347 CASTxB6 Cell 122


title: Hippocampus P347 CASTxB6 Cell 137


title: Hippocampus P347 CASTxB6 Cell 114


title: Hippocampus P347 CASTxB6 Cell 116


title: Hippocampus P347 CASTxB6 Cell 127


title: Hippocampus P347 CASTxB6 Cell 117


title: Hippocampus P347 CASTxB6 Cell 130


title: Hippocampus P347 CASTxB6 Cell 112


title: Hippocampus P347 CASTxB6 Cell 110


title: Hippocampus P347 CASTxB6 Cell 106


title: Hippocampus P347 CASTxB6 Cell 113


title: Hippocampus P347 CASTxB6 Cell 109


title: Hippocampus P347 CASTxB6 Cell 105


title: Hippocampus P347 CASTxB6 Cell 108


title: Hippocampus P347 CASTxB6 Cell 107


title: Hippocampus P347 CASTxB6 Cell 103


title: Hippocampus P347 CASTxB6 Cell 101


title: Hippocampus P347 CASTxB6 Cell 102


title: Hippocampus P347 CASTxB6 Cell 104


title: Hippocampus P347 CASTxB6 Cell 100


title: Hippocampus P347 CASTxB6 Cell 119


title: Hippocampus P347 CASTxB6 Cell 099


title: Hippocampus P347 CASTxB6 Cell 098


title: Hippocampus P347 CASTxB6 Cell 097


title: Hippocampus P347 CASTxB6 Cell 096


title: Hippocampus P347 CASTxB6 Cell 095


title: Hippocampus P347 CASTxB6 Cell 093


title: Hippocampus P347 CASTxB6 Cell 091


title: Hippocampus P347 CASTxB6 Cell 111


title: Hippocampus P347 CASTxB6 Cell 090


title: Hippocampus P347 CASTxB6 Cell 094


title: Hippocampus P347 CASTxB6 Cell 088


title: Hippocampus P347 CASTxB6 Cell 115


title: Hippocampus P347 CASTxB6 Cell 089


title: Hippocampus P347 CASTxB6 Cell 086


title: Hippocampus P347 CASTxB6 Cell 087


title: Hippocampus P347 CASTxB6 Cell 085


title: Hippocampus P347 CASTxB6 Cell 080


title: Hippocampus P347 CASTxB6 Cell 083


title: Hippocampus P347 CASTxB6 Cell 082


title: Hippocampus P347 CASTxB6 Cell 081


title: Hippocampus P347 CASTxB6 Cell 084


title: Hippocampus P347 CASTxB6 Cell 077


title: Hippocampus P347 CASTxB6 Cell 078


title: 0001200370T

description: Gene expression without any treatment

value: ⅠB

value: yes

value: moderate


title: Hippocampus P347 CASTxB6 Cell 079


title: Hippocampus P347 CASTxB6 Cell 092


title: Hippocampus P347 CASTxB6 Cell 075


title: Hippocampus P347 CASTxB6 Cell 073


title: Hippocampus P347 CASTxB6 Cell 071


title: Hippocampus P347 CASTxB6 Cell 072


title: Hippocampus P347 CASTxB6 Cell 064


title: Hippocampus P347 CASTxB6 Cell 065


title: Hippocampus P347 CASTxB6 Cell 063


title: Hippocampus P347 CASTxB6 Cell 069


title: Hippocampus P347 CASTxB6 Cell 070


title: Hippocampus P347 CASTxB6 Cell 062


title: Hippocampus P347 CASTxB6 Cell 076


title: Hippocampus P347 CASTxB6 Cell 061


title: Hippocampus P347 CASTxB6 Cell 060


title: Hippocampus P347 CASTxB6 Cell 066


title: Hippocampus P347 CASTxB6 Cell 057


title: Hippocampus P347 CASTxB6 Cell 074


title: Hippocampus P347 CASTxB6 Cell 067


title: Hippocampus P347 CASTxB6 Cell 052


title: Hippocampus P347 CASTxB6 Cell 059


title: Hippocampus P347 CASTxB6 Cell 056


title: Hippocampus P347 CASTxB6 Cell 051


title: Hippocampus P347 CASTxB6 Cell 058


title: Hippocampus P347 CASTxB6 Cell 053


title: Hippocampus P347 CASTxB6 Cell 054


title: Hippocampus P347 CASTxB6 Cell 049


title: Hippocampus P347 CASTxB6 Cell 055


title: Hippocampus P347 CASTxB6 Cell 068


title: Hippocampus P347 CASTxB6 Cell 045


title: Hippocampus P347 CASTxB6 Cell 047


title: Hippocampus P347 CASTxB6 Cell 050


title: Hippocampus P347 CASTxB6 Cell 048


title: Hippocampus P347 CASTxB6 Cell 044


title: Hippocampus P347 CASTxB6 Cell 042


title: Hippocampus P347 CASTxB6 Cell 037


title: Hippocampus P347 CASTxB6 Cell 043


title: Hippocampus P347 CASTxB6 Cell 036


title: Hippocampus P347 CASTxB6 Cell 038


title: Hippocampus P347 CASTxB6 Cell 035


title: Hippocampus P347 CASTxB6 Cell 033


title: Hippocampus P347 CASTxB6 Cell 034


title: Hippocampus P347 CASTxB6 Cell 046


title: Hippocampus P347 CASTxB6 Cell 041


title: Hippocampus P347 CASTxB6 Cell 029


title: Hippocampus P347 CASTxB6 Cell 024


title: Hippocampus P347 CASTxB6 Cell 025


title: Hippocampus P347 CASTxB6 Cell 028


title: Hippocampus P347 CASTxB6 Cell 026


title: Hippocampus P347 CASTxB6 Cell 023


title: Hippocampus P347 CASTxB6 Cell 022


title: Hippocampus P347 CASTxB6 Cell 032


title: Hippocampus P347 CASTxB6 Cell 020


title: Hippocampus P347 CASTxB6 Cell 031


title: Hippocampus P347 CASTxB6 Cell 030


title: Hippocampus P347 CASTxB6 Cell 039


title: Hippocampus P347 CASTxB6 Cell 040


title: Hippocampus P347 CASTxB6 Cell 019


title: Hippocampus P347 CASTxB6 Cell 018


title: Hippocampus P347 CASTxB6 Cell 021


title: Hippocampus P347 CASTxB6 Cell 017


title: Hippocampus P347 CASTxB6 Cell 011


title: Hippocampus P347 CASTxB6 Cell 027


title: Hippocampus P347 CASTxB6 Cell 013


title: Hippocampus P347 CASTxB6 Cell 015


title: Hippocampus P347 CASTxB6 Cell 012


title: Hippocampus P347 CASTxB6 Cell 006


title: Hippocampus P347 CASTxB6 Cell 009


title: Hippocampus P347 CASTxB6 Cell 005


title: Hippocampus P347 CASTxB6 Cell 014


title: Hippocampus P347 CASTxB6 Cell 007


title: Hippocampus P347 CASTxB6 Cell 004


title: Hippocampus P347 CASTxB6 Cell 003


title: Hippocampus P347 CASTxB6 Cell 008


title: Hippocampus P309 B6xCAST Cell 192


title: Hippocampus P309 B6xCAST Cell 189


title: Hippocampus P309 B6xCAST Cell 191


title: Hippocampus P347 CASTxB6 Cell 016


title: Hippocampus P309 B6xCAST Cell 187


title: Hippocampus P347 CASTxB6 Cell 001


title: Hippocampus P309 B6xCAST Cell 190


title: Hippocampus P347 CASTxB6 Cell 002


title: Hippocampus P309 B6xCAST Cell 183


title: Hippocampus P309 B6xCAST Cell 188


title: Hippocampus P309 B6xCAST Cell 182


title: Hippocampus P309 B6xCAST Cell 178


title: Hippocampus P309 B6xCAST Cell 185


title: Hippocampus P309 B6xCAST Cell 181


title: Hippocampus P347 CASTxB6 Cell 010


title: Hippocampus P309 B6xCAST Cell 175


title: Hippocampus P309 B6xCAST Cell 176


title: Hippocampus P309 B6xCAST Cell 179


title: Hippocampus P309 B6xCAST Cell 177


title: Hippocampus P309 B6xCAST Cell 174


title: Hippocampus P309 B6xCAST Cell 173


title: Hippocampus P309 B6xCAST Cell 171


title: Hippocampus P309 B6xCAST Cell 186


title: Hippocampus P309 B6xCAST Cell 184


title: Hippocampus P309 B6xCAST Cell 172


title: Hippocampus P309 B6xCAST Cell 169


title: Hippocampus P309 B6xCAST Cell 168


title: Hippocampus P309 B6xCAST Cell 167


title: Hippocampus P309 B6xCAST Cell 166


title: Hippocampus P309 B6xCAST Cell 180


title: Hippocampus P309 B6xCAST Cell 163


title: Hippocampus P309 B6xCAST Cell 160


title: Hippocampus P309 B6xCAST Cell 164


title: Hippocampus P309 B6xCAST Cell 159


title: Hippocampus P309 B6xCAST Cell 162


title: Hippocampus P309 B6xCAST Cell 161


title: Hippocampus P309 B6xCAST Cell 158


title: Hippocampus P309 B6xCAST Cell 152


title: Hippocampus P309 B6xCAST Cell 156


title: Hippocampus P309 B6xCAST Cell 170


title: Hippocampus P309 B6xCAST Cell 155


title: Hippocampus P309 B6xCAST Cell 151


title: Hippocampus P309 B6xCAST Cell 154


title: Hippocampus P309 B6xCAST Cell 157


title: Hippocampus P309 B6xCAST Cell 150


title: Hippocampus P309 B6xCAST Cell 148


title: Hippocampus P309 B6xCAST Cell 165


title: Hippocampus P309 B6xCAST Cell 147


title: Hippocampus P309 B6xCAST Cell 145


title: Hippocampus P309 B6xCAST Cell 146


title: Hippocampus P309 B6xCAST Cell 142


title: Hippocampus P309 B6xCAST Cell 143


title: Hippocampus P309 B6xCAST Cell 137


title: Hippocampus P309 B6xCAST Cell 139


title: Hippocampus P309 B6xCAST Cell 153


title: Hippocampus P309 B6xCAST Cell 140


title: Hippocampus P309 B6xCAST Cell 135


title: Hippocampus P309 B6xCAST Cell 133


title: Hippocampus P309 B6xCAST Cell 136


title: Hippocampus P309 B6xCAST Cell 134


title: Hippocampus P309 B6xCAST Cell 131


title: Hippocampus P309 B6xCAST Cell 132


title: Hippocampus P309 B6xCAST Cell 127


title: Hippocampus P309 B6xCAST Cell 119


title: Hippocampus P309 B6xCAST Cell 122


title: Hippocampus P309 B6xCAST Cell 121


title: Hippocampus P309 B6xCAST Cell 126


title: Hippocampus P309 B6xCAST Cell 125


title: Hippocampus P309 B6xCAST Cell 120


title: Hippocampus P309 B6xCAST Cell 129


title: Hippocampus P309 B6xCAST Cell 128


title: Hippocampus P309 B6xCAST Cell 149


title: Hippocampus P309 B6xCAST Cell 123


title: Hippocampus P309 B6xCAST Cell 130


title: Hippocampus P309 B6xCAST Cell 138


title: Hippocampus P309 B6xCAST Cell 141


title: Hippocampus P309 B6xCAST Cell 124


title: Hippocampus P309 B6xCAST Cell 113


title: Hippocampus P309 B6xCAST Cell 116


title: Hippocampus P309 B6xCAST Cell 115


title: Hippocampus P309 B6xCAST Cell 114


title: Hippocampus P309 B6xCAST Cell 117


title: Hippocampus P309 B6xCAST Cell 144


title: Hippocampus P309 B6xCAST Cell 112


title: Hippocampus P309 B6xCAST Cell 110


title: Hippocampus P309 B6xCAST Cell 109


title: Hippocampus P309 B6xCAST Cell 108


title: Hippocampus P309 B6xCAST Cell 118


title: Hippocampus P309 B6xCAST Cell 107


title: Hippocampus P309 B6xCAST Cell 092


title: Hippocampus P309 B6xCAST Cell 093