title: CBF1_DBDnoCoil

city: Saint Louis

first: Christian

last: Shively

state: MO

address: 4523 Clayton Avenue

department: Genetics

institute: Washington University in St Louis

description: "Calling Card" Assay for in vivo Transcription Factor Binding: a retrotransposon is directed into the genome at loci bound by a given transcription factor

library_source: genomic

data_processing:
Library strategy: Calling Card
Paired-End sequence reads were filtered for presence of Read1 initial 5bp barcode followed by unique 17-mer sequence (AATTCACTACGTCAACA) and Read2 initial 8bp barcode.
80bp of Read1 insert sequence was mapped to the 2008 S. cerevisiae reference genome (R-61-1-1) sequence using NovoAlign with default parameter settings. (Insertion position and number of reads mapping to each insertion is given in gnashy file.)
Number of insertions into each S. cerevisiae intergenic region was normalized to a total of 100,000 retrotransposon insertions per experiment and p-value was generated using poisson statistics.  (Significantly bound intergenic regions file)
Genome_build: 2008 S. cerevisiae reference genome (R-61-1-1)
Supplementary_files_format_and_content: .gnashy - a table indicating genomic position (chromosome, chromosome coordinate) of the retrotransposon insertion and number of reads aligning to that position
Supplementary_files_format_and_content: .gnashy.txt - Significantly bound intergenic regions file giving S. cerevisiae intergenic region, flanking ORFs (standard and systematic names), number of detected retrotransposon "calling card" insertions, normalized number of insertions (TPH), hyper-geometric p-value

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: The indicated yeast strain was co-transformed with a plasmid carrying the indicated transcription factor fused at the C-terminus to Sir4p and a plasmid carrying a barcoded HIS3-carrying Ty5 retrotransposon under the control of the GAL1/10 promoter.  A single clone was then incubated for 3 days on selective media with galactose as the carbon source.  Plates were then sequentially replica-plated to YPD (2 days), followed by SC-HIS with 5'FOA agar plates (3 days).

extract_protocol:
Genomic DNA was extracted from all cells using standard glass bead-beating, phenol chloroform isoamyl alcohol purification, and NH4Ac ethanol protocol.
Genomc DNA was digested in three separate restriction enzyme digests (HinPI1, HpaII, and Taq-alphaI), self-ligated with T4 DNA ligase, and an inverse PCR reaction was performed to amplify genomic DNA downstream of each inserted Ty5 retrotransposon.
"Calling Card" Assay to identify in vivo genomic targets of DNA-binding factors
"Calling Card" Assay performed as previously described: 1. "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins." Wang H, Mayhew D, Chen X, Johnston M, Mitra RD.  Genome Research, 2011, May 21(5):748-55. PMID 21471402. 2. "Calling Card Analysis in Budding Yeast." Mayhew D, Mitra RD.  Cold Spring Harbor Protocols, 2016, Feb 1, 2016(2). PMID 26832687.

tag: genotype

value: sir4D cbf1D

tag: transcription factor

value: Cbf1p bHLH


title: 12-20W13M4LN17

status: Public on Jul 18 2019

type: RNA

city: La Jolla

first: Luc

last: Teyton

state: CA

address: 10550 North Torrey Pines Road

country: USA

institute: TSRI

data_processing: Custom R analysis pipeline

label: EVAGREEN

molecule: total RNA

organism: Mus musculus

source_name: LymphNode

label_protocol: IAg7 tetramers with PE fluorphores. Stain at 4C for 60 minutes

extract_protocol: Tetramer used to stain CD4+ T cells specific to either 12-20 or 13-21 of the insulin Beta chain from various NOD mice tissues.

tag: cell type

value: CD4+ T cell

tag: strain

value: NOD/ShiLtJ

tag: iag7 tetramer

tag: age (in weeks)


title: 12-20W13M4LN16


title: P1_E11_exp1_K562_60min4sU

type: SRA

city: Solna

first: Gert-Jan

last: Hendriks

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description:
exp1_readcounts.csv
exp1_newcounts.csv
exp1_oldcounts.csv

library_source: transcriptomic

data_processing:
NASC-seq: Trimming of reads was performed with trimgalore
NASC-seq: Reads were aligned to Hg38 using STAR aligner
NASC-seq: Duplicates were removed with Picard
NASC-seq: Data was further processed using the NASC-seq analysis pipeline
NASC-seq: Cell filtering for processing was performed, cells with less than 100000 total reads, less than 50000 mapping reads or less than 10% of reads mapping were removed from the analysis.
TT-seq data processing. Paired-end 75 base reads with additional 6 base reads of barcodes were demultiplexed and mapped with STAR (Dobin and Gingeras 2015) to the Hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li, Handsaker et al. 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Read counts per gene were calculated using HTSeq (Anders, Pyl et al. 2015). The resulting count tables were used as input for differential expression analysis using the R/Bioconductor implementation of DESeq2.
Genome_build: Hg38
Supplementary_files_format_and_content: NASC-seq: The readcounts.csv file contains the readcounts for all features for all cells (even those filtered out during NASC-seq pipeline processing) for the corresponding experiment
Supplementary_files_format_and_content: NASC-seq: The newcounts.csv contains the 'counts' for reads that are considered newly produced for the corresponding experiment. Since we calculate fractions of total reads, this field may contain decimal values. Please note that we cannot caluclate the fraction of reads that is new/old for lowly expressed genes, (i.e. less than 16 reads), which results in the introduction of NA values.
Supplementary_files_format_and_content: NASC-seq: The oldcounts.csv contains the 'counts' for reads that are considered pre-existing for the corresponding experiment. Since we calculate fractions of total reads, this field may contain decimal values. Please note that we cannot caluclate the fraction of reads that is new/old for lowly expressed genes, (i.e. less than 16 reads), which results in the introduction of NA values.
Supplementary_files_format_and_content: TT-seq: DESeq2_results .csv files contain results from differential expression analysis using DESeq2 setting lfcThreshold = 1.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol:
NASC-seq: Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% Penicillin/Streptomycin (HyClone) at 37°C under 5% CO2.
TT-seq: Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% Penicillin/Streptomycin (HyClone) at 37°C under 5% CO2.

extract_protocol:
NASC-seq: Cells were distributed to NASC-seq lysis buffer with FACS.
TT-seq: Total RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was extracted according to Dolken et al., RNA, 2008 and fragmented with a BioRuptor Next Gen (Diagenode) at high power for one cycle of 30’’/30’’ ON/OFF (see also Schwalb et al., 2016)
NASC-seq: Libraries were prepared using the NASC-seq protocol
TT-seq: Sequencing libraries were prepared with the Ovation Universal RNA-Seq System (NuGEN) following the manufacturer's’ instructions

treatment_protocol:
NASC-seq: On the day of the experiment, Jurkat cells were seeded to a density of 1*10^6 cells/ml and stimulated with 50ng/μl phorbol 12-myristate 13-acetate (PMA) and 1μM ionomycin (Sigma) or treated with solvent control (DMSO, Sigma) for the indicated time at 37°C under 5% CO2. NASC-seq (Jurkat cells): Cells were labelled grown with 4sU (50μM) during the entire stimulus.
NASC-seq: K562 cells were passaged the day before the experiment and labeled with 4sU (50μM) for 60 minutes.
TT-seq: On the day of the experiment, Jurkat cells were seeded to a density of 1*10^6 cells/ml and stimulated with 50ng/μl phorbol 12-myristate 13-acetate (PMA) and 1μM ionomycin (Sigma) or treated with solvent control (DMSO, Sigma) for the indicated time at 37°C under 5% CO2. During the last 5 minutes of each time point cells were labelled in media with 500μM 4sU (Sigma) at 37°C under 5% CO2. Cells were harvested by centrifugation at 1400xg for 2 min.

tag: 4su labelling

value: 60min 4sU

tag: method

value: NASC-seq

tag: molecule

value: polyA RNA


title: CBF1_DBDwCoil

value: Cbf1p bHLH-ZIP


title: P1_D8_exp1_K562_60min4sU


title: 12-20W13M4LN14


title: 12-20W13M4LN13


title: P1_D7_exp1_K562_60min4sU


title: TEF1prom_TYE7_gcr2ko

value: sir4D gcr2D


title: 12-20W13M4LN12


title: 12-20W13M4LN7


title: 12-20W13M4LN11


title: P1_E1_exp1_K562_unlabelled

value: no 4sU labelling


title: P1_D5_exp1_K562_60min4sU


title: P1_D6_exp1_K562_60min4sU


title: 12-20W13M4LN10


title: CBF1


title: 12-20W13M4LN8


title: CST6


title: TEF1prom_TYE7


title: 12-20W13M4LN6


title: 12-20W13M4LN18


title: P1_D4_exp1_K562_60min4sU


title: 12-20W13M4LN9


title: 12-20W13M4LN5


title: 12-20W13M4LN4


title: P1_D2_exp1_K562_unlabelled


title: CB-103 10 µM rep2

city: Palo Alto

first: Mark

last: Mercola

address: 1651 Page Mill Road

department: Department of Medicine

institute: Stanford University School of Medicine

description:
Sample 14 H17
H17_USR17002558

data_processing:
FastQC (v0.11.5) and MultiQC (v1.3) were used to assess read quality.
Adapter and quality trimming of reads were performed with Trimmomatic (v0.36).
Reads were mapped to genome GRCh37 (hg19) using STAR (v2.5.3a) with UCSC gene annotations, and on average 19.1 million uniquely mapped reads were counted. Uniquely mapped reads were summarized at the gene level with featureCounts (v1.28.1) from the Rsubread module.
Differential expression was performed with DESeq2 (v1.17.39). Genes having a fold-change of greater than 1.5 and a p-value of less than 0.05 were considered significant.
To compare small molecule (CB-103, DAPT and RIN1) treatment to siRNA knockdown of RBPJ, transcripts were examined that showed a fold change > 2 (P < 0.05) by the specific treatment by either the small molecules or RBPJ siRNA relative to their respective controls (DMSO vehicle or control siRNA), and showed variation <40% between techniques (DMSO-vehicle vs. control siRNA).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Results from final data processing step
DAPT_vs_DMSO.txt: Differential expression between treatment with gamma secretase inhibitor DAPT and DMSO vehicle. Genes included are those that showed <40% change in expression between negative control conditions (control siRNA vs DMSO vehicle) to remove any contribution due to the techniques (siRNA transfection or compound treatment).
RIN1_2uM_vs_DMSO.txt: Differential expression between treatment with experimental compound RIN1 and DMSO vehicle. Genes included are those that showed <40% change in expression between negative control conditions (control siRNA vs DMSO vehicle) to remove any contribution due to the techniques (siRNA transfection or compound treatment).
CB-103_10uM_vs_DMSO.txt: Differential expression between treatment with experimental compound CB-103 and DMSO vehicle. Genes included are those that showed <40% change in expression between negative control conditions (control siRNA vs DMSO vehicle) to remove any contribution due to the techniques (siRNA transfection or compound treatment).
siRBPJ_vs_siCTRL.txt: Differential expression between treatment with siRNA against RBPJ (CUCCCAAGAUUGAUAAUUA, Dharmacon) and non-targeting control (Dharmacon catalogue number D-001810-01). Genes included are those that showed <40% change in expression between negative control conditions (control siRNA vs DMSO vehicle) to remove any contribution due to the techniques (siRNA transfection or compound treatment).

source_name: Jurkat cells

growth_protocol: Jurkat cells were grown in RPMI 1640 media supplemented with 10% fetal bovine serum, glutamax and penicillin/streptomicin.

extract_protocol:
Total RNA was extracted using Quick RNA miniprep (Zymo Research R1055) following kit protocol including the DNAse treatment step.
Library construction was performed by Novogene with the following protocol: mRNA was enriched using oligo(dT) beads, fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/μl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM); Eukaryotic transcription (250~300 bp insert cDNA library)

treatment_protocol: Treatment was done in growth media. For compound treatment cells were seeded at 0.5 million cells/ml. Compound treatment duration was 8 hours. Final DMSO concentration was 0.1% for all compound samples. For siRNA treatment: transfection by electroporation (Neon, Thermo Fisher Scientific), 100 ul tip, 100 ul cells at 20 million/ml, 10 ul siRNA at 100 uM, 3 pulsed of 10 msec duration, 1350 V. siRNAs: Dharmacon J-007772-06 (CUCCCAAGAUUGAUAAUUA) for RBPJ NM_203283, and nont-targeting control D-001810-01. After electroporation cells were seeded at 0.25 million/ml and collected 48 hours later.

tag: treatment

value: CB-103 10 microM 8 hrs

tag: cell line

value: Jurkat


title: P1_D3_exp1_K562_unlabelled


title: CB-103 10 µM rep1

description:
Sample 13 H11
H11_USR17002552


title: 12-20W13M4LN3


title: P1_D12_exp1_K562_60min4sU


title: 12-20W13M4LN15


title: DAPT 10 µM rep2

description:
Sample 12 H14
H14_USR17002555

value: DAPT 10 microM 8 hrs


title: DAPT 10 µM rep1

description:
Sample 11 H8
H8_USR17002549L


title: 12-20W13M4LN2


title: 13-21W13M4I23

source_name: Islets


title: 13-21W13M4I22


title: 13-21W13M4I21


title: 13-21W13M4I20


title: P1_D11_exp1_K562_60min4sU


title: P1_D1_exp1_K562_unlabelled


title: P1_D10_exp1_K562_60min4sU


title: RIN1 2 µM rep1

description:
Sample 8 H6
H6_USR17002547L

value: RIN1 2 microM 8 hrs


title: P1_C9_exp1_K562_60min4sU


title: RIN1 2 µM rep3

description:
Sample 10 H15
H15_USR17002556


title: 13-21W13M4I18


title: RIN1 2 µM rep2

description:
Sample 9 H9
H9_USR17002550L


title: 13-21W13M4I19


title: 13-21W13M4I16


title: 13-21W13M4I17


title: DMSO vehicle control rep3

description:
Sample 7 H13
H13_USR17002554

value: 0.1 % DMSO 8 hrs


title: P1_C8_exp1_K562_60min4sU


title: 13-21W13M4I15


title: 12-20W13M4LN1


title: P1_C7_exp1_K562_60min4sU


title: 13-21W13M4I13


title: 13-21W13M4I24


title: DMSO vehicle control rep1

description:
Sample 5 H5
H5_USR17002546L


title: DMSO vehicle control rep2

description:
Sample 6 H7
H7_USR17002548L


title: 13-21W13M4I14


title: 13-21W13M4I12


title: 13-21W13M4I11


title: P1_C6_exp1_K562_60min4sU


title: 13-21W13M4I10


title: P1_C5_exp1_K562_60min4sU


title: siRNA RBPJ rep2

description:
Sample 4 H4
H4_USR17002545L

value: siRNA RBPJ J-007772-06 48 hs


title: 13-21W13M4I8


title: siRNA RBPJ rep1

description:
Sample 3 H1
H1_USR17002542L


title: 13-21W13M4I5


title: 13-21W13M4I7


title: siRNA control rep2

description:
Sample 2 H3
H3_USR17002544L

value: siRNA control D-001810-01 48 hs


title: siRNA control rep1

description:
Sample 1 H2
H2_USR17002543L


title: 13-21W13M4I6


title: P1_C4_exp1_K562_60min4sU


title: P1_C3_exp1_K562_unlabelled


title: P1_C2_exp1_K562_unlabelled


title: 13-21W13M4I3


title: 13-21W13M4I2


title: 12-20W13M4I23


title: P1_C12_exp1_K562_60min4sU


title: 12-20W13M4I22


title: 13-21W13M4I1


title: P1_C11_exp1_K562_60min4sU


title: 12-20W13M4I21


title: 13-21W13M4I9


title: P1_C10_exp1_K562_60min4sU


title: 12-20W13M4I20


title: sgCtrl_Input

city: New York

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Alignment using Bowtie 2 v2.2.9 default parameters
Formatting using Samtools v 1.7, --view BAM file conversion, quality score min of 30 (-q 30), -sort Bamfile sort by chromosome and location, -rmdup duplicate removal, -index Bam file index
Peak calling using MACS2 v2.1.1.20160309, using processed BAM file, input controls, and replicates combined per IP. p<0.00000005, narrow peak calling (broad peaks for H3k27me3),
Signal files using Deeptools v 3.0.0, normalized using RPKM (--normalizeUsing RPKM), binned at 5bp (--bs 5), reads centered (--center reads), extend over half the length of the sequneced library (--extendReads 125), smooth signal (--smooth 250), remove ENCODE blacklist regions (--blackListFileName)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files are peak files for each ChIP seqeincing run, combining 2 biological replicates per IP/condition to generate a final peak list.  BigWig files are normalized

source_name: ChIP Sequencing of Input for sgCHD1 LNCaP Cells

growth_protocol: Cells were grown to 80% confluence on poly-L-lysine coated plates in 5%FBS supplemented RPMI-1640

extract_protocol:
20 million cells/replicate were fixed using 1% formaldehyde for 10 minutes at 24C, quenched for 5 minutes with 0.125M glycine, and stored at -80C until use. Pellets were then thawed on ice and lysed using 1% SDS_lysis buffer, sonicated for 27 cycles (30on/30ff) using a temperature controlled bioruptor, and spun down at max speed for 10 minutes.  Clarified chromatin was then incubated with primary antibody overnight, and genomic DNA washed and isolated the next morning.
ChIP sequencing libraries (20ng DNA/sample) were constructed using the KAPA Hyper Prep Kit (Illuminia- Kapa biosystems Cat # KK8502, NimbleGen SeqCap Adapter Kit A- Roche Cat # 07 141 530 001) according to the manufactures instructions.  Libraries were assessed for quality, purity, and size using DNA High Sensitivity Bioanalyzer chips, and those passing QC were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems KK4854).  Libraries were pooled to a final concentration of 10nM and sequenced using the Illumina HiSeq 4000

treatment_protocol: Cells were treated with 10nM DHT for 3 hours before harvesting.

value: 10nM DHT 3 hours

value: LNCaP


title: sgCtrl_AR1

source_name: ChIP Sequencing for AR in sgCtrl LNCaP cells post 10nM DHT


title: 12-20W13M4I19

value: CD4+ T cell


title: sgCtrl_AR2


title: 12-20W13M4I18

value: NOD/ShiLtJ


title: sgCHD1_AR2

source_name: ChIP Sequencing for AR in sgCHD1 LNCaP cells post 10nM DHT


title: 12-20W13M4I17


title: P1_C1_exp1_K562_unlabelled


title: 13-21W13M4I4


title: 12-20W13M4I16


title: 12-20W13M4I15


title: 12-20W13M4I13


title: 12-20W13M4I14


title: sgCHD1_Input

source_name: ChIP Sequencing of Input for sgCtrl LNCaP Cells


title: P1_B8_exp1_K562_60min4sU

value: 60min 4sU


title: 12-20W13M4I10


title: sln1_16h_rep2

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

country: United Kingdom

institute: University of Exeter

description:
98-sln1_16h_2_TTAGGC_L006
Δsln1 developing appressoria 16 hrs

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were filtered using the fastq-mcf program from the ea-utils package (https://expressionanalysis.github.io/ea-utils/) applying –x 0.01, –q 20, –p 10, and –u
Reads were mapped to the Magnaporthe oryzae 70-15 reference genome version 8 using the TopHat2 package
Counts of reads mapping to each gene in the M. oryzae genome were generated using the htseq-count function of the HTSeq package
Relative gene expression was quantified using DESeq
Genome_build: Magnaporthe oryzae 70-15 reference genome version 8
Supplementary_files_format_and_content: 16h_expression_all.txt  containing relative gene expression (baseMean) of every gene in each strain, generated by DESeq
Supplementary_files_format_and_content: *.count.txt containing raw counts for every gene in each strain (output from htseq-count)

organism: Pyricularia oryzae

source_name: Guy11 - Δsln1

extract_protocol:
Total RNA was then extracted using Qiagen RNeasy Plant Mini kit, according to manufacturer's instructions. RNA-seq  libraries were prepared using 5 µg of total RNA with ScriptSeq RNA-Seq Library Preparation Kit from Illumina according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

tag: genotype/variation

value: sln1 null mutant

tag: tissue

value: developing conidia


title: 12-20W13M4I9


title: P1_B9_exp1_K562_60min4sU

value: NASC-seq

value: polyA RNA


title: 12-20W13M4I8


title: P1_B7_exp1_K562_60min4sU


title: sln1_16h_rep1

description:
97-sln1_16h_1_ATCACG_L006
Δsln1 developing appressoria 16 hrs


title: 12-20W13M4I6


title: guy11_16h_rep2

description:
48_guy11_16h_CGTACG_L004
wild-type developing appressoria 16 hrs

value: wild type


title: P1_B5_exp1_K562_60min4sU


title: P1_B6_exp1_K562_60min4sU


title: buf1_16h_rep2

description:
96-buf1_16h_2_CTTGTA_L006
Δbuf1 developing appressoria 16 hrs

source_name: Guy11 - Δbuf1

value: buf1 null mutant


title: buf1_16h_rep1

description:
95-buf1_16h_1_CAGATC_L006
Δbuf1 developing appressoria 16 hrs


title: 12-20W13M4I5


title: P1_B3_exp1_K562_unlabelled

value: no 4sU labelling


title: 12-20W13M4I2


title: guy11_16h_rep1

description:
47_guy11_16h_GTTTCG_L004
wild-type developing appressoria 16 hrs


title: 12-20W13M4I3


title: rho4_16h_rep2

description:
32_rho4_t16_2_GCCAAT_L006
Δrho4 developing appressoria 16 hrs

source_name: Guy11 - Δrho4

value: rho4 null mutant


title: 12-20W13M4I1


title: P1_B2_exp1_K562_unlabelled


title: 13-21W7M7LN24

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN23

description: Insulin7weeksMouse7(Islets and LN).csv


title: rho4_16h_rep1

description:
31_rho4_t16_1_ACAGTG_L006
Δrho4 developing appressoria 16 hrs


title: P1_B12_exp1_K562_60min4sU


title: 12-20W13M4I12


title: 12-20W13M4I7


title: cdc42_16h_rep2

description:
30_cdc42_t16_2_TGACCA_L006
Δcdc42 developing appressoria 16 hrs

source_name: Guy11 - Δcdc42

value: cdc42 null mutant


title: 13-21W7M7LN22

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN21

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN20

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_B4_exp1_K562_60min4sU


title: P1_B11_exp1_K562_60min4sU


title: cdc42_16h_rep1

description:
29_cdc42_t16_1_CGATGT_L006
Δcdc42 developing appressoria 16 hrs


title: P1_B1_exp1_K562_unlabelled


title: P1_B10_exp1_K562_60min4sU


title: 12-20W13M4I4


title: 13-21W7M7LN18

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN17

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN15

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN16

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN14

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_A9_exp1_K562_60min4sU


title: 13-21W7M7LN13

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_A7_exp1_K562_60min4sU


title: P1_A8_exp1_K562_60min4sU


title: 13-21W7M7LN10

description: Insulin7weeksMouse7(Islets and LN).csv


title: control rep35

city: Columbia

first: Susan

last: Nagel

state: Missouri

address: One Hospital Drive

institute: University of Missouri

data_processing:
checked the quality of the data using FastQC
remove reads with low‐quality bases, adapter sequences, and other contaminating sequences using Cutadapt
Bowtie2 was used to build the index of reference genome
Each sample’s reads were aligned against the reference genome hg38 using Bowtie2
we used Samtools and Picard for sorting and removing duplicate reads, respectively
we segmented the genome sequence into 1,000 bases tiling windows and then recorded the number of reads that are mapped to each methylated regions. Read counts are the number of aligned reads that uniquely map to the hg38 reference genome. Several R packages (MEDIPS, BSgenome, BSgenome.Hsapiens.UCSC.hg38)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes the raw read counts of each 1,000 bases tiling windows for all samples

source_name: endometrial tissue

extract_protocol:
Endometrial tissue was lysed using Qiagen ATL buffer supplemented with Proteinase K at 55C overnight. DNA was extracted using the Qiagen DNAeasy Blood and Tissue kit
To produce methyl enriched DNA fragments, sonicated DNA was subjected to the Methylated-CpG Island Recovery Assay (MethylCollector Ultra – Active Motif). Enriched methyl DNA was then subjected to library construction using the NEBNext DNA library prep kit for Illumina (New England Biolabs)

value: endometrial tissue

tag: disease state

value: control


title: disease rep42

value: endometriosis


title: control rep33


title: control rep34


title: disease rep41


title: P1_A6_exp1_K562_60min4sU


title: 13-21W7M7LN9

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN8

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep40


title: 13-21W7M7LN19

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN7

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_A5_exp1_K562_60min4sU


title: disease rep39


title: 13-21W7M7LN5

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_D9_exp1_K562_60min4sU


title: control rep32


title: 13-21W7M7LN6

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN3

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_A4_exp1_K562_60min4sU


title: 13-21W7M7LN4

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_A3_exp1_K562_unlabelled


title: 13-21W7M7LN12

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN2

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN11

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep38


title: P1_A2_exp1_K562_unlabelled


title: 12-20W7M7LN23

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7LN1

description: Insulin7weeksMouse7(Islets and LN).csv


title: control rep31


title: 12-20W7M7LN21

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_A11_exp1_K562_60min4sU


title: control rep30


title: P1_A12_exp1_K562_60min4sU


title: 12-20W7M7LN20

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN18

description: Insulin7weeksMouse7(Islets and LN).csv


title: P1_A10_exp1_K562_60min4sU


title: disease rep37


title: 12-20W7M7LN17

description: Insulin7weeksMouse7(Islets and LN).csv


title: control rep29


title: disease rep36


title: 12-20W7M7LN15

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN16

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN14

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN13

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep35


title: CUTRUN.CTCF_rep1

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Library strategy: CUT&RUN
Cut-C data are processed using HiC-Pro pipeline. The parameters are default parameter, except restriction site and minimum cis distance threshold are unset.
Cut-C  bigWig are generated from alignment ( bwt2paris.bam file) produced by HiC-Pro pipe line; first mate are decoupled from second mate to prevent inclusion of non-genomic region.
CUT&RUN reads are trimmed using TrimGalore, the params: trim_galore --stringency 5 --gzip --paired --trim1 --length 30 -q 0
CUT&RUN data are aligned using Bowtie, the params: --threads 3 -m 1 -v 2 -S -I 0 -X 2000
CUT&RUN deduplication is done using Picard MarkDuplicates, the params: REMOVE_DUPLICATES=TRUE
CUT&RUN alignement BAM file are converted to bedgraph using MACS2 before finally converted to bigWig using UCSC bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig for Cut-C data from are processed from HiC-Pro output as described above.  The contact file (allValidPairs) are obtained from HiC-Pro pipeline final output. bigWig for CUT&RUN are processed using step as described above.

source_name: CUT&RUN CTCF

growth_protocol: HEK293T cells were grown on DMEM medium supplemented with 10% FBS and 1% Penicillin/ Streptomycin.

extract_protocol:
CUT-C: Ligated DNA were collected by reverse-crosslinking and DNA extraction. The biotin-tagged DNA were collected by Streptavidin beads. CUT&RUN: The released DNA fragment were extracted using DNA extraction kit.
CUT-C: Library was prepared using standard Illumina protocol, CUT&RUN: library was prepared with Accel-NGS 1S Plus DNA Library Kit (Swift Biosciences)

treatment_protocol: CUT-C: Crosslink with 1% formaldehyde, cell lysis, Mnase-tethered cleavage at antibody-bound sites, endo-chew, addition of biotin-tagged nucleotide, proximity ligation. CUT&RUN: CUT&RUN protocol (Skene et al., 2018 Nature Protocols) was followed with minor modifications

tag: preparation type

value: CUT&RUN

tag: antibody

value: CTCF


title: control rep28


title: disease rep34


title: 12-20W7M7LN12

description: Insulin7weeksMouse7(Islets and LN).csv

value: CD4+ T cell


title: 12-20W7M7LN10

description: Insulin7weeksMouse7(Islets and LN).csv

value: NOD/ShiLtJ


title: 12-20W7M7LN11

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN9

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN19

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN7

description: Insulin7weeksMouse7(Islets and LN).csv


title: CUTC.H3K4me3_rep2

data_processing:
Library strategy: Cut-C
Cut-C data are processed using HiC-Pro pipeline. The parameters are default parameter, except restriction site and minimum cis distance threshold are unset.
Cut-C  bigWig are generated from alignment ( bwt2paris.bam file) produced by HiC-Pro pipe line; first mate are decoupled from second mate to prevent inclusion of non-genomic region.
CUT&RUN reads are trimmed using TrimGalore, the params: trim_galore --stringency 5 --gzip --paired --trim1 --length 30 -q 0
CUT&RUN data are aligned using Bowtie, the params: --threads 3 -m 1 -v 2 -S -I 0 -X 2000
CUT&RUN deduplication is done using Picard MarkDuplicates, the params: REMOVE_DUPLICATES=TRUE
CUT&RUN alignement BAM file are converted to bedgraph using MACS2 before finally converted to bigWig using UCSC bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig for Cut-C data from are processed from HiC-Pro output as described above.  The contact file (allValidPairs) are obtained from HiC-Pro pipeline final output. bigWig for CUT&RUN processed using step as described above.

source_name: Cut-C H3K4me3

value: Cut-C


title: CUTRUN.H3K4me3_rep1

data_processing:
Library strategy: CUT&RUN
Cut-C data are processed using HiC-Pro pipeline. The parameters are default parameter, except restriction site and minimum cis distance threshold are unset.
Cut-C  bigWig are generated from alignment ( bwt2paris.bam file) produced by HiC-Pro pipe line; first mate are decoupled from second mate to prevent inclusion of non-genomic region.
CUT&RUN reads are trimmed using TrimGalore, the params: trim_galore --stringency 5 --gzip --paired --trim1 --length 30 -q 0
CUT&RUN data are aligned using Bowtie, the params: --threads 3 -m 1 -v 2 -S -I 0 -X 2000
CUT&RUN deduplication is done using Picard MarkDuplicates, the params: REMOVE_DUPLICATES=TRUE
CUT&RUN alignement BAM file are converted to bedgraph using MACS2 before finally converted to bigWig using UCSC bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig for Cut-C data from are processed from HiC-Pro output as described above.  The contact file (allValidPairs) are obtained from HiC-Pro pipeline final output. bigWig for CUT&RUN processed using step as described above.

source_name: CUT&RUN H3K4me3


title: 12-20W7M7LN8

description: Insulin7weeksMouse7(Islets and LN).csv


title: CUTC.H3K4me3_rep1


title: 12-20W7M7LN6

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN5

description: Insulin7weeksMouse7(Islets and LN).csv


title: CUTC.CTCF_rep1

source_name: Cut-C CTCF


title: P1_A1_exp1_K562_unlabelled


title: control rep27


title: 12-20W7M7LN2

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep32


title: 12-20W7M7LN1

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep31


title: 13-21W7M7I23

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN3

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5+Cmplt_G5

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

data_processing:
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform according to the SmartSeq2 protocol (Picelli S et al. 2014) with some modifications (Trombetta JJ et al., 2014) on an Illumina NextSeq500.
Data was separated by barcode and aligned utilizing STAR v2.4.2a (Dobin A et al. 2015) and gene-level abundance was estimated using tximport package (Soneson C et al., 2016). TMM (trimmed mean of M-values) normalization was performed using edgeR (Robinson MD et al., 2010) and identification of differential gene transcripts was performed with the limma-voom function (Law CW et al. 2014).
Genome_build: hg19, human genome (GRCh38), version 24 (Ensembl 83) annotations
Supplementary_files_format_and_content: tab-delimited text file including log2 CPM from voom

growth_protocol: Human arterial endothelial cells (ECs) were isolated from unused large artery pieces harvested from organ donors (agreement PFS08-017 of the French regulatory institution “Agence de la Bio-Medicine”). Arteries were incubated with collagenase A (2.2U/ml; Roche, Meyland, France) for 40 min at 37°C and cells harvested by mild scrapping of the lumen. ECs were selected using CD31-Dynabeads (Invitrogen, Cergy Pontoise, France) for 20 min at 4°C, washed three times, plated on plastic dishes and grown in Endothelial Cell Basal Medium (Promocell, Heidelberg, Germany) supplemented with 10% FCS, glutamine (200mM), penicillin and streptomycin (100 UI/ml), ECGS (0.004ml/ml), hEGF (0.1ng/ml), hbFGF (1ng/ml), hydrocortisone (1ug/ml) and Heparin (90ug/ml), at 37°C in a 5%CO2. After expansion, primary EC cultures were frozen in 10% DMSO-FCS in liquid nitrogen at passage 1 or 2. These cells were characterized by their morphology in culture and by anti-CD31 and anti-CD146 endothelial markers.

extract_protocol:
Cells were harvested after a 4 h incubation, and RNAs were collected in 1 ml of Trizol and stored at -80°C until RNA extraction for sequencing. Total RNA was isolated using Trizol method (Life Technologies SAS) combined with Rneasy mini kit procedure (Qiagen). RNA quality was assessed using the Agilent 6000 Pico Kit as instructed by the manufacturer. All RNA samples yield maximum quality with the RNA integrity number (RIN) above 9.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads, polyA mRNA was converted to cDNA and amplified cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Sequencing was carried out as paired-end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: After thawing, primary EC cultures from 10 individual donors were seeded in 12-wells plates. Post-confluent monolayers of ECs were incubated for 4h in a total volume of 150µl of Neu5Gc-free according to the various conditions. Two final concentrations of IA-purified anti-Neu5Gc were: a/ 1.5 ng/uL for the pre- and post-immunization samples, mimicking the average concentration of anti-Neu5Gc in normal individual sera 22 measured by the same ELISA20 and, b/ an additional concentration of 9 ng/uL, for Elicited antibodies which can reach high concentration in vivo. ECs were also stimulated with TNFα (500U/ml) or human complement alone (i.e. a lyophilized pool of human sera- Sigma S1764 - St Louis, MO, US) used at a final dilution of 1:2.

tag: source patient id

value: endothelial cells (EC)

value: Elicited anti-Neu5Gc antibodies 1.5ng + complement


title: Post_1.5+Cmplt_G3


title: Post_1.5+Cmplt_G2


title: 13-21W7M7I21

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I20

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I22

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep30


title: disease rep29


title: 13-21W7M7I18

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep33


title: 13-21W7M7I17

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I16

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep28


title: 13-21W7M7I19

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I15

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7LN4

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5+Cmplt_G9


title: 13-21W7M7I13

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5+Cmplt_G1


title: 13-21W7M7I12

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I11

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I10

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep26


title: Post_1.5+Cmplt_G8


title: Post_1.5+Cmplt_G6


title: control rep26


title: disease rep25


title: Post_1.5+Cmplt_G4


title: 13-21W7M7I7

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I9

description: Insulin7weeksMouse7(Islets and LN).csv


title: 13-21W7M7I8

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5+Cmplt_G10


title: 13-21W7M7I6

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5_sans_E5

value: Elicited anti-Neu5Gc antibodies 1.5ng


title: Post_1.5+Cmplt_G7


title: 13-21W7M7I4

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep27


title: 12-20W7M7I24

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I23

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5_sans_E3


title: Post_1.5_sans_E2


title: 13-21W7M7I3

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep24


title: disease rep23


title: control rep24


title: Post_1.5_sans_E4


title: 12-20W7M7I22

description: Insulin7weeksMouse7(Islets and LN).csv


title: control rep23


title: 12-20W7M7I21

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I20

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I19

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5_sans_E10


title: disease rep22


title: 13-21W7M7I5

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I18

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I17

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I16

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5_sans_E1


title: Post_1.5_sans_E9


title: control rep22


title: 13-21W7M7I2

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep21


title: 12-20W7M7I15

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I14

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I13

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I12

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5_sans_E8


title: 12-20W7M7I11

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_1.5_sans_E6


title: disease rep19


title: disease rep20


title: Post_1.5_sans_E7


title: disease rep18


title: 12-20W7M7I9

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I10

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_9+Cmplt_H5

value: Elicited anti-Neu5Gc antibodies 9ng + complement


title: control rep21


title: 12-20W7M7I6

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I7

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_9+Cmplt_H3


title: 12-20W7M7I5

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep17


title: 12-20W7M7I3

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_9+Cmplt_H2


title: 12-20W7M7I4

description: Insulin7weeksMouse7(Islets and LN).csv


title: disease rep16


title: disease rep15


title: 12-20W7M7I1

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M7I2

description: Insulin7weeksMouse7(Islets and LN).csv


title: Post_9+Cmplt_H10


title: 12-20W7M2b44

source_name: Blood


title: 12-20W7M2b45


title: control rep20


title: control rep25


title: 12-20W7M7I8

description: Insulin7weeksMouse7(Islets and LN).csv


title: 12-20W7M2b36


title: 12-20W7M2b34


title: 12-20W7M2b35


title: 12-20W7M2b33


title: Post_9+Cmplt_H8


title: disease rep14


title: Post_9+Cmplt_H7


title: control rep18


title: 12-20W7M2b31


title: 12-20W7M2b30


title: 12-20W7M2b32


title: Post_9+Cmplt_H4


title: disease rep13


title: 12-20W7M2b29


title: 12-20W7M2b28


title: Post_9_sans_F5

value: Elicited anti-Neu5Gc antibodies 9ng


title: 12-20W7M2b38


title: Post_9_sans_F3


title: disease rep12


title: Post_9+Cmplt_H9


title: 12-20W7M2b26


title: 12-20W7M2b27


title: disease rep11


title: 12-20W7M2b25


title: 12-20W7M2b24


title: disease rep10


title: control rep19


title: Post_9_sans_F2


title: Post_9_sans_F4


title: 12-20W7M2b22


title: 12-20W7M2b23


title: 12-20W7M2b21


title: 12-20W7M2b20


title: Post_9+Cmplt_H6


title: 12-20W7M2b19


title: control rep16


title: Post_9_sans_F10


title: control rep17


title: 12-20W7M2b17


title: Post_9_sans_F1


title: 12-20W7M2b16


title: control rep14


title: Post_9_sans_F9


title: control rep15


title: 12-20W7M2b15


title: control rep13


title: 12-20W7M2b14


title: 12-20W7M2b13


title: control rep12


title: 12-20W7M2b12


title: Post_9_sans_F6


title: 12-20W7M2b10


title: 12-20W7M2b11


title: Pre_1.5_sans_D5

value: natural anti-Neu5Gc antibodies 1.5ng


title: Post_9_sans_F7


title: 12-20W7M2b8


title: 12-20W7M2b9


title: 12-20W7M2b7


title: control rep10


title: 12-20W7M2b6


title: 12-20W7M2b18


title: 12-20W7M2b5


title: Pre_1.5_sans_D2


title: control rep11


title: Pre_1.5_sans_D3


title: control rep9


title: Post_9_sans_F8


title: control rep8


title: 12-20W7M2b3


title: 12-20W7M2b2


title: 12-20W7M2b1


title: 12-20W7M2b4


title: control rep7


title: control rep6


title: Pre_1.5_sans_D4


title: 12-20W7M1b48


title: control rep5


title: 12-20W7M1b46


title: 12-20W7M1b45


title: Pre_1.5_sans_D9


title: Pre_1.5_sans_D1


title: control rep4


title: 12-20W7M1b44


title: 12-20W7M1b42


title: 12-20W7M1b43


title: control rep3


title: 12-20W7M1b40


title: 12-20W7M1b41


title: Pre_1.5_sans_D6


title: 12-20W7M1b39


title: Pre_1.5_sans_D8


title: Pre_1.5_sans_D7


title: Pre_1.5_sans_D10


title: 12-20W7M1b38


title: control rep2


title: 12-20W7M1b37


title: 12-20W7M1b36


title: Cmplt_C5


title: 12-20W7M1b35


title: Cmplt_C3


title: 12-20W7M1b34


title: 12-20W7M1b47


title: Cmplt_C2


title: 12-20W7M1b33


title: 12-20W7M1b32


title: 12-20W7M1b31


title: disease rep7


title: disease rep8


title: Cmplt_C4


title: 12-20W7M1b30


title: disease rep6


title: 12-20W7M1b29


title: disease rep9


title: Cmplt_C9


title: 12-20W7M1b27


title: Cmplt_C10


title: disease rep4


title: disease rep5


title: Cmplt_C1


title: control rep1


title: 12-20W7M1b25


title: 12-20W7M1b24


title: disease rep3


title: Cmplt_C8


title: 12-20W7M1b22


title: 12-20W7M1b21


title: Cmplt_C6


title: 12-20W7M1b23


title: 12-20W7M1b19


title: disease rep1


title: Cmplt_C7


title: TNF_B5


title: 12-20W7M1b18


title: 12-20W7M1b16


title: 12-20W7M1b28


title: 12-20W7M1b26


title: 12-20W7M1b15


title: TNF_B3


title: 12-20W7M1b14


title: 12-20W7M1b13


title: β-catenin siRNA HepG2_biological_rep3

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: HepG2 cells transfected with β-catenin siRNA

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: HepG2 cells

tag: transfection

value: β-catenin siRNA


title: 12-20W7M1b12

tag: cell type


title: β-catenin siRNA HepG2_biological_rep2

source_name: HepG2 cells transfected with β-catenin siRNA


title: β-catenin siRNA HepG2_biological_rep1


title: 12-20W7M1b11

tag: strain


title: disease rep2


title: TNF_B4


title: TNF_B2


title: 12-20W7M1b10

tag: iag7 tetramer


title: 12-20W7M1b20

tag: age (in weeks)


title: 12-20W7M1b8


title: 12-20W7M1b6


title: TNF_B10


title: 12-20W7M1b17


title: Ctrl siRNA HepG2_biological_rep1

description: HepG2 cells transfected with control siRNA

value: control siRNA


title: Ctrl siRNA HepG2_biological_rep2

source_name: HepG2 cells transfected with control siRNA


title: TNF_B9


title: 12-20W7M1b5


title: TNF_B1


title: 12-20W7M1b3


title: 12-20W7M1b2


title: TNF_B8


title: 12-20W7M1b1


title: sgCHD1_DHT_rep2

description: ATACsequencing in sgCHD1LNCaP cells post 10nM DHT

data_processing:
Data processing and peak calling was performed by the Center for Functional Cancer Epigenetics at The Dana Farber Cancer Institute, utilizing their established pipeline.
Peaks were called using MACS2 v2.1.1 FDR 0.01, narrow peak calling
Final peak files were generated for each cell line and condition by merging replicates.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files are peak files for each ATAC condition, combining 2 biological replicates  to generate a final peak list.

source_name: LNCaP

extract_protocol: 50k cells in biological duplicate were submitted to Center for Functional Cancer Epigenetics at Dana Farber research institute for ATAC library preparation using the Omni ATAC protocol.

treatment_protocol: Cells were starved of hormone in 5% CDT media for 72 hours prior to treatment with 10nM DHT for 4 hours before harvesting.

value: 10nM DHT 4 hours


title: sgCHD1_ETOH_rep2


title: 13-213LN24

description: 314(insulin 7 weeks).csv

source_name: LymphNode


title: Ctrl siRNA HepG2_biological_rep3


title: 13-213LN23

description: 314(insulin 7 weeks).csv


title: TNF_B6


title: TNF_B7


title: 13-213LN19

description: 314(insulin 7 weeks).csv


title: sgCHD1_DHT_rep1


title: 13-213LN20

description: 314(insulin 7 weeks).csv


title: 13-213LN18

description: 314(insulin 7 weeks).csv


title: UnTTT_A5

value: Untreated


title: 13-213LN22

description: 314(insulin 7 weeks).csv


title: Ctrl_ETOH_rep1

description: ATACsequencing in sgCtrl LNCaP cells post 10nM DHT


title: 13-213LN21

description: 314(insulin 7 weeks).csv


title: UnTTT_A3


title: 13-213LN17

description: 314(insulin 7 weeks).csv


title: Ctrl_DHT_rep2


title: 13-213LN15

description: 314(insulin 7 weeks).csv


title: 12-20W7M1b4


title: Ctrl_DHT_rep1


title: UnTTT_A2


title: 13-213LN16

description: 314(insulin 7 weeks).csv


title: Ctrl_ETOH_rep2


title: 13-213LN13

description: 314(insulin 7 weeks).csv


title: sgCHD1_ETOH_rep1


title: UnTTT_A4


title: 13-213LN14

description: 314(insulin 7 weeks).csv


title: 13-213LN12

description: 314(insulin 7 weeks).csv


title: sgCHD1_AR1

value: 10nM DHT 3 hours

value: LNCaP


title: 13-213LN11

description: 314(insulin 7 weeks).csv


title: UnTTT_A10


title: 13-213LN10

description: 314(insulin 7 weeks).csv


title: 13-213LN9

description: 314(insulin 7 weeks).csv


title: 13-213LN8

description: 314(insulin 7 weeks).csv


title: UnTTT_A9


title: UnTTT_A8


title: 13-213LN7

description: 314(insulin 7 weeks).csv


title: H3K27me3_2

source_name: ChIP Sequencing for H3K27me3 in LNCaP cells post 10nM DHT


title: 13-213LN5

description: 314(insulin 7 weeks).csv


title: 13-213LN3

description: 314(insulin 7 weeks).csv


title: UnTTT_A7


title: H3K4me3_2

source_name: ChIP Sequencing for H3K4me3 in LNCaP cells post 10nM DHT


title: 13-213LN4

description: 314(insulin 7 weeks).csv


title: cMyc_3

source_name: ChIP Sequencing for cMyc in LNCaP cells post 10nM DHT


title: cMyc_1


title: UnTTT_A6


title: H3K4me3_3


title: 12-203LN24

description: 314(insulin 7 weeks).csv


title: BV2-mix3

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010). The RT (Read Count) data were processed based on Quantile normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor (Gentleman et al.,2004).
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: microglia

growth_protocol: HT22 and BV-2 cells were maintained in Dulbecco's Modified Eagle's medium (Hyclone/Thermo, Rockford, IL), supplemented with 10% fetal bovine serum (FBS) (Hyclone/Thermo, Rockford, IL) and 1% penicillin/streptomycin in a 5% CO2 at 37℃. Human brain vascular pericyte (HBVP) was purchased from ScienCell Research Laboratories (Carlsbad, CA, USA) and maintained pericyte medium (PM) supplemented with 2% FBS, 1% pericyte growth supplement (PGS), and 1% penicillin/streptomycin in a 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. In brief, each 500ng total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, Inc., USA).

treatment_protocol: HT22 cells were plated on 96 well microplates at a density of 5 x 10^3/well and treated with hydrogen peroxide (H2O2) (250 μM) and each herbal extract for 6 h. BV-2 cells were pretreated with each herbal extract for 2 h and then stimulated with LPS (1 μ/mL) for an additional 22 h. HBVP were plated onto 6 well plates and maintained to 90% confluence in 2 ml of culture media. Cells were treated with TGF-ß (10 ng/mL) and each herbal extract for 24 h.   Seven crude herbal extracts forming UGS, including Uncariae Ramulus et Uncus (C1), Atractylodis Rhizoma Alba (C2), Poria Sclerotium (C3), Bupleuri Radix (C4), Angelicae Gigantis Radix (C5), Cnidii Rhizoma (C6), and Glycyrrhizae Radix et Rhizoma (C7) were purchased from Kwangmyungdang Pharmaceutical Co. LTD (Ulsan, Republic of Korea). In the preparation of mixture groups (Mix1 ~ Mix3), the ratios of the two herbal extracts reproduced those contained in UGS. To prepare Mix1, Uncariae Ramulus et Uncus (C1) and Atractylodis Rhizoma Alba (C2) were mixed in the ratio 3:4. For Mix 2, Poria Sclerotium (C3) and Bupleuri Radix (C4) were mixed in the ratio 2:1. For Mix 3, Angelicae Gigantis Radix (C5) and Cnidii Rhizoma (C6) and were mixed in the ratio 1:1.

value: Mouse BV-2 Microglial Cell Line


title: 13-213LN2

description: 314(insulin 7 weeks).csv

value: CD4+ T cell


title: BV2-C7


title: 13-213LN1

description: 314(insulin 7 weeks).csv

value: NOD/ShiLtJ


title: H3K27me3_3


title: BV2-mix2


title: CHD1_3

source_name: ChIP Sequencing for CHD1 in LNCaP cells post 10nM DHT


title: CHD1_2


title: 12-203LN20

description: 314(insulin 7 weeks).csv


title: 12-203LN22

description: 314(insulin 7 weeks).csv


title: 12-203LN23

description: 314(insulin 7 weeks).csv


title: BV2-mix1


title: 12-203LN21

description: 314(insulin 7 weeks).csv


title: 12-203LN19

description: 314(insulin 7 weeks).csv


title: 13-213LN6

description: 314(insulin 7 weeks).csv


title: 12-203LN18

description: 314(insulin 7 weeks).csv


title: 12-203LN17

description: 314(insulin 7 weeks).csv


title: AR_2

source_name: ChIP Sequencing for AR in LNCaP cells post 10nM DHT


title: AR_3


title: 12-203LN16

description: 314(insulin 7 weeks).csv


title: 12-203LN13

description: 314(insulin 7 weeks).csv


title: 12-203LN14

description: 314(insulin 7 weeks).csv


title: LN_sgCHD1_8-3

data_processing:
Human cell line reads (FASTQ files) were mapped to the human reference genome sequence (hg19) using STAR v2.4.0j (Dobin et al., 2013), and mouse organoid reads were mapped to the mouse reference genome sequence (mm10) using STAR v2.4.0j.
BAM files were subsequently converted into mapped-read format (MRF) using RSEQtools (Habegger et al., 2011).
The read count of each gene was calculated via HTSeq (Anders et al. 2014) using GENCODE as reference gene annotation set.  Quantification of gene expression was performed via RSEQtools, and expression levels (RPKM) were estimated.
Differentially expression analyses were performed using DESeq2 (ref) based on the gene read count data.  Multiple-hypothesis testing was considered by using Benjamini-Hochberg (BH; FDR) correction.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: First column represents GENCODE gene name, and second represents the read count for each gene.

growth_protocol: Isogenic LNCaP cells were grown in androgen deprived media for 72 hours. Murine organoids were grown in 2D in complete prostate organoid media for 48 hours and harvested for RNA in biological triplicate.

extract_protocol: RNA seq library preps for human were generated using Poly-A kit while the murine organoid libraries were generated using Ribo-Zero.  The murine organoids were sequenced to 150bp , paired end.

treatment_protocol: LNCaP cells were stimulated with 1nM DHT (or vehicle) for 3 and 8 hours in biological triplicate.

value: LnCap cell line

tag: genotype

value: CHD1 loss


title: BV2-Control


title: 12-203LN11

description: 314(insulin 7 weeks).csv


title: BV2-LPS


title: HT22_C7

source_name: neuronal cells

value: Mouse Hippocampal Neuronal Cell Line


title: 12-203LN10

description: 314(insulin 7 weeks).csv


title: 12-203LN9

description: 314(insulin 7 weeks).csv


title: 12-203LN8

description: 314(insulin 7 weeks).csv


title: 12-203LN7

description: 314(insulin 7 weeks).csv


title: LN_sgCHD1_8-1


title: HT22_mix3


title: HT22_mix2


title: LN_sgCHD1_3-3


title: 12-203LN6

description: 314(insulin 7 weeks).csv


title: HT22_mix1


title: 12-203LN5

description: 314(insulin 7 weeks).csv


title: 12-203LN4

description: 314(insulin 7 weeks).csv


title: LN_sgCHD1_3-2


title: HT22_UGS


title: BV2-UGS


title: 12-203LN15

description: 314(insulin 7 weeks).csv


title: 12-203LN3

description: 314(insulin 7 weeks).csv


title: 12-203LN2

description: 314(insulin 7 weeks).csv


title: 12-203LN12

description: 314(insulin 7 weeks).csv


title: LN_sgCHD1_0-3


title: LN_sgCHD1_8-2


title: HT22_H202


title: 12-203LN1

description: 314(insulin 7 weeks).csv


title: 13-214I4

description: 314(insulin 7 weeks).csv

source_name: Islets


title: 13-214I3

description: 314(insulin 7 weeks).csv


title: 13-214I2

description: 314(insulin 7 weeks).csv


title: HT22_Control


title: 13-214I1

description: 314(insulin 7 weeks).csv


title: LN_sgCHD1_0-1


title: 13-213I3

description: 314(insulin 7 weeks).csv


title: 13-213I2

description: 314(insulin 7 weeks).csv


title: MS_09_KO5

city: San Diego

first: Brian

middle: Patrick

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data QC by FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and mapping to the mouse reference genome (mm10) by STAR (Dobin, A. et al. 2014) with default parameters were performed in illumine BaseSpace (https://basespace.illumina.com).
FeatureCounts (Liao,Y et al., 2014) was used to count the reads mapped to the annotated mouse genes.
EdgeR- based R pipeline in SARTools was used to identify differentially expressed genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized read count values for each Sample

source_name: melanoma tumor

growth_protocol: 100,000 melanoma celle Yummer1.7 were inject s.c. in wt or siah2 KO mice and the tumors were collected 10 days after.

extract_protocol:
Total RNA was extracted from tumors or cells using TRIzol (Ambion) and treated with DNase I.
Poly A selected RNA libraries were prepared for sequencing using the NEB Ultra II Directional RNA library kit.

value: Siah2 KO

tag: tumor source

value: melanoma cells Yummer1.7 (100,000cells) were injected s.c on flunk of the mouse


title: LN_Ctrl_8-3

value: Control


title: MS_10_KO6


title: LN_Ctrl_8-2


title: 12-204I2

description: 314(insulin 7 weeks).csv


title: LN_sgCHD1_3-1


title: 13-213I1

description: 314(insulin 7 weeks).csv


title: MS_08_KO3


title: 12-204I1

description: 314(insulin 7 weeks).csv


title: 12-201I8

description: 314(insulin 7 weeks).csv


title: 12-201I7

description: 314(insulin 7 weeks).csv


title: LN_Ctrl_3-3


title: 12-201I6

description: 314(insulin 7 weeks).csv


title: LN_Ctrl_8-1


title: LN_Ctrl_3-2


title: 12-201I5

description: 314(insulin 7 weeks).csv


title: 12-201I4

description: 314(insulin 7 weeks).csv


title: MS_05_WT6

value: WT


title: LN_sgCHD1_0-2


title: MS_06_KO1


title: LN_Ctrl_3-1


title: 12-201I2

description: 314(insulin 7 weeks).csv


title: MS_04_WT5


title: LN_Ctrl_0-3


title: 12-201I3

description: 314(insulin 7 weeks).csv


title: 12-201I1

description: 314(insulin 7 weeks).csv


title: MS_03_WT4


title: LN_Ctrl_0-2


title: 12-203I3

description: 314(insulin 7 weeks).csv


title: MS_02_WT3


title: MS_07_KO2


title: LN_Ctrl_0-1


title: 12-203I1

description: 314(insulin 7 weeks).csv


title: MS_01_WT2


title: 13B12LN44

description: 13-21B 12 weeks UPDATED.csv


title: G1297_ON_Input

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
the low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1. Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm10) with BWA 0.7.12 .
Peaks were called using the MACS2 plus IDR framework developed by the ENCODE project.
Mapped reads were visualized using igv-2.3. The heatmaps for ChIP-Seq data were drawn using the ngsplot-2.47 program.
Super enhancers were identified by H3K27ac with ROSE pipelines. Super enhancers identified in this study were assigned to the transcripts whose TSS were within the super enhancers.
BigWig (bw) files were generated using igvtools (Version 2.3.91 Broad Institute) and wigToBigWig (version 4, UCSC). The data were normalized as RPM (reads per million).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: murine EWS/ATF1-induced sarcoma cell line

extract_protocol:
Purified ChIP DNA (5 ng per sample) was used for generation of sequencing libraries with TruSeq ChIP Sample Prep Kit (Illumina).
The resultant DNA libraries were assessed on an Agilent Bioanalyzer and quantified with KAPA Library Quantification Kits (KAPA BIOSYSTEMS). The libraries were sequenced to generate single-end 86 bp reads using NextSeq 500 (illumina).

tag: chip antibody


title: 141299

city: Tallinn

first: Agne

last: Velthut-Meikas

address: Akadeemia tee 15

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

description: ESPcounts.csv

data_processing:
Quality control and adapter trimming of raw sequences was performed using Trimmomatic version 0.36. All sequences were scanned with 4 base long sliding window and reads were dropped if the average quality of base pair was below 30 according to Phred +33 quality score system or if total read length was less than 17.
Identification of miRNAs from sequencing reads was performed by miRDeep2 algorithm according to miRBase version 21. Standard settings were used.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: counts

source_name: endometrium

extract_protocol:
Qiagen miRNeasy protocol for endometrium samples and PaxGene Blood miRNA protocol for blood samples
Illumina TruSeq Small RNA Library Preparation Guide

tag: patient id

tag: lh day

tag: group

value: IVF

tag: country

value: Spain

tag: age


title: 141273

description: ESPcounts.csv

source_name: blood


title: 13B12LN43

description: 13-21B 12 weeks UPDATED.csv

data_processing: Custom R analysis pipeline


title: 13B12LN42

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S44

description: 13-21B 12 weeks UPDATED.csv

source_name: Spleen


title: 13B12LN41

description: 13-21B 12 weeks UPDATED.csv


title: G1297_NanogKRAB_HA_48h

tag: cell line

tag: genotype/variation

value: Nanog-KRAB-introduced

value: anti HA antibody(Monoclonal Mouse IgG 1-κ):nacalai cat# 06340-54 Lot#M4H0340


title: 141272

description: ESPcounts.csv


title: G1297_Ebf1KRAB_HA_48h


title: 13B12LN40

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN39

description: 13-21B 12 weeks UPDATED.csv


title: 141271

description: ESPcounts.csv


title: 12-203I4

description: 314(insulin 7 weeks).csv


title: 13B12LN35

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN36

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN37

description: 13-21B 12 weeks UPDATED.csv


title: 12-203I2

description: 314(insulin 7 weeks).csv


title: 13B12LN34

description: 13-21B 12 weeks UPDATED.csv


title: 141266

description: ESPcounts.csv


title: 13B12LN33

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN32

description: 13-21B 12 weeks UPDATED.csv


title: 141264

description: ESPcounts.csv


title: 13B12LN31

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN30

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN29

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN28

description: 13-21B 12 weeks UPDATED.csv


title: 141262

description: ESPcounts.csv


title: 141261

description: ESPcounts.csv


title: 141270

description: ESPcounts.csv


title: 13B12LN38

description: 13-21B 12 weeks UPDATED.csv


title: 141259

description: ESPcounts.csv


title: 141263

description: ESPcounts.csv


title: 140436

description: ESPcounts.csv


title: 140435

description: ESPcounts.csv


title: 140438

description: ESPcounts.csv


title: WT-3

tag: tissue

value: organoid


title: Hi-C Tet2/3 DKO iNKT transferred and expanded Biol. Rep. 2

first: Isaac

middle: F.

last: López-Moyado

address: 9420 Athena Cir

department: Division of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

description: Hi-C

data_processing:
For WGBS analysis, we employed BSMAP (v2.9) (Xi and Li, 2009) to align paired-end reads from bisulfite-treated samples to the mm10 mouse reference genome allowing 4 mismatches. Reads mapping to multiple locations in the reference genome with the same mapping score were removed as well as the 5' ends bearing quality lower than 20 (mapping parameters: -n 1 -v 4 -w 2 -r 0 -q 20 -R -p 8). Duplicate reads caused by PCR amplification were removed by BSeQC (v1.0.3) (Lin et al., 2013) using default parameters. An effective genome size of 1.87e9 (as suggested in BSeQC for Mus musculus genome) was employed to calculate maximum coverage at the same genomic location. In addition, BSeQC was employed for removing DNA methylation artifacts introduced by end repair during adaptor ligation. For paired-end sequencing, overlapping segments of two mates of a pair were reduced to only one copy to avoid considering the same region twice during the DNA methylation quantification. To estimate CpG DNA methylation, we employed the methratio.py tool included in BSMAP (v2.9) (Xi and Li, 2009), merging DNA methylation at each CpG di-nucleotide (combining CpG methylation ratios on both DNA strands).
Hi-C analysis was performed using HOMER (Heinz et al., 2010) and its Hi-C data analysis suite. Reads corresponding to each extreme of a fragment were trimmed after the corresponding restriction site (e.g. MboI in the case of the iNKT datasets) using HOMER (Heinz et al., 2010) homerTools trim and independently mapped employing BWA-aln (v0.7.13) (single-end mode) (Li and Durbin, 2010). Reads were filtered out if they had a MAPQ score of less than 30, and only reads that were at least 25 bp were considered for the rest of the analysis. Only reads falling within the autosomes were considered for the analysis (no sex chromosomes included). Independently-mapped reads were paired using the makeTagDirectory command, allowing only 1 tag per bp (-tbp 1). Reads were filtered to remove uninformative reads (contiguous genomic fragments, self-ligation, re-ligation, and reads originating from regions of unusually high tag density) and also filtered based on the distance tor restriction sites (-genome mm10 -removePEbg -restrictionSite GATC -both -removeSelfLigation -removeSpikes 10000 5). To perform the principal component analysis (PCA) of Hi-C data (A/B compartment identification), we used the tool runHiCpca.pl on the normalized interaction matrix, with the options -res 50000 -superRes 100000 -genome mm10.
For total RNA-seq analysis, quality and adapter trimming was performed on raw RNA-seq reads using TrimGalore! 431 v0.4.5 with default parameters, retaining reads with minimal length of 25 bp. Ribosomal RNA reads were filtered out using Tagdust2. Resulting reads were aligned to mouse genome mm10 using STAR v2.5.3a (Dobin et al., 2013) with alignment parameter --outFilterMismatchNmax 4 --outFilterMultimapNmax 100 --winAnchorMultimapNmax 200. We employed TETranscripts (Jin et al., 2015) to quantify gene and transposable element transcript abundances. We used this package on mode -multi to be able to use ambiguously mapped reads to generate the count tables to then perform the differential expression analysis. We used the transcript annotations of the mouse genome mm10, and the repeat element annotation from UCSC RepeatMasker track of mouse genome mm10.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation summary matrices were generated using the methratio.py tool included in BSMAP (v2.9), and summarize the ratio of bisulfite-unconverted to total cytosines (C_count/[C_count+CT_count]). BedGraph files were generated using HOMER's tool runHiCpca.pl on the normalized interaction matrix, and contain the PC1 values which aid in the Hi-C A/B compartment identification. The matrix of raw counts of sequencing reads was generated using TETranscripts, and contains the raw counts of sequencing reads overlapping transcript and repeat element features in all experimental conditions, to be used in downstream differential expression analysis.

extract_protocol:
Between 0.6 and 1.5x10^6 iNKT cells were fixed in complete medium containing 1% Formaldehyde, then quenched with 125mM glycine and washed twice with an excess of PBS. Cells were then resuspended in lysis buffer containing 0.5% SDS and lysed at 62°C for 7 minutes. This step also allows to remove proteins that were not fixed to the chromatin. SDS was further quenched with 1% Triton-X-100 at 37°C for 15 minutes. Next, permeabilized nuclei were reacted with 100 units of MboI overnight at 37°C. After subsequent washing and inactivation of MboI, the restriction sites were further filled in with Biotin-14-dATP and Klenow polymerase at room temperature for 40 minutes. Samples were transferred into a ligation solution containing 600 units of T4 DNA ligase. Proximity ligation was stopped by addition of 2-fold molar excess of EDTA, and samples were decrosslinked at 65°C for 16h00. DNA was further purified by proteinase K digestion and phenol/chloroform extraction.
800 ng of DNA was sonicated to an average of 300bp fragments length, and was used for subsequent library preparation that includes (1) blunting of DNA, (2) A-tailing, (3) ligation of sequencing adapters, and (4) amplification of library.

value: Tet2/3 DKO (Tet2-/- ;Tet3fl/fl;CD4Cre)

value: Spleen

value: iNKT

tag: expansion stage

value: Transferred and expanded in congenic recipients

tag: strain background


title: WGBS (MethylC-seq) Tet2/3 DKO iNKT transferred and expanded Biol. Rep. 1

description: WGBS (MethylC-seq)

extract_protocol:
After isolation of the cells, DNA was isolated using the PureLink DNA isolation kit (Life Technologies), according to the instructions of the manufacturer.
DNA was fragmented to an average size of 200 bp using the Adaptive Focused Acoustics Covaris S2 instrument. Briefly, fully unmethylated lambda DNA (Promega) was spiked into the mouse genomic DNA at a ratio of 1:200. DNA was end-repaired using the End Repair (Illumina Epicentre) and A-tailed (using Klenow fragment, NEB). Ligation of methylated adapters (NeBNext Multiplex Oligos for Illumina, NEB) was performed using Quick Ligase Kit (NEB). DNA was bisulfite-treated using the MethylCode Bisulfite Conversion Kit (Life Technologies). The bisulfite treated DNA was amplified for 4 cycles -so as to ensure high complexity of the libraries- using Kapa HiFi Uracil+ (Kapa Biosystems).

tag: cell type


title: Total RNA-seq WT iNKT thymus Biol. Rep. 2

description:
Total (ribodepleted) RNA-seq
NKT_ribofree.cntTable

source_name: Thymus

extract_protocol:
10 million cells were sorted and then whole RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
Ribo-zero RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) with minor modifications. The starting RNA was 800 ng. Ribosomal RNAs were depleted using magnetic beads. Next, RNA was fragmented, and cDNA was synthesized using Superscript II (Invitrogen). After A-tailing and adaptor ligation, libraries were generated by amplifying the cDNA for 12 cycles.

value: Wild Type

value: Thymus


title: Hi-C WT iNKT spleen

description: Hi-C


title: Hi-C Tet2/3 DKO iNKT transferred and expanded Biol. Rep. 3

description: Hi-C


title: WGBS (MethylC-seq) Tet2/3 DKO iNKT transferred and expanded Biol. Rep. 2

description: WGBS (MethylC-seq)


title: Hi-C WT iNKT thymus

description: Hi-C


title: Total RNA-seq Tet2/3 DKO iNKT thymus Biol. Rep. 1

value: Young mice (3-4 weeks old)


title: 13B12LN16

description: 13-21B 12 weeks UPDATED.csv

extract_protocol: Tetramer used to stain CD4+ T cells specific to either 12-20 or 13-21 of the insulin Beta chain from various NOD mice tissues.

value: CD4+ T cell

tag: strain

value: NOD/ShiLtJ


title: 13B12LN18

description: 13-21B 12 weeks UPDATED.csv

tag: iag7 tetramer


title: 13B12LN15

description: 13-21B 12 weeks UPDATED.csv

tag: age (in weeks)


title: 13B12LN21

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN20

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN24

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN22

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN26

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN25

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN23

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN27

description: 13-21B 12 weeks UPDATED.csv


title: Total RNA-seq WT iNKT thymus Biol. Rep. 1

tag: genotype


title: Hi-C Tet2/3 DKO iNKT transferred and expanded Biol. Rep. 1

description: Hi-C


title: 13B12LN19

description: 13-21B 12 weeks UPDATED.csv


title: Total RNA-seq Tet2/3 DKO iNKT thymus Biol. Rep. 2


title: 140433

description: ESPcounts.csv


title: 13B12LN14

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN17

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN13

description: 13-21B 12 weeks UPDATED.csv


title: WT-2


title: 140434

description: ESPcounts.csv


title: 140432

description: ESPcounts.csv


title: 13B12LN12

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN9

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN5

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN10

description: 13-21B 12 weeks UPDATED.csv


title: WT-1


title: 13B12LN4

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN6

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN2

description: 13-21B 12 weeks UPDATED.csv


title: 140419

description: ESPcounts.csv


title: 13B12LN3

description: 13-21B 12 weeks UPDATED.csv


title: 140422

description: ESPcounts.csv


title: 13B12LN8

description: 13-21B 12 weeks UPDATED.csv


title: CRE-3

value: CHD1 loss


title: 140431

description: ESPcounts.csv


title: 140424

description: ESPcounts.csv


title: 13B12LN1

description: 13-21B 12 weeks UPDATED.csv


title: 140420

description: ESPcounts.csv


title: CRE-1


title: 13B12S31

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S38

description: 13-21B 12 weeks UPDATED.csv


title: 13B12LN11

description: 13-21B 12 weeks UPDATED.csv


title: 140418

description: ESPcounts.csv


title: 13B12LN7

description: 13-21B 12 weeks UPDATED.csv


title: CRE-2


title: 140421

description: ESPcounts.csv


title: 13B12S26

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S25

description: 13-21B 12 weeks UPDATED.csv


title: 140417

description: ESPcounts.csv


title: 13B12S18

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S20

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S16

description: 13-21B 12 weeks UPDATED.csv


title: 131212

description: ESPcounts.csv

value: CONTROL


title: 13B12S13

description: 13-21B 12 weeks UPDATED.csv


title: 131213

description: ESPcounts.csv


title: 131215

description: ESPcounts.csv


title: 13B12S12

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S7

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S6

description: 13-21B 12 weeks UPDATED.csv


title: 131214

description: ESPcounts.csv


title: 131211

description: ESPcounts.csv


title: 13B12S3

description: 13-21B 12 weeks UPDATED.csv


title: Liver_NAFLD [2019KA6]

city: Otaku

first: Fumika

last: Shigiyama

state: Tokyo

department: Diabetes, Metabolism and Endocrinology

institute: Toho University Graduate School of Medicine

hyb_protocol: The procedure of hybridization is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manual.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000 using GeneChip Command Console Software ver3.2. The procedure of scan is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manual.

data_processing: Data is processed by RMA-Sketch algorithm using Expression ConsoleTM Software ver.1.3.0.

label: biotin

source_name: Human Liver biopsy sample

label_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manual. 100ng Total RNA was used for this assay.

extract_protocol: Total RNA was extracted from flash frozen ~10 mg liver biopsy using the RNeasy mini kit (Qiagen, Tokyo, Japan). RNA was reverse-transcribed into cDNA using the QuantiTect Reverse Transcription Kit (Qiagen, Hilden, Germany).

tag: diagnosis

value: Nonalcoholic fatty liver disease (NAFLD)

value: Liver


title: 131210

description: ESPcounts.csv

value: Spain


title: Liver_NAFLD [2019KA10]


title: 13B12S24

description: 13-21B 12 weeks UPDATED.csv


title: 13B12S2

description: 13-21B 12 weeks UPDATED.csv


title: Liver_NAFLD [2019KA14]


title: 13B12S14

description: 13-21B 12 weeks UPDATED.csv


title: Liver_NAFLD [2019A44]


title: 13A12S43

description: 13-21A 12 weeks UPDATED.csv


title: 131209

description: ESPcounts.csv


title: 13A12S44

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN44

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2019A47]


title: 13B12S4

description: 13-21B 12 weeks UPDATED.csv


title: 131208

description: ESPcounts.csv


title: Liver_NAFLD [2019A36]


title: 13A12LN43

description: 13-21A 12 weeks UPDATED.csv


title: 131207

description: ESPcounts.csv


title: 13A12LN42

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2019A39]


title: Liver_NAFLD [2019A43]


title: 13A12LN40

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2019A34]


title: 13B12S42

description: 13-21B 12 weeks UPDATED.csv


title: Liver_NAFLD [2019A4]


title: 13A12LN39

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2018A26]


title: 131206

description: ESPcounts.csv


title: 13A12LN38

description: 13-21A 12 weeks UPDATED.csv


title: 131205

description: ESPcounts.csv


title: Liver_NAFLD [2018KA3]


title: 13A12LN41

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2018A28]


title: 131204

description: ESPcounts.csv


title: 13A12LN36

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN33

description: 13-21A 12 weeks UPDATED.csv


title: 131067

description: ESPcounts.csv


title: 13A12LN30

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN31

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN29

description: 13-21A 12 weeks UPDATED.csv


title: 131068

description: ESPcounts.csv


title: 13A12LN34

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN32

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN28

description: 13-21A 12 weeks UPDATED.csv


title: 131065

description: ESPcounts.csv


title: 13A12LN37

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN27

description: 13-21A 12 weeks UPDATED.csv


title: 131066

description: ESPcounts.csv


title: 13A12LN26

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2018A20]


title: 131064

description: ESPcounts.csv


title: Liver_NAFLD [2018A18]


title: Liver_NAFLD [2018A13]


title: 13A12LN35

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2018A9]


title: 13A12LN25

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN23

description: 13-21A 12 weeks UPDATED.csv


title: 131063

description: ESPcounts.csv


title: 13A12LN22

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN21

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN20

description: 13-21A 12 weeks UPDATED.csv


title: 131062

description: ESPcounts.csv


title: 13A12LN19

description: 13-21A 12 weeks UPDATED.csv


title: 131060

description: ESPcounts.csv


title: 131061

description: ESPcounts.csv


title: 13A12LN18

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN17

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN15

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN24

description: 13-21A 12 weeks UPDATED.csv


title: 131059

description: ESPcounts.csv


title: 13A12LN14

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN12

description: 13-21A 12 weeks UPDATED.csv


title: 131058

description: ESPcounts.csv


title: Liver_NAFLD [2018A8]


title: 131057

description: ESPcounts.csv


title: 13A12LN11

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN13

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN8

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN7

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2018A12]


title: 13A12LN6

description: 13-21A 12 weeks UPDATED.csv


title: 131056

description: ESPcounts.csv


title: Liver_NAFLD [2018A6]


title: Liver_NAFLD [2015A23]


title: Liver_NAFLD [2015A26]


title: 13A12LN16

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2015A28]


title: Liver_NAFLD [2018A3]


title: 131055

description: ESPcounts.csv


title: Liver_NAFLD [2015A20]


title: Liver_NAFLD [2015A22]


title: 13A12LN10

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN5

description: 13-21A 12 weeks UPDATED.csv


title: 13A12LN4

description: 13-21A 12 weeks UPDATED.csv


title: 131051

description: ESPcounts.csv


title: 131048

description: ESPcounts.csv


title: Liver_NAFLD [2015A19]


title: Liver_NAFLD [2018A23]


title: 13A12LN1

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2015A18]


title: Liver_NAFLD [2015A21]


title: 131052

description: ESPcounts.csv


title: 13A12LN2

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S41

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2015A17]


title: 13A12LN3

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S38

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S37

description: 13-21A 12 weeks UPDATED.csv


title: 131047

description: ESPcounts.csv


title: Liver_NAFLD [2015A16]


title: 13A12S31

description: 13-21A 12 weeks UPDATED.csv


title: 131045

description: ESPcounts.csv


title: 13A12S35

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S25

description: 13-21A 12 weeks UPDATED.csv


title: 131044

description: ESPcounts.csv


title: 131046

description: ESPcounts.csv


title: Liver_NAFLD [2015A14]


title: 13A12S23

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2015A15]


title: 13A12S14

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S24

description: 13-21A 12 weeks UPDATED.csv


title: 131043

description: ESPcounts.csv


title: 131042

description: ESPcounts.csv


title: Liver_NAFLD [2015A12]


title: Liver_NAFLD [2015A13]


title: Liver_NAFLD [2015A11]


title: 13A12S36

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S13

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S34

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S12

description: 13-21A 12 weeks UPDATED.csv


title: 13951

description: ESPcounts.csv

value: IVF


title: 131041

description: ESPcounts.csv


title: 13A12S8

description: 13-21A 12 weeks UPDATED.csv


title: 13950

description: ESPcounts.csv


title: 13A12S4

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S17

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S22

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S7

description: 13-21A 12 weeks UPDATED.csv


title: Liver_NAFLD [2015A10]


title: Liver_NAFLD [2015A8]


title: Liver_NAFLD [2015A7]


title: Liver_NAFLD [2015A6]


title: 13A12S9

description: 13-21A 12 weeks UPDATED.csv


title: 13A12S10

description: 13-21A 12 weeks UPDATED.csv


title: 13942

description: ESPcounts.csv


title: 13A12S1

description: 13-21A 12 weeks UPDATED.csv


title: 13910

description: ESPcounts.csv


title: 13A12S2

description: 13-21A 12 weeks UPDATED.csv


title: 13909

description: ESPcounts.csv


title: Liver_NAFLD [2015A4]


title: 13B6LN40

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN39

description: 13-21B 6weeks UPDATED.csv


title: 13908

description: ESPcounts.csv


title: 13943

description: ESPcounts.csv


title: 13B6LN38

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN37

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN36

description: 13-21B 6weeks UPDATED.csv


title: 13907

description: ESPcounts.csv


title: 13B6LN35

description: 13-21B 6weeks UPDATED.csv


title: 13A12S3

description: 13-21A 12 weeks UPDATED.csv


title: 13B6LN42

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN34

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN33

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN41

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN31

description: 13-21B 6weeks UPDATED.csv


title: 13906

description: ESPcounts.csv


title: 13B6LN32

description: 13-21B 6weeks UPDATED.csv


title: 13905

description: ESPcounts.csv


title: 13B6S44

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_123

city: Boston

first: Yang

last: Luo

state: Massachusetts

address: 77 avenue louis pasteur, room 255

institute: Harvard Medical School

data_processing:
Low input gene expression quantification was performed with Kallisto version 0.43.1 (Bray et al, Nature Biotechnology, 2016), using the Ensembl 83 annotation.
Normalized expression are log2(tpm+1) values. Expressed genes those with a log2(TMPM+1) > 1 in at least 95% of the samples.
Genome_build: hg19

source_name: THP1 clonal cell line

growth_protocol: 10% complete RPMI (1640 + 50mL FBS + 0.5mLBME + 5.5mL Pen/Strep + 5mL NEAA + 2mL Lglut + 7.5mL HEPES + 5mL NaPyruvate)

extract_protocol:
Qiagen Rneasy minikit (Qiagen, catalogue no. 74104)
Smartseq2 (Broad Institute Genomics Platform)

treatment_protocol: CRISPR/Cas9 disruption of 3q23 genomic region around rs73226617, and single-cell sorts of edited THP1 cells after 2 weeks

value: Wildtype amplicon size, intact genomic sequence


title: 13B6LN30

description: 13-21B 6weeks UPDATED.csv

source_name: LymphNode


title: 13902

description: ESPcounts.csv


title: Liver_NAFLD [2015A3]


title: WT liver_rep3

city: Seoul

first: Sang Geon

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

institute: Seoul National University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k 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: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: WT liver_rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Male WT and Gα12 mice in 95% C57BL/6 background (n=3, each) were fed ad libitum with free access to water and food.

extract_protocol: RNA was prepared using the TRIzol (TaKaRa BIO, Otsu, Shiga Japan) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After an overnight fast, the 8-week-old mice were sacrificed. Livers from these mice were then dissected and RNA was isolated with a Qiagen RNeasy Mini kit. RNA quality was validated with the Agilent 2100 Bioanalyzer.

tag: gender

value: male

value: C57BL/6 and 129/Sv

value: liver

value: 8 weeks

tag: diet

value: chow diet, overnight fasting


title: Gα12 KO liver_rep2

source_name: Gα12 KO liver_rep2


title: clone_replicate2_122


title: Gα12 KO liver_rep1

source_name: Gα12 KO liver_rep1


title: Gα12 KO liver_rep3

source_name: Gα12 KO liver_rep3


title: WT liver_rep1

source_name: WT liver_rep1


title: WT liver_rep2

source_name: WT liver_rep2


title: 13B6LN29

first: Luc

institute: TSRI

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN28

description: 13-21B 6weeks UPDATED.csv


title: 13901

description: ESPcounts.csv

tag: patient id

tag: lh day


title: 13B6LN25

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_18


title: 13B6LN26

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN24

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN27

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_114


title: 13899

description: ESPcounts.csv

tag: group

tag: country


title: 13B6LN23

description: 13-21B 6weeks UPDATED.csv


title: 13900

description: ESPcounts.csv

tag: age


title: 13B6LN22

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_116

tag: cell line


title: clone_replicate2_13


title: 13893

description: ESPcounts.csv


title: 13B6LN20

description: 13-21B 6weeks UPDATED.csv


title: 13894

description: ESPcounts.csv


title: 13B6LN21

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_14


title: clone_replicate2_8


title: 13B6LN19

description: 13-21B 6weeks UPDATED.csv


title: 13890

description: ESPcounts.csv


title: 13B6LN17

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_135

value: Wildtype amplicon size, edited genomic sequence


title: 13889

description: ESPcounts.csv


title: 13B6LN15

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN16

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_133


title: 13888

description: ESPcounts.csv


title: 13B6LN13

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN12

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN11

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_124


title: clone_replicate2_125


title: 13B6LN9

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN10

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN7

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_24


title: 13885

description: ESPcounts.csv


title: 13882

description: ESPcounts.csv


title: 13B6LN5

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_20


title: 13B6LN4

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN18

description: 13-21B 6weeks UPDATED.csv


title: 13886

description: ESPcounts.csv


title: 13B6LN3

description: 13-21B 6weeks UPDATED.csv


title: 13B6LN1

description: 13-21B 6weeks UPDATED.csv


title: 13881

description: ESPcounts.csv


title: 13B6S42

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_12


title: 13880

description: ESPcounts.csv


title: clone_replicate2_15


title: clone_replicate2_131


title: 13B6S41

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_80

value: Detectable genomic deletion in amplicon


title: 13B6LN8

description: 13-21B 6weeks UPDATED.csv


title: 13B6S40

description: 13-21B 6weeks UPDATED.csv


title: 13610

description: ESPcounts.csv


title: 13B6LN6

description: 13-21B 6weeks UPDATED.csv


title: 13887

description: ESPcounts.csv


title: 13B6S39

description: 13-21B 6weeks UPDATED.csv


title: 13B6S38

description: 13-21B 6weeks UPDATED.csv


title: 13B6S37

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_102


title: 13B6S36

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_79


title: 13590

description: ESPcounts.csv


title: 13B6S34

description: 13-21B 6weeks UPDATED.csv


title: 13B6S35

description: 13-21B 6weeks UPDATED.csv


title: 13B6S33

description: 13-21B 6weeks UPDATED.csv


title: 13606

description: ESPcounts.csv


title: 13B6LN2

description: 13-21B 6weeks UPDATED.csv


title: 13586

description: ESPcounts.csv


title: 13879

description: ESPcounts.csv


title: 13B6S32

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate2_66


title: NOTNV75LH8E

description: ESTcounts.csv

value: Estonia


title: 13B6S30

description: 13-21B 6weeks UPDATED.csv

value: CD4+ T cell


title: 13B6S28

description: 13-21B 6weeks UPDATED.csv

value: NOD/ShiLtJ


title: clone_replicate1_123


title: 13B6S27

description: 13-21B 6weeks UPDATED.csv


title: NOTNV75LH2E

description: ESTcounts.csv


title: 13B6S25

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate1_116


title: clone_replicate1_122


title: 13B6S24

description: 13-21B 6weeks UPDATED.csv


title: 13B6S23

description: 13-21B 6weeks UPDATED.csv


title: NOTNV73LH8E

description: ESTcounts.csv


title: NOTNV71LH8E

description: ESTcounts.csv


title: clone_replicate1_114


title: 13B6S21

description: 13-21B 6weeks UPDATED.csv


title: 13B6S19

description: 13-21B 6weeks UPDATED.csv


title: NOTNV62LH8E

description: ESTcounts.csv


title: NOTNV59LH8E

description: ESTcounts.csv


title: 13B6S31

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate1_18


title: clone_replicate2_160


title: clone_replicate2_68


title: 13B6S26

description: 13-21B 6weeks UPDATED.csv


title: NOTNV78LH8E

description: ESTcounts.csv


title: NOTNV58LH8E

description: ESTcounts.csv


title: 13B6S22

description: 13-21B 6weeks UPDATED.csv


title: 13B6S29

description: 13-21B 6weeks UPDATED.csv


title: 13B6S18

description: 13-21B 6weeks UPDATED.csv


title: 13B6S17

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate1_14


title: 13B6S16

description: 13-21B 6weeks UPDATED.csv


title: 13B6S20

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate1_13


title: 13B6S15

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate1_8


title: NOTNV52LH8E

description: ESTcounts.csv


title: 13B6S13

description: 13-21B 6weeks UPDATED.csv


title: NOTNV48LH8E

description: ESTcounts.csv


title: clone_replicate1_135


title: 13B6S12

description: 13-21B 6weeks UPDATED.csv


title: 13B6S14

description: 13-21B 6weeks UPDATED.csv


title: NOTNV48LH2E

description: ESTcounts.csv


title: 13B6S10

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title: 13B6S9

description: 13-21B 6weeks UPDATED.csv


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description: 13-21B 6weeks UPDATED.csv


title: 13B6S11

description: 13-21B 6weeks UPDATED.csv


title: 13B6S5

description: 13-21B 6weeks UPDATED.csv


title: clone_replicate1_131


title: NOTNV47LH2E

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title: clone_replicate1_124


title: NOTNV44LH8E

description: ESTcounts.csv


title: clone_replicate1_125


title: NOTNV47LH8E

description: ESTcounts.csv


title: 13B6S4

description: 13-21B 6weeks UPDATED.csv


title: NOTNV44LH8B

description: ESTcounts.csv


title: 13B6S7

description: 13-21B 6weeks UPDATED.csv


title: 13B6S2

description: 13-21B 6weeks UPDATED.csv


title: NOTNV43LH8E

description: ESTcounts.csv


title: 13B6S1

description: 13-21B 6weeks UPDATED.csv


title: 13B6S6

description: 13-21B 6weeks UPDATED.csv


title: 13A6S44

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV43LH8B

description: ESTcounts.csv


title: clone_replicate1_20


title: 13A6S43

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN44

description: 13-21 A 6weeks UPDATED.csv


title: clone_replicate1_133


title: clone_replicate1_15


title: 13A6LN43

description: 13-21 A 6weeks UPDATED.csv


title: clone_replicate1_24


title: clone_replicate1_12


title: NOTNV41LH8E

description: ESTcounts.csv


title: 13A6LN42

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN40

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV41LH8B

description: ESTcounts.csv


title: clone_replicate1_80


title: 13B6S3

description: 13-21B 6weeks UPDATED.csv


title: 13A6LN38

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN39

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN41

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV40LH8E

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description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN35

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV40LH2E

description: ESTcounts.csv


title: clone_replicate1_79


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description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN33

description: 13-21 A 6weeks UPDATED.csv


title: NOTNV39LH8E

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description: 13-21 A 6weeks UPDATED.csv


title: NOTNV40LH2B

description: ESTcounts.csv


title: 13A6LN30

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN29

description: 13-21 A 6weeks UPDATED.csv


title: clone_replicate1_68


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description: ESTcounts.csv


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description: 13-21 A 6weeks UPDATED.csv


title: clone_replicate1_102


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description: 13-21 A 6weeks UPDATED.csv


title: NOTNV36LH8E

description: ESTcounts.csv


title: 13A6LN26

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN25

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN22

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN24

description: 13-21 A 6weeks UPDATED.csv


title: 13A6LN21

description: 13-21 A 6weeks UPDATED.csv