title: Cal27 ATAC-seq

data_processing:
Nextera adapters were trimmed from the raw fastq files by using cutadapt with parameters “-m 5 -e 0.10 -a CTGTCTCTTATA -A CTGTCTCTTATA” and then aligned to human reference genome hg38 using bowtie2 with parameters “-X2000 --mm --local”
Improper mapped, poorly mapped and unmatched reads were filtered from the resultant raw bam files using samtools view with parameters “-F 1804 -f 2 -q30”
Duplicates were marked by “picard MarkDuplicate” and removed by “samtools view”
Final bam files were generated after removing mitochondrial reads by “awk” command
Replicate Bam files were merged using “samtools merge” and converted to tagAlign format using bedtools bamtobed with parameters “-bedpe -mate1 -I” and “awk”
To account for the cutting offset of Tn5 transposase, mapping position was shifted using “awk”
Peaks were called from tagAlign files using MACS2 callpeak with parameters “-g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits”
Bedgraph files output from MACS2 were converted to BigWig files using bedGraphToBigWig
NarrowPeak files from individual ATAC-seq replicates and pooled peak files from MACS2 were sorted for high P-value peaks (>= 13 -log10 [p < 0.05]) with “awk”
high P-value pooled peaks were intersected with high P-value peaks from each replicate using bedtools intersect with the -u parameter
In order to exclude promoter proximal peaks the Gencode hg38 annotation was downloaded and TSS +/- 2kb were filtered out with “awk”. High p-value peaks were intersected with the Gencode TSS annotation with bedtools intersect with the -v parameter
Promoter distal high p-value ATAC peaks were intersected with H3K27Ac ChIP-seq peaks from each specific cell line to identify ATAC peaks located within regions of H3K27Ac using bedtools intersect with the -wa parameter.
Motifs were identified from these peaks using HOMER findMotifsGenome with the parameter “-size given”
Genome_build: hg38
Supplementary_files_format_and_content: BigWig (bw) files contain IGV-viewable read density data, visualized as peaks. Browser Extensible Data (BED) files contain the subset of significant (p < 0.05), TSS distal, H3K27Ac overlapping peaks.

extract_protocol:
Approximately 50,000 nuclei were resuspended in 20µL ice-cold Tagmentation Buffer, and incubated with 1µL Tagmentation enzyme (Illumina, #FC-121-1030) at 37 °C for 30 min with shaking 500 rpm. The tagmentated DNA was purified using MinElute PCR purification kit (Qiagen, #28004).
libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541) with primer extension at 72°C for 5 min, denaturation at 98°C for 30s, followed by 8 cycles of denaturation at 98°C for 10s, annealing at 63°C for 30s and extension at 72°C for 60s. Amplified libraries were then purified using MinElute PCR purification kit (Qiagen, #28004), and two size selection steps were performed using SPRIselect bead (Beckman Coulter, #B23317) at 0.55X and 1.5X bead-to-sample volume rations, respectively. Each library was then sequenced on an Illumina NextSeq500 or HiSeq4000 to a depth of >= 20 million usable reads pairs

tag: tagmentation enzyme

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1038


title: LNZ308 H3K27ac ChIP seq

status: Public on Dec 17 2019

type: SRA

city: La Jolla

first: Nathan

last: Jameson

state: CALIFORNIA

address: 9500 Gilman Dr

department: Pathology

country: USA

institute: UC San Diego

library_source: genomic

data_processing:
Raw reads were aligned to hg19 with the Bowtie2 software with default parameters
Non-uniquely mapped reads were removed with “awk” command
Peaks were called by first creating TagDirectories of H3K27Ac and Input samples using the “makeTagDirectory” command in HOMER. Peaks were identified from the H3K27Ac tag directories using the input directories for normalization with the “findPeaks” command from HOMER with the following parameters: -style histone -size 250 -minDist 250.
Genome-wide read coverage was calculated by igvtools count
Genome_build: hg19
Supplementary_files_format_and_content: tiled data files (tdf) include average feature density for each sample for easy viewing in IGV; Browser Extensible Data (BED) files contain H3K27Ac peak calls with the given parameters across the whole genome

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain

growth_protocol: GBM cell lines U87, T98G, LN229, LNZ308, SF767 and head and neck cell lines HN12, Cal27 and Detroit562 were maintained in DMEM (Hyclone, #SH30022.01) supplemented with 10% fetal bovine serum (Atlanta Biologicals, #S12450) and 1% penicillin-streptomycin (Gibco, #15140-122) and grown as adherent cultures. GBM neurosphere cell lines GSC23 and TS576 were maintained in DMEM/F12 (Gibco, #11320-033) supplemented with B27 supplement (Gibco, #12504-044) and 1% penicillin-streptomycin and grown in suspension.

extract_protocol:
Chromatin was sheared in diluted lysis buffer (1% SDS, 50mM Tris-HCl, 20mM EDTA, 1x protease inhibitor) to 200-500bp using a Covaris M220 Focused-Ultrasonicator with the following parameters: 10 minutes, peak incident power 75, duty factor 10%, 200 cycles/burst. 3ug antibody anti-H3K27Ac (Active Motif, #39133) was incubated with Dynabeads Protein G beads (Invitrogen, #10004D) for 4 hours. Beads were washed 3 times with 5mg/ml BSA, and incubated with 50% crosslinked chromatin (500ul) and 50% ChIP master mix (1% Triton-X, 0.1% DOC, 1X protease inhibitor, 1x TE) at 4°C overnight. 10% of the chromatin was not exposed to antibody and was used as control (input). Immunoprecipitated DNA was washed with RIPA buffer (50mM Hepes, 1% NP-40, 0.7% DOC, 0.5M LiCl, 1mM EDTA, 1x protease inhibitor) and eluted from the beads in elution buffer (10mM Tris, 1mM EDTA, 1% SDS). Along with input, immunoprecipitated DNA was reverse crosslinked at 65°C overnight, and purified via Phenol:Chloroform extraction
DNA libraries were prepared with either the TruSeq ChiP Library Prep Kit (Illumina, #IP-202-1012) or the Accel-NGS 2S Plus DNA Library kit (Swift Bioscience, #21024) and sequenced using 75 bp single-end sequencing method on an Illumina Hi-seq 4000

tag: cell line

tag: tissue

value: Brain

tag: tumor type

value: GBM

tag: chip antibody

value: anti-H3K27Ac (Active Motif, #39133)


title: liver_normal diet_biological rep5

type: RNA

city: Gunma

first: Tsudoi

last: Toyoda

address: 54 Nakaorui-machi, Takasaki-shi

country: Japan

institute: Tkasaki University of Health and Welfare

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to a Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) with the GeneChip 3' IVT PLUS Reagent kit (Thermo Fisher Scientific). The array was stained using the GeneChip Hybridization, Wash and Stain kit and on a GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: The fluorescence signals of probes were scanned with a GeneChip Scanner 3000 7G (Thermo Fisher Scientific) and converted to an intensity value with Affymetrix GeneChip Command Console software (Thermo Fisher Scientific).

data_processing: The signal intensity of probe sets was normalized by the distribution free weighted method. Data were compared between control and the MSx groups by rank products method. Probe sets with false discovery rate < 0.001 were considered as showing significant differences in expression. Probe sets sorted as both up- and downregulated were excluded, and the remaining probe sets were treated as differentially expressed genes. Normalization and between-group comparisons were performed with R v.3.2.2 (https://cran.r-project.org/) and Bioconductor v.3.1 (http://www.bioconductor.org/).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: normal diet

label_protocol: Biotinylated cRNA was prepared from purified total RNA with the GeneChip 3' IVT PLUS Reagent kit (Thermo Fisher Scientific).

growth_protocol: Male KK-Ay mice (4 weeks old) were purchased from CLEA Japan (Tokyo, Japan). The mice were individually housed in a room maintained at 21°C–23°C and 50%–70% relative humidity on a 12:12-h light/dark cycle. Control and MSx diets were prepared based on the AIN-93G formula by Oriental Yeast Co. (Tokyo, Japan) . After 4 days of acclimation, the mice were divided into two groups (n = 8 each) with approximately equal mean body weights. Mice were fed the control or MSx diet for 42 days and allowed free access to the diet and ultrapure water during this period.

extract_protocol: Total RNA was isolated from liver with TRIzol reagent (Thermo Fisher Scientific) and purified with an RNeasy Mini kit and RNase-Free DNase Set (Qiagen, Venlo, the Netherlands).

treatment_protocol: The liver was treated with RNAlater (Thermo Fisher Scientific, Waltham, MA, USA) at 4°C overnight and stored at −80°C until use.

tag: strain

value: KK-A[y]

tag: gender

value: male

tag: age

value: 11 weeks old

value: liver

tag: diet

value: normal diet


title: liver_normal diet_biological rep8


title: HN12 ATAC-seq

source_name: Tongue

value: HNSCC

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1037


title: MBC03.shWDR5.Rep1

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description:
genes.counts.txt
genes.edgeR_results_MBC03.txt

library_source: transcriptomic

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to o the human (hg19) and mouse (mm10) reference genome using TopHat2 with the option “--b2-very-sensitive”. After removing the reads aligned to the mouse genome, only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (Rsubread version 1.5.1), summarized across all exons as annotated in the NCBI build 37.2, with default options
Differentially expressed genes in biological triplicates of shLuc and shWDR5 cancer cell line were identified using EdgeR R-package v3.2.2.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: The file gene.counts.txt contains the raw read counts for each samples. The file edgeR_results_*.txt contains differentially expressed genes in biological triplicates of shLuc and shWDR5 Breast Cancer PDXs.

source_name: Human Breast Cancer PDXs

growth_protocol: See additional columns of the SAMPLES section

extract_protocol: 2.5x10^4 cells are lysed and processed according to TRUSeq RNA Sample Prep Kit Illumina protocol. Briefly, after cell lysis the poly-A containing mRNA molecules were purified using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis follows, using DNA Polymerase I and RNase H. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library for HiSeq 2000 Illumina sequencing.

tag: cell type

value: Human Breast Cancer PDXs primary cells

tag: growth protocol

value: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine, 1% Pen/Strep, 10mM HEPES, 5 µg/ml Insulin, 0.5 µg/ml Hydrocortisone, 10 ng/ml EGF, 10 NG/ML Cholera Toxin

tag: treatment

value: Cells were infected with pRSI-U6-shWDR5-UbiC-TagRFP-2A-Puro vector and selectioned with 3µg/ml of Puromycin


title: U87 Input


title: liver_MSx-added diet_biological rep2

source_name: MSx-added diet

value: MSx-added diet


title: liver_normal diet_biological rep4


title: liver_normal diet_biological rep2


title: liver_normal diet_biological rep1


title: liver_normal diet_biological rep3


title: SF767 ATAC-seq

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1036


title: liver_normal diet_biological rep6


title: Detroit562 ATAC-seq

source_name: Pharynx

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1039


title: MBC02.shWDR5.Rep3

description:
genes.counts.txt
genes.edgeR_results_MBC02.txt

treatment_protocol: See additional columns of the SAMPLES section


title: MBC03.shWDR5.Rep3


title: MBC03.shWDR5.Rep2


title: MBC02.shWDR5.Rep2


title: MBC02.shWDR5.Rep1


title: TS576 ATAC-seq

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1035


title: LN229 ATAC-seq

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1032


title: MBC10.shWDR5.Rep3

description:
genes.counts.txt
genes.edgeR_results_MBC10.txt


title: MBC10.shWDR5.Rep2


title: T98G ATAC-seq

value: GBM

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1031


title: U87 ATAC-seq

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1030


title: MBC07.shWDR5.Rep3

description:
genes.counts.txt
genes.edgeR_results_MBC07.txt


title: MBC10.shWDR5.Rep1


title: MBC07.shWDR5.Rep2


title: MBC07.shWDR5.Rep1


title: transgen_expt_2_input

city: Atlanta

first: David

middle: J.

last: Katz

state: GA

address: 615 Michael St.

department: Cell Biology

institute: Emory University School of Medicine

data_processing:
Reads were and aligned to genome WS220/ce10 using Bowtie2 (Langmead & Salzberg 2012) using default settings.
Peaks were called with MACS v2.1.1 (Feng et al 2012) using the following parameters: --bw 150 -q .01 --nomodel --broad. Peaks were required to be present in at least two replicates from the same genotype and generation, and the union of all peaks was used for the final peak list.
bamCoverage in deepTools2 (Ramirez et al 2016) was used to generate bedGraph coverage tracks in 10-bp bins, with blacklisted regions from McMurchy et al 2017 excluded, using the following parameters: -bs 10, -e 200, --normalizeUsing None. Z-score was used to normalize coverage in 10-bp bins for each replicate, and the average for each bin was calculated from all three replicates. bedGraphs were converted to bigWig coverage tracks using UCSC bedGraphToBigWig utility.
Genome_build: ce10
Supplementary_files_format_and_content: bigWig files are average z-score normalized coverage tracks. bed files are the list of H3K9me2 peaks identified in each transgenerational experiment.

organism: Caenorhabditis elegans

source_name: mixed stage populations

growth_protocol: Animals were cultured with OP50 on 10-cm NGM agar plates at 20C.

extract_protocol:
Mixed-stage populations were collected by washing off plates with PBS, pelleted in 500 ul of PBS, and flash frozen. Frozen pellets were disrupted by a 7-ml Type B glass Dounce homogenizer, fixed for ten minutes with 1% formaldehyde (diluted from 37% (w/v)) at 37°C and quenched with 125 mM glycine. ChIP samples were processed with a Chromatin Immunoprecipitation Assay Kit (EMD Millipore) according to manufacturer’s instructions. Samples were sonicated using a Diagenode Bioruptor UCD-200 at 4°C for 15 minutes on high, with a cycle of 45s on and 15s off. 1/20th of sample volume was taken for input controls. For immunoprecipitation, extracts were incubated overnight at 4°C with 10ul of H3K9me2 antibody (ab1220, Abcam). DNA was extracted by phenol-chloroform and ethanol precipitated.
Libraries were prepared by HAIB-GSL (for HiSeq) or GGBC (for NextSeq).

value: mixed

value: whole animal

tag: Stage


title: MBC26.shWDR5.Rep3

description:
genes.counts.txt
genes.edgeR_results_MBC26.txt


title: transgen_expt_2_jhdm-1_midgen


title: MBC26.shWDR5.Rep2


title: transgen_expt_2_jhdm-1_earlygen


title: transgen_expt_2_N2_midgen

description: second N2 replicate for jhdm-1 transgen expt (expt 2) is same data as in transgen_expt_1_N2_midgen_rep3.fastq.gz


title: transgen_expt_2_N2_earlygen

description: second N2 replicate for jhdm-1 transgen expt (expt 2) is same data as in transgen_expt_1_N2_earlygen_rep3.fastq.gz


title: MBC26.shWDR5.Rep1


title: MBC03.shLuc.Rep3

value: Cells were infected with pRSI-U6-shLuc-UbiC-TagRFP-2A-Puro vector and selectioned with 3µg/ml of Puromycin


title: MBC03.shLuc.Rep2


title: GSC23 ATAC-seq

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1034


title: MBC03.shLuc.Rep1


title: LNZ308 ATAC-seq

value: TDE1 Tagment DNA Enzyme, Illumina, #FC-121-1033


title: transgen_expt_1_wdr-5_midgen


title: transgen_expt_1_input


title: transgen_expt_1_wdr-5_earlygen


title: transgen_expt_1_N2_lategen


title: MBC02.shLuc.Rep2


title: transgen_expt_1_N2_midgen


title: transgen_expt_1_wdr-5_lategen


title: MBC02.shLuc.Rep3


title: MBC02.shLuc.Rep1


title: transgen_expt_1_N2_earlygen


title: MBC10.shLuc.Rep2


title: MBC10.shLuc.Rep3


title: MBC07.shLuc.Rep3


title: Cap-G binding in 3rd instar larval nSyb posistive neurons_Dam Only_rep2

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Library strategy: DamID-seq
For Targeted DamID, sequencing reads were mapped to release 6 of the Drosophila genome using Bowtie2 (see PMID: 26112292 for details of the damidseq_pipeline).
Reads were extended to adjacent GATC sites and binned for each GATC fragment
GATC fragments without any reads were excluded, followed by quantile normalisation and pseudocount addition.
Ratio files (log2) were then generated from the experimental and Dam-only control data.
Genome_build: BDGP6
Supplementary_files_format_and_content: log2 normalised fold changes between the experimental and Dam-only control as an average gff file (averageof the biological replicate gff files produced by the damidseq_pipeline)

organism: Drosophila melanogaster

source_name: x30 dissected 3rd instar larval brains

growth_protocol: Flies were maintained on standard fly media.

extract_protocol:
For Targeted DamID experiments, genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016). For RNA-seq experiments, total RNA was extracted from dissected 3rd instar larvae CNS, 35 per replicate, using a standard TRIzol extraction protocol. RNA libraries and sequencing was performed by BGI (www.bgi.com).
Targeted DamID libraries were generated using the Illumina Truseq Library Kit. RNA-seq libraries were generated by BGI (www.bgi.com).

treatment_protocol: For Targeted DamID experiments, animals were raised at 18 degrees, then shifted to 29 degrees 24 h before DNA extraction. For RNA-seq experiments, animals were raised at 25 degrees.

value: brain

value: nSyb positive neurons

tag: developmental stage

value: 3rd instar larvae


title: Cap-G binding in 3rd instar larval nSyb posistive neurons_Dam Only_rep1


title: Cap-G binding in 3rd instar larval nSyb posistive neurons_Dam_nSyb_CapG_rep2


title: MBC07.shLuc.Rep2

value: Human Breast Cancer PDXs primary cells

value: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine, 1% Pen/Strep, 10mM HEPES, 5 µg/ml Insulin, 0.5 µg/ml Hydrocortisone, 10 ng/ml EGF, 10 NG/ML Cholera Toxin


title: Cap-G binding in 3rd instar larval nSyb posistive neurons_Dam_nSyb_CapG_rep1


title: Cap-G binding in 3rd instar larval elav positive neurons_Dam Only rep2

value: elav positive neurons


title: MBC07.shLuc.Rep1


title: Cap-G binding in 3rd instar larval elav positive neurons_Dam Only rep1


title: MBC26.shLuc.Rep3


title: MBC26.shLuc.Rep2


title: MBC26.shLuc.Rep1


title: Cap-G binding in 3rd instar larval elav positive neurons_Dam-Elav_CapG_rep1


title: Cap-G binding in 3rd instar larval elav positive neurons_Dam-Elav_CapG_rep2


title: MCF10DCIS.COM.shWDR5.Rep3

description:
genes.counts.txt
genes.edgeR_results.txt

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were aligned to the hg19 human reference genome and to the Homo Sapiens transcriptome (NCBI build 37.2) using TopHat2 v2.1.0 with the option “--b2-very-sensitive”. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (Rsubread version 1.5.1), summarized across all exons as annotated in the NCBI build 37.2, with default options
Differentially expressed genes in biological triplicates of shLuc and shWDR5 cancer cell line were identified using EdgeR R-package v3.2.2.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: The file gene.counts.txt contains the raw read counts for each samples. The file edgeR_results.txt contains differentially expressed genes in biological triplicates of shLuc and shWDR5 cancer cell line

source_name: Human Breast Cancer (BC) cell line

extract_protocol: 1.5x10^6 cells are lysed and processed according to TRUSeq RNA Sample Prep Kit Illumina protocol. Briefly, after cell lysis the poly-A containing mRNA molecules were purifeid using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis follows, using DNA Polymerase I and RNase H. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library for HiSeq 2000 Illumina sequencing.

value: MCF10DCIS.COM cancer cell line

value: DMEM/F12 supplemented with 5% Horse Serum, 2mM L-Glutamine, 1% Pen/Strep, 10mM HEPES and 1.05mM CaCl2

value: Cells were infected with pRSI-U6-shWDR5-UbiC-TagRFP-2A-Puro vector and selectioned with 3µg/ml of Puromycin


title: Cap-G binding in 3rd instar larval neuroblasts_Dam Only_rep1

value: neuroblasts


title: MCF10DCIS.COM.shWDR5.Rep2


title: Cap-G binding in 3rd instar larval neuroblasts_Dam Only_rep2


title: MCF10DCIS.COM.shWDR5.Rep1


title: Cap-G binding in 3rd instar larval neuroblasts_Dam-wor_CapG_rep1


title: Cap-G binding in 3rd instar larval neuroblasts_Dam-wor_CapG_rep2


title: MCF10DCIS.COM.shLuc.Rep2


title: MBC10.shLuc.Rep1


title: MCF10DCIS.COM.shLuc.Rep3


title: MCF10DCIS.COM.shLuc.Rep1


title: NB4_RARA_ChIA-PET

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

data_processing:
Library strategy: ChIA-PET
Filtering linker sequence in ChIA-PET using in-house script
Mapping ChIA-PET reads to reference genome using BWA MEM (version 0.7.16)
Deduplicating ChIA-PET reads using Picard (MarkDuplicates)
Peak-calling for ChIA-PET using MACS (v.1.4.2)
Producing 2D contact map of ChIA-PET using Juicer tool (version 1.6.1)
Mapping ChIP-Seq reads from ABI SOLiD sequencing platform (csfasta+QV.qual) using SOLiD BioScope (version 1.0.1)
Mapping ChIP-Seq reads from Illumina sequencing platform using BWA-MEM (version 0.7.16), and peak-calling using MACS (version 1.4.2)
Mapping RNA-Seq reads uinsg Bowtie2, and processing using edge R
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt format for peak (bed), loop (bedpe), binary data format for Juicebox (hic)

growth_protocol: Both U937-PR9 and NB4 cells were cultured in RPMI 1640 (ThermoFisher, A10491), supplemented with 10% fetal bovine serum (ThermoFisher, 10082147). These cells were cultured at 37 ℃ , 5% CO2, and ambient oxygen levels.

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 ×150bp) was used for ChIA-PET libraries  with Illumina Hiseq 2500 or Illumina Nextseq 500.

treatment_protocol: The U937-PR9 cells were treated with 100 μM ZnSO4 (Sigma, Z0251) for 4 hours for ChIA-PET and ChIP-Seq experiment. The U937-PR9 cells were treated with 100 μM ZnSO4  and then collected these cells at 4, 6, 12, 24 hours for RNA-Seq experiment. These cells was preincubated with 100 μM ZnSO4 for 4 hours and then treated with ATRA (Sigma, R2625) for 24 and 48 hours used for RNA-Seq experiment. NB4 cells were treated with ATRA for 24 and 48 hours used for RNA-Seq experiment.

tag: method

value: ChIA-PET

tag: factor

value: RARA (Santa Cruz, catalog# sc-551X)

tag: molecule subtype

value: nuclear chromatin


title: MCF10DCIS.COM.shWDR5.H3K4me3.Rep1

description: Chromatin IP against H3K4me3

data_processing:
Reads were quality filtered according to the Illumina pipeline, then were mapped to the hg19 human reference genome using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
ChIP-seq agaist WDR5: Peak calling was performed using MACS2 (version 2.1.0.20150731) with the "--nomodel",  “--pvalue 0.001" and "--extsize 200" flags and arguments to identify regions in the genome that are enriched to WDR5 in the MCF10DCIS.COM shLuc cell line against both input and MCF10DCIS.COM shWDR5 cell line.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: *.bdg files were generated by MACS2

extract_protocol:
ChIP lysates were generated from 10-15x10^6 cells. Briefly, after cross-linking (1% formaldehyde), cells were lysed in SDS buffer (100 mM NaCl, 50 mM Tris HCl pH 8.1, 5 mM EDTA pH 8, 0.5% SDS, and protease inhibitors) and sonicated in IP buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.1, 5 mM EDTA pH 8, 0.3% SDS, 1.7% Triton X-100) prior to overnight incubation with antibodies against respective antibodies. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified by using Qubit for dsDNA (Thermo Fisher Scientific).
ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

value: original BC cell line

tag: antibody

value: Anti-H3K4me3 (Active Motif 39159)


title: MCF10DCIS.COM.shWDR5.WDR5

description: Chromatin IP against WDR5

value: Anti-WDR5 (Antibody from Diego Pasini Lab)


title: MCF10DCIS.COM.Input

description: Control IP DNA


title: PLC/PRF5 MTR4 KD 2

city: Shenzhen

first: Lili

last: Yu

state: Guangdong

address: No. 3025 Shennan Middle Road, Shenzhen

department: The Eighth affiliated hospital

country: China

institute: Sun Yat-Sen University

data_processing:
RNA-seq reads were mapped to the human genome (H. sapiens, GRCh38) and transcriptome (Ensembl, release 84) using the software hisat2 (v2.1.0) with the default parameters.
Read counts were calculated using htseq-count
DEseq2 was used to do differential expressed gene analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample ...

source_name: Hepatocellular Carcinoma Cell Line

growth_protocol: PLC/PRF5 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Total RNA was extracted using RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: knockdown MTR4

tag: cell line

tag: genotype/variation

value: MTR4 KD


title: I-IRI-h-6

city: Busan

first: Sang Heon

last: Song

state: Seo-gu

address: 179 Gudeok-ro

department: Internal Medicine

country: South Korea

institute: Pusan National University Hospital

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was performed to assess the quality of RNA-seq.
RNA-seq data were quantified by salmon with parameters -p 8 --seqBias --gcBias --useVBOpt --numBootstraps 30 --validateMappings
The abundance of the transcripts in the samples was calculated to obtain both TPM (Transcripts Per Million) and the un-normalized counts of sequencing reads.
Differential expression analysis was performed using R (version 3.5.1) with DESeq2 Bioconductor package
SOM algorithm implemented in MATLAB 2018b software.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: kidney tissue

extract_protocol:
Total RNA was isolated from kidney cortex from five male patients at each condition using mirVana™ miRNA Isolation Kit (ThermoFisher, Inc., Seoul, Korea). Samples with RNA integrity numbers > 7 were prepared using Illumina TruSeq Standard mRNA Prep kit (Catalog # RS-122-2103; Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: kidney

value: male

tag: condition

value: ischemia


title: P-IRI-h-6

value: pre-ischemia


title: P-IRI-h-5


title: I-IRI-h-5


title: R10-IRI-h-5

value: reperfusion


title: PLC/PRF5 control 2

value: control


title: PLC/PRF5 control 3


title: R10-IRI-h-6


title: PLC/PRF5 MTR4 KD 1


title: PLC/PRF5 control 1


title: MCF10DCIS.COM.shLuc.H3K4me3.Rep1

description: Chromatin IP against H3K4me3

value: Cells were infected with pRSI-U6-shLuc-UbiC-TagRFP-2A-Puro vector and selectioned with 3µg/ml of Puromycin


title: T-cell_donor_14

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

data_processing:
Casava 1.9
RNA-seq reads were processed with CirComPara v0.1.3: reads were  co-linearly mapped to reference genome with HISAT2 and processed with Cufflinks; co-linearly unmapped reads were analyzed with CIRI, segemehl, CIRCexplorer and findcirc to analyze circRNAs
Gene annotation Ensembl GRCh38 v87
Genome_build: hg38
Supplementary_files_format_and_content: circRNA_expression_per_sample.csv reports circRNAs' backsplice genomic coordinates, the overlapping gene(s) and the read count (as defined by CirComPara) for each sample as a comma separated table with circrna IDs and host genes in rows and samples as columns; gene_expression_FPKM_table.csv reports linear gene expression in FPKM for each sample as a comma separated table with genes as rows and samples as columns.

source_name: Peripheral blood

extract_protocol:
Mononuclear cells (PBMCs) were isolated from peripheral blood of healthy adult donors (Department of Transfusional Medicine, University Hospital of Padova) with LymphoprepTM density gradient centrifugation (STEMCELL Technologies, Vancouver, BC, Canada) followed by haemolysis (0.5M EDTA pH 8.0). CD45+ population was separated by sorting with FACS AriaTM III (Becton Dickinson, NJ07417, USA) into B-cells, T-cells and monocytes, after labeling with anti CD19, CD3, CD14 antibodies (Beckman Coulter, CA 92821, USA). Total RNA was extracted with TRIzol reagent (Thermo Fisher Scientific, Waltham, Massachusetts) and precipitated with isopropanol. Samples with RNA integrity number (RIN) > 7, assessed with Agilent 2100 Bioanalyzer (Santa Clara, CA, USA), were used for sequencing.
RNA library was prepared with TruSeq Stranded Total RNA Ribo-Zero Gold kit. Paired-end reads 100–125 bp

value: normal

tag: marker


title: MCF10DCIS.COM.shLuc.WDR5

description: Chromatin IP against WDR5

value: DMEM/F12 supplemented with 5% Horse Serum, 2mM L-Glutamine, 1% Pen/Strep, 10mM HEPES and 1.05mM CaCl2


title: T-cell_donor_12


title: R10-IRI-h-2

tag: gender


title: P-IRI-h-2


title: P-IRI-h-3


title: I-IRI-h-4


title: I-IRI-h-2


title: I-IRI-h-3


title: R10-IRI-h-3


title: P-IRI-h-4


title: NB4_RNAPII_ChIA-PET

value: RNAPII (Biolegend, catalog# 920102)


title: T-cell_donor_01


title: PLC/PRF5 MTR4 KD 3


title: T-cell_donor_07


title: R10-IRI-h-4


title: Healthy-blood-3

city: New York

first: Stuart

last: Weisberg

state: NY

address: 650 W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

description:
DM0023
Healthy donor sample

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
We performed data quality control using RNA-SeQC (Wang et al., 2012).
We computed read counts using HTSeq (Anders et al., 2014).
Genome_build: Human: NCBI/build37.2 (GRCh37)
Supplementary_files_format_and_content: *.counts.txt: Computed read counts using HTSeq are provided with gene named in tab-delimited txt files.

source_name: blood CD8+ TEM

extract_protocol:
RNA was isolated from cell pellets using the RNeasy Mini Kit (QIAGEN) and quantitated using an Agilent 2100 Bioanalyzer (Agilent Technologies).
We prepared RNA-Seq libraries using Illumina TruSeq RNA prep kit with poly-A pulldown and sequenced them on the Illumina HiSeq 2500 with 101bp single-end reads at the Columbia Genome Center.

treatment_protocol: CD3+CD8+CD69+TEM (CD45RA−CCR7−) cells were sorted from the pancreas, jejunum and PLN of five individual organ donors, and CD8+ TEM cells (CD45RA−CCR7−CD69−) were sorted from peripheral blood of healthy donors.

value: Blood

value: DAPIlo CD45+CD3+CD8+CD45RA-CCR7-

tag: isolation

value: primary, sorted


title: D333 PLN TRM

description:
DS013
Organ donor sample

source_name: PLN TRM

value: Pancreas draining lymph node

value: DAPIlo CD45+CD3+CD8+CD45RA-CCR7-CD69+

tag: organ donor


title: Monocyte_donor_05

tag: cell type


title: Monocyte_donor_08


title: Monocyte_donor_07


title: Healthy-blood-2

description:
DM0022
Healthy donor sample


title: Monocyte_donor_06


title: Healthy-blood-1

description:
DM0021
Healthy donor sample


title: D333 Jejunum TRM

description:
DS011
Organ donor sample

source_name: Jejunum TRM

value: Jejunum


title: B-cell_donor_13


title: B-cell_donor_07


title: D332 Jejunum TRM

description:
DS009
Organ donor sample


title: D325 Pancreas TRM

description:
DS008
Organ donor sample

source_name: Pancreas TRM

value: Pancreas


title: B-cell_donor_14


title: D325 Jejunum TRM

description:
DS007
Organ donor sample


title: B-cell_donor_05


title: D318 Jejunum TRM

description:
DS005
Organ donor sample


title: D318 PLN TRM

description:
DS003
Organ donor sample


title: D318 Pancreas TRM

description:
DS004
Organ donor sample


title: bovine in treat group 3

city: Beijing

first: suyu

last: quan

address: Yuanmingyuan West Road No.2, Haidian Distric

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

description: 1_all_miRNA_counts.xls, 2_all_miRNA_TPM.xls, 3_diff_expressed_miRNA.xls

data_processing:
Cutadapt (version 1.14), fastx_toolkit (version 0.0.13) and NGSQCToolkit (version 2.3.3) were used to get clean reads.
Clean reads were matched with Rfam (version 10.0), and rRNA, snRNA, cis-reg, tRNA and other specific sequences were annotated.
The transcripts were filtered using bowtie.
MiRBase (version 22.0) was used for miRNA alignment to annotate known miRNAs.
Novel miRNA prediction of unannotated sequences was performed with miRDeep2. Novel miRNA secondary structure prediction was performed using RNAfold.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The TPM (transcript per million) metric represented the miRNA expression level.

organism: Bos taurus

source_name: milk  EV

growth_protocol: Six Holstein cows (n=3, 101±10 DIM, 574±36 kg BW, 32±2 kg milk/d) were utilized in the experimental period while housed in 6 environmentally control chambers and exposed to constant 20°C, 40% humidity.

extract_protocol:
Total Exosome Isolation kit (from other body fluids) (Invitrogen, Catalog Number: 4484453) was used for the isolation of milk EVs. The miRNeasy Mini Kit (QIAGEN, Catalog Number: 217004) was used to extract EV-miRNAs.
TruSeq Small RNA Sample Prep Kits (no. RS-200-0012, Illumina), Qubit dsDNA Assay Kit (no. Q328520, Life Technologies), Qubit RNA Assay Kit (no. Q32852, Life Technologies), SuperScript II Reverse Transcriptase (no.18064-014, Invitrogen) and DNA loading dye (no.LC6678, Invitrogen) were utilized in this step, following the manufacturer’s instructions. Briefly, 3' adapter and 5' adapter were ligated to the end of the RNA molecules. Then the libraries were reverse transcribed and PCR amplified subsequently. The cDNA constructs were purified and recovered, and the libraries was checked and normalized eventually.

treatment_protocol: Control cows were fed with TMR while treat cows were fed with feed that partly replaced alfalfa hay with whole cotton seed and soybean hull.

tag: strain

value: Holstein cow

value: milk

value: female, mid lactation

tag: diet

value: whole cotton seed and soybean hull


title: D325 PLN TRM

description:
DS006
Organ donor sample


title: MG1655_2

city: San Diego

first: Anand

last: Sastry

state: CA

department: Bioengineering

institute: University of California, San Diego

description: Escherichia coli K-12 MG1655

data_processing:
Raw sequencing reads were mapped to the reference genomes using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode. Only 1100 genes common across all strains were quantified.
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample

organism: Escherichia coli

source_name: E. coli MG1655

growth_protocol: glycerol stocks of E. coli strains were inoculated into M9 minimal media with 2g/L glucose, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: media

value: M9 minimal media w/ 2g/L glucose


title: PP2_WGBS_rep1

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using BSMap (Xi and Li, 2009) in bisulfite mode with default parameters. CpG methylation was called as described in (Ziller et al., 2013), excluding low-quality, duplicate, and >10%-mismatched reads.
Genome_build: hg19
Supplementary_files_format_and_content: bed. Column headers are: Chr, Start, End, methylatedCpG/TotalCpG, Score, Strand

source_name: HUES 8 hESC line

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).

extract_protocol:
DNA was fragmented with a Covaris S2 sonicator for 6min, purified using the DNA Clean and Concentrator kit (Zymo Research), and bisulfite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research).
Sequencing libraries were generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences), pooled, and sequenced on a HiSeq 4000 instrument.

value: HUES 8 hESC line

value: hPSC-derived pancreatic progenitor 2

tag: Stage

value: Stage 4 day 5


title: D304 Pancreas TRM

description:
DS001
Organ donor sample


title: bovine in treat group 1

tag: developmental stage


title: 9CRAL.D120-3

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: 9CRAL supplemented H9 clone at differentiation D120 replicate 3

data_processing:
Raw reads passing chastity filter were trimmed for Illumina adapters in Trimmomatic (v0.36) (Bolger et al., 2014).
Trimmed reads were quantified at the transcript level using kallisto (v0.45.0) prior to summarizing to gene level using tximport (v1.8) using the option “countFromAbundance=lengthScaledTPM” in the R enviroment.
The gene level count values from tximport were normalized using TMM and converted to count per million (CPM) using edgeR (v3.20.9)
Differential expression analysis was performed using limma (v3.34.9).
Genome_build: GRCm38.p7 assembly using Ensembl v82 annotation

molecule: polyA RNA

source_name: retinal organoid

growth_protocol: Human embryonic stem cell (ESC) line CRX-GFP H9 was a subclone carrying a green fluorescent protein (GFP) marker under the control of the cone‐rod homeobox (CRX) promoter   as previously reported (Kaewkhaw et al 2015). Human induced pluripotent stem cell (iPSC) line PEN8E, NEI377 and ESP were reprogrammed from skin biopsies using integration-free Sendai virus or mRNA carrying the four Yamanaka factors (Shimada et al, 2017) and their genome integrity and pluripotency have been evaluated (Shimada et al, 2017; Lukovic et al, manuscript in preparation). H9, PEN8E and NEI377 were maintained in Essential 8 medium (E8; ThermoFisher Scientific) and ESP was maintained in mTeSR1® (StemCell Technologies), with all lines sustained on BD MatrigelTM human embryonic stem cell-qualified Basement Membrane Matrix (Corning)-coated plates under hypoxia (5% O2).  PSCs were passaged every 3-4 days at 70-80% confluency using the EDTA-based protocol (Beers et al., 2012).  To start differentiation, all lines were detached and dissociated into small clumps with the EDTA dissociation protocol (Beers et al., 2012) and cultured in polyHEMA-coated or Ultra Low Attachment Culture Dishes (Corning) in E8 with 10 mM Y-27632 (Tocris) to form embryoid bodies (EBs). Neural-induction medium (NIM) consisting of DMEM/F-12 (1:1), 1% N2 supplement (ThermoFisher Scientific), 1x MEM non-essential amino acids (NEAA), and 2 µg/ml heparin (MilliporeSigma) was added at differentiation day (D)1 and D2 to reach a final ratio of 3:1 and 1:1 NIM:E8, respectively. Starting at D3, EBs were cultured in 100% NIM for an additional 4 days. EBs were collected at D7 and plated onto BD MatrigelTM Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning)-coated plates. On D16, medium was changed to photoreceptor induction medium (PIM) consisting of DMEM/F-12 (3:1) with 2% B27 without Vitamin A, 1% antibiotic-antimycotic solution (ThermoFisher Scientific), and 1X NEAA. Medium was changed daily.   Upon appearance of optic vesicles (OVs; typically, D21-28) with neuroepithelium morphology, regions were excised with tungsten needles under magnification and transferred to suspension culture in polyHEMA-coated or Ultra Low Attachment 10-cm2 Culture Dishes (Corning) in PIM. After D42, PIM was supplemented with 10% fetal bovine serum (FBS;  ThermoFisher Scientific), 100 mM Taurine (MilliporeSigma), 2 mM GlutaMAX (ThermoFisher Scientific). Starting at D63, PIM was supplemented with 1 mM retinoid (MilliporeSigma) 3 times a week and switched to 0.5 mM  at D92. 1% N2 supplement was included starting at D92. Medium for H9 and PEN8E-derived organoids was supplemented with 20 ng/ml insulin-like growth factor 1 (IGF1; ThermoFisher Scientific) and 55 nM beta-mercaptoethanol (2-ME; ThermoFisher Scientific) from dissection till the end of differentiation. 9-cis retinal (9CRAL; MilliporeSigma) was added at the described concentrations and corresponding time period during media change. Organoids for dataset PEN8E_2 were cultured with 10 ng/ml IGF1 from D42 to D200 and all-trans retinoic acid (ATRA; MilliporeSigma) was supplemented to PIM at 1 µM 5 times per week and at 0.5 µM twice a week for D63-92 and D92-180, respectively. ESP-derived organoid cultures were maintained the same with PEN8E_2 organoids, except No IGF1 was used. For all experiments directly comparing 9CRAL and ATRA, media changes were performed in the dark under dim red light to reduce isomerization of the retinoids. Retinal organoids were collected in the dark and processed in the light as described for all other experiments.

extract_protocol:
Trizol
Illumina Standed mRNA-seq

tag: stem cells type

value: ESC

tag: retinoic acid

tag: differentiation day


title: D304 Jejunum TRM

description:
DS002
Organ donor sample


title: MG1655_1

description: Escherichia coli K-12 MG1655


title: D333 Pancreas TRM

description:
DS012
Organ donor sample


title: D332 Pancreas TRM

description:
DS010
Organ donor sample


title: EDL933_2

description: Escherichia coli O157:H7 EDL933

source_name: E. coli O157:H7 EDL933


title: 9CRAL.D120-1

description: 9CRAL supplemented H9 clone at differentiation D120 replicate 1

tag: cell line


title: 9CRAL.D120-2

description: 9CRAL supplemented H9 clone at differentiation D120 replicate 2


title: EDL933_1

description: Escherichia coli O157:H7 EDL933


title: W3110_2

description: Escherichia coli W3110

source_name: E. coli W3110


title: 9CRAL.D90-1

description: 9CRAL supplemented H9 clone at differentiation D90 replicate 1


title: 9CRAL.D90-2

description: 9CRAL supplemented H9 clone at differentiation D90 replicate 2


title: W3110_1

description: Escherichia coli W3110


title: bovine in treat group 2


title: ATRA.D120-2

description: ATRA supplemented H9 clone at differentiation D120 replicate 2

value: ATRA


title: HS_2

description: Escherichia coli HS

source_name: E. coli HS

value: HS


title: ATRA.D120-3

description: ATRA supplemented H9 clone at differentiation D120 replicate 3


title: ATRA.D120-1

description: ATRA supplemented H9 clone at differentiation D120 replicate 1


title: HS_1

description: Escherichia coli HS


title: ATRA.D90-2

description: ATRA supplemented H9 clone at differentiation D90 replicate 2


title: Crooks_1

description: Escherichia coli Crooks

source_name: E. coli Crooks

value: Crooks


title: ATRA.D90-1

description: ATRA supplemented H9 clone at differentiation D90 replicate 1


title: PEN8E_2.D201-2

description: PEN8E_2 clone at differentiation D201 replicate 2

value: iPSC


title: CFT073_2

description: Escherichia coli CFT073

source_name: E. coli CFT073


title: CFT073_1

description: Escherichia coli CFT073


title: Crooks_2

description: Escherichia coli Crooks


title: PEN8E_2.D201-1

description: PEN8E_2 clone at differentiation D201 replicate 1


title: PEN8E_2.D152-2

description: PEN8E_2 clone at differentiation D152 replicate 2


title: BL21_1

description: Escherichia coli BL21(DE3)

source_name: E. coli BL21(DE3)


title: PEN8E_2.D152-1

description: PEN8E_2 clone at differentiation D152 replicate 1


title: PEN8E_2.D200-1

description: PEN8E_2 clone at differentiation D200 replicate 1


title: BL21_2

description: Escherichia coli BL21(DE3)


title: PEN8E_2.D91-2

description: PEN8E_2 clone at differentiation D91 replicate 2


title: PEN8E_2.D122-1

description: PEN8E_2 clone at differentiation D122 replicate 1


title: PEN8E_2.D91-1

description: PEN8E_2 clone at differentiation D91 replicate 1


title: PEN8E_2.D38-1

description: PEN8E_2 clone at differentiation D38 replicate 1


title: NEI377.D203-1

description: NEI377 clone at differentiation D203 replicate 1


title: NEI377.D200-1

description: NEI377 clone at differentiation D200 replicate 1


title: NEI377.D120-3

description: NEI377 clone at differentiation D120 replicate 3


title: NEI377.D145-1

description: NEI377 clone at differentiation D145 replicate 1


title: NEI377.D153-1

description: NEI377 clone at differentiation D153 replicate 1


title: NEI377.D120-2

description: NEI377 clone at differentiation D120 replicate 2


title: NEI377.D120-1

description: NEI377 clone at differentiation D120 replicate 1


title: NEI377.D90-3

description: NEI377 clone at differentiation D90 replicate 3


title: NEI377.D90-4

description: NEI377 clone at differentiation D90 replicate 4


title: NEI377.D90-5

description: NEI377 clone at differentiation D90 replicate 5


title: NEI377.D90-6

description: NEI377 clone at differentiation D90 replicate 6


title: NEI377.D90-2

description: NEI377 clone at differentiation D90 replicate 2


title: NEI377.D38-1

description: NEI377 clone at differentiation D38 replicate 1


title: NEI377.D38-2

description: NEI377 clone at differentiation D38 replicate 2


title: Prostate, Met_Bcat

city: Duarte

first: Zijie

last: Sun

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

data_processing:
The sequencing library templates were prepared for sequencing using the Illumina TruSeq SR Cluster V4-cBot-HS Kit.
Real-time analysis (RTA) 1.18.64 software was used to process the image analysis and base calling
RNA sequences were aligned to mouse genome assembly mm9 using TopHat v2
Ensemble gene expression levels were calculated using HTseq-count
Bioconductor package edgeR was used to normalize the data and calculate P value and log2 fold change among groups.
Genome_build: UCSC: Mouse genome assembly mm9
Supplementary_files_format_and_content: The processed data file is a text file that contains the raw reads for each sample aligned to the mm9 reference genome

source_name: Prostate Tissue

extract_protocol:
Prostate tissues were homogenized in RNA-Bee (TEL-TEST, Inc.), and total RNA was isolated as recommended by manufacturer
RNA concentration was measured by NanoDrop 1000 (Thermo Fisher Scientific, Waltham Massachusetts, US) and RNA integrity was determined using Bioanalyzer (Agilent). Library construction of 200 ng total RNA for each sample was made using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) (Kapa Biosystems, Wilmington, USA). Using 10 cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (Thermo Fisher Scientific). Each library was quantified using a Qubit fluorometer (Life Technologies) and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). Sequencing was performed on an Illumina® Hiseq 2500 (Illumina, San Diego, CA, USA) instrument using the TruSeq SR Cluster Kit V4-cBot-HS (Illumina®) to generate 51 bp single-end reads sequencing with v4 chemistry. Quality control of RNA-Seq reads was performed using FastQC.

value: Prostate

tag: tissue condition

value: Fresh tumor tissue

tag: age

value: 16 months postnatal

tag: genotype


title: Prostate, Bcat_Only

tag: tissue


title: NEI377.D90-1

description: NEI377 clone at differentiation D90 replicate 1


title: ESP.D186-1

description: ESP clone at differentiation D186 replicate 1

value: ESP


title: ESP.D186-2

description: ESP clone at differentiation D186 replicate 2


title: ESP.D186-3

description: ESP clone at differentiation D186 replicate 3


title: NEI377.D202-1

description: NEI377 clone at differentiation D202 replicate 1


title: ESP.D172-3

description: ESP clone at differentiation D172 replicate 3


title: B6_Th1_Zbtb7b

city: MONTREAL

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: Th1 cells were stimulated for 2h anti-CD3 [5ug/mL], anti-CD28 [3ug/mL], IL-12 [10ng/mL], IL18 [10ng/ul] and IFNg [400U/ml])

data_processing:
Reads quality filtered according to the Illumina pipeline
The sequence reads were mapped to the mouse mm9 reference genome assembly with Bowtie 1.0.0 using the following settings: --best --trim5 2 mm9 (Langmead et al., 2009).
To identify significant TF binding events, we processed the mapped sequence reads with MACS 1.4.1 using matching number of Input control reads to ThPOK ChIP-seq sample (Zhang et al., 2008).
The resulting transcription factor peak lists were filtered to remove regions longer than 3kb because they were artifacts generated from high background sequences, and contiguous peaks were separated with PeakSplitter (Salmon-Divon et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: B6_Th1_Zbtb7b_split_filtered_FINAL_CENTER.bed = list of transcription factor binding peaks called by MACS and splitted by PeakSplitter

source_name: Primary Th1 polarized CD4+ T cells

growth_protocol: Th1 cells were obtained by isolating lymph nodes and spleens from B6 WT mice and naïve CD4+ T cells were enriched using the EasySep Mouse Naïve CD4+ T cell Isolation kit (StemCell). Cells were polarized into the Th1 helper cells for 6 days using plate-bound anti-CD3 (5ug/mL), in complete RPMI medium (RPMI-1610, 10% FBS, 1X P/S and 1X non-essential amino acids) containing anti-CD28 (3ug/mL), IL-12 (10ng/mL), IL-2 (10ng/mL) and anti-IL-4 (10ug/mL), with medium replenished after 3 days. Th1 polarization was assessed by staining cells with eFluor450 anti-CD4 (GK1.5), PE anti-CD4 (IM-7) and APC anti-CD62L (MEL-14)) and analyzed by FACS.

extract_protocol:
Ten million Th1 cells per ChIP were crosslinked for 10 min at room temperature with 1% formaldehyde added in culture medium. Crosslink was stopped with ice-cold PBS containing 0.125M glycine for 5min. Nuclei were prepared by sequential incubation on ice for 5min in buffer A [10mM Tris-HCl (pH 8), 10mM EDTA, 0.25% Triton X-100], and for 30min in buffer B [10mM Tris-HCl (pH 8), 1mM EDTA, 200mM NaCl] (all buffers include proteases inhibitors). Nuclei were resuspended in sonication buffer [10mM Tris-HCl (pH 8), 1mM EDTA, 0.5% SDS, 0.5% Triton X-100, 0.05% NaDOC, 140mM NaCl] and sonicated with a Branson Digital Sonifier (Branson Ultrasonics) to an average size of 250bp. Sonicated chromatin was incubated overnight on a rotating platform at 4°C with a mixture of 20μl Protein A and 20μl Protein G Dynabeads (Invitrogen) pre-bound with 5μg of anti-ThPOK (sc-79127X) antibody from Santa Cruz Biotechnologies. Immune complexes were washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash B [1% Triton X-100, 0.1% SDS, 150mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash C [1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8), Wash D (1% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH 8]; and TEN buffer [50mM NaCl, 10mM Tris-HCl pH 8, 1mM EDTA]. After de-crosslinking by overnight incubation at 65°C, the ChIP and Input DNA was purified with QIAquick PCR purification columns following manufacturer’s instructions (Qiagen).
The ChIP-seq libraries were prepared using the Kapa ChIP Library kit (Kapa Biosystems) and sequenced on a HiSeq 2500 (Illumina) using a 50bp paired-end configuration, with sonicated input DNA as control.

value: Primary Th1 polarized CD4+ T cells

tag: antibody

value: anti-ThPOK (SantaCruz, sc-79127X)


title: B6_Th1_Input

treatment_protocol: Th1 cells were stimulated for 2h anti-CD3 [5ug/mL], anti-CD28 [3ug/mL], IL-12 [10ng/mL], IL18 [10ng/ul] and IFNg [400U/ml]

value: input


title: RNAseq Eed CKO FGO rep2

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
All RNA-seq data were mapped to the mouse reference genome (mm9) by TopHat (version 2.0.11). The gene expression level was calculated by Cufflinks (version 2.0.2)(Trapnell et al., 2012) using the refFlat database from the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Full-grown oocytes

extract_protocol:
To isolate PGCs, germinal ridges were isolated from E11.5 and E13.5 embryos. To obtain the single cell su¬spension, the germinal ridges were digested with 0.25% trypsin-EDTA at 37°C for 10min. For E13.5 embryos, the germinal ridges were digested separately based on the gender. GFP-positive PGCs were sorted and collected by FACS.WT oocytes were collected from wild-type C57BL/6N females. Briefly, growing oocytes were isolated by mechanical dissection using a 26 gauge needle in M2 medium. Growing oocytes I were isolated from 7 or 10d old mice and growing oocytes II were from 14d old mice. Full-grown oocytes were isolated from superovulated 8-week-old mice 46 h after PMSG injection. The whole ovaries were clipped mechanically with a razor blade. To remove the granulosa cells, the dissociated oocyte-granulosa cell complexes were transferred into M2 medium containing 0.1% hyaluronidase and digested for 5 min. Oocytes were then crosslinked with 1% formaldehyde after removing the zona pellucida by acidic Tyrode’s solution treatment. Eedfl/wt and EedmNull late 2-cell embryos were harvested by mating Eedfl/fl  or Eedfl/fl;Gdf9-Cre females with PWK/PhJ males.
sisHi-C libraries were produced as described (Du et al., 2017). Briefly, PGCs, oocytes or embryos were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Then formaldehyde was quenched with glycine for 10 min at RT. After being washed with 1 × PBS, the samples were incubated in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min and the chromatin was solubilized with 0.5% SDS. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP, the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, Cat # 65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Extaq (Takara), and the products were purified and size-selected with AMPure XP beads （Beckman Coulter, Cat # A63881）  RNA-seq libraries of Eedfl/fl and Eed CKO FGOs were prepared as previously described (Brind'Amour et al., 2018). Total RNA was isolated from about 25 oocytes with TRIzol (Thermo, 10296028), and ribosomal RNA was depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S) according to the manufacturer’s instruction. Double-stranded cDNA was synthesized using NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S). Library preparation was performed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s instruction.  CUT&RUN libraries of Eedfl/fl and Eed-/- oocytes were conducted as previously described (Skene and Henikoff, 2017). A low constant amount of yeast DNA was added to each reaction as spike-in DNA.

treatment_protocol: To collect oocytes undergoing germinal vesicle break down (GVBD), the full-grown oocytes with granulosa cells removed were firstly cultured in M2 medium supplemented with 5μM milrinone. Then half of the FGOs were washed out of milrinone and cultured at 37℃ to allow synchronized resumption of meiosis. After 2-4hours of incubation, oocytes that exit meiosis arrest and lose the GV were collected. The other half of the FGOs cultured with milrinone were collected at the same time as control.

value: Full-grown oocytes


title: RNAseq Eed flfl FGO rep3


title: RNAseq Eed CKO FGO rep1


title: Gdnf-EGFP/Rpl10a-ES2243_IP1

first: Eric

middle: F

last: Schmidt

address: 1230 York Avenue

institute: The Rockefeller University

description:
Ribosomal-bound RNA
1206_Gdnf_TRAP_ES2243_IP1_GCCAAT_L002

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Cerebral cortex

growth_protocol: Not applicable

extract_protocol:
The cerebral cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: No treatment

tag: animal line

value: Gdnf-TRAP ES2243

tag: application

value: RNA-seq

tag: sample type

value: Immunopurified (IP)


title: Gdnf-EGFP/Rpl10a-ES2243_IP2

description:
Ribosomal-bound RNA
1207_Gdnf_TRAP_ES2243_IP2_CTTGTA_L002


title: RNAseq Eed flfl FGO rep2


title: RNAseq Eed CKO FGO rep3


title: RNAseq Eed flfl FGO rep1


title: ESP.D172-2

description: ESP clone at differentiation D172 replicate 2


title: ESP.D172-1

description: ESP clone at differentiation D172 replicate 1


title: ESP.D123-4

description: ESP clone at differentiation D123 replicate 4


title: ESP.D123-3

description: ESP clone at differentiation D123 replicate 3


title: ESP.D123-2

description: ESP clone at differentiation D123 replicate 2


title: Hi-C Scc1 CKO SN FGO 72

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiC-Lib (Imakaev et al., 2012), Mirnylib (Imakaev et al., 2012) and Cooler v0.7.2 (Abdennur et al., 2017).
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the  pairs. readID/chr1/pos1/chr2/pos2/ strand1/strand2/pair type code/. Details of the files could be found: https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md

extract_protocol:
Fully grown denuded GV (germinal vesicle) oocytes were isolated from 2-3 month old Scc1 flox/flox and Scc1 flox/flox;Zp3-Cre female mice by puncturing of ovaries with hypodermic needles. Oocytes were incubated for at least 2 hours before the procedure to ensure viability. Before formaldehyde fixation, the zona pellucida was removed by treatment with Acidic Tyrode's solution (Sigma). Oocytes were fixed in with 2% formaldehyde for 15 minutes at room temperature. Oocytes were washed through drops of complete M2. For SN and NSN distinction oocytes were stained for 15 min with 0.2 μg/ml Hoechst (33342, Invitrogen). Cells were then imaged using a confocal microscope (LSM510 Axiovert 200M, Zeiss) and sorted according to their chromatin structure before proceeding with the Hi-C protocol.
Single-nucleus Hi-C libraries were produced as described (Flyamer et al., 2017).

tag: genotype/variation

value: Scc1 flox/flox;Zp3-Cre


title: Hi-C Scc1 CKO SN FGO 70


title: Hi-C Scc1 CKO SN FGO 71


title: ESP.D88-3

description: ESP clone at differentiation D88 replicate 3


title: Hi-C Scc1 CKO SN FGO 68


title: Hi-C Scc1 CKO SN FGO 73


title: ESP.D123-1

description: ESP clone at differentiation D123 replicate 1


title: ESP.D88-2

description: ESP clone at differentiation D88 replicate 2


title: ESP.D88-1

description: ESP clone at differentiation D88 replicate 1


title: Hi-C Scc1 CKO SN FGO 67


title: ESP.D60-3

description: ESP clone at differentiation D60 replicate 3


title: Hi-C Scc1 CKO SN FGO 66


title: ESP.D60-2

description: ESP clone at differentiation D60 replicate 2


title: Hi-C Scc1 CKO SN FGO 64


title: ESP.D123-5

description: ESP clone at differentiation D123 replicate 5


title: Hi-C Scc1 CKO SN FGO 65


title: ESP.D25-7

description: ESP clone at differentiation D25 replicate 7


title: Hi-C Scc1 CKO SN FGO 63


title: ESP.D25-5

description: ESP clone at differentiation D25 replicate 5


title: ESP.D25-6

description: ESP clone at differentiation D25 replicate 6


title: ESP.D25-4

description: ESP clone at differentiation D25 replicate 4


title: Hi-C Scc1 CKO SN FGO 61


title: Hi-C Scc1 CKO SN FGO 60


title: ESP.D25-3

description: ESP clone at differentiation D25 replicate 3


title: ESP.D25-2

description: ESP clone at differentiation D25 replicate 2


title: Hi-C Scc1 CKO NSN FGO 58


title: Hi-C Scc1 CKO SN FGO 69


title: Hi-C Scc1 CKO NSN FGO 56


title: PEN8E.D150-1

description: PEN8E clone at differentiation D150 replicate 1


title: Hi-C Scc1 CKO NSN FGO 54


title: ESP.D25-1

description: ESP clone at differentiation D25 replicate 1


title: ESP.D60-1

description: ESP clone at differentiation D60 replicate 1


title: PEN8E.D200-1

description: PEN8E clone at differentiation D200 replicate 1


title: PEN8E.D200-2

description: PEN8E clone at differentiation D200 replicate 2


title: Hi-C Scc1 CKO NSN FGO 55


title: Hi-C Scc1 CKO NSN FGO 57


title: PEN8E.D150-2

description: PEN8E clone at differentiation D150 replicate 2


title: Hi-C Scc1 CKO NSN FGO 52


title: Hi-C Scc1 CKO SN FGO 62


title: Hi-C Scc1 CKO NSN FGO 53


title: Hi-C Scc1 CKO SN FGO 59


title: Hi-C Scc1 CKO NSN FGO 49


title: Hi-C Scc1 CKO NSN FGO 50


title: Hi-C Scc1 CKO NSN FGO 51


title: Hi-C Scc1 CKO NSN FGO 47


title: Hi-C Scc1 CKO NSN FGO 48


title: PEN8E.D120-1

description: PEN8E clone at differentiation D120 replicate 1


title: PEN8E.D75-2

description: PEN8E clone at differentiation D75 replicate 2


title: PEN8E.D120-2

description: PEN8E clone at differentiation D120 replicate 2


title: PEN8E.D105-2

description: PEN8E clone at differentiation D105 replicate 2


title: Hi-C Scc1 CKO NSN FGO 46


title: PEN8E.D90-2

description: PEN8E clone at differentiation D90 replicate 2


title: PEN8E.D90-1

description: PEN8E clone at differentiation D90 replicate 1


title: Hi-C Scc1 CKO NSN FGO 45


title: PEN8E.D67-1

description: PEN8E clone at differentiation D67 replicate 1


title: Hi-C Scc1 CKO NSN FGO 44


title: PEN8E.D37-3

description: PEN8E clone at differentiation D37 replicate 3


title: Hi-C Scc1 CKO NSN FGO 43


title: PEN8E.D60-1

description: PEN8E clone at differentiation D60 replicate 1


title: PEN8E.D37-1

description: PEN8E clone at differentiation D37 replicate 1


title: PEN8E.D37-2

description: PEN8E clone at differentiation D37 replicate 2


title: Hi-C Scc1 CKO NSN FGO 42


title: Hi-C Scc1 CKO NSN FGO 39


title: Hi-C Scc1 CKO NSN FGO 40


title: Hi-C Scc1 CKO NSN FGO 41


title: H9.D200-2

description: H9 clone at differentiation D200 replicate 2

value: ESC


title: PEN8E.D75-1

description: PEN8E clone at differentiation D75 replicate 1


title: H9.D200-1

description: H9 clone at differentiation D200 replicate 1


title: H9.D150-1

description: H9 clone at differentiation D150 replicate 1


title: Hi-C Scc1 flfl SN FGO 35

value: Scc1 flox/flox


title: Hi-C Scc1 flfl SN FGO 36


title: PEN8E.D105-1

description: PEN8E clone at differentiation D105 replicate 1


title: Hi-C Scc1 flfl SN FGO 37


title: H9.D150-2

description: H9 clone at differentiation D150 replicate 2


title: Hi-C Scc1 flfl SN FGO 38


title: H9.D120-2

description: H9 clone at differentiation D120 replicate 2


title: H9.D90-2

description: H9 clone at differentiation D90 replicate 2


title: Hi-C Scc1 flfl SN FGO 33


title: Hi-C Scc1 flfl SN FGO 34


title: Hi-C Scc1 flfl SN FGO 31


title: Hi-C Scc1 flfl SN FGO 32


title: H9.D120-1

description: H9 clone at differentiation D120 replicate 1


title: H9.D67-3

description: H9 clone at differentiation D67 replicate 3


title: H9.D67-2

description: H9 clone at differentiation D67 replicate 2


title: H9.D37-2

description: H9 clone at differentiation D37 replicate 2


title: PEN8E.D60-2

description: PEN8E clone at differentiation D60 replicate 2


title: Hi-C Scc1 flfl SN FGO 29


title: Hi-C Scc1 flfl SN FGO 28


title: H9.D67-1

description: H9 clone at differentiation D67 replicate 1


title: Hi-C Scc1 flfl SN FGO 27


title: H9.D37-1

description: H9 clone at differentiation D37 replicate 1


title: Hi-C Scc1 flfl SN FGO 26


title: H9.D90-1

description: H9 clone at differentiation D90 replicate 1


title: Hi-C Scc1 flfl SN FGO 25


title: Hi-C Scc1 flfl SN FGO 24


title: Hi-C Scc1 flfl NSN FGO 19


title: Hi-C Scc1 flfl SN FGO 23


title: Hi-C Scc1 flfl SN FGO 22


title: Hi-C Scc1 flfl NSN FGO 18


title: Hi-C Scc1 flfl NSN FGO 16


title: Hi-C Scc1 flfl NSN FGO 17


title: Hi-C Scc1 flfl NSN FGO 15


title: Hi-C Scc1 flfl NSN FGO 13


title: Hi-C Scc1 flfl SN FGO 30


title: M6

first: Yu

last: Cao

state: Beijing

address: Xiyuan hospital, Haidian District, Beijing, China

department: Institute of Geriatrics

institute: Xiyuan Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the Rat reference genome using the bwa aligner.The mapped reads were then compared to the Rfam database and  miRbase21.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Genome_build: rn6
Supplementary_files_format_and_content: An excel includes all RPM values for each Sample.

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Total RNA was isolated from hippocampi using the Trizol (invitrogen) according to the manufacturer's protocol. RNA purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0.
RNAs were ligated with 3’RNA adapter, and followed by 5’adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA).

treatment_protocol: Bilateral common carotid arteries occlusion

tag: strain

value: wistar

value: 10 weeks

tag: tissure

value: hippcampus

tag: treatment

value: 2-VO operation


title: M5


title: M3


title: M8


title: M7


title: hESCs-LB-D24-4

city: Baltimore

first: S. Amer

last: Riazuddin

state: Maryland

address: 600 N. Wolfe St

institute: Johns Hopkins University School of Medicine

description:
mRNA library
hESCs-derived LB-D24

data_processing:
The base calls were assigned through the Illumina Real Time Analysis (RTA) software (Ver. 1.17.20) and base call files were converted from a binary format (BCL) to flat file format (qseq.txt) using Illumina BCL Converter software (Ver. 1.9.4). Qseq.txt files were de-multiplexed to single sample FASTQ files using de-multiplexer software written at Center for Inherited Disease Research (CIDR), Johns Hopkins University as part of CIDRSeqSuite (Ver. 7.1.0; unpublished).
The raw RNA-Seq reads (FASTQ) were processed and analyzed using Lasergene Genomics Suite. The paired-end reads were assembled with SeqMan NGen (Ver. 12), using default parameters. The human reference genome (GRCh38.p11) was used for the mapping of RNA-Seq reads. The ArrayStar (Ver, 12) was used for normalization, differential gene expression and statistical analysis of mapped paired-end reads using the default parameters. The expression data quantification and normalization were calculated using the RPKM value for each gene.
In parallel, we created expression profile to examine the genes differential expression in iPSCs-derived lentoid bodies compared with hESCs-derived lentoid bodies using Spotfire DecisionSite with Functional Genomics software. All transcripts’ log2-fold changes between hESCs- and iPSCs-derived LB-D24 were analyzed to determine the standard deviation (s.d.) from their mean of 0, which represents no change. We chose a ≥ 2 s.d., the cutoff value for differentially expressed genes.
Genome_build: Human reference genome (GRCh38.p11)
Supplementary_files_format_and_content: Excel spread sheets including gene expression values (RPKM) for each Sample

source_name: Human ESCs-derived LB-D24

growth_protocol: Briefly, 60-70 hESCs and iPSCs colonies with approximately 25 cells each colony, were cultured in mTeSR1 medium on a Matrigel-coated 35-mm plate. The hESCs and iPSCs were treated with mTeSR1 medium containing 100 ng/ml of Noggin four hours post-plating, which continued for six days (day 0 to day 6). On day 6, ~60-65 differentiating hESCs and iPSCs along with adjacent epithelial-like cells were mechanically isolated and reseeded in Matrigel-coated 35-mm plates containing a cocktail of 100 ng/ml of basic fibroblast growth factor (bFGF), 20 ng/ml bone morphogenetic protein 7 (BMP7) and 20 ng/ml bone morphogenetic protein 4 (BMP4) for nine days (day 6 to day 15). On day 10, cell colonies that did not form “fried egg” morphologies were mechanically discarded while the cells clusters forming the “fried egg” morphologies were continued to be treated with 100 ng/ml of bFGF, 20 ng/ml BMP7 and 20 ng/ml BMP4 until day 15. On day 15, cell clusters were treated with 100 ng/ml bFGF along with 20 ng/ml Wnt3a to differentiate lens epithelial cells into lens fiber cells until the day of harvesting.

extract_protocol:
The differentiated lentoid bodies were harvested on day 24 for total RNA isolation and subsequent next-generation based RNA sequencing.
Total RNA was subjected to RNA-Seq library preparation using NEBNext Ultra II RNA Library Prep Kit for Illumina. Approximately, 1.0 µg high-quality total RNA (≥ 8.0 RIN Score) was used for polyadenylated RNA selection using oligo dT beads, followed by the fragmentation of selected polyadenylated RNA. The fragmented RNA was used as a template for cDNA synthesis by reverse transcriptase with random primers. The cDNA was end-repaired to incorporate the specific index adapters for multiplexing, followed by a purification step and amplification for 15 cycles. The quality and functionality of the final amplified libraries were examined on an Agilent 2100 Bioanalyzer (Agilent) and quantitative PCR (qPCR) according to the manufacturer’s instructions.

tag: cell type

value: hESCs-derived LB-D24


title: hiPSCs-LB-D24-7

description:
mRNA library
hiPSCs-derived LB-D24

source_name: Human iPSCs-derived LB-D24

value: iPSCs-derived LB-D24


title: hiPSCs-LB-D24-5

description:
mRNA library
hiPSCs-derived LB-D24


title: K5

value: sham-operated


title: hiPSCs-LB-D24-6

description:
mRNA library
hiPSCs-derived LB-D24


title: hiPSCs-LB-D24-8

description:
mRNA library
hiPSCs-derived LB-D24


title: hESCs-LB-D24-3

description:
mRNA library
hESCs-derived LB-D24


title: Hi-C Scc1 flfl NSN FGO 21

tag: developmental stage


title: hESCs-LB-D24-2

description:
mRNA library
hESCs-derived LB-D24


title: Hi-C Scc1 flfl NSN FGO 20


title: hESCs-LB-D24-1

description:
mRNA library
hESCs-derived LB-D24


title: Hi-C Scc1 flfl NSN FGO 11


title: Hi-C Scc1 flfl NSN FGO 10


title: K4


title: K3


title: Hi-C Scc1 flfl NSN FGO 9


title: Hi-C Scc1 flfl NSN FGO 14


title: K1


title: Hi-C Scc1 flfl NSN FGO 7


title: ny1_ny1M95_3

city: bronx

first: Nicholas

last: Baker

address: 1300 Morris Park Avenue

department: genetics

institute: albert einstein college of medicine

data_processing:
The library is sequenced using Illumina HiSeqTM 2000
Then raw reads is subjected to quality control (QC)
After QC, raw reads are filtered into clean reads for alignment to the reference sequences.
Genome_build: dm6
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample;Excel files for differentially expressed genes determined using DESEQ2; Excel files for different expression between wildtype (frt82_w) and rpS12 mutant (ny1_ny1),  wildtype and Xrp1 mutant (m2-73_w), wild type and RpS3+/- rpS12G97D/G97D(ny1_ny1M95), Xrp1 mutant and rpS12 mutant, RpS3 mutant (M95_w) and RpS17 mutant (M67_w), RpS3 mutant and RpS3 rpS12 double mutant (ny1_ny1M95), RpS3 rpS12 double mutant and Xrp1 RpS3 double mutant (m2-73_M95), and rpS12 and RpS3 rpS12 double mutant.  The raw data for some of these samples (frt_w, M95_w, M67_w, and m2-73_M95) was deposited previously (GSE112864)

source_name: 3rd instar wing disc

growth_protocol: eggs laid in 4h cohorts were raised at 25°C on yeast-glucose medium supplemented with 20μg/ml tetracycline to minimize potential differences in microbiome between genotypes.

extract_protocol:
from each genotype, ~50 wing discs were dissected into Trizol reagent (25 discs into 250μL) and frozen at -80°C. Following thawing and centrifugation (12000g 15 min 4°C), the aqueous phase was precipitated with an equal volume of isopropanol (10 min room temperature). The pellet was recovered by centrifugation (12000g 15 min 4°C), washed with RNAse-free 75% ethanol twice, and air dried (5-10 min room temperature) after removing the remaining ethanol with a filtered RNAse-free pipette tip. Samples were resuspended in RNAse-free water, analyzed by nanodrop spectroscopy and Bioanalyzer and satisfactory samples stored at -80°C
library was constructed by Beijing Genomics Institute. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

treatment_protocol: third-instar larvae were harvested 24±2h before puparium formation

value: w11-18 ; rpS12G97D/rpS12G97D p{hs-neor FRT}80B  M(3R)RpS3

value: 3rd instar

value: wing disc


title: Hi-C Scc1 flfl NSN FGO 8

value: Full-grown oocytes


title: ny1_ny1_3

description: M95_w-VS-ny1_ny1M95.DEseq2_Method.GeneDiffExp.xls


title: Hi-C Scc1 flfl NSN FGO 6


title: ny1_ny1M95_2

description: ny1_ny1M95-VS-m2-73_M95.DEseq2_Method.GeneDiffExp.xls


title: ny1_ny1_2

description: M95_w-VS-M67_w.DEseq2_Method.GeneDiffExp.xls


title: ny1_ny1_1

description: m2-73_w-VS-ny1_ny1.DEseq2_Method.GeneDiffExp.xls


title: Hi-C Scc1 flfl NSN FGO 2


title: ny1_ny1M95_1

description: ny1_ny1-VS-ny1_ny1M95.DEseq2_Method.GeneDiffExp.xls


title: Hi-C Scc1 flfl NSN FGO 3


title: Hi-C Scc1 flfl NSN FGO 1


title: m2-73_w_2

description: frt82_w-VS-ny1_ny1.DEseq2_Method.GeneDiffExp.xls


title: m2-73_w_3

description: frt82_w-VS-ny1_ny1M95.DEseq2_Method.GeneDiffExp.xls


title: m2-73_w_1

description: frt82_w-VS-m2-73_w.DEseq2_Method.GeneDiffExp.xls


title: Hi-C Scc1 flfl NSN FGO 12


title: K2


title: CI

city: Bar Harbor

first: Christopher

middle: Lee

state: ME

address: 600 Main Street

department: Research

description:
CI_GES15_04151_CAGATC_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed

data_processing:
Basecalls performed using CASAVA
ChIP-seq and ATAC-seq reads were aligned using bwa v.0.7.15 or bowtie v.0.12.9
ChIP-seq and ATAC-seq peaks were called using MACS v.1.4.2
Genome_build: mm10
Supplementary_files_format_and_content: processed files are tab-delimited txt files representing the position of identified ChIP or ATAC peaks in mm10 coordinates followed by read counts. Also provided are bedgraph files for DMC1 ChIP and HELLS ChIP.

source_name: C57BL/6J_male germ cells_ChIP-seq

growth_protocol: Isolation of enriched germ cells was conducted from male mice at 12-14 days post-partum. Or whole testis collected from 6 week old male mice.

extract_protocol:
Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11,11)
For ATAC-seq samples and histone ChIP-seq germ cells were enzymatically disaggregated using Liberase enzyme. For testis samples nuclei were first crosslinked in tubules and nuclei extracted using Dounce homogenizer.

value: 12-14 days post-partum

tag: tissue/cell type

value: male germ cells

tag: chromatin fragmentation

value: MNase

tag: chip antibody


title: CK

description:
CK_GES15_05228_ACAGTG_LaneALL
processed data file:
peakome_k9ac.counts.tsv


title: CJ

description:
CJ_GES15_05227_TGACCA_LaneALL
processed data file:
peakome_k9ac.counts.tsv


title: CH

description:
CH_GES15_04150_GCCAAT_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed
peakome_k9ac.counts.tsv


title: Hi-C Scc1 flfl NSN FGO 5


title: CG

description:
CG_GES15_04149_ACAGTG_LaneALL
processed data file:
peakome_k9ac.counts.tsv


title: CF

description:
CF_GES15_04148_TGACCA_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed


title: CB

description:
CB_GES15_03992_CTTGTA_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed


title: Hi-C Scc1 flfl NSN FGO 4


title: BW

description:
BW_GES15_03987_TGACCA_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed


title: BV

description:
BV_GES15_03986_TTAGGC_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed
peakome_k9ac.counts.tsv


title: BY

description:
BY_GES15_03989_GCCAAT_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed


title: BR

description:
BR2_GES15_02486_GGCTAC_LaneALL
processed data file:
BxC_EMASE_counts.mm10.tsv

source_name: (B6xCAST) F1_male germ cells_ChIP-seq

value: (B6xCAST) F1


title: AX

description:
AX2-GES14-04830_CTTGTA_AC57KHANXX_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed


title: AN

description:
AN2_GES14_00608_CTTGTA_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed


title: AL

description:
AL2_GES14_00065_TTAGGC_LaneALL
processed data file:
chromHMM_11state_reordered_dense.bed


title: ATAC17

description:
ATAC17-GES16-00134_LaneALL
processed data file:
BxC_EMASE_counts.mm10.tsv

source_name: (B6xCAST) F1_male germ cells_ATAC-seq

extract_protocol:
TDE1 Tagment DNA Enzyme
For ATAC-seq samples and histone ChIP-seq germ cells were enzymatically disaggregated using Liberase enzyme. For testis samples nuclei were first crosslinked in tubules and nuclei extracted using Dounce homogenizer.


title: ATAC18

description:
ATAC18-GES16-00135_LaneALL
processed data file:
BxC_EMASE_counts.mm10.tsv


title: A549_Pirf_24h_Rep4

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

country: Germany

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

data_processing: Data has been log-transformed and normalized (percentile shift) within the Agilent GeneSpring V13 software

growth_protocol: 24h  at 37°C and 5%CO2

extract_protocol: Qiagen Rneasy according to manufacturers instructions

treatment_protocol: 1.5 mg/ml of Pirfenidone or respective volume of PBS

tag: cell line

tag: treatmnet

value: Pirfenidone

tag: treatment  time


title: A549_PBS_24h_Rep3

scan_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

value: PBS


title: ATAC14

institute: The Jackson Laboratory

description:
2015-DS033-LIB-33002-ATAC14-CGTACTAG_S2_LaneALL
processed data file:
atac_b6_ki_peakome.blacklisted.counts.tsv

tag: age


title: ATAC16

description: 2015-DS033-LIB-33004-ATAC16-TCCTGAGC_S4_LaneALL

source_name: DBA/2J_male germ cells_ATAC-seq


title: ATAC15

description: 2015-DS033-LIB-33003-ATAC15-AGGCAGAA_S3_LaneALL


title: A549_Pirf_24h_Rep3

label_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions


title: A549_PBS_24h_Rep4


title: A549_6h_Pirf_Rep2

growth_protocol: 24h or 6h at 37°C and 5%CO2

treatment_protocol: 1.5 mg/ml or 0.75 mg/ml of Pirfenidone or respective volume of PBS


title: A549_Pirf_24h_Rep1


title: A549_PBS_24h_Rep1


title: A549_Pirf_24h_Rep2


title: A549_6h_Pirf_Rep3


title: H1975_0-75mg_Pirf_24h_Rep3

treatment_protocol: 0.75 mg/ml of Pirfenidone or respective volume of PBS


title: A549_PBS_24h_Rep2


title: A549_6h_PBS_Rep3


title: ATAC13

description:
2015-DS033-LIB-33001-ATAC13-TAAGGCGA_S1_LaneALL
processed data file:
atac_b6_ki_peakome.blacklisted.counts.tsv


title: A549_6h_PBS_Rep2


title: A549_6h_Pirf_Rep1


title: ATAC4

description:
2015-DS032-LIB-32001-ATAC-4-TCCTGAGC_LaneALL
processed data file:
atac_b6_ki_peakome.blacklisted.counts.tsv

source_name: C57BL/6J_male germ cells_ATAC-seq


title: H1975_0-75mg_Pirf_24h_Rep1


title: H1975_0-75mg_Pirf_24h_Rep2


title: ATAC7

description:
2015-DS032-LIB-32002-ATAC7-CTCTCTAC_LaneALL
processed data file:
atac_b6_ki_peakome.blacklisted.counts.tsv


title: Hi-C Ring1 KO Rnf2 flfl FGO rep3

description:
Hi-C Ring1 KO Rnf2 flfl FGO rep3
processed data file:
Ring1_KO_Rnf2_flfl_FGO_rep123_allValidPairs.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Cmpartment analysis are done as previously described (Lieberman et al., 2009)
TAD calling is done with insulation score as previously described ( Crane et al., 2015)
CUT&RUN reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together. And the mouse profiles were normalized to the yeast reads.
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: Hi-C Ring1 KO Rnf2 flfl FGO

extract_protocol:
To isolate PGCs, germinal ridges were isolated from E11.5 and E13.5 embryos. To obtain the single cell su¬spension, the germinal ridges were digested with 0.25% trypsin-EDTA at 37°C for 10min. For E13.5 embryos, the germinal ridges were digested separately based on the gender. GFP-positive PGCs were sorted and collected by FACS.WT oocytes were collected from wild-type C57BL/6N females. Briefly, growing oocytes were isolated by mechanical dissection using a 26 gauge needle in M2 medium. Growing oocytes I were isolated from 7 or 10d old mice and growing oocytes II were from 14d old mice. Full-grown oocytes were isolated from superovulated 8-week-old mice 46 h after PMSG injection. The whole ovaries were clipped mechanically with a razor blade. To remove the granulosa cells, the dissociated oocyte-granulosa cell complexes were transferred into M2 medium containing 0.1% hyaluronidase and digested for 5 min. Oocytes were then crosslinked with 1% formaldehyde after removing the zona pellucida by acidic Tyrode’s solution treatment. Eedfl/wt and EedmNull late 2-cell embryos were harvested by mating Eedfl/fl  or Eedfl/fl;Gdf9-Cre females with PWK/PhJ males.
sisHi-C libraries were produced as described (Du et al., 2017). Briefly, PGCs, oocytes or embryos were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Then formaldehyde was quenched with glycine for 10 min at RT. After being washed with 1 × PBS, the samples were incubated in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min and the chromatin was solubilized with 0.5% SDS. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP, the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, Cat # 65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Extaq (Takara), and the products were purified and size-selected with AMPure XP beads （Beckman Coulter, Cat # A63881）  RNA-seq libraries of Ring1-/-Rnf2fl/fl and Ring1/Rnf2 dKO oocytes were prepared as follows. Cumulus oocyte complexes were isolated from ovaries of approx. 3 months old females. Granulosa cells were removed by repeated pipeting using a fine-pulled capilary glass needle in M2 medium. Oocytes were washed twice in M2 medium and subsequently washed twice in DNA suspension Buffer (TEKnova, Cat # PNT0221). For RNA isolation, 15 GV oocytes from one mouse were pooled and RNA was extracted using the RNAEasy Micro Kit (Qiagen,Cat # 74004) according to the manufacturer’s instructions. RNA was amplified and converted to cDNA using the Ovation v2 Kit (NuGen, Cat # 7102). Sequencing libraries were prepared with the Truseq DNA LT kit (Illumina, Cat # FC-121-2001).  CUT&RUN libraries of Eedfl/fl and Eed-/- oocytes were conducted as previously described (Skene and Henikoff, 2017). A low constant amount of yeast DNA was added to each reaction as spike-in DNA.


title: Hi-C Ring1 Rnf2 dKO FGO rep3

description:
Hi-C Ring1 Rnf2 dKO FGO rep3
processed data file:
Ring1_Rnf2_dKO_FGO_rep123_allValidPairs.txt.gz

source_name: Hi-C Ring1 Rnf2 dKO FGO


title: Hi-C Eed flwt late 2cell rep1

description:
Hi-C Eed flwt late 2cell rep1
processed data file:
Eed_flwt_late_2cell_rep12_maternal_allValidPairs.txt.gz
Eed_flwt_late_2cell_rep12_paternal_allValidPairs.txt.gz
Eed_flwt_late_2cell_rep12_allValidPairs.txt.gz

source_name: Hi-C Eed flwt late 2cell

value: C57BL/6N x PWK/PhJ

value: late 2-cell embryos


title: Hi-C Eed mNull late 2cell rep1

description:
Hi-C Eed mNull late 2cell rep1
processed data file:
Eed_mNull_late_2cell_rep12_maternal_allValidPairs.txt.gz
Eed_mNull_late_2cell_rep12_paternal_allValidPairs.txt.gz
Eed_mNull_late_2cell_rep12_allValidPairs.txt.gz

source_name: Hi-C Eed mNull late 2cell


title: JIM460A6_S47_L008: spleen-4

first: Patricia

last: Barral

address: Guy's Campus

department: Immunobiology

institute: King's College London

data_processing:
cutadapt  v1.7.1 with a minlength of 25 and a quality of 10
quantify reads using rsem (v1.2.31) with bowtie2 (v2.2.9)
Genome_build: GRCm38
Supplementary_files_format_and_content: fastq are gzipped, rsem are tab delimited columns of expected counts

source_name: iNKT cells

extract_protocol:
RNA was isolated using RNA Mini Kit (QIAGEN). RNAseq including cDNA library preparation was processed at the Advanced sequencing facility in the Francis Crick Institute (London, UK).
NuGEN Ovation Ultralow (v2) kit was used for library preparation

treatment_protocol: NKT cells were sort-purified from lymphoid tissues from WT C57BL/6 mice (as CD1d-tetramer+TCR-b+B220-CD11b-CD11c-CD8-). Four biological replicates were performed.

value: iNKT

tag: tissue

value: SPLEEN

tag: unit

tag: batch

value: First


title: JIM460A8_S49_L008: iLN-4

value: INGLN


title: H1975_0-75mg_Pirf_6h_Rep3


title: JIM460A7_S48_L008: mLN-4

value: MLN


title: H1975_0-75mg_Pirf_6h_Rep1


title: H1975_0-75mg_Pirf_6h_Rep2


title: H1975_0-75mg_PBS_ctrl_24h_Rep1


title: H1975_0-75mg_PBS_ctrl_24h_Rep2


title: JIM460A5_S46_L008: thymus-3

value: THYMUS


title: H1975_0-75mg_PBS_ctrl_24h_Rep3


title: H1975_0-75mg_PBS_ctrl_6h_Rep3


title: H1975_0-75mg_PBS_ctrl_6h_Rep2


title: H1975_0-75mg_PBS_ctrl_6h_Rep1


title: JIM460A3_S44_L008: iLN-3


title: A549_0-75mg_Pirf_6h_Rep3


title: JIM460A2_S43_L008: mLN-3


title: JIM460A1_S42_L008: spleen-3


title: JIM460A10_S51_L008: thymus-4


title: A549_0-75mg_Pirf_24h_Rep1


title: MNR_D_1

first: Victor

middle: KM

last: Han

state: Ontario

address: 1151 Richmond St

department: Biochemistry

institute: University of Western Ontario

description:
MNR Litter D
fetal_counts.txt
M7D

data_processing:
Hiseq 2500 was used at McGill University and Genome Innovation Centre, D00278.
Fastqc was used to ensure all samples obtained good quality reads, then reads were aligned to the mm9 transcriptome using bowtie2 (default settings).
Sample tables were merged into a master count table in R console.
Transcripts were collapsed to the gene level in the R console using Biomart "ensembl_transcript_id" and "ensembl_gene_id" from the may 2012 mm9 archived version.
Data was normalized and differential expression was determined using DESeq2, ALDex2 and EdgeR tools.
Genome_build: mm9
Supplementary_files_format_and_content: Individual sample raw counts aligned to the transcriptome but not yet collapsed to the gene level; master count table is raw counts for all samples collapsed to the gene level

source_name: Right liver lobe

extract_protocol:
Frozen tissue was pulverized then homogenized. Total RNA was isolated with TRIzol the PureLink Mini RNA kit (Invitrogen, USA) using the manufactuer's on-column DNAseI protocol.
Libraries were created with the NEBNext® UltraTM Directional RNA library Prep Kit for Illumina® at McGill University and Genome Quebec Innovation Center (Quebec, CA) according to the manufacter's protocol

value: CD-1 IGS

tag: stress

value: maternal nutrient restriction (MNR)

value: fetal liver

value: Embryonic day 18.5

tag: litter

value: D


title: A549_0-75mg_Pirf_6h_Rep2


title: MNR_C_1

description:
MNR, Litter C
fetal_counts.txt
M5C

tag: strain

value: C


title: MNR_E_1

description:
MNR Litter E
fetal_counts.txt
M9E

value: E


title: MNR_E_2

description:
MNR Litter E
fetal_counts.txt
M10E


title: MNR_D_2

description:
MNR Litter D
fetal_counts.txt
M8D


title: A549_0-75mg_PBS_ctrl_24h_Rep1


title: AF16_HS_rep2

city: La Jolla

first: Jacob

last: Garrigues

address: 9500 Gilman Dr.

description:
AF_4_S10_L003
Heat-shocked sample replicate 2
processed data file: Cbr_AF16_NHS.HS_normalized.counts.txt

data_processing:
Default base-calling software for the Illumina HiSeq 4000 platform was used
Sequenced reads were aligned to the mRNA transcriptome using Salmon v0.13.1 with default parameters and automatic library type detection enabled
Salmon-derived counts (TPMs) for each transcript were processed using DESeq2 v1.18.1 with default parameters and a parametric fit type to obtain gene-level normalized counts
Genome_build: ce11 for C. elegans, cb4 for C. briggsae
Supplementary_files_format_and_content: tab-delimited text files include DESeq2-normalized counts for protein-coding genes

organism: Caenorhabditis briggsae

source_name: AF16_HS_whole L2 stage worm

growth_protocol: Worms were grown under standard conditions at 20 C until heat shock was performed

extract_protocol:
L2 stage worms were collected and washed, flash frozen on dry ice, and RNA was harvested using Trizol reagent
Illumina TruSeq Stranded Total RNA Library Prep Gold Kit was used with 1 ug of total RNA for the construction of sequencing libraries

treatment_protocol: Control (NHS) worms were maintained at 20 C, while heat-shocked (HS) worms were placed in a 34 C water bath for 30 minutes before collection

value: L2 stage

value: heat-shocked (HS)

value: Whole worm


title: AF16_NHS_rep2

description:
AF_3_S9_L003
Control sample replicate 2
processed data file: Cbr_AF16_NHS.HS_normalized.counts.txt

source_name: AF16_NHS_whole L2 stage worm

value: control (NHS)


title: AF16_HS_rep3

description:
AF_6_S12_L003
Heat-shocked sample replicate 3
processed data file: Cbr_AF16_NHS.HS_normalized.counts.txt


title: AF16_NHS_rep3

description:
AF_5_S11_L003
Control sample replicate 3
processed data file: Cbr_AF16_NHS.HS_normalized.counts.txt


title: A549_0-75mg_Pirf_24h_Rep2

value: Pirfenidone


title: AF16_HS_rep1

description:
AF_2_S8_L003
Heat-shocked sample replicate 1
processed data file: Cbr_AF16_NHS.HS_normalized.counts.txt


title: A549_0-75mg_PBS_ctrl_24h_Rep3

value: PBS


title: A549_0-75mg_PBS_ctrl_6h_Rep3


title: A549_0-75mg_Pirf_24h_Rep3


title: MNR_B_2

city: London

description:
MNR, Litter B
fetal_counts.txt
M4B

value: B


title: A549_0-75mg_PBS_ctrl_24h_Rep2


title: A549_0-75mg_PBS_ctrl_6h_Rep2


title: MNR_A_2

description:
MNR, Litter A
fetal_counts.txt
M2A

value: A


title: MNR_B_1

description:
MNR, Litter B
fetal_counts.txt
M3B


title: MNR_C_2

description:
MNR, Litter C
fetal_counts.txt
M6C


title: CON_E_2

description:
Control, Litter E
fetal_counts.txt
C9E

value: control


title: A549_0-75mg_PBS_ctrl_6h_Rep1


title: CON_D_2

description:
Control, Litter D
fetal_counts.txt
C10D


title: A549_6h_PBS_Rep1


title: CON_E_1

description:
Control, Litter E
fetal_counts.txt
C8E


title: AF16_NHS_rep1

description:
AF_1_S7_L003
Control sample replicate 1
processed data file: Cbr_AF16_NHS.HS_normalized.counts.txt


title: Progeny1-1276 [a550818-4325018-051918-783_H12]

type: genomic

city: Gainesville

first: Jianping

last: Wang

state: Florida

address: 2033 Mowry Road

department: Agronomy

institute: University of Florida

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The Affymetrix bioinformatics team processed the raw intensities in cell intensity files (.CEL) to obtain normalized intensities for each probe set. Further, these normalized intensities were converted to genotype calls with the Axiom Genotyping Algorithm version one
primary data description: Genotype Call (SNP call): AA=0, AB=1, BB=2, NoCall="-"; 'Signal' = Summarized signal

label: Biotin

organism: Saccharum officinarum

source_name: Progeny from cross Green German and IND81-146

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: These plant samples were maintained at the United States Department of Agriculture (USDA), Agricultural Research Service (ARS) Sugarcane Field Station at Canal Point, FL, which were under nature condition.

extract_protocol: Genomic DNA samples were extracted using MagJET Plant Genomic DNA Kit (Thermo Fisher Scientific, MA, USA).

treatment_protocol: Young leaf tissues were collected and stored at -80 °C for DNA extraction.

value: Sugarcane yellow leaf virus free


title: CON_D_1

description:
Control, Litter D
fetal_counts.txt
C7D

value: CD-1 IGS


title: MNR_A_1

description:
MNR, Litter A
fetal_counts.txt
M1A

value: maternal nutrient restriction (MNR)


title: CON_C_2

description:
Control, Litter C
fetal_counts.txt
C6C

value: fetal liver


title: Progeny1-1320 [a550818-4325018-051918-783_H10]


title: CON_C_1

description:
Control, Litter C
fetal_counts.txt
C5C

value: Embryonic day 18.5


title: CON_B_2

description:
Control, Litter B
fetal_counts.txt
C4B