title: shCtrl-1: Cancer associated fibroblasts expressing shCtrl construct, biological replicate 1

description: Gene expression data from human CAFs expressing shCtrl construct, biological replicate 1

source_name: CAFs expressing shCtrl construct

value: shCtrl


title: DAPK1 ko clone 10/8 3

status: Public on May 01 2019

type: RNA

city: Erlangen

first: Regine

last: Schneider-Stock

state: Bavaria

address: Universitaetsstrasse 22

department: Department of Pathology

country: Germany

institute: University Hospital Erlangen

description: DAPK1 ko cancer cell line

hyb_protocol: The Nanostring hybridization reaction containing 3 µl Reporter CodeSet, 5 µl hybridization buffer, 2 µl Capture ProbeSet and 5 µl total RNA (100 ng) was conducted for 16 h at 65°C. After hybridization, labelled RNA was processed automatedly according to the manufacturer's instructions for approximately 2.5 to 3 h through the NanoString nCounter Prep Station, where mRNA specific magnetic beads separation and mRNA immobilization on the cartridge surface takes place.

scan_protocol: Automated counting and tabulating of signals of the reporter probes was performed using the nCounter Digital Analyzer (Nanostring), a multi-channel epifluorescence scanner specifically configured for use with Nanostring's nCounter cartridges, and standard settings.

data_processing:
Data were processed internally using the nCounter Digital Analyzer (Nanostring). The number of mRNA specific reporter signals counted corresponds to number of respective mRNA molecules counted and present in the sample. For each sample, one Reported Code Count (RCC) file is generated, which contains the gene expression raw data. RCC files were downloaded from the nCounter Digital Analyzer and imported into the nSolver Analysis Software 3.0 (Nanostring) for data processing, quality control and analysis. Finally, housekeeping gene (geometric mean of 40 genes) normalization for quantitating gene expression levels, positive control normalization for background noise correction and data analysis was performed using nSolver™ Analysis Software 3.0 (NanoString Technologies, Hamburg, Germany) and standard settings. The fold-change of counts was determined by averaging results per DAPK1 ko cell line and comparing them to average counts of HCT116 cells.
Matrix tables contain normalized counts, raw data and fold change (FC) data of nine samples (see samples list above) obtained from the nSolver Analysis Software 3.0. Fold changes of counts were determined by averaging results per DAPK1 ko cell line (n = 1-3) and by comparing them to the average counts of HCT116 cells (n = 3) and are given in excel sheet Grouped FC all ko clones. Two further sheets present individual fold change data of all replicates (HCT116: n = 3, clone 7/6: n = 2, clone 10/8: n = 3, clone 21/9: n=1) and fold changes grouped per ko clone.

label: Reporter CodeSet & Capture ProbeSet (PanCancer Progression Panel, Nanostring)

molecule: total RNA

organism: Homo sapiens

source_name: HCT116_DAPK1 ko clone 10/8

label_protocol: 100 ng (contaied in 5 µl) of total RNA per sample was labeled with the Reporter CodeSet & Capture ProbeSet included in the following kit: XT_PGX_HuV1_CancerProg_CSO XT-CSO-PROG1-12(Cat. no. 115000152, Nanostring).

growth_protocol: All cell lines HCT116 and DAPK1 ko clones 7/6, 10/8 and 21/9  were cultured in a 100 cm cell culture dish and maintained in RPMI medium supplemented with 1% penicillin/streptomycin and 10% FBS.

extract_protocol: Cell harvesting was performed on ice. Cells were scraped off from the cell culture plates and cell pellets were prepared by centrifugation at 5000 rpm fr 5 min at 4 °C. Cells were washed with PBS, centrifugation was repeated, supernatants were discarded and dry cell pellets were frozen in liquid nitrogen and stred at -80°C. RNA was isolated from frozen cell pellets using the QIAzol Lysis Reagent (Qiagen) and RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: No treatment was applied.

tag: cell line

value: HCT116 DAPK1 ko clone 10/8

tag: tissue

value: colorectal carcinoma


title: CD4+Foxp3- CD4conv-2

type: SRA

city: Paris

first: Felipe

middle: Leal

last: Valentim

state: Île-de-France

address: Bâtiment Cervi, 4ème étage, pièce 052

country: France

institute: INSERM/UPMC

library_source: transcriptomic

data_processing:
Nextera adaptor removal: Trimmomatic (Bolger et al., 2014)
Reads alignment : hisat2 (Kim et al., 2015)
Read counts: featureCounts (Liao et al., 2014)
Read counts normalization: DESeq2 (Anders and Huber, 2010)
SAM to BAM conversion: samtools (Li et al., 2009)
Genome_build: Ensembl genome (Yates et al., 2016) version GRCm38
Supplementary_files_format_and_content: reads_count.gene_level.txt: Raw read counts as outputed by featureCounts

organism: Mus musculus

source_name: CD4conv Non-pregnant uterus

extract_protocol:
Uterine and uDLN Tregs and uterine CD4conv were isolated by cell sorting using FACS ARIA (BD Biosciences) after enrichment in CD4+ cells was performed using the EasySep Mouse APC Positive Selection Kit (Stemcell 18452). Groups of 20 mice per non-pregnant sample and 3 to 8 mice per pregnant sample were made and 4 samples were collected per cell type.
RNA was purified with the RNAqueous®-Micro Total RNA Isolation Kit (Invitrogen AM1931). cDNA was prepared with the SMART-Seq v4 Ultra Low Input RNA Kit. Indexed paired-end libraries were done with the Nextera® XT Library Prep Kit and the Nextera XT Index Kit. The quality control was done in Tapestation and Quantifluor. Illumina sequencing of the 16 samples in 2x150, 50 million reads/sample was done with the NextSeq 500 High Output Kit v2 (300 cycles) sequencer (Illumina Inc) generating paired end reads of approximately 2 x 150 bp in length. The samples were sequenced in two batches; CD4conv and uTreg E6-E8 samples in the first batch, and uDLN Treg NP and uTreg NP samples in the second batch.

tag: strain

value: BALB/c background Foxp3IRES-GFP (Bettelli et al. 2006)

value: Uterus

tag: cell type

tag: pregnancy stage

value: Non-pregnant


title: shCtrl-2: Cancer associated fibroblasts expressing shCtrl construct, biological replicate 2

city: Chicago

first: Mark

middle: Adam

last: Eckert

state: IL

address: 929 East 57th St, W107

department: OB/GYN

country: USA

institute: University of Chicago

description: Gene expression data from human CAFs expressing shCtrl construct, biological replicate 2

hyb_protocol: 5.5 ug of the fragmented and labeled cDNA was hybridized to Mouse Clariom S  array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix  GeneChip  Pico Reagent Kit guide (Thermo Fisher Scientific, Inc).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL intensity files were generated by GeneChip Command Console Software (AGCC, Thermo Fisher Scientific, Inc)

data_processing: Transcriptome Analysis Software 4.0 (TAS 4.0) Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA)

label: biotin

label_protocol: 700 pg of total RNA was used to generate double strand cDNA and the Ds cDNA was fragmented and biotin labeled according to Affymetrix  GeneChip  Pico Reagent Kit manual (Thermo Fisher Scientific, Inc).

growth_protocol: All cell lines were grown in methionine-free DMEM supplemented with 10% dialyzed fetal bovine serum and 10 micromolar methionine for 21 days before collection.

extract_protocol: RNA was extracted with the Qiagen AllPrep DNA/RNA Mini Kit per manufacturer's instructions. RNA integrity was checked on a bioanalyzer (Agilent,Inc). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis

treatment_protocol: All cell lines were stably infected with the indicated constructs and no additional treatment was performed.

value: Cancer associated fibroblasts (CAFs)

tag: expression construct


title: Donor_2_d2

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

institute: INSERM

data_processing:
Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v1.2.1).
Fastq files were then run with count application (Cell Ranger v1.2.1) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: purified Vgd2

extract_protocol: Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 14 cycles used for cDNA amplification and 12 cycles for library amplification

tag: subject id

value: purified TCRVdelta 2 gammadelta T lymphocytes

tag: cmv status

value: CMV+


title: shCtrl-3: Cancer associated fibroblasts expressing shCtrl construct, biological replicate 3

description: Gene expression data from human CAFs expressing shCtrl construct, biological replicate 3


title: cerebral cortex A2 rep 3

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.114 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files contain RPKM values for each sample

organism: Macaca fascicularis

source_name: cerebral cortex

extract_protocol:
Total RNAs were individually extracted using the Ambion Magmax™-96 total RNA isolation kit (Life Sciences) according to the manufacturer’s instructions. Briefly, 5 mg of tissue was placed in the lysis solution and homogenised in Qiagen Tissuelyzer™ for a period of 30 sec. Nucleic acids were captured onto magnetic beads, washed and treated with DNase. Total RNA was then eluted in 50 μl elution buffer. RNA quality and concentration was measured using an RNA Pico chip on an Agilent Bioanalyzer.
The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) producing a 275bp fragment including adapters in average size. In the final step before sequencing, eight individual libraries were normalised and pooled together using the adapter indices supplied by the manufacturer. Pooled libraries have then been clustered on the cBot Instrument from Illumina using the TruSeq SR Cluster Kit v3 - cBot - HS(GD-401-3001, Illumina Inc, San Diego, CA)  sequencing was then performed as 2x85bp, paired reads and 7 bases index read on an Illumina HiSeq3000 instrument using the TruSeq SBS Kit HS- v3  (50-cycle) (FC-401-3002, Illumina Inc, San Diego, CA).

value: cerebral cortex

tag: animal

tag: Sex

value: female


title: Weight-losing (ID041_071F)

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen

department: Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Affymetrix Human Clariom D Assay, and then washed and stained slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: These arrays were pre-processed with RMA, which includes normalization, summarization of probes to probesets, and background correction. Prior to further analysis, collapseRows R function (Miller et al., 2011) was used to convert and collapse the transcript abundance quantification detected by Affymetrix probe sets to mapped FANTOM-CAT IDs. 48368 probe sets annoated as locus type coding or multiple complex were filtered for in order to include only protein-coding genes. Subsequently, probe sets with gene name absent, indicated as miRNA, transcript identified by AceView, uncharacterized LOC or uncharacterized protein were excluded, leaving 26064 transcripts for further analysis.

source_name: Subcutaneous adipose tissue

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: Not relevant.

extract_protocol: Total RNA was isolated using the RNeasy kit (cat no. 217004, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Biopsies from the abdominal subcutaneous adipose tissue depot were obtained from the surgical incision. Samples were immediately frozen in liquid nitrogen and kept at -70C for subsequent DNA and RNA preparation.

value: White adipose tissue

tag: gender

tag: age

tag: weight change

value: Weight-losing

tag: time point

value: Baseline


title: cerebral cortex A2 rep 2


title: Donor_2_d1

source_name: purified Vgd1

value: purified TCRVdelta 1 gammadelta T lymphocytes


title: Weight-stable (ID043_006F)

value: Weight-stable


title: DAPK1 ko clone 10/8 2

description: DAPK1 ko cancer cell line


title: cerebral cortex A2 rep 1


title: Weight-losing (ID045_033F)


title: Dinoroseobacter shibae ∆191kb_3

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Genome_build: strain specific (indicated for each sample): NC_009952.1, NC_009955.1 NC_009956.1, NC_009957.1, NC_009958.1, NC_009959.1, NC_018290.1, NC_018291.1, NC_018287.1, NC_018288.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

organism: Dinoroseobacter shibae

source_name: strain grown in Marine broth

extract_protocol:
The pestled bacterial cell powder was covered with 1 ml TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA) and incubated for 5 min at room temperature. The further steps for total RNA isolation starting with the centrifugation at 12,000g for 10 min at 4°C were performed with the RNeasy mini kit (Qiagen, Hilden, Germany) as previously described (Wang et al. 2014). After DNase treatment, the total RNA was resolved in 50 µl ultrapure DEPC-treated H2O. Successful removal of genomic DNA was verified via PCR with specific primers against the 78 kb chromid (P737: 5´-GCTCTGCACCATTTCTTTTCG-3´,  P738: 5´-CGAGGCGGTTTGGTGTGTAGT-3´) using 1 µl of total RNA as a template. Depletion of ribosomal RNA was performed with the mRNA Ribo-Zero Magnetic Kit (Epicentre, Madison, WI, USA) according to the manufacturer´s instructions.
Single end, strand specific cDNA libraries were prepared using the Scriptseq v2 RNA-Seq Library Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturers protocol. For sequencing equal volumes of libraries (12 pM) were multiplexed on a single lane. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 - HS (Illumina, San Diego, CA, USA) for 50 cycles resulting in 50 bp reads. Image analysis and base calling were performed using the Illumina pipeline v 1.8 (Illumina, San Diego, CA, USA).

tag: replicons present

tag: biological replicate

tag: technical replicate


title: DAPK1 ko clone 10/8 1

description: DAPK1 ko cancer cell line

tag: cell line


title: DAPK1 ko clone 7/6 2

description: DAPK1 ko cancer cell line

source_name: HCT116_DAPK1 ko clone 7/6

value: HCT116 DAPK1 ko clone 7/6

tag: tissue


title: kidney cortex A1 rep 3

source_name: kidney cortex

value: kidney cortex


title: Dinoroseobacter shibae ∆191kb_2


title: kidney cortex A1 rep 2


title: kidney cortex A1 rep 1


title: Weight-gaining (ID040_153E)

value: Weight-gaining

value: Follow-up


title: Weight-stable (ID037_049F)


title: DAPK1 ko clone 7/6 1

description: DAPK1 ko cancer cell line

value: colorectal carcinoma


title: HCT116 wt 3

description: Wildtype cancer cell line HCT116


title: HCT116 wt 2

description: Wildtype cancer cell line HCT116


title: HCT116 wt 1

description: Wildtype cancer cell line HCT116


title: Dinoroseobacter shibae DSM16493T_2


title: liver A1 rep 3

source_name: liver

value: liver


title: liver A1 rep 2


title: liver A1 rep 1


title: Zoloft 471: Whole hippocampus, 24hr post fluid percussion injury+Zoloft drug treatment, rep3

city: Northbrook

first: Michael

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: miRNA expression of whole hippocampus 24hr post-injury

hyb_protocol: For mRNA: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Rat Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.  For miRNA: Labeled target was applied to Agilent miRNA 8x60K v21 arrays (Design ID# 070154) and hybridized overnight.

scan_protocol: Slides were washed and scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Rattus norvegicus

label_protocol: For mRNA: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the Total RNA sample.  Briefly, Total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.  For miRNA: Total RNA samples were dephosphorylated, denatured, and end-labeled according to Agilent's protocols.

growth_protocol: Adult male Sprague-Dawley rats (350 g–400 g) from vendor Charles Rivers were housed 2 per cage with food and water ad libitum in a vivarium with these constant conditions: light cycle (6∶00–18∶00) temperature (21°C–23°C), and humidity (40%–50%).

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Rats were subjected to experimental severe fluid percussion brain injury (with and without drug treatments), or sham injury and brains were removed 24 hours later, stored in RNA later and total RNA isolated at GenUs Biosystems.

tag: strain

value: Sprague-Dawley

value: male

value: hippocampus


title: Weight-losing (ID033_008F)


title: cerebral cortex A1 rep 3


title: Weight-losing (ID034_137E)


title: WGBS_CMD1_KO_2

city: Shanghai

first: Guoliang

last: Xu

address: 320 Yueyang Road

country: China

institute: Shanghai institute of biochemistry and cell biology

description:
Cells are treated under high light exposure
WT_cmd1_WGBS_Methylation_all.xlsx

library_source: genomic

data_processing:
After quality control (FastQC Version 0.11.5) and adapter trimming (Trimmomatic V0.36), the clean reads were aligned to the C. reinhardtii genome (V5.5, Phytozome) using BSMAP version v2.9
Raw methylation estimates were called for cytosines covered at least ten reads.
Commonly detected cytosine sites were averaged across replicates to increase robustness. To determine the methylation status of genes, methylation ratios of cytosines within the promoter region (2kb upstream and 1kb downstream of TSS) were collected and compared between wild-type and CMD1 mutant samples with Wilcoxon signed-rank test and corrected for false discovery rate (FDR) with the Benjamini & Hochberg method
Fold changes and percentage of differences were also calculated. Differentially methylated genes were identified with FDR values below 0.05 and at least 1.5-fold deviation. Functional enrichment was analyzed with Gene Ontology annotation and Fisher's exact test.
Genome_build: V5.5, Phytozome
Supplementary_files_format_and_content: Excel file include average methylation level of genes for each sample.

molecule: genomic DNA

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii

growth_protocol: All strains were cultured mixotrophically in Tris/acetate/phosphate (TAP) medium on a rotary shaker at 25 °C and maintained at a light intensity of 20 μmol photons·m-2·s-1.

extract_protocol:
Total RNA was extracted from C. reinhardtii using CTAB method
For the library preparation, the genomic DNA together with ~2% unmethylated lambda DNA (Thermo Scientific) was firstly shared by Covaris S220 for the generation of fragments (~300 bp). Then about 500 ng shared DNA was converted and purified with EZ DNA Methylation-Direct Kit (Zymo Research) following the manufacturer’s instructions. The DNA library was prepared using TruSeq DNA Methylation Kit (Illumina) according to the vendor’s manual

treatment_protocol: Cells were transferred to Sueoka's high salt medium (HSM) at 1 ×10^5/ml and exposed to light intensity (300μE)

tag: genotype

value: cmd1 KO


title: WGBS_CMD1_KO_1


title: Dinoroseobacter shibae ∆191kb_1


title: Dinoroseobacter shibae DSM16493T_3


title: Weight-stable (ID038_003F)


title: Zoloft 469: Whole hippocampus, 24hr post fluid percussion injury+Zoloft drug treatment, rep1


title: Weight-losing (ID031_031F)


title: cerebral cortex A1 rep 2

value: cerebral cortex


title: WGBS_WT_1

value: WT


title: Weight-stable (ID028_058F)

value: White adipose tissue

value: female


title: cerebral cortex A1 rep 1


title: RNA-seq_CMD1_KO_3

description:
Cells are treated under high light exposure
WT_cmd1_RNA_seq_FPKM_all.xlsx

data_processing:
quality control (FastQC Version 0.11.5) and adapter trimming (Trimmomatic40 V0.36)
the clean reads were aligned to the C. reinhardtii genome (V5.5, Phytozome) using TopHat2 (version v2.1.1) with default settings
The transcription levels of annotated genes (FPKM, fragments per kilobase of transcript per million mapped reads) were quantified and normalized using Cufflinks (v2.0.0) with default parameters
genes with adjusted P value < 0.05 and at least 2-fold-change were considered to be differentially expressed
Genome_build: C. reinhardtii genome (V5.5, Phytozome)
Supplementary_files_format_and_content: Excel file include FPKM data for each samples.

extract_protocol:
Total RNA was extracted from C. reinhardtii using TrizolTM (Thermo) according to the instruction’s manual
The RNA library was prepared using TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the vendor’s manual

treatment_protocol: Cells were transferred to Sueoka's high salt medium (HSM) at 1 ×10^5/ml and exposed to light intensity (300μE). Three biological replicates were repeated. WT_1/cmd1_1; WT_2/cmd1_2; WT_3/cmd1_3


title: Prozac 459: Whole hippocampus, 24hr post fluid percussion injury+Prozac drug treatment, rep3


title: Dinoroseobacter shibae DSM16493T_1


title: Weight-losing (ID032_023F)

value: Weight-losing

value: Baseline


title: CK7_3A

city: Houston

first: Peter

middle: Y

last: Lwigale

state: Texas

address: 6100 Main street

department: BioSciences

institute: Rice University

data_processing:
Raw reads produced by Illumina HS2000 are subjected to quality control (QC) to remove reads with adaptors, with more than 10% unknowns, and low quality reads. Resultiung clean reads are stored in FASTQ format.
Bowtie2 and HISAT were used to map clean reads to reference gene and genome, respectively. An average mapping ratio of 76.26% to the reference gene and 93.10% to the genome were generated with Galgal5 reference assembly (FASTA format) and annotated gene model (GTF format) from Ensembl database
Transcripts were normalized and presented as Fragments Per Kilobase Million (FPKM).
Differentially expressed genes (DEGs) were screened for using NOISeq method with parameter of abs(log2) ≥1 and probability ≥0.8.
Biological functions of DEGs were analyzed by DAVID Bioinformatics Resources 6.8. Data was further subjected to GO and KEGG pathway enrichment analyses.
Supplementary_files_format_and_content: FPKM values for each sample

organism: Gallus gallus

source_name: keratocytes and endothelium

extract_protocol:
E3 periocular neural crest, E5 corneal endothelium, or E7 corneal endothelium and keratocytes were isolated and flash frozen in Trizol. Quality control was performed with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real -Time PCR System.
Standard Illumina protocols

value: keratocytes and endothelium

tag: developmental stage

value: embryonic day 7


title: Prozac 456: Whole hippocampus, 24hr post fluid percussion injury+Prozac drug treatment, rep1


title: Prozac 458: Whole hippocampus, 24hr post fluid percussion injury+Prozac drug treatment, rep2


title: RNA-seq_CMD1_KO_1


title: Weight-stable (ID025_155E)

value: Weight-stable


title: Zoloft 470: Whole hippocampus, 24hr post fluid percussion injury+Zoloft drug treatment, rep2


title: CK5_2A

source_name: corneal endothelium

value: corneal endothelium

value: embryonic day 5


title: Weight-stable (ID024_126E)

value: Follow-up


title: Imipramine 466: Whole hippocampus, 24hr post fluid percussion injury+Imipramine, rep3


title: Weight-losing (ID029_004F)


title: CK7_1A


title: RNA-seq_WT_3


title: CK5_3A


title: Weight-losing (ID027_061F)


title: Imipramine 465: Whole hippocampus, 24hr post fluid percussion injury+Imipramine, rep2


title: RNA-seq_WT_1


title: RNA-seq_WT_2


title: Imipramine 464: Whole hippocampus, 24hr post fluid percussion injury+Imipramine, rep1


title: CK7_2A


title: Weight-gaining (ID022_129E)

value: Weight-gaining


title: RNA-seq_CMD1_KO_2


title: Weight-losing (ID020_148E)


title: TBI 454: Whole hippocampus, 24hr post fluid percussion injury, rep2

value: Sprague-Dawley


title: CK5_1A


title: Weight-gaining (ID018_059F)


title: TBI 453: Whole hippocampus, 24hr post fluid percussion injury, rep1

value: male


title: CK3_2A

source_name: periocular neural crest

value: periocular neural crest

value: embryonic day 3


title: CK3_3A


title: Weight-stable (ID021_044F)


title: CK3_1A


title: Weight-stable (ID023_005F)


title: Weight-losing (ID017_133E)


title: TBI 460: Whole hippocampus, 24hr post fluid percussion injury, rep3

value: hippocampus


title: E7B

city: Heidelberg

first: Jacob

last: Musser

address: Meyerhofstrasse 1

institute: European Molecular Biology Laboratory

description:
E7B
E7B_ggemu_scaled

data_processing:
Basecalls performed using CASAVA
reads mapped to chicken, emu, or alligator genomes using Tophat2 version 2.0.6. using default parameters and setting the -GTF option
read counts generated using HTSEQ version 0.5.3p9 implemented in python version 2.7.2. We set the option requiring reads to map to the correct strand, and resolved issues with multiple mappings using the option "intersection-nonempty".
TPM (transcript per million) relative expression values were calculated for all genes using the following method: Wagner GP, Kin K, Lynch VJ. 2012. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theor Biosci. 131:281-285.
We applied a scaling factor to all emu TPM values (.55x) and alligagtor TPM values (.62) to account for differences in the number of annotated genes. This value was calculated using the method outlined here: Musser, J. M. & Wagner, G. P. Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called ‘species signal’. J Exp Zool (Mol Dev Evol) 324, 588–604 (2015).
Genome_build: Chicken reads were mapped to ensembl WASHUC2 release version 68. Emu reads were mapped to a preliminary version of the Emu genome generated by the Alan Baker Lab at the University of Toronto. Alligator reads were mapped to american alligator genome allmis1.
Genome_build: Chicken:  WASHUC2 (https://may2012.archive.ensembl.org/Gallus_gallus/Info/Index)
Genome_build: Alligator: Allmis1 (https://hgdownload-test.gi.ucsc.edu/goldenPath/allMis1/bigZips/)
Genome_build: Emu:  preliminary version from Allan Baker's Lab is not available publicly
Supplementary_files_format_and_content: the final scaled TPM values for all chicken, emu, and alligator one-to-one orthologs that were used for analyses. The matrix uses chicken gene identifiers from the WASHUC2 version of the chicken genome (the data from Emu and Alligator are only for the 1-1 orthologs to chicken).

organism: Dromaius novaehollandiae

source_name: feather placode dorsal tract epidermis

growth_protocol: Bird eggs were incubated with rotation in a G.Q.F 1502 Sportsmen Incubator at 37.8 degrees celsius (chicken) or 35.5 degrees celsius (emu). Alligator egg incubation is described in detail in Musser et al. 2015.

extract_protocol:
Total RNA was extracted using a Qiagen Rneasy kit.
polyA enriched strand-specific library was constructed using a proprietary method developed by the Yale Center for Genome Analysis

treatment_protocol: Skin samples were dissected and placed in a minimal amount of 10 mg/mL dispase and incubated at 4 degrees celsius for 13 hours to permit clean separation of epidermis.

value: Hamburger and Hamilton Stage 33/34

value: feather placode dorsal tract epidermis


title: Sham 457: Whole hippocampus, 24hr post sham treatment, rep1


title: E16C

description:
E16C_001_ATCAC_L001
E16C_ggemu_scaled

source_name: claw morphogenesis epidermis

value: Hamburger and Hamilton stage 38

value: claw morphogenesis epidermis


title: RNA_THP1_2hrPMA_rep2

city: Nashville

first: Emily

last: Hodges

state: TN

address: 2212 Garland Ave.

department: Biochemistry

institute: Vanderbilt University

description:
RNA-seq of THP1 Monocytes: 2hrs 162nM PMA treatment
THP1_PMAtimecourse_RNAseq_DESeq2_NormalizedCountsTable.txt

data_processing:
Trimming: All sequencing library reads were trimmed of adapters using TrimGalore script wrapper for Cutadapt (Martin, 2011) and FastQC. Version: trim_galore 0.4.0. Command: trim_galore --fastqc --fastqc_args "--outdir ${FASTQC_DIR}" --clip_R1 9 --clip_R2 9 --paired --retain_unpaired --output_dir ${TRIM_DIR} ${R1} ${R2}
Mapping: Standard ATAC reads were mapped with bowtie2. Version: bowtie2 2.2.6. Command: bowtie2 -p 8 --no-discordant --no-mixed -X 1000 -x ${INDEX} -1 ${R1} -2 ${R2} -S ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All bisulfite converted samples were mapped with WALT. Version: WALT v1.0. Command: walt -m 8 -t 6 -i ${INDEX} -1 ${R1} -2 ${R2} -o ${MAPPED_DIR}/${MAPPED}.sam
Mapping: All RNA-seq reads were mapped with STAR. Version: STAR_2.6.1a. Command: STAR --runThreadN 4 --genomeDir /data/hodges_lab/human_genome/GRCh38_Gencode24 --sjdbGTFfile /data/hodges_lab/human_genome/GRCh38_Gencode24/gencode.v24.primary_assembly.annotation.gtf --readFilesCommand zcat --readFilesIn --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
ATAC peak calling: All peak calling was done with MACS2. Version: MACS2 2.1.1. Command: macs2 callpeak -t ${MAPPED_DIR}/${MAPPED}.shifted.bam -f BAMPE -n ${MACS_DIR}/${MAPPED} -g hs -q 0.005 -B --SPMR --keep-dup all --broad --broad-cutoff 0.005
DNA methylation analysis: The Methpipe suite of tools was used for all CpG methylation analysis. Version: Methpipe 3.4.3
Differential RNA-seq analysis: DESeq2 was use to calculate differential RNA expression across the time course. Version: DESeq2 1.18.1. R-Version: 3.4.3
Differential ATAC-seq analysis: TCseq was used to calculate differential chromatin accessibility across the time course. Version: 1.6.1. R-version: 3.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are broadPeak output bed files from MACS2, meth files are a tab delimited text file of CpG methylation values for all symmetic CpGs in hg19, meth files are generated as output from Methpipe
Supplementary_files_format_and_content: DEseq2 normalized transcript abundance table

source_name: THP-1 Monocyte

growth_protocol: THP1 monocytes were cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 units penicillin/streptomycin and 1mM sodium pyruvate. During routine culture THP1 cells were maintained at a density of 0.5-2E6 cells/mL. All cells were regularly screened for mycoplasma contamination using the Lonza MycoAlert kit.

extract_protocol: THP1 cells were harvested from each PMA stimulation time point by pelleting approximately 1E6 cells at 4°C, 500 R.C..F for 5 minutes. After removal of supernatant, cell pellet was homogenized with Trizol by repeatedly pipetting up/down with a 1mL micropipette tip. RNA was purified according to the Triozol manufacturere protocol. Libraries were prepared using manufacturer protocols in the SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian kit available from Takara Bio USA, Inc (catalog # 634873)

treatment_protocol: Differentiation of THP1 monocytes was induced with RPMI medium carrying PMA at a concentration of 100ng/mL (162nM). THP1 monocyte PMA stimulation time points were harvested with a combination of aspiration (for suspended cells) and trypsin (for adherent cells). The final collection of each time point was pelleted at 4°C, 500 R.C.F for 5 minutes. After pelleting cells were resuspended in ice cold PBS and cell counted using an automated cell counter (Biorad). This cell suspension was divided as input material for RNA extraction, genomic DNA extraction and ATAC reactions.

tag: pma stimulation time point

value: 2 hr


title: Sham 461: Whole hippocampus, 24hr post sham treatment, rep2


title: RNA_THP1_1hrPMA_rep2

description:
RNA-seq of THP1 Monocytes: 1hrs 162nM PMA treatment
THP1_PMAtimecourse_RNAseq_DESeq2_NormalizedCountsTable.txt

value: 1 hr


title: E15C

description:
E15C_006_GCCAAT_L008
E15C_ggemu_scaled


title: RNA_THP1_0.5hrPMA_rep2

description:
RNA-seq of THP1 Monocytes: 0.5hrs 162nM PMA treatment
THP1_PMAtimecourse_RNAseq_DESeq2_NormalizedCountsTable.txt


title: E27R

description:
E27R_003_TTAGG_L001
E27R_ggemu_scaled

source_name: reticulate scale morphogenesis tract epidermis

value: Hamburger and Hamilton stage 40


title: E25R

description:
E25R_002_CGATG_L001
E25R_ggemu_scaled

value: reticulate scale morphogenesis tract epidermis


title: Control diet fed 9_7E

city: Vancouver

first: Alexander

middle: G

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

country: Canada

institute: The University of British Columbia

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.14

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: Raw expression data were background corrected, normalized and log transformed using the oligo package of the Bioconductor open-source project in the R statistical environment.

source_name: Mouse utero-placental tisses at Gd10.5 of pregnancy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Whole Transcript (WT) Expression Arrays protocol.

extract_protocol: RNA from purified murine uterine natural killer cells was isolated using a protocol that combines Trizol LS + Qiagen clean-up columns + DNase treatment to remove any contaminant gDNA. Quality control was performed using Agilent Bioanalyzer, only samples with RIN values >8 were used.

treatment_protocol: 9 week old female C57BL6/J mice were subjected to 13 week high-fat high-sucrose diet or a matched low-fat no-sucrose(control) diet prior pregnancy with diet regime maintained throughout pregnancy.

value: utero-placental tissue

tag: condition

value: Control


title: RNA_THP1_24hrPMA_rep1

description:
RNA-seq of THP1 Monocytes: 24hrs 162nM PMA treatment
THP1_PMAtimecourse_RNAseq_DESeq2_NormalizedCountsTable.txt

value: 24 hr


title: Weight-stable (ID014_079E)

value: White adipose tissue

value: female

value: Weight-stable

value: Follow-up

tag: subject id


title: Weight-gaining (ID010_136E)

value: Weight-gaining


title: Weight-gaining (ID011_046F)

value: Baseline


title: Control diet fed 4_3E

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.13


title: E17S

description:
E17S_CTTGTA_L002
E17S_ggemu_scaled

source_name: scutate scale morphogenesis tract epidermis


title: High fat diet fed Diet-indued obese 30_18C

description:
High fat diet fed
Gene expression from uetrine natural killer cells at GD10.8

value: Diet-indued obese


title: RNA_THP1_2hrPMA_rep1


title: Control diet fed 38_21C

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.12


title: RNA_THP1_1hrPMA_rep1


title: Weight-gaining (ID015_122E)


title: Weight-losing (ID013_099E)

value: Weight-losing


title: E16S

description:
E16S_GCCAAT_L002
E16S_ggemu_scaled

value: scutate scale morphogenesis tract epidermis


title: High fat diet fed Diet-indued obese resistant 37_18E

description:
High fat diet fed
Gene expression from uetrine natural killer cells at GD10.11

value: Diet-indued obese resistant


title: E24BF3

description:
E24BF3_008_ACTTG_L002
E24BF3_ggemu_scaled

source_name: feather morphogenesis flank/femoral tract epidermis

value: Hamburger and Hamilton Stage 36


title: Weight-stable (ID012_066F)

source_name: Subcutaneous adipose tissue


title: High fat diet fed Diet-indued obese resistant 33_14D

description:
High fat diet fed
Gene expression from uetrine natural killer cells at GD10.10


title: RNA_THP1_0.5hrPMA_rep1


title: Weight-stable (ID009_131E)


title: Weight-gaining (ID007_080E)


title: Control diet fed 32_15E

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.9


title: Control diet fed 27_13B

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.6


title: High fat diet fed Diet-indued obese 3_4E

description:
High fat diet fed
Gene expression from uetrine natural killer cells at GD10.7


title: Control diet fed 26_17A

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.5


title: Control diet fed 24_13D


title: RNA_THP1_0hrPMA_rep2

description:
RNA-seq of THP1 Monocytes: 0hrs 162nM PMA treatment
THP1_PMAtimecourse_RNAseq_DESeq2_NormalizedCountsTable.txt

value: 0 hr


title: RNA_THP1_0hrPMA_rep1


title: Weight-stable (ID005_007F)


title: E18BFL

description:
E18BFL_GCCAAT_L007
E18BFL_ggemu_scaled

value: feather morphogenesis flank/femoral tract epidermis


title: Weight-stable (ID006_039F)


title: E18MB

description:
E18MB
E18MB_ggemu_scaled

source_name: feather morphogenesis dorsal tract epidermis


title: RNA_THP1_24hrPMA_rep2


title: E23C

description:
E23C_012_CTTGTA_L008
E23C_ggemu_scaled

source_name: claw placode epidermis

value: claw placode epidermis


title: E11B

description:
E11B.gz
E11B_ggemu_scaled

value: feather morphogenesis dorsal tract epidermis


title: AA26LFC

description:
AA26LFC_005_ACAGT_L002
AA26LFC_ggam_scaled

organism: Alligator mississippiensis

source_name: foot claw morphogenesis epidermis

value: Ferguson stage 22

value: foot claw morphogenesis epidermis


title: High fat diet fed Diet-indued obese 2_6B

description:
High fat diet fed
Gene expression from uetrine natural killer cells at GD10.12

value: utero-placental tissue


title: AA24LFC

description:
AA24LFC_004_TGACC_L001
AA24LFC_ggam_scaled


title: E21R

description:
E21R_GCCAAT_L001
E21R_ggemu_scaled

source_name: reticulate scale placode tract epidermis

value: Hamburger and Hamilton Stage 39


title: A190Fem

description:
A190Fem_CTTGTA_L003
A190Fem_ggam_scaled

source_name: asymmetric (femoral) scale morphogenesis tract epidermis

value: Feguson stage 23/24


title: A189Fem

description:
A189Fem_GCCAAT_L003
A189Fem_ggam_scaled

value: asymmetric (femoral) scale morphogenesis tract epidermis


title: E11S

description:
E11S_ACAGTG_L002
E11S_ggemu_scaled

source_name: scutate scale placode tract epidermis

value: Hamburger and Hamilton Stage 37

value: scutate scale placode tract epidermis


title: Weight-losing (ID003_103E)

value: White adipose tissue

value: female

value: Follow-up


title: High fat diet fed Diet-indued obese 18_2C

value: Diet-indued obese


title: A164F

description:
A164F_CTTGTA_L007
A164F_ggam_scaled

source_name: symmetric (flank) scale morphogenesis tract epidermis

value: Ferguson stage 23


title: Weight-stable (ID001_078F)

value: Weight-stable

value: Baseline


title: High fat diet fed Diet-indued obese resistant 17_4C

value: Diet-indued obese resistant


title: Weight-gaining (ID002_032F)

value: Weight-gaining


title: E10S

description:
E10S_TGACCA_L002
E10S_ggemu_scaled


title: E9FL

description:
E9FL_ACAGTG_L007
E9FL_ggemu_scaled

source_name: feather placode flank/femoral tract epidermis

value: Hamburger and Hamilton Stage 33/34


title: A162F

description:
A162F_GCCAAT_L007
A162F_ggam_scaled

value: symmetric (flank) scale morphogenesis tract epidermis


title: E6FL

description:
E6FL_TGACCA_L007
E6FL_ggemu_scaled

value: feather placode flank/femoral tract epidermis


title: 17AM: Chicken_PHF 5

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene Expression in PHF treated birds

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 ° C and hybridized on to a Agilent's chicken GXP_8X60k Array (AMADID: 049081) designed by Genotypic Technology Private limited, bangalore using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method . Gene Based analysis was performed.

source_name: Breast Muscle

label_protocol: The samples for Gene expression were labeled using Agilent Quick Amp Kit, One-Color (Lot # 6275010). 600ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Birds were supplemented with PHF for 42 days and breast muscle were collected.

extract_protocol: RNA was extracted from  he muscle tissue using Qiagen Lipid tissue kit.

value: Breast Muscle


title: AA29LFC

description:
AA29LFC_007_CAGAT_L002
AA29LFC_ggam_scaled

source_name: foot claw placode epidermis

value: Ferguson stage 21

value: foot claw placode epidermis


title: 18AM: Chicken_PHF 6

description: Gene Expression in PHF treated birds


title: High fat diet fed Diet-indued obese resistant 16_4D

description:
High fat diet fed
Gene expression from uetrine natural killer cells at GD10.9

value: utero-placental tissue


title: E9B2

description:
E9B2_TGACCA_L006
E9B2_ggemu_scaled

source_name: feather placode dorsal tract epidermis

value: feather placode dorsal tract epidermis


title: AA28LFC

description:
AA28LFC_006_GCCAA_L002
AA28LFC_ggam_scaled


title: High fat diet fed Diet-indued obese 15_10B


title: Mango 1 month Old

city: St. Lucia

first: Muhammad

middle: Umair

last: Ahsan

state: QLD

address: 306 Carmody Rd., The University of Queensland (UQ)

country: Australia

institute: The University of Queensland

data_processing:
Raw read files were processed with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapters, with trimmed reads of lengths less than 30 nt retained. Reads mapping to ribosomal RNAs were removed using BBduk (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/). The SCRAM pipeline was used for quantifying miRNA reads (Fletcher, Boden et al. 2018). Normalisation of read counts was based on reads per million reads between 20 and 24 nt. Reference mature Arabidopsis and rice miRNA sequences for mapping were obtained from miRbase (http://www.mirbase.org/).
Supplementary_files_format_and_content: reads count, mature miRNA count

organism: Mangifera indica

source_name: youngest juvenile tree_leaf

growth_protocol: Samples from 1 month old trees, youngest fully expanded leaf arising from the primary unbranched shoot was collected. For mature/already flowering trees planted in field, the general sampling strategy was to collect leaves from 15 different positions on each of three replicate trees (3 biological replicates) to capture an average for each tree regardless of potential leaf-specific variation. The sampling age for mature/already flowering avocado and macadamia was chosen as 10 year old field grown trees since avocado and macadamia has 7 to 10 year juvenile phase. On the other hand, Mango cultivar Kensington Pride starts flowering in about 3-5 years, hence 5 year old trees were selected as mature already flowering samples.

extract_protocol:
Total RNA of collected samples was extracted using a MasterPure Plant RNA Purification kit (Epicentre, Madison, WI, USA) according to the manufacturer’s protocol
NEXTflex Small RNA-Seq Kit v3 was utilized to prepare small RNA libraries per manufacturer’s instructions (Bioo Scientific Corporation, Austin, TX, USA). Briefly, 1μg of total RNA extracted using the above method from 1 month and 10 year old trees (5 year old mango) avocado, macadamia and mango tree leaves waeres utilzed. During 3’ adapter ligation step the samples are incubated at 20 °C overnight. Then first strand cDNA was synthesised using NEB #M0253 kit according to manufacturer protocol using the NEXTflex RT Primer (New England Biolabs Inc., Beverly, MA, USA). Incubation at 25 °C for 10 minutes was followed by extension at 37 °C for 40 minutes and Inactivation of the enzyme at 65 °C for 20 minutes. NEXTflex reagents and primers were used for 17 cycles of PCR amplification. PCR products between 130 and 180bp were cut from a 3% MetaPhor Agarose gel. The QIAquick gel extraction kit (QIAGEN, Venlo, The Netherlands) was used to isolate this DNA before libraries were sent to the Queensland University of Technology Australia, genomics laboratory for quantification and sequencing on Illumina TruSeq (Illumina, San Diego, CA, USA) as a 76 cycle single read library.

tag: cultivar

value: Kensington Pride

value: 1 month (juvenile)

value: fully expanded newly emerged leaves


title: Control diet fed 14_3A

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.7

value: Control


title: 16AM: Chicken_PHF 4

description: Gene Expression in PHF treated birds


title: 15AM: Chicken_PHF 3

description: Gene Expression in PHF treated birds


title: 14AM: Chicken_PHF 2

description: Gene Expression in PHF treated birds


title: 13AM: Chicken_PHF 1

description: Gene Expression in PHF treated birds


title: Control diet fed 11_1B


title: A83Fem

description:
A83Fem_ACAGTG_L003
A83Fem_ggam_scaled

source_name: asymmetric (femoral) scale placode tract epidermis


title: High fat diet fed Diet-indued obese 13_6C

description:
High fat diet fed
Gene expression from uetrine natural killer cells at GD10.6

source_name: Mouse utero-placental tisses at Gd10.5 of pregnancy

value: Diet-indued obese


title: 6AM: Chicken_Control 6

description: Gene Expression in control birds


title: AN1404_Rep1

city: Baltimore

middle: R.

last: Marten

state: MD

address: 1000 Hilltop Circle

department: Chemical, Biochemical, and Environmental Engineering

institute: University of Maryland Baltimore County

data_processing:
Sequenced reads were trimmed for adaptor sequence,RNA-Seq output data  was checked for base quality and aligned to the reference genome of Aspergillus nidulans  (www.aspgd.org/) using bowtie2 and the read counts were normalized using HT-Seq.  Differential expression analysis was done using DESeq software (Anders and Huber, 2010)
Genome_build: Aspergillus nidulans
Supplementary_files_format_and_content: Tab-delimited text files include Differential expression log2fold values for each sample

organism: Aspergillus nidulans

source_name: MpkA kinase deletion

growth_protocol: Spores were spread on MAGV plates [2% malt extract, 1.5% agar, 2% glucose, 1mL/L Hutner’s solution (FGSC), 1mL/L vitamin solution (FGSC)] and incubated for 2 days at 28⁰C. Harvested cells (1x107 spores) were inoculated into 50mL of rich, low pH media [YGV: 0.5% yeast extract, 2% glucose, 1mL/L Hutner’s solution (FGSC), 1mL/L vitamin solution (FGSC) adjusted to pH 3.3 with 1M HCl] and grown for 12 hours at 250 rpm and 28⁰C. This flask was used to seed 1.2L of YGV media in a 2.8L Fernbach flask at 250 rpm and 28⁰C. After approximately 20 hours (or until late exponential growth phase), mycelia were harvested and immediately frozen with liquid nitrogen and stored at -80⁰C.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 ((Illumina, Inc. San Diego, CA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: -mpkA


title: Mac 10 year old

organism: Macadamia integrifolia

source_name: mature/already flowering tree_leaf

value: 10 year old (mature/already flowering)


title: Mac 1 month old


title: AN1404_Rep2


title: A82Fem

description:
A82Fem_TGACCA_L003
A82Fem_ggam_scaled

value: asymmetric (femoral) scale placode tract epidermis


title: Mango 5 year old

value: 5 year old (mature/already flowering)


title: A152F

description:
A152F_ACAGTG_L007
A152F_ggam_scaled

source_name: symmetric (flank) scale placode tract epidermis

value: Ferguson stage 22


title: AN1405_Rep2

source_name: Parental strain

value: parental strain


title: 5AM: Chicken_Control 5

description: Gene Expression in control birds


title: A151F

description:
A151F_TGACCA_L007
A151F_ggam_scaled

value: symmetric (flank) scale placode tract epidermis


title: Avo 10 year old

organism: Persea americana

value: Hass


title: Avo 1 month old


title: 26-3-4_RNAseq

status: Public on Apr 30 2019

city: Columbia

first: Melvin

middle: John

last: Oliver

state: Missouri

address: 206 Curtis Hall

department: Plant Genetics Unit

institute: USDA-ARs

data_processing:
Performed by MU Core: Base calling and quality scoring for the NextSeq 500 platform is performed by an updated implementation of Real-Time Analysis (RTA), called RTA v2.
adaptor removal performed by MU core
RNA-seq reads were aligned to the maize B73 genome and gene models (RefGen_v3 (Release 5b+)) with CLC Workbench (Version 6.8.1) using the following parameters:
Low quality nucleotides were trimmed using default trim tool settings with the following exceptions: trim quality score limit = 0.03; Trim 5' terminal nucleotides = 12; Trim 3' terminal nucleotides = 2.
Sequences with more than two ambiguous nucleotides, low-quality sequences (<0.02), and reads < 36 nt were filtered.
Genome_build: maize B73 genome and gene models (RefGen_v3 (Release 5b+))
Supplementary_files_format_and_content: Tables (.csv) including raw counts were generated with CLC Workbench (Version 6.8.1). Normalized read count tables (.csv) of read counts per million were generated with EdgeR.

organism: Zea mays

source_name: seedling_water potentials of -0.3 MPa (mild water deficit stress)

growth_protocol: Briefly, surface sterilized maize seeds (B73) were imbibed for 24 hours at room temperature in an aerated 1mM CaSO4 solution. Imbibed seeds were planted in boxes of vermiculite hydrated to the drip point with 1mM CaSO4, and germinated in the dark at 29  1ºC at near-saturation humidity until primary roots had reached 15-25 mm. Seedlings were transplanted to plastic boxes, each containing vermiculite moistened with 1mM CaSO4 to achieve water potentials of -0.02 MPa (well-watered), -0.3 MPa (mild water deficit stress), or -1.6 MPa (severe water deficit stress), and grown in the dark at 29 °C and near saturation humidity. At 26 hours after transplanting the primary root growth zone, consisting of the apical 1 cm of the primary root, was harvested from each seedling.

extract_protocol:
Total RNA was extracted using the RNEasy Plant Mini Kit (Qiagen, Carlsbad, CA) and treated with Turbo DNase (Life Technologies, Carlsbad, CA) to remove contaminating genomic DNA.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Libraries were prepared using the NEBNext mRNA Library Prep Master Mix Set for Illumina and according to kit's instructions. Briefly, polyA mRNA was purified from 1 µg total RNA using the Dynabeads mRNA DIRECT Purification kit. After mRNA fragmentation and cDNA synthesis, adaptors were ligated and library fragments of ~100 bp were selected using AMPure XP beads. DNA fragments were PCR amplified with Illumina primers for 10 cycles. Libraries were sequenced on the Illumina NextSeq 500 platform following the manufacturer's protocols.
RNA-seq each library was split into four parts for sequencing on independent lanes so as to remove any lane bias

treatment_protocol: Water deficit treatments were applied in a non-transpiring vermiculite culture system.Sharp R.E., Silk W.K., & Hsiao T.C. (1988). Growth of the maize primary root at low water potentials I. Spatial distribution of expansive growth.  Plant Physiology 87 (1):50-57.

value: B73 inbred line

tag: treatment

value: mild water deficit

value: seedling 1-cm primary root growth zone


title: 26-16-2_RNAseq

source_name: seedling_water potentials of -1.6 MPa (severe water deficit stress)

value: severe water deficit


title: 26-16-5_RNAseq


title: 26-3-3_RNAseq


title: 26-16-1_RNAseq


title: 3BM: Chicken_Control 3

description: Gene Expression in control birds

value: Breast Muscle


title: 4AM: Chicken_Control 4

description: Gene Expression in control birds


title: 26-WW-3_RNAseq

source_name: seedling_water potentials of -0.02 MPa (well-watered)

value: well-watered


title: 26-WW-2_RNAseq


title: 1AM: Chicken_Control 1

description: Gene Expression in control birds


title: 26-WW-1_RNAseq


title: AN1405_Rep1


title: 2BM: Chicken_Control 2

description: Gene Expression in control birds


title: RNA-seq_HAP1_WT_r3_C631

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
RNA-seq in HAP1 cell line, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Reads were trimmed with Trimmomatic and aligned to the GRCh37/hg19 assembly of the human genome using Bowtie1 with the following parameters: "-q -p 6 -a -m 100-minins 0-maxins 5000-fr-sam-chunkmbs 200".
Duplicate reads were removed with Picard’s MarkDuplicates utility with standard parameters before transcript quantification with BitSeq using the Markov chain Monte Carlo method and standard parameters.
To obtain gene-level quantifications, we assigned the expression values of its highest expressed transcript to each gene.
Differential gene-level expression between each knockout and wild-type cells was performed with DESeq2 from the raw count data with a significance threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Each csv file contains read counts for each sample at gene level

molecule: polyA RNA

source_name: HAP1 cell line

growth_protocol: HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.

extract_protocol:
RNA extraction was performed with Qiagen RNeasy Mini Kit (Cat No. 74106) according to the manufacturer's instructions.
Total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

tag: library

value: RNA-seq

tag: replicate

tag: clone

tag: knockout

value: WT


title: RNA-seq_HAP1_SMARCD3_r1_2480_12

description:
RNA-seq in HAP1 cell line knockout for SMARCD3, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_WT_r2_C631

description:
RNA-seq in HAP1 cell line, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD3_r3_2480_12

description:
RNA-seq in HAP1 cell line knockout for SMARCD3, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD3_r2_2480_12

description:
RNA-seq in HAP1 cell line knockout for SMARCD3, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_WT_r1_C631

description:
RNA-seq in HAP1 cell line, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD2_r3_2782_10

description:
RNA-seq in HAP1 cell line knockout for SMARCD2, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD2_r1_2782_10

description:
RNA-seq in HAP1 cell line knockout for SMARCD2, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCC1_r2_2476_12

description:
RNA-seq in HAP1 cell line knockout for SMARCC1, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD1_r1_2478_6

description:
RNA-seq in HAP1 cell line knockout for SMARCD1, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCC1_r1_2476_12

description:
RNA-seq in HAP1 cell line knockout for SMARCC1, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCC1_r3_2476_12

description:
RNA-seq in HAP1 cell line knockout for SMARCC1, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD1_r2_2478_6

description:
RNA-seq in HAP1 cell line knockout for SMARCD1, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: 26-3-1_RNAseq


title: RNA-seq_HAP1_SMARCA4_r3_2878_6

description:
RNA-seq in HAP1 cell line knockout for SMARCA4, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD2_r2_2782_10

description:
RNA-seq in HAP1 cell line knockout for SMARCD2, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCA4_r1_2878_6

description:
RNA-seq in HAP1 cell line knockout for SMARCA4, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCD1_r3_2478_6

description:
RNA-seq in HAP1 cell line knockout for SMARCD1, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCA4_r2_2878_4

description:
RNA-seq in HAP1 cell line knockout for SMARCA4, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCA4_r1_2878_4


title: RNA-seq_HAP1_PHF10_r2_2778_11

description:
RNA-seq in HAP1 cell line knockout for PHF10, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCA2_r3_4055_12

description:
RNA-seq in HAP1 cell line knockout for SMARCA2, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_PHF10_r3_2778_11

description:
RNA-seq in HAP1 cell line knockout for PHF10, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCA4_r3_2878_4


title: RNA-seq_HAP1_SMARCA4_r2_2878_6


title: RNA-seq_HAP1_SMARCA2_r1_4055_12

description:
RNA-seq in HAP1 cell line knockout for SMARCA2, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_SMARCA2_r2_4055_12

description:
RNA-seq in HAP1 cell line knockout for SMARCA2, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_PBRM1_r1_1135_10

description:
RNA-seq in HAP1 cell line knockout for PBRM1, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF3_r3_2776_1

description:
RNA-seq in HAP1 cell line knockout for DPF3, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_PHF10_r1_2778_11

description:
RNA-seq in HAP1 cell line knockout for PHF10, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_PBRM1_r3_1135_10

description:
RNA-seq in HAP1 cell line knockout for PBRM1, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_PBRM1_r2_1135_10

description:
RNA-seq in HAP1 cell line knockout for PBRM1, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF2_r3_2777_4

description:
RNA-seq in HAP1 cell line knockout for DPF2, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF3_r1_2776_1

description:
RNA-seq in HAP1 cell line knockout for DPF3, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF2_r2_2777_4

description:
RNA-seq in HAP1 cell line knockout for DPF2, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF3_r2_2776_1

description:
RNA-seq in HAP1 cell line knockout for DPF3, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF2_r1_2777_4

description:
RNA-seq in HAP1 cell line knockout for DPF2, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BRD9_r2_934_10

description:
RNA-seq in HAP1 cell line knockout for BRD9, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF1_r3_2779_11

description:
RNA-seq in HAP1 cell line knockout for DPF1, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BRD9_r3_934_10

description:
RNA-seq in HAP1 cell line knockout for BRD9, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF1_r2_2779_11

description:
RNA-seq in HAP1 cell line knockout for DPF1, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_DPF1_r1_2779_11

description:
RNA-seq in HAP1 cell line knockout for DPF1, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BRD9_r1_934_10

description:
RNA-seq in HAP1 cell line knockout for BRD9, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL7B_r3_4278_8

description:
RNA-seq in HAP1 cell line knockout for BCL7B, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BRD7_r1_923_10

description:
RNA-seq in HAP1 cell line knockout for BRD7, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BRD7_r2_923_10

description:
RNA-seq in HAP1 cell line knockout for BRD7, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL7B_r1_4278_8

description:
RNA-seq in HAP1 cell line knockout for BCL7B, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL7B_r2_4278_8

description:
RNA-seq in HAP1 cell line knockout for BCL7B, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL7A_r3_2434_10

description:
RNA-seq in HAP1 cell line knockout for BCL7A, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL7A_r2_2434_10

description:
RNA-seq in HAP1 cell line knockout for BCL7A, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL11B_r3_2432_10

description:
RNA-seq in HAP1 cell line knockout for BCL11B, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL11B_r1_2432_10

description:
RNA-seq in HAP1 cell line knockout for BCL11B, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL11A_r3_2426_10

description:
RNA-seq in HAP1 cell line knockout for BCL11A, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL11B_r2_2432_10

description:
RNA-seq in HAP1 cell line knockout for BCL11B, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: 4C-seq_Enhancer1_F1-control_Rep2

city: Nijmegen

first: Hendrik

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

data_processing:
Library strategy: 4C-seq
4C-seq experiments were performed as described previously65 with minor modifications. Briefly, 10 million cells were cross-linked for 10 minutes with 2% paraformaldehyde in ES-culture medium, quenched with glycine and lysed in 30 ml lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP-40, 1X protease inhibitors) for 30 minutes at 4 ̊ C . Nuclei were then incubated with 0.25% SDS for 30min in NEB buffer3 followed Triton X-100 treatment for 30 min both at 37 ̊ C. Nuclei were then digested with 700U DpnII enzyme (NEB) over night at 37 ̊C. Enzyme was inactivated at 65 ̊C for 15 min followed by  ‘in nuclei’ ligation at 16 ̊C with 2000U T4 ligase (NEB)66. Samples were then treated with protease K and RNAse A and DNA was purified by phenol–chloroform (Sigma: 77618-500ml). DNA was further digested with 50U BfaI enzyme, purified with QIAquick PCR Purification columns followed by second ligation at 16 ̊ C. 1000ng of 4C-seq library was amplified with bait-specific inverse primers using Expand Long template PCR sytem (Roche 11759060001) for 28 PCR cycles (Table S1). PCR products were then purified and 50ng DNA was used for library preparation using KAPA Hyperprep kit (Roche 07962363001) and 5 PCR cycles. Libraries were sequenced on the Illumina NextSeq500 to obtain paired-end sequenced of 50bp-long reads
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks

source_name: Mouse Embryonic Stem Cells

growth_protocol: E14Tg2a or F1-hybride ESCs were cultured in standard culture medium on gelatin coated-dishes without feeder cells. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal calf serum, L-glutamine (2 nM), Na-Pyruvate (1 mM), non-essential amino acids (0.1 mM each), Penicillin Streptomycin, 2-mercaptoethanol (55 µM) and LIF (1000 U/ml, Milipore). For serum free culture, cells were maintained in NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore). For EpiLSC-differentiation, 2i-ESCs were seeded in ~15,000 cells per cm2 density on Fibronectin (10 μg/ml) coated dishes and in NDiff 227 (StemCells, Inc.) supplemented with Penicillin Streptomycin (Gibco), 20 ng/ml ActivinA (R&D systems), 12 ng/ml bFGF (R&D systems) and 1% knock out serum replacement (Gibco) and cells were maintained for 72h in this culture.

extract_protocol:
Briefly, 10 million cells were cross-linked for 10 minutes with 2% paraformaldehyde in ES-culture medium, quenched with glycine and lysed in 30 ml lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP-40, 1X protease inhibitors) for 30 minutes at 4°C  . Nuclei were then incubated with 0.25% SDS for 30 minutes in NEB buffer3 followed by Triton X-100 treatment for 30 minutes both at 37°C. Nuclei were then digested with 700 units DpnII enzyme (NEB) overnight at 37 ̊C. Enzyme was inactivated at 65 ̊C for 15 min followed by  ‘in nuclei’ ligation at 16 ̊C with 2,000 units T4 ligase (NEB)66. Samples were then treated with protease K and RNAseA and DNA was purified by phenol–chloroform (Sigma: 77618-500ml). DNA was further digested with 50 units BfaI, purified with QIAquick PCR purification columns followed by second ligation at 16°C. Next, 1000 ng of 4C-seq library was amplified with bait-specific inverse primers using Expand Long template PCR sytem (Roche 11759060001) for 28 PCR cycles.
PCR products were then purified and 50 ng DNA was used for library preparation using KAPA Hyperprep kit (Roche 07962363001) and 5 PCR cycles.  Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and were size selected using bead purification protocol (200bp-1500bp).  Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina Nextseq500  machines and generated 50bp pair end reads.

tag: background strain

tag: cell type

value: Mouse Embryonic Stem Cells

tag: chip antibody


title: 4C-seq_Enhancer1_F1-control_Rep1


title: 4C-seq_Enhancer1_CRISPR-clone_Rep2


title: RNA-seq_HAP1_ARID2_r1_907_9

description:
RNA-seq in HAP1 cell line knockout for ARID2, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv

tag: cell line


title: 4C-seq_Myc_serum_Rep4

value: serum

value: Myc


title: RNA-seq_HAP1_BRD7_r3_923_10

description:
RNA-seq in HAP1 cell line knockout for BRD7, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_ARID2_r2_907_9

description:
RNA-seq in HAP1 cell line knockout for ARID2, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL11A_r1_2426_10

description:
RNA-seq in HAP1 cell line knockout for BCL11A, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_ARID1B_r3_582_7

description:
RNA-seq in HAP1 cell line knockout for ARID1B, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: 4C-seq_Myc_serum_Rep3


title: RNA-seq_HAP1_ARID1B_r2_582_7

description:
RNA-seq in HAP1 cell line knockout for ARID1B, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: 4C-seq_Myc_serum_Rep2


title: 4C-seq_Myc_serum_Rep1


title: RNA-seq_HAP1_BCL7A_r1_2434_10

description:
RNA-seq in HAP1 cell line knockout for BCL7A, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: 4C-seq_Myc_2i_Rep4


title: 4C-seq_Myc_2i_Rep3


title: 4C-seq_Myc_2i_Rep2


title: RNA-seq_HAP1_ARID1B_r1_582_7

description:
RNA-seq in HAP1 cell line knockout for ARID1B, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: 4C-seq_Myc_2i_Rep1


title: RNA-seq_HAP1_ARID1A_r2_618_3

description:
RNA-seq in HAP1 cell line knockout for ARID1A, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_BCL11A_r2_2426_10

description:
RNA-seq in HAP1 cell line knockout for BCL11A, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_ARID1A_r2_618_10


title: RNA-seq_HAP1_ARID2_r3_907_9

description:
RNA-seq in HAP1 cell line knockout for ARID2, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_ARID1A_r3_618_10

description:
RNA-seq in HAP1 cell line knockout for ARID1A, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv


title: 4C-seq_Enhancer1_CRISPR-clone_Rep1


title: RNA-seq_HAP1_ARID1A_r1_618_3

description:
RNA-seq in HAP1 cell line knockout for ARID1A, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: RNA-seq_HAP1_ACTB_r3_2471_10

description:
RNA-seq in HAP1 cell line knockout for ACTB, replicate 3
baf_complex.rnaseq.expression_counts.gene_level.csv

value: ACTB


title: Yy1-ChIP-serum-Rep2

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 and reads with mapping quality less than 15 were discarded. PCR duplicates were removed from mapped BAM files and in case of pair-end sequencing, paired fragments were kept only when both reads were mapped uniquely to the same genomic region (unique and concordant alignments). Fragment size modeling was then applied on filtered BAM files (http://code.google.com/p/phantompeakqual-tools/) and peaks were called using MACS2  (http://github.com/taoliu/MACS/) and with default (narrow) settings.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth.

growth_protocol: E14Tg2a or F1 ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were transfered from serum-medium to   NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore) for 72h or maintained for long term (>4 weeks) in 2i medium (2i_LT)

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) in ES-medium. Fixed cells were sonicated using a Diagenode Bioruptor UCD-300 for 4x1 minutes (30 seconds on; 30 seconds off). 50µl of chromatin (500,000 cells) were used with 0.5-1µg of H3K27ac antibody (Diagenode) and incubated overnight at 4ºC with rotation. For TF-ChiP-seq, 15-million cells were used per ChIP together with 15 μg anti-GFP antibody (ab290, Abcam) and 3 ChIP-samples were pooled to yield chromatin equal to 30-million cells per transcription factor. Antibody-chromatin complexes were incubated with protein-A/G magnetic beads, eluted, Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C. Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB. De-crosslinked DNA was used for library construction using KAPA Hifi kit according to manufacturer’s instruction.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina NextSeq 500 machines and generated 42 bp pair end reads.

value: YY1 (Active Motif, 61779)


title: Yy1-ChIP-2i-Rep1


title: Yy1-ChIP-serum-Rep1


title: Yy1-ChIP-EpiLSCs-Rep2

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium on gelatin coated-dishes without feeder cells. For serum culture, Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal calf serum, L-glutamine (2 nM), Na-Pyruvate (1 mM), non-essential amino acids (0.1 mM each), Penicillin Streptomycin, 2-mercaptoethanol (55 µM) and LIF (1000 U/ml, Milipore) was used. For serum free culture, cells were transferred from serum-medium to NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore) or maintained for long term (>4 weeks) in 2i medium (2i_LT). For EpiLSC-differentiation, 2i-ESCs were seeded at ~15,000 cells per cm2 on Fibronectin (10 μg/ml) coated dishes and in NDiff 227 (StemCells, Inc.) supplemented with Penicillin Streptomycin (Gibco), 20 ng/ml Activin-A (R&D systems), 12 ng/ml bFGF (R&D systems) and 1% knock-out serum replacement (Gibco), and cells were maintained for 72h in this culture.

value: EpiLSCs


title: Yy1-ChIP-2i-Rep2


title: RNA-seq_HAP1_ACTB_r2_2471_10

description:
RNA-seq in HAP1 cell line knockout for ACTB, replicate 2
baf_complex.rnaseq.expression_counts.gene_level.csv


title: Yy1-ChIP-EpiLSCs-Rep1


title: Smc1-ChIP-serum-Rep2

value: SMC1 (Bethyl, A300-055A)


title: ChIP-seq_HAP1_WT_SMARCA4_r2

description:
ChIP-seq for SMARCA4 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Library quality was assessed with the phantomPeakQualtools scripts (Landt SG, Genome Research 2012).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair
Supplementary_files_format_and_content: csv file contains read counts for each sample in each regulatory element

extract_protocol:
ChIPmentation was carried out as described (Schmidl et al, Nature Methods 2015). Cells were washed once with PBS and fixed with 1% paraformaldehyde in up to 1ml PBS for 10 min at room temperature. Glycine was added to stop the reaction. Cells were collected at 500 g for 10min at 4 C, washed twice with cold PBS supplemented with 1 mM phenylmethyl sulfonyl fluoride (PMSF). The pellet was lysed in sonication buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 0.25% SDS, 1uL protease inhibitors (Sigma) and 1 mM PMSF) and sonicated with a Covaris S220 sonicator to a range of 200-700 bp. Lysates were centrifuged at full speed for 5min at 4 C, and the supernatant transferred to a new tube. The lysate was then brought to RIPA buffer conditions (final concentration: 10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1uL protease inhibitors (Sigma) and 1 mMPMSF) to a volume of 200 ml per IP. For each immunoprecipitation, 10 ml magnetic Protein A (Life Technologies) were washed twice and resuspended in PBS supplemented with 0.1% BSA. The antibody was added and bound to the beads by rotating 2 h at 4 C. Used antibodies were H3K4me1 (0.5 mg per IP, Diagenode pAb-194-050), H3K27ac (1 mg per IP, Diagenode pAB-196-050) and H3K27me3 (1 mg per IP, Millipore 07-499). For control libraries, an IP with 2.5 mg of a nonspecific IgG rabbit antibody was used. Blocked antibody-conjugated beads were then placed on a magnet, supernatant was removed and the sonicated lysate was added to the beads followed by incubation for 3-4 h at 4 C on a rotator. Beads were washed subsequently with RIPA (twice), RIPA-500 (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS and 0.1% DOC) (twice) and RIPA-LiCl (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 250mM LiCl, 1% Triton X-100, 0.5% DOC and 0.5% NP40) (twice). Beads were washed once with cold Tris-Cl pH 8.0, to remove detergent, salts and EDTA. Beads were washed once more with cold Tris-Cl pH 8.0.
DNA was purified with SPRI AMPure XP beads (sample-to-beads ratio 1:2) or Qiagen MinElute columns. One microlitre of each library was amplified in a 10-ml qPCR reaction containing 0.15 mM primers, 1uL SYBR Green and 5 ml Kapa HiFi HotStart ReadyMix (Kapa Biosystems), to estimate the optimum number of enrichment cycles with the following programme: 72 oC for 5min, 98 oC for 30 s, 24 cycles of 98 oC for 10 s, 63 oC for 30 s and 72 oC for 30 s, and a final elongation at 72 oC for 1min. Kapa HiFi HotStart ReadyMix was incubated at 98 oC for 45 s before preparation of all PCR reactions (qPCR and final enrichment PCR). Final enrichment of the libraries was performed in a 50-ml reaction using 0.75 mM primers and 25 ml Kapa HiFi HotStart ReadyMix. Libraries were amplified for N+1 cycles, where N is equal to the rounded-up Cq value determined in the qPCR reaction. Enriched libraries were purified using SPRI AMPure XP beads at a beads-to-sample ratio of 1:1, followed by a size selection using AMPure XP beads to recover libraries with a fragment length of 200-400 bp. Library preparation was performed using custom Nextera primers as described for ATAC-seq. The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform and the 50-bp single-end configuration.

value: ChIP-seq

tag: ip


title: Control diet fed 20_19E

description:
Control diet fed
Gene expression from uetrine natural killer cells at GD10.13

tag: tissue

value: utero-placental tissue

value: Control


title: ChIP-seq_HAP1_WT_SMARCA4_r1

description:
ChIP-seq for SMARCA4 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: Smc1-ChIP-EpiLSCs-Rep2


title: RNA-seq_HAP1_ARID1A_r3_618_3


title: ChIP-seq_HAP1_WT_SMARCA2_r1

description:
ChIP-seq for SMARCA2 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_WT_PBRM1_r1

description:
ChIP-seq for PBRM1 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_WT_PolII_r1

description:
ChIP-seq for PolII on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv

value: PolII


title: Smc1-ChIP-2i-Rep2


title: Smc1-ChIP-EpiLSCs-Rep1


title: ChIP-seq_HAP1_WT_Input_8x_r1

description:
ChIP-seq for Input_8x on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv

value: Input


title: RNA-seq_HAP1_ARID1A_r1_618_10


title: ChIP-seq_HAP1_WT_Input_25_r2

description:
ChIP-seq for Input_25 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: RNA-seq_HAP1_ACTB_r1_2471_10

description:
RNA-seq in HAP1 cell line knockout for ACTB, replicate 1
baf_complex.rnaseq.expression_counts.gene_level.csv


title: ChIP-seq_HAP1_WT_Input_20_r1

description:
ChIP-seq for Input_20 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: Smc1-ChIP-2i-Rep1


title: CTCF-ChIP-serum-Rep2

value: CTCF (Millipore, 07-729)


title: CTCF-ChIP-serum-Rep1


title: ChIP-seq_HAP1_WT_IgG_r2

description:
ChIP-seq for IgG on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv

value: IgG


title: ChIP-seq_HAP1_WT_Input_1x_r1

description:
ChIP-seq for Input_1x on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: CTCF-ChIP-EpiLSCs-Rep1


title: ChIP-seq_HAP1_WT_H3K27ac_r1

description:
ChIP-seq for H3K27ac on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: CTCF-ChIP-2i-Rep1


title: CTCF-ChIP-EpiLSCs-Rep2


title: ChIP-seq_HAP1_WT_IgG_r1

description:
ChIP-seq for IgG on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: Smc1-ChIP-serum-Rep1


title: H3K27ac_Esrrb-cre-Tx-2iLT-Rep2

growth_protocol:
E14Tg2a or F1 ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were transfered from serum-medium to   NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore) for 72h or maintained for long term (>4 weeks) in 2i medium (2i_LT).
For CRE-recombination, cells were treated with 4-hydroxy tamoxifen (0.5 μM) for 2 days.

value: H3K27ac (Diagenode C15410196 )


title: ChIP-seq_HAP1_WT_ARID2_PA5_r2

description:
ChIP-seq for ARID2_PA5 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_WT_BRD4_r1

description:
ChIP-seq for BRD4 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_WT_ARID2_NB_r1

description:
ChIP-seq for ARID2_NB on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIP-seq_HAP1_WT_ARID1B_r1

description:
ChIP-seq for ARID1B on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: H3K27ac_Esrrb-cre-NoTx-2iLT-Rep2


title: H3K27ac_Esrrb-cre-Tx-2iLT-Rep1


title: H3K27ac_Esrrb-cre-NoTx-2iLT-Rep1


title: ChIPmentation_HAP1_WT_IgG_921-7_r2

description:
ChIPmentation for IgG on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv

value: ChIPmentation


title: ChIP-seq_HAP1_WT_ARID1A_r1

description:
ChIP-seq for ARID1A on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: H3K27ac_Esrrb-cre-NoTx-serum-Rep2


title: H3K27ac_Esrrb-cre-Tx-serum-Rep1


title: H3K27ac_Esrrb-cre-Tx-serum-Rep2


title: ChIPmentation_HAP1_WT_IgG_921-7_r1

description:
ChIPmentation for IgG on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: H3K27ac_Esrrb-cre-NoTx-serum-Rep1


title: ChIPmentation_HAP1_WT_IgG_1102-3_r1


title: ChIPmentation_HAP1_WT_H3K9me3_921-7_r2

description:
ChIPmentation for H3K9me3 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: CTCF-ChIP-2i-Rep2


title: ChIPmentation_HAP1_WT_H3K9me3_921-7_r1

description:
ChIPmentation for H3K9me3 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIPmentation_HAP1_WT_H3K9me3_1102-3_r1


title: 4C-seq_Spry4_ser_2

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium on gelatin coated-dishes without feeder cells. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal calf serum, L-glutamine (2 nM), Na-Pyruvate (1 mM), non-essential amino acids (0.1 mM each), Penicillin Streptomycin, 2-mercaptoethanol (55 µM) and LIF (1000 U/ml, Milipore). For serum free culture, cells were maintained in NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore). For EpiLSC-differentiation, 2i-ESCs were seeded in ~15,000 cells per cm2 density on Fibronectin (10 μg/ml) coated dishes and in NDiff 227 (StemCells, Inc.) supplemented with Penicillin Streptomycin (Gibco), 20 ng/ml ActivinA (R&D systems), 12 ng/ml bFGF (R&D systems) and 1% knock out serum replacement (Gibco) and cells were maintained for 72h in this culture.


title: 4C-seq_Spry4_ser_4


title: ChIPmentation_HAP1_WT_H3K4me3_921-7_r2

description:
ChIPmentation for H3K4me3 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spry4_ser_1


title: 4C-seq_Spry4_Epi_2

value: EpiLSC


title: ChIPmentation_HAP1_WT_H3K4me3_1102-3_r1

description:
ChIPmentation for H3K4me3 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spry4_Epi_4

value: Mouse Embryonic Stem Cells


title: ChIP-seq_HAP1_WT_ARID1A_r2

description:
ChIP-seq for ARID1A on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spry4_Epi_3


title: ChIPmentation_HAP1_WT_H3K4me1_921-7_r1

description:
ChIPmentation for H3K4me1 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIPmentation_HAP1_WT_H3K4me3_921-7_r1


title: ChIPmentation_HAP1_WT_H3K4me1_1102-3_r2

description:
ChIPmentation for H3K4me1 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spry4_2i_4


title: ChIPmentation_HAP1_WT_H3K27me3_921-7_r2

description:
ChIPmentation for H3K27me3 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spry4_2i_2


title: 4C-seq_Spry4_ser_3

value: serum


title: ChIPmentation_HAP1_WT_H3K36me3_921-7_r1

description:
ChIPmentation for H3K36me3 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spic_ser_3


title: ChIPmentation_HAP1_WT_H3K36me3_921-7_r2

description:
ChIPmentation for H3K36me3 on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spry4_2i_1


title: 4C-seq_Spic_ser_4


title: ChIPmentation_HAP1_WT_H3K36me3_1102-3_r1


title: ChIPmentation_HAP1_WT_H3K27me3_1102-3_r1

description:
ChIPmentation for H3K27me3 on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spic_ser_2


title: ChIPmentation_HAP1_WT_H3K27ac_1102-3_r3

description:
ChIPmentation for H3K27ac on HAP1 cell line, replicate 3
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIPmentation_HAP1_WT_H3K27ac_921-7_r2

description:
ChIPmentation for H3K27ac on HAP1 cell line, replicate 2
baf_complex.chipseq_peaks.raw_coverage.csv


title: ChIPmentation_HAP1_WT_H3K27ac_1102-3_r2


title: ChIPmentation_HAP1_WT_H3K4me1_921-7_r2


title: 4C-seq_Spry4_Epi_1


title: ChIPmentation_HAP1_WT_H3K27ac_1102-3_r1_t6

description:
ChIPmentation for H3K27ac on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv


title: 4C-seq_Spic_Epi_3


title: 4C-seq_Spic_Epi_4


title: ChIPmentation_HAP1_WT_H3K27ac_1102-3_r1_t2


title: 4C-seq_Spic_Epi_2


title: 4C-seq_Spic_Epi_1


title: ATAC-seq_HAP1_WT_r2_C631

description:
ATAC-seq  on HAP1 cell line, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: Each csv file contains read counts for each sample for each regulatory element

extract_protocol: 50000 cells were resuspended in 25 µl transposase reaction mix (0.05% digitonin, 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880).

value: ATAC-seq

value: WT


title: ChIPmentation_HAP1_WT_CTCF_921-7_r1

description:
ChIPmentation for CTCF on HAP1 cell line, replicate 1
baf_complex.chipseq_peaks.raw_coverage.csv

value: CTCF


title: 4C-seq_Spry4_2i_3


title: 4C-seq_Spic_2i_3


title: 4C-seq_Spic_2i_2


title: ATAC-seq_HAP1_WT_r1_C631

description:
ATAC-seq  on HAP1 cell line, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Spic_ser_1


title: 4C-seq_Spic_2i_1


title: ATAC-seq_HAP1_SMARCD3_r1_2480_12

description:
ATAC-seq  on HAP1 cell line with SMARCD3 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Prdm14_ser_4


title: ATAC-seq_HAP1_SMARCD2_r2_2782_10

description:
ATAC-seq  on HAP1 cell line with SMARCD2 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCD2_r1_2782_10

description:
ATAC-seq  on HAP1 cell line with SMARCD2 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCD1_r2_2478_6

description:
ATAC-seq  on HAP1 cell line with SMARCD1 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Prdm14_ser_1


title: 4C-seq_Prdm14_Epi_4


title: ATAC-seq_HAP1_SMARCD3_r2_2480_12

description:
ATAC-seq  on HAP1 cell line with SMARCD3 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCC1_r2_2476_12

description:
ATAC-seq  on HAP1 cell line with SMARCC1 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCD1_r1_2478_6

description:
ATAC-seq  on HAP1 cell line with SMARCD1 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Spic_2i_4


title: 4C-seq_Prdm14_Epi_3


title: 4C-seq_Prdm14_ser_3


title: 4C-seq_Prdm14_Epi_2


title: 4C-seq_Prdm14_Epi_1


title: ATAC-seq_HAP1_SMARCA4_r2_2878_4

description:
ATAC-seq  on HAP1 cell line with SMARCA4 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Prdm14_2i_4


title: ChIPmentation_HAP1_WT_H3K27ac_1102-3_r1_t3


title: 4C-seq_Prdm14_2i_2


title: ATAC-seq_HAP1_SMARCA4_r1_2878_4

description:
ATAC-seq  on HAP1 cell line with SMARCA4 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Prdm14_ser_2


title: ATAC-seq_HAP1_SMARCA2_r2_4055_12

description:
ATAC-seq  on HAP1 cell line with SMARCA2 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Klf4_ser_4


title: ATAC-seq_HAP1_PHF10_r2_2778_11

description:
ATAC-seq  on HAP1 cell line with PHF10 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCA2_r1_4055_12

description:
ATAC-seq  on HAP1 cell line with SMARCA2 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Klf4_ser_2


title: 4C-seq_Klf4_ser_1


title: 4C-seq_Klf4_Epi_4


title: 4C-seq_Klf4_ser_3


title: ATAC-seq_HAP1_PHF10_r1_2778_11

description:
ATAC-seq  on HAP1 cell line with PHF10 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_PBRM1_r1_1135_10

description:
ATAC-seq  on HAP1 cell line with PBRM1 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Klf4_Epi_3


title: 4C-seq_Klf4_Epi_2


title: ATAC-seq_HAP1_DPF2_r2_2777_4

description:
ATAC-seq  on HAP1 cell line with DPF2 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_DPF3_r2_2776_1

description:
ATAC-seq  on HAP1 cell line with DPF3 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCA4_r2_2878_6


title: 4C-seq_Klf4_Epi_1


title: ATAC-seq_HAP1_DPF3_r1_2776_1

description:
ATAC-seq  on HAP1 cell line with DPF3 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Klf4_2i_4


title: ATAC-seq_HAP1_SMARCA4_r1_2878_6


title: ATAC-seq_HAP1_DPF1_r2_2779_11

description:
ATAC-seq  on HAP1 cell line with DPF1 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Prdm14_2i_1


title: ATAC-seq_HAP1_DPF1_r1_2779_11

description:
ATAC-seq  on HAP1 cell line with DPF1 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_SMARCC1_r1_2476_12

description:
ATAC-seq  on HAP1 cell line with SMARCC1 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Klf4_2i_2


title: 4C-seq_Klf4_2i_3


title: 4C-seq_Prdm14_2i_3


title: ATAC-seq_HAP1_BRD9_r2_934_10

description:
ATAC-seq  on HAP1 cell line with BRD9 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Klf4_2i_1


title: ATAC-seq_HAP1_PBRM1_r2_1135_10

description:
ATAC-seq  on HAP1 cell line with PBRM1 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_BRD9_r1_934_10

description:
ATAC-seq  on HAP1 cell line with BRD9 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Fgf5_ser_4


title: ATAC-seq_HAP1_DPF2_r1_2777_4

description:
ATAC-seq  on HAP1 cell line with DPF2 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_BRD7_r2_923_10

description:
ATAC-seq  on HAP1 cell line with BRD7 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Fgf5_ser_1


title: 4C-seq_Fgf5_Epi_4


title: ATAC-seq_HAP1_BCL7B_r2_4278_8

description:
ATAC-seq  on HAP1 cell line with BCL7B knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_BCL7B_r1_4278_8

description:
ATAC-seq  on HAP1 cell line with BCL7B knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Fgf5_ser_3