title: 4sU-RNA - 2-3 hpi Rep 1

value: human foreskin fibroblasts

value: 60 min 500 uM 4sU at 2-3 h p.i.


title: RBG18356_Plate5_D2_Gata3_sg2

status: Public on Oct 26 2020

type: SRA

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
TFnet_exon_counts.csv
TFnet_intron_counts.csv

library_source: transcriptomic

data_processing:
sequencing reads alignment with STAR (default settings)
Counting of reads to exons or introns, summarised per gene - featureCounts. Ensembl v93 genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: csv files with either total number of reads mapping to exonic or intronic regions, summed per gene.

molecule: polyA RNA

organism: Mus musculus

source_name: Hoxb8-FL cell line

growth_protocol: Hoxb8-FL cells were grown in: DMEM with 10% FCS, 5% Flt3L-conditioned medium, 50 uM 2-Mercaptoethanol, 1% Penicillin + Streptomycin, 1% Glutamine solution, 1 uM β-Estradiol, unless otherwise indicated

extract_protocol:
375 BFP+/7AAD (live) cells were sorted using flow cytometry into Smart-Seq2 lysis plates.
small-scale bulk RNA-Seq was performed using a modified version of Smart-Seq2 (Picelli et al. Nature Protocols 2014). Please see the accompanying publication for a detailed protocol.

treatment_protocol: Cells were transduced with constructs carrying sgRNAs expression cassetes (Perturb-Seq GBC library backbone) targeting indicated genes.

tag: tissue

value: bone marrow

tag: cell type

value: early hematopoietic progenitor cells

tag: genotype

value: Cas9 expressing, Hoxb8 expressing

tag: treatment

value: Treated with Gata3_sg2

tag: day

tag: antibody


title: 4sU-RNA - 0-1 hpi Rep 1

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
newly transcribed RNA (4sU-RNA)
Purified from total RNA using 4sU-tagging

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: gene read counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 13 were infected at 60% confluency 24h after the last split.

extract_protocol:
Total RNA was prepared using Trizol. Newly transcribed RNA was purified as described in Rädle et al., JoVE 2013.
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (only for total RNA). No rRNA depletion was performed for the 4sU-RNA samples!

treatment_protocol: Cells were infected for 15 min with HSV-1 strain 17 at an MOI of 10 followed by PBS wash and media replacement. 500µM 4-thiouridine was added to the cell culture at the indicated time points.

tag: time post infection

value: 60 min 500 uM 4sU at 0-1 h p.i.

tag: infection with

value: vhs-null mutant of herpes simplex virus 1, strain 17


title: 4sU-RNA - mock Rep 1

value: 60 min 500 uM 4sU prior to infection

value: mock


title: 4sU-RNA - 1-2 hpi Rep 1

value: 60 min 500 uM 4sU at 1-2 h p.i.


title: RBG18357_Plate5_E2_Gata3_sg2


title: Total RNA - 8hpi Rep 1

description:
total RNA
Total RNA prepared using Trizol

source_name: Total RNA

value: 8 h p.i.


title: RBG18354_Plate5_B2_Gata3_sg2


title: RBG18355_Plate5_C2_Gata3_sg2


title: RBG18353_Plate5_A2_Gata3_sg2


title: RBG18352_Plate5_H1_Gata3_sg1

value: Treated with Gata3_sg1


title: Total RNA - 2hpi Rep 1

value: 2 h p.i.


title: Total RNA - 6hpi Rep 1

value: 6 h p.i.


title: Total RNA - 4hpi Rep 1

value: 4 h p.i.


title: RBG18351_Plate5_G1_Gata3_sg1


title: Total RNA - mock Rep 1


title: dVhs_Cr_2: Chromatin-associated RNA, delta-Vhs, 8h p.i., Rep 2

description: Chromatin-associated RNA isolated from delta-Vhs infected HFF at 8h p.i.

source_name: Chromatin-associated RNA

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 15 were infected with HSV-1 strain 17 or its vhs-null mutant at an MOI of 10

extract_protocol:
Subcellular RNA fractions were prepared combinig the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013)
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina)  with Ribo-Zero Human/Mouse/Rat (only for total RNA).

treatment_protocol: Cells were infected for 15 min using an MOI of 10. 15 min after infection (time point 0h), cell culture media was replaced with fresh media. Cells were harvested prior to or at 8h p.i. Subcellular RNA fractions were prepared and subjected to standard RNA-seq including rRNA deplation

value: delta-Vhs 8h p.i.

tag: replicate

value: Repicate 2

tag: molecule subtype

value: Subcellular RNA fraction


title: RBG18349_Plate5_E1_Gata3_sg1

value: bone marrow


title: pNorB2

city: Madison

first: Caitilyn

last: Allen

state: WI

address: Russell Labs 1630 Linden Drive

department: Plant Pathology

country: USA

institute: University of Wisconsin-Madison

data_processing:
Illumina CASAVA v1.8 used for basecalling
Reads were filtered for quality, removing reads with adaptor contamination, greater than 10% uncertain nucleotides, or more than 50% of nucleotides with a Qpred less than or equal to 5. Over 95% of reads were of good quality, and were mapped to the R. solanacearum GMI1000 genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000009125.1) using Bowtie2 -2.2.3
Gene expression was calculated using HTseq v0.6.1
Differential gene expression was calculated using DESeq 1.18.0. P-values calculated by DESeq were adjusted to control for the false discovery rate (FDR) using the Benjamini-Hochberg approach
Genome_build: GCA_000009125.1
Supplementary_files_format_and_content: .txt file including raw readcounts for each sample

organism: Ralstonia solanacearum

source_name: ∆norB bacteria in tomato stem tissue

growth_protocol: Phenol-Chloroform: 21 day old Bonny Best tomatoes were inoculated with ~2000 CFU of each bacteria strain through the cut petiole of the first true leaf. Plants were grown at 28˚C with a 12 hr photoperiod. Seedlings were transplanted after 14 days. After transplanting, plants were watered on alternate days with 1/2 strength Hoagland solution.

extract_protocol:
Phenol-Chloroform: At 3 dpi, approximately 0.1 g of stem tissue was collected from the site of inoculation, immediately frozen in liquid nitrogen, and stored at -80˚C. Another ~0.1 g of tissue was collected from directly below the inoculation site and was ground in bead beater tubes using a PowerLyzer (Qiagen, Hilden, Germany) for two cycles of 2200 rpm for 90 s in each with a 4 min rest between cycles. This material was then dilution plated to measure bacterial colonization. From each biological replicate, we chose six plants with the most similar level of colonization. RNA was extracted from these using a modified hot phenol-chloroform method (DOI: 10.1128/mBio.00114-12). Between 4 and 5 individual plants were pooled per biological replicate. Nucleic acid sample quality was checked using a nanodrop, Agilent bioanalyzer, and qRT-PCR primers Actin_F/R. All samples had RIN values of above 7.2.
NEBNext® µLtraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswitch, MA, USA) following the manufacturer’s recommendation and starting with 3 mg of RNA per sample

tag: strain

value: {delta}norB

tag: growth protocol

value: Bacteria in tomato stem tissue

tag: tomato variety

value: Bonny Best

value: Untreated

tag: age

value: 3 dpi

tag: extraction method

value: Phenol-Chloroform


title: pNorB1


title: pNorB3


title: RBG18348_Plate5_D1_Gata3_sg1

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing


title: dVhs_Cy_2: Cytoplasmic RNA, delta-Vhs, 8h p.i., Rep 2

description: Cytoplasmic RNA isolated from delta-Vhs infected HFF at 8h p.i.

source_name: Cytoplasmic RNA

value: human foreskin fibroblasts


title: pNarG2

source_name: ∆narG bacteria in tomato stem tissue

value: {delta}narG


title: pNarG1


title: pNarG3


title: pWT2

source_name: WT bacteria in tomato stem tissue

value: WT


title: pWT3


title: dVhs_To_2: Total RNA, delta-Vhs, 8h p.i., Rep 2

description: Total RNA isolated from delta-Vhs infected HFF at 8h p.i.


title: pWT1


title: norB3

source_name: ∆norB bacterial culture, 0.1% oxygen

growth_protocol: Column: 50 mL of modified Van den Mooter medium (DOI: 10.1128/mBio.02471-14) with 30 mM potassium nitrate was inoculated with R. solanacearum to an initial concentration of 10^7 CFU/mL. (OD600=0.01). The cultures were then incubated without shaking at 28˚C in 0.1% oxygen for 12 hours.

extract_protocol:
Column: After 16h total incubation, sub-samples were collected for dilution plating to determine CFU/ml and the tubes were capped and centrifuged at room temperature for 5 min at 8000 rpm. The supernatant was removed and pellets were frozen in liquid nitrogen. RNA extractions were carried out using a modified version of the Quick-RNATM MiniPrep kit (Zymo Research, Irvine, CA, USA), as follows. Pellets were resuspended in 400 µL of ice cold TE pH 8 with 1 mg/mL lysozyme, 0.25 µL Superase Inhibitor (Ambion, Austin, TX, USA), and 80 µL of 10% SDS, vortexed for 10s, transferred to a new 2 mL tube, and shaken at ~300 rpm for 2 min. 800 µL of RNA-Lysis lysis buffer was added, the tubes were vortexed again for 10 s, cleaned according to the kit manufacturer’s instructions, and eluted in 100 µL of water. Nucleic acid concentrations were estimated using a nanodrop, normalized to 200 ng/uL, and cleaned using the DNA-free DNAse kit (Invitrogen, Carlsbad, CA, USA). Samples were incubated at 37C for 1 hour, with 2 µL more of DNAse added at 30 min. After DNAse inactivation, samples were further cleaned by chloroform extraction, then precipitated overnight at -20˚C with 100 𝜇M Sodium Acetate pH 5.5 and 66 % ethanol. Samples were checked for concentration on a Nanodrop, for DNA contamination by PCR using the qRT-PCR primers serC_F/R, and for RNA integrity (RIN) using an Agilent Bioanalyzer 21000 (Agilent, Santa Clara, CA, USA). All samples had RIN values above 7.3.
NEBNext® µLtraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswitch, MA, USA) following the manufacturer’s recommendation and starting with 3 mg of RNA per sample

treatment_protocol: Column: At 12 hpi, CysNO or hydrogen peroxide were added to final concentrations of 1 mM or 100 uM, respectively, as required.

value: Bacterial culture, 0.1% oxygen

value: 16 hpi

value: Column


title: dVhs_Cr_1: Chromatin-associated RNA, delta-Vhs, 8h p.i., Rep 1

value: delta-Vhs 8h p.i.

value: Repicate 1


title: RBG18346_Plate5_B1_Gata3_sg1

value: bone marrow

value: Treated with Gata3_sg1


title: norB2

value: {delta}norB


title: dVhs_Nu_1: Nucleoplasmic RNA, delta-Vhs, 8h p.i., Rep 1

description: Nucleoplasmic RNA isolated from delta-Vhs infected HFF at 8h p.i.

source_name: Nucleoplasmic RNA

value: Subcellular RNA fraction


title: RBG17273_Exp1_TC_C10_Gata3sg2_12d

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
exp1_exon_counts.csv
exp1_intron_counts.csv

extract_protocol:
75 BFP+/7AAD (live) cells were sorted using flow cytometry into Smart-Seq2 lysis plates.
small-scale bulk RNA-Seq was performed using a modified version of Smart-Seq2 (Picelli et al. Nature Protocols 2014). Please see the accompanying publication for a detailed protocol.

value: Treated with Gata3_sg2


title: RBG18350_Plate5_F1_Gata3_sg1


title: narG3

source_name: ∆narG bacterial culture, 0.1% oxygen

value: Untreated


title: dVhs_Nu_2: Nucleoplasmic RNA, delta-Vhs, 8h p.i., Rep 2

value: Repicate 2


title: narG2


title: RBG17272_Exp1_TC_B10_Gata3sg2_12d

value: early hematopoietic progenitor cells


title: narG1


title: RBG18347_Plate5_C1_Gata3_sg1

value: Cas9 expressing, Hoxb8 expressing


title: dVhs_To_1: Total RNA, delta-Vhs, 8h p.i., Rep 1

value: human foreskin fibroblasts


title: RBG17271_Exp1_TC_A10_Gata3sg2_12d


title: H2O22

source_name: WT bacterial culture, 0.1% oxygen

value: 100 uM hydrogen peroxide


title: RBG18345_Plate5_A1_Gata3_sg1


title: RBG17270_Exp1_TC_H9_control_12d

value: Treated with control vector


title: CysNO2

value: WT

value: Bacterial culture, 0.1% oxygen

value: 1 mM CysNO


title: H2O23

value: 16 hpi

value: Column


title: RBG17269_Exp1_TC_G9_control_12d

value: bone marrow


title: H2O21


title: CysNO3


title: WT_Cr_2: Chromatin-associated RNA, HSV-1 8h p.i., Rep 2

description: Chromatin-associated RNA isolated from HSV-1 infected HFF at 8h p.i.

value: HSV-1 8h p.i.

value: Replicate 2


title: WT_Nu_2: Nucleoplasmic RNA, HSV-1 8h p.i., Rep 2

description: Nucleoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.

value: Subcellular RNA fraction


title: norB1

value: {delta}norB


title: GMI2

value: Untreated


title: RBG17268_Exp1_TC_F9_control_12d


title: GMI1


title: dVhs_Cy_1: Cytoplasmic RNA, delta-Vhs, 8h p.i., Rep 1

value: delta-Vhs 8h p.i.

value: Repicate 1


title: RBG17267_Exp1_TC_E9_control_12d

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing


title: mock_Nu_2: Nucleoplasmic RNA, Mock, Rep 2

description: Nucleoplasmic RNA isolated from mock infected HFF

value: human foreskin fibroblasts

value: Mock


title: WT_Cy_2: Cytoplasmic RNA, HSV-1 8h p.i., Rep 2

description: Cytoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.


title: RBG17266_Exp1_TC_D9_control_12d

value: Treated with control vector


title: CysNO1

value: WT

value: Bacterial culture, 0.1% oxygen


title: mock_Cy_2: Cytoplasmic RNA, Mock, Rep 2

description: Cytoplasmic RNA isolated from mock infected HFF


title: mock_Cr_2: Chromatin-associated RNA, Mock, Rep 2

description: Chromatin-associated RNA isolated from mock infected HFF


title: RBG17265_Exp1_TC_C9_control_12d


title: RBG17263_Exp1_TC_A9_control_12d


title: GMI3

value: 16 hpi


title: RBG17264_Exp1_TC_B9_control_12d


title: WT_To_2: Total RNA, HSV-1 8h p.i., Rep 2

description: Total RNA isolated from HSV-1 infected HFF at 8h p.i.


title: WT_Nu_1: Nucleoplasmic RNA, HSV-1 8h p.i., Rep 1


title: mock_To_2: Total RNA, Mock, Rep 2

description: Total RNA isolated from mock infected HFF


title: RBG17262_Exp1_TC_H8_Gata3sg2_7d

value: Treated with Gata3_sg2


title: WT_Cy_1: Cytoplasmic RNA, HSV-1 8h p.i., Rep 1


title: WT_Cr_1: Chromatin-associated RNA, HSV-1 8h p.i., Rep 1


title: RBG17261_Exp1_TC_G8_Gata3sg2_7d

value: bone marrow


title: WT_To_1: Total RNA, HSV-1 8h p.i., Rep 1

value: HSV-1 8h p.i.


title: RBG17260_Exp1_TC_F8_Gata3sg2_7d


title: A10443

type: RNA

city: Xuzhou

first: Jing

last: Yang

state: Jiangsu

address: Room 519, Building A, The Department of Immunology, Xuzhou Medical University

country: China

institute: Xuzhou Medical University

hyb_protocol: Biotin labeled aRNA  was fragmented at 94°C for 35 minutes following the manufacturers instructions. On completion of the fragmentation reaction, 130ul Agilent hybridization buffer was added to the fragmentation mixture and hybridized to GeneChip primeview human Microarrays (901838) for 16 hours at 45°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed in GeneChip Fluidics Station 450.

scan_protocol: Slides were scanned immediately by GeneChip Scanner 3000.

data_processing: Primary array processing was conducted using Affymetrix GeneChip® Command Console® Software (AGCC, version 1.1), and subsequent analysis was performed using the Affymetrix Expression Console (EC, version 1.1).

label: Biotin

source_name: parental cells

label_protocol: Biotin labeled aRNA was prepared from approximate 50 ng total RNA using a GeneChip 3’IVT Express Kit (Affymetrix) according to the manufacturer's instructions, followed by purification using GeneChip 3’IVT Express Kit.  Purified aRNA yield were checked with the nanodrop 2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from parental cells  and alisertib resistance cells by Trizol.

value: cell line

value: colorectal cancer


title: RBG17259_Exp1_TC_E8_Gata3sg2_7d


title: 1183

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

description: Gene expression data from age-defined primary dermal fibroblasts

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 microarray plates using the Affymetrix GeneTitan instrument

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The PLIER algorithm, quantile normalization, was performed in R as the processing protocol to normalize the data for subsequent analysis.

label: biotin

source_name: primary dermal fibroblasts

label_protocol: Biotinylated cRNA were prepared  using the Affymetrix HT 3’ IVT Express kit (Cat. #901253) on a Beckman Biomek FXp Laboratory Automation Workstation (Beckman Cat. #A31842).

growth_protocol: Primary skin fibroblasts were grown from foreskin samples obtained from donors from the Royal Victoria Infirmary (Newcastle upon Tyne, UK). Ethical approval for this work was granted by the Newcastle and North Tyneside Research Ethics Committee (Ref 08/H0906/95), and the research use of the samples was in accordance with the terms of the written, informed patient consent. The study was performed in accordance with the principles of the Declaration of Helsinki. Fibroblasts were cultured from the dermis following separation from the epidermis via dispase treatment. Cells were grown in DMEM containing 10% fetal calf serum and penicillin/streptomycin. Cells were grown from Caucasian male donors aged between 17 to 84 years old.

extract_protocol: RNA was extracted from skin cells using an RNeasy Mini Kit (Qiagen, UK)

treatment_protocol: untreated

tag: age group

value: young


title: A10446

source_name: alisertib resistance cells


title: A10441


title: A10445


title: 499


title: Tender_6: Tender group, individual 6

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

country: Spain

institute: INIA

description: Gene expression data from Longissimus dorsi tissue

data_processing:
FastQC was used to evaluate the quality of the raw sequencing data
The sequences were trimmed to remove the sequencing adaptor and poly A and T tails with Trim Galore setting default values (stringency of 6bp) and paired-end reads where kept when both pairs were longer than 40 bp.
Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using TopHat v2.1.0 applying default settings, except the reads were aligned first to the ENSEMBLE (Sscrofa11.1) transcriptome annotation (-G option) and the distance between pairs was set to 50 bp. (inner-mean distance) and the standard deviation at 150 bp.
Transcripts were assembled and quantified in FPKM using Cufflinks v2.2.1
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sus scrofa

source_name: Longissimus dorsi, male

growth_protocol: Pigs fattened in a free-range system based on the ad libitum intake of acorns and grass.

extract_protocol:
RiboPure RNA isolation kit
Paired-end libraries were prepared using TruSeq SBS Kit v3-(Illumina, San Diego CA) for each sample. Multiplex sequencing of the libraries was carried out on a HiSeq2000 sequence analyzer (Illumina, Inc) with four samples per lane, according to the manufacturer’s instruction at Centro Nacional de Análisis Genómico. Paired-end reads of 76 bp were generated.

treatment_protocol: Longissimus dorsii muscle were manteined at -80 ºC

tag: Sex

value: male

value: Longissimus dorsi

tag: shear force

tag: ebv shear force


title: mock_Cr_1: Chromatin-associated RNA, Mock, Rep 1

tag: cell type

value: Repicate 1

value: Subcellular RNA fraction


title: Tender_5: Tender group, individual 5

tag: tissue


title: RBG17258_Exp1_TC_D8_Gata3sg2_7d

value: early hematopoietic progenitor cells

tag: genotype

value: Cas9 expressing, Hoxb8 expressing

tag: treatment

tag: day


title: Tender_4: Tender group, individual 4


title: 533

value: old


title: 1180


title: 1082


title: A10444


title: 1003


title: mock_Nu_1: Nucleoplasmic RNA, Mock, Rep 1

value: human foreskin fibroblasts

tag: time post infection

value: Mock


title: A10442


title: Tender_2: Tender group, individual 2


title: Tender_3: Tender group, individual 3


title: RBG17257_Exp1_TC_C8_Gata3sg2_7d

tag: antibody


title: Tender_1: Tender group, individual 1


title: mock_Cy_1: Cytoplasmic RNA, Mock, Rep 1

tag: replicate

tag: molecule subtype


title: Tough_6: Tough group, individual 6


title: 1142


title: RBG17256_Exp1_TC_B8_Gata3sg2_7d


title: RBG17255_Exp1_TC_A8_Gata3sg2_7d


title: Tough_5: Tough group, individual 5


title: Tough_3: Tough group, individual 3


title: Tough_2: Tough group, individual 2


title: RBG17254_Exp1_TC_H7_control_7d

value: Treated with control vector


title: Tough_4: Tough group, individual 4


title: 423


title: Tough_1: Tough group, individual 1


title: mC_brain_platypus

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

library_source: genomic

data_processing:
CASAVA v1.8.2
Adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.8 before methylation quantification with CGmaptools
Genome_build: Monodelphis domestica we used ENSEMBL Monodelphis_domestica.BROADO5.dna.toplevel.fa
Genome_build: Ornithorhynchus anatinus we used ENSEMBL Ornithorhynchus_anatinus.OANA5.dna.toplevel.fa
Genome_build: Gallus gallus we used ENSEMBL Gallus_gallus.Galgal4.dna.toplevel.fa
Genome_build: Callorhinchus milii we used calMil1 (GCA_000165045.2)
Genome_build: Lethenteron camtschaticum we used LetJap1.0 (GCA_000466285.1)
Genome_build: Apis mellifera we used ENSEMBL Apis_mellifera.GCA_000002195.1.31.dna.genome.fa
Genome_build: Octopus bimaculoides we used ENSEMBL Octopus_bimaculoides.PRJNA270931.dna.toplevel.fa
Genome_build: Branchiostoma lanceolatum we used ENSEMBL Branchiostoma_lanceolatum.BraLan2.dna.toplevel.fa
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2/CGmaptools (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).

molecule: genomic DNA

organism: Ornithorhynchus anatinus

source_name: frontal cortex

extract_protocol:
DNeasy Blood & Tissue kit (Qiagen)
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

tag: source

value: Frozen sample


title: RBG17253_Exp1_TC_G7_control_7d


title: RBG17252_Exp1_TC_F7_control_7d


title: mC_brain_opossum

organism: Monodelphis domestica

source_name: brain


title: RBG17251_Exp1_TC_E7_control_7d

source_name: Hoxb8-FL cell line


title: mC_brain_elephant_shark

organism: Callorhinchus milii


title: Colistin_rep3

city: Berkeley

first: Gabriel

last: Mitchell

state: California

address: 1951 Oxford Street

department: Department of Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
The HiSeq instrument control software was HD 3.4.0.38 and the Illumina real-time-analysis software version was RTA 2.7.7.
The data were converted to fastq files and demultiplexed with Illumina bcl2fastq/2.20.0.422.
Raw reads were preprocessed using HTStream v1.0.0, trimming Illumina adapters and evaluating run quality. Processed reads were aligned to the genome using BWA mem v0.7.16a. A gene expression table was then created using the featureCounts function from the R package Rsubread.
Genome_build: Escherichia_coli_str_k_12_substr_mg1655.ASM584v2
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Normalized gene counts (counts per million) for every gene and every sample.

organism: Escherichia coli

source_name: Bacterial culture

growth_protocol: A single colony of E. coli MG1655 was inoculated into cation-adjusted Mueller-Hinton broth and incubate 16-18 h at 37oC with shaking. Cultures were diluted in fresh media to an A600nm of 0.1, incubated at 37oC with shaking until an A600nm of 0.8-1.0 (~2h) prior to antibiotic treatments.

extract_protocol:
Cultures were treated with RNAprotect. Bacterial cultured were lyzed and RNA was extracted using the PureLink RNA Mini Kit (Ambion life technologies, Invitrogen, Carlsbad, California, USA), treated with DNAse and cleaned using the RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA). The quality and the quantity of each RNA samples was analyzed using a bioanalyzer and the Qubit technology.
Dual-barcode indexed RNA-seq libraries were generated from 50 ng total RNA each, using the Kapa Hyper Stranded RNA-seq kit (KapaBiosystems/Roche, Basel, Switzerland) following the instructions of the manufacturer. Libraries were analyzed via micro-capillary gel electrophoresis on a LabChip GX system (PerkinElmer, Waltham, MA), quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA) and pooled in equimolar ratios. The pool was quantified by qPCR with a Kapa Library Quant kit (KapaBiosystems/Roche) and sequenced on one lane of an Illumina HiSeq 4000 (Illumina, San Diego, CA) with single-end 100 bp reads.

treatment_protocol: Antibiotics were added to each cultures, which were further incubated for 1 h at 37oC with shaking.

tag: strain

value: 4ug/ml colistin


title: CSA13_rep3

value: 8 ug/ml CSA13


title: B184_0.2_biological rep1

city: Gothenburg

first: Qi

last: Qi

address: Kemivägen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
The raw reads from each sample were mapped to the R64 reference genome using TopHat (v 2.0.12), with 84.0—87.6% of the reads successfully mapped.
Cufflinks version 2.2.1 was used to calculate FPKM values, and the feature counts module of the Subread package (v 1.4.6) was used to determine raw read counts.
Genome_build: R64
Supplementary_files_format_and_content: tab-delimited text file includes gene counts values for each sample

organism: Saccharomyces cerevisiae

source_name: cell pellets

extract_protocol:
Refer to QIAGEN RNeasy Mini Handbook
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: dilution rate/h

tag: protein productivity

value: high


title: CSA131_rep3

value: 8 ug/ml CSA131


title: B184_0.2_biological rep2


title: Untreated_rep3

value: Untreated


title: MH34_0.2_biological rep2

value: medium


title: RBG17250_Exp1_TC_D7_control_7d

value: bone marrow


title: MH34_0.2_biological rep1


title: LL37_rep2

value: 256 ug/ml LL37


title: LL37_rep3


title: AAC_0.2_biological rep2

value: AAC

value: low


title: RBG17249_Exp1_TC_C7_control_7d

value: early hematopoietic progenitor cells


title: CSA131_rep2


title: AAC_0.2_biological rep1


title: B184_0.1_biological rep2


title: RBG17248_Exp1_TC_B7_control_7d

value: Cas9 expressing, Hoxb8 expressing


title: B184_0.1_biological rep1


title: RBG17247_Exp1_TC_A7_control_7d


title: MH34_0.1_biological rep1


title: Colistin_rep2


title: RBG18572_Plate7_D7_Lmo2_sg1

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
TFnet_exon_counts.csv
TFnet_intron_counts.csv

value: Treated with Lmo2_sg1


title: RBG18586_Plate7_B9_Lmo2_sg3

value: Treated with Lmo2_sg3


title: RBG17246_Exp1_TC_H6_Gata3sg2_5d

value: Treated with Gata3_sg2


title: AAC_0.1_biological rep2


title: RBG17245_Exp1_TC_G6_Gata3sg2_5d


title: AAC_0.1_biological rep1


title: 1006

tag: age

tag: age group

value: old


title: Untreated_rep2


title: PDGFR_1.5Y_3

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna

data_processing:
Illumina BCL files files demultiplexed using bcl2fastq2v2.2.0
adapters were trimmed from demultiplexed fastq files using CutAdaptV2.4 using the following parameters; -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --pair-filter=any -m 40
RRBS alignment index was generated using mm10 reference genome and BSBoltV0.1.2 with the following parameters; -rrbs
Trimmed fastq files aligned to human reference mm10 using BSBoltV0.1.2 using the following parameters; -BT2-k 10 -discord
Methylation calls made using BSBoltV0.1.2 using the following parameters; -min-qual 25 -min 5
Genome_build: mm10
Supplementary_files_format_and_content: Cgmap files, contain CpG sites with a minimum of 10x coverage; genomic coordinates, methylation value (0-1), number of methylated Cs and number of total Cs.

source_name: PDGFR⍺ cardiac fibroblasts

growth_protocol: Hearts of 14-week-old and 1.5 year old animals were used for determination of differences in DNA methylation of either PDGFR⍺ cardiac fibroblasts isolated from those hearts or whole heart tissue.

extract_protocol:
DNA was first extracted from whole hearts or cardiac fibroblasts (Qiagen All prep DNA/RNA mini kit, Catalog 80204).
Illumina NovaSeq SP platform (paired-end, 150bp)

treatment_protocol: Cardiac fibroblasts were isolated using Flow cytometry.

value: PDGFRalpha cardiac fibroblasts

value: 1.5-year old


title: PDGFR_1.5Y_1


title: RBG17244_Exp1_TC_F6_Gata3sg2_5d


title: LL37_rep1


title: PDGFR_1.5Y_2


title: PDGFR_14W_3

value: 14-week old


title: PDGFR_14W_2


title: RBG17243_Exp1_TC_E6_Gata3sg2_5d


title: CSA13_rep1

value: 8 ug/ml CSA13


title: PDGFR_14W_1


title: Heart_1.5Y_3

source_name: Whole heart

value: cardiac cells


title: CSA13_rep2


title: Heart_1.5Y_2


title: MH34_0.1_biological rep2


title: mock_To_1: Total RNA, Mock, Rep 1

source_name: Total RNA

value: human foreskin fibroblasts

value: Mock

value: Repicate 1

value: Subcellular RNA fraction


title: Colistin_rep1

value: 4ug/ml colistin


title: Heart_1.5Y_1


title: Untreated_rep1

value: Untreated


title: RBG17241_Exp1_TC_C6_Gata3sg2_5d

value: bone marrow

value: early hematopoietic progenitor cells


title: Heart_14W_3


title: Heart_14W_2


title: RBG17240_Exp1_TC_B6_Gata3sg2_5d

value: Cas9 expressing, Hoxb8 expressing


title: CTL CFs YAP 8SA - CFs from healthy donor overexpressing YAP rep3

city: Brno

first: Ana

middle: Rubina

last: Perestrelo

address: Studentska

department: CTM

country: Czech Republic

institute: ICRC

description:
Sample 4_rep3
CTL123_rep3

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
Quality trimming of raw reads performed using Trimmomatic version 0.36 with parameters CROP:250 LEADING:3  TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35
Sequenced reads were mapped to hg38 genome (with Ensembl GRCh38 version 94 annotation) using STAR version 2.5.3a as splice-aware short read aligner and the default parameters, with the exception of --outFilterMismatchNoverLmax 0.1 and --twopassMode basic
The gene counts were produced using featureCounts version 1.6.320 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000
The merged file summing up gene counts from DCMA (Sample 2) and DCMB (Sample 3) was produced and named DCM
The differential gene expression analysis was calculated for samples of overexpressed control (Sample 4), DCMA (Sample 2), DCMB (Sample 3) and merged sample DCM against the control (Sample 1) using Bioconductor package DESeq2 version 1.20.0
Genome_build: Ensembl GRCh38 version 94
Supplementary_files_format_and_content: DEseq2 table with differential gene expression data

source_name: Cardiac fibroblasts derived from human heart tissue

growth_protocol: Patient-derived primary CFs were isolated by explant outgrowth on pre-gelatinized plates and sorted for a Thy1 (CD90)-positive and PECAM-1 (CD31)-negative population.  YAP over-expression stable CF lines were obtained by lentiviral infection. Freshly isolated CFs were cultured in Claycomb media (Sigma 51800C) supplemented with 15% FBS (Sigma), L-Glutamine (2 mM, Biowest) and 1% Penicillin/Streptomycin. After isolation, the cells were maintained in DMEM/F12 supplemented with 10% FBS (Sigma), L-Glutamine (2 mM, Biowest) and 1% Penicillin/Streptomycin. Once the cells reached 80% confluence, the CFs were expanded 1:3-1:5 or at a seeding density of 5,000cells/cm2, and the cell culture medium was replaced daily.

extract_protocol:
CFs at 80% confluency were detached from culture plates and total RNA was extracted using a High Pure RNA Isolation Kit (Roche), according to the manufacturer’s instructions.
Sequencing library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) according to manufacturer’s instructions. In brief, 200-300 ng of total RNA was used as input to the NEBNext poly(A) mRNA Magnetic Isolation Module and the enriched samples were then fragmented and transcribed into cDNA. Following universal adapter ligation, samples were barcoded using dual indexing primers.

treatment_protocol: With the exception of healthy CFs' manipulation to overexpress YAP, the restant primary cultures did not suffer any treatment

value: primary cardiac fibroblasts

tag: disease state

value: healthy

value: wt overexpressing YAP


title: RBG17239_Exp1_TC_A6_Gata3sg2_5d

value: Treated with Gata3_sg2


title: CTL CFs YAP 8SA - CFs from healthy donor overexpressing YAP rep2

description:
Sample 4_rep2
CTL123_rep2


title: Heart_14W_1


title: CSA131_rep1

value: 8 ug/ml CSA131


title: RBG17238_Exp1_TC_H5_control_5d

value: Treated with control vector


title: RBG33059_Plate21_H12_noB_Spi1_sg3

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
Tfnet_interactions_exon_counts.csv
Tfnet_interactions_intron_counts.csv

data_processing:
For RNA-Seq: sequencing reads alignment with STAR (default settings). Aligned as single-end data.
For RNA-seq: Counting of reads to exons or introns, summarised per gene - featureCounts. Ensembl v93 genome annotation. Only read1 used for counting.
Genome_build: mm10
Supplementary_files_format_and_content: csv files with either total number of reads mapping to exonic or intronic regions, summed per gene.

growth_protocol: Hoxb8-FL cells were grown in: DMEM with 10% FCS, 5% Flt3L-conditioned medium, 50 uM 2-Mercaptoethanol, 1% Penicillin + Streptomycin, 1% Glutamine solution, either with or without 1 uM β-Estradiol

treatment_protocol:
treatment1:  Cells were transduced with constructs carrying sgRNAs expression cassettes (Perturb-Seq GBC library backbone) targeting indicated genes. Cells were harvested 48h after transduction.
treatment2:  30h after transduction cells were washed with media and cultured for another 18h either with or without beta-estradiol.

tag: cell line

value: Treated with Spi1_sg3

value: cultured without beta-estradiol

tag: time

value: day 2


title: RBG33058_Plate21_G12_noB_Spi1_sg3

tag: tissue

tag: cell type


title: RBG33056_Plate21_E12_noB_Spi1_sg3

tag: genotype


title: RBG33055_Plate21_D12_noB_Spi1_sg3


title: RBG17242_Exp1_TC_D6_Gata3sg2_5d

tag: treatment

tag: day


title: RBG17237_Exp1_TC_G5_control_5d

tag: antibody


title: CTL CFs YAP 8SA - CFs from healthy donor overexpressing YAP rep1

description:
Sample 4_rep1
CTL123_rep1


title: RBG33054_Plate21_C12_noB_Spi1_sg3


title: 1190

value: old


title: RBG33057_Plate21_F12_noB_Spi1_sg3


title: RBG33053_Plate21_B12_noB_Spi1_sg3


title: RBG33052_Plate21_A12_noB_Spi1_sg3


title: RBG17236_Exp1_TC_F5_control_5d


title: DCMB CFs- CFs from DCM patient B rep3

description:
Sample 3_rep3
DCMB_rep3

value: dilated cardiomyopathy and heart failure

value: wt


title: RBG33051_Plate21_H11_noB_Spi1_sg2

value: Treated with Spi1_sg2


title: DCMB CFs- CFs from DCM patient B rep2

description:
Sample 3_rep2
DCMB_rep2


title: RBG33050_Plate21_G11_noB_Spi1_sg2


title: RBG17235_Exp1_TC_E5_control_5d


title: DCMB CFs- CFs from DCM patient B rep1

description:
Sample 3_rep1
DCMB_rep1


title: RBG17234_Exp1_TC_D5_control_5d


title: RBG33048_Plate21_E11_noB_Spi1_sg2


title: RBG33047_Plate21_D11_noB_Spi1_sg2


title: RBG33049_Plate21_F11_noB_Spi1_sg2


title: DCMA CFs - CFs from DCM patient A rep3

description:
Sample 2_rep3
DCMA_rep3


title: RBG17233_Exp1_TC_C5_control_5d


title: RBG33045_Plate21_B11_noB_Spi1_sg2


title: RBG33044_Plate21_A11_noB_Spi1_sg2


title: DCMA CFs - CFs from DCM patient A rep1

description:
Sample 2_rep1
DCMA_rep1


title: RBG17231_Exp1_TC_A5_control_5d


title: CTL CFs - CFs from healthy donor rep3

description:
Sample 1_rep3
CTL_rep3


title: RBG33043_Plate21_H10_noB_Spi1_sg1

value: Treated with Spi1_sg1


title: RBG17232_Exp1_TC_B5_control_5d

value: bone marrow


title: RBG17230_Exp1_TC_H4_Gata3sg2_4d

value: early hematopoietic progenitor cells


title: RBG33042_Plate21_G10_noB_Spi1_sg1

value: Cas9 expressing, Hoxb8 expressing


title: RBG33041_Plate21_F10_noB_Spi1_sg1


title: RBG33038_Plate21_C10_noB_Spi1_sg1


title: RBG17229_Exp1_TC_G4_Gata3sg2_4d


title: RBG33039_Plate21_D10_noB_Spi1_sg1


title: RBG33037_Plate21_B10_noB_Spi1_sg1


title: RBG33040_Plate21_E10_noB_Spi1_sg1


title: RBG17228_Exp1_TC_F4_Gata3sg2_4d


title: CTL CFs - CFs from healthy donor rep2

description:
Sample 1_rep2
CTL_rep2

value: primary cardiac fibroblasts


title: CTL CFs - CFs from healthy donor rep1

description:
Sample 1_rep1
CTL_rep1

value: healthy


title: RBG33035_Plate21_H9_emptyV

value: Treated with controlNT

value: control (full media)


title: W1118_Adult_A_4

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

state: CA

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
Fastq files were processed using Cell Ranger (3.1.0) pipeline using default parameters.
Reference transcriptome package for Cell Ranger was generated using Drosophila melanogaster genome sequence and gene annotations from FlyBase (release 6.29).
Single-cell transcriptomes from DGRP samples were demultiplexed based on parental genotypes using demuxlet (version 2) with default parameters.
Single-cell data analysis was performed using Seurat package (3.1.2). The results of the analysis are provided in ** files
Genome_build: FlyBase 6.29
Supplementary_files_format_and_content: (0) README file with description of datasets; (1) Raw counts for the final merged dataset in 10X format (separately for main and early datasets );(2) Metadata for single cells with sample identities and cluster identities; (3) tSNE embeddings

organism: Drosophila melanogaster

extract_protocol:
FACS-sorted single-cell suspension
Single-cell RNA-Seq libraries were generated using Chromium Single Cell Reagent Kit V3 according to the manufacturer's protocol.
Single-cell RNA-Seq

value: optic lobes

value: 96h APF


title: RBG33036_Plate21_A10_noB_Spi1_sg1


title: DCMA CFs - CFs from DCM patient A rep2

description:
Sample 2_rep2
DCMA_rep2


title: RBG17227_Exp1_TC_E4_Gata3sg2_4d

value: Treated with Gata3_sg2


title: RBG33033_Plate21_F9_emptyV


title: RBG33046_Plate21_C11_noB_Spi1_sg2

value: cultured without beta-estradiol


title: W1118_Adult_A_3


title: RBG17226_Exp1_TC_D4_Gata3sg2_4d


title: RBG33034_Plate21_G9_emptyV

value: day 2


title: RBG33031_Plate21_D9_emptyV


title: W1118_Adult_A_2


title: RBG33032_Plate21_E9_emptyV


title: RBG17224_Exp1_TC_B4_Gata3sg2_4d


title: RBG33030_Plate21_C9_emptyV


title: RBG33028_Plate21_A9_emptyV


title: W1118_Adult_A_1


title: RBG33029_Plate21_B9_emptyV


title: W1118_72h_A_4

value: 72h APF


title: RBG17225_Exp1_TC_C4_Gata3sg2_4d


title: RBG33026_Plate21_G8_Spi1_sg3

value: Treated with Spi1_sg3


title: RBG33025_Plate21_F8_Spi1_sg3


title: RBG33024_Plate21_E8_Spi1_sg3


title: RBG33027_Plate21_H8_Spi1_sg3


title: W1118_72h_A_2


title: RBG33023_Plate21_D8_Spi1_sg3


title: RBG17222_Exp1_TC_H3_control_4d

value: Treated with control vector


title: W1118_72h_A_3


title: RBG33022_Plate21_C8_Spi1_sg3


title: RBG17221_Exp1_TC_G3_control_4d


title: RBG17220_Exp1_TC_F3_control_4d


title: RBG17223_Exp1_TC_A4_Gata3sg2_4d


title: W1118_72h_A_1


title: W1118_48h_B_4

value: 48h APF


title: RBG17219_Exp1_TC_E3_control_4d


title: W1118_48h_B_3


title: RBG33020_Plate21_A8_Spi1_sg3


title: RBG33021_Plate21_B8_Spi1_sg3


title: RBG33019_Plate21_H7_Spi1_sg2

value: Treated with Spi1_sg2


title: RBG33018_Plate21_G7_Spi1_sg2

value: bone marrow


title: RBG33017_Plate21_F7_Spi1_sg2

value: early hematopoietic progenitor cells


title: RBG17217_Exp1_TC_C3_control_4d

value: Cas9 expressing, Hoxb8 expressing


title: RBG33015_Plate21_D7_Spi1_sg2


title: W1118_48h_B_1


title: RBG33016_Plate21_E7_Spi1_sg2


title: RBG33013_Plate21_B7_Spi1_sg2


title: RBG33012_Plate21_A7_Spi1_sg2


title: W1118_48h_A_4


title: W1118_48h_B_2


title: W1118_48h_A_3


title: RBG33014_Plate21_C7_Spi1_sg2


title: RBG33009_Plate21_F6_Spi1_sg1

value: Treated with Spi1_sg1


title: RBG33010_Plate21_G6_Spi1_sg1


title: RBG17214_Exp1_TC_H2_Gata3sg2_3d


title: W1118_48h_A_2


title: RBG17213_Exp1_TC_G2_Gata3sg2_3d


title: RBG33007_Plate21_D6_Spi1_sg1


title: W1118_24h_A_4

value: 24h APF


title: RBG33004_Plate21_A6_Spi1_sg1


title: W1118_48h_A_1


title: RBG33005_Plate21_B6_Spi1_sg1


title: RBG17212_Exp1_TC_F2_Gata3sg2_3d


title: RBG33003_Plate21_H5_R26

value: Treated with controlR26


title: RBG33006_Plate21_C6_Spi1_sg1

value: control (full media)


title: RBG17218_Exp1_TC_D3_control_4d


title: RBG33002_Plate21_G5_R26


title: RBG17211_Exp1_TC_E2_Gata3sg2_3d


title: W1118_24h_A_3

value: optic lobes


title: RBG17210_Exp1_TC_D2_Gata3sg2_3d


title: RBG17216_Exp1_TC_B3_control_4d


title: RBG33000_Plate21_E5_R26


title: RBG33011_Plate21_H6_Spi1_sg1


title: RBG17215_Exp1_TC_A3_control_4d


title: RBG32999_Plate21_D5_R26


title: W1118_24h_A_2


title: RBG32998_Plate21_C5_R26


title: RBG33008_Plate21_E6_Spi1_sg1


title: RBG17209_Exp1_TC_C2_Gata3sg2_3d


title: W1118_24h_A_1


title: RBG17208_Exp1_TC_B2_Gata3sg2_3d


title: RBG32996_Plate21_A5_R26


title: RBG32997_Plate21_B5_R26


title: DGRP_All_B_8

value: 0-96h APF


title: RBG32987_Plate21_H3_noB

value: Treated with controlNT


title: DGRP_All_B_7


title: RBG32986_Plate21_G3_noB

value: cultured without beta-estradiol


title: DGRP_All_B_6


title: RBG32985_Plate21_F3_noB

value: day 2


title: RBG17207_Exp1_TC_A2_Gata3sg2_3d

value: Treated with Gata3_sg2


title: RBG17205_Exp1_TC_G1_control_3d


title: RBG17206_Exp1_TC_H1_control_3d


title: RBG32983_Plate21_D3_noB


title: RBG32984_Plate21_E3_noB


title: RBG32982_Plate21_C3_noB


title: RBG33001_Plate21_F5_R26


title: DGRP_All_B_4


title: RBG17203_Exp1_TC_E1_control_3d


title: RBG17204_Exp1_TC_F1_control_3d


title: RBG32981_Plate21_B3_noB


title: RBG32978_Plate21_G2_noB


title: RBG32980_Plate21_A3_noB


title: RBG32979_Plate21_H2_noB


title: DGRP_All_B_2


title: RBG32974_Plate21_C2_noB


title: DGRP_All_B_3


title: RBG32976_Plate21_E2_noB


title: RBG17200_Exp1_TC_B1_control_3d


title: DGRP_All_A_8


title: RBG32972_Plate21_A2_noB


title: DGRP_All_B_1


title: DGRP_All_A_7


title: RBG32970_Plate21_G1_emptyV


title: RBG17199_Exp1_TC_A1_control_3d


title: RBG32973_Plate21_B2_noB


title: DGRP_All_A_6


title: DGRP_All_B_5


title: RBG32969_Plate21_F1_emptyV


title: RBG32966_Plate21_C1_emptyV


title: RBG17202_Exp1_TC_D1_control_3d


title: BG530_Ebf1_Hoxb8FL

description: ChIP-Seq from Hoxb8-FL cells grown under self-renewal conditions, repeat 3

data_processing:
Reads aligned to mm10 using Bowtie2.
bedGraphs created using bedtools.
bigWigs created using UCSC utilities.
Peaks called using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content:bigWig: density profile of mapped reads;  bed: peaks

extract_protocol:
Cells were fixed in 1% formaldehyde, isolated chromatin was fragment and immunoprecipitated using the indicated antisera.
ChIP followed by Illumina TruSeq library generation. Please see the accompanying publication for a detailed protocol.

treatment_protocol: No treatment

value: Not treated


title: RBG32965_Plate21_B1_emptyV


title: RBG32968_Plate21_E1_emptyV


title: RBG32975_Plate21_D2_noB


title: RBG17201_Exp1_TC_C1_control_3d

value: Treated with control vector


title: BG528_Ebf1_Hoxb8FL

description: ChIP-Seq from Hoxb8-FL cells grown under self-renewal conditions, repeat 1


title: RBG32964_Plate21_A1_emptyV


title: BG529_Ebf1_Hoxb8FL

description: ChIP-Seq from Hoxb8-FL cells grown under self-renewal conditions, repeat 2


title: RBG32967_Plate21_D1_emptyV


title: DGRP_All_A_5


title: RBG32977_Plate21_F2_noB


title: DGRP_All_A_4


title: RBG32971_Plate21_H1_emptyV


title: RBG32962_Plate20_G12_noB_Cebpa_sg3

value: Treated with Cebpa_sg3


title: BG527_Tcf3_Hoxb8FL


title: RBG32960_Plate20_E12_noB_Cebpa_sg3


title: DGRP_All_A_3


title: BG526_Tcf3_Hoxb8FL


title: RBG32959_Plate20_D12_noB_Cebpa_sg3


title: BG525_Tcf3_Hoxb8FL


title: RBG32957_Plate20_B12_noB_Cebpa_sg3


title: DGRP_All_A_1


title: BG524_Gata3_Hoxb8FL


title: RBG32956_Plate20_A12_noB_Cebpa_sg3


title: RBG32955_Plate20_H11_noB_Cebpa_sg2

value: Treated with Cebpa_sg2


title: RBG32963_Plate20_H12_noB_Cebpa_sg3

value: bone marrow


title: RBG32954_Plate20_G11_noB_Cebpa_sg2

value: early hematopoietic progenitor cells


title: BG523_Gata3_Hoxb8FL

value: Cas9 expressing, Hoxb8 expressing


title: RBG32951_Plate20_D11_noB_Cebpa_sg2


title: RBG32953_Plate20_F11_noB_Cebpa_sg2


title: BG521_Cebpa_Hoxb8FL

value: Cebpa


title: RBG32952_Plate20_E11_noB_Cebpa_sg2


title: RBG32949_Plate20_B11_noB_Cebpa_sg2


title: BG520_Cebpa_Hoxb8FL


title: RBG32950_Plate20_C11_noB_Cebpa_sg2


title: RBG32961_Plate20_F12_noB_Cebpa_sg3


title: RBG32946_Plate20_G10_noB_Cebpa_sg1

value: Treated with Cebpa_sg1


title: RBG32947_Plate20_H10_noB_Cebpa_sg1


title: RBG32948_Plate20_A11_noB_Cebpa_sg2


title: RBG32945_Plate20_F10_noB_Cebpa_sg1


title: BG519_Cebpa_Hoxb8FL


title: DGRP_All_A_2


title: BG364_Cebpb_Hoxb8FL

description: ChIP-Seq from Hoxb8-FL cells grown under self-renewal conditions

value: Cebpb


title: RBG32941_Plate20_B10_noB_Cebpa_sg1


title: RBG32958_Plate20_C12_noB_Cebpa_sg3


title: RBG32943_Plate20_D10_noB_Cebpa_sg1


title: BG363_Cebpa_Hoxb8FL

description: ChIP-Seq from Hoxb8-FL cells grown under self-renewal conditions, repeat 4


title: RBG32942_Plate20_C10_noB_Cebpa_sg1


title: RBG32937_Plate20_F9_emptyV

value: control (full media)


title: RBG32936_Plate20_E9_emptyV


title: RBG32938_Plate20_G9_emptyV


title: BG357_Gfi1b_Hoxb8FL


title: BG353_Fli1_Hoxb8FL


title: RBG32939_Plate20_H9_emptyV


title: RBG32935_Plate20_D9_emptyV


title: BG354_Lyl1_Hoxb8FL


title: RBG32934_Plate20_C9_emptyV


title: RBG32933_Plate20_B9_emptyV


title: BG352_Lmo2_Hoxb8FL


title: RBG32944_Plate20_E10_noB_Cebpa_sg1


title: BG522_Gata3_Hoxb8FL


title: RBG32930_Plate20_G8_Cebpa_sg3


title: BG351_Erg_Hoxb8FL

value: Erg


title: RBG32929_Plate20_F8_Cebpa_sg3


title: RBG32931_Plate20_H8_Cebpa_sg3


title: RBG32927_Plate20_D8_Cebpa_sg3


title: RBG32928_Plate20_E8_Cebpa_sg3


title: BG349_AcK27_Hoxb8FL


title: RBG32932_Plate20_A9_emptyV


title: BG350_Runx1_Hoxb8FL


title: RBG32940_Plate20_A10_noB_Cebpa_sg1


title: RBG32925_Plate20_B8_Cebpa_sg3


title: RBG32926_Plate20_C8_Cebpa_sg3


title: BG348_PU1_Hoxb8FL


title: BG355_Gfi1_Hoxb8FL


title: RBG32924_Plate20_A8_Cebpa_sg3


title: RBG32921_Plate20_F7_Cebpa_sg2


title: RBG32923_Plate20_H7_Cebpa_sg2


title: RBG32920_Plate20_E7_Cebpa_sg2


title: BG345_Scl_Hoxb8FL


title: RBG32922_Plate20_G7_Cebpa_sg2


title: RBG32918_Plate20_C7_Cebpa_sg2


title: 48h KO Replicate 03

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

institute: Francis Crick Institute

description:
48 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A13_S16_L003

data_processing:
Read Trimming and adapter removal was performed with Trimmomatic (version 0.36)
Read alignment and gene expression quantification was performed with RSEM (v 1.2.31) and STAR (v 2.5.2a)
Differential expression analysis was carried out with DESeq2 package ( version 1.18.1 ) with R version 3.4.1
Genome_build: Ensembl GRCm38 release 86
Supplementary_files_format_and_content: Tab-delimited text include normalized counts per gene and per sample (generated by DESeq2).

source_name: DN3 and DN4 thymocytes  (Thy1.2+CD44-)

extract_protocol:
RNA was extracted from sorted Thy1.2+ CD44- thymocytes with TRIzol and the Qiagen RNAeasy Mini Kit
Stranded polyA-enriched libraries were made using the KAPA mRNA HyperPrep Kit (Roche)
RNAseq libraries were sequenced on an Illumina HiSeq 4000 using a 75 base single-end read strategy

treatment_protocol: Mice were injected intraperitonealy with 150 µg anti-CD3e for the indicated time points (3, 24 and 48h). Uninjected mice were used for the 0h timepoint.

value: 7-8 weeks

value: Thymus

value: DN3 and DN4 thymocytes  (Thy1.2+CD44-)

value: 48 hours


title: RBG32915_Plate20_H6_Cebpa_sg1

extract_protocol:
375 BFP+/7AAD (live) cells were sorted using flow cytometry into Smart-Seq2 lysis plates.
small-scale bulk RNA-Seq was performed using a modified version of Smart-Seq2 (Picelli et al. Nature Protocols 2014). Please see the accompanying publication for a detailed protocol.

value: day 2


title: 48h KO Replicate 01

description:
48 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A11_S6_L001


title: 48h KO Replicate 02

description:
48 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A12_S7_L001


title: mC_NeuralTube_amphioxus

organism: Branchiostoma lanceolatum

source_name: Neural tube

extract_protocol:
DNeasy Blood & Tissue kit (Qiagen)
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 300 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: Collected in Banyuls, France


title: 24h KO Replicate 02

description:
24 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A24_S21_L003

value: 24 hours


title: RBG32913_Plate20_F6_Cebpa_sg1


title: RBG32919_Plate20_D7_Cebpa_sg2


title: 24h KO Replicate 03

description:
24 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A25_S29_L004


title: RBG32917_Plate20_B7_Cebpa_sg2


title: RBG32916_Plate20_A7_Cebpa_sg2


title: BG347_Meis1_Hoxb8FL

value: Not treated


title: ChIPseq_H3K9me3_G9aDKO

city: Hong Kong

first: Qinghong

last: Jiang

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie v1.2 with parameters -v 3 -m 1 --best --strata.
Duplicates were then removed by Picard MarkDuplicates v2.9.0.
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

source_name: Embryonic stem cell

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 80% confluency.

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with Mnase. The histone-DNA complexes were then isolated with antibodies.
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were crosslinked using 1% formaldehyde for 10minutes at room temperature then quenched with glycine.

tag: chip antibody

value: H3K9me3 (abcam:ab8898)

value: Embryonic stem cell


title: ChIPseq_input_G9aDKO_H3K9me3

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with Mnase.
ChIP libraries were prepared for sequencing using standard Illumina protocols


title: ChIPseq_SMC3_TT2_G9ai-NT-D14

extract_protocol:
Crosslinked cells were lysed and chromatin were sonicated. Histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 250uM UNC0638 (G9a inhibitor, Selleck Chemicals) for 4 days, followed by 10 days of recovery culture then collect. Cells were crosslinked using 1% formaldehyde for 10minutes at room temperature then quenched with glycine.

value: Anti-SMC3 (abcam:ab9263)

value: WT


title: ChIPseq_SMC3_TT2_G9ai-D2

treatment_protocol: Cells were treated with 250uM UNC0638 (G9a inhibitor, Selleck Chemicals) and collect on day 2. Cells were crosslinked using 1% formaldehyde for 10minutes at room temperature then quenched with glycine.


title: ChIPseq_input_TT2_DMSO-NT-D14

extract_protocol:
Crosslinked cells were lysed and chromatin were sonicated.
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 250uM DMSO and collect on day 14. Cells were crosslinked using 1% formaldehyde for 10minutes at room temperature then quenched with glycine.


title: RBG32911_Plate20_D6_Cebpa_sg1

value: bone marrow

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing


title: ChIPseq_SMC3_TT2_G9ai_Control


title: ChIPseq_SMC3_TT2_DMSO-NT-D14


title: RBG32914_Plate20_G6_Cebpa_sg1

value: Treated with Cebpa_sg1

value: control (full media)


title: RBG32910_Plate20_C6_Cebpa_sg1


title: ChIPseq_input_TT2_G9ai-NT-D14


title: mC_brain_arctic_lamprey

organism: Lethenteron camtschaticum

value: Frozen sample


title: 24h KO Replicate 01

description:
24 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A23_S20_L003

value: 7-8 weeks

value: Thymus


title: RBG32908_Plate20_A6_Cebpa_sg1


title: 3h KO Replicate 02

description:
3 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A18_S25_L004

value: DN3 and DN4 thymocytes  (Thy1.2+CD44-)

value: 3 hours


title: 3h KO Replicate 03

description:
3 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A19_S26_L004


title: RBG32909_Plate20_B6_Cebpa_sg1

value: day 2


title: RBG32907_Plate20_H5_R26

value: Treated with controlR26


title: ChIPseq_input_TT2_G9ai-D2


title: RBG32912_Plate20_E6_Cebpa_sg1


title: 0h KO Replicate 02

description:
0 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A5_S10_L002

value: 0 hours


title: 0h KO Replicate 03

description:
0 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A6_S11_L002


title: 3h KO Replicate 01

description:
3 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A17_S24_L004


title: RBG32905_Plate20_F5_R26

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
Tfnet_interactions_exon_counts.csv
Tfnet_interactions_intron_counts.csv


title: ChIPseq_input_G9aDKO_SMC3


title: ChIPseq_input_TT2_G9ai_Control


title: 48h HET Replicate 03

description:
48 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A10_S5_L001

value: 48 hours


title: ChIPseq_input_TT2_SMC3

value: Embryonic stem cell


title: 0h KO Replicate 04

description:
0 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 4
sample name:
KOE855A7_S12_L002


title: ChIPseq_input_J1_SMC3


title: RBG32906_Plate20_G5_R26


title: 48h HET Replicate 02

description:
48 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A9_S14_L002


title: RNA-seq_brain_queen_honeybee

organism: Apis mellifera

source_name: whole brain

extract_protocol:
Trizol
Illumina TruSeq stranded poly-A selected mRNA kit

value: Reared at UWA, Australia


title: RBG32903_Plate20_D5_R26


title: RBG32902_Plate20_C5_R26


title: ChIPseq_input_DnmtDKO_SMC3

value: Dnmt 3a/3b-/-


title: RBG32904_Plate20_E5_R26

value: bone marrow


title: P5 (3)

city: New York

first: Yeojin

last: Lee

state: NY

address: 650 WEST 168TH STREET, BB 1108

institute: Columbia University Medical Center

hyb_protocol: The labelled cDNA was hybridized to Affymetrix Mouse Gene ST 1.0 chips following the manufacturer's instructions.

scan_protocol: standard Affymetrix protocol

data_processing: Expression values for all probes were normalized and determined using the robust multi-array average (RMA) method with an Affymetrix Expression Console (Irizarry et al., 2003). Normalized data were analyzed using Transcriptome Analysis Console 2.0.

source_name: Sorted Cxcl12-DsRed+ stromal cells from P5 livers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

tag: developmental stage

value: liver

value: CD45-Ter119-Cxcl12-DsRed+ stromal cells


title: P5 (2)


title: E15.5 (1)

source_name: Sorted Cxcl12-DsRed+ stromal cells from E15.5 livers


title: P10 (3)

source_name: Sorted Cxcl12-DsRed+ stromal cells from P10 livers


title: P10 (1)


title: P10 (2)


title: E15.5 (3)


title: P5 (1)


title: E15.5 (2)


title: ChIPseq_input_G9aCM_SMC3

tag: strain


title: mC_brain_queen_honeybee

tag: source


title: ChIPseq_input_DnmtTKO_SMC3


title: 0h KO Replicate 01

description:
0 hours Wnk1fl/fl/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A4_S9_L002

tag: age


title: 24h HET Replicate 01

description:
24 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A20_S27_L004

value: 24 hours


title: RBG32899_Plate20_H3_noB

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing

value: Treated with controlNT

value: cultured without beta-estradiol


title: RBG32901_Plate20_B5_R26

value: control (full media)


title: 24h HET Replicate 03

description:
24 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A22_S19_L003

value: 7-8 weeks

value: Thymus

value: DN3 and DN4 thymocytes  (Thy1.2+CD44-)


title: ChIPseq_SMC3_G9aKO

value: Anti-SMC3 (abcam:ab9263)


title: RBG32900_Plate20_A5_R26

value: Treated with controlR26

value: day 2


title: ChIPseq_SMC3_J1

value: Embryonic stem cell

value: WT


title: ChIPseq_SMC3_TT2


title: tsa15 rep1 Input

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: UBC

data_processing:
Fastq files were aligned to saccer3 using BWA
Samtools was used to filter for mapped reads with a mapping quality score of at least 10
Bedtools and AWK were used to convert the BAM files into bed files of mapped DNA fragments
Fragments smaller than 500 bp and larger than 90 bp were selected for using AWK
Coverage per million fragments was calculated and converted to wig file format
Genome_build: saccer3
Supplementary_files_format_and_content: wig files, coverage in 1bp intervals

source_name: yeast_H3K23ac +TSA Input

growth_protocol: Yeast strains were arrested in G1 with alpha factor, treated with 25 μM TSA for 15 minutes, and crosslinked with 1% formaldehyde for 15 minutes

extract_protocol: Cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with αHA (Roche, cat no. 12013819001), αH3K4me3 (Abcam, cat no. ab1012), αH3K23ac (Active Motif, cat no. 39131), or αIgG (Millipore, cat no. PP64) antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE. The immunoprecipitated DNA was subjected to Illumina HiSeq paired-end sequencing.  Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) Agencourt AMPure XP solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent High Sensitivity chip to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).

treatment_protocol: 1% formaldehyde crosslinking

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 bar1::KAN

tag: growth stage

tag: treated with

value: 25 μM TSA for 15 min


title: tsa15 rep1 H3K23ac

source_name: yeast_H3K23ac +TSA IP

value: H3K23ac (Active Motif, 39131, Lot:104)


title: ChIPseq_SMC3_G9aDKO


title: 3h HET Replicate 03

description:
3 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A16_S23_L004

value: 3 hours


title: tsa15 rep2 Input


title: tp0 rep2 Input

source_name: yeast_H3K23ac Input

growth_protocol: Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes

value: no TSA


title: 24h HET Replicate 02

description:
24 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A21_S28_L004

value: 24 hours


title: 48h HET Replicate 01

description:
48 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A8_S13_L002

value: 48 hours


title: RBG32896_Plate20_E3_noB

source_name: Hoxb8-FL cell line

value: bone marrow

tag: cell line

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing

value: Treated with controlNT

value: cultured without beta-estradiol


title: RBG32898_Plate20_G3_noB

tag: time


title: tsa15 rep2 H3K23ac


title: RBG32897_Plate20_F3_noB

tag: tissue


title: ChIPseq_SMC3_DnmtTKO

value: Anti-SMC3 (abcam:ab9263)

tag: cell type


title: 3h HET Replicate 02

description:
3 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A15_S18_L003

tag: genotype

value: 7-8 weeks

value: Thymus

value: DN3 and DN4 thymocytes  (Thy1.2+CD44-)


title: ChIPseq_SMC3_G9aCM

value: Embryonic stem cell


title: tp0 rep2 H3K23ac

source_name: yeast_H3K23ac IP

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 bar1::KAN


title: 3h HET Replicate 01

description:
3 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A14_S17_L003


title: 0h HET Replicate 03

description:
0 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 3
sample name:
KOE855A3_S4_L001

value: 0 hours


title: RBG32895_Plate20_D3_noB

value: day 2


title: ChIPseq_SMC3_DnmtDKO

value: Dnmt 3a/3b-/-


title: tp0 rep1 Input

value: no TSA


title: RBG32894_Plate20_C3_noB


title: tp0 rep1 H3K23ac

value: H3K23ac (Active Motif, 39131, Lot:104)


title: 0h HET Replicate 02

description:
0 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 2
sample name:
KOE855A2_S3_L001


title: ChIPseq_input_G9aKO_SMC3


title: RBG32893_Plate20_B3_noB


title: 0h HET Replicate 01

description:
0 hours Wnk1fl/+/CD2Cre/Rag1KO Mouse 1
sample name:
KOE855A1_S2_L001


title: Hi-C_TT2_Rep2

description: Rep2_Run4 fastq files were sequenced on a MGISEQ-2000RS instrument.

data_processing:
The alignment was processed by Juicer v1.5.6 (Durand et al., 2016) with restriction enzyme as MboI (GATCGATC) and mm10 as the reference genome, and all the other parameters of Juicer were set to default.
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C files were genreated from Juicer; The contents are contact matrices.
Supplementary_files_format_and_content: BigWig files for directionality index were generated by Hi-C Domain Caller and UCSC utilities; Scores represent directionality index under 25kb resolution for replicates merged samples

extract_protocol:
Nuclei were isolated and DNA within nucleus is digested, ligated then sonicated. Cis-interacting DNA were isolated using T1 streptavidin beads pull down.
Hi-C libraries were prepared using Illumina Truseq DNA adapters. Extra conversion steps were performed for libaries sequenced on the MGI2000-RS (BGI) using the MGIEasy App-A Conversion Kit.

value: WT


title: Hi-C_J1_Rep2


title: RBG32892_Plate20_A3_noB

value: bone marrow


title: RA_GS_2

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 (v2.0.9).
bedtools was used to get read counts for genes (bedtools multicov -split -D).
read counts were obtained for each sample for RNA-seq data.
The reads were normalized (based on Generalized Linear Models ) using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including CPM for each sample

source_name: Mouse embryonic fibroblast(MEF)

extract_protocol:
Total RNA extraction was performed using Trizol (Invitrogen) and RNA-seq library was generated using the Illumina TruSeq method according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina True-seq RNA sample prep kit v2, according to the manufacturer’s protocol.

value: Pontin RA

tag: media

value: Glucose starvation


title: RA_GS_1


title: RBG32891_Plate20_H2_noB

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing

value: Treated with controlNT


title: Untagged_100u_Mnase_HA-IP

source_name: Yeast

growth_protocol:
Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes
Cells were grown in YPD

extract_protocol: MNase ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with 100u microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.  Sequencing libraries were prepared as described previously (Maltby et al. 2012; Martin et al. 2017). Briefly, 2 ng of ChIP or input material was end-repaired, A-tailed, and adapters ligated, before PCR amplification with indexed primers. We performed 10 and 11 rounds of PCR amplification for MNase and sonication ChIP-seq experiments, respectively. All DNA purification steps used SPRI (Solid Phase Reversible Immobilization) magnetic beads. Samples were pooled, gel-purified (50 bp - 600 bp region) and sequenced on an Illumina HiSeq 2500.

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 SPT16-HA6::HIS3


title: epl1.485 rep2 pt15 MNase Input

extract_protocol: MNase ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.  Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using NucleoMag solid phase reversible immobilization paramagnetic beads. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) NucleoMag solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent Tape Station to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 epl1.485-6HA::HIS


title: Untagged_100u_Mnase-Input


title: Hi-C_G9a_Rep2


title: epl1.485 rep1 pt15 MNase Input

growth_protocol: Yeast strains were arrested in G1 with alpha factor, treated with 400 μg/mL 1,10-phenanthroline monohydrate for 15 minutes, and crosslinked with 1% formaldehyde for 15 minutes


title: RBG32890_Plate20_G2_noB

value: cultured without beta-estradiol


title: RA_CTL_2

value: Normal


title: Hi-C_G9aCM_Rep2

value: Embryonic stem cell


title: RBG32889_Plate20_F2_noB


title: WT_GS_2

value: Pontin WT


title: Hi-C_DnmtTKO_Rep2


title: epl1.485 rep2 pt15 H4K8ac

value: H4K8ac (Abcam ab45166, clone EP1002Y)


title: epl1.485 rep1 pt15 H4K8ac


title: WT_GS_1


title: RBG32887_Plate20_D2_noB

value: day 2


title: RA_CTL_1


title: Hi-C_TT2_Rep1


title: epl1.485 rep2 tp0 H4K8ac


title: RBG32886_Plate20_C2_noB


title: WT_CTL_2


title: epl1.485 rep1 tp0 H4K8ac


title: Hi-C_J1_Rep1


title: RBG32885_Plate20_B2_noB


title: WT_CTL_1


title: Hi-C_G9aKO_Rep1


title: RBG32884_Plate20_A2_noB


title: epl1.485 6HA rep2 tp pt15 Sonicated Input

description: Yeast strains were arrested in G1 with alpha factor, treated with 400 μg/mL 1,10-phenanthroline monohydrate for 15 minutes, and crosslinked with 1% formaldehyde for 15 minutes

extract_protocol: Sonication ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in lysis buffer and sonicated to produce an average fragment size of 250 bp (30 seconds on / 30 seconds off for 15 mintues total sonication time in Diagenode Biorupter). Sonicated lysates were clarified by centrifugation at 9000g for 10 minutes, and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.  Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using NucleoMag solid phase reversible immobilization paramagnetic beads. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) NucleoMag solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent Tape Station to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).


title: epl1.485 rep2 tp0 MNase Input


title: Hi-C_G9aDKO_Rep1


title: epl1.485 6HA rep2 tp pt15 Sonicated HA IP


title: RBG32883_Plate20_H1_emptyV

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
Tfnet_interactions_exon_counts.csv
Tfnet_interactions_intron_counts.csv

value: control (full media)


title: RBG32882_Plate20_G1_emptyV


title: Hi-C_G9aCM_Rep1


title: epl1.485 6HA rep2 tp0 Sonicated Input

description: Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes


title: SPJ4575_H3Flag_FlagChIP

first: Songtao

last: Jia

state: New York

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University

description: ChIP-seq

data_processing:
The raw reads were trimmed by Trimmomatic (v0.35) to remove remaining adapter contaminants and low-quality regions. The trimmed reads were aligned to the S. pombe reference genome (Ensembl assembly version: ASM294v2.29) by bwa (v0.7.12-r1039) (http://bio-bwa.sourceforge.net/). The read-mapping files were further processed by Samtools (v1.2) picard-tools (v2.0.1) (http://broadinstitute.github.io/picard/) and GATK (v3.5) for indexing, sorting, PCR duplicates removal, and local-realignment around Indels. The per-based mapping depth was calculated by bedtools (v2.25.0) and the sliding window analyses were further performed using a 100-bp window size and 50-bp step size.
Genome_build: ASM294v2.29
Supplementary_files_format_and_content: tdf: coverage tracks

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in YEA until mid-log phase

extract_protocol:
Log-phase yeast cells were incubated at 18 ̊C for 2 hours and then fixed for 30 minutes in 3% freshly made formaldehyde. The crosslinking reaction was stopped by the addition of 2.5 M Glycine to make a final concentration of 0.125 M. The cells were pelleted and washed with PBS (phosphate buffered saline) before resuspended in ChIP lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1% Triton X-100, 0.1% Deoxycholate supplemented with cOmplete protease inhibitors cocktail (Roche)). Ice cold glass beads were added and the mixtures were vigorously disrupted in a bead- beater. The lysates were collected and subjected to sonication to reduce chromatin size to 500– 1000 base pairs. The cleared cell lysates were incubated with anti-Flag (Sigma) over night at 4 ̊C. Protein G beads were then added to isolate the antibodies and associated chromatin fragments. The beads were then washed with ChIP lysis buffer twice, ChIP lysis buffer containing 0.5 M NaCl, Wash buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA), and TE (50 mM Tris pH 8.0, 1 mM EDTA). The bound chromatin fragments were eluted with TES (50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS) and the crosslinking was reversed by incubating at 65 ̊C overnight. The protein DNA mixture were then subjected to proteinase K treatment and phenol:chloroform extraction before the DNA was precipi- tated by ethanol.
Libraries were prepared according to TruSeq ChIP sample preparation guide (Illumina)

value: YEA

value: A2220, M2 Flag agarose


title: CS170_H3K9MFlag_FlagChIP

description: ChIP-seq


title: CS161_FlagClr4K9M_FlagChIP

description: ChIP-seq

value: Flag-Clr4, hht3-K9M-GFP


title: epl1.485 6HA rep2 tp0 Sonicated HA IP


title: Hi-C_DnmtDKO_Rep2

value: Dnmt 3a/3b-/-


title: SPJ390_FlagClr4_FlagChIP

description: ChIP-seq


title: RBG32881_Plate20_F1_emptyV

value: bone marrow


title: Hi-C_DnmtDKO_Rep1


title: RBG32880_Plate20_E1_emptyV

value: early hematopoietic progenitor cells


title: Hi-C_DnmtTKO_Rep1


title: BR172_notag_FlagChIP

description: ChIP-seq

value: WT


title: RBG32879_Plate20_D1_emptyV

value: Cas9 expressing, Hoxb8 expressing

value: Treated with controlNT


title: RNA_TT2_G9ai_Control

data_processing:
The reads from RNA-seq library were aligned to GRCm38/mm10 genome assembly and GENCODE vM15 transcriptome assembly separately with STAR v2.5.3a.
Only alignments belong to genomic uniquely aligned reads were kept in both alignment process.
Fragments per kilobase per million (FPKM) of annotated genes were quantified by RSEM from transcriptomic alignments.
Genome_build: mm10
Supplementary_files_format_and_content: Annotated genes' quantification results were generated by RSEM; Fragment counts, TPM and FPKM were included in the tsv file.
BigWig files were generated by STAR v2.5.3a and UCSC utilites; Scores represent RPM signal for piled up genomic alignments

extract_protocol:
Total RNA were extracted using Rneasy Mini Kit (Qiagen) according to manufacturer protocols.
RNA-seq libraries were prepared using Smart-seq2 protocol.

treatment_protocol: Cells are treated with 250uM UNC0638 (G9a inhibitor, Selleck Chemicals) or DMSO as control and collect on day 2, 4 and 14.


title: epl1.485 6HA rep1 tp pt15 Sonicated HA IP

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 epl1.485-6HA::HIS


title: epl1.485 6HA rep1 tp0 Sonicated HA IP


title: RELB-1-LPS

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
Reads obtained from Illumina sequencing were assessed for quality using FASTQC version 0.11.7 (Andrews, 2018). Salmon version 0.11.3 (Patro et al., 2017) was used for quasi-mapping-based quantification of transcript abundances from the paired end reads over a reference set of human transcript sequences obtained from Gencode version 29 (Frankish et al., 2018). Transcript-level counts generated by Salmon were summarized to gene-level counts using tximport R/Bioconductor package version 1.2.3 (Soneson et al., 2015).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.txt.gz - gzipped tab delimited text file containing a matrix of read counts over genes summarized using tximport R/Bioconductor package
Supplementary_files_format_and_content: tpm.txt.gz - gzipped tab delimited text file containing a matrix of normalized read counts over genes in transcript per million summarized using tximport R/Bioconductor package
Supplementary_files_format_and_content: effective_length.txt.gz - gzipped tab delimited text file containing a matrix of effective gene lengths estimated by tximport R/Bioconductor package

source_name: U937_RELB-/- (KO)_LPS

growth_protocol: RPMI1640 + 10% FBS + 1x Sodium Pyruvate + 1x Pan/Strep

extract_protocol:
Total RNA was extracted from bulk cells in two steps, RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) and the aqueous phase was processed using Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). Purified RNA samples were quality checked using Agilent RNA 6000 Pico assay (Agilent Technologies, Paolo Alto, CA). Reverse transcription and amplification were performed according to established method (Picelli et al., 2014).
cDNA was synthesized from 2ng of purified total RNA using modified oligo(dT) primers along with 1ul of a 1: 50,000 dilution of ERCC RNA Spike in control (Ambion® Thermo Fisher Scientific). To generate sufficient quantities of cDNA for downstream library preparation steps, 13 cycles of PCR amplification was performed. The quantity and integrity of cDNA was assessed using DNA High Sensitivity Reagent Kit, Perkin Elmer LabChip GX (PerkinElmer, Waltham, MA, USA). Subsequently, pooled cDNA libraries were prepared (250 pg of cDNA per sample) using Nextera XT Kit (Illumina, San Diego, CA, USA) with dual indices for de-multiplexing. The libraries were qPCR quantified (Kapa Biosystems, Wilmington, MA) to ascertain the loading concentration. Samples were subjected to an indexed PE sequencing run of 2x151 cycles on an Illumina HiSeq 4000.

treatment_protocol: Untreated or treated with 500 ng/ml LPS

tag: knockout

value: RELB-/- (KO)

tag: treatment

value: LPS

tag: time point

tag: sample batch

value: A


title: RELB-2-LPS

value: B


title: Hi-C_G9aDKO_Rep2

value: Embryonic stem cell


title: RBG32878_Plate20_C1_emptyV

extract_protocol:
375 BFP+/7AAD (live) cells were sorted using flow cytometry into Smart-Seq2 lysis plates.
small-scale bulk RNA-Seq was performed using a modified version of Smart-Seq2 (Picelli et al. Nature Protocols 2014). Please see the accompanying publication for a detailed protocol.

value: day 2


title: RELB-1-Untreated

source_name: U937_RELB-/- (KO)_Untreated

value: Untreated


title: RNA_TT2_G9ai_250nM_D4


title: RELB-2-Untreated


title: epl1.485 6HA rep1 tp pt15 Sonicated Input

tag: chip antibody


title: RBG32875_Plate19_H12_noB_Meis1_sg4

value: Treated with Meis1_sg4

value: cultured without beta-estradiol


title: RNA_TT2_G9ai_250nM_D2


title: epl1.485 rep1 tp0 MNase Input


title: cREL-2-Untreated

source_name: U937_cREL-/- (KO)_Untreated

value: cREL-/- (KO)


title: RNA_TT2_G9ai_250nM_D14


title: RBG32877_Plate20_B1_emptyV

value: control (full media)


title: RNA_J1


title: RNA_G9aDKO


title: RBG32873_Plate19_F12_noB_Meis1_sg4

value: bone marrow


title: EPL1HA6 rep2 tp pt15 Sonicated Input

source_name: EPL1HA6 tp pt15 Sonicated Input

extract_protocol:
Sonication ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in lysis buffer and sonicated to produce an average fragment size of 250 bp (30 seconds on / 30 seconds off for 15 mintues total sonication time in Diagenode Biorupter). Sonicated lysates were clarified by centrifugation at 9000g for 10 minutes, and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.
Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using NucleoMag solid phase reversible immobilization paramagnetic beads. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) NucleoMag solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent Tape Station to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 EPL1-6HA


title: epl1.485 6HA rep1 tp0 Sonicated Input


title: RBG32876_Plate20_A1_emptyV

value: early hematopoietic progenitor cells


title: RNA_G9aCM


title: RNA_TT2

value: WT


title: cREL-2-LPS

source_name: U937_cREL-/- (KO)_LPS


title: EPL1HA6 rep1 tp pt15 Sonicated Input


title: epl1.485 rep1 tp0 MNase HA IP


title: EPL1HA6 rep1 tp0 Mnase HA IP


title: RBG32874_Plate19_G12_noB_Meis1_sg4

value: Cas9 expressing, Hoxb8 expressing


title: cREL-1-LPS


title: EPL1HA6 rep2 tp0 Sonicated Input

source_name: EPL1HA6 tp0 Sonicated Input


title: RBG32872_Plate19_E12_noB_Meis1_sg4


title: p65-3-LPS

value: C


title: cREL-1-Untreated


title: RBG32870_Plate19_C12_noB_Meis1_sg4


title: RBG32871_Plate19_D12_noB_Meis1_sg4


title: WGBS_CpG_TT2

data_processing:
WGBS reads were aligned by Bismark v0.19.0 (Krueger and Andrews, 2011) to the GRCm38/mm10 reference assembly.
PCR duplicates were then removed by Picard MarkDuplicates v2.9.0.
Individual CG methylation levels were extracted for CG sites with reads coverage of ≥5
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by UCSC utilites; Scores represent the ratio of methylated C for each CG site with reads coverage ≥5

source_name: Embryonic stem cell

extract_protocol:
Genomic DNA were isolated using Bradley Buffer.
MethylC-seq libraries are prepared using NEBNext® DNA Library Prep Reagent Set for Illumina based on manufacturer protocol.


title: EPL1HA6 rep1 tp0 Sonicated Input


title: RNA_DnmtTKO


title: EPL1HA6 rep2 tp pt15 Sonicated HA IP

source_name: EPL1HA6 tp pt15 Sonicated HA IP


title: RBG32869_Plate19_B12_noB_Meis1_sg4


title: p65-3-Untreated

source_name: U937_p65-/- (KO)_Untreated


title: WGBS_CpG_G9aKO


title: p65-2-LPS


title: p65-2-Untreated


title: WGBS_CpG_G9aDKO


title: RNA_DnmtDKO

data_processing:
The reads from RNA-seq library were aligned to GRCm38/mm10 genome assembly and GENCODE vM15 transcriptome assembly separately with STAR v2.5.3a.
Only alignments belong to genomic uniquely aligned reads were kept in both alignment process.
Fragments per kilobase per million (FPKM) of annotated genes were quantified by RSEM from transcriptomic alignments.
Genome_build: mm10
Supplementary_files_format_and_content:  Annotated genes' quantification results were generated by RSEM; Fragment counts, TPM and FPKM were included in the tsv file.
BigWig files were generated by STAR v2.5.3a and UCSC utilites; Scores represent RPM signal for piled up genomic alignments

value: Dnmt 3a/3b-/-


title: RBG32867_Plate19_H11_noB_Meis1_sg3

value: Treated with Meis1_sg3


title: p65-1-LPS

value: LPS

value: A


title: RBG32866_Plate19_G11_noB_Meis1_sg3


title: WGBS_CpG_G9aCM

value: Embryonic stem cell


title: p65-1-Untreated


title: EPL1HA6 rep2 tp0 Sonicated HA IP

source_name: EPL1HA6 tp0 Sonicated HA IP


title: EPL1HA6 rep1 tp0 Sonicated HA IP


title: EPL1HA6 rep2 tp pt15 Input

source_name: EPL1HA6 tp pt15 Input

extract_protocol:
MNase ChIP-seq: cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE.
Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using NucleoMag solid phase reversible immobilization paramagnetic beads. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) NucleoMag solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent Tape Station to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).


title: RBG32865_Plate19_F11_noB_Meis1_sg3

value: day 2


title: ChIPseq_input_J1_H3K9me2

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with Mnase.
ChIP libraries were prepared for sequencing using standard Illumina protocols


title: RBG32864_Plate19_E11_noB_Meis1_sg3


title: EPL1HA6 rep1 tp pt15 Input


title: p52-2-Untreated

source_name: U937_p52-/- (KO)_Untreated

value: Untreated


title: EPL1HA6 rep1 tp pt15 Sonicated HA IP


title: ChIPseq_input_G9aKO_H3K9me2


title: EPL1HA6 rep2 tp0 Input

source_name: EPL1HA6 tp0 Input


title: RBG32868_Plate19_A12_noB_Meis1_sg4

source_name: Hoxb8-FL cell line

value: Treated with Meis1_sg4


title: RBG32863_Plate19_D11_noB_Meis1_sg3

value: cultured without beta-estradiol


title: EPL1HA6 rep1 tp0 Input


title: p52-1-LPS

value: B


title: RBG32862_Plate19_C11_noB_Meis1_sg3


title: p52-1-Untreated


title: EPL1HA6 rep2 tp pt15 H4K8ac

source_name: EPL1HA6 tp pt15 H4K8ac

value: H4K8ac (Abcam ab45166, clone EP1002Y)


title: ChIPseq_input_G9aCM_H3K9me2


title: RBG32861_Plate19_B11_noB_Meis1_sg3

value: bone marrow


title: p50-2-LPS


title: ChIPseq_input_DnmtTKO_H3K9me2


title: RBG32860_Plate19_A11_noB_Meis1_sg3


title: ChIPseq_input_TT2_H3K9me2


title: p50-2-Untreated

source_name: U937_p50-/- (KO)_Untreated


title: p52-2-LPS


title: RBG32859_Plate19_H10_noB_Meis1_sg1

value: Treated with Meis1_sg1


title: ChIPseq_input_DnmtDKO_H3K9me2


title: p50-1-LPS


title: EPL1HA6 rep1 tp0 H4K8ac

source_name: EPL1HA6 tp0 H4K8ac

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 EPL1-6HA


title: ChIPseq_input_TT2_H3K27ac_Rep2

value: WT


title: p50-1-Untreated


title: ChIPseq_input_G9aDKO_H3K9me2


title: pt15 rep2 H3K23ac

source_name: pt15 H3K23ac

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 bar1::KAN

value: H3K23ac (Active Motif, 39131, Lot:104)


title: ChIPseq_input_J1_H3K27ac_Rep2


title: ChIPseq_input_TT2_H3K27acRep1_H3K4me3


title: tsa15 rep2 H4K12ac

description:
Associated MNase input deposited at GSM2443150
BM133_GTCCGC_L002

source_name: tsa15 H4K12ac


title: RBG32857_Plate19_F10_noB_Meis1_sg1

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing


title: pt15 rep2 H4K12ac

source_name: pt15 H4K12ac


title: RBG32856_Plate19_E10_noB_Meis1_sg1