title: SU-DHL-8 cells_siCtrl input (m6A-Seq)

tag: cell line


title: 000008555669_D01

status: Public on Apr 08 2021

type: SRA

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

country: USA

institute: UCSD

library_source: transcriptomic

data_processing:
STAR
Rsubread: FeatureCounts
DESeq from Bioconductor
Genome_build: UCSC mm10
Supplementary_files_format_and_content: gct

molecule: total RNA

organism: Mus musculus

source_name: D7 TIL P14

extract_protocol:
Cells were sorted into TCL lysis buffer and RNA was captured and purified on RNAClean XP beads
PrepX RNA-seq library preperation kit (Integenex)

tag: strain

tag: age

value: 6-12 Weeks

tag: tissue

value: Tumor


title: 000008555669_D02


title: SU-DHL-8 cells_siWTAP input (m6A-Seq)

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

country: China

institute: Soochow University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2 (version 2.1.0.20151222) was employed to perform m6A peak calling.Then using Hommer (version:4.7.2) to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus m6A motif by DREME (version:4.11.1) and MEME (version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich (version:2.0.7).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

molecule: polyA RNA

organism: Homo sapiens

source_name: SU-DHL-8 cells

extract_protocol:
m6A antibody immunoprecipitation RNA was quality control with QubitTM (Thermo Fisher Scientifc, USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). Then, 100ng RNA was used for library building following NEBNext® Ultra™ RNA Library Prep Kit protocol for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®2.0 (Life Technologies, USA) and then sequenced on Illumina platformat sing-end /pair end reads for 50bp/150bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sirna

value: siWTAP

tag: genotype

value: WTAP knockdown

tag: ip antibody


title: PROseq_TGFb_siMeox1_Set2

city: San Francisco

first: Pawel

last: Przytycki

state: California

address: 1650 Owens Street

department: GIDB

institute: Gladstone Institutes

data_processing:
Cluster generation, sequencing, and base calling was performed on Illumina HiSeq 4000
Sequenced reads were trimmed for adaptor sequence and low-quality reads removed using Trimmomatic.
Reads were mapped to the mm10 genome with Bowtie 2. All the downstream analysis was done using Homer. Reads Per Kilobase of exon per Megabase of library size (RPKM) for every gene were calculated to quantify nascent transcription.
Library strategy: PROseq
Genome_build: Mm10
Supplementary_files_format_and_content: We provide BigWig files for PROseq We provide bed files and bigWig files for ChIPseq.

source_name: Cardiac fibroblasts

growth_protocol:
A Tcf21MCM mouse was crossed with a Rosa26-Ai6 mouse (Jackson Laboratory stock# 007906). At 10 weeks of age, intraperitoneal injection of Tamoxifen (75 mg tamoxifen/kg) was done for 5 days (once a day). Tamoxifen was prepared following Jackson Laboratory guidelines https://www.jax.org/research-and-faculty/resources/cre-repository/tamoxifen#). After 5 days of injection, the mouse was sacrificed and the non-CM cells isolated as described in a previous section of this method. 100k ZsGreen positive cells were sorted with BD AriaII sorter and cultured for 3 days at 37C in a humidified incubator with 5% CO2 and maintained in FB medium: high glucose DMEM (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Hyclone, GE Healthcare), 1x Non-Essential Amino Acid (NEAA), 10U/ml penicillin/streptomycin and 1mM sodium pyruvate (all from Life Technologies). For immortalization, FB were seeded at 105 per 100 mm plate in the afternoon. Next morning, 2 hours before infection, fresh media was added on plates. The SV40 T Antigen Cell Immortalization Kit (Alstem, #CILV01) was used. 5 µl/well lentivirus supernatant (vials have 20ul) in the presence of Polybrene (added to a final concentration of 5 µg/ml). The next day, remove viral supernatant and switch again to FM medium. After 72 hours incubation, subculture the cells into 2 × 100 mm dishes and add the appropriate amount of puromycin for stable cell-line generation (1ug/ml for mouse cardiac FBs).
After 10 days after puromycin selection, multiple clones were picked for expansion. For daily cell culture, FBs were split every 3-4 days and the media was changed every other day. For the FB TGF-β stimulation, FBs were seeded at 1x105/well of 6 well plate at day 1. On day 2, the media was changed to same basal media with 0.5% FBS. On the day 3, TGF-1(Peprotech) was added into the media at concentration of 10ng/ml. Cells were collected on day 5 for RNA extraction and subsequent gene expression analysis with real time PCR.

extract_protocol:
After 48h of TGF-b treatment, fibroblast cells were washed 3 times with cold PBS and then sequentially swelled in swelling buffer (10mM Tris-HCl pH7.5, 2mM MgCl2, 3mM CaCl2) for 10 min on ice, harvested, and lysed in lysis buffer (swelling buffer plus 0.5% NP-40, 20 units of SUPERase-In, and 10% glycerol). The resultant nuclei were washed two more times with 5ml lysis buffer and finally resuspended in 100 μl of freezing buffer (50mM Tris-HCl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 20 units of SUPERase-In, 1% sarkosyl, 100 M A/GTP, 100 μM biotin-11-C/UTP (Perkin-Elmer) and incubated for 5 min at 30°C. The resultant nuclear-runon RNA (NRO-RNA) was then extracted with TRIzol® LS reagent (Life Technologies, Cat# 10296–028) following manufacturer’s instructions. NRO-RNA was fragmented to 200–500nt by alkaline base hydrolysis on ice for 30 min and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8, Excessive salt and residual NTPs were removed by using P-30 column (Bio-Rad, Cat# 732–6250), followed by treatment with DNase I (Promega Cat# M6101) and antarctic phosphatase (NEB Cat# M0289L). Fragmented nascent RNA was bound to 10 μl of MyOne Streptavidin C1 dynabeads (Invitrogen, Cat# 65001) following the manufacturer’s instructions. The beads were washed twice in high salt (2 M NaCl, 50 mM Tris-HCl pH 7.5, 0.5% Triton X-100, 0.5 mM EDTA), once in medium salt (1M NaCl, 5 mM Tris-HCl pH 7.5, 0.1% Triton X-100, 0.5 mM EDTA), and once in low salt (5 mM Tris-HCl pH 7.5, 0.1% Triton X-100). Bound RNA was extracted from the bead using Trizol (Invitrogen, Cat# 15596–018) in two consecutive extractions, and the RNA fractions were pooled, followed by ethanol precipitation.
Libraries were generated using the NEBNext® Multiplex Small RNA Library Prep Set. (NEB, Cat#E7300S) following the manufacturer’s instructions. The cDNA products were separated on a 10% polyacrylamide TBE-urea gel and only those fragments migrating between 200–500bp were excised and recovered by gel extraction. Finally, libraries were quantified by Qubit and sent to sequence SR75 bp on a HiSeq 4000 platform (Illumina).

tag: cell type

value: Cardiac fibroblasts

tag: treatment

value: TGFb

tag: type of experiment

value: PRO seq


title: 000008555669_C02


title: 000008555669_F01


title: PROseq_TGFb_Set2


title: 000008555669_B02


title: 000008555669_A02


title: PROseq_Unstim_Set2

value: Vehicle


title: SU-DHL-8 cells_siWTAP m6A (m6A-Seq)

value: m6A antibody (Synaptic Systems, 202003)


title: 000008555669_B01


title: PROseq_TGFb_siCtrl_Set1


title: 000008555669_A01


title: 000008555669_G02

source_name: D7 Spleen P14

value: Spleen


title: 000008555669_C01


title: PROseq_TGFb_siMeox1_Set1


title: PROseq_TGFb_Set1


title: 000008555669_H01


title: WT_2

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

country: Germany

institute: Würzburg University

data_processing:
READemption 0.4.3, align, coverage (as previoulsy described Smirnov et al. 2016)
Genome_build: NC_016810.1,NC_017720.1,NC_017718.1,NC_017719.1

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

growth_protocol: LB media, 37 °C, indicated OD

extract_protocol:
PCI extraction, DNase I treatment
NEBNext® Small RNA Library Prep (Illumina)

treatment_protocol: lysis by beads, FLAG-CoIP

tag: growth

value: WT

value: anti-FLAG


title: 000008555669_F02


title: WT_1


title: 000008555669_G01


title: 000008555669_H02


title: 000008555669_E03

source_name: D11 TIL P14


title: ProQ_3XFLAG_2


title: 000008555669_F03


title: 000008555669_E01


title: PROseq_TGFb_siCtrl_Set2


title: FinO3xFLAG_1


title: 000008555669_D03


title: 000008555669_C03


title: Nr18_ID_006034_FinO_OD_2plus9h_2xpur


title: PROseq_Unstim_Set1


title: 000008555669_A03


title: TAC_JQ1_bulkRNAseq_CMs_Rep3

description:
EDGER.Rawcounts_Sham_TAC_TACJQ1.csv
BulkRNAseq_CM_DE_TAC_vs_TACJQ1.csv

data_processing:
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Reads were mapped to the mm10 reference mouse genome using STAR (v 2.7.3a) and assigned to Ensembl genes. We quantified gene expression using raw counts and kept the protein coding genes that showed an average FPKM value across the samples >0.5 FPKM. We then performed differential expression gene testing with DESeq25 (v.1.24.0 R package) using default settings.
Genome_build: Mm10
Supplementary_files_format_and_content: We provide barcodes.tsv files, matrix.mtx files and features.tsv files (for single cell RNA seq) or peaks.bed files (for single cell ATAC seq) generated by the 10x Genomics cellranger command. We provide BigWig files for PROseq and 4C. We provide bed files and bigWig files for ChIPseq. We provide excel files for differential expression analysis with Reads Per Kilobase of exon per Megabase of library size (RPKM) for every gene.

source_name: Heart tissue (Cardiomyocyte cells)

extract_protocol:
Briefly, after proper anesthesia level was reached, thoracotomy was performed, and mouse heart was isolated. The isolated heart was cannulated and perfused with perfusion buffer (120.4 mM NaCl, 14.7 mM KCl, 0.6 mM KH2PO4, 0.6 mM Na2HPO4, 1.2 mM MgSO4, 10 mM Na-HEPES, 4.6 mM NaHCO3, 30 mM taurine, 10 mM 2,3-butanedione monoxime, and 5.5 mM glucose, pH 7.0) in a Langendorff perfusion system (Radnoti 120108EZ) for 5-10 minutes at 37 °C. The cannulated heart was then digested by digestion buffer (perfusion buffer with 300 units/mL collagenase II (Worthington Biochemical) and 50 μM CaCl2) for about 10 min at 37 °C. At the end of digestion, the atria and great vessels were removed and the ventricular tissue was transferred to and gently teased into small pieces in stop buffer (perfusion buffer with 10% fetal bovine serum) at 37 °C. After gently pipetting, cell suspension was passed through a 250uM strainer in a falcon tube and then at 30xg for 3 minutes at room temperature (RT). Then, the supernatant - containing most of the non-cardiomyocytes (CMs) - was divided from the pellet (containing the CM fraction). The non-CM fraction was centrifuged again at 30xg for 3 minutes at RT and the supernatant kept. The supernatant was then filtered with a cell strainer (70um) and finally centrifuged at 400xg for 3 minutes at RT for eliminating debris. The non-CM pellet was finally resuspended in 1mL cold PBS 0.5% BSA. 30k cells were counted with trypan blue using a hemocytometer and then used for subsequent 10X Genomics Chromium single cell RNAseq preparation. For single cell ATAC, 500k isolated and purified non-CMs were resuspended in 100uL lysis buffer (Tris-HCl 10mM pH 7.4, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, P40 0.1%, Digitonin 0.01%, BSA 1% in Nuclease-free water), pipetted 10 times and kept on ice for 5 minutes. Nuclei were then washed 1mL 1X PBS with 1% BSA and then centrifuged at for 5 minutes at 4C. The nuclei pellet was resuspended in 1mL 1X PBS with 1% BSA and filtered with a 10uM strainer (pluriSelect #43-50010-00). Nuclei were then counted with DAPI using a hemocytometer and finally 30k non-CM nuclei used for subsequent 10X Genomics Chromium single cell ATACseq preparation. The CM-fraction was, after the first centrifugation, centrifugated again at 30xg for 3 minutes at RT in stopping buffer and the supernatant was discarded. The CM pellet was finally centrifuged at 400xg for 3 minutes in stopping buffer at RT and after discarding the supernatant, the cell pellet was lysed in Qiazol (miRNeasy kit - Qiagen) for subsequent RNA extraction.
Total RNA from CMs was extracted using miRNeasy kit (Qiagen) according to the manufacturer’s instructions and quantified with Nanodrop (Thermo scientific). After RNA quality control with bioanalyzer Agilent 2100 (Agilent Technologies), Paired-end Poly(A)-enriched RNA libraries were prepared with the ovation RNA-seq Universal kit (NuGEN; strand specific) from the Gladstone Genomic core for 9 samples: Sham (x3), TAC-Veh (x3) and TAC-JQ1 (x3). High-throughput sequencing was done using a PE75 run on a NextSeq 500 instrument (Illumina).

tag: heart surgery

value: TAC

value: Bulk RNA seq

value: Heart tissue (Cardiomyocyte cells)


title: TAC_JQ1_bulkRNAseq_CMs_Rep2


title: 000008555669_E02


title: ProQ_3XFLAG_1


title: Nr16_ID_006032_FinO_OD_2plus3h_2xpur


title: Nr15_ID_006031_FinO_OD_2_2xpur


title: TAC_bulkRNAseq_CMs_Rep3

description:
EDGER.Rawcounts_Sham_TAC_TACJQ1.csv
BulkRNAseq_CM_DE_Sham_vs_TAC.csv
BulkRNAseq_CM_DE_TAC_vs_TACJQ1.csv


title: TAC_JQ1_bulkRNAseq_CMs_Rep1


title: Nr14_ID_006030_FinO_OD_05_2xpur


title: Nr12_ID_006028_ProQ_OD_2plus9h


title: Nr10_ID_006026_ProQ_OD_2plus3h


title: Nr13_ID_006029_FinO_OD_015_2xpur


title: TAC_bulkRNAseq_CMs_Rep1


title: TAC_bulkRNAseq_CMs_Rep2


title: Nr09_ID_006025_ProQ_OD_2


title: Nr08_ID_006024_ProQ_OD_05


title: Nr07_ID_006023_ProQ_OD_015


title: Sham_bulkRNAseq_CMs_Rep1

description:
EDGER.Rawcounts_Sham_TAC_TACJQ1.csv
BulkRNAseq_CM_DE_Sham_vs_TAC.csv

value: Sham


title: Sham_bulkRNAseq_CMs_Rep2


title: Sham_bulkRNAseq_CMs_Rep3


title: Nr06_ID_006022_WT_OD_2plus9h


title: 000008555669_B03


title: Corticosterone GR ChIP - GH2008constant_180_rep1

city: Bristol

first: Benjamin

middle: P

last: Flynn

state: County (optional)

address: Dorothy Hodgkin Building, Whitson street

country: United Kingdom

institute: University of Bristol

description: ChIP-Seq

library_source: genomic

data_processing:
Basecalling RTA 1.18.61 Illumina instrument run time analysis software
Adapters removed by Trimmomatic-0.36, -phredd33 SE
Aligned using bowite2 (default parameters)
Duplicate tags removed by samtools (default parameters) and normalised to a total of 10 million by makeTagDirectory -single -genome rn6 -checkGC (HOMER v4.9.1)
Approximate ChIP-fragment densities compiled for visualisation purposes (i.e. UCSC genome browser) for each replicate by makeUCSCfile (HOMER v4.9.1)
Enrichment of GR tags to 1 % input control, were identified by findPeaks (HOMER v4.9.1) using relaxed settings -F1 -L1 -P.1 -LP.01 -poisson .1 -style factor. Replicate concordance was assessed using an irreproducible discovery rate (IDR v2.0.3) set to 0.01. Overlapping enrichments between replicates were merged using mergePeaks (HOMER v4.9.1) and filtered according to the IDR estimated confidence threshold. Overlapping confident enrichment regions were merged again (mergePeaks) to create a single list of enriched GR locations across conditions.
pSer2 Pol2 enrichment regions were manually restricted to transcript coding regions larger than twice the fragment length (> 320b) and limited to 10 Kb from the transcriptional start site (TSS) based upon Ensemble release Rnor_6.0.92 co-ordinates.
Raw tags counted within GR and pSer2 Pol2 regions by annotatePeaks.pl -raw  (HOMER v4.9.1)
Input tags subtracted and differential enrichment identified by DESeq2 analysis by getDifferentialExpression.pl -AvsA -log2fold 0  (HOMER v4.9.1) (n=2)
Input tags subtracted and differential enrichment identified by DESeq2 analysis by getDifferentialExpression.pl -AvsA -log2fold 0 -norm2total  (HOMER v4.9.1) (n=2)
List of IDR filtered enriched regions after 140 min (PLS_GR_140_peaks.txt) and 180 min (PLS_GR_180_peaks.txt) pulsatile CORT infusion, 140 min (CNS_GR_140_peaks.txt) and 180 min (CNS_GR_180_peaks.txt) constant CORT infusion, 140 min and 180 min VEH infusion (VEH_GR_peaks.txt) and resultant merged regions from all treatments (GR_peaks.txt). Approximate ChIP-fragment densities are compiled for visualisation purposes (i.e. UCSC genome browser) for each replicate (all bedGraph.gz files). Final matrix includes peak ID (column 1), GR enrichment locations (columns 2-5), whether a region was enriched to input control by each infusion condition (column 6-10),normalised tag counts (columns 27-36) and DESeq2 results, formatted by log2 fold change, Wald test p-value, Benjamin-Hochberg adjusted p-value and wether an enriched peak was detected for either compared treatment (columns 37-75) (GRChIP_allresults.txt).
Enrichment regions were manually restricted to transcript coding regions larger than twice the fragment length (> 320b) and limited to 10 Kb from the transcriptional start site (TSS) based upon Ensemble release Rnor_6.0.92 co-ordinates (pSer2Pol2_intragenic_regions.txt). Approximate ChIP-fragment densities are compiled for visualisation purposes (i.e. UCSC genome browser) for each replicate (all bedGraph.gz files). Final matrix includes gene ID (column 1), chr pSer2 Pol2 enrichment locations and strand (columns 3-6), normalised tag counts (columns 22-31) and DESeq2 results, formatted by log2 fold change, Wald test p-value and Benjamin-Hochberg adjusted p-value (columns 32-61) (pSer2Pol2ChIP_allresults.txt).
Genome_build: rn6

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
ChIP-Seq  Dissection and fixing  Liver was dissected and 0.4 g fixed in 1 % (v/v) formaldehyde (Sigma, UK), phosphate buffered saline (1.37 M NaCl, 2.68 mM KCl, 10.14 mM Na2HPO4, pH 7.4) solution for 10 min at room temperature. Formaldehyde cross-linking was quenched with addition of glycine (final conc. 125 mM) for 5 min and washed three times in ice cold phosphate buffered saline supplemented with 2 mM NaF, 0.2 mM sodium orthovanadate and 1X cOmplete protease inhibitor (Roche Diagnostics). Fixed liver was stored at -80 °C in 0.2 g samples in 500 µl of S1 Buffer (10 mM HEPES, pH 7.9, 10 mM KCl, 15 mM MgCl2, 0.1 mM (EDTA), pH 8) supplemented with 0.5 mM Dithiothreitol and 2 mM NaF, 0.2 mM sodium orthovanadate and 1X cOmplete protease inhibitor.   ChIP assay  Samples were thawed slowly on ice and adjusted to a final volume of 1 ml/ sample with supplemented S1 buffer and Dounce homogenised. Lysate was centrifuged at 4000 rpm (4 °C) and lysed in supplemented (2mM NaF and 0.2 mM sodium orthovanadate and 1X cOmplete protease inhibitor) sodium dodecyl sulphate (SDS) lysis buffer (2 % SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.1)). Chromatin was sonicated using a Branson Sonifier 450 (Branson Ultrasonics, Danbury, CT, USA) to 300-500 bp fragments with multiple 10-sec bursts at 10 % output and centrifuged at 13,000 rpm at 4 °C to remove cellular debris from the chromatin suspension. Sheared chromatin was stored at -80 °C.  ChIP buffers were prepared in house, as described in the EZ ChIP kit protocol (Upstate Biotechnology, Lake Placid, NY, USA) with some modifications for use with animal tissue (as described where relevant). Sheared chromatin was removed from -80 °C storage and thawed slowly on ice, diluted to 50 µg in 100 µl of SDS lysis buffer and 0.9 ml with supplemented (2mM NaF, 0.2 mM NaVan and 1X cOmplete protease inhibitor) ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl). Inputs were immunoprecipitated against either a GR antibody cocktail (2 µg of PA1-510A, 4 µl of PA1511A (Thermo Fisher, USA) and 4 µg of M-20X sc-1004X (Santa Cruz, USA)) or the serine 2 phosphorylated RNA polymerase II complex (2 µl ab5095 (Abcam, UK)). Rabbit IgG antibodies were used as negative control (2 µg of sc-2027 (Santa Cruz, USA)). Inputs were incubated overnight at 4 °C and incubated with protein A Dynabeads for 4 hrs (Sigma-Aldrich, UK). To reduce non-specific binding, the DNA-Antibody-Dynabead slurries were sequentially washed with 150 mM salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1), 500 mM salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1), LiCl buffer (0.25 M LiCl, 1 % IGEPAL-CA630, 1 % deoxycholic acid sodium salt, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and twice in TE buffer (10 mM Tris-HCl, 1 mM EDTA) (pH 8.0). Complexes were eluted from the Dynabeads in 1 % SDS 100 mM and 0.1M NaHCO3. NaCl was added (300 mM final concentration) and crosslinks reversed overnight at 65 °C. RNA was removed using RNase treatment (Roche Diagnostics) at 65 °C and protein was digested using proteinase K (Ambion, Huntington, UK) after adjusting each solution with EDTA (1 mM final) and Tris-HCl (4 mM final) at 45 °C. DNA was extracted using 25:24:1 phenol-chloroform-isoamyl alcohol (Sigma, UK) followed by 24:1 chloroform-isoamyl alcohol (Sigma, UK). DNA in the aqueous phase was precipitated overnight at -20 °C in 2.5 VOL 100 % ethanol and 20 µg glycogen (Sigma-Aldrich, UK). DNA was pelleted by centrifugation at 13,000 rpm, 4 °C and washed in 70 % Ethanol (13,000 rpm, 4 °C), air dried and suspended in 40 µl nuclease free water (Ambion, Huntington, UK).  For each ChIP-seq replicate/condition/timepoint, liver samples from 6 rats were collected (72 rats in total). From each replicate/condition/timepoint, 10 x 100ug chromatin aliquots were prepared and immunoprecipitated with antibodies to either GR or pSer2 Pol2 before pooled, concentrated using a UniVapo Vacuum concentrator (Transcriptomics facility, UOB) to approx. 35 µl and sequenced. Note: Two separate ChIP-seq experiments were performed independently to allow for concordant peak calling analysis as previously described
ChIP-Seq  Library prepared according to TrueSeq SBS v3-HS kit protocol (Illumina)

value: Sprague Dawley

tag: Sex

value: Male

value: Liver

value: Corticosterone infusion - constant - 180min

tag: chip antibody

value: 2ug PA1-510A, 4ul PA1511A (Thermo Fisher, USA) and 4ug M-20X sc-1004X (Santa Cruz, USA)


title: Nr05_ID_006021_WT_OD_2plus6h


title: Nr04_ID_006020_WT_OD_2plus3h


title: Unstim_CF_Peak9_ViewPoint_4C

data_processing:
Library strategy: 4C
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
The analysis was done as described in Krijger et al., Methods, 2019. In brief, reads were demultiplexed and low-quality reads removed using Trimmomatic.
Reads were mapped to the mm10 genome with Bowtie 2. Reads were counted on restriction fragment ends and read count normalization and smoothing was performed. Peak calling over background has been performed using de function “doPeakC” directly on the rds files produced by the pipeline as in Krijger et al., Methods, 2019.
Genome_build: Mm10
Supplementary_files_format_and_content: We provide barcodes.tsv files, matrix.mtx files and features.tsv files (for single cell RNA seq) or peaks.bed files (for single cell ATAC seq) generated by the 10x Genomics cellranger command. We provide BigWig files for PROseq and 4C. We provide bed files and bigWig files for ChIPseq. We provide excel files for differential expression analysis with Reads Per Kilobase of exon per Megabase of library size (RPKM) for every gene.

growth_protocol: A Tcf21MCM mouse was crossed with a Rosa26-Ai6 mouse (Jackson Laboratory stock# 007906). At 10 weeks of age, intraperitoneal injection of Tamoxifen (75 mg tamoxifen/kg) was done for 5 days (once a day). Tamoxifen was prepared following Jackson Laboratory guidelines https://www.jax.org/research-and-faculty/resources/cre-repository/tamoxifen#). After 5 days of injection, the mouse was sacrificed and the non-CM cells isolated as described in a previous section of this method. 100k ZsGreen positive cells were sorted with BD AriaII sorter and cultured for 3 days at 37C in a humidified incubator with 5% CO2 and maintained in FB medium: high glucose DMEM (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Hyclone, GE Healthcare), 1x Non-Essential Amino Acid (NEAA), 10U/ml penicillin/streptomycin and 1mM sodium pyruvate (all from Life Technologies). For immortalization, FB were seeded at 105 per 100 mm plate in the afternoon. Next morning, 2 hours before infection, fresh media was added on plates. The SV40 T Antigen Cell Immortalization Kit (Alstem, #CILV01) was used. 5 µl/well lentivirus supernatant (vials have 20ul) in the presence of Polybrene (added to a final concentration of 5 µg/ml). The next day, remove viral supernatant and switch again to FM medium. After 72 hours incubation, subculture the cells into 2 × 100 mm dishes and add the appropriate amount of puromycin for stable cell-line generation (1ug/ml for mouse cardiac FBs).   After 10 days after puromycin selection, multiple clones were picked for expansion. For daily cell culture, FBs were split every 3-4 days and the media was changed every other day. For the FB TGF-β stimulation, FBs were seeded at 1x105/well of 6 well plate at day 1. On day 2, the media was changed to same basal media with 0.5% FBS. On the day 3, TGF-1(Peprotech) was added into the media at concentration of 10ng/ml. Cells were collected on day 5 for RNA extraction and subsequent gene expression analysis with real time PCR.

extract_protocol:
After 48h of TGFb treatment, fibroblast cells were washed 3 times with cold PBS and then sequentially cross-linked with 1% formaldehyde for 10 min. The reaction was quenched by addition of glycine to a final concentration of 0.125 M. Cells were washed once again with cold PBS and nuclei were extracted by incubation 10min in ice with 5 ml of ice-cold lysis buffer (10 mM Tris–HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40 + protease inhibitor). Nuclei were resuspended in restriction enzyme buffer (NEB Cat#B7006S) and incubated with 0.3 % SDS for 1h at 37 C and further incubated with 2% Triton X-100 for 1h. 400U of DpnII restriction enzyme (NEB Cat#R0543S) was added and incubated overnight. Restriction enzyme was heat inactivated at 65C for 20 min. Ligation of DNA regions in close physical proximity was performed using 1000U of T4 DNA ligase (NEB M0202M) overnight. The following day, 300µg of proteinase K were added and decrosslinking was performed at 65C overnight. After de-crosslinking, DNA was purified using phenol/chloroform precipitation and the second digestion was performed by adding 400U of NlaIII restriction enzyme (NEB Cat#R0125S), then incubation at 65C for 4h. After the second digestion, ligation of DNA was performed again using T4 DNA ligase as described above. 4C-seq libraries were amplified using PCR with primer containing partial Illumina sequence adaptors (1st primer: gttcagagttctacagtccgacgatc; 2nd primer: agacgtgtgctcttccgatct). The first primer was designed on each view point and the second primer designed beside the closest NlaIII cutting site to the view point. Full-length Illumina sequencing adaptors and barcodes were added by the second round of PCR. Finally, libraries were quantified by Qubit and library quality checked with bioanalyzer Agilent 2100 (Agilent Technologies).
High-throughput sequencing was done using a SE75 run on a NextSeq 500 instrument (Illumina

value: Cardiac fibroblasts


title: Nr03_ID_006019_WT_OD_2


title: TGFb_CF_Peak9_ViewPoint_4C

value: TGFb


title: Nr02_ID_006018_WT_OD_05


title: Nr01_ID_006017_WT_OD_015


title: Unstim_CF_Meox1_ViewPoint_4C


title: TGFb_CF_Meox1_ViewPoint_4C


title: CO25_Treg_2_S9

city: Concepcion

first: Estefania

last: Nova-Lamperti

email: enova@udec.cl, enovalamperti@gmail.com

state: BioBio-Concepcion

address: Victor Lamas

department: Clinical Biochemistry and Immunology

country: Chile

institute: Universidad de Concepción

data_processing:
Quality check verified with FastQC software package and summarized with MultiQC softare package.
Reads were aligned to the human reference genome using STAR aligner software.
Expression values were calculated with by RSEM v.1.3.1 from which TPM values for each gene were extracted.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix with the raw counts

source_name: Peripheral Blood Tregs

extract_protocol:
Cells were washed after co-cultured and harvested using Trizol reagent. RNA was isolated with Direct-Zol RNA MicroPrep w/Zymo-Spin columns. RNA-seq was performed using the QIAGEN Human Inflammation and Immunity Transcriptome RNA targeted panel (QIAGEN)
RNA libraries were prepared for sequencing using standard QIAgen protocols

treatment_protocol: A standardized piece of tissue (weight about 0.1 g) from the oral cancer and control samples was cut and incubated in X-VIVO15 (LONZA) serum-free medium for 48 h at 37 ºC. After the incubation the medium was collected, debris was eliminated by centrifugation and filtration (0.22um), and the medium with all proteins and factors secreted from the tissue (Secretome) was stored by -80 ºC until use.

value: Treg

tag: secretome

value: OSCC

tag: donor


title: CO25_Teff_2_S10

source_name: Peripheral Blood Teff

value: Teff


title: CO16_Teff_2_S12

value: Not Malignant


title: CO16_Treg_2_S11


title: CO19_Treg_1_S7


title: CO16_Treg_1_S5


title: CO12_Teff_1_S4


title: Blood_H3K4me3_K5

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

description:
K5
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to the reference hg38 genome using Bowtie2 v2.2.7.
Peaks were identified using MACS 2.1.2 using the following parameters: -g hs --keep-dup all --broad --nomodel --shift 37 --extsize 73
To compare the H3K4me3 ChIP datasets of the CD-exposed and control samples, differential peaks were identified using the following steps: first, from all of the peaks called using MACS2 we retained only peaks with average values above the median; Second, we selected peaks with fold changes above 1.5 and FDR < 0.1. Statistical significance was calculated using R package Limma v3.38.3, which was designed to work with a limited number of replicates.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigwig files, bed file containing differential peaks.

source_name: Blood H3K4me3

extract_protocol:
Starting with 200µL of umbilical cord blood, we performed ChIP using 0.5µg of anti-H3K4me3 antibody (Millipore - 07-473). Immunoprecipitated DNA was purified using Qiagen MinElute kit.
Sequencing libraries were prepared using NEBNext® ChIP-seq Library Prep Master Mix Set for Illumina® (NEB, E6240).

treatment_protocol: Umbilical cord blood was sampled at the delivery and CD concentration was assessed by mass spectrometry.

tag: exposure group

value: CD

value: Umbilical cord blood


title: Blood_H3K4me3_K6

description:
K6
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: Blood_H3K4me3_K3

description:
K3
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: Blood_H3K4me3_K1

description:
K1
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: Blood_H3K4me3_K2

description:
K2
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: Blood_H3K4me3_K4

description:
K4
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: Blood_H3K4me3_C6

description:
C6
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6

value: Control


title: CO16_Teff_1_S6


title: Nr11_ID_006027_ProQ_OD_2plus6h

value: anti-FLAG


title: Blood_H3K4me3_C4

description:
C4
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: CO12_Treg_1_S3


title: Blood_H3K4me3_C3

description:
C3
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: Blood_H3K4me3_C5

description:
C5
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: CO19_Teff_1_S8


title: Blood_H3K4me3_C1

description:
C1
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: CO11_Treg_1_S1


title: CO11_Teff_1_S2


title: Blood_H3K4me3_C2

description:
C2
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6


title: Blood_H3K4me3_Input

description:
Input
DNA from 12 samples (H3K4me3): 6 controls, 6 exposed + 1 Input DNA. Blood_H3K4me3_Input : Library from Input, DNA Blood_H3K4me3_C1 : Library from DNA of C1, Blood_H3K4me3_C2 : Library from DNA of C2 Blood_H3K4me3_C3 : Library from DNA of C3, Blood_H3K4me3_C4 : Library from DNA of C4, Blood_H3K4me3_C5 : Library from DNA of C5, Blood_H3K4me3_C6 : Library from DNA of C6, Blood_H3K4me3_K1 : Library from DNA of CD1, Blood_H3K4me3_K2 : Library from DNA of CD2, Blood_H3K4me3_K3 : Library from DNA of CD3, Blood_H3K4me3_K4 : Library from DNA of CD4, Blood_H3K4me3_K5 : Library from DNA of CD5, Blood_H3K4me3_K6 : Library from DNA of CD6

source_name: Blood Input


title: HF-3177_RNAseq_rep2

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

data_processing:
The raw sequencing reads were trimmed using Trim Galore version 0.4.3 (options: --stringency 3 -q 20 -e .20 --length 15 --paired) and aligned to the hg19 genome using hisat 2.1.0 (options: --dta-cufflinks). The transcripts were assembled using Cufflinks 2.2.1. and the final expression level were quantified using Cuffdiff (options: --library-type fr-firststrand).
Illumina RTA-1.18 software used for basecalling
Genome_build: hg19

source_name: Glioblastoma neurosphere cell suspensions

growth_protocol: Tumor specimens were dissociated and cultured as neurospheres in DMEM/F12 medium (11330-032, Gibco) supplemented with N-2 supplement (17502-048, Gibco) and growth factors (EGF and FGF-basic). Cells with passages between 15 and 26 were used for experiments.

extract_protocol:
Total RNA was isolated in biological replicates using AllPrep DNA/RNA Mini Kit (80204, QIAGEN).
Strand-specific RNA libraries were generated from 300 ng of total RNA following the manuals of KAPA Stranded mRNA Sequencing Kit (KK8502, KAPA Biosystems). Libraries were sequenced on Illumina platform with 75 bp paired-end sequencing.

tag: source

value: Glioblastoma


title: HF-3035_RNAseq_rep2


title: N2-iMG-rep3

city: Taipei

first: Yu-Hui

last: Wong

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

data_processing:
N1-iMG and N2-iMG libraries were sequenced using the Illumina HiSeq 4000 system; N2-iPSC and N2-iN libraries were sequenced using the Illumina NovaSeq 6000 system. Image analysis and base calling were conducted by the Control Software + OLB + GAPipeline-1.6 (Illumina) on the instrument.
Reads were first mapped to a reference genome of human (GRCh37; hg19) using HISAT2 (version 2.0.1).
Per-gene expression levels (read counts) were quantitated using HTSEQ (v 0.6.1).
According to the read counts quantitated by HTSEQ, the fragments per kilobase of transcript per million mapped reads (FPKM) was calculated by the formula “total exon fragments / (mapped reads [millions] x exon length [KB])”.
FPKM from different experiments was then normalized using Median of ratios method (DESeq2, v 1.6.3).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including FPKM values of each gene for each sample

source_name: induced microglia

growth_protocol:
[iMG] HiPSCs that had been infected with both FUW-rtTA and pTetO-CEBPA-T2A-SPI1-T2A-Puro were seeded on day -1.  On day 0, the cells had reached at least 70% confluency; at this point the culture medium was replaced with DMEM/F12 (Gibco) supplemented with N2 (Gibco) and non-essential amino acids (NEAA, Gibco). The medium also contained human BMP4 (50 ng/ml, PeproTech), basic FGF (bFGF/FGF2 50 ng/ml, PeproTech) and activin-A (20 ng/ml, PeproTech).  Doxycycline (2 μg/ml, Sigma) was added to promote TetO downstream gene expression and retained in the medium until the end of the experiment.  On day 1, the medium was replaced with DMEM/F12/N2/NEAA containing human VEGF (50 ng/ml, PeproTech), SCF (50 ng/ml, PeproTech) and FGF2 (20 ng/ml).  Puromycin (1 μg/ml, Gibco) was also added for 24 hours to select for successfully infected cells.  On day 2, the medium was replaced with DMEM/F12/N2/NEAA containing human IL-34 (10 ng/ml, PeproTech), M-CSF (10 ng/ml, PeproTech) and TGFβ-1 (10 ng/ml, PeproTech).  Two days later, the medium was replaced with DMEM/F12/N2/NEAA containing human IL-34 (100 ng/ml), M-CSF (20 ng/ml) and TGFβ-1 (20 ng/ml).  After day 4, half medium was removed and replaced with fresh DMEM/F12/N2/NEAA containing human IL-34 (100 ng/ml), M-CSF (20 ng/ml), GM-CSF (20 ng/ml, PeproTech) and TGFβ-1 (20 ng/ml); this was repeated every 3 days from this point onwards. Cells were assayed on days 9.
[iPSCs] Human iPSCs were routinely maintained in Essential 8™ (E8) medium (Gibco, USA) on vitronectin (VTN-N, Gibco, USA) coated dishes at 37°C in a 5% CO2 incubator.
[iN] HiPSC-derived neurons were generated using a published protocol (Zhang et al., 2013) with modifications.  HiPSCs that had been infected with FUW-rtTA and pTetO-Ngn2-puro were seeded on day -1.  On day 0, when the cells reached at least 70% confluency, the culture medium was replaced with DMEM/F12 supplemented with N2, NEAA, human BDNF (10 ng/ml, PeproTech), human NT-3 (10 ng/ml, PeproTech) and mouse laminin (0.2 μg/ml, Gibco).  Doxycycline (2 μg/ml) was added to induce TetO-regulated Ngn2 expression and retained in the medium until the end of the experiment.  On day 1, puromycin (1 μg/ml) was added to kill any uninfected cells.  On day 2, puromycin was removed and the cells were replated in Neurobasal medium supplemented with B-27 supplement (Gibco), GlutaMAX (Gibco), mouse laminin (0.2 μg/ml), human BDNF (10 ng/ml) and NT-3 (10 ng/ml) on poly-L-lysine and laminin coated dishes (~105 cells/mL).  On day 4, cytosine arabinoside (Ara-C, 2 μM, Sigma) was added to the medium to inhibit non-neuronal cell proliferation and was then removed on day 6.  After day 6, 50% of the medium was changed every 4 days. Cells were assayed on days 20.

extract_protocol:
Total RNA was isolated using a Tissue Total RNA Mini Kit (Geneaid, Taiwan) by following the manufacturer’s instructions. 2 μg of total RNA with a RIN value above 9.7 was used to prepare the appropriate libraries.
Next generation sequencing library preparation was constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using  a NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).  The mRNA fragmentation and priming was performed using NEBNext RNA First Strand Synthesis Reaction Buffer and NEBNext Random Primers.  First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix.  The purified double-stranded cDNA obtained by AxyPrep Mag PCR Clean-up (Axygen) was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tail; this was done in a single reaction, and was followed by a T-A ligation to add adaptors to both ends.  Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size being 300 bp) were recovered.  Each sample was then amplified by PCR for 11 cycles using the P5 and P7 primers, with both primers carrying sequences that are able to anneal with the flow cell in order to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing.  The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: cell line

value: Microglia derived from iPSC


title: HF-3177_RNAseq_rep1


title: N2-iMG-rep1


title: N2-iMG-rep2


title: N1-iMG-rep3


title: HF-3035_RNAseq_rep1


title: HF-3016_RNAseq_rep2


title: N1-iMG-rep2


title: HF-2927_RNAseq_rep1


title: HF-2927_RNAseq_rep2


title: KP18003

city: Farmington

first: Carolyn

last: Paisie

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

description: single cell RNAseq of human CD33+ cells enriched from the liver of humanized NSG-SGM3 mice at 12 week after transplanted with human CD34+ cells from cord blood

data_processing:
Cell Ranger v2.2 with GRCh38
Data sets from liver and spleen of two independent experiments were normalized using Harmony
Genome_build: GRCh38
Supplementary_files_format_and_content: FASTQ files containing both barcode reads and transcript reads

extract_protocol:
Enriched human CD33+ cells from liver and spleen of hNSG-SGM3 mice were resuspended in PBS containing 0.04% BSA and the cell numbers were counted on Contess II automated cell counter (ThermoFisher), and approximately 12,000 cells were loaded per channel on Chromium microfluidic chips (10x Genomics).
Single cell capture, barcoding and library preparation were performed using the 10X Chromium version 2 chemistry according to the manufacturer’s protocol (10x Genomics).  The quality of cDNA and libraries were checked on an Agilent 4200 TapeStation, quantified by KAPA qPCR, and sequencing on a HiSeq 4000 (Illumina) to an average depth of 50,000 reads per cell.

tag: host mouse strain

value: untreated


title: N1-iMG-rep1


title: KP19001

description: single cell RNAseq of human CD33+ cells enriched from the spleen of humanized NSG-SGM3 mice at 12 week after transplanted with human CD34+ cells from cord blood

tag: tissue

value: Spleen


title: HF-2354_RNAseq_rep1


title: HF-3177_chia-pet

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categaries: PET reads, single tag reads and no-linker reads. Tags identified (>=16bp) and reads without linkers were mapped to hg19 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped,multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categaries were merged and used for peak calling with MACS v2.1.1.20160309 (options: --keep-dup all --nomodel --extsize 250 -B --SPMR -g hs). CPU furhter clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5,-20 -3 5,480 -t 16 -O). The cis-interaction significance was assessed with ChiaSigScaled (https://github.com/cheehongsg/ChiaSigScaled ; options: -c 3 -t 16 -p -m 8000). Cis-interactions with member size >=3 and FDR < 0.05 were reported. The complete list trans interaction was reported here while additional filtering were applied (e.g. exclude singletons ) for corresponding analyses in publication. (see details in publication).
Illumina RTA-1.18 software used for basecalling
Genome_build: hg19

extract_protocol:
10 million cells were dual-crosslinked with 1.5mM EGS (21565, Thermo Fisher) for 45 min followed by 1% formaldehyde (F8775, Sigma) for 20 min at room temperature and then quenched with 0.125 M Glycine (G8898, Sigma) for 10 min. The crosslinked cells were washed with PBS twice and lysed in 100 ul 0.55% SDS with incubation at room temperature, 62°C and 37°C sequentially for 10 min each, which was followed by 37°C for 30 min with addition of 25 ul 25% Triton-X 100 to quench SDS and 37°C overnight with addition of 50 ul AluI (R0137L, NEB), 50 μl 10 × CutSmart buffer and 275 μl H2O to fragmentize the chromatin. The pelleted digested nuclei were resuspended in 500 ul A-tailing solution containing 50 μl 10 × CutSmart buffer, 10 μl BSA (B9000S, NEB), 10 μl 10 mM dATP (N0440S, NEB), 10 μl Klenow (3’- 5’ exo-) (M0202L, NEB), and 420 μl H2O  with 1 hr incubation at room temperature and then subjected to proximity ligation by adding 200 μl 5 × ligation buffer (B6058S, NEB), 6 μl biotinylated bridge linker (200 ng/ul), 10 μl T4 DNA ligase (M0202L, NEB) and 284 μl H2O and incubating at 16°C overnight. The ligated chromatins were then sheared by sonication and immunoprecipitated with anti-RNApolII antibody (920102, Biolegend).
The ChIPped DNA were tagmented using the Nextera DNA Sample Preparation Kit (Illumina). The linker ligated ChIA-PET constructs were selected using streptavidin magnetic beads. The magnetic beads were blocked with sheared gDNA prior to the selection. The streptavidin selected constructs were amplified with PCR and purified.

value: RNA polymerase II (920102, Biolegend)


title: PC3_ecDNA_negative-chia-pet

description: ChIAPET

data_processing:
ChIA-PET data was processed by ChIA-PET Utilities (CPU) (https://github.com/cheehongsg/CPU). CPU (options: stat -s -p -T 18 -t 16) removed the adaptors, and grouped the reads into three categaries: PET reads, single tag reads and no-linker reads. Tags identified (>=18bp) and reads without linkers were mapped to hg19 using BWA alignment and mem according to the tag/read length. CPU further separated the mapping results into uniquely-mapped,multiply-mapped, and unmapped classes with the pairing consideration (options: pair -S -t 16) and removed duplicates generated by PCR amplification (dedup -g -t 16). Next, the non-redundant uniquely-mapped reads from 3 categaries were merged. CPU furhter clustered the non-redundant uniquely-mapped pair-end tags and grouped them as intra-chromosomal PET clusters (cis-interactions) and inter-chromosomal PET clusters (trans-interactions) (options: cluster -s 8000 -M -B 1000 -5 5,-20 -3 5,480 -t 16 -O).
Illumina RTA-1.18 software used for basecalling
Genome_build: hg19

source_name: PC3 from NCI60

growth_protocol: PC3 cell lines are cultured in F-12K medium (30-2004, ATCC) with 10% FBS.

value: The PC3 was initiated from a bone metastasis of a grade IV prostatic adenocarcinoma from a 62-year-old male Caucasian.


title: KP18002


title: HF-2354_RNAseq_rep2


title: HF-3016_chia-pet


title: HF-3035_chia-pet


title: 1d_Male_elav_H3K9me3_4

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

description: Sequential Chromatag-ChIP for elav neuron chromatin

data_processing:
ChIP-seq reads were pre-processed using Trimmomatic’s ILLUMINACLIP (v. 0.33) option to remove Illumina adaptor sequences. Pre-processed ChIP-seq reads were aligned to the D. melanogaster dm6 UCSC genome assembly using Bowtie2 (v.2.2.5), allowing up to 6 mismatches. Only uniquely aligned reads were considered and individual replicate and pooled replicate (all replicates) BAM files were generated with SAMtools (v. 1.2) for downstream analyses.
MACS2 (v.2.1.0) peaks were called for each histone modification (H3K27ac, H3K36me3, H3K4me3, H3K9me3, H3K27me3) at each time point (48hr APF, 1-day adult, 10-12 day adult) for each sex in fru P1 or elav neurons, relative to sex and stage-specific input chromatin library controls for individual and all (pooled) replicates. We performed “narrow” peak calling for histone modifications with more compact enrichment patterns (H3K27ac and H3K4me3) and the “broad” peak option for modifications with diffuse enrichment (H3K36me3, H3K9me3, and H3K27me3) on all individual biological replicates and on all (pooled) replicate data using the following “callpeak” parameters: --gsize dm -p 1e-2 --call-summits --fix-bimodal.
Input normalized BigWig files for all histone modifications for all replicate (pooled) data were obtained using Deeptools bamCompare function to subtract input ChIP-seq signal from histone modification .BAM files obtained from concatinating individual replicate .BAM files.
Genome_build: UCSC dm6 (BDGP Release 6 plus ISO1 MT)

organism: Drosophila melanogaster

source_name: Whole head

growth_protocol: For 48hr APF stage: pupae were sex-sorted at white pre-pupal stage and aged to 48hr after Puparium formation (APF) on Bromophenol blue agar plates at 25˚C on a 12 hour light and 12 hour dark cycle. Adult stage flies were reared and maintained on standard cornmeal food at 25°C on a 12 12-h light/12-h dark cycle.

extract_protocol: The adult heads were separated from their bodies by vortexing frozen animals. The heads were sifted through liquid nitrogen-cooled mesh sieves #25 and #40 (with heads retained in the #40 sieve). The sequential ChIP methodology presented here is based on a previously published ChIP protocol (Negre et al. 2006). Frozen adult heads or frozen whole body pupae (~0.3g) were dounce homogenized in 5ml of Buffer A1 (60mM KCL, 15mM NaCl, 4mM MgCl2, 15mM HEPES (pH 7.6), 0.5% TritonX-100, 0.5mM DTT, 10mM sodium butyrate, and Roche cOmplete Protease Inhibitor cocktail EDTA-free, product 5056489001), with 1% methanol-free formaldehyde (Pierce, 20% solution product 28906) for crosslinking at room temperature for 10 min. The crosslinking reaction was quenched using 540\265l 2.5M Glycine and incubated for 5 minutes at room temperature. Cross-linked homogenates were centrifuged at 4000g for 5 minutes at 4\272C and the nuclear pellets were resuspended in Buffer A1. The nuclear pellets were washed 3 more times by centrifugation at 4000g for 5 minutes at 4\272C with resuspension in 3ml of buffer A1. The nuclear pellets were washed an additional time with 1x Lysis Buffer without SDS (140mM NaCl, 15mM HEPES (pH 7.6), 1mM EDTA (pH 8.0), 0.5mM EGTA, 1% TritonX-100, 0.5mM DTT, 0.1% sodium deoxycholate, 10mM sodium butyrate, and Roche cOmplete Protease Inhibitor Cocktail EDTA-free) to remove all traces of Buffer A1 before the next lysis step. After one additional spin at 4000g for 5 minutes at 4\272C, the washed nuclear pellet was resuspended in Lysis Buffer containing 1% SDS and 0.5% N-Laurosylsarcosine and incubated at 4\272C, rotating for 1 hour. Nuclear lysates were quickly spun down for 10 seconds at 2000g and supernatant transferred to sonication tubes (Covaris; product 520130) for shearing. Chromatin was sheared for 25 minutes using a Covaris E220 (duty cycle: 5.0, peak incident power: 140, cycles per burst: 200). The sheared chromatin was transferred to microcentrifuge tubes and rotated for 10 min. at 4\272C. Next, the sheared chromatin was centrifuged at 18,000g for 5 minutes at 16 \272C. The supernatant was transferred to a new microcentrifuge tube and the centrifugation step was repeated twice. The final supernatant was split into two 0.5ml aliquots (material from ~0.15g frozen tissue) and brought to a 1.5ml volume with 1x Lysis Buffer without SDS. The sheared chromatin was then aliquoted into 250\265l volumes and stored at -80\272C. To perform the sequential ChIP, 750\265l of 1x Lysis Buffer without SDS was added to the 250\265l of the thawed sheared chromatin. The sheared chromatin was incubated with 50\265l of magnetic protein A/G beads (Pierce, product 88803) and 5\265g of each respective antibody at 4\272C overnight. The magnetic protein A/G beads were then washed four times with 1ml of Lysis Buffer wash (140mM NaCl, 15mM HEPES (pH 7.6), 1mM EDTA (pH 8.0), 0.5mM EGTA, 1% TritonX-100, 0.05% SDS, 0.5mM DTT, 0.1% sodium deoxycholate, 10mM sodium butyrate, and Roche cOmplete Protease Inhibitor Cocktail EDTA-free) and twice with TE (10mM Tris-HCL (pH 8.0), 1mM EDTA) for 10 minutes each, rotating at 4 \272C. Beads were incubated in 100\265l ChIP elution buffer (100mM NaHCO3, 80mM NaOH, 1% SDS) at room temperature, rotating for 30-60 minutes to elute chromatin. The eluate was diluted 1:10 with Lysis Buffer without SDS and incubated on magnetic streptavidin beads (Invitrogen Dynabeads MyOne Streptavidin C1) for 4hrs-overnight rotating at 4\272C. The beads were washed as above and chromatin was reverse crosslinked on beads in ChIP elution buffer (with 0.04mg/ml proteinase K, 0.01mg/ml RNaseA) at 65 \272C overnight. DNA was purified with a DNA purification and concentration kit (Machery-Nagel, product 740609). ChIPseq libraries were prepared using the NEBNext ChIP-seq library preparation kit. Libraries were size selected using AMPure XP beads (Beckman) and clean up steps were performed using the Machery Nagel PCR cleanup kit. A final wash was performed using the AMpure XP beads according to kit protocol to remove primers.

treatment_protocol: Approximately 1000 sex-sorted flies that were 48hr after pupal formation (APF, +/- 1hr), 16-24hrs post eclosion, or 10-12 days post eclosion were used for each ChIP independent biological replicate (n=4 and n=3 for 10-12 day adult female libraries). Flies were collected and sex sorted at the white prepupal stage, 0-8hrs post-eclosion, or 0-48hrs post-eclosion for appropriate aging to their respective time points and snap frozen in liquid nitrogen between ZT1 and ZT2. All flies collected under anesthetization were allowed to recover for at least 16hrs before freezing took place. All frozen animals were stored at -80°C until they were processed for downstream experiments.

tag: developmental stage

value: Male

value: elav


title: 1d_Male_elav_H3K9me3_3


title: 1d_Male_elav_H3K9me3_2


title: KP19002

value: Liver


title: 1d_Female_elav_H3K9me3_3

value: Female


title: 1d_Female_elav_H3K9me3_2


title: HF-2354_chia-pet


title: 1d_Female_elav_H3K9me3_1


title: cocktail rep4

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Bascalling performed using RTA 1.18.64.0
The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) (Li and Durbin 2009) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v1.4.1) (Trapnell, Pachter et al. 2009) against the Mus musculus genome (mm10) and a maximum of 6 mismatches.  Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC RefSeq mm10). rRNA loci are masked on the genome for downstream analysis.
Aligned reads are subjected to FPKM estimation with Cufflinks (v1.3.0) (Trapnell, Williams et al. 2010, Roberts, Trapnell et al. 2011). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with UCSC RefSeq annotation (mm10) of genes with at least one protein coding transcript were allowed and counted towards the number of mapped hits used in the FPKM denominator.
Furthermore, the aligned reads were counted with HTSeq (0.6.1p1)
The genes were subjected to differential expression analysis with DESeq2 (v1.6.3; Bioconductor) (Love, Huber et al. 2014). The effect of samples originating from the same mouse was blocked.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample (standard output Cufflinks); tab-delimited text file containing the differential expression analysis plus mean FPKM values  (DESeq2)

source_name: cocktail aCSF_acute brain slice

growth_protocol: 4-week-old mice were deeply anesthetized using isoflurane (Abbot Animal Health, IL, USA; IsoFlo), decapitated and their brains quickly chilled in ice-cold oxygenated (95% O2/ 5% CO2) dissection buffer (110 mM choline chloride, 25 mM NaHCO3, 1.25 mM NaH2PO4, 2.5 mM KCl, 0.5 mM CaCl2, 7 mM MgCl2, 11.6 mM  ascorbic acid, 3.1 mM pyruvic acid, and 25 mM D-glucose). Coronal brain slices (350µm) containing auditory cortex were cut in ice-cold dissection buffer using a Vibratome (Leica Biosystems, Germany; VT1000S) and immediately incubated for 15 min recovery phase in dissection buffer at 32°C. This was followed by phase in which slices rested in oxygenated (95% O2/5% CO2) artificial cerebrospinal fluid (aCSF; 118 mM NaCl, 2.5 mM KCl, 26.5 mM NaHCO3, 1 mM NaH2PO4, 1 mM MgCl2, 2 mM CaCl2, and 20 mM D-glucose) for 45min at room temperature (RT).

extract_protocol:
Brain slice hemispheres that underwent incubation protocol in cocktail or control aCSF, were placed under a dissection microscope and auditory cortices dissected while submerged in bubbled aCSF. Total RNA from dissected auditory cortices was isolated by Trizol (800µl / auditory cortex; Life technologies, Grand Island, NY, USA).
One microgram of total RNA was used for poly-A selection with a Dynabeads mRNA purification kit (Invitrogen, CA, USA) followed by cDNA generation (NEB 1st strand and NEB 2nd strand ultra directional Kits; New England BioLabs, Frankfurt am Main, Germany). Libraries were prepared using a NEBNext Ultra DNA kit (New England BioLabs, Frankfurt am Main, Germany) and quantified with a Library Quantification kit for Illumina platforms (Kapa Biosystems, Inc., Wilmington, MA, USA).

treatment_protocol: After the initial 15min of recovery in Choline Chloride, slices were cut along the midline into two hemispheres under a dissection microscope and incubated in aCSF for 45 min. One hemisphere of each brain slice was then transferred to fresh aCSF for 1hour, the complementary hemisphere underwent incubation in cocktail aCSF (50µM (-)-Bicuculline methiodide, 100µM DL-Norepinephrin hydrochloride, 50µM Carbamolylcholine chloride, 100µM Dopamine hydrochloride, 40µM Ascorbic Acid and 100µM Serotonin hydrochloride (Sigma-Aldrich, MO, USA)) for 1h.

tag: strain

tag: age

value: 4-week old

tag: mouse id

value: mouse 4

tag: incubated in

value: cocktail aCSF for 1hr

value: acute brain slice


title: cocktail rep2

value: mouse 2


title: cocktail rep6

value: mouse 6


title: 1d_Male_elav_H3K4me3_3

tag: cell type


title: 1d_Male_elav_H3K4me3_2


title: control rep6

source_name: control aCSF_acute brain slice

value: artificial cerebrospinal fluid (aCSF) for 1hr


title: 1d_Female_elav_H3K9me3_4


title: cocktail rep5

value: mouse 5


title: HF-3016_RNAseq_rep1

value: Glioblastoma


title: 1d_Male_elav_H3K4me3_1


title: 1d_Female_elav_H3K4me3_4


title: 1d_Female_elav_H3K4me3_3


title: cocktail rep3

value: mouse 3


title: control rep3


title: 1d_Female_elav_H3K4me3_2


title: cocktail rep1

value: mouse 1


title: control rep2


title: control rep5


title: 1d_Female_elav_H3K4me3_1


title: 1d_Male_elav_H3K4me3_4


title: control rep4


title: 1d_Male_elav_H3K36me3_4


title: control rep1


title: MCF7-RNF2-PD_rep2

city: Beijing

first: Howard

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description:
AP-seq PD rep2 in MCF7 cell
MCF7-RNF2-Detect-seq_on-target.bed
MGISEQ-2000

data_processing:
Library strategy: Detect-seq
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software with the following command: "cutadapt --times 1  -e 0.1  -O 3  --quality-cutoff 25  -m 50 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -A  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o {read1.out}  -p {read2.out}  {read1.in}  {read2.in}"
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome, hg38 for HEK293T and MCF7, mm10 for mESC, with bowtie2 aligner. And only record the best hit of alignment for each read.
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Remove duplication step: The sorted BAM files are removed the PCR amplification bias with the PICARD MarkDuplicates command.
Peak calling step: The final AP site peak are generated by the macs2 software
Genome_build: mm10, hg38
Supplementary_files_format_and_content: The bigwig files are generated by the deeptools bamCoverage software with parameters as follows: "bamCoverage --bam {input} -o {output} -of bigwig --scaleFactor 1 --binSize 10  --normalizeUsing RPKM"

source_name: MCF-7 cells

growth_protocol: The HEK293T and MCF7 is separately cultivated in DMEM and MEM with 10% FBS and 1% PS at 37°C cultivator with 5% CO2. The subculture of cells was performed every 2–3 days and only passage 3-10 were used for experiments. All the cells were routinely tested for Mycoplasma contamination with TransDetect PCR Mycoplasma Detection Kit (TRANSGEN BIOTECH, FM311-01).

extract_protocol:
Genomic DNA was freshly extracted using CWBIO universal genomic DNA kit (CWbiotech, CW2298M) and stored in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) at -80 °C.
Extracted genomic DNA was fragmented into ~300 bp through Covaris Focused-ultrasonicator™ Instrument (ME220), followed by a purification using DNA Clean & Concentrator-5 (Vistech, DC2005). ~5 ug DNA fragments and 10 pg spike-in model sequences were subjected to end repair with NEBNext End Repair Module (NEB, E6050), and 1 μl E. coli ligase (NEB, M0205) was added to repair nicks in DNA. Then hydroxylamine protection of endogenous 5fC was performed in 100 mM MES buffer (pH 5.0), 10 mM O-ethylhydroxylamine (EtONH2, Aldrich, 274992) at 37 °C for 6 h. The product underwent 5fC protection was diluted 2.5 times and purified with DNA Clean & Concentrator-5. Next, dA-tailing procedure was carried out using NEBNext dA-Tailing Module (NEB, E6053) followed by a DNA purification with 1.8 × AMPure XP beads.   DNA damage that may interfere the subsequent labeling step was repaired in a mixture of 2 μl endonuclease IV (Endo IV, NEB, M0304), 1 μl Bst full-length polymerase (NEB, M0328), 2 μl Taq ligase (NEB, M0208), 1 μl NAD+ (NEB, B9007), 1 μl dNTP (2.5 mM each) in NEBuffer 3 for 1 h at 37 °C and 1 h at 45 °C. DNA was purified and subjected to in vitro BER labeling reaction containing a mixture of 1 μl UDG (NEB, M0280), 1.5 μl Endo IV, 0.8 μl Bst full-length polymerase, 1.7 μl Taq ligase, 1 μl NAD+, 200 nM biotin-dUTP, 800 nM d5fCTP, 200 nM dATP and 200 nM dGTP in NEBuffer 3 for 40 min at 37 °C. The DNA was incubated with 75 mM of malononitrile in 10 mM Tris-HCl (pH 7.0) at 37°C for 20 h in an enclosed thermomixer (Eppendorf, 850 rpm), away from light. The reaction product was then purified with 1.8 × AMPure XP beads.  Labeled fragments were enriched by streptavidin C1 beads (Invitrogen) following the manufacturer's instruction. Y adaptor (see Supplementary Note 1) was ligated (NEBNext Quick Ligation Module, E6056) to double-stranded DNA on streptavidin C1 beads so that free adaptor can be removed by three-times washing of 1×B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20). After washing once with 1× SSC buffer (pH 7.0), beads with biotinylated DNA strands were resuspended in freshly prepared 0.15 M NaOH and incubated at room temperature for 10 min, followed by a sequential washing of 1× SSC buffer (7.0) and 1× TE buffer (pH 7.5) for once. The DNA was eluted from C1 beads using deionized water after heating at 95 °C for 3 min.   Eluted DNA was finally subjected to library amplification with indexed primers (NEB). To obtain sufficient DNA template, 2 rounds of amplification were first performed by using MightyAmp DNA polymerase (Takara), which was proved to read through regions containing biotin-dU and d5fC-malononitrile sites more easily. The PCR product was recovered via DNA Clean & Concentrator-5 and then PCR amplified for ~12 cycles using NEBNext® Q5® Hot Start HiFi PCR Master Mix (NEB, M0543). The constructed libraries were checked using the Agilent 2100 bioanalyzer. Sequencing was performed by Illumina Hiseq X Ten.

treatment_protocol: 6.4 × 106 of HEK293T cells or 2.5 × 106 of MCF-7 cells were seeded into 6-well culture plates (Corning) for 16 h growth. Adherent cells were transfected with 4 μg BE and 2720 ng sgRNA plasmids per well using lipofectamine LTX following the manufacturer’s protocol. Cells were then collected after 72 h of transfection.

value: breast derived epithelial cells

tag: genotype

value: Wild Type

tag: experiment

value: PD

value: AP-seq


title: 1d_Male_elav_H3K36me3_2

tag: Sex

value: Male

value: elav


title: MCF7-RNF2-Input_rep1

description:
AP-seq Input rep1 in MCF7 cell
MCF7-RNF2-Detect-seq_on-target.bed
MGISEQ-2000

value: Input


title: 1d_Male_elav_H3K36me3_1

tag: chip antibody


title: MCF7-RNF2-Input_rep2

description:
AP-seq Input rep2 in MCF7 cell
MCF7-RNF2-Detect-seq_on-target.bed
MGISEQ-2000


title: 1d_Male_elav_H3K9me3_1


title: MCF7-HEK4-PD_rep2

description:
AP-seq PD rep2 in MCF7 cell
MCF7-HEK4-Detect-seq_pRBS.bed
MGISEQ-2000


title: MCF7-HEK4-Input_rep1

description:
AP-seq Input rep1 in MCF7 cell
MCF7-HEK4-Detect-seq_pRBS.bed
MGISEQ-2000


title: 1d_Male_elav_H3K36me3_3


title: MCF7-HEK4-Input_rep2

description:
AP-seq Input rep2 in MCF7 cell
MCF7-HEK4-Detect-seq_pRBS.bed
MGISEQ-2000


title: 1d_Female_elav_H3K36me3_4

value: Female


title: MCF7-sgRNADel_rep2.HEK4-on-target

description:
sgRNADel_rep2.HEK4-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx

data_processing:
Library strategy: Targeted amplicon sequencing
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software with the following command: "cutadapt --times 1  -e 0.1  -O 3  --quality-cutoff 25  -m 100 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -A  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o {read1.out}  -p {read2.out}  {read1.in}  {read2.in}"
Alignment step: All FASTQ files are aligned by bwa mem (version = 0.7.15) with default parameters. More information please query www.detect-seq.com
Genome_build: hg38
Supplementary_files_format_and_content: Processed data contains the primer and experiment design information of all target amplicon sequencing data.

extract_protocol:
Genomic DNA was freshly extracted using CWBIO universal genomic DNA kit (CWbiotech, CW2298M) and stored in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) at -80 °C.
Regions flanking the targeting sites were selected for the design of primers, whose overhangs contained the paired Illumina adaptor sequences. In addition, a 10-nt barcode was also added into each primer pairs to lower the detection limit from 10-1 to 10-5 (Primers are listed in the Supplementary). The first round of PCR amplification was performed with NEBNext® Q5® Hot Start HiFi PCR Master Mix (NEB, M0543L) using ~10 ng of genomic DNA as an input template. After ~10 cycles of amplification, the PCR products were purified with 1 × Agencourt AMPure XP beads and eluted with ddH2O. Purified DNA samples were then subjected to the second round of amplification for ~15 cycles and assigned with different indexes followed by a purification with 0.8 × AMPure XP beads. The libraries were quantified with Qubit 2.0 Fluorometer (INVITROGEN) and pooled together for high-throughput sequencing by Illumina HiSeq X Ten (Genetron Health, Beijing).    All FASTQ files in this dataset, have already been grouped by barcode. Meanwhile, the Illumina sequencing errors were trying to be corrected as well (decrease error rate from ~0.1% to ~0.005%). The Python scripts used in this step are available by request to correspondents.

value: Targeted Amplicon Sequencing


title: MCF7-sgRNADel_rep2.RNF2-on-target

description:
sgRNADel_rep2.RNF2-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_elav_H3K36me3_3


title: MCF7-sgRNADel_rep1.HEK4-on-target

description:
sgRNADel_rep1.HEK4-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_H3K27me3_4


title: MCF7-RNF2.All_rep2.RNF2-on-target

description:
RNF2.All_rep2.RNF2-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx

value: BE4max + sgRNA (RNF2)


title: 1d_Female_elav_H3K36me3_2


title: MCF7-sgRNADel_rep1.RNF2-on-target

description:
sgRNADel_rep1.RNF2-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: MCF7-RNF2.All_rep1.RNF2-on-target

description:
RNF2.All_rep1.RNF2-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_elav_H3K36me3_1


title: 1d_Male_elav_H3K27me3_3


title: 1d_Male_elav_H3K27me3_2


title: MCF7-HEK4.All_rep2.HEK4-on-target

description:
HEK4.All_rep2.HEK4-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx

value: BE4max + sgRNA (HEK293T site4)


title: 1d_Female_elav_H3K27me3_4


title: 1d_Female_elav_H3K27me3_2


title: MCF7-HEK4.All_rep1.HEK4-on-target

description:
HEK4.All_rep1.HEK4-on-target in MCF7 cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_H3K27ac_4


title: 1d_Female_elav_H3K27me3_3


title: 1d_Female_elav_H3K27me3_1


title: 293T-sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-53

description:
sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-53 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx

source_name: HEK293T cells

value: embryonic kidney derived epithelial cells


title: 1d_Male_elav_H3K27ac_2


title: 1d_Male_elav_H3K27ac_3


title: 293T-sgRNADel_rep2.EMX1-on-target

description:
sgRNADel_rep2.EMX1-on-target in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-93

description:
sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-93 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_H3K27ac_1

description: Sequential Chromatag-ChIP for elav neuron chromatin


title: 1d_Male_elav_H3K27me3_1


title: 293T-sgRNADel_rep2.VEGFA-Site2-on-target

description:
sgRNADel_rep2.VEGFA-Site2-on-target in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_elav_H3K27ac_4


title: 293T-sgRNADel_rep2.EMX1-Detect-pRBS-4

description:
sgRNADel_rep2.EMX1-Detect-pRBS-4 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep2.EMX1-Detect-Extend-21

description:
sgRNADel_rep2.EMX1-Detect-Extend-21 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep2.EMX1-Detect-Extend-14

description:
sgRNADel_rep2.EMX1-Detect-Extend-14 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep2.EMX1-Detect-pRBS-11

description:
sgRNADel_rep2.EMX1-Detect-pRBS-11 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep2.EMX1-Detect-pRBS-21

description:
sgRNADel_rep2.EMX1-Detect-pRBS-21 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_H3_3


title: 1d_Female_elav_H3K27ac_2


title: 1d_Female_elav_H3K27ac_1


title: 293T-sgRNADel_rep2.EMX1-Detect-pRBS-14

description:
sgRNADel_rep2.EMX1-Detect-pRBS-14 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_H3_4


title: 293T-sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-56

description:
sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-56 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_H3_2


title: Nr17_ID_006033_FinO_OD_2plus6h_2xpur

tag: growth

tag: ip antibody

value: anti-FLAG


title: 293T-sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-120

description:
sgRNADel_rep2.VEGFA-Site2-Detect-pRBS-120 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-on-target

description:
sgRNADel_rep1.VEGFA-Site2-on-target in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-56

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-56 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-93

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-93 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-53

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-53 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_Input_4

description: ChIP input chromatin

value: ChIP Input

value: whole head


title: 1d_Female_elav_H3_2


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-67

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-67 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_Input_3

description: ChIP input chromatin


title: 1d_Female_elav_H3_1


title: 1d_Female_elav_H3_3


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-344

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-344 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_elav_H3_4


title: 1d_Male_elav_H3_1


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-304

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-304 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-270

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-270 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-314

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-314 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_elav_Input_1

description: ChIP input chromatin


title: 1d_Male_elav_Input_2

description: ChIP input chromatin


title: 1d_Female_elav_Input_3

description: ChIP input chromatin


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-264

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-264 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-237

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-237 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-120

description:
sgRNADel_rep1.VEGFA-Site2-Detect-pRBS-120 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: FinO3xFLAG_2


title: 293T-sgRNADel_rep1.VEGFA-Detect-Extend-16

description:
sgRNADel_rep1.VEGFA-Detect-Extend-16 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_elav_Input_1

description: ChIP input chromatin


title: 1d_Female_elav_Input_2

description: ChIP input chromatin


title: 293T-sgRNADel_rep1.VEGFA-Detect-Extend-15

description:
sgRNADel_rep1.VEGFA-Detect-Extend-15 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Detect-Extend-14

description:
sgRNADel_rep1.VEGFA-Detect-Extend-14 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K9me3_4

description: Sequential Chromatag-ChIP for fru P1 neuron chromatin

value: fru P1


title: 10d_Male_H3K9me3_2


title: 10d_Male_H3K9me3_3


title: 10d_Male_H3K9me3_1


title: 293T-sgRNADel_rep1.VEGFA-Detect-Extend-11

description:
sgRNADel_rep1.VEGFA-Detect-Extend-11 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_H3K9me3_4


title: 10d_Female_H3K9me3_3


title: 10d_Female_H3K9me3_1


title: 293T-sgRNADel_rep1.HEK239T-site4-Detect-pRBS-98

description:
sgRNADel_rep1.HEK239T-site4-Detect-pRBS-98 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_elav_Input_4

description: ChIP input chromatin


title: 293T-sgRNADel_rep1.EMX1-on-target

description:
sgRNADel_rep1.EMX1-on-target in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K4me3_4


title: 293T-sgRNADel_rep1.EMX1-Detect-pRBS-7

description:
sgRNADel_rep1.EMX1-Detect-pRBS-7 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.EMX1-Detect-pRBS-4

description:
sgRNADel_rep1.EMX1-Detect-pRBS-4 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K4me3_2


title: 293T-sgRNADel_rep1.EMX1-Detect-pRBS-21

description:
sgRNADel_rep1.EMX1-Detect-pRBS-21 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_H3K4me3_4


title: 293T-sgRNADel_rep1.EMX1-Detect-pRBS-11

description:
sgRNADel_rep1.EMX1-Detect-pRBS-11 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.EMX1-Detect-pRBS-14

description:
sgRNADel_rep1.EMX1-Detect-pRBS-14 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.EMX1-Detect-Extend-21

description:
sgRNADel_rep1.EMX1-Detect-Extend-21 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K4me3_1


title: 293T-sgRNADel_rep1.VEGFA-Detect-Extend-12

description:
sgRNADel_rep1.VEGFA-Detect-Extend-12 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K36me3_4


title: 293T-sgRNADel_rep1.HEK239T-site4-Detect-pRBS-18

description:
sgRNADel_rep1.HEK239T-site4-Detect-pRBS-18 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-9

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-9 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx

value: BE4max + sgRNA (VEGFA site2)


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-80

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-80 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-on-target

description:
VEGFA.All_rep1.VEGFA-Site2-on-target in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.VEGFA-Detect-Extend-13

description:
sgRNADel_rep1.VEGFA-Detect-Extend-13 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_H3K4me3_1


title: 10d_Female_H3K4me3_3


title: 10d_Male_H3K36me3_3


title: 10d_Male_H3K36me3_2


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-93

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-93 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K27me3_3

description: Sequential Chromatag-ChIP for fru P1 neuron chromatin


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-79

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-79 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K27me3_4


title: 10d_Male_H3K36me3_1


title: 10d_Female_H3K36me3_3


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-67

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-67 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K4me3_3


title: 10d_Female_H3K27me3_1


title: 10d_Female_H3K36me3_1


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-64

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-64 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-5

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-5 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-sgRNADel_rep1.EMX1-Detect-Extend-14

description:
sgRNADel_rep1.EMX1-Detect-Extend-14 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-56

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-56 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-345

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-345 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K27me3_1


title: 10d_Male_H3K27me3_2


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-53

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-53 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K27ac_3


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-54

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-54 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-344

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-344 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_H3K27me3_4


title: 10d_Female_H3K27me3_3


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-48

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-48 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-4

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-4 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_H3K36me3_4


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-338

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-338 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-335

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-335 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_H3K27ac_3


title: 10d_Male_H3K27ac_4


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-342

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-342 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-304

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-304 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-331

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-331 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_H3K27ac_1

description: Sequential Chromatag-ChIP for fru P1 neuron chromatin


title: 10d_Male_H3_3


title: 10d_Male_H3K27ac_2


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-298

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-298 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-341

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-341 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-275

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-275 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-33

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-33 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-270

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-270 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3K27ac_1


title: 10d_Female_H3_3


title: 10d_Female_H3K27ac_4


title: 10d_Female_H3_1


title: 10d_Female_H3_4


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-262

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-262 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_H3_2


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-261

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-261 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_Input_4

value: Whole head


title: 10d_Male_H3_4


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-218

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-218 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx

value: Wild Type


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-253

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-253 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Male_Input_3


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-237

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-237 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_Input_4


title: 10d_Male_Input_2


title: 10d_Male_H3_1


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-160

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-160 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-264

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-264 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K9me3_3


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-189

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-189 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-158

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-158 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K9me3_2


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-120

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-120 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_Input_3


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-154

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-154 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K9me3_4

description: Sequential Chromatag-ChIP for fru P1 neuron chromatin


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-153

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-153 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K9me3_1


title: 1d_Female_H3K9me3_3


title: 1d_Female_H3K9me3_4


title: 10d_Male_Input_1


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-24

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-24 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-102

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-102 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-20

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-20 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 10d_Female_Input_1


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-16

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-16 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-22

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-22 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-132

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-132 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-15

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-15 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-14

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-14 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-13

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-13 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K4me3_4


title: 1d_Male_H3K4me3_3


title: 293T-VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-10

description:
VEGFA.All_rep1.VEGFA-Site2-Detect-pRBS-10 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_H3K9me3_1


title: 1d_Male_H3K4me3_1


title: 1d_Female_H3K4me3_4


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-12

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-12 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_H3K4me3_3


title: 293T-VEGFA.All_rep1.VEGFA-Detect-Extend-11

description:
VEGFA.All_rep1.VEGFA-Detect-Extend-11 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-HEK4.All_rep1.HEK239T-site4-on-target

description:
HEK4.All_rep1.HEK239T-site4-on-target in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_H3K4me3_1


title: 1d_Female_H3K9me3_2


title: 1d_Male_H3K36me3_3


title: 1d_Male_H3K4me3_2


title: 293T-HEK4.All_rep1.HEK239T-site4-Detect-pRBS-98

description:
HEK4.All_rep1.HEK239T-site4-Detect-pRBS-98 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-HEK4.All_rep1.HEK239T-site4-Detect-pRBS-85

description:
HEK4.All_rep1.HEK239T-site4-Detect-pRBS-85 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-EMX1.All_rep2.EMX1-on-target

description:
EMX1.All_rep2.EMX1-on-target in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx

value: BE4max + sgRNA (EMX1)


title: 1d_Male_H3K36me3_2

description: Sequential Chromatag-ChIP for fru P1 neuron chromatin


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-9

description:
EMX1.All_rep2.EMX1-Detect-pRBS-9 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-HEK4.All_rep1.HEK239T-site4-Detect-pRBS-56

description:
HEK4.All_rep1.HEK239T-site4-Detect-pRBS-56 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-7

description:
EMX1.All_rep2.EMX1-Detect-pRBS-7 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K36me3_1


title: 1d_Female_H3K36me3_4


title: 1d_Female_H3K36me3_3


title: 1d_Female_H3K36me3_2


title: 1d_Female_H3K36me3_1


title: 1d_Female_H3K4me3_2


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-4

description:
EMX1.All_rep2.EMX1-Detect-pRBS-4 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-3

description:
EMX1.All_rep2.EMX1-Detect-pRBS-3 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-21

description:
EMX1.All_rep2.EMX1-Detect-pRBS-21 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K27me3_4


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-14

description:
EMX1.All_rep2.EMX1-Detect-pRBS-14 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-11

description:
EMX1.All_rep2.EMX1-Detect-pRBS-11 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-15

description:
EMX1.All_rep2.EMX1-Detect-pRBS-15 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Male_H3K36me3_4


title: 1d_Male_H3K27me3_2


title: 1d_Male_H3K27me3_1


title: 1d_Male_H3K27me3_3


title: 1d_Female_H3K27me3_4


title: 293T-EMX1.All_rep2.EMX1-Detect-Potential-2

description:
EMX1.All_rep2.EMX1-Detect-Potential-2 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 293T-EMX1.All_rep2.EMX1-Detect-pRBS-10

description:
EMX1.All_rep2.EMX1-Detect-pRBS-10 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_H3K27me3_3


title: 293T-EMX1.All_rep2.EMX1-Detect-Potential-1

description:
EMX1.All_rep2.EMX1-Detect-Potential-1 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx


title: 1d_Female_H3K27me3_2


title: 1d_Female_H3K27me3_1


title: 293T-EMX1.All_rep2.EMX1-Detect-Extend-6

description:
EMX1.All_rep2.EMX1-Detect-Extend-6 in HEK293T cell
20200615-TargetSeq_experiment_design_processed_data.xlsx