title: DM T3 RNA 1

status: Public on Sep 01 2021

city: Heraklion

first: Christos

last: Delidakis

address: 100 N Plastira St

country: Greece

institute: FORTH-IMBB

data_processing:
Fastq files were downloaded from Illumina-BaseSpace and mapped to dm6 genes (iGenomes UCSC/dm6) using hisat2 version 2.1.0 (--score-min L 0,-0.5)
Bedgraphs were generated using genomecov (bedtools (https://doi.org/10.1093/bioinformatics/btq033), v2.25.0) and uploaded in UCSC genome browser for visualization
Gene counts were computed with htseq-count (-s yes, version 0.11.2)
Differential analysis was performed with SARTools (version 1.5.1) (https://doi.org/10.1371/journal.pone.0157022 ) with default parameters using the edgeR package.
Genome_build: dm6
Supplementary_files_format_and_content: individual bedgraph files depicting  expression levels per gene  and coordinates of the genes in dm6 Drosophila genome
Supplementary_files_format_and_content: supplementary files contain Matrix tables with raw gene counts for every gene and every sample, Fold change(FC), log2FC, p value and p.adj for the indicated comparisons of genotypes

organism: Drosophila melanogaster

source_name: Allograft tumour T3

extract_protocol:
150 larval brains per replica carrying GFP positive actin>F/O clones overexpressing UAS-HA-mγ, UAS-HA-dpn  (DM) were hand dissected, dissociated with collagenase and GFP positive cells were purified by FACS sorting and stored in Trizol. In parallel, larval brains of the same genotype were allografted into adult w1118 host flies and grown for 8-10 days. 25 T0 host flies were sacrificed per replica and the GFP tumour masses were collected in Trizol. Some tumour masses were used to generate more advanced allograft stages. In the forth allograft stage (T3), 25 host flies were again sacrificed per replica and GFP tumour masses were stored in Trizol.  RNA was extracted according to standard protocols.
NGS libraries were generated using total RNA as input with polyA mRNA magnetic isolation kit (NEB) and the NEB Ultra II RNA library kit for Illumina kit according to manufactures protocol, using 13 cycles of amplification. Libraries were sequenced on Illumina Nextseq 500 on 1 x 75 High flowcell.

tag: genotype

value: actinF/O>DM[dpn and E(spl)m{gamma}] overactivation

value: 4th allograft DM tumour (T3) from w1118 adult hosts

value: T3 allograft DM tumours grown for 8-10 days post 4rth transplantation in w1118 adult host flies


title: AOCS18.5_B_FNeg_3

status: Public on Sep 03 2021

type: SRA

city: Melbourne

first: Elizabeth

middle: Louise

last: Christie

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

library_source: transcriptomic

data_processing:
bcl2fastq (v2.20.0.422) was used to demultiplex the sequencing data and convert base call (BCL) files into FASTQ files
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8)
Reads were trimmed for low quality, adapters, N content and poly-A tails using fastq-mcf (v1.05)
Contamination was checked using FastQ Screen (v0.11.4)
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b)
Mapped reads were sorted using Picard Tools (v2.17.3)
Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4)
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the “intersection-nonempty” mode
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts, gene by sample matrix

molecule: total RNA

organism: Homo sapiens

source_name: HGSOC cell

growth_protocol: Cells were seeded (5x10^5-1.5x10^6 cells/plate) in 10cm plates with exponentially growing cells collected 48-72hrs after seeding (approximately 70-80% confluency).

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase digestion. 1ug of RNA was submitted for sequencing.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using standard Illumina protocols

treatment_protocol: Cell lines were grown in RPMI 1640 (GIBCO, USA) media supplemented with 10% HyClone Fetal Bovine Serum (GE Healthcare, USA) and 1% Penicillin-Streptomycin-Glutamine (GIBCO). Cells were cultured in a humidified atmosphere at 37°C containing 5% CO2.

tag: cell line

tag: slc25a40-abcb1 fusion status

value: Fusion Negative


title: AOCS18.5_D_FNeg_1


title: AOCS18.5_C_FNeg_1


title: DM T3 RNA 4

tag: tissue

tag: age


title: AOCS18.5_B_FNeg_1


title: DM T0 RNA 3

source_name: Allograft tumour T0

value: 1st allograft DM tumour (T0) from w1118 adult hosts

value: T0 allograft DM tumours grown for 8-10 days post 1st transplantation in w1118 adult host flies


title: DM FACs RNA2

source_name: Larval CNS

value: larval CNS(FACs sorted GFP positive DM cells)

value: 3rd instar larvae, 4 days post actinF/O>DM clone induction


title: DM T3 RNA 2


title: DM T0 RNA 4


title: DM T0 RNA 2


title: DM FACs RNA4


title: DM FACs RNA1

value: actinFLipout [actinF/O]>DM[dpn and E(spl)m{gamma}] overactivation


title: P30_StrVasc_scRNA_Cisplatin

status: Public on Aug 17 2021

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

country: USA

institute: National Institute on Deafness and Other Communication Disorders

description: P30 Stria Vascularis single cell capture cisplatin treated

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the CellRanger v3.0.1 pipeline using default settings.
Dataset pre-processing, clustering, and data visualization were performed using Scanpy (v1.4.5) package.
Computational removal of doublets was performed using Scrublet (v0.2.1)
Differential expression analysis was performed using DEsingle (v1.6.0).
Regulatory network inference was performed using pySCENIC (v0.10.0).
Genome_build: GRCm38 with custom transcript annotation with introns (pre-mRNA)
Supplementary_files_format_and_content: CellRanger v3.0.1 gene counts matrices.

molecule: polyA RNA

organism: Mus musculus

source_name: P30 Stria Vascularis

extract_protocol:
Single cell suspension from stria vascularis: Published protocol from 10x genomics was used to create a single cell suspension . Briefly, stria vascularis from ~6 P30 animals were isolated and collected in 3ml DMEM F-12 media. Following collection, 10 μL trypsin was added to the tube and incubated for 7 minutes at 37° C. After incubation 150 μL liquid was removed and replaced with 150 μL 10% FBS in DMEM.  The tissue was triturated for 2 minutes to dissociate single cells and then passed through a 20 μm filter.  200 μL of supernatant was removed, leaving a 100 μL final volume. Cells were counted in a Luna cell counter and a cellular density of 1x10^6 cells/ml was used to load onto the 10X genomics chip.
Library preparation was performed according to the manufacturer’s instructions for the 10x Genomics Chromium platform (10x Genomics). The libraries were sequenced on four lanes on a NextSeq500 sequencer (Illumina).

tag: strain

value: CBA/J mice (strain 000656)

value: Stria Vascularis

tag: technique

value: Single cell RNA-seq


title: RNA-AST3-12

status: Public on Jun 15 2021

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
The raw data generated was first assessed for quality using FastQC . Reads were pre-processed to remove the adapter sequences and removal of the low-quality bases (<q30). Pre-processing of the data was done with Cutadapt. An average of 97% of high-quality reads were retained for the downstream analysis.
HISAT2, a splice aligner program, was used to align the sequencing data to the human reference genome using the default parameters. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Reads were then classified into aligned reads (which align to the reference genome) and unaligned reads.
Cufflinks was used to estimate and calculate transcript abundance and normalized read count using Fragments Per Kilobase of transcript per Million mapped reads (or FPKM). Cuffdiff () was then used to identify the differentially expressed transcripts expressed as log2fold change values.
Genome_build: Reference based transcriptome analysis was conducted for the six samples. The reference genome used was GRCh38.p10 Genome Reference Consortium Human Build 38 patch release 10 (GRCh38.p10), downloaded from the Ensemble database.
Supplementary_files_format_and_content: Excel sheet with normalized counts for each sample, log2 fold change, p-value, gene identifier.

source_name: human dopamine neurons derived from iPSCs

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). RNA samples with a measured 28S/18S > 1 and RNA integrity number (RIN) ≥ 7 were used for RNAseq library construction.
RNA-seq library were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.
Approximately 125 ng of total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Barcoded libraries were sized on the bioanalyzer and quantitated by QUBIT. Six individually prepared libraries (n=3 for AST and n=3 for NST) were pooled by equimolar and sequenced by Illumina HiSeq 3000 2X100 cycles run (Illumina Inc., CA, U.S.A). RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression & Genotyping Core, University of Florida (UF).

tag: cell type

value: Cell line


title: RNA-AST1-10


title: RNA-NAS2-8


title: RNA-AST2-11


title: RNA-NAS1-7


title: RNA-NAS3-9


title: Round_Pale_R1

status: Public on Jun 30 2021

data_processing:
Following sequencing, data processing was done using the standard Illumina pipeline and Fastq files were generated for data processing and assembly.
Fast QC was used to evaluate the RNA sequencing quality and Trimmomatic was used to trim low quality reads with a phred score < 20, within a windows of 4 base pairs.The reads after trimming with length < 100 were removed from downstream analysis. The remaining high quality reads were aligned to a Daphnia pulex reference genome using Bowite14 with default parameters
Transcript expression data were obtained at both the gene and isoform level using RSEM5. Expression level estimation was generated as fragments per kilobase of transcript sequence per million mapped fragments (FPKM) value. A small value (0.001) was added to the gene expression for the genes with expression value of 0 to statistically evaluate the data. PCA and cluster analysis were performed to identify outlier samples and no outliers were detected.
Genome_build: http://arthropods.eugenes.org/EvidentialGene/daphnia/daphnia_pulex/daphnia_pulex_genes2017/genes/
Supplementary_files_format_and_content: Excel sheet with normalized counts of genes and isoforms for each sample, and fold change between the two phenotypes in each lake

organism: Daphnia pulicaria

source_name: Adult

extract_protocol:
Thirty animals from each of the four lakes were added directly to 8 mL of RNALater solution. Total RNA was extracted with Trizol Reagent (Thermo Fisher) following the instruction.
The RNA samples were then purified with NEBNext rRNA Depletion kit (NEB E6310). The libraries were constructed using the NEBNext UltraII Directional RNA Library Prep kit for Illumina (NEB E7760) and the NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB E7335).

tag: lake

value: Round

tag: phenotype

value: Pale


title: Black_Pale_R1

value: Black


title: Doe_Red_R1

value: Doe

value: Red


title: Round_Red_R1


title: Doe_Pale_R1


title: Long_Red_R1

value: Long


title: Black_Red_R1


title: Long_Pale_R1


title: 5452_NB

status: Public on Nov 26 2020

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

data_processing:
The raw reads with quality score < 15 were filtered, and then mapped to bovine genome (ARS-UCD1.2.98;https://bovinegenome.elsiklab.missouri.edu/downloads/ARS-UCD1.2 ) using the STAR software. The number of reads uniquely aligned to each gene was calculated using FeatureCounts.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Blood

extract_protocol:
Total RNA was extracted from Tempus tubes using a Preserved Blood RNA Purification Kit (Norgen Biotek Corp.,Thorlord ON, ), and the Nanodrop 1000 (Thermo Scientifc, Willmingotn, DE, USA) and 2200 RNA Screentape Tapestation System (Agilent Technologies Inc, Cedar Creek, TX) were used respectively to quantify and measure the RNA integrity Number for each sample.
All samples had RIN values above 8,0 and were all used for library construction and RNA-seq was performed with samples in 4 separate pools of 12 samples each, with pool 4 having 11 samples.
Total RNA was purified using poly-T oligo-attached magnetic beads and mRNA libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA).

tag: disease status

value: Healthy penmate


title: 5783_NB


title: 5528_NB


title: 5638_NB


title: 5697_NB


title: 5564_NB


title: Patient 10 HNSCC11

status: Public on Mar 09 2021

type: RNA

city: Baltimore

first: Rania

middle: Hassan

last: Younis

address: 650 W Batimore St

department: Oncology and Diagnostic Sciences

institute: University of Maryland School of Dentistry

hyb_protocol: Hybridization was carried in a regular thermal cycler. The hybridized mix was purified using magnetic beads in the nCounter machine in the institute of genome sciences (IGS) University of Maryland, Baltimore.

scan_protocol: nCounter digital analyser scan with 555FOVs was used and image acquisition was on the ncounter SPRINT system

data_processing: Data analysis was carried using IO-360 platform 770 genes code sets using the nSolver 4.0 software basic and advanced costumed analysis.

label: Fluorescent

source_name: Head and neck cancer

label_protocol: Biotinylated capture probes and color coded reporter probes were used for the hybridization complex, according to the manufacturer's protocol

extract_protocol:
Three to five slides of 5 um thick FFPE tissue sections of prospectively collected HNSCC tumor tissue were used for RNA extraction using Rneasy FFPE kit (Qiagen, catalog no 73504). The tumor rich areas and 3-4mm of peritumoral stromal were identified and manually micro-dissected by a surgical oral pathologist (RY) guided by H&E stained section.
RNA quality control (QC) analysis was run on nanochip, to ensure required 200nt in 50-300ng with no prior amplification or enzymatic reaction.

value: Head and neck squamous cell carcinoma

tag: gender

value: Male

tag: location

value: Caucasian

tag: race

value: Oropharynx

tag: Stage

value: I

tag: soluble sema4d

value: High levels

tag: histological inflammatory subtype sema4 score

value: Immune-excluded


title: 9357_NB


title: 5644_NB


title: Patient 6 HNSCC07

value: Female

value: II


title: 9362_NB


title: 5291_NB


title: 9313_NB


title: 5921_NB


title: 5764_NB


title: 9819_NB


title: 9909_NB


title: 9518_NB


title: fetal skeletal muscle at F18, biological rep1

status: Public on May 10 2021

city: Prague 2

first: Jana

last: Krizova

state: Non United States Or Canada

address: Ke Karlovu 2

department: Department of Pediatrics and Inherited Metabolic Disorders

country: Czech Republic

institute: Charles University in Prague, First Faculty of Medicine, and General University Hospital in Prague

description:
RaGene1_120313W_JZ16_A18
RaGene1_120313W_JZ01_A18
Gene expression data from fetal skeletal muscle tissue.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 °C on Rat Gene 1.0 ST Array. Arrays were scanned according to the protocol described in WT Sense Target Labeling Assay Manual (FS450_0007).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Expression console, using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Rattus norvegicus

source_name: Rat 18-day old fetal skeletal muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (RIN>8) using Ambion WT kit.

growth_protocol: The animals were kept and all rat tissues were obtained in the Department of Genetics of Model Diseases, Institute of Physiology CAS (Prague, Czech Republic). The experiments were performed in agreement with the Animal Protection Law of the Czech Republic and were approved by the Ethics Committee of the Institute of Physiology AS CR (Prague, Czech Republic).

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

treatment_protocol: The fetuses were delivered by Caesarean section after sacrifice of pregnant Wistar rat mothers. Adult P90 controls were collected. All tissues were snap frozen in liquid nitrogen immediately. Tissues were stored for further analyses at -80 °C.

value: Wistar rat

value: 18-day old fetus

value: skeletal muscle


title: 5700_BRD

value: BRD


title: fetal skeletal muscle at F18, biological rep5

description:
RaGene1_120313W_JZ20_E18
RaGene1_120313W_JZ01_E18
Gene expression data from fetal skeletal muscle tissue.


title: fetal skeletal muscle at F18, biological rep4

description:
RaGene1_120313W_JZ19_D18
RaGene1_120313W_JZ01_D18
Gene expression data from fetal skeletal muscle tissue.


title: fetal skeletal muscle at F18, biological rep3

description:
RaGene1_120313W_JZ18_C18
RaGene1_120313W_JZ01_C18
Gene expression data from fetal skeletal muscle tissue.


title: 9535_NB


title: fetal skeletal muscle at F18, biological rep2

description:
RaGene1_120313W_JZ17_B18
RaGene1_120313W_JZ01_B18
Gene expression data from fetal skeletal muscle tissue.


title: 9887_BRD


title: 5080_BRD


title: 9777_BRD


title: 9900_BRD


title: 9436_NB


title: 5242_BRD


title: 5725_BRD


title: 9877_BRD


title: 9332_BRD


title: 9830_BRD


title: 9556_BRD


title: 5972_BRD


title: 5321_BRD


title: 9986_BRD


title: 9836_BRD


title: 9499_BRD


title: 9627_BRD


title: 5994_BRD


title: 5913_BRD


title: 5696_BRD


title: 5979_BRD


title: 9504_BRD


title: 5327_BRD


title: 5969_BRD


title: 9497_BRD


title: APC-3

status: Public on Oct 23 2020

city: GLASGOW

first: Karen

last: Pickering

state: Scotland

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: CRUK Beatson institute

description: Small intestinal tissue subjected to tamoxifen induced genetic recombination in vivo

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Matrix of raw counts

source_name: Small intestine

extract_protocol:
RNA extraction perfomed with Qiagen RNeasy kit using Qiagen protocols
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

tag: genotype

value: VilCreER+ Apcfl/fl

tag: genetic background


title: APC-1


title: APC-2


title: APC Kras-3

value: VilCreER+ Apcfl/fl KrasG12D/+


title: APC Kras-1


title: APC Kras-4


title: Patient 3 PA scRNA-seq

status: Public on Oct 21 2020

city: La Jolla

first: Ali

last: Torkamani

state: CA

address: 3344 North Torrey Pines Court, Suite 300

department: Scripps Research Translational Institute

institute: Scripps Research

data_processing:
Library strategy: scRNA-Seq
10X Genomics cellranger count version 3.0.2 with default parameters was used, processing 4 lanes of paired-end fastq files (8 fastq files per sample) into expression matrix data files. This was repeated for each of the 6 samples. The resulting processed files (tar archives) have names formatted as 0?dat2019???????CARcon???_featurebcmatrixfiltered.tar. Concurrently, an h5 molecule info file was created by the same cellranger count processing step, and this h5 files is used for a further aggregation processing step. The 6 sample molecule info files created have the name format 0?dat2019???????CARcon???_moleculeinfo.h5. The GRCh38 transcriptome was used for mapping and alignment by the cellranger count software.
The 6 samples were aggregated together into a single processed file using 10X Genomics cellranger aggr version 3.0.2. Default parameters were applied, including --normalize mapped.
Genome_build: GRCh38 transcriptome
Supplementary_files_format_and_content: There are two processed file types containing similar information. The tar archive files contain 3 text files each and are embodiments of expression data. These are features.tsv.bz, barcodes.tsv.gz, and matrix.mtx.gz. The features file contains the gene ids (rows), the barcodes file contains the cell ids (columns), and the matrix.mtx file contains a sparse representation of the expression data, in the form of row number, column number, and UMI count, separated by spaces. The other processed file is a molecule_info file.h5 containing compressed molecule information typical of 10X Genomics single cell experiments The h5 processed file and is used for producing the aggregated cell data set (tar file).

source_name: Carotid artery proximal adjacent

extract_protocol:
AC and PA  artery tissue from patients undergoing  endarterectomy and was immediately collected from the operating room and transferred on ice for tissue dissociation. Samples were weighed, minced with surgical blades, then placed in conical tubes with pronase (5000U/ml) and collagenase II (0.1% solution). Tissue was then incubated at 37C for one hour with continuous gentle agitation. 30min into the incubation period, DNase I solution was added, and the entire solution remained incubated for an additional 30min. Pipetting mixture up and down every 10min helped break tissue apart. After one-hour incubation was complete, 10% FBS+Complete EC media (Cell Applications, Inc) was immediately added to dissociated tissue to quench enzymatic activity. The sample was then inverted a few times and then set down for 30sec, allowing all debris to settle at the bottom. The entire solution was carefully transferred, without settled debris, to another conical tube (use pipettor to transfer solution near debris pellet carefully, removing all solution but leaving pellet at bottom of tube). Sample was then centrifuged at 500g for 5min and supernatant discarded. Cell pellet was resuspended in 5mL 1X RBC lysis buffer and incubated at RT for 5min. 30mL 1X PBS was added to stop the reaction and the sample was then spun immediately at 500g for 5min at RT. The supernatant was discarded, and cell pellet resuspended in 10mL FACS buffer composed of: 1X PBS, 2.5mM EDTA, 25mM HEPES, 1% FBS (heat-inactivated), and 1% Pen-Strep. To wash excess reagents, the sample is centrifuged again at 500g for 5min, supernatant discarded, then cell pellet is again resuspended in 2mL FACS buffer. 2ul of 5mM DRAQ5 is added to each tube, and solution is pipetted up and down a few times. Next, solution is triturated with P1000 and entire sample sieved through 100uM cell strainer fitted onto 50mL conical tube. This step is repeated next through a 40uM cell strainer. The solution is placed on ice and immediately transported for FACS. Cells were sorted on a MoFLo Astrios EQ cell sorter (Beckman Coulter) with a 100 µm nozzle tip at a sheath pressure of 20 psi. Cells were distinguished from cellular debris by gating DRAQ5 positive events and doublets excluded using appropriate FSC and SSC gating. (Extended Data Fig. 1a-d). Cells isolated represented <1% of the total particles in the sample which was then transported for evaluation of viability and subsequent sequencing. Cells were then processed on the 10X Genomics Chromium single cell 3’ v3 gene expression platform. Cells were counted and checked for viability using a Countess II Automated Cell Counter (Thermo Fisher).
Sequencing libraries were prepared as recommended in the user manual with cell target numbers ranging between 6,000 – 22,000 cells per sample. Completed sequencing libraries were then sequenced on an Illumina NextSeq500 using 28 x 91 paired-end reads with 8 base i7 index reads to demultiplex different samples. Aggregating our 6 samples (3 patient-matched PA and AC samples) resulted in 51,981 cells, a sequencing depth of 15,549 reads/cell, 1,339 median genes/cell and 3,776 UMI/cell.

value: carotid

value: proximal adjacent


title: APC Kras-2


title: MCF7_3324_rep2_RNA

status: Public on Oct 15 2020

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description: bowtie_paired_MCF7_3324_2.gene.mmseq; MCF7_CTRL_3324_treated_cells_raw_reads_2017-04-03.txt; MCF7_CTRL_3324_normalized_readcounts_2017-04-03.txt

data_processing:
The RNA-seq data were mapped using Bowtie mapper against human transcriptome version GRCh37.72 and MMseq to calculate FPKM and raw reads. We used the reads with minimal mapping quality score of 10.
Genome_build: GRCh37.72
Supplementary_files_format_and_content: MMSeq caulculation files, and merged expression data file.

source_name: MCF7 treated with 3324

growth_protocol: MCF7 cells (purchased from ATCC) were cultured in Dulbecco's Modified Eagle Medium  (DMEM; EuroClone), supplemented with 10% heat-inactivated fetal bovine serum (FBS; Sigma-Aldrich),  antimicrobials (100 U/mL penicillin, 100 μg/mL streptomycin, 250 ng/mL amphotericin-B) and 2mM Lglutamine  (EuroClone).

extract_protocol:
The total RNA of cells was extracted using Trizol (Life Technologies) according to manufacturer’s instructions. After DNase treatment, 5 μg of extracted RNA was depleted from ribosomal RNA using Ribo-Zero Gold Kit (Epicenter Madison, Winsconsin, USA). After fragmentation of the rRNA-depleted RNA, 500ng was reverse-transcribed using Super Script III Reverse Transcriptase (Invitrogen) and random primers (Invitrogen) following the manufacturer’s instructions.
Total RNA was extracted from cells using the QIAGEN RNeasy RNA extraction kit (QIAGEN, Netherlands), using on-column DNaseI treatment. Ribosomal RNA was removed using the riboZero rRNA removal kit (Illumina). RNA was then fragmented into 200bp fragments by incubation for 7.5 min at 95°C in fragmentation buffer (200 mM Tris-acetate, 500 mM Potassium Acetate, 150 mM Magnesium Acetate [pH 8.2]). First strand cDNA synthesis was performed using SuperScript III (Life Technologies), followed by synthesis of the second cDNA strand. Library preparation was performed using the KAPA hyperprep kit (KAPA Biosystems). Quality of cDNA and the efficiency of ribosomal RNA removal was confirmed using quantitative RT-PCR using the IQ Sybr Supermix, with primers for GAPDH, 18S and 28S rRNA.   Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 min at 20°C and then for 30 min at 65°C.Subsequently adapters were ligated by adding 30μl ligation buffer, 10 Kapa l DNA ligase, 5 μl diluted adaptor in a total volume of 110μl and incubated for 15 min at 15°C. Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20 μl elution buffer. After post-ligation cleanup, samples were incubated with 3 uL USER enzyme for 15 min at 37°C to digest the 2nd cDNA strand. Libraries were amplified by adding 25 μl 2x KAPA HiFi Hotstart ReadyMix and 5μl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis. Sequencing was performed using Illumina NextSeq 500 machines and generated 43bp single end reads.

treatment_protocol: MCF7 cells were treated DMSO or 25microM of MC3324 inhibitor.

tag: cell line

value: Human breast cancer cells

tag: passages


title: 98_Wapl-C20_24h_RNA_rep2

description: Sample 98

data_processing:
ChIP-seq: Calibrated ChIP-seq data were analyzed based on a modified method described in previously (Orlando et al., 2014). Raw sequencing data was mapped to a concatenated reference genome (mm10 and hg19) using Bowtie 2 mapper (version 2.3.4.1) (Langmead et al., 2009). The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools (version 1.9) (Li et al., 2009). The coverage files (bigWig files) were generated by applying the above computed scaling factor using deepTools (version 2.5.4) (Ramírez et al., 2014), and further calibrated based on average enrichment of the ChIP-seq experiments under direct comparison using their spike-in reference.; Standard ChIP-seq data were mapped to a mm10 reference. The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools. The coverage files of uncalibrated ChIP-seq data and the data of pluripotency factors (due to absence of these factors in HEK293T cells) were generated using “normalize to 1X genome coverage” methods in deepTools. Peak calling was performed using MACS2 (version 2.1.1.20160309) (Liu, 2014) at a q-value cutoff of 0.01.
RNA-seq: Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Hi-C: Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
4C-seq: The raw sequence data was mapped using our 4C mapping pipeline (http://github.com/deWitLab/4C_mapping ).
TT-seq: Raw TT-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) with the following settings adjusted for nascent RNA sequencing: (1) microexon-search, and (2) fr-firststrand. The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene (the entire gene) in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The downstream analysis of TT-seq data was performed using the same settings as RNA-seq for proper data comparison using A DESeq2 package.
ATAC-seq: ATAC-seq data were were mapped against mm10 reference genome using BWA-MEM. The mapped reads with mapping quality score <15, as well as optical PCR duplicates, were discarded using SAMtools. The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. Alignment of ATAC-seq was performed the same as ChIP-seq data.
Genome_build: mm10
Supplementary_files_format_and_content: 1. ChIP-seq: bigWig files; 2. RNA-seq: bigWig files, HTSeq raw read count tables, DESeq2 normalized ratio tables; 3. Hi-C: Hi-C iced matrix, genome abs.bed file; 4. 4C-seq: interaction coverage file, viewpoint information file.

growth_protocol: E14Tg2a (129/Ola isogenic background) and the derived cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 104 U of Leukemia Inhibitory Factor/LIF (Millipore), MEK inhibitor PD0325901 (1 µM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 µM, Cayman Chemical) and 1-Thioglycerol (1.5x10-4 M, Sigma-Aldrich). The cell lines were passaged every 2 days in daily culture. During the protein depletion experiments, the cells were seeded overnight before the start of the time course in the following densities: For a 96 h time course, 2.5 k, 35 k, 150 k, and 400 k cells were seeded in 24-well, 6-well, 10-cm and 15-cm plates, respectively. For 24 h time course, 5 k, 0.5 M, and 4 M cells were seeded in chamber slide (ThermoFisher Scientific), 6-well and 15-cm plates, respectively. The media were refreshed every 2 days during a time course.

extract_protocol:
1. ChIP-seq: All the ChIP-seq experiments, except for H3K27me3, were performed in presence of 10% HEK293T cells as an internal reference using a published protocol with small modifications (Liu et al., 2017). For chromatin preparation, the mouse embryonic stem cells were mixed with 10% HEK293T cells and cross-linked by a final concentration of 1% formaldehyde for 10 min. The cross-linking reaction was quenched using 2.0 M glycine. The cross-linked cells were then lysed and sonicated to obtain ~300 bp chromatin using Bioruptor Plus sonication device (Diagenode). For ChIP assays, antibodies were first coupled with Protein G beads (ThermoFisher Scientific), and then the sonicated chromatin were incubated overnight at 4oC with the antibody coupled Protein G beads. After over incubation, captured chromatin was washed, eluted and de-crosslinked. The released DNA fragments were purified using MiniElute PCR Purification Kit (Qiagen). The ChIP experiments were performed using the following antibodies: (1) WAPL (16370-1-AP, Proteintech), (2) CTCF (07-729, Merck Millipore), (3) RAD21 (ab154769, Abcam), (4) SOX2 (AF2018, R&D Systems), (5) OCT4 (AF1759, R&D Systems), (6) NANOG (RCAB002P-F, Cosmo Bio Co.), (7) MED1 (A300-793A, Bethyl Laboratories), (8) H3K4me3 (pAb-003-050, Diagenode), (9) H3K27ac (ab4729, Abcam), and (10) H3K27me3 (pAb-195-050, Diagenode); 2. RNA-seq: RNA was isolated following a standard TRIzol RNA isolation protocol (Ambion). The cells were lysed using 1 ml of TRIzol reagent, and 200 µl chloroform was added to the lysates. The mixture was vortexed and centrifuged at 12,000 g at 4°C for 15 min. Upper phase was homogenized with 0.5 ml of 100% isopropanol, incubated at room temperature for 10 min, and centrifuged at 4°C for 10 min. The resulted RNA pellet was washed with 75% ice-cold ethanol, dried at room temperature for 10 min, and resuspended in RNase-free water. The isolated RNA was treated with DNase using RNeasy Mini Kit (Qiagen); 3. Hi-C: Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). For each template, 10 million cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI, and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down; 4. 4C-seq was performed as previously described (Geeven et al., 2018; van de Werken et al., 2012) using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). We used MboI as the first restriction enzyme and Csp6I as the second restriction fragment; 5. TT-seq libraries were prepared following a published protocol (Gregersen et al., 2020). The untreated and 500 nM treated WAPL-AID cells (6 and 24 h) were labeled using 2 mM 4SU for 10 min. Total RNA from the labeled cells was isolated and fragmented. Then 4SU labeled RNA fragments were biotinylated and enriched using streptavidin MicroBeads; 6. ATAC-seq libraries were prepared following a published protocol (Liu et al. 2017). Nuclei were isolated, permeabilized, and tagmented using in-house produced Tn5 transposase.
1. ChIP-seq: ChIP-seq libraries were prepared according to the protocol of KAPA HTP Library Preparation Kit (Roche); 2. RNA-seq libraries were prepared using a TruSeq Stranded RNA LT Kit (Illumina); 3. Hi-C libraries were prepared using a standard end-repair and A-tailing method; 4. 4C-seq libraries were prepared using a two-step PCR method for indexing described first in (Haarhuis et al., 2017); 5. TT-seq libraries were prepared using KAPA RNA HyperPrep Kits (Roche) and KAPA Dual-Indexed Adapter Kits (Roche); 6. The resulted DNA fragments underwent two sequential 9-cycle PCR amplification and the fragments < 700 bp were purified using SPRI beads (Liu et al., 2017).
Illumina Hi-C 2500 (ChIP-seq, RNA-seq and 4C-seq: 65 bp single-end), Illumina Hi-C X (Hi-C: 150 bp paired-end), Illumina NextSeq 550 (TT-seq, ATAC-seq: 75 bp paired-end)

treatment_protocol: WAPL and RAD21 depletion were induced by treating the cells with a final concentration of 500 µM IAA (I5148-10G, Sigma Aldrich). OCT4- and NANOG-FKBP proteins were depleted by adding a final concentration of 500 nM dTAG-13 molecule (requested from Dr. Nathanael S. Gray from Dana-Faber Cancer Institute) (Nabet et al., 2018). All the time series experiments were performed by inducing protein degradation at different time points and harvest the samples in the end of the time course.

tag: genetic modification

value: OsTir1; WAPL-AID-eGFP

value: Embyonic stem cell


title: MCF7_3324_rep1_RNA

description: bowtie_paired_MCF7_3324_1.gene.mmseq; MCF7_CTRL_3324_treated_cells_raw_reads_2017-04-03.txt; MCF7_CTRL_3324_normalized_readcounts_2017-04-03.txt


title: MCF7_control_rep1_RNA

description: bowtie_paired_MCF7_control_1.gene.mmseq; MCF7_CTRL_3324_treated_cells_raw_reads_2017-04-03.txt; MCF7_CTRL_3324_normalized_readcounts_2017-04-03.txt

source_name: MCF7 control


title: 104_Wapl-C6_NPC_0h_RNA_rep2

description: Sample 104

value: Neural precursor cell


title: MCF7_control_rep2_RNA

description: bowtie_paired_MCF7_control_2.gene.mmseq; MCF7_CTRL_3324_treated_cells_raw_reads_2017-04-03.txt; MCF7_CTRL_3324_normalized_readcounts_2017-04-03.txt


title: 91_Sox2FKBP-0h_antiRad21

description: Sample 91

library_source: genomic

molecule: genomic DNA


title: 103_Wapl-C6_NPC_0h_RNA_rep1

description: Sample 103


title: 101_Wapl-C20_96h_RNA_rep1

description: Sample 101


title: 97_Wapl-C20_24h_RNA_rep1

description: Sample 97


title: 96_Wapl-C20_6h_RNA_rep2

description: Sample 96


title: 95_Wapl-C20_6h_RNA_rep1

description: Sample 95


title: 92_Sox2FKBP-24h_antiRad21

description: Sample 92


title: 102_Wapl-C20_96h_RNA_rep2

description: Sample 102


title: 85_Rad21-AID_24h_4C_Sik1_rep1

description: 67-90_Viewpoint_4C_samples_2019-07-26.txt

data_processing:
Library strategy: 4C-seq
ChIP-seq: Calibrated ChIP-seq data were analyzed based on a modified method described in previously (Orlando et al., 2014). Raw sequencing data was mapped to a concatenated reference genome (mm10 and hg19) using Bowtie 2 mapper (version 2.3.4.1) (Langmead et al., 2009). The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools (version 1.9) (Li et al., 2009). The coverage files (bigWig files) were generated by applying the above computed scaling factor using deepTools (version 2.5.4) (Ramírez et al., 2014), and further calibrated based on average enrichment of the ChIP-seq experiments under direct comparison using their spike-in reference.; Standard ChIP-seq data were mapped to a mm10 reference. The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools. The coverage files of uncalibrated ChIP-seq data and the data of pluripotency factors (due to absence of these factors in HEK293T cells) were generated using “normalize to 1X genome coverage” methods in deepTools. Peak calling was performed using MACS2 (version 2.1.1.20160309) (Liu, 2014) at a q-value cutoff of 0.01.
RNA-seq: Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Hi-C: Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
4C-seq: The raw sequence data was mapped using our 4C mapping pipeline (http://github.com/deWitLab/4C_mapping ).
Genome_build: mm10
Supplementary_files_format_and_content: 1. ChIP-seq: bigWig files; 2. RNA-seq: bigWig files, HTSeq raw read count tables, DESeq2 normalized ratio tables; 3. Hi-C: Hi-C iced matrix, genome abs.bed file; 4. 4C-seq: interaction coverage file, viewpoint information file.

extract_protocol:
1. ChIP-seq: All the ChIP-seq experiments, except for H3K27me3, were performed in presence of 10% HEK293T cells as an internal reference using a published protocol with small modifications (Liu et al., 2017). For chromatin preparation, the mouse embryonic stem cells were mixed with 10% HEK293T cells and cross-linked by a final concentration of 1% formaldehyde for 10 min. The cross-linking reaction was quenched using 2.0 M glycine. The cross-linked cells were then lysed and sonicated to obtain ~300 bp chromatin using Bioruptor Plus sonication device (Diagenode). For ChIP assays, antibodies were first coupled with Protein G beads (ThermoFisher Scientific), and then the sonicated chromatin were incubated overnight at 4oC with the antibody coupled Protein G beads. After over incubation, captured chromatin was washed, eluted and de-crosslinked. The released DNA fragments were purified using MiniElute PCR Purification Kit (Qiagen). The ChIP experiments were performed using the following antibodies: (1) WAPL (16370-1-AP, Proteintech), (2) CTCF (07-729, Merck Millipore), (3) RAD21 (ab154769, Abcam), (4) SOX2 (AF2018, R&D Systems), (5) OCT4 (AF1759, R&D Systems), (6) NANOG (RCAB002P-F, Cosmo Bio Co.), (7) MED1 (A300-793A, Bethyl Laboratories), (8) H3K4me3 (pAb-003-050, Diagenode), (9) H3K27ac (ab4729, Abcam), and (10) H3K27me3 (pAb-195-050, Diagenode); 2. RNA-seq: RNA was isolated following a standard TRIzol RNA isolation protocol (Ambion). The cells were lysed using 1 ml of TRIzol reagent, and 200 µl chloroform was added to the lysates. The mixture was vortexed and centrifuged at 12,000 g at 4°C for 15 min. Upper phase was homogenized with 0.5 ml of 100% isopropanol, incubated at room temperature for 10 min, and centrifuged at 4°C for 10 min. The resulted RNA pellet was washed with 75% ice-cold ethanol, dried at room temperature for 10 min, and resuspended in RNase-free water. The isolated RNA was treated with DNase using RNeasy Mini Kit (Qiagen); 3. Hi-C: Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). For each template, 10 million cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI, and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down; 4. 4C-seq was performed as previously described (Geeven et al., 2018; van de Werken et al., 2012) using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). We used MboI as the first restriction enzyme and Csp6I as the second restriction fragment.
1. ChIP-seq: ChIP-seq libraries were prepared according to the protocol of KAPA HTP Library Preparation Kit (Roche); 2. RNA-seq libraries were prepared using a TruSeq Stranded RNA LT Kit (Illumina); 3. Hi-C libraries were prepared using a standard end-repair and A-tailing method; 4. 4C-seq libraries were prepared using a two-step PCR method for indexing described first in (Haarhuis et al., 2017)

value: OsTir1; RAD21-AID-eGFP


title: 80_Wapl-C6_0h_4C_Elf3_rep2


title: 86_Rad21-AID_24h_4C_Sik1_rep2


title: 89_Rad21-AID_24h_4C_Elf3_rep1


title: 77_Wapl-C6_24h_4C_Sik1_rep1


title: 79_Wapl-C6_0h_4C_Elf3_rep1


title: 88_Rad21-AID_0h_4C_Elf3_rep2


title: 82_Wapl-C6_24h_4C_Elf3_rep2


title: 81_Wapl-C6_24h_4C_Elf3_rep1


title: 84_Rad21-AID_0h_4C_Sik1_rep2


title: 78_Wapl-C6_24h_4C_Sik1_rep2


title: 87_Rad21-AID_0h_4C_Elf3_rep1


title: 75_Wapl-C6_0h_4C_Sik1_rep1


title: 73_Wapl-C6_24h_4C_Klf9_rep1


title: 76_Wapl-C6_0h_4C_Sik1_rep2


title: 90_Rad21-AID_24h_4C_Elf3_rep2


title: 83_Rad21-AID_0h_4C_Sik1_rep1


title: 69_Wapl-C6_24h_4C_Klf4_rep1


title: 71_Wapl-C6_0h_4C_Klf9_rep1


title: 64_Rad21-AID_24h_RNA_rep2

description:
59-64_Rad21AID_RNA_htseqcounts_unnormalized_2019-07-26.txt
59-64_Rad21AID_RNA_normalized_ratio_2019-07-26.txt

data_processing:
ChIP-seq: Calibrated ChIP-seq data were analyzed based on a modified method described in previously (Orlando et al., 2014). Raw sequencing data was mapped to a concatenated reference genome (mm10 and hg19) using Bowtie 2 mapper (version 2.3.4.1) (Langmead et al., 2009). The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools (version 1.9) (Li et al., 2009). The coverage files (bigWig files) were generated by applying the above computed scaling factor using deepTools (version 2.5.4) (Ramírez et al., 2014), and further calibrated based on average enrichment of the ChIP-seq experiments under direct comparison using their spike-in reference.; Standard ChIP-seq data were mapped to a mm10 reference. The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools. The coverage files of uncalibrated ChIP-seq data and the data of pluripotency factors (due to absence of these factors in HEK293T cells) were generated using “normalize to 1X genome coverage” methods in deepTools. Peak calling was performed using MACS2 (version 2.1.1.20160309) (Liu, 2014) at a q-value cutoff of 0.01.
RNA-seq: Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Hi-C: Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
4C-seq: The raw sequence data was mapped using our 4C mapping pipeline (http://github.com/deWitLab/4C_mapping ).
Genome_build: mm10
Supplementary_files_format_and_content: 1. ChIP-seq: bigWig files; 2. RNA-seq: bigWig files, HTSeq raw read count tables, DESeq2 normalized ratio tables; 3. Hi-C: Hi-C iced matrix, genome abs.bed file; 4. 4C-seq: interaction coverage file, viewpoint information file.


title: 68_Wapl-C6_0h_4C_Klf4_rep2


title: 63_Rad21-AID_24h_RNA_rep1


title: 67_Wapl-C6_0h_4C_Klf4_rep1


title: 74_Wapl-C6_24h_4C_Klf9_rep2


title: 59_Rad21-AID_0h_RNA_rep1


title: 60_Rad21-AID_0h_RNA_rep2


title: 62_Rad21-AID_6h_RNA_rep2


title: 70_Wapl-C6_24h_4C_Klf4_rep2


title: 72_Wapl-C6_0h_4C_Klf9_rep2


title: 58_PT_96h_RNA_rep2

description:
45-58_WaplC6_Parental_RNA_htseqcounts_unnormalized_2019-07-26.txt
45-58_WaplC6_Parental_RNA_normalized_ratio_2019-07-26.txt


title: 54_Wapl-C6_96h_RNA_rep2


title: 57_PT_96h_RNA_rep1


title: 56_PT_0h_RNA_rep2


title: 55_PT_0h_RNA_rep1


title: 51_Wapl-C6_48h_RNA_rep1


title: 43_Nanog-FKBP_0h_antiMed1

value: NANOG-FKBP-eGFP


title: 61_Rad21-AID_6h_RNA_rep1


title: 52_Wapl-C6_48h_RNA_rep2


title: 49_Wapl-C6_24h_RNA_rep1


title: 53_Wapl-C6_96h_RNA_rep1


title: 46_Wapl-C6_0h_RNA_rep2


title: 47_Wapl-C6_6h_RNA_rep1


title: 44_Nanog-FKBP_24h_antiMed1


title: 48_Wapl-C6_6h_RNA_rep2


title: 38_Wapl-C6_24h_antiMed1


title: 39_Rad21-AID_0h_antiMed1


title: 36_Rad21-AID_24h_antiNanog


title: 37_Wapl-C6_0h_antiMed1


title: 35_Rad21-AID_0h_antiNanog


title: 42_Oct4-FKBP_24h_antiMed1


title: 45_Wapl-C6_0h_RNA_rep1


title: 50_Wapl-C6_24h_RNA_rep2


title: 34_Wapl-C6_24h_antiOct4


title: 41_Oct4-FKBP_0h_antiMed1


title: 33_Wapl-C6_0h_antiOct4


title: 40_Rad21-AID_24h_antiMed1


title: 32_Wapl-C6_24h_antiSox2


title: 30_Wapl-C6_24h_antiNanog


title: 28_Wapl-C6_96h_antiH3K27me3


title: 27_Wapl-C6_0h_antiH3K27me3


title: 25_Wapl-C6_24h_antiH3K27ac


title: 26_Wapl-C6_96h_antiH3K27ac


title: 24_Wapl-C6_6h_antiH3K27ac


title: 23_Wapl-C6_0h_antiH3K27ac


title: 22_Wapl-C6_96h_antiH3K4me3


title: 20_Wapl-C6_6h_antiH3K4me3


title: 21_Wapl-C6_24h_antiH3K4me3


title: 19_Wapl-C6_0h_antiH3K4me3


title: 130_Wapl-C6_24on24off_4Cwashoff_Klf4SE_rep2

description: Sample 130

data_processing:
Library strategy: 4C-seq
ChIP-seq: Calibrated ChIP-seq data were analyzed based on a modified method described in previously (Orlando et al., 2014). Raw sequencing data was mapped to a concatenated reference genome (mm10 and hg19) using Bowtie 2 mapper (version 2.3.4.1) (Langmead et al., 2009). The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools (version 1.9) (Li et al., 2009). The coverage files (bigWig files) were generated by applying the above computed scaling factor using deepTools (version 2.5.4) (Ramírez et al., 2014), and further calibrated based on average enrichment of the ChIP-seq experiments under direct comparison using their spike-in reference.; Standard ChIP-seq data were mapped to a mm10 reference. The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools. The coverage files of uncalibrated ChIP-seq data and the data of pluripotency factors (due to absence of these factors in HEK293T cells) were generated using “normalize to 1X genome coverage” methods in deepTools. Peak calling was performed using MACS2 (version 2.1.1.20160309) (Liu, 2014) at a q-value cutoff of 0.01.
RNA-seq: Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Hi-C: Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
4C-seq: The raw sequence data was mapped using our 4C mapping pipeline (http://github.com/deWitLab/4C_mapping ).
TT-seq: Raw TT-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) with the following settings adjusted for nascent RNA sequencing: (1) microexon-search, and (2) fr-firststrand. The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene (the entire gene) in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The downstream analysis of TT-seq data was performed using the same settings as RNA-seq for proper data comparison using A DESeq2 package.
ATAC-seq: ATAC-seq data were were mapped against mm10 reference genome using BWA-MEM. The mapped reads with mapping quality score <15, as well as optical PCR duplicates, were discarded using SAMtools. The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. Alignment of ATAC-seq was performed the same as ChIP-seq data.
Genome_build: mm10
Supplementary_files_format_and_content: 1. ChIP-seq: bigWig files; 2. RNA-seq: bigWig files, HTSeq raw read count tables, DESeq2 normalized ratio tables; 3. Hi-C: Hi-C iced matrix, genome abs.bed file; 4. 4C-seq: interaction coverage file, viewpoint information file.


title: 18_Nanog-FKBP_24h_antiRad21


title: 17_Nanog-FKBP_0h_antiRad21


title: 129_Wapl-C6_24on24off_4Cwashoff_Klf4SE_rep1

description: Sample 129


title: 15_Oct4-FKBP_0h_antiRad21_rep2


title: 31_Wapl-C6_0h_antiSox2


title: 128_Wapl-C6_24h_4Cwashoff_Klf4SE_rep2

description: Sample 128


title: 14_Oct4-FKBP_24h_antiRad21_rep1


title: 13_Oct4-FKBP_0h_antiRad21_rep1


title: 29_Wapl-C6_0h_antiNanog


title: 11_WaplNPC-C6_0h_antiRad21_rep2


title: 12_WaplNPC-C6_24h_antiRad21_rep2


title: 127_Wapl-C6_24h_4Cwashoff_Klf4SE_rep1

description: Sample 127


title: 126_Wapl-C6_0h_4Cwashoff_Klf4SE_rep2

description: Sample 126


title: 10_WaplNPC-C6_24h_antiRad21_rep1


title: 124_Wapl-C6_24on24off_4Cwashoff_Sik1promoter_rep2

description: Sample 124


title: 125_Wapl-C6_0h_4Cwashoff_Klf4SE_rep1

description: Sample 125


title: 8_Wapl-C20_24h_antiRad21


title: 123_Wapl-C6_24on24off_4Cwashoff_Sik1promoter_rep1

description: Sample 123


title: 16_Oct4-FKBP_24h_antiRad21_rep2


title: 121_Wapl-C6_24h_4Cwashoff_Sik1promoter_rep1

description: Sample 121


title: 122_Wapl-C6_24h_4Cwashoff_Sik1promoter_rep2

description: Sample 122


title: 7_Wapl-C20_0h_antiRad21


title: 120_Wapl-C6_0h_4Cwashoff_Sik1promoter_rep2

description: Sample 120


title: 6_Wapl-C6_24h_antiRad21


title: 5_Wapl-C6_0h_antiRad21


title: 4_Wapl-C6_24h_antiCtcf


title: 118_NANOG-FKBP_24h_ATAC

description: Sample 118


title: 116_OCT4-FKBP_24h_ATAC

description: Sample 116


title: 3_Wapl-C6_0h_antiCtcf


title: 115_OCT4-FKBP_0h_ATAC

description: Sample 115


title: 1_Wapl-C6_0h_antiWapl


title: 114_SOX2-FKBP_24h_ATAC

description: Sample 114


title: 113_SOX2-FKBP_0h_ATAC

description: Sample 113


title: 109_Wapl-C6_6h_TTseq_rep1

description: Sample 109

data_processing:
Library strategy: TT-seq
ChIP-seq: Calibrated ChIP-seq data were analyzed based on a modified method described in previously (Orlando et al., 2014). Raw sequencing data was mapped to a concatenated reference genome (mm10 and hg19) using Bowtie 2 mapper (version 2.3.4.1) (Langmead et al., 2009). The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools (version 1.9) (Li et al., 2009). The coverage files (bigWig files) were generated by applying the above computed scaling factor using deepTools (version 2.5.4) (Ramírez et al., 2014), and further calibrated based on average enrichment of the ChIP-seq experiments under direct comparison using their spike-in reference.; Standard ChIP-seq data were mapped to a mm10 reference. The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools. The coverage files of uncalibrated ChIP-seq data and the data of pluripotency factors (due to absence of these factors in HEK293T cells) were generated using “normalize to 1X genome coverage” methods in deepTools. Peak calling was performed using MACS2 (version 2.1.1.20160309) (Liu, 2014) at a q-value cutoff of 0.01.
RNA-seq: Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Hi-C: Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
4C-seq: The raw sequence data was mapped using our 4C mapping pipeline (http://github.com/deWitLab/4C_mapping ).
TT-seq: Raw TT-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) with the following settings adjusted for nascent RNA sequencing: (1) microexon-search, and (2) fr-firststrand. The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene (the entire gene) in “Mus Musculus GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The downstream analysis of TT-seq data was performed using the same settings as RNA-seq for proper data comparison using A DESeq2 package.
ATAC-seq: ATAC-seq data were were mapped against mm10 reference genome using BWA-MEM. The mapped reads with mapping quality score <15, as well as optical PCR duplicates, were discarded using SAMtools. The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. Alignment of ATAC-seq was performed the same as ChIP-seq data.
Genome_build: mm10
Supplementary_files_format_and_content: 1. ChIP-seq: bigWig files; 2. RNA-seq: bigWig files, HTSeq raw read count tables, DESeq2 normalized ratio tables; 3. Hi-C: Hi-C iced matrix, genome abs.bed file; 4. 4C-seq: interaction coverage file, viewpoint information file.


title: 110_Wapl-C6_6h_TTseq_rep2

description: Sample 110


title: 112_Wapl-C6_24h_TTseq_rep2

description: Sample 112


title: 9_WaplNPC-C6_0h_antiRad21_rep1


title: 107_Wapl-C6_0h_TTseq_rep1

description: Sample 107


title: 111_Wapl-C6_24h_TTseq_rep1

description: Sample 111


title: 108_Wapl-C6_0h_TTseq_rep2

description: Sample 108


title: 119_Wapl-C6_0h_4Cwashoff_Sik1promoter_rep1

description: Sample 119


title: H3K4me3-TestisPortion-P7-Wt-To-R2-L6089

status: Public on Oct 09 2020

city: Berlin

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: To_Histones_segmentation_TestisPortion.bed

data_processing:
Each ChIPseq sample was mapped to the talOcc4 genome using STAR v2.6.1d (Dobin et al., 2013). In order to force an unspliced end-to-end alignment of the 50bp reads and to report only unique alignments the following options were applied: --alignEndsType EndToEnd   alignIntronMax 1   outFilterMatchNminOverLread 0.94 --outFilterMismatchNmax 5 --outFilterMultimapNmax 1.
Histone modification data was segmented genome-wide and classified into 7 modification states by applying the tool EpiCseg (Mammana et al., 2015).  If a state was supported by <50 regions the respective genomic regions were excluded from segmentation and EpiCseg was rerun.
Genome_build: talOcc4, mm9

organism: Talpa occidentalis

source_name: Testicular part of the ovotestis

extract_protocol:
Chromatin immunoprecipitations were performed using the iDeal ChIP-seq kit for Histones (Cat. No. C01010051) according guidelines.
Whole fixed gonads were sonicated with a Bioruptor (45 cycles 30sec on, 30 sec off at high power) in the shearing buffer from the kit. 5 mg of chromatin was used in each immunoprecipitation with 1mg of the following specific histones antibodies: anti-H3K4me3, Millipore, cat. No. 07-473; anti-H3K4me1, Diagenode, cat. No. C15410037; anti-H3K27ac, Diagenode, cat. No. C15410174; anti-H3K27me3, Millipore, cat. No. 07-449. Libraries were prepared using the Nextera adaptors and sequenced

treatment_protocol: Gonads from P7 mole animals and from E13.5 mouse embryos were fixed at 1% FA, snap freeze and store at -80°C.

value: Wild type

tag: embryonic stage

value: Post-partum day 7


title: H3K4me3-Testis-P7-Wt-To-R2-L6077

source_name: Testis


title: H3K4me3-OvaryPortion-P7-Wt-To-R1-L6082

description: To_Histones_segmentation_OvaryPortion.bed

source_name: Ovarian part of the ovotestis


title: H3K4me1-TestisPortion-P7-Wt-To-R2-L6731


title: H3K4me3-TestisPortion-P7-Wt-To-R1-L6088


title: H3K4me1-Testis-P7-Wt-To-R2-L6730


title: H3K4me1-Testis-P7-Wt-To-R1-L6179


title: H3K27ac-TestisPortion-P7-Wt-To-R2-L6091


title: 2_Wapl-C6_24h_antiWapl


title: H3K27ac-TestisPortion-P7-Wt-To-R1-L6090


title: H3K27ac-Testis-P7-Wt-To-R2-L6079


title: 117_NANOG-FKBP_0h_ATAC

description: Sample 117


title: H3K4me1-OvaryPortion-P7-Wt-To-R1-L6180


title: bulk [NextFlex_NB_0319_006_S6]

status: Public on Sep 10 2020

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

institute: UMCG Groningen

description:
bulk
mechanical

data_processing:
The NEXTflex barcode (9 base pairs) was stripeed from the sequence, using a custom bash script. The barcode was saved in a separate file for further use.
The sequencing reads were aligned with HISAT2 (version 2.1.0) to the GRCh38.92 reference genome with Ensembl annotation.
Further processing was done with samtools (version 1.9) and Picard Tools (version 1.140). This included sorting, assigning reads to a read group, verification of mate pair information and marking duplicates.
After these processing steps, reads were quantified using featureCounts (Subread version 1.6.2)
Reads from bulk samples were deduplicated using a bash script by BIOO Scientific (v2, date 11/1/14) , using the NEXTflex barcode that was saved in the additional file.
Genome_build: Homo.sapiens.GRCh38.92
Supplementary_files_format_and_content: A tab-delimited text file per sample containing gene counts used for bulk-sequencing (n=25).
Supplementary_files_format_and_content: UMItools_GEO.py: Demultiplexing and alignment pipeline.
Supplementary_files_format_and_content: readinCBC.csv contains the custom cell barcodes for Smartseq2 sequencing data.

source_name: brain

extract_protocol:
Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of viable (DAPI-, DRAQ5+), CD45+, CD11B+ cells.
All 25 RNA samples, with RIN values varying between 5.1 and 9.9, were enriched for poly(A)+ messenger RNA using NEXTflex Poly(A) Beads (BIOO Scientific, #NOVA-512980) according to the protocol in the manual. Fourteen µL of this mRNA-enriched poly(A)-tailed RNA was used as the input for the NEXTflex Rapid Directional qRNA-Seq kit (Bioo Scientific, #NOVA-5130-04). Library preparation was performed according to the manufacturers protocol. Quality and concentration of libraries from individual samples were assessed using the High Sensitivity dsDNA kit (Agilent, 067-4626) on a 2100 Bioanalyzer (Agilent) and a Qubit 2.0 Fluorometer (Life Technologies). Subsequently, individual libraries were combined into 3 sequencing pools with equal molar input per sample. 75bp paired-end sequencing was performed on an Illumina NextSeq 500 system. PhiX was added at 5% to both pools as an internal control before sequencing.

value: microglia

tag: donor group

value: CTR+

tag: donor id

tag: brain bank

value: NetherlandsBrainBank

tag: brain region

value: LPS

tag: sequencing pool

tag: age

value: M

tag: ph csf

tag: post mortem delay (h.mm)

tag: sorter

tag: passedpreprocessingqc

value: YES


title: H3K27ac-OvaryPortion-P7-Wt-To-R2-L6085


title: bulk [BE_RNAseq_Pool_II_013_S13]

description: mechanical

data_processing:
The NEXTflex barcode (9 base pairs) was stripeed from the sequence, using a custom bash script. The barcode was saved in a separate file for further use.
The sequencing reads were aligned with HISAT2 (version 2.1.0) to the GRCh38.92 reference genome with Ensembl annotation.
Further processing was done with samtools (version 1.9) and Picard Tools (version 1.140). This included sorting, assigning reads to a read group, verification of mate pair information and marking duplicates.
After these processing steps, reads were quantified using featureCounts (Subread version 1.6.2)
Reads from bulk samples were deduplicated using a bash script by BIOO Scientific (v2, date 11/1/14) , using the NEXTflex barcode that was saved in the additional file.
Genome_build: Homo.sapiens.GRCh38.92
Supplementary_files_format_and_content: A tab-delimited text file per sample containing gene counts used for bulk-sequencing (n=25).
Reads from bc-Smart-seq2 single cells were demultiplexed based on cell barcodes using UMI-tools (version 0.5.3)
Reads without cell barcode or UMIs were removed and remaining raw reads were aligned to the human genome using HiSat2 (v.2.1.0) in single-end mode.
Primary counts were quantified with the function featureCounts (Subread version 1.6.0) using the flag –primary and -R BAM to save the BAM file.
PCR duplicates were removed and unique molecules were counted per gene and per cell using the function UMI-tools count
Genome_build: Homo.sapiens.GrCh38.91
Supplementary_files_format_and_content: A tab-delimited text file per sample containing gene counts of 1 pool (~84 single cells). Pools were combined into 20 superpools and used for bc-Smart-Seq2 single cell RNA sequencing (193 pools, n = 16 samples).
Reads from 10x Genomics Chromium single cells were demultiplexed and aligned to the GRCh38 genome with Ensembl transcriptome annotation with Cell Ranger using default parameters.
The demultiplexed fastq files were used as input for the 10x Genomics pipeline Cell ranger.
Barcode filtering was performed with the R package DropletUtils with a threshold of > 100 UMIs per barcode.
Genome_build: Homo.sapiens.GrCh38
Supplementary_files_format_and_content: A tab-separated barcodes text file, a tab-separated gene text file and a market exchange format (MEX) sparse count matrix per sample.
Supplementary_files_format_and_content: UMItools_GEO.py: Demultiplexing and alignment pipeline.
Supplementary_files_format_and_content: readinCBC.csv contains the custom cell barcodes for Smartseq2 sequencing data.

extract_protocol:
Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of viable (DAPI-, DRAQ5+), CD45+, CD11B+ cells.
All 25 RNA samples, with RIN values varying between 5.7 and 9.9, were enriched for poly(A)+ messenger RNA using NEXTflex Poly(A) Beads (BIOO Scientific, #NOVA-512980) according to the protocol in the manual. Fourteen µL of this mRNA-enriched poly(A)-tailed RNA was used as the input for the NEXTflex Rapid Directional qRNA-Seq kit (Bioo Scientific, #NOVA-5130-04). Library preparation was performed according to the manufacturers protocol. Quality and concentration of libraries from individual samples were assessed using the High Sensitivity dsDNA kit (Agilent, 067-4626) on a 2100 Bioanalyzer (Agilent) and a Qubit 2.0 Fluorometer (Life Technologies). Subsequently, individual libraries were combined into 2 sequencing pools of 13 samples each with equal molar input. 75bp paired-end sequencing was performed on an Illumina NextSeq 500 system. PhiX was added at 5% to both pools as an internal control before sequencing.
single cell RNA-Seq, bc-Smart-seq2 :Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, viable (DAPI-, DRAQ5+), CD45+, CD11B+ cells.
single cell RNA-Seq, bc-Smart-seq2 : After cell lysis and barcoded poly-dT primer annealing, RNA was reverse-transcribed with a biotinylated barcoded template switching oligo (BC-TSO). Primer-dimers and small fragments were removed by exonuclease treatment. cDNA libraries were amplified and multiplexed. When cDNA libraries showed an average size of 1.5-2 kb, libraries were tagmented and indexed according to the Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1024) with an input of 500 pg cDNA. Samples were sequence on an Ilumina NextSeq 500. using 75 bp paired-end reads. Read 1 comprises the poolbarcode and read 2 the cDNA.
10X Genomics: Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of viable (DAPI-, DRAQ5+), CD45+, CD11B+ cells.
10X Genomics: The single-cell barcoded libraries were constructed according to the instructions of the Single Cell 3’ Reagent Kits v2 (10x Genomics). Briefly, cells were loaded into a slot of a Chromium chip and GEMs were incubated in a thermal cycler to generate barcoded cDNA. After amplification, the cDNA was fragmented and processed for sequencing by ligating adapters and sample indices. The libraries were sequenced on an Illumina NextSeq 500 system with a sequencing depth up to 20,000 reads per cell.

tag: cell type

value: CTR

value: GFS

tag: gender

value: F


title: bulk [NextFlex_NB_0319_012_S12]

description:
bulk
mechanical

value: AD


title: H3K27ac-Testis-P7-Wt-To-R1-L6178

tag: genotype


title: bulk [BE_RNAseq_Pool_II_012_S12]

description: mechanical


title: bulk [BE_RNAseq_Pool_II_011_S11]

description: mechanical


title: H3K4me3-Testis-P7-Wt-To-R1-L6076


title: bulk [BE_RNAseq_Pool_II_010_S10]

description: mechanical


title: H3K4me1-TestisPortion-P7-Wt-To-R1-L6181


title: H3K4me3-OvaryPortion-P7-Wt-To-R2-L6083


title: bulk [NextFlex_NB_0319_002_S2]

description:
bulk
mechanical


title: bulk [BE_RNAseq_Pool_II_006_S6]

description: mechanical


title: H3K4me1-OvaryPortion-P7-Wt-To-R2-L6732


title: bulk [BE_RNAseq_Pool_II_002_S2]

description: mechanical


title: bulk [BE_RNAseq_Pool_I_012_S1]

description: mechanical


title: bulk [BE_RNAseq_Pool_I_010_S3]

description: mechanical


title: bulk [BE_RNAseq_Pool_I_011_S2]

description: mechanical


title: bulk [BE_RNAseq_Pool_II_001_S1]

description: mechanical


title: H3K27ac-OvaryPortion-P7-Wt-To-R1-L6084


title: bulk [BE_RNAseq_Pool_I_008_S11]

description: mechanical


title: bulk [BE_RNAseq_Pool_I_009_S12]

description: mechanical


title: bulk [NextFlex_NB_0319_003_S3]

description:
bulk
mechanical


title: bulk [BE_RNAseq_Pool_I_006_S9]

description: mechanical


title: bulk [BE_RNAseq_Pool_I_003_S6]

description: mechanical


title: bulk [BE_RNAseq_Pool_I_004_S7]

description: mechanical


title: bulk [BE_RNAseq_Pool_I_001_S4]

description: mechanical


title: bulk [BE_RNAseq_Pool_II_009_S9]

description: mechanical


title: 10x_genomics [10X_Donor2019-010]

value: MCI


title: single_cell_barcoded_SmartSeq2 [54-3]

value: Sony


title: single_cell_barcoded_SmartSeq2 [60-1]

value: XDP


title: single_cell_barcoded_SmartSeq2 [62-4]


title: single_cell_barcoded_SmartSeq2 [63-2]


title: 10x_genomics [10X_Donor2018-135]


title: bulk [BE_RNAseq_Pool_I_013_S13]

description: mechanical


title: single_cell_barcoded_SmartSeq2 [59-2]


title: bulk [BE_RNAseq_Pool_II_004_S4]

description: mechanical


title: single_cell_barcoded_SmartSeq2 [55-4]


title: bulk [BE_RNAseq_Pool_I_005_S8]

description: mechanical


title: single_cell_barcoded_SmartSeq2 [57-2]


title: single_cell_barcoded_SmartSeq2 [61-1]


title: single_cell_barcoded_SmartSeq2 [58-3]


title: single_cell_barcoded_SmartSeq2 [55-2]


title: bulk [BE_RNAseq_Pool_I_002_S5]

description: mechanical


title: single_cell_barcoded_SmartSeq2 [49-4]


title: single_cell_barcoded_SmartSeq2 [51-1]


title: single_cell_barcoded_SmartSeq2 [60-4]


title: single_cell_barcoded_SmartSeq2 [50-4]


title: single_cell_barcoded_SmartSeq2 [47-3]


title: single_cell_barcoded_SmartSeq2 [46-3]


title: single_cell_barcoded_SmartSeq2 [54-4]


title: single_cell_barcoded_SmartSeq2 [56-2]


title: single_cell_barcoded_SmartSeq2 [55-3]


title: single_cell_barcoded_SmartSeq2 [58-1]


title: single_cell_barcoded_SmartSeq2 [59-3]


title: single_cell_barcoded_SmartSeq2 [50-2]


title: single_cell_barcoded_SmartSeq2 [57-3]


title: single_cell_barcoded_SmartSeq2 [59-4]


title: single_cell_barcoded_SmartSeq2 [62-1]


title: single_cell_barcoded_SmartSeq2 [58-4]


title: single_cell_barcoded_SmartSeq2 [49-1]


title: single_cell_barcoded_SmartSeq2 [46-1]


title: single_cell_barcoded_SmartSeq2 [47-4]


title: single_cell_barcoded_SmartSeq2 [56-3]


title: single_cell_barcoded_SmartSeq2 [53-2]


title: single_cell_barcoded_SmartSeq2 [57-1]


title: single_cell_barcoded_SmartSeq2 [50-3]


title: single_cell_barcoded_SmartSeq2 [45-1]


title: single_cell_barcoded_SmartSeq2 [53-3]


title: single_cell_barcoded_SmartSeq2 [51-4]


title: single_cell_barcoded_SmartSeq2 [49-3]


title: single_cell_barcoded_SmartSeq2 [60-2]


title: single_cell_barcoded_SmartSeq2 [52-3]


title: single_cell_barcoded_SmartSeq2 [58-2]


title: single_cell_barcoded_SmartSeq2 [55-1]


title: single_cell_barcoded_SmartSeq2 [46-2]


title: single_cell_barcoded_SmartSeq2 [59-1]


title: single_cell_barcoded_SmartSeq2 [52-4]


title: single_cell_barcoded_SmartSeq2 [60-3]


title: single_cell_barcoded_SmartSeq2 [54-1]


title: single_cell_barcoded_SmartSeq2 [48-2]


title: single_cell_barcoded_SmartSeq2 [53-4]

value: AntwerpUniversityHospital


title: single_cell_barcoded_SmartSeq2 [40-2]

value: Astrios


title: single_cell_barcoded_SmartSeq2 [57-4]


title: single_cell_barcoded_SmartSeq2 [32-3]


title: single_cell_barcoded_SmartSeq2 [27-3.2]


title: single_cell_barcoded_SmartSeq2 [56-4]


title: single_cell_barcoded_SmartSeq2 [54-2]

value: NO


title: single_cell_barcoded_SmartSeq2 [52-2]


title: single_cell_barcoded_SmartSeq2 [48-4]


title: single_cell_barcoded_SmartSeq2 [43-1.2]


title: single_cell_barcoded_SmartSeq2 [45-3]


title: single_cell_barcoded_SmartSeq2 [51-2]


title: single_cell_barcoded_SmartSeq2 [47-2]


title: single_cell_barcoded_SmartSeq2 [52-1]


title: single_cell_barcoded_SmartSeq2 [43-2]


title: single_cell_barcoded_SmartSeq2 [50-1]


title: single_cell_barcoded_SmartSeq2 [51-3]


title: single_cell_barcoded_SmartSeq2 [33-2]


title: single_cell_barcoded_SmartSeq2 [48-1]


title: single_cell_barcoded_SmartSeq2 [53-1]


title: single_cell_barcoded_SmartSeq2 [45-4]


title: single_cell_barcoded_SmartSeq2 [42-1]


title: single_cell_barcoded_SmartSeq2 [46-4]


title: single_cell_barcoded_SmartSeq2 [49-2]


title: single_cell_barcoded_SmartSeq2 [44-1.2]


title: single_cell_barcoded_SmartSeq2 [29-1]


title: single_cell_barcoded_SmartSeq2 [48-3]


title: single_cell_barcoded_SmartSeq2 [37-3]


title: single_cell_barcoded_SmartSeq2 [15-2.2]


title: single_cell_barcoded_SmartSeq2 [43-4]


title: single_cell_barcoded_SmartSeq2 [30-3.3]


title: single_cell_barcoded_SmartSeq2 [5-4.2]


title: single_cell_barcoded_SmartSeq2 [35-4]


title: single_cell_barcoded_SmartSeq2 [32-4]


title: single_cell_barcoded_SmartSeq2 [29-3]


title: single_cell_barcoded_SmartSeq2 [27-2.2]


title: single_cell_barcoded_SmartSeq2 [39-1]


title: single_cell_barcoded_SmartSeq2 [27-1]


title: single_cell_barcoded_SmartSeq2 [45-2]


title: single_cell_barcoded_SmartSeq2 [42-3]


title: single_cell_barcoded_SmartSeq2 [41-3]


title: single_cell_barcoded_SmartSeq2 [29-4]


title: single_cell_barcoded_SmartSeq2 [33-1]


title: single_cell_barcoded_SmartSeq2 [32-2]


title: single_cell_barcoded_SmartSeq2 [43-3]


title: single_cell_barcoded_SmartSeq2 [27-4]


title: single_cell_barcoded_SmartSeq2 [39-3]


title: single_cell_barcoded_SmartSeq2 [37-4]


title: single_cell_barcoded_SmartSeq2 [30-3.2]


title: single_cell_barcoded_SmartSeq2 [42-2]


title: single_cell_barcoded_SmartSeq2 [30-1]


title: single_cell_barcoded_SmartSeq2 [42-4]


title: single_cell_barcoded_SmartSeq2 [35-2]


title: single_cell_barcoded_SmartSeq2 [24-1]


title: single_cell_barcoded_SmartSeq2 [39-2]


title: single_cell_barcoded_SmartSeq2 [29-2]


title: single_cell_barcoded_SmartSeq2 [41-2]


title: single_cell_barcoded_SmartSeq2 [44-4]


title: single_cell_barcoded_SmartSeq2 [37-2]


title: single_cell_barcoded_SmartSeq2 [43-1]


title: single_cell_barcoded_SmartSeq2 [26-4]


title: single_cell_barcoded_SmartSeq2 [14-4]


title: single_cell_barcoded_SmartSeq2 [41-4]


title: single_cell_barcoded_SmartSeq2 [37-1]


title: single_cell_barcoded_SmartSeq2 [30-3]


title: single_cell_barcoded_SmartSeq2 [40-1]


title: single_cell_barcoded_SmartSeq2 [44-3]


title: single_cell_barcoded_SmartSeq2 [27-2]


title: single_cell_barcoded_SmartSeq2 [35-1]


title: single_cell_barcoded_SmartSeq2 [30-2]


title: single_cell_barcoded_SmartSeq2 [41-1]


title: single_cell_barcoded_SmartSeq2 [24-4]


title: single_cell_barcoded_SmartSeq2 [39-4]


title: single_cell_barcoded_SmartSeq2 [14-3]


title: single_cell_barcoded_SmartSeq2 [26-3]


title: single_cell_barcoded_SmartSeq2 [40-4]


title: single_cell_barcoded_SmartSeq2 [24-3]


title: single_cell_barcoded_SmartSeq2 [30-4]


title: single_cell_barcoded_SmartSeq2 [24-2]


title: single_cell_barcoded_SmartSeq2 [44-1]


title: single_cell_barcoded_SmartSeq2 [40-3]


title: single_cell_barcoded_SmartSeq2 [33-4]


title: single_cell_barcoded_SmartSeq2 [35-3]


title: single_cell_barcoded_SmartSeq2 [26-1]


title: single_cell_barcoded_SmartSeq2 [33-3]


title: single_cell_barcoded_SmartSeq2 [44-2]


title: single_cell_barcoded_SmartSeq2 [26-2]


title: single_cell_barcoded_SmartSeq2 [13-3]


title: single_cell_barcoded_SmartSeq2 [14-1]


title: single_cell_barcoded_SmartSeq2 [13-4]


title: single_cell_barcoded_SmartSeq2 [13-1]


title: single_cell_barcoded_SmartSeq2 [14-2]


title: single_cell_barcoded_SmartSeq2 [2-4]


title: single_cell_barcoded_SmartSeq2 [2-3]


title: single_cell_barcoded_SmartSeq2 [11-4.2]


title: single_cell_barcoded_SmartSeq2 [32-1]


title: single_cell_barcoded_SmartSeq2 [12-1]


title: single_cell_barcoded_SmartSeq2 [12-2]


title: single_cell_barcoded_SmartSeq2 [12-3]


title: single_cell_barcoded_SmartSeq2 [12-4]


title: single_cell_barcoded_SmartSeq2 [20-1]


title: single_cell_barcoded_SmartSeq2 [2-2]


title: single_cell_barcoded_SmartSeq2 [15-3]


title: single_cell_barcoded_SmartSeq2 [15-4]


title: single_cell_barcoded_SmartSeq2 [5-4]


title: single_cell_barcoded_SmartSeq2 [11-4]


title: single_cell_barcoded_SmartSeq2 [5-1]


title: single_cell_barcoded_SmartSeq2 [5-2]


title: single_cell_barcoded_SmartSeq2 [5-3]


title: VilCreER APCfl/fl - 3

status: Public on Aug 26 2020

description:
Small intestinal tissue subjected to tamoxifen induced genetic recombination in vivo
GSE112226_DESeq2.WT_vs_APC.full_results

source_name: Whole intestine

value: VilCreER+ APCfl/fl

tag: genetic background


title: single_cell_barcoded_SmartSeq2 [15-1]

value: microglia


title: WT - 3

value: VilCreER+


title: single_cell_barcoded_SmartSeq2 [11-3]

value: NetherlandsBrainBank


title: VilCreER APCfl/fl - 2


title: VilCreER APCfl/fl - 1


title: single_cell_barcoded_SmartSeq2 [13-2]

value: CTR+

value: LPS


title: WT - 2


title: single_cell_barcoded_SmartSeq2 [11-1]

value: YES


title: single_cell_barcoded_SmartSeq2 [11-2]

value: CTR


title: SLEX low sample, replicate 1

status: Public on Aug 24 2020

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
SLEX low sample, replicate 1
SLEX_RNAseq.txt

data_processing:
RNA-seq data were aligned using bowtie2 against the hg38 version of the human genome, and RSEM v1.2.12 software was used to estimate raw read counts and RPKM using Ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: CD4+ T cells

extract_protocol:
Genomic RNA was extracted from the homogenized sample with miRNeasy mini kit with on-column DNase I treament according to the manufacturer’s protocol (Qiagen, Hilden, Germany).
The NEBNext Ultra RNA Library Prep Kit for Illumina was used to prepare the RNA sequencing libraries following the manufacturer's recommendations (NEB)

tag: slexlevel

value: low

tag: replicate


title: SLEX high sample, replicate 4

description:
SLEX high sample, replicate 4
SLEX_RNAseq.txt

value: high


title: WT - 1


title: nTreg_ChIPseq_Foxp3_sgBrd9+Foxp3

status: Public on Jul 07 2020

city: San Diego

first: Diana

middle: C.

last: Hargreaves

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

description: ChIP-seq for Foxp3 in nTregs expressing Foxp3 construct, transduced with sgBrd9

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq, ChIP-seq and ATAC-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bed files. ChIP-seq peaks for Foxp3, BRD9, BRG1 and PHF10 were found by using the findPeaks program in HOMER with the parameter "-style factor" versus the appropriate ChIP input experiments as background. ChIP-seq peaks for H3K27ac were called using the parameter "-style histone." ATAC-seq peaks were called using the parameter "-style dnase." For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: Bed file Columns: (1) peak ID (2) chrom (3) chromStart (4) chromEnd (5) strand. DiffExpOutput tab delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM for each experiment (13) Log2 fold change (14) p value (15) adjusted p value

source_name: nTregs isolated from Foxp3Thy1.1/Rosa-Cas9 mice

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq, 7.5e6 nTregs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Foxp3, BRG1, BRD9, PHF10 and H3K27ac then bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. For ATAC-seq, 50k nTregs per replicate were washed with cold PBS and resuspension buffer (RB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) before lysis in RB with 0.1% NP40. Cells were then incubated in transposition mix containing Tn5 transposase for thirty minutes at 37degC.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions. ATAC-seq -- purified DNA was ligated with adapters (NuGEN), amplified and size selected for sequencing.

tag: genotype/variation

value: nTregs

tag: perturbation

tag: overexpression construct

tag: antibody source

value: In-house made Foxp3 antibody


title: nTreg_ChIPseq_Foxp3_sgBrd9+MIGR

description: ChIP-seq for Foxp3 in nTregs expressing MIGR control, transduced with sgBrd9

value: MIGR control


title: single_cell_barcoded_SmartSeq2 [15-2]

tag: donor group

tag: donor id

tag: brain bank

tag: brain region

value: F

value: XDP


title: nTreg_ChIPseq_Input_sgBrd9+Foxp3

description: Input for ChIP-seq in nTregs expressing Foxp3 construct, transduced with sgBrd9


title: nTreg_ChIPseq_Input_sgNT+Foxp3

description: Input for ChIP-seq in nTregs expressing Foxp3 construct, transduced with sgNT

value: sgNT


title: SLEX low sample, replicate 4

description:
SLEX low sample, replicate 4
SLEX_RNAseq.txt


title: nTreg_ChIPseq_Input_sgBrd9+MIGR

description: Input for ChIP-seq in nTregs expressing MIGR control, transduced with sgBrd9


title: SLEX low sample, replicate 3

description:
SLEX low sample, replicate 3
SLEX_RNAseq.txt


title: nTreg_ChIPseq_Input_sgNT+MIGR

description: Input for ChIP-seq in nTregs expressing MIGR control, transduced with sgNT


title: SLEX high sample, replicate 5

description:
SLEX high sample, replicate 5
SLEX_RNAseq.txt


title: SLEX low sample, replicate 2

description:
SLEX low sample, replicate 2
SLEX_RNAseq.txt


title: SLEX high sample, replicate 1

description:
SLEX high sample, replicate 1
SLEX_RNAseq.txt


title: nTreg_ChIPseq_Input_Replicate3_forBRD9

description: Input for ChIP-seq in Tregs Replicate 3 for BRD9


title: SLEX high sample, replicate 2

description:
SLEX high sample, replicate 2
SLEX_RNAseq.txt


title: nTreg_ChIPseq_Foxp3_sgNT+Foxp3

description: ChIP-seq for Foxp3 in nTregs expressing Foxp3 construct, transduced with sgNT


title: nTreg_ChIPseq_Foxp3_sgNT+MIGR

description: ChIP-seq for Foxp3 in nTregs expressing MIGR control, transduced with sgNT


title: nTreg_RNAseq_sgPhf10_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPhf10, replicate 1

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, transcript per milion (TPM) reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-58) TPM for each experiment

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.
Strand-specific polyA+ RNA-seq

tag: sg-guide


title: SLEX high sample, replicate 3

description:
SLEX high sample, replicate 3
SLEX_RNAseq.txt


title: nTreg_RNAseq_sgArid2_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid2, replicate 1


title: nTreg_RNAseq_sgBrd7_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd7, replicate 2


title: nTreg_ChIPseq_sgNT_BRD9

description: ChIP-seq for BRD9 in Tregs transduced with sgNT

value: BRD9 Active Motif #61537


title: nTreg_ChIPseq_BRD9_Replicate3

description: ChIP-seq for BRD9 in Tregs Replicate 3


title: nTreg_RNAseq_sgArid2_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid2, replicate 2


title: nTreg_RNAseq_sgPhf10_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPhf10, replicate 3


title: nTreg_RNAseq_sgPhf10_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPhf10, replicate 2


title: nTreg_RNAseq_sgPbrm1-2_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPbrm1-2, replicate 1


title: nTreg_RNAseq_sgPbrm1-2_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPbrm1-2, replicate 2


title: nTreg_RNAseq_sgBrd7_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd7, replicate 3


title: nTreg_RNAseq_sgBrd7_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd7, replicate 1


title: nTreg_RNAseq_sgPbrm1_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPbrm1, replicate 3


title: nTreg_RNAseq_sgGltscr1/1l_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgGltscr1/1l, replicate 1


title: nTreg_RNAseq_sgPbrm1_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPbrm1, replicate 2


title: nTreg_RNAseq_sgGltscr1/1l_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgGltscr1/1l, replicate 2


title: nTreg_RNAseq_sgGltscr1_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgGltscr1, replicate 2


title: nTreg_RNAseq_sgGltscr1_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgGltscr1, replicate 1


title: nTreg_RNAseq_sgPbrm1_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPbrm1, replicate 1


title: nTreg_RNAseq_sgGltscr1/1l_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgGltscr1/1l, replicate 3


title: nTreg_RNAseq_sgSmarcd1_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgSmarcd1, replicate 2


title: nTreg_RNAseq_sgArid2_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid2, replicate 3


title: nTreg_RNAseq_sgGltscr1_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgGltscr1, replicate 3


title: nTreg_RNAseq_sgSmarcd1_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgSmarcd1, replicate 1


title: nTreg_RNAseq_sgBrd9-2_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd9-2, replicate 1


title: nTreg_RNAseq_sgBrd9-2_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd9-2, replicate 2


title: nTreg_RNAseq_sgBrd9_Rep5

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd9, replicate 3


title: nTreg_RNAseq_sgBrd9_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd9, replicate 1


title: nTreg_RNAseq_sgBrd9_Rep4

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd9, replicate 2


title: nTreg_RNAseq_sgPbrm1-2_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgPbrm1-2, replicate 3


title: nTreg_RNAseq_sgDpf1/2_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgDpf1/2, replicate 3


title: nTreg_RNAseq_sgDpf1/2_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgDpf1/2, replicate 1


title: nTreg_RNAseq_sgDpf2_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgDpf2, replicate 3


title: nTreg_RNAseq_sgArid1a-2/1b-2_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a-2/1b-2, replicate 3


title: nTreg_RNAseq_sgDpf1/2_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgDpf1/2, replicate 2


title: nTreg_RNAseq_sgDpf2_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgDpf2, replicate 1


title: nTreg_RNAseq_sgSmarcd1_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgSmarcd1, replicate 3


title: nTreg_RNAseq_sgArid1a-2/1b-2_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a-2/1b-2, replicate 2


title: nTreg_RNAseq_sgDpf2_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgDpf2, replicate 2


title: nTreg_RNAseq_sgArid1a/1b_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a/1b, replicate 2


title: nTreg_RNAseq_sgArid1a/1b_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a/1b, replicate 1


title: nTreg_RNAseq_sgArid1a-2_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a-2, replicate 2


title: nTreg_RNAseq_sgArid1a-2_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a-2, replicate 3


title: nTreg_RNAseq_sgArid1a-2_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a-2, replicate 1


title: nTreg_RNAseq_sgBrd9-2_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgBrd9-2, replicate 3


title: nTreg_RNAseq_sgArid1a_Rep2

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a, replicate 2


title: nTreg_RNAseq_sgArid1a_Rep1

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgArid1a, replicate 1


title: nTreg_RNAseq_sgNT_Rep4

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgNT, replicate 2


title: nTreg_RNAseq_sgNT_Rep3

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgNT, replicate 1


title: nTreg_RNAseq_sgPbrm_Rep2

description:
RNA-seq in nTregs transduced with sgPbrm, replicate 2.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgPbrmvssgNT_DiffExpOutput.txt

data_processing:
Basecalls performed using RTA (Illumina).
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq, ChIP-seq and ATAC-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bed files. ChIP-seq peaks for Foxp3, BRD9, BRG1 and PHF10 were found by using the findPeaks program in HOMER with the parameter "-style factor" versus the appropriate ChIP input experiments as background. ChIP-seq peaks for H3K27ac were called using the parameter "-style histone." ATAC-seq peaks were called using the parameter "-style dnase." For RNA-Seq, Reads Per Kilobase of exon per million mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bed file Columns: (1) peak ID (2) chrom (3) chromStart (4) chromEnd (5) strand.
Supplementary_files_format_and_content: DiffExpOutput tab-delimited text file Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) FPKM for each experiment (13) Log2 fold change (14) p value (15) adjusted p value.

extract_protocol:
For ATAC-seq, 50k nTregs per replicate were washed with cold PBS and resuspension buffer (RB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) before lysis in RB with 0.1% NP40. Cells were then incubated in transposition mix containing Tn5 transposase for thirty minutes at 37degC. Purified DNA was ligated with adapters (NuGEN), amplified and size selected for sequencing.
For ChIP-Seq, 7.5e6 nTregs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Foxp3, BRG1, BRD9, PHF10 and H3K27ac then bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing. ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions.
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.

tag: treatment

tag: guide rna

value: sgPbrm


title: nTreg_RNAseq_sgNT_Rep5

description:
TPM_Treg_sgSWISNF.txt
RNA-seq in nTregs transduced with sgNT, replicate 3


title: nTreg_RNAseq_sgNT_Rep1

description:
RNA-seq in nTregs transduced with sgNT, replicate 1.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgFoxp3vssgNT_DiffExpOutput.txt
processed data: nTreg_sgBrd9vssgNT_DiffExpOutput.txt
processed data: nTreg_sgPbrmvssgNT_DiffExpOutput.txt

tag: cell type


title: nTreg_RNAseq_sgPbrm_Rep1

description:
RNA-seq in nTregs transduced with sgPbrm, replicate 1.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgPbrmvssgNT_DiffExpOutput.txt


title: nTreg_RNAseq_dBRD9_Rep2

description:
RNA-seq in nTregs treated with dBRD9, replicate 2.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_dBRD9vsDMSO_DiffExpOutput.txt

value: 2.5 uM dBRD9


title: nTreg_RNAseq_sgBrd9_Rep2

description:
RNA-seq in nTregs transduced with sgBrd9, replicate 2.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgBrd9vssgNT_DiffExpOutput.txt


title: nTreg_RNAseq_sgFoxp3_Rep1

description:
RNA-seq in nTregs transduced with sgFoxp3, replicate 1.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgFoxp3vssgNT_DiffExpOutput.txt


title: nTreg_RNAseq_sgBrd9_Rep1

description:
RNA-seq in nTregs transduced with sgBrd9, replicate 1.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgBrd9vssgNT_DiffExpOutput.txt


title: nTreg_RNAseq_sgFoxp3_Rep2

description:
RNA-seq in nTregs transduced with sgFoxp3, replicate 2.
Strand-specific polyA+ RNA-seq.
processed data: nTreg_sgFoxp3vssgNT_DiffExpOutput.txt