title: ATACseq_WT_Dome_BR2


title: Quantseq_14som_SATB2_MUT_BR1

status: Public on Sep 02 2021

type: SRA

city: Pune

first: Sanjeev

last: Galande

state: Maharashtra

address: Dr. Homi bhabha road, Pashan

department: Biology

country: India

institute: IISER Pune

description:
3' mRNA quantseq Lexogen
processed data file:
14_somite_quantseq_normCPM.txt

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed for quality using Trimmomatic and aligned to the daRer10 genome assembly using STAR aligner. Counts for each gene feature was estimated using the FeatureCounts package from Rsubread. Differential expression analysis was performed for replicates using EdgeR.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

molecule: polyA RNA

organism: Danio rerio

source_name: Whole embryo

growth_protocol: embryos were grown at 28.5 degrees till the desired stage is reached. Stages were determined visually

extract_protocol:
Single embryos were harvested in 100 μl RNA iso-plus total RNA extraction reagent (DSS Takara, India) at 80% epiboly, 6 ss and 14 ss stages of zebrafish embryonic development. Samples were homogenized by vigorous vortexing to assure complete lysis followed by addition of 15 ul of CHCl3. Aqueous layer was separated by centrifugation at 12000 xg for 15 minutes at 4oC. The aqueous layer was collected in a separate tube and an equal volume of isopropanol containing GlycoBlue coprecipitant (Invitrogen, USA) was added. The aqueous fraction was stored at -20oC until further processing. Meanwhile, the organic fraction was processed for DNA extraction by precipitating with 150 μl of 100% ethanol and incubated for 10 minutes at RT. Samples were centrifuged for 10 minutes at high speed and the pellet was washed with 70% ethanol (twice). After drying, DNA pellets were resuspended in low TE and used for genotyping as described before. Once the genotype for each embryo was confirmed, the corresponding RNA fractions were processed further. RNA from 2-3 samples were pooled to get sufficient amounts to prepare libraries.
Extracted RNA samples were quantified using Nanodrop 2000 and RNA integrity was determined using Agilent bioanalyzer 2100. Samples with RNA integrity number (RIN) > 8 were used to prepare sequencing libraries using Quantseq 3’ mRNA seq library kit (Lexogen GMBH, Austria) as per the instructions from the manufacturer. Briefly, 300 ng of RNA was used for poly-A capturing and subjected to first and second-strand synthesis. All cDNA samples were amplified for 10-15 cycles depending on cycle number estimation by qPCR (PCR add-on kit, Lexogen GMBH, Austria). Amplified libraries were purified using two rounds of 0.8x volume of Hi-prep PCR purification kit (MagBio Genomics, USA). The concentration of libraries was estimated using the Qubit dsDNA HS system (Thermo Fisher Scientific). Finally, all the libraries were pooled and subjected to high throughput sequencing using 76 bp SE chemistry on Nextseq 550.

tag: genotype/varaition

tag: strain

value: TU

tag: Stage

value: 14 somite (16hpf)


title: donor3_highAβ

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

country: USA

institute: University of Colorado Boulder

data_processing:
QC and adapters trimmed using fastp.
Reads aligned and counted using STAR.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene counts for each sample.

organism: Homo sapiens

source_name: Primary human astrocytes

growth_protocol: Primary astrocytes were grown in astrocyte-specific growth medium (from corresponding suppliers) and sub-cultured when semi-confluent.

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
PolyA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit.

treatment_protocol: Passage 2-3 cells were treated when semi-confluent for 24 h with combinations of Aβ, C1q, TNF-α and IL-1α pre-diluted in fresh media.

tag: treatment

value: 1 µM Aβ

tag: donor age

value: fetal

tag: supplier/gender

value: Sciencell/male


title: TS072611B_INPUT

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Reads were aligned to hg19 with bowtie2 (v2.2.5) using default settings.
Reads in ENCODE blacklisted regions were removed with samtools (v1.9).
Peaks were called with MACS2 (v2.1.0.20150420) with the parameters --nomodel --shiftsize=150 (ChIP) or --nomodel --shiftsize=50 (FAIRE) and input controls.
DiffBind (v2.14.0) was used to derive consensus peak sets for each histone mark and accessible chromatin, requiring peaks to overlap in at least three samples for each ChIP-seq or FAIRE-seq assay in order to be merged and retained. The consensus peaksets for each assay were then concatenated and merged to derive a list of putative regulatory elements with bedtools2 (v2.29.2).
DiffBind was then used to determine differentially bound/accessible regions between sample groups for each assay. ChIPseeker (v1.22.0) was used to annotate peaks with hg19 UCSC knownGene annotations.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format files containing peaks for each sample as called by MACS2.

molecule: genomic DNA

source_name: CD19+ B cells

extract_protocol:
Cells were formaldehyde cross-linked (1% final concentration) for 10 minutes in RPMI with 10% FBS. Quenching was performed by addition of 1M glycine (125 mM final concentration) with gentle mixing for 10 minutes at room temperature. Cells were washed with cold PBS and lysed in an SDS buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0) with protease inhibitors before chromatin was fragmented using a Diagenode Bioruptor to an average size of less than 300 bp as determined using an Agilent Bioanalyzer 2100. Lysates were immunoprecipitated with the listed antibodies conjugated to Protein-A Dynabeads (5 ug antibody incubated with beads for 2-4 hours at 4°C) overnight at 4°C. The beads were then washed with the following buffers each for 3 minutes at 4°C - low salt buffer (150 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), high salt buffer (500 mM NaCl, 50 mM Tris pH 8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH 8.0, 0.5% Na deoxycholate, 1% NP40), and TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). After washing, crosslinks were reversed overnight at 65°C in 250 uL elution buffer (1% SDS, 100 mM NaHCO3) followed by addition of proteinaseK and incubation at 56°C for 1 hour.  DNA was purified with QIAquick PCR purification columns.
At least 3 ng of DNA was used to for indexed library preparation using Illumina TruSeq adapters and standard Illumina protocols. Fragments were size selected (average fragment-size: 200-400 bp for ChIP; 50-200 for FAIRE) using Agencourt AMPure XP beads prior to amplification. Samples were pooled (6-10 per lane) and sequenced.

tag: tissue

value: tonsil

tag: disease state

value: healthy

tag: antibody

value: input


title: CLL140_snp

type: genomic

hyb_protocol: 0.5 ug of DNA was hybridized according to manufacturer's instructions.

data_processing: Genotypes were called from CEL files using the Affymetrix Genotyping Console (v4.2.0.26) with the BIRDSEED v2 algorithm with default settings. Copy number analysis was performed with the Affymetrix Genotyping Console using regional GC correction and default settings. The DNAcopy R package was used for circular binary segmentation on raw data. cnvkit and the copynumber R package were used for CNV thresholding using log2 ratio values of -0.2 and 0.2.

label: Biotin

label_protocol: Per manufacturer's instructions

extract_protocol: Genomic DNA was extracted from sorted B CD19+ B cells using a Qiagen Dneasy Blood and Tissue kit.

value: peripheral blood

value: chronic lymphocytic leukemia


title: RNAseq_Dome_Satb2_Momix_BR1

description:
processed data file:
Dome_Satb2OE_normCPM_SATB2OE.txt
Dome_Satb2MO_normCPM.txt

data_processing:
Sequencing reads were trimmed for quality using Trimmomatic and aligned to daRer10 genome assembly using HISAT2 aligner. Counts for each gene feature was estimated using the FeatureCounts package from Rsubread. Differential expression analysis was performed for replicates using EdgeR. A volcano plot for significantly differentially expressed genes was generated using the PlotVolcano tool from the Galaxy server. Gene ontology analysis for upregulated and downregulated genes were performed using a web-based tool, gProfiler.
Genome_build: DanRer10 or mm10
Supplementary_files_format_and_content: Tab deliminated Txt files containing normalised CPM counts, BigWig fles and consensus peak file in bed format, Feature matrix CellRanger output

extract_protocol:
For Satb2 overexpression studies, 3x-Flag-Satb2 mRNA was injected at 1 cell stage and embryos were harvested at 4.5 hpf and were lysed in RNA iso plus (DSS-Takara, India) to extract total RNA. Each sample consisted of at least 10 embryos per experiment. For Satb2 knock-down studies, 4 ng morpholino mix was injected at 1 cell stage and embryos were harvested at 4.5 hpf.
Approximately 500 ng of Total RNA with RIN > 9 was used as a starting material to prepare mRNA sequencing libraries using the SENSE mRNA seq kit (Lexogen GMBH, Austria). All cDNA samples were amplified for 10-15 cycles depending on cycle number estimation by qPCR using the PCR add-on kit (Lexogen GMBH, Austria). Amplified libraries were purified using two rounds of 0.8x volume of Hi-prep PCR purification kit. The concentration of libraries was estimated using the Qubit 4 DNA HS system (Thermo Scientific). Finally, all the libraries were pooled and subjected to high throughput sequencing using 100 bp PE chemistry on Hiseq 2500 (Macrogen, Korea).

treatment_protocol: Knockdown using  SATB2 morpholinos from 1 cell stage

value: Wild-Type

value: AB/TU

value: Dome (4.5 hpf)


title: donor3_lowAβ

value: 10 nm Aβ


title: donor3_cytokineduplet

value: 10 nm TNF-α IL-1α


title: TS121511A_INPUT


title: donor3_Aβcytokineduplet

value: 10 nm Aβ TNF-α IL-1α


title: donor3_control

value: control


title: TS072611A_INPUT


title: RNAseq_Dome_SATB2OE_BR2

treatment_protocol: overexpression of 3XFLAG-SATB2 from 1 cell stage


title: Quantseq_6som_SATB2_MUT_BR2

description:
3' mRNA quantseq Lexogen
processed data file:
6_somite_quantseq_normCPM.txt

value: TU

value: 6 somite (12hpf)


title: TS072111A_INPUT


title: RNAseq_Dome_SATB2OE_BR1


title: Quantseq_6som_WT_BR2


title: RNAseq_Dome_Ctrl_BR3


title: Quantseq_6som_SATB2_MUT_BR1


title: TS061611B_INPUT


title: RNAseq_Dome_Ctrl_BR2


title: donor2_Aβcytokineduplet

value: Lonza/female


title: donor2_highAβ

value: 1 µM Aβ

value: fetal


title: TS060911A_INPUT

value: tonsil


title: Quantseq_6som_WT_BR1


title: donor2_cytokinetriplet

value: 10 nm C1q TNF-α IL-1α


title: RNAseq_Dome_Ctrl_BR1


title: Quantseq_80epi_MUT_Rep2

description:
3' mRNA quantseq Lexogen
processed data file:
80_epi_quantseq_normCPM.txt

value: 80% epiboly (8hpf)


title: donor2_cytokineduplet


title: Quantseq_80epi_MUT_BR1


title: TS061611A_INPUT

value: healthy

value: input


title: donor2_lowAβ


title: TS050411_INPUT


title: RNAseq_Dome_SATB2OE_BR3

value: Wild-Type


title: FL153_snp

value: lymph node

value: follicular lymphoma


title: rny-1 mRNA

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: rRNA depleted (mRNA-seq)

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic version 0.17 for mRNA-seq or Cutadapt for sRNA-seq
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2 version 2.0.0-beta7
Read counting was performed with HTSeq
Differential Gene expression analysis performed with DESeq2
Genome_build: Streptococcus pneumoniae D39 (RefSeq NC_008533) genome and D39 plasmid pDP1 sequence (RefSeq NC_005022)

molecule: total RNA

organism: Streptococcus pneumoniae D39

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.1 - 0.15

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
For samples 1-6, the library was generated by first removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria. Samples were then subjected to RNA fragmentation using the Ambion RNA fragmentation kit (AM8740). Fragmented RNA was subjected to RNA 5' polyphosphatase (Epicenter) treatment, which was performed to facilitate the 5' adapter ligation step. Small RNA libraries were generated by Macrogen using TruSeq® small RNA library kit (Illumina).  For samples 7-14, rRNA-depleted samples were directly used for mRNA-seq library preparation using ScriptSeqTM v2 RNA-seq Library preparation kit (Epicenter).

tag: genotype

value: rny deletion mutant


title: Quantseq_80epi_WT_BR2


title: TS042811A_INPUT


title: Quantseq_80epi_WT_BR1


title: Tcf4tr/+ P12 mice

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq 2.20.0.422.
R1 (28p) corresponds to a 16bp cell barcode + 12bp UMI barcode and R2 (91bp) contains the biological read. I1 corresponds to the 8bp Illumina I7 index of each read.
A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 2020-A, GRCm38/vM23) using 10X Genomics Cellranger count version 4.0.0
Genome_build: GRCm38/vM23
Supplementary_files_format_and_content: Counts matrices are in Matrix Market CSR format and gzipped.  Rows correspond to genes in the associated features.tsv.gz and columns correspond to cell-barcodes in associated barcodes.tsv.gz

organism: Mus musculus

source_name: Ventral parafacial region

extract_protocol:
Brainstem slices were prepared using a vibratome in ice cold, high sucrose slicing solution. Slicing solution was equilibrated with a 5% CO2-95% O2 gas mixture before use. Transverse brainstem slices (300 μm thick) were prepared and then immediately enzymatically treated at 34°C with protease XVIII (6 mg/mL) for 6 minutes. After enzyme incubation, slices were washed three times in cold dissociation solution and then transferred to an enzyme inhibitor mix containing trypsin inhibitor (10 mg/mL) and bovine serum albumin (BSA, 10 mg/mL) in cold sucrose dissociation solution. Shortly thereafter, slices were transferred to a glass Petri dish on ice. Using a plastic transfer pipette and scalpel, each region of interest was micro-dissected out of the slices and manually separated into sterile microcentrifuge tubes. Tissue chunks were then warmed to 34°C for 10 minutes before trituration.
A single cell suspension was achieved by trituration using a 25 and 30 gauge needles sequentially, attached to a 2 mL syringe. Samples were triturated for an average of 5 minutes. Immediately after, the samples were placed back on ice and filtered through a 30-micron filter into sterile microcentrifuge tubes for cell viability assessment. Cell viability for each sample was assessed on a Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded for capture onto an individual lane of a Chromium Controller (10X Genomics). Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform according to the manufacturer’s protocol (#CG00052) using version 3 (V3) chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR. Each library was sequenced on 16.67% of an Illumina NovaSeq 6000 S4 lane, targeting 6,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.

value: Brain

tag: batch

tag: condition

value: Heterozygous truncation


title: TS040611B_INPUT


title: donor1_Aβcytokineduplet-3

value: 10 nm Aβ TNF-α IL-1α

value: Gibco/male


title: TS020212B_INPUT


title: OT1-sgSOCS1-Tum-Rep1

city: Paris

first: Aurélien

last: Sutra del Galy

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Sequences were aligned with STAR and counts were generated by HTSeq using the annotations from mm10.
Raw counts were normalized to log2 transformed Counts using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: txt

growth_protocol: OT1 Mock or sgSOCS1 were sorted by flow cytometry from B16-OVA tumors in C57BL6 mice after harvest and liberase digestion

extract_protocol:
RNA was extracted using signle cell kit norgen biotek according to manufacturer's instructions. samples were digested with DNAse (qiagen) prior to elution.
SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian
Sequencing was performed on Novaseq 6000 sequencer in 100bp paired-end reads

treatment_protocol: Cells were lysed in RLT buffer supplemented with 10% of beta-mercaptoethanol

value: Tumor

tag: cell type

value: OT1 CD8 TCRtransgenic


title: donor2_control

value: control

value: Lonza/female


title: CUT&Tag_H3K9me3_BCAA_rep1

city: Xi'an

first: Fuyang

last: Zhang

state: Shaanxi

address: 127 West Changle Rd

department: Cardiology

country: China

institute: Xijing hospital

data_processing:
Library strategy: CUT&Tag
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Reads distributions (from bigwig) across gene are presented as an average plot (average of reads signals across all genes). The deeptools tool is used for this analysis.
Peaks were annotated by the function of annotatePeak of ChIPseeker.
Genome_build: rn6
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: broadpeak

organism: Rattus norvegicus

source_name: Adipose-derived mesenchymal stem cells

growth_protocol: customized BCAA-free DMEM/HG containing 10% FBS and 1% penicillin/streptomycin

extract_protocol:
histone-DNA complexes were isolated with antibody (H3K9me3, abclonal, A2360)
libraries were prepared by library construction NEBNext kit according to the manufacturer’s protocols

treatment_protocol: treated with vehicle or 3.432mM BCAA for 12 hours.

value: Adipose-derived mesenchymal stem cells

value: Sprague Dawley

value: treated with 3.432mM BCAA for 12 hours in the presence of 100uM hydrogen peroxide

tag: cut&tag antibody

value: H3K9me3 (abclonal, A2360)


title: TS020212A_INPUT

value: tonsil

value: healthy

value: input


title: OT1-sgSOCS1-Tum-Rep3


title: CUT&Tag_H3K9me3_BCAA_IgG

value: rabbit normal IgG (Millipore, 12-370)


title: FL3A145_INPUT

value: lymph node

value: follicular lymphoma


title: OT1-Mock-Tum-Rep3

source_name: Mock


title: RNA-seq_BCAA_rep3

data_processing:
(RNA-Seq) Trimmomatic software were used to remove adapter and low quality reads. [Bolger et al., Bioinformatics, 2014]
(RNA-Seq) Quality distribution plot and base content distribution were generated by FASTQC.
(RNA-Seq) STAR is used to align clean reads to reference genome. [Dibin et al., STAR: ultrafast universal RNA-seq aligner.Bioinformatics, 2013]
(RNA-Seq) Read counts for individual transcripts of each sample were produced with HTSeq-count. [Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 2015]
Genome_build: rn6
Supplementary_files_format_and_content: raw counts

extract_protocol:
RNA was isolated using TRIzol reagent. A total of 3 μg of RNA per sample was utilized for RNA library preparation with the NEBNext® UltraTM RNA Library Prep Kit for Illumina® for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: TS012612B_INPUT


title: TS012612A_INPUT


title: donor1_cytokinetriplet-2

value: 10 nm C1q TNF-α IL-1α

value: fetal


title: CUT&Tag_H3K9me3_CON_IgG

value: treated with vehicle for 12 hours in the presence of 100uM hydrogen peroxide


title: donor1_cytokinetriplet-1

value: Gibco/male


title: donor1_cytokinetriplet-3


title: donor1_Aβcytokineduplet-1

value: 10 nm Aβ TNF-α IL-1α


title: donor1_Aβcytokineduplet-2


title: RNA-seq_BCAA_rep2


title: OT1-Mock-Tum-Rep1

value: Tumor

value: OT1 CD8 TCRtransgenic


title: OT1-sgSOCS1-Tum-Rep2


title: FL3A119_INPUT


title: OT1-Mock-Tum-Rep2


title: CUT&Tag_H3K9me3_CON_rep1

value: Adipose-derived mesenchymal stem cells


title: Tcf4+/+ P12 mice

value: Brain

value: Wild Type


title: FL313_INPUT


title: RNA-seq_BCAA_rep1

value: Sprague Dawley

value: treated with 3.432mM BCAA for 12 hours in the presence of 100uM hydrogen peroxide


title: FL301_INPUT


title: donor1_highAβ-3

value: 1 µM Aβ


title: Marilyn-sgSOCS1-DLN-Rep2

source_name: Murine primary T cells TCR -transgenic

growth_protocol: Marilyn Mock or sgSOCS1 were sorted by flow cytometry from draining lymph nodes in female C57BL6 mice bearing MB49 tumors

value: Draining Lymph node

value: Marilyn CD4 T cells

tag: genetic modification


title: Marilyn-Mock-DLN-Rep2

value: Mock


title: RNA-seq_CON_rep3


title: FL255_INPUT

value: lymph node

value: follicular lymphoma

value: input


title: donor1_highAβ-2

value: fetal


title: Marilyn-Mock-DLN-Rep3


title: RNA-seq_CON_rep1

value: treated with vehicle for 12 hours in the presence of 100uM hydrogen peroxide


title: donor1_cytokineduplet-3

value: 10 nm TNF-α IL-1α

value: Gibco/male


title: Marilyn-sgSOCS1-DLN-Rep3


title: cochlear duct P7

city: Shanghai

first: Jianyong

last: Chen

state: Yangpu

address: 1665 Kongjiang Rd

department: Otorhinolaryngology Head and Neck Surgery

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

description: Single-cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
Sample demultiplexing, barcode processing and single-cell 3’ gene counting by using the Cell Ranger pipeline
sc-RNA-seq data were aligned to Rattus norvegicus reference genome
The Cell Ranger output was loaded into Seurat(version 3.1.1) be used for dimensional reduction, clustering, and analysis of sc-RNA-sequenceing data.
all genes expressed in less than 1 cell were removed, number of genes expressed per cell > 500 as low and <5000 as high cut-off、UMI counts less than 500、the percent of mitochondrial-DNA derived gene-expression <25%.
Genome_build: Rattus norvegicus UCSC
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cochlea

extract_protocol:
The cochlear duct tissues were placed in a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice, the tissues were transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers. Tissues were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I)
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cells according to the manufacturer's instructions of the 10X Genomics Chromium Single-Cell 3' kit (V3). The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou, China) at a minimum depth of 20,000 reads per cell.

value: Sprague-Dawley

value: greater epithelial ridge cell

tag: age

value: post natal day 7


title: Marilyn-sgSOCS1-DLN-Rep1


title: donor1_highAβ-1


title: FL238_INPUT


title: donor1_lowAβ-2

value: 10 nm Aβ


title: FL153_INPUT


title: donor1_cytokineduplet-2


title: RNA-seq_CON_rep2

value: Adipose-derived mesenchymal stem cells

value: Sprague Dawley


title: donor1_lowAβ-3


title: cochlear duct P1

description: Single-cell

value: post natal day 1


title: rny-3 sRNA

description: rRNA depleted (sRNA-seq)

value: rny deletion mutant


title: FL174_INPUT


title: DL551_INPUT

value: diffuse large B cell lymphoma


title: rny-1 sRNA

description: rRNA depleted (sRNA-seq)


title: FL120_INPUT


title: donor1_control-3

value: control


title: DL3A538_INPUT

value: lymph node


title: pnp-3 sRNA

description: rRNA depleted (sRNA-seq)

value: pnp deletion mutant


title: Effector OT-I, biological replicate 3

type: RNA

city: La Jolla

first: Jennifer

last: Hope

state: CA

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

description: miRNA expression data in anti-influenza effector OT-I CD8+ T cells

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data was normalized and analyzed using Affymetrix Expression Console (default settings) and miRBASE version 21.

label: biotin

source_name: Effector (CD44+CD62L-) CD8+ T cell

label_protocol: Standard Affymetrix protocol

extract_protocol: Samples frozen in TRIReagent and total RNA was isolated using chloroform/isopropanol based extraction.

treatment_protocol: In vivo influenza virus infection.

tag: gender

value: Female

value: Lung


title: Effector OT-I, biological replicate 4


title: pnp-2 sRNA

description: rRNA depleted (sRNA-seq)


title: donor1_cytokineduplet-1

value: fetal


title: FL202_INPUT

value: follicular lymphoma

value: input


title: D270T54|CD8KO3D28

data_processing:
Sequences were aligned with STAR and counts were generated by HTSeq using the annotations from mm10.
Raw counts were normalized to log2 transformed Counts using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: CD8 CAR T cells

growth_protocol: CD4 CAR and CD8 CAR Mock or sgSOCS1 were sorted by flow cytometry from the bone marrow of NALM6 bearing NSG mice

value: Bone Marrow

tag: time point

value: Day 28


title: Naïve OT-I, biological replicate 4

description: miRNA expression data in naïve OT-I CD8+ T cells

source_name: Naïve (CD44-CD62L+) CD8+ T cell

value: Spleen


title: Marilyn-Mock-DLN-Rep1

value: Draining Lymph node

value: Marilyn CD4 T cells

value: Mock


title: Naïve OT-I, biological replicate 5


title: pol5_SQK1-IR_smallRNA-seq

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
Shortstack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads and Bowtie was used to map the reads specifically to the transgene.
Genome_build: Araport11
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under 16-hour day conditions at 22°C in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds unless otherwise noted.

extract_protocol:
Total RNA was isolated with Trizol reagent (Invitrogen) and enriched for small RNAs using the mirVana microRNA Isolation Kit (Ambion).
Size-enriched small RNAs were used in the Illumina TruSeq Small RNA Library Preparation Kit.
Multiplexed libraries were sequenced on Illumina HiSeq2500 or HiSeq4000 or NextSeq550.

tag: ecotype

value: Columbia


title: Col_SQK1-IR_smallRNA-seq

source_name: inflorescence (stage 1-12) immature flower buds


title: D270T52|CD8KO1D28


title: Effector OT-I, biological replicate 2


title: rny-2 sRNA

description: rRNA depleted (sRNA-seq)

value: rny deletion mutant


title: DL237_INPUT

value: diffuse large B cell lymphoma


title: donor1_lowAβ-1

value: 10 nm Aβ

value: Gibco/male


title: donor1_control-2

value: control


title: DL3A193_INPUT

value: lymph node


title: FL139_INPUT


title: Thymus-Satb1KO-scRNASeq-rep1

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-Seq data process pipline. Rawdata were filtered by fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6, --sensitive); Uniq mapped  ChIP-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files of  ChIP-Seq were generated by BEDtools(v2.29.2); Bed files of ChIP-Seq were got from Bam file by using HOMER (v4.10.4) with parameters (-style histone).
ATAC-Seq data process pipline. Clean reads  were obtained following quality filtering and adapter trimming using fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6 --sensitive -X 2000); Uniq mapped  ATAC-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files were generated by BEDtools (v2.29.2); Peak files were got from Bam file by using MACS2(v2.2.4) with parameters(-t input_file –q 0.01 -f BAM --nomodel --shift -100 --extsize 200 -keep-dup all).
3C-HTGTS data process pipline. Paired-end illumina sequencing fastq data were remove adaptor and low-quality reads with using fastp (v0.20.0); Filtered Reads were extracted from the sequence file after quality control through cutadapt(v1.18), Pear(v0.9.6), etc., which contain both NestPrimer and AdapterPrimer reads pairs. We merged them for Read1 and Read2, and single-ended reads were mapped to mouse genome mm10 with bowtie2(v2.3.5.1); The SAM files after mapping reads were obtained using samtools (v1.7),including removing the unmapped, multi-mapped reads and mapping to the reads on chrM; The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics and standardization,including removing reads for non-specific ligation and self-ligation. Then,we normalized bedGraph file using CPM(Counts per million in cis)normalization method, and visualized on IGV. Finally, we organized the results report and visualized it with R.
4C-Seq data process pipline. Clean reads were obtained following quality filtering and adaptor trimming using trim_glore (v0.6.4) with parameter(--paired -q 20),and reads were processed by cutadapt(v1.18); The first MboI enzyme fragment behind the viewpoint was extracted and mapped to mm10 genome assembly by bowtie2(v2.3.5.1) with parameter(-p 8 --sensitive). Reads numbers were counted and normalized by the total mapped reads per sample after self-ligation remove, and then differential interactions were identified by 4C-ker.
Hi-C data process pipline. Reads were obtained following quality filtering and adaptor trimming using fastp(v0.20.0) with default parameters. Hi-C mapping, filtering, correction, and binning were performed with the HiC-Pro(v2.11.1) software.The paired-end reads were mapped to the mm10 mouse reference genome.Singleton, multi-mapped, low-quality,unmapped,dumped, dangling, self-circle paired-end reads, and PCR duplicates were all removed by HiC-Pro after mapping.We generated raw contact matrices at 10-kb,20-kb,50-kb,100-kb,500-kb,1-Mb resolutions.For raw contact matrices correction from Hi-C data,we used the iterative correction method(ICE) through HiC-Pro(v2.11.1)software.The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format at fragment resolution.Visualization of Hi-C contact matrices was done via juicerbox. A/B compartment analysis was performed at 250-kb resolution using a publicly available script (matrix2compartment.pl).A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries.Chromatin loops in Satb1WT and Satb1CKO DP cells were called using Fit-Hi-C(v2.0.7).
5' RACE data process pipline. Reads were obtained following quality filtering and adaptor trimming using  fastp(v0.20.0) with default parameters.  Then the clean reads were analyzed with MIXCR(v2.1.10) to derive unique clonotypes based on CDR3 homology. Reads that comprise the clonotypes of interest (with matching VJ genes to Mus Musculus library antibody) were extracted for further analysis. The corresponding germline sequences were retrieved from IMGT, the international ImMunoGeneTics database.
Bulk RNA-Seq data process pipline. Clean data were obtained by removing reads containing adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. All the downstream analysis were based on the clean data with high quality. Reads were aligned to the mouse transcriptome using Hisat2(v2.1.0) and Ensemble gene annotation. Gene count data generated by featureCounts(v2.0.0) of subread software was used as input to DESeq2(v1.30.0) to generate differential expression data as well as normalised count tables.
scRNA-Seq data process pipline. The cleaned data was generated by Cell Ranger(v2.2.0) and filtered for the low quality reads and unrelated sequence. The data was aligned to mouse mm10 reference genome. Data merging, thresholding, normalization, principal component analysis, clustering analysis, visualization , differential gene expression analysis and cell cycle phases analysis were carried out in Seurat(v2.3.4) according to their recommended steps.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks. We used deepTools(v3.5.0) to generate bedGraph files. The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.

source_name: Thymocytes

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
For ChIP-Seq, DP thymocytes were perforated and dealed with MNase.Histone-DNA particles were precipitated with antibody. DNA were purified by PCR Purification Kit.For library preparation, DNAseq libraries were made using Tn5 DNA Library preparation kit.
For ATAC-Seq, a total of 50,000 cell pellets were washed with PBS, cells lysed on ice for 3 minutes in 50 μL ice-cold Lysis Buffer, and resuspended in 1mL ice-cold RBS-Wash and pelleted at 4°C at 500 × g for 10 minutes. Tagmentation was performed in 1 × Tagmentation Buffer (10mM Tris pH 7.4, 5mM MgCl2, 10% DMF, 33% PBS, 0.1% TWEEN 20, 0.01% Digitonin) using 100nM Tn5 Transposase for 30 minutes at 37°C. DNA was purified using PCR Purification Kit according to the manufacturer’s instructions. DNA was eluted into a volume of 20 μl and stored at -20°C prior to library preparation.For library preparation, PCR were performed using Kappa High-Fidelity DNA Polymerase with 1 cycle of 5 minutes at 72°C for gap filling. And a PCR for another 10-15 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina HiSeq 2000 platform to obtain 150 bp paired-end reads.
For 3C-HTGTS, in brief, 10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. MboI was inactivated by adding 10%SDS at 37°C for 30 min . To reduce the SDS concentration, the solution was diluted with T4 ligase buffer containing 1% Triton X-100, followed by incubation at 37°C for 1h. T4 ligase was added to each sample and incubated for overnight at 16°C.Crosslinks were reversed and samples were treated with Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol.The 3C libraries were sonicated to 300-500bp Sonicated DNA was linearly amplified with a biotinylated primer that anneals baits . The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor.The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer. And a final PCR for another 10-15 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina HiSeq 2000 platform to obtain 150 bp paired-end reads.
For 4C-Seq, chromatin was crosslinked for 10 minutes at room temperature in 1X PBS/10% FBS containing 4% formaldehyde. Crosslinking was blocked by glycine addition. Following cell lysis, nuclei pellets were resuspended in 1.2X Buffer2 (NEB), followed by SDS addition. The samples were incubated while shaking for 60 minutes at 37°C. TritonX-100 was added in order to quench SDS. Crosslinked chromatin was primarily digested using MboI . Ligation was performed in the presence of T4 DNA Ligase in diluted conditions. Chromatin reverse crosslinking was carried out using proteinase K ,phenol-chloroform and DNA were purified by ethanol precipitation. Secondary restriction was performed using NlaIII. Secondary ligation was carried out with T4 DNA Ligase in diluted conditions. Ligated DNA products were then extracted using phenol-chloroform with ethanol precipitation and purified.4C-seq library preparation was achieved by inverse PCR using 100 ng template DNA (for 10 reactions in total),. The viewpoint-directed inverse PCR primers carrying Illumina P5 or P7 sequencing adapters as below: Ets2 forward primer:5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgcccgggagcagcgtggatc-3’;Ets2 veserce primer: 5’-TCTTTCCCTACACGACGCTCTTCCGATCTcgagcacttaggcgccatct-3’.
For Hi-C, 5-10 million  DP thymocytes were crosslinked at 1% formaldehydeand and quenched by 200mM glycine for 5min at room terperature. After two washes with cold PBS,cells were pelleted and kept at -80°C until use. Subsequently, crosslinked cell were lysed and chromatins were digested with 150 U MboI overnight at 37 °C. Next, MboI was inactivated at 62 °C for 20min, fragmented ends were  biotinylated with biotin-dCTP using the Klenow large fragment for 60-90 min at 37 °C, and the sample was diluted and proximity ligated for 4 h at room temperature. Crosslinks DNA were reversed by the addition of SDS, ProteinaseK, and NaCl, and allowed to incubate overnight at 68 °C. DNA was purified by phenol/chloroform, followed by ethanol precipitation and resuspended in 100ul nuclease-free dH2O. DNA was treated with T4 DNA polymerase to remove unligated biotinylated ends and shared to 300-500bp by sonication Subsequently,The ligated junctions were pulled down with Dynabeads MyOne Streptavidin C1 magnetic beads.End-repair, A-tailing, adapter-ligation and PCR amplification reactions were performed on the biotinylated fragments bound to the beads. After purification of the PCR products, the final libraries were sequenced on an Illumina HiSeq 2000 platform to obtain 150 bp paired-end reads.
For 5' RACE, the 1ug RNA was used for the reverse transcription (RT). The cDNA libraries were performed with oligo(dT)  primer by 5′Rapid amplification of complementary DNA ends(5’RACE) . During the reverse transcription reaction , A SMART oligonucleotide was ligated to  the 5’end of each cDNA . The TCR library is then prepared by touchdown PCR amplification using a set of primers: a forward primer to the adaptor and a reverse primer to the constant region of the TCR  . Touchdown PCR was performed under the conditions of 95°C for 3 min, followed by 15 cycles of 98 °C forc15 s, 65 °C(decrease 0.7°C/cycles) for 15 s and 72 °C for 1 min,  20 cycles of 98 °C for 15 s, 60 °C for 15 s and 72 °C for 1 min and one cycle 10 min at 72°C. PCR products, ranged from 300-700bp were gel purified by DNA Gel Purification Kit. Illumina paired end adapters were ligated to TCR libraries, followed by 2rd round PCR with Illumina P5/P7 adaptor primers under 30s at 95°C , 15s at 65 °C, 60s  at 72°C for 10-15 cycles , Plus a final extenaion for 10 min at 72°C. Ampure bead purified PCR product. Finally, the TCR libraries were sequenced on an Illumina HiseqXtenPE150 (2 × 150 nt).
For Bulk RNA-Seq, the sorted DP cells were isolated using a TRIzol. The total RNA was quantified and qualified by Agilent 2100 Bioanalyzer and NanoDrop2000 .Subsequently, 1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase(NEB) and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix(NEB). The purified double-stranded cDNA were subjected to end repair, 3'-dA tailing and adapter ligation.Size selection of adapter ligated DNA were performed prior to PCR amplification. The ligated DNA was then amplified by 10-15 PCR amplification cycles with Illumina P5/P7 primers. The PCR products were cleaned up using beads, validated using an Qsep100 and quantified by Qubit3.0 Fluorometer. Libraries were a 2x150bp paired-end (PE) sequenced on a NextSeq 550 on an Illumina HiSeq instrumen
For scRNA-Seq, thymocytes were isolated from thymus. Cell viability was assessed and the samples (cell viability >80%) were prepared for single-cell library construction. The single-cell library was constructed using the ChromiumTM Controller and ChromiumTM Single Cell 3’ Reagent Version 2 Kit (10x Genomics, Pleasanton, CA) according to the manufacturer’s instructions. The PCR products were then quality and quantitated by Agilent 2100 bioanalyzer and  QPCR. The final libraries were sequenced using the Illumina Hiseq 4000 (BGI-Shenzhen, China).

tag: strain

value: Thymus

value: Thymocytes


title: donor1_control-1

tag: treatment

value: fetal


title: Thymus-Satb1WT-scRNASeq-rep1


title: DL252_INPUT

value: input


title: Naïve OT-I, biological replicate 3

value: Female


title: D270T53|CD8KO2D28

value: Bone Marrow

value: Day 28


title: DL135_INPUT


title: DP-Satb1WT-RNASeq-rep3

value: DP thymocytes


title: Effector OT-I, biological replicate 1

value: Lung


title: pnp-1 sRNA

description: rRNA depleted (sRNA-seq)

value: pnp deletion mutant


title: SOX2 & FMOD knockout_replicate 3

city: Copenhagen

first: victor

last: oria

state: Zealand

address: Ole Maaløes Vej 5, 4th Floor

department: BRIC

country: Denmark

institute: University of Copenhagen

hyb_protocol: Affymetrix GeneChip® WT Plus Reagent Kit (ThermoFisher, Santa Clara, CA) was used for the preparation of samples and generation of ss-cDNA for hybridization. 250 ng of total RNA were used for input. All the reactions and hybridizations were carried out according to the manufacturer's protocol.

scan_protocol: GeneChip Scanner 3000

data_processing: The raw data was first processed with R package oligo (Carvalho BS, Irizarry RA (2010). “A Framework for Oligonucleotide Microarray Preprocessing.” Bioinformatics, 26 (19), 2363-7. ISSN 1367-4803, doi: 10.1093/bioinformatics/btq431) and then normalized with RMA (Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):e15. doi:10.1093/nar/gng015).

source_name: Cultured Cl.2A cell line

label_protocol: Biotin

growth_protocol: Opti-MEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution

extract_protocol: Total RNA extraction using Rneasy Mini Kit (Qiagen) according to manufacturer's protocol. Extracted RNA was treated with RNAse Free DNAse kit to remove traces of geomic DNA prior to analysis

value: Cell line


title: SOX2 knockout_replicate 3


title: SOX2 & FMOD knockout_replicate 1


title: SOX2 & FMOD knockout_replicate 2


title: DL273_INPUT


title: SOX2 knockout_replicate 2


title: DL188_INPUT


title: CLL396_INPUT

value: peripheral blood

value: chronic lymphocytic leukemia


title: D270T51|CD8WT3D28

value: Mock


title: D270T50|CD8WT2D28


title: Naïve OT-I, biological replicate 1

value: Spleen


title: D270T48|CD4KO3D28

source_name: CD4 CAR T cells


title: SOX2 knockout_replicate 1


title: D270T49|CD8WT1D28


title: DL191_INPUT

value: diffuse large B cell lymphoma


title: Naïve OT-I, biological replicate 2


title: D270T46|CD4KO1D28


title: D270T43|CD4WT1D28


title: DP-Satb1KO-RNASeq-rep1


title: CLL347_INPUT


title: CLL412_INPUT


title: Thymus-ETS2SEKO-RACE-TCRA-rep2

data_processing:
Library strategy: 5' RACE
Illumina Casava1.7 software used for basecalling.
ChIP-Seq data process pipline. Rawdata were filtered by fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6, --sensitive); Uniq mapped  ChIP-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files of  ChIP-Seq were generated by BEDtools(v2.29.2); Bed files of ChIP-Seq were got from Bam file by using HOMER (v4.10.4) with parameters (-style histone).
ATAC-Seq data process pipline. Clean reads  were obtained following quality filtering and adapter trimming using fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6 --sensitive -X 2000); Uniq mapped  ATAC-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files were generated by BEDtools (v2.29.2); Peak files were got from Bam file by using MACS2(v2.2.4) with parameters(-t input_file –q 0.01 -f BAM --nomodel --shift -100 --extsize 200 -keep-dup all).
3C-HTGTS data process pipline. Paired-end illumina sequencing fastq data were remove adaptor and low-quality reads with using fastp (v0.20.0); Filtered Reads were extracted from the sequence file after quality control through cutadapt(v1.18), Pear(v0.9.6), etc., which contain both NestPrimer and AdapterPrimer reads pairs. We merged them for Read1 and Read2, and single-ended reads were mapped to mouse genome mm10 with bowtie2(v2.3.5.1); The SAM files after mapping reads were obtained using samtools (v1.7),including removing the unmapped, multi-mapped reads and mapping to the reads on chrM; The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics and standardization,including removing reads for non-specific ligation and self-ligation. Then,we normalized bedGraph file using CPM(Counts per million in cis)normalization method, and visualized on IGV. Finally, we organized the results report and visualized it with R.
4C-Seq data process pipline. Clean reads were obtained following quality filtering and adaptor trimming using trim_glore (v0.6.4) with parameter(--paired -q 20),and reads were processed by cutadapt(v1.18); The first MboI enzyme fragment behind the viewpoint was extracted and mapped to mm10 genome assembly by bowtie2(v2.3.5.1) with parameter(-p 8 --sensitive). Reads numbers were counted and normalized by the total mapped reads per sample after self-ligation remove, and then differential interactions were identified by 4C-ker.
Hi-C data process pipline. Reads were obtained following quality filtering and adaptor trimming using fastp(v0.20.0) with default parameters. Hi-C mapping, filtering, correction, and binning were performed with the HiC-Pro(v2.11.1) software.The paired-end reads were mapped to the mm10 mouse reference genome.Singleton, multi-mapped, low-quality,unmapped,dumped, dangling, self-circle paired-end reads, and PCR duplicates were all removed by HiC-Pro after mapping.We generated raw contact matrices at 10-kb,20-kb,50-kb,100-kb,500-kb,1-Mb resolutions.For raw contact matrices correction from Hi-C data,we used the iterative correction method(ICE) through HiC-Pro(v2.11.1)software.The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format at fragment resolution.Visualization of Hi-C contact matrices was done via juicerbox. A/B compartment analysis was performed at 250-kb resolution using a publicly available script (matrix2compartment.pl).A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries.Chromatin loops in Satb1WT and Satb1CKO DP cells were called using Fit-Hi-C(v2.0.7).
5' RACE data process pipline. Reads were obtained following quality filtering and adaptor trimming using  fastp(v0.20.0) with default parameters.  Then the clean reads were analyzed with MIXCR(v2.1.10) to derive unique clonotypes based on CDR3 homology. Reads that comprise the clonotypes of interest (with matching VJ genes to Mus Musculus library antibody) were extracted for further analysis. The corresponding germline sequences were retrieved from IMGT, the international ImMunoGeneTics database.
Bulk RNA-Seq data process pipline. Clean data were obtained by removing reads containing adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. All the downstream analysis were based on the clean data with high quality. Reads were aligned to the mouse transcriptome using Hisat2(v2.1.0) and Ensemble gene annotation. Gene count data generated by featureCounts(v2.0.0) of subread software was used as input to DESeq2(v1.30.0) to generate differential expression data as well as normalised count tables.
scRNA-Seq data process pipline. The cleaned data was generated by Cell Ranger(v2.2.0) and filtered for the low quality reads and unrelated sequence. The data was aligned to mouse mm10 reference genome. Data merging, thresholding, normalization, principal component analysis, clustering analysis, visualization , differential gene expression analysis and cell cycle phases analysis were carried out in Seurat(v2.3.4) according to their recommended steps.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks. We used deepTools(v3.5.0) to generate bedGraph files. The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.


title: DP-Satb1WT-RNASeq-rep2


title: CLL378_INPUT


title: DP-Satb1KO-RNASeq-rep3


title: DP-Satb1KO-RNASeq-rep2


title: CLL158_INPUT


title: D270T40|CD8KO1D7

value: Day 7


title: D270T42|CD8KO3D7


title: Col_AGO4-IP_rep3

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt. For AGO4-IP small RNA processing please refer to the Methods section of the manuscript associated with this GSE entry.
Shortstack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads and Bowtie was used to map the reads specifically to the transgene.
Genome_build: Araport11
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

value: Columbia

value: inflorescence (stage 1-12) immature flower buds

tag: molecule subtype

value: AGO4-IP small RNA


title: FMOD knockout_replicate 3


title: FMOD knockout_replicate 2


title: CB021314_INPUT

source_name: CD19+CD10+CD44lowCXCR4+ B cells

value: tonsil

value: healthy

value: input


title: DP-Satb1WT-RNASeq-rep1

value: Thymus


title: Thymus-ETS2SEWT-RACE-TCRA-rep2

value: Thymocytes


title: D270T44|CD4WT2D28

value: Bone Marrow

value: Day 28


title: Col_AGO4-IP_rep2


title: CLL140_INPUT


title: D270T45|CD4WT3D28


title: CLL144_INPUT


title: D270T47|CD4KO2D28


title: D270T38|CD8WT2D7


title: Control_replicate 3

value: Cell line


title: D270T41|CD8KO2D7


title: Control_replicate 1


title: D270T37|CD8WT1D7


title: Col_35S-EVD_mock-IP_rep3

value: mock-IP small RNA


title: CC021314_INPUT

source_name: CD19+CD10+CD44lowCXCR4- B cells


title: D270T36|CD4KO3D7


title: Thymus-Bcl6SEWT-RACE-TCRA-rep1


title: KO_3

city: Nanjing

first: Anliang

last: Xia

address: 321 Zhongshan Road

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: liver tumor

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver tumor

value: DEN+CCl4 for 5 months

value: lnc-CTHCC-/-


title: DP-Satb1KO-HiC-rep2

value: DP thymocytes


title: Col_35S-EVD_mock-IP_rep1


title: DP-Satb1WT-HiC-rep2


title: FMOD knockout_replicate 1


title: D270T33|CD4WT3D7

value: Day 7

value: Mock


title: DP-Satb1WT-HiC-rep1


title: Thymus-ETS2SEWT-RACE-TCRA-rep1


title: Thymus-Bcl6SEKO-RACE-TCRA-rep1


title: Control_replicate 2


title: Col_AGO4-IP_rep1

value: Columbia

value: inflorescence (stage 1-12) immature flower buds


title: Col_35S-EVD_EVD-only_AGO4-IP_rep2

value: AGO4-IP small RNA


title: D270T32|CD4WT2D7


title: D270T39|CD8WT3D7


title: Thymus-ETS2SEKO-RACE-TCRA-rep1


title: KO_1


title: D270T34|CD4KO1D7


title: KO_2


title: WT_1

value: wild type


title: Col_35S-EVD_AGO4-IP_rep3


title: KO-2

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description:
KO-2
Villin-Cre-PPARa-LoxP.txt

data_processing:
Samples passed the quality controls stablished in the FastQC software v.0.11.2.
Were mapped to mouse reference genome mm10 with TopHat v2.0.13
Its alignment was checked with Picard Tools v1.80
Gene expression counts were obtained with the HTSeq software v.0.6.1
Normalized counts (CPM) were obtained by edgeR library v.3.10.5 in R
Genome_build: Mouse reference genome mm10
Supplementary_files_format_and_content: txt file containing all the gene expressions for all the samples. Each column is a sample. Each row is a gene.

source_name: Duodenum

growth_protocol: Mice were maintained on a 12h-light/12h-dark cycle with free access to water and food

extract_protocol:
RNA was extracted with TRIzol (ThermoFisher, Waltham, MA, USA)
Sequencing libraries were prepared with the TruSeq stranded mRNA protocol (Illumina, San Diego, CA, USA) and were sequenced in a HiSeq 2500 (Illumina) obtaining 100 base single read fragments

treatment_protocol: The sacrifice day, mice were starved from 12:00 until 18:00. At 18:00 food was reintroduced and mice were sacrificed at 00:00.

value: Duodenum

value: Ppar alpha loxP/loxP;Villin-Cre (intestinal PPAR-alpha KO)

tag: biological replicate


title: KO-4

description:
KO-4
Villin-Cre-PPARa-LoxP.txt


title: Thymus-ETS2SEKO-ETS2p-4C-rep1

data_processing:
Library strategy: 4C-Seq
Illumina Casava1.7 software used for basecalling.
ChIP-Seq data process pipline. Rawdata were filtered by fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6, --sensitive); Uniq mapped  ChIP-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files of  ChIP-Seq were generated by BEDtools(v2.29.2); Bed files of ChIP-Seq were got from Bam file by using HOMER (v4.10.4) with parameters (-style histone).
ATAC-Seq data process pipline. Clean reads  were obtained following quality filtering and adapter trimming using fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6 --sensitive -X 2000); Uniq mapped  ATAC-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files were generated by BEDtools (v2.29.2); Peak files were got from Bam file by using MACS2(v2.2.4) with parameters(-t input_file –q 0.01 -f BAM --nomodel --shift -100 --extsize 200 -keep-dup all).
3C-HTGTS data process pipline. Paired-end illumina sequencing fastq data were remove adaptor and low-quality reads with using fastp (v0.20.0); Filtered Reads were extracted from the sequence file after quality control through cutadapt(v1.18), Pear(v0.9.6), etc., which contain both NestPrimer and AdapterPrimer reads pairs. We merged them for Read1 and Read2, and single-ended reads were mapped to mouse genome mm10 with bowtie2(v2.3.5.1); The SAM files after mapping reads were obtained using samtools (v1.7),including removing the unmapped, multi-mapped reads and mapping to the reads on chrM; The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics and standardization,including removing reads for non-specific ligation and self-ligation. Then,we normalized bedGraph file using CPM(Counts per million in cis)normalization method, and visualized on IGV. Finally, we organized the results report and visualized it with R.
4C-Seq data process pipline. Clean reads were obtained following quality filtering and adaptor trimming using trim_glore (v0.6.4) with parameter(--paired -q 20),and reads were processed by cutadapt(v1.18); The first MboI enzyme fragment behind the viewpoint was extracted and mapped to mm10 genome assembly by bowtie2(v2.3.5.1) with parameter(-p 8 --sensitive). Reads numbers were counted and normalized by the total mapped reads per sample after self-ligation remove, and then differential interactions were identified by 4C-ker.
Hi-C data process pipline. Reads were obtained following quality filtering and adaptor trimming using fastp(v0.20.0) with default parameters. Hi-C mapping, filtering, correction, and binning were performed with the HiC-Pro(v2.11.1) software.The paired-end reads were mapped to the mm10 mouse reference genome.Singleton, multi-mapped, low-quality,unmapped,dumped, dangling, self-circle paired-end reads, and PCR duplicates were all removed by HiC-Pro after mapping.We generated raw contact matrices at 10-kb,20-kb,50-kb,100-kb,500-kb,1-Mb resolutions.For raw contact matrices correction from Hi-C data,we used the iterative correction method(ICE) through HiC-Pro(v2.11.1)software.The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format at fragment resolution.Visualization of Hi-C contact matrices was done via juicerbox. A/B compartment analysis was performed at 250-kb resolution using a publicly available script (matrix2compartment.pl).A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries.Chromatin loops in Satb1WT and Satb1CKO DP cells were called using Fit-Hi-C(v2.0.7).
5' RACE data process pipline. Reads were obtained following quality filtering and adaptor trimming using  fastp(v0.20.0) with default parameters.  Then the clean reads were analyzed with MIXCR(v2.1.10) to derive unique clonotypes based on CDR3 homology. Reads that comprise the clonotypes of interest (with matching VJ genes to Mus Musculus library antibody) were extracted for further analysis. The corresponding germline sequences were retrieved from IMGT, the international ImMunoGeneTics database.
Bulk RNA-Seq data process pipline. Clean data were obtained by removing reads containing adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. All the downstream analysis were based on the clean data with high quality. Reads were aligned to the mouse transcriptome using Hisat2(v2.1.0) and Ensemble gene annotation. Gene count data generated by featureCounts(v2.0.0) of subread software was used as input to DESeq2(v1.30.0) to generate differential expression data as well as normalised count tables.
scRNA-Seq data process pipline. The cleaned data was generated by Cell Ranger(v2.2.0) and filtered for the low quality reads and unrelated sequence. The data was aligned to mouse mm10 reference genome. Data merging, thresholding, normalization, principal component analysis, clustering analysis, visualization , differential gene expression analysis and cell cycle phases analysis were carried out in Seurat(v2.3.4) according to their recommended steps.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks. We used deepTools(v3.5.0) to generate bedGraph files. The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.

tag: tissue

value: Thymus

value: Thymocytes


title: KO-1

description:
KO-1
Villin-Cre-PPARa-LoxP.txt


title: WT_2


title: Col_35S-EVD_EVD-only_AGO4-IP_rep3


title: WT-3

description:
WT-3
Villin-Cre-PPARa-LoxP.txt

value: Ppar-alpha loxP/loxP (control)


title: D270T35|CD4KO2D7

value: Bone Marrow


title: 8 caki cl2b_(miRNA-4_0)

city: Donsotia-San Sebastian

first: charles

last: lawrie

address: Paseo Mikeletegi, 83- planta 3

department: Oncology

country: Spain

institute: Biodonostia Research Institute

description: miRNA  expression data from  clone 2  of Caki sunitinib resistant ccRCC cell line

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA processed in affymetrix TAC (v.4.0.2)

source_name: ccRCC Caki sunitinib resistant cell line

label_protocol: standard Affymetrix protocol

growth_protocol: cells were grown over several months either with sunitinib (two clones per cell line) or without (parental cell lines).

extract_protocol: RNA was extracted for cells with Trizol using standard protocols

treatment_protocol: Sunitinib concentrations were increased incrementally by 0.5uM steps until the IC50 values reached >10uM

tag: cell line

value: clear cell renal cell carcinoma (ccRCC)

tag: drug resistance

value: sunitinib resistant


title: 9 caki cl2c_(miRNA-4_0)


title: Thymus-ETS2SEWT-ETS2p-4C-rep1

tag: genotype


title: Col_35S-EVD_mock-IP_rep2

value: mock-IP small RNA


title: 7 caki cl2a_(miRNA-4_0)


title: KO-3

description:
KO-3
Villin-Cre-PPARa-LoxP.txt


title: Thymus-ETS2SEKO-ETS2p-4C-rep2


title: suvh2_suvh9_rep1

value: total small RNA


title: Col_35S-EVD_EVD-only_AGO4-IP_rep1


title: D270T31|CD4WT1D7


title: 6 caki cl1c_(miRNA-4_0)

description: miRNA  expression data from  clone 1 of Caki sunitinib resistant ccRCC cell line


title: suvh2_suvh9_rep2


title: WT-2

description:
WT-2
Villin-Cre-PPARa-LoxP.txt


title: 4 caki cl1a_(miRNA-4_0)


title: 3 caki Pc_(miRNA-4_0)

description: miRNA expression data from Caki  ccRCC cell line

source_name: ccRCC Caki cell line

value: sunitinib sensitive


title: drm1-drm2


title: Thymus-ETS2SEWT-ETS2p-4C-rep2


title: ago4_ago6_ago9


title: Thymus-Bcl6SEKO-Bcl6p-3C-HTGTS-rep1

data_processing:
Library strategy: 3C-HTGTS
Illumina Casava1.7 software used for basecalling.
ChIP-Seq data process pipline. Rawdata were filtered by fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6, --sensitive); Uniq mapped  ChIP-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files of  ChIP-Seq were generated by BEDtools(v2.29.2); Bed files of ChIP-Seq were got from Bam file by using HOMER (v4.10.4) with parameters (-style histone).
ATAC-Seq data process pipline. Clean reads  were obtained following quality filtering and adapter trimming using fastp(v0.20.0) with default parameters, and reads were mapped to the mm10 genome assembly using bowtie2 (v2.3.5.1) with parameters (-p 6 --sensitive -X 2000); Uniq mapped  ATAC-seq reads pairs were got after pcr duplication removing by Picard (v2.22.8) and samtools (v1.7); RPKM normalized BigWig files were generated by BEDtools (v2.29.2); Peak files were got from Bam file by using MACS2(v2.2.4) with parameters(-t input_file –q 0.01 -f BAM --nomodel --shift -100 --extsize 200 -keep-dup all).
3C-HTGTS data process pipline. Paired-end illumina sequencing fastq data were remove adaptor and low-quality reads with using fastp (v0.20.0); Filtered Reads were extracted from the sequence file after quality control through cutadapt(v1.18), Pear(v0.9.6), etc., which contain both NestPrimer and AdapterPrimer reads pairs. We merged them for Read1 and Read2, and single-ended reads were mapped to mouse genome mm10 with bowtie2(v2.3.5.1); The SAM files after mapping reads were obtained using samtools (v1.7),including removing the unmapped, multi-mapped reads and mapping to the reads on chrM; The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics and standardization,including removing reads for non-specific ligation and self-ligation. Then,we normalized bedGraph file using CPM(Counts per million in cis)normalization method, and visualized on IGV. Finally, we organized the results report and visualized it with R.
4C-Seq data process pipline. Clean reads were obtained following quality filtering and adaptor trimming using trim_glore (v0.6.4) with parameter(--paired -q 20),and reads were processed by cutadapt(v1.18); The first MboI enzyme fragment behind the viewpoint was extracted and mapped to mm10 genome assembly by bowtie2(v2.3.5.1) with parameter(-p 8 --sensitive). Reads numbers were counted and normalized by the total mapped reads per sample after self-ligation remove, and then differential interactions were identified by 4C-ker.
Hi-C data process pipline. Reads were obtained following quality filtering and adaptor trimming using fastp(v0.20.0) with default parameters. Hi-C mapping, filtering, correction, and binning were performed with the HiC-Pro(v2.11.1) software.The paired-end reads were mapped to the mm10 mouse reference genome.Singleton, multi-mapped, low-quality,unmapped,dumped, dangling, self-circle paired-end reads, and PCR duplicates were all removed by HiC-Pro after mapping.We generated raw contact matrices at 10-kb,20-kb,50-kb,100-kb,500-kb,1-Mb resolutions.For raw contact matrices correction from Hi-C data,we used the iterative correction method(ICE) through HiC-Pro(v2.11.1)software.The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format at fragment resolution.Visualization of Hi-C contact matrices was done via juicerbox. A/B compartment analysis was performed at 250-kb resolution using a publicly available script (matrix2compartment.pl).A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries.Chromatin loops in Satb1WT and Satb1CKO DP cells were called using Fit-Hi-C(v2.0.7).
5' RACE data process pipline. Reads were obtained following quality filtering and adaptor trimming using  fastp(v0.20.0) with default parameters.  Then the clean reads were analyzed with MIXCR(v2.1.10) to derive unique clonotypes based on CDR3 homology. Reads that comprise the clonotypes of interest (with matching VJ genes to Mus Musculus library antibody) were extracted for further analysis. The corresponding germline sequences were retrieved from IMGT, the international ImMunoGeneTics database.
Bulk RNA-Seq data process pipline. Clean data were obtained by removing reads containing adapter, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. All the downstream analysis were based on the clean data with high quality. Reads were aligned to the mouse transcriptome using Hisat2(v2.1.0) and Ensemble gene annotation. Gene count data generated by featureCounts(v2.0.0) of subread software was used as input to DESeq2(v1.30.0) to generate differential expression data as well as normalised count tables.
scRNA-Seq data process pipline. The cleaned data was generated by Cell Ranger(v2.2.0) and filtered for the low quality reads and unrelated sequence. The data was aligned to mouse mm10 reference genome. Data merging, thresholding, normalization, principal component analysis, clustering analysis, visualization , differential gene expression analysis and cell cycle phases analysis were carried out in Seurat(v2.3.4) according to their recommended steps.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks. We used deepTools(v3.5.0) to generate bedGraph files. The hicpro2juicebox.sh utility was used to convert the allValidPairs output of the pipeline into Juicebox .hic format.


title: Thymus-Bcl6SEWT-Bcl6p-3C-HTGTS-rep1


title: Col_35S-EVD_AGO4-IP_rep2


title: DP-Satb1WT-ETS2p-3C-HTGTS-rep2

value: DP thymocytes


title: DP-Satb1KO-HiC-rep1


title: MM4

city: Toronto

first: Danielle

last: Croucher

state: Ontario

address: 101 College Street

department: Medical Biophysics

country: Canada

institute: University of Toronto

data_processing:
CellRanger softerware suite v2 (10x Genomics)
Genome_build: mm10/GRCm38 + hg38/GRCh38 MYC
Supplementary_files_format_and_content: R object containing QC-passed cell barcodes only and all metadata

source_name: RBC-lysed BM

extract_protocol:
BM were extracted from hind-leg bones, dissociated into a single cell suspension using mechanical disruption (syringe) and RBC's lysed. Single-cell RNA-sequencing profiles were then generated using the 10x Genomics Chromium Single Cell 3' Solution V2 protocol
Single-cell library preparation was carried out as per the 10X Genomics Chromium single-cell protocol using the v2 chemistry reagent kit (10X Genomics, Plesanton, CA, USA). Cell suspensions were loaded onto individual channels of a Chromium Single-Cell Chip along with reverse transcription (RT) master mix and single cell 3’ gel beads, aiming for 1000 – 10,000 captured cells per sample. Following generation of gel bead-in-emulsions (GEMs), cDNA underwent a two-stage purification process with Dynal MyONE Silane beads (Thermo Fisher Scientific), followed by SPRISelect beads (Beckman Coulter). RT and cDNA amplification were performed using a 96-well Veriti Thermocycler (Life Technologies). Amplified cDNA was purified using SPRIselect beads and sequencing libraries were generated with unique sample indexes (SI). Dual sided SPRIselect cleanup was used to clean up samples and size select. Samples were quantified by Kapa Library Quantification kit (Roche) and normalised to achieve the desired median read depth per cell. Libraries were sequenced on an Illumina 2500 in Highoutput mode at the Princess Margaret Genomics Centre (Toronto, ON) using the 10X Genomics recommended sequencing parameters.


title: DP-Satb1KO-ETS2p-3C-HTGTS-rep1


title: MM7


title: MM6


title: MM5


title: Col_35S-EVD_AGO4-IP_rep1


title: Cont3


title: pol5_35S-EVD_smallRNA-seq


title: WT-1

description:
WT-1
Villin-Cre-PPARa-LoxP.txt


title: DP-Satb1KO-ETS2p-3C-HTGTS-rep2


title: 5 caki cl1b_(miRNA-4_0)


title: DP-Satb1WT-ETS2p-3C-HTGTS-rep1


title: DP-Satb1KO-Bcl6p-3C-HTGTS-rep2


title: ago2_35S-EVD


title: pol4_35S-EVD_smallRNA-seq


title: A498 cl2c_(miRNA-4_0)

description: miRNA expression data from  clone 2 of  498 sunitinib resistant ccRCC cell line

source_name: ccRCC A498 sunitinib resistantcell line


title: met1_35S-EVD_smallRNA-seq


title: 1 caki Pa_(miRNA-4_0


title: DP-Satb1WT-Bcl6p-3C-HTGTS-rep2


title: DP-Satb1KO-Bcl6p-3C-HTGTS-rep1


title: drm2_35S-EVD_smallRNA-seq


title: ND5


title: Cont2


title: A498 cl1c_(miRNA-4_0)

description: miRNA expression data from  clone 1 of  498 sunitinib resistant ccRCC cell line


title: A498 cl2b_(miRNA-4_0)


title: ND4


title: 2 caki Pb_(miRNA-4_0)


title: dcl2-dcl4_35S-EVD_smallRNA-seq


title: DP-Satb1KO-ATAC-rep2


title: dcl2-dcl3-dcl4_35S-EVD_smallRNA-seq


title: A498 cl1a_(miRNA-4_0)

source_name: ccRCC A498 sunitinib resistant cell line


title: A498 cl2a_(miRNA-4_0)


title: A498 cl1b_(miRNA-4_0)


title: Cont1


title: drm1-drm2_35S-EVD_smallRNA-seq


title: MM1


title: DP-Satb1WT-ATAC-rep2


title: dcl1-dcl2-dcl3-dcl4_35S-EVD_smallRNA-seq


title: MM2


title: DP-Satb1WT-Bcl6p-3C-HTGTS-rep1


title: A498 Pc_(miRNA-4_0)

description: miRNA expression data from A498 ccRCC cell line

source_name: ccRCC A498 cell line


title: AMG3


title: A498 Pb_(miRNA-4_0)


title: Col_T3A-EVD_smallRNA-seq


title: dcl1-het-dcl2-dcl3-dcl4_35S-EVD_smallRNA-seq


title: A498 Pa_(miRNA-4_0).


title: dcl1_35S-EVD_smallRNA-seq


title: MM3


title: DP-Satb1KO-ATAC-rep1


title: DP-Satb1WT-ATAC-rep1


title: 9-786 cl2c_(miRNA-4_0)

description: miRNA expression data from cl2  786-O resistant  ccRCC cell line

source_name: ccRCC 786 sunitinib resistant cell line


title: Col_RHD6-IR_root_smallRNA-seq

source_name: roots

value: roots


title: DP-Satb1WT-H3K27me3-input


title: Col_EVD-only_smallRNA-seq

value: Columbia


title: AMG1


title: DP-Satb1KO-H3K4me3-input


title: DP-Satb1KO-H3K27me3-rep2

tag: chip antibody


title: Col_35S-EVD_T3A-EVD_smallRNA-seq

value: inflorescence (stage 1-12) immature flower buds


title: ND1


title: 7-786 cl2a_(miRNA-4_0)


title: 8-786 cl2b_(miRNA-4_0)


title: cmt2-cmt3_35S-EVD_smallRNA-seq


title: ND3


title: dcl3_35S-EVD_smallRNA-seq


title: ago4-ago6-ago9_35S-EVD_smallRNA-seq


title: 3-786 Pc_(miRNA-4_0)

description: miRNA expression data from 786-O ccRCC cell line

source_name: ccRCC 786 cell line


title: Col_35S-EVD_EVD-only_smallRNA-seq

source_name: inflorescence (stage 1-12) immature flower buds


title: 6-786 cl1c_(miRNA-4_0)

description: miRNA expression data from cl1  786-O resistant  ccRCC cell line


title: ND2


title: DP-Satb1KO-H3K4me3-rep2

source_name: Thymocytes


title: 2-786 Pb_(miRNA-4_0)


title: pol5_RHD6-IR_smallRNA-seq


title: DP-Satb1WT-H3K27me3-rep1


title: AMG2


title: 5-786 cl1b_(miRNA-4_0)


title: Col_35S-EVD_T3_smallRNA-seq


title: DP-Satb1WT-H3K4me3-input


title: DP-Satb1KO-H3K27me3-rep1


title: ago6_35S-EVD_smallRNA-seq


title: DP-Satb1WT-H3K4me3-rep2


title: DP-Satb1KO-H3K27me3-input


title: 1-786 Pa_(miRNA-4_0)


title: cmt2_35S-EVD_smallRNA-seq


title: Col_RHD6-IR_smallRNA-seq


title: 4-786 cl1a_(miRNA-4_0)


title: DP-Satb1WT-H3K27me3-rep2


title: Col_35S-EVD_smallRNA-seq


title: DP-Satb1KO-H3K4me3-rep1


title: ago4-4_35S-EVD_smallRNA-seq


title: N_122

status: Public on Sep 01 2021

city: New York

first: Michelle

middle: E

last: Ehrlich

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: 4 Months old RAT striatum-N

data_processing:
Paired-end reads were aligned to reference genome using HISAT2
FeatureCounts was used to count the read numbers mapped per gene
Readcounts were adjusted by TMM normalisation
edgeR R package was used to perform differential expression analysis.
P-values were adjusted using Benjamini Hochberg method
.txt file containing a matrix of genes with readcounts against samples

source_name: striatum

extract_protocol:
The striatum  from one hemisphere was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA sequencing was performed by Novogene (https://en.novogene.com) on an Illumina Novaseq 6000 S4 flow cells platform

tag: injection group

value: N-TAF MiRNA

value: Sprague Dawley

tag: age of injection


title: ago4-6_35S-EVD_smallRNA-seq


title: DP-Satb1WT-H3K4me3-rep1

tag: cell type


title: S019_BL

city: Dublin

first: Antoinette

last: Perry

address: Science West, University College Dublin, Belfield, Dublin, Ireland

country: Ireland

institute: University College Dublin

description: prostate cancer cfDNA sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: samples were scanned using na Illumina BeadArrayTM reader

data_processing: .idat files were quality filtered and converted to beta values using the minfi R package. Normalization method = FunNorm.

label: Cy5 and Cy3

source_name: Peripheral blood plasma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted Qiagen QIAamp Circulating Nucleic Acid Kit according to standard instructions

value: plasma

tag: patient diagnosis

value: advanced stage prostate cancer (PCa)

tag: subject id

tag: collection time-point

value: Baseline


title: N_121

description: 4 Months old RAT striatum-N


title: S019_FU5

description: prostate cancer cfDNA sample


title: S009_FU4

description: prostate cancer cfDNA sample


title: S019_FU4

description: prostate cancer cfDNA sample


title: N_119

description: 4 Months old RAT striatum-N


title: S008_FU1

description: prostate cancer cfDNA sample


title: S019_FU3

description: prostate cancer cfDNA sample


title: S009_BL

description: prostate cancer cfDNA sample


title: S009_FU3

description: prostate cancer cfDNA sample


title: S009_FU2

description: prostate cancer cfDNA sample


title: N_90

description: 4 Months old RAT striatum-N


title: S029_FU2

description: prostate cancer cfDNA sample


title: S029_FU4

description: prostate cancer cfDNA sample


title: S007_BL

description: prostate cancer cfDNA sample


title: N_123

description: 4 Months old RAT striatum-N


title: S009_FU1

description: prostate cancer cfDNA sample


title: S019_FU2

description: prostate cancer cfDNA sample


title: S007_FU3

description: prostate cancer cfDNA sample


title: S007_FU2

description: prostate cancer cfDNA sample


title: S029_FU1

description: prostate cancer cfDNA sample


title: N_73

description: 4 Months old RAT striatum-N


title: S008_FU2

description: prostate cancer cfDNA sample


title: S008_BL

description: prostate cancer cfDNA sample


title: S019_FU1

description: prostate cancer cfDNA sample


title: S008_FU3

description: prostate cancer cfDNA sample


title: C_N_94

description: 4 Months old RAT striatum-C/N

value: C/N-TAF MiRNA


title: S020_FU5

description: prostate cancer cfDNA sample


title: S007_NTS1

description: prostate cancer cfDNA sample


title: C_N_76

description: 4 Months old RAT striatum-C/N


title: N_71

description: 4 Months old RAT striatum-N


title: C_N_92

description: 4 Months old RAT striatum-C/N


title: S020_FU4

description: prostate cancer cfDNA sample


title: S007_FU1

description: prostate cancer cfDNA sample


title: S020_NTS1

description: prostate cancer cfDNA sample


title: C_N_125

description: 4 Months old RAT striatum-C/N


title: C_N_95

description: 4 Months old RAT striatum-C/N


title: C_N_96

description: 4 Months old RAT striatum-C/N


title: C_N_97

description: 4 Months old RAT striatum-C/N


title: C_N_80

description: 4 Months old RAT striatum-C/N


title: CT_88

description: 4 Months old RAT striatum-Ct

value: control miRNA


title: CT_129

description: 4 Months old RAT striatum-Ct


title: S007_FU5

description: prostate cancer cfDNA sample


title: S020_FU3

description: prostate cancer cfDNA sample


title: S020_FU1

description: prostate cancer cfDNA sample


title: CT_126

description: 4 Months old RAT striatum-Ct


title: S017_FU3

description: prostate cancer cfDNA sample


title: S020_FU2

description: prostate cancer cfDNA sample


title: S017_FU4

description: prostate cancer cfDNA sample


title: S017_FU2

description: prostate cancer cfDNA sample


title: CT_128

description: 4 Months old RAT striatum-Ct


title: S017_FU5

description: prostate cancer cfDNA sample


title: S017_FU1

description: prostate cancer cfDNA sample


title: 776-48h-mmH3K9-50-bio-rep-4-tech-rep-1

city: Grand Forks

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Preliminary quality control analysis of FastQ files was performed using FastQC v.0.11.2.
The three prime adapters were trimmed from the reads using scythe v0.981. Quality trimming was carried out using sickle v1.33.
To remove contaminating cellular reads, reads aligning to African green monkey (Chlorocebus sabeus1.1) or human (hg19) genomes were removed.
Duplicate fragments were removed using the Picard Tools (Broad) Mark Duplicates function.
Bam files were filtered to contain only fragments between 100-150bp using an awk script.
Replicate bam files were merged together using samtools v1.3.1.
Bedgraphs normalized to 1x Coverage were generated from filtered, deduplicated reads using Deeptools v2.5.4.
Genome_build: GCA_000837645.1 (ViralProj14024)
Supplementary_files_format_and_content: *_depthNorm.bedgraph: BedGraphs normalized to 1x Coverage were generated from deduplicated reads using Deeptools v2.5.4.

organism: Betapolyomavirus macacae

extract_protocol:
The samples obtained from ChIP analyses were first purified using Zymo Research ChIP DNA Clean and Concentrator columns according to the supplied protocol.
Libraries were prepared using the New England Biolabs Next UltraII kit according to the protocol supplied with the kit with one exception. All reagent volumes were reduced by half for the preparation of libraries with no apparent effect on library quality or quantity.

tag: strain/background

tag: genotype/variation

value: WT

tag: time

tag: virion

value: No

tag: gradient


title: 776-48h-mmH3K9-50-bio-rep-5-tech-rep-1


title: S017_BL

description: prostate cancer cfDNA sample


title: S013_FU3

description: prostate cancer cfDNA sample


title: N_72

description: 4 Months old RAT striatum-N

tag: strain


title: S013_FU4

description: prostate cancer cfDNA sample

tag: tissue


title: S013_FU5

description: prostate cancer cfDNA sample


title: S013_FU1

description: prostate cancer cfDNA sample


title: LW50 WT A

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Adapters and low-quality bases from the RNA-seq reads were removed using Cutadapt
The filtered reads were mapped to the mouse genome (GRCm38) using TopHat2
htseq was used to estimate the expression counts of the genes
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression counts in tabular format

source_name: Intestinal organoid

growth_protocol: Small intestinal organoids were derived following standard protocols from healthy tissue of 8-12 weeks old mice (n = 3) of the strains Rnaseh2b_Xbp1fl/fl and ΔIEC, Rnaseh2bVilCreΔIEC, Xbp1VilCreΔIEC and Rnaseh2b_p53VilCreΔIEC. Cells were grown on 24-well plates in a combination of Matrigel and IntestiCult™ Organoid Growth Medium (STEMCELL Technologies).

extract_protocol:
Organoids were washed in PBS and RNA was extracted following the RNeasy Kit (Qiagen) according to manufacturer's protocol.
RNA libraries were prepared using TruSeq stranded mRNA Kit (Illumina) according to manufacturer’s instructions. All samples were sequenced using an Illumina HiSeq 4000 with single-end sequencing of 50bp reads


title: LW50 Xbp1KO A


title: LW50 WT C


title: HaCaT, TGF-β1

city: Fukuoka

first: Hatta

last: Mitsutoki

state: Fukuoka

address: 2-15-1 Tamura,Sawara-ku

department: Physiological Science and Molecular Biology

country: Japan

institute: Fukuoka Dental College

description: Gene expression (EMT)

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: HaCaT, TGF-β1-treated, 48h

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: NucleoSpin RNA Kit (Macherey-Nagel)

tag: cell line

value: HaCaT

tag: treatment


title: HaCaT, CTRL

description: Gene expression (Control)

source_name: HaCaT, Non-treated, 48h

value: Control


title: S013_FU2

description: prostate cancer cfDNA sample


title: LW50 Xbp1KO B

tag: genotype


title: S002_FU3

description: prostate cancer cfDNA sample


title: CT_82

description: 4 Months old RAT striatum-Ct


title: S002_FU2

description: prostate cancer cfDNA sample


title: HaCaT, TY1-SNAI2

description: Gene expression (SNAI2 overexpression)

source_name: HaCaT stably expressing TY1-SNAI2

value: SNAI2 overexpression


title: 776-48h-HH3-50-bio-rep-5-tech-rep-1

tag: chip antibody


title: LW50 WT B


title: 776-48h-mmH3K9-30-bio-rep-5-tech-rep-1


title: 776-48h-mmH3K9-50-bio-rep-3-tech-rep-1


title: HaCaT, TY1

description: Gene expression (Control)

source_name: HaCaT stably expressing TY1-tag


title: S002_FU1

description: prostate cancer cfDNA sample


title: LW50 Xbp1KO C


title: LW50 H2BKO B


title: 776-48h-HH3-50-bio-rep-3-tech-rep-1


title: S002_FU5

description: prostate cancer cfDNA sample


title: S029_BL

description: prostate cancer cfDNA sample


title: 776-48h-HH3-50-bio-rep-4-tech-rep-1


title: 776-48h-HH3-30-bio-rep-5-tech-rep-1


title: 776-48h-HH3-30-bio-rep-4-tech-rep-1


title: 776-48h-HH3-10-bio-rep-4-tech-rep-1


title: H2Bp53DKO 1


title: 776-48h-mmH3K9-30-bio-rep-3-tech-rep-1


title: LW50 H2BKO C


title: S013_BL

description: prostate cancer cfDNA sample


title: 776-48h-mmH3K9-10-bio-rep-4-tech-rep-1


title: 776-48h-HH3-30-bio-rep-3-tech-rep-1


title: S002_FU4

description: prostate cancer cfDNA sample


title: 776-48h-mmH3K9-10-bio-rep-5-tech-rep-1


title: LW45 DKO 1


title: 776-48h-RNA-P2-bio-rep-9-tech-rep-1


title: RMB3879

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

description: Liver total cells, B6, no treatment

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38_M13 from GENCODE using RSEM program version 1.3.0 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program.
TPM (Transcripts Per Million) table were generated by RSEM 1.3.0.
Genome_build: GRCm38_M13
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: liver NPCs

growth_protocol: C57BL/6 were housed in SPF conditions and organs were harvested when mice were 8 wk-old

extract_protocol:
Liver digested by collagenase/DNAse for 30 mins
Smartseq2

treatment_protocol: Cells form 3 mice were independently prepared and pooled before the sorting

tag: sorting

value: sorted alive CD45+ CD3- CD19- CD49b- Ly6G- CD64+ F4/80+ cells

tag: kit

value: Smart Seq -Nextera XT v2

value: liver macrophages


title: LW50 H2BKO A


title: 776-48h-RNA-P2-bio-rep-7-tech-rep-1


title: LW45 DKO 4


title: 776-48h-dmH3K9-bio-rep-7-tech-rep-1


title: 776-48h-HH3-10-bio-rep-5-tech-rep-1


title: RMB3875

description: Liver total cells, B6, no treatment

tag: cell type


title: LW50 DKO A


title: 776-48h-mmH3K9-10-bio-rep-3-tech-rep-1


title: 776-48h-dmH3K4-bio-rep-4-tech-rep-1


title: H2Bp53DKO 3


title: RMB3878

description: Liver total cells, B6, no treatment


title: RMB3865

description: Liver total cells, B6, no treatment


title: RMB3872

description: Liver total cells, B6, no treatment


title: 776-48h-HH3-10-bio-rep-3-tech-rep-1


title: RMB3864

description: Liver total cells, B6, no treatment


title: RMB3876

description: Liver total cells, B6, no treatment


title: RMB3874

description: Liver total cells, B6, no treatment


title: RMB3863

description: Liver total cells, B6, no treatment


title: 776-48h-dmH3K9-bio-rep-4-tech-rep-1


title: 776-48h-dmH3K4-bio-rep-5-tech-rep-1


title: 776-48h-dmH3K4-bio-rep-6-tech-rep-1


title: 776-48h-mmH3K9-30-bio-rep-4-tech-rep-1


title: RMB3866

description: Liver total cells, B6, no treatment


title: RMB3873

description: Liver total cells, B6, no treatment


title: 776DV-dmH3K9-bio-rep-5-tech-rep-1

value: Yes


title: RMB3869

description: Liver total cells, B6, no treatment


title: 776-48h-RNA-P2-bio-rep-8-tech-rep-1


title: RMB3867

description: Liver total cells, B6, no treatment


title: 776-48h-dmH3K9-bio-rep-6-tech-rep-1


title: 776-48h-mmH3K9-30-bio-rep-2-tech-rep-1


title: RMB3860

description: Liver total cells, B6, no treatment


title: RMB3859

description: Liver total cells, B6, no treatment


title: H2Bp53DKO 2


title: cs1085DV-mmH3K9-bio-rep-2-tech-rep-1


title: RMB3868

description: Liver total cells, B6, no treatment


title: 776DV-dmH3K9-bio-rep-4-tech-rep-1


title: cs1085DV-mmH3K9-bio-rep-1-tech-rep-1


title: 776-48h-dmH3K9-bio-rep-5-tech-rep-1


title: RMB3870

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-10-bio-rep-1-tech-rep-1


title: 776-48h-dmH3K9-bio-rep-3-tech-rep-1


title: 776-48h-mmH3K9-50-bio-rep-1-tech-rep-1


title: RMB3871

description: Liver total cells, B6, no treatment


title: 776-48h-dmH3K9-bio-rep-2-tech-rep-1


title: 776-48h-HH3-10-bio-rep-2-tech-rep-1


title: RMB3851

description: Liver total cells, B6, no treatment


title: 776-48h-HH3-10-bio-rep-1-tech-rep-1


title: RMB3849

description: Liver total cells, B6, no treatment


title: RMB3861

description: Liver total cells, B6, no treatment


title: 776-48h-HH3-50-bio-rep-1-tech-rep-1


title: RMB3862

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-10-bio-rep-2-tech-rep-1


title: RMB3847

description: Liver total cells, B6, no treatment


title: 776DV-dmH3K9-bio-rep-2-tech-rep-1


title: 776-48h-HH3-50-bio-rep-2-tech-rep-1


title: RMB3846

description: Liver total cells, B6, no treatment


title: cs1085DV-mmH3K9-bio-rep-3-tech-rep-1


title: 776-48h-dmH3K4-bio-rep-3-tech-rep-1


title: RMB3877

description: Liver total cells, B6, no treatment


title: 776DV-dmH3K9-bio-rep-3-tech-rep-1


title: RMB3858

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-50-bio-rep-2-tech-rep-1


title: RMB3839

description: Liver total cells, B6, no treatment


title: RMB3853

description: Liver total cells, B6, no treatment


title: 776DV-tmH3K9-bio-rep-6-tech-rep-1


title: RMB3857

description: Liver total cells, B6, no treatment


title: RMB3856

description: Liver total cells, B6, no treatment


title: RMB3854

description: Liver total cells, B6, no treatment


title: 776DV-tmH3K9-bio-rep-4-tech-rep-1


title: 776-48h-mmH3K9-30-bio-rep-1-tech-rep-1


title: 776-48h-HH3-30-bio-rep-2-tech-rep-1


title: 776-48h-HH3-30-bio-rep-1-tech-rep-1


title: RMB3838

description: Liver total cells, B6, no treatment


title: RMB3850

description: Liver total cells, B6, no treatment


title: RMB3852

description: Liver total cells, B6, no treatment


title: 776DV-tmH3K9-bio-rep-5-tech-rep-1


title: RMB3855

description: Liver total cells, B6, no treatment


title: 776DV-tmH3K9-bio-rep-3-tech-rep-1


title: 776-48h-tmH3K4-bio-rep-5-tech-rep-1


title: RMB3836

description: Liver total cells, B6, no treatment


title: RMB3834

description: Liver total cells, B6, no treatment


title: RMB3843

description: Liver total cells, B6, no treatment


title: RMB3845

description: Liver total cells, B6, no treatment


title: 776DV-HH4-bio-rep-5-tech-rep-1


title: RMB3841

description: Liver total cells, B6, no treatment


title: 776DV-mmH4K20-bio-rep-4-tech-rep-1


title: RMB3831

description: Liver total cells, B6, no treatment


title: RMB3848

description: Liver total cells, B6, no treatment


title: RMB3842

description: Liver total cells, B6, no treatment


title: 776-48h-dmH3K4-bio-rep-2-tech-rep-1


title: 776DV-dmH3K9-bio-rep-1-tech-rep-1


title: RMB3844

description: Liver total cells, B6, no treatment


title: RMB3840

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K4-bio-rep-5-tech-rep-1


title: 776-48h-RNA-P2-bio-rep-6-tech-rep-1


title: 776DV-tmH3K9-bio-rep-7-tech-rep-1


title: RMB3828

description: Liver total cells, B6, no treatment


title: RMB3837

description: Liver total cells, B6, no treatment


title: RMB3832

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-bio-rep-10-tech-rep-1


title: 776-48h-RNA-P2-bio-rep-5-tech-rep-1


title: 776-48h-mmH3K9-bio-rep-9-tech-rep-1


title: RMB3833

description: Liver total cells, B6, no treatment


title: RMB3821

description: Liver total cells, B6, no treatment


title: RMB3835

description: Liver total cells, B6, no treatment


title: 776-48h-HH4-bio-rep-5-tech-rep-1


title: 776-48h-tmH3K9-bio-rep-4-tech-rep-1


title: 776-48h-HH3-bio-rep-4-tech-rep-1


title: 776DV-HH3-bio-rep-6-tech-rep-1


title: RMB3819

description: Liver total cells, B6, no treatment


title: 776-48h-HH4-bio-rep-8-tech-rep-1


title: 776-48h-HH4-bio-rep-4-tech-rep-1


title: RMB3829

description: Liver total cells, B6, no treatment


title: 776-48h-RNA-P2-bio-rep-4-tech-rep-1


title: 776-48h-tmH3K4-bio-rep-3-tech-rep-1


title: 776-48h-tmH3K9-bio-rep-3-tech-rep-1


title: RMB3827

description: Liver total cells, B6, no treatment


title: RMB3820

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K4-bio-rep-4-tech-rep-1


title: RMB3825

description: Liver total cells, B6, no treatment


title: RMB3816

description: Liver total cells, B6, no treatment


title: RMB3826

description: Liver total cells, B6, no treatment


title: RMB3815

description: Liver total cells, B6, no treatment


title: 776-48h-tmH3K9-bio-rep-6-tech-rep-1


title: RMB3822

description: Liver total cells, B6, no treatment


title: 776-48h-HH4-bio-rep-7-tech-rep-1


title: RMB3824

description: Liver total cells, B6, no treatment


title: RMB3823

description: Liver total cells, B6, no treatment


title: RMB3812

description: Liver total cells, B6, no treatment


title: 776-48h-HH3-bio-rep-3-tech-rep-1


title: RMB3830

description: Liver total cells, B6, no treatment


title: 776DV-mmH4K20-bio-rep-2-tech-rep-1


title: 776-48h-HH4-bio-rep-2-tech-rep-1


title: 776-48h-HH4-bio-rep-6-tech-rep-1


title: 776-48h-tmH3K4-bio-rep-4-tech-rep-1


title: RMB3809

description: Liver total cells, B6, no treatment


title: RMB3810

description: Liver total cells, B6, no treatment


title: RMB3808

description: Liver total cells, B6, no treatment


title: RMB3818

description: Liver total cells, B6, no treatment


title: 776-48h-tmH3K9-bio-rep-5-tech-rep-1


title: 776-48h-RNA-P2-bio-rep-3-tech-rep-1


title: 776DV-HH4-bio-rep-4-tech-rep-2


title: RMB3807

description: Liver total cells, B6, no treatment


title: RMB3804

description: Liver total cells, B6, no treatment


title: 776DV-HH3-bio-rep-5-tech-rep-1


title: RMB3817

description: Liver total cells, B6, no treatment


title: 776DV-mmH4K20-bio-rep-1-tech-rep-1


title: 776DV-mmH4K20-bio-rep-1-tech-rep-2


title: RMB3802

description: Liver total cells, B6, no treatment


title: RMB3803

description: Liver total cells, B6, no treatment


title: 776-48h-tmH3K9-bio-rep-2-tech-rep-1


title: 776-48h-tmH3K4-bio-rep-2-tech-rep-2


title: RMB3813

description: Liver total cells, B6, no treatment


title: 776DV-HH3-bio-rep-5-tech-rep-2


title: RMB3814

description: Liver total cells, B6, no treatment


title: 776DV-HH3-bio-rep-4-tech-rep-2


title: 776-48h-HH4-bio-rep-3-tech-rep-1


title: RMB3796

description: Liver total cells, B6, no treatment


title: 776-48h-RNA-P2-bio-rep-2-tech-rep-2


title: 776-48h-RNA-P2-bio-rep-2-tech-rep-1


title: RMB3795

description: Liver total cells, B6, no treatment


title: RMB3793

description: Liver total cells, B6, no treatment


title: RMB3811

description: Liver total cells, B6, no treatment


title: 776DV-mmH4K20-bio-rep-3-tech-rep-1


title: 776DV-HH4-bio-rep-4-tech-rep-1


title: 776-48h-HH3-bio-rep-2-tech-rep-1


title: RMB3794

description: Liver total cells, B6, no treatment


title: RMB3805

description: Liver total cells, B6, no treatment


title: RMB3790

description: Liver total cells, B6, no treatment


title: 776DV-HH4-bio-rep-3-tech-rep-1


title: 776DV-HH3-bio-rep-3-tech-rep-1


title: 776-48h-mmH3K9-bio-rep-8-tech-rep-1


title: RMB3797

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K4-bio-rep-3-tech-rep-1


title: 776DV-HH4-bio-rep-3-tech-rep-2


title: RMB3806

description: Liver total cells, B6, no treatment


title: RMB3786

description: Liver total cells, B6, no treatment


title: 776DV-mmH3K20-bio-rep-1-tech-rep-1


title: 776-48h-tmH3K4-bio-rep-2-tech-rep-1


title: 776DV-HH3-bio-rep-4-tech-rep-1


title: RMB3801

description: Liver total cells, B6, no treatment


title: 776DV-mmH3K9-bio-rep-5-tech-rep-1


title: 776DV-mmH3K9-bio-rep-7-tech-rep-1


title: RMB3799

description: Liver total cells, B6, no treatment


title: 776DV-mmH3K9-bio-rep-6-tech-rep-1


title: RMB3800

description: Liver total cells, B6, no treatment


title: RMB3784

description: Liver total cells, B6, no treatment