title: lung,PCW5.5, rep1 [10x303w4]

data_processing:
Reads were aligned to the human reference genome  and libraries were demultiplexed and aligned with the 10X Genomics pipeline CellRanger (version 3.0.2).
Loom files were generated for each sample by running Velocyto (0.17.17) 76 in order to map molecules to unspliced and spliced transcripts.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: lung

extract_protocol:
 The tissues were triturated with glass Pasteur pipettes every 15-20 min to enhance dissociation. After digestion, the cell suspension was filtered in a 15ml Falcon tube using a 30μm cell strainer (CellTrics, Sysmex), to remove clumps and debris. The cell suspension was kept ice cold and was diluted (roughly 1:2) with ice cold HBSS. The filtered cells were pelleted at 200g for 5 min at 4 °C and the pellet resuspended in a small volume of calcium- and magnesium-free HBSS (Gibco, cat no. 14170) and transferred to 1.5ml Eppendorf tubes precoated with 30% BSA (A9576, Sigma-Aldrich). A Bürker chamber was used for cell counting.
Single-cell RNAseq was carried out with the Chromium Single Cell 3´ Reagent Kit v2 and v3. Cell suspensions were counted and diluted to concentrations of 800 – 1200 cells/μl for a target recovery of 5000 cells on the Chromium platform. Downstream procedures including cDNA synthesis, library preparation and sequencing were performed according to the manufacturer’s instructions (10X Genomics Inc.). Libraries were sequenced on an Illumina NovaSeq 6000 (Illumina). We aimed to obtain 75.000 and 200.000 sequencing reads/cell for the v2 and v3 libraries respectively to match the different performances of the Chromium Single Cell 3´ Reagent v2 and v3 Kits and to achieve sufficient sequencing saturation. Across all 39 libraries we obtained an average of 187242 reads/cell.

value: lung

tag: technology

value: Chromium

tag: library technology

tag: gender

value: female


title: Lung,7,rep1

status: Public on Jan 17 2023

type: SRA

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

description: 10X Genomics

library_source: transcriptomic

data_processing:
Sequenced ST libraries were processed using Space Ranger 1.0.0 Pipeline (10X Genomics).
Reads were aligned to the human reference genome to obtain an expression matrix.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
One of the two lungs (preferentially the left), from each donor, was snap frozen in cryomatrix and further used for histological analyses. We cut 10-12μm-thick tissue sections with a cryostat (Leica CM3050S or analogue) and collected them onto poly-lysine coated slides (VWR Cat No. 631-0107)
Spatial Gene Expression libraries (n=9) (6-13 pcw) were generated with the Visium Spatial Gene Expression Slide & Reagent kit (PN-1000184; 10X Genomics Inc.), according to manufacturer's protocol

tag: tissue

value: Lung

tag: age

tag: donor


title: Lung,7,rep2

description: 10X Genomics


title: Lung,7,rep4

description: 10X Genomics


title: Lung,7,rep7

description: 10X Genomics


title: Lung,7,rep3

description: 10X Genomics


title: Lung,12,rep4

description: 10X Genomics


title: lung,PCW5.5, rep2 [10x303w3]

library_source: transcriptomic single cell


title: Lung,8,rep2

description: 10X Genomics


title: lung,PCW7, rep1 [10x299w3]


title: lung,PCW7, rep2 [10x299w4]


title: lung,PCW7, rep3 [10x299w5]


title: lung,PCW7, rep4 [10x299w6]


title: Lung,9,rep2

description: 10X Genomics


title: lung,PCW6, rep2 [10x289w3]

value: male


title: lung,PCW10, rep1 [10x285w3]


title: lung,PCW10, rep2 [10x285w4]


title: lung,PCW11.5, rep5 [10X274w2]


title: lung,PCW11.5, rep4 [10X272w4]


title: lung,PCW11.5, rep3 [10X272w3]


title: lung,PCW11.5, rep6 [10X274w3]


title: lung,PCW11.5, rep1 [10X272w1]


title: lung,PCW11.5, rep2 [10X272w2]


title: lung,PCW12, rep3 [10X263w3]


title: Lung,7,rep5

description: 10X Genomics


title: lung,PCW12, rep1 [10X263w1]


title: lung,PCW14, rep7 [10X256w1]


title: lung,PCW14, rep6 [10X253w8]


title: lung,PCW14, rep5 [10X253w7]


title: lung,PCW14, rep4 [10X253w6]


title: lung,PCW14, rep1 [10X253w3]


title: lung,PCW14, rep2 [10X253w4]


title: lung,PCW14, rep3 [10X253w5]


title: lung,PCW13, rep5 [10X247w3]


title: lung,PCW13, rep3 [10X247w1]


title: lung,PCW13, rep4 [10X247w2]


title: lung,PCW13, rep2 [10X214w2]


title: lung,PCW6, rep3 [10x289w4]


title: lung,PCW5, rep1 [10X180w1]


title: lung,PCW12, rep1 [10X189w1]


title: lung,PCW13, rep1 [10X214w1]


title: lung,PCW8, rep1 [10X158w3]


title: lung,PCW6, rep1 [10X151w1]


title: lung,PCW8.5, rep2 [10X166w2]


title: lung,PCW12, rep2 [10X263w2]


title: lung,PCW13, rep6 [10X247w4]


title: Myocardial scar control_8

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
bio_rep_8
Reads_per_gene.csv

data_processing:
To assure high sequence quality, Illumina reads were quality- and adapter-trimmed via Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Processed reads were subsequently mapped to the mouse genome (GRCm39) using STAR v2.7.2b with default parameters. Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package. Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction). The count output was utilized to identify differentially expressed genes using DESeq2 version 1.24.0. Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”. Differential expression of genes was assumed at an adjusted p-value (padj) after Benjamini-Hochberg correction < 0.05 and |log2FoldChange| ≥ 1.
genome build/assembly: GRCm39
Supplementary files format and content: tsv; gene barcode matrices and feature barcode matrix
Supplementary files format and content: csv; raw gene count, clonotypes and contigs

molecule: polyA RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Infarcted heart tissue was dissected and stored in RNA later solution at 4°C overnight. Afterwards, samples were stored at -80°C until RNA extraction. RNA was extracted from mouse cardiac tissue (infarcted area) by using the tissue RNA isolation kit (RNeasy mini – Qiagen) according to the manufacturer's instructions
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥7.5. DNA libraries suitable for sequencing were prepared from 50 ng of total RNA, with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume). After 17 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~310 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

value: heart

tag: cell line

value: primary cells

tag: cell type

value: cardiac cells

tag: genotype

tag: treatment

value: control non-T-cell transferred

tag: time point

value: 5 days post-surgery


title: Myocadial scar TCR-M Treg transfer_1

description:
bio_rep_1
Reads_per_gene.csv

value: receiving adoptive transfer of Treg-polarized myosin-specific T-cells


title: GBM5_1_short read spatial transcriptomics

city: Chengdu

first: Yuan

last: Wang

state: Sichuan

address: No.17 People's South Road

country: China

institute: Sichuan university

data_processing:
ST RNA-seq alignment process was completed by spaceranger (version 1.1.0)
Seurat V4 workflow
Genome_build: hg38
Supplementary_files_format_and_content: spaceranger workflow outcome

extract_protocol:
Surgically removed human glioma samples were snap-frozen in isopentane/liquid nitrogen, embedded in pre-chilled OCT (Tissue-Tek O.C.T. Compound, SAKURA), and then cryosectioned into 10 μm sections at -20℃. Sections with obvious tumor areas were collected. Frozen tissue sections on Visium Tissue Optimization Slides were fixed with pre-chilled methanol. H&E staining was performed according to the Tissue Optimization Guide (CG000238 Rev A, 10X Genomics), and subjected to bright-field imaging under a Leica DM6B microscope. Sections were permeabilized with 0.1N HCl at different durations. The released mRNA was captured by probes on the slides, and reverse transcribed to cDNA marked by fluorescently labeled nucleotides. Tissue was then removed from the slides with a digestive enzyme, leaving the fluorescently labeled cDNA, which was visualized under a Leica DM6B microscope. Based on the signal intensity, we determined the optimal permeabilization duration for human brain tumor samples was 12min
Follwed by protocol of spatial transcriptomics based 10X technology

tag: replicates

tag: integrated diagnosis

value: Glioblastoma, IDH-wt

tag: primary/ recurrent

value: Primary

tag: who grade

value: IV

tag: p53 ihc

value: Positive

tag: idh1 mutant

value: No

tag: tert mutant (c228t or c250t)

tag: mgmt promoter methylation

value: Yes

tag: h3f3a mutant

tag: hist1h3b mutant

tag: gfap ihc

tag: oligo2 ihc

tag: ki_67 labeling index (cc)


title: Myocardial scar control_6

description:
bio_rep_6
Reads_per_gene.csv

tag: tissue

tag: cell line

tag: cell type


title: GBM5_2_short read spatial transcriptomics

value: GBM5 peritumor

value: Peritumor tissue


title: Myocadial scar TCR-M Treg transfer_3

description:
bio_rep_3
Reads_per_gene.csv

tag: genotype

tag: treatment

tag: time point


title: Myocadial scar TCR-M Treg transfer_5

description:
bio_rep_5
Reads_per_gene.csv


title: Myocardial scar control_3

description:
bio_rep_3
Reads_per_gene.csv


title: Myocardial scar control_2

description:
bio_rep_2
Reads_per_gene.csv


title: Myocardial scar control_4

description:
bio_rep_4
Reads_per_gene.csv


title: Myocadial scar TCR-M Treg transfer_6

description:
bio_rep_6
Reads_per_gene.csv


title: Myocadial scar TCR-M Treg transfer_4

description:
bio_rep_4
Reads_per_gene.csv


title: Myocadial scar TCR-M Treg transfer_2

description:
bio_rep_2
Reads_per_gene.csv


title: Myocardial scar control_5

description:
bio_rep_5
Reads_per_gene.csv


title: Myocardial scar control_7

description:
bio_rep_7
Reads_per_gene.csv


title: lung,PCW12, rep2 [10X189w2]

value: lung

tag: age

tag: technology

value: Chromium

tag: library technology

tag: gender


title: GBM3_short read spatial transcriptomics

tag: replicates

tag: integrated diagnosis

tag: primary/ recurrent

tag: who grade

tag: p53 ihc

tag: idh1 mutant

tag: tert mutant (c228t or c250t)


title: GBM4_short read spatial transcriptomics

value: Secondary glioblastoma

tag: mgmt promoter methylation

tag: h3f3a mutant

tag: hist1h3b mutant

tag: gfap ihc

tag: oligo2 ihc

tag: ki_67 labeling index (cc)


title: GBM1_short read spatial transcriptomics


title: DMG5_short read spatial transcriptomics

value: Diffuse midline glioma, H3K27M-mutant


title: DMG4_short read spatial transcriptomics

value: Recurrent


title: GBM2_short read spatial transcriptomics

value: Negative


title: DMG3_short read spatial transcriptomics


title: lung,PCW8.5, rep1 [10X140w1]

tag: tissue

tag: age

value: female


title: DMG2_short read spatial transcriptomics


title: DMG1_short read spatial transcriptomics


title: WT_nt_12

city: Iowa City

first: John

middle: F

last: Engelhardt

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

country: USA

institute: University of Iowa

description:
TPM_12
TPM_WT_nt_12

data_processing:
Samples were aligned and processed through RSEM, using Bowtie2 alignment
Gene-level TPM as reported by RSEM were used for analysis
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample

source_name: Brain

growth_protocol: Primary neonatal neural stem cells were cultured and propagated in serum-free medium (SFM) DMEM/F12 supplemented with EGF, FGF (Sigma), insulin, transferrin, sodium selenite (ITSS) (Roche) and B-27 supplement (Invitrogen)

extract_protocol:
Total RNA was prepared using RNAeasy Plus kit (Qiagen) following manufacturer's instructions.
Ribosome depletion and library construction were performed by the University of Washington

treatment_protocol: 48 hours after plating Ncf1–/– NSCs were treated with mouse recombinant Igfbp2 (100 ng/ml). 48 hours after treatment, total RNA was prepaired using RNAeasy Plus kit (Qiagen)

value: Brain

tag: cell line

tag: cell type

value: Neural Stem Cells

tag: genotype

value: WT

tag: treatment


title: WT_nt_11

description:
TPM_11
TPM_WT_nt_11

value: Primary


title: WT_nt_10

description:
TPM_10
TPM_WT_nt_10


title: Myocardial scar control_1

description:
bio_rep_1
Reads_per_gene.csv

value: heart

value: primary cells

value: cardiac cells

value: control non-T-cell transferred

tag: time point

value: 5 days post-surgery


title: NCF1KO_IGFBP2_06

description:
TPM_6
TPM_NCF1KO_IGFBP2_06

value: NCF1 KO


title: NCF1KO_nt_01

description:
TPM_1
TPM_NCF1KO_nt_01


title: NCF1KO_IGFBP2_07

description:
TPM_7
TPM_NCF1KO_IGFBP2_07


title: NCF1KO_nt_04

description:
TPM_4
TPM_NCF1KO_nt_04


title: NCF1KO_IGFBP2_05

description:
TPM_5
TPM_NCF1KO_IGFBP2_05


title: NCF1KO_IGFBP2_08

description:
TPM_8
TPM_NCF1KO_IGFBP2_08


title: Infect WT HSC using antibody against H2K27ac [Cut&Run]

city: Houston

first: Duy

middle: Tri

last: Le

state: Texas

address: 1102 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

library_source: genomic

data_processing:
library strategy: CUT&RUN
FASTQ files were preprocessed using HTS stream
CUT&RUN alignment (Bowtie2)
Peaks were called uing MACS v2.2 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: narrow peaks

molecule: genomic DNA

source_name: Hematopoietic Stem Cells

growth_protocol: HSCs were isolated via whole bone marrow from naïve or infected mice

extract_protocol:
Leg and hip bones were isolated and HSCs were purified via FACS sorting following mechanical isolation and c-kit+ magnetic cell enrichment. HSCs (LK CD150+ CD48-) were washed with Wash Buffer (50mL total with 20 mM HEPES pH 7.5, 150mM NaCl, 0.5 mM Spermidine, and one Roche Complete protein inhibitor tablet) and bound to Concanavalin A-coated magnetic beads (Bang Laboratories L200731C) for 15 minutes room temperature. Sample slurries were magnetically separated, washed, and incubated with primary antibody diluted in wash buffer containing 0.05% digitonin (Dig Wash) overnight at 4 °C. Slurries were then magnetically separated and washed with Dig Wash three times and then incubated with protein A-MNase (pA-MN, Epicypher 15-1016) for 1 hour at 4 °C. Slurries were magnetically separated and washed, resuspended in 200uL Dig Wash, and placed on an iced heating block. 2uL of 2mM CaCl2 was added to catalyze the pA-MN reaction and digestion. After 45 minutes, one equal volume of Stop Buffer (340mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.05 mg/mL glycogen, 5 ug/mL RNase A, 2 pg/mL heterologous spike-in DNA) was added to end the reaction, and sample slurries were then incubated for 30 minutes at 37 °C to release fragments and then magnetically separated. The supernatant was collected, and DNA was purified via phenol-chloroform extraction and ethanol precipitation. Samples were resuspended in molecular-grade water after ethanol precipitation.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were in the presence of 1-month M. avium infection.

value: murine Hematpoietic stem cells

tag: strain

value: 1-month Mycobacterium avium infection


title: WT_nt_09

description:
TPM_9
TPM_WT_nt_09


title: Infect WT HSC using antibody against mouse IgG [Cut&Run]


title: Infected Batf2 KO HSC replicate 3

data_processing:
FASTQ files were preprocessed using HTS stream
RNA seq alignment (STAR)
Differential expression (DE) analysis of gene expression was performed using R package filterByExpr()
differential expresion analysis using deSeq2
Geneset enrichment analysis was done by sorting gene lists according to their increasing p-value and running tmodCERNOtest() function from the tmod R package (Weiner 3rd and Domaszewska)
Panel plots with geneset enrichment were plotted with tmodPanelPlot() from tmod, other plots were plotted using ggplot2.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every sample

extract_protocol:
Leg and hip bones were isolated and HSCs were purified via FACS sorting following mechanical isolation and c-kit+ magnetic cell enrichment. DNA and RNA were isolated with the RNeasy Kit (Qiagen, Cat#74004). RNA-seq libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Usa).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were in the presence and absence of 1-month M. avium infection.

value: C57BL/9 Batf2 KO

value: 1-month Mycobacterium aivum infection


title: Infected Batf2 KO HSC replicate 4


title: Infect WT HSC using antibody against BATF2 [Cut&Run]


title: NCF1KO_nt_03

description:
TPM_3
TPM_NCF1KO_nt_03


title: NCF1KO_nt_02

description:
TPM_2
TPM_NCF1KO_nt_02


title: Infected Batf2 KO HSC replicate 2


title: Infected Batf2 KO HSC replicate 1


title: WT-HFD-M3

city: Philadelphia

first: Ying

last: Shao

state: Pennsylvania

address: 3500 N Broad St, MERB1083A

institute: Temple University

data_processing:
FASTQ files were mapped to the mouse mm10 genome using STAR Aligner.
BAM alignment files were imported into Qlucore Omics Explorer and used to generate expression data (transcripts per million, TPM).
Assembly: Mus musculus (UCSC version mm10, based on GRCm38.p6)
Supplementary files format and content: gene TPM values for each Sample

source_name: Hepatic macrophages from liver

extract_protocol:
Hepatic macrophages from liver were isolated and directly lysed in TRIzol, and RNA was harvested using miRNeasy Mini kit.
Total RNA libraries were prepared by using Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara). In short, 250 pg -10 ng total RNA from each sample was reverse-transcribed via random priming and reverse transcriptase. Full-length cDNA was obtained with SMART (Switching Mechanism At 5' end of RNA Template) technology. The template-switching reaction was used to keep the strand orientation of the RNA. The ribosomal cDNA was hybridized to mammalian-specific R-Probes and then cleaved by ZapR. Libraries containing Illumina adapter with TruSeq HT indexes were subsequently pooled and loaded to the Hiseq 2500. Single end reads at 75 bp with 30 million reads per sample were generated for bioinformatic analysis.

tag: phenotype

value: wildtype

value: High fat diet

value: Hepatic macrophages from liver


title: WT-NCD-M1

value: Normal chow diet


title: C11-HFD-M2

value: Caspase-11 konck out


title: WT-NCD-M2


title: WT-NCD-M3


title: WT-HFD-M1


title: C11-HFD-M1


title: C11-NCD-M2


title: C11-NCD-M1


title: WT-HFD-M2


title: C11-NCD-M3


title: C11-HFD-M3


title: Batf2 KO HSC replicate 4

value: naïve


title: Batf2 KO HSC replicate 3


title: infected WT HSC replicate 1


title: infected WT HSC replicate 4


title: WT HSC replicate 4


title: WT HSC replicate 3


title: WT HSC replicate 1


title: WT HSC replicate 2


title: SRF control lungs

city: Princeton

first: Katharine

last: Goodwin

state: NJ

address: Hoyt Laboratory, 25 William St

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: pooled cells from 6 lungs

data_processing:
Basecalls performed using RTA version 1.18.64.0
Concatenated fastq files from both lanes of flowcell
Demultiplexed reads using barcode_splitter 0.18.2 (https://bitbucket.org/princeton_genomics/barcode_splitter)
Single cell analysis (alignment, cell identification, gene counts, etc.) performed by CellRanger count version 3.0.2
Single cell analysis by Seurat (v3)
Assembly: Mus musculus reference genome mm10-3.0.0
Supplementary files format and content: 10x Cell Ranger HDF5 formatted matrix files

extract_protocol:
Lungs were isolated from embryos at the stages of interest and then dissociated with dispase at room temperature for 10 minutes, with additional mechanical dissociation using fine tungsten needles to create single-cell suspensions. Dispase was inactivated by adding DMEM/F12 medium (without HEPES) supplemented with 5% heat-inactivated fetal bovine serum (FBS; Atlanta Biologicals) and antibiotics (50 units/ml of penicillin and streptomycin) and the cell suspensions were then passed through 40-μm-diameter mesh filters.
Cells were loaded and processed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 on the Chromium Controller (10X Genomics) following manufacturer protocols. Individual cells were encapsulated in droplets with individual gel beads carrying unique barcoded primers and lysed. Then, cDNA fragments were synthesized, barcoded, and amplified by PCR. Illumina sequencing libraries were prepared from the amplified cDNA from each sample group using the Nextra DNA library prep kit (Illumina). Libraries were sequenced on NovaSeq 6000 S Prime flowcells (Illumina) as paired-end 28 + 94 nucleotide reads, following manufacturer protocols.

value: lung

value: Srf-flox/flox


title: SRF mutant lungs

description: pooled cells from 7 lungs


title: CC.9

city: Madison

first: Tracy

last: Hagemann

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

description: astrocyte transcripts isolated from purified ribosomes

data_processing:
base calling: bcl2fastq-1.8.4
All samples passed quality control as defined by fastqc thresholds
Reads were mapped back to the genome using the short read aligner Bowtie (Langmead et al., 2009), followed by RSEM (Li et al., 2011) to estimate gene expression.
Bowtie version 1.2.0, default parameters, RSEM version 1.2.30, default parameters, R version 3.3.0
Assembly: GRCm38, mm10
Supplementary files format and content: .csv file with expression estimation with RSEM.

source_name: corpus callosum

extract_protocol:
Immunoprecipitated polysome preparation (Heiman et al. (2014). Nat Protoc 9, 1282-1291), followed by Agilent Absolutely RNA Microprep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Stranded RNA w/ polyA selection.
RNA-Seq, mouse, 1x100bp, 25M reads

tag: strain background

value: corpus callosum

tag: molecule subtype

value: translated RNA


title: CC.8


title: CC.6


title: CC.5


title: CC.1

value: WT


title: CC.2


title: CC.3


title: Hip.1

source_name: hippocampus

value: hippocampus


title: CC.4


title: Hip.9


title: Batf2 KO HSC replicate 1


title: infected WT HSC replicate 2


title: Hip.5


title: Hip.8


title: Hip.2


title: Hip.7


title: Hip.6


title: KO_scRNAseq

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

data_processing:
The preprocessing was followed by a pipeline provided by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression).
The process of converting raw sequencing data (bcl files) into fastqs and aligning to the human reference genome [http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz, v.3.0.0, hg19] were performed using a Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
The Cell Ranger count module was used to generate the raw gene expression matrix.
Genome_build: mm10
Supplementary_files_format_and_content: 10x cell ranger count output (raw gene expression matrix, cell barcode and gene information table)

source_name: stomach

growth_protocol: sstr2 knockout and wild type mice were used for single-cell RNA sequencing

extract_protocol:
Sample extraction was prepared using Chromium Single cell 3' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocols.
Sequencing library was prepared using Chromium Single cell 3' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocols.

value: gastric tissue

value: Sstr2 KO


title: Hip.3


title: Hip.4


title: SSTR2_WT_19

data_processing:
perfored trim-galore for trim off the adapter sequences or low-quality reads
Aligned to the mouse reference genome (mm10) using Bismark
Duplicated reads were removed using Bismark command "deduplicate_bismark"
methylation level calculated by Bismark command "bismark_methylation_extractor --no_overlap --comprehensive --cutoff 5 --bedgraph"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, methylation value

growth_protocol: Mouse tissues

extract_protocol:
QIAmp DNA mini kit was used for gDNA extraction
Library was constructed using the Illumina TruSeq DNA methylation kit according to the manufactures instruction

treatment_protocol: For bisulfite conversion, we used EZ DNA methylation Gold kit

value: Sstr2 WT


title: SSTR2_WT_24


title: SSTR2_KO_35


title: SSTR2_KO_23


title: Forebrain EtOH-exposed rep16

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.90
Genome_build: mm10
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

source_name: Forebrain

extract_protocol:
Genomic DNA was extracted from tissues and cell lines using QIAamp DNA Micro Kit (Qiagen) as per manufacturer protocols
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published prototol (Legault, LM. Bio-Protocol, 2019).  Briefly, DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplificaton.

treatment_protocol: Prenatal exposure

value: Forebrain

value: Embryonic day 10.5

value: Wild type

tag: exposure

value: Ethanol


title: Batf2 KO HSC replicate 2

value: murine Hematpoietic stem cells

value: C57BL/9 Batf2 KO


title: infected WT HSC replicate 3

value: 1-month Mycobacterium aivum infection


title: CC.7


title: SSTR2_KO_22


title: SSTR2_WT_12


title: WT_scRNAseq


title: Forebrain EtOH-exposed rep15


title: Forebrain EtOH-exposed rep14


title: Forebrain EtOH-exposed rep13


title: Forebrain EtOH-exposed rep11


title: Forebrain EtOH-exposed rep7


title: Forebrain EtOH-exposed rep6


title: Forebrain EtOH-exposed rep9


title: Forebrain EtOH-exposed rep3


title: Forebrain EtOH-exposed rep12


title: Forebrain EtOH-exposed rep10


title: Forebrain EtOH-exposed rep5


title: Forebrain EtOH-exposed rep4


title: Forebrain Ctrl rep4

value: Saline


title: Forebrain Ctrl rep3


title: Forebrain Ctrl rep6


title: Forebrain EtOH-exposed rep2


title: Forebrain Ctrl rep5


title: Forebrain Ctrl rep2


title: Forebrain Ctrl rep1


title: Lung,8.5,rep1

description: 10X Genomics

value: Lung

tag: donor


title: Lung,6,rep3

description: 10X Genomics


title: Lung,6,rep1

description: 10X Genomics


title: Lung,6,rep4

description: 10X Genomics


title: Lung,6,rep2

description: 10X Genomics


title: CMT

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

description: three castrated and testosterone treatment inividuals pooled

data_processing:
Raw sequencing data were evaluated by FAST-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), an online bioinformatics program used to characterize quality distributions of nucleotides, position-specific sequencing qualities, GC contents, the proportions of PCR duplication, and k-mer frequencies
Raw reads after quality control testing were then mapped to the reference pig genome version 10.2 (Sscrofa 10.2), using MapSplice version v2.1.8.
counting counts for each sample
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: text fiel with raw counts

organism: Sus scrofa

source_name: Renal

extract_protocol:
Kidney tissues from pigs were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA from pigs of the same group was pooled together in equal amounts to generate a mixed sample. Sequencing libraries were prepared using a Ion Total RNA-Seq Kit v2.0 (Life Technologies, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: three groups of pigs were fed a high-fat and high-cholesterol diet

value: Chinese Wuzhishan Pigs

value: kidney

value: 6–7 months old

tag: diet

value: high-fat and high-cholesterol diet (HFC)

tag: condition

value: castrated with testosterone replacement


title: CM

description: three castrated individuals pooled

value: castrated


title: IM

description: three intact individuals pooled

value: intact


title: Forebrain EtOH-exposed rep8


title: CPEK_Plasma1

city: Gwanak

first: Pattawika

last: Lertpatipanpong

state: Seoul

department: College of Veterinary Medicine

institute: Seoul National University

data_processing:
After sequencing, the quality of reads was evaluated and to decrease the bias of the analysis result using FastQC software (version 0.11.7) and Trimmomatic program (version 0.38).
Read data were mapped to the reference genome (CanFam3.1) using the HISAT2 program (version 2.1.0).
The transcript assembly was conducted using the StringTie program (version 2.1.3b).
Assembly: CanFam3.1
Supplementary files format and content: txt file include read count, FPKM and TPM values for all genes as matrix table
Supplementary files format and content: txt file include read count, FPKM and TPM values for all transcripts as matrix table

organism: Canis lupus familiaris

source_name: CPEK cells, CAMP 30s

growth_protocol: Canine Epidermal Keratinocytes (CPEK) were grown in DMEM supplement with 10% FBS, 50 units/ml of penicillin and  100 ug/ml of streptomycin.

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). The total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA Reference Guide # 1000000040498 v00
RNA-seq libraries were created using a TruSeq Stranded mRNA Library Prep Kit for the Illumina platform.

treatment_protocol: Canine keratinocytes (CPEK) were incubated at 37C in 5%CO2 and grown until reach 80-90% confluence. The cells were directly reated with CAMP (cold asmospheric microwave plasma) for 30s and further incubation for 15 min. After that, culture media was replaced by new fresh complete media and further incubated for 24h before collecting total RNA. Gas-treated CPEK cells were used as control.

value: CPEK

value: epidermal keratinocytes

value: WT

value: CAMP 30s


title: CPEK_Plasma2


title: CPEK_GAS3

source_name: CPEK cells, Gas control

value: Gas control


title: CPEK_GAS2


title: Forebrain EtOH-exposed rep1

value: Forebrain

value: Embryonic day 10.5

value: Wild type

value: Ethanol


title: ATAC_seq, time point 72h, TGF-beta1 treated, replication 1

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

institute: Albert-Ludwigs-Universität Freiburg

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic version 0.38 (quality cutoff: 20)
ATAC-seq reads were aligned to the Ensembl GRCh38 genome using Bowtie2 version 2.4.5. with a maximum insert size of 1000 Only uniquely mapping reads with at most two mismatches were retained.
PCR duplicates were removed with Picard MarkDuplicates 2.18.2. Reads mapping to the mitochondrial chromosome were filtered out and properly paired mapping reads were retained using SAMTools version 1.4.1.
ATAC-seq peaks were called using Genrich version 0.5. using the ATAC-seq mode and setting as thresholds AUC > 200 and adj. p-value < 0.01
Assembly: Ensembl GRCh38
Supplementary files format and content: BAM, encodepeaks

growth_protocol: MCF10A cells were cultivated in GibcoTM Advanced DMEM/F12 with 5 % (v/v) horse serum, 1 % (v/v) penicillin/streptomycin, 20 ng/ml human EGF, 0.5 μg/ml hydrocortisone, 0.1 μg/ml cholera toxin, and 10 μg/ml insulin at 37 °C and 5 % CO2

extract_protocol:
From each experimental condition, 5x104 viable cells were taken to prepare ATAC-seq reactions following the Omni-ATAC protocol [Corces et al., An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature Methods 2017, 14, 959–962, doi:10.1038/nmeth.4396)
Libraries were constructed using the Illumina Tagment DNA enzyme and buffer kit (#20034197, Illumina, San Diego, CA, USA) as  described as in the Omni-ATAC protocol [Corces et al., An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature Methods 2017, 14, 959–962, doi:10.1038/nmeth.4396)

treatment_protocol: Cells received recombinant human TGFβ1 (#100-21, PeproTech, Rocky Hill, NJ, USA) at a final concentration of 5 ng/ml, or a corresponding volume of solvent solution containing 0.1 % BSA in PBS. TGFβ1 and solvent were refreshed every 48 h in experiments with extended treatment times.

value: immortalized human mammary epithelial cell line

tag: time

value: 72 hours


title: ATAC_seq, time point 6h, TGF-beta1 treated, replication 2

value: 6 hours


title: CPEK_GAS1


title: ATAC_seq, time point 24h, TGF-beta1 treated, replication 2

value: 24 hours


title: ATAC_seq, time point 0, solvent treated, replication 2

value: Solvent

value: 0 hour


title: ATAC_seq, time point 72h, TGF-beta1 treated, replication 2


title: ATAC_seq, time point 24h, TGF-beta1 treated, replication 1


title: ATAC_seq, time point 6h, TGF-beta1 treated, replication 1


title: Lung,8.5,rep2

description: 10X Genomics

value: Lung


title: mESC-dPiga-H3K4me3-BS03468A

city: New York

first: Matthew

middle: T

last: Maurano

state: New York

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

description: H3K4me3 ChIP

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)

growth_protocol: mESCs were cultured as described in (Brosh et al. 2021) on plates coated with 0.1% gelatin (EMD Millipore ES006-B) in 80/20 medium comprising 80% 2i medium and 20% mESC medium. 2i medium contained a 1:1 mixture of Advanced DMEM/F12 (ThermoFisher 12634010) and Neurobasal-A (ThermoFisher 10888022) supplemented with 1% N2 Supplement (ThermoFisher 17502048), 2% B27 Supplement (ThermoFisher 17504044), 1% glutamax (ThermoFisher 35050061), 1% Pen-Strep (ThermoFisher 15140122), 0.1 mM 2-mercaptoethanol (Sigma M3148), 1,250 U/mL LIF (ESGRO ESG1107l), 3 μM CHIR99021 (R&D Systems 4423), and 1 μM PD0325901 (Sigma PZ0162). mESC medium contained knockout DMEM (ThermoFisher 10829018) supplemented with 15% FBS (BenchMark 100- 106), 0.1 mM 2-mercaptoethanol, 1% glutamax, 1% MEM nonessential amino acids (ThermoFisher 11140050), 1% nucleosides (EMD Millipore ES008-D), 1% Pen-Strep, and 1,250 U/mL LIF. Cells were grown at 37 °C in a humidified atmosphere of 5% CO2 and passaged on average twice per week.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Sheared chromatin from crosslinked mESCs was immunoprecipitated using H3K4me3 antibody (Diagenode C15410003-50) conjugated to M-280 Dynabeads (Invitrogen 11204D), followed by reverse crosslinking and treatment with Proteinase K/RNase A prior to DNA library preparation.

treatment_protocol: Cells were engineered with different landing pads and payloads as described and were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript.

value: C57BL6/6J x CAST/EiJ F1 hybrid mESC

value: C57BL6/6J x CAST/EiJ F1 hybrid

tag: internal id


title: mESC-Sox2_DistalLCR_DHS19andCTCF25toDHS26-BS18425A

description: Captured genomic DNA

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)
Library strategy: Capture-seq

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Capture genomic DNA libraries were prepared with in-solution hybridization capture (Capture-seq) on total DNA libraries using baits for relevant genomic DNA and custom synthetic sequences.

tag: clone id

tag: payload id


title: mESC-Sox2_DistalLCR_DHS20andCTCF25toDHS26-BS18427A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andCTCF25toDHS26-BS18424A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20andCTCF25toDHS26-BS18428A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20andCTCF25toDHS26-BS18429A

description: Captured genomic DNA


title: CPEK_Plasma3

tag: cell line

value: CPEK

value: epidermal keratinocytes


title: mESC-Sox2_DistalLCR_CTCF25toDHS26-BS17983A

description: Captured genomic DNA

tag: cell type


title: mESC-Sox2_DistalLCR_CTCF25toDHS26-BS17979A

description: Captured genomic DNA

tag: genotype


title: mESC-Sox2_DistalLCR_CTCF25toDHS26-BS17980A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andDHS20-BS17978A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_CTCF25toDHS26-BS17981A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andCTCF25toDHS26-BS18422A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andDHS20-BS17977A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andDHS20-BS17975A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andDHS20-BS17976A

description: Captured genomic DNA


title: ATAC_seq, time point 0, solvent treated, replication 1

value: WT

tag: treatment


title: mESC-Sox2_DistalLCR_CTCF25toDHS26-BS17984A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andDHS20-BS17973A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20-BS17971A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20-BS17968A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20andCTCF25toDHS26-BS18426A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20-BS17969A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS19andCTCF25toDHS26-BS18421A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20-BS17966A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20-BS17967A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS20-BS17970A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_CTCF25toDHS26-BS17982A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dC~d8TFBSandDHS24dT-BS17964A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dC~d8TFBSandDHS24dT-BS17963A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dC~d8TFBSandDHS24dT-BS17962A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS26~minimal-BS16654A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dC~d7TFBSandDHS24dT-BS16645A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dC~d8TFBSandDHS24dT-BS17960A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dCandDHS24dT-BS16636A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dC~d8TFBSandDHS24dT-BS17961A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17~dDistalCTCF-BS17891A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17~dDistalCTCF-BS17890A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17~dDistalCTCF-BS17887A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17~dDistalCTCF-BS17886A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17~dDistalCTCF-BS17889A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17-BS17885A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17-BS17884A

description: Captured genomic DNA


title: mESC-Sox2_DistalLCR_DHS23dC~d8TFBSandDHS24dT-BS17965A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17-BS17879A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17-BS17881A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17-BS17880A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_126kb~dProximalLCRandCTCF17-BS17870A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17-BS17882A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_126kb~dProximalLCRandCTCF17-BS17866A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_126kb~dProximalLCRandCTCF17-BS17871A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_126kb~dProximalLCRandCTCF17-BS17867A

description: Captured genomic DNA


title: mESC-Sox2_Sox2_126kb~dProximalLCRandCTCF17-BS17868A

description: Captured genomic DNA


title: BAC-Sox2_DistalLCR_CTCF25toDHS26-BS17725A

description: BAC DNA

library_source: other

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)
Library strategy: DNA-seq

molecule: other

extract_protocol: Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.


title: BAC-Sox2_DistalLCR_DHS23dC~d8TFBSandDHS24dT-BS17722A

description: BAC DNA


title: BAC-Sox2_DistalLCR_DHS19andDHS20-BS17724A

description: BAC DNA


title: BAC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17~dDistalCTCF-BS17341A

description: BAC DNA


title: BAC-Sox2_DistalLCR_DHS19andCTCF25toDHS26-BS18295A

description: BAC DNA


title: BAC-Sox2_DistalLCR_DHS20-BS17723A

description: BAC DNA


title: BAC-Sox2_Sox2_d5pProximal~dCTCF13toCTCF14andCTCF17-BS17063A

description: BAC DNA


title: BAC-Sox2_Sox2_126kb~dProximalLCRandCTCF17-BS14083A

description: BAC DNA


title: 2 mg/kg of lipid nanoparticle with Dsi-RNA CL_03

city: Aachen

first: Matthias

last: Bartneck

address: Pauwelsstraße 30

department: Internal medicine III

institute: University Hospital Aachen

data_processing:
The FASTQ files were generated using bcl2fastq (Illumina). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.5 implemented in Nextflow 21.10.6 using Docker 20.10.12 with the minimal command.
In brief, lane-level reads were trimmed using Trim Galore 0.6.7 and aligned to the mouse genome (GRCm39) using STAR 2.7.9a. Reads were mapped to a composite genome made by concatenating the reference genome and 92 ERCC ExFold RNA Spike-In Mixes sequences (ThermoFisher).
Gene-level and transcript-level quantification was done by Salmon v1.5.2. All analysis was performed using custom scripts in R version 4.1.1 using the DESeq2 v.1.32.0 framework.
Supplementary files format and content: Excel file contains the normalized reads for all samples.
Supplementary files format and content: The fastaq files are the raw data.

source_name: Liver

extract_protocol:
The RNeasy mini kit from Qiagen including tissue homogenizer (Retch mill) and QIAShredder tubes were used to extract the RNA from tissue. RNA quality from all samples was very good.
RNA sequencing was done using Collibiri 3’ mRNA Library Prep Kit (for Illumina). We used a NextSeq 500/550 High Output v2.5 kit. We employed ERCC RNA Spike-in Mix (Thermofisher).

treatment_protocol: The animals received the lipid nanoparticles with different dosages of Dsi-RNA positive control and were killed with 10% isoflurane for analysis after 24 hours. Livers were perfused with PBS.

tag: tissue

value: Liver

value: IV injection of the particles, then killed after 24 hours


title: 2 mg/kg of lipid nanoparticle with Dsi-RNA CL_16


title: BLT-1 injection (1mg/kg), wait 24 hours, then IV injection of particles (0.2 mg/kg), then killed after 24 hours CL_19

value: BLT-1 injection (1mg/kg), waiting 24 hours, then IV injection of the particles (0.2 mg/kg), then killed after 24 hours


title: 2 mg/kg of lipid nanoparticle with Dsi-RNA CL_36


title: BLT-1 injection (1mg/kg), wait 24 hours, then IV injection of particles (0.2 mg/kg), then killed after 24 hours CL_06


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_39


title: BLT-1 injection (1mg/kg), wait 24 hours, then IV injection of particles (0.2 mg/kg), then killed after 24 hours CL_07


title: mESC-Sox2_Sox2_126kb~dProximalLCRandCTCF17-BS17869A

description: Captured genomic DNA

tag: strain


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_31


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_18


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_17


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_38


title: BAC-Sox2_DistalLCR_DHS20andCTCF25toDHS26-BS18296A

description: BAC DNA


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_5


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_30


title: Control CL_29

description: Control


title: 0.2 mg/kg of lipid nanoparticle with Dsi-RNA CL_4


title: Control CL_28

description: Control


title: Control CL_15

description: Control


title: Control CL_14

description: Control


title: Control CL_27

description: Control


title: Control CL_02

description: Control


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS09396A

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)
Library strategy: Captured genomic DNA

growth_protocol: mESCs were cultured on gelatin-coated plates coated in 80/20 medium comprising 80% 2i medium and 20% mESC medium and with 1% Pen-strep.

extract_protocol:
Capture genomic DNA libraries were prepared with in-solution hybridization capture (Capture-seq) on total DNA libraries using baits for relevant genomic DNA and custom synthetic sequences.
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).


title: BLT-1 injection (1mg/kg), wait 24 hours, then IV injection of particles (0.2 mg/kg), then killed after 24 hours CL_20


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS09400A


title: Control CL_01

description: Control


title: mESC-Sox2_DistalLCR_dDHS23toDHS27-BS09394A


title: mESC-Sox2_DistalLCR_dDHS19toDHS20-BS09044A


title: mESC-Sox2_DistalLCR_dDHS23toDHS27-BS09393A


title: mESC-Sox2_DistalLCR_dDHS23toDHS27-BS09390A


title: mESC-Sox2_DistalLCR_dDHS19toDHS20-BS09045A


title: mESC-Sox2_DistalLCR_dDHS19toDHS20-BS09042A


title: mESC-Sox2_DistalLCR_dDHS19toDHS20-BS09041A


title: mESC-Sox2_DistalLCR_dDHS19toDHS20-BS09043A


title: mESC-Sox2_DistalLCR_dCTCF28-BS09039A


title: mESC-Sox2_DistalLCR_dDHS19toDHS20-BS09040A


title: mESC-Sox2_DistalLCR_WT-BS08967A


title: mESC-Sox2_DistalLCR_dDHS26toDHS27andCTCF28-BS09037A


title: mESC-Sox2_DistalLCR_dDHS20-BS09031A


title: mESC-Sox2_DistalLCR_WT-BS08964A


title: mESC-Sox2_DistalLCR_dDHS20-BS09032A


title: mESC-Sox2_DistalLCR_DHS26~minimal~d4TFBS-BS16661A


title: mESC-Sox2_DistalLCR_dCTCF28-BS09038A


title: mESC-Sox2_DistalLCR_DHS26~minimal~d4TFBS-BS16657A


title: mESC-Sox2_DistalLCR_DHS26~minimal~d4TFBS-BS16658A


title: mESC-Sox2_DistalLCR_DHS26~minimal~d4TFBS-BS16659A


title: mESC-Sox2_DistalLCR_DHS26~minimal~d4TFBS-BS16660A


title: mESC-Sox2_DistalLCR_DHS26~minimal~d4TFBS-BS16656A


title: mESC-Sox2_DistalLCR_dDHS23toDHS27-BS09395A


title: mESC-Sox2_DistalLCR_dDHS23toDHS27-BS09392A


title: mESC-Sox2_DistalLCR_DHS26~minimal-BS16650A


title: mESC-Sox2_DistalLCR_DHS26~minimal-BS16651A


title: mESC-Sox2_DistalLCR_DHS26~minimal-BS16652A


title: mESC-Sox2_DistalLCR_DHS26~minimal-BS16649A


title: mESC-Sox2_DistalLCR_DHS23dC~d7TFBSandDHS24dT-BS16643A


title: mESC-Sox2_DistalLCR_DHS23dC~d7TFBSandDHS24dT-BS16647A


title: mESC-Sox2_DistalLCR_DHS23dC~d7TFBSandDHS24dT-BS16646A


title: mESC-Sox2_DistalLCR_DHS23dCandDHS24dT-BS16639A


title: mESC-Sox2_DistalLCR_DHS23dCandDHS24dT-BS16640A


title: mESC-Sox2_DistalLCR_DHS23dCandDHS24dT-BS16638A


title: mESC-Sox2_DistalLCR_DHS23dC~d7TFBSandDHS24dT-BS16642A


title: mESC-Sox2_DistalLCR_DHS24~NuclearreceptorAndSox-BS16546A


title: mESC-Sox2_DistalLCR_DHS24~NuclearreceptorAndSox-BS16545A


title: mESC-Sox2_DistalLCR_DHS23dCandDHS24dT-BS16637A


title: mESC-Sox2_DistalLCR_DHS24~NuclearreceptorAndSox-BS16547A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandESRRAandForkhead-BS16541A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandESRRAandForkhead-BS16539A


title: mESC-Sox2_DistalLCR_DHS24~NuclearreceptorAndSox-BS16544A


title: mESC-Sox2_DistalLCR_DHS24~NuclearreceptorAndSox-BS16543A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandESRRAandForkhead-BS16536A


title: mESC-Sox2_DistalLCR_DHS26~minimal-BS16655A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandESRRAandForkhead-BS16537A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandForkhead-BS16535A


title: mESC-Sox2_DistalLCR_DHS23dCandDHS24dT-BS16641A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandForkhead-BS16531A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandForkhead-BS16530A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandForkhead-BS16534A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandForkhead-BS16533A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandNuclearreceptorandSox-BS16525A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandNuclearreceptorandSox-BS16526A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandForkhead-BS16524A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandNuclearreceptorandSox-BS16529A


title: mESC-Sox2_DistalLCR_DHS23dC~d7TFBSandDHS24dT-BS16648A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandForkhead-BS16532A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandForkhead-BS16523A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandForkhead-BS16521A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandForkhead-BS16522A


title: mESC-Sox2_DistalLCR_DHS24andDHS26-BS16448A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandForkhead-BS16519A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandESRRAandForkhead-BS16540A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandESRRAandForkhead-BS16542A


title: mESC-Sox2_DistalLCR_DHS24andDHS26-BS16447A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandNuclearreceptorandSox-BS16527A


title: mESC-Sox2_DistalLCR_DHS24andDHS26-BS16444A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRBandForkhead-BS16520A


title: mESC-Sox2_DistalLCR_DHS23andDHS26-BS16438A


title: mESC-Sox2_DistalLCR_DHS23andDHS26-BS16439A


title: mESC-Sox2_DistalLCR_DHS23andDHS26-BS16436A


title: mESC-Sox2_DistalLCR_DHS26-BS16435A


title: mESC-Sox2_DistalLCR_DHS26-BS16434A


title: mESC-Sox2_DistalLCR_DHS26-BS16433A


title: mESC-Sox2_DistalLCR_DHS26-BS16432A


title: mESC-Sox2_DistalLCR_DHS23andDHS26-BS16437A


title: mESC-Sox2_DistalLCR_DHS24dT~mut4TFBS-BS15834A


title: mESC-Sox2_DistalLCR_DHS24dT~mut4TFBS-BS15833A


title: mESC-Sox2_DistalLCR_DHS24dT~mut4TFBS-BS15832A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandESRRB-BS15830A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandESRRB-BS15829A


title: mESC-Sox2_DistalLCR_DHS24dT~mut4TFBS-BS15831A


title: mESC-Sox2_DistalLCR_DHS24andDHS26-BS16443A


title: mESC-Sox2_DistalLCR_DHS24dT~dForkhead-BS15824A


title: mESC-Sox2_DistalLCR_DHS24dT~dForkhead-BS15823A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandESRRB-BS15827A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRA-BS15821A


title: mESC-Sox2_DistalLCR_DHS24dT~dForkhead-BS15822A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRA-BS15820A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRA-BS15818A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRA-BS15819A


title: mESC-Sox2_DistalLCR_DHS24dT~dNuclearreceptorAndSOX-BS15817A


title: mESC-Sox2_DistalLCR_DHS24dT~dNuclearreceptorAndSOX-BS15814A


title: mESC-Sox2_DistalLCR_DHS24dT~dNuclearreceptorAndSOX-BS15813A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRB-BS15812A


title: mESC-Sox2_DistalLCR_DHS26-BS16431A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRB-BS15811A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRB-BS15810A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRB-BS15809A


title: mESC-Sox2_hDistalLCR_orthoDHS24-BS15715A


title: mESC-Sox2_hDistalLCR_orthoDHS24-BS15714A


title: mESC-Sox2_DistalLCR_DHS26-BS16429A


title: mESC-Sox2_hDistalLCR_orthoDHS23toDHS24-BS15709A


title: mESC-Sox2_hDistalLCR_orthoDHS23toDHS24-BS15707A


title: mESC-Sox2_hDistalLCR_orthoDHS23toDHS24-BS15708A


title: mESC-Sox2_hDistalLCR_orthoDHS23toDHS24-BS15706A


title: mESC-Sox2_DistalLCR_DHS24andDHS26-BS16446A


title: mESC-Sox2_hDistalLCR_orthoDHS24-BS15712A


title: mESC-Sox2_DistalLCR_DHS24dT~d4TFBS-BS14910A


title: mESC-Sox2_DistalLCR_DHS24dT~d4TFBS-BS14908A


title: mESC-Sox2_DistalLCR_DHS24dT-BS14906A


title: mESC-Sox2_DistalLCR_DHS24dT~d4TFBS-BS14907A


title: mESC-Sox2_DistalLCR_DHS24dT~d4TFBS-BS14909A


title: mESC-Sox2_DistalLCR_DHS24dT-BS14902A


title: mESC-Sox2_DistalLCR_DHS24dT-BS14904A


title: mESC-Sox2_DistalLCR_DHS24dT-BS14903A


title: mESC-Sox2_DistalLCR_DHS24dT-BS14901A


title: mESC-Sox2_DistalLCR_dDHS20toCTCF28-BS13418A


title: mESC-Sox2_DistalLCR_DHS24dT~dESRRAandESRRB-BS15828A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~CTCF~Divergent-BS15808A


title: mESC-Sox2_DistalLCR_DHS24dT~dForkhead-BS15826A


title: mESC-Sox2_hDistalLCR_orthoDHS23toDHS24-BS15710A


title: mESC-Sox2_DistalLCR_DHS24dT-BS14900A


title: mESC-Sox2_hDistalLCR_orthoDHS24-BS15711A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~CTCF~Divergent-BS15804A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~CTCF~Divergent-BS15806A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~CTCF~Divergent-BS15802A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~CTCF~Divergent-BS15803A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~dCTCF-BS15801A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~dCTCF-BS15797A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~dCTCF-BS15799A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~dCTCF-BS15796A


title: mESC-Sox2_DistalLCR_2xDHS24-BS14764A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~dCTCF-BS15800A


title: mESC-Sox2_DistalLCR_2xDHS24-BS14762A


title: mESC-Sox2_DistalLCR_2xDHS24-BS14763A


title: mESC-Sox2_DistalLCR_2xDHS24-BS14761A


title: mESC-Sox2_DistalLCR_2xDHS24-BS14760A


title: mESC-Sox2_DistalLCR_DHS19andDHS20andCTCF25toDHS26-BS15624A


title: mESC-Sox2_DistalLCR_2xDHS24-BS14759A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS15620A


title: mESC-Sox2_DistalLCR_DHS19andDHS20andCTCF25toDHS26-BS15623A


title: mESC-Sox2_DistalLCR_DHS19andDHS20andCTCF25toDHS26-BS15622A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS15617A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS15614A


title: mESC-Sox2_DistalLCR_DHS19andDHS20andCTCF25toDHS26-BS15621A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS15619A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS15615A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS15618A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS23andDHS24-BS15606A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS23andDHS24-BS15604A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15613A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15612A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15611A


title: mESC-Sox2_DistalLCR_DHS23andCTCF25-BS15431A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15610A


title: mESC-Sox2_DistalLCR_DHS23andCTCF25-BS15429A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS23andDHS24-BS15605A


title: mESC-Sox2_DistalLCR_DHS23andCTCF25-BS15430A


title: mESC-Sox2_DistalLCR_DHS24toCTCF25~inverted-BS15602A


title: mESC-Sox2_DistalLCR_DHS23andCTCF25-BS15432A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15608A


title: mESC-Sox2_DistalLCR_DHS23toDHS26-BS15424A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS23andDHS24-BS15603A


title: mESC-Sox2_DistalLCR_DHS23toDHS26-BS15427A


title: mESC-Sox2_DistalLCR_DHS23toDHS26-BS15428A


title: mESC-Sox2_DistalLCR_DHS23andDHS24-BS15422A


title: mESC-Sox2_DistalLCR_DHS24dT~dNuclearreceptorAndSOX-BS15816A


title: mESC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15609A


title: mESC-Sox2_DistalLCR_DHS23toDHS26-BS15426A


title: mESC-Sox2_DistalLCR_DHS23andDHS24-BS15419A


title: mESC-Sox2_DistalLCR_DHS23andDHS24-BS15418A


title: mESC-Sox2_DistalLCR_DHS23-BS15417A


title: mESC-Sox2_DistalLCR_DHS24toCTCF25~inverted-BS15600A


title: mESC-Sox2_DistalLCR_DHS23andDHS24-BS15420A


title: mESC-Sox2_DistalLCR_DHS23-BS15414A


title: mESC-Sox2_DistalLCR_DHS24toCTCF25~inverted-BS15599A


title: mESC-Sox2_DistalLCR_DHS23-BS15415A


title: mESC-Sox2_DistalLCR_DHS23andDHS24-BS15421A


title: mESC-Sox2_DistalLCR_DHS23~DHS24~DHS26~CTCF25-BS14757A


title: mESC-Sox2_DistalLCR_DHS23~DHS24~DHS26~CTCF25-BS14758A


title: mESC-Sox2_DistalLCR_DHS23~DHS24~DHS26~CTCF25-BS14754A


title: mESC-Sox2_DistalLCR_DHS23~DHS24~DHS26~CTCF25-BS14756A


title: mESC-Sox2_DistalLCR_DHS23~CTCF25~DHS24-BS14746A


title: mESC-Sox2_DistalLCR_DHS23~CTCF25~DHS24-BS14749A


title: mESC-Sox2_DistalLCR_DHS23~CTCF25~DHS24-BS14750A


title: mESC-Sox2_DistalLCR_DHS23~CTCF25~DHS24-BS14751A


title: mESC-Sox2_DistalLCR_DHS23~CTCF25~DHS24-BS14748A


title: mESC-Sox2_DistalLCR_CTCF25~DHS23~DHS24-BS14745A


title: mESC-Sox2_DistalLCR_DHS23~CTCF25~DHS24-BS14747A


title: mESC-Sox2_DistalLCR_CTCF25~DHS23~DHS24-BS14742A


title: mESC-Sox2_DistalLCR_CTCF25~DHS23~DHS24-BS14741A


title: mESC-Sox2_DistalLCR_CTCF25~DHS23~DHS24-BS14739A


title: mESC-Sox2_DistalLCR_DHS24~DHS23~CTCF25-BS14736A


title: mESC-Sox2_DistalLCR_CTCF25~DHS23~DHS24-BS14740A


title: mESC-Sox2_DistalLCR_DHS24~DHS23~CTCF25-BS14738A


title: mESC-Sox2_DistalLCR_CTCF25~DHS23~DHS24-BS14743A


title: mESC-Sox2_DistalLCR_DHS24~DHS23~CTCF25-BS14737A


title: mESC-Sox2_DistalLCR_DHS24~DHS23~CTCF25-BS14735A


title: mESC-Sox2_DistalLCR_DHS23-BS15413A


title: mESC-Sox2_DistalLCR_dDHS23toDHS24-BS16427A


title: mESC-Sox2_DistalLCR_dDHS20toDHS27-BS16428A


title: mESC-Sox2_DistalLCR_dDHS23toDHS24-BS16424A


title: mESC-Sox2_DistalLCR_DHS23~DHS24~DHS26~CTCF25-BS14752A


title: mESC-Sox2_DistalLCR_dDHS23toDHS24-BS16425A


title: mESC-Sox2_DistalLCR_DHS24toCTCF28-BS12378A


title: mESC-Sox2_DistalLCR_DHS24toCTCF25-BS13432A


title: mESC-Sox2_DistalLCR_DHS24toCTCF28-BS12377A


title: mESC-Sox2_DistalLCR_DHS24toCTCF25-BS13431A


title: mESC-Sox2_DistalLCR_DHS24toCTCF25-BS13430A


title: mESC-Sox2_DistalLCR_DHS24-BS13425A


title: mESC-Sox2_DistalLCR_DHS24-BS13426A


title: mESC-Sox2_DistalLCR_DHS24-BS13427A


title: mESC-Sox2_DistalLCR_DHS23toCTCF25~inverted-BS12021A


title: mESC-Sox2_DistalLCR_DHS24toCTCF25-BS13429A


title: mESC-Sox2_DistalLCR_DHS23toCTCF25-BS13422A


title: mESC-Sox2_DistalLCR_DHS23toCTCF25~inverted-BS12022A


title: mESC-Sox2_DistalLCR_dDHS23toDHS24-BS16426A


title: mESC-Sox2_DistalLCR_DHS23toCTCF25-BS13420A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS12019A


title: mESC-Sox2_DistalLCR_DHS23toCTCF25-BS13421A


title: mESC-Sox2_DistalLCR_dDHS23toCTCF25-BS16422A


title: mESC-Sox2_DistalLCR_dDHS23toCTCF25-BS16418A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS12018A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS12017A


title: mESC-Sox2_DistalLCR_dDHS23toDHS24-BS16423A


title: mESC-Sox2_DistalLCR_DHS23toDHS27-BS12014A


title: mESC-Sox2_DistalLCR_DHS23toDHS27-BS12016A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS15932A


title: mESC-Sox2_DistalLCR_DHS24-BS13428A


title: mESC-Sox2_DistalLCR_dDHS23toCTCF25-BS16419A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS15931A


title: mESC-Sox2_Sox2_dProxEnhancers-BS10992A


title: mESC-Sox2_DistalLCR_WT~inverted-BS12008A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS15930A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS15929A


title: mESC-Sox2_DistalLCR_DHS23toDHS27-BS15925A


title: mESC-Sox2_DistalLCR_DHS24toCTCF28-BS12376A


title: mESC-Sox2_Sox2_dIntervening-BS10991A


title: mESC-Sox2_DistalLCR_WT~inverted-BS12012A


title: mESC-Sox2_DistalLCR_WT~inverted-BS12010A


title: mESC-Sox2_Sox2_dIntervening-BS10987A


title: mESC-Sox2_DistalLCR_DHS23toDHS27-BS15928A


title: mESC-Sox2_Sox2_dProxEnhancers-BS10993A


title: mESC-Sox2_Sox2_dIntervening-BS10990A


title: mESC-Sox2_Sox2_dIntervening-BS10988A


title: mESC-Sox2_Sox2_d3pProximal-BS10981A


title: mESC-Sox2_DistalLCR_dDHS21-BS16416A


title: mESC-Sox2_DistalLCR_DHS23toDHS27-BS15926A


title: mESC-Sox2_Sox2_d3p5pProximal-BS10975A


title: mESC-Sox2_Sox2_d3p5pProximal-BS10976A


title: mESC-Sox2_DistalLCR_dDHS21-BS16414A


title: mESC-Sox2_DistalLCR_dDHS21-BS16413A


title: mESC-Sox2_Sox2_d3pProximal-BS10980A


title: mESC-Sox2_DistalLCR_dDHS20toDHS23~3-BS16412A


title: mESC-Sox2_DistalLCR_dDHS21-BS16411A


title: mESC-Sox2_DistalLCR_dDHS21andCTCF28-BS10973A


title: mESC-Sox2_DistalLCR_dDHS26-BS11218A


title: mESC-Sox2_DistalLCR_DHS24dT~d4TFBS-BS14911A


title: mESC-Sox2_DistalLCR_DHS23toDHS27~CTCF~Divergent-BS15807A


title: mESC-Sox2_DistalLCR_dDHS26-BS10968A


title: mESC-Sox2_DistalLCR_dDHS24-BS10963A


title: mESC-Sox2_DistalLCR_dDHS24-BS10962A


title: mESC-Sox2_DistalLCR_dCTCF25-BS10960A


title: mESC-Sox2_DistalLCR_dDHS24-BS10961A


title: mESC-Sox2_DistalLCR_dCTCF25-BS10959A


title: mESC-Sox2_DistalLCR_dDHS21-BS10971A


title: mESC-Sox2_DistalLCR_dDHS23-BS10956A


title: mESC-Sox2_DistalLCR_dDHS23-BS10955A


title: mESC-Sox2_DistalLCR_dDHS21-BS16415A


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS12373A


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS13416A


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS13419A


title: mESC-Sox2_DistalLCR_dDHS21-BS10972A


title: mESC-Sox2_DistalLCR_dDHS27-BS10954A


title: mESC-Sox2_DistalLCR_dCTCF25andDHS26andCTCF28-BS10951A


title: mESC-Sox2_Sox2_143kb-BS09725A


title: mESC-Sox2_DistalLCR_dDHS27-BS11216A


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS12371A


title: mESC-Sox2_Sox2_143kb-BS09722A


title: mESC-Sox2_DistalLCR_dDHS26-BS10969A


title: mESC-Sox2_Sox2_126kb~dProximalLCR-BS08818A


title: mESC-Sox2_Sox2_126kb~dProximalLCR-BS08817A


title: mESC-Sox2_DistalLCR_dCTCF25andDHS26andCTCF28-BS10953A


title: mESC-Sox2_Sox2_101kb~dDistalLCR-BS09720A


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08353A


title: mESC-Sox2_Sox2_143kb-BS07692A


title: mESC-Sox2_Sox2_101kb~dDistalLCR-BS09717A


title: mESC-Sox2_Sox2_101kb~dDistalLCR-BS09716A


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08352A


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS14899A


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08348A


title: mESC-Sox2_DistalLCR_dDHS21toDHS22-BS12372A


title: BAC-Sox2_DistalLCR_DHS26~minimal-BS16318A

extract_protocol:
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).


title: LP-LCR-BS08118A

source_name: LP-LCR


title: LP-Sox2-BS09181A


title: BAC-Sox2_DistalLCR_DHS23dC~d7TFBSandDHS24dT-BS16317A


title: BAC-Sox2_DistalLCR_DHS26~minimal~d4TFBS-BS16319A


title: LP-LCR-BS09993A


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08347A


title: BAC-Sox2_DistalLCR_DHS24~NuclearreceptorAndSox-BS16315A


title: BAC-Sox2_DistalLCR_DHS24dT~dESRRBandESRRAandForkhead-BS16314A


title: BAC-Sox2_DistalLCR_DHS24dT~dESRRAandForkhead-BS16313A


title: BAC-Sox2_DistalLCR_DHS24dT~dESRRBandForkhead-BS16311A


title: BAC-Sox2_DistalLCR_DHS24dT~dESRRAandNuclearreceptorandSox-BS16312A


title: Mut6, MM0299 treatment

city: Dallas

first: Deepak

last: Nijhawan

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern

data_processing: Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene.

growth_protocol: Mut6 were grown in a defined medium as described in the paper.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was sent to BGI genomics for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by BGI genomics

treatment_protocol: Cells were treated with DMSO or 100 nM MM0299 for 24 hour.

value: Brain tumor


title: BAC-Sox2_DistalLCR_DHS24dT~mut4TFBS-BS16081A


title: BAC-Sox2_DistalLCR_DHS23dCandDHS24dT-BS16316A


title: BAC-Sox2_DistalLCR_DHS24andDHS26-BS16071A


title: BAC-Sox2_DistalLCR_DHS26-BS16054A


title: BM5

city: St. Louis

first: Ravi

last: Vij

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
BM5

data_processing:
Single cell RNA sequence data was de-multiplexed to FASTQ, aligned to the human reference genome (GRCh38), and transposed into gene-by-cell UMI count matrices using the proprietary software tool Cell Ranger (v3.0.0) from 10x Genomics.
Seurat v3.0.0 [11] was used for all subsequent analysis. First, all data underwent quality filtering (as recommended by Seurat) to remove barcodes with: too few total transcript counts (< 300); too few genes expressed (< 200) or too few UMIs (< 1,000), indicating possible debris;  too many genes expressed (> 50,000) and too many UMIs (> 10,000), indicating the presence of multiplet; or too high proportion of mitochondrial gene expression over the total transcript counts (> 20%), indicating a dying cell. Each sample was scaled and normalized using Seurat’s ‘SCTransform’ function to correct for batch effects (with parameters: vars.to.regress = c("nCount_RNA", "percent.mito"), return.only.var.genes = F).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (RNA count matrices).

source_name: Donor BMMC, aspirate, scRNAseq

extract_protocol:
Bone marrow mononuclear cells (BMMCs) were isolated using Ficoll-Paque purification and cryopreserved in a 1:10 mixture of dimethyl sulfoxide and fetal bovine serum. Upon thawing in 37⁰C water baths, whole BMMCs from WashU cohort 1 were loaded onto the 10X Genomics Chromium Controller using 10x Genomics Chromium Single Cell 3’v2 Library Kits. BMMCs aliquots from WashU Cohort 2, MMRF, and healthy donors were centrifuged upon thawing at 300G for 5 min to pellet cells. All supernatant was removed. To prepare cells for the Miltenyi Dead Cell Removal Kit, cells were resuspended in 100 uL of  beads and incubated at room temperature for 15 minutes. Cells were then run through the DepeleS selection using the autoMACS®Pro Separator. The negative fraction (live cells) were pelleted by centrifugation at 450G for 5 minutes. Cells were finally resuspended in ice cold phosphate buffer saline (PBS) and 0.5% BSA and loaded onto the 10x Genomics Chromium Controller. WashU Cohort 2 and healthy donor samples were loaded using 10x Genomics Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.2. MMRF cohort samples were loaded using 10x Genomics Chromium Controller and using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.3.
Using the 10x Genomics Chromium Single Cell and Chromium instrument, approximately 16,500 to 20,000 cells were partitioned into nanoliter droplets to achieve single cell resolution for a maximum of 10,000 individual cells per sample. The resulting cDNA was tagged with a common 16nt cell barcode and 10nt Unique Molecular Identifier during reverse transcription. Full length cDNA from poly-A mRNA transcripts was enzymatically fragmented and size selected for ~400bp cDNA amplicons optimal for library construction (10x Genomics). The concentration of the 10x single cell library was determined through qPCR (Kapa Biosystems) or automated electrophoresis (Agilent TapeStation) to produce cluster counts appropriate for the HiSeq 4000 or NovaSeq 6000 platform (Illumina). 26x98bp sequence data were generated targeting between 25K-50K read pairs/cell, which provided digital gene expression profiles for each individual cell.

value: BMMC

value: Bone Marrow


title: BAC-Sox2_DistalLCR_DHS24dT~dForkhead-BS16079A


title: BAC-Sox2_DistalLCR_DHS24dT~dESRRA-BS16078A


title: BM2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
BM2


title: BM4

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
BM4


title: BAC-Sox2_DistalLCR_DHS23andDHS26-BS16062A


title: BAC-Sox2_DistalLCR_DHS24dT~dNuclearreceptorAndSOX-BS16077A


title: mESC-Sox2_Sox2_46kbp~dDistalLCR-BS08351A


title: ND_170607

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
ND_170607
Raw files already available on dbGaP accession number phs000159


title: ND_090617

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
ND_090617
Raw files already available on dbGaP accession number phs000159


title: BAC-Sox2_hDistalLCR_orthoDHS24-BS14982A


title: BAC-Sox2_DistalLCR_DHS24dT~dESRRB-BS16076A


title: ND_083017

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
ND_083017
Raw files already available on dbGaP accession number phs000159


title: BAC-Sox2_hDistalLCR_orthoDHS23toDHS24-BS14981A


title: MMY98423

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY98423

source_name: Patient BMMC, aspirate, scRNAseq, WU cohort 2

tag: diagnosis

value: Multiple myeloma (MM)


title: BAC-Sox2_DistalLCR_DHS24dT~d4TFBS-BS14581A


title: ND_170531

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
ND_170531
Raw files already available on dbGaP accession number phs000159


title: BAC-Sox2_DistalLCR_DHS24dT-BS14580A


title: MMY80649

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY80649


title: MMY74196

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY74196


title: Mut6, DMSO

value: DMSO


title: BAC-Sox2_DistalLCR_DHS23toDHS27~dCTCF-BS15358A


title: BAC-Sox2_DistalLCR_2xDHS24-BS14579A


title: MMY70893

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY70893


title: BAC-Sox2_DistalLCR_DHS24dT~dESRRAandESRRB-BS16080A


title: MMY47218

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY47218


title: BAC-Sox2_DistalLCR_DHS19andDHS20andCTCF25toDHS26-BS14573A


title: BAC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS14934A


title: BAC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS26-BS14930A


title: MMY67868

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY67868


title: MMY34600

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY34600


title: MMY40511

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY40511


title: BAC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15353A


title: MMY34339

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY34339


title: BAC-Sox2_DistalLCR_DHS23toDHS26~invertedCTCF25-BS15352A


title: BAC-Sox2_DistalLCR_DHS23toDHS26~invertedDHS23andDHS24-BS15343A


title: BAC-Sox2_DistalLCR_DHS24toCTCF25~inverted-BS14559A


title: BAC-Sox2_DistalLCR_DHS23andCTCF25-BS14551A


title: MMY83942

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY83942


title: BAC-Sox2_DistalLCR_DHS23toDHS26-BS14544A


title: MMY18273

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY18273


title: BAC-Sox2_DistalLCR_DHS23andDHS24-BS14542A


title: MMY21940

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY21940


title: 81012_2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
81012_2

source_name: Patient BMMC, aspirate, scRNAseq, WU cohort 1


title: BAC-Sox2_DistalLCR_DHS23toDHS27~CTCF~Divergent-BS15360A


title: 81012_1

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
81012_1


title: BAC-Sox2_DistalLCR_DHS23-BS14530A


title: BAC-Sox2_DistalLCR_DHS23~DHS24~DHS26~CTCF25-BS14098A


title: BAC-Sox2_DistalLCR_DHS23~CTCF25~DHS24-BS14095A


title: 77570

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
77570


title: 60359_2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
60359_2


title: 59114_4

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
59114_4


title: 58408_1

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
58408_1


title: 59114_1

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
59114_1


title: BAC-Sox2_DistalLCR_DHS24~DHS23~CTCF25-BS14086A


title: BAC-Sox2_DistalLCR_DHS24toCTCF28-BS11296A


title: 58408_2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
58408_2


title: BAC-Sox2_DistalLCR_CTCF25~DHS23~DHS24-BS14093A


title: BAC-Sox2_DistalLCR_dDHS23toDHS24-BS15553A


title: BAC-Sox2_DistalLCR_DHS24-BS12693A


title: 83942

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
83942


title: BAC-Sox2_DistalLCR_DHS23toCTCF25~inverted-BS11120A


title: MMY22933

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMY22933


title: 57075_3

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
57075_3


title: BAC-Sox2_DistalLCR_DHS23toCTCF25-BS12688A


title: 56203_2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
56203_2


title: BAC-Sox2_DistalLCR_dDHS23toCTCF25-BS15563A


title: 47491_2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
47491_2


title: BAC-Sox2_DistalLCR_DHS23toDHS27~inverted-BS11111A


title: 60359_1

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
60359_1


title: BAC-Sox2_DistalLCR_DHS23toDHS27-BS11108A


title: 37692_2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
37692_2


title: 27522_6

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
27522_6


title: BAC-Sox2_DistalLCR_DHS24toCTCF25-BS12697A


title: 27522_5

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
27522_5


title: BAC-Sox2_DistalLCR_WT~inverted-BS11101A


title: BAC-Sox2_Sox2_dProxEnhancers-BS09860A


title: mESC-Sox2_Sox2_d3pProximal-BS11221A


title: 27522_3

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
27522_3


title: 27522_2

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
27522_2


title: BAC-Sox2_DistalLCR_dDHS19toDHS20-BS08434A


title: 27522_1

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
27522_1


title: BAC-Sox2_Sox2_d3p5pProximal-BS09846A


title: BAC-Sox2_DistalLCR_dDHS21-BS08687A


title: BAC-Sox2_Sox2_d3pProximal-BS09853A


title: MMRF_2259

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_2259

source_name: Patient BMMC, aspirate, scRNAseq, MMRF cohort


title: 56203_1

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
56203_1


title: 25183

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
25183


title: 47491_1

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
47491_1


title: MMRF_2251

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_2251


title: BAC-Sox2_DistalLCR_dDHS24-BS08441A


title: BAC-Sox2_DistalLCR_dCTCF25-BS09485A


title: MMRF_1777

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1777


title: BAC-Sox2_DistalLCR_dDHS26-BS08996A


title: MMRF_1720

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1720


title: BAC-Sox2_DistalLCR_dCTCF28-BS08436A


title: BAC-Sox2_DistalLCR_dDHS23-BS08989A


title: BAC-Sox2_DistalLCR_dDHS21toDHS22-BS08756A


title: MMRF_1424

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1424


title: BAC-Sox2_DistalLCR_dDHS27-BS08745A


title: 27522_4

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
27522_4


title: MMRF_1686

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1686


title: BAC-Sox2_Sox2_dIntervening-BS09854A


title: MMRF_1641

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1641


title: MMRF_1267

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1267


title: BAC-Sox2_DistalLCR_dDHS23toDHS27-BS08737A


title: MMRF_2168

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_2168


title: MMRF_1967

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1967


title: MMRF_2038

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_2038


title: BAC-Sox2_Sox2_143kb-BS02964A


title: MMRF_1941

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1941


title: MMRF_1537

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1537


title: MMRF_1640

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1640


title: MMRF_1505

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1505


title: MMRF_1413

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1413


title: BAC-Sox2_DistalLCR_WT-BS08167A


title: BAC-Sox2_Sox2_126kb~dProximalLCR-BS02961A


title: BAC-Sox2_Sox2_46kbp~dDistalLCR-BS02957A


title: scRNAseq of myeloid cells from room air (RA) mice

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
The raw reads in fastq format was processed using 10X genomics cellranger analysis package. OIR and RA samples will be pooled using cellranger aggr pipeline.
The cellranger pipeline outputs containing gene-by-cell expression data from the aggregated libraries were imported into R package Seurat 4.0 to create a Seurat object. Quality control measures were implemented in Seurat to filter out cells expressing > 6000 genes. Cells with a higher percentage of mitochondrial genes were also excluded from the subsequent analysis. Normalization and scaling were performed within Seurat before subsequent analysis such as PCA, umap, tSNE, and clustering analyses. Visualization of the scRNA data was performed using Seurat tSNEplot, Vinplot, Featureplot, Dotplot, and DoHeatmap functions. Cell cycle analysis was performed using the Seurat cell cycle scoring function. A cell cycle gene signature containing 97 cell cycle-related genes(86) were used to derive the G1/S and G2/M scores.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: FACS-sorted F4/80 and CD11 cells

growth_protocol: Postnatal mice were euthanized at postnatal (P)17 days and retinas were collected and digested to obtain single cell suspension. F4/80 and CD11b cells were sorted with FACS equipment.

extract_protocol:
FACS-sorted F4/80 and CD11b positive cells were processed for scRNAseq libraries using the Chromium Controller (10X Genomics).
scRNAseq libraries were generated for approximately 2,000 cells per sample using 10X 3’ single cell mRNAseq V3 reagents.  The scRNAseq libraries were sequenced using Illumina NextSeq 500 sequencer to collect approximately 80k reads per cell.  Each cell was tagged with a Unique Molecular Identifier (UMI) sequence, which represents the identity of each single cell throughput the analysis pipeline.
Single cell RNA-Seq

treatment_protocol: Postnatal mice were subjected to model of oxygen-induced retinopathy. Then mice were euthanized at postnatal (P)17 days and retinas were collected and digested to obtain single cell suspension. F4/80 and CD11b cells were sorted with FACS equipment.

value: retina

value: F4/80 and CD11 cells

tag: disease state

value: control


title: BAC-Sox2_Sox2_101kb~dDistalLCR-BS02959A


title: MMRF_1695

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1695


title: Suv39hdn_Chromosomes_2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina RTA 2.11.3 software used for basecalling and bcl2fastq2_2.20.0 for converting base call (BCL) files into FASTQ files.
Raw reads were trimmed with Trim Galore! (trim_galore_v0.4.4) with arguments "--trim-n --paired".
The trimmed reads were then aligned to USCS mm10 using bowtie2 (bowtie2/2.2.9), with arguments "-p8 -t –very-sensitive -X 2000".
Samtools (1.2) was applied for sorting the reads and picardtools MarkDuplicates (1.90) was used for marking duplicated reads. R bioconductor package ATACseqQC (Ou et al., 2018) was applied for removing duplicated reads, reads without properly mapped mates, and reads mapped to chrMT.
alignmentSieve function from deeptools (Ramírez et al., 2014) was applied for shifting ATACseq reads (Buenrostro et al., 2013) and keeping nucleosome-free reads (fragment length <=100 bps) with arguments "--ATACshift --minFragmentLength 0 --maxFragmentLength 100". Peaks were called from nucleosome-free fragments with MACS2 (-f BAMPE)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bed files

source_name: Suv39h dn Mitotic Chromosomes

growth_protocol: ESCs were grown in KO-DMEM medium supplemented with 15% FCS, non-essential amino acids, L-glutamine, 2-mercaptoethanol, antibiotics and 1000 U/ml of leukaemia inhibitory factor (LIF).

extract_protocol:
For ATAC-seq on asynchronous cells, nuclei were obtained by resuspending 5 x 104 cells in 50 μl of ATAC-resuspension buffer (10 mM Tris–HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Igepal CA-630; 0.1% Tween-20; 0.01% Digitonin) for 3 min on ice before adding 1 ml of ATAC-resuspension buffer without Igepal and Digitonin and pelleting nuclei at 500 g (10 min at 4°C). For ATAC-seq on purified mitotic chromosomes, condensed chromosomes were released from arrested cells using polyamine buffer, stained with Hoechst 33258 and Chromomycin A3, purified by flow cytometry using a Becton Dickinson Influx equipped with specialised air-cooled lasers and pelleted at 10,000 g (10 min at 4°C).
To perform ATAC-seq, nuclei, mitotic cells (5 x 10^4) or purified chromosomes (2 x 10^6) were resuspended in 50 μl transposase mixture (25 μl Illumina TD buffer, 22.5 μl H2O, and 2.5 μl Illumina TDE1 transposase) and incubated at 37°C for 30 min with shaking at 1,000 rpm. DNA was purified (Qiagen MinElute kit) and amplified with seven cycles of PCR (NEBNext High Fidelity master mix). Libraries were purified twice with Ampure XP beads (Beckman Coulter), including removal of large fragments with 0.5x beads.

treatment_protocol: For mitotic cells and chromosomes, rapidly dividing cultures of ESCs were arrested in metaphase using demecolcine (0.1 μg/ml for 6 h), and cells were collected by mitotic shake-off shake off and 1X PBS wash.

value: Suv39h dn

tag: sample

value: Purified mitotic chromosomes

value: Embryonic stem cells


title: scRNAseq of myeloid cells from OIR mice

value: oxygen-induced retinopathy (OIR)


title: Suv39hdn_Chromosomes_1


title: Suv39hdn_Mitotic_2

source_name: Suv39h dn Mitotic Cells

value: Mitotic cells


title: MMRF_1325

description:
two instrument models were used to produce reads: Illumina HiSeq 4000/NovaSeq 6000
10x Genomics
MMRF_1325


title: BAC-Sox2_DistalLCR_dCTCF25andDHS26andCTCF28-BS08739A


title: Suv39hdn_Mitotic_1


title: HCT116.DKO12.pLenti.FasL.NP.rep2

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

description: Single Read

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples

source_name: Korean Collection for Type Cultures (KCTC) and edited by Synthego

extract_protocol:
Cell lysates were subjected to pull down with a GW182 FLAG-GST-T6B peptide isolated using anti-FLAG M2 Magnetic beads. RNA was extracted using Trizol followed by an ethanol precipitation.
Small RNA-Seq libraries were generated using illumina TruSeq small RNA adapters. RNA 19-35 nucleotides were size selected by Urea-PAGE gel extraction after each round of adapter ligation. The final library ~156 bp was size selected on an agarose-TBE gel. Final cDNA quality was assessed by Agilent Bioanalyzer and DNA concetration was determined by Qubit.

treatment_protocol: HCT116 cells were spin-infected with pLenti-CD95L wild-type, NP, GUA, or pLenti empty vector in the presence of 8 ug/ml polybrene. Infected cells were selected with 2 mg/ml puromycin. Cells were flash frozen 100 hours after infection.

value: HCT116 Drosha CD95 d.k.o. clone #12

tag: treatment/infection

value: Cells were transduced with pLenti -CD95L NP


title: HCT116.DKO12.pLenti.FasL.GUA.rep1

description: Single Read

value: Cells were transduced with pLenti -CD95L GUA


title: HCT116.DKO12.pLenti.FasL.GUA.rep2

description: Single Read


title: HCT116.DKO12.pLenti.FasL.NP.rep1

description: Single Read


title: BAC-Sox2_DistalLCR_dDHS20-BS08431A


title: Suv39hdn_Asynchr_1

source_name: Suv39h dn Asynchronous Cells

value: Asynchronous cells


title: Suv39hdn_Asynchr_2


title: HCT116.DKO12.pLenti.FasL.wt.rep2

description: Single Read

value: Cells were transduced with pLenti -CD95L wild-type


title: HCT116.DKO12.pLenti.FasL.wt.rep1

description: Single Read


title: WT_Chromosomes_1

source_name: WT Mitotic Chromosomes

value: Wild-type


title: WT_Chromosomes_2


title: HCT116.DKO12.pLenti.rep2

description: Single Read

value: Cells were transduced with pLenti empty vector


title: WT_Mitotic_1

source_name: WT Mitotic Cells


title: WT_Asynchr_1

source_name: WT Asynchronous Cells


title: WT_Asynchr_2


title: HCT116.Ago123.ko.pLenti.FasL.NP.rep2

description: Single Read

source_name: David Corey (UT Southwestern) PMID: 32501500

treatment_protocol: HCT116 w.t., Drosha k.o., and Ago 1/2/3 k.o. cells were spin-infected with pLenti-CD95L NP or pLenti empty vector in the presence of 8 ug/ml polybrene. Infected cells were selected with 2 mg/ml puromycin. Cells were flash frozen 100 hours after infection.


title: HCT116.Drosha.ko.pLenti.FasL.NP.rep2

description: Single Read

source_name: Korean Collection for Type Cultures

value: HCT116 Drosha k.o. clone #40


title: HCT116.Ago123.ko.pLenti.rep2

description: Single Read


title: HCT116.Ago123.ko.pLenti.FasL.NP.rep1

description: Single Read


title: HCT116.Ago123.ko.pLenti.rep1

description: Single Read


title: AB6378

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: paired-end (read2 used to read cell and molecule barcodes only)

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
M_metadata_s.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Left limb- autopod

growth_protocol: Experiments were performed in the Weizmann Institute of Science

extract_protocol:
Forelimb tissues were disassociated using enzymatic digestion. E10.5-E11.5 forelimbs were digested with pre-heated 0.25% trypsin in DMEM medium (ThermoFisher) and incubated for 10 min at 37°C, gently pipetting every 3 min. E12.5-E14.5 forelimbs were digested with 1.5 mg/ml  collagenase type V (Sigma-Aldrich) in DMEM at 37°C for 10-15 min, gently pipetting every 5 min until the tissue completely dissolved. The digestion reaction was stopped by addition of DMEM supplemented with 10% FBS and 1% Pen-Strep. Cell suspensions were filtered through a 40-µm nylon mesh and collected by centrifugation at 1000 rpm for 7 min at 4°C. Supernatant was removed and cells were resuspended in 500 µl ice-cold MACS buffer (with 0.5% BSA and 2 mM EDTA in PBS) and used immediately for fluorescence-activated cell sorting (FACS).
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Induction of Cre recombinase was performeds by administration of 5 mg/ml tamoxifen in corn oil X5 body weight by oral gavage. For harvesting of embryos, timed-pregnant females were euthanized by cervical dislocation.

tag: organ

value: limb

tag: selection marker

value: tomato-

tag: mouse id

tag: timepoint

tag: replicate


title: HCT116.Drosha.ko.pLenti.FasL.NP.rep1

description: Single Read


title: AB6376


title: HCT116.Drosha.ko.pLenti.rep2

description: Single Read


title: AB6379

value: tomato+


title: HCT116.Drosha.ko.pLenti.rep1

description: Single Read


title: AB6374

source_name: Left limb-proximal


title: AB6377


title: AB6375


title: AB6373


title: HCT116.Parental.pLenti.FasL.NP.rep2

description: Single Read

value: HCT116 wild-type


title: HCT116.Parental.pLenti.FasL.NP.rep1

description: Single Read


title: AB6372


title: AB6371


title: HCT116.Parental.pLenti.rep1

description: Single Read


title: HCT116.DKO12.pLenti.rep1

description: Single Read


title: HCT116.Parental.pLenti.rep2

description: Single Read


title: HCT116.DKO12.pLenti.FasL.SIL.rep2

description: Single Read

treatment_protocol: HCT116 cells were spin-infected with pLenti-CD95L wild-type, NP, Zero, SIL, or pLenti empty vector in the presence of 8 ug/ml polybrene. Infected cells were selected with 2 mg/ml puromycin. Cells were flash frozen 100 hours after infection.

value: Cells were transduced with pLenti -CD95L SIL


title: WT_Mitotic_2


title: HCT116.DKO12.pLenti.FasL.SIL.rep1

description: Single Read