title: Cop1_sgRNA2_Rep2

status: Public on Apr 30 2021

type: SRA

city: Boston

first: Xiaoqing

last: Wang

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.4.0 with parameters --outFilterMultimapNmax 1 --outFilterMatchNmin 35
Primary aligned reads were counted using htseq-count -m union -s no -t exon
The DESeq2 R package version 1.10 was used for differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: 4T1 mouse breast cancer cells

extract_protocol:
Cancer cell were collected, flash frozen on dry ice, and RNA was harvested using QIAGEN DAN/RNA mini kit (Cat#80204). Illumina TruSeq RNA Library Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IFNgamma, 20ng/ml, 24 hours

tag: strain

value: BALB/c

tag: cell line

tag: treatment

value: vehicel


title: Cop1_sgRNA1_IFNgamma_Rep2

value: IFNgamma


title: Cop1_sgRNA2_IFNgamma_Rep1


title: Cop1_sgRNA2_IFNgamma_Rep2


title: Cop1_sgRNA1_Rep1


title: Rosa26_sgRNA_IFNgamma_Rep1


title: Cop1_sgRNA1_Rep2


title: Cop1_sgRNA2_Rep1


title: Cop1_sgRNA1_IFNgamma_Rep1


title: ESC_1

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

description: Sample 35

data_processing:
Sequenced reads were processed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 CROP:100 HEADCROP:10 SLIDINGWINDOW:4:15 MINLEN:36
Quality reads were aligned to the mm9 genome (and hg18 in samples with spike-in) using RSEM-1.2.4 with a mismatch per seed set to 2 and seed length set to 28 (-bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28).
Differentially expressed (DE) genes were called with EBSeq using the human matrix for normalization (MedianNorm(human_matrix)) or normalizing against the mouse matrix if no human spike in control. Genes with PPDE > 0.95 and PostFC > 2 were considered DE.
RSEM-1.2.4 was used to calculate TPM values
Genome_build: mm9, hg18
Supplementary_files_format_and_content: text file containing genes, transcript ID, length, counts, transcripts per million (TPM), and FPKM.

molecule: polyA RNA

source_name: V6.5 Mouse Embryonic Stem Cells

growth_protocol: MEFs were maintained in MEF media (DMEM, 10% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, and 2-Mercaptoethanol (4 μl/500ml)), and ESCs and reprogramming cells were grown on irradiated feeder MEFs and maintained in ESC media (knock-out DMEM, 15% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, 2-Mercaptoethanol (4 μl/525ml), and leukemia inhibitory factor).

extract_protocol:
RNA was extracted with TRIzol and chloroform, cleaned using the Qiagen Rneasy Mini kit, and Dnase treated (Qiagen 79254) for 30 min. 1 ug of RNA was used for library construction. For the Tc and Sort samples (#1-22, paired-end sequencing), 20 ng of 293T RNA was added as a human spike in control.
TruSeq RNA Sample Preparation kit V2 (RS-122-2002) was used to construct cDNA libraries

value: feeder depletion 24 hours prior to harvest

tag: cell type

value: V6.5 Mouse Embryonic Stem Cells


title: Exp_d2_Cdh1_dot1li_2

description: Sample 34

source_name: day 2 reprogramming MEFs

value: Cdh1 lentivirus; 2 days of doxycyline and SGC0946

tag: genotype

value: homozygous Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (Col1a1 locus), heterozygous reverse tetracycline transactivator (Rosa26 locus)

value: E13.5 Mouse embryonic fibroblasts

tag: sample type

value: Cdh1 expression


title: Exp_d2_Cdh1_control_2

description: Sample 32

value: Cdh1 lentivirus; 2 days of doxycyline and DMSO


title: Rosa26_sgRNA_IFNgamma_Rep2


title: Exp_d2_Cdh1_control_1

description: Sample 31


title: Exp_d2_empty_dot1li_2

description: Sample 30

value: empty lentivirus; 2 days of doxycyline and SGC0946


title: Exp_d2_empty_dot1li_1

description: Sample 29


title: Exp_MEF_Cdh1_2

description: Sample 26

value: Cdh1 lentivirus


title: Exp_MEF_emtpy_2

description: Sample 24

source_name: MEFs

value: empty lentivirus


title: Exp_MEF_emtpy_1

description: Sample 23


title: Rosa26_sgRNA_Rep2


title: Exp_d2_empty_control_1

description: Sample 27

value: empty lentivirus; 2 days of doxycyline and DMSO


title: Exp_MEF_Cdh1_1

description: Sample 25


title: ESC_2

description: Sample 36


title: Rosa26_sgRNA_Rep1


title: K0035-E3-s

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

description: mRNA-seq

data_processing:
FASTQ TO BAM
bulk: FEATURECOUNTS
bulk: EDGER
single-cell: Cell Ranger
single-cell: Seurat
Genome_build: mm10
Supplementary_files_format_and_content: batch corrected counts from featureCounts
Supplementary_files_format_and_content: Processed data file is in excel and is CPM data for all genes in all samples.

source_name: microglia

growth_protocol: All animal experiments were approved by the University of Pittsburgh Institutional Animal Care and Use Committee. All procedures were carried out in accordance with the approved guidelines. APP23 transgenic mice (C57Bl6 background) expressing human APP751 familial Swedish AD mutation (APPK670N, M671L) were crossed to wild-type C57BL/6 mice to generate APP23 hemizygous mice

extract_protocol:
Mice were anesthetized with Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with cold 0.1 M PBS, pH 7.4: left hemisphere fixed in 4% paraformaldehyde for histology. The cortex was dissected from the other and snap frozen on dry ice for RNA and protein isolation
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated by Novogene.
scRNA libraries were generated with Chromium single cell 3’ chip kit v3 for scRNA-seq (10x Genomics) according to the manufacturer’s instructions and then the quality assessed using Agilent Bioanalyzer 2100. Sequencing was performed using NovaSeq (Illumina) by MedGenome Inc. with a custom sequencing setting (28bp for Read1 and 91bp for Read2) to obtain an average sequencing depth of 45K reads/cell.

treatment_protocol: The following mouse lines were bred to generated experimental mice: Wild-type C57BL/6J (WT; JAX), human APOE3 and APOE4 targeted replacement mice (E3 & E4; Taconic), Trem2em2ADiuj/J mice (Trem2ko; JAX) and 129P2(Cg)-Cx3cr1tm1Litt/J (Cx3cr1GFP; JAX). Human APOE3 and APOE4 targeted replacement mice were bred to Abca1tm1Jdm/J mice (Abca1ko; JAX) to generate APOE3/Abca1het and APOE4/Abca1het (E3het & E4het). Likewise, human APOE3 and APOE4 targeted replacement mice were bred to Trem2em2ADiuj/J mice (Trem2ko; JAX) to generate APOE3/Trem2ko and APOE4/Trem2ko (E3/Trem2ko & E4/Trem2ko).

value: microglia

tag: Sex

value: Male

tag: infusion

tag: single/dual

value: Single

tag: time


title: K0043-E4-s

description: mRNA-seq


title: K0043-E4-d

description: mRNA-seq

value: Dual


title: K0034-E4-s

description: mRNA-seq


title: K0044-E3-d

description: mRNA-seq


title: K0041-E3-s

description: mRNA-seq


title: K0044-E3-s

description: mRNA-seq


title: K0042-E4-s

description: mRNA-seq


title: K0042-E4-d

description: mRNA-seq


title: Exp_d2_Cdh1_dot1li_1

description: Sample 33


title: Exp_d2_empty_control_2

description: Sample 28


title: K0015-E3-s

description: mRNA-seq


title: K0035-E3-d

description: mRNA-seq


title: K0015-E3-d

description: mRNA-seq


title: K0008-E4-d

description: mRNA-seq


title: K0034-E4-d

description: mRNA-seq


title: K0008-E4-s

description: mRNA-seq


title: K0138-AbE4-s

description: mRNA-seq


title: K0118-AbE4-s

description: mRNA-seq


title: K0135-AbE4-d

description: mRNA-seq


title: K0136-AbE3-s

description: mRNA-seq


title: K0137-AbE3-s

description: mRNA-seq


title: K0118-AbE4-d

description: mRNA-seq


title: K0137-AbE3-d

description: mRNA-seq


title: K0101-AbE3-s

description: mRNA-seq


title: K0126-AbE3-d

description: mRNA-seq


title: K0136-AbE3-d

description: mRNA-seq


title: X0095-AbE4-N

description: mRNA-seq

source_name: neuron

value: neuron


title: A2000-AbE4-N

description: mRNA-seq


title: A1999-AbE4-N

description: mRNA-seq


title: X0107-AbE3-N

description: mRNA-seq


title: X0103-AbE4-N

description: mRNA-seq


title: K0007-E3-d

description: mRNA-seq


title: X0102-AbE3-N

description: mRNA-seq


title: X0093-AbE3-N

description: mRNA-seq


title: X0094-AbE3-N

description: mRNA-seq


title: K0126-AbE3-s

description: mRNA-seq


title: K0138-AbE4-d

description: mRNA-seq


title: F1805-AbE3-N

description: mRNA-seq


title: F1806-AbE3-N

description: mRNA-seq


title: K0102-AbE4-d

description: mRNA-seq


title: K0102-AbE4-s

description: mRNA-seq


title: A2001-AbE4-M

description: mRNA-seq


title: A2000-AbE4-M

description: mRNA-seq


title: A1999-AbE4-M

description: mRNA-seq


title: F1805-AbE3-M

description: mRNA-seq


title: F1786-AbE4-M

description: mRNA-seq


title: F1786-AbE4-N

description: mRNA-seq


title: A2001-AbE4-N

description: mRNA-seq


title: K0135-AbE4-s

description: mRNA-seq


title: X0108-AbE4-M

description: mRNA-seq


title: X0103-AbE4-M

description: mRNA-seq


title: X0095-AbE4-M

description: mRNA-seq


title: X0102-AbE3-M

description: mRNA-seq


title: X0101-AbE3-M

description: mRNA-seq


title: X0094-AbE3-M

description: mRNA-seq


title: X0107-AbE3-M

description: mRNA-seq


title: X0106-Ab-M

description: mRNA-seq

value: Ab


title: X0093-AbE3-M

description: mRNA-seq


title: X0090-Ab-M

description: mRNA-seq


title: X0098-Ab-M

description: mRNA-seq


title: X0105-sAb-M

description: mRNA-seq

value: sAb


title: X0100-sAb-M

description: mRNA-seq


title: X0089-Ab-M

description: mRNA-seq


title: X0097-Ab-M

description: mRNA-seq


title: X0092-sAb-M

description: mRNA-seq


title: F1806-AbE3-M

description: mRNA-seq


title: X0091-sAb-M

description: mRNA-seq


title: 7527AA_MSCB-187

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse or human genome reference.
Gene quantification was performed using UMI information to correct for amplification biases.
Genome_build: human: GRCh38. Gencode release 26.  Mouse: GRCm38. Gencode release M15.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

source_name: bladder

extract_protocol:
Short-term cultured pancreatic islet cells were isolated from a healthy pancreas donor. The culturing process favor the enrichment of pancreatic islet cells while large eliminating endothelial and immune cell types. Primary bladder epithelial cells were isolated by FACS (CD45-, CD140a-, CD31-, Ter119-) from a healthy mouse.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014). This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes (bases 1 to 6 and 7 to 14, respectively). Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

value: primary bladder epithelial cell


title: 7527AA_MSCB-191


title: 7527AA_MSCB-189


title: 7527AA_MSCB-186


title: 7527AA_MSCB-190


title: X0104-AbE4-M

description: mRNA-seq


title: 7527AA_MSCB-192


title: 7527AA_MSCB-188


title: 7527AA_MSCB-184


title: 7527AA_MSCB-183


title: 7527AA_MSCB-181


title: 7527AA_MSCB-180


title: 7527AA_MSCB-177


title: 7527AA_MSCB-179


title: X0099-sAb-M

description: mRNA-seq


title: 7527AA_MSCB-178


title: 7527AA_MSCB-174


title: 7527AA_MSCB-182


title: 7527AA_MSCB-173


title: 7527AA_MSCB-172


title: 7527AA_MSCB-170


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title: 7527AA_MSCB-175


title: 7527AA_MSCB-168


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title: 7527AA_MSCB-164


title: 7527AA_MSCB-160


title: 7527AA_MSCB-165


title: 7527AA_MSCB-161


title: 7527AA_MSCB-162


title: 7527AA_MSCB-166


title: 7527AA_MSCB-159


title: 7527AA_MSCB-157


title: 7527AA_MSCB-155


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title: 7527AA_MSCB-142


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title: 7527AA_MSCB-135


title: 7527AA_MSCB-133


title: 7527AA_MSCB-132


title: 7527AA_MSCB-134


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title: 7527AA_MSCB-120


title: 7527AA_MSCB-122


title: 7527AA_MSCB-117


title: 7527AA_MSCB-118


title: 7527AA_MSCB-119


title: 7527AA_MSCB-121


title: 7527AA_MSCB-123


title: 7527AA_MSCB-116


title: 7527AA_MSCB-113


title: 7527AA_MSCB-112


title: 7527AA_MSCB-111


title: 7527AA_MSCB-110


title: 7527AA_MSCB-115


title: 7527AA_MSCB-108


title: 7527AA_MSCB-114


title: 7527AA_MSCB-106


title: 7527AA_MSCB-109


title: 7527AA_MSCB-104


title: 7527AA_MSCB-103


title: 7527AA_MSCB-105


title: 7527AA_MSCB-101


title: 7527AA_MSCB-102


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title: 7527AA_MSCB-097


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title: 7527AA_MSCB-087


title: 7527AA_MSCB-084


title: 7527AA_MSCB-088


title: 7527AA_MSCB-085


title: 7527AA_MSCB-083


title: K0101-AbE3-d

description: mRNA-seq


title: X0101-AbE3-N

description: mRNA-seq


title: 7527AA_MSCB-082


title: 7527AA_MSCB-074


title: 7527AA_MSCB-066


title: 7527AA_MSCB-069


title: 7527AA_MSCB-068


title: 7527AA_MSCB-078


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title: 7527AA_MSCB-080


title: 7527AA_MSCB-081


title: 7527AA_MSCB-073


title: 7527AA_MSCB-072


title: 7527AA_MSCB-077


title: 7527AA_MSCB-065


title: 7527AA_MSCB-075


title: 7527AA_MSCB-067


title: 7527AA_MSCB-070


title: 7527AA_MSCB-058


title: 7527AA_MSCB-079


title: 7527AA_MSCB-056


title: 7527AA_MSCB-062


title: 7527AA_MSCB-076


title: 7527AA_MSCB-063


title: 7527AA_MSCB-053


title: 7527AA_MSCB-064


title: 7527AA_MSCB-061


title: 7527AA_MSCB-057


title: 7527AA_MSCB-060


title: 7527AA_MSCB-059


title: 7527AA_MSCB-054


title: 7527AA_MSCB-055


title: 7527AA_MSCB-052


title: 7527AA_MSCB-051


title: 7527AA_MSCB-047


title: 7527AA_MSCB-045


title: 7527AA_MSCB-049


title: 7527AA_MSCB-048


title: 7527AA_MSCB-041


title: 7527AA_MSCB-044


title: 7527AA_MSCB-043


title: 7527AA_MSCB-042


title: 7527AA_MSCB-038


title: 7527AA_MSCB-036


title: 7527AA_MSCB-039


title: 7527AA_MSCB-034


title: 7527AA_MSCB-050


title: 7527AA_MSCB-031


title: 7527AA_MSCB-032


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title: 7527AA_MSCB-035


title: 7527AA_MSCB-033


title: 7527AA_MSCB-029


title: 7527AA_MSCB-027


title: 7527AA_MSCB-030


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title: 7527AA_MSCB-040


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title: 7527AA_MSCB-016


title: 7527AA_MSCB-020


title: 7527AA_MSCB-012


title: 7527AA_MSCB-002


title: 7527AA_MSCB-003


title: 7527AA_MSCB-005


title: 7527AA_MSCB-011


title: 7526AA_MSCB-191


title: 7526AA_MSCB-192


title: 7527AA_MSCB-001


title: 7527AA_MSCB-021


title: 7527AA_MSCB-004


title: 7527AA_MSCB-014


title: 7526AA_MSCB-190


title: 7526AA_MSCB-188


title: 7526AA_MSCB-187


title: 7527AA_MSCB-010


title: 7527AA_MSCB-006


title: 7527AA_MSCB-009


title: 7526AA_MSCB-189


title: 7526AA_MSCB-185


title: 7526AA_MSCB-184


title: 7526AA_MSCB-180


title: 7526AA_MSCB-181


title: 7526AA_MSCB-183


title: 7526AA_MSCB-182


title: 7526AA_MSCB-178


title: 7526AA_MSCB-177


title: 7526AA_MSCB-172


title: 7526AA_MSCB-175


title: 7526AA_MSCB-176


title: 7526AA_MSCB-174


title: 7526AA_MSCB-171


title: 7526AA_MSCB-173


title: 7526AA_MSCB-170


title: 7526AA_MSCB-169


title: 7526AA_MSCB-186


title: 7526AA_MSCB-165


title: 7526AA_MSCB-164


title: 7526AA_MSCB-168


title: 7526AA_MSCB-166


title: 7526AA_MSCB-162


title: 7526AA_MSCB-163


title: 7526AA_MSCB-160


title: 7526AA_MSCB-179


title: 7526AA_MSCB-159


title: 7526AA_MSCB-157


title: 7526AA_MSCB-158


title: 7526AA_MSCB-156


title: 7526AA_MSCB-155


title: 7526AA_MSCB-152


title: 7526AA_MSCB-154


title: 7526AA_MSCB-150


title: 7526AA_MSCB-167


title: 7526AA_MSCB-149


title: 7526AA_MSCB-148


title: 7526AA_MSCB-146


title: 7526AA_MSCB-142


title: 7526AA_MSCB-161


title: 7526AA_MSCB-141


title: 7526AA_MSCB-140


title: 7526AA_MSCB-137


title: 7526AA_MSCB-136


title: 7526AA_MSCB-139


title: 7526AA_MSCB-135


title: 7526AA_MSCB-138


title: 7526AA_MSCB-134


title: 7526AA_MSCB-133


title: 7526AA_MSCB-132


title: 7526AA_MSCB-130


title: 7526AA_MSCB-129


title: 7526AA_MSCB-131


title: 7526AA_MSCB-151


title: 7526AA_MSCB-128


title: 7526AA_MSCB-153


title: 7526AA_MSCB-127


title: 7526AA_MSCB-143


title: 7526AA_MSCB-144


title: 7526AA_MSCB-147


title: 7526AA_MSCB-123


title: 7526AA_MSCB-145


title: 7526AA_MSCB-125


title: 7526AA_MSCB-121


title: 7526AA_MSCB-122


title: 7526AA_MSCB-118


title: 7526AA_MSCB-117


title: 7526AA_MSCB-120


title: 7526AA_MSCB-116


title: 7526AA_MSCB-115


title: 7526AA_MSCB-114


title: 7526AA_MSCB-111


title: 7526AA_MSCB-109


title: 7526AA_MSCB-108


title: 7526AA_MSCB-113


title: 7526AA_MSCB-126


title: 7526AA_MSCB-106


title: 7526AA_MSCB-105


title: 7526AA_MSCB-104


title: 7526AA_MSCB-103


title: 7526AA_MSCB-107


title: 7526AA_MSCB-102


title: 7526AA_MSCB-101


title: 7526AA_MSCB-124


title: 7526AA_MSCB-099


title: 7526AA_MSCB-100


title: 7526AA_MSCB-098


title: 7526AA_MSCB-097


title: 7526AA_MSCB-119


title: 7526AA_MSCB-096


title: 7526AA_MSCB-095


title: 7526AA_MSCB-094


title: 7526AA_MSCB-110


title: 7526AA_MSCB-112


title: 7526AA_MSCB-091


title: 7526AA_MSCB-092


title: 7526AA_MSCB-090


title: 7526AA_MSCB-089


title: 7526AA_MSCB-088


title: 7526AA_MSCB-087


title: 7526AA_MSCB-082


title: 7526AA_MSCB-083


title: 7526AA_MSCB-085


title: 7526AA_MSCB-086


title: 7526AA_MSCB-084


title: 7526AA_MSCB-081


title: 7526AA_MSCB-080


title: 7526AA_MSCB-079


title: 7526AA_MSCB-077


title: 7526AA_MSCB-078


title: 7526AA_MSCB-075


title: 7526AA_MSCB-074


title: 7526AA_MSCB-076


title: 7526AA_MSCB-073


title: 7526AA_MSCB-072


title: 7526AA_MSCB-071


title: 7526AA_MSCB-070


title: 7526AA_MSCB-068


title: 7526AA_MSCB-069


title: 7526AA_MSCB-093


title: 7526AA_MSCB-065


title: 7526AA_MSCB-063


title: 7526AA_MSCB-062


title: 7526AA_MSCB-064


title: 7526AA_MSCB-061


title: 7526AA_MSCB-060


title: 7526AA_MSCB-058


title: 7526AA_MSCB-056


title: 7526AA_MSCB-052


title: 7526AA_MSCB-057


title: 7526AA_MSCB-053


title: 7526AA_MSCB-050


title: 7526AA_MSCB-054


title: 7526AA_MSCB-055


title: 7526AA_MSCB-067


title: 7526AA_MSCB-048


title: 7526AA_MSCB-043


title: 7526AA_MSCB-047


title: 7526AA_MSCB-042


title: 7526AA_MSCB-039


title: 7526AA_MSCB-045


title: 7526AA_MSCB-044


title: 7526AA_MSCB-040


title: 7526AA_MSCB-046


title: 7526AA_MSCB-066


title: 7526AA_MSCB-041


title: 7526AA_MSCB-051


title: 7526AA_MSCB-049


title: 7526AA_MSCB-038


title: 7526AA_MSCB-035


title: 7526AA_MSCB-034


title: 7526AA_MSCB-032


title: 7526AA_MSCB-059


title: 7526AA_MSCB-037


title: 7526AA_MSCB-031


title: 7526AA_MSCB-025


title: 7526AA_MSCB-029


title: 7526AA_MSCB-024


title: 7526AA_MSCB-011


title: 7526AA_MSCB-020


title: 7526AA_MSCB-017


title: 7526AA_MSCB-015


title: 7526AA_MSCB-014


title: 7526AA_MSCB-008


title: 7526AA_MSCB-019


title: 7526AA_MSCB-027


title: 7526AA_MSCB-013


title: 7526AA_MSCB-006


title: 7526AA_MSCB-021


title: 7526AA_MSCB-023


title: 7526AA_MSCB-026


title: 7526AA_MSCB-022


title: 7526AA_MSCB-016


title: 7526AA_MSCB-028


title: 7526AA_MSCB-012


title: 7526AA_MSCB-009


title: 7526AA_MSCB-018


title: 7526AA_MSCB-007


title: 7526AA_MSCB-036


title: 7526AA_MSCB-005


title: 7526AA_MSCB-004


title: 7526AA_MSCB-003


title: 7526AA_MSCB-030


title: 7526AA_MSCB-033


title: 7526AA_MSCB-010


title: 7526AA_MSCB-001


title: 7003AA_MSCB-192


title: 7003AA_MSCB-188


title: 7003AA_MSCB-182


title: 7526AA_MSCB-002


title: 7003AA_MSCB-185


title: 7003AA_MSCB-189


title: 7003AA_MSCB-177


title: 7003AA_MSCB-190


title: 7003AA_MSCB-175


title: 7003AA_MSCB-191


title: 7003AA_MSCB-173


title: 7003AA_MSCB-186


title: 7003AA_MSCB-172


title: 7003AA_MSCB-184


title: 7003AA_MSCB-174


title: 7003AA_MSCB-183


title: 7003AA_MSCB-187


title: 7003AA_MSCB-181


title: 7003AA_MSCB-179


title: 7003AA_MSCB-180


title: 7003AA_MSCB-171


title: 7003AA_MSCB-176


title: 7003AA_MSCB-170


title: 7003AA_MSCB-169


title: 7003AA_MSCB-165


title: 7003AA_MSCB-178


title: 7003AA_MSCB-167


title: 7003AA_MSCB-168


title: 7003AA_MSCB-163


title: 7003AA_MSCB-164


title: 7003AA_MSCB-162


title: 7003AA_MSCB-166


title: 7003AA_MSCB-160


title: 7003AA_MSCB-159


title: 7003AA_MSCB-161


title: 7003AA_MSCB-157


title: 7003AA_MSCB-158


title: 7003AA_MSCB-154


title: 7003AA_MSCB-149


title: 7003AA_MSCB-148


title: 7003AA_MSCB-156


title: 7003AA_MSCB-155


title: 7003AA_MSCB-153


title: 7003AA_MSCB-152


title: 7003AA_MSCB-151


title: 7003AA_MSCB-144


title: 7003AA_MSCB-150


title: 7003AA_MSCB-146


title: 7003AA_MSCB-147


title: 7003AA_MSCB-145


title: 7003AA_MSCB-143


title: 7003AA_MSCB-142


title: 7003AA_MSCB-138


title: 7003AA_MSCB-141


title: 7003AA_MSCB-137


title: 7003AA_MSCB-140


title: 7003AA_MSCB-136


title: 7003AA_MSCB-139


title: 7003AA_MSCB-135


title: 7003AA_MSCB-134


title: 7003AA_MSCB-133


title: 7003AA_MSCB-131


title: 7003AA_MSCB-130


title: 7003AA_MSCB-132


title: 7003AA_MSCB-129


title: 7003AA_MSCB-128


title: 7003AA_MSCB-127


title: wild type E. coli - P1vir infection time 10 min - rep. 1

city: Gdansk

first: Grzegorz

middle: M.

last: Cech

state: Pomorskie

address: Wita Stwosza 59 pok. A242

department: Department of Bacterial Molecular Genetics

country: Poland

institute: Uniwersytet Gdański, Wydział Biolog

description:
DE_results_WT_10_upregulated_genes; DE_results_WT_10_limma; DE_results_WT_10_downregulated_genes
WT_t-10_Exp1

data_processing:
Quality and adapter trimming of short reads was performed using Trimmomatic (Bolgeret al. 2014)
Short reads matching known rRNA sequences were removed using HISAT2 aligner (Kim et al. 2015)
Read quality reports before and after quality filtering were prepared using FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Filtered reads were aligned to the reference genomes using Burrows-Wheeler Aligner with selected BWA-MEM algorithm (Li and Durbin 2009)
Sambamba software was used for BAM files processing (Tarasov et al. 2015)
Hierarchical clustering of RNA–Seq samples (Pearson correlation metric, centroid linkage) based on the expression values of all genes was performed using standard R functions (R Core Team 2016) and variance stabilizing transformation provided by DESeq2 package (Love et al. 2014).
Differential expression analysis between designated groups of samples was performed using voom+limma (Ritchie 2015) pipeline (Law et al. 2016). FDR threshold of 0.01 and fold change threshold of 1.1 were used during the analysis.
FastQC read quality reports before and after quality control was done as well as, read mapping quality reports created by Qualimap
Genome_build: Escherichia coli K12 MG1655 (NC_000913)
Genome_build: P1 phage (NC_005856)
Supplementary_files_format_and_content: DE_results_WT_30_upregulated_genes  - upredulation of host genes, 30 min of infection in wild type cells
Supplementary_files_format_and_content: DE_results_WT_30_limma - upredulation of phage genes, 30 min of infection in wild type cells
Supplementary_files_format_and_content: DE_results_WT_30_downregulated_genes - downredulation of host genes, 30 min of infection in wild type cells
Supplementary_files_format_and_content: DE_results_WT_10_upregulated_genes - upredulation of host genes, 10 min of infection in wild type cells
Supplementary_files_format_and_content: DE_results_WT_10_limma - upredulation of phage genes, 10 min of infection in wild type cells
Supplementary_files_format_and_content: DE_results_WT_10_downregulated_genes - downredulation of host genes, 10 min of infection in wild type cells
Supplementary_files_format_and_content: DE_results_dksA_30_upregulated_genes - upredulation of host genes, 30 min of infection in dksA mutant
Supplementary_files_format_and_content: DE_results_dksA_30_limma - upredulation of phage genes, 30 min of infection in dksA mutant
Supplementary_files_format_and_content: DE_results_dksA_30_downregulated_genes - downredulation of host genes, 30 min of infection in dksA mutant
Supplementary_files_format_and_content: DE_results_dksA_10_upregulated_genes - upredulation of host genes, 10 min of infection in dksA mutant
Supplementary_files_format_and_content: DE_results_dksA_10_limma - upredulation of phage genes, 10 min of infection in dksA mutant
Supplementary_files_format_and_content: DE_results_dksA_10_downregulated_genes - downredulation of host genes, 10 min of infection in dksA mutant
Supplementary_files_format_and_content: gene_counts - unnormalized read counts
Supplementary_files_format_and_content: gene_tpm - Table storing normalized TPM

organism: Escherichia coli str. K-12 substr. MG1655

source_name: mammalians intestine

growth_protocol: Bacterial wild type and dksA strains were cultured in LB broth containing 10 mM CaCl2 at 37°C with shaking to OD600 = 0.2

extract_protocol:
RNA isolation was performed using RNeasy Mini Kit (Qiagen) according the manufac-turer's protocol. The elution step was performed twice using 50 µl of RNase-free water on the same column to increase RNA yields. The RNA preparation was digested with DNase using TURBO DNA-free™ Kit (Ambion), according the manufacturer's protocol. Samples were stored at −80°C. The purity and integrity of RNA was assessed using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and Agilent RNA 6000 Nano Kit, according the manufacturer's protocol. RNA depleted of ribosomal RNA with Ribo-Zero rRNA removal Kit Bacteria (Illumina).
Library prepared with TruSeq Stranded Total RNA Sample Prep Kit (Illumina).

treatment_protocol: P1vir phage was added at final MOI = 10. One-ml samples were immediately withdrawn to previously prepared 1.5 ml tubes containing 250 µlaqua-phenol (5% phenol in 96% ethanol). Samples were withdrawn at 0, 10 and 30 minutes after P1vir infection

tag: background strain

value: wild type

tag: strain id

value: infected with P1vir phage

tag: phage name

value: Bacteriophage P1vir

tag: infection time

value: 10 min

tag: replicate number

value: experiment 1


title: wild type E. coli - P1vir infection time 10 min - rep. 2

description:
DE_results_WT_10_upregulated_genes; DE_results_WT_10_limma; DE_results_WT_10_downregulated_genes
WT_t-10_Exp2

value: experiment 2


title: wild type E. coli - P1vir infection time 30 min - rep. 2

description:
DE_results_WT_10_upregulated_genes; DE_results_WT_10_limma; DE_results_WT_10_downregulated_genes
WT_t-30_Exp2

value: 30 min


title: wild type E. coli - P1vir infection time 30 min - rep. 1

description:
DE_results_WT_10_upregulated_genes; DE_results_WT_10_limma; DE_results_WT_10_downregulated_genes
WT_t-30_Exp1


title: wild type E. coli - P1vir infection time 30 min - rep. 3

description:
DE_results_WT_10_upregulated_genes; DE_results_WT_10_limma; DE_results_WT_10_downregulated_genes
WT_t-30_Exp3

value: experiment 3


title: wild type E. coli - P1vir infection time 0 min - rep. 3

value: untreated

value: 0 min = no phage


title: wild type E. coli - P1vir infection time 10 min - rep. 3

description:
DE_results_WT_10_upregulated_genes; DE_results_WT_10_limma; DE_results_WT_10_downregulated_genes
WT_t-10_Exp3


title: 7003AA_MSCB-125


title: 7003AA_MSCB-126


title: 7003AA_MSCB-124


title: wild type E. coli - P1vir infection time 0 min - rep. 2


title: wild type E. coli - P1vir infection time 0 min - rep. 1


title: E. coli dksA mutant - P1vir infection time 30 min - rep. 3

description:
DE_results_dksA_10_upregulated_genes; DE_results_dksA_10_limma; DE_results_dksA_10_downregulated_genes
dksA_t-30_Exp3


title: 7003AA_MSCB-123


title: E. coli dksA mutant - P1vir infection time 30 min - rep. 2

description:
DE_results_dksA_10_upregulated_genes; DE_results_dksA_10_limma; DE_results_dksA_10_downregulated_genes
dksA_t-30_Exp2


title: 7003AA_MSCB-121


title: 7003AA_MSCB-122


title: E. coli dksA mutant - P1vir infection time 30 min - rep. 1

description:
DE_results_dksA_10_upregulated_genes; DE_results_dksA_10_limma; DE_results_dksA_10_downregulated_genes
dksA_t-30_Exp1


title: 7003AA_MSCB-120


title: E. coli dksA mutant - P1vir infection time 10 min - rep. 2

description:
DE_results_dksA_10_upregulated_genes; DE_results_dksA_10_limma; DE_results_dksA_10_downregulated_genes
dksA_t-10_Exp2


title: 7003AA_MSCB-119


title: E. coli dksA mutant - P1vir infection time 10 min - rep. 3

description:
DE_results_dksA_10_upregulated_genes; DE_results_dksA_10_limma; DE_results_dksA_10_downregulated_genes
dksA_t-10_Exp3


title: 7003AA_MSCB-118


title: E. coli dksA mutant - P1vir infection time 10 min - rep. 1

description:
DE_results_dksA_10_upregulated_genes; DE_results_dksA_10_limma; DE_results_dksA_10_downregulated_genes
dksA_t-10_Exp1


title: E. coli dksA mutant - P1vir infection time 0 min - rep. 3


title: 7003AA_MSCB-116


title: 7003AA_MSCB-117


title: 7003AA_MSCB-115


title: E. coli dksA mutant - P1vir infection time 0 min - rep. 2


title: 7003AA_MSCB-114


title: 7003AA_MSCB-113


title: 7003AA_MSCB-110


title: 7003AA_MSCB-108


title: 7003AA_MSCB-111


title: antigen-specific CD8+ T cells Trp2 (Dct) wild-type bulk cells replicate 1

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
bulk RNA
WT1

data_processing:
Illumina bcl2fastq (bulk RNAseq) or 10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Read mapping was performed via Hisat2 (Bulk RNAseq) or Cell Ranger count (scRNAseq) using the mouse reference genome (mm10).
Gene level quantification was completed using Subread featureCounts (bulk RNASeq) or Cell Ranger count software.
Raw counts data was imported into R for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized read count values for each sample

source_name: antigen-specific CD8+ T cells

growth_protocol: Trp2/Kb-specific cells were isolated from pre-immune WT and Dct-/- mice using tetramer enrichment followed by fluorescence-activated cell sorting on double tetramer positive cells.

extract_protocol:
Bulk RNAseq (samples 1-6): cells were isolated from three separate cohorts, with each cohort comprising eight WT and eight Dct-/- mice; Qiagen RNEasy Plus Mini Kit was used to extract RNA. Single cell RNA-seq (scRNAseq samples 1 and 2): sorted cells were supplied as input to the 10x Genomics single cell protocol.
Bulk: Clontech StrandedRNA Pico Mammalian workflow was used for library preparation; scRNAseq: Chromium Single Cell Immune Profiling was used for library preparation. Samples were prepared for sequencing using standard Illumina protocols.

value: antigen-specific CD8+ T cells

value: wildtype

tag: tissue

value: spleen


title: antigen-specific CD8+ T cells Trp2 (Dct) wild-type bulk cells replicate 2

description:
bulk RNA
WT2


title: antigen-specific CD8+ T cells Trp2 (Dct) knockout bulk cells replicate 3

description:
bulk RNA
KO3

value: Dct-/-


title: antigen-specific CD8+ T cells Trp2 (Dct) knockout bulk cells replicate 2

description:
bulk RNA
KO2


title: antigen-specific CD8+ T cells Trp2 (Dct) wild-type bulk cells replicate 3

description:
bulk RNA
WT3


title: M251

city: Galveston

first: Kubra

last: Naqvi

state: TX

address: 301 University blvd

institute: University of Texas Medical Branch

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.7.5c) using the Gencode GRCm primary genome assembly and vM25 annotation file.
Reads were aligned to the mouse reference using the STAR software version 2.7.5c with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR.
Differential gene expression was analyzed with the R (version 4.0.2) software DESeq2 (version 1.28.1)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene

source_name: WT_8 weeks infected_lung

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Poly-A plus RNA was enriched from  ~0.1 ug of total RNA and used to generate libraries using the NEBNext Ultra II Kit.

tag: genotype/variation

value: WT

value: 8 weeks infected

value: lung


title: 7003AA_MSCB-112

value: primary bladder epithelial cell


title: 7003AA_MSCB-109


title: 7003AA_MSCB-106


title: antigen-specific CD8+ T cells Trp2 (Dct) knockout bulk cells replicate 1

description:
bulk RNA
KO1

tag: strain


title: M253


title: 7003AA_MSCB-107


title: 7003AA_MSCB-105


title: 7003AA_MSCB-104


title: E. coli dksA mutant - P1vir infection time 0 min - rep. 1


title: M243

source_name: MGL-1-/-_8 weeks infected_lung


title: 7003AA_MSCB-102


title: M241


title: 7003AA_MSCB-101


title: 7003AA_MSCB-100


title: M250


title: M239


title: M203

source_name: WT_2 weeks infected_lung

value: 2 weeks infected


title: M202


title: M249


title: M201


title: 7003AA_MSCB-097


title: M248


title: 7003AA_MSCB-098


title: 7003AA_MSCB-095


title: 7003AA_MSCB-099


title: 7003AA_MSCB-103


title: 7003AA_MSCB-096


title: M244


title: M188

source_name: MGL-1-/-_2 weeks infected_lung


title: M194


title: 7003AA_MSCB-092


title: M191


title: 7003AA_MSCB-093


title: 7003AA_MSCB-091


title: M189


title: 7003AA_MSCB-094


title: M197


title: M240


title: 7003AA_MSCB-090


title: 7003AA_MSCB-089


title: M87

value: uninfected


title: M186


title: 7003AA_MSCB-088


title: M86


title: M199


title: 7003AA_MSCB-087


title: M85


title: M84


title: 7003AA_MSCB-086


title: 7003AA_MSCB-084


title: M83


title: M50


title: 7003AA_MSCB-083


title: 7003AA_MSCB-081


title: M48


title: 7003AA_MSCB-082


title: M47


title: 7003AA_MSCB-080


title: 7003AA_MSCB-079


title: M49


title: 7003AA_MSCB-077


title: 7003AA_MSCB-076


title: 7003AA_MSCB-078


title: 7003AA_MSCB-074


title: Screen-s2_day12_U_B_2

city: STANFORD

first: Jeffrey

middle: Michael

last: Granja

state: CA

address: 279 Campus Drive W

department: Genetics

institute: Stanford University

description:
CRISPR Screen
processed data file:
Screen-Matrices-Combined-sgRNA-Counts.tsv
Screen-Matrices-Mageck-Results-Gene-Summary.txt

library_source: genomic

data_processing:
ATAC-seq:
Fastq reads were trimmed using cutadapt and then aligned to the genome with bowtie 2 and then filtered for high quality read paired alignment.
Mitochondrial and picard identified pcr duplicates were then discarded.
Macs2 was then used to identify peak regions that were reproducible across replicate samples and then to create a sample by peak matrix.
Bulk RNA-seq:
Fastq reads were trimmed using cutadapt and then pseudo aligned to the genome with Kallisto.
Counts were then compiled from each sample to build a sample by gene counts matrix.
Single Cell ATAC-seq:
The Cell Ranger ATAC Software Suite (version 1.2.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the Tn5 transposase made cuts
Regions of enriched accessibility, i.e. peaks were identified with MACS2
Barcodes likely associated with whole cells were identified by analyzing the number of fragments (1000) mapped near TSS regions (enriched over background) and a peak-barcode matrix is defined
CRISPR Screen:
Fastq reads were aligned to sgRNA barcodes using casTLE (implementing bowtie).
Counts were then compiled from each sample across both screen halves and normalized.
The counts matrix was then used as input to MaGeCK for downstream analysis.
Genome_build: mm10/hg38
Supplementary_files_format_and_content:
Processed ATAC-seq/scATAC-seq data is provided as an R SummarizedExperiment object. This object contains counts alongth with row and column metadata corresponding to the individual cells and peak/motif/gene chromatin accessibility. Fragments file contain Tn5 corrected cut sites per sample or cell.
Processed RNA-seq data is provided in an xlsx file containing counts/tpm for each sample per gene. Additionally, Kallisto generated transcript abundances per sample are provided.
Processed CRISPR Screen data using casTLE (bowtie) is provided as a counts table for each sgRNA count sample per gene and a table of results from MAGeCK analysis.
*insertion.bw: Sample Bigwig file of chromatin accessibilty
*Fragments.tsv.gz: Sample Fragments Files containing Tn5 cut sites of chromatin accessibility
*chromVAR-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing samples by TF accessibility.
*Peak-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing samples by peak accessibility.
*abundance.tsv: Sample transcript abundances from Kallisto.
bRNA-Matrices-Initial-LKB1-Resoration.xlsx: Matrix excel file containing transcript abundances and counts for each sample with descriptions.
bRNA-Matrices-Mouse-Tumor-Metastases-Matrices.xlsx: Matrix excel file containing transcript abundances and counts for each sample with descriptions.
Save_LKB1_ArchRProject.zip: Saved ArchRProject from ArchR for scATAC-seq mouse data.
*singlecell.csv: 10x Genomics Single Cell QC statistics file.
*fragments.tsv.gz: Sample Fragments Files containing Tn5 cut sites per cell of chromatin accessibility
*chromVAR-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing cells by TF accessibility.
scATAC-LKB1-GeneScoreMatrix-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing cells by gene accessibility.
scATAC-LKB1-PeakMatrix-Summarized-Experiment.rds: Matrix summarized experiment file (R object) containing cells by peak accessibility.
Screen-Counts-s1*counts.csv: Counts file from casTLE for each sample of CRISPR screen half 1.
Screen-Counts-s1_s2*counts.csv: Counts file from casTLE for each sample of CRISPR screen half 2. (Repeat of sample from half 1)
Screen-Counts-s2*counts.csv: Counts file from casTLE for each sample of CRISPR screen half 2.
Screen-Matrices-Combined-sgRNA-Counts.tsv: Combined Matrix file of all samples for CRISPR screen.
Screen-Matrices-Mageck-Results-Gene-Summary.txt: Results file from MaGeCK analysis of CRISPR screen data.

molecule: genomic DNA

source_name: Immortalized cell line

extract_protocol:
Genomic DNA was extracted from each sample in technical duplicate with the Qiagen Blood Maxi Kit and eluted in Buffer EB.
Screen library preparation was performed as previously described (Morgens et al Nature Communications 2017; doi: 10.1038/ncomms15178)

tag: cell line

tag: tissue/cell type

value: lung cancer

value: vehicle

tag: timepoint of treatment

value: 12 days

tag: source

value: mouse derived

tag: growth media

value: DMEM; 10% FBS; 1% pen-strep


title: Screen-s2_day12_U_B_1

tag: treatment


title: Screen-s2_day12_R_B_2


title: 7003AA_MSCB-073

tag: cell type


title: Screen-s2_day12_R_B_1


title: Screen-s2_day12_R_A_2


title: 7003AA_MSCB-085


title: Screen-s2_day12_R_A_1


title: M51


title: 7003AA_MSCB-071


title: Screen-s2_day10_U_B

value: 10 days


title: 7003AA_MSCB-070


title: Screen-s2_day10_U_A


title: 7003AA_MSCB-069


title: Screen-s2_day0_2

value: 0 days


title: 7003AA_MSCB-067


title: Screen-s1_s2_day12_R_B_1


title: 7003AA_MSCB-066


title: Screen-s2_day12_U_A_2


title: 7003AA_MSCB-068


title: Screen-s2_day12_U_A_1


title: Screen-s2_day0_1


title: 7003AA_MSCB-075


title: 7003AA_MSCB-063


title: 7003AA_MSCB-064


title: 7003AA_MSCB-072


title: Screen-s1_day12_U_B_1


title: 7003AA_MSCB-061


title: 7003AA_MSCB-062


title: Screen-s1_day12_U_A_2


title: Screen-s1_day12_R_B_2


title: 7003AA_MSCB-060


title: Screen-s1_day12_R_A_2


title: 7003AA_MSCB-059


title: Screen-s1_day12_R_B_1


title: 7003AA_MSCB-058


title: 7003AA_MSCB-057


title: Screen-s1_day12_R_A_1


title: Screen-s1_s2_day0_1


title: 7003AA_MSCB-065


title: 7003AA_MSCB-055


title: Screen-s1_day0_2


title: Screen-s1_day0_1


title: scATAC-aSP95_KP_Primary_21A

description:
Single Cell ATAC-seq
processed data file:
Save_LKB1_ArchRProject.zip
scATAC-LKB1-PeakMatrix-Summarized-Experiment.rds
scATAC-LKB1-GeneScoreMatrix-Summarized-Experiment.rds
scATAC-LKB1-ChromVAR-Summarized-Experiment.rds

source_name: Mouse lung adenocarcinoma primary tumors and metastases

extract_protocol:
Up to 50,000 FACS-isolated lung adenocarcinoma cells were viably cryopreserved in BAMBANKER freezing media (Wako Chemicals 302-14681) so that scATAC-seq could be performed on all cells at the same time. Cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the pelleted nuclei were resuspended in Diluted Nuclei Buffer (10x Genomics). The nuclei stock concentration was determined for each cell line using Trypan Blue and a total of 5,000 nuclei from each cell line were pooled together and loaded into the 10x Genomics scATAC-seq (v1) transposition reaction.
scATAC-seq library preparation was performed as recommended by the manufacturer (10x Genomics scATAC-seq (v1)).


title: 7003AA_MSCB-053


title: 7003AA_MSCB-054


title: 7003AA_MSCB-052


title: Screen-s1_day12_U_B_2


title: scATAC-aSP87_KP_Female


title: scATAC-aSP82_KP_Primary_15B


title: Screen-s1_day12_U_A_1


title: 7003AA_MSCB-050


title: scATAC-aSP72_KPL_Male


title: 7003AA_MSCB-049


title: 7003AA_MSCB-048


title: 7003AA_MSCB-047


title: Screen-s1_day10_U_B


title: scATAC-aSP71_KPL_Primary_13C


title: scATAC-aSP59_KPL_Female


title: Screen-s1_day10_U_A


title: scATAC-aSP68_KPL_Primary_13B


title: bRNA-KPT.Primary-CC1032T4-R-JBS3

description:
Bulk mRNA-seq
processed data file:
bRNA-Matrices-Mouse-Tumor-Metastases-Matrices.xlsx

extract_protocol:
RNA was extracted from up to 50,000 FACS-isolated lung adenocarcinoma cells using the AllPrep DNA/RNA Micro Kit (Qiagen). RNA quality of each tumor sample was assessed using the RNA6000 PicoAssay for the Bioanalyzer 2100 (Agilent) as per the manufacturer's instructions. All of the RNA used for RNA-seq had an RNA integrity number (RIN) > 8.0.
RNA-sequencing libraries were generated as previously described (Chuang et al Nature Medicine 2017; doi: 10.1038/nm.4285) and sequenced using 200-cycle kits on an Illumina HiSeq 2000.


title: 7003AA_MSCB-056


title: 7003AA_MSCB-043


title: 7003AA_MSCB-045


title: 7003AA_MSCB-044


title: 7003AA_MSCB-046


title: 7003AA_MSCB-042


title: bRNA-KPLT.Primary-JB0890T8-JBS6


title: 7003AA_MSCB-051


title: bRNA-KPT.Met-CC1032LN-R-JBS20


title: bRNA-KPLT.Primary-JB0754T5-JBS5


title: 7003AA_MSCB-041


title: 7003AA_MSCB-040


title: bRNA-KPLT.Primary-JB0887T4-JBS7


title: 7003AA_MSCB-039


title: bRNA-KPLT.Met-JB0851LIVER-JBS18


title: scATAC-aSP81_KP_Male


title: bRNA-KPLT.Met-JB0751LN-JBS17


title: bRNA-KPLT.Met-JB0751HEART-JBS19


title: bRNA-Initial_LU2_vehicle_Rep2

description:
Bulk mRNA-seq
processed data file:
bRNA-Matrices-Initial-LKB1-Resoration.xlsx

extract_protocol:
Adherent cells were rinsed with PBS, trypsinized for 5 minutes at 37 degrees C, pelleted, and cell pellets were frozen at -80 degrees C. Cell pellets were processed to total RNA using the RNeasy Plus Mini Kit (Qiagen) according to standard protocols. RNA quality was assessed using the Bioanalyzer 2100 (Agilent). All of the RNA used for RNA-seq had an RNA integrity number (RIN) of 10.0.
500ng total RNA for each sample was processed into libraries using the TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced according to standard protocols.

value: 6 days


title: 7003AA_MSCB-037


title: 7003AA_MSCB-038


title: 7003AA_MSCB-036


title: bRNA-Initial_LU2_vehicle_Rep1


title: 7003AA_MSCB-035


title: bRNA-Initial_LU2_4OHT_Rep2


title: 7003AA_MSCB-033


title: 7003AA_MSCB-032


title: bRNA-Initial_LU1_vehicle_Rep2


title: 7003AA_MSCB-031


title: bRNA-Initial_LU1_4OHT_Rep1


title: bRNA-Initial_LU1_vehicle_Rep1


title: bRNA-Initial_LU1_4OHT_Rep2


title: 7003AA_MSCB-027


title: bRNA-Initial_LU2_4OHT_Rep1


title: 7003AA_MSCB-028


title: bRNA-Initial_LR2_4OHT_Rep1


title: 7003AA_MSCB-029


title: 7003AA_MSCB-025


title: bRNA-Initial_LR2_4OHT_Rep2


title: bRNA-Initial_LR2_vehicle_Rep2


title: bRNA-Initial_LR2_vehicle_Rep1


title: 7003AA_MSCB-024


title: 7003AA_MSCB-023


title: bRNA-Initial_LR1_vehicle_Rep1


title: bRNA-Initial_LR1_vehicle_Rep2


title: 7003AA_MSCB-034


title: bRNA-Initial_LR1_4OHT_Rep2


title: bRNA-Initial_LR1_4OHT_Rep1


title: bATAC-TKO_LR1_sgSik_2_vehicle_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-TKO-Peak-Summarized-Experiment.rds
bATAC-Matrices-TKO-chromVAR-Summarized-Experiment.rds

extract_protocol:
50,000 cultured cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the resulting nuclei were then transposed and processed for bulk ATAC-seq (Corces et al. Nature Methods 2017).
Omni-ATAC-seq (Corces et al. Nature Methods 2017,  doi:10.1038/nmeth.4396)


title: 7003AA_MSCB-021


title: 7003AA_MSCB-020


title: bATAC-TKO_LR1_sgSik_2_vehicle_Rep1


title: 7003AA_MSCB-019


title: 7003AA_MSCB-022


title: 7003AA_MSCB-030


title: 7003AA_MSCB-018


title: bATAC-TKO_LR1_sgSik_2_4OHT_Rep2


title: bATAC-TKO_LR1_sgSik_2_4OHT_Rep1


title: 7003AA_MSCB-026


title: 7003AA_MSCB-016


title: bATAC-TKO_LR1_sgSik_1_vehicle_Rep2


title: 7003AA_MSCB-015


title: 7003AA_MSCB-014


title: 7003AA_MSCB-013


title: 7003AA_MSCB-012


title: bATAC-TKO_LR1_sgSik_1_4OHT_Rep2


title: bATAC-TKO_LR1_sgSik_1_vehicle_Rep1


title: bATAC-TKO_LR1_sgSafe_2_vehicle_Rep2


title: 7003AA_MSCB-011


title: bATAC-TKO_LR1_sgSafe_2_vehicle_Rep1


title: 7003AA_MSCB-010


title: bATAC-TKO_LR1_sgSafe_2_4OHT_Rep1


title: bATAC-TKO_LR1_sgSafe_2_4OHT_Rep2


title: 7003AA_MSCB-009


title: 7003AA_MSCB-008


title: 7003AA_MSCB-007


title: bATAC-TKO_LR1_sgSafe_1_vehicle_Rep1


title: 7003AA_MSCB-005


title: 7003AA_MSCB-006


title: bATAC-TKO_LR1_sgSafe_1_4OHT_Rep2


title: bATAC-TKO_LR1_sgSafe_1_4OHT_Rep1


title: 7003AA_MSCB-003


title: 7003AA_MSCB-004


title: bATAC-TKO_LR1_sgNuak_2_vehicle_Rep2


title: 7003AA_MSCB-017


title: bATAC-TKO_LR1_sgNuak_2_vehicle_Rep1


title: bATAC-TKO_LR1_sgSik_1_4OHT_Rep1


title: bATAC-TKO_LR1_sgNuak_2_4OHT_Rep1


title: 7003AA_MSCB-001


title: 7003AA_MSCB-002


title: bATAC-TKO_LR1_sgNuak_2_4OHT_Rep2


title: 7002AA_MSCB-191


title: 7002AA_MSCB-192


title: bATAC-TKO_LR1_sgNuak_1_vehicle_Rep2


title: bATAC-TKO_LR1_sgNuak_1_vehicle_Rep1


title: bATAC-TKO_LR1_sgNuak_1_4OHT_Rep2


title: 7002AA_MSCB-190


title: bATAC-TKO_LR1_sgNuak_1_4OHT_Rep1


title: bATAC-TKO_LR1_sgSafe_1_vehicle_Rep2


title: 7002AA_MSCB-189


title: bATAC-TKO_LR1_sgMark_2_vehicle_Rep2


title: bATAC-TKO_LR1_sgMark_2_vehicle_Rep1


title: bATAC-TKO_LR1_sgMark_2_4OHT_Rep2


title: 7002AA_MSCB-185


title: 7002AA_MSCB-184


title: 7002AA_MSCB-187


title: 7002AA_MSCB-188


title: bATAC-TKO_LR1_sgMark_1_4OHT_Rep2


title: bATAC-TKO_LR1_sgMark_1_vehicle_Rep2


title: 7002AA_MSCB-182


title: bATAC-TKO_LR1_sgMark_1_vehicle_Rep1


title: 7002AA_MSCB-186


title: 7002AA_MSCB-183


title: 7002AA_MSCB-179


title: bATAC-TKO_LR1_sgMark_1_4OHT_Rep1


title: 7002AA_MSCB-181


title: 7002AA_MSCB-174


title: bATAC-TKO_LR1_sgLkb1_1_vehicle_Rep1


title: 7002AA_MSCB-175


title: bATAC-TKO_LR1_sgLkb1_2_vehicle_Rep2


title: bATAC-TKO_LR1_sgLkb1_2_vehicle_Rep1


title: bATAC-TKO_LR1_sgLkb1_2_4OHT_Rep2


title: bATAC-TKO_LR1_sgMark_2_4OHT_Rep1


title: 7002AA_MSCB-173


title: 7002AA_MSCB-176


title: 7002AA_MSCB-180


title: bATAC-TKO_LR1_sgLkb1_1_vehicle_Rep2


title: bATAC-TKO_LR1_sgLkb1_2_4OHT_Rep1


title: bATAC-TKO_LR1_sgLkb1_1_4OHT_Rep2


title: 7002AA_MSCB-178


title: 7002AA_MSCB-177


title: bATAC-TKO_LR1_sgLkb1_1_4OHT_Rep1


title: bATAC-TKO_LR1_sgAmpk_2_vehicle_Rep2


title: 7002AA_MSCB-172


title: 7002AA_MSCB-171


title: 7002AA_MSCB-170


title: bATAC-TKO_LR1_sgAmpk_2_4OHT_Rep1


title: bATAC-TKO_LR1_sgAmpk_2_vehicle_Rep1


title: 7002AA_MSCB-167


title: 7002AA_MSCB-166


title: 7002AA_MSCB-169


title: 7002AA_MSCB-168


title: bATAC-TKO_LR1_sgAmpk_2_4OHT_Rep2


title: 7002AA_MSCB-165


title: bATAC-TKO_LR1_sgAmpk_1_4OHT_Rep1


title: bATAC-TKO_LR1_sgAmpk_1_vehicle_Rep1


title: bATAC-TKO_LR1_sgAmpk_1_vehicle_Rep2


title: bATAC-TC_LR2_4OHT_6h_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-TC-Peak-Summarized-Experiment.rds
bATAC-Matrices-TC-chromVAR-Summarized-Experiment.rds

value: 6 hours


title: bATAC-TKO_LR1_sgAmpk_1_4OHT_Rep2


title: 7002AA_MSCB-164


title: 7002AA_MSCB-163


title: bATAC-TC_LR2_4OHT_6h_Rep1


title: bATAC-TC_LR2_4OHT_6d_Rep2


title: bATAC-TC_LR2_4OHT_6d_Rep1


title: 7002AA_MSCB-161


title: bATAC-TC_LR2_4OHT_4d_Rep2

value: 4 days


title: 7002AA_MSCB-162


title: 7002AA_MSCB-160


title: bATAC-TC_LR2_4OHT_4d_Rep1


title: bATAC-TC_LR2_4OHT_48h_Rep1

value: 48 hours


title: 7002AA_MSCB-156


title: 7002AA_MSCB-158


title: 7002AA_MSCB-159


title: 7002AA_MSCB-157


title: bATAC-TC_LR2_4OHT_36h_Rep2

value: 36 hours


title: bATAC-TC_LR2_4OHT_48h_Rep2


title: bATAC-TC_LR2_4OHT_36h_Rep1


title: 7002AA_MSCB-155


title: bATAC-TC_LR2_4OHT_24h_Rep2

value: 24 hours


title: 7002AA_MSCB-154


title: 7002AA_MSCB-153


title: bATAC-TC_LR2_4OHT_24h_Rep1


title: bATAC-TC_LR2_4OHT_12_Rep2

value: 12 hours


title: 7002AA_MSCB-152

value: primary bladder epithelial cell


title: bATAC-TC_LR2_4OHT_12_Rep1


title: 7002AA_MSCB-149


title: 7002AA_MSCB-150


title: 7002AA_MSCB-151


title: 7002AA_MSCB-148


title: bATAC-TC_LR2_4OHT_0h_Rep1

value: 0 hours


title: bATAC-TC_LR2_4OHT_0h_Rep2


title: bATAC-TC_LR1_4OHT_6h_Rep1


title: bATAC-TC_LR1_4OHT_6d_Rep1


title: 7002AA_MSCB-145


title: 7002AA_MSCB-146


title: 7002AA_MSCB-147


title: bATAC-TC_LR1_4OHT_6h_Rep2


title: bATAC-TC_LR1_4OHT_6d_Rep2


title: 7002AA_MSCB-144


title: 7002AA_MSCB-143


title: bATAC-TC_LR1_4OHT_48h_Rep2


title: bATAC-TC_LR1_4OHT_4d_Rep1


title: 7002AA_MSCB-142


title: 7002AA_MSCB-141


title: bATAC-TC_LR1_4OHT_4d_Rep2


title: 7002AA_MSCB-140


title: bATAC-TC_LR1_4OHT_36h_Rep2


title: bATAC-TC_LR1_4OHT_48h_Rep1


title: 7002AA_MSCB-138


title: 7002AA_MSCB-137


title: bATAC-TC_LR1_4OHT_12_Rep2


title: bATAC-TC_LR1_4OHT_12_Rep1


title: 7002AA_MSCB-135


title: 7002AA_MSCB-136


title: 7002AA_MSCB-134


title: bATAC-TC_LR1_4OHT_0h_Rep2


title: bATAC-TC_LR1_4OHT_0h_Rep1


title: 7002AA_MSCB-130


title: 7002AA_MSCB-132


title: 7002AA_MSCB-133


title: bATAC-SOX_LR2_Sox17_vehicle_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-SOX_LR2-Peak-Summarized-Experiment.rds
bATAC-Matrices-SOX_LR2-chromVAR-Summarized-Experiment.rds


title: 7002AA_MSCB-129


title: bATAC-SOX_LR2_sgSox17_2_vehicle_Rep2


title: bATAC-SOX_LR2_Sox17_4OHT_Rep2


title: 7002AA_MSCB-128


title: bATAC-TC_LR1_4OHT_36h_Rep1


title: 7002AA_MSCB-139


title: bATAC-SOX_LR2_sgSox17_2_vehicle_Rep1


title: bATAC-SOX_LR2_sgSox17_2_4OHT_Rep2


title: bATAC-TC_LR1_4OHT_24h_Rep2


title: bATAC-TC_LR1_4OHT_24h_Rep1


title: bATAC-SOX_LR2_sgSox17_2_4OHT_Rep1


title: 7002AA_MSCB-127


title: bATAC-SOX_LR2_sgSox17_1_vehicle_Rep2


title: 7002AA_MSCB-125


title: 7002AA_MSCB-124


title: 7002AA_MSCB-122


title: 7002AA_MSCB-123


title: 7002AA_MSCB-121


title: 7002AA_MSCB-131


title: bATAC-SOX_LR2_sgSox17_1_vehicle_Rep1


title: bATAC-SOX_LR2_sgSox17_1_4OHT_Rep2


title: bATAC-SOX_LR2_Sox17_4OHT_Rep1


title: bATAC-SOX_LR2_sgSox17_1_4OHT_Rep1


title: 7002AA_MSCB-120


title: bATAC-SOX_LR2_sgSafe_1_vehicle_Rep2


title: bATAC-SOX_LR2_sgSafe_1_vehicle_Rep1


title: bATAC-SOX_LR2_sgSafe_1_4OHT_Rep2


title: 7002AA_MSCB-119


title: 7002AA_MSCB-116


title: bATAC-SOX_LR2_Sox17_vehicle_Rep1


title: 7002AA_MSCB-126


title: 7002AA_MSCB-117


title: 7002AA_MSCB-115


title: 7002AA_MSCB-114


title: bATAC-SOX_LR2_GFP_vehicle_Rep1


title: bATAC-SOX_LR1_sgSox17_2_Sox17_vehicle_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-SOX_LR1-Peak-Summarized-Experiment.rds
bATAC-Matrices-SOX_LR1-chromVAR-Summarized-Experiment.rds


title: 7002AA_MSCB-113


title: bATAC-SOX_LR1_sgSox17_2_Sox17_vehicle_Rep1


title: bATAC-SOX_LR2_GFP_4OHT_Rep1


title: 7002AA_MSCB-118


title: 7002AA_MSCB-112


title: bATAC-SOX_LR2_GFP_4OHT_Rep2


title: 7002AA_MSCB-110


title: bATAC-SOX_LR1_sgSox17_2_Sox17_4OHT_Rep2


title: bATAC-SOX_LR2_sgSafe_1_4OHT_Rep1


title: 7002AA_MSCB-109


title: 7002AA_MSCB-108


title: 7002AA_MSCB-107


title: bATAC-SOX_LR1_sgSox17_2_BFP_vehicle_Rep2


title: bATAC-SOX_LR1_sgSox17_2_BFP_4OHT_Rep2


title: bATAC-SOX_LR1_sgSox17_2_BFP_vehicle_Rep1


title: 7002AA_MSCB-106


title: 7002AA_MSCB-105


title: bATAC-SOX_LR2_GFP_vehicle_Rep2


title: bATAC-SOX_LR1_sgSox17_2_BFP_4OHT_Rep1


title: bATAC-SOX_LR1_sgSafe_1_BFP_vehicle_Rep2


title: 7002AA_MSCB-104


title: 7002AA_MSCB-103


title: bATAC-SOX_LR1_sgSafe_1_BFP_vehicle_Rep1


title: bATAC-SOX_LR1_sgSafe_1_BFP_4OHT_Rep2


title: bATAC-SOX_LR1_sgSafe_1_BFP_4OHT_Rep1


title: bATAC-SIK_LR1_sgSik3_2_vehicle_Rep1

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-SIK_Set1-Peak-Summarized-Experiment.rds
bATAC-Matrices-SIK_Set1-chromVAR-Summarized-Experiment.rds
bATAC-Matrices-SIK_Set2-Peak-Summarized-Experiment.rds
bATAC-Matrices-SIK_Set2-chromVAR-Summarized-Experiment.rds


title: 7002AA_MSCB-111


title: bATAC-SOX_LR1_sgSox17_2_Sox17_4OHT_Rep1


title: bATAC-SIK_LR1_sgSik3_2_4OHT_Rep1


title: 7002AA_MSCB-099


title: 7002AA_MSCB-098


title: 7002AA_MSCB-100


title: 7002AA_MSCB-096


title: bATAC-SIK_LR1_sgSik3_1_vehicle_Rep1


title: 7002AA_MSCB-097


title: 7002AA_MSCB-101


title: bATAC-SIK_LR1_sgSik3_1_4OHT_Rep2


title: bATAC-SIK_LR1_sgSik3_1_vehicle_Rep2


title: 7002AA_MSCB-093


title: bATAC-SIK_LR1_sgSik3_1_4OHT_Rep1


title: bATAC-SIK_LR1_sgSik2_2_vehicle_Rep2


title: 7002AA_MSCB-102


title: bATAC-SIK_LR1_sgSik2_2_vehicle_Rep1


title: 7002AA_MSCB-090


title: bATAC-SIK_LR1_sgSik2_2_4OHT_Rep2


title: bATAC-SIK_LR1_sgSik3_2_vehicle_Rep2


title: 7002AA_MSCB-089


title: 7002AA_MSCB-088


title: bATAC-SIK_LR1_sgSik3_2_4OHT_Rep2


title: bATAC-SIK_LR1_sgSik2_2_4OHT_Rep1


title: bATAC-SIK_LR1_sgSik2_1_vehicle_Rep2


title: 7002AA_MSCB-087


title: bATAC-SIK_LR1_sgSik2_1_vehicle_Rep1


title: 7002AA_MSCB-086


title: bATAC-SIK_LR1_sgSik2_1_4OHT_Rep2


title: 7002AA_MSCB-095


title: 7002AA_MSCB-085


title: 7002AA_MSCB-084


title: 7002AA_MSCB-094


title: 7002AA_MSCB-092


title: 7002AA_MSCB-091


title: 7002AA_MSCB-081


title: bATAC-SIK_LR1_sgSik1_2_vehicle_Rep1


title: bATAC-SIK_LR1_sgSik2_1_4OHT_Rep1


title: bATAC-SIK_LR1_sgSik1_2_4OHT_Rep2


title: bATAC-SIK_LR1_sgSik1_2_4OHT_Rep1


title: 7002AA_MSCB-082


title: bATAC-SIK_LR1_sgSik1_1_vehicle_Rep1


title: 7002AA_MSCB-079


title: 7002AA_MSCB-078


title: bATAC-SIK_LR1_sgSik1_1_4OHT_Rep2


title: 7002AA_MSCB-077


title: bATAC-SIK_LR1_sgSik1_1_4OHT_Rep1


title: 7002AA_MSCB-076


title: bATAC-SIK_LR1_sgSik_2_vehicle_Rep2


title: 7002AA_MSCB-075


title: bATAC-SIK_LR1_sgSik_2_vehicle_Rep1


title: 7002AA_MSCB-074


title: 7002AA_MSCB-083


title: bATAC-SIK_LR1_sgSik_2_4OHT_Rep1


title: bATAC-SIK_LR1_sgSik1_2_vehicle_Rep2


title: bATAC-SIK_LR1_sgSik_1_vehicle_Rep2


title: 7002AA_MSCB-072


title: 7002AA_MSCB-071


title: 7002AA_MSCB-080


title: bATAC-SIK_LR1_sgSik1_1_vehicle_Rep2


title: 7002AA_MSCB-073


title: 7002AA_MSCB-069


title: 7002AA_MSCB-066


title: 7002AA_MSCB-070


title: 7002AA_MSCB-068


title: bATAC-SIK_LR1_sgSik_1_4OHT_Rep2


title: bATAC-SIK_LR1_sgSafe_2_4OHT_Rep2


title: 7002AA_MSCB-067


title: bATAC-SIK_LR1_sgSik_1_4OHT_Rep1


title: bATAC-SIK_LR1_sgSafe_2_vehicle_Rep1


title: bATAC-SIK_LR1_sgSafe_2_vehicle_Rep2


title: 7002AA_MSCB-065


title: bATAC-SIK_LR1_sgSafe_1_vehicle_Rep1


title: 7002AA_MSCB-062


title: bATAC-SIK_LR1_sgSafe_2_4OHT_Rep1


title: bATAC-SIK_LR1_sgSik_1_vehicle_Rep1


title: bATAC-SIK_LR1_sgSafe_1_vehicle_Rep2


title: 7002AA_MSCB-064


title: 7002AA_MSCB-063


title: 7002AA_MSCB-061


title: bATAC-SIK_LR1_sgSafe_1_4OHT_Rep2


title: bATAC-SIK_LR1_sgLkb1_2_vehicle_Rep1


title: bATAC-SIK_LR1_sgLkb1_2_vehicle_Rep2


title: 7002AA_MSCB-060


title: bATAC-SIK_LR1_sgSik_2_4OHT_Rep2


title: 7002AA_MSCB-058


title: bATAC-SIK_LR1_sgLkb1_2_4OHT_Rep2


title: bATAC-SIK_LR1_sgLkb1_2_4OHT_Rep1


title: 7002AA_MSCB-057


title: bATAC-SIK_LR1_sgLkb1_1_vehicle_Rep2


title: bATAC-SIK_LR1_sgLkb1_1_4OHT_Rep1


title: bATAC-Mouse_KPL_Primary_5B_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-Mouse-Peak-Summarized-Experiment.rds
bATAC-Matrices-Mouse-chromVAR-Summarized-Experiment.rds

extract_protocol:
Up to 50,000 FACS-isolated lung adenocarcinoma cells were viably cryopreserved in BAMBANKER freezing media (Wako Chemicals 302-14681) so that bulk ATAC-seq could be performed on all cells at the same time. Cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the resulting nuclei were then transposed and processed for bulk ATAC-seq (Corces et al. Nature Methods 2017).
Omni-ATAC-seq (Corces et al. Nature Methods 2017,  doi:10.1038/nmeth.4396)

value: Mouse lung adenocarcinoma primary tumors and metastases


title: bATAC-SIK_LR1_sgLkb1_1_vehicle_Rep1

value: lung cancer


title: 7002AA_MSCB-052


title: 7002AA_MSCB-055


title: 7002AA_MSCB-054


title: bATAC-SIK_LR1_sgLkb1_1_4OHT_Rep2


title: 7002AA_MSCB-053


title: 7002AA_MSCB-056


title: bATAC-Mouse_KPL_Primary_5B_Rep1


title: bATAC-SIK_LR1_sgSafe_1_4OHT_Rep1


title: bATAC-Mouse_KPL_Primary_5A_Rep2


title: 7002AA_MSCB-051


title: 7002AA_MSCB-050


title: 7002AA_MSCB-049


title: 7002AA_MSCB-059


title: bATAC-Mouse_KPL_Primary_5A_Rep1


title: bATAC-Mouse_KPL_Primary_4C_Rep2


title: 7002AA_MSCB-048


title: bATAC-Mouse_KPL_Primary_4B_Rep1


title: bATAC-Mouse_KPL_Primary_4C_Rep1


title: 7002AA_MSCB-046


title: bATAC-Mouse_KPL_Primary_4B_Rep2


title: 7002AA_MSCB-044


title: bATAC-Mouse_KPL_Primary_4A_Rep2


title: 7002AA_MSCB-045


title: bATAC-Mouse_KPL_Primary_4A_Rep1


title: 7002AA_MSCB-043


title: bATAC-Mouse_KPL_Primary_13C_Rep2


title: 7002AA_MSCB-040


title: bATAC-Mouse_KPL_Primary_13D_Rep2


title: 7002AA_MSCB-041


title: 7002AA_MSCB-039


title: 7002AA_MSCB-038


title: bATAC-Mouse_KPL_Primary_13C_Rep1


title: bATAC-Mouse_KPL_Primary_13B_Rep2


title: bATAC-Mouse_KPL_Primary_13B_Rep1


title: 7002AA_MSCB-037


title: bATAC-Mouse_KPL_Primary_13A_Rep2


title: 7002AA_MSCB-036


title: 7002AA_MSCB-035


title: bATAC-Mouse_KPL_Primary_13A_Rep1


title: 7002AA_MSCB-047


title: bATAC-Mouse_KPL_Primary_11B_Rep2


title: 7002AA_MSCB-033


title: bATAC-Mouse_KPL_Primary_11B_Rep1


title: 7002AA_MSCB-034


title: 7002AA_MSCB-032


title: 7002AA_MSCB-031


title: bATAC-Mouse_KPL_Primary_11A_Rep2


title: 7002AA_MSCB-030


title: bATAC-Mouse_KPL_Primary_10E_Rep2


title: 7002AA_MSCB-042


title: bATAC-Mouse_KPL_Primary_13D_Rep1


title: bATAC-Mouse_KPL_Primary_10E_Rep1


title: bATAC-Mouse_KPL_Metastasis_5C_Rep2


title: bATAC-Mouse_KPL_Primary_10B_Rep1


title: 7002AA_MSCB-029


title: bATAC-Mouse_KPL_Primary_10B_Rep2


title: bATAC-Mouse_KPL_Metastasis_5C_Rep1


title: 7002AA_MSCB-026


title: 7002AA_MSCB-027


title: bATAC-Mouse_KPL_Metastasis_13G_Rep2


title: 7002AA_MSCB-025


title: 7002AA_MSCB-028


title: 7002AA_MSCB-024


title: bATAC-Mouse_KPL_Metastasis_13G_Rep1


title: 7002AA_MSCB-022


title: 7002AA_MSCB-023


title: bATAC-Mouse_KPL_Metastasis_13F_Rep2


title: bATAC-Mouse_KPL_Primary_11A_Rep1


title: 7002AA_MSCB-021


title: 7002AA_MSCB-020


title: 7002AA_MSCB-019


title: bATAC-Mouse_KPL_Metastasis_10F_Rep2


title: bATAC-Mouse_KPL_Metastasis_10F_Rep1


title: bATAC-Mouse_KPL_Metastasis_10A_Rep2


title: 7002AA_MSCB-018


title: 7002AA_MSCB-017


title: 7002AA_MSCB-016


title: bATAC-Mouse_KP_Primary_7C_Rep2


title: bATAC-Mouse_KPL_Metastasis_10A_Rep1


title: bATAC-Mouse_KP_Primary_7C_Rep1


title: 7002AA_MSCB-015


title: bATAC-Mouse_KP_Primary_7B_Rep2


title: bATAC-Mouse_KP_Primary_7B_Rep1


title: bATAC-Mouse_KP_Primary_7A_Rep2


title: 7002AA_MSCB-012


title: 7002AA_MSCB-013


title: 7002AA_MSCB-014


title: bATAC-Mouse_KP_Primary_7A_Rep1


title: 7002AA_MSCB-011


title: bATAC-Mouse_KPL_Metastasis_13F_Rep1


title: bATAC-Mouse_KP_Primary_22A_Rep1


title: 7002AA_MSCB-009


title: bATAC-Mouse_KP_Primary_22A_Rep2


title: bATAC-Mouse_KP_Primary_1A_Rep1


title: bATAC-Mouse_KP_Primary_1A_Rep2


title: 7002AA_MSCB-006


title: bATAC-Mouse_KP_Primary_17C_Rep2


title: 7002AA_MSCB-010


title: bATAC-Mouse_KP_Primary_18A_Rep1


title: 7002AA_MSCB-008


title: 7002AA_MSCB-005


title: 7002AA_MSCB-004


title: bATAC-Mouse_KP_Primary_18A_Rep2


title: 7002AA_MSCB-007


title: 7002AA_MSCB-003


title: 7002AA_MSCB-002


title: 7002AA_MSCB-001


title: bATAC-Mouse_KP_Primary_16B_Rep2


title: bATAC-Mouse_KP_Primary_17C_Rep1


title: bATAC-Mouse_KP_Primary_16B_Rep1


title: 7001AA_MSCB-192


title: bATAC-Mouse_KP_Primary_16A_Rep1


title: 7001AA_MSCB-190


title: 7001AA_MSCB-191


title: bATAC-Mouse_KP_Primary_16A_Rep2


title: 7001AA_MSCB-189


title: bATAC-Mouse_KP_Primary_14B_Rep2


title: bATAC-Mouse_KP_Primary_15C_Rep1


title: bATAC-Mouse_KP_Primary_15C_Rep2


title: 7001AA_MSCB-187


title: 7001AA_MSCB-185


title: 7001AA_MSCB-188


title: bATAC-Mouse_KP_Primary_14A_Rep2


title: bATAC-Mouse_KP_Primary_14B_Rep1


title: 7001AA_MSCB-186


title: bATAC-Mouse_KP_Primary_14A_Rep1


title: bATAC-Mouse_KP_Metastasis_21C_Rep2


title: 7001AA_MSCB-183


title: 7001AA_MSCB-184


title: bATAC-Mouse_KP_Metastasis_21C_Rep1


title: bATAC-Mouse_KP_Metastasis_17F_Rep2


title: bATAC-Mouse_KP_Metastasis_17F_Rep1


title: 7001AA_MSCB-181


title: 7001AA_MSCB-182


title: 7001AA_MSCB-180


title: bATAC-Mouse_KP_Metastasis_17E_Rep1


title: bATAC-Mouse_KP_Metastasis_17E_Rep2


title: 7001AA_MSCB-178


title: 7001AA_MSCB-179


title: bATAC-Mouse_KP_Metastasis_15D_Rep2


title: bATAC-Initial_LU2_4OHT_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-Initial-Peak-Summarized-Experiment.rds
bATAC-Matrices-Initial-chromVAR-Summarized-Experiment.rds


title: bATAC-Mouse_KP_Metastasis_15D_Rep1


title: 7001AA_MSCB-175


title: 7001AA_MSCB-177


title: 7001AA_MSCB-176


title: bATAC-Initial_LU2_vehicle_Rep2

value: vehicle


title: bATAC-Initial_LU2_vehicle_Rep1


title: 7001AA_MSCB-174


title: bATAC-Initial_LU1_4OHT_Rep1


title: bATAC-Initial_LU1_4OHT_Rep2


title: 7001AA_MSCB-172


title: bATAC-Initial_LU2_4OHT_Rep1


title: 7001AA_MSCB-167


title: bATAC-Initial_LR2_vehicle_Rep1


title: bATAC-Initial_LR2_4OHT_Rep1


title: 7001AA_MSCB-169


title: 7001AA_MSCB-170


title: 7001AA_MSCB-173


title: bATAC-Initial_LU1_vehicle_Rep1


title: bATAC-Initial_LR1_vehicle_Rep2


title: bATAC-Initial_LR2_vehicle_Rep2


title: 7001AA_MSCB-168


title: 7001AA_MSCB-165


title: bATAC-Initial_LR2_4OHT_Rep2


title: 7001AA_MSCB-164


title: bATAC-Initial_LU1_vehicle_Rep2


title: bATAC-Initial_LR1_vehicle_Rep1


title: 7001AA_MSCB-163


title: 7001AA_MSCB-166


title: 7001AA_MSCB-161


title: 7001AA_MSCB-162


title: 7001AA_MSCB-160


title: 7001AA_MSCB-171


title: bATAC-CMTC_LR1_sgTrim28_4OHT_48h_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-CMTC-Peak-Summarized-Experiment.rds
bATAC-Matrices-CMTC-chromVAR-Summarized-Experiment.rds


title: 7001AA_MSCB-158


title: 7001AA_MSCB-157


title: bATAC-CMTC_LR1_sgTrim28_4OHT_48h_Rep1


title: 7001AA_MSCB-156


title: bATAC-CMTC_LR1_sgTrim28_4OHT_12h_Rep2


title: bATAC-CMTC_LR1_sgTrim28_4OHT_24h_Rep2


title: bATAC-CMTC_LR1_sgTrim28_4OHT_24h_Rep1


title: 7001AA_MSCB-154


title: bATAC-CMTC_LR1_sgTrim28_4OHT_12h_Rep1


title: 7001AA_MSCB-153


title: bATAC-Initial_LR1_4OHT_Rep2


title: bATAC-Initial_LR1_4OHT_Rep1


title: 7001AA_MSCB-152


title: 7001AA_MSCB-151


title: bATAC-CMTC_LR1_sgSuz12_4OHT_48h_Rep1


title: 7001AA_MSCB-159


title: bATAC-CMTC_LR1_sgSuz12_4OHT_24h_Rep2


title: 7001AA_MSCB-150


title: bATAC-CMTC_LR1_sgTrim28_4OHT_0h_Rep1


title: 7001AA_MSCB-148


title: 7001AA_MSCB-149


title: bATAC-CMTC_LR1_sgSuz12_4OHT_12h_Rep1


title: bATAC-CMTC_LR1_sgSuz12_4OHT_12h_Rep2


title: bATAC-CMTC_LR1_sgSuz12_4OHT_24h_Rep1


title: bATAC-CMTC_LR1_sgSuz12_4OHT_0h_Rep2


title: 7001AA_MSCB-147


title: bATAC-CMTC_LR1_sgSuz12_4OHT_0h_Rep1


title: 7001AA_MSCB-145


title: 7001AA_MSCB-155


title: 7001AA_MSCB-144


title: 7001AA_MSCB-143


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_48h_Rep1


title: bATAC-CMTC_LR1_sgTrim28_4OHT_0h_Rep2


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_48h_Rep2


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_24h_Rep2


title: bATAC-CMTC_LR1_sgSuz12_4OHT_48h_Rep2


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_12h_Rep2


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_24h_Rep1


title: 7001AA_MSCB-140


title: 7001AA_MSCB-141


title: 7001AA_MSCB-142


title: 7001AA_MSCB-139


title: 7001AA_MSCB-137


title: 7001AA_MSCB-138


title: bATAC-CMTC_LR1_sgSafe_4OHT_48h_Rep2


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_0h_Rep1


title: 7001AA_MSCB-136


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_12h_Rep1


title: 7001AA_MSCB-135


title: bATAC-CMTC_LR1_sgSafe_4OHT_48h_Rep1


title: bATAC-CMTC_LR1_sgSuv39h1_4OHT_0h_Rep2


title: 7001AA_MSCB-134


title: 7001AA_MSCB-146


title: bATAC-CMTC_LR1_sgSafe_4OHT_24h_Rep2


title: bATAC-CMTC_LR1_sgSafe_4OHT_24h_Rep1


title: 7001AA_MSCB-132


title: 7001AA_MSCB-131


title: 7001AA_MSCB-130


title: bATAC-CMTC_LR1_sgSafe_4OHT_12h_Rep1


title: 7001AA_MSCB-129


title: bATAC-CMTC_LR1_sgSafe_4OHT_0h_Rep1


title: 7001AA_MSCB-128


title: bATAC-CMTC_LR1_sgLkb1_4OHT_48h_Rep2


title: bATAC-CMTC_LR1_sgLkb1_4OHT_48h_Rep1


title: 7001AA_MSCB-126


title: bATAC-CMTC_LR1_sgLkb1_4OHT_24h_Rep1


title: bATAC-CMTC_LR1_sgLkb1_4OHT_24h_Rep2


title: 7001AA_MSCB-125


title: 7001AA_MSCB-124


title: 7001AA_MSCB-133


title: 7001AA_MSCB-123


title: 7001AA_MSCB-122


title: bATAC-CMTC_LR1_sgLkb1_4OHT_0h_Rep2


title: bATAC-CMTC_LR1_sgLkb1_4OHT_12h_Rep2


title: bATAC-CMTC_LR1_sgEed_4OHT_48h_Rep2


title: 7001AA_MSCB-119


title: bATAC-CMTC_LR1_sgSafe_4OHT_12h_Rep2


title: bATAC-CMTC_LR1_sgSafe_4OHT_0h_Rep2


title: bATAC-CMTC_LR1_sgEed_4OHT_24h_Rep2


title: 7001AA_MSCB-120


title: bATAC-CMTC_LR1_sgEed_4OHT_48h_Rep1


title: bATAC-CMTC_LR1_sgEed_4OHT_24h_Rep1


title: 7001AA_MSCB-117


title: bATAC-CMTC_LR1_sgEed_4OHT_12h_Rep2


title: bATAC-CMTC_LR1_sgEed_4OHT_12h_Rep1


title: 7001AA_MSCB-127


title: 7001AA_MSCB-115


title: bATAC-CMTC_LR1_sgEed_4OHT_0h_Rep2


title: 7001AA_MSCB-114


title: bATAC-CMTC_LR1_sgLkb1_4OHT_0h_Rep1


title: 7001AA_MSCB-121


title: bATAC-CMTC_LR1_sgLkb1_4OHT_12h_Rep1


title: 7001AA_MSCB-112


title: 7001AA_MSCB-113


title: bATAC-CM_LR1_sgTrim28_vehicle_Rep2

description:
Bulk ATAC-seq
processed data file:
bATAC-Matrices-CM-Peak-Summarized-Experiment.rds
bATAC-Matrices-CM-chromVAR-Summarized-Experiment.rds


title: 7001AA_MSCB-109


title: 7001AA_MSCB-111


title: bATAC-CM_LR1_sgSuz12_vehicle_Rep2


title: 7001AA_MSCB-118


title: bATAC-CM_LR1_sgSuz12_vehicle_Rep1


title: 7001AA_MSCB-107


title: 7001AA_MSCB-106


title: bATAC-CM_LR1_sgTrim28_vehicle_Rep1


title: bATAC-CM_LR1_sgSuz12_4OHT_Rep2


title: 7001AA_MSCB-116


title: 7001AA_MSCB-110


title: 7001AA_MSCB-105


title: bATAC-CM_LR1_sgSuz12_4OHT_Rep1


title: bATAC-CM_LR1_sgSuv39h1_vehicle_Rep2


title: 7001AA_MSCB-104


title: 7001AA_MSCB-103


title: 7001AA_MSCB-102


title: bATAC-CMTC_LR1_sgEed_4OHT_0h_Rep1


title: bATAC-CM_LR1_sgSuv39h1_vehicle_Rep1


title: bATAC-CM_LR1_sgSuv39h1_4OHT_Rep2


title: 7001AA_MSCB-101


title: bATAC-CM_LR1_sgSuv39h1_4OHT_Rep1


title: bATAC-CM_LR1_sgTrim28_4OHT_Rep1


title: bATAC-CM_LR1_sgTrim28_4OHT_Rep2


title: 7001AA_MSCB-108


title: 7001AA_MSCB-100


title: bATAC-CM_LR1_sgSmchd1_vehicle_Rep1


title: bATAC-CM_LR1_sgSmchd1_vehicle_Rep2


title: bATAC-CM_LR1_sgSmchd1_4OHT_Rep1


title: bATAC-CM_LR1_sgSmchd1_4OHT_Rep2


title: 7001AA_MSCB-099


title: 7001AA_MSCB-098


title: 7001AA_MSCB-097


title: 7001AA_MSCB-096


title: bATAC-CM_LR1_sgSmarce1_vehicle_Rep1


title: 7001AA_MSCB-095


title: bATAC-CM_LR1_sgSmarce1_vehicle_Rep2


title: 7001AA_MSCB-094


title: bATAC-CM_LR1_sgSmarce1_4OHT_Rep2


title: 7001AA_MSCB-091


title: bATAC-CM_LR1_sgSmarce1_4OHT_Rep1


title: 7001AA_MSCB-092


title: bATAC-CM_LR1_sgSafe_4OHT_Rep2


title: bATAC-CM_LR1_sgSafe_4OHT_Rep1


title: 7001AA_MSCB-090


title: bATAC-CM_LR1_sgLkb1_vehicle_Rep1


title: bATAC-CM_LR1_sgLkb1_vehicle_Rep2


title: 7001AA_MSCB-089


title: 7001AA_MSCB-088


title: 7001AA_MSCB-085


title: bATAC-CM_LR1_sgLkb1_4OHT_Rep1


title: 7001AA_MSCB-087


title: bATAC-CM_LR1_sgLkb1_4OHT_Rep2


title: 7001AA_MSCB-084


title: 7001AA_MSCB-086


title: bATAC-CM_LR1_sgEed_vehicle_Rep1


title: bATAC-CM_LR1_sgEed_vehicle_Rep2


title: 7001AA_MSCB-093


title: 7001AA_MSCB-082


title: bATAC-CM_LR1_sgEed_4OHT_Rep1


title: bATAC-CM_LR1_sgDnmt3a_vehicle_Rep2


title: bATAC-CM_LR1_sgSafe_vehicle_Rep2


title: 7001AA_MSCB-080


title: 7001AA_MSCB-081


title: 7001AA_MSCB-078


title: bATAC-CM_LR1_sgDnmt3a_vehicle_Rep1


title: bATAC-CM_LR1_sgEed_4OHT_Rep2


title: 7001AA_MSCB-079


title: bATAC-CM_LR1_sgDnmt3a_4OHT_Rep1


title: bATAC-CM_LR1_sgDnmt3a_4OHT_Rep2


title: bATAC-CM_LR1_sgCited2_vehicle_Rep1


title: 7001AA_MSCB-076


title: bATAC-CM_LR1_sgCited2_vehicle_Rep2


title: 7001AA_MSCB-075


title: bATAC-CM_LR1_sgCited2_4OHT_Rep1


title: bATAC-CM_LR1_sgCited2_4OHT_Rep2


title: 7001AA_MSCB-074


title: 7001AA_MSCB-083


title: bATAC-CM_LR1_sgArid1a_vehicle_Rep2


title: 7001AA_MSCB-072


title: 7001AA_MSCB-073


title: bATAC-CM_LR1_sgArid1a_vehicle_Rep1


title: bATAC-CM_LR1_sgArid1a_4OHT_Rep2


title: bATAC-CM_LR1_sgArid1a_4OHT_Rep1


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Twice Tumour derived BL6 mouse, Immune evasive rep3 [BiSulfite-seq]

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

country: United Kingdom

institute: University of Edinburgh

description:
NPE_IE_3
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt

data_processing:
Reads were trimmed with TrimGalore (version 0.5.0). NuGen diversity adaptors were removed with a Python script supplied by NuGen “trimRRBSdiversityAdaptCustomers.py” (version 1.11 https://github.com/nugentechnologies/NuMetRRBS)
Reads were then aligned to the mm10 in silico bisulfite transformed genome with the bisulphite sequencing aligner Bismark (version 0.16.3 with Bowtie version 2.2.6 using parameters: -N 0 -L 20)
PCR duplicates were then removed using a Python script from NuGen “nudup.py” (version 2.3 https://github.com/tecangenomics/nudup)
Methylation estimation was completed using the Bismark methylation extractor.
Genome_build: mm10
Supplementary_files_format_and_content: Three sets of tab-delimited files for mouse NSCs, and engineered NSCs containing percentage methylated, total counts, methyalted counts, per CpG site.

source_name: Mouse Neural Stem Cell

growth_protocol: All cell lines were maintained in standard NSC media: serum-free basal medium supplemented with N2 and B27 (Life Technologies), laminin (Cultrex, 2 mg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml).

extract_protocol:
DNA was extracted from cells using the Qiagen DNeasy Blood and Tissue kit
Libraries were prepared from 200ng of each DNA sample using the Ovation RRBS Methyl-Seq System 1- 16 (Tecan Genomics Inc, #0353) according to the provided protocol

value: Mouse Neural Stem Cell

tag: type

value: Cell line

tag: genotype

value: Nf1-/- Pten-/- EGFRvIII


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Twice Tumour derived BL6 mouse, Immune evasive rep2 [BiSulfite-seq]

description:
NPE_IE_2
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-071


title: 7001AA_MSCB-077


title: 7001AA_MSCB-068


title: 7001AA_MSCB-070


title: 7001AA_MSCB-067


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep6 [BiSulfite-seq]

description:
NPE_BL6_TD_6
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-066


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Twice Tumour derived BL6 mouse, Immune evasive rep1 [BiSulfite-seq]

description:
NPE_IE_1
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-065


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep4 [BiSulfite-seq]

description:
NPE_BL6_TD_4
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep3 [BiSulfite-seq]

description:
NPE_BL6_TD_3
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-063


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep2 [BiSulfite-seq]

description:
NPE_BL6_TD_2
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-062


title: 7001AA_MSCB-064


title: 7001AA_MSCB-061


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep1 [BiSulfite-seq]

description:
NPE_BL6_TD_1
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from NSG mouse rep3 [BiSulfite-seq]

description:
NPE_NSG_TD_3
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from NSG mouse rep2 [BiSulfite-seq]

description:
NPE_NSG_TD_2
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-060


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from NSG mouse rep1 [BiSulfite-seq]

description:
NPE_NSG_TD_1
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-058


title: 7001AA_MSCB-069


title: 7001AA_MSCB-056


title: 7001AA_MSCB-057


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep6 [BiSulfite-seq]

description:
NPE_6
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep5 [BiSulfite-seq]

description:
NPE_5
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-054


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep4 [BiSulfite-seq]

description:
NPE_4
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep5 [BiSulfite-seq]

description:
NPE_BL6_TD_5
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep3 [BiSulfite-seq]

description:
NPE_3
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO rep3 [BiSulfite-seq]

description:
NP_3
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-055


title: 7001AA_MSCB-051


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep2 [BiSulfite-seq]

description:
NPE_2
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep1 [BiSulfite-seq]

description:
NPE_1
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-052


title: Nf1 KO, Pten KO rep2 [BiSulfite-seq]

description:
NP_2
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-053


title: Nf1 KO, Pten KO rep1 [BiSulfite-seq]

description:
NP_1
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-048


title: 7001AA_MSCB-050


title: WT rep6 [BiSulfite-seq]

description:
BL6_WT_6
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt

value: WT


title: WT rep4 [BiSulfite-seq]

description:
BL6_WT_4
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-047


title: 7001AA_MSCB-059


title: WT rep3 [BiSulfite-seq]

description:
BL6_WT_3
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: WT rep5 [BiSulfite-seq]

description:
BL6_WT_5
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-045


title: 7001AA_MSCB-044


title: 7001AA_MSCB-046


title: WT rep2 [BiSulfite-seq]

description:
BL6_WT_2
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: 7001AA_MSCB-043


title: WT rep1 [BiSulfite-seq]

description:
BL6_WT_1
RRBS_percent_methylation.txt
RRBS_T_methylation.txt
RRBS_M_methylation.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Twice Tumour derived from BL6 mouse, Immune evasive rep1 [RNA-seq]

description:
NPE_IE_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt

data_processing:
Paired end RNA sequencing reads were trimmed with Trimgalore (version 0.5.0) with default parameters and aligned to mm10 genome using Kallisto (version 0.44.0).
Read counts were summarised via the package Tximport (version 1.8.0) and subsequent normalisation was completed via DESeq2 (version 1.27.32) as regularised-logarithm transformation (rlog).
Genome_build: mm10
Supplementary_files_format_and_content: Three sets of tab-delimited files for mouse NSCs, and engineered NSCs containing raw counts, and normalised counts as calculated by DESeq2 (rlog and FPM).

extract_protocol:
RNA was isolated and gDNA eliminated using the RNeasy Mini Kit (Qiagen, 74104)
Libraries were prepared from 500ng of each total-RNA sample using the TruSeq Stranded mRNA Library Kit (20020594) according to the provided protocol.


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Twice Tumour derived from BL6 mouse, Immune evasive rep2 [RNA-seq]

description:
NPE_IE_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-041


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Twice Tumour derived from BL6 mouse, Immune evasive rep3 [RNA-seq]

description:
NPE_IE_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-040


title: 7001AA_MSCB-039


title: 7001AA_MSCB-049


title: 7001AA_MSCB-038


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep3 [RNA-seq]

description:
NPE_BL6_TD_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-037


title: 7001AA_MSCB-042


title: 7001AA_MSCB-036


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from NSG mouse rep3 [RNA-seq]

description:
NPE_NSG_TD_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep1 [RNA-seq]

description:
NPE_BL6_TD_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from NSG mouse rep2 [RNA-seq]

description:
NPE_NSG_TD_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-034


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from BL6 mouse rep2 [RNA-seq]

description:
NPE_BL6_TD_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-035


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Tumour derived from NSG mouse rep1 [RNA-seq]

description:
NPE_NSG_TD_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-033


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep2 [RNA-seq]

description:
NPE_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep3 [RNA-seq]

description:
NPE_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-032


title: Nf1 KO, Pten KO, EGFRvIII overexpression rep1 [RNA-seq]

description:
NPE_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: Nf1 KO, Pten KO rep3 [RNA-seq]

description:
NP_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-030


title: Nf1 KO, Pten KO rep2 [RNA-seq]

description:
NP_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-031


title: 7001AA_MSCB-029


title: 7001AA_MSCB-028


title: PDGFRa overexpression rep3 [RNA-seq]

description:
PDGFRA_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt

value: PDGFRa


title: PDGFRa overexpression rep2 [RNA-seq]

description:
PDGFRA_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-027


title: Nf1 KO, Pten KO rep1 [RNA-seq]

description:
NP_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-026


title: 7001AA_MSCB-025


title: EGFRvIII overexpression rep2 [RNA-seq]

description:
EGFRvIII_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt

value: EGFRvIII


title: PDGFRa overexpression rep1 [RNA-seq]

description:
PDGFRA_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: Nf1 KO rep3 [RNA-seq]

description:
NF1_KO_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-023


title: 7001AA_MSCB-024


title: 7001AA_MSCB-021


title: 7001AA_MSCB-020


title: Nf1 KO rep2 [RNA-seq]

description:
NF1_KO_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: EGFRvIII overexpression rep3 [RNA-seq]

description:
EGFRvIII_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: EGFRvIII overexpression rep1 [RNA-seq]

description:
EGFRvIII_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-019


title: 7001AA_MSCB-022


title: Nf1 KO rep1 [RNA-seq]

description:
NF1_KO_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: Pten KO rep3 [RNA-seq]

description:
PTEN_KO_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt

value: Pten-/-


title: Pten KO rep2 [RNA-seq]

description:
PTEN_KO_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-018


title: Pten KO rep1 [RNA-seq]

description:
PTEN_KO_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-017


title: 7001AA_MSCB-016


title: Trp53 KO rep3 [RNA-seq]

description:
P53_KO_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-015


title: 7001AA_MSCB-014


title: Trp53 KO rep2 [RNA-seq]

description:
P53_KO_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: WT rep3 [RNA-seq]

description:
BL6_WT_3
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-013


title: Trp53 KO rep1 [RNA-seq]

description:
P53_KO_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: WT rep1 [RNA-seq]

description:
BL6_WT_1
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: WT rep2 [RNA-seq]

description:
BL6_WT_2
RNAseq_normalised_counts.txt
RNAseq_Mouse_fpm.txt
RNAseq_Mouse_raw_counts.txt


title: 7001AA_MSCB-010


title: TFH_Tbetneg lymph node_3

city: New York

first: Michail

last: Schizas

address: 1275 York ave

institute: Memorial sloan Kettering

data_processing:
alignment
read quantification per gene
normalization of gene enrichment using DESeq
Supplementary_files_format_and_content: all_gene_exp.xlsx

source_name: TFH_Tbetneg lymph node

extract_protocol:
RNA was extracted from Trizol™ and prepared for sequencing by the Integrated Genomics Core at Memorial Sloan Kettering Cancer Center.
Libraries were constructed using SMARTer RNA-seq kits (Takara) according to the manufacturer's protocols

value: T-bet-TFH

value: Lymph node


title: 7001AA_MSCB-011


title: TFH_Tbetneg lymph node_2


title: 7001AA_MSCB-008


title: TFH_Tbetpos lymph node_3

source_name: TFH_Tbetpos lymph node

value: T-bet+TFH


title: 7001AA_MSCB-006


title: TFH_Tbetpos lymph node_2


title: 7001AA_MSCB-009


title: 7001AA_MSCB-007


title: 7001AA_MSCB-004


title: TFH_Tbetneg lymph node_1


title: TFH_Tbetpos lymph node_1


title: 7001AA_MSCB-003


title: TH1 lymph node_2

source_name: TH1 lymph node


title: 7001AA_MSCB-002


title: 7001AA_MSCB-001


title: TH1 lymph node_1


title: TH1 lymph node_3


title: Input

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Library strategy: 5hmC immunoprecipitation seq
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 using STAR with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
Peaks were called via MUSIC (https://github.com/gersteinlab/MUSIC) and unified peaks were used for recounting via bigWigAverageOverBed (UCSC Tools)
Annotation of peaks was done via UROPA (https://github.com/loosolab/UROPA) against Gencode V 16
Genome_build: mm10_GRCm38

source_name: Lung smooth muscle cells

extract_protocol:
1.5 µg genomic DNA was extracted from control and Tet3 inactivated SMCs by using the AllPrep® DAN/RNA Micro Kit (Qiagen). 1 µg of sheared DNA, 4 µg of 5hmC monoclonal antibody (EpiGentek Cat. #A-1018) were incubated with 8 µl of protein A/G beads. Captured DNA was eluted in 15 µl H2O and input DNA was used for end polishing, adaptor ligation, and library amplification using indexed primers.  Purified library DNA was eluted in 12 µl of water.
Intactness of the library was verified using a Bioanalyer and KAPA qPCR Library Quantification. 10 nM of sample libraries were subjected to next generation sequencing using an Illuminar HiSeq 4000. Reads were processed with a set of public available tools as described for RNAseq. Mapping was performed by STAR against the mouse genome (version mm10). Deduplication of reads was done by Picard (http://broadinstitute.github.io/picard/; Broad Institute). In order to find broader regions enriched for reads, the peak caller MUSIC was employed. Annotation of peaks was performed via UROPA using the GENCODE annotation (V.16). Recounting of different regions (unified peaks (all replicates), promoters, and genes) was calculated using bigWigAverageOverBed (UCSC Tools). To compare peaks and regions from different samples and conditions, read counts were submitted to DESeq2 for normalization.

value: Lung smooth muscle cells

tag: antibody


title: 7000AA_MSCB-190


title: 7000AA_MSCB-192


title: Tet3_Mut_2

value: 5hmC (Epigentek)


title: 7001AA_MSCB-005

value: primary bladder epithelial cell


title: WT_Rep2


title: 7000AA_MSCB-189


title: 7000AA_MSCB-188


title: 7000AA_MSCB-186


title: 7000AA_MSCB-187


title: WT_Rep1


title: 7000AA_MSCB-185


title: Tet3_Mut_1


title: Sort_CDH1pos_control_2

description: Sample 20

source_name: day 5.5 reprogramming MEFs

value: 3.5 days of doxycycline; FACS sort CDH1+; days 3.5-5.5 doxycycline and DMSO

value: homozygous Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (Col1a1 locus), heterozygous reverse tetracycline transactivator (Rosa26 locus)

value: E13.5 Mouse embryonic fibroblasts

tag: sample type

value: CDH1 sort


title: Sort_CDH1pos_dot1li_1

description: Sample 21

value: 3.5 days of doxycycline; FACS sort CDH1+; days 3.5-5.5 doxycycline and SGC0946


title: Sort_CDH1pos_dot1li_2

description: Sample 22


title: Sort_CDH1pos_control_1

description: Sample 19


title: 7000AA_MSCB-184


title: Sort_CDH1neg_dot1li_1

description: Sample 17

value: 3.5 days of doxycycline; FACS sort CDH1-; days 3.5-5.5 doxycycline and SGC0946


title: 7000AA_MSCB-191


title: 7000AA_MSCB-181


title: 7000AA_MSCB-179


title: 7000AA_MSCB-180


title: 7000AA_MSCB-178


title: 7000AA_MSCB-177


title: 7001AA_MSCB-012


title: Tc_d4mid_2

description: Sample 12

source_name: day 4 reprogramming MEFs

value: 4 days of doxycycline; days 0-2 DMSO, days 2-4 SGC0946

value: Timecourse


title: Tc_d4dot1li_2

description: Sample 14

value: 4 days of doxycycline and SGC0946


title: Tc_d4dot1li_1

description: Sample 13


title: Tc_d4mid_1

description: Sample 11


title: 7000AA_MSCB-176


title: 7000AA_MSCB-173


title: Sort_CDH1neg_dot1li_2

description: Sample 18


title: 7000AA_MSCB-175


title: 7000AA_MSCB-174


title: Sort_CDH1neg_control_2

description: Sample 16

value: 3.5 days of doxycycline; FACS sort CDH1-; days 3.5-5.5 doxycycline and DMSO


title: 7000AA_MSCB-171


title: 7000AA_MSCB-183


title: Tc_d4control_2

description: Sample 8

value: 4 days of doxycycline and DMSO


title: Tc_d4early_1

description: Sample 9

value: 4 days of doxycycline; days 0-2 SGC0946, days 2-4 DMSO


title: Tc_d2dot1li_2

description: Sample 6

source_name: day 2 reprogramming MEFs

value: 2 days of doxycycline and SGC0946


title: Tc_d4control_1

description: Sample 7


title: Tc_d2dot1li_1

description: Sample 5


title: Tc_d4early_2

description: Sample 10


title: Sort_CDH1neg_control_1

description: Sample 15


title: 7000AA_MSCB-170

source_name: bladder


title: 7000AA_MSCB-182


title: 7000AA_MSCB-169


title: 7000AA_MSCB-168


title: Tc_d2control_1

description: Sample 3

value: 2 days of doxycycline and DMSO


title: Tc_mef_2

description: Sample 2

source_name: MEFs


title: Tc_d2control_2

description: Sample 4


title: 7000AA_MSCB-166


title: 7000AA_MSCB-165


title: 7000AA_MSCB-164


title: HSCs_e2-1

city: Shanghai

first: Ya

last: Gao

state: China

address: zhizaoju road

country: China

institute: Shanghai 9th People’s Hospital Schoolof Medicine ShanghaiJia

data_processing:
RNA quantity and quality were measured using a NanoDrop ND-1000. The cDNA library was constructed using KAPA Stranded RNA-Seq Library Preparation Kit (Illumina) following the manufacturer’s protocol.
The final double-stranded cDNA samples were verified with an Agilent 2100 Bioanalyzer (Agilent Technologies).
After cluster generation (TruSeq SR Cluster Kit v3-cBot-HS, Illumina), sequencing was performed on an Illumina HiSeq 4000 sequencing platform.
Image analysis, base calling, and error estimation were performed using Illumina/Solexa Pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
Raw data were pre-processed using Solexa CHASTITY and Cutadapt to remove adaptor sequences, ribosomal RNA, and other contaminants that may interfere with clustering and assembly. The trimmed reads are mapped to the corresponding reference genome using HISAT2 (version 2.0.4) for RNA-seq, and StringTie (version 1.2.3) was used to reconstruct the transcriptome.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression_Gene.xlsx inclucing: Track_ID : Gene_Name : Locus : Strand : Gene_Type : etc.

source_name: mice primary Hepatic Stellate Cells

growth_protocol: Primary HSCs were derived from C57BL/6 mice followed researcher’s instruction(Weiskirchen, Sabine, et al. "Isolation and culture of primary murine hepatic stellate cells." Fibrosis. Humana Press, New York, NY, 2017. 165-191). Cells were cultured in DMEM (Gibco, Grand Island, New York, USA) supplemented with 10% exosomes-depleted fetal bovine serum (FBS, Gibco), 1% penicillin and 1% streptomycin, and incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After cell cultures reached 90% confluency, cells were washed with PBS and incubated with freshly prepared complete medium containing exosome-free FBS for 48 h. Exosomes were collected from Np cells, Panc02 and KPC culture medium. HSCs were devided to 3 groups: C1-3 ( adding Exosomes from Primary mice pancreatic duct epithelial cells); E1.1-3 ( adding Exosomes from mice pancreatic adenocarcinoma cell lines -KPC) ; E2.1-3 ( adding Exosomes from mice pancreatic adenocarcinoma cell lines -Panc02).

value: mice primary Hepatic Stellate Cells

value: mice liver


title: HSCs_e2-2


title: 7000AA_MSCB-172

value: primary bladder epithelial cell


title: HSCs_e2-3


title: 7000AA_MSCB-163


title: 7000AA_MSCB-162


title: HSCs_e1-3


title: HSCs_e1-2


title: 7000AA_MSCB-160


title: HSCs_control-3


title: 7000AA_MSCB-161


title: HSCs_e1-1


title: 7000AA_MSCB-158


title: HSCs_control-2


title: HSCs_control-1


title: 7000AA_MSCB-159


title: 7000AA_MSCB-157


title: 7000AA_MSCB-155


title: Tc_mef_1

description: Sample 1

extract_protocol:
RNA was extracted with TRIzol and chloroform, cleaned using the Qiagen Rneasy Mini kit, and Dnase treated (Qiagen 79254) for 30 min. 1 ug of RNA was used for library construction. For the Tc and Sort samples (#1-22, paired-end sequencing), 20 ng of 293T RNA was added as a human spike in control.
TruSeq RNA Sample Preparation kit V2 (RS-122-2002) was used to construct cDNA libraries


title: 7000AA_MSCB-167


title: 7000AA_MSCB-154