title: sgNEG_rep4_immune_sort_RNAseq

city: Cold Spring Harbor

first: Tim

middle: D D

last: Somerville

state: NY

address: 1 Bungtown Road

department: CSHL

institute: Cold Spring Harbor Laboratory

description: Fibroblast_and_Immune_sort_sgTP63_vs_sgNEG.txt

data_processing:
For xenograft RNA-seq analysis, paired end 150bp sequencing reads were mapped to the mm10 or hg38 genomes using HISAT2 with standard parameters.The alignment sam files were converted to bam format using the samtools view command. To disambiguate between the human and mouse reads, Disambiguate was run on the bam files. For all other RNA-seq analysis, single-end 50bp sequencing reads were mapped to the hg38 or mm10 genomes using hisat2 with default settings.
Structural RNAs were masked
For xenograft RNA-seq analysis, unambiguous reads were used for RNA quantification and differential expression analysis using DESeq2. For all other RNA-seq analysis, differentially expressed genes were identified using Cuffdiff, normalized to total mapped reads.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: txt files generated from DESeq2 or Cuffdiff

source_name: flow sorted mouse immune cells from orthotopic panreatic tumors in NSG mice

growth_protocol: Human PDA cells used for conditioned media experiments were cultured in DMEM with 5%FBS and P/S. mPSCs were cultured in the indicated conditioned media or control media. For T3M4 and KLM1 cells used for dox-inducible knock out of TP63, cells were cultured in RPM1 with 10%FBS and P/S.

extract_protocol:
RNA was extracted using TRIzol following manufacture’s protocol. 0.5-2ug total RNA was used for constructing RNA-seq library
RNA-seq libraries were constructed using the Illumina TruSeq sample prep kit v2 following manufacture’s protocol. Briefly, RNA was polyA selected and enzymatically fragmented. cDNA was synthesized using Super Script II master mix, followed by end repair, A-tailing and PCR amplification.

tag: mouse strain

value: NSG

tag: treatment time

value: flow sorted at end point


title: sgTP63#4_rep3_immune_sort_RNAseq

status: Public on Apr 27 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: treatment

value: flow sorted mouse immune cells from orthotopic panreatic tumors in NSG mice


title: sgNEG_rep1_immune_sort_RNAseq


title: sgNEG_rep3_immune_sort_RNAseq


title: sgNEG_rep2_immune_sort_RNAseq


title: sgTP63#4_rep2_immune_sort_RNAseq


title: sgTP63#4_rep1_immune_sort_RNAseq


title: sgTP63#4_rep4_immune_sort_RNAseq


title: sgTP63#4_rep3_fibroblast_sort_RNAseq

source_name: flow sorted mouse fibroblasts cells from orthotopic panreatic tumors in NSG mice


title: sgTP63#4_rep4_fibroblast_sort_RNAseq

value: flow sorted mouse fibroblasts cells from orthotopic panreatic tumors in NSG mice


title: sgTP63#4_rep1_fibroblast_sort_RNAseq


title: sgTP63#4_rep2_fibroblast_sort_RNAseq


title: CD275 rep3

type: RNA

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: Gene expression data from CD275+ iPS derived DE/ADE cells, biological replicate 3

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression data were RMA normalized using the oligo package (version 1.42.0) and then filtered to retain only probe sets with a minimum intensity of 10 in at least 3 samples

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: H9, Mel1-NKX6.1-GFPand iPSCs were cultured on 1:30 diluted Geltrex (Invitogen, U.K, Cat#A1413302) in StemMACS IPS-Brew medium (Miltenyi Biotech,Germany, Cat#130-104-368).  At ~70–80% confluency, cultures were rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen, Cat#14190) followed by incubation with 0.5 mM EDTA (Applichem, Cat#12604-021) for 2–3 min at 37 °C. Single cells were rinsed with IPS-Brew, and spun at 1,300 r.p.m. for 3 mins. The resulting cell pellet was suspended in IPS-Brew medium supplemented with Y-27632 (10 μM; Sigma-Aldrich; MO, Cat#Y0503) and the single cell suspension was seeded at ~1.5–2 × 105 cells/cm2 on Geltrex-coated surfaces. Cultures were fed every day with IPS-Brew medium and differentiation was initiated 12 h following seeding, resulting in ~90% starting confluency.

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol: The cells were differentiated towards definitive endoderm using MCDB131 medium supplemented with 0.5 % BSA (Sigma, Cat#10775835001), 100 ng/ml Activin A (Peprotech, Cat#120-14-300) and 25 ng/ml WNT3A (Peprotech, Cat#315-20) for the first day. For the next 2 days, the cells were treated with MCDB131 supplemented with 0.5 % BSA and 100ng/ml Activin A.

tag: cell type

value: CD275+ iPS derived DE/ADE cells


title: CD177 rep1

description: Gene expression data from CD177+ iPS derived DE/ADE cells, biological replicate 1

scan_protocol: According to the Affymetrix expression protocol

value: CD177+ iPS derived DE/ADE cells


title: CD184 rep3

description: Gene expression data from CXCR4+ (CD184+) iPS derived DE/ADE cells, biological replicate 3


title: CD184 rep2

description: Gene expression data from CXCR4+ (CD184+) iPS derived DE/ADE cells, biological replicate 2


title: CD177 rep3

description: Gene expression data from CD177+ iPS derived DE/ADE cells, biological replicate 3


title: CD275 rep2

description: Gene expression data from CD275+ iPS derived DE/ADE cells, biological replicate 2


title: CD184 rep1

description: Gene expression data from CXCR4+ (CD184+) iPS derived DE/ADE cells, biological replicate 1


title: sgNEG_rep3_fibroblast_sort_RNAseq


title: CD275 rep1

description: Gene expression data from CD275+ iPS derived DE/ADE cells, biological replicate 1


title: CD177 rep2

description: Gene expression data from CD177+ iPS derived DE/ADE cells, biological replicate 2


title: sgNEG_rep1_fibroblast_sort_RNAseq


title: sgNEG_rep4_fibroblast_sort_RNAseq


title: sgNEG_rep2_fibroblast_sort_RNAseq


title: mPSCs_plus_SUIT2_conditioned_media_RNAseq

description: mPSCs_treated_with_conditioned_or_control_media.txt

source_name: mouse pancreatic stellate cells 5

value: mPSC5 cells cultured with conditioned media from SUIT2 cells

value: day 4 post addition of media


title: mPSCs_plus_control_media_rep1_RNAseq

value: mPSC5 cells cultured with control media


title: mPSCs_plus_control_media_rep2_RNAseq


title: mPSCs_plus_AsPC1_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from AsPC1 cells


title: mPSCs_plus_PATU8988S_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from PATU8988S cells


title: mPSCs_plus_MIAPaca2_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from MIAPaca2 cells


title: mPSCs_plus_CAPAN2_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from CAPAN2 cells


title: mPSCs_plus_CFPAC1_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from CFPAC1 cells


title: mPSCs_plus_PANC0403_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from PANC0403 cells


title: mPSCs_plus_KLM1_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from KLM1 cells


title: mPSCs_plus_T3M4_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from T3M4 cells


title: mPSCs_plus_HPAFII_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from HPAFII cells


title: M016.X1

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Read mapping was performed using TopHat version 2.0.9
Read counts per gene were quantified using HTSeq version 0.5.4
Read counts were normalised using DEseq2.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Read count table

source_name: Melanoma PDX

growth_protocol: Tumor fragments of ~5mm3 were used for subcutaneous transplantation into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice, which was performed under anesthesia. Tumor outgrowth was measured twice a week with a caliper. Before reaching the maximum allowed tumor size of 1000 mm3, mice were sacrificed, tumors were removed and tumor pieces were snap-frozen and stored at -80°C for RNAseq analysis.

extract_protocol: RNA isolated by Trizol, according to manufacturers protocol.RNA libraries were prepared for sequencing using standard Illumina protocols

tag: origin

value: Patient derived xenograft (PDX) sample

tag: derived from

value: melanoma metastases

tag: host strain

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse


title: N2A138_PAR-CLIP

city: Hangzhou

first: Dongli

last: Pan

state: Zhejiang

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description:
small RNA
Cells overexpressing miR-138, uninfected

data_processing:
Reads were trimmed to discard adapters and low-quality reads and reads less than 21 base long using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/).
Using the “grep” command to retain only reads that contain this sequence CACCAGC (binding site of the miR-138 seed region). These reads were aligned with the mouse (mm10 version) genome using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml)
Counts of reads aligned to 5’ UTR, CDS and 3’ UTR of each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral or mouse/human gene

source_name: N2A138 cells derived from Neuro-2a cells

extract_protocol:
RNA crosslinked and immunoprecipitate with Agonaute was extracted according to standard PAR-CLIP protocol (Danan, C., Manickavel, S., and Hafner, M. (2016). PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. Methods in molecular biology 1358, 153-173.)
RNA libraries were prepared for sequencing using TruSeq Small RNA Library Preparation Kit (Illumina)

treatment_protocol: For infection, cells were infected with wild-type HSV-1 (strain KOS) for 4 and 8 hpi (MOI = 1) before PAR-CLIP

tag: tissue

value: Brain

tag: cell line

tag: genotype

value: overexpressing miR-138

tag: infection status

value: uninfected


title: miR-138_N2A3

description: miR-138 transfected Neuro-2a cells

data_processing:
Reads were trimmed to remove adapters, low-quality reads, and reads less than 30 bases long using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic)
The trimmed reads were aligned with the human (hg19 build) or mouse (mm10 build) using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml).
Counts of reads aligned to each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
Genome_build: hg19 (human), mm10 (mouse)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral gene

source_name: Neuro-2a cells

extract_protocol:
Total RNAs were purified using an RNeasyPlus Mini Kit following the manufacturer’s instructions (Qiagen)
mRNAs were isolated using a Takara mRNA Isolation Kit. Libraries were prepared using a PrepX RNA-seq Library Preparation Kit

treatment_protocol: Neuro-2a cells were transfected with 40 nM of a miR-138 or scrambled mimic for 24 h before performing RNAseq

tag: transfected with

value: miR-138 mimic


title: Control_N2A3

description: Control transfected Neuro-2a cells

value: control mimic


title: Control_N2A1

description: Control transfected Neuro-2a cells


title: Control_N2A2

description: Control transfected Neuro-2a cells


title: miR-138_N2A2

description: miR-138 transfected Neuro-2a cells


title: miR-138_N2A1

description: miR-138 transfected Neuro-2a cells


title: Caco2 V600E_shControl_1

city: Berlin

first: Bertram

last: Klinger

address: Chariteplatz 1

institute: Charite Universitätsmedizin

data_processing:
Quality control was performed using FastQC
Reads were mapped using STAR aligner v2.7.3a
Mapped reads were counted using subread featureCounts
Read counts were normalised using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimeted file of DESeq2 normalised read counts

source_name: colon cancer cell line

growth_protocol: CaCo2 wt shControl, CaCo2 wt shSFPQ and CaCo2 BRAFV600E shControl, CaCo2 BRAFV600E shSFPQ were grown in DMEM supplemented with 10% FCS, Pen/Strep (100 U/ ml / 100µg/ml) and Ultraglutamine (2 mM) at 37°C with 5 % CO2

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit
Illumina TruSeq® Stranded Total RNA Library Prep

treatment_protocol: Upon attachment doxycycline (2 µg/ml) was added to induce transgene expression

value: colon cancer cell line

tag: genotype/variation

value: BRAF V600E

tag: shRNA

value: sh Control

tag: treated with

value: doxycycline for 96h


title: Caco2_V600E_shSFPQ_1

value: SFPQ shRNA


title: Caco2wt_shSFPQ_2

value: BRAF wt


title: Caco2wt_shSFPQ_1


title: Caco2_V600E_shSFPQ_2


title: Caco2 V600E_shControl_2


title: MCF10AT1_BPAplusBa_P_60_S8_pool3

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

country: France

institute: university Lyon1

description: exposed during 60 days to 10-10 M of bisphenol-A (BPA) and 10-10M  benzo[a]pyrene (B[a]P) replicat 3

data_processing:
base calling and quality assessment were realised using NCS v.1.2.1.7 and RTA v 2.1.3
demultiplexing were realised using Bcl2fastQ v 2.15.0.4
Trimmed reads were aligned on human genome (hg19) using TopHat-2 v. 2.1.0
Data normalization (FPKM) were performed using Cufflinks software v.2.1.1
Transcripts were considered as differentially expressed when p-value of a student non-parametric t-test was <=0,05
Genome_build: hg19
Supplementary_files_format_and_content: gene_id; Locus length; coverage;FPKM

growth_protocol: MCF10AT1 and MCF10AT1-derived cancerous MCF10CAC1a.cl1 were purchased from Karmanos Institute and maintained in complete DMEM/HAM's F12 medium with 5% horse serum and additional supplements. 100 ng/mL cholera enterotoxin, 10 mg/mL insulin, 0.5 mg/mL hydrocortisol, 20 ng/mL epidermal growth factor (Sigma, Saint Louis, USA) 100 units/mL penicillin and 100 mg/mL streptomycin. Treatment : B[a]P and BPA were purchased from Sigma (Saint Louis, USA). 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), used as a control, was purchased from LGC Standard (Molsheim, France). MCF10AT1 cells were chronically exposed or not to 10-10 M of B[a]P or to 10-10 M BPA, alone or in combination, during 60 days (20 passages) in phenol red-free DMEM/Ham’s F12 medium with 5% steroid-depleted, dextran-coated and charcoal-treated horse serum, containing the above-mentioned supplements (further referred to as DCC medium). Unexposed MCF10CA1a.cl1 cells were grown concomitantly in the same medium for 60 days and named MCF10CA1a.cl160d. Media and treatments were changed every 2 days. Cells were frozen every 2 weeks

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer’s protocol and treated by DNAse
Ribosomal depletion was performed with the Ribo-zero gold kit (Epicentre). Libraries were performed from 20 ng ribosomal depleted RNA with the NEXTFLEX® Rapid Directional RNA-Seq Library Prep Kit (BIOO-Scientific). Libraries were sequenced using an Illumina NextSeq 500 platform (flow cell highoutput V2) and a 75 bp paired-end sequencing with approximately 30-35 million reads per sample

value: Early-transformed human mammary cells

tag: agent


title: Caco2wt_shControl_1


title: MCF10CA1a_cl1_NT_60_S9_pool3

description: unexposed cells replicat 3

value: MCF10AT1-derived cancerous cells

value: unexposed cells


title: MCF10CA1a_cl1_NT_60_S9_pool2

description: unexposed cells replicat 2


title: MCF10AT1_BPA_60_S6_pool3

description: exposed during 60 days to 10-10 M of  bisphenol-A (BPA) replicat 3


title: N2Aanti138_PAR-CLIP

description:
small RNA
Cells antagonizing miR-138, uninfected

source_name: N2Aanti138 cells derived from Neuro-2a cells

value: antagonizing miR-138


title: MCF10AT1_BA_P_60_S7_pool3

description: exposed during 60 days to 10-10 M of benzo[a]pyrene (B[a]P) replicat 3


title: mPSCs_plus_BxPC3_conditioned_media_RNAseq

value: mPSC5 cells cultured with conditioned media from BxPC3 cells

value: day 4 post addition of media


title: MCF10AT1_NT_60_S5_pool3

description: unexposed cells replicat 3


title: MCF10AT1_BPAplusBa_P_60_S8_pool2

description: exposed during 60 days to 10-10 M of bisphenol-A (BPA) and 10-10M  benzo[a]pyrene (B[a]P) replicat 2


title: MCF10AT1_BPA_60_S6_pool2

description: exposed during 60 days to 10-10 M of  bisphenol-A (BPA) replicat 2


title: MCF10AT1_BA_P_60_S7_pool2

description: exposed during 60 days to 10-10 M of benzo[a]pyrene (B[a]P) replicat 2


title: MCF10CA1a_cl1_NT_60_S9_pool1

description: unexposed cells replicat 1


title: MCF10AT1_NT_60_S5_pool2

description: unexposed cells replicat 2


title: MCF10AT1_BPAplusBa_P_60_S2_pool1

description: exposed during 60 days to 10-10 M of bisphenol-A (BPA) and 10-10M  benzo[a]pyrene (B[a]P) replicat 1


title: MCF10AT1_BA_P_60_S1_pool1

description: exposed during 60 days to 10-10 M of benzo[a]pyrene (B[a]P) replicat 1


title: MCF10AT1_BPA_60_S6_pool1

description: exposed during 60 days to 10-10 M of  bisphenol-A (BPA) replicat 1


title: Caco2wt_shControl_2


title: KLM1_48hr_dox_sgTP63#4_rep3_RNAseq

value: KLM1 cells transduced with YXP-Cas9 vector and sgTP63#4 and dox treated for 48 hours

value: 48 hous post dox treatment


title: MCF10AT1_NT_60_S5_pool1

description: unexposed cells replicat 1


title: KLM1_48hr_dox_sgNEG_rep3_RNAseq

value: KLM1 cells transduced with YXP-Cas9 vector and sgNEG and dox treated for 48 hours


title: KLM1_48hr_dox_sgTP63#4_rep2_RNAseq


title: KLM1_48hr_dox_sgTP63#4_rep1_RNAseq


title: KLM1_48hr_dox_sgNEG_rep2_RNAseq


title: T3M4_48hr_dox_sgTP63#4_rep3_RNAseq

value: T3M4 cells transduced with YXP-Cas9 vector and sgTP63#4 and dox treated for 48 hours


title: T3M4_48hr_dox_sgTP63#4_rep1_RNAseq


title: T3M4_48hr_dox_sgNEG_rep2_RNAseq

value: T3M4 cells transduced with YXP-Cas9 vector and sgNEG and dox treated for 48 hours


title: T3M4_48hr_dox_sgNEG_rep3_RNAseq


title: sgTP63#4_rep3_cancer_cell_sort_RNAseq

source_name: flow sorted human KLM1 cells from orthotopic panreatic tumors in NSG mice

value: flow sorted at end point


title: sgTP63#4_rep4_cancer_cell_sort_RNAseq

value: flow sorted human KLM1 cells from orthotopic panreatic tumors in NSG mice


title: sgNEG_rep1_cancer_cell_sort_RNAseq


title: sgNEG_rep3_cancer_cell_sort_RNAseq


title: sgTP63#4_rep2_cancer_cell_sort_RNAseq


title: sgNEG_rep2_cancer_cell_sort_RNAseq


title: sgNEG_rep4_cancer_cell_sort_RNAseq


title: sgTP63#4_rep1_cancer_cell_sort_RNAseq


title: PANC1_RNAseq

value: PANC1 cells grown in reduced media of DMEM supplemented with 5% FBS


title: PATU8988S_RNAseq

value: PATU8988S cells grown in reduced media of DMEM supplemented with 5% FBS


title: SUIT2_RNAseq

value: SUIT2 cells grown in reduced media of DMEM supplemented with 5% FBS


title: AsPC1_RNAseq

value: AsPC1 cells grown in reduced media of DMEM supplemented with 5% FBS


title: KLM1_RNAseq

value: KLM1 cells grown in reduced media of DMEM supplemented with 5% FBS


title: PANC0403_RNAseq

value: PANC0403 cells grown in reduced media of DMEM supplemented with 5% FBS


title: MIAPaca2_RNAseq

value: MIAPaca2 cells grown in reduced media of DMEM supplemented with 5% FBS


title: T3M4_RNAseq

value: T3M4 cells grown in reduced media of DMEM supplemented with 5% FBS


title: CFPAC1_RNAseq

value: CFPAC1 cells grown in reduced media of DMEM supplemented with 5% FBS


title: T3M4_48hr_dox_sgTP63#4_rep2_RNAseq


title: KLM1_48hr_dox_sgNEG_rep1_RNAseq


title: BxPC3_RNAseq

value: BxPC3 cells grown in reduced media of DMEM supplemented with 5% FBS


title: HPAFII_RNAseq

source_name: HPAFII

value: HPAFII cells grown in reduced media of DMEM supplemented with 5% FBS


title: KLM1_H3K27ac_ChIPseq

library_source: genomic

data_processing:
50bp single end sequencing reads were mapped to hg19 genome using Bowtie2 using default settings
PCR duplicates were removed from sequencing reads using SAM Tools rmdup.
MACS 1.4.2 was used to call peaks with input genomic DNA as control with other default parameters: 1e-05 Pvalue cutoff for peak detection, 10-30 within MFOLD range
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files converted from wiggle file generated from MACS peaks calling

molecule: genomic DNA

growth_protocol: Human PDA cells were cultured in RPMI with 10%FBS and P/S.

extract_protocol:
After cross-link, cells were incubated with cell lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40) and then resuspended and sonicated in nuclei lysis buffer (50mM Tris pH8.0, 10mM EDTA, 1%SDS) for 15mins, followed by ChIP
Library was constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture’s protocol. Briefly, ChIP DNA was end repaired, followed by A tailing and size selection (250-500 bp) by gel electrophoresis. 15 PCR cycles were used for final library amplification and the library was analyzed on Bioanalyzer using high sensitivity DNA chip (Agilent) on Bio-analyzer.

treatment_protocol: Cell cultures were collected and cross-likned with formaldehyde at room temperature for 15 mins.

value: wt cells

tag: chip antibody

value: ab4729, abcam


title: CAPAN2_RNAseq

value: CAPAN2 cells grown in reduced media of DMEM supplemented with 5% FBS


title: T3M4_48hr_dox_sgNEG_rep1_RNAseq

value: T3M4 cells transduced with YXP-Cas9 vector and sgNEG and dox treated for 48 hours

value: 48 hous post dox treatment


title: T3M4_H3K27ac_ChIPseq


title: ChIP_input_NFL_OE

city: Stanford

first: Gerlinde

last: Wernig

state: CA

address: 265 Campus Drive

department: Pathology

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

description:
primary human normal lung fibroblast with JUN overexpression
ChIP-SEQ

data_processing:
Reads were trimmed for adaptor sequence, then mapped to hg38 using bowtie2, duplicate fragments were then removed using Picard.
MACS2 was used to call all reported ATAC-seq peaks. Peaks were filtered using the consensus excludable ENCODE blacklist.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files, peaks

source_name: primary human normal lung fibroblast

extract_protocol: FOR ChIP, Around 10,000,000 cells were used for each chromatin immunoprecipitation.

value: primary lung fibroblasts

tag: treatent

value: JUN overexpression


title: ATAC_NFL_OE_2

description:
primary human normal lung fibroblast with JUN overexpression
ATAC-SEQ

extract_protocol:
FOR ATAC, Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
FOR ATAC, Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.


title: miR-138_293T2

description: miR-138 transfected 293T cells

source_name: 293T cells

value: Kidney

value: miR-138 mimic


title: ATAC_NFL_OE_1


title: ChIP_input_NLF

description:
primary human normal lung fibroblast
ChIP-SEQ

value: wild type


title: miR-138_293T3

description: miR-138 transfected 293T cells


title: ATAC_NLF_2

description:
primary human normal lung fibroblast
ATAC-SEQ


title: miR-138_293T1

description: miR-138 transfected 293T cells


title: Control_293T1

description: Control transfected 293T cells

value: control mimic


title: RWPE-1_rep3

city: Dallas

first: Ram

last: Mani

state: Texas

address: 5323 Harry Hines Blvd NB6.444

institute: UT Southwestern Medical Center

data_processing:
Quality control using FastQC
Remove reads mapped to ribosome RNA using bowtie
Map to genome using Tophat, and remove duplicates by samtools
Expression level calculation by eXpress
Deffirential expession analysis by DESeq2
Genome_build: hg19

source_name: RWPE-1 (ATCC number:CRL-11609)

growth_protocol: All cell lines were cultured following ATCC guidelines. RWPE-1 was cultured in Keratinocyte serum free medium, supplemented with bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF). LNCaP and DU145 were cultured in RPMI supplemented with 10% FBS (vol/vol) and VCaP was cultured in DMEM supplemented with 10% FBS (vol/vol).

extract_protocol:
RNA was extracted using the RNeasy kit from QIAGEN, employing an on-column DNase treatment. RNA was assessed by Tape Station (Agilent). Using a bead based approach, mRNA from the samples was isolated and used to construct a RNA-seq library using the KAPA mRNA Hyper prep kit (KAPA Biosystems).
After cDNA conversion, Truseq adapters were ligated to the DNA, and PCR amplified with minimal number of cycles to obtain RNA-seq libraries.

treatment_protocol: About 7-10 million cells were seeded in a 10sq.cm plate and harvested 16 hours later.

tag: replicate

value: Epithelial cells derived from the peripheral zone of a histologically normal adult human prostate


title: RWPE-1_rep2


title: Input_for_T3M4_H3K27ac_ChIPseq


title: RWPE-1_rep1


title: Input_for_KLM1_H3K27ac_ChIPseq


title: LNCaP_rep1

source_name: LNCaP (ATCC number:CRL-1740)

value: LNCaP

value: Prostate cancer cells from Lymph node


title: LNCaP_rep3


title: LNCaP_rep2


title: LNCaP Input

data_processing:
Mapping to genome using bowtie
Peak calling using MACS2
Genome_build: hg19

growth_protocol: RPMI 1640 medium supplemented with 10% (vol/vol) FBS in a 5% CO2 incubator at 37 °C

extract_protocol:
Chromatin Immunoprecpitations were performed using HighCell ChIP kit following manufacturer's protocol (Diagenode). The ChIP DNA was isolated and purified (IPure Kit, Diagenode) from samples.
Next- generation sequencing library preparation using KAPA Hyper Prep kit (KAPA Biosystems) using TruSeq adapters (Integrated DNA Technologies). A quality check of the purified libraries was carried out using the Bioanalyzer 2100 (Agilent).

treatment_protocol: Around 8 million LNCap and 16 million DU145 cells were plated in T75 flasks. The cells were harvested and, fixed in 1% formaldehyde, and quenched using 125mM glycine. The fixed cells were lysed using the Protein G High Cell ChIP kit (Diagenode) and the chromatin was sheared using a Bioruptor (Diagenode).

tag: antibody

tag: protein

value: Metastatic, Prostate cancer cell from left supraclavicular lymph node  from Lymph node


title: DU145_rep1

source_name: DU145 (ATCC number:HTB-81)

tag: cell type

value: Prostate cancer cells from Brain metastasis


title: LNCaP AR

value: Androgen Receptor (06-680, Millipore, Lot number 2746312)

value: Androgen Receptor


title: DU145 H3K27ac

source_name: DU145 (ATCC number: HTB-81)

value: Histone H3K27ac antibody (39133 Active Motif, Lot number 01518010)

value: Acetylated Histone H3 at Lysine 27

value: Metatstatic, Prostate cancer cells from Brain


title: DU145 CTCF

value: CTCF antibody (3418S Cell Signaling Technology, Lot number 3

value: CTCF


title: ATAC_NLF_1

growth_protocol: Human fibroblasts were obtained from lungs of patients that underwent transplantation (IRB 18891). The tissue was chopped and incubated with Collagenase I (1 mg/ml, Thermo Fisher Scientific) and DNAse I (20 ug/ml, Sigma) for 30 min, centrifuged at 600 g for 5 min and filtered (70 um) to remove non-homogenized pieces of tissue. Tissue homogenate was treated with ACK lysing buffer (Thermo Fisher) for 10-15 min, centrifuged for 600 g, washed twice in DMEM with 10% fetal bovine serum (Gibco) and plated at a density of approximately 500,000 cells/cm2 in DMEM with 10% fetal bovine serum, 1% penicillin/streptomycin (Thermo Fisher Scientific) and Ciproﬂoxacin 10 µg/mL, Corning) and kept in an incubator at 37 °C 95%O2/5%CO2. Media was changed after 24h. For lentiviral-based transduction, primary fibroblasts were washed with PBS prior to transfection. 500 μl Cas9-gRNAJUN-Puromycin (knock out) or IRES-Hygro-TetO-JUN (doxycyclin inducible overexpression) lentivirus,  was added with in fresh medium with 4ug/mL polybrene (Sigma). Medium was replaced after incubation for 24 h at 37 °C 95%O2/5%CO2 and infected cells selected with 1 ug/mL puromycin or 500 ug/mL hygromycin in DMEM 10% FSB for 3 days.

value: primary lung fibroblasts


title: ChIP_NFL_OE

value: JUN overexpression


title: VCaP_rep2

source_name: VCaP (ATCC number: CRL-2876)

value: VCaP

value: Prostate cancer from Vertebral metastasis


title: ChIP_NLF

value: wild type


title: DU145 Input


title: VCaP

data_processing:
Data processing using ChIAPET2
Genome_build: hg19

extract_protocol:
The ChIP DNA fragments were proximity ligated using a bridge linker, and the proximity-ligated products were selected out and used to construct a library using the Nextera Sequencing technology (Illumina).
Nextera

treatment_protocol: About 200 million cells per cell line were cross-linked using 1.5mM ethylene glycol bis(succinimidyl succinate) (EGS) (35 minutes), and 1% Formaldehyde (8 minutes), and quenched using 0.125M Glycine (5 minutes) at room temperature. The cells were lysed and the chromatin was sheared and used for ChIP using the RNApolII antibody (Diagenode).

value: RNA polymerase 2 (920102 Biolegend, Lot number B217159)


title: Control_293T2

description: Control transfected 293T cells

value: Kidney

value: control mimic


title: Control_293T3

description: Control transfected 293T cells


title: RWPE-1

value: Epithelial cells derived from the peripheral zone of a histologically normal adult human prostate


title: LNCaP

value: LNCaP

value: Metastatic, Prostate cancer cell from left supraclavicular lymph node  from Lymph node


title: DU145


title: DU145_rep2

value: Prostate cancer cells from Brain metastasis


title: IPF1KO rep1

data_processing:
the adaptors were removed using cutadapt program v 1.9.1
The reads were then mapped onto the human genome hg19 assembly using Bowtie2. The standard default settings were modified to allow mapped paired-end fragments up to 2 kb.
Only the reads with mapping quality greater than 30 were kept, and the duplicated reads were removed using picard tools v1.126. the reads from mitochondria were also removed.
Convert PE BAM to tagAlign (BED 3+3 format) using bedtools v 2.26 functions
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist.
Peaks raw abundance was edstimated using bedtools v 2.26 functions
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited narrowPeak files generated by macs2, and the bigwig files generated by slopBed, bedClip and bedGraphToBigWig from KentTools (ucsc_tools)

source_name: Lung fibroblasts

growth_protocol: Human fibroblasts were obtained from lungs of patients that underwent transplantation (IRB 18891). The tissue was chopped and incubated with Collagenase I (1 mg/ml, Thermo Fisher Scientific) and DNAse I (20 ug/ml, Sigma) for 30 min, centrifuged at 600 g for 5 min and filtered (70 um) to remove non-homogenized pieces of tissue. Tissue homogenate was treated with ACK lysing buffer (Thermo Fisher) for 10-15 min, centrifuged for 600 g, washed twice in DMEM with 10% fetal bovine serum (Gibco) and plated at a density of approximately 500,000 cells/cm2 in DMEM with 10% fetal bovine serum, 1% penicillin/streptomycin (Thermo Fisher Scientific) and Ciproﬂoxacin 10 µg/mL, Corning) and kept in an incubator at 37 °C 95%O2/5%CO2. Media was changed after 24h and cells were cultured until 80-90% confluent before each passage. For lentiviral-based transduction, cells in passage 2 were washed with PBS prior to transfection. 500 μl Cas9-gRNAJUN-Puromycin lentivirus was added with in fresh medium with 4ug/mL polybrene (Sigma). Medium was replaced after incubation for 24 h at 37 °C 95%O2/5%CO2 and cells were kept at 37 °C 95%O2/5%CO2 for 48h. Infected cells selected with 1 ug/ml in DMEM 10% FSB for 3 days. After selection, cells were cultured until 80-90% confluent.

extract_protocol:
Lysates were clarified from tagmented DNA and libraries were prepared using indexing primers included in the Nextera Index kit (Illumine, FC-121-1030) and NEBNext High-Fidelity 2Ã— PCR Master Mix (NEB, M 0541S).
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols.

tag: passages

value: JUN-/-


title: IPF1KO rep2


title: IPF1 rep1


title: Kras+ Rac1 fl/fl rep3

city: Vienna

first: Melanie

last: Floderer

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were trimmed using trim_galore v0.3.7 and reads mapping to known mitochondrial and ribosomal sequences were removed using bowtie2 v2.1.0. Thereafter, reads were aligned to the Mus musculus genome mm10 (iGenomes) using star v2.5.0a and reads in genes were counted with featureCounts from subread v1.4.6.
Gene expression measurements in fragments per kilobase per million reads (FPKM) and transcripts per million (TPM) were calculated using RSEM v1.2.25.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with per gene tpm for each sample

source_name: Primary pneumocytes

growth_protocol: Primary pneumocytes were purified as described in Schramek et al. Nat Genet. 2011 and Rao et al. Genes & Development. 2017. In brief, lungs were dissected from 8–12-week-old mice, infused with IMDM containing 600 U/mL collagenase IV (Worthington) and 200 U/mL DNase (Worthington) through the trachea, and incubated for 1 h at 37°C. After the isolation, cells were maintained in Ham's F-12 media supplemented with 15 mM HEPES, 0.8 mM CaCl2, 0.25% BSA, ITS (Sigma) and 2% FCS, at 37ºC and 5% CO2 conditions. Cells were infected with Adeno-Cre (MOI = 100) in vitro for 2 h at 37°C and harvested after 4 days of culture.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit (Cat# ) was used with ? ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Lung

tag: age

value: 8 weeks

value: LSL-KrasG12D/+ Rac1fl/fl

value: KrasG12D-induced primary pneumocytes after 4 days of Adeno-cre infection


title: Kras+ Rac1 fl/fl rep2

tag: tissue


title: Kras+Hace1 KO Rac1 fl/fl rep1

tag: genotype

value: LSL-KrasG12D/+ Hace1-/- Rac1fl/fl


title: Kras+Hace1 KO Rac1 fl/fl rep2


title: Kras+ Hace1 KO rep3

value: LSL-KrasG12D/+ Hace1-/-


title: Kras+ WT rep2


title: Kras+ WT rep1


title: Kras+ Hace1 KO rep1


title: Kras+ Hace1 KO rep2


title: VCaP_rep1

tag: cell line

value: VCaP


title: Kras+ Rac1 fl/fl rep1


title: IPF1 rep2

value: primary lung fibroblasts


title: Kras+ WT rep3


title: RBG19872_KitHi_E11.5_G2VLo

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were aligned to Mus musculus genome (GRCm38.81) using G-SNAP (version 2015-09-29) with the following parameters: –B 5 –n 1 –N 1 –Q. HTSeq-count (version 0.6.0) was run to assign mapped reads to Ensembl genes (GRCm38.81).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

source_name: IAHC cells

growth_protocol: Gata2V/+ embryos were generated by timed matings of C57BL/6HsdJOla (Ly5.2) wild-type females with Gata2V/V (Kaimakis et al., 2016) males (>10 backcrosses onto C57BL/6HsdJOla).Transplantations were performed with B6.SJL-PtprcaPepcb/BoyCrl (Ly5.1/5.1, 2-4 month old) recipients and carrier spleen cells.

extract_protocol:
AGM (aorta-gonad-mesonephros) regions (including trunk portion of the vitelline and umbilical arteries) of E10/11 embryos were dissected as previously described (Medvinsky et al., 2008). Single cell suspensions were prepared by enzymatically digesting tissues at 37°C in 0.125% type 1 collagenase (C0130, Sigma-Aldrich) for 45 min, after which tissues were further mechanically disrupted with a P1000 pipette. Cells were subsequently passed over a 0.35 µm strainer, collagenase washed away with PBS+10%FBS+1%P/S (PFP), spun down (234g) and resuspended in PFP for flow cytometric antibody staining. Cells were incubated at 4°C for 30 min in PFP with directly conjugated antibodies against CD31 (CD31-BV605, 1:100, cat# 102427, Biolegend), cKit (cKit-BV421, 1:200, cat.# 562609, BD) and CD27 (CD27-APC, 1:75, cat.# 17-0271-82. eBioscience). Excess of antibodies was washed away with PFP before fluorescence activated cell sorting (FACS) on an AriaII (BD). Dead cell exclusion was by Hoechst 33342 and gates were set based on unstained WT and fluorescence-minus-one (FMO) controls. Sorted single cells were collected in 50% FBS/PBS for functional analyses (transplantation + bulk CFU-C assay). Both collagenase and FCS were batch tested for optimal AGM conditions.
Pooled libraries were run on the Illumina Hi-Seq 2500.
Libraries were prepared using the Illumina Nextera XT Libraries were prepared using the Illumina Nextera XT DNA preparation kit.

tag: condition

tag: days

value: IAHC cells

tag: cluster (all cells)

tag: cluster (nocd27+ cells)

tag: clustertype (nocd27+ cells)


title: RBG19896_KitHi_E11.5_G2VLo

value: EC


title: RBG19765_KitHi_E11.5_CD27+


title: RBG19860_KitHi_E11.5_G2VLo


title: RBG19836_KitHi_E11.5_G2VLo


title: RBG19717_KitHi_E11.5_CD27+


title: RBG19729_KitHi_E11.5_CD27+


title: RBG19753_KitHi_E11.5_CD27+


title: RBG19824_KitHi_E11.5_G2VLo


title: RBG19777_KitHi_E11.5_CD27+


title: RBG19908_KitHi_E11.5_G2VLo


title: RBG19789_KitHi_E11.5_CD27+


title: RBG19884_KitHi_E11.5_G2VLo


title: RBG19848_KitHi_E11.5_G2VLo


title: RBG19883_KitHi_E11.5_G2VLo


title: RBG19895_KitHi_E11.5_G2VLo


title: RBG19871_KitHi_E11.5_G2VLo


title: RBG19907_KitHi_E11.5_G2VLo


title: RBG19859_KitHi_E11.5_G2VLo


title: RBG19741_KitHi_E11.5_CD27+


title: RBG19823_KitHi_E11.5_G2VLo


title: RBG19764_KitHi_E11.5_CD27+


title: RBG19788_KitHi_E11.5_CD27+


title: RBG19835_KitHi_E11.5_G2VLo


title: RBG19776_KitHi_E11.5_CD27+


title: RBG19752_KitHi_E11.5_CD27+


title: RBG19847_KitHi_E11.5_G2VLo


title: RBG19705_KitHi_E11.5_CD27+


title: mPSCs_plus_PANC1_conditioned_media_RNAseq

source_name: mouse pancreatic stellate cells 5

tag: treatment

value: mPSC5 cells cultured with conditioned media from PANC1 cells

tag: treatment time

value: day 4 post addition of media


title: RBG19716_KitHi_E11.5_CD27+


title: RBG19906_KitHi_E11.5_G2VLo


title: RBG19704_KitHi_E11.5_CD27+


title: RBG19870_KitHi_E11.5_G2VLo


title: RBG19882_KitHi_E11.5_G2VLo


title: RBG19894_KitHi_E11.5_G2VLo


title: RBG19728_KitHi_E11.5_CD27+


title: RBG19846_KitHi_E11.5_G2VLo


title: RBG19787_KitHi_E11.5_CD27+


title: RBG19775_KitHi_E11.5_CD27+


title: RBG19751_KitHi_E11.5_CD27+


title: RBG19727_KitHi_E11.5_CD27+


title: RBG19858_KitHi_E11.5_G2VLo


title: RBG19739_KitHi_E11.5_CD27+


title: RBG19703_KitHi_E11.5_CD27+


title: RBG19715_KitHi_E11.5_CD27+


title: RBG19834_KitHi_E11.5_G2VLo


title: RBG19822_KitHi_E11.5_G2VLo


title: RBG19893_KitHi_E11.5_G2VLo


title: RBG19905_KitHi_E11.5_G2VLo


title: RBG19740_KitHi_E11.5_CD27+


title: RBG19857_KitHi_E11.5_G2VLo


title: RBG19881_KitHi_E11.5_G2VLo


title: RBG19869_KitHi_E11.5_G2VLo


title: RBG19833_KitHi_E11.5_G2VLo


title: RBG19821_KitHi_E11.5_G2VLo


title: RBG19845_KitHi_E11.5_G2VLo


title: RBG19774_KitHi_E11.5_CD27+


title: RBG19763_KitHi_E11.5_CD27+


title: RBG19750_KitHi_E11.5_CD27+


title: RBG19762_KitHi_E11.5_CD27+


title: RBG19738_KitHi_E11.5_CD27+


title: RBG19702_KitHi_E11.5_CD27+


title: RBG19892_KitHi_E11.5_G2VLo


title: RBG19714_KitHi_E11.5_CD27+


title: RBG19880_KitHi_E11.5_G2VLo


title: RBG19868_KitHi_E11.5_G2VLo


title: RBG19856_KitHi_E11.5_G2VLo


title: RBG19726_KitHi_E11.5_CD27+


title: RBG19785_KitHi_E11.5_CD27+


title: RBG19832_KitHi_E11.5_G2VLo


title: RBG19820_KitHi_E11.5_G2VLo


title: RBG19773_KitHi_E11.5_CD27+


title: RBG19761_KitHi_E11.5_CD27+


title: RBG19725_KitHi_E11.5_CD27+


title: RBG19891_KitHi_E11.5_G2VLo


title: RBG19749_KitHi_E11.5_CD27+


title: RBG19713_KitHi_E11.5_CD27+


title: RBG19903_KitHi_E11.5_G2VLo


title: RBG19737_KitHi_E11.5_CD27+


title: RBG19879_KitHi_E11.5_G2VLo


title: RBG19867_KitHi_E11.5_G2VLo


title: RBG19855_KitHi_E11.5_G2VLo


title: RBG19843_KitHi_E11.5_G2VLo


title: RBG19831_KitHi_E11.5_G2VLo


title: RBG19784_KitHi_E11.5_CD27+


title: RBG19819_KitHi_E11.5_G2VLo


title: RBG19904_KitHi_E11.5_G2VLo


title: RBG19844_KitHi_E11.5_G2VLo


title: RBG19748_KitHi_E11.5_CD27+


title: RBG19736_KitHi_E11.5_CD27+


title: RBG19724_KitHi_E11.5_CD27+


title: RBG19712_KitHi_E11.5_CD27+


title: RBG19700_KitHi_E11.5_CD27+


title: RBG19786_KitHi_E11.5_CD27+


title: RBG19890_KitHi_E11.5_G2VLo


title: RBG19701_KitHi_E11.5_CD27+


title: RBG19866_KitHi_E11.5_G2VLo


title: RBG19842_KitHi_E11.5_G2VLo


title: RBG19878_KitHi_E11.5_G2VLo


title: RBG19830_KitHi_E11.5_G2VLo


title: RBG19783_KitHi_E11.5_CD27+


title: RBG19747_KitHi_E11.5_CD27+


title: RBG19818_KitHi_E11.5_G2VLo


title: RBG19771_KitHi_E11.5_CD27+


title: RBG19759_KitHi_E11.5_CD27+


title: RBG19735_KitHi_E11.5_CD27+


title: RBG19723_KitHi_E11.5_CD27+


title: RBG19711_KitHi_E11.5_CD27+


title: RBG19772_KitHi_E11.5_CD27+


title: RBG19901_KitHi_E11.5_G2VLo


title: RBG19760_KitHi_E11.5_CD27+


title: RBG19699_KitHi_E11.5_CD27+


title: RBG19889_KitHi_E11.5_G2VLo


title: RBG19865_KitHi_E11.5_G2VLo


title: RBG19877_KitHi_E11.5_G2VLo


title: RBG19853_KitHi_E11.5_G2VLo


title: RBG19841_KitHi_E11.5_G2VLo


title: RBG19782_KitHi_E11.5_CD27+


title: RBG19902_KitHi_E11.5_G2VLo


title: RBG19817_KitHi_E11.5_G2VLo


title: RBG19854_KitHi_E11.5_G2VLo


title: RBG19770_KitHi_E11.5_CD27+


title: RBG19758_KitHi_E11.5_CD27+


title: RBG19746_KitHi_E11.5_CD27+


title: RBG19722_KitHi_E11.5_CD27+


title: RBG19888_KitHi_E11.5_G2VLo


title: RBG19698_KitHi_E11.5_CD27+


title: RBG19710_KitHi_E11.5_CD27+


title: RBG19876_KitHi_E11.5_G2VLo


title: RBG19734_KitHi_E11.5_CD27+


title: RBG19864_KitHi_E11.5_G2VLo


title: RBG19852_KitHi_E11.5_G2VLo


title: RBG19816_KitHi_E11.5_G2VLo


title: RBG19781_KitHi_E11.5_CD27+


title: RBG19769_KitHi_E11.5_CD27+


title: RBG19840_KitHi_E11.5_G2VLo


title: RBG19745_KitHi_E11.5_CD27+


title: RBG19757_KitHi_E11.5_CD27+


title: RBG19721_KitHi_E11.5_CD27+


title: RBG19733_KitHi_E11.5_CD27+


title: RBG19697_KitHi_E11.5_CD27+


title: RBG19829_KitHi_E11.5_G2VLo


title: RBG19899_KitHi_E11.5_G2VLo


title: RBG19887_KitHi_E11.5_G2VLo


title: RBG19709_KitHi_E11.5_CD27+


title: RBG19875_KitHi_E11.5_G2VLo


title: RBG19863_KitHi_E11.5_G2VLo


title: RBG19851_KitHi_E11.5_G2VLo


title: RBG19827_KitHi_E11.5_G2VLo


title: RBG19839_KitHi_E11.5_G2VLo


title: RBG19815_KitHi_E11.5_G2VLo


title: RBG19780_KitHi_E11.5_CD27+


title: RBG19768_KitHi_E11.5_CD27+


title: RBG19756_KitHi_E11.5_CD27+


title: RBG19828_KitHi_E11.5_G2VLo


title: RBG19744_KitHi_E11.5_CD27+


title: RBG19696_KitHi_E11.5_CD27+


title: RBG19720_KitHi_E11.5_CD27+


title: RBG19732_KitHi_E11.5_CD27+


title: RBG19898_KitHi_E11.5_G2VLo


title: RBG19886_KitHi_E11.5_G2VLo


title: RBG19874_KitHi_E11.5_G2VLo


title: RBG19838_KitHi_E11.5_G2VLo


title: RBG19826_KitHi_E11.5_G2VLo


title: RBG19814_KitHi_E11.5_G2VLo


title: RBG19767_KitHi_E11.5_CD27+


title: RBG19779_KitHi_E11.5_CD27+


title: RBG19731_KitHi_E11.5_CD27+


title: RBG19862_KitHi_E11.5_G2VLo


title: RBG19755_KitHi_E11.5_CD27+


title: RBG19695_KitHi_E11.5_CD27+


title: RBG19707_KitHi_E11.5_CD27+


title: RBG19743_KitHi_E11.5_CD27+


title: RBG19873_KitHi_E11.5_G2VLo


title: RBG19861_KitHi_E11.5_G2VLo


title: RBG19719_KitHi_E11.5_CD27+


title: RBG19885_KitHi_E11.5_G2VLo


title: RBG19897_KitHi_E11.5_G2VLo


title: RBG19849_KitHi_E11.5_G2VLo


title: RBG19825_KitHi_E11.5_G2VLo


title: RBG19708_KitHi_E11.5_CD27+


title: RBG19837_KitHi_E11.5_G2VLo


title: RBG19813_KitHi_E11.5_G2VLo


title: RBG19766_KitHi_E11.5_CD27+


title: RBG19742_KitHi_E11.5_CD27+


title: RBG19850_KitHi_E11.5_G2VLo


title: RBG19778_KitHi_E11.5_CD27+


title: RBG19718_KitHi_E11.5_CD27+


title: RBG19706_KitHi_E11.5_CD27+


title: RBG19730_KitHi_E11.5_CD27+


title: RBG19754_KitHi_E11.5_CD27+


title: RBG19694_KitHi_E11.5_CD27+


title: RBG19693_KitHi_E11.5_G2VLo


title: RBG19681_KitHi_E11.5_G2VLo


title: RBG19645_KitHi_E11.5_G2VLo


title: RBG19669_KitHi_E11.5_G2VLo


title: RBG19609_KitHi_E11.5_G2VLo


title: RBG19633_KitHi_E11.5_G2VLo


title: RBG19621_KitHi_E11.5_G2VLo


title: RBG19644_KitHi_E11.5_G2VLo


title: RBG19632_KitHi_E11.5_G2VLo


title: RBG19680_KitHi_E11.5_G2VLo


title: RBG19692_KitHi_E11.5_G2VLo


title: RBG19656_KitHi_E11.5_G2VLo


title: RBG19668_KitHi_E11.5_G2VLo


title: RBG19620_KitHi_E11.5_G2VLo


title: RBG19691_KitHi_E11.5_G2VLo


title: RBG19631_KitHi_E11.5_G2VLo


title: RBG19619_KitHi_E11.5_G2VLo


title: RBG19608_KitHi_E11.5_G2VLo


title: RBG19666_KitHi_E11.5_G2VLo


title: RBG19655_KitHi_E11.5_G2VLo


title: RBG19679_KitHi_E11.5_G2VLo


title: RBG19667_KitHi_E11.5_G2VLo


title: RBG19642_KitHi_E11.5_G2VLo


title: RBG19678_KitHi_E11.5_G2VLo


title: RBG19689_KitHi_E11.5_G2VLo


title: RBG19654_KitHi_E11.5_G2VLo


title: RBG19606_KitHi_E11.5_G2VLo


title: RBG19618_KitHi_E11.5_G2VLo


title: RBG19665_KitHi_E11.5_G2VLo


title: RBG19677_KitHi_E11.5_G2VLo


title: RBG19641_KitHi_E11.5_G2VLo


title: RBG19653_KitHi_E11.5_G2VLo


title: RBG19629_KitHi_E11.5_G2VLo


title: RBG19605_KitHi_E11.5_G2VLo


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title: RBG19459_KitHi_E11.5_G2VLo


title: RBG19411_KitHi_E11.5_G2VLo


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title: RBG19315_KitHi_E11.5_G2VLo


title: RBG19482_KitHi_E11.5_G2VLo


title: RBG19494_KitHi_E11.5_G2VLo


title: RBG19458_KitHi_E11.5_G2VLo


title: RBG19470_KitHi_E11.5_G2VLo


title: RBG19364_KitHi_E11.5_G2VLo


title: RBG19446_KitHi_E11.5_G2VLo


title: RBG19483_KitHi_E11.5_G2VLo


title: RBG19434_KitHi_E11.5_G2VLo


title: RBG19398_KitHi_E11.5_G2VLo


title: RBG19410_KitHi_E11.5_G2VLo


title: RBG19422_KitHi_E11.5_G2VLo


title: RBG19374_KitHi_E11.5_G2VLo


title: RBG19386_KitHi_E11.5_G2VLo


title: RBG19362_KitHi_E11.5_G2VLo


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title: RBG19326_KitHi_E11.5_G2VLo


title: RBG19493_KitHi_E11.5_G2VLo


title: RBG19314_KitHi_E11.5_G2VLo


title: RBG19481_KitHi_E11.5_G2VLo


title: RBG19338_KitHi_E11.5_G2VLo


title: RBG19433_KitHi_E11.5_G2VLo


title: RBG19445_KitHi_E11.5_G2VLo


title: RBG19421_KitHi_E11.5_G2VLo


title: RBG19397_KitHi_E11.5_G2VLo


title: RBG19409_KitHi_E11.5_G2VLo


title: RBG19385_KitHi_E11.5_G2VLo


title: RBG19373_KitHi_E11.5_G2VLo


title: RBG19361_KitHi_E11.5_G2VLo


title: RBG19337_KitHi_E11.5_G2VLo


title: RBG19349_KitHi_E11.5_G2VLo


title: RBG19313_KitHi_E11.5_G2VLo


title: RBG19325_KitHi_E11.5_G2VLo


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title: RBG19456_KitHi_E11.5_G2VLo


title: RBG19444_KitHi_E11.5_G2VLo


title: RBG19432_KitHi_E11.5_G2VLo


title: RBG19420_KitHi_E11.5_G2VLo


title: RBG19408_KitHi_E11.5_G2VLo


title: RBG19457_KitHi_E11.5_G2VLo


title: RBG19384_KitHi_E11.5_G2VLo


title: RBG19360_KitHi_E11.5_G2VLo


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title: RBG19335_KitHi_E11.5_G2VLo


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title: RBG19466_KitHi_E11.5_G2VLo


title: RBG19478_KitHi_E11.5_G2VLo


title: RBG19418_KitHi_E11.5_G2VLo


title: RBG19406_KitHi_E11.5_G2VLo


title: RBG19394_KitHi_E11.5_G2VLo


title: RBG19430_KitHi_E11.5_G2VLo


title: RBG19455_KitHi_E11.5_G2VLo


title: RBG19334_KitHi_E11.5_G2VLo


title: RBG19442_KitHi_E11.5_G2VLo


title: RBG19322_KitHi_E11.5_G2VLo


title: RBG19370_KitHi_E11.5_G2VLo


title: RBG19382_KitHi_E11.5_G2VLo


title: RBG19310_KitHi_E11.5_G2VLo


title: RBG19395_KitHi_E11.5_G2VLo


title: RBG7553_KitHi_E11_G2VInt


title: RBG7565_KitHi_E11_G2VInt


title: RBG19383_KitHi_E11.5_G2VLo


title: RBG7564_KitHi_E11_G2VInt


title: RBG7527_KitHi_E11_G2VInt


title: RBG7539_KitHi_E11_G2VInt


title: RBG7540_KitHi_E11_G2VInt


title: RBG7563_KitHi_E11_G2VInt


title: RBG7551_KitHi_E11_G2VInt


title: RBG7552_KitHi_E11_G2VInt


title: RBG19454_KitHi_E11.5_G2VLo


title: RBG7562_KitHi_E11_G2VInt


title: T47D cells, Hypoxia rep 2

city: Edmonton

first: Laura

middle: Jiyoung

last: Lee

state: Alberta

address: 5-120 Katz Group Centre

department: Oncology

country: Canada

institute: University of Alberta

data_processing:
Read quality in fastq files were checked with FastQC (v0.11.5)
Fastq files were trimmed for adapter sequences using Skewer (v0.1.127)
Reads were aligned to hg19 human reference genome using STAR (v2.5.2a)
Read quantification via FeatureCounts (v1.5.1) was performed using Refseq annotations
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files show read counts with associated genomic coordinates and gene ID. These files were generated with FeatureCounts

source_name: Breast cancer

growth_protocol: T47D cells were grown in adherent culture with RPMI media supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using 5Prime RNA extraction kit
Libraries were prepared using mRNA stranded library preparation from NEB

treatment_protocol: Cells were placed in a hypoxia incubation chamber set to 0.5% O2. Normoxia control cells were grown under normal tissue culture conditions.

value: breast cancer cells

value: Hypoxia (0.5% O2, 48 hours)


title: T47D cells, Hypoxia rep 1


title: RBG19346_KitHi_E11.5_G2VLo


title: RBG7538_KitHi_E11_G2VInt


title: T47D cells, Normoxia rep 1

value: Control (20% O2)


title: RBG7561_KitHi_E11_G2VInt


title: RBG7549_KitHi_E11_G2VInt


title: RBG7537_KitHi_E11_G2VInt


title: RBG7541_KitHi_E11_G2VInt


title: RBG19469_KitHi_E11.5_G2VLo


title: RBG7572_KitHi_E11_G2VInt


title: RBG7525_KitHi_E11_G2VInt


title: RBG7571_KitHi_E11_G2VInt


title: RBG7524_KitHi_E11_G2VInt


title: DMEM_IP_1_S25

city: Portland

first: Mara

last: Sherman

state: OR

address: 2730 SW Moody Avenue CL6C

institute: Oregon Health & Science University

data_processing:
Reads trimmed using default paramters of Trim Galore! Version 0.4.3
Trimmed reads aligned to human reference genome GRCh38, release 87 using bowtie2 (version 2.3.4)
Alignments filtered for reads with MAPQ score >= 11 using samtools (version 1.3.1)
Duplicates removed using picard tools (version 2.9.0)
Peaks called using MACS2 (version 2.1.1.20160309)
Peaks filtered for known chromosomes only
common peaks shared between replicates determined by findOverlapsOfPeaks() from ChIPpeakAnno R package (version 3.14.2)
common peaks shared between treatments determined by findOverlapsOfPeaks() from ChIPpeakAnno R package (version 3.14.2)
Genome_build: GRCh38

source_name: DMEM

growth_protocol: Cells were maintained in DMEM + 10% FBS. At the start of the experiment, cells were washed once with sterile PBS and switched to fresh, serum-free DMEM for 48 hours.

extract_protocol:
Lysates were clarified from sonicated nuclei and MYC-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: MIAPaCa2 cells after 48-hour serum starvation were treated with fresh DMEM or conditioned media (CM) from cancer-associated fibroblasts for 3 hours.

value: Pancreatic ductal adenocarcinoma

tag: chip antibody

value: Cell Signaling Technology MYC Antibody #9402


title: RBG7560_KitHi_E11_G2VInt


title: DMEM_Input_S23


title: RBG7548_KitHi_E11_G2VInt


title: RBG7550_KitHi_E11_G2VInt


title: RBG7523_KitHi_E11_G2VInt


title: CM_Input_S24

source_name: conditioned media


title: CM_IP_2_S29


title: RBG7570_KitHi_E11_G2VInt


title: DMSO+DMF MED1 ChIP-seq

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 50
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Colon Carcinoma

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
sonication

treatment_protocol: Cells were treated with DMSO for 24 hours, washed once with media, followed by 6 hour DMF treatment.

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog

tag: agent

value: DMSO+DMF

value: Colon


title: JQ1+Cisplatin MED1 ChIP-seq

treatment_protocol: Cells were treated with 1uM JQ1 for 24 hours, washed once with media, followed by 50uM cisplatin treatment.


title: DMSO+Cisplatin MED1 ChiP-seq

treatment_protocol: Cells were treated with DMSO for 24 hours, washed once with media, followed by 6 hour 50uM cisplatin treatment.

value: DMSO+Cisplatin


title: T47D cells, Normoxia rep 2

tag: cell type


title: RBG7559_KitHi_E11_G2VInt


title: RBG7547_KitHi_E11_G2VInt


title: JQ1+DMF MED1 ChIP-seq

treatment_protocol: Cells were treated with 1uM JQ1 for 24 hours, washed with media, followed by a 6 hour DMF treatment.


title: SR-74_inf

city: Philadelphia

first: James

last: Garifallou

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC1014

department: Neonatology

institute: Children's Hospital of Philadelphia

description:
Infected Sample untreated
SR-74_inf_3451129796_S1

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v2  per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled,  and sequenced on an Illumina Hiseq sequencer in a paired-end, single indexing run. Sequencing for each library  targeted 20,000 mean reads per cell. We had a mean of 39,227 reads per cell post-normalization with 2,165 median  genes per cell. Data was then processed using the Cellranger pipeline (10x genomics, v.3.0.2) for demultiplexing and  alignment of sequencing reads to the GRCh38 transcriptome and creation of feature-barcode matrices. Individual  single cell RNAseq libraries were aggregated using the cellranger aggr pipeline. Libraries were normalized for  sequencing depth across all libraries during aggregation. Secondary analysis on the aggregated feature barcode matrix  was performed using the Seurat package (v.3.0) within the R computing environment. Briefly, cells expressing less  than 200 or more than 5000 genes were excluded from further analysis. Additionally, cells expressing >20%  mitochondrial genes were excluded from the dataset.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcode ID, feature ID and count matrix

source_name: human-induced pluripotent stem cell (HiPSC)

growth_protocol: scRNAseq Uninfected  iNeurons were differentiated as described  and re-plated on DIV2 to Matrigel coated Nunc Lab-Tek II  8-well chamber slides at 70k cells/well in iN media. On DIV5 of iNeuron differentiation, the iAstrocytes were added at 50k cells/well. On DIV7 of iNeuron differentiation, iMicroglia were added at 100k cell/well. Cultures were taken out to DIV21 of iNeuron differentiation.    scRNAseq Uninfected+EFZ  iNeurons were differentiated as described  and re-plated on DIV2 to Matrigel coated Nunc Lab-Tek II  8-well chamber slides at 70k cells/well in iN media. On DIV5 of iNeuron differentiation, the iAstrocytes were added at 50k cells/well. On DIV7 of iNeuron differentiation, iMicroglia were added at 100k cell/well. Cultures were taken out to DIV21 of iNeuron differentiation.    scRNAseq Infected  iNeurons were differentiated as described  and re-plated on DIV2 to Matrigel coated Nunc Lab-Tek II  8-well chamber slides at 70k cells/well in iN media. On DIV5 of iNeuron differentiation, the iAstrocytes were added at 50k cells/well. On DIV7 of iNeuron differentiation, iMicroglia were added at 100k cell/well. Cultures were taken out to DIV21 of iNeuron differentiation.    scRNAseq Infected+EFZ  iNeurons were differentiated as described  and re-plated on DIV2 to Matrigel coated Nunc Lab-Tek II  8-well chamber slides at 70k cells/well in iN media. On DIV5 of iNeuron differentiation, the iAstrocytes were added at 50k cells/well. On DIV7 of iNeuron differentiation, iMicroglia were added at 100k cell/well. Cultures were taken out to DIV21 of iNeuron differentiation.

extract_protocol:
Dataset consists of a total of six single-cell datasets generated using the 10x Genomics Chromium platform. Prior to GEM generation, the sample’s concentration (cells/ul) and viability (%) were determined by staining the cells with trypan blue and by manually counting using an inverted microscope.
Next-generation sequencing libraries were prepared following the 10X Single Cell v2 protocol without modification. Sample quality was evaluated using Agilent’s Bioanalyzer High Sensitivity reagent kit following cDNA amplification and library construction. The completed libraries were quantified using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were diluted to 2nM and sequenced in a paired-end, single-indexed format on the Illumina HiSeq2500 using the Rapid Run v2 chemistry. Cells were sequenced at a depth of 50.000 reads/cell.

treatment_protocol:
scRNAseq Uninfected+EFZ: EFZ was added at 20nM at each media exchange starting in the iMicroglia at what would be day 6 of the infection, through the full timeline of the tri-culture
scRNAseq Infected: iMicroglia were infected as decribed, and added to the tri-culture at d15 of the infection
scRNAseq Infected+EFZ: iMicroglia were infected as described and EFZ was added at 20nM at each media exchange starting in the iMicroglia at day 6 of the infection, through the full timeline of the tri-culture

value: Tri-culture of differentiated HiPSC into neurons, astrocytes, and microglia

tag: infection status

value: Infected with HIV

value: Untreated


title: RBG7569_KitHi_E11_G2VInt


title: RBG7558_KitHi_E11_G2VInt


title: SR-74_ia

description:
Infected Sample treated with anti-retroviral (replicate1)
SR-74_ia_4207436210_S1

value: Treated with Anti-retroviral


title: RBG7546_KitHi_E11_G2VInt

value: IAHC cells


title: SR-74_ca

description:
Uninfected control sample treated with anti-retroviral
SR-74_ca_6425713259_S1

value: Uninfected


title: DMEM_IP_2_S26


title: SR-74_ctl

description:
Uninfected and untreated control sample
SR-74_ctl_6636632695_S1


title: WT15_HIV

data_processing:
RNA-seq reads were demultiplexed using the DRAGEN genome pipeline (Goyal et al., 2017). FASTQ files were  aligned to hg19 reference using the STAR (v.2.6.1) (Dobin et al., 2013) aligner with default settings to produce BAM files
Generated BAM  files were read into the R statistical computing environment. Gene counts were obtained using the  GenomicAlignments package. FeatureCounts matrix was produced
Genome_build: hg19
Supplementary_files_format_and_content: Counts Matrix

growth_protocol: Bulk RNAseq iMg  iPSCs were differentiated into common myeloid progenitors (CMPs) according to the published protocol (Paluru et al., 2014) by the Human Pluripotent Stem Cell Core (CHOP). CMPs were plated at 333K cells / well in a 24-well Cellbind plate (Corning 3337). CMPs were differentiated in iMg media (RPMI 1640 media  with 10% FBS,  IL-34 (100ng/mL), , CSF-1 (25ng/mL), and  TGF-β1 (50ng/mL). Half media changes were performed every two days for 11 days.    Bulk RNAseq MDM  We receive donated buffy coat from New York Blood Center  Buffy coat was diluted 1:1 with PBS (without Ca2+ and Mg2+) . 15 mLs of Ficoll  was added to 50mL conical tubes. 25mLs of Buffy Coat/PBS was slowly layered onto the Ficoll. The PBMCs are spun and the supernatant was discarded, and the pellet resuspended in 10mLs of Red Blood Cell Lysis buffer. Cells were shaking at RT for 10 minutes. Cells were spun. The supernatant was discarded, and the pellet was resuspended in DMEM with 10% FBS + Gentamicin.  The PBMCs were plated on 6-well tissue culture plate for 5 days. On day 5, a full media exchange was performed  and added 10ng/mL Human GM-CSF. A half media exchange was performed on day 7. At day 10, RNA was collected    BulkRNAseq iAst  iPSCs transfected with the NGN2 virus were put through the first two days of the iNeuron differentiation. On day 3, cells were exposed to Astrocyte differentiation media: N2 media (without BDNF, NT-3, laminin, and doxycycline), 10% FBS, B-27 with vitamin-A, FGF-2 (20ng/mL) and EGF (20ng/mL). After 30 days, EGF was removed and FGF2 reduced to 5ng/mL. After 70 total days, cells were switched into Astrocyte Media for the 20 days.     Bulk RNAseq human astrocytes  human astrocytes were obtained from Sciencell. Cells were plated on PLL-coated plates  and grown for two weeks in Astrocyte media (Sciencell) and then RNA was extracted.

extract_protocol:
Bulk RNAseq iMg  Cells were washed twice with RT PBS, then lifted with StemPro accutase and spun down at 1,500 rpm for 5 min. Fresh cells were processed through Qiashredder and RNeasy mini kit  and frozen at -80°C.    Bulk RNAseq MDM  Cells were washed twice with RT PBS, then lifted with StemPro accutase and spun down at 1,500 rpm for 5 min. Fresh cells were processed through Qiashredder and RNeasy mini kit  and frozen at -80°C.    BulkRNAseq iAst  Cells were washed twice with RT PBS, then lifted with StemPro accutase and spun down at 1,500 rpm for 5 min. Fresh cells were processed through Qiashredder and RNeasy mini kit  and frozen at -80°C.    Bulk RNAseq human astrocytes  Cells were washed twice with RT PBS, then lifted with StemPro accutase and spun down at 1,500 rpm for 5 min. Fresh cells were processed through Qiashredder and RNeasy mini kit  and frozen at -80°C.
Next-generation sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA library preparation kit, using high quality RNA (RIN >= 8.7) and 200ng of input. Libraries were assessed for quality using the PerkinElmer Labchip GX and qPCR using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were diluted to 2nM and sequenced in a paired-end (2 x 100bp), dual-indexed format on the Illumina HiSeq2500 using the High Output v4 chemistry.

treatment_protocol: Bulk RNAseq iMg  For HIV infected sampls, at D11 of the iMg differentiation, iMg were infected with 50ng/mL JAGO stran HIV. A full media exchange was perfomred 24 hours later. Full media exchanges occurred ever 3 days for 15 days.    Bulk RNAseq MDM  n/a    BulkRNAseq iAst  n/a    Bulk RNAseq human astrocytes  n/a

value: iPSC lines for the iMg

value: exposed to 50ng/mL of JAGO strain HIV (UPenn Center  of Aids Research; CFAR) for 24 hours

tag: treatment group


title: SR-74_ia2

description:
Infected Sample treated with anti-retroviral (replicate2)
SR-74_ia2_3572755499_S2


title: WT15

value: untrt


title: RBG7534_KitHi_E11_G2VInt


title: CM_IP_1_S28


title: RBG7557_KitHi_E11_G2VInt


title: RBG7545_KitHi_E11_G2VInt


title: RBG7568_KitHi_E11_G2VInt


title: HA_25417

value: human astrocytes


title: HA_n3


title: RBG7520_KitHi_E11_G2VInt


title: 30C1_iAst

value: IPSC-derived astrocytes


title: 6C4_iAst


title: RBG7533_KitHi_E11_G2VInt


title: RBG7567_KitHi_E11_G2VInt


title: WT4_876


title: RBG7535_KitHi_E11_G2VInt


title: WT6_HIV_869


title: RBG7556_KitHi_E11_G2VInt


title: RBG7544_KitHi_E11_G2VInt


title: WT10_869


title: MDM3_847

value: monocyte derived macrophage


title: RBG7532_KitHi_E11_G2VInt


title: HA_835


title: MDM1_808


title: RBG7519_KitHi_E11_G2VInt


title: RBG7566_KitHi_E11_G2VInt


title: WT10_HIV_389


title: WT6_286


title: RBG7543_KitHi_E11_G2VInt


title: RBG7555_KitHi_E11_G2VInt


title: SC_263


title: RBG7531_KitHi_E11_G2VInt


title: RBG7542_KitHi_E11_G2VInt


title: MDM2_165


title: si_ERK3_t24_R3

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0b)
The ENSEMBL Homo_sapiens.GRCh38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v79) was used.
Exploratory data analysis was performed with the pcaExplorer package (version version 2.8.0, Marini et al., 2019)
Differential expression analysis was performed with DESeq2 (version 1.22.1), setting the False Discovery Rate to 0.05
Accurate estimation of the effect sizes (in terms of log fold change) is performed using the apeglm shrinkage estimator (version 1.4.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts as input matrix to DESeq2

source_name: Human Colonic Primary Epithelial Cells (HCPECs_

growth_protocol: Minimum Essential Medium Eagle’s (MEM) supplemented with 10% heat inactivated FBS, 2 mM L-glutamine and 1 mM sodium pyruvate.

extract_protocol:
After the stimulation cells were washed with cold PBS and lysed with Trizol (Cat# 15596018, Ambion) according to the manufacturer’s instructions. Total RNA was quantified by a Qubit 2.0 fluorometer (Invitrogen) and quality was assessed using Agilent’s bioanalyzer 2100 and a RNA 6000 Nano chip (Agilent). Samples with RNA integrity number (RIN) > 8 were further subjected for RNA library preparation. Barcoded cDNA libraries were prepared from 300 ng of total RNA using the NEBnext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the provided instruction. Library quantity was assessed on a Qubit 2.0 using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s Bioanalyzer 2100 and a HS DNA assay chip. Barcoded RNA-Seq libraries were onboard clustered using HiSeq Rapid SR Cluster Kit v2 using 8pM and 59 bps were sequenced on an Illumina HiSeq2500 using a HiSeq Rapid SBS kit v2.
Barcoded cDNA libraries were prepared from 300 ng of total RNA using the NEBnext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the provided instruction.
Library quantity was assessed on a Qubit 2.0 using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s Bioanalyzer 2100 and a HS DNA assay chip.
Barcoded RNA-Seq libraries were onboard clustered using HiSeq Rapid SR Cluster Kit v2 using 8pM and 59 bps were sequenced on an Illumina HiSeq2500 using a HiSeq Rapid SBS kit v2.

treatment_protocol: Three biological replicates of HCPEC were seeded in 12-well plates at initial density of 2x105 cells/well. 24 h later cells were transiently transfected with either control siRNA (siCo) or siRNA targeting ERK3 (siERK3). 24 h post-transfection medium was exchanged for MEM-FBS and other supplements and cells were stimulated with LPS (200 ng/ml) for 24 h.

tag: stimulation

value: 24h LPS


title: RBG7554_KitHi_E11_G2VInt


title: RBG7530_KitHi_E11_G2VInt


title: RBG7517_KitHi_E11_G2VInt

value: EC


title: RBG7433_KitHi_E11_G2VInt


title: control_t0_R3


title: control_t24_R3

value: siCo


title: RBG7505_KitHi_E11_G2VInt


title: RBG7493_KitHi_E11_G2VInt


title: si_ERK3_t24_R2


title: RBG7481_KitHi_E11_G2VInt


title: control_t24_R2


title: RBG7469_KitHi_E11_G2VInt


title: si_ERK3_t24_R1


title: control_t0_R2


title: si_ERK3_t0_R1


title: RBG7516_KitHi_E11_G2VInt


title: RBG7457_KitHi_E11_G2VInt


title: control_t24_R1


title: RBG7504_KitHi_E11_G2VInt


title: control_t0_R1


title: RBG7480_KitHi_E11_G2VInt


title: si_ERK3_t0_R3


title: si_ERK3_t0_R2


title: RBG7456_KitHi_E11_G2VInt


title: P2672_N729-S506

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 and QC assessment 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.
Smart-seq2 libraries were mapped as paired-end reads using STAR 2.5.4b and RSEM 1.3.0 for the quantification.
10x RNA-Seq libraries: We processed sequencing reads with CellRanger v3.0.0 for the PBMC data and v3.0.2 for the CLL and T-cell activation data. We used the human GRCh38 assembly as reference genome. To specify the hashtag oligonucleotide (HTO) libraries, the cDNA libraries and the HTO sequences, we followed the “Feature Barcoding Analysis” pipeline, available at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis. We set the --chemistry and --expect-cells flags of cellranger count to “SC3Pv3" and “5000”, respectively. We demultiplexed cell hashtags as described in Stoeckius et al. for each batch and donor separately. Briefly, we normalized hashtag oligonucleotide (HTO) counts using a centered log ratio (CLR), in which each count is divided by the geometric mean of a HTO across cells and log-transformed. We then clustered barcodes using k-medoids with k equal to the number of conditions (k=4 for batch 03, and k=8 for batch 04), which allowed us to identify the background distribution of each HTO. We re-clustered Male 04 with k=3, as no clear signal for the HTO “24h 4ºC” was detected. Subsequently, we considered the top 0.5% normalized HTO counts of the background distribution as outliers and excluded them. We classified barcodes to a given condition if the normalized HTO counts of that condition exceeded the 0.99 quantile. We discarded both barcodes that were assigned to more than one condition (multiplets) and barcodes that were not assigned to any condition (negatives). In subsequent datasets (CLL and T-cell activation), we demultiplexed the HTO with Seurat’s built-in functions.
10X ATAC-Seq libraries were processed with the Cell Ranger ATAC 1.1.0 pipeline
Quality control and normalization: We performed quality control (QC) and normalization separately for each dataset (PBMC, CLL, T-cell activation). Following the guidelines from Luecken et al.], we inspected the distributions of three main QC metrics: library size (total UMI), library complexity (number of detected genes) and mitochondrial expression. Importantly, we analyzed these metrics jointly to ensure that cells with high mitochondrial expression were not metabolically active. Finally, we analyzed one of the CLL donors independently as it showed markedly different distributions in QC metrics. We classified as damaged cells those barcodes with an aberrantly low number of UMI and genes, or with an abnormally high mitochondrial expression. Likewise, we classified as doublets those barcodes that possessed and aberrantly large library size and complexity. We also leveraged DoubletFinder to detect doublets that shared the same HTO and were not outliers in any qc metric. We ruled out genes that were detected in less than 10 (CLL) or 15 cells (T-cell activation). Finally, we used the Scran 1.10.2 package to normalize UMI counts with cell-based size factors.
Smart-seq2 validation: To confirm that the results obtained from 10x Genomics-derived data were technology-independent, we profiled the transcriptome of 376 CD3+ T-cells with Smart-seq2[30]. The cells originated from the same donors as in the 10x Genomics experiments, and were distributed across four 96-well plates (all time points per plate). We discarded 60 cells that either had <75,000 or >1,000,000 total counts, <435 detected genes or a mitochondrial expression >20%. Similarly, we filtered out 6,542 genes that had an average expression across cells <1. We normalized gene counts with the Scran package, which removed the batch effect between plates.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression matrices:    10x Genomics and ATAC-Seq: Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. It also contains tab-separated values (TSV) files with feature and barcode sequences corresponding to row and column indices respectively. In addition, for ATAC-Seq data, a BED file with the genome coordinates for the peaks is included.      Smart-seq2: Tab-separated values (TSV) files containing gene expression values as row counts.

source_name: blood

extract_protocol:
Peripheral venous blood samples were collected by venipuncture from two voluntary blood donors, one male and one female. Blood samples were collected in ACD-tubes and stored at room temperature (RT) or 4ºC. In the former condition peripheral blood mononuclear cells (PBMC) were isolated at 2, 8, 24 and 48 h. For samples stored at 4ºC, PBMC were isolated at 24 and 48hrs. PBMC separation was performed using Ficoll density gradient centrifugation. For each condition, 12 ml of blood were diluted with an equal volume of pre-warmed RPMI 1640 culture medium (Lonza). The diluted blood was then carefully layered onto a Leucosep tube (Greiner Bio‐One) prefilled with 15 ml of Ficoll-Plus (GE Healthcare Biosciences AB) and centrifuged for 15 min at 800 x g and RT (without acceleration and brake). After centrifugation, PBMC were collected with a sterile Pasteur pipette into a 50 ml tube, diluted up to 10 ml with pre-warmed RPMI medium and centrifuged for 10 min, at 400 x g and RT. Following a second washing step with 5 ml of RPMI medium and a 5 min centrifugation, PBMC were resuspended in 8 aliquots of freezing media. Freezing media consisted of RPMI 1640 with 20% heat-inactivated fetal bovine serum (Sigma-Aldrich), 10% DMSO (Sigma-Aldrich) and Penicillin-Streptomycin 1:1000 (Lonza). 1 ml aliquots, with approximately 1x10e6 cells/ml, were gradually frozen using a commercial freezing box (Mr. Frosty, Nalgene) at -80°C for 24 h and then stored in a vapor–phase liquid nitrogen tank at -150ºC.
Cryopreserved (-80ºC) PBMC samples were rapidly thawed in a 37ºC water bath. Each sample was transferred into a 15 ml Falcon using a 1000 ul cut tip without mixing by pipetting. Next, 1 ml of 37ºC pre-warmed media (Hibernate-A supplemented with 10% FCS; ThermoFisher) was added drop-wise with gentle swirling of the sample. After 1 min incubation, 2 ml of pre-warmed media were added and incubated for 1 min. Next, 5 ml pre-warmed media was gently added, inverted and incubated (1 min). This step was repeated once. Finally, the samples were centrifuged at 700 x g for 5 min (4ºC). The supernatant was removed and the pellets re-suspended in 100 ul of Cell staining buffer (BioLegend). Of note, we did not observe an increase of damaged/dead cells (cell viability staining) towards the later time points with an average viability of 95% (range: 88-98%) across time points. An increased fraction of debris could be observed at 24 and 48 hours, which, however, did not result in reduced data quality (e.g. proportion of excluded cells) during data analysis (Additional file 7: Table 6).
CLL patient samples were obtained from freshly extracted blood, stored either at RT or 4ºC. Mononuclear cells were isolated after Ficoll density gradient centrifugation, at 2, 4, 6, 8 and 24 h after patient blood extraction. The cells were directly cryopreserved with freezing media (RPMI 1640 with 20% FBS and 10% DMSO), in the concentration of 5-10x10e6 cells/ml, according to standarized protocol. The tumor cell content of all the samples was >80%, as assassed by immunostaining of CD19, CD20, CD5 and CD45 followed by flow cytometry. All patients gave informed consent for their participation in the study according to International Cancer Genome Consortium (ICGC) guidelines.
Cell hashing was performed following manufacturer’s instructions (Cell hashing and Single Cell Proteogenomics Protocol Using TotalSeq™ Antibodies; BioLegend). Therefore, samples were incubated 10 min at 4ºC with Human TruStain FcX™ Fc Blocking reagent (BioLegend). Next, sample-specific TotalSeq antibodies (anti-human Hashtag 1-8, Biolegend) were added with subsequent incubation on ice for 45 min. Cells were washed once with cold 1X PBS supplemented with 0.0005% BSA (ThermoFisher) and pelleted at 700 x g for 5 minute. A single cell solution was obtained resuspending the pellet in 1X PBS (0.0005% BSA) and filtering it through a 40 µm cell strainer. The cells were counted in an automatic cell counter (Countess v.2, ThermoFisher).
Single-cell ATAC sequencing:
For the single-cell ATAC-seq experiments, we analyzed one PBMC and one CLL sample isolated after 0 h, 8 h and 24 h of blood storage at room temperature before cryopreservation. Frozen samples were rapidly thawed in a 37°C water bath. Each sample was transferred into a 15 ml Falcon using a 1000 µl cut tip without mixing by pipetting. Next, 1 ml of 37°C pre-warmed media (Hibernate-A supplemented with 10% FCS) was added drop-wise with gentle swirling of the sample. After 1 min of RT incubation, additional 2 ml of pre-warmed media were added. The samples were again kept at RT for 1 min, before 5 ml of pre-warmed media were gently added. This step was repeated once. Then, samples were centrifuged at 700 x g for 5 min. Supernatant was removed and the pellets resuspended in 500 µl of PBS supplemented with 0.05% BSA. Cell concentration and viability were determined with a TC20™ Automated Cell Counter.
Nuclei isolation was performed following the “Nuclei Isolation for Single Cell ATAC Sequencing demonstrated protocol” (10x Genomics). Briefly, 1,000,000 cells from the CLL sample and 300,000 cells from PBMC, were transferred to a 1.5 ml microcentrifuge tube and centrifuged at 500 x g for 5 min at 4°C. The supernatant was removed without disrupting the cell pellet and 100 µl of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette-mixed 10 times. Samples were then incubated on ice during 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette-mixed. Nuclei were centrifuged at 500 x g for 5 min at 4°C and the supernatant removed without disrupting the pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 1,540-3,850 nuclei/µl, suitable for a Target Nuclei Recovery of 5000. The resulting nuclei concentration was determined using a with a TC20 Automated Cell Counter.
Single cell 3’ libraries were prepared using the 10x Genomics Single Cell 3’ Reagent Kit v2, together with the 10x Chromium Controller microfluidic platform according to manufacturer’s instructions (10x Genomics). In summary, our hashed samples (adjusted to 1000 cells/ul) were loaded into a 10x Chip A, together with the RT mix, barcoded beads and partioning oil. After 10x Chromium Controller processing, reaction was incubated 45 min at 53ºC and 5 min at 85ºC. Next, the cDNA was purified with silane magnetic beads. The cDNA amplification was performed using the cDNA amplification primer, plus a Hashtag oligonucleotide (HTO, Supplementary Table 4), and 25 PCR cycles. In order to separate the TotalSeq™ Hashtag fraction from the amplified cDNA a second purification was performed (see TotalSeq™-A Cell Hashing and TotalSeq™-A Antibodies Protocol for Simultaneous Proteomics and Transcriptomics with 10X Single Cell 3' Reagent Kit v2 protocol) and HTO specifically amplified and indexed (Supplementary Table 3. Finally, sequencing of HTO (5%) and cDNA (95%) libraries was carried out on a HSeq2500 (Illumina).
For Smart-seq2 libraries, we profiled the transcriptome of 376 PBMC. The cells originated from the same donors as in the 10x Genomics experiments, and were distributed across four 96-well plates (all conditions per plate). We discarded 60 cells that either had <75,000 or >1,000,000 total counts, <435 detected genes or a mitochondrial expression >20%. Similarly, we filtered out 6,542 genes that had an average expression across cells <1. We normalized gene counts with the Scran package, which removed the batch effect between plates.
scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits User Gu

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