title: MDA-ER-beta E2 #1

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

data_processing: The data were normalized using Faster cyclic loess (Fastlo) in R

source_name: MDA-ER-beta E2

extract_protocol: Total RNA was extracted from cells using Trizol per the manufacturer's recommendation.

treatment_protocol: MDA-MB-231-ER-beta cells were plated in 10 cm dishes and allowed to grow to approximately 80% confluence in DMEM/F12 medium containing 10% charcoal stripped FBS and Doxycycline (100 ng/ml, to induce ER-beta expression).  Cells were subsequently treated with ethanol vehicle or 1 nM estradiol for 5 days.  Media was changed on day 3 to refresh treatments.

value: Triple Negative Breast Cancer Cell Line

tag: treated with

value: 17-beta estradiol for 5 days


title: F0-CO-6d

status: Public on Aug 23 2018

type: SRA

city: Mainz

first: Piyush

last: More

address: Langenbeckstrasse 1

department: Department of Pharmacology

country: Germany

institute: University Medical Center, Johannes Gutenberg University of Mainz

description: F0 mice

library_source: transcriptomic

data_processing:
Quality of raw sequencing reads was checked using FastQC version 0.11.5 (Babraham Bioinformatics, Cambridge, UK)
RNA-Seq reads were aligned to the GRCm38 genome (GENCODE) using STAR aligner version 2.5.3a (Dobin A et al., Bioinformatics, 2013, 29(1):15-21) with the option "--quantMode GeneCounts"
Differential gene expression analysis was performed using edgeR version 3.20.1 (Robinson MD et al., Bioinformatics, 2010, 26(1):139-140)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include mapped gene counts for each sample
Supplementary_files_format_and_content: XLS files include differential gene expression analysis using edgeR

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: All animal experiments conformed to the Guide for the Care and Use of Laboratory Animals published by the US National Institutes of Health, and they were approved by the responsible local ethics committee. C57BL/6J were obtained from Envigo (Venray, Netherlands). Maximally 5 animals per cage were kept on a 12 h light cycle at a temperature of 20–24°C and 45-65% humidity. Females were housed individually beginning with the last three days before giving birth.

extract_protocol:
Total hepatic RNA was isolated from livers of adult mice using TriFast (PeqLab, Erlangen, Germany). The hepatic RNA from newborn mice was isolated with RNeasyKit (Qiagen, Hilden, Germany).
The library was prepareed using TruSeq RNA Library Prep Kit (Illumina) at Star SEQ GmbH, Mainz, Germany

treatment_protocol: Three-day-old F0 mice were injected with TCPOBOP (3 mg/kg, i.p.) in corn oil or with corn oil alone.

tag: strain

tag: age

value: 5-6 days

tag: tissue

value: Liver

tag: treatment

value: Corn oil


title: H3_ChIP-seq_biotin_Parental_rep2

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

library_source: genomic

data_processing:
Base calling software: Casava 1.8.2
Reads were aligned to  human genome assembly (GRCh37/hg19) using Bowtie v. 1.1.2 with parameters -m1 --best.
PCR duplicates were removed using rmDup v. 2-0  and unique mapped reads were extended to 500bp to account for the average library size.
Reads were summed in 250 bp non-overlapping bins and values were normalized to Reads Per Million (RPM).
Peak calling was performed with MACS v. 2.0.9 under broad domain parameters using Parental ChIP-seq of Total H3 from each experiment as a reference.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedgraph files were generated using Galaxy. Scores represent the sum of RPM in 250bp windows

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa S3 cells

growth_protocol: Human HeLa S3 cells were grown in suspension in spinners in DMEM medium (Thermo Fisher Scientific) supplemented with dialyzed FBS (Invitrogen) and penicillin and streptomycin at 37ºC and 5% CO2.

extract_protocol:
Fixed cells were lysed during 20 min in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with proteases inhibitors, passed through a 21G needle and sonicated using a Bioruptor nextGen (Diagenode) to obtain chromatin frgament size of 250-500bp. Sonicated chromatin was centrifuged at 14000rpm at 4ºC for 10 min and the supernatant used for subsequent steps. Chromatin associated to each histone mark was obtained by incubating sonicated chromatin with the corresponding antibody.After ChIP, chromatin was separated from Protein A agarose beads by an incubation with Elution buffer (10 mM Tris HCL, 1 mM EDTA, 2 % SDS, 15 mM DTT, pH 8 supplemented with protease inhibitors) for 30 min at 37 ºC in rotation. Supernatant was diluted 20 times with RIPA and chromatin was then incubated with MyOne Streptavidin T1 beads. For single streptavidin pull-downs, 30 μg of input chromatin was used in the following steps. Briefly, MyOne streptavidin T1 beads were blocked by incubating with 1μg/ml free biotin (Sigma) for 10 min at room temperature. Beads were then washed three times with RIPA buffer and chromatin was pre-cleared with blocked beads for 1 h at 4 ºC. After pre-clearing, supernatant was incubated with new non-blocked T1 streptavidin beads over night at 4 ºC. Beads were then washed for 5 min rotating at room temperature, once with RIPA buffer, twice with 2 % SDS, once with RIPA 0.5 M NaCl, once with 1X LiCl buffer and twice with TE buffer. Chromatin was then purified and decrosslinked.
Libraries were costructed using the NEB Next Ultra DNA Library prep kit (New England Biolabs) following manufacturer’s instructions.Samples were indexed and 4 different samples sequenced together.

treatment_protocol: For all ChOR-seq and ChIP-seq, HeLa S3 cells were synchronized at the G1/S border by single thymidine block (2 mM, 17 h) and released into fresh media containing deoxycytidine (24 μM). Parental samples were collected 1 hour before labelling. 3h and 15 min after release, DNA was labelled during 20 min with medium containing biotin-dUTP and Nascent chromatin was collected (T0). For each time-course experiment, replicated DNA was isolated by single Streptavidin pull-down on Nascent chromatin. Harvested cells were immediately fixed in 1% formaldehyde for 15 min.  Fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT.

tag: cell line

value: HeLa S3

tag: cell type

value: cervical carcinoma

tag: ezh2i treatment

value: Non treated

tag: spike-in

value: NO

tag: labelling

value: biotin-dUTP

tag: cell cycle

value: Early S (2 h and 15 min after release)

tag: antibody

value: Total H3 (Abcam, Cat No. Ab179, RRID:AB_302613)


title: Live male pupa shipped april 2017 for HiC library preparation - replicate 2

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

description:
processed data file:
AGWG.0_0.hic, AGWG.0_30.hic, AGWG.0_asm.scaffold_track.txt, AGWG.0_asm.superscaf_track.txt, AGWG.0.assembly, AGWG.0.hic, AGWG.1_0.hic, AGWG.1_30.hic, AGWG.1_asm.scaffold_track.txt, AGWG.1_asm.superscaf_track.txt, AGWG.1.assembly, AGWG.1.hic, AGWG.1.review.assembly, AGWG.draft_0.hic, AGWG.draft_30.hic, AGWG.draft_asm.scaffold_track.txt, AGWG.draft_asm.superscaf_track.txt, AGWG.draft.assembly, AGWG.draft.fasta.gz, AGWG.draft.hic, AGWG.draft.mnd.txt.gz, AGWG.edits.txt, AGWG.final.fasta.gz, AGWG.HiC.fasta.gz, AGWG.rawchrom_0.hic, AGWG.rawchrom_30.hic, AGWG.rawchrom_asm.scaffold_track.txt, AGWG.rawchrom_asm.superscaf_track.txt, AGWG.rawchrom.hic, AGWG.rawchrom_tiled_0.hic, AGWG.rawchrom_tiled_30.hic, AGWG.rawchrom_tiled.asm, AGWG.rawchrom_tiled_asm.scaffold_track.txt, AGWG.rawchrom_tiled_asm.superscaf_track.txt, AGWG.rawchrom_tiled.assembly, AGWG.rawchrom_tiled.hic, AGWG.rawchrom_tiled.review_0.hic, AGWG.rawchrom_tiled.review_30.hic, AGWG.rawchrom_tiled.review.asm, AGWG.rawchrom_tiled.review_asm.scaffold_track.txt, AGWG.rawchrom_tiled.review_asm.superscaf_track.txt, AGWG.rawchrom_tiled.review.assembly, AGWG.rawchrom_tiled.review.hic, alignments.txt, contributing_2D_asm.txt, Liverpool2_30.hic, Liverpool2.hic, mega_30.hic, mega.hic, not_contributing_2D_asm.txt, overlap_qc_track_2D_asm.txt, overlaps_2D_asm_post_tiling.txt, overlaps_2D_asm.txt, overlaps_2D_input.txt, suspect_2D.at.step.0.txt, suspect.at.step.0.bed

data_processing:
library strategy: Hi-C
The paired end reads were processed against the draft genome assemblies using Juicer tool for Hi-C experiments (Durand et al. 2016) to produce merged_nodups.txt files, a duplicate-free list of paired alignments of Hi-C reads to the draft fasta.
The merged_nodups.txt files were used as input into a 3D-DNA Hi-C assembly pipeline (see Dudchenko et al. 2017), with algorithmic modification included at https://github.com/theaidenlab/AGWG-merge and a review step in Juicebox Assembly Tools (Dudchenko et al. 2018) to create chromosome-length assembly fasta files.
The paired end reads were processed against the chromosome-length assemblies using Juicer tool for Hi-C experiments (Durand et al. 2016) to create genome-wide Hi-C contact maps compatible with Juicebox visualization tool for Hi-C contact maps (hic-files). Additional filtration was applied for contact matrices for Samples 2 and 3 (Aedes aegypti) to remove contact pairs from poly-G reads.
A detailed description of the procedure can be found at https://github.com/theaidenlab/AGWG-merge
Genome_build: AaegL5.0
Supplementary_files_format_and_content:
AGWG.draft.fasta.gz: the FALCON-Unzip output
AGWG.draft.mnd.gz: list of paired alignments of Hi-C reads (combined from three in situ Hi-C experiments SRR6294665, SRR6294663, SRR6294664) to the draft FALCON-Unzip fasta as generated by the Juicer pipeline
AGWG.draft.assembly: text file format, generated by 3D-DNA and Juicebox Assembly Tools, that stores the relationship between the original draft sequences and the output assembly
AGWG.draft.hic, AGWG.draft_0.hic and AGWG.draft_30.hic: Hi-C contact maps in the .hic file format compatible with Juicebox and Juicebox Assembly Tools thresholded at mapping quality 1, 0 and 30, respectively, generated by 3D-DNA visualization module
AGWG.draft_asm.scaffold_track.txt and AGWG.draft_asm.superscaf_track.txt: 2D annotation tracks marking down the boundaries of scaffolds and superscaffolds, respectively, as generated by 3D-DNA visualization module
AGWG.0.assembly: .assembly file generated by 3D-DNA for preliminary scaffolding
AGWG.0.hic, AGWG.0_0.hic, AGWG.0_30.hic: Hi-C contact maps, as generated by the 3D-DNA pipeline visualization module, thresholded at mapping quality 1, 0 and 30, respectively, for preliminary scaffolding
AGWG.0_asm.scaffold_track.txt and AGWG.0_asm.superscaf_track.txt: 2D annotation tracks for preliminary scaffolding, as generated by 3D-DNA visualization module for preliminary scaffolding
suspect_2D.at.step.0.txt, suspect_2D.at.step.0.bed, AGWG.edits.txt: files, annotating misjoined regions in the draft contigs
AGWG.1.assembly: .assembly file generated by 3D-DNA for scaffolding the input contigs after misjoin correction
AGWG.1.hic, AGWG.1_0.hic, AGWG.1_30.hic: Hi-C contact maps as generated by the 3D-DNA pipeline visualization module, thresholded at mapping quality 1, 0 and 30, respectively, for round of scaffolding after misjoin correction
AGWG.1_asm.scaffold_track.txt and AGWG.1_asm.superscaf_track.txt: 2D annotation tracks for scaffolding after misjoin correction as generated by 3D-DNA visualization module
AGWG.1.review.assembly: .assembly file as exported by Juicebox Assembly Tools to polish and split the AGWG.1.assembly into chromosomes
AGWG.rawchrom.hic, AGWG.rawchrom_0.hic, AGWG.rawchrom_30.hic: Hi-C contact maps as generated by the 3D-DNA pipeline visualization module, thresholded at mapping quality 1, 0 and 30, respectively, for reviewed assembly results
AGWG.rawchrom_asm.scaffold_track.txt and AGWG.rawchrom_asm.superscaf_track.txt: 2D annotation tracks for reviewed assembly as generated by 3D-DNA visualization module
alignments.txt, overlaps_2D_input.txt, overlaps_2D_asm.txt, overlaps_2D_asm_post_tiling.txt:list of all pairwise alignments between nearby contigs that fit the alignment score, overlap length, position and sequence identity criteria to be marked as alternative haplotypes, as generated by the 3D-DNA merge module, as well as the associated 2D track files
AGWG.rawchrom_tiled.asm, AGWG.rawchrom_tiled.assembly:assembly file listing merge blocks -- chains of overlapping contigs organized based on alignment information -- as identified by the 3D-DNA merge module and a Juicebox Assembly Tools-compatible version of the same file
AGWG.rawchrom_tiled.hic, AGWG.rawchrom_tiled_0.hic, AGWG.rawchrom_tiled_30.hic:Hi-C contact maps as generated by the 3D-DNA pipeline visualization module, thresholded at mapping quality 1, 0 and 30, respectively, for automatic tiling
AGWG.rawchrom_tiled_asm.scaffold_track.txt, AGWG.rawchrom_tiled_asm.superscaf_track.txt:2D annotation tracks for automatic tiling as generated by 3D-DNA visualization module
AGWG.rawchrom_tiled.review.asm, AGWG.rawchrom_tiled.review.assembly:the curated version of the file AGWG.rawchrom_tiled.asm listing chains of overlapping contigs and the Juicebox Assembly Tools-compatible version of the same file
AGWG.rawchrom_tiled.review.hic, AGWG.rawchrom_tiled.review_0.hic, AGWG.rawchrom_tiled.review_30.hic: Hi-C contact maps as generated by the 3D-DNA pipeline visualization module, thresholded at mapping quality 1, 0 and 30, respectively, for the tiled assembly after curation
AGWG.rawchrom_tiled.review_asm.scaffold_track.txt, AGWG.rawchrom_tiled.review_asm.superscaf_track.txt: 2D annotation tracks for this step as generated by 3D-DNA visualization module, illustrating the assembly with tiled alternative haplotypes
AGWG.final.fasta.gz: haploid contigs generated by 3D-DNA via merging overlapping sequences within individual merge blocks
overlap_qc_track_2D_asm.txt, contributing_2D_asm.txt and not_contributing_2D_asm.txt: 2D track files that facilitate comparison of iterative and pairwise alignments as well as classify individual contig contributions to final haploid reference, as generated by the 3D-DNA merge module
AGWG.HiC.fasta.gz: final chromosome-length scaffolds as generated by the 3D-DNA finalize module
Liverpool1.hic, Liverpool1_30.hic: Hi-C contact maps created by realigning the Hi-C data from SRR6294665 experiment to the haploid chromosome-length AaegL5 reference, as generated by the Juicer pipeline, thresholded at mapping quality 1 and 30, respecitvely
Liverpool2.hic, Liverpool2_30.hic: Hi-C contact maps created by realigning the Hi-C data from SRR6294663 experiment to the haploid chromosome-length AaegL5 reference, as generated by the Juicer pipeline, thresholded at mapping quality 1 and 30, respectively
Liverpool3.hic, Liverpool3_30.hic: Hi-C contact maps created by realigning the Hi-C data from SRR6294664 experiment to the haploid chromosome-length AaegL5 reference, as generated by the Juicer pipeline, thresholded at mapping quality 1 and 30, respectively
mega.hic, mega_30.hic: contact maps, created by combining data from all three Hi-C experiments listed above

organism: Aedes aegypti

source_name: Live male pupa shipped april 2017 for HiC-library

extract_protocol:
Insect tissue was crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
Standard Illumina library construction protocol. 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 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the NextSeq500 following the manufacturer's protocols.
In situ Hi-C (Rao, Huntley et al., 2014)

tag: Sex

value: male

tag: developmental stage

value: pupa


title: U87_shPRMT2_input

status: Public on Aug 22 2018

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

country: China

institute: Tianjin medical university

data_processing:
RNA-seq analysis was completed by BGI company(Shenzhen,China). For ChIP-seq, Clean reads were obtained from sequencing company.
Clean reads were aligned to human reference genome (hg19) using Bowtie2 version 2.2.9. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS version 1.4.2. and ChIPseeker package respectively.
Heatmaps and average profiles were generated by deepTools V2.4.0.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include FPKM values for each sample. For ChIP-seq, bigwig files were generated using deepTools V2.4.0, score represents the normalized coverage of  DNA fragments at a given genomic coordinate.

growth_protocol: The glioblastoma cell lines U87 was cultured in DMEM containing 10% fetal bovine serum (FBS). TPC1115 was obtained from fresh surgical specimens of human primary GBMs and cultured as either monolayer or tumorspheres in DMEM/F12 medium supplemented with N2, B27 (Gibco), 20 ng/ml human Fibroblast Growth Factor-basic (bFGF, Sino Biological, Beijing, China), 20 ng/ml Epidermal Growth Factor-basic (EGF, Sino Biological, Beijing, China).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Construction of ChIP-seq library was completed according to Illumina's instructions accompanying the NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs #E7370)

treatment_protocol: U87 cells were infected with shPRMT2 lentivirus

value: glioblastoma cells

tag: transfected with

value: shPRMT2 lentivirus

tag: chip antibody


title: F0-TCPOBOP-6d

description: F0 mice

value: TCPOBOP


title: F0-TCPOBOP-3m

description: F0 mice

value: 3 months


title: MDA-ER-beta E2 #1 rpt

type: RNA

city: Cambridge

country: United Kingdom

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Doxycycline-inducible ER-beta expressing MDA-MB-231cells were maintained in phenol red-free DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS), 1% antibiotic-antimycotic (AA), 5 mg/L blasticidin S and 500 mg/L zeocin.

value: Triple Negative Breast Cancer Cell Line

value: 17-beta estradiol for 5 days


title: MDA-ER-beta Veh. #3 rpt

source_name: MDA-ER-beta Veh.

value: ethanol vehicle for 5 days


title: U87_shPRMT2_H3K27me3

value: H3K27me3 (Cell Signaling Technology, Cat#9733)


title: Input_biotin_rep1

value: HeLa S3

value: Mid S (3 h and 15 min after release)


title: MDA-ER-beta Veh. #3


title: T7 primase (residue: 1-271) at 5 uM concentration

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: no hybridiztion

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

label: Alexa 488

molecule: protein

organism: Escherichia phage T7

source_name: T7 primase

label_protocol: Proteins were tagged with N-terminal His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen).

growth_protocol: We have used T7 primase containing His tag at the N terminus. The T7 primase domain (residue: 1-271) was constructed, over-produced and purified as previously described (Zhu B, Lee S-J, Richardson CC JBC 2009 284(35)23842). Briefly, the coding region of T7 gene 4 primase domain was inserted into pET28b (EMD Biosciences), and the coding region in this plasmid was confirmed by DNA sequencing.

extract_protocol: Extraction protocol is based on a modified protocol described before (Ilic S et al., 2016 Sci. Reports), except that the purification step was based upon Ni-NTA purification and a subsequent step of gel filtration. For expression of His-tagged protein, a starter culture was used to inoculate 1 L of LB medium containing 50 µg/mL kanamycin. When the culture optical density (600 nm) reached approximately 0.7, it was induced for protein overexpression with 0.5 mM isopropyl-β-D-thiogalactopyranoside (IPTG) for 3 h at 37°C. The cells were harvested by centrifugation (4,700 x g for 20 minutes). The cell pellet was resuspended in buffer A (50 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.1mM DTT) containing 0.25 mg/ml Lysozyme and 1 mM PMSF and incubated on ice for 1 h. After four freeze-thaw cycles, streptomycin sulfate was added until it reached a concentration of 1%. After centrifugation at 15,000 × g for 30 minutes, supernatant was diluted with buffer A and loaded onto a prepacked Ni-NTA affinity column (GE Healthcare) in the presence of 10 mM imidazole. T7 primase bound to the Ni-NTA column was eluted using buffer A containing a gradient of imidazole from 10 to 500 mM. Fractions containing primase were combined and ammonium sulfate was added (0.4 g/ml). The precipitate was dissolved in 5 mL buffer A and was loaded onto a superdex S-200HR column and eluted using Buffer B (50 mM Tris-HCl pH 7.5, 0.1mM DTT, 1mM EDTA, 50mM NaCl). The fractions containing purified T7 DNA primase were combined and dialyzed against buffer C (50mM Tris-HCl pH 7.5, 1mM DTT, 1mM EDTA, 50% glycerol) and stored at -20oC. The purified His tagged protein was ~95% pure as determined by SDS-PAGE analysis and has comparable activity as the wild type gene 4 protein. In addition, it has been shown previously that the tag at the N-terminus  supports the growth of T7∆4 phage (Zhu B, Lee S-J, Richardson CC JBC 2009 284(35)23842), thus the tag does not affect our analysis.

tag: protein

value: T7 primase

tag: protein concentration


title: Live male pupa shipped april 2017 for HiC library preparation - replicate 1

description:
processed data file:
AGWG.0_0.hic, AGWG.0_30.hic, AGWG.0_asm.scaffold_track.txt, AGWG.0_asm.superscaf_track.txt, AGWG.0.assembly, AGWG.0.hic, AGWG.1_0.hic, AGWG.1_30.hic, AGWG.1_asm.scaffold_track.txt, AGWG.1_asm.superscaf_track.txt, AGWG.1.assembly, AGWG.1.hic, AGWG.1.review.assembly, AGWG.draft_0.hic, AGWG.draft_30.hic, AGWG.draft_asm.scaffold_track.txt, AGWG.draft_asm.superscaf_track.txt, AGWG.draft.assembly, AGWG.draft.fasta.gz, AGWG.draft.hic, AGWG.draft.mnd.txt.gz, AGWG.edits.txt, AGWG.final.fasta.gz, AGWG.HiC.fasta.gz, AGWG.rawchrom_0.hic, AGWG.rawchrom_30.hic, AGWG.rawchrom_asm.scaffold_track.txt, AGWG.rawchrom_asm.superscaf_track.txt, AGWG.rawchrom.hic, AGWG.rawchrom_tiled_0.hic, AGWG.rawchrom_tiled_30.hic, AGWG.rawchrom_tiled.asm, AGWG.rawchrom_tiled_asm.scaffold_track.txt, AGWG.rawchrom_tiled_asm.superscaf_track.txt, AGWG.rawchrom_tiled.assembly, AGWG.rawchrom_tiled.hic, AGWG.rawchrom_tiled.review_0.hic, AGWG.rawchrom_tiled.review_30.hic, AGWG.rawchrom_tiled.review.asm, AGWG.rawchrom_tiled.review_asm.scaffold_track.txt, AGWG.rawchrom_tiled.review_asm.superscaf_track.txt, AGWG.rawchrom_tiled.review.assembly, AGWG.rawchrom_tiled.review.hic, alignments.txt, contributing_2D_asm.txt, Liverpool3_30.hic, Liverpool3.hic, mega_30.hic, mega.hic, not_contributing_2D_asm.txt, overlap_qc_track_2D_asm.txt, overlaps_2D_asm_post_tiling.txt, overlaps_2D_asm.txt, overlaps_2D_input.txt, suspect_2D.at.step.0.txt, suspect.at.step.0.bed


title: U87_shPRMT2_H3K9me3

value: H3K9me3 (Cell Signaling Technology, Cat#13969)


title: U87_shPRMT2_H3K4me3

value: H3K4me3 (Cell Signaling Technology, Cat#9751)


title: Live male pupa shipped april 2017 for HiC library preparation - replicate 3

description:
processed data file:
AGWG.0_0.hic, AGWG.0_30.hic, AGWG.0_asm.scaffold_track.txt, AGWG.0_asm.superscaf_track.txt, AGWG.0.assembly, AGWG.0.hic, AGWG.1_0.hic, AGWG.1_30.hic, AGWG.1_asm.scaffold_track.txt, AGWG.1_asm.superscaf_track.txt, AGWG.1.assembly, AGWG.1.hic, AGWG.1.review.assembly, AGWG.draft_0.hic, AGWG.draft_30.hic, AGWG.draft_asm.scaffold_track.txt, AGWG.draft_asm.superscaf_track.txt, AGWG.draft.assembly, AGWG.draft.fasta.gz, AGWG.draft.hic, AGWG.draft.mnd.txt.gz, AGWG.edits.txt, AGWG.final.fasta.gz, AGWG.HiC.fasta.gz, AGWG.rawchrom_0.hic, AGWG.rawchrom_30.hic, AGWG.rawchrom_asm.scaffold_track.txt, AGWG.rawchrom_asm.superscaf_track.txt, AGWG.rawchrom.hic, AGWG.rawchrom_tiled_0.hic, AGWG.rawchrom_tiled_30.hic, AGWG.rawchrom_tiled.asm, AGWG.rawchrom_tiled_asm.scaffold_track.txt, AGWG.rawchrom_tiled_asm.superscaf_track.txt, AGWG.rawchrom_tiled.assembly, AGWG.rawchrom_tiled.hic, AGWG.rawchrom_tiled.review_0.hic, AGWG.rawchrom_tiled.review_30.hic, AGWG.rawchrom_tiled.review.asm, AGWG.rawchrom_tiled.review_asm.scaffold_track.txt, AGWG.rawchrom_tiled.review_asm.superscaf_track.txt, AGWG.rawchrom_tiled.review.assembly, AGWG.rawchrom_tiled.review.hic, alignments.txt, contributing_2D_asm.txt, Liverpool1_30.hic, Liverpool1.hic, mega_30.hic, mega.hic, not_contributing_2D_asm.txt, overlap_qc_track_2D_asm.txt, overlaps_2D_asm_post_tiling.txt, overlaps_2D_asm.txt, overlaps_2D_input.txt, suspect_2D.at.step.0.txt, suspect.at.step.0.bed


title: U87_shPRMT2_H3R8me2a

value: H3R8me2a (Novus Biologicals, Cat#NB21-1062, Lot A-1)


title: MDA-ER-beta E2 #3

tag: treated with


title: U87_shPRMT2_H3K4me1

value: H3K4me1 (Cell Signaling Technology, Cat#5326)


title: MDA-ER-beta E2 #2


title: U87_scramble_input

value: scramble control


title: U87_scramble_H3K27ac


title: U87_shPRMT2_H3K27ac


title: U87_scramble_H3K4me1


title: RhBMDMsinfected with M. tuberculosis H37Rv isogenic dosS deletion mutant strain  for 4 hour- Replicate 2

city: Covington

first: Uma

middle: S

last: Gautam

state: LA

address: 18703 Three Rivers Road

department: Bacteriology and Parasitology

institute: TNPRC

description: Biological replicate 1 of 3

scan_protocol: As described in previous publication Gautam et al 2010 PMID: 26270051 As described in previous publication Gautam et al 2010 PMID: 26270051

data_processing: Data analysis procedures have been described in detail in the above referenced previous publications from our group. Briefly, data was extracted from 16 BIT TIFF files scanned using GenePix 4000B scanner (5um res) using GenePix pro 7.0 and then uploaded to Spotfire DecisionSite for Microarray Analysis. Array data was then filtered for abberant SNR, flags etc and normalized using the S+ ArrayAnalyzer LOWESS normalization script resident within Spotfire. Statistical significance was determined using Spotfire. Analyzed data were then exported to Excel.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis H37Rv isogenic dosS deletion mutant bacterial RNA isolated from infected RhBMDMs at 0 hour (0 hour means 4hr incubation of macrophages with M. tuberculosis H37Rv isogenic mutant strain of dosS gene deletion)

growth_protocol: Rh-BMDMs were cultured as previously described (Mehra et al 2010 PMCID: PMC3052882 and Dutta et al 2012 PMCID: PMC3250399 and M. tuberculosis cultures were grwon following th eprotocol decribed by Gautam et al 2010 (PMID: 26270051 )

tag: strain/genotype

tag: source

value: Intraphagosomal M. tuberculosis H37Rv isogenic mutant bacterial RNA isolated from infected macrophages 4 hr post infection

source_name: M. tuberculosis H37Rv isogenic dosS deletion mutant bacterial RNA isolated from in vitro grown cultures in 7H9 media and not in macrophages were used as baseline control

value: H37Rv isogenic mutant bacterial strain of dosS gene deletion

value: M. tuberculosis H37Rv isogenic mutant bacterial RNA isolated from in vitro grown cultures and not in macrophages


title: RhBMDMsinfected with M. tuberculosis H37Rv isogenic dosS deletion mutant strain  for 4 hour- Replicate 3

description: Biological replicate 1 of 3

hyb_protocol: As described in previous publication Gautam et al 2010 PMID: 26270051

value: H37Rv isogenic mutant strain of dosS gene deletion


title: U87_scramble_H3K9me3

value: glioblastoma cells

value: H3K9me3(Cell Signaling Technology, Cat#13969)


title: U87_scramble_H3K4me3


title: arle-14 ChIP rep1

first: Susan

middle: E.

last: Mango

state: MA

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Reads were aligned to the C. elegans reference genome (ce10) with Bowtie2 (version 2.3.1), using default parameters and '--very-sensitive'.
Log-likelihood-ratio tracks were created using MACS2 (version 2.1.1.20160309).  For each sample: $ macs2 callpeak -t ${sample}_ChIP.bam -c ${sample}_Input.bam -f BAMPE -g ce --keep-dup all --bdg --SPMR; macs2 bdgcmp -t ${sample}_treat_pileup.bdg -c ${sample}_control_lambda.bdg -o ${sample}_logLR.bdg -m logLR -p 0.00001
LogLR tracks were converted to BigWig using linux sort and the UCSC tool bedGraphToBigWig.  For each sample: $ sort -k1,1 -k2,2n ${sample}_logLR.bdg > ${sample}_logLR_sort.bdg; bedGraphToBigWig ${sample}_logLR_sort.bdg ce10genome.txt ${sample}_logLR.bw
Correlations of the logLR-bigWig files were calculated using the UCSC tool wigCorrelate.
Genome_build: ce10
Supplementary_files_format_and_content: bigWigs of log-likelihood-ratio tracks produced by 'macs2 bdgcmp'

organism: Caenorhabditis elegans

source_name: embryonic lysate

growth_protocol: Mix-staged embryos were collected from adult worms by bleaching. Embryos were shaken at 200rpm at 20oC in CSM medium (100mM NaCl, 5.6mM K2HPO4, 4.4mM KH2PO4, 10μg/ml cholesterol, 10mM potassium citrate, 2mM CaCl2, 2mM MgSO4, 1X trace metals.) without food. Once the embryos hatched and became L1s, concentrated NA22 bacteria were added to the culture. Synchronized embryos were harvested by bleaching after 62-66 hours when most worms carried 1-8 embryos, frozen in liquid nitrogen and stored at -80oC.

extract_protocol:
H3K9me2 ChIP was done as described previously (Hsu et. al, Science 2015) with the following changes: Embryos frozen in liquid nitrogen were thawed on ice and fixed in 1.5% Formaldehyde (Electron Microscopy Sciences, #15686) for 15 minutes at room temperature. Using the QSonica Q800 Sonicator, samples were sonicated at 30% amplitude, 30 seconds ON, 30 seconds OFF for a total of 15 minutes at 4oC, yielding 100-300 base pair fragments. 6μl of MABI0307 H3K9me2 antibody was coupled to 25μl beads (Pierce Protein A/G magnetic beads, #88802) for 8 hours at 4oC prior to ChIP. 40 μg of chromatin was used per ChIP reaction and chromatin was pre-cleared for 2 hours at 4°C using uncoupled magnetic beads (Pierce #88802). To elute the bound immunocomplexes, 150 μL of elution buffer (50mM NaHCO3, 140mM NaCl, 1% SDS) was added to each tube and heated at 65°C for 15 minutes.
The ChIP-Seq libraries were generated by using the Apollo 324 System and PrepX ILM DNA Library Kit from IntergenX. After adaptor ligation, the input and ChIP DNA were enriched by PCR amplification using NEBNext High-Fidelity 2X PCR master Mix with Q5 polymerase and PrepX PCR primer with the following PCR conditions: 30 seconds at 98°C, [10 seconds at 98°C, 30 seconds at 60°C, 30 seconds at 72°C] for 8 cycles for Input libraries and 11 cycles for ChIP libraries, followed by 5 minutes at 72°C (~15 uL adaptor ligated DNA, 25 uL NEBNext High-Fidelity 2X PCR master Mix, 2uL Universal PCR primer, brought to to 50ul with Nuclease-Free water). The enriched DNA was then purified using 50 uL (1:1 ratio of DNA volume and beads) of PCR Clean DX Beads (Aline) and size selected by Pippin Prep, 180-600bp. 1 uL of each library was applied to measure the concentration using a Qubit dsDNA assay kit (Invitrogen). 1 ng of DNA from each library was checked by a TapeStation (Agilent Technologies). Input and ChIP libraries were pooled such that they had the same expected number of sequence reads.

value: anti-H3K9me2  (MABI0307)

tag: genotype


title: arle-14 Input rep2


title: arle-14 ChIP rep2


title: MDA-ER-beta Veh. #2

tag: cell line

value: Triple Negative Breast Cancer Cell Line

value: ethanol vehicle for 5 days


title: RhBMDMsinfected with M. tuberculosis H37Rv wild type strain for 4 hour- Replicate 2

description: Biological replicate 1 of 3

source_name: M. tuberculosis H37Rv bacterial RNA isolated from infected RhBMDMs at 0 hour (0 hour means 4hr incubation of macrophages with M. tuberculosis H37Rv )

label_protocol: As described in previous publication Gautam et al 2010 PMID: 26270051

value: H37Rv wild type strain

value: Intraphagosomal M. tuberculosis H37Rv bacterial RNA isolated from infected macrophages 4 hr post infection

source_name: M. tuberculosis H37Rv bacterial RNA isolated from in vitro grown cultures in 7H9 media and not in macrophages were used as baseline control

value: M. tuberculosis H37Rv bacterial RNA isolated from in vitro grown cultures and not in macrophages


title: RhBMDMsinfected with M. tuberculosis H37Rv wild type strain for 4 hour- Replicate 3

description: Biological replicate 1 of 3

extract_protocol: As described in previous publication Gautam et al 2010 PMID: 26270051


title: U87_scramble_H3R8me2a

tag: cell type


title: RhBMDMsinfected with M. tuberculosis H37Rv isogenic dosS deletion mutant strain  for 4 hour- Replicate 1

description: Biological replicate 1 of 3


title: U87_scramble_H3K27me3

value: H3K27me3 (Cell Signaling Technology, Cat#9733)


title: arle-14 Input rep1


title: RhBMDMsinfected with M. tuberculosis H37Rv wild type strain for 4 hour- Replicate 1

description: Biological replicate 1 of 3


title: MDA-ER-beta Veh. #1


title: TransAscl1Rep3

city: Stanford

first: Lei

middle: Stanley

last: Qi

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

description:
Ascl1 trans-differentiated Tuj1+ neurons
embryonic fibroblast

data_processing:
Reads were aligned with STAR v2.5 to both ENSEMBL transcriptome and mm10 genome.
Differential gene expression between groups was assessed by edgeR
Genome_build: mm10
Supplementary_files_format_and_content: logCPM.txt is a table of gene-level moderated log counts per million per sample computed by edgeR

growth_protocol: CamES-derived neuronal cells driven by sgRNAs were purified with PSA-NCAM at day 12. MEF-derived neuronal cells driven by the overexpression of cDNAs were purified with PSA-NCAM at day 12.

extract_protocol:
Total RNA was purified using RNeasy Plus Mini Kit (Qiagen).
Library preparation and next-generation sequencing were performed by Novogene Corporation, Chula Vista, CA.

tag: source cell type

value: Mef


title: TransNeurog1Ezh2Rep1

description:
Ezh2+Neurog1 trans-differentiated Tuj1+ neurons
embryonic fibroblast


title: TransEzh2Brn2Rep1

description:
Ezh2+Brn2 trans-differentiated Tuj1+ neurons
embryonic fibroblast


title: TransEzh2Brn2Rep2

source_name: Ezh2+Brn2 trans-differentiated Tuj1+ neurons


title: TransNeurog1Ezh2Rep2

source_name: Ezh2+Neurog1 trans-differentiated Tuj1+ neurons


title: Suz12Rep3

description:
Suz12 induced Tuj1 positive neurons
embryonic stem cells

source_name: Suz12 induced Tuj1 positive neurons

value: CamES


title: TransEzh2Brn2Rep3


title: TransNeurog1Ezh2Rep3


title: TransAscl1Rep2

source_name: Ascl1 trans-differentiated Tuj1+ neurons


title: Suz12Rep4


title: Suz12Rep1


title: Suz12Rep2


title: Neurog1Rep3

description:
Neurog1 induced Tuj1 positive neurons
embryonic stem cells

source_name: Neurog1 induced Tuj1 positive neurons


title: Neurog1Rep1


title: JunRep4

description:
Jun induced Tuj1 positive neurons
embryonic stem cells

source_name: Jun induced Tuj1 positive neurons


title: JunRep3


title: TransAscl1Rep1


title: JunRep1


title: Ezh2Rep2

description:
Ezh2 induced Tuj1 positive neurons
embryonic stem cells

source_name: Ezh2 induced Tuj1 positive neurons


title: Neurog1Ezh2Rep4

description:
Neurog1 + Ezh2 induced Tuj1 positive neurons
embryonic stem cells


title: Neurog1Rep4


title: Neurog1Rep2


title: CamEsRep6

description:
dCas9-SunTag expressing mouse embryonic stem cells
embryonic stem cells

value: CRISPRa mouse embryonic stem cells


title: CamEsRep3

source_name: dCas9-SunTag expressing mouse embryonic stem cells


title: Neurog1Ezh2Rep2

source_name: Neurog1 + Ezh2 induced Tuj1 positive neurons


title: MefRep3

description:
mouse embryonic fibroblasts
embryonic fibroblast

source_name: mouse embryonic fibroblasts

value: Mouse embryonic fibroblast


title: CamEsRep1


title: Ascl1Rep2

description:
Asc1 induced Tuj1 positive neurons
embryonic stem cells

source_name: Asc1 induced Tuj1 positive neurons


title: MefRep2


title: MefRep1


title: JunRep2


title: Ezh2Rep3


title: Neurog1Ezh2Rep1


title: Neurog1Ezh2Rep3


title: Ascl1Rep4


title: CamEsRep2


title: Ascl1Rep1


title: Ascl1Rep3


title: Ezh2Rep1


title: G3

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Sequencing reads were trimmed to 50 bp and mapped to the mouse genome (mm9) using Tophat v2.1.1. Mapped reads (~95% of total reads) were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: mm9
Supplementary_files_format_and_content: The gene expression table is tab-delimited and is in the following format: <GeneSymbol> <FPKM>

source_name: mouse primary embryo fibroblast

growth_protocol: Isolation of primary mouse embryonic fibroblasts (MEF): The embryos were removed from the uterus and freed from surrounding membranes in a sterile dish. After rinsing for several times in a culture dish containing PBS, the embryos were transferred to a fresh culture dish and minced with scissors until they could be pipetted (clumps about 1 mm in diameter). Trypsin/EDTA solution was then added, and the clumps were incubated at 37°C for 10-15 min with periodical pipetting. The digestion was monitored by checking the suspension under a microscope. After passing through 70 µm nylon filter, the pellet was re-suspended and plated in culture medium).

extract_protocol:
RNA were isolated from WT, Gadd45a-/-, G3Terc-/- and G3-dKO MEF cells using TRI reagent.
RNA was pre-treated with DNase and processed following Illumina manufacturer’s instructions: magnetic beads with oligo (dT) were used to isolate polyadenylated mRNA (polyA+ mRNA) from the total RNA. Fragmentation buffer containing divalent cations was added for shearing mRNA to short fragments of 200 to 700 nucleotides in length. These short fragments were used as templates to synthesize the first-strand cDNA using random hexamer-primer. Second-strand cDNA was synthesized using buffer including dNTPs, RNase H, and DNA polymerase I. The products were purified with QIAquick PCR Purification Kit and then subjected to end preparation, dA tailing, sequencing adapter ligation and PCR amplification.

tag: genotype/variation

value: G3 Terc-/-

value: primary embryo fibroblast

tag: strain


title: CamEsRep4


title: WT

value: Wild-type


title: KO


title: Ezh2Rep4


title: CamEsRep5


title: G3KO

value: G3 Gadd45-/-Terc-/- (dKO)


title: Nr4a1-/- VAT AP rep4

city: Pittsburgh

first: Yang

last: Zhang

state: PA

address: 100 Technology Dr.

department: Medicine

institute: University of Pittsburgh

description:
YZ16_KO_V_MACS_4
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts

data_processing:
Sequence alignment (BAM) files: Sequencing reads are aligned to the reference genome  using the RNA-specific STAR aligner.
Experimental QC: In addition to the quality-control performed following sequencing  (FastQC), we use the Broad Institute's RNA-SeQC tool to assess the quality of the  experiment following sequence alignment
Normalized read-count files: We use the featureCounts tool to count sequencing  reads mapping to the reference genome at the gene level. The counts are  subsequently normalized between samples (using DESeq) to control for  experimental sources of variation (e.g. library depth). These count-based files are the  basis of many current RNA-Seq genomic analyses.
Second normalized read-count files: We will use the RUV-Seq tool to normalize the  sequencing reads mapping to the reference genome to spike-in gene sets: ERCC RNA  Spike-in Mix
Differential expression analysis: Using the DESeq software suite, differential expression  analysis is performed between the desired experimental contrasts for both normalization  methods independently.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited output files (opened with spreadsheet programs  such as MS Excel) summarize the analysis results, indicating summary expression data  and P-values for differential transcript expression on the gene level.

source_name: adipose progenitors

extract_protocol:
Purification of total RNA isolated from APs of Nr4a1+/+ and Nr4a1-/- mice was performed using an RNeasy Micro Kit (Qiagen). Genomic DNA was removed using a DNA-free DNA removal kit (Ambion). RNA was analyzed by Qubit® RNA BR Assay Kit (ThermoFisher Scientific) according to the manufacturer’s instructions.
Sequencing libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit (NEB). RNA-Seq experiments were run using Single Read 75 flowcells on an Illumina NextSeq 500 platform.

tag: strains

tag: fat tissue location

value: visceral

tag: age


title: Nr4a1-/- VAT AP rep3

description:
YZ15_KO_V_MACS_3
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: RhBMDMs infected with MtbΔdosR for 24 hour- Replicate 2

description: Biological replicate 1 of 2

scan_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844; Dutta et al 2012 PMCID: PMC3250399; Mehra et al 2012 PMCID:PMCID: PMC3308902; Mehra et al 2013 PMID: 23255564 Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

organism: Macaca mulatta

source_name: MtbΔdosR mutant infected Rhesus Bone Marrow Derived Macrophages, 24 hour

growth_protocol: Rh-BMDMs were cultured as previously described (Mehra et al 2010 PMCID: PMC3052882 and Dutta et al 2012 PMCID: PMC3250399

extract_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844 and Dutta et al 2012 PMCID: PMC3250399

value: 4-5 years old

value: Rhesus Bone Marrow Derived Macrophages

tag: macrophages

value: infected with Mtb{delta}dosR

tag: culture/treatment

value: Indian Rhesus macaque bone marrow derived macrophages were cultured and infected with MtbΔdosR

source_name: Uninfected Rhesus Bone Marrow Derived Macrophages

tag: infection

value: Uninfected


title: Nr4a1-/- VAT AP rep2

description:
YZ14_KO_V_MACS_2
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: RhBMDMs infected with MtbΔdosT for 24 hour- Replicate 2

description: Biological replicate 1 of 2

hyb_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844; Dutta et al 2012 PMCID: PMC3250399; Mehra et al 2012 PMCID:PMCID: PMC3308902; Mehra et al 2013 PMID: 23255564

source_name: MtbΔdosT mutant infected Rhesus Bone Marrow Derived Macrophages, 24 hour

value: infected with Mtb{delta}dosT

value: Indian Rhesus macaque bone marrow derived macrophages were cultured and infected with MtbΔdosT


title: RhBMDMs SiRNA-Silenced for TNF and infected with MtbΔdosS for 24 hour- Replicate 1

description: Biological replicate 1 of 2

source_name: MtbΔdosS mutant infected Rhesus Bone Marrow Derived Macrophages, 24 hour

label_protocol: As described in previous publications including Mehra et al 2010 PMCID: PMCID: PMC2930844; Dutta et al 2012 PMCID: PMC3250399; Mehra et al 2012 PMCID:PMCID: PMC3308902; Mehra et al 2013 PMID: 23255564

value: silenced for TNF expression and infected with Mtb{delta}dosS

value: Indian Rhesus macaque bone marrow derived macrophages were cultured, silenced for TNF and  infected with MtbΔdosS


title: RhBMDMs infected with MtbΔdosR for 24 hour- Replicate 1

description: Biological replicate 1 of 2


title: Nr4a1-/- SAT AP rep3

description:
YZ11_KO_SQ_MACS_3
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts

value: subcutaneous


title: RhBMDMs SiRNA-Silenced for TNF and infected with MtbΔdosS for 24 hour- Replicate 2

description: Biological replicate 1 of 2


title: RhBMDMs infected with MtbΔdosS for 24 hour- Replicate 1

description: Biological replicate 1 of 2

source_name: MtbΔdosS mutant infected Rhesus Bone Marrow Derived Macrophages, 24 hour incubation

value: infected with Mtb{delta}dosS

value: Indian Rhesus macaque bone marrow derived macrophages were cultured and infected with MtbΔdosS


title: AP isolated from VAT from biological replicate 3

hyb_protocol: Following fragmentation,  41 uL of cDNA were hybridized for 16 hr at 45 C on GeneChip GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.

label: Biotin

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA using amplification kit WT PLUS, Lot # 4220250, followed by labeling 5.5 ug cDNA using kit WT PLUS, Lot # 4220250.

growth_protocol: Fresh isolated cells and tissues

extract_protocol: Total RNA were extracted by Qiagen Rneasy Micro Kit.

tag: white adpose tissue ocation

value: visceral adipose tissue


title: Unfractionated AT specimens from SAT from biological replicate 1

source_name: adipose tissue

value: subcutaneous adipose tissue


title: Nr4a1-/- SAT AP rep1

description:
YZ9_KO_SQ_MACS_1
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: Unfractionated AT specimens from VAT from biological replicate 3


title: AP isolated from VAT from biological replicate 1


title: RhBMDMs infected with MtbΔdosT for 24 hour- Replicate 1

description: Biological replicate 1 of 2


title: Nr4a1-/- VAT AP rep1

description:
YZ13_KO_V_MACS_1
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: RhBMDMs infected with MtbΔdosS for 24 hour- Replicate 2

description: Biological replicate 1 of 2


title: Nr4a1+/+ VAT AP rep4

description:
YZ8_WT_V_MACS_4
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts

value: wild type


title: AP isolated from SAT from biological replicate 2


title: AP isolated from SAT from biological replicate 3


title: Unfractionated AT specimens from VAT from biological replicate 2


title: AP isolated from SAT from biological replicate 1


title: Nr4a1-/- SAT AP rep4

description:
YZ12_KO_SQ_MACS_4
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: Unfractionated AT specimens from SAT from biological replicate 2


title: Nr4a1-/- SAT AP rep2

description:
YZ10_KO_SQ_MACS_2
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: AP isolated from VAT from biological replicate 2


title: Nr4a1+/+ VAT AP rep3

description:
YZ7_WT_V_MACS_3
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: Unfractionated AT specimens from SAT from biological replicate 3


title: Unfractionated AT specimens from VAT from biological replicate 1


title: Nr4a1+/+ SAT AP rep3

description:
YZ3_WT_SQ_MACS_3
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: VAT AP rep1

data_processing:
Bowtie2 was used to align sequencing reads to the mm9 genome build.
MACS2 narrowPeak was used to call peaks for ATAC-seq Comparisons of genomic loci were performed with BEDOPS and mapping reads to genomic loci was performed with Bamliquidator
Enhancer identification was carried out using ROSE2
Network construction utilized the coltron python package
Genome_build: mm9

growth_protocol: Fresh isolated AP from mouse adipose tissue.

extract_protocol:
Samples were washed in PBS, then lysed in 10 mM Tris-HCL 0.1% IGEPAL buffer, followed by transposition reaction using Nextera DNA Transposase for 30 minutes at 37 degrees.  DNA was then isolated using Qiagen MinElute PCR purification.
Sequencing libraries were generated as described (Buenrostro Nat Methods 2013) by PCR with Nextera index sequences.

treatment_protocol: No additional treatment

value: 16 wks


title: VAT AP rep2

value: visceral


title: Nr4a1+/+ VAT AP rep1

description:
YZ5_WT_V_MACS_1
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: Nr4a1+/+ VAT AP rep2

description:
YZ6_WT_V_MACS_2
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: jimpy 1D oligodendrocyte differentiation

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

description: Oligodendrocyte progenitor cells induced to form oligodendrocytes for one day, according to Najm et al. 2011.

data_processing:
Raw reads were processed as described (Macosko et al., 2015). The sequenced libraries yielded 50-base paired-end reads. For read one bases 21-50 were trimmed since only bases 1-20 contain the identifiers (bases 1-12 represent the cell barcode and bases 13-20 denote the unique molecular identifier [UMI]).
Read one with quality scores of less than 10 were removed. Read two was trimmed at the 3’ end if ployA tails were present and at the 5’ end if the template switching oligo adapter sequence appeared.
The resulting reads were aligned to iGenomes mm9 RefSeq transcriptome using STAR v.2.5 (Dobin et al., 2013) with default settings.
Mapped reads were filtered to contain only uniquely mapped, exonic reads. PCR duplicates with the same coordinates, cell barcode, and UMI were discarded.
Reads were then grouped by cell barcode, generating a digital UMI-count matrix quantifying the number of unique transcripts per gene.
Genome_build: mm9
Supplementary_files_format_and_content: DGE(Digital gene expression) table was generated.   Row stands for genes; Column stands for single cells.  Number is the transcripts number(UMI) of any given gene in any given cell

molecule: polyA RNA

growth_protocol: OPCs were differentiated to oligodendrocytes for 1 day in oligodendrocyte differentiation media which consisted of N2B27 media DMEM/F12 (11320082, Thermo Fisher), 1x N2 supplement (AR009, R&D Systems), 1x B-27 without vitamin A supplement (12587-010, Thermo Fisher), and 1x Glutamax (35050061, Thermo Fisher) supplemented with 100ng/mL noggin (3344-NG, R&D Systems), 10ng/mL neurotrophin-3 (NT-3; 267-N3, R&D Systems), 50 μM cAMP (D0260, Sigma), 100ng/mL insulin-like growth factor-1 (IGF-1; 291-G1, R&D Systems) NT-3, and 40ng/mL triiodothyronine (thyroid hormone; T-6397, Sigma).

extract_protocol:
Drop-Seq was performed as previously described (Macosko et al., 2015). In brief, three individual syringes containing cell suspension at 200,000 cells/mL) barcoded mRNA capture beads (MACOSKO-2011-10, ChemGenes) in lysis buffer (prepared according to instructions in Drop-Seq protocol (Macosko et al., 2015) at 200,000 beads/mL, and QX200 droplet generation oil (186-4006, Bio-Rad), respectively, were placed in a Legato™ 100 pump (788100, Analytical West). Each output was connected to a custom-made PDMS co-flow microfluidic droplet generation device (Nanoshift) under microscope supervision. Cell and bead flow was set to 4,000uL/hr, and oil flow was set to 15,000uL/hr during droplet generation. These settings were optimized to allow at most one bead per one cell. Droplets were collected and then broken to release beads.
First strand cDNA synthesis with incorporation of a PCR handle was performed on the collected beads using the Maxima H Minus Reverse Transcriptase (EP0752, Thermo Fisher). The resulting full-length cDNA library was prepared for sequencing as described (Macosko et al., 2015)

value: B6CBACa/J Aw-J/A

tag: source (ipsc line)


title: wild-type 1D oligodendrocyte differentiation


title: Nr4a1+/+ SAT AP rep2

description:
YZ2_WT_SQ_MACS_2
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: Nr4a1+/+ SAT AP rep4

description:
YZ4_WT_SQ_MACS_4
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts


title: Thalamus [P60THRep1P2]

city: Boston

first: Arpiar

last: Saunders

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
P60THRep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt

data_processing:
Sequencing was performed on an Illumina NextSeq500 using a 75 cycle kit (Read1: 20bp; Read2: 50 bp).
Sequencing Reads were aligned against the GRCm38.81 mouse genome draft using STAR.
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1.
A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: *.raw.dge.txt: Digital gene expression matrix; comma-delimited file with columns = cells, and rows = transcript counts.
Supplementary_files_format_and_content: metacells.BrainCellAtlas_Saunders_version_2018.04.01.csv: Comma-delimited digital gene expression matrix (ncol = 565, nrow =32307).

source_name: P60-70 Male Mice

extract_protocol: Drop-seq (Macosko et al. 2014 Cell).

treatment_protocol: Acute brain slices digested for 3 hrs with a protease cocktail before titration, centrifugation to isolate debris-depleted single cells.

tag: strain/background

tag: gender

value: Male

tag: tissue

value: Thalamus


title: Thalamus [P60THRep4P2]

description:
P60THRep4P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep4P3]

description:
P60SNRep4P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt

value: Substantia Nigra/Ventral Tegmental Area


title: Thalamus [P60THRep4P1]

description:
P60THRep4P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep3P1]

description:
P60THRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep2P2]

description:
P60THRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep1P1]

description:
P60THRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Nr4a1+/+ SAT AP rep1

description:
YZ1_WT_SQ_MACS_1
raw_count_matrix.sort.primary.counts
normalized_count_matrix.sort.primary.counts

tag: genotype


title: SAT AP rep2


title: SAT AP rep1


title: Thalamus [P60THRep6P2]

description:
P60THRep6P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep6P1]

description:
P60THRep6P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep5P2]

description:
P60THRep5P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep5P1]

description:
P60THRep5P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep3P2]

description:
P60THRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep2P3]

description:
P60THRep2P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Thalamus [P60THRep2P1]

description:
P60THRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Thalamus.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep4P2]

description:
P60SNRep4P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep3P3]

description:
P60SNRep3P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep4P1]

description:
P60SNRep4P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep3P2]

description:
P60SNRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep2P2]

description:
P60SNRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep2P3]

description:
P60SNRep2P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep1P2]

description:
P60SNRep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep1P1]

description:
P60SNRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep2P1]

description:
P60SNRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Striatum [P60STRRep1P1]

description:
P60STRRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt

value: Striatum


title: Hippocampus [P60HippoRep5P2]

description:
P60HippoRep5P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt

value: Hippocampus


title: Hippocampus [P60HippoRep4P3]

description:
P60HippoRep4P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Striatum [P60STRRep1P4]

description:
P60STRRep1P4
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt


title: Striatum [P60STRRep2P2]

description:
P60STRRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt


title: Striatum [P60STRRep2P1]

description:
P60STRRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt


title: Hippocampus [P60HippoRep6P3]

description:
P60HippoRep6P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Striatum [P60STRRep3P1]

description:
P60STRRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt


title: Hippocampus [P60HippoRep6P2]

description:
P60HippoRep6P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Striatum [P60STRRep1P2]

description:
P60STRRep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt


title: Hippocampus [P60HippoRep5P1]

description:
P60HippoRep5P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Striatum [P60STRRep1P3]

description:
P60STRRep1P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt


title: Hippocampus [HippoRep3P2]

description:
HippoRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Substantia Nigra/Ventral Tegmental Area [P60SNRep3P1]

description:
P60SNRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60SubstantiaNigra.raw.dge.txt


title: Hippocampus [HippoRep3P3]

description:
HippoRep3P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Hippocampus [P60HippoRep5P3]

description:
P60HippoRep5P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Hippocampus [HippoRep3P1]

description:
HippoRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Hippocampus [HippoRep2P1]

description:
HippoRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Hippocampus [P60HippoRep1P1]

description:
P60HippoRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Hippocampus [HippoRep2P2]

description:
HippoRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Hippocampus [P60HippoRep4P2]

description:
P60HippoRep4P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: Hippocampus [P60HippoRep1P2]

description:
P60HippoRep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep4P2]

description:
P60GPNBRep4P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt

value: GlobusPallidus Externus/Nucleus Basalis


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep7P1]

description:
P60GPNBRep7P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: Striatum [P60STRRep3P2]

description:
P60STRRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Striatum.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep6P1]

description:
P60GPNBRep6P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: Hippocampus [P60HippoRep4P1]

description:
P60HippoRep4P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep6P2]

description:
P60GPNBRep6P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: Hippocampus [P60HippoRep6P1]

description:
P60HippoRep6P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Hippocampus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep5P1]

description:
P60GPNBRep5P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep4P1]

description:
P60GPNBRep4P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep1P1]

description:
P60GPNBRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep3P2]

description:
P60GPNBRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: Entopeduncular/Subthalamic Nuclei [P60ENTSTNRep1P1]

description:
P60ENTSTNRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60EntoPeduncular.raw.dge.txt

value: Entopeduncular/Subthalamic Nuclei


title: Posterior Cortex [P60PCRep1P2]

description:
P60PCRep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt

value: Posterior Cortex


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep3P1]

description:
P60GPNBRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep2P1]

description:
P60GPNBRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: Entopeduncular/Subthalamic Nuclei [P60ENTSTNRep3P1]

description:
P60ENTSTNRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60EntoPeduncular.raw.dge.txt


title: Posterior Cortex [P60PCRep1P1]

description:
P60PCRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Posterior Cortex [P60PCRep6P2]

description:
P60PCRep6P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Posterior Cortex [P60PCRep6P1]

description:
P60PCRep6P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep3P3]

description:
P60GPNBRep3P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: GlobusPallidus Externus/Nucleus Basalis [P60GPNBRep2P2]

description:
P60GPNBRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60GlobusPallidus.raw.dge.txt


title: Posterior Cortex [P60PCRep4P2]

description:
P60PCRep4P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Posterior Cortex [P60PCRep4P1]

description:
P60PCRep4P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Entopeduncular/Subthalamic Nuclei [P60ENTSTNRep4P1]

description:
P60ENTSTNRep4P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60EntoPeduncular.raw.dge.txt


title: Posterior Cortex [P60PCRep3P2]

description:
P60PCRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Posterior Cortex [P60PCRep6P3]

description:
P60PCRep6P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Posterior Cortex [P60PCRep3P3]

description:
P60PCRep3P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Control 14

city: Kingston

first: David

middle: M

last: Maslove

state: Ontario

address: 76 Stuart St.

department: Critical Care Medicine

country: Canada

institute: Queen's University

description: Gene expression from whole blood collected from crtically ill patient in ICU

hyb_protocol: 16 hr at 45°C

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Gene expression generated from Affymetrix PrimeVIew array. Image files were captured using an Affymetrix GeneChip Scanner 3000. CEL files were subsequently preprocessed using PLIER normalization.

source_name: Whole blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Extracted from PAXgene whole blood RNA collection tubes

treatment_protocol: Patients were treated with either lactoferrin or placebo delivered enetrally

tag: batch

value: C

tag: rin

tag: day

value: Control

tag: Sex


title: patient 62 Day.3

value: FALSE

value: TRUE

value: Placebo


title: Control 17


title: Control 5


title: Control 18


title: Control 8


title: Control 16


title: patient 69 Day.1

value: Lactoferrin


title: Control 15


title: patient 69 Day.3


title: Control 21


title: Control 20


title: Control 19


title: patient 69 Day.7


title: Control 13


title: Posterior Cortex [P60PCRep2P2]

description:
P60PCRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Posterior Cortex [P60PCRep2P1]

description:
P60PCRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: Posterior Cortex [P60PCRep4P3]

description:
P60PCRep4P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: patient 67 Day.3

value: Female


title: patient 68 Day.3


title: Posterior Cortex [P60PCRep3P1]

description:
P60PCRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cortex_noRep5_POSTERIORonly.raw.dge.txt


title: patient 68 Day.1


title: patient 66 Day.1


title: patient 65 Day.1


title: patient 64 Day.21


title: patient 64 Day.7


title: patient 64 Day.1


title: patient 63 Day.21


title: Cerebellum [P60CBRep3P2]

description:
P60CBRep3P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt

value: Cerebellum


title: SJNB8 Trametinib 2

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix),

source_name: Neuroblastoma cell line SJNB8, unmodified; treated with Trametinib

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: NMB and SJNB8 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

treatment_protocol: NMB cells were transduced with pInducer virus particles with doxycycline-inducible expression of NRAS or pLentiCRISPR with a gRNA targeting NF1. SJNB8 cells were treated with 1uM Trametinib or equal amounts of solvent (DMSO) for 6 hours prior to harvesting.

tag: cell line

tag: genotype/variation

value: wildtype cells with Trametinib


title: patient 64 Day.3

value: Male


title: SJNB8 Trametinib 3


title: patient 63 Day.7


title: SJNB8 Trametinib 1


title: Cerebellum [P60CBRep3P1]

description:
P60CBRep3P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt


title: NMB pInd NRAS +dox 2

source_name: Neuroblastoma cell line NMB with doxycycline-inducible expression of NRAS Q61V (plus dox)

value: NMB


title: NMB pLCR NF1 3

source_name: Neuroblastoma cell line NMB with CRISPR induced knockout of NF1

value: CRISPR induced knockout of NF1


title: SJNB8 DMSO 1

source_name: Neuroblastoma cell line SJNB8, unmodified

value: wildtype cells with DMSO vehicle


title: patient 67 Day.1


title: NMB pInd NRAS +dox 3

value: doxycycline-inducible expression of NRAS Q61V (plus dox)


title: patient 63 Day.3


title: NMB pLCR NF1 2


title: patient 60 Day.1


title: patient 63 Day.14


title: patient 59 Day.1


title: SJNB8 DMSO 3


title: patient 58 Day.28


title: patient 58 Day.14


title: SJNB8 DMSO 2


title: NMB pLCR NF1 1


title: patient 63 Day.1


title: NMB pInd NRAS +dox 1


title: patient 58 Day.21


title: patient 58 Day.7


title: Control 12


title: NMB pInd NRAS -dox 3

source_name: Neuroblastoma cell line NMB with doxycycline-inducible expression of NRAS Q61V (minus dox)


title: NMB pInd NRAS -dox 2

value: doxycycline-inducible expression of NRAS Q61V (minus dox)


title: Cerebellum [P60CBRep2P1]

description:
P60CBRep2P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt


title: Cerebellum [P60CBRep1P3]

description:
P60CBRep1P3
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt


title: Cerebellum [P60CBRep2P2]

description:
P60CBRep2P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt


title: Control 11


title: Cerebellum [P60CBRep1P2]

description:
P60CBRep1P2
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt


title: Cerebellum [P60CBRep1P1]

description:
P60CBRep1P1
Single-cell gene expression data based on 3' transcript counts.
mRNA (cDNA)
processed data file: F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt


title: population.iRBC.28

city: Stockholm

first: Rickard

last: Sandberg

address: Solnavägen 9  Solna

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Aligned reads with STAR version 2.3 to combined genomes of P.falciparum(Pf3D7v3) and human (hg19) with the outSAMstrandField  set to 'intronMotif'.
Calculated expression values with rpkmforgenes.py (available at https://github.com/danielramskold/S3_species-specific_sequencing) with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and gene annotation for the UCSC genome browser Ensembl track and Plasmodb release 11.1 annotation for P.falciparum (Pf3D7v3).
Principal component analysis done using prcomp function and t-stochastic neighbour embedding performed using tsne version 0.1-3 in R.
Single-cell differential expression analysis done using SCDE version 2.8.0.
Genome_build: Combined Pf3D7v3 (Plasmodb release 11.1) and hg19 (UCSF Human Genome Assembly)
Supplementary_files_format_and_content: Tab-delimited text with each row and column corresponding to P. falciparum genes and samples respectively. The first 208 fields represent the read counts and the next 208 are the normalized gene expression measurements (RPKM).

organism: Plasmodium falciparum

extract_protocol: SmartSeq2 (Picelli S, Nat Methods. 2013, PubMed PMID: 24056875)

tag: strain

value: A

tag: library quality

value: high

tag: group

value: population

value: two


title: population.iRBC.23

value: one


title: population.iRBC.26


title: population.iRBC.25


title: Control 10

value: C

value: Control

tag: age


title: population.iRBC.24


title: population.iRBC.22


title: NMB pInd NRAS -dox 1


title: NMB wild type 3

source_name: Neuroblastoma cell line NMB, unmodified

value: wildtype


title: population.iRBC.21


title: Control 9


title: NMB wild type 2


title: wild-type 1D oligodendrocytes (i.wt-1.4)

description: Oligodendrocyte progenitor cells induced to form oligodendrocytes for one day, according to Najm et al. 2011.

data_processing:
Reads were aligned to the mm9 genome using TopHat v2.0.6 without providing a reference transcriptome.
Abundance of transcripts from the iGenomes mm9 RefSeq reference were measured using Cufflinks v2.0.2.
FPKMs were quantile normalized.
Genome_build: mm9
Supplementary_files_format_and_content: cufflinks fpkm_tracking format

source_name: Differentiating oligodendrocytes

growth_protocol: For samples 1-6 OPCs were grown in N2B27 media which contained DMEM/F12 (11320082, Thermo Fisher), 1x N2 supplement (AR009, R&D Systems), 1x B-27 without vitamin A supplement (12587-010, Thermo Fisher), and 1x Glutamax. N2B27 media was futher supplemented with 20 ng/mL fibroblast growth factor 2 (FGF2; 233-FB, R&D Systems), 20 ng/mL platelet-derived growth factor-AA (PDGF-AA; 221-AA, R&D Systems). For samples 7-12 OPCs were differentiated to oligodendrocytes for 1 day in oligodendrocyte differentiation media which consisted of N2B27 media supplemented with 100ng/mL noggin (3344-NG, R&D Systems), 10ng/mL neurotrophin-3 (NT-3; 267-N3, R&D Systems), 50 μM cAMP (D0260, Sigma), 100ng/mL insulin-like growth factor-1 (IGF-1; 291-G1, R&D Systems) NT-3, and 40ng/mL triiodothyronine (thyroid hormone; T-6397, Sigma).

extract_protocol:
Cells were homogenized in TRIzol (15596026, Thermo Fisher). All samples were chloroform extracted and phase separated. RNA was isolated using the miRNeasy Mini kit (217004, Qiagen).
Sequencing libraries were generated using the TruSeq Stranded Total RNA kit (20020596, Illumina) after rRNA depletion with RiboZero Gold (MRZG126, Illumina) followed by 100bp paired-end sequencing. Sequencing was performed on an Illumina HiSeq 2500 at the Case Western Reserve University School of Medicine Genomics Core Facility

value: B6CBACa/J Aw-J/A


title: jimpy 1D oligodendrocytes (i.jp-1.4)


title: population.iRBC.27


title: Control 7


title: Control 6


title: jimpy 1D oligodendrocytes (i.jp-1.5)


title: jimpy 1D oligodendrocytes (i.jp-1.6)


title: wild-type 1D oligodendrocytes (i.wt-1.3)


title: population.iRBC.20

value: five


title: NMB wild type 1


title: Control 4


title: population.iRBC.19


title: Control 3


title: jimpy OPCs (i.jp-1.6)

description: Oligodendrocyte progenitor cells cultured according to Najm et al. 2011.

source_name: oligodendrocyte progenitor cells


title: wild-type 1D oligodendrocytes (i.wt-1.0)


title: population.iRBC.18


title: Control 1


title: jimpy OPCs (i.jp-1.5)


title: Control 2


title: population.iRBC.16


title: population.iRBC.17


title: patient 62 Day.1

value: FALSE

value: TRUE

value: Placebo


title: patient 61 Day.3

value: Male


title: patient 58 Day.3

value: Lactoferrin


title: patient 61 Day.1


title: jimpy OPCs (i.jp-1.4)


title: patient 60 Day.7

value: Female


title: patient 29 Day.1


title: patient 58 Day.1


title: population.iRBC.15


title: wild-type OPCs (i.wt-1.3)


title: population.iRBC.14


title: wild-type OPCs (i.wt-1.0)


title: population.iRBC.13


title: population.iRBC.11


title: patient 60 Day.3


title: wild-type OPCs (i.wt-1.4)


title: population.iRBC.10


title: population.iRBC.9


title: VTA-205

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads obtained from mouse brain cells were mapped to mm10 using TopHat2v2.1.0. Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v75 annotation. Differential expression analysis was done using the voom-limma R package at FDR cutoff of 0.05 (5% False Discovery Rate) and a log fold change cutoff of < -0.05 or > 0.05 was applied.
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text file generated using HTSeq-count against Ensembl v75 annotation

source_name: Brain

growth_protocol: Male C57BL/6J mice were obtained from The Jackson Laboratory.

extract_protocol:
RNA from mouse brain samples was extracted using an RNeasy micro kit using Trizol, followed by DNase 1 treatment, as described by the manufacturer (Qiagen). RNA integrity number (RIN) and concentration were assessed using a Bioanalyzer (Agilent).
Libraries were constructed using the ScriptSeq Complete Gold Kit (Epicentre, Illumina) preceded by ribosomal RNA depletion.

treatment_protocol: C57BL/6J male mice underwent cocaine or saline SA followed by 24 hr or 30 d of WD. At the 30 d WD time-point, animals were challenged with a single IP injection of cocaine or saline within the drug SA and transcriptional analysis was conducted on tissue collected 1 hr later.

value: Brain

tag: region

value: Ventral tegmental area

tag: self-administration

value: Saline

tag: challenge


title: VTA-204


title: VTA-214

value: Cocaine


title: VTA-223


title: patient 27 Day.3

value: A


title: population.iRBC.12

value: high

value: population


title: population.iRBC.8

value: two


title: patient 28 Day.1


title: patient 26 Day.14


title: patient 26 Day.3


title: population.iRBC.7


title: patient 26 Day.1


title: population.iRBC.5


title: population.iRBC.6


title: patient 26 Day.7


title: VTA-201


title: population.iRBC.4


title: VTA-193


title: VTA-203


title: patient 27 Day.1


title: VTA-195


title: patient 25 Day.3


title: patient 24 Day.14


title: population.iRBC.2


title: VTA-175


title: patient 24 Day.3


title: patient 24 Day.7


title: population.iRBC.3


title: VTA-191


title: VTA-171


title: population.iRBC.1


title: patient 25 Day.1


title: patient 24 Day.1


title: VTA-162


title: sc.iRBC.180

value: low

value: single-cell

value: one


title: sc.iRBC.178


title: VTA-144


title: sc.iRBC.179

value: four


title: VTA-145


title: VTA-182


title: patient 23 Day.7

value: TRUE

value: FALSE


title: VTA-122

value: Male


title: patient 22 Day.7

value: Placebo


title: sc.iRBC.176


title: sc.iRBC.175


title: patient 23 Day.3

value: Female

value: Lactoferrin


title: sc.iRBC.177


title: VTA-115

value: Brain

value: Ventral tegmental area


title: sc.iRBC.173


title: patient 21 Day.3


title: sc.iRBC.174


title: VTA-113

value: Saline

value: Cocaine


title: VTA-143


title: VTA-161


title: sc.iRBC.172

value: A


title: VTA-091


title: sc.iRBC.170


title: VTA-094


title: VTA-074


title: sc.iRBC.171


title: sc.iRBC.169


title: VTA-085


title: patient 23 Day.1


title: patient 20 Day.7


title: VTA-065


title: patient 19 Day.7


title: patient 22 Day.1


title: patient 22 Day.3


title: patient 20 Day.3


title: patient 19 Day.3


title: patient 19 Day.14


title: patient 20 Day.1


title: sc.iRBC.168


title: patient 19 Day.1


title: sc.iRBC.165

value: moderate


title: sc.iRBC.164


title: VTA-043


title: sc.iRBC.167

value: two


title: VTA-053


title: sc.iRBC.163


title: VTA-011


title: patient 17 Day.7


title: patient 18 Day.3


title: patient 18 Day.7


title: VTA-035


title: VTA-055


title: patient 18 Day.1


title: patient 18 Day.14


title: VTA-072


title: sc.iRBC.162


title: patient 17 Day.3


title: PFC-205

value: Prefrontal cortex


title: sc.iRBC.160

value: single-cell


title: patient 17 Day.1


title: sc.iRBC.158


title: PFC-214


title: PFC-203


title: sc.iRBC.159


title: sc.iRBC.157

value: three


title: PFC-204


title: PFC-223


title: sc.iRBC.166

value: low


title: sc.iRBC.155


title: PFC-194


title: patient 16 Day.1

value: TRUE


title: sc.iRBC.161

value: four


title: patient 16 Day.7

value: Male

value: FALSE


title: patient 16 Day.14


title: patient 15 Day.28


title: PFC-201


title: PFC-193


title: PFC-195


title: sc.iRBC.154


title: sc.iRBC.156


title: sc.iRBC.152


title: PFC-191


title: sc.iRBC.151


title: sc.iRBC.153


title: sc.iRBC.150


title: sc.iRBC.149


title: patient 15 Day.21


title: patient 15 Day.14


title: patient 14 Day.3

value: Placebo


title: PFC-183


title: patient 14 Day.1


title: PFC-171


title: PFC-185


title: sc.iRBC.147


title: patient 13 Day.3

value: Lactoferrin


title: patient 15 Day.7


title: PFC-162

value: Brain


title: patient 13 Day.1


title: patient 12 Day.1


title: PFC-182


title: sc.iRBC.146


title: PFC-161


title: sc.iRBC.148


title: PFC-175


title: sc.iRBC.144


title: PFC-151


title: PFC-145


title: patient 12 Day.3


title: patient 14 Day.7


title: sc.iRBC.145


title: patient 11 Day.3

value: Female


title: sc.iRBC.142


title: PFC-144

value: Saline


title: PFC-143


title: sc.iRBC.140


title: patient 11 Day.1


title: sc.iRBC.143


title: sc.iRBC.139


title: PFC-115

value: Cocaine


title: sc.iRBC.141

value: A


title: sc.iRBC.137

value: moderate


title: patient 4 Day.1


title: PFC-122


title: PFC-125


title: patient 10 Day.7


title: patient 3 Day.7


title: patient 3 Day.3


title: patient 2 Day.3


title: patient 2 Day.1


title: PFC-094


title: patient 10 Day.3


title: sc.iRBC.138

value: two


title: patient 3 Day.1


title: sc.iRBC.135


title: PFC-105

value: Prefrontal cortex


title: PFC-085


title: PFC-083


title: PFC-111


title: PFC-091


title: sc.iRBC.133

value: single-cell


title: sc.iRBC.134


title: patient 9 Day.14


title: sc.iRBC.136


title: patient 10 Day.1


title: patient 1 Day.28


title: sc.iRBC.131


title: PFC-074


title: patient 9 Day.28


title: sc.iRBC.130


title: PFC-073


title: sc.iRBC.129


title: sc.iRBC.132


title: PFC-072


title: sc.iRBC.128


title: PFC-065


title: patient 9 Day.3


title: PFC-035


title: patient 9 Day.7


title: PFC-043


title: patient 9 Day.1


title: patient 8 Day.15


title: PFC-011


title: sc.iRBC.121


title: patient 8 Day.3


title: sc.iRBC.124


title: PFC-014


title: PFC-031


title: patient 8 Day.1


title: patient 1 Day.21


title: PFC-012


title: patient 8 Day.7


title: PFC-053


title: sc.iRBC.127


title: sc.iRBC.120


title: NAc-225

value: Nucleus accumbens


title: sc.iRBC.125


title: sc.iRBC.119


title: patient 8 Day.14


title: patient 7 Day.7


title: sc.iRBC.123


title: patient 7 Day.3


title: patient 6 Day.3


title: NAc-223


title: patient 6 Day.7


title: sc.iRBC.122


title: NAc-214


title: NAc-205


title: patient 5 Day.1


title: sc.iRBC.117


title: patient 6 Day.1


title: sc.iRBC.126


title: NAc-204


title: NAc-201


title: sc.iRBC.115


title: sc.iRBC.116


title: NAc-195


title: NAc-203


title: sc.iRBC.114


title: sc.iRBC.113


title: NAc-193


title: patient 57 Day.7

value: B


title: patient 4 Day.7

value: TRUE


title: NAc-194


title: patient 57 Day.3


title: sc.iRBC.112


title: patient 4 Day.3


title: patient 4 Day.14


title: sc.iRBC.118


title: patient 57 Day.1


title: NAc-183


title: NAc-191


title: NAc-185


title: sc.iRBC.109


title: sc.iRBC.110


title: NAc-175


title: sc.iRBC.108


title: sc.iRBC.106


title: NAc-182


title: sc.iRBC.105


title: patient 56 Day.21


title: patient 54 Day.7


title: patient 56 Day.7


title: patient 54 Day.14


title: NAc-171


title: NAc-162


title: patient 56 Day.28


title: NAc-161


title: patient 56 Day.14


title: sc.iRBC.107


title: patient 55 Day.1


title: sc.iRBC.103


title: sc.iRBC.104


title: NAc-151


title: sc.iRBC.102


title: NAc-145


title: NAc-125


title: sc.iRBC.101


title: NAc-122


title: sc.iRBC.100


title: patient 54 Day.3


title: patient 54 Day.1


title: patient 53 Day.3


title: sc.iRBC.111


title: NAc-115


title: patient 51 Day.3


title: patient 53 Day.7


title: sc.iRBC.99


title: NAc-111


title: NAc-113


title: NAc-094


title: sc.iRBC.97


title: sc.iRBC.98


title: sc.iRBC.95


title: NAc-091


title: NAc-105


title: sc.iRBC.94


title: sc.iRBC.93


title: patient 51 Day.1


title: patient 48 Day.1


title: patient 50 Day.1


title: sc.iRBC.96

value: one


title: patient 52 Day.1


title: patient 49 Day.1


title: patient 52 Day.14


title: sc.iRBC.90

value: high

tag: sub-population

value: four


title: patient 47 Day.3

value: Male

value: FALSE

value: Placebo


title: sc.iRBC.91


title: NAc-074

value: Brain


title: NAc-083

value: Saline


title: patient 47 Day.1


title: sc.iRBC.89


title: NAc-053

value: Cocaine


title: NAc-073


title: NAc-055


title: patient 46 Day.3


title: sc.iRBC.88

value: A


title: NAc-052


title: sc.iRBC.87


title: patient 46 Day.7


title: sc.iRBC.92


title: NAc-085


title: patient 45 Day.1

value: Lactoferrin


title: patient 44 Day.3

value: Female


title: NAc-035


title: sc.iRBC.84


title: patient 44 Day.7


title: patient 45 Day.3


title: sc.iRBC.86


title: NAc-031


title: sc.iRBC.85


title: sc.iRBC.83


title: sc.iRBC.81


title: sc.iRBC.82


title: patient 44 Day.1


title: NAc-014


title: Hipp-225

value: Ventral hippocampus


title: Hipp-223


title: NAc-012


title: Hipp-205


title: patient 43 Day.1


title: sc.iRBC.80

value: single-cell


title: patient 42 Day.7


title: patient 42 Day.3


title: sc.iRBC.78


title: patient 41 Day.1


title: sc.iRBC.79


title: patient 41 Day.14


title: patient 42 Day.1


title: patient 40 Day.1


title: sc.iRBC.77


title: patient 40 Day.3


title: Hipp-203


title: Hipp-201


title: sc.iRBC.76


title: Hipp-204


title: Hipp-191


title: sc.iRBC.72

value: two


title: sc.iRBC.74

value: three


title: Hipp-195


title: Hipp-185


title: sc.iRBC.73


title: sc.iRBC.71


title: patient 38 Day.7

value: B

value: TRUE


title: patient 38 Day.3


title: Hipp-194


title: patient 39 Day.1


title: sc.iRBC.69

value: high


title: sc.iRBC.75


title: Hipp-183


title: patient 37 Day.21


title: Hipp-182


title: sc.iRBC.70


title: Hipp-175


title: sc.iRBC.68


title: patient 37 Day.3


title: Hipp-171


title: patient 31 Day.14


title: sc.iRBC.65


title: sc.iRBC.66


title: patient 31 Day.1


title: Hipp-214


title: patient 37 Day.14


title: sc.iRBC.63


title: sc.iRBC.64


title: Hipp-162


title: sc.iRBC.67


title: Hipp-144


title: Hipp-125


title: Hipp-161


title: patient 31 Day.7


title: patient 30 Day.21


title: patient 37 Day.1


title: Hipp-151


title: sc.iRBC.62


title: Hipp-115


title: Hipp-122


title: sc.iRBC.61


title: patient 32 Day.14


title: sc.iRBC.60


title: patient 50 Day.3


title: Hipp-111


title: patient 30 Day.14


title: Hipp-113


title: sc.iRBC.59


title: sc.iRBC.58


title: Hipp-105


title: patient 32 Day.7


title: sc.iRBC.56


title: Hipp-091


title: patient 31 Day.3


title: sc.iRBC.57


title: Hipp-085


title: patient 36 Day.3


title: patient 32 Day.1


title: patient 32 Day.3


title: patient 30 Day.7


title: Hipp-074


title: patient 36 Day.1


title: sc.iRBC.54


title: Hipp-073


title: patient 36 Day.7


title: patient 39 Day.3


title: sc.iRBC.53


title: sc.iRBC.51


title: Hipp-072


title: Hipp-065


title: sc.iRBC.50


title: sc.iRBC.52


title: patient 35 Day.1


title: patient 30 Day.3


title: patient 34 Day.21


title: Hipp-055


title: Hipp-052


title: sc.iRBC.45


title: Hipp-035


title: Hipp-053


title: sc.iRBC.47


title: patient 34 Day.14


title: Hipp-043


title: sc.iRBC.46


title: sc.iRBC.44


title: Hipp-031


title: patient 34 Day.3


title: Cpu-225

value: Dorsal striatum


title: sc.iRBC.48


title: patient 34 Day.1

value: Male


title: patient 33 Day.28

value: FALSE


title: sc.iRBC.43


title: sc.iRBC.42


title: Hipp-014


title: sc.iRBC.49


title: sc.iRBC.41


title: Cpu-223


title: patient 33 Day.14


title: patient 33 Day.7


title: patient 33 Day.21


title: patient 33 Day.1


title: sc.iRBC.40


title: sc.iRBC.39


title: Cpu-214


title: Cpu-204


title: sc.iRBC.38


title: sc.iRBC.36


title: Cpu-205


title: patient 31 Day.21

value: Placebo


title: Cpu-203

value: Brain


title: Cpu-201

value: Saline


title: patient 30 Day.1


title: sc.iRBC.37


title: Cpu-195

value: Cocaine


title: sc.iRBC.34

value: A


title: Cpu-191


title: sc.iRBC.33


title: Cpu-193


title: Cpu-185


title: Cpu-183


title: Cpu-182


title: PDA_tumor_80

city: Brussels

first: Sylvain

last: Brohée

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: pancreatic tumor

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by submitter

tag: death


title: sc.iRBC.30

value: one


title: PDA_tumor_78


title: sc.iRBC.29


title: PDA_tumor_76


title: Cpu-194

tag: tissue


title: sc.iRBC.35


title: Cpu-175


title: PDA_tumor_79


title: PDA_tumor_74


title: PDA_tumor_75


title: sc.iRBC.31


title: sc.iRBC.32


title: PDA_tumor_77


title: PDA_tumor_73


title: Cpu-171


title: PDA_tumor_72


title: PDA_tumor_70


title: PDA_tumor_69


title: sc.iRBC.27


title: PDA_tumor_68


title: PDA_tumor_71


title: sc.iRBC.26


title: sc.iRBC.25


title: sc.iRBC.28


title: Cpu-161


title: Cpu-162


title: PDA_tumor_67


title: Cpu-151


title: sc.iRBC.23


title: sc.iRBC.24


title: Cpu-145


title: Cpu-143


title: sc.iRBC.22


title: sc.iRBC.21


title: Cpu-125


title: Cpu-122


title: sc.iRBC.20


title: sc.iRBC.19


title: Cpu-115


title: PDA_tumor_65


title: sc.iRBC.18


title: Cpu-113


title: Cpu-111


title: Cpu-091


title: sc.iRBC.16


title: sc.iRBC.17


title: PDA_tumor_63


title: PDA_tumor_62


title: sc.iRBC.55


title: Cpu-105


title: Hipp-094


title: PDA_tumor_61


title: PDA_tumor_66


title: PDA_tumor_60


title: PDA_tumor_58


title: PDA_tumor_64


title: sc.iRBC.15


title: Cpu-085


title: patient 35 Day.3


title: PDA_tumor_57


title: sc.iRBC.14


title: PDA_tumor_56


title: PDA_tumor_55


title: PDA_tumor_59


title: Cpu-083


title: PDA_tumor_54


title: sc.iRBC.12


title: sc.iRBC.11


title: Cpu-072


title: sc.iRBC.10


title: sc.iRBC.13


title: sc.iRBC.9


title: sc.iRBC.8


title: Cpu-074


title: Cpu-055


title: Cpu-073


title: Cpu-053


title: PDA_tumor_53


title: Cpu-035


title: PDA_tumor_52


title: sc.iRBC.5


title: Cpu-052


title: sc.iRBC.7


title: PDA_tumor_51


title: sc.iRBC.6


title: PDA_tumor_47


title: Cpu-031


title: PDA_tumor_45


title: sc.iRBC.4


title: Cpu-065


title: Cpu-014


title: Cpu-012


title: PDA_tumor_50


title: PDA_tumor_48


title: PDA_tumor_49


title: sc.iRBC.2


title: PDA_tumor_44


title: sc.iRBC.1


title: PDA_tumor_43


title: Cpu-011


title: BLA-223

value: Basolateral amygdala


title: BLA-225


title: PDA_tumor_46