title: NK cells input

status: Public on Oct 15 2020

type: SRA

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

library_source: genomic

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human genome (hg38) using STAR2.4.2a with parameters --alignIntronMax 1 and --outFilterMultimapNmax 1
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg38
Supplementary_files_format_and_content:
txt = txt file with MACS2 peak calling results
BW = signal map in bigWIG format (UCSC)
BED = narrowPeak BED file containing MACS peaks

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: Mature NK cells were isolated from peripheral blood. Mononuclear cells in buffy coats were isolated by Lymphoprep density gradient centrifugation, followed by CD3 and CD19 cell removal by anti-CD3/19-biotine labeling and subsequent anti-biotin MACS depletion. Enriched NK cells were subsequently sorted as CD56+CD3- (residual CD3+ and CD19+ cells were identified via streptavidin staining) using a BD FACSAria III cell sorter.

tag: cell type

value: peripheral blood mononuclear cells

tag: cell subtype

value: Mature NK cells

tag: gating


title: NK cells ETS1 ChIP

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot #


title: BFKB8488A_3_8D_HFD_eWAT_SVF_Mac1

status: Public on Dec 31 2018

city: South San Francisco

first: Junichiro

last: Sonoda

state: CA

address: 1 DNA WAY

department: Cancer Immunology

country: USA

institute: Genentech

description:
sample name in processed data file: SAM24295036
NGS905update_counts.xls

library_source: transcriptomic

data_processing:
Illumina Casava 1.8
Sequencing reads were filtered to have at least an average base quality of 23 and were then aligned to GRCm38  using GSNAP
Expression counts per gene were obtained by counting the number of reads aligned uniquely to each gene locus as defined by NCBI and Ensembl gene annotations and RefSeq mRNA sequences
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file with gene expression counts

molecule: total RNA

organism: Mus musculus

source_name: Fat Pad: Epididymal

growth_protocol: C57Bl/6J mice were on High Fat Diet (HFD) till they weight 38-42g (18-20 weeks old).

extract_protocol:
RNeasy Kit (Qiagen, Hilden, Germany)
N=3 M1 samples bFKB1 treated, N=3 M2 samples bFKB1 treated

treatment_protocol: Male mice were maintained on High Fat Diet (HFD) and at thermoneutral temperature throughout the study. Mice received bFKB1 at 10mg/kg i.p., and tissue harvested after 8 days.

tag: tissue

value: Fat Pad:Epididymal

tag: strain

value: M1 macrophage

tag: treatment

tag: replicate

tag: gender

value: male


title: BFKB8488A_2_8D_HFD_eWAT_SVF_Mac1

description:
sample name in processed data file: SAM24295034
NGS905update_counts.xls


title: BFKB8488A_1_8D_HFD_eWAT_SVF_Mac1

description:
sample name in processed data file: SAM24295032
NGS905update_counts.xls


title: BFKB8488A_3_8D_HFD_eWAT_SVF_Mac2

description:
sample name in processed data file: SAM24295037
NGS905update_counts.xls

value: M2 macrophage


title: IMP2 WT IP RNA rep1

city: Boston

first: Ning

last: Dai

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Male, 6 weeks after birth, two weeks on HFD.
mRNA interacting with IMP2 protein

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm10 using STAR.
Transcript abundance was calculated using HTseq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include read count values for each Sample.

source_name: mouse skeletal muscle

growth_protocol:
6 weeks after birth, two weeks on HFD.
With/without IMP2 in muscle.

extract_protocol:
QIAGEN RNase kit.
Libraries were constructed according to Illumina TruSeq high throughput kit.

tag: strain/background

tag: genotype/variation

value: Wild Type

value: Male

tag: age

value: 6 weeks

value: Skeletal muscle

value: 2 weeks HFD

tag: ip antibody

value: IMP2 (home-made customized antibodies)


title: IMP2 WT IP RNA rep2


title: BFKB8488A_1_8D_HFD_eWAT_SVF_Mac2

description:
sample name in processed data file: SAM24295033
NGS905update_counts.xls


title: IMP2 KO IP RNA rep2

value: IMP2 null


title: BFKB8488A_2_8D_HFD_eWAT_SVF_Mac2

description:
sample name in processed data file: SAM24295035
NGS905update_counts.xls


title: IMP2 KO Total rep3

description:
Male, 6 weeks after birth, two weeks on HFD.
total mRNA


title: IMP2 WT Total rep3


title: IMP2 WT Total rep1


title: IMP2 KO Total rep1


title: IMP2 KO Total rep2


title: IMP2 WT Total rep2


title: IMP2 KO IP RNA rep1


title: DISC1_Mutant_Treatment_THC_5471

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

data_processing:
Basecalls performed using CASAVA version 1.8.4
FastQC used to assess FASTQ file properties
Alignment to mm10 using Bowtie2 (version 2.2.2) with RSEM (version 1.2.21) defaults
Expression levels of known genes calculated with RSEM and NCBI RefSeq annotation
Differential expression calculated with edgeR (version 3.10.2)
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: hippocampus

extract_protocol:
Total RNA purified from hippocampus
riboZero used to remove ribosomal RNA
Paired end sequencing (100 bp x 2) using a HiSeq2500 instrument to a depth of 75 million reads

treatment_protocol: aDN-DISC1 mice treated with vehicle or Δ9-THC

value: C57BL/6 background

tag: genotype

value: DISC1 mutant

value: THC


title: DISC1_Control_Treatment_THC_5463


title: DISC1_Mutant_Treatment_Vehicle_5446

value: Vehicle


title: DISC1_Control_Treatment_Vehicle_5450


title: DISC1_Mutant_Treatment_THC_5462


title: DISC1_Mutant_Treatment_THC_5460


title: DISC1_Control_Treatment_Vehicle_5456


title: DISC1_Control_Treatment_THC_5461


title: Cold_AP_2

description:
NGS905_counts.xls
sample name in processed data file: SAM24329992

data_processing:
Illumina Casava 1.8
Sequencing reads were filtered to have at least an average base quality of 23 and were then aligned to GRCm38  using GSNAP
Expression counts per gene were obtained by counting the number of reads aligned uniquely to each gene locus as defined by NCBI and Ensembl gene annotations and RefSeq mRNA sequences. Samtools was used for read counting.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file with gene expression counts

growth_protocol: C57Bl/6J mice were fed High Fat Diet (HFD) starting at 6 weeks old untill their weight increased to 38-42g (18-20 weeks old).

extract_protocol:
FACS sorted cells from 5 mice will be pooled as one sample for RNAseq gene expression analysis.  Total RNA was extracted using the Qiagen RNeasy Micro Kit. Poly A enrichment was performed with Oligo dT bead selection. The resulting poly-A+ RNA was fragmented and cDNA was synthesized using Superscript II and random primers. Libraries were prepared according to standard Illumina protocol, using the Illumina TruSeq mRNA Sample Prep Kit v2.
TruSeq RNA Library Prep Kit v2 (Illumina, USA)

treatment_protocol: Male mice were on High Fat Diet (HFD) throughout the study. One group of these mice were held in thermoneutral condition (29-30 degrees C) for control (Group1, Warm). Mice that were exposed to cold were transferred from thermoneutral condition to 18 degrees C temperature controlled chamber for 7 days adaptation before reducing the chamber temperature to 4 degree C (Group2, Cold).  The mice were be euthanized at day 14 after 7 days of the 4 degree C cold exposure.

value: Epididymal fat

tag: Sex

tag: cell type

value: AP (adipose progenitor)

tag: temperature

value: Cold


title: Cold_AP_3

description:
NGS905_counts.xls
sample name in processed data file: SAM24329991


title: DISC1_Control_Treatment_THC_5440


title: Warm_AP_2

description:
NGS905_counts.xls
sample name in processed data file: SAM24329989

value: Thermoneutral


title: DISC1_Control_Treatment_Vehicle_5455


title: DISC1_Mutant_Treatment_Vehicle_5448


title: Cold_AP_1

description:
NGS905_counts.xls
sample name in processed data file: SAM24329993

value: male


title: DISC1_Mutant_Treatment_Vehicle_5447


title: Warm_AP_1

description:
NGS905_counts.xls
sample name in processed data file: SAM24329990


title: Warm_AP_3

description:
NGS905_counts.xls
sample name in processed data file: SAM24329988


title: Cold_M1_2

description:
NGS905_counts.xls
sample name in processed data file: SAM24295028

value: M1 macrophage


title: Cold_M1_3

description:
NGS905_counts.xls
sample name in processed data file: SAM24295030


title: Cold_M2_3

description:
NGS905_counts.xls
sample name in processed data file: SAM24295031

value: M2 macrophage


title: Cold_M2_2

description:
NGS905_counts.xls
sample name in processed data file: SAM24295029


title: Cold_M1_1

description:
NGS905_counts.xls
sample name in processed data file: SAM24295026


title: Cold_M2_1

description:
NGS905_counts.xls
sample name in processed data file: SAM24295027


title: Warm_M2_2

description:
NGS905_counts.xls
sample name in processed data file: SAM24295023


title: Warm_M2_3

description:
NGS905_counts.xls
sample name in processed data file: SAM24295025


title: Warm_M1_3

description:
NGS905_counts.xls
sample name in processed data file: SAM24295024


title: Warm_M1_2

description:
NGS905_counts.xls
sample name in processed data file: SAM24295022


title: Warm_M2_1

description:
NGS905_counts.xls
sample name in processed data file: SAM24295021


title: Warm_M1_1

description:
NGS905_counts.xls
sample name in processed data file: SAM24295020


title: mouse14_kidney_5min_RiboSeq

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description:
processed data file:
mouse13-16_kidney_5min_RiboSeq.coverage.txt

data_processing:
library strategy: Ribo-seq
To remove illumina adapter from Ribo-seq libraries run "cutadapt -u 1 -m 23 -a AGATCGGAAGAGCACACGTCT --discard-untrimmed -o output.fastq input.fastq"
mRNA-seq sequences were aligned with TopHat 2.1.0 using following settings: tophat --transcriptome-index --no-discordant --no-mixed --no-novel-juncs
The NCBI mouse genome build GRCm38.p3 and the Mus musculus Annotation Release 105 were used as a reference. When aligning mRNA-seq and ribosome profiling reads for expression and translation efficiency estimation we used the following strategy. Only full chromosomes were left and all non-chromosomal and mitochondrial records removed. Furthermore, only RefSeq and BestRefSeq records were left in the transcriptome annotation, while Gnomon predictions were discarded along with pseudogenes. Read count per gene was accessed by HTseq-count software
To plot time-dependent ribosome occupancy, we employed a different strategy. First, using a gene bank (gbk) file, which comes in a package with the genome assembly and annotation, we extracted RefSeq and BestRefSeq records for every gene including CDS, 5’-UTR and 3’-UTR lengths and sequences. Among them, we identified the longest isoform for every gene, prioritized as CDS > 5’UTR > 3’UTR. 5’-UTRs were trimmed by 100 nucleotides. If either or UTRs were shorter than 100 nucleotides, we filled it with up to 100 based on genomic coordinates. The full list of sequences is collected in the mRNA_100.fna file. To prepare a list of non-redundant genes, we run blast of all vs. all (blastall -p blastn -m 8 -b 500 -v 500 -e 0.001). Gene pairs that are too similar at the level of nucleotide sequence were excluded. In addition to the e-score, we enforced a requirement of the high-homology stretch being at least 50 nt long, and if it was longer, the similarity had to be at least 90% to treat these genes as homologous and redundant. A total of 13,685 genes passed every threshold. This reference set ensured unambiguous alignment of ribosome footprints. Resulting sequences are collected in the mRNA_100unique.fna file.
Custom Perl and R scripts were used to calculate the footprint coverage profiles of individual genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts contain raw read count of individual genes; footprint coverage contains gene coverage profiles

extract_protocol:
Frozen tissue was lysed a glass-Teflon Dounce homogenizer: 20 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 1 mM DTT, 1% Triton-X100, 0.1 mg/ml cycloheximide. The lysate was incubated with 4:1 mixture of ribonucleases T1 and S7 for 30 min at room temperature with gentle agitation. Lysate fractionation was performed by ultracentrifugation for 3 h at 35.000 rpm in an SW41 rotor (Beckman, Optima L-20K) at 4⁰ C in 10-50% sucrose, 20 mM Tris-HCl pH 7.5, 100 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.1 mg/ml cycloheximide. After the centrifugation, gradients were passed through a UV detector (Bio-Rad) and the absorption at 254 nm was recorded. The fraction containing monosomes was collected in a single tube. The volume of the sample was brought to 50 ul by concentrating it using 100 kDa filters (Amicon Ultra, Millipore). Then, the sample was diluted to 500 ul with a buffer containing 10 mM Tris-HCl pH 7.5, 2 mM EDTA, 1% SDS. RNA was extracted by hot acid phenol (Ambion) and precipitated by the glycogen-ethanol method (1/10 volume of 3 M sodium acetate, 1/100 volume of glycogen, 2.5 volumes of pure ethanol, 1-hour incubation at -20 followed by centrifugation). RNA was loaded on a 15% polyacrylamide TBE-urea gel and the band containing ribosomal footprints around 28-30 nucleotides was cut.
DNA adapter (rApp-AGATCGGAAGAGCACACGTCT- ddC) was ligated to the 3' end of RNA footprint. Illumina flanking sequences were added through reverse transcription and consequent Circligation technique.

tag: internal animal id

value: 13 weeks old mouse

tag: inhibitors

value: harringtonine 5 min

tag: injection route

value: retro-orbital

value: kidney

tag: molecule subtype

value: ribosome footprints


title: mouse16_kidney_5min_RiboSeq

tag: tissue


title: mouse15_kidney_5min_RiboSeq

tag: strain


title: mouse13_kidney_5min_RiboSeq


title: mouse16_liver_5min_RiboSeq

description:
processed data file:
mouse13-16_liver_5min_RiboSeq.coverage.txt

value: liver


title: mouse15_liver_5min_RiboSeq


title: mouse14_liver_5min_RiboSeq


title: Treg_MT Foxp3 RNA-Seq biological replicate 1

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

data_processing:
For CHIP-Seq: Reads were mapped to the mouse mm10 genome sequence (GRCm38) with BWA (version 0.7.16a-r1181), and BAM files were generated with SAMtools (version 1.5), using the following commands: bwa aln -o 1 -l 32 -t 4 -k 2 -m 80000000 [reference] [fastq] > [aln] ; bwa samse -n 10 [reference] [aln] [fastq] | samtools view -Sbh - > [bamfile]
Duplicates removal was performed using PICARD MarkDuplicates tool (version 2.17.10)
Bigwig files were generated from BAM files using deepTools bamCoverage (version 3.0.1) with parameters --binSize 10 --normalizeUsing RPGC --ignoreForNormalization chrX ---extendReads [insert size]
ChIP-seq peaks were called using MACS2 callpeak (version 2.1.1.20160309) with parameters --bdg -q 0.01 --keep-dup all
Differential peaks between the WT and MT samples were calculated using bdgdiff module in MACS2
Bigwig files and aligned peaks were visualised using the Interactive Genome Browser (IGV)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files containing the number of reads per 10 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)
Supplementary_files_format_and_content: text files containing ChIP-Seq peak genomic coordinates, length, summit, pileup, pvalue, fold enrichment, qvalue and name over input as determined by MACS2
For RNA-Seq: Quality of raw FASTQ sequences was assessed using FASTQC (v0.11.5).
Raw reads were adaptor-trimmed and quality-filtered using Cutadapt version 1.14 (-q 20,20)
Reads were aligned to the GRCm38/mm10 mouse genome reference with the STAR Aligner (version 020201)
Gene expression quantification was done with STAR (using the --quantMode GeneCounts option) to generate uniquely mapped read counts at the gene level
Differential expression analysis was performed with DESeq2 (v.1.16.0) using the count matrix as input
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing the raw reads count matrix
For HiChIP: Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Genome_build: mm9
Supplementary_files_format_and_content: Output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.

source_name: M370I Treg cells

growth_protocol: Treg cells sorted from lymph nodes and spleens

extract_protocol:
Cells were harvested from mice that were approximately 3-4 weeks old. Lymph nodes and spleen cells were sorted based on CD4, CD25,GITR and Fr4 or CD4, CD25, Foxp3-GFP. Cells were fixed with formaldehyde, nuclei were extracted and sonicated. For RNA-seq total RNA was extracted using Quiagen's RNeasy Kit and TRIzol reagent
ChIP DNA was prepared for high throughput sequencing library using Accel-NGS 2S Plus DNA library kit
ChIP-seq and HiChIP with Illumina Hiseq4000, Illumina HiSeq 2500 single-end 50bp sequencing platform for RNA-seq

treatment_protocol: Crosslinked with 1% formaldehyde. IP with Foxp3 antibody; custom polyclonal antibody that has been affinity purified, IP with H3K27ac antibody for HiChIP (Abcam ab4729)

value: Treg cells

value: mutant M370I


title: mouse13_liver_5min_RiboSeq


title: Treg_MT Foxp3 RNA-Seq biological replicate 2


title: Treg_WT Foxp3 RNA-Seq biological replicate 2

source_name: WT Treg cells

value: Wild-type


title: Treg_WT Foxp3 RNA-Seq biological replicate 1


title: D7_Glu

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

country: France

institute: CNRS

data_processing:
Sequencing quality control: Image analysis and base calling were performed using the NextSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software. The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
The reads were subjected to standard quality control (QC) and filter criteria according to the following parameters: (1) trimming and cleaning reads that aligned to primers and/or adaptors,(2) reads with over 50% of low-quality bases (quality value ≤15) in one read, and (3) reads with over 10% unknown bases (N bases). We have used a software called Trimmomatic to remove primers and also to remove bad quality reads. After filtering, we removed short reads (<36bp), the remaining reads are called "clean reads" and stored as FASTQ format.
Once we did confident in the quality of our sequencing data, we proceeded to align the clean reads within FASTQ files to a reference sequence. Alignments have been performed using Bowtie2 (v2.1.0)  tool against human GRCh37 reference genome and with GMAP against HIV genome.  Bowtie2 behavior was adjusted to support local alignment by set to sensitive. Ouputs were stored in BAM files which contain all the alignments.  BAM files have been sorted to compute gene level raw counts from mapped reads in each library.
Genome_build: GRCh37 and HIV YU2 strain
Supplementary_files_format_and_content: One text file by sample (tab delimited) with a first column for gene identification. The next column corresponds to the raw read counts (non-normalized).
Supplementary_files_format_and_content: Probe design includes several targets (NimbleGen Tiled Regions) such as Mir124 Loci and HIV region. We selected reads dedicated to these regions. Reads from Mir loci were counted per library (Mir124_expression_profile.pdf) whereas reads from HIV regions were assembled into contigs (contigs_stats.xlsx). Thus in our analysis it's not possible to find gene level raw counts from others regions because probe design was built to target only regions from specific chromosome.

source_name: blood

extract_protocol:
Total RNA was extracted from infected and uninfected PBMC samples using TRIzol reagent (Invitrogen) following the manufacturer's protocol.
After KAPA Hyper Prep (ROCHE) library preparation from 1µg total RNA, we proceeded with SeqCap EZ capture (ROCHE) following the manufacturer's recommendations. Hybrid selection was performed with a custom SeqCap EZ Choice Library (Roche NimbleGen).

treatment_protocol: Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal.

value: PBMC cells

tag: agent

value: HIV YU-2 strain

tag: treatment

value: GLUCURONIDE

tag: donor

value: Donor 7


title: D8_Glu

value: Donor 8


title: D6_Glu

value: Donor 6


title: D4_Glu

value: Donor 4


title: D1_Glu

value: Donor 1


title: D8_464


title: D6_464


title: D5_464

value: Donor 5


title: D5_Glu


title: D7_DMSO

value: DMSO


title: D1_464


title: D8_DMSO


title: D6_DMSO


title: D5_DMSO


title: D4_464


title: D4_DMSO


title: Sample-45: MRucRi_5

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

data_processing:
The libraries were sequenced as single-end, 75 base read length on an Illumina NextSeq 500 with a raw read count between 47 and 60 million reads per sample.
The reads were aligned to the reference human genome (hg19) using HISAT2 which achieved high overall alignment in all samples (>97%).
The number of reads that aligned to each protein coding gene were counted using htseq-count.
Count files were used to calculate gene TPMs and for EdgeR analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file contaning raw read count values of protein coding genes for each sample (Genes x Samples)

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucRi) in 5% oxygen culture condition

growth_protocol: Human ESC and iPSC were cultured in six-well tissue culture plates (Thermo Scientific) coated with Matrigel (BD Bioscience) under an atmosphere of 5 % CO2/air at 37°C in mTeSR1 medium (STEMCELL Technologies). Cells were passaged every 5–6 days.

extract_protocol:
RNAs were extracted with STAT60 (Tel-Test) and 1-bromo-3-chloro-propane (Sigma).
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

treatment_protocol: Human ESC and iPSC colonies were exposed to dispase (1 mg/mL) (STEMCELL Technologies) for 5-7 min at 37 °C and then were broken into small clumps with the Stempro EZpassage (Invitrogen) cutting tool. The method for TB differentiation has been described elsewhere with slight modifications (Amita et al 2013 PNAS). Cells were passaged onto Matrigel coated dishes into DME/F12 medium (Thermo Scientific) with knock-out serum replacement (KOSR, Invitrogen) that had been conditioned by mouse embryonic fibroblasts for 24 h (MEF-CM) and supplemented with FGF2 (4 ng/ml). After 24 h, the conditioned medium was replaced with daily changes of non-conditioned DME/F12/KOSR medium lacking FGF2 (hESC medium), but containing BMP4 (10 ng/ml), A83-01 (1 μM) and PD173074 (0.1 μM) (BAP treatment) for up to 6 days. Control cultures (undifferentiated) were maintained in MEF-CM containing 4 ng/ml FGF2.

value: iPSC derived from umbilical cord of EOPE pregnancy

tag: gender

value: female


title: Sample-43: MRucQi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucQi) in 5% oxygen culture condition


title: D1_DMSO


title: D7_464


title: Sample-42: MRucPi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucPi) in 20% oxygen culture condition


title: Sample-40: MRucMi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucMi) in 20% oxygen culture condition

value: male


title: Sample-39: MRucMi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucMi) in 5% oxygen culture condition


title: Sample-37: MRucLi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucLi) in 5% oxygen culture condition


title: Sample-36: MRucKi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucKi) in 20% oxygen culture condition


title: Sample-35: MRucKi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucKi) in 5% oxygen culture condition


title: Sample-48: MRucSi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucSi) in 20% oxygen culture condition


title: Sample-47: MRucSi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucSi) in 5% oxygen culture condition


title: Sample-44: MRucQi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucQi) in 20% oxygen culture condition


title: Sample-41: MRucPi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucPi) in 5% oxygen culture condition


title: Sample-38: MRucLi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucLi) in 20% oxygen culture condition


title: Sample-33: MRucJi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucJi) in 5% oxygen culture condition


title: Sample-46: MRucRi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucRi) in 20% oxygen culture condition


title: Sample-30: MRucGi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucGi) in 20% oxygen culture condition


title: Sample-31: MRucIi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucIi) in 5% oxygen culture condition


title: Sample-29: MRucGi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucGi) in 5% oxygen culture condition


title: Sample-32: MRucIi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucIi) in 20% oxygen culture condition


title: Sample-25: MRucDi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucDi) in 5% oxygen culture condition


title: Sample-17: MRuc9i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc9i) in 5% oxygen culture condition

value: iPSC derived from umbilical cord of normal pregnancy


title: Sample-23: MRucBi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucBi) in 5% oxygen culture condition


title: Sample-22: MRucAi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucAi) in 20% oxygen culture condition


title: Sample-26: MRucDi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucDi) in 20% oxygen culture condition


title: Sample-24: MRucBi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucBi) in 20% oxygen culture condition


title: Sample-18: MRuc9i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc9i) in 20% oxygen culture condition


title: Sample-21: MRucAi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucAi) in 5% oxygen culture condition


title: Sample-16: MRuc8i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc8i) in 20% oxygen culture condition


title: Sample-13: MRuc7i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc7i) in 5% oxygen culture condition


title: Sample-28: MRucEi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucEi) in 20% oxygen culture condition


title: Sample-27: MRucEi_5

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucEi) in 5% oxygen culture condition


title: Sample-20: MRuc10i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc10i) in 20% oxygen culture condition


title: Sample-19: MRuc10i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc10i) in 5% oxygen culture condition


title: Sample-4: H9 WA09_20

source_name: trophoblasts collected at day 6 BAP treatment of H9 hESC (WA09) in 20% oxygen culture condition

value: ESC derived from human blastocysts (H9, NIH code WA09)


title: Sample-5: MRuc3i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc3i) in 5% oxygen culture condition


title: Sample-9: MRuc5i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc5i) in 5% oxygen culture condition


title: Sample-1: H1 WA01_5

source_name: trophoblasts collected at day 6 BAP treatment of H1 hESC (WA01) in 5% oxygen culture condition

value: ESC derived from human blastocysts (H1, NIH code WA01)


title: Sample-2: H1 WA01_20

source_name: trophoblasts collected at day 6 BAP treatment of H1 hESC (WA01) in 20% oxygen culture condition


title: Sample-7: MRuc4i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc4i) in 5% oxygen culture condition


title: Sample-8: MRuc4i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc4i) in 20% oxygen culture condition


title: Sample-3: H9 WA09_5

source_name: trophoblasts collected at day 6 BAP treatment of H9 hESC (WA09) in 5% oxygen culture condition


title: HUES9.day0

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description: processed data file: Txi_gene$counts.csv

data_processing:
Raw reads were mapped to the human reference transcriptome (Ensembl, release 92) using Kallisto. Tximport was used to import transcript-level count data into R and summarize to gene-level.
Data were normalized using the DESeq2 package, and filtering was carried out to remove unexpressed and lowly expressed genes.
Differentially expressed genes (FDR < 0.05 and log2 fold change >= 0.59) were identified using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Txi_gene$counts.csv: Comma-separated text file.

source_name: human embryonic stem cell (hESC)

growth_protocol: hESCs were cultured on MEFs at 4% oxygen and passaged manually to expand in preparation for RNA isolation and trophoblastic cell differentiation.

extract_protocol:
Total RNA was isolated for all samples at the same time using TRIzol (Invitrogen). RNA quality was assessed using an Agilent BioAnalyzer.
TruSeq Stranded mRNA Library Preparation Kit (Illumina).
RNA-Sequencing (Illumina NextSeq 500), two runs.

treatment_protocol: Mechanical disslocatin was used to passage hESC colonies onto Matrigel coated plates with Mef-conditioned medium containing b-FGF. 24 hours after plating, we added differentiation medium lacking β-FGF and containing 50ng/mL BMP4, 1 µM A83-01 (Tocris), and 0.1 µM PD173074 (Tocris) to differentiate cells to trophoblastic progenitor cells. Media was refreshed every 48 hours and cells were harvested at day 5 of differentiation.

tag: cell line

tag: passage

tag: differentiation status

value: day 0


title: H9.day5

value: day 5


title: HUES8.day5


title: HUES7.day5


title: HUES8.day0


title: HUES9.day5


title: H9.day0


title: HUES7.day0


title: Sample-6: MRuc3i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc3i) in 20% oxygen culture condition


title: H1.day0


title: H1.day5


title: Sample-34: MRucJi_20

source_name: trophoblasts collected at day 6 BAP treatment of EOPE-iPSC (MRucJi) in 20% oxygen culture condition


title: Sample-10: MRuc5i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc5i) in 20% oxygen culture condition


title: Sample-15: MRuc8i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc8i) in 5% oxygen culture condition


title: Sample-11: MRuc6i_5

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc6i) in 5% oxygen culture condition


title: Sample-12: MRuc6i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc6i) in 20% oxygen culture condition


title: Sample-14: MRuc7i_20

source_name: trophoblasts collected at day 6 BAP treatment of CTL-iPSC (MRuc7i) in 20% oxygen culture condition


title: Skin_3001/004 V9 (P)_rep5

type: RNA

city: muenster

first: karin

last: loser

state: nrw

address: von-esmarch-str. 58

department: dermatology

country: Germany

institute: university of muenster

description: Gene expression data from psoriasis plaque

hyb_protocol: DNA targets were hybridized for 17h at 45°C on GeneChip Human Transcriptome Arrays 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol (Affymetrix GeneChip Wash, Stain and Scan Kit, 900720).

scan_protocol: Subsequently, the GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: For microarray data analysis, the Affymetrix Expression Console and Transcriptome Analysis Console was used. The robust multi-array (RMA) averaging method was applied for background correction, quantile normalization, and probe summarization.

label: Biotin

source_name: Skin biopsy (lesional, 16 wk secukinumab), patient with moderate to severe plaque type psoriasis

label_protocol: The fragmented and biotinylated DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol (Affymetrix GeneChip® WT PLUS Reagent Kit, 902280) from 100 ng total RNA starting material and 5.5 µg cDNA intermediate product.

growth_protocol: Skin biopsies were taken from psoriasis patients at baseline (lesional and non-lesional skin, V2), after 16 weeks of treatment with subcutaneous secukinumab (lesional skin, V9) and after

extract_protocol: RNA was extracted from frozen skin samples using affinity chromatographgy columns according to the manufacturer's instructions (Analytik Jena, Jena, Germany).

treatment_protocol:
the 16 week randomized, double-blind, placebo contgrolled withdrawal phase (lesional skin, V14). Samples from patients who received secukinumab during the withdrawal phase are
labelled with V, samples from patients who received placebo during the withdrawal phase are labelled with P.

value: Skin

tag: disease state

value: Plaque-type psoriasis patient

tag: skin type

value: psoriasis plaque


title: Skin_3001/004 V2 non-les. (P)_rep5

description: Gene expression data from non-affected skin

source_name: Skin biopsy (non-lesional, baseline), patient with moderate to severe plaque type psoriasis

value: non-affected skin


title: Skin_3001/004 V2 (P)_rep5

source_name: Skin biopsy (lesional, baseline), patient with moderate to severe plaque type psoriasis


title: Skin_3009/005 V2 (V)_rep5


title: Skin_3013/008 V2 non-les. (P)_rep4


title: Skin_3001/004 V14 (P)_rep5

source_name: Skin biopsy (lesional, 16 wk secukinumab + 16 wk placebo), patient with moderate to severe plaque type psoriasis


title: Skin_3009/005 V9 (V)_rep5


title: Skin_3013/008 V14 (P)_rep4


title: Skin_3013/008 V9 (P)_rep4


title: CHB8.day0

tag: Sex


title: CHB8.day5


title: Skin_3009/004 V2 non-les. (V)_rep3


title: Skin_3009/001 V9 (P)_rep1


title: Skin_3013/008 V2 (P)_rep4


title: Skin_3025/005 V2 (P)_rep2


title: Skin_3009/005 V14 (V)_rep5

source_name: Skin biopsy (lesional, 16 wk secukinumab + 16 wk secukinumab), patient with moderate to severe plaque type psoriasis


title: Skin_3013/010 V2 (P)_rep3


title: Skin_3009/004 V9 (V)_rep3


title: Skin_3004/012 V14 (V)_rep2


title: Skin_3009/001 V2 non-les. (P)_rep1


title: Skin_3010/005 V2 non-les. (V)_rep4


title: Skin_3025/005 V9 (P)_rep2


title: Skin_3009/004 V14 (V)_rep3


title: Skin_3010/005 V9 (V)_rep4


title: Skin_3025/005 V14 (P)_rep2


title: Skin_3010/005 V2 (V)_rep4


title: Skin_3013/010 V2 non-les. (P)_rep3


title: Skin_3025/005 V2 non-les. (P)_rep2


title: Skin_3009/004 V2 (V)_rep3


title: Skin_3009/001 V14 (P)_rep1


title: Skin_3004/012 V2 (V)_rep2


title: Skin_3009/005 V2 non-les. (V)_rep5


title: Skin_3013/010 V14 (P)_rep3


title: Skin_3013/010 V9 (P)_rep3


title: Skin_3010/005 V14 (V)_rep4


title: Skin_3004/014 V2 non-les. (V)_rep1


title: Skin_3004/014 V14 (V)_rep1


title: Skin_3004/014 V2 (V)_rep1


title: Skin_3004/012 V9 (V)_rep2


title: Skin_3004/012 V2 non-les. (V)_rep2


title: Skin_3009/001 V2 (P)_rep1


title: Skin_3004/014 V9 (V)_rep1


title: A6.1001200147

city: Stanford

first: Qingyun

last: Li

address: 299 Campus Drive

department: Neurobiology

institute: Stanford University

description: Gpnmb_Clec7a_143_Microglia_processed_data.csv

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing 143 microglia (enriched for P7 PAM) and mapped gene counts (including counts for ERCC spike-ins).

source_name: Microglia

extract_protocol:
Cerebella (CB) were dissected out and put into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia (enriched for PAM with Gpnmb and Clec7a surface markers) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+Gpnmb+Clec7a+ gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.

tag: genotype

value: wild type

value: CB

tag: age

tag: gate

value: Y


title: A5.1001200146


title: A4.1001200147


title: A2.1001200147


title: A2.1001200146


title: A10.1001200146


title: A3.1001200146


title: A4.1001200146


title: A11.1001200147


title: A1.1001200147


title: A5.1001200147


title: A12.1001200146


title: A6.1001200146


title: A12.1001200147


title: A3.1001200147


title: H8.1001200165

description: C57BL6J_TREM2KO_369_Microglia_processed_data.csv

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing 369 microglia (from wild type and Trem2 KO) and mapped gene counts (including counts for ERCC spike-ins).

extract_protocol:
The whole brain was dissected out and put into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ or CD45lowCD11b+Gpnmb+Clec7a+ gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.

value: Brain


title: A1.1001200146


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title: H6.1001200165

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title: E8.1001200162


title: E7.1001200162


title: E7.1001200163


title: E6.1001200165


title: E9.1001200163


title: E6.1001200162


title: E6.1001200160


title: E9.1001200160


title: E7.1001200165


title: E8.1001200160


title: E6.1001200163


title: E5.1001200163


title: E5.1001200165


title: E5.1001200162


title: E7.1001200160


title: E4.1001200165


title: E5.1001200160


title: E4.1001200163


title: E4.1001200162


title: E3.1001200163


title: E3.1001200165


title: E3.1001200162


title: E4.1001200160


title: E2.1001200163


title: E2.1001200165


title: E2.1001200162


title: E12.1001200163


title: E12.1001200162


title: E12.1001200160


title: E12.1001200165


title: E10.1001200165


title: E11.1001200160


title: E2.1001200160


title: E10.1001200162


title: E1.1001200165


title: E10.1001200160


title: E11.1001200162


title: E10.1001200163


title: E1.1001200163


title: D9.1001200165


title: E1.1001200160


title: D9.1001200163


title: D9.1001200160


title: D9.1001200162


title: D8.1001200165


title: D8.1001200163


title: D8.1001200160


title: D7.1001200165


title: D8.1001200162


title: D7.1001200162


title: E11.1001200163


title: D7.1001200163


title: E11.1001200165


title: D6.1001200165


title: D6.1001200160


title: D6.1001200162


title: D6.1001200163


title: E1.1001200162


title: D5.1001200165


title: D4.1001200162


title: D5.1001200163


title: D4.1001200160


title: D5.1001200162


title: D5.1001200160


title: D4.1001200165


title: D3.1001200165


title: D3.1001200163


title: D2.1001200163


title: D2.1001200165


title: D3.1001200160


title: D7.1001200160


title: D12.1001200165


title: E3.1001200160


title: D12.1001200163


title: D12.1001200162


title: D12.1001200160


title: D11.1001200163


title: D11.1001200162


title: D2.1001200162


title: D2.1001200160


title: D10.1001200162


title: D10.1001200160


title: D10.1001200163


title: D10.1001200165


title: D4.1001200163


title: D11.1001200160


title: D1.1001200165


title: D1.1001200163


title: D11.1001200165


title: D1.1001200162


title: C9.1001200163


title: D3.1001200162


title: D1.1001200160


title: C9.1001200165


title: C9.1001200160


title: C9.1001200162


title: C8.1001200165


title: C8.1001200162


title: C8.1001200160


title: C8.1001200163


title: C7.1001200165


title: C7.1001200163


title: C6.1001200163


title: C7.1001200162


title: C6.1001200160


title: C6.1001200162


title: C5.1001200165


title: C5.1001200163


title: C5.1001200160


title: C2.1001200165


title: C4.1001200162


title: C2.1001200163


title: C3.1001200162


title: C3.1001200160


title: C4.1001200165


title: C3.1001200165


title: C2.1001200162


title: C2.1001200160


title: C7.1001200160


title: C12.1001200162


title: C6.1001200165


title: C12.1001200163


title: C11.1001200163


title: C11.1001200165


title: C11.1001200162


title: C11.1001200160


title: C5.1001200162


title: C10.1001200165


title: C4.1001200163


title: C4.1001200160


title: C10.1001200163


title: C10.1001200162


title: C10.1001200160


title: C3.1001200163


title: C12.1001200165


title: C1.1001200165


title: C1.1001200162


title: B9.1001200165


title: B9.1001200162


title: B9.1001200163


title: B9.1001200160


title: C12.1001200160


title: B8.1001200162


title: C1.1001200160


title: B8.1001200160


title: B8.1001200163


title: B7.1001200165


title: B7.1001200163


title: B7.1001200162


title: B7.1001200160


title: B6.1001200165


title: B6.1001200163


title: B6.1001200162


title: B5.1001200165


title: B4.1001200165


title: B4.1001200163


title: C1.1001200163


title: B5.1001200162


title: B5.1001200160


title: B4.1001200160


title: B5.1001200163


title: B3.1001200162


title: B3.1001200165


title: B3.1001200160


title: B2.1001200165


title: B8.1001200165


title: B2.1001200162


title: B2.1001200163


title: B2.1001200160


title: B12.1001200165


title: B12.1001200163


title: B12.1001200160


title: B11.1001200165


title: B11.1001200163


title: B11.1001200162


title: B6.1001200160


title: B11.1001200160


title: B10.1001200163


title: B4.1001200162


title: B10.1001200165


title: B10.1001200162


title: B10.1001200160


title: B3.1001200163


title: B1.1001200162


title: B1.1001200160


title: B1.1001200163


title: B1.1001200165


title: A9.1001200163


title: A9.1001200165


title: A8.1001200163


title: A8.1001200165


title: A9.1001200160


title: A7.1001200163


title: A6.1001200163


title: A8.1001200162


title: B12.1001200162


title: A6.1001200160


title: A5.1001200165


title: A4.1001200165


title: A6.1001200162


title: A7.1001200165


title: A5.1001200163


title: A4.1001200163


title: A3.1001200165


title: A3.1001200163


title: A5.1001200162


title: A4.1001200162


title: A3.1001200162


title: A2.1001200165


title: A2.1001200163


title: A2.1001200162


title: A2.1001200160


title: A7.1001200162


title: A12.1001200165


title: A12.1001200162


title: A12.1001200160


title: A12.1001200163


title: A11.1001200163


title: A11.1001200165


title: A11.1001200160


title: A10.1001200165


title: A1.1001200163


title: A10.1001200163


title: A1.1001200165


title: A10.1001200162


title: A1.1001200162


title: A3.1001200160


title: STR_rep2

description: BulkRNAseq_P60_regions_processed_data.csv

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing 12 samples (3 replicates each region, 4 regions) and mapped gene counts.

extract_protocol:
Cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR) were dissected out on ice. Tissues from the same region were pooled from 3-5 mice into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. For each sample, 3000 live cells in the TMEM119+ gate (also CD45lowCD11b+) were sorted into a 1.5ml Eppendorf tube containing 350ul RLT buffer. RNA was extracted using RNeasy Micro Kit and eluted with 14ul nuclease-free water.
To make cDNA, Smart-Seq v4 ultra low input RNA kit was used following manufacture’s instruction (9.5ul RNA input). cDNA was amplified for 9 cycles, and cDNA concentrations were measured with Qubit. Libraries were prepared using Nextera XT DNA Sample Prep Kit (380pg cDNA per sample) following the standard protocol. Nextera XT 24 Indexes were used during whole transcriptomes amplification (13 cycles). Library quality was assessed with Bioanalyzer and Qubit. Nextseq sequencing was performed to a depth of (1.6±0.33) E+07 raw reads per sample and (1.07±0.24) E+07 mapped reads per sample. This led to the detection of 11727±563 genes, comparable to 11407±2177 genes detected in P60 microglia from our previously published dataset (Bennett et al. PNAS. 2016).

value: STR


title: STR_rep1


title: HIP_rep2

value: HIP


title: CTX_rep3

value: CTX


title: CB_rep2


title: CB_rep1


title: CTX_rep2


title: CTX_rep1


title: CB_rep3


title: HIP_rep1


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_H09_S381)

city: Cambridge

first: Sanjay

last: Prakadan

address: 77 Massachusetts Ave, E25-356

institute: Massachusetts Institute of Technology

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_H09_S381)
BH.tumor.rsem.full.txt

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
TopHat was used to align data
RSEM was used to generate estimates of transcripts per million reads for each single cell
Regression analysis was done as described in manuscript
Genome_build: mm10
Supplementary_files_format_and_content: Transformed, filtered RSEM TPM Matrices:
[BH.tumor.rsem.full.txt.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH4.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH4.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH5.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH5.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH7.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH7.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH8.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH8.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH9.rsem.full.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y
[BH9.rsem.regress.txt]  Murine Transcripts per million estimate by RSEM, log transformed (base 2), over all cells in analysis. F(x,y) = log2(TPM+1), where F(x,y) is value in matrix for gene x, cell y

source_name: Transcriptome of single tumor cell captured by flow cytometry

extract_protocol:
Smart-seq 2
Illumina Nextera XT

tag: cell type

tag: time point

tag: treatment status

value: treated

tag: origin

value: Tumor


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_H06_S378)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_H06_S378)
BH.tumor.rsem.full.txt

value: single tumor cell captured by flow cytometry


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_H08_S380)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_H08_S380)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_H02_S374)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_H02_S374)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_H05_S377)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_H05_S377)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G11_S371)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G11_S371)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_H01_S373)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_H01_S373)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G08_S368)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G08_S368)
BH.tumor.rsem.full.txt


title: A1.1001200160

tag: strain

tag: tissue


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G04_S364)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G04_S364)
BH.tumor.rsem.full.txt


title: HIP_rep3


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G05_S365)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G05_S365)
BH.tumor.rsem.full.txt


title: STR_rep3


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G10_S370)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G10_S370)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G09_S369)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G09_S369)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G02_S362)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G02_S362)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F11_S359)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F11_S359)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F12_S360)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F12_S360)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F10_S358)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F10_S358)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G03_S363)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G03_S363)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F09_S357)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F09_S357)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F08_S356)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F08_S356)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F06_S354)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F06_S354)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F07_S355)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F07_S355)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F05_S353)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F05_S353)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F04_S352)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F04_S352)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F01_S349)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F01_S349)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E12_S348)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E12_S348)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G06_S366)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G06_S366)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E11_S347)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E11_S347)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_G01_S361)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_G01_S361)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E05_S341)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E05_S341)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E07_S343)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E07_S343)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E06_S342)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E06_S342)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E08_S344)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E08_S344)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E10_S346)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E10_S346)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E02_S338)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E02_S338)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E03_S339)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E03_S339)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E01_S337)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E01_S337)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E04_S340)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E04_S340)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D10_S334)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D10_S334)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D09_S333)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D09_S333)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D11_S335)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D11_S335)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F02_S350)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F02_S350)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D06_S330)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D06_S330)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_F03_S351)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_F03_S351)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D05_S329)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D05_S329)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D01_S325)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D01_S325)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D03_S327)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D03_S327)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D02_S326)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D02_S326)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D08_S332)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D08_S332)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C12_S324)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C12_S324)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C11_S323)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C11_S323)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D12_S336)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D12_S336)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C10_S322)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C10_S322)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C09_S321)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C09_S321)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_D04_S328)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_D04_S328)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C08_S320)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C08_S320)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C06_S318)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C06_S318)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C07_S319)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C07_S319)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_E09_S345)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_E09_S345)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C01_S313)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C01_S313)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C02_S314)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C02_S314)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B10_S310)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B10_S310)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B09_S309)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B09_S309)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_C04_S316)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_C04_S316)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B06_S306)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B06_S306)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B05_S305)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B05_S305)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B11_S311)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B11_S311)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B04_S304)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B04_S304)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B03_S303)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B03_S303)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B02_S302)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B02_S302)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B08_S308)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B08_S308)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A12_S300)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A12_S300)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A11_S299)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A11_S299)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B01_S301)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B01_S301)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A10_S298)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A10_S298)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A08_S296)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A08_S296)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_B07_S307)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_B07_S307)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A05_S293)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A05_S293)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A06_S294)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A06_S294)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A03_S291)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A03_S291)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A04_S292)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A04_S292)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A07_S295)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A07_S295)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH9_Lung_A01_S289)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH9_Lung_A01_S289)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H12_S96)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H12_S96)
BH.tumor.rsem.full.txt

value: untreated


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H08_S92)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H08_S92)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H09_S93)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H09_S93)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H10_S94)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H10_S94)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H07_S91)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H07_S91)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H11_S95)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H11_S95)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H06_S90)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H06_S90)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H05_S89)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H05_S89)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H04_S88)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H04_S88)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G10_S82)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G10_S82)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G12_S84)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G12_S84)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_H01_S85)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_H01_S85)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G11_S83)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G11_S83)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G09_S81)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G09_S81)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G07_S79)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G07_S79)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G08_S80)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G08_S80)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G06_S78)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G06_S78)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G04_S76)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G04_S76)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G01_S73)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G01_S73)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G03_S75)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G03_S75)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F12_S72)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F12_S72)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_G02_S74)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_G02_S74)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F07_S67)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F07_S67)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F10_S70)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F10_S70)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F06_S66)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F06_S66)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F05_S65)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F05_S65)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F02_S62)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F02_S62)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F03_S63)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F03_S63)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F01_S61)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F01_S61)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_E12_S60)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_E12_S60)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_F04_S64)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_F04_S64)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_E09_S57)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_E09_S57)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_E10_S58)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_E10_S58)
BH.tumor.rsem.full.txt


title: Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with JQ1 (BH7_Lung_E11_S59)

description:
Sorted, primary lung tumor single cells from mouse with small cell lung cancer, treated with bromodomain inhibitor JQ1 (BH7_Lung_E11_S59)
BH.tumor.rsem.full.txt