title: 1-1-0-0-BTN30-C23-1782070104-20ul-1-IL5359-N709-N506 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_Input_ovary2_SE

status: Public on Jul 15 2016

type: SRA

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Colorado Denver

library_source: genomic

data_processing:
Data were first mapped to an Ascaris germline draft genome (AgBionano_v1.9) using bowtie2. For CENP-A paired-end reads, we only used reads that aligned concordantly to the genome (on average 77% with insertion size < 1,500 bp) for further analysis. For these concordantly aligned paired-end reads, the entire sequences bordered by the paired-end reads were used for genome mapping and coverage analysis. For CENP-A single-end libraries, the reads were extended to the average nucleosome DNA sizes for data analysis.
For each stage, the Input vs. CENP-A ChIP-seq data were compared using the MACS2 callpeak module (-p 1e-3 --broad --broad-cutoff 0.1) to identify CENP-A enriched regions. The summits for each CENP-A enriched regions were also identified using the callpeak module (-p 1e-3 --call-summits). Overlapping peak regions from two biological replicates were defined as CENP-A peaks (peak size cutoff >= 1 kb).
Genome_build: Ascaris germline genome (AgBionano_v1.9) http://nematodes.org/genomes/ascaris_suum/
Supplementary_files_format_and_content: Microsoft excel file with defined peaks regions and read coverage values

molecule: genomic DNA

organism: Ascaris suum

source_name: Ascaris tissue or embryos

growth_protocol: Ascaris fertilized eggs were harvested from female uteri by treatment with 0.5 N NaOH, followed by extensive washing in water, and then stored at 4 °C with 5 volumes of PBS (pH 2.0). For embryonation, the fertilized eggs from final proximal region of the uterus (Zygote-4 = 0 hr embryos) were incubated at 30 °C in PBS (pH 2.0) with constant (100 rpm) shaking for the desired time. The outer shell/membranes were de-coated with 0.4 N KOH/1.4% sodium hypochlorite at 4 °C (zygotes from regions 1-4) or 30°C (developing embryos and larvae) for 180 or 90 minutes, respectively, prior to RNA preparation.

extract_protocol:
DNA was isolated by phenol:chloroform extraction and precipitated with ethanol in the presence of 10 µg of glycogen
Standard Illumina protocol

tag: tissue

value: ovary


title: 1-1-0-0-BTN30-C12-1782070104-6ul-1-IL5359-N705-N505 BTN30 Mic-scRNA-Seq

city: Stanford

first: Stephen

last: Quake

state: CA

address: 450 Serra Mall

institute: Stanford Department of Bioengineering

description: polyA RNA Mic-scRNA-Seq

library_source: transcriptomic

data_processing:
Aligned using STAR
Genes which overlapped with intergenic regions, introns, or multiples genes removed
Number of reads aligning to each gene counted
Genome_build: mm10
Supplementary_files_format_and_content: matrix, samples as rows and genes as columns. data is is log10(counts per million reads)

molecule: polyA RNA

organism: Mus musculus

source_name: striatum

extract_protocol:
Acute brain slices were cut from 5-7 weeks old male mouse and after papain treatment dissociated mechanically (SI Methods). Live cells were purified by either magnetic bead-activated cell sorting (MACS;Miltenyi Biotec) or by fluorescence-activated cell sorting (FACS). For cell type specific isolation genetically labeled MSN subtypes D1-, D2-MSN, and astrocytes were purified by FACS.
Single cells were captured on a microfluidic chip on the C1 system (Fluidigm) and whole-transcriptome amplified cDNA was prepared on chip using theSMARTer Ultra LowRNAkit for Illumina (Clontech). For smart-seq2 protocol, three MSN populations (D1-MSN tdTom+, D1-MSN GFP+ and tdTom+/GFP+ MSNs) sorted individually into 96 well plates with lysis buffer and spun down and frozen at -80°C and amplified using the protocol as described previously (Picelli et al., 2013). Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

tag: experiment

tag: major cell type

value: Neuron

tag: protocol

value: Mic-scRNA-Seq


title: 1-1-0-0-BTN30-C14-1782070104-20ul-1-IL5359-N710-N505 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_Input_ovary3_SE


title: 1-1-0-0-BTN30-C18-1782070104-6ul-1-IL5359-N701-N506 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_Input_ovary1_SE


title: CenpA_Input_L1_SE

value: embryo


title: CenpA_Input_7day_SE


title: 1-1-0-0-BTN30-C07-1782070104-20ul-1-IL5359-N702-N505 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN30-C10-1782070104-12ul-1-IL5359-N707-N505 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_Input_60hr_SE


title: 1-1-0-0-BTN30-C06-1782070104-6ul-1-IL5359-N710-N504 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_Input_0hr_SE


title: CenpA_Input_5day_SE


title: CenpA_testis2_SE

value: testis


title: 1-1-0-0-BTN28-C88-1772078265-10ul-1-IL5359-N711-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN30-C02-1782070104-14ul-1-IL5359-N707-N504 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN30-C03-1782070104-12ul-1-IL5359-N706-N504 BTN30 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_ovary3_SE


title: CenpA_ovary2_SE


title: CenpA_60hr_SE


title: CenpA_7day_SE


title: 1-1-0-0-BTN28-C73-1772078265-4ul-1-IL5359-N711-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_L1_SE


title: CenpA_5day_SE


title: 1-1-0-0-BTN28-C59-1772078265-6ul-1-IL5359-N712-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_0hr_SE


title: CenpA_testis1_SE


title: 1-1-0-0-BTN28-C54-1772078265-2ul-1-IL5359-N708-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_Input_46hr_SE


title: 1-1-0-0-BTN28-C83-1772078265-4ul-1-IL5359-N704-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: MP6_K562_MUT-_2

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

data_processing:
CASAVA Illumina in house
TopHat alignment
Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: gtf annotaton file

molecule: total RNA

organism: Homo sapiens

source_name: K562, uninduced

growth_protocol: K562 cells were grown in RPMI-1640 media supplemented with 10% fetal bovin serum.

extract_protocol:
RNA was prepared by Trizol extraction
Ribosomal RNA was depleted by RNAseH hybridization based technique. Illumina compatible cDNA library was prepared from rRNA depleted libraries by standard approaches

treatment_protocol: Doxycycline induction was performed with 1 ug/ml of doxycyline for 48 hours

tag: cell line

tag: transgene


title: MP4_K562_WT-_1


title: MP2_K562_MUT-_1


title: 1-1-0-0-BTN28-C51-1772078265-4ul-1-IL5359-N705-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C69-1772078265-0ul-1-IL5359-N707-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C42-1772078265-8ul-1-IL5359-N709-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: CenpA_testis3_SE


title: 1-1-0-0-BTN28-C48-1772078265-4ul-1-IL5359-N704-N504 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: sh492 rep1

city: DOWNERS GROVE

first: Cai

last: Roberts

state: IL

address: 555 31ST STREET, SCIENCE HALL 322-E

department: Pharmacology

institute: Midwestern University

data_processing:
Fastq files were uploaded to the online Galaxy platform (http://usegalaxy.org)
Cufflinks to assemble alignments into transcripts
Tophat to align reads to genome
Cuffmerge to combine cufflinks outputs into a gtf file
Cuffdiff to determine differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: Excel files containing FPKM values, log2 fold changes, and statistics

source_name: Ovcar8 cell line

growth_protocol: Cells were maintained at standard cell culture conditions in RPMI 1640 supplemented with 0.4 mg/ml G418, 10% fetal bovine serum, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Kit from Qiagen (Cat. No. 74134) and RNA quality comfirmed by absorbance spectra.
Illumina TruSeq workflow

treatment_protocol: None.

value: Ovary

tag: transfection


title: sh492 rep2


title: MP5_K562_MUT+_2

source_name: K562, Doxycline induced


title: CenpA_ovary1_SE


title: CenpA_46hr_SE


title: 1-1-0-0-BTN28-C68-1772078265-4ul-1-IL5359-N706-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C39-1772078265-2ul-1-IL5359-N707-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: MP3_K562_WT+_1


title: MP7_K562_WT+_2


title: TWIST rep2


title: 1-1-0-0-BTN28-C38-1772078265-4ul-1-IL5359-N706-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: MP1_K562_MUT+_1


title: 1-1-0-0-BTN28-C40-1772078265-2ul-1-IL5359-N708-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: latehEC_15c

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: processed data file: EC_Model_Human_counts.gct

data_processing:
Illumina CASAVA v1.8.2  software used for basecalling and fastq file generation
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Cynomolgus monkey genome version 5.0 (Ebeling et al. 2011, PMID: 21862625. Equivalent to MacFas_Jun2011)for monkey samples or to the human genome (GRCh38/hg38) for human samples, respectively, using bowtie2
Reads Counts were calculated using HTSeq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted to generate read count values at the gene level for each sample
Genome_build: Cynomolgus monkey genome version 5.0 (Ebeling et al. 2011, PMID: 21862625. Equivalent to MacFas_Jun2011)and human genome (GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited gct files include read count values at the gene level for each sample, entrez-gene-ID, gene-symbol

source_name: human endothelial cell

growth_protocol: Cynomolgus monkey IPSCs (cIPSCs) were established from fibroblasts derived from kidney fibroblasts from a female, 14 year old Cynomolgus monkey using Sendai virus particles (Invitrogen Cytotune) and the Yamanaka factors (Oct4, Sox2, Klf4, C-Myc). cIPSCs  were cultured on matrigel (BD Bioscience) coated plates supplemented with Y-27632 (Calbiochem). Human IPSCs (hIPSC) derived from neonatal foreskin fibroblasts were cultured on matrigel-coated plates in mTesR1 (StemCell Technologies) medium including supplements. Human primary cells (from Lonza: HUVEC, HSVEC; from Cascade Biologics: HPAEC) were grown until confluency in EGM-2 medium (Lonza).

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ACTGAT

treatment_protocol: IPSCs were detached using Accutase (Stem Cell Technologies) and seeded on growth factor reduced matrigel (BD Bioscience) in the corresponding stem cell medium (mTesR1 for hIPSCs, MT medium for cIPSCs) supplemented with 10 µM Rock Inhibitor Y-27632. After 24 hours, cells were washed with PBS and covered with priming medium consisting of N2B27 supplemented with 25ng/ml BMP4 (Gibco) and 1 µM CP21 (Roche). After priming period (between 3-4 days), cells were washed and medium was switched to induction medium consisting of StemPro34-SFM complete (Gibco) supplemented with 200ng/ml VEGF (Peprotech) and 2µM Forskolin. Induction medium was changed every other day.  At day 6 of differentiation, ECs were dissociated with Accutase or 0.05% Trypsin-EDTA and MACS-separated using CD144 MicroBeads (Miltenyi Biotec) and an autoMACSpro separator (Miltenyi Biotec). Positive sorted cells were replated on human fibronectin (Sigma-Aldrich) coated dishes in EC expansion medium consisting of StemPro-34 SFM supplemented with 50ng/ml VEGF.

tag: cell type

value: IPSC-derived endothelial cell (EC)

tag: time

tag: treatment

value: N2B27-CP21-BMP4 (3d), Stempro-VEGF-FSK (2d), Stempro-VEGF (9d)

tag: macs-separation

value: CD144+, MACS-separated using CD144 MicroBeads (Miltenyi Biotec)


title: 1-1-0-0-BTN28-C37-1772078265-8ul-1-IL5359-N705-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: latehEC_15b

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GTTTCG


title: 1-1-0-0-BTN28-C35-1772078265-10ul-1-IL5359-N703-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C43-1772078265-6ul-1-IL5359-N712-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: latehEC_15a

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ATTCCT


title: hIPSC_0c

source_name: human induced pluripotent stem cell

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: CGTACG

value: induced pluripotent stem cell (IPSC)


title: 1-1-0-0-BTN28-C31-1772078265-4ul-1-IL5359-N712-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C27-1772078265-6ul-1-IL5359-N710-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: hIPSC_0b

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GATCAG


title: hIPSC_0a

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: TTAGGC


title: TWIST rep1


title: 394_human_HSVEC

source_name: Human adult saphenous vein endothelial cells (HSVEC)

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GAGTGG

value: primary endothelial cell

value: confluency


title: 399_human_pulmonary_artery

source_name: Human Pulmonary Artery Endothelial Cells  (HPAEC)

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GTGGCC


title: 1-1-0-0-BTN28-C21-1772078265-4ul-1-IL5359-N704-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C19-1772078265-4ul-1-IL5359-N705-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C13-1772078265-0ul-1-IL5359-N701-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 388_human_HUVECs_Lonza_AE_C

source_name: Human Umbilical Vein Endothelial Cells (HUVEC) Lonza AE_C

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ACTTGA


title: 387_human_HUVECs_Lonza_AE_batchA

source_name: Human Umbilical Vein Endothelial Cells (HUVEC) Lonza AE_batchA

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ATCACG


title: 1-1-0-0-BTN28-C08-1772078265-6ul-1-IL5359-N709-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C07-1772078265-6ul-1-IL5359-N710-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN23-C67-1772078216-IL5326-701-506 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C04-1772078265-8ul-1-IL5359-N706-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 386_human_HUVECs_Lonza_RNCB_CL00577

source_name: Human Umbilical Vein Endothelial Cells (HUVEC) Lonza RNCB CL00577

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: TAGCTT


title: 1-1-0-0-BTN23-C61-1772078216-IL5326-701-505 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN23-C45-1772078216-IL5326-701-504 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: KAP1 Naive

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Illumina pipeline Casava 1.82
Sequenced reads were de-multiplexed to attribute each read to a DNA sample and then aligned to reference human genome hg19 with bowtie2
NGS.plot R package was used to generate the plots using the BAM files
Genome_build: hg19
Supplementary_files_format_and_content: png plots

extract_protocol:
Pellets were lysed, resuspended in 1mL of LB1 on ice for 10min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, resuspend in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS and protease inhibitors) and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 60 min), yielding genomic DNA fragments with a bulk size of 100-300 bp
Libraries of immunoprecipitated chromatin and total input control from ChIP were performed with single-end adaptors as previously described (Rowe et al., 2013b). Sequencing was performed on an Illumina HiSeq 2500 (Illumina), with each library sequenced in 100-bp reads run.

treatment_protocol: Cells were cross-linked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution (11% Formaldehyde Sigma 2525459, 50mM HEPES pH 7.5, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) to the growth media followed by quenching with 100 mM glycine. Cells were washed twice with PBS, then the supernatant was aspirated and the cell pellet was flash frozen in liquid nitrogen.

tag: medium

tag: chip antibody

tag: antibody manufacturer and catalog number

value: Abcam ab10483


title: 1-1-0-0-BTN23-C41-1772078216-IL5326-702-502 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C34-1772078265-4ul-1-IL5359-N702-N503 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: KAP1 Primed

value: hESM


title: 1-1-0-0-BTN23-C38-1772078216-IL5326-701-501 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: shSETD2 Dnmt3b ChIP-seq

city: Barcelona

first: Debayan

last: Datta

state: Barcelona

address: C. Baldiri Reixac 10

department: Oncology

country: Spain

institute: IRB Barcelona

data_processing:
The ChIP-seq datasets were aligned to the human genome build hg19 using Bowtie version 1.01. The parameters used were -k 1, -m 1, -n 2.
Peaks of Dnmt3A and Dnmt3B were called using MACS 1.4.1 using the parameters -p 1e-5, -w, -S and -g hs.
For Histone marks, MACS2 was used with parameters -broad, -q 0.01 -g hs.
Genome_build: hg19
Supplementary_files_format_and_content: The BED files were obtained from the output of MACS/MACS2.

source_name: Epidermal Stem Cells

growth_protocol: Human Epidermal Stem Cells were isolated from neonatal foreskin samples and cultured with a feeder layer of fibroblasts (J2-3T3) as described previously (Gandarillas and Watt, 1997). Undifferentiated epSC were grown in Keratinocyte Serum-Free Medium with supplements (KSFM; GIBCO). For calcium-induced differentiation, after reaching 70% confluence KSFM was exchanged for EMEM (Lonza) supplemented with 8% chelated FBS, EGF (10 ng/ml), 1% penicillin/streptomycin, and 1.2mM CaCl2. After 48 hr differentiated keratinocytes were collected.

extract_protocol: EpiSC and differentiated keratinocytes were trypsinized and crosslinked in 1% formaldehyde (FA) for 10 min at room temperature (RT). For ChIPs from EBs, crosslinking was performed for 30 min at RT in 4% FA. Crosslinking was quenched with 0.125 M glycine. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 15 min in a Bioruptor (Diagenode). Soluble material was quantified by Bradford assays. To immunoprecipitate transcription factors, 2000 mg of protein and 100 mg of immunoprecipitated histone/histone modifications were used. Antibodies (10ug for DnmtA/3B and 3ug for histone modifications) were incubated overnight with the chromatin. Immunocomplexes were recovered with 30 ul of protein A bead slurry (Healthcare. Cat # 17-5280-01). Immunoprecipitated material was washed three times with low salt buffer and one time with high salt buffer. DNA complexes were decrosslinked at 65_C overnight, and DNA was then eluted in 50 ul of water using the PCR purification kit (QIAGEN)

treatment_protocol: Epidermal Stem Cells growing in KSM media were infected with precipitated lentiviral particles produced by 293T cells transfected with the mentioned plasmids. Cells were collected for ChIP assay after 5 days of puromycin selection

tag: passage

value: Foreskin

tag: chip-antibody

value: DNMT3B Novus (NB300-516)


title: 1-1-0-0-BTN23-C01-1772078216-IL5326-701-502 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: shSETD2 Dnmt3a ChIP-seq

value: DNMT3A SantaCruz (H-295)


title: 1-1-0-0-BTN28-C25-1772078265-6ul-1-IL5359-N708-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-dd-BTN22-C48-14ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: shDnm3b Dnmt3b Chip-seq


title: 1-1-0-0-BTN28-C18-1772078265-2ul-1-IL5359-N702-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Dnmt3b EpSC  ChIp-seq replicate 2


title: 1-0-g-d-BTN24-C19-54ul-IL5195-704-502 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN24-C93-22ul-IL5195-705-504 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-d-BTN24-C43-38ul-IL5195-702-508 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN24-C90-46ul-IL5195-710-503 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Medip Seq shTET2


title: 1-0-g-d-BTN24-C09-46ul-IL5195-702-502 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: HydroxyMedip Seq shDnmt3b

value: 5-Hydroxymethylcytosine (Active Motif, Cat:39769)


title: HydroxyMedip Seq shDnmt3a


title: 1-0-g-d-BTN22-C18-30ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Neuron


title: Dnmt3a EpSC  ChIp-seq replicate 2


title: Medip Seq ShCTRL


title: 1-1-0-0-BTN28-C26-1772078265-6ul-1-IL5359-N709-N502 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Mic-scRNA-Seq


title: HydroxyMedip Seq shCTRL


title: 1-0-g-0-BTN24-C82-30ul-IL5195-701-508 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: H3K36me3 Chip-Seq KC

source_name: Differentiated Keratinocytes

value: H3K36me3 (Abcam Cat:ab9050)


title: 1-0-g-0-BTN24-C51-18ul-IL5195-706-503 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: H3K36me3  Chip-Seq EpiSC


title: 1-0-g-0-BTN24-C52-54ul-IL5195-709-505 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN24-C77-10ul-IL5195-710-507 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: H3K27ac rep3 Chip-Seq KC

value: H3K27ac (Merck Millipore. Cat 07-360)


title: H3K27ac rep 2 Chip-Seq EpiSC


title: 1-0-g-0-BTN24-C21-46ul-IL5195-702-504 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN24-C06-30ul-IL5195-706-508 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN22-C92-8ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: shDnm3a Dnmt3a Chip-seq


title: 1-0-g-0-BTN22-C71-18ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN22-C46-10ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Naive  - WIBR3

data_processing:
Illumina pipeline Casava 1.82
Reads were mapped to the human genome (hg19) using TopHat (v2.0.11) in sensitive mode (tophat --library-type fr-firststrand -g 1 --no-novel-juncs --no-novel-indels –b2-sensitive)
Gene counts were generated using HTSeq-count (0.6.1)
Repeats counts were generated using the multiCov tool from the bedtools (2.25) software
Genome_build: hg19
Supplementary_files_format_and_content: read counts on genes (pileup files): htseq-cout output; read counts on repeats: bedtools multiBamCov output

source_name: human ES

growth_protocol: Conventional (primed) human ESC lines were maintained on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeders in human embryonic stem cell medium (hESM) and passaged mechanically using a drawn Pasteur pipette or enzymatically by treatment for 20 minutes with 1 mg/mL Collagenase Type IV (Gibco) followed by sequential sedimentation steps in hESM to remove single cells. Naive human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium. For conversion of pre-existing primed human ESC lines, we seeded 2 x 105 trypsinized single cells on a MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (Stemgent, 10 μM). 2 days later medium was switched to 5i/L/A or 4i/L/A (no IM12)-containing naive human ESC medium. Following an initial wave of cell death, naive colonies appeared within 10 days and were expanded polyclonally using Accutase (Gibco) on a MEF feeder layer. Naive cells generated with DOX-inducible KLF2 and NANOG transgenes (Theunissen et al., 2014) were maintained in 2i/L/DOX with optional inclusion of 10 μM ROCK inhibitor Y-27632. To adapt DOX-dependent naive cells to transgene-free culture conditions, 1 x 105 single cells were seeded on a MEF feeder layer in 2i/L/DOX and DOX was withdrawn the next day. For re-priming, semi-confluent cultures of naive cells were switched to hESM with ROCK inhibitor Y-27632 (10 μM) and passaged with Collagenase on MEFs. Neuronal precursor cells (NPCs) were derived from re-primed cells using a published differentiation protocol (Cohen et al., 2007). To culture naive human cells described by Gafni et al. (2013), we used the KSR-based version of the NHSM protocol. Tissue culture media were filtered using a low protein-binding binding 0.22 μm filter (Corning). All experiments in this paper were performed under physiological oxygen conditions (5% O2, 3% CO2). Detailed media compositions are described in Supplemental Experimental Procedures.

extract_protocol: Illumina Truseq Stranded RNA

tag: es state

value: naive


title: Naive - WIBR2


title: Naive (transgene-dependent) - WIBR3 OCT4-ΔPE-GFP +K2N cl. 12

value: naive TD


title: 1-0-g-0-BTN22-C51-10ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

extract_protocol:
Acute brain slices were cut from 5-7 weeks old male mouse and after papain treatment dissociated mechanically (SI Methods). Live cells were purified by either magnetic bead-activated cell sorting (MACS;Miltenyi Biotec) or by fluorescence-activated cell sorting (FACS). For cell type specific isolation genetically labeled MSN subtypes D1-, D2-MSN, and astrocytes were purified by FACS.
Single cells were captured on a microfluidic chip on the C1 system (Fluidigm) and whole-transcriptome amplified cDNA was prepared on chip using theSMARTer Ultra LowRNAkit for Illumina (Clontech). For smart-seq2 protocol, three MSN populations (D1-MSN tdTom+, D1-MSN GFP+ and tdTom+/GFP+ MSNs) sorted individually into 96 well plates with lysis buffer and spun down and frozen at -80°C and amplified using the protocol as described previously (Picelli et al., 2013). Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.


title: X-reporter line, Naive, Double positive - WIBR2 MECP2 reporter (cl. 299) (XX)

value: 5i/L/A (CH)


title: Naive (transgene-dependent) - WIBR3 OCT4-ΔPE-GFP +K2N cl. 16


title: 1-0-g-0-BTN22-C28-8ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN22-C32-26ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: X-reporter line, Naive, Double positive - WIBR2 MECP2 reporter (cl. 298) (XX) -2

value: 5i/L/A (IM)


title: Male Naive ES - WIN1 (XY) - 2


title: 1-0-g-0-BTN22-C27-14ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN24-C07-18ul-IL5195-703-508 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN22-C22-10ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN22-C13-8ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN22-C89-8ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: X-reporter line, Primed,  Red only - WIBR2 MECP2 reporter (cl. 298) Red (XX)

value: primed


title: Male Primed iPS - NPC 1.1 #13 (XY)

source_name: human iPS

value: NPC 1.1


title: 1-0-g-0-BTN22-C10-14ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: X-reporter line, Primed, Green only - WIBR2 MECP2 reporter (cl. 299) GFP (XX)


title: Male Primed iPS - NPC 1.1 #4 (XY)


title: 1-0-g-0-BTN22-C02-6ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: X-reporter line, Naive, Double positive - WIBR2 MECP2 reporter (cl. 298) (XX)


title: 1-0-1-1-BTN35-C39-1782070112-30ul-1-IL5413-N703-N508 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Male Primed ES - WIBR1 (XY)


title: Male Naive ES - WIN1 (XY)


title: 1-0-1-1-BTN35-C22-1782070112-22ul-1-IL5413-N702-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-g-0-BTN22-C15-10ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: MEDIP-Seq KC

data_processing:
The ChIP-seq datasets were aligned to the human genome build hg19 using Bowtie version 1.01. The parameters used were -k 1, -m 1, -n 2.
Peaks of Dnmt3A and Dnmt3B were called using MACS 1.4.1 using the parameters -p 1e-5, -w, -S and -g hs. For Methylation and HydroxyMethylation peaks, the p-value cutoff was set to 1e-3.
For Histone marks, MACS2 was used with parameters -broad, -q 0.01 -g hs.
Genome_build: hg19
Supplementary_files_format_and_content: The BED files were obtained from the output of MACS/MACS2.

tag: tissue


title: Input Dnmt3AB Chip-Seq KC

value: none, input


title: 1-0-1-1-BTN35-C20-1782070112-18ul-1-IL5413-N711-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

tag: experiment


title: HydroxyMedip-Seq EpiSC


title: 1-0-1-1-BTN35-C16-1782070112-22ul-1-IL5413-N706-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

tag: major cell type


title: 1-0-1-1-BTN35-C05-1782070112-12ul-1-IL5413-N704-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

tag: protocol


title: MP8_K562_WT-_2

extract_protocol:
RNA was prepared by Trizol extraction
Ribosomal RNA was depleted by RNAseH hybridization based technique. Illumina compatible cDNA library was prepared from rRNA depleted libraries by standard approaches

tag: cell line


title: MEDIP-Seq EpiSC


title: Input HydroxyMedip-Seq KC


title: 1-0-1-1-BTN34-C41-1782070111-30ul-1-IL5413-N703-N504 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: HydroxyMedip-Seq KC


title: Input Dnmt3AB ChIP-Seq EpiSC


title: 1-0-1-1-BTN34-C39-1782070111-30ul-1-IL5413-N702-N504 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-1-BTN27-C03-1771026164-IL5326-704-501 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Astro


title: 1-0-1-0-BTN35-C76-1782070112-18ul-1-IL5413-N709-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-1-BTN27-C36-1771026164-IL5326-710-504 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C75-1782070112-18ul-1-IL5413-N708-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C71-1782070112-2ul-1-IL5413-N704-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C68-1782070112-12ul-1-IL5413-N701-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C65-1782070112-14ul-1-IL5413-N708-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C66-1782070112-8ul-1-IL5413-N709-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-1-BTN35-C36-1782070112-18ul-1-IL5413-N711-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C64-1782070112-14ul-1-IL5413-N707-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-1-BTN35-C25-1782070112-12ul-1-IL5413-N706-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Input HydroxyMedip-Seq EpiSC


title: 1-0-1-0-BTN35-C58-1782070112-22ul-1-IL5413-N712-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C57-1782070112-22ul-1-IL5413-N710-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_L1_GR_rep1

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: ChIP-seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al., Nature method, 2012)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.

source_name: Mammary

growth_protocol: C57BL/6 mice were purchased from Charles River. Wap-delE1a, -delE1b, -delE1c, -delE2, -delE3, -delE1a_delE2, -delE2_delE3 and -delE1a_delE2_delE3  were inter-bred to maintain homozygosity. Genotyping was confirmed by PCR followed by the DNA sequencing using genomic DNAs from a tail snip. All animals were handled and housed in accordance with the guidelines of the National Institute of Diabetes, Digestive and Kidney Diseases Animal Care and Use Committee.

extract_protocol:
Frozen-stored mammary tissues from L1 and p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Mammary epithelial cells were isolated from fresh L1 and p13 mammary tissues. Antibodies against STAT5A (Santa Cruz, sc-1081), GR (Thermo Scientific, PA1-511A), MED1 (Bethyl laboratory, A300-793A), H3K27ac (Abcam, Ab4729), NFIB (Santa Cruz, sc-5567), ELF5 (Santa Cruz, sc-9645), RNA Pol II (Abcam, Ab5408) and H3K4me3 (Milllipore, 17-614) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Mammary gland

tag: state

value: lactation day 1

tag: genotype

value: GR (Thermo Scientific, PA1-511A)


title: 1-0-1-0-BTN35-C56-1782070112-10ul-1-IL5413-N709-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_L1_H3K27ac_rep1

description: ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: ChIPSeq_Wap-delE1a_delE2_L1_H3K27ac_rep2

description: ChIP-seq


title: ChIPSeq_Wap-delE1a_delE2_L1_STAT5A_rep1

description: ChIP-seq

value: STAT5A (Santa Cruz, sc-1081)


title: ChIPSeq_Wap-delE2_delE3_L1_STAT5A

description: ChIP-seq


title: ChIPSeq_Wap-delE1a_delE2_delE3_L1_H3K27ac_rep2

description: ChIP-seq


title: 1-0-1-1-BTN27-C71-1771026164-IL5326-709-508 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C54-1782070112-22ul-1-IL5413-N706-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Neuron


title: 1-0-1-1-BTN34-C38-1782070111-46ul-1-IL5413-N701-N504 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_delE3_L1_H3K27ac_rep1

description: ChIP-seq


title: 1-0-1-0-BTN35-C53-1782070112-30ul-1-IL5413-N705-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C55-1782070112-8ul-1-IL5413-N708-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_delE3_L1_GR_rep2

description: ChIP-seq


title: ChIPSeq_Wap-delE1a_delE2_delE3_L1_GR_rep1

description: ChIP-seq


title: 1-0-1-0-BTN35-C40-1782070112-22ul-1-IL5413-N704-N508 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_delE3_L1_STAT5A_rep1

description: ChIP-seq


title: 1-0-1-0-BTN35-C21-1782070112-46ul-1-IL5413-N710-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C26-1782070112-10ul-1-IL5413-N707-N507 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_L1_GR_rep2

description: ChIP-seq


title: STHdh Q111/Q111, replicate 1

city: Ashburn

first: Zhe

last: Liu

state: Virginia

address: 19700 Helix Dr.

department: Janelia Farm Research Campus

institute: Howard Hughes Medical Institute

description:
Directional mRNA-seq
Processed data file: Differential_Gene_Expression_Summary.txt

data_processing:
Reads Mapping: Bowtie 2
Differential Gene expression analysis: Cuffdiff
Significance Thresholding: R
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Differential_Gene_Expression_Summary.txt: Tab-delimited text file contains FPKMs averaged for the replicates.

growth_protocol: Regular STHdh culture conditions.

extract_protocol:
Total RNA was extracted with TRIzol LS Reagent (Invitrogen).
Libraries were prepared with ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre). Single-end 50bp reads.

value: STHdh Q111/Q111

tag: genotype/variation

tag: cell type

value: striatal neuron cell line expressing mutant huntingtin

tag: Stage

value: undifferentiated


title: STHdh Q111/Q111 + Sp1 overexpression, replicate 2

treatment_protocol: Transient expression of Sp1.

tag: transient overexpression


title: STHdh Q111/Q111, replicate 2


title: STHdh Q7/Q111, replicate 2

value: STHdh Q7/Q111

value: striatal neuron cell line expressing WT and mutant huntingtin


title: STHdh Q111/Q111 + Sp1 overexpression, replicate 1


title: STHdh Q7/Q111, replicate 1


title: 1-0-1-0-BTN35-C17-1782070112-18ul-1-IL5413-N705-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: STHdh Q7/Q7, replicate 2

value: STHdh Q7/Q7

value: striatal neuron cell line expressing WT huntingtin


title: 1-0-1-0-BTN35-C14-1782070112-18ul-1-IL5413-N701-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_L1_STAT5A_rep2

description: ChIP-seq

tag: chip antibody


title: 1-0-1-0-BTN35-C13-1782070112-30ul-1-IL5413-N702-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: STHdh Q7/Q7, replicate 1


title: 1tts_BTN2_C96_IL3971-708-508_CAGAGAGG-CTAAGCCT BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Microglia


title: 1-0-1-0-BTN35-C03-1782070112-18ul-1-IL5413-N712-N504 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ttg_BTN13_C37_IL4884-701-503_TAAGGCGA-TATCCTCT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: OPC


title: STH-Sp1-ChIP-Exo

description:
ChIP-exo enriched genomic DNA.
Processed data file: PeakRegions.txt

data_processing:
Reads Mapping: Bowtie2
Strand separation: Customized
Peak Calling: MACS2
Thresholding: R
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text file contains the genomic localizations of ChIP-exo mapped peak-pairs.

source_name: STHdh Q7/Q7, Sp1 ChIP

growth_protocol: Regular STHdh culturing protocol.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to "Rhee, H.S., and Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419" with custom-made Illumina adapters. Single-end 50bp reads.

value: Anti-Sp1 (home-made, antigen purified)


title: 1ttg_BTN13_C54_IL4884-704-504_TCCTGAGC-AGAGTAGA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

source_name: striatum

value: Ependy-C


title: 1tt_BTN2_C84_IL3971-705-507_GGACTCCT-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Vascular


title: 1-0-1-0-BTN34-C94-1782070111-30ul-1-IL5413-N711-N504 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-1-0-0-BTN28-C55-1772078265-2ul-1-IL5359-N711-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C77_IL3971-710-506_CGAGGCTG-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C73_IL3971-706-506_TAGGCATG-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C68_IL3971-703-506_AGGCAGAA-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C80-1782070111-12ul-1-IL5413-N710-N503 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C78-1782070111-4ul-1-IL5413-N708-N503 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: ChIPSeq_Wap-delE1a_delE2_delE3_L1_STAT5A_rep2

description: ChIP-seq

value: Mammary gland

value: lactation day 1


title: 1tt_BTN2_C60_IL3971-706-505_TAGGCATG-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C61_IL3971-709-505_GCTACGCT-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C75-1782070111-30ul-1-IL5413-N705-N503 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN35-C18-1782070112-22ul-1-IL5413-N704-N506 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C57_IL3971-704-505_TCCTGAGC-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C64-1782070111-30ul-1-IL5413-N709-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C53_IL3971-712-504_GTAGAGGA-AGAGTAGA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C51_IL3971-709-504_GCTACGCT-AGAGTAGA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C90_IL3971-712-507_GTAGAGGA-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C62_IL3971-710-505_CGAGGCTG-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C47_IL3971-707-508_CTCTCTAC-CTAAGCCT BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C59-1782070111-38ul-1-IL5413-N704-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C46_IL3971-706-508_TAGGCATG-CTAAGCCT BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C42_IL3971-711-507_AAGAGGCA-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C38_IL3971-708-507_CAGAGAGG-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Macrophage


title: 1tt_BTN2_C34_IL3971-703-507_AGGCAGAA-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C53-1782070111-12ul-1-IL5413-N711-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Neuron


title: 1tt_BTN2_C29_IL3971-708-506_CAGAGAGG-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C52-1782070111-10ul-1-IL5413-N710-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C37_IL3971-707-507_CTCTCTAC-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C31_IL3971-711-506_AAGAGGCA-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C88_IL3971-701-508_TAAGGCGA-CTAAGCCT BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C28_IL3971-707-506_CTCTCTAC-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C20_IL3971-712-505_GTAGAGGA-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C50-1782070111-22ul-1-IL5413-N705-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ttgg_BTN13_C49_IL4884-702-502_CGTACTAG-CTCTCTAT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C19_IL3971-701-506_TAAGGCGA-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C15_IL3971-707-505_CTCTCTAC-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C42-1782070111-46ul-1-IL5413-N704-N504 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C04_IL3971-710-504_CGAGGCTG-AGAGTAGA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C03_IL3971-707-504_CTCTCTAC-AGAGTAGA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C72_IL3972-712-504_GTAGAGGA-AGAGTAGA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C36-1782070111-38ul-1-IL5413-N712-N503 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C67_IL3972-704-504_TCCTGAGC-AGAGTAGA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C26-1782070111-38ul-1-IL5413-N703-N503 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C70_IL3972-710-504_CGAGGCTG-AGAGTAGA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C59_IL3972-711-502_AAGAGGCA-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C80_IL3972-705-506_GGACTCCT-ACTGCATA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C56_IL3972-705-502_GGACTCCT-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C57-1782070111-18ul-1-IL5413-N701-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN2_C43_IL3971-702-508_CGTACTAG-CTAAGCCT BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C24-1782070111-38ul-1-IL5413-N712-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C55_IL3972-704-502_TCCTGAGC-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C23-1782070111-22ul-1-IL5413-N701-N503 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C21-1782070111-30ul-1-IL5413-N710-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C43_IL3972-701-508_TAAGGCGA-CTAAGCCT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C42_IL3972-709-507_GCTACGCT-AAGGAGTA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C18-1782070111-8ul-1-IL5413-N707-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C33_IL3972-703-506_AGGCAGAA-ACTGCATA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C29_IL3972-708-505_CAGAGAGG-GTAAGGAG BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C27_IL3972-703-505_AGGCAGAA-GTAAGGAG BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C26_IL3972-702-505_CGTACTAG-GTAAGGAG BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C51-1782070111-6ul-1-IL5413-N706-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C22_IL3972-709-504_GCTACGCT-AGAGTAGA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C16-1782070111-46ul-1-IL5413-N708-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C25_IL3972-701-505_TAAGGCGA-GTAAGGAG BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C13-1782070111-14ul-1-IL5413-N706-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C17_IL3972-708-503_CAGAGAGG-TATCCTCT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C48_IL3972-709-508_GCTACGCT-CTAAGCCT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C11_IL3972-708-502_CAGAGAGG-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C14_IL3972-702-503_CGTACTAG-TATCCTCT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C06-1782070111-10ul-1-IL5413-N707-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C16_IL3972-709-503_GCTACGCT-TATCCTCT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C10_IL3972-709-502_GCTACGCT-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C15-1782070111-6ul-1-IL5413-N705-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C04-1782070111-30ul-1-IL5413-N709-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C21_IL3972-701-504_TAAGGCGA-AGAGTAGA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C45_IL3972-703-508_AGGCAGAA-CTAAGCCT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C06_IL3972-707-501_CTCTCTAC-TAGATCGC BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C09_IL3972-701-502_TAAGGCGA-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C03-1782070111-30ul-1-IL5413-N701-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C46_IL3972-707-508_CTCTCTAC-CTAAGCCT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C05_IL3972-708-501_CAGAGAGG-TAGATCGC BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C02-1782070111-18ul-1-IL5413-N702-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C05-1782070111-22ul-1-IL5413-N708-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C02_IL3972-702-501_CGTACTAG-TAGATCGC BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C03_IL3972-701-501_TAAGGCGA-TAGATCGC BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tt_BTN1_C01_IL3972-703-501_AGGCAGAA-TAGATCGC BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ttQ_BTN2_C86_IL3971-710-507_CGAGGCTG-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN28-C53-1772078265-4ul-1-IL5359-N707-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ttQ_BTN2_C79_IL3971-702-507_CGTACTAG-AAGGAGTA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C01-1782070111-22ul-1-IL5413-N703-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C78_IL4884-708-504_CAGAGAGG-AGAGTAGA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ttQ_BTN2_C09_IL3971-702-505_CGTACTAG-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C51-1771026164-IL5326-704-505 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Astro


title: 1tg_BTN14_C74_IL4884-707-501_CTCTCTAC-TAGATCGC BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C64_IL4884-708-503_CAGAGAGG-TATCCTCT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Oligo


title: 1tg_BTN14_C62_IL4884-706-508_TAGGCATG-CTAAGCCT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C33-1771026164-IL5326-708-504 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C65_IL4884-708-507_CAGAGAGG-AAGGAGTA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C77-1771026164-IL5326-706-501 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C59_IL4884-708-506_CAGAGAGG-ACTGCATA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C75_IL4884-706-507_TAGGCATG-AAGGAGTA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C32-1771026164-IL5326-707-508 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C60_IL4884-708-508_CAGAGAGG-CTAAGCCT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C41_IL4884-707-508_CTCTCTAC-CTAAGCCT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Ependy-Sec


title: 1-0-1-0-BTN27-C30-1771026164-IL5326-706-504 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ttQ_BTN2_C67_IL3971-702-506_CGTACTAG-ACTGCATA BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C40_IL4884-707-505_CTCTCTAC-GTAAGGAG BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C38_IL4884-706-505_TAGGCATG-GTAAGGAG BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C40-1771026164-IL5326-705-501 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C23_IL4884-707-507_CTCTCTAC-AAGGAGTA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C27-1771026164-IL5326-704-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN14_C06_IL4884-707-502_CTCTCTAC-CTCTCTAT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C94_IL4884-704-505_TCCTGAGC-GTAAGGAG BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C93_IL4884-702-504_CGTACTAG-AGAGTAGA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C08-1771026164-IL5326-707-507 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C84_IL4884-703-508_AGGCAGAA-CTAAGCCT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C78_IL4884-703-507_AGGCAGAA-AAGGAGTA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C68_IL4884-702-505_CGTACTAG-GTAAGGAG BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN34-C49-1782070111-22ul-1-IL5413-N704-N501 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C65_IL4884-704-502_TCCTGAGC-CTCTCTAT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN23-C76-1772078216-IL5326-702-507 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C53_IL4884-704-501_TCCTGAGC-TAGATCGC BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C55_IL4884-702-503_CGTACTAG-TATCCTCT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN23-C56-1772078216-IL5326-701-507 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C51_IL4884-702-506_CGTACTAG-ACTGCATA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C41_IL4884-703-504_AGGCAGAA-AGAGTAGA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C39_IL4884-702-501_CGTACTAG-TAGATCGC BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C40_IL4884-702-508_CGTACTAG-CTAAGCCT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C34_IL4884-702-507_CGTACTAG-AAGGAGTA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN27-C13-1771026164-IL5326-703-502 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN23-C24-1772078216-IL5326-702-501 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C30_IL4884-703-505_AGGCAGAA-GTAAGGAG BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C07_IL4884-701-508_TAAGGCGA-CTAAGCCT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN23-C27-1772078216-IL5326-701-503 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C17_IL4884-703-502_AGGCAGAA-CTCTCTAT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C25_IL4884-701-501_TAAGGCGA-TAGATCGC BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN1_C58_IL3972-710-502_CGAGGCTG-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN2_C07_IL3971-703-505_AGGCAGAA-GTAAGGAG BTN02 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C08_IL4884-701-506_TAAGGCGA-ACTGCATA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN24-C79-10ul-IL5195-706-507 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN24-C46-8ul-IL5195-707-505 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C64_IL4884-703-506_AGGCAGAA-ACTGCATA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN23-C96-1772078216-IL5326-702-505 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN1_C57_IL3972-706-502_TAGGCATG-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN1_C51_IL3972-706-501_TAGGCATG-TAGATCGC BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C43_IL4884-701-504_TAAGGCGA-AGAGTAGA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN1_C08_IL3972-702-502_CGTACTAG-CTCTCTAT BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C67_IL4884-710-505_CGAGGCTG-GTAAGGAG BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C82_IL4884-712-506_GTAGAGGA-ACTGCATA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN24-C23-8ul-IL5195-708-501 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1tg_BTN13_C31_IL4884-701-502_TAAGGCGA-CTCTCTAT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN24-C18-2ul-IL5195-707-501 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-dd-BTN22-C47-1ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C61_IL4884-710-504_CGAGGCTG-AGAGTAGA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-1-0-BTN23-C48-1772078216-IL5326-702-503 BTN23 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN24-C08-2ul-IL5195-703-502 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN24-C81-6ul-IL5195-705-503 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C41_IL4884-711-505_AAGAGGCA-GTAAGGAG BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C59_IL4884-712-505_GTAGAGGA-GTAAGGAG BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C34_IL4884-711-503_AAGAGGCA-TATCCTCT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C33_IL4884-710-501_CGAGGCTG-TAGATCGC BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C31_IL4884-709-504_GCTACGCT-AGAGTAGA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C18_IL4884-711-502_AAGAGGCA-CTCTCTAT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C12_IL4884-711-501_AAGAGGCA-TAGATCGC BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C27_IL4884-709-508_GCTACGCT-CTAAGCCT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: NSC


title: 1t_BTN14_C19_IL4884-706-506_TAGGCATG-ACTGCATA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN24-C45-8ul-IL5195-704-505 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN15_C15_IL4884-709-502_GCTACGCT-CTCTCTAT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN35-C45-1782070112-12ul-1-IL5413-N707-N508 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN14_C12_IL4884-707-503_CTCTCTAC-TATCCTCT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-d-BTN22-C52-4ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN14_C05_IL4884-707-506_CTCTCTAC-ACTGCATA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN13_C89_IL4884-704-503_TCCTGAGC-TATCCTCT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN35-C47-1782070112-2ul-1-IL5413-N708-N508 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN35-C51-1782070112-12ul-1-IL5413-N702-N505 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN34-C45-1782070111-4ul-1-IL5413-N707-N504 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN14_C31_IL4884-706-502_TAGGCATG-CTCTCTAT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN34-C44-1782070111-4ul-1-IL5413-N706-N504 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN13_C32_IL4884-701-507_TAAGGCGA-AAGGAGTA BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN35-C43-1782070112-2ul-1-IL5413-N705-N508 BTN35 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1qt_BTN15_C47_IL4884-711-506_AAGAGGCA-ACTGCATA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN13_C02_IL4884-701-505_TAAGGCGA-GTAAGGAG BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gs_BTN3_C05_IL3971-703-501_AGGCAGAA-TAGATCGC BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1t_BTN13_C23_IL4884-703-503_AGGCAGAA-TATCCTCT BTN13 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gs_BTN3_C57_IL3971-707-501_CTCTCTAC-TAGATCGC BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN34-C11-1782070111-4ul-1-IL5413-N703-N502 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN34-C29-1782070111-2ul-1-IL5413-N707-N503 BTN34 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ggs_BTN3_C33_IL3971-703-503_AGGCAGAA-TATCCTCT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN28-C50-1772078265-0ul-1-IL5359-N704-N501 BTN28 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C91-1771026164-IL5326-707-506 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C95-1771026164-IL5326-710-502 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C53_IL4709-711-501_AAGAGGCA-TAGATCGC BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C49_IL4709-704-501_TCCTGAGC-TAGATCGC BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C54_IL4709-712-501_GTAGAGGA-TAGATCGC BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C80-1771026164-IL5326-708-502 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C61_IL4709-704-503_TCCTGAGC-TATCCTCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C87-1771026164-IL5326-704-507 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C41_IL4709-708-507_CAGAGAGG-AAGGAGTA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C37_IL4709-701-507_TAAGGCGA-AAGGAGTA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C90_IL4690-710-506_CGAGGCTG-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C88_IL4690-702-507_CGTACTAG-AAGGAGTA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C45_IL4709-703-508_AGGCAGAA-CTAAGCCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C76-1771026164-IL5326-705-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C82_IL4690-701-507_TAAGGCGA-AAGGAGTA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C72-1771026164-IL5326-710-505 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ggs_BTN3_C61_IL3971-701-502_TAAGGCGA-CTCTCTAT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C69-1771026164-IL5326-708-507 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C73_IL4690-710-505_CGAGGCTG-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C67_IL4690-708-505_CAGAGAGG-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1ggsQ_BTN3_C19_IL3971-705-502_GGACTCCT-CTCTCTAT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C70-1771026164-IL5326-709-502 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C79_IL4690-711-505_AAGAGGCA-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C59_IL4690-712-506_GTAGAGGA-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C41_IL4690-704-506_TCCTGAGC-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C46_IL4690-703-506_AGGCAGAA-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C39_IL4690-706-505_TAGGCATG-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C66-1771026164-IL5326-706-506 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C63-1771026164-IL5326-704-506 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C67-1771026164-IL5326-707-505 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C62_IL4690-709-505_GCTACGCT-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN7_C32_IL4709-702-506_CGTACTAG-ACTGCATA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C28_IL4690-701-506_TAAGGCGA-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C19_IL4690-704-505_TCCTGAGC-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C80_IL4690-701-502_TAAGGCGA-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C59-1771026164-IL5326-709-507 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C36_IL4690-707-506_CTCTCTAC-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C57-1771026164-IL5326-708-506 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C69_IL4690-703-502_AGGCAGAA-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C65_IL4690-706-503_TAGGCATG-TATCCTCT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C62-1771026164-IL5326-703-508 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C57_IL4690-702-502_CGTACTAG-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C54_IL4690-707-503_CTCTCTAC-TATCCTCT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C53-1771026164-IL5326-705-507 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C49_IL4690-711-501_AAGAGGCA-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C61_IL4690-712-501_GTAGAGGA-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C41_IL4690-709-502_GCTACGCT-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C47_IL4690-710-502_CGAGGCTG-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C37_IL4690-702-501_CGTACTAG-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C32_IL4690-704-501_TCCTGAGC-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C47-1771026164-IL5326-709-506 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C24_IL4690-706-502_TAGGCATG-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C46-1771026164-IL5326-709-501 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C30_IL4690-702-503_CGTACTAG-TATCCTCT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C04_IL4690-711-502_AAGAGGCA-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN6_C31_IL4690-703-505_AGGCAGAA-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C87_IL3971-708-503_CAGAGAGG-TATCCTCT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C93_IL3971-701-504_TAAGGCGA-AGAGTAGA BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C43-1771026164-IL5326-707-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C49-1771026164-IL5326-703-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C42-1771026164-IL5326-706-505 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C69_IL3971-706-502_TAGGCATG-CTCTCTAT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C41-1771026164-IL5326-705-506 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C26_IL3971-711-502_AAGAGGCA-CTCTCTAT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C35-1771026164-IL5326-709-505 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C47_IL3971-702-504_CGTACTAG-AGAGTAGA BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C01_IL3971-701-501_TAAGGCGA-TAGATCGC BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C26-1771026164-IL5326-703-507 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C73_IL4709-706-505_TAGGCATG-GTAAGGAG BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C23-1771026164-IL5326-709-504 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C90_IL4709-710-507_CGAGGCTG-AAGGAGTA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C70_IL4709-710-504_CGAGGCTG-AGAGTAGA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C45-1771026164-IL5326-708-505 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C69_IL4709-706-504_TAGGCATG-AGAGTAGA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C19-1771026164-IL5326-707-501 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C63_IL4709-706-503_TAGGCATG-TATCCTCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C18-1771026164-IL5326-706-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C59_IL4709-711-502_AAGAGGCA-CTCTCTAT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C43_IL4709-701-508_TAAGGCGA-CTAAGCCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C42_IL4709-709-507_GCTACGCT-AAGGAGTA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C71_IL3971-709-502_GCTACGCT-CTCTCTAT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C17-1771026164-IL5326-705-505 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C40_IL4709-707-507_CTCTCTAC-AAGGAGTA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C36_IL4709-709-506_GCTACGCT-ACTGCATA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C20_IL3971-704-502_TCCTGAGC-CTCTCTAT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C34_IL4709-707-506_CTCTCTAC-ACTGCATA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C16-1771026164-IL5326-704-508 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gch_BTN5_C44_IL4690-706-501_TAGGCATG-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C33_IL4709-703-506_AGGCAGAA-ACTGCATA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN3_C10_IL3971-709-501_GCTACGCT-TAGATCGC BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C35_IL4709-708-506_CAGAGAGG-ACTGCATA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C21-1771026164-IL5326-708-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C14-1771026164-IL5326-703-506 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C31_IL4709-701-506_TAAGGCGA-ACTGCATA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C30_IL4709-709-505_GCTACGCT-GTAAGGAG BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C28_IL4709-707-505_CTCTCTAC-GTAAGGAG BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C27_IL4709-703-505_AGGCAGAA-GTAAGGAG BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C26_IL4709-702-505_CGTACTAG-GTAAGGAG BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C11-1771026164-IL5326-709-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C25_IL4709-701-505_TAAGGCGA-GTAAGGAG BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C10-1771026164-IL5326-708-508 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C20_IL4709-702-504_CGTACTAG-AGAGTAGA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C06-1771026164-IL5326-706-502 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C07-1771026164-IL5326-706-508 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C18_IL4709-707-503_CTCTCTAC-TATCCTCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C16_IL4709-709-503_GCTACGCT-TATCCTCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C15-1771026164-IL5326-704-502 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1gg_BTN5_C07_IL4690-707-501_CTCTCTAC-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C15_IL4709-701-503_TAAGGCGA-TATCCTCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C01-1771026164-IL5326-703-501 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C14_IL4709-702-503_CGTACTAG-TATCCTCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C12_IL4709-707-502_CTCTCTAC-CTCTCTAT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C08_IL4709-702-502_CGTACTAG-CTCTCTAT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C06_IL4709-707-501_CTCTCTAC-TAGATCGC BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C02_IL4709-702-501_CGTACTAG-TAGATCGC BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C01_IL4709-703-501_AGGCAGAA-TAGATCGC BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-0-BTN27-C31-1771026164-IL5326-707-502 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-1-BTN27-C12-1771026164-IL5326-710-503 BTN27 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN6_C84_IL4690-709-506_GCTACGCT-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-0-BTN24-C70-12ul-IL5195-709-508 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-0-BTN24-C59-22ul-IL5195-710-505 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN7_C24_IL4709-707-504_CTCTCTAC-AGAGTAGA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN6_C22_IL4690-706-506_TAGGCATG-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN6_C55_IL4690-707-505_CTCTCTAC-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-0-BTN24-C29-18ul-IL5195-708-502 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN6_C09_IL4690-701-505_TAAGGCGA-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN6_C15_IL4690-702-505_CGTACTAG-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN6_C33_IL4690-705-505_GGACTCCT-GTAAGGAG BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C48_IL4690-703-503_AGGCAGAA-TATCCTCT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-0-BTN22-C34-8ul-1 BTN22 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C38_IL4690-705-501_GGACTCCT-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Sutent BX41-8

city: Lausanne

first: Sadegh

last: Saghafinia

address: Route Cantonale

department: SV

institute: EPFL

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Mus musculus (v. GRCm38) genome using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using Mus_musculus (Ensembl version GRCm38.74) gene annotation.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: mouse pancreatic neuroendocrine insulinoma/PanNET

extract_protocol:
Total RNA was prepared using miRNAeasy mini kit
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

treatment_protocol: Mice were treated 4D starting at 15.5W

tag: tumor type

value: mouse PanNET = RIP1TAG2 model (Hanahan 1985 Nature 315 115-22).

tag: tumor stage

value: islet tumor or insulinoma

tag: treatment

value: sunitinib monotherapy (sutent)


title: 1g_BTN7_C23_IL4709-708-504_CAGAGAGG-AGAGTAGA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Sutent BX41-6


title: 1g_BTN5_C34_IL4690-707-502_CTCTCTAC-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1-0-0-0-BTN24-C76-8ul-IL5195-701-507 BTN24 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C33_IL4690-709-501_GCTACGCT-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C25_IL4690-701-501_TAAGGCGA-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C23_IL4690-708-502_CAGAGAGG-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Sutent BX41-5


title: 1g_BTN5_C22_IL4690-701-503_TAAGGCGA-TATCCTCT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C19_IL4690-708-501_CAGAGAGG-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN6_C47_IL4690-705-506_GGACTCCT-ACTGCATA BTN06 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Sutent BX44-12


title: 1g_BTN5_C10_IL4690-712-502_GTAGAGGA-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: RS BZ51-7

value: rapamycin + sunitinib combination therapy (RS)


title: 1g_BTN5_C08_IL4690-703-501_AGGCAGAA-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: RS BZ51-5


title: 1g_BTN5_C12_IL4690-705-502_GGACTCCT-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN3_C51_IL3971-702-501_CGTACTAG-TAGATCGC BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN3_C24_IL3971-707-502_CTCTCTAC-CTCTCTAT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: RS BZ50-4


title: RS BZ75-10


title: 1g_BTN3_C15_IL3971-711-501_AAGAGGCA-TAGATCGC BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN3_C04_IL3971-704-501_TCCTGAGC-TAGATCGC BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: RS BZ50-1


title: 1g_BTN14_C53_IL4884-708-505_CAGAGAGG-GTAAGGAG BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C06_IL4690-704-502_TCCTGAGC-CTCTCTAT BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 7_B6_S409_Ctr

value: control saline treatment


title: 1chg_BTN7_C13_IL4709-703-503_AGGCAGAA-TATCCTCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 3_B6_S409_Ctr


title: 1g_BTN14_C43_IL4884-706-503_TAGGCATG-TATCCTCT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: B6_3_S409_Saline


title: 1_BTN15_C94_IL4884-712-508_GTAGAGGA-CTAAGCCT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN14_C22_IL4884-708-502_CAGAGAGG-CTCTCTAT BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN1_C19_IL3972-703-504_AGGCAGAA-AGAGTAGA BTN01 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C63_IL4884-710-507_CGAGGCTG-AAGGAGTA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C92_IL4884-710-506_CGAGGCTG-ACTGCATA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C88_IL4884-712-507_GTAGAGGA-AAGGAGTA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: B6_2_S409_Saline


title: 1g_BTN3_C73_IL3971-701-503_TAAGGCGA-TATCCTCT BTN03 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN14_C47_IL4884-708-501_CAGAGAGG-TAGATCGC BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C69_IL4884-710-508_CGAGGCTG-CTAAGCCT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1g_BTN5_C45_IL4690-710-501_CGAGGCTG-TAGATCGC BTN05 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: B1a-H3K4me3-R3

city: Farmington

first: Jethro

last: Johnson

address: 10 Discovery Drive

institute: Jackson Laboratory for Genomic Medicine

data_processing:
fastq files were created with CASAVA 1.8.1
ChIP-seq reads were trimmed to a common length (40bp) and aligned to the mm10 genome assembly using BWA version 0.7.8 with the following configurations: -l 28 -k 2 -n 4
Aligned input samples were pooled and peaks were called  at a p value threshold of 0.005 using macs2 version 2.0.10 with default parameters.
An optimal peak set was generated for each cell type using the ENCODE Irreproducibility Discovery Rate (IDR) pipeline using a pooled consistency threshold of q < 0.005.
Genome_build: mm10
Supplementary_files_format_and_content: ENCODE narrowPeak

source_name: B1A B cells

extract_protocol:
Female mouse C57BL/6 B cell populations were sorted on BD FACSAriaII, BD Influx or Beckman Coulter MoFlo XDP cell sorters; collected cells were centrifuged and cross-linked with 1% formaldehyde and sonicated to shear the chromatin to ~500bp fragments; DNA was isolated with antibodies and purified by phenol-chloroform extraction
Libraries were prepared with Illumina's DNA Sample prep kit according to the manufacturer's instructions

value: Peritoneal cavity

tag: age

value: 7-9 weeks

tag: Sex

value: Female

tag: immunization

tag: flow strategy


title: 1t_BTN15_C58_IL4884-712-504_GTAGAGGA-AGAGTAGA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

tag: experiment

tag: major cell type

tag: protocol


title: 1_BTN15_C45_IL4884-710-503_CGAGGCTG-TATCCTCT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Microglia


title: 1_BTN15_C42_IL4884-712-501_GTAGAGGA-TAGATCGC BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Ependy-C


title: 1_BTN15_C39_IL4884-710-502_CGAGGCTG-CTCTCTAT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: B1a-H3K4me3-R1

tag: strain

tag: tissue


title: 1_BTN15_C20_IL4884-709-506_GCTACGCT-ACTGCATA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: B1a-H3K4me1-R3


title: B1a-H3K4me3-R2


title: B1a-H3K4me1-R2


title: 1_BTN15_C22_IL4884-711-508_AAGAGGCA-CTAAGCCT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C19_IL4884-709-507_GCTACGCT-AAGGAGTA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C11_IL4884-711-504_AAGAGGCA-AGAGTAGA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: B1a-H3K4me1-R1


title: 1_BTN15_C03_IL4884-709-501_GCTACGCT-TAGATCGC BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C04_IL4884-711-507_AAGAGGCA-AAGGAGTA BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN14_C25_IL4884-706-501_TAGGCATG-TAGATCGC BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN15_C02_IL4884-709-505_GCTACGCT-GTAAGGAG BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: B1a-input-R3


title: B1a-input-R2


title: B1a-input-R1


title: 1_BTN11_C21_IL4791-711-508_AAGAGGCA-CTAAGCCT BTN11 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN11_C55_IL4791-709-508_GCTACGCT-CTAAGCCT BTN11 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN11_C30_IL4791-712-507_GTAGAGGA-AAGGAGTA BTN11 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN14_C08_IL4884-706-504_TAGGCATG-AGAGTAGA BTN14 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN11_C10_IL4791-711-501_AAGAGGCA-TAGATCGC BTN11 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Germinal-H3K4me3-R3

source_name: Germinal Center B cells

value: Spleen

value: 7 weeks

value: SRBC


title: 1_BTN15_C25_IL4884-709-503_GCTACGCT-TATCCTCT BTN15 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Mic-scRNA-Seq


title: 1_BTN10_C70_IL4791-707-508_CTCTCTAC-CTAAGCCT BTN10 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Oligo


title: Germinal-H3K4me3-R1


title: Germinal-H3K4me3-R2


title: 1_BTN10_C60_IL4791-704-508_TCCTGAGC-CTAAGCCT BTN10 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN10_C36_IL4791-708-508_CAGAGAGG-CTAAGCCT BTN10 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Ependy-Sec


title: 1_BTN10_C89_IL4791-701-501_TAAGGCGA-TAGATCGC BTN10 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: 1_BTN10_C16_IL4791-705-508_GGACTCCT-CTAAGCCT BTN10 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq


title: Germinal-H3K4me1-R2


title: 1_BTN10_C10_IL4791-702-508_CGTACTAG-CTAAGCCT BTN10 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: OPC


title: 1Dg_BTN7_C86_IL4709-705-507_GGACTCCT-AAGGAGTA BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq

value: Macrophage


title: Germinal-H3K4me1-R1


title: Germinal-input-R3


title: 1Dg_BTN7_C44_IL4709-702-508_CGTACTAG-CTAAGCCT BTN07 Mic-scRNA-Seq

description: polyA RNA Mic-scRNA-Seq