title: transcriptome data induced by rice straw

status: Public on Nov 22 2015

city: Nanjing

first: youzhi

last: miao

state: JiangSu

address: No.1 WeiGang, XuanWu, NanJing, JiangSu province, China

department: College of Resources & Environmental Science

institute: Nanjing Agricultural University, Nanjing, China

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Aspergillus fumigatus Z5 using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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 and normalized by the size of the meta-transcript and by the size of the library.
Using the MA-plot-based method with Random Sampling model in the DEGseq program package, the differences in expression levels between samples were calculated for each individual gene. Differences were determined to be significant if FDR scores were ≤ 0.001.
Genome_build: Aspergillus fumigatus Z5; PRJNA231983; AZZA00000000
Supplementary_files_format_and_content: tab-delimited xlsx files include read numbers and RPKM values for each gene.

source_name: filamentous fungi

growth_protocol: Conidia of Z5 were incubated at 45 ℃, 145rpm for 20 hours with sucrose as the sole carbon source, and then the mycelia were transformed into the medium, which contained xylan, cellulose and rice straw as the sole carbon souce, respectively, to induce those relatived genes expression.

extract_protocol:
The frozen mycelia were disrupted by grinding in liquid nitrogen, and total RNA was extracted using RNeasy Plant Mini Kit (Qiagen).
Messenger RNA was purified from the total RNA with a Micropoly(A)PuristTM mRNA purification kit (Ambion, America). Double-stranded cDNA was synthesized according to Ng’s full-length cDNA synthesis protocol with some modifications. GsuI-oligo dT was used as the primer for first-strand cDNA synthesis from 10 μg of mRNA, using 1,000 units of Superscript II reverse transcriptase (Invitrogen, America). The diol group of the CAP structure of mRNA was then oxidized by NaIO4 (Sigma, America) and linked to biotin hydrazide. Dynal M280 streptavidin Dynabeads (Invitrogen, America) were used to select biotinylated RNA/cDNA. The first-strand cDNA was then released by alkaline hydrolysis. Next, adaptors were ligated to the 5’-end of the first-strand cDNA by DNA ligase (TaKaRa, Dalian, China), and the second-strand cDNA was synthesized through primer extension using Ex Taq polymerase (TaKaRa, Dalian, China). Last, the polyA tail and 5’ adaptors were removed by GsuI digestion. The synthesized cDNA was fractioned ultrasonically into 300-800 bp fragments and purified using Ampure beads (Agencourt, America). The prepared cDNAs were transformed into libraries with the TruSeq DNA Sample Prep Kit – Set A (Illumina, America), clonally amplified using the TruSeq PE Cluster Kit (Illumina, America) and sequenced with Illumina equipment according to the manufacturer's instructions.

tag: carbon source

value: rice straw


title: transcriptome data induced by cellulose

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Aspergillus fumigatus

tag: strain

value: cellulose


title: transcriptome data induced by xylan

value: xylan


title: transcriptome data induced by sucrose

value: sucrose


title: p39 - 12 month male AL+LA

city: Manchester

first: Shona

middle: Hiedi

last: Wood

address: Oxford road

country: United Kingdom

institute: University of Manchester

description: Ribodepleted RNA

data_processing:
counts: csfasta and quals were mapped to the ensembl reference genome rn5 ensembl 75 http://www.ensembl.org/Rattus_norvegicus/Info/Index by bowtie using forward reads only. Raw counts per gene were estimated by the python script HTSeq count (http://www-huber.embl.de/users/anders/HTSeq/).
Genome_build: rn5

organism: Rattus norvegicus

source_name: cerebral cortex

growth_protocol: The non-supplemented CRM diet was supplied by Dietex International, Witham, UK. The lipoic acid supplemented diet was the CRM diet enriched with a racemic mixture of DL-thioctic acid (a-lipoic acid) obtained from Fisher Scientific U.K., Limited, at 1.5 g/kg by the Special Diet Systems Division of Dietex International. A previous experiment supplied the rat brain tissue for this study (Merry et al. 2008). All animal husbandry procedures undertaken in this study were carried out in accordance with the provisions of the United Kingdom Animals (Scientific Procedures) Act 1986. Male BN rats (SubstrainBN/SsNOlaHSD) were obtained from Harlan UK at 21–28 days of age and maintained under barrier conditions on a 12-h light: 12-h dark cycle (08:00–20:00). The health status of the rats was monitored at regular intervals through the screening of sentinel animals. All animals were caged in groups of four and fed the non-supplemented CRM diet ad libitum until 2 months of age, when they were transferred to single housing and assigned randomly to one of 6 dietary groups as summarised in Table 4. All rats fed ad libitum and CR were sacrificed at 6, 12, and 28 months of age. CR fed animals were fed either the CRM diet, or the lipoic acid supplemented CRM diet at 55% the daily food intake of control rats, to maintain their body weight at approximately 55% that of age- matched ad libitum fed animals. The diet of animals maintained on a DR regime was supplied daily as pre-weighed ratios between 10:30 and 11:00 h. The daily food ration supplied to DR animals was the same for age-matched animals irrespective of whether they were fed the CRM diet, or the lipoic acid supplemented CRM diet. Six dietary feeding combinations were studied to compare the effect of ad libitum or DR feeding with, and without lipoic acid supplementation, on transcription. Survival trajectories for these groups were previously determined [7].  All groups were run simultaneously and so experienced identical husbandry and housing conditions. None of the animals exhibited any signs of pathology when sacrificed.

extract_protocol: RNA was extracted from the cerebral cortex using Qiagen's tissuelyser II and RNeasy lipid tissue kit. The quality of the extracted RNA was assessed using the Agilent 2100 bioanalyser, all RNA integrity numbers (RINs) were above 8 indicating that good quality RNA had been extracted. The samples were pooled 2 by 2 (leaving 3 samples per age group). Ribosomal RNA was removed from the pooled samples using a Eukaryote ribominus kit (Invitrogen) and confirmed with the Agilent 2100 bioanalyser. The library preparation protocol was carried out according to the manufacturer’s instructions: the RNA was fragmented and cleaned up using spin columns (Invitrogen) and SOLiD RNA adapters were then hybridized and ligated to the samples. Reverse transcription was performed to generate cDNA. The cDNA was purified, size selected, amplified and then purified again (as detailed in the SOLiD protocol). The size distribution of the cDNA library was assessed using the bioanalyser. The samples were then subject to emulsion PCR and sequenced using the SOLiD system 5500xl. Multiplex paired-end sequencing of RNA libraries with barcodes.

tag: age

value: 12 month

tag: treatment

value: 12 months ad libitum plus lipoic acid

tag: tissue

value: cerebral cortex


title: p38 - 12 month male AL+LA

description: Ribodepleted RNA

treatment_protocol: The non-supplemented CRM diet was supplied by Dietex International, Witham, UK. The lipoic acid supplemented diet was the CRM diet enriched with a racemic mixture of DL-thioctic acid (a-lipoic acid) obtained from Fisher Scientific U.K., Limited, at 1.5 g/kg by the Special Diet Systems Division of Dietex International. A previous experiment supplied the rat brain tissue for this study (Merry et al. 2008). All animal husbandry procedures undertaken in this study were carried out in accordance with the provisions of the United Kingdom Animals (Scientific Procedures) Act 1986. Male BN rats (SubstrainBN/SsNOlaHSD) were obtained from Harlan UK at 21–28 days of age and maintained under barrier conditions on a 12-h light: 12-h dark cycle (08:00–20:00). The health status of the rats was monitored at regular intervals through the screening of sentinel animals. All animals were caged in groups of four and fed the non-supplemented CRM diet ad libitum until 2 months of age, when they were transferred to single housing and assigned randomly to one of 6 dietary groups as summarised in Table 4. All rats fed ad libitum and CR were sacrificed at 6, 12, and 28 months of age. CR fed animals were fed either the CRM diet, or the lipoic acid supplemented CRM diet at 55% the daily food intake of control rats, to maintain their body weight at approximately 55% that of age- matched ad libitum fed animals. The diet of animals maintained on a DR regime was supplied daily as pre-weighed ratios between 10:30 and 11:00 h. The daily food ration supplied to DR animals was the same for age-matched animals irrespective of whether they were fed the CRM diet, or the lipoic acid supplemented CRM diet. Six dietary feeding combinations were studied to compare the effect of ad libitum or DR feeding with, and without lipoic acid supplementation, on transcription. Survival trajectories for these groups were previously determined [7].  All groups were run simultaneously and so experienced identical husbandry and housing conditions. None of the animals exhibited any signs of pathology when sacrificed.


title: p36 - 28 month male AL+LA

description: Ribodepleted RNA

value: 28 month

value: 28 months ad libitum plus lipoic acid


title: p35 - 28 month male AL+LA

description: Ribodepleted RNA


title: p34 - 28 month male AL+LA

description: Ribodepleted RNA


title: p33 - 28 month male CRswCR+LA

description: Ribodepleted RNA

value: 28 months calorie restriction switched to calorie restriction plus lipoic acid at 12 months


title: p32 - 28 month male CRswCR+LA

description: Ribodepleted RNA


title: p31 - 28 month male CRswCR+LA

description: Ribodepleted RNA


title: p30 - 28 month male CRswAL+LA

description: Ribodepleted RNA

value: 28 months calorie restriction switched to ad libitum plus lipoic acid at 12 months


title: p28 - 28 month male CRswAL+LA

description: Ribodepleted RNA


title: p29 - 28 month male CRswAL+LA

description: Ribodepleted RNA


title: p27 - 28 month male CRswAL

description: Ribodepleted RNA

value: 28 months calorie restriction switched to ad libitum at 12 months


title: p26 - 28 month male CRswAL

description: Ribodepleted RNA


title: p25 - 28 month male CRswAL

description: Ribodepleted RNA


title: p24 - 28 month male AL+LAswCR

description: Ribodepleted RNA

value: 28 months ad libitum plus lipoic acid switched to calorie restriction at 12 months


title: p22 - 28 month male AL+LAswCR

description: Ribodepleted RNA


title: p19 - 28 month male ALswCR

description: Ribodepleted RNA

value: 28 months ad libitum switched to calorie restriction at 12 months


title: p21 - 28 month male ALswCR

description: Ribodepleted RNA


title: p20 - 28 month male ALswCR

description: Ribodepleted RNA


title: p37 - 12 month male AL+LA

description: Ribodepleted RNA


title: p18 - 28 month male CR

description: Ribodepleted RNA

value: 28 months calorie restriction


title: p17 - 28 month male CR

description: Ribodepleted RNA


title: p12 - 6 month male CR

description: Ribodepleted RNA

value: 6 month

value: 6 months calorie restriction


title: p13 - 12 month male CR

description: Ribodepleted RNA

value: 12 months calorie restriction


title: p16 - 28 month male CR

description: Ribodepleted RNA


title: p15 - 12 month male CR

description: Ribodepleted RNA


title: p11 - 6 month male CR

description: Ribodepleted RNA


title: p10 - 6 month male CR

description: Ribodepleted RNA


title: p8 - 28 month male AL

description: Ribodepleted RNA

value: 28 months ad libitum


title: p7 - 28 month male AL

description: Ribodepleted RNA


title: p9 - 28 month male AL

description: Ribodepleted RNA


title: p4 - 12 month male AL

description: Ribodepleted RNA

value: 12 months ad libitum


title: Pou3f1_inputD2.fastq

status: Public on Nov 23 2015

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
Raw reads were mapped to mm9 with TopHat version 1.4.1
FPKM for each gene as expression value was assigned by cufflinks version 1.3.0
Cuffdiff was used to identify differentially expressed genes
ChIP-seq reads were aligned with SOAP version 2.20 to the mouse genome build mm9
findPeaks software of Homer was used to identify Oct6 binding peaks with 4 fold more normalized tags in experiment group than control
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, bed file includes the tag density

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cell

growth_protocol: Mouse embryonic stem cells(mESCs) (R1 and R1/E) were maintained on a layer of mitomycin C-treated mouse embryonic fibroblast feeder cells in standard medium supplemented with 1,000 U/mL mouse leukemia inhibitory factor (LIF). Unbiased ESC differentiation in serum-containing medium was performed as described previously (Zhang, T., et al.,2013)

extract_protocol:
For ChIP-seq, cell lysates were clarified from sonicated nuclei and Pou3f1-DNA complexes were precipitated with Pou3f1 antibody (Santa Cruz, sc-11661, Lot# C2012), then genomic DNA was recoveried and purified for subsequent library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiation cells with or without Pou3f1 overexpression

tag: cell line

value: Pou3f1-overexpressing ESC

tag: time

value: ESC neural differentiation day2

tag: chip antibody

value: none (input)


title: p23 - 28 month male AL+LAswCR

description: Ribodepleted RNA

value: cerebral cortex


title: p3 - 6 month male AL

description: Ribodepleted RNA

value: 6 months ad libitum


title: p6 - 12 month male AL

description: Ribodepleted RNA

value: 12 month


title: p2 - 6 month male AL

description: Ribodepleted RNA


title: p1 - 6 month male AL

description: Ribodepleted RNA


title: ATAC_IFN.rep1

status: Public on Nov 21 2015

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description: genomic DNA in accessible regions

data_processing:
Library strategy: ATAC-Seq
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie1.1.1 with –m 1 option
Data were filtered using sickle1.2 and cutadapt1.8.3
duplicated reads were removed using Picard Tools(1.138)  MarkDuplicates
reads were piled up using macs2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bdg2bw (https://gist.github.com/taoliu/2469050)

source_name: Splenic B cell

extract_protocol:
B cells were negatively isolated using magnetic beads (EasySep Mouse B Cell Isolation Kit, STEMCELL Technologies). DNA was tagged and fragmented by Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) after permeabilization.
PCR was performed using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) and the amplified DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter)

treatment_protocol: subcutaneous injection of 10,000U IFNa (Recombinant Mouse IFN Alpha A3, R&D, cat # 12100-1)

value: 5 weeks old

tag: Sex

value: male

tag: time point


title: ATAC_ctrl.rep1

description: genomic DNA in accessible regions

value: no IFN


title: ATAC_IFN.rep2

description: genomic DNA in accessible regions


title: ATAC_ctrl.rep2

description: genomic DNA in accessible regions


title: pol2_24hr

data_processing:
Basecalls performed using CASAVA-1.8.2 for HiSeq2500 and 1.4.1.2 - RTA 2.4.6 for NextSeq500
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie1.1.1 with –m 1 option
Data were filtered using sickle1.2 and cutadapt1.8.3
duplicated reads were removed using Picard Tools(1.138)  MarkDuplicates
reads were piled up using macs2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bdg2bw (https://gist.github.com/taoliu/2469050)

extract_protocol:
B cells were negatively isolated using magnetic beads (EasySep Mouse B Cell Isolation Kit, STEMCELL Technologies). Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody conjugated to magnetic beads.
Libraries were prepared according to a general protocol for ChIP-seq. Briefly, DNA was end-repaired using End-It DNA End-Repair Kit (Epicentre) followed by a single adenine nucleotide overhang attachment by Klenow fragment (Klenow Fragment 3'>5' exo-, New England Biolabs). The adaptor oligo mix was ligated by T4 DNA Ligase (LigaFast Rapid DNA Ligation System, Promega). Then the adapter ligated DNA was amplified by PCR employing NEBNext High-Fidelity 2X PCR Master Mix (NEB) and a set of indexed primers. Libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter).

tag: antibody

value: Pol2 (Santa Cruz Biotechnology, N-20)


title: pol2_4hr


title: p14 - 12 month male CR

description: Ribodepleted RNA


title: pol2_48hr


title: H3K4me1

value: merged

value: H3K4me1 (1:1 mixture of ab8895, abcam and 07-436, EMD Millipore)


title: pol2_8hr


title: EpiCon_R2_RNAseq

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: RNAseq

data_processing:
RNA-Seq reads (51bp, single-ended) were aligned to the mouse genome (NCBI37/mm9) using the software TopHat2
Transcript assembly and differential expression was determined using Cufflinks with Refseq mRNAs to guide assembly
Analysis of RNA-seq data was done using the cummeRbund package in R
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: mouse skin

growth_protocol: Epi-SCs  were FASC-purified from ETS2(T72D) suepr-activated mice and control mice.

extract_protocol: FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >9. Library preparation using the Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 2000 machines.

treatment_protocol: No treatment

value: skin

value: Female

tag: age or tumor stage

tag: sorting markers

value: integrin α6, CD34, Sca1 and RFP


title: pol2_2hr


title: EpiETS2_T72D_OE_R2_RNAseq

description: RNAseq


title: p5 - 12 month male AL

description: Ribodepleted RNA


title: EpiETS2_T72D_OE_R1_RNAseq

description: RNAseq


title: Input_EpiSC_H3K27ac_nanoChIPseq_R2

description: input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software MACS (Version 1.4.2) with input as controls.
wig files created using IGVtools with 25bp windows with no extension to reads.
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows

source_name: Mouse back skin

growth_protocol: SCC-SCs were FACS-purifed from the allograft SCC and EpiSCs were FACS-purified from control and ETS2(T72D) super-activated skin.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Nano-ChIPseqs were conducted as previously reported (Adli and Bernstein, Nature Protocol, 2011) and libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, ChIP DNA was primed and amplified using designed primers for 15 cycles and digested with BciV1 restriction enzyme. After digestion, the DNA was ligated with Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 17 cycles and library fragments of 200-500 bp (insert plus adaptor and PCR primer sequences) were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tumor stage

value: RFP, integrin α6, Sca-1, CD34

value: No


title: ETS2_T72D_OE_EpiSC_H3K27ac_naanoChIPseq_R1

description: Chromatin IP against H3K27ac

value: CD1;ETS2(T72D) overexpression

value: H3K27ac (abcam, ab4729)


title: pol2_30min


title: EpiCon_R1_RNAseq

description: RNAseq


title: Control_EpiSC_H3K27ac_nanoChIPseq_R1

description: Chromatin IP against H3K27ac


title: Input_EpiSC_H3K27ac_nanoChIPseq_R1

description: input DNA


title: ETS2_T72D_OE_EpiSC_H3K27ac_naanoChIPseq_R2

description: Chromatin IP against H3K27ac


title: EpiSC_RNAseq

description: RNAseq

data_processing:
RNA-Seq reads (51bp, single-ended) were aligned to the mouse genome (NCBI37/mm9) using the software TopHat (version 2.0.4)
Transcript assembly and differential expression was determined using Cufflinks with Refseq mRNAs to guide assembly
Analysis of RNA-seq data was done using the cummeRbund package in R
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Mouse back skins

growth_protocol: Skin SCC-SC, HF-SC and Epi-SC were FACS-purifed from the allograt SCC and normal back skins of indicated ages of mice

value: integrin α6, CD34 and Sca1


title: SCC_SC_H3K27ac_nanoChIPseq

description: Chromatin IP against H3K27ac

source_name: Mouse skin SCC

value: 3 weeks after tumor graft

value: GFP, integrin α6, integrin β1


title: SCC_SC_H3K27ac_ChIP-seq_rep2

description: Chromatin IP against H3K27ac

growth_protocol: SCC-SC were FACS-purifed from the allograft SCC.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: HFSC_RNAseq

description: RNAseq


title: SCC_SC_RNA-seq

description: RNAseq


title: pol2_0hr


title: SCC_SC_Input_DNA_rep2

description: input DNA


title: pol2_1hr


title: Tcf7 +/+ 20wk [S178_wt]

city: Worcester

first: Yu

last: Liu

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

description: Sample 178

data_processing:
The fastq files were obtained using Illumina CASAVA v1.8
The quality of fastq reads was examined by FASTQC and low quality 5' nucleotides were removed before mapping
The fastq read were mapped on human geneome (mm9) using Tophat 1.4.1
The read counts were calculated using customed R scripts to calculate transcript union reads per million reads (truRPMs)
Genome_build: mm9
Supplementary_files_format_and_content: Excel spread sheet was provided for coding gene expression of all the samples in this study

growth_protocol: 8 week old and 20 week old animals

extract_protocol:
Total RNA with Trizol
The sequencing libraries were constructed using RiboZero and Illumina TruSeq RNA preparation kit following the kit instructions.

treatment_protocol: Regular mouse chow and high-fat (45%) diet

tag: strain background

tag: genotype/variation

value: wild type; Tcf7 +/+

value: 20 weeks

tag: diet

value: high-fat (45%)

value: Mouse Islets


title: Tcf7 +/+ 20wk [S188_wt]

description: Sample 188


title: SCC_SC_Input_DNA_rep1

description: input DNA


title: SCC_SC_H3K27ac_ChIP-seq_rep1

description: Chromatin IP against H3K27ac


title: Tcf7 +/+ 8wk [S146_wt]

description: Sample 146

value: 8 weeks

value: low-fat (10%)


title: Primed_MED1_R2

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
genome build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

organism: Homo sapiens

source_name: Embryonic stem cells

growth_protocol: cultured in primed ES cells medium

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

treatment_protocol: normal primed hESCs

tag: cell type

value: Primed

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog

tag: system

value: Embryo


title: Tcf7 -/- 20wk [S175_ko]

description: Sample 175

value: knockout; Tcf7 -/-

tag: age

tag: tissue


title: Primed_OCT4_R2

value: Santa Cruz


title: Control_EpiSC_H3K27ac_nanoChIPseq_R2

description: Chromatin IP against H3K27ac

value: Female

tag: strain

value: RFP, integrin α6, Sca-1, CD34

value: skin


title: Primed_MED1_R1

tag: chip antibody


title: Tcf7 +/+ 8wk [S139_wt]

description: Sample 139


title: Primed_OCT4_R1


title: Primed_CTCF_R2

value: CTCF

value: Millipore


title: Tcf7 -/- 8wk [S140_ko]

description: Sample 140


title: Primed_H3K27ac_R2

growth_protocol: Primed hESCs were cultured as previously described (Theunissen et al., 2014). Primed hESCs were maintained on mitomycin C-inactivated MEF feeder layers and passaged every 7-10 days. When passaging primed hESCs, clumps of cells were partially dissociated with collagenase type IV (GIBCO, 17104-019), and then subjected to two sedimentation steps in stationary 50 cm tubes for 10 minutes at room temperature in primed hESC medium to remove single cells. Primed hESC medium (500 ml) consisted of 400 ml of Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12, Invitrogen, 11320), 75 ml Fetal Bovine Serum (FBS, Hyclone, SH30071.03HI), 25 ml KnockOutTM Serum Replacement (KSR, Invitrogen, 10828-028), supplemented with 1 mM glutamine (Invitrogen, 25030-024), 1% nonessential amino acids (Invitrogen, 11140-050), penicillin-streptomycin (Invitrogen, 15140-122), 0.1 mM β- mercaptoethanol (Sigma, M6250-100ML), and 4 ng/ml FGF2 (R&D systems, 233-FB- 025).

value: Abcam


title: Primed_Input


title: Primed_H3K27ac_R1


title: Naive_OCT4_R2

growth_protocol:
Naive hESCs were cultured as previously described (Theunissen et al., 2014). For the induction of naive hESCs, primed hESCs were cultured for 24 hr in the primed hESC medium described above, further supplemented with 10 μM ROCK inhibitor Y- 27632 (Stemgent, 04-0012). Colonies were then trypsinized to form a single cell suspension and cells were plated onto a MEF feeder layer in the primed hESC medium + ROCK inhibitor described above. 24 hr later, the medium was switched to 5i/L/A naive hESC medium. The 5i/L/A naive hESC medium (500 ml) used for induction and maintenance of naive hESCs was made up of 240 ml DMEM/F12, 240 ml Neurobasal (Invitrogen, 21103), 5 ml N2 supplement (Invitrogen, 17502048) and 10 ml B27 supplement (Invitrogen, 17504044), supplemented with 10 μg recombinant human LIF (purified in-lab from E. coli), 1 mM glutamine, 1% nonessential amino acids, 0.1 mM β- mercaptoethanol, penicillin-streptomycin, 50 μg/ml BSA (Sigma, A4737-25G), and the following small molecules and cytokines: 1 μM PD0325901 (Stemgent, 04-0006), 1 μM IM-12 (Enzo, BML-WN102-0005), 0.5 μM SB590885 (R&D systems, 2650/10), 1 μM WH-4-023 (A Chemtek) 10 μM Y-27632 (Stemgent, 04-0012), and 10 ng/ml Activin A (Peprotech, 120-14). Following an initial wave of widespread cell death, dome-shaped naive hESC colonies appeared within 10 days and could be expanded and maintained in 5i/L/A naive hESC medium.
Naive hESCs were maintained on mitomycin C-inactivated MEF feeder cells and passaged every 5-7 days. The naive hESCs were passaged by dissociating cells with accutase (GIBCO, A1110501), and then centrifuging cells at 1000 rpm for 5 minutes at room temperature in neutralization medium (DMEM supplemented with 10% FBS, 1 mM glutamine, 1% nonessential amino acids, penicillin-streptomycin, and 0.1 mM β- mercaptoethanol). To harvest cells for downstream experiments, primed and naive hESCs were trypsinized and subsequently pre-plated on gelatin-coated dishes to deplete MEF feeder cells. All cell culture experiments were performed under physiological oxygen conditions (5% O2, 3% CO2).

value: Naive


title: Naive_OCT4_R1


title: Naive_MED1-R2


title: Tcf7 -/- 20wk [S181_ko]

description: Sample 181

value: 20 weeks


title: Naive_MED1-R1


title: Naive_Input


title: Naive_CTCF_R2


title: Naive_CTCF_R1


title: Naive_H3K27ac_R2


title: Primed_SMC1_ChIAPET_biologicalReplicate2_run2

description:
ChIA-PET against Smc1 in primed hESCs
Primed_SMC1_ChIAPET_B2_unique_interchromosomal.bed12

data_processing:
Library strategy: ChIA-PET
Images analysis and base calling was done using the solexa pipeline.
The raw sequences from the paired-end sequencing were analyzed for the presence of the PET linker barcodes and trimmed using Cutadapt with the parameters “-m 17 -a forward=ACGCGATATCTTATCTGACT -a reverse=AGTCAGATAAGATATCGCGT --overlap 10” (Martin, 2011) Specifically, we trimmed the 3’ sequence immediately after a perfect match of at least the first 10nt of the linker sequences. After removing the linkers and the 3’ sequence following the linkers, only the 5’ ends of the trimmed PETs of at least 17bp in length were retained for effective mapping to the reference genome. The PET sequences that had PET linkers on at least one end of the PET were used for downstream analyses.
The sequences of the two ends of PET sequences were separately mapped to the hg19 human genome using the bowtie algorithm with the option “-k 1 -m 1 -v 1”.  These criteria retained only the uniquely mapped reads, with at most a single mismatch for further analysis. Aligned reads were paired with mates and were filtered for redundant sequences to avoid bias from PCR amplification in the library preparation procedure. PET sequences with identical genomic coordinates and strand information at both ends were collapsed into a single PET sequence.
Genome_build: hg19
Supplementary_files_format_and_content: BED12 file: The PET sequences were categorized into intrachromosomal PETs, where the two ends of a PET were on the same chromosome, and interchromosomal PETs, where the two ends were on different chromosomes. The unique intrachromosomal PETs are parsed into BED12 format file.

extract_protocol:
400 million naive or primed hES cells were cross-linked by 1% formaldehyde at RT 10 mintues and were sonicated to solubilize the chromatin. The chromatin complexes contain DNA fragments with an average size of 300-800 bp were immunoprecipitated by using SMC1a antibody.
The ChIA-PET libraries were generated in three stages. In the first stage, ChIP was performed using 25 μg anti-SMC1 antibody (Bethyl Labs, A300-055A) and 250 μl protein G Dynabeads (Life technology, 10004D). This stage was the same as the experimental procedure described in the ChIP-seq library generation. The second stage was the ligation of the DNA fragments based on proximity. The ChIP-DNA with beads were washed once with TE buffer, then incubated with the end blunting mix (containing 7.2 μl T4 DNA polymerase (New England Biolabs, M0203S) and 7 μl 10 mM dNTP (Life Technologies, 18427013) in 700 μl total volume) at 37 °C for 40 min. The beads were then washed three times with ChIA-PET wash buffer (10 mM Tris-HCl pH7.5, 1 mM EDTA, 500 mM NaCl). The beads were incubated with klenow (3’-5’ exo-) master mix (containing 7 μl klenow fragment (3’-5’ exo-) (New England Biolabs, M0212S) and 7 μl 10 mM dATP (New England Biolabs, N0440S) in 700 μl total volume) at 37 °C for 50 min. The beads were then washed three times with ChIA-PET wash buffer. The beads were then incubated with proximity ligation mix (containing 42 μl T4 DNA ligase (Life Technologies, 46300018) and 4 μl bridge linker (200 ng/ μl including Forward: /5Phos/CGCGATATC/iBiodT/TATCTGACT; Reverse: /5Phos/GTCAGATAAGATATCGCGT) in 14 ml total volume) at 16 °C for 22 hr. The beads were then washed three times with ChIA-PET wash buffer. The beads were then incubated with an exonuclease reaction mix (containing 6 μl lambda exonuclease (New England Biolabs, M0262S), and 6 μl exonuclease I  (New England Biolabs, M0293S) in 700 μl total volume) at 37 °C for 1 hr. The DNA was eluted and reverse crosslinked with proteinase K (Life Technologies, AM2546) at 55 °C overnight. The DNA was purified by phenol-chloroform extraction and ethanol precipitation. The third stage was the tagmentation of ligated products, purification of the tagmented DNA fragments, amplification of the DNA by PCR, size selection and paired-end sequencing. The ChIA-PET proximity ligation products were tagmented with Tn5 Transposase (5 μl Tn5 transposase (Illumina, FC-121-1030) for 50 ng DNA) at 55 °C for 5 min, then at 10 °C for 10 min. The tagmented DNA was purified using a Zymo column (VWR, 100554-654) following the manufacturer’s instructions. The tagmented DNA was affinity purified with M280 streptavidin beads (50 μl for each library, Life Technologies, 11205D), followed by washing five times with 2×SSC/0.5% SDS and then two times with 1× B&W buffer (5 mM Tris-HCl pH7.5, 0.5 mM EDTA, 1 M NaCl). The buffer was discarded and the immobilized DNA library on beads was gently resuspended in 30 μl EB buffer (QIAGEN). The PCR amplifications of the DNA libraries were performed by using the Nextera DNA Sample Preparation Kit (Illumina, FC-121-1031) for 10-12 cycles. The DNA was selected for the size range of 300-500 bp and was purified by gel extraction. The ChIA-PET library was sequenced by paired-end sequencing (100×100) on the Illumina HiSeq 2000.
Linker Forward: /5Phos/CGCGATATC/iBiodT/TATCTGACT; Reverse: /5Phos/GTCAGATAAGATATCGCGT

treatment_protocol: None.

tag: antibody catalog number

value: Bethyl A300-055A


title: Tcf7 -/- 8wk [S142_ko]

description: Sample 142

value: Mouse Islets


title: Primed_SMC1_ChIAPET_biologicalReplicate1_run2

description:
ChIA-PET against Smc1 in primed hESCs
Primed_SMC1_ChIAPET_B1_unique_interchromosomal.bed12


title: Primed_SMC1_ChIAPET_biologicalReplicate1_run1


title: Primed_SMC1_ChIAPET_biologicalReplicate1_run3


title: Primed_CTCF_R1

value: Upstate/Millipore


title: Naive_SMC1_ChIAPET_biologicalReplicate2_run2

description:
ChIA-PET against Smc1 in naive hESCs
Naive_SMC1_ChIAPET_B2_unique_interchromosomal.bed12


title: Naive_SMC1_ChIAPET_biologicalReplicate2_run1


title: Stat1_IFN.rep2

value: 5 weeks old

tag: Sex

value: male

tag: treatment

tag: time point

value: Stat1 (Santa Cruz Biotechnology, sc-592)


title: Naive_SMC1_ChIAPET_biologicalReplicate1_run1

description:
ChIA-PET against Smc1 in naive hESCs
Naive_SMC1_ChIAPET_B1_unique_interchromosomal.bed12


title: Naive_SMC1_ChIAPET_biologicalReplicate1_run3


title: Stat1_ctrl.rep2

value: no IFN

tag: antibody


title: Stat1_IFN.rep1


title: Stat2_IFN.rep2

value: Stat2 (EMD Millipore, #07-140)


title: Naive_SMC1_ChIAPET_biologicalReplicate1_run2


title: Stat2_IFN.rep1


title: Stat1_ctrl.rep1


title: Stat2_ctrl.rep2


title: Stat2_ctrl.rep1


title: Naive_H3K27ac_R1

value: Embryo


title: pT_Spec_RpoE_10mins_rep2.bam

city: Indianapolis

first: Dharanesh

last: Gangaiah

state: Indiana

address: 635 Barnhill drive, MS 420

department: Department of Microbiology and Immunology

institute: Indiana University School of Medicine

data_processing:
Image analysis and base calling were performed with the HiSeq Control software and the Real Time Analysis software.
Demultiplexing was performed with the Illumina CASAVA software.
Sequenced reads were mapped with the Burrows-Wheeler Alignment tool
The total number of reads corresponding to the coding region of each gene was determined with the NGSUtils suite
Gene List was generated using an FDR cutoff of  0.1 and a fold change cutoff of 2 fold
Genome_build: AE017143
Supplementary_files_format_and_content: Excel Sheet includes RPKM values for each sample as well as calculated fold change, p-value, and FDR.

organism: [Haemophilus] ducreyi

source_name: bacteria

growth_protocol: Bacteria were grown in gonococcal broth supplemented with 5% fetal bovine serum, 1% IsoVitalex and 50 μg/ml hemin (Aldrich Chemical Co.) in a 33°C waterbath.

extract_protocol:
Bacteria were collected and RNA was harvested using Trizol reagent. The Ribo-Zero Magnetic kit was used to remove rRNA and the Illumina TruSeq Stranded mRNA sample preparation kit (Cat# RS-122-2101) was used with 10 to 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: growth phase

value: Midlog

value: 10 minutes after induction


title: pT_Spec_10mins_rep4.bam


title: pT_Spec_RpoE_10mins_rep1.bam


title: pT_Spec_10mins_rep2.bam


title: pT_Spec_RpoE_5mins_rep4.bam

value: 5 minutes after induction


title: pT_Spec_10mins_rep1.bam


title: pT_Spec_RpoE_5mins_rep3.bam


title: pT_Spec_5mins_rep3.bam


title: pT_Spec_5mins_rep4.bam


title: pT_Spec_5mins_rep2.bam


title: pT_Spec_RpoE_5mins_rep1.bam


title: pT_Spec_5mins_rep1.bam


title: pT_Spec_RpoE_5mins_rep2.bam


title: pT_Spec_RpoE_0mins_rep4.bam

value: 0 minutes


title: pT_Spec_0mins_rep4.bam


title: pT_Spec_0mins_rep2.bam


title: pT_Spec_0mins_rep3.bam


title: pT_Spec_RpoE_0mins_rep2.bam


title: pT_Spec_RpoE_10mins_rep4.bam


title: pT_Spec_0mins_rep1.bam


title: deltacpxR_stationary_rep3

extract_protocol:
Bacteria was collected and RNA was harvested using Trizol reagent. The Ribo-Zero Magnetic kit was used to remove rRNA and the Illumina TruSeq Stranded mRNA sample preparation kit (Cat# RS-122-2101) was used with 10 to 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Stationary


title: deltacpxR_stationary_rep2


title: deltacpxR_stationary_rep4


title: deltacpxA_stationary_rep1


title: deltacpxA_stationary_rep2


title: deltacpxA_stationary_rep4


title: deltacpxA_stationary_rep3


title: pT_Spec_10mins_rep3.bam


title: 35000HP_stationary_rep4


title: Primed_SMC1_ChIAPET_biologicalReplicate2_run1


title: pT_Spec_RpoE_0mins_rep1.bam


title: 35000HP_stationary_rep2


title: 35000HP_stationary_rep3


title: 35000HP_stationary_rep1


title: deltacpxR_stationary_rep1


title: deltacpxR_transition_rep4

value: Transition


title: deltacpxA_transition_rep4


title: deltacpxR_transition_rep1


title: deltacpxA_transition_rep3


title: deltacpxR_transition_rep3


title: pT_Spec_RpoE_0mins_rep3.bam


title: deltacpxA_transition_rep1


title: deltacpxA_transition_rep2


title: 35000HP_transition_rep1


title: 35000HP_transition_rep4


title: 35000HP_transition_rep2


title: deltacpxR_midlog_rep4

value: Mid-log


title: 35000HP_transition_rep3


title: deltacpxA_midlog_rep2


title: deltacpxA_midlog_rep3


title: deltacpxR_midlog_rep3


title: deltacpxR_midlog_rep1


title: deltacpxA_midlog_rep4


title: 35000HP_midlog_rep3


title: 35000HP_midlog_rep4


title: pT_Spec_RpoE_10mins_rep3.bam


title: deltacpxR_midlog_rep2


title: 35000HP_midlog_rep1


title: P36-ND

city: Kunming

first: Tianqing

last: Li

address: No. Boda Road, Yuhua Area, Chenggong New Town

institute: Primate Translational Medicine Research Center, Kunming University of Science and Technology

description: Differenatiated neurons from the 36th passage NESCs

data_processing:
Fastx (version:0.0.13) software was used to get clean reads. The following describe the detailed information:
Remove the poor reads with poor quality, in which the percentage of Q>20 is less than 50%. Q=-10logerror_ratio
Remove the reads with Q <10 in 3'-terminal. Or, the error_ratio of base is < 0.1.
Remove the all linker sequences in the reads.
Remove the N base in the reads
Remove the reads with the length of less than 20.
Genome_build: Genome mapping was performed by spliced mapping algorithm of Tophat (version:2.0.9) software for clean reads. The reference of genome is Ensembl Macaca_mulatta.MMUL_1.72; the link address is the following:
Genome_build: ftp://ftp.ensembl.org/pub/release-72/fasta/macaca_mulatta/dna/Macaca_mulatta.MMUL_1.72.dna.toplevel.fa.gz.

organism: Macaca mulatta

source_name: monkey differentiated neurons from NESCs

growth_protocol: For NESCs, monkey embryonic stem cell-derived NESCs were cultured in NESCs culture media composed of Neurobasal media including 1xB27,1x N2, 1xNEAA, 1% Glutmax, 3 μM CHIR99021, 5μM SB431542, 10ng/ml bFGF, and 1000U/ml hLIF.  0.025% trypsin was used to digest NESCs when passaging to encourage cell propagation. NESCs were routinely passaged to 1:8 to 1:16 ratios every 3-4 days. For NT formation, NESCs were continually cultured 8-10 days before passaging. For RPGCs, NESCs were cultured in NESCs culture media without 3 μM CHIR99021 for 7 days. For differentiated neurons, NESCs were cultured on laminin (5μg/ml) and gelatin (0.05%) coated plates in differentiation media (SDM) [Neurobasal supplemented with N2, B27, NEAA and Glutmax] for 13 days.

extract_protocol:
500 ng mRNA of each sample was used to produce its respective sequence library.
mRNA was fragmented using the fragmentation Buffer (Ambion) and double-stranded cDNA was then synthesized using SuperScript II (Invitrogen) RT and random primers. Libraries were prepared according to Illumina's instructions. Sequencing was then performed in a HiSeq 2500 apparatus (Illumina) according to the TruSeq RNA Sample Preparation Guide (Illumina).

tag: neural tube morphology

value: neuronal mophorlogy

tag: culture media

value: NESC differentiation media

tag: single cell passage and self-ograinzation into neural tubes

value: no


title: deltacpxR_transition_rep2


title: Biopsy439

source_name: H. ducreyi-infected pustules from humans

growth_protocol: RNA was directly extracted from H. ducreyi-infected pustules and no growth conditions were involved for this study.

extract_protocol:
RNA was harvested from pustules using Trizol reagent. The Ribo-Zero Gold rRNA Removal kit (Epidemiology) was used to remove rRNA and the Illumina TruSeq Stranded mRNA sample preparation kit (Cat# RS-122-2101) was used with 10 to 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Unknown

value: end point pustules


title: P36-NNC

description: RPGCs were converted from

source_name: monkey radial glial progenitor cells

value: lack of NT formation

value: NESC culture meida without CHIR99021

value: weak


title: P36-N

description: the 36th passage NESCs

source_name: monkey neuroepithelial stem cells (NESCs)

value: Neural tube formation at high cell density

value: NESC culture meida containg bFGF, LIF, CHIR99021 and SB431542

value: strong


title: P24-N

description: the 24th passage NESCs


title: Biopsy413


title: Biopsy412


title: GPR65-WT-IL1B_IL6_IL23-96h (population, rep1)

status: Public on Nov 20 2015

city: Berkeley

first: Nir

last: Yosef

state: CA

address: Berkeley

department: EECS

institute: UC Berkeley

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-WT-b623-96h
sample date (yymmdd): 140205

data_processing:
base calling software
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text. Standard cufflinks output with columns for: (tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status)

source_name: CD4 T cells

growth_protocol: C57BL/6 WT and CD4-/-(2663) mice were obtained from Jackson Laboratory. IL-17A–GFP+ mice were obtained from Biocytogen. All animals, unless noted otherwise, were housed and maintained in a conventional pathogen-free facility at the Harvard Institute of Medicine in Boston. All experiments were performed in accordance to the guidelines outlined by the Harvard Medical Area Standing Committee on Animals at the Harvard Medical School. In addition, spleens and lymph nodes from GPR65−/− mice were provided by Li Yang (IACUC protocol: J195b), originally generated by Dr. Owen Witte. PLZP−/− mice were provided by Pier Paolo Pandolfi at the Beth Israel Deaconess Medical Center (IACUC protocol: 082-2014), and TOSO−/− mice were generously provided by John Coligan at the National Institute of Allergy and Infectious Diseases.

extract_protocol:
Cells were washed, stained and sorted for CD3 (Biolegend), CD4 (Biolegend), 7AAD and IL-17A-GFP+.
population controls were generated by extracting total RNA using a RNeasy plus Micro RNA kit (Qiagen) according to manufacturer’s recommendations. Subsequently, 1 μL of RNA in water was added to 2  μL of lysis reaction mix, thermocycled using cycling conditions I described in Supplementary Experimental Procedures in corresponding publication. Next, 4  μL of the RT Reaction Mix were added, and the mixture was thermocycled using cycling conditions II. Finally, 1  μL of the total RT reaction was added to 9 μL of PCR mix, and that mixture was thermocycled using cycling conditions III. Products were quantified, diluted to 0.125 ng/ μL, and libraries were prepared, cleaned, and tested as described in Supplementary Experimental Procedures in corresponding publication.

treatment_protocol: CD4+ T cells were purified from spleen and LNs using anti-CD4 microbeads (Miltenyi Biotech) and then stained in PBS with 1% FCS for 20 min at room temperature with anti-CD4-PerCP, anti-CD62L-APC and anti-CD44-PE antibodies (all Biolegend). Naive CD4+CD62lhighCD44low T cells were sorted using a BD FACSAria cell sorter, or provided by collaborator as sorted cells, shipped on ice overnight. Sorted cells were activated with plate-bound anti-CD3 (2 μg/ml) and anti-CD28 (2 μg/ml) in the presence of cytokines. For Th17 differentiation, the following reagents were used: 2 ng/ml recombinant human TGF-β1 (Miltenyi Biotec), 25 ng/ml recombinant mouse IL-6 (Miltenyi Biotec), 20 ng/ml recombinant mouse IL-23 (R&D Biosystems) and 20 ng/ml recombinant mouse IL-1β (Miltenyi Biotec).

tag: cell type

value: CD4 T cells


title: GPR65-KO-No_cytokines_added-96h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-KO-Th0-96h
sample date (yymmdd): 140205


title: GPR65-KO-IL1B_IL6_IL23-96h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-KO-b623-96h
sample date (yymmdd): 140205


title: GPR65-WT-TGFB1_IL6-96h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-WT-T16-96h
sample date (yymmdd): 140205


title: GPR65-KO-TGFB1_IL6-96h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-KO-T16-96h
sample date (yymmdd): 140205


title: TGFB1_IL6-unsorted-48h (population, rep1)

description: Gaublomme_et_al_2015_populations_invitro_T16-48h-1

growth_protocol: C57BL/6 WT and CD4-/-(2663) mice were obtained from Jackson Laboratory. IL-17A–GFP+ mice were obtained from Biocytogen. All animals, unless noted otherwise, were housed and maintained in a conventional pathogen-free facility at the Harvard Institute of Medicine in Boston. All experiments were performed in accordance to the guidelines outlined by the Harvard Medical Area Standing Committee on Animals at the Harvard Medical School.

treatment_protocol: CD4+ T cells were purified from spleen and LNs using anti-CD4 microbeads (Miltenyi Biotech) and then stained in PBS with 1% FCS for 20 min at room temperature with anti-CD4-PerCP, anti-CD62L-APC and anti-CD44-PE antibodies (all Biolegend). Naive CD4+CD62lhighCD44low T cells were sorted using a BD FACSAria cell sorter. Sorted cells were activated with plate-bound anti-CD3 (2 μg/ml) and anti-CD28 (2 μg/ml) in the presence of cytokines. For Th17 differentiation, the following reagents were used: 2 ng/ml recombinant human TGF-β1 (Miltenyi Biotec), 25 ng/ml recombinant mouse IL-6 (Miltenyi Biotec), 20 ng/ml recombinant mouse IL-23 (R&D Biosystems) and 20 ng/ml recombinant mouse IL-1β (Miltenyi Biotec).


title: TGFB1_IL6-unsorted-48h (population, rep2)

description: Gaublomme_et_al_2015_populations_invitro_T16-48h-2


title: GPR65-WT-No_cytokines_added-96h (population, rep2)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-WT-Th0-96-1
sample date (yymmdd): 140219


title: GPR65-WT-TGFB1_IL6-96h (population, rep2)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-WT-T16-96-1
sample date (yymmdd): 140219


title: 35000HP_midlog_rep2


title: Biopsy437


title: GPR65-WT-IL1B_IL6_IL23-96h (population, rep2)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-WT-B623-96-1
sample date (yymmdd): 140219


title: IL1B_IL6_IL23--IL17A/GFP+-48h (population, rep2)

description: Gaublomme_et_al_2015_populations_invitro_B623-48h-IL17A-2


title: TGFB1_IL6-IL17A/GFP+-48h (population, rep3)

description: Gaublomme_et_al_2015_populations_invitro_T16-48h-IL17A-3


title: deltacpxA_midlog_rep1


title: TGFB1_IL6-IL17A/GFP+-48h (population, rep1)

description: Gaublomme_et_al_2015_populations_invitro_T16-48h-IL17A-1


title: GPR65-WT-No_cytokines_added-96h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-WT-Th0-96h
sample date (yymmdd): 140205


title: P5-N

description: the 5th passage NESCs

value: moderate


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC95_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519

source_name: TGFB1_IL6-48h-IL-17A/GFP+ (single cell batch 8)

extract_protocol:
Cells were washed, stained and sorted for CD3 (Biolegend), CD4 (Biolegend), 7AAD and IL-17A-GFP+.
Cell lysis and SMART-Seq (Ramskold et al., 2012) whole transcriptome amplification (WTA) was performed on the C1 chip using the Fluidigm C1 Single-Cell Auto Prep System (C1 System) with the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech). WTA products were harvested from the C1 chip, and cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents (Illumina) as per manufacturer’s recommendations, with minor modifications. Specifically, reactions were run at ¼ the recommended volume, the tagmentation step was extended to 10 minutes, and the extension time during the PCR step was increased from 30s to 60s. After the PCR step, all 96 samples were pooled without library normalization, cleaned twice with 0.9x AMPure XP SPRI beads (Beckman Coulter), and eluted in buffer TE. The pooled libraries were quantified using Quant-IT DNA High-Sensitivity Assay Kit (Invitrogen) and examined using a high sensitivity DNA chip (Agilent). Finally, samples were sequenced deeply using either a HiSeq 2000 or a HiSeq 2500 sequencer.


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC92_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC90_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC91_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


title: IL1B_IL6_IL23--IL17A/GFP+-48h (population, rep1)

description: Gaublomme_et_al_2015_populations_invitro_B623-48h-IL17A-1


title: TGFB1_IL6-IL17A/GFP+-48h (population, rep4)

description: Gaublomme_et_al_2015_populations_invitro_T16-48h-IL17A-4


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC79_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC78_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC9_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC94_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC74_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC70_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


title: TGFB1_IL6-IL17A/GFP+-48h (population, rep2)

description: Gaublomme_et_al_2015_populations_invitro_T16-48h-IL17A-2


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC73_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC77_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC66_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC86_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC63_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC81_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC64_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC68_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC55_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC65_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC57_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC56_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC58_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC60_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC62_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC75_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC54_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC51_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC50_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC80_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC53_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC48_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC67_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC49_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC34_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC41_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC29_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC27_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC30_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC23_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC46_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC26_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC28_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC42_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC22_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC44_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC45_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC2_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC19_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC40_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC24_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC39_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC47_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC38_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC32_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC16_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC33_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC20_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC21_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC18_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC3_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC13_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC15_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC14_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC10_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC96_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828

source_name: TGFB1_IL6-48h-IL-17A/GFP+ (single cell batch 7)


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC95_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC11_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC9_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_140519_T16_IL17A_48h_SC1_408
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 140519


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC94_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC90_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC88_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC84_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC86_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC82_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC80_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC8_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC76_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC72_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC73_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC74_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC71_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC70_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC69_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC64_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC68_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC62_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC63_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC60_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC65_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC57_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC52_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC54_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC51_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC79_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC5_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC61_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC58_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC77_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC78_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC48_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC43_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC47_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC45_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC49_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC41_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC40_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC46_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC44_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC4_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC35_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC32_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC6_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC36_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC30_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC3_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC34_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC33_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC26_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC24_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC23_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC20_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC28_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC19_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC22_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC2_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC14_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC17_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC13_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC18_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC11_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC12_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC80_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118

source_name: TGFB1_IL6-48h-IL-17A/GFP+ (single cell batch 9)


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC78_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC54_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC62_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC53_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC72_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC74_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC33_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC26_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC25_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC24_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC22_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC14_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC19_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC51_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC16_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130828_48h_t16_il17pos_SC1_185
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130828


title: Tgfb1_IL6_48hr_130715_T16_48h_SC86_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC86_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715

source_name: TGFB1_IL6-48h (single cell batch 6)


title: Tgfb1_IL6_48hr_130715_T16_48h_SC93_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC93_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC92_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC92_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC95_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC95_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC90_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC90_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC70_56
CD4+ T cells from IL-17A–GFP+mice  differentiated into Th17 cells in-vitro with Tgfb1 + IL6. GFP+ cells were sorted and profiled after 48hr
sample date (yymmdd): 130118


title: Tgfb1_IL6_48hr_130715_T16_48h_SC91_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC91_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC89_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC89_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC85_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC85_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC9_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC9_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC83_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC83_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC81_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC81_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC78_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC78_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC74_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC74_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC73_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC73_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC76_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC76_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC82_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC82_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715


title: Tgfb1_IL6_48hr_130715_T16_48h_SC8_144

description:
Gaublomme_et_al_2015_single-cells_Tgfb1_IL6_48hr_130715_T16_48h_SC8_144
CD4+ T cells from C57BL/6 WT mice differentiated into Th17 cells in-vitro with Tgfb1 + IL6. Cells were profiled after 48hr
sample date (yymmdd): 130715