title: Sample_903_ILC3neg_Mtb


title: Single Basal Cell TAGGCATG-CTAAGCCT

status: Public on Jun 04 2018

type: SRA

city: Bruxelles

first: Alexandra

last: Van Keymeulen

address: 808, route de Lennik CP602

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description: SmartSEQ2 scRNAseq

library_source: transcriptomic

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated matrix containing raw transcript counts

molecule: total RNA

organism: Mus musculus

source_name: Rosa-tdTomato

growth_protocol: E14 Lgr5-GFP embryos were collected and the whole skin containing the mammary buds was dissected. Female tissues were placed in HBSS + 300U/ml collagenase (Sigma) + 300μg/ml hyaluronidase (Sigma) and digested for 1h30 at 37°C under shaking. EDTA at a final concentration of 5mM was added for 3min to the resultant organoid suspension, followed by a wash in 10% FBS/PBS and labelling in 2% FBS/PBS before filtration through a 40μm mesh. Adult mammary glands were dissected and the lymph nodes removed. Tissues were briefly washed in HBSS, and chopped in 1mm3 pieces. Chopped tissues were placed in HBSS + 300 U/ml collagenase (Sigma) + 300μg/ml hyaluronidase (Sigma) and digested 2h at 37°C under agitation. Physical dissociation using a P1000 pipette was done every 15mins throughout the enzymatic digestion time. EDTA at a final concentration of 5mM was added for 5 min to the resultant organoid suspension, followed by 0,25% Trypsin-EGTA for 1 min before filtration through a 70-μm mesh, 2 successive washes in 2% FBS/PBS and labelling.

extract_protocol:
Samples were incubated in 250μl of 2% FBS/PBS with fluorochrome-conjugated primary antibodies for 30min, with shaking every 10min. Primary antibodies were washed with 2% FBS/PBS, and cells were resuspended in 2.5mg/ml DAPI (Invitrogen) before analysis. The following primary antibodies were used: APC-conjugated anti-CD45 (1:100, clone 30-F11, eBiosciences), APC-conjugated anti-CD31 (1:100, clone 390, eBiosciences), APC- conjugated anti-CD140a (1:100, clone APA5, eBiosciences) and PE-conjugated anti- CD49f (1:200, clone GoH3, eBiosciences) for embryos; PECy7-conjugated anti- CD24 (1:100, clone M1/69, BD Biosciences), APC-conjugated anti-CD29 (1:100, clone eBioHMb1-1, eBiosciences), PE-conjugated anti-CD45 (1:100, clone 30-F11, eBiosciences), PE-conjugated anti-CD31 (1:100, clone MEC 13.33, BD Biosciences), PE-conjugated anti-CD140a (1:100, clone APA5, eBiosciences) for adult MGs. Data analysis and cell sorting was performed on a FACSAria sorter using the FACS DiVa software (BD Biosciences). Dead cells were excluded with DAPI; CD45+, CD31+ and CD140a+ cells were excluded (Lin+) before analysis of the GFP+ cells.
Single cell transcriptomes were generated using a modified Smartseq-2 protocol74. 1μL lysis buffer in 384 well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer, 2.5mM dNTPs, 2.5μM oligo-dT30-VN and ERCC controls at a final dilution of 1:100 million. Reverse transcription and PCR was performed according to the Smartseq-2 protocol with reduced volumes: 1μl of reverse B372transcription mix instead of 5.7μl and 3μl PCR Master mix instead of 12.5μl. cDNA was amplified for 24 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8x ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 30μl buffer EB (Qiagen) and transferred to 384_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermofisher) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit. After initial quality control 24 samples were discarded with cDNA yields of less than 21ng. These samples were replaced with 24 cells from another 384 well plate from the same cell sort by plate reformatting with an acoustic dispenser (LabCyte Echo 525). Next generation sequencing library preparation was performed using a Nextera XT DNA library preparation kit with volumes reduced by one-tenth (Illumina) using an acoustic dispenser. In brief, 100pg of cDNA in a volume of 500nL was tagmented by adding 1.5μl Tn5-buffer mix and incubating for 10 min at 55°C. Tagmented samples were barcoded with Nextera index sets A - D and amplified with 11 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6x ratio. Library pools were eluted in buffer EB and quality control performed using an Agilent 2100 BioAnalyser and High Sensitiviy DNA chip before adjusting to a concentration of 4nM. The diluted pools were quantified using a KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before a final dilution to 2nM. The pool of 384 samples was sequenced on 2 lanes of a HiSeq2500 in high output mode v4 chemistry with 1x100bp read length.
scRNAseq

tag: library type

value: Nextera XT

tag: facs


title: Single Basal Cell GGACTCCT-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Sample_903_ILC2_uninf

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

description: group 2 ILC from uninfected lung tissue

data_processing:
Sequence reads were trimmed for adaptor sequence and mapped to hg19 human genome using STAR v2.5.3a
Read counts were calculated using htseq-count.
Expression analysis performed with edgeR v3.12.1
Genome_build: hg19
Supplementary_files_format_and_content: processed data files include raw counts of uniquely mapped sequence reads with ensemble transcript ID per sample.

organism: Homo sapiens

source_name: Lung

extract_protocol:
Cells sorted into RLT buffer and RNA extracted with Qiagen micro RNA kit.
cDNA generation and amplification with SMartSeq v4 kit. Sequence libraries prepared with Nextera XT kit.

tag: cell type

tag: infection

value: uninf


title: Oga Fed L1, biological replicate 2

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

country: USA

institute: NIDDK/NIH

hyb_protocol: C. elegans whole genome expression array chips were washed and stained in the Affymetrix Fluidics Station 400s

scan_protocol: Chips were scanned with an Affymetrix Scanner with standard settings

data_processing: Data was analyzed by Micrarray Suite 5.0 (MAS5) and by RMA using the program Partek

label: biotin

organism: Caenorhabditis elegans

source_name: oga-1(ok1207) L1 animall

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA

growth_protocol: Embryos were isolated from wild type and mutant gravid adults by bleach treatment and shaken gently with good aeration in sterile buffer to hatch and collected 48 hours later. Synchronized L1 animals were plated on NGM with food for 3 hours, collected, washed, and used for total RNA preparation.

extract_protocol: Trizol extraction of total RNA was performed according to standard protocols

treatment_protocol: Synchronized L1 animals were isolated for wild type and two mutant strains: loss of the O-GlcNAc transferase ogt-1(ok430) and loss of the O-GlcNAcase oga-1(ok1207).  Animals were plated on NGM with E. coli (OP50) and allowed to feed for 3 hours prior to collection and RNA isolation.

tag: genotype/variation

value: oga mutant

tag: development stage


title: Single Embryonal Progenitor Cell AGGCAGAA-CTAAGCCT

description: SmartSEQ2 scRNAseq

value: CD49f Hi/Lgr5 Hi


title: Single Basal Cell CGTACTAG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCCTGAGC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Ogt Fed L1, biological replicate 3

source_name: ogt-1(ok430) L1 animal

value: ogt mutant


title: Oga Fed L1, biological replicate 1

source_name: oga-1(ok1207) L1 animal


title: Ogt Fed L1, biological replicate 1


title: Ogt Fed L1, biological replicate 2


title: Single Basal Cell TAAGGCGA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCGACGTC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: WT Fed L1, biological rep2

source_name: Wild Type L1 animal

value: wild type


title: Oga Fed L1, biological replicate 3


title: Sample_903_ILC3neg_uninf

description: group 3 ILC (NKp44 negative) from uninfected lung tissue


title: Sample_903_ILC1_Mtb

description: group 1 ILC from Mtb infected lung tissue

value: Mtb


title: WT Fed L1, biological rep3


title: WT Fed L1, biological rep1


title: Single Basal Cell TGCAGCTA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_susp_uninf

description: whole cell suspension from uninfected lung tissue

value: susp


title: Single Basal Cell CCTAAGAC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ACTGAGCG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_susp_Mtb

description: whole cell suspension  from Mtb infected lung tissue


title: Single Basal Cell ATGCGCAG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TAGCGCTC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_NK_uninf

description: natural killer cells from uninfected lung tissue

value: NK


title: Sample_903_ILC2_Mtb

description: group 2 ILC from Mtb infected lung tissue


title: Sample_903_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Single Embryonal Progenitor Cell TACGCTGC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GCGTAGTA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_ILC3pos_uninf

description: group 3 ILC (NKp44 positive) from uninfected lung tissue


title: Single Basal Cell CGGAGCCT-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ATCTCAGG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_NK_Mtb

description: natural killer cells from Mtb infected lung tissue


title: Single Basal Cell ACTCGCTA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGAGCTAC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GTAGAGGA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_ILC3neg_uninf


title: Sample_875_ILC3pos_Mtb

description: group 3 ILC (NKp44 positive) from Mtb infected lung tissue


title: Single Basal Cell GCTCATGA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell AAGAGGCA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_ILC2_uninf

description: group 2 ILC from uninfected lung tissue


title: Single Basal Cell CGAGGCTG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CTCTCTAC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_ILC3neg_Mtb

description: group 3 ILC (NKp44 negative) from Mtb infected lung tissue


title: Single Embryonal Progenitor Cell CGATCAGT-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGACTCCT-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TAGGCATG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCCTGAGC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Sample_875_ILC2_Mtb


title: Single Basal Cell CGTACTAG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell AGGCAGAA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TAAGGCGA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TGCAGCTA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCGACGTC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGATCAGT-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_875_ILC1_Mtb


title: Single Basal Cell TAGCGCTC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_869_susp_Mtb


title: Single Basal Cell TACGCTGC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CCTAAGAC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ATGCGCAG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GCGTAGTA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_869_ILC3pos_uninf


title: Sample_869_susp_uninf


title: Sample_869_ILC3pos_Mtb


title: Single Basal Cell GCTCATGA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_875_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Sample_869_ILC3neg_uninf


title: Sample_869_NK_uninf


title: Single Basal Cell ATCTCAGG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGGAGCCT-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell AAGAGGCA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGAGGCTG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_869_ILC3neg_Mtb


title: Single Basal Cell CTCTCTAC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TAGGCATG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_869_ILC2_uninf

description: group 2 ILC from uninfected lung tissue


title: Single Basal Cell GTAGAGGA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ACTGAGCG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGACTCCT-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCCTGAGC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_869_ILC2_Mtb


title: Single Basal Cell AGGCAGAA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGTACTAG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_869_NK_Mtb


title: Single Basal Cell GGAGCTAC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Sample_869_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Single Basal Cell TAAGGCGA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCGACGTC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ACTCGCTA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TGCAGCTA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_869_ILC1_Mtb


title: Single Basal Cell CGATCAGT-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_susp_uninf


title: Single Basal Cell CCTAAGAC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ACTGAGCG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_susp_Mtb


title: Single Basal Cell TAGCGCTC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ATGCGCAG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGGAGCCT-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_NK_Mtb


title: Sample_860_NK_uninf


title: Single Basal Cell GCGTAGTA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGAGCTAC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_ILC3pos_Mtb


title: Single Basal Cell ATCTCAGG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_ILC3pos_uninf


title: Single Basal Cell ACTCGCTA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GCTCATGA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GTAGAGGA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGAGGCTG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell AAGAGGCA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_ILC3neg_uninf


title: Sample_860_ILC3neg_Mtb


title: Single Basal Cell TAGGCATG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CTCTCTAC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGACTCCT-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCCTGAGC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_ILC2_Mtb


title: Sample_860_ILC2_uninf

description: group 2 ILC from uninfected lung tissue


title: Single Basal Cell AGGCAGAA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TACGCTGC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Single Basal Cell CGTACTAG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Sample_860_ILC1_Mtb


title: Single Basal Cell TAAGGCGA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TCGACGTC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_susp_uninf


title: Single Embryonal Progenitor Cell TGCAGCTA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_susp_Mtb


title: Single Basal Cell CCTAAGAC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_NK_uninf


title: Single Basal Cell CGATCAGT-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ACTGAGCG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TAGCGCTC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_NK_Mtb


title: Single Basal Cell CGGAGCCT-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TACGCTGC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_ILC3pos_uninf


title: Single Basal Cell GCGTAGTA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ATGCGCAG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGAGCTAC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ACTCGCTA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_903_NK_uninf


title: Single Basal Cell ATCTCAGG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GCTCATGA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_ILC3pos_Mtb


title: Sample_857_ILC3neg_uninf


title: Sample_857_ILC3neg_Mtb


title: Single Basal Cell AAGAGGCA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GTAGAGGA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_ILC2_uninf

description: group 2 ILC from uninfected lung tissue


title: Single Basal Cell TAGGCATG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CTCTCTAC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGAGGCTG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGACTCCT-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_ILC2_Mtb


title: Single Basal Cell TCCTGAGC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGTACTAG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: 50 Cell Control Embryonal Progenitor TAAGGCGA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Sample_857_ILC1_Mtb


title: Single Basal Cell TCGACGTC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell AGGCAGAA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TGCAGCTA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGATCAGT-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CCTAAGAC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TAGCGCTC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ATGCGCAG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TACGCTGC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGGAGCCT-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCGTAGTA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGAGCTAC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ATCTCAGG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GCTCATGA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell AAGAGGCA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CTCTCTAC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GTAGAGGA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell TAGGCATG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell GGACTCCT-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Sample_857_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Single Basal Cell CGAGGCTG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: 50 Cell Control Luminal CGTACTAG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell ACTGAGCG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Macrophage, HFD, Ly6c+ / Cd9-, rep4

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Ly6c_r4

data_processing:
Bulk RNA-seq reads were aligned to UCSC mm9 genome using STAR aligner. Raw read counts were measured within RefSeq genes using featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: Raw tag count by featureCount

source_name: eWAT macrophage

growth_protocol: All experiments used male age-matched C57BL/6J mice housed at four or five animals per cage. High-fat diet studies were conducted by feeding mice a purified-ingredient diet composed of 60:20:20 kcal percentage of fat:carbohydrate:protein (Research Diets, D12492)

extract_protocol:
For bulk RNA-seq of sort-purified cell populations, libraries were prepared using the SMARTer Stranded RNA-seq kit (Clontech) and TruSeq RNA library prep kit (Illumina). For bulk RNA-seq of adipose tissue, total RNA was isolated from snap-frozen tissue samples. Tissues were mechanically homogenized in 500μL TRIzol (Life Technologies) in a TissueLyser (Qiagen) for 4 min, at a frequency of 22s−1. After homogenization, samples were centrifuged at 4°C and homogenates transferred to a fresh tube for RNA extraction with chloroform. Aqueous chloroform fractions were mixed with equal volumes of 70% ethanol/30% water and RNA further purified with RNeasy Mini spin columns (Qiagen) and oncolumn DNase-digestion (Qiagen). One microgram of purified DNase-treated total RNA from biological replicates was processed with a Ribo-Zero Magnetic rRNA removal kit (Epicentre, MRZH11124).
Bulk adipose RNA libraries were prepared using a TruSeq Stranded Total RNA Library Prep Gold (Illumina, 200020599) and standard Illumina protocol.

treatment_protocol: [ex-vivo macrophages] Epididymal white adipose tissue (eWAT) depots were isolated from mice. Adipose samples were placed in 1 mL of DMEM and individual depots were finely minced under sterile conditions with a razorblade prior to digestion in 5 mL DMEM with 6 mg/1 mL collagenase D (Roche) or 3 mg/1 mL collagenase IV (Gibco) at 37° C in a shaking incubator for 30 min. Cells were pelleted at 700g and adipocyte fraction removed. After resuspension of the stromal fraction in 5mL of MACS buffer (1x PBS, 2% calf serum, 25 mM HEPES, 2 mM EDTA) for cell sorting, cells were purified through a 100 μm filter (Falcon), pelleted at 700g, and re-suspended in 1 mL of RBC lysis buffer (0.15 M NH4Cl, .01 M NaHCO3, 0.0013 M EDTA) for 5 minutes at room temperature. Cells were washed again in MACS buffer prior to staining for sorting.  [BMDM] Bone marrow cells were isolated under sterile conditions and cultured in the presence of mCSF at a density of 5x106 cells/10 mL of complete media for a period of six days. On day six of culture, cells were re-plated at a density of 3x106 cells and cultured for a period of 24 hours in the presence of BSA (control), LPS (5 ng/mL), or IL-4 (10 ng/mL).  [Adoptive Transfer] 75-125K cells were sort-purified from obese, CD45.2+ donors and transferred via intraperitoneal injection three times over the course of one week into lean, CD45.1+ recipients. Recipient mice were allowed to rest 24-48 hours prior to sacrifice for subsequent eWAT RNA-seq.

tag: condition

value: High fat diet

tag: strain

tag: tissue

value: Epididymal white adipose tissue (eWAT)

value: adipose tissue macrophage (ATM)

tag: cell sorting

value: Ly6c+ / Cd9-


title: Macrophage, HFD, Ly6c+ / Cd9-, rep2

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Ly6c_r2


title: Macrophage, HFD, Ly6c+ / Cd9-, rep1

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Ly6c_r1


title: Single Basal Cell TCCTGAGC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTCGCTA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: eWAT_B6_HFD_35

description:
Fluidigm C1
gene.fpkm_table.gz

data_processing:
Sequencing reads from scRNA-seq were aligned to UCSC mm9 genome using default options in STAR aligner. Reads aligned to chrM were discarded. Gene expression levels were quantified and normalized using cuffquant and cuffnorm
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression level in FPKM scale normalized by cuffnorm

molecule: polyA RNA

source_name: scRNA-seq, eWAT_B6_HFD_35

extract_protocol:
Libraries were prepared from sort-purified cell populations via a C1 platform (Fluidigm) and barcoded via Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were prepared from sort-purified cell populations via a C1 platform (Fluidigm) and barcoded via Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: Epididymal white adipose tissue (eWAT) depots were isolated from mice. Adipose samples were placed in 1 mL of DMEM and individual depots were finely minced under sterile conditions with a razorblade prior to digestion in 5 mL DMEM with 6 mg/1 mL collagenase D (Roche) or 3 mg/1 mL collagenase IV (Gibco) at 37° C in a shaking incubator for 30 min. Cells were pelleted at 700g and adipocyte fraction removed. After resuspension of the stromal fraction in 5mL MACS buffer (1x PBS, 2% calf serum, 25 mM HEPES, 2 mM EDTA) for cell sorting, cells were purified through a 100 μm filter (Falcon), pelleted at 700g, and re-suspended in 1 mL of RBC lysis buffer (0.15 M NH4Cl, .01 M NaHCO3, 0.0013 M EDTA) for 5 minutes at room temperature. Cells were washed again in MACS buffer prior to staining for sorting.

tag: diet


title: eWAT_B6_HFD_34

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_34


title: eWAT_B6_HFD_36

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_36


title: eWAT_B6_HFD_33

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_33


title: Single Basal Cell AGGCAGAA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: eWAT_B6_HFD_31

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_31


title: 50 Cell Control Basal TAAGGCGA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: eWAT_B6_HFD_30

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_30


title: eWAT_B6_HFD_29

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_29


title: Macrophage, HFD, Ly6c+ / Cd9-, rep3

description:
featureCount.ATM.Cd9_vs_Lc.txt
ATM_Ly6c_r3


title: eWAT_B6_HFD_27

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_27


title: eWAT_B6_HFD_28

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_28


title: eWAT_B6_HFD_26

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_26


title: eWAT_B6_HFD_25

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_25


title: eWAT_B6_HFD_32

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_32


title: WA27788_BASELINE_PBO__Patient_1163

city: South San Francisco

first: Janina

last: Reeder

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

description:
US91903684_254014310044_S01_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE

hyb_protocol: Equimolar target/reference mixes were hybridised to custom Agilent 60-mer arrays (EPI_8X60_3P_004; Epistem) according to the manufacturer's instructions.

scan_protocol: Slides were scanned for Cy5 and Cy3 on an Agilent Technologies Microarray Scanner G2505c (Serial number US91903684) at a 3uM resolution producing a 20Bit tiff image. Array data was extracted from the scanned images using the default Agilent 2 colour extraction protocol GE2_105_Dec08 in Agilent feature extraction version 10.5.1.

data_processing: Raw microarray data were processed using the R programming language and packages from the Bioconductor project (http://www.bioconductor.org). Preprocessing of the probe set intensities included background correction, normalisation (Loess), and replicate averaging, excluding control probes and feature filtering (removal of features not associated with a Gene ID and duplicate Gene IDs).

source_name: Equimolar cDNA Pool

label_protocol: An equimolar pool of all amplified cDNA samples was used to incorporate Cy3 fluorophore using an RNAamp Cy3/Cy5 labelling kit (Epistem).

growth_protocol: RNA amplification was performed using 10 ng total RNA and the RNAamp RNA Nano amplification kit (Epistem, Manchester, UK). Amplified cDNA was assessed quantitatively (NanoDrop) and qualitatively (Bioanalyzer; Agilent).

extract_protocol: Skin samples were homogenised in TRIzol® (ThermoFisher Scientific, Waltham, MA, USA) using a polytron homogeniser, and total RNA was isolated according to the manufacturer's protocol.

treatment_protocol: Storage of human tissue in RNAlater®

tag: sample type

value: reference

label_protocol: Individual cDNA test samples were labelled with Cy5, using an RNAamp Cy3/Cy5 labelling kit (Epistem).

value: skin biopsy

tag: disease state

value: systemic sclerosis (SSc)

tag: subject

tag: treatment

value: placebo

tag: time point

value: BASELINE

tag: gender

value: M

tag: age

tag: mrss


title: WA27788_WEEK 24_PBO__Patient_1326

description:
US91903684_254014310081_S01_GE2_105_Dec08_2_EH_2_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1326

value: WEEK 24

value: F


title: WA27788_BASELINE_PBO__Patient_1325

description:
US91903684_254014310037_S01_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1120

description:
US91903684_254014310080_S01_GE2_105_Dec08_2_EH_1_1
SSc placebo BASELINE


title: eWAT_B6_HFD_23

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_23

tag: cell type


title: WA27788_WEEK 24_PBO__Patient_1493

description:
US91903684_254014310081_S01_GE2_105_Dec08_2_EH_1_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1493


title: WA27788_BASELINE_PBO__Patient_1324

description:
US91903684_254014310044_S01_GE2_105_Dec08_2_EH_1_2
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1238

description:
US91903684_254014310037_S01_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1493

description:
US91903684_254014310081_S01_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1326

description:
US91903684_254014310081_S01_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: eWAT_B6_HFD_21

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_21


title: eWAT_B6_HFD_22

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_22


title: eWAT_B6_HFD_20

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_20


title: WA27788_WEEK 24_PBO__Patient_1116

description:
US91903684_254014310042_S01_GE2_105_Dec08_2_EH_2_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1116


title: WA27788_BASELINE_PBO__Patient_1431

description:
US91903684_254014310035_S01_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1116

description:
US91903684_254014310042_S01_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1174

description:
US91903684_254014310042_S01_GE2_105_Dec08_2_EH_1_3
SSc placebo BASELINE


title: WA27788_WEEK 24_PBO__Patient_1120

description:
US91903684_254014310080_S01_GE2_105_Dec08_2_EH_1_2
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1120


title: WA27788_WEEK 24_PBO__Patient_1431

description:
US91903684_254014310035_S01_GE2_105_Dec08_2_EH_2_2
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1431


title: WA27788_WEEK 24_PBO__Patient_1174

description:
US91903684_254014310042_S01_GE2_105_Dec08_2_EH_1_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1174


title: eWAT_B6_HFD_19

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_19


title: eWAT_B6_HFD_24

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_24


title: eWAT_B6_HFD_17

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_17


title: eWAT_B6_HFD_18

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_18


title: eWAT_B6_HFD_16

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_16


title: WA27788_WEEK 24_PBO__Patient_1461

description:
US91903684_254014310035_S01_GE2_105_Dec08_2_EH_1_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1461


title: eWAT_B6_HFD_15

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_15


title: WA27788_WEEK 24_PBO__Patient_1292

description:
US91903684_254014310039_S01_GE2_105_Dec08_2_EH_2_3
SSc placebo WEEK 24

source_name: Equimolar cDNA Pool

source_name: WA27788_WEEK 24_PBO__Patient_1292


title: WA27788_BASELINE_PBO__Patient_1461

description:
US91903684_254014310035_S01_GE2_105_Dec08_2_EH_1_2
SSc placebo BASELINE


title: eWAT_B6_HFD_14

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_14


title: WA27788_WEEK 24_PBO__Patient_1238

description:
US91903684_254014310037_S01_GE2_105_Dec08_2_EH_1_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1238


title: WA27788_BASELINE_PBO__Patient_1006

description:
US91903684_254014310038_S01_GE2_105_Dec08_2_EH_2_1
SSc placebo BASELINE


title: eWAT_B6_HFD_12

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_12


title: eWAT_B6_HFD_13

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_13


title: eWAT_B6_HFD_11

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_11


title: eWAT_B6_HFD_10

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_10


title: eWAT_B6_HFD_8

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_8


title: eWAT_B6_HFD_7

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_7


title: WA27788_BASELINE_PBO__Patient_1137

description:
US91903684_254014310034_S01_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: eWAT_B6_HFD_5

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_5


title: eWAT_B6_HFD_6

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_6


title: WA27788_WEEK 24_PBO__Patient_1137

description:
US91903684_254014310034_S01_GE2_105_Dec08_2_EH_1_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1137


title: eWAT_B6_HFD_4

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_4


title: WA27788_WEEK 24_PBO__Patient_1358

description:
US91903684_254014310049_S01_GE2_105_Dec08_2_EH_2_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1358


title: WA27788_BASELINE_PBO__Patient_1292

description:
US91903684_254014310034_S01_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1358

description:
US91903684_254014310049_S01_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: WA27788_WEEK 24_PBO__Patient_1063

description:
US91903684_254014310047_S01_GE2_105_Dec08_2_EH_1_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1063


title: WA27788_BASELINE_PBO__Patient_1063

description:
US91903684_254014310047_S01_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1107

description:
US91903684_254014310050_S01_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: WA27788_WEEK 24_PBO__Patient_1019

description:
US91903684_254014310047_S01_GE2_105_Dec08_2_EH_2_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1019


title: WA27788_BASELINE_PBO__Patient_1129

description:
US91903684_254014310043_S01_GE2_105_Dec08_2_EH_2_1
SSc placebo BASELINE

source_name: Equimolar cDNA Pool


title: WA27788_WEEK 24_PBO__Patient_1242

description:
US91903684_254014310046_S01_GE2_105_Dec08_2_EH_2_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1242


title: eWAT_B6_HFD_9

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_9


title: eWAT_B6_HFD_2

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_2


title: eWAT_B6_HFD_3

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_3


title: eWAT_B6_HFD_0

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_0


title: WA27788_WEEK 24_PBO__Patient_1479

description:
US91903684_254014310046_S01_GE2_105_Dec08_2_EH_1_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1479


title: WA27788_WEEK 24_PBO__Patient_1330

description:
US91903684_254014310049_S01_GE2_105_Dec08_2_EH_1_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1330


title: WA27788_BASELINE_PBO__Patient_1242

description:
US91903684_254014310046_S01_GE2_105_Dec08_2_EH_2_3
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1479

description:
US91903684_254014310046_S01_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1330

description:
US91903684_254014310049_S01_GE2_105_Dec08_2_EH_1_2
SSc placebo BASELINE


title: WA27788_WEEK 24_PBO__Patient_1097

description:
US91903684_254014310071_S02_GE2_105_Dec08_2_EH_2_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1097


title: WA27788_WEEK 24_PBO__Patient_1122

description:
US91903684_254014310071_S02_GE2_105_Dec08_2_EH_2_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1122


title: WA27788_WEEK 24_PBO__Patient_1328

description:
US91903684_254014310071_S02_GE2_105_Dec08_2_EH_1_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1328


title: WA27788_BASELINE_PBO__Patient_1328

description:
US91903684_254014310071_S02_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: eWAT_B6_HFD_1

description:
Fluidigm C1
gene.fpkm_table.gz

source_name: scRNA-seq, eWAT_B6_HFD_1


title: WA27788_BASELINE_PBO__Patient_1097

description:
US91903684_254014310071_S02_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: 15d_WT_H3K27me3_ChIPSeq_input_rep2

city: Shanghai

first: Hui

last: Wang

email: wanghuisimm@sioc.ac.cn, mazj@sioc.ac.cn

address: Qiuyue Road 26

country: China

institute: Chinese Academy of Science

library_source: genomic

data_processing:
For ChIP-Seq, Sequencing reads were mapped to reference genome dm6 or mm10 respectively with Bowtie2 by default parameter. The peak regions were identified by homer function findPeaks with parameter –style histone -F 2 -size 3000 -minDist 5000. The overlapped peaks of replicate data-sets were found using homer function mergePeaks by default parameter. Bedtools were used to compare the peaks between different genotypes and aging stages. To get inter-peak regions, we used Bedtools to subtracted the peak regions from whole genome.
Genome_build: dm6 and mm10
Supplementary_files_format_and_content: bigwig files were generated by deeptools.

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Flies were cultured in standard media at 25ºC with 60% humidity unless otherwise specified. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype male flies were collected at the day of eclosion and transferred to new vials every other day during aging process.

extract_protocol:
For ChIP-Seq, 5% mouse epigenome was used as internal control for H3K27me3 IP.
ChIP libraries were prepared according to instructions of NEB DNA library prep kit (NEB, E7370L). RNA libraries were prepared according to instructions of NEB Ultra RNA library prep kit (NEB, E7530L).

treatment_protocol: Flies were harvested at the given age.

tag: genotype

value: 15 day

value: muscle


title: 30d_WT_H3K27me3_ChIPSeq_rep2

value: 30 day

tag: chip antibody

value: H3K27me3 (Millipore 07-449)


title: 3d_WT_H3K27me3_ChIPSeq_input_rep2

value: 3 day


title: 30d_WT_H3K27me3_ChIPSeq_input_rep2


title: 15d_WT_H3K27me3_ChIPSeq_rep2


title: WA27788_BASELINE_PBO__Patient_1436

description:
US91903684_254014310070_S02_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: WA27788_WEEK 24_PBO__Patient_1436

description:
US91903684_254014310070_S02_GE2_105_Dec08_2_EH_2_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1436


title: WA27788_WEEK 24_PBO__Patient_1049

description:
US91903684_254014310069_S02_GE2_105_Dec08_2_EH_2_2
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1049


title: WA27788_WEEK 24_PBO__Patient_1158

description:
US91903684_254014310070_S02_GE2_105_Dec08_2_EH_1_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1158


title: WA27788_BASELINE_PBO__Patient_1122

description:
US91903684_254014310071_S02_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: WA27788_WEEK 24_PBO__Patient_1500

description:
US91903684_254014310067_S02_GE2_105_Dec08_2_EH_2_1
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1500


title: WA27788_WEEK 24_PBO__Patient_1053

description:
US91903684_254014310068_S02_GE2_105_Dec08_2_EH_2_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1053


title: WA27788_BASELINE_PBO__Patient_1057

description:
US91903684_254014310043_S01_GE2_105_Dec08_2_EH_1_2
SSc placebo BASELINE

source_name: Equimolar cDNA Pool


title: WA27788_BASELINE_PBO__Patient_1158

description:
US91903684_254014310070_S02_GE2_105_Dec08_2_EH_1_2
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1262

description:
US91903684_254014310043_S01_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1500

description:
US91903684_254014310067_S02_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: 3d_WT_H3K27me3_ChIPSeq_rep2


title: WA27788_BASELINE_PBO__Patient_1049

description:
US91903684_254014310069_S02_GE2_105_Dec08_2_EH_2_1
SSc placebo BASELINE


title: 30d_WT_H3K27me3_ChIPSeq_input_rep1


title: 15d_WT_H3K27me3_ChIPSeq_input_rep1


title: WA27788_BASELINE_PBO__Patient_1053

description:
US91903684_254014310068_S02_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: 30d_WT_H3K27me3_ChIPSeq_rep1


title: 15d_WT_H3K27me3_ChIPSeq_rep1


title: pupae_H3K27me3_ChIPSeq_input_rep2

value: 7day pupae

value: pupae


title: 3d_WT_H3K27me3_ChIPSeq_rep1


title: WA27788_WEEK 24_PBO__Patient_1045

description:
US91903684_254014310066_S02_GE2_105_Dec08_2_EH_2_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1045


title: WA27788_WEEK 24_PBO__Patient_1001

description:
US91903684_254014310067_S02_GE2_105_Dec08_2_EH_2_4
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1001


title: WA27788_BASELINE_PBO__Patient_1045

description:
US91903684_254014310066_S02_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1000

description:
US91903684_254014310065_S02_GE2_105_Dec08_2_EH_1_2
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1348

description:
US91903684_254014310066_S02_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1395

description:
US91903684_254014310045_S01_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1214

description:
US91903684_254014310046_S01_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: WA27788_BASELINE_PBO__Patient_1414

description:
US91903684_254014310064_S02_GE2_105_Dec08_2_EH_2_2
SSc placebo BASELINE


title: WA27788_WEEK 24_PBO__Patient_1348

description:
US91903684_254014310066_S02_GE2_105_Dec08_2_EH_1_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1348


title: larva_H3K27me3_ChIPSeq_input_rep1

value: 96 hour larva

value: larva


title: 3d_WT_H3K27me3_ChIPSeq_input_rep1


title: larva_H3K27me3_ChIPSeq_rep2


title: pupae_H3K27me3_ChIPSeq_rep2


title: embryo_H3K27me3_ChIPSeq_rep2

value: 30min - 1 hour embryo

value: embryo


title: pupae_H3K27me3_ChIPSeq_input_rep1


title: larva_H3K27me3_ChIPSeq_rep1


title: WA27788_WEEK 24_PBO__Patient_1414

description:
US91903684_254014310064_S02_GE2_105_Dec08_2_EH_2_1
SSc placebo WEEK 24

value: reference

source_name: WA27788_WEEK 24_PBO__Patient_1414

value: skin biopsy

value: systemic sclerosis (SSc)


title: embryo_H3K27me3_ChIPSeq_input_rep1


title: pupae_H3K27me3_ChIPSeq_rep1


title: embryo_H3K27me3_ChIPSeq_input_rep2


title: larva_H3K27me3_ChIPSeq_input_rep2


title: embryo_H3K27me3_ChIPSeq_rep1


title: TSZ_mRNA_Seq_rep1

first: Zaijun

last: Ma

institute: Chinese Academy Science

description:
DMSO_vs_TSZ_DESeq.csv
TNF-alpha_vs_TSZ_DESeq.csv
TSZ_vs_TSZ_Nec-1s_DESeq.csv

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to hg38 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue

source_name: TSZ, HT-29 cells

growth_protocol: HT-29 cells were cultured in McCoy's 5A medium (GIBCO, Grand Island, NY, USA), supplemented with 10% FBS (Gibco), penicillin and streptomycin.

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa)
RNA libraries were prepared according to instructions of NEB Ultra RNA library prep kit (NEB, E7530L).

treatment_protocol: HT-29 were treated with DMSO, 10 ng/ml TNF-α (T), or the combination of 10 ng/ml TNF-α (T), 50 nM SM-164 (S) and 20 μM zVAD (Z) in the presence or absence of 10 μM Nec-1s for 8 h.

value: colon

tag: cell line

value: colon adenocarcinoma cell line HT29

value: TNF-α, SM-164, zVAD


title: TSZ_mRNA_Seq_rep3


title: TNF-α_mRNA_Seq_rep2

description:
DMSO_vs_TNF-alpha_DESeq.csv
TNF-alpha_vs_TSZ_DESeq.csv
TNF-alpha_vs_TSZ_Nec-1s_DESeq.csv

source_name: TNF-α, HT-29 cells

value: TNF-α


title: TSZ,Nec-1s_mRNA_Seq_rep3

description:
DMSO_vs_TSZ_Nec-1s_DESeq.csv
TSZ_vs_TSZ_Nec-1s_DESeq.csv

source_name: TSZ,Nec-1s, HT-29 cells

value: TNF-α, SM-164, zVAD,Nec-1s


title: TSZ,Nec-1s_mRNA_Seq_rep1


title: WA27788_WEEK 24_PBO__Patient_1033

description:
US91903684_254014310069_S02_GE2_105_Dec08_2_EH_1_4
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1033

value: placebo

value: WEEK 24

value: F


title: TSZ,Nec-1s_mRNA_Seq_rep2


title: AW7-K8P63-BC1.1

data_processing:
Approximately 19 million of paired-end reads per sample were mapped against the mouse reference genome (GRCm38/mm10) using STAR software to generate read alignments for each sample. Annotations Mus_musculus.GRCm38.87.gtf were obtained from ftp.Ensembl.org. After transcripts assembling, gene level counts were obtained using HTSeq. Fold change of mean gene expression for the duplicates were used to calculate the level of differential gene expression. Heatmap of the 500 most variable genes across the 8 samples and corresponding clustering dendrogram were drawn with heatmap.2 function of the R package gplots (citation R). Euclidian distance with complete linkage agglomeration method was used for clustering.
Genome_build: grcm38
Supplementary_files_format_and_content: CP20M-Wuidart (count normalized by 20M mapped reads

source_name: mammary gland

growth_protocol: Mice – Lgr5-EGFP-IRES-CreER18 and Rosa-tdTomato63 mice were obtained from the Jackson Laboratory. Rosa-Confetti15 mice were provided by H. Clevers; K14rtTA transgenic mice64 were provided by Elaine Fuchs; TetO-Cre mice65 were provided by Andreas Nagy; Rosa26-ΔNp63-IRES-GFP mice57 were provided by Wim Declercq. The generation of K5CreER and of K8rtTA were previously described9, 66. All experimental mice used in this study were females of mixed genetic backgrounds. No statistical methods were used to predetermine sample size. The experiments were not randomized. The investigators were not blinded to allocation during experiments and outcome assessment. Mice colonies were maintained in a certified animal facility in accordance with European guidelines. The experiments were approved by the local ethical committee (CEBEA).

extract_protocol:
RNAseq and analysis of bulk samples40000 LCs and 5000 BCs were isolated by FACS as described above and collected into kit lysis buffer. RNA was extracted using absolutely RNA nanoprep kit (Stratagene).
RNA quality was checked using a Bioanalyzer 2100 (Agilent technologies). Indexed cDNA libraries were obtained using the Ovation Solo RNA-Seq System (NuGen) following manufacturer recommendation. The multiplexed libraries (18 pM) were loaded on flow cells and sequences were produced using a NovaSeq 6000 S2 Reagent Kit (200 cycles) from a NovaSeq 6000 System (Illumina).

treatment_protocol: Targeting Confetti, tdTomato or ΔNp63-IRES-GFP expression in the MG – For clonal lineage tracing, K14rtTA/TetO-Cre/Rosa-Confetti embryos were induced at E13 by intravenous (IV) injection in the tail vein of the pregnant mother with 1µg/g of Doxycycline (diluted in sterile PBS, Sigma) and sacrificed 2 days later (E15) or 5 days after delivery (P5). K5CreER/Rosa-Confetti newborn pups (P1) were induced by intraperitoneal (IP) injection of 50µg of Tamoxifen (diluted in sunflower seed oil, Sigma) and sacrificed 21 days later. For lineage tracing at saturation, K14rtTA/TetO-Cre/Rosa-tdTomato or K14rtTA/TetO-Cre/Rosa-ΔNp63-IRES-GFP embryos were induced at E13 by IV injection in the tail vein of the pregnant mother with 15µg/g of Doxycycline (diluted in sterile PBS) and sacrificed 5 days after delivery (P5). K8rtTA/TetO-Cre/Rosa-Confetti female mice were induced at 4w old with Doxycyclin treatment during 7 days consisting in the combination of Doxycylin 10g/kg in diet (Bio-Serv), 2g/l in drinking water (AG Scientific) and 3 intraperitoneal injections of 2 mg in 200µl PBS.

value: mammary gland

value: female

tag: mouse strain

tag: cell surface markers


title: AW8-K8P63-BC2.2

tag: tissue


title: WA27788_WEEK 24_PBO__Patient_1026

description:
US91903684_254014310064_S02_GE2_105_Dec08_2_EH_2_3
SSc placebo WEEK 24

source_name: WA27788_WEEK 24_PBO__Patient_1026


title: AW6-CD1-BC2.2


title: WA27788_BASELINE_PBO__Patient_1026

description:
US91903684_254014310064_S02_GE2_105_Dec08_2_EH_2_4
SSc placebo BASELINE

value: BASELINE


title: AW5-CD1-BC1.1


title: AW4-K8P63-LC2.2


title: DMSO_mRNA_Seq_rep3

description:
DMSO_vs_TNF-alpha_DESeq.csv
DMSO_vs_TSZ_DESeq.csv
DMSO_vs_TSZ_Nec-1s_DESeq.csv

source_name: DMSO, HT-29 cells

value: DMSO


title: AW2-CD1-LC2.2


title: DMSO_mRNA_Seq_rep2


title: DMSO_mRNA_Seq_rep1


title: AW1-CD1-LC1.1


title: TNF-α_mRNA_Seq_rep3


title: TSZ_mRNA_Seq_rep2


title: WA27788_BASELINE_PBO__Patient_1396

description:
US91903684_254014310067_S02_GE2_105_Dec08_2_EH_1_4
SSc placebo BASELINE


title: CLL-M12_H3K27ac

status: Public on Jun 03 2018

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

description: Raw data available via dbGaP Study Accession phs000939

data_processing:
Reads were aligned to the hg19 genome assembly using BWA. Data were filtered to remove PCR duplicates and reads mapping to >2 genomic sites.
Genome_build: hg19
Supplementary_files_format_and_content:tdf files were generated with IGVtools view

source_name: Chronic lymphocytic leukemia M12

extract_protocol:
Cells were crosslinked by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a Branson sonifier in a 1% SDS-containing lysis buffer. Samples were diluted 1:10 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples, 1:10 diluted sonicated chromatin (whole cell extract; wce), was added directly to the reverse crosslinking step without immunoprecipitation.
Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced (38 bp x 2) on illumina NextSeq.

value: Lymph node

tag: tissue/cell type

value: Chronic lymphocytic leukemia biopsy

value: H3K27ac (Active Motif)


title: MCL-M10_wce

source_name: Mantle cell lymphoma M10

value: Mantle cell lymphoma biopsy

value: input


title: MCL-M06_wce

source_name: Mantle cell lymphoma M06


title: MCL-M08_wce

source_name: Mantle cell lymphoma M08


title: CLL-M12_wce


title: MCL-M08_H3K27ac


title: MCL-M10_H3K27ac


title: CLL-M13_wce

source_name: Chronic lymphocytic leukemia M13


title: CLL-M10_wce

source_name: Chronic lymphocytic leukemia M10


title: CLL-M13_RBPJ

value: RBPJ (Cell Signaling)


title: CLL-M10_H3K27ac


title: AIREKO [kw_tuft_144]

city: Stanford

first: Aparna

middle: Rajiv

last: Rajpurkar

state: CA

address: 279 Campus Drive

department: Genetics

institute: Stanford University

description:
kw_tuft_144
Corresponds with batch 2 of methods, 50 cell positive control
Removed before processing
all_wt_counts.txt.gz
Removed before processing

data_processing:
Reads were aligned to the GRCm38 build of the Mus musculus genome using STAR (release 020201) with standard parameters. Initial cell filtering was performed by setting a minimum threshold of 40% total reads mapping to the genome.
Read counting to genes was performed with featureCounts (version 1.5.3) from the Subread package. Non-default parameters used were --primary. Gene filtering was performed by setting a minimum threshold of 10 reads in a total of  5 cells. Cell filtering was performed by requiring a minimum of 750 genes expressed with 10 reads. Futhermore, we required cells to have a minimum of 100,000 total reads mapping to known genes and less than 10% of reads mapping to mitochondrial genes. This retained 197 WT cells and 95 AireKO cells for downstream analysis.
Normalization was performed using the indeXplorer pipeline (https://git.embl.de/velten/indeXplorer) (version ad03ee7f), depending on SCDE version 2.6.0. Normalized files are provided. Mitochondrial read count effect was regressed out of the data. All downstream analysis was performed using R version 3.4.0.
All analysis code and pipelines are provided at the publically available repository https://github.com/mTEC-pipelines/tufts-pipelines.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression matriix of post-normalized read counts for all retained cells.
Supplementary_files_format_and_content: aireko_counts.txt: tab-separated file of raw counts, aireKO samples
Supplementary_files_format_and_content: all_wt_counts.txt: tab-separated file of raw counts, wild-type samples
Supplementary_files_format_and_content: POR_all_data.txt: tab-separated file of normalized expression counts
Supplementary_files_format_and_content: samples_all.txt: tab-separated metadata file with sample batch information
Supplementary_files_format_and_content: POR_all_data.rda: Rdata file of normalized expression counts

source_name: Thymus epithelium

extract_protocol:
For thymic epithelium, thymi were isolated, cleaned of fat and transferred to DMEM + 2% FBS on ice. Thymi were minced with a razor blade and tissue pieces were moved with a glass Pasteur pipette to 15 ml tubes and vortexed briefly in 10 ml of media. Fragments were allowed to settle before removing the media and replacing it with 4 ml of digestion media containing 2% FBS, 100 μg mL-1 DNase I (Roche), and 100 μg mL-1 Liberase TM (Sigma-Aldrich) in DMEM. Tubes were moved to a 37° C water bath and fragments were triturated through a glass Pasteur pipette at 0 min and 6 min to mechanically aid digestion. At 12 min, tubes were spun briefly to pellet undigested fragments and the supernatant was moved to 20 ml of 0.5% BSA (Sigma-Aldrich), 2 mM EDTA (TekNova), in PBS (MACS buffer) on ice to stop the enzymatic digestion. This was repeated twice for a total of three 12 min digestion cycles, or until there were no remaining tissue fragments. The single cell suspension was then pelleted and washed once in MACS Buffer. Density-gradient centrifugation using a three-layer Percoll gradient (GE Healthcare) with specific gravities of 1.115, 1.065, and 1.0 was used to enrich for stromal cells. Cells isolated from the Percoll- light fraction, between the 1.065 and 1.0 layers, were then washed and resuspended for staining. Cells were stained with fluorescently labeled antibodies and sorted via flow cytometry into single wells of 96 well plates containg 5 ul of lysis buffer. cDNA libraries were prepared using the standard smartSeq-2 protocol including ERCC control RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Flare25/Flare25 Aire-/-

value: 6 weeks

tag: Sex

value: Mixed

tag: mouse status

value: Naive

tag: sorting gate


title: Control 1 Beads with IL-6 stim

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: 3,6 ug of Biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Clariom S Human (Affymetrix-Thermofisher) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The raw CEL files were imported and analyzed using 'affy' package in R language. Data was normalized using RMA normalization and log2 transformed.

source_name: Control Beads with IL-6 stim

label_protocol: 25 ng of total RNA is reverse transcribed  following the Ovation PicoSL V2 (Nugen). Briefly, the resulting double strand cDNA is used for SPIA amplification. 3,6 ug of amplified cDNA are fragmented and biotin labelled using Encore Biotin Module (Nugen).

extract_protocol: RNeasy Minikit Qiagen

treatment_protocol: Naive CD4+ T cells from patients or controls were stimulated with CD2/CD3/CD28-coated beads (Miltenyi) + IL-6 (100ng/mL). HVS-transformed Saimiri T cells were used without stimulation.

tag: subject status

value: control

value: blood

value: Naive CD4+ T cells

tag: stimulated with


title: Control 4 Beads with IL-6 stim

value: CD2/CD3/CD28-coated beads (Miltenyi) + IL-6 (100ng/mL)


title: Neg ctl [kw_tuft_143]

description:
kw_tuft_143
Corresponds with batch 2 of methods, no cell negative control (all other processing steps identical to methods)
Removed before processing
Removed before processing
Removed before processing

source_name: Neg ctl

value: Neg ctl

value: not applicable


title: WT [kw_tuft_142]

description:
kw_tuft_142
Corresponds with batch 2 of methods, 50 cell positive control
Removed before processing
aireko_counts.txt.gz
Removed before processing


title: Neg ctl [kw_tuft_141]

description:
kw_tuft_141
Corresponds with batch 2 of methods, no cell negative control (all other processing steps identical to methods)
Removed before processing
Removed before processing


title: AIREKO [kw_tuft_9]

description:
kw_tuft_9
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: Control 2 Beads with IL-6 stim


title: AIREKO [kw_tuft_8]

description:
kw_tuft_8
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: CLL-M13_NICD1

value: NICD1 (Cell signaling)


title: Patient 7 Beads with IL-6 stim

source_name: Patient Beads with IL-6 stim

value: patient with an autosomal recessive form of hyper-IgE syndrome (HIES)


title: AIREKO [kw_tuft_6]

description:
kw_tuft_6
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_7]

description:
kw_tuft_7
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_5]

description:
kw_tuft_5
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: Patient 4 Beads with IL-6 stim


title: MCL-M06_H3K27ac

value: Lymph node


title: AIREKO [kw_tuft_47]

description:
kw_tuft_47
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_48]

description:
kw_tuft_48
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_41]

description:
kw_tuft_41
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_46]

description:
kw_tuft_46
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_44]

description:
kw_tuft_44
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_45]

description:
kw_tuft_45
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_38]

description:
kw_tuft_38
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_42]

description:
kw_tuft_42
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_36]

description:
kw_tuft_36
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_43]

description:
kw_tuft_43
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_40]

description:
kw_tuft_40
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_35]

description:
kw_tuft_35
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_39]

description:
kw_tuft_39
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_4]

description:
kw_tuft_4
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_34]

description:
kw_tuft_34
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_33]

description:
kw_tuft_33
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_37]

description:
kw_tuft_37
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_30]

description:
kw_tuft_30
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_32]

description:
kw_tuft_32
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_26]

description:
kw_tuft_26
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_3]

description:
kw_tuft_3
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_24]

description:
kw_tuft_24
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_25]

description:
kw_tuft_25
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_29]

description:
kw_tuft_29
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_28]

description:
kw_tuft_28
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_27]

description:
kw_tuft_27
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_31]

description:
kw_tuft_31
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_21]

description:
kw_tuft_21
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_23]

description:
kw_tuft_23
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_22]

description:
kw_tuft_22
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_192]

description:
kw_tuft_192
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_190]

description:
kw_tuft_190
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_19]

description:
kw_tuft_19
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_186]

description:
kw_tuft_186
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_185]

description:
kw_tuft_185
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_20]

description:
kw_tuft_20
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_2]

description:
kw_tuft_2
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_18]

description:
kw_tuft_18
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_189]

description:
kw_tuft_189
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_187]

description:
kw_tuft_187
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_184]

description:
kw_tuft_184
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_183]

description:
kw_tuft_183
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_181]

description:
kw_tuft_181
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_180]

description:
kw_tuft_180
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_182]

description:
kw_tuft_182
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_179]

description:
kw_tuft_179
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_178]

description:
kw_tuft_178
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_171]

description:
kw_tuft_171
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_173]

description:
kw_tuft_173
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_175]

description:
kw_tuft_175
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_177]

description:
kw_tuft_177
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_176]

description:
kw_tuft_176
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_169]

description:
kw_tuft_169
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_174]

description:
kw_tuft_174
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_191]

description:
kw_tuft_191
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_168]

description:
kw_tuft_168
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_172]

description:
kw_tuft_172
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_188]

description:
kw_tuft_188
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_170]

description:
kw_tuft_170
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_163]

description:
kw_tuft_163
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_167]

description:
kw_tuft_167
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_17]

description:
kw_tuft_17
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_162]

description:
kw_tuft_162
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_159]

description:
kw_tuft_159
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_166]

description:
kw_tuft_166
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_164]

description:
kw_tuft_164
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_165]

description:
kw_tuft_165
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_161]

description:
kw_tuft_161
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_156]

description:
kw_tuft_156
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_160]

description:
kw_tuft_160
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_16]

description:
kw_tuft_16
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_158]

description:
kw_tuft_158
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_157]

description:
kw_tuft_157
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: TNF-α_mRNA_Seq_rep1

description:
DMSO_vs_TNF-alpha_DESeq.csv
TNF-alpha_vs_TSZ_DESeq.csv
TNF-alpha_vs_TSZ_Nec-1s_DESeq.csv

value: colon

value: colon adenocarcinoma cell line HT29

tag: treatment

value: TNF-α


title: AIREKO [kw_tuft_153]

description:
kw_tuft_153
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda

tag: age


title: AIREKO [kw_tuft_152]

description:
kw_tuft_152
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_154]

description:
kw_tuft_154
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_151]

description:
kw_tuft_151
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_155]

description:
kw_tuft_155
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_15]

description:
kw_tuft_15
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_147]

description:
kw_tuft_147
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_149]

description:
kw_tuft_149
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_148]

description:
kw_tuft_148
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_14]

description:
kw_tuft_14
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_146]

description:
kw_tuft_146
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_145]

description:
kw_tuft_145
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_12]

description:
kw_tuft_12
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_11]

description:
kw_tuft_11
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_13]

description:
kw_tuft_13
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_10]

description:
kw_tuft_10
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_99]

description:
kw_tuft_99
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_1]

description:
kw_tuft_1
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda

value: 5 weeks


title: WT [kw_tuft_97]

description:
kw_tuft_97
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_96]

description:
kw_tuft_96
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_98]

description:
kw_tuft_98
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_92]

description:
kw_tuft_92
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_93]

description:
kw_tuft_93
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_94]

description:
kw_tuft_94
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_95]

description:
kw_tuft_95
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_91]

description:
kw_tuft_91
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: AIREKO [kw_tuft_150]

description:
kw_tuft_150
Corresponds with batch 2 of methods
POR_all_data.txt.gz
aireko_counts.txt.gz
POR_all_data.rda

value: Flare25/Flare25 Aire-/-


title: WT [kw_tuft_90]

description:
kw_tuft_90
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda

value: 6 weeks


title: WT [kw_tuft_89]

description:
kw_tuft_89
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda

value: Mixed


title: WT [kw_tuft_86]

description:
kw_tuft_86
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda

value: Naive


title: WT [kw_tuft_85]

description:
kw_tuft_85
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_88]

description:
kw_tuft_88
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_87]

description:
kw_tuft_87
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_83]

description:
kw_tuft_83
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_82]

description:
kw_tuft_82
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_80]

description:
kw_tuft_80
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_81]

description:
kw_tuft_81
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_79]

description:
kw_tuft_79
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_78]

description:
kw_tuft_78
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_75]

description:
kw_tuft_75
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_76]

description:
kw_tuft_76
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_74]

description:
kw_tuft_74
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: CLL-M13_H3K27ac

description: Raw data available via dbGaP Study Accession phs000939

value: Chronic lymphocytic leukemia biopsy

value: H3K27ac (Active Motif)


title: WT [kw_tuft_71]

description:
kw_tuft_71
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_70]

description:
kw_tuft_70
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_69]

description:
kw_tuft_69
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: AW3-K8P63-LC1.1

value: mammary gland

tag: gender

value: female


title: WT [kw_tuft_64]

description:
kw_tuft_64
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_67]

description:
kw_tuft_67
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_65]

description:
kw_tuft_65
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_68]

description:
kw_tuft_68
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_66]

description:
kw_tuft_66
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_62]

description:
kw_tuft_62
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_61]

description:
kw_tuft_61
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_63]

description:
kw_tuft_63
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_84]

description:
kw_tuft_84
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_57]

description:
kw_tuft_57
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_59]

description:
kw_tuft_59
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_60]

description:
kw_tuft_60
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_77]

description:
kw_tuft_77
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_56]

description:
kw_tuft_56
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_58]

description:
kw_tuft_58
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_54]

description:
kw_tuft_54
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_72]

description:
kw_tuft_72
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_55]

description:
kw_tuft_55
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_52]

description:
kw_tuft_52
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_53]

description:
kw_tuft_53
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_140]

description:
kw_tuft_140
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_50]

description:
kw_tuft_50
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_73]

description:
kw_tuft_73
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_51]

description:
kw_tuft_51
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_137]

description:
kw_tuft_137
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_49]

description:
kw_tuft_49
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_139]

description:
kw_tuft_139
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_134]

description:
kw_tuft_134
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_135]

description:
kw_tuft_135
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_132]

description:
kw_tuft_132
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_133]

description:
kw_tuft_133
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_126]

description:
kw_tuft_126
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_128]

description:
kw_tuft_128
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_127]

description:
kw_tuft_127
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_124]

description:
kw_tuft_124
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_121]

description:
kw_tuft_121
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_122]

description:
kw_tuft_122
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_117]

description:
kw_tuft_117
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_138]

description:
kw_tuft_138
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_120]

description:
kw_tuft_120
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_123]

description:
kw_tuft_123
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_114]

description:
kw_tuft_114
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_110]

description:
kw_tuft_110
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_119]

description:
kw_tuft_119
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_111]

description:
kw_tuft_111
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_116]

description:
kw_tuft_116
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_118]

description:
kw_tuft_118
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_115]

description:
kw_tuft_115
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_131]

description:
kw_tuft_131
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_113]

description:
kw_tuft_113
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_129]

description:
kw_tuft_129
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_130]

description:
kw_tuft_130
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_136]

description:
kw_tuft_136
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_112]

description:
kw_tuft_112
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_108]

description:
kw_tuft_108
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_125]

description:
kw_tuft_125
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_107]

description:
kw_tuft_107
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_105]

description:
kw_tuft_105
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_104]

description:
kw_tuft_104
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_103]

description:
kw_tuft_103
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_102]

description:
kw_tuft_102
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_101]

description:
kw_tuft_101
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_109]

description:
kw_tuft_109
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_100]

description:
kw_tuft_100
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.8.featurecounts]

description:
June5_KW.8.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.4.featurecounts]

description:
June5_KW.4.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.6.featurecounts]

description:
June5_KW.6.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.31.featurecounts]

description:
June5_KW.31.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.7.featurecounts]

description:
June5_KW.7.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.27.featurecounts]

description:
June5_KW.27.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.30.featurecounts]

description:
June5_KW.30.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.28.featurecounts]

description:
June5_KW.28.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.23.featurecounts]

description:
June5_KW.23.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.26.featurecounts]

description:
June5_KW.26.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.24.featurecounts]

description:
June5_KW.24.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.22.featurecounts]

description:
June5_KW.22.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.21.featurecounts]

description:
June5_KW.21.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.2.featurecounts]

description:
June5_KW.2.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.20.featurecounts]

description:
June5_KW.20.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.1.featurecounts]

description:
June5_KW.1.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.19.featurecounts]

description:
June5_KW.19.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.18.featurecounts]

description:
June5_KW.18.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [kw_tuft_106]

description:
kw_tuft_106
Corresponds with batch 2 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.9.featurecounts]

description:
June5_KW.9.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.16.featurecounts]

description:
June5_KW.16.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.14.featurecounts]

description:
June5_KW.14.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.5.featurecounts]

description:
June5_KW.5.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.15.featurecounts]

description:
June5_KW.15.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.3.featurecounts]

description:
June5_KW.3.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.29.featurecounts]

description:
June5_KW.29.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.11.featurecounts]

description:
June5_KW.11.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.9.featurecounts]

description:
June29_KW.9.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.25.featurecounts]

description:
June5_KW.25.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.10.featurecounts]

description:
June5_KW.10.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.95.featurecounts]

description:
June29_KW.95.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.12.featurecounts]

description:
June5_KW.12.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.13.featurecounts]

description:
June5_KW.13.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.91.featurecounts]

description:
June29_KW.91.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.92.featurecounts]

description:
June29_KW.92.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.94.featurecounts]

description:
June29_KW.94.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June5_KW.17.featurecounts]

description:
June5_KW.17.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.8.featurecounts]

description:
June29_KW.8.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.89.featurecounts]

description:
June29_KW.89.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.88.featurecounts]

description:
June29_KW.88.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.87.featurecounts]

description:
June29_KW.87.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.86.featurecounts]

description:
June29_KW.86.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.90.featurecounts]

description:
June29_KW.90.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.84.featurecounts]

description:
June29_KW.84.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.83.featurecounts]

description:
June29_KW.83.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.82.featurecounts]

description:
June29_KW.82.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.93.featurecounts]

description:
June29_KW.93.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.85.featurecounts]

description:
June29_KW.85.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.80.featurecounts]

description:
June29_KW.80.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.81.featurecounts]

description:
June29_KW.81.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.79.featurecounts]

description:
June29_KW.79.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.78.featurecounts]

description:
June29_KW.78.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.77.featurecounts]

description:
June29_KW.77.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: neg ctl [June29_KW.96.featurecounts]

description:
June29_KW.96.featurecounts
Corresponds with batch 1 of methods, 0 cell control (all other processing steps identical to methods)
Removed before processing
all_wt_counts.txt.gz
Removed before processing

source_name: neg ctl

value: neg ctl


title: WT [June29_KW.7.featurecounts]

description:
June29_KW.7.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.76.featurecounts]

description:
June29_KW.76.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.75.featurecounts]

description:
June29_KW.75.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.74.featurecounts]

description:
June29_KW.74.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.73.featurecounts]

description:
June29_KW.73.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.72.featurecounts]

description:
June29_KW.72.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.71.featurecounts]

description:
June29_KW.71.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.70.featurecounts]

description:
June29_KW.70.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.6.featurecounts]

description:
June29_KW.6.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.68.featurecounts]

description:
June29_KW.68.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.67.featurecounts]

description:
June29_KW.67.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda


title: WT [June29_KW.69.featurecounts]

description:
June29_KW.69.featurecounts
Corresponds with batch 1 of methods
POR_all_data.txt.gz
all_wt_counts.txt.gz
POR_all_data.rda