title: A1_N712_S508

description:
polyA RNA
single cell


title: A1_N712_S505

status: Public on Mar 28 2016

type: SRA

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

country: USA

institute: UCSF

description:
polyA RNA
single cell

library_source: transcriptomic

data_processing:
Bulk RNA-seq: Strand-specific reads were aligned to the human reference genome, Ensembl GRCh37/hg19 release 75, using TopHat v2.0.10 with the flags (--library-type fr-firststrand –microexon-search). De novo transcriptome assembly was performed separately on rRNA depletion total RNA-seq alignments, and on polyA selection RNA-seq alignments, using Cufflinks v2.2.1 with the flags (-M ensembl_75_mtRNA_rRNA.gtf -b genome.fa -u --library-type fr-firststrand --max-multiread-fraction 0.25 --3-overhang-tolerance 2000). Transcriptome assemblies at all developmental stages and replicates were merged, separately for rRNA depletion total RNA-seq and polyA selection RNA-seq, with the Ensembl 75/GENCODE 19 reference transcriptome, using Cuffmerge. To identify transcripts novel compared to Ensembl, we utilized Cuffcompare class codes and extracted those assembled transcripts classified as: i – novel intronic, u – novel intergenic, x – novel antisense. All novel transcripts under 200 nt in length were removed. Of the remaining transcripts, we determined minimal read coverage thresholds based on whether Cufflinks classified previously annotated transcripts as having “full_read_support.” By analyzing the true positive rate vs. false positive rate of classifying known genes as obtaining “full_read_support” at various coverage thresholds, we determined the minimum coverage to be 1.4 for polyA and 1.67 for total RNA-seq (at FDR = 0.05). Starting with just the polyA RNA-seq data, transcripts with read coverage above 1.4 in both biological replicates of at least one developmental stage were included in the reference and considered to be expressed in the neocortex. Due to limited availability of early fetal tissue, the GW14.5 sample was treated as the biological duplicate of the GW13 sample. Novel transcripts that were predicted to have protein coding capability by one or more of the following methods were classified as transcripts of uncertain coding potential (TUCP): CPAT, threshold = 0.364; CPC, threshold = 0; Pfam. For comparing to the Pfam database, the longest potential open reading frame (ORF) of each novel transcript was obtained, and any putative ORF that had a significant match for a protein domain annotated in Pfam A or Pfam B resulted in the parent transcript being classified as a TUCP. All remaining novel lncRNAs and TUCPs were then named according to recently proposed nomenclature standards, for instance LINC-[nearest mRNA] for intergenic lncRNAs and [nearest mRNA]-AS for antisense lncRNAs, and were then merged to the Ensembl 75 reference transcriptome, resulting in the polyA Full reference transcriptome. The polyA Stringent reference transcriptome was produced by removing all novel single-exon lncRNAs and TUCPs. Known lncRNAs from Ensembl were obtained by identifying transcripts with one of the following biotype classifications: “3prime_overlapping_ncrna,” “antisense,” “lincRNA,” “processed_transcript,” “sense_intronic,” and “sense_overlapping.” The same pipeline, with the coverage threshold of 1.67, was performed for reads derived from the total RNA-seq. Gene-level fragment counts for each polyA and total RNA sample were quantified using featureCounts v1.4.6, using the flags: -p -s 2 -B -C -t exon -g gene_id. Count tables were normalized to TPM (Transcripts per Million) for internal comparisons and visualizations of bulk RNA-seq. To identify differentially expressed genes, we used DESeq2 on gene-level fragment counts derived from the polyA samples and polyA Full reference transcriptome. Pairwise negative binomial significance tests were performed between developmental stages using biological duplicates, and the union of genes that were significant at FDR < 0.01 were classified as differentially expressed.
Single Cell RNA-seq: Paired end 100 reads from single cell cDNA libraries were quality trimmed using Trim Galore with the flags: -q 20 --nextera --length 20. Trimmed reads were aligned to the human reference genome, Ensembl GRCh37/hg19 release 75, augmented with the 92 ERCC Spike-In Control sequences, using TopHat v2.0.10 with the flags: --transcriptome-index=polya_stringent_reference.gtf --prefilter-multihits. The polyA Stringent reference transcriptome, derived from whole tissue RNA-seq as described above, was used as a transcriptome guide. Gene-level fragment counts were quantified using featureCounts v1.4.6 with the flags: -p -B -C. Counts were normalized by transcriptome size factors according to DESeq. 50 additional single cell libraries were also included, which were deposited in SRP041736.

molecule: polyA RNA

organism: Homo sapiens

source_name: Cerebral Cortex

extract_protocol:
Single-cell capture and cell lysis using Fluidigm C1.
RT and whole transcriptome amplifcation on the Fluidigm C1 IFC; library indexed  by illumina Nextera DNA Sample Prep Kit

tag: tissue

value: Cerebral Cortex

tag: developmental stage


title: A1_N712_S503

description:
polyA RNA
single cell


title: brm-1 ref6-1 rep1

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline
The raw reads were aligned to the Arabidopsis genome (TAIR10) using tophat2. The reads mapped to more than one positions were removed.
The raw counts of gene were generated by perl script.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel files of raw counts

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
RNAs from 14-day-seedlings of wild-type, brm-1, ref6-1, and brm-1 ref6-1 were isolated by the Plant/Fungi Total RNA Purification Kit (Norgen) and then treated by RNase-free DNase (Qiagen). To minimize variations, RNAs from three biological replicates were pooled
RNA libraries were built using the Illumina TruSeq RNA library preparation protocol. The libraries were sequenced on an Illumina HiSeq 2500 using a paired end recipe (2x100 bp) with TruSeq v3 chemistry.

value: Seedling

tag: genotype/variation

value: brm-1 ref6-1


title: ref6-1 rep3


title: A1_N712_S504

description:
polyA RNA
single cell


title: brm-1 ref6-1 rep2


title: A1_N712_S502

description:
polyA RNA
single cell


title: brm-1 ref6-1 rep3


title: ref6-1 rep2


title: brm-1 rep3


title: ref6-1 rep1


title: brm-1 rep1


title: A1_N711_S508

description:
polyA RNA
single cell


title: A1_N711_S505

description:
polyA RNA
single cell


title: A1_N712_S501

description:
polyA RNA
single cell


title: A2_N701_S501

description:
polyA RNA
single cell


title: brm-1 rep2


title: A1_N711_S507

description:
polyA RNA
single cell


title: A1_N711_S504

description:
polyA RNA
single cell


title: WT rep1

value: WT


title: A1_N711_S503

description:
polyA RNA
single cell


title: S1_-P1_#04

city: Taipei

first: Tzyy-Jen

last: Chiou

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description: Pi starvation 1-day

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by adaptor sequence, and low-quality sequences were eliminated. Sequences were mapped to Arabidopsis thaliana reference (TAIR10) whole genome using CLC Genomics Workbench 7.0.4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. The number of reads mapping to the exons of a transcript were counted and normalized by the kilobase size of a transcript and by the megabase size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: xlsx file includes description, RPKM values and normalized values for each Sample

source_name: plant seedlings

growth_protocol: Seeds were surface sterilized and germinated on agar plates with one-half modified Hoagland nutrient solution containing 250 μM KH2PO4, 1% sucrose, and 1% bactoagar.

extract_protocol:
Total RNA was isolated using RNAzol (Molecular Research Center).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Pi-sufficient (+Pi) and Pi-deficient (−Pi) media were supplemented with 250 µM for 10-day and 10 µM KH2PO4 for additional 1-day or 3-days, respectively.

value: shoot

tag: treatment

value: Pi starvation

tag: time

value: 1 day

tag: plant


title: A1_N710_S505

description:
polyA RNA
single cell


title: A1_N710_S508

description:
polyA RNA
single cell


title: A1_N710_S504

description:
polyA RNA
single cell


title: MKN45.H3K27ac

city: Daejeon

first: sujin

last: Baek

address: Gwahank-ro 125

department: MGRC

country: South Korea

institute: KRIBB

library_source: genomic

data_processing:
mapped to hg19 using bwa
Peak abundance were calculated  using MACS (v.1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: bed file

molecule: genomic DNA

extract_protocol:
A protocol generated at Myer`s laboratory (http://hudsonalpha.org/myers-lab/protocols)
libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: chip antibody


title: A1_N710_S501

description:
polyA RNA
single cell


title: A1_N709_S508

description:
polyA RNA
single cell


title: MKN45.input

value: input


title: A1_N709_S507

description:
polyA RNA
single cell


title: Wild-type_r1

city: No.12 Zhongguancun South Street, Haidian

first: Jun

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

description: Biological replicate 1

data_processing:
FastaQ files of each sample was aligned against Arabidopsis Genome TAIR 10 using TopHat.
Mapped sequences were assembled into transcripts using Cufflinks.
Assembled transcripts of each sample were summarized and merged into transcription units using Cuffcompare.
Expression level of each gene or transcription unit are presented by Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: Arabidopsis Genome Annotation TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample produced by Cufflinks,Cuffcompare and Cuffdiff.

source_name: embryos at the mature-green stage

growth_protocol: Arabidopsis plant  materials were grown under long day conditions at 22℃. Embryos were isolociated at the mature-green stages.

extract_protocol: All samples were harvested and frozen immediately in liquid nitrogen until use. Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen). RNA sequence libraries were prepared with TruSeq RNA sample Prep V2 kit according to the instructions (Illumina). Sequences were determined by HiSeq 2000 sequencing system in the genomic center in Rockefeller University.

tag: genotype


title: SNU638.input


title: SNU719.input


title: SNU719.H3K27ac


title: A1_N709_S506

description:
polyA RNA
single cell


title: WT rep3


title: WT rep2


title: A1_N709_S502

description:
polyA RNA
single cell


title: clf-28_r2

description: Biological replicate 2


title: SNU638.H3K27ac


title: SNU016.input


title: clf-28_r1

description: Biological replicate 1


title: A1_N709_S501

description:
polyA RNA
single cell


title: MKN1.H3K27ac


title: A1_N708_S502

description:
polyA RNA
single cell


title: A1_N710_S502

description:
polyA RNA
single cell


title: KATOIII.input

description: KATOIII-input

source_name: KATOIII-input

value: KATOIII


title: A1_N707_S507

description:
polyA RNA
single cell


title: SNU016.H3K27ac


title: A1_N707_S506

description:
polyA RNA
single cell


title: A1_N708_S508

description:
polyA RNA
single cell


title: A1_N707_S503

description:
polyA RNA
single cell


title: AGS.H2K27ac

value: AGS


title: KATOIII.H3K27ac


title: AGS.input

description: AGS-input

source_name: AGS-input


title: A1_N706_S507

description:
polyA RNA
single cell


title: A1_N709_S503

description:
polyA RNA
single cell


title: A1_N707_S505

description:
polyA RNA
single cell


title: A1_N706_S506

description:
polyA RNA
single cell


title: A1_N706_S505

description:
polyA RNA
single cell


title: A1_N706_S504

description:
polyA RNA
single cell


title: MKN1.input


title: A1_N706_S503

description:
polyA RNA
single cell


title: A1_N706_S502

description:
polyA RNA
single cell


title: A1_N705_S507

description:
polyA RNA
single cell


title: csc1_dc2

description: differentiated cell  (csc1-clone2)

data_processing:
Base calling performed using CASAVA version 1.7
mapped to hg19 whole genome using bwa v.0.5.9
Methylation levels were called using pysam (-2 kb~500 bp from TSS).  Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated  using a standard protocol. The rpkm values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: differentiated cell

extract_protocol:
Standard DNA extraction protocol using Qiagen prep kit
Libraries were prepared according to Illumina's instructions.

tag: patient

tag: cell type

value: differentiated cell


title: csc1_dc2_RNA-Seq

description: differentiated cell (csc1-clone2)

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using Tophat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated  using a standard protocol. The rpkm values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

extract_protocol:
Standard RNA extraction protocol using Qiagen RNA mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: csc1_dc3_RNA-Seq

description: differentiated cell (csc1-clone3)


title: csc1_sc2_RNA-Seq

description: gastric cancer stem cell (csc1-clone2)

source_name: gastric cancer stem cell

value: gastric cancer stem cell


title: csc1_sc3

description: gastric cancer stem cell  (csc1-clone3)


title: A1_N705_S506

description:
polyA RNA
single cell


title: csc1_sc2

description: gastric cancer stem cell (csc1-clone2)


title: csc1_sc3_RNA-Seq

description: gastric cancer stem cell (csc1-clone3)


title: csc1_dc3

description: differentiated cell (csc1-clone3)


title: A1_N705_S505

description:
polyA RNA
single cell


title: A1_N705_S503

description:
polyA RNA
single cell


title: A1_N705_S502

description:
polyA RNA
single cell


title: mRNA_STAT5AAB_CD4_iTreg_IL2_96h_rpt2_C248_OS1082.fq

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description:
sample54_RNA39
exp ID: 131126_0083_s18
lab data ID: 1082
processed data file: Villarino RPKM table.xlsx
sample54_RNA39

data_processing:
ChIP-seq alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were aligned to mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Only uniquely mapped, non-redundant reads were used for peak calling.
ChIP-seq peaks: Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0 E-05.
RNA-seq alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to mouse genome mm9 using TopHat 2.0.8.
RNA-seq RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
Genome_build: mm9
Supplementary_files_format_and_content: bw for ChIP-seq peak files, excel for a RPKM file

organism: Mus musculus

growth_protocol:
growth protocol 1: ChIPseq IL-2 cultures: CD4+ T cells were enriched from pooled spleens and lymph nodes of 8-12 week-old mice by magnetic separation (negative selection beads by Miltenyi Biotec). Naïve CD4+ CD44-low CD25- cells were then  purified by cell sorting (FACSAria III; Becton Dickinson) and activated with plate-bound anti-mouse CD3 (10 μg/ml; Clone 17A2) and soluble anti-mouse CD28 (1 μg ml; Clone 37.51) in the presence of blocking antibodies for mouse IL-2, mouse IL-4 and mouse IFN-g (10 μg/ml each; Clones S4B6, BVD6-24G2 and XMG1.2)(All antibodies from BioXcell). These were cultured with recombinant human IL-2 (10 U/ml; NIH/NCI BRB Preclinical Repository) for 48 hours, then pulsed with 100 U/ml human IL-2 for 1 hour prior to fixing with 1% formaldehyde for ChIPseq library preparation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 1 million cells/ml in flat bottomed, 24 well tissue culture-treated plates (CoStar).
growth protocol 2: Ex vivo Naive CD4+ T cells: CD4+ T cells were enriched from pooled spleens and lymph nodes of 8-12 week-old mice by magnetic separation (negative selection beads by Miltenyi Biotec). CD4+ CD44-low CD25- cells were then  purified by cell sorting (FACSAria III; Becton Dickinson) and immediately resuspended in Trizol ragent (Invitrogen) for subsequent RNA isolation.
growth protocol 3: Ex vivo nTreg T cells: CD4+ T cells were enriched from pooled spleens and lymph nodes of 8-12 week-old mice by magnetic separation (negative selection beads by Miltenyi Biotec). CD4+ CD25-high Neuropilin+ nTreg  cells were then purified by cell sorting (FACSAria III; Becton Dickinson) and immediately resuspended in Trizol ragent (Invitrogen) for subsequent RNA isolation.
growth protocol 4: In vitro IL-7 cultures: CD4+ T cells were enriched from pooled spleens and lymph nodes of 8-12 week-old mice by magnetic separation (negative selection beads by Miltenyi Biotec). Niave CD4+ CD44-low CD25- cells were then  purified by cell sorting (FACSAria III; Becton Dickinson) and cultured overnight (12 hours) in the presence of recombinant mouse IL-7 (20 ng/ml; eBioscience). These were then collected and resuspended in Trizol ragent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 0.5 million cells/ml in flat bottomed, 96 well tissue culture-treated plates (CoStar).
growth protocol 5: In vitro IL-2 cultures: CD4+ T cells were enriched from pooled spleens and lymph nodes of 8-12 week-old mice by magnetic separation (negative selection beads by Miltenyi Biotec). Naïve CD4+ CD44-low CD25- cells were then  purified by cell sorting (FACSAria III; Becton Dickinson) and activated with plate-bound anti-mouse CD3 (10 μg/ml; Clone 17A2) and soluble anti-mouse CD28 (1 μg ml; Clone 37.51) in the presence of blocking antibodies for mouse IL-2, mouse IL-4 and mouse IFN-g (10 μg/ml each; Clones S4B6, BVD6-24G2 and XMG1.2)(All antibodies from BioXcell). These were cultured with recombinant human IL-2 (100 U/ml; NIH/NCI BRB Preclinical Repository) for 72 hours, then collected and resuspended in Trizol ragent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 0.5 million cells/ml in flat bottomed, 96 well tissue culture-treated plates (CoStar).
growth protocol 6: Retroviral transduction with IL-2: CD4+ T cells were enriched from pooled spleens and lymph nodes of 8-12 week-old mice by magnetic separation (negative selection beads by Miltenyi Biotec). Naïve CD4+ CD44-low CD25- cells were then purified by cell sorting (FACSAria III; Becton Dickinson) and activated with plate-bound anti-mouse CD3 (10 μg/ml; Clone 17A2) and soluble anti-mouse CD28 (1 μg ml; Clone 37.51) in the presence of blocking antibodies for mouse IL-2, mouse IL-4 and mouse IFN-g (10 μg/ml each; Clones S4B6, BVD6-24G2 and XMG1.2)(All antibodies from BioXcell). 48 hours later, these were retrovirally transduced (1 hour 'spinfections' at 2200 RPM, 18° C), then cultured for an additional 48 hours in the presence of recombinant human IL-2 (10 U/ml; NIH/NCI BRB Preclinical Repository), collected and resuspended in Trizol ragent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 1.5-2.0 million cells/ml in flat bottomed, 24 well tissue culture-treated plates (CoStar).
growth protocol 7: In vitro iTreg cultures with IL-2: CD4+ T cells were enriched from pooled spleens and lymph nodes of 8-12 week-old mice by magnetic separation (negative selection beads by Miltenyi Biotec). Naïve CD4+ CD44-low CD25- cells were then  purified by cell sorting (FACSAria III; Becton Dickinson) and activated with plate-bound anti-mouse CD3 (10 μg/ml; Clone 17A2) and soluble anti-mouse CD28 (1 μg ml; Clone 37.51) in the presence of blocking antibodies for mouse IL-2, mouse IL-4 and mouse IFN-g (10 μg/ml each; Clones S4B6, BVD6-24G2 and XMG1.2)(All antibodies from BioXcell). These were cultured with recombinant human IL-2 (100 U/ml; NIH/NCI BRB Preclinical Repository) and recombinant human TGF-b (5 ng/ml; R&D Systems) for 96 hours, then collected and resuspended in Trizol ragent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 0.5 million cells/ml in flat bottomed, 96 well tissue culture-treated plates (CoStar).

extract_protocol:
ChIP-seq: Cells were chemically cross-linked by 1% formaldehyde. Lysates were made by sonication (10,000,000 cells/sample) and protein-DNA complexes isolated using the indicated antibodies.
ChIP-seq: Single-end libraries were prepared for STAT5-bound fragments, along with un-precipitated input controls, using the NEBNext ChIP-Seq Library Prep kit for Illumina (New England Biolabs). Briefly, DNA fragments were end-repaired to generate phosphorylated blunt ends. These were then treated with Taq polymerase and dATP to generate 3-prime 'A' base overhangs for ligation to adapters containing complementary 'T' base overhangs. After ligation, DNA was PCR amplified for 15 cycles with indexed primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-seq: Indexed libraries were multiplexed and sequenced for 50 single read cycles on Illumina HiSeq 2000 or 2500 instruments according to the manufacturer's instructions.
RNA-seq: RNA was extracted from 50-500K cells by phenol-chloroform method with GlycoBlue as co-precipitant (7 μg per sample; Life Technologies).
RNA-seq: Single-end libraries were prepared from 0.1-0.5 μg of total RNA using the TruSeq RNA Sample Preparation Kit V2 (Illumina)
RNA-seq: Indexed libraries were multiplexed and sequenced for 50 single read cycles on Illumina HiSeq 2000 or 2500 instruments according to the manufacturer's instructions.

tag: strain

value: mixed 129/C5BL/6

value: STAT5A-/- STAT5B+/-

value: mouse primary CD4+ T cells

tag: culture condition

value: 96 hour in vitro iTreg culture with IL-2 (growth protocol 7)


title: mRNA_STAT5BBA_CD4_iTreg_IL2_96h_rpt2_C249_OS1083.fq

description:
sample55_RNA40
exp ID: 131126_0083_s19
lab data ID: 1083
processed data file: Villarino RPKM table.xlsx
sample55_RNA40

value: STAT5A+/- STAT5B-/-


title: A1_N704_S506

description:
polyA RNA
single cell

value: Cerebral Cortex


title: mRNA_WT_CD4_iTreg_IL2_96h_rpt2_C247_OS1081.fq

description:
sample53_RNA38
exp ID: 131126_0083_s17
lab data ID: 1081
processed data file: Villarino RPKM table.xlsx
sample53_RNA38


title: A1_N704_S504

description:
polyA RNA
single cell


title: mRNA_STAT5BBA_CD4_IL7_12h_rpt2_C139_OS748.fq

description:
sample42_RNA27
exp ID: 130517_0055_s22
lab data ID: 748
processed data file: Villarino RPKM table.xlsx
sample42_RNA27

value: 12 hour in vitro culture with IL-7 (growth protocol 4)


title: mRNA_WT_CD4_IL7_12h_rpt2_C137_OS746.fq

description:
sample40_RNA25
exp ID: 130517_0055_s20
lab data ID: 746
processed data file: Villarino RPKM table.xlsx
sample40_RNA25


title: mRNA_STAT5AAB_CD4_IL7_12h_rpt2_C138_OS747.fq

description:
sample41_RNA26
exp ID: 130517_0055_s21
lab data ID: 747
processed data file: Villarino RPKM table.xlsx
sample41_RNA26


title: mRNA_STAT5BBA_CD4_Naive_ExVivo_rpt3_C133_OS745.fq

description:
sample39_RNA24
exp ID: 130517_0055_s19
lab data ID: 745
processed data file: Villarino RPKM table.xlsx
sample39_RNA24

value: ex vivo naive CD4+ T cells (growth protocol 2)


title: A1_N704_S503

description:
polyA RNA
single cell


title: Med-2

city: Corvallis

first: Luis

last: Sayavedra-Soto

state: OR

address: Cordley Hall 2082

department: Botany and Plant Pathology

institute: Oregon State University

data_processing:
The mRNA-Seq reads were analyzed using the CLC Main Workbench (CLC bio, Aarhus, DK). The module for empirical analysis of differential gene expression (DGE) was used as described (Robinson and Smyth 2008) with default values of the software and normalized to reads per kilobase per million (RPKM). Significant DGE for two-group comparisons was determined for all three possible but non-reciprocal pair-wise comparisons (P-value threshold ≤0.05). Fold change in mRNA abundance indicates the difference in mRNA transcripts between the control (replete IC) and the treatment (IC-limited). If the relative abundance of a transcript in the control was smaller than in the treatment, the number was given a positive value; conversely, if the transcript count was larger in the control than in the treatment, the number was given a negative value.
Genome_build: N.europaea: gi|30407130|emb|AL954747.1| Nitrosomonas europaea ATCC 19718, complete genome
Supplementary_files_format_and_content: Excell Microsoft's software; data; matrix processed data, CLC data output

organism: Nitrosomonas europaea

source_name: Bacterial cells_1.0 mM carbonate Med

growth_protocol: Chemostat culture experiments were carried out at 30 °C in 2 liter bioreactors (Applikon Biotechnology ADI1025-ADI1010) with stirring at 600 rpm, constant aeration (0.2-µm-filtered atmospheric air), and pH maintained at 7.5. Bioreactors were treated with Sigmacote (Sigma-Aldrich, St. Louis, MO) to inhibit biofilm formation. Medium consisted of 30 mM (NH4)2SO4 as described (Perez et al. 2015), with the exception that K2HPO4 and NaH2PO4 (25 and 2.5 mM, respectively) were added to buffer the medium to pH 8. Chemostat cultures were inoculated with 2% volume exponential phase batch cultures and grown in batch mode until ≥ 20 mM ammonium (NH4+) was consumed. At this point, medium feed commenced and continuous culturing began. Continuous cultures were allowed at least three population doublings to reach steady state, which was defined as one population doubling with ≤ 5% change in cell density. Approximately 200 µl aliquots of chemostat cultures were plated periodically on Luria-Bertani agar plates to confirm axenic culture conditions.

extract_protocol: Cells from three biological replicates for each treatment were lysed by sonication and the total RNA was extracted with an RNeasy Mini Kit (Qiagen, Germantown, MD). MICROBExpress RNA Isolation Kit was used to deplete rRNA from the total RNA (Ambion/Life Technologies, NY). Illumina-targeted RNA Expression Kit and at least 200 ng of depleted RNA were used to prepare mRNA-Seq libraries, and the libraries were sequenced (100mer paired-end) on a HISEq 2000 Sequencer (Illumina, San Diego, CA) at the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University.

treatment_protocol: Continuous cultures were maintained at steady state under three different inorganic carbon (IC) conditions: IC replete (2 mM Na2CO3, 100 mL min-1 0.2-µm-filtered atmospheric air), 1.0 mM Na2CO3, and 0.2 mM Na2CO3 (both IC-limiting conditions with 50 mL min-1 0.2-µm-filtered atmospheric air). The rationale for providing IC via medium addition and aeration was that aeration with CO2-free air resulted in removal of all IC from the system. This effect would be similar to sparging medium with inert gas to remove oxygen. The pH under replete conditions was controlled with addition of 10% (w/v) Na2CO3 as necessary. In IC-limiting treatments, pH was maintained with addition of 0.4 M NaOH as necessary. The same growth medium was used in the three IC conditions, with the exception of Na2CO3 levels among treatments.

tag: carbonate conc.

value: 1.0 mM carbonate Med


title: mRNA_STAT5AAB_CD4_Naive_ExVivo_rpt3_C132_OS744.fq

description:
sample38_RNA23
exp ID: 130517_0055_s18
lab data ID: 744
processed data file: Villarino RPKM table.xlsx
sample38_RNA23


title: Med-1


title: mRNA_WT_CD4_Naive_ExVivo_rpt3_C131_OS743.fq

description:
sample37_RNA22
exp ID: 130517_0055_s17
lab data ID: 743
processed data file: Villarino RPKM table.xlsx
sample37_RNA22

value: WT


title: Hi-3

source_name: Bacterial cells_replete carbonate High

value: replete carbonate High


title: Low-3

source_name: Bacterial cells_0.2 mM carbonate Low

value: 0.2 mM carbonate Low


title: Low-1


title: A1_N704_S507

description:
polyA RNA
single cell


title: A1_N704_S502

description:
polyA RNA
single cell


title: Low-2


title: Hi-1


title: Hi-2


title: A1_N703_S505

description:
polyA RNA
single cell


title: Med-3

extract_protocol: Cells from three biological replicates for each treatment were lysed by sonication and the total RNA was extracted with an RNeasy Mini Kit (Qiagen, Germantown, MD). MICROBExpress RNA Isolation Kit was used to deplete rRNA from the total RNA (Ambion/Life Technologies, NY). Illumina-targeted RNA Expression Kit and at least 200 ng of depleted RNA were used to prepare mRNA-Seq libraries, and the libraries were sequenced (100mer paired-end) on a HISEq 2000 Sequencer (Illumina, San Diego, CA) at the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University.


title: A1_N704_S505

description:
polyA RNA
single cell


title: mRNA_STAT5BBA_CD4_IL7_12h_rpt3_C174_OS742.fq

description:
sample36_RNA21
exp ID: 130517_0055_s16
lab data ID: 742
processed data file: Villarino RPKM table.xlsx
sample36_RNA21


title: mRNA_STAT5AAB_CD4_IL7_12h_rpt3_C173_OS741.fq

description:
sample35_RNA20
exp ID: 130517_0055_s15
lab data ID: 741
processed data file: Villarino RPKM table.xlsx
sample35_RNA20


title: A1_N704_S501

description:
polyA RNA
single cell


title: A1_N703_S504

description:
polyA RNA
single cell


title: A1_N703_S502

description:
polyA RNA
single cell


title: mRNA_STAT5BBA_CD4_Th0_IL2_72h_rpt2_C180_OS591.fq

description:
sample33_RNA18
exp ID: 130329_0049_s18
lab data ID: 591
processed data file: Villarino RPKM table.xlsx
sample33_RNA18

value: 72 hour in vitro culture with IL-2 (growth protocol 5)


title: mRNA_STAT5BBA_CD4_Th0_IL2_72h_rpt1_C151_OS576.fq

description:
sample30_RNA15
exp ID: 130329_0049_s3
lab data ID: 576
processed data file: Villarino RPKM table.xlsx
sample30_RNA15


title: mRNA_WT_CD4_Th0_IL2_72h_rpt2_C178_OS589.fq

description:
sample31_RNA16
exp ID: 130329_0049_s16
lab data ID: 589
processed data file: Villarino RPKM table.xlsx
sample31_RNA16


title: A1_N703_S503

description:
polyA RNA
single cell


title: A1_N702_S507

description:
polyA RNA
single cell


title: mRNA_STAT5AAB_CD4_Th0_IL2_72h_rpt2_C179_OS590.fq

description:
sample32_RNA17
exp ID: 130329_0049_s17
lab data ID: 590
processed data file: Villarino RPKM table.xlsx
sample32_RNA17


title: mRNA_STAT5AAB_CD4_Th0_IL2_72h_rpt1_C150_OS575.fq

description:
sample29_RNA14
exp ID: 130329_0049_s2
lab data ID: 575
processed data file: Villarino RPKM table.xlsx
sample29_RNA14


title: A1_N702_S506

description:
polyA RNA
single cell


title: A1_N702_S505

description:
polyA RNA
single cell


title: csc3-sc_RNA-Seq

description: gastric cancer stem cell-csc3 patient


title: mRNA_WT_Naive_CD4_IL7_12h_rpt3_C172_OS740.fq

description:
sample34_RNA19
exp ID: 130517_0055_s14
lab data ID: 740
processed data file: Villarino RPKM table.xlsx
sample34_RNA19


title: normal2_RNA-Seq

description: gastric normal tissue2

source_name: gastric normal tissue

value: gastric normal tissue


title: csc3-dc_RNA-Seq

description: cancer associated fibroblast -csc3 patient


title: csc2-sc_RNA-Seq

description: gastric cancer stem cell-csc2 patient


title: csc3-mc_RNA-Seq

source_name: mixture of several clones

value: mixture of several clones


title: Input_WT_CD4_Th0_IL2_48h_rpt1_OS1055

description:
sample5_ChIP5
exp ID: 131126_0082_s24
lab data ID: 1055
sample5_ChIP5

value: 48 hour in vitro culture with IL-2 (growth protocol 1)

value: input


title: A1_N703_S506

description:
polyA RNA
single cell


title: normal1_RNA-Seq

description: gastric normal tissue1


title: Input_STAT5AA_CD4_Th0_IL2_48h_rpt1_OS1056

description:
sample6_ChIP6
exp ID: 131126_0082_s25
lab data ID: 1056
sample6_ChIP6

value: mixed 129/C5BL/6

value: STAT5A-/- STAT5B+/+


title: A1_N702_S503

description:
polyA RNA
single cell


title: A1_N702_S501

description:
polyA RNA
single cell


title: A1_N702_S508

description:
polyA RNA
single cell


title: mRNA_WT_CD4_Th0_IL2_72h_rpt1_C149_OS574.fq

description:
sample28_RNA13
exp ID: 130329_0049_s1
lab data ID: 574
processed data file: Villarino RPKM table.xlsx
sample28_RNA13

value: mouse primary CD4+ T cells


title: Input_STAT5AB_CD4_Th0_IL2_48h_rpt1_OS1057

description:
sample7_ChIP7
exp ID: 131126_0082_s26
lab data ID: 1057
sample7_ChIP7

value: STAT5A+/- STAT5B+/-


title: csc2-mc_RNA-Seq


title: csc1-sc_RNA-Seq

description: gastric cancer stem cell-csc1 patient

value: gastric cancer stem cell


title: csc2-dc_RNA-Seq

description: cancer associated fibroblast -csc2 patient

value: differentiated cell


title: csc1-mc_RNA-Seq


title: csc1-dc_RNA-Seq

description: cancer associated fibroblast -csc1 patient


title: panSTAT5_STAT5AB_CD4_Th0_IL2_48h_rpt1_OS1035

description:
sample4_ChIP4
exp ID: 131126_0082_s4
lab data ID: 1035
sample4_ChIP4

value: pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4)


title: A1_N701_S507

description:
polyA RNA
single cell

value: Cerebral Cortex


title: csc3-n

source_name: normal

value: normal


title: csc3-sc

description: gastric cancer stem cell-csc3


title: panSTAT5_STAT5BB_CD4_Th0_IL2_48h_rpt1_OS1034

description:
sample3_ChIP3
exp ID: 131126_0082_s3
lab data ID: 1034
sample3_ChIP3

value: STAT5A+/+ STAT5B-/-


title: panSTAT5_STAT5AA_CD4_Th0_IL2_48h_rpt1_OS1033

description:
sample2_ChIP2
exp ID: 131126_0082_s2
lab data ID: 1033
sample2_ChIP2


title: csc3-dc

description: differentiated cell-csc3


title: A1_N701_S506

description:
polyA RNA
single cell


title: A1_N702_S504

description:
polyA RNA
single cell


title: A1_N701_S505

description:
polyA RNA
single cell


title: csc2-n


title: csc2-sc

description: gastric cancer stem cell-csc2


title: panSTAT5_WT_CD4_Th0_IL2_48h_rpt1_OS1032

description:
sample1_ChIP1
exp ID: 131126_0082_s1
lab data ID: 1032
sample1_ChIP1

value: WT


title: csc2-dc

description: differentiated cell-csc2


title: csc1-dc

description: differentiated cell-csc1


title: A1_N701_S508

description:
polyA RNA
single cell


title: csc1-sc

description: gastric cancer stem cell-csc1


title: A1_N701_S503

description:
polyA RNA
single cell


title: mRNA_STAT5BBA_CD4_iTreg_IL2_96h_rpt1_C234_OS976.fq

description:
sample52_RNA37
exp ID: 130815_0208_s34
lab data ID: 976
processed data file: Villarino RPKM table.xlsx
sample52_RNA37

value: STAT5A+/- STAT5B-/-

value: 96 hour in vitro iTreg culture with IL-2 (growth protocol 7)


title: OTII_CD8a_2

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
reads were aligned to Mouse Ensembl genes using the STAR version 2.3.0 software
Differential expression was determined by use of the Cufflinks software with default settings
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM

source_name: naïve OT-II CD4 T cells

extract_protocol:
1. Naive OT-II CD4 T cell extraction: peripheral lymphnodes and spleens were dissected on ice and mechanically disrupted in RPMI/10% FBS. Naïve CD4 T cells were pre-enriched by negative selection using biotinylated antibodies against CD8α, CD25, CD11c, CD11b, TER-119, NK1.1, and B220 and anti-biotin MACS beads (Miltenyi Biotec) and sorted as Aqua–CD11c–CD8α–MHCII–Vα2+CD4+CD25–CD62hiCD44lo. 2. Mesenteric lymphnodes from eight week old male C57Bl6 mice reared in the SPF facility of Rockefeller University were dissected into cold HBSS supplemented with Mg2+ and Ca2+, finely chopped and incubated in 400 U/ml Collagenase D (Roche) in HBSS for 25 min at 37°C, 5% CO2. Collagenase was quenched on ice by addition of final 10% FCS. Single cell suspensions were extracted from connective tissue by taking up and resuspending the digests five times. Mesenteric dendritic cells were pre-enriched using anti-CD11c MACS beads (Miltenyi Biotec) and LS MACS Separation Columns (Miltenyi Biotec). Cells were sorted using FACS Aria cell sorter flow cytometer (Becton Dickinson).Dendritic were sorted as Aqua–CD45+Lin–(CD3–B220–NK1.1–CD19–) CD11chi, and the subpopulations further as MHCIIintCD8α+CD11blo, MHCIIintCD8α–CD11b+, MHCIIhiCD103+CD11b– and MHCIIhiCD103+CD11b+. 3. After 24 h of co-culture with DCs, OT-II cells were sorted as Aqua-CD11c–CD8α–MHCII–Vα2+CD4+. RNA from sorted cell pellets was extracted and column-purified using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems). Genomic DNA was removed by on-column digest with DNAse I (Qiagen), according to the PicoPure RNA Isolation kit manual.
RNA libraries were prepared using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech Laboratories) and sequenced using 50 base pair paired end reading on a HiSeq 2500 instrument (Illumina).

treatment_protocol: Sorted and Cell TraceTM stained naïve OT-II cells were cultured for24h in flat bottom 96 well plates OT-II in the presence of sorted mLN DC subpopulations, 1 μg/ml anti-IL4 and 1 μg/ml anti-IFN-γ antibody in RPMI/10 % FBS. Antigen was provided as 1 μg/ml of OT-II peptide (chicken OVA323-339, amino acid sequence ISQAVHAAHAEINEAGR, made by the Rockefeller University Proteomics Resource Center). Cells were co-cultured at a 5:1 T cell/DC ratio (100,000 to 20,000 or 50,000 to 10,000).

value: C57BL/6 CD45.1 OT-II

tag: organ

value: spleen and  lymphnodes

value: CD4 T cells


title: A1_N701_S501

description:
polyA RNA
single cell


title: GW23_2_total

description:
ribozero total RNA
bulk tissue

extract_protocol:
Trizol followed by DNAse I treatment; QIAGEN Rneasy columns
illumina Truseq Stranded Total RNA with Ribo-Zero Gold

tag: replicate


title: mRNA_STAT5BBA_CTL_RV_IL2_24h_rpt2_C218_OS951.fq

description:
sample48_RNA33
exp ID: 130815_0208_s09
lab data ID: 951
processed data file: Villarino RPKM table.xlsx
sample48_RNA33

value: retrovirally transduced and cultured with IL-2 for 24 hours (growth protocol 6)


title: OTII_CD8a_1


title: OTII_CD11b_3


title: mRNA_WT_CD4_iTreg_IL2_96h_rpt1_C232_OS974.fq

description:
sample50_RNA35
exp ID: 130815_0208_s32
lab data ID: 974
processed data file: Villarino RPKM table.xlsx
sample50_RNA35

value: mixed 129/C5BL/6


title: mRNA_STAT5BBA_CTL_RV_IL2_24h_rpt1_C208_OS949.fq

description:
sample46_RNA31
exp ID: 130815_0208_s07
lab data ID: 949
processed data file: Villarino RPKM table.xlsx
sample46_RNA31


title: OTII_CD8a_3


title: mRNA_STAT5BBA_S5A_RV_IL2_24h_rpt2_C219_OS952.fq

description:
sample49_RNA34
exp ID: 130815_0208_s10
lab data ID: 952
processed data file: Villarino RPKM table.xlsx
sample49_RNA34


title: GW21_2_total

description:
ribozero total RNA
bulk tissue


title: mRNA_STAT5AAB_CD4_nTreg_ExVivo_rpt2_C129_OS944.fq

description:
sample44_RNA29
exp ID: 130815_0208_s02
lab data ID: 944
processed data file: Villarino RPKM table.xlsx
sample44_RNA29

value: STAT5A-/- STAT5B+/-

value: ex vivo nTreg cells (growth protocol 3)


title: GW21_1_total

description:
ribozero total RNA
bulk tissue


title: OTII_CD11b_1


title: mRNA_STAT5BBA_CD4_IL7_12h_rpt1_C96_OS389.fq

description:
sample27_RNA12
exp ID: 121221_0175_s10
lab data ID: 389
processed data file: Villarino RPKM table.xlsx
sample27_RNA12

value: mouse primary CD4+ T cells

value: 12 hour in vitro culture with IL-7 (growth protocol 4)


title: GW16_2_total

description:
ribozero total RNA
bulk tissue


title: mRNA_STAT5AAB_CD4_IL7_12h_rpt1_C95_OS388.fq

description:
sample26_RNA11
exp ID: 121221_0175_s9
lab data ID: 388
processed data file: Villarino RPKM table.xlsx
sample26_RNA11


title: mRNA_WT_CD4_nTreg_ExVivo_rpt2_C128_OS943.fq

description:
sample43_RNA28
exp ID: 130815_0208_s01
lab data ID: 943
processed data file: Villarino RPKM table.xlsx
sample43_RNA28


title: mRNA_WT_Naive_CD4_IL7_12h_rpt1_C94_OS387.fq

description:
sample25_RNA10
exp ID: 121221_0175_s8
lab data ID: 387
processed data file: Villarino RPKM table.xlsx
sample25_RNA10


title: Wild-type_r2

description: Biological replicate 2


title: GW16_1_total

description:
ribozero total RNA
bulk tissue


title: mRNA_STAT5AAB_CD4_Naive_ExVivo_rpt2_C92_OS385.fq

description:
sample23_RNA8
exp ID: 121221_0175_s6
lab data ID: 385
processed data file: Villarino RPKM table.xlsx
sample23_RNA8

value: ex vivo naive CD4+ T cells (growth protocol 2)


title: mRNA_WT_CD4_Naive_ExVivo_rpt2_C91_OS384.fq

description:
sample22_RNA7
exp ID: 121221_0175_s5
lab data ID: 384
processed data file: Villarino RPKM table.xlsx
sample22_RNA7


title: ref6 BRM-BRM-GFP ab290 #2

data_processing:
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline
ChIP-seq reads were aligned to the Arabidopsis genome (TAIR10) using BOWTIE2 version 2.2.5.
The program MACS v1.4 was used to identify ChIP-enriched domains (peaks).
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files report peaks

organism: Arabidopsis

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with H3K27me3 or GFP antibody.
Ten ng of ChIP DNA  was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Hiseq 2000 was used for high-throughput sequencing of the ChIP-seq library.

value: Seedling

tag: age

value: ref6-1 mutant background with ProBRM-BRM-GFP transgene

tag: antibody

value: GFP (ab290, abcam)


title: GW23_1_total

description:
ribozero total RNA
bulk tissue

tag: tissue

value: Cerebral Cortex

tag: developmental stage


title: GW13_1_total

description:
ribozero total RNA
bulk tissue


title: mRNA_STAT5BBA_CD4_nTreg_ExVivo_rpt1_C90_OS382.fq

description:
sample21_RNA6
exp ID: 121221_0175_s3
lab data ID: 382
processed data file: Villarino RPKM table.xlsx
sample21_RNA6

tag: genotype/variation


title: mRNA_STAT5AAB_CD4_iTreg_IL2_96h_rpt1_C233_OS975.fq

description:
sample51_RNA36
exp ID: 130815_0208_s33
lab data ID: 975
processed data file: Villarino RPKM table.xlsx
sample51_RNA36


title: mRNA_STAT5BBA_CD4_Naive_ExVivo_rpt2_C93_OS386.fq

description:
sample24_RNA9
exp ID: 121221_0175_s7
lab data ID: 386
processed data file: Villarino RPKM table.xlsx
sample24_RNA9


title: Brmref6K271

value: brm-1 ref6-1

value: H3K27me3 (Millipore, catalog# 07-449, lot# 1959680)


title: Brmref6K272


title: mRNA_STAT5AAB_CD4_nTreg_ExVivo_rpt1_C89_OS381.fq

description:
sample20_RNA5
exp ID: 121221_0175_s2
lab data ID: 381
processed data file: Villarino RPKM table.xlsx
sample20_RNA5


title: GW23_1_polya

description:
polyA RNA
bulk tissue

extract_protocol:
Trizol followed by DNAse I treatment; QIAGEN Rneasy columns
illumina Truseq Stranded mRNA


title: OTII_CD11b_2


title: mRNA_WT_CD4_nTreg_ExVivo_rpt1_C88_OS380.fq

description:
sample19_RNA4
exp ID: 121221_0175_s1
lab data ID: 380
processed data file: Villarino RPKM table.xlsx
sample19_RNA4

value: WT


title: Ref6K272


title: CD8a_3

source_name: mesenteric lymphnode dendritic cells

extract_protocol:
Mesenteric lymphnodes from eight week old male C57Bl6 mice reared in the SPF facility of Rockefeller University were dissected into cold HBSS supplemented with Mg2+ and Ca2+, finely chopped and incubated in 400 U/ml Collagenase D (Roche) in HBSS for 25 min at 37°C, 5% CO2. Collagenase was quenched on ice by addition of final 10% FCS. Single cell suspensions were extracted from connective tissue by taking up and resuspending the digests five times. Mesenteric dendritic cells were pre-enriched using anti-CD11c MACS beads (Miltenyi Biotec) and LS MACS Separation Columns (Miltenyi Biotec). Cells were sorted using FACS Aria cell sorter flow cytometer (Becton Dickinson).Dendritic were sorted as Aqua–CD45+Lin–(CD3–B220–NK1.1–CD19–) CD11chi, and the subpopulations further as MHCIIintCD8α+CD11blo, MHCIIintCD8α–CD11b+, MHCIIhiCD103+CD11b– and MHCIIhiCD103+CD11b+. RNA from sorted cell pellets was extracted and column-purified using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems). Genomic DNA was removed by on-column digest with DNAse I (Qiagen), according to the PicoPure RNA Isolation kit manual.
RNA libraries were prepared using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech Laboratories) and sequenced using 50 base pair paired end reading on a HiSeq 2500 instrument (Illumina).

value: mesenteric lymphnodes

value: dendritic cells


title: mRNA_STAT5BBA_CD4_nTreg_ExVivo_rpt2_C130_OS945.fq

description:
sample45_RNA30
exp ID: 130815_0208_s03
lab data ID: 945
processed data file: Villarino RPKM table.xlsx
sample45_RNA30

value: STAT5A+/- STAT5B-/-


title: GW21_2_polya

description:
polyA RNA
bulk tissue


title: mRNA_STAT5BBA_CD4_Naive_ExVivo_rpt1_C79_OS328.fq

description:
sample18_RNA3
exp ID: 121126_0170_s16
lab data ID: 328
processed data file: Villarino RPKM table.xlsx
sample18_RNA3


title: mRNA_STAT5BBA_S5A_RV_IL2_24h_rpt1_C209_OS950.fq

description:
sample47_RNA32
exp ID: 130815_0208_s08
lab data ID: 950
processed data file: Villarino RPKM table.xlsx
sample47_RNA32

value: retrovirally transduced and cultured with IL-2 for 24 hours (growth protocol 6)


title: GW21_1_polya

description:
polyA RNA
bulk tissue


title: CD8a_1


title: Ref6K271


title: mRNA_STAT5AAB_CD4_Naive_ExVivo_rpt1_C78_OS327.fq

description:
sample17_RNA2
exp ID: 121126_0170_s15
lab data ID: 327
processed data file: Villarino RPKM table.xlsx
sample17_RNA2

value: mixed 129/C5BL/6


title: GW23_2_polya

description:
polyA RNA
bulk tissue


title: CD8a_2


title: Ref6input

value: none (input)


title: Brmref6input


title: CD11b_3


title: GW14.5_1_total

description:
ribozero total RNA
bulk tissue


title: mRNA_WT_CD4_Naive_ExVivo_rpt1_C77_OS326.fq

description:
sample16_RNA1
exp ID: 121126_0170_s14
lab data ID: 326
processed data file: Villarino RPKM table.xlsx
sample16_RNA1


title: GW14.5_1_polya

description:
polyA RNA
bulk tissue


title: Input_STAT5AA_CD4_Th0_IL2_48h_rpt2_OS3401

description:
sample14_ChIP14
exp ID: 151211_0411_s08
lab data ID: 3401
sample14_ChIP14

value: STAT5A-/- STAT5B+/+

value: 48 hour in vitro culture with IL-2 (growth protocol 1)

value: input


title: brminput


title: brmK272


title: GW16_1_polya

description:
polyA RNA
bulk tissue


title: CD11b_2


title: CD103+CD11b+_3


title: Input_STAT5AB_CD4_Th0_IL2_48h_rpt2_OS3402

description:
sample15_ChIP15
exp ID: 151211_0411_s09
lab data ID: 3402
sample15_ChIP15

value: STAT5A+/- STAT5B+/-

value: mouse primary CD4+ T cells


title: CD11b_1


title: GW13_1_polya

description:
polyA RNA
bulk tissue


title: brmK271

value: Seedling


title: CD103+CD11b+_2


title: WTK272


title: Input_WT_CD4_Th0_IL2_48h_rpt2_OS3397

description:
sample12_ChIP12
exp ID: 151211_0411_s04
lab data ID: 3397
sample12_ChIP12


title: CD103+CD11b+_1


title: panSTAT5_STAT5AB_CD4_Th0_IL2_48h_rpt2_OS3399

description:
sample11_ChIP11
exp ID: 151211_0411_s06
lab data ID: 3399
sample11_ChIP11

value: pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4)


title: WTinput


title: CD103+CD11b-_3


title: WTK271


title: panSTAT5_STAT5BB_CD4_Th0_IL2_48h_rpt2_OS3395

description:
sample9_ChIP9
exp ID: 151211_0411_s02
lab data ID: 3395
sample9_ChIP9

value: STAT5A+/+ STAT5B-/-


title: CD103+CD11b-_1


title: panSTAT5_STAT5AA_CD4_Th0_IL2_48h_rpt2_OS3396

description:
sample10_ChIP10
exp ID: 151211_0411_s03
lab data ID: 3396
sample10_ChIP10


title: CD103+CD11b-_2


title: GW16_2_polya

description:
polyA RNA
bulk tissue

value: Cerebral Cortex


title: panSTAT5_WT_CD4_Th0_IL2_48h_rpt2_OS3394

description:
sample8_ChIP8
exp ID: 151211_0411_s01
lab data ID: 3394
sample8_ChIP8


title: Cell96-A12 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2

status: Public on Mar 27 2016

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: AML mouse ckit+ splenocytes from mouse 2

data_processing:
FASTQ sequence files were aligned to the mouse genome version 10 (mm10) using TopHat2 with de novo junction discovery and separately to mm9 using RSEM.
The fastq files were aligned to mouse genome mm10 using BowTie 2 and TopHat 2 (Kim et al., 2013; Trapnell et al., 2009). BAM files were further processed in AltAnalyze 2.0.9 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010). To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold. RSEM gene-expression TPM values were all subjected to the same defaults in AltAnlayze for statistical analysis.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005). All gene set enrichment analyses were performed using GSEA v.2.2.0 (Mootha et al., 2003; Subramanian et al., 2005).
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: primary AML

growth_protocol: Mice were euthanized with carbon dioxide and cervical dislocation. Spleens were harvested from moribund Flt3ITD/ITD;Dnmt3afl/- MxCre and  Flt3ITD/ITD;Dnmt3afl/fl controls.  Splenocytes were isolated from freshly sacrificed mice and crushed between two glass slides. Red blood cells were lysed using Ammonium-Chloride-Potassium (ACK) buffer (Gibco), washed, and filtered to obtain single cells suspensions for downstream applications.

extract_protocol:
Single CD117+ (c-Kit+) cells were prepared using the C1™ Single-Cell Auto Prep System (Fluidigm, San Fransisco, CA), according to the manufacturer’s instructions.  In short, sorted cells were counted and resuspended at a concentration of 333,333 cells per 1 mL DPBS then loaded onto a primed C1 Single-Cell Auto Prep Integrated Fluidic Chip for mRNA-Seq (5-10 µm). After the fluidic step, cell separation was visually scored to identify wells containing single live cells. In two independent rounds, 52 and 56 cells were captured.
Cells were lysed on the chip and reverse transcription was performed using the Clontech SMARTer® Kit with the mRNA Seq: RT + Amp (1771x) according to the manual. After the reverse transcriptase step, cDNAs were transferred to a 96 well plate and diluted with 6 µl C1™ DNA Dilution Reagent. cDNAs were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit (Agilent Technologies (Santa Clara, CA). Libraries for the first 48 visually validated cells from each of the two independent captures were prepared using the Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA).  In each single-cell library preparation, a total of 125pg cDNA was tagmented at 55 °C for 20 minutes. Next, libraries were pooled and purified on the AMPure® bead-based magnetic separation Kit prior to a final quality control check using both the Qubit® dsDNA HS Assay Kit (Life Tecnologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit. The majority of cDNA fragments were confirmed to be between 200-602 bp, qualifying the libraries for sequencing. All 96 single-cell RNA-Seq libraries were sequenced on one HiSeq 2500 gel.

treatment_protocol: To isolated c-Kit+ leukemic stem/progenitor populations, freshly isolated single cells suspensions were incubated with CD117 MicroBeads and separated on an AutoMACS Pro separator (Miltenyi, San Diego, CA) according to manufacturer specifications. RNA was extracted from cKit+ purified splenocytes using TriZol (Invitrogen) according to manufacturers instructions.

tag: sample type

value: cKit+ splenocytes

value: acute myeloid leukemia


title: Cell94-C11 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell93-B11 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell95-G11 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell92-A11 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell91-E10 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell89-C10 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell88-B10 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell90-D10 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell87-A10 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell86-H9 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Input_STAT5BB_CD4_Th0_IL2_48h_rpt2_OS3398

description:
sample13_ChIP13
exp ID: 151211_0411_s05
lab data ID: 3398
sample13_ChIP13


title: Cell85-G9 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell83-B9 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell82-F8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell75-E7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell80-C8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell79-B8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell78-H7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell76-F7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell70-E5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell61-H3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell64-E4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell73-B7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell68-C5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell60-G3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell66-A5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell67-B5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell77-G7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell63-D4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell71-E6 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell84-F9 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell74-D7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell59-E3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell58-D3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell56-E2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell57-H2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell69-D5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell54-A2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell55-D2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell53-H1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell51-E1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell50-B1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell49-A1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell62-A4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell7-F2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1

description: AML mouse ckit+ splenocytes from mouse 1


title: Cell81-E8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell8-G2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell9-H2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell48-H12 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell5-B2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell47-F12 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell52-G1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell43-G11 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell46-D12 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell44-A12 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell42-F11 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell41-E11 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell4-H1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell45-B12 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell65-F4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell40-G10 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell39-C10 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell38-E9 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell6-E2 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell35-E8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell36-H8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell33-B8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell30-F7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell31-G7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell29-E7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell28-D7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell32-H7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell3-F1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell25-E6 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell22-A6 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell23-B6 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell27-B7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell37-D9 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell72-G6 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-2


title: Cell20-F5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell34-C8 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell2-D1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell19-E5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell18-A5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell13-H3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell12-F3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell14-B4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell15-D4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell11-E3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell26-A7 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell10-B3 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Cell1-A1 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Double KO study NG66 rep2

city: Research Triangle Park

first: Perry

middle: J

last: Blackshear

state: NC

address: 111 T.W. alexander drive

department: LST

institute: NIEHS

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for data quality using sickle version 1.210 with parameters "pe -q 20 -l 20"
Trimmed sequence reads were aligned to mm10 using TopHat v2.0.4, with an associated transcript GTF file, using parameters "--solexa-quals --library-type fr-unstranded", "--mate-inner-dist" using average insert size minus the read lengths, "--mate-std-dev" using 10 percent the average insert size, and "--GTF" using the attached mm10_genes.gtf file representing mm10 transcripts.
Splice junction data from TopHat2 were merged based upon identical start and stop positions to produce union junction tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Junction bed files are in bed12 format, suitable for viewing in UCSC genome browser so the splice sites are thin and anchors are thick.

source_name: Spleen tissue mRNA

extract_protocol:
RNA was isolated from spleen using GE Healthcare RNA isolation kit. RNA was quantified on Tecan's Infinite 200PRO Nanoquant.
Libraries were prepared according to Illumina's Instructions

treatment_protocol: No treatment

value: Spleen

value: Double KO (TNFR1-/-, TNFR2-/-)


title: Double KO study NG66 rep4


title: Cell21-H5 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Double KO study NG66 rep3


title: Double KO study NG66 rep1


title: Wildtype study NG108 rep4

value: Wildtype


title: 9798 Flt3ITD/ITD,Dnmt3afl/fl MPN

description: MPN control mouse #9798 ckit+ splenocytes

source_name: primary MPN

extract_protocol:
RNA was extracted according to Meyer et al., 2009. RNA quality and quantity were measured by Agilant Bioanalyzer. Then samples with a RIN>8.0 were processed by poly-A selection, stranded True-seq, paired-end 75 base pair (bp), 40 million reads.
RNAs were detected by RNAseq analysis using paired-end 75 nucleotide (nt) sequencing and 40 million reads for all samples. RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits.

value: myeloproliferative neoplasm


title: 9796 Flt3ITD/ITD,Dnmt3afl/fl MPN

description: MPN control mouse #9796 ckit+ splenocytes


title: 9927 Flt3ITD/ITD,Dnmt3afl/fl MPN

description: MPN control mouse #9927 ckit+ splenocytes


title: Cell17-G4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Triple KO study NG66 rep4

value: Triple KO (Zfp36-/-, TNFR1-/-, TNFR2-/-)


title: Triple KO study NG66 rep3


title: Triple KO study NG66 rep2


title: Triple KO study NG66 rep1


title: Cell16-F4 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: Wildtype study NG66 rep4


title: Wildtype study NG66 rep3


title: Wildtype study NG66 rep2


title: Wildtype study NG66 rep1


title: XX-650-23 input DNA

status: Public on Mar 26 2016

city: Stanford

first: Kathleen

middle: M

last: Sakamoto

address: CCSR 1215C, 235 Campus Drive

department: Pediatrics

institute: Stanford University

data_processing:
RNAseq reads were mapped to human genome hg19 using tophat(Version 2.0.6) with refseq gene annotation
uniquely mapped reads were counted using htseq-count with refseq  gene annotation
genes with 0 counts across all samples were filtered out
ChIP-seq reads were mapped to human genome hg19 using Bowtie
Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis.Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects
The genome was tiled into 100-bp windows. Each read was extended by 150 bases (we refer to tags as the extend read counts within a bin) and was counted as one read to each window to which it partially or fully matched
The total counts of the input and ChIP samples were normalized to each other
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes raw gene counts values for each RNA-Seq Sample. Bed files includes peaks for ChIP-Seq Samples.

source_name: KG1 cells

growth_protocol: KG1 cells were p maintained with IMDM (Gibco) supplemented with 10% FBS (Fisher Scientific) and 1% PSG (Gibco).

extract_protocol:
Chromatin were digested by Micrococcal nuclease and then sonicated using SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology) following themanufacturer’s protocol. CREB-DNA complexes were isolated with antibody.
Libraries were prepared using the Illumina Truseq RNA samples prep kit per manufacturer’s instructions.

treatment_protocol: KG1 cells were plated at a density of 2-4x105 cells/ml, and treated with 5μM XX-650-23 in 0.1% DMSO or 0.1% DMSO alone.

value: acute myeloid leukemia cell line KG1

tag: treatment

tag: chip ab


title: DMSO input DNA

tag: cell line


title: XX-650-23 CREB_ChIPSeq

value: CREB (Millipore, 17-600)


title: DMSO CREB_ChIPSeq


title: XX-650-23 rep2

description:
XX_rep2
XX_RNAseq_rawCounts.txt.gz

extract_protocol:
RNA was prepared using the Aurum Total RNA Mini Kit (Bio-Rad)
Libraries were prepared using the Illumina Truseq RNA samples prep kit per manufacturer’s instructions.


title: XX-650-23 rep1

description:
XX_rep1
XX_RNAseq_rawCounts.txt.gz


title: DMSO rep2

description:
DMSO_rep2
XX_RNAseq_rawCounts.txt.gz


title: Wildtype study NG108 rep2

tag: genotype


title: Wildtype study NG108 rep1


title: DMSO rep1

description:
DMSO_rep1
XX_RNAseq_rawCounts.txt.gz


title: Wildtype study NG108 rep3


title: Cell24-D6 cKit+ Flt3ITD/ITD,Dnmt3afl/- MxCre  AML-1


title: J_4-50_4-4-89

status: Public on Mar 25 2016

city: Toronto

first: Arturas

last: Petronis

address: 250 College St Rm606

country: Canada

institute: Centre for Addiction and Mental Health

description: Sample name: H4.4/Ind89

data_processing:
Analysis of the padlock BS-seq data was completed using a custom pipeline based on the Bismark tool
Reads were first trimmed and residual adapter sequences removed using Trimmomatic-0.32.
Reads that did not align to phiX were aligned to the target reference genome (GRCh37/hg19 or GRCm38/mm10).
Percent modification was estimated as the fraction of spanning reads that retained the reference “C”, and were not converted to “T” from the bisulfite treatment.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files with coverage of modified and unmodified cytosines, with fields: chromosome, position, type, # reads with modified cytosine, # reads with unmodified cytosine

source_name: Jejunum lacking enterocytes

growth_protocol: Human jejunum surgical samples, blood and sperm was examined as well as mouse jejunum

extract_protocol:
DNA from tissues were extracted by standard phenol chloroform extraction
Bisulfite padlock probes technique was used to interrogate the lactase gene region and minichromosome maintenance deficient 6 gene of humans and mice

tag: individual

value: Bisulfite-converted Padlock

tag: Sex

value: M

value: CT

value: Jejunum lacking enterocytes


title: J_4-49_4-4-88

description: Sample name: H4.4/Ind88

value: F

value: CC


title: J_4-38_4-4-72

description: Sample name: H4.4/Ind72


title: J_4-39_4-4-73

description: Sample name: H4.4/Ind73


title: J_4-48_4-4-87

description: Sample name: H4.4/Ind87


title: J_4-1_4-4-7

description: Sample name: H4.4/Ind7


title: J_4-33_4-4-68

description: Sample name: H4.4/Ind68


title: J_4-31_4-4-60

description: Sample name: H4.4/Ind60


title: J_4-30_4-4-59

description: Sample name: H4.4/Ind59

value: TT


title: J_4-29_4-4-58

description: Sample name: H4.4/Ind58


title: J_4-28_4-4-57

description: Sample name: H4.4/Ind57


title: J_4-41_4-4-74

description: Sample name: H4.4/Ind74


title: J_4-27_4-4-56

description: Sample name: H4.4/Ind56


title: E_3-24_4-4-45

description: Sample name: H4.4/Ind45

source_name: Enterocytes

tag: relative lactase mrna expression

tag: cell type

value: Enterocytes


title: J_4-44_4-4-77

description: Sample name: H4.4/Ind77


title: E_3-23_4-4-44

description: Sample name: H4.4/Ind44


title: E_3-22_4-4-43

description: Sample name: H4.4/Ind43


title: J_3-27_4-4-42

description: Sample name: H4.4/Ind42


title: J_4-24_4-4-41

description: Sample name: H4.4/Ind41


title: J_3-23_4-4-38

description: Sample name: H4.4/Ind38


title: J_4-23_4-4-40

description: Sample name: H4.4/Ind40


title: J_4-22_4-4-39

description: Sample name: H4.4/Ind39


title: J_4-32_4-4-67

description: Sample name: H4.4/Ind67


title: J_4-20_4-4-37

description: Sample name: H4.4/Ind37


title: E_4-17_4-4-35

description: Sample name: H4.4/Ind35


title: E_4-18_4-4-36

description: Sample name: H4.4/Ind36


title: J_4-54_4-4-3

description: Sample name: H4.4/Ind3


title: J_3-20_4-4-29

description: Sample name: H4.4/Ind29


title: J_3-21_4-4-30

description: Sample name: H4.4/Ind30


title: E_4-14_4-4-32

description: Sample name: H4.4/Ind32


title: J_3-17_4-4-27

description: Sample name: H4.4/Ind27


title: J_3-15_4-4-25

description: Sample name: H4.4/Ind25


title: J_3-16_4-4-26

description: Sample name: H4.4/Ind26


title: J_4-12_4-4-24

description: Sample name: H4.4/Ind24


title: E_3-19_4-4-34

description: Sample name: H4.4/Ind34


title: J_3-19_4-4-28

description: Sample name: H4.4/Ind28


title: J_4-11_4-4-23

description: Sample name: H4.4/Ind23


title: J_4-7_4-4-19

description: Sample name: H4.4/Ind19


title: J_4-10_4-4-22

description: Sample name: H4.4/Ind22


title: J_4-4_4-4-10

description: Sample name: H4.4/Ind10


title: B_8_4-3-7

description: Sample name: H4.3/Ind7

source_name: Blood

value: Blood


title: J_4-5_4-4-11

description: Sample name: H4.4/Ind11


title: B_9_4-3-8

description: Sample name: H4.3/Ind8


title: B_LAC26_4-3-67

description: Sample name: H4.3/Ind67


title: WGA_4-3-68

description:
Sample name: H4.3/Ind68
For WGA samples, a genome devoid of DNA modifications was used to verify the efficiency of the bisulfite conversion reactions.

source_name: WGA

value: Intestine


title: E_3-17_4-4-33

description: Sample name: H4.4/Ind33


title: B_21_4-3-65

description: Sample name: H4.3/Ind65


title: B_LAC25_4-3-66

description: Sample name: H4.3/Ind66


title: E_3-15_4-4-31

description: Sample name: H4.4/Ind31


title: J_4-34_4-4-69

description: Sample name: H4.4/Ind69


title: B_17_4-3-64

description: Sample name: H4.3/Ind64


title: B_10_4-3-62

description: Sample name: H4.3/Ind62


title: B_16_4-3-63

description: Sample name: H4.3/Ind63


title: B_5_4-3-61

description: Sample name: H4.3/Ind61


title: B_4_4-3-60

description: Sample name: H4.3/Ind60


title: B_10_4-3-9

description: Sample name: H4.3/Ind9


title: B_7_4-3-6

description: Sample name: H4.3/Ind6


title: J_4-9_4-4-21

description: Sample name: H4.4/Ind21


title: B_1_4-3-59

description: Sample name: H4.3/Ind59


title: B_LAC29_4-3-56

description: Sample name: H4.3/Ind56


title: B_6_4-3-5

description: Sample name: H4.3/Ind5


title: B_LAC30_4-3-57

description: Sample name: H4.3/Ind57


title: B_LAC27_4-3-54

description: Sample name: H4.3/Ind54


title: B_LAC18_4-3-45

description: Sample name: H4.3/Ind45


title: B_LAC26_4-3-53

description: Sample name: H4.3/Ind53


title: B_LAC19_4-3-46

description: Sample name: H4.3/Ind46


title: B_LAC28_4-3-55

description: Sample name: H4.3/Ind55


title: B_LAC25_4-3-52

description: Sample name: H4.3/Ind52


title: B_LAC24_4-3-51

description: Sample name: H4.3/Ind51


title: B_LAC23_4-3-50

description: Sample name: H4.3/Ind50


title: B_LAC22_4-3-49

description: Sample name: H4.3/Ind49


title: B_LAC21_4-3-48

description: Sample name: H4.3/Ind48


title: B_LAC20_4-3-47

description: Sample name: H4.3/Ind47


title: B_LAC11_4-3-38

description: Sample name: H4.3/Ind38


title: B_LAC17_4-3-44

description: Sample name: H4.3/Ind44


title: B_LAC8_4-3-35

description: Sample name: H4.3/Ind35


title: B_LAC10_4-3-37

description: Sample name: H4.3/Ind37


title: B_LAC31_4-3-58

description: Sample name: H4.3/Ind58


title: B_LAC5_4-3-32

description: Sample name: H4.3/Ind32


title: B_LAC14_4-3-41

description: Sample name: H4.3/Ind41


title: B_LAC16_4-3-43

description: Sample name: H4.3/Ind43


title: B_LAC15_4-3-42

description: Sample name: H4.3/Ind42


title: B_LAC13_4-3-40

description: Sample name: H4.3/Ind40


title: B_5_4-3-4

description: Sample name: H4.3/Ind4


title: B_LAC12_4-3-39

description: Sample name: H4.3/Ind39


title: B_LAC1_4-3-28

description: Sample name: H4.3/Ind28


title: B_LAC7_4-3-34

description: Sample name: H4.3/Ind34


title: B_LAC9_4-3-36

description: Sample name: H4.3/Ind36


title: B_LAC6_4-3-33

description: Sample name: H4.3/Ind33


title: B_28_4-3-27

description: Sample name: H4.3/Ind27


title: B_LAC4_4-3-31

description: Sample name: H4.3/Ind31


title: B_25_4-3-24

description: Sample name: H4.3/Ind24


title: B_24_4-3-23

description: Sample name: H4.3/Ind23


title: B_3_4-3-3

description: Sample name: H4.3/Ind3


title: B_27_4-3-26

description: Sample name: H4.3/Ind26


title: B_20_4-3-19

description: Sample name: H4.3/Ind19


title: B_21_4-3-20

description: Sample name: H4.3/Ind20


title: B_2_4-3-2

description: Sample name: H4.3/Ind2


title: B_LAC3_4-3-30

description: Sample name: H4.3/Ind30


title: B_22_4-3-21

description: Sample name: H4.3/Ind21


title: B_23_4-3-22

description: Sample name: H4.3/Ind22


title: B_18_4-3-17

description: Sample name: H4.3/Ind17


title: B_LAC2_4-3-29

description: Sample name: H4.3/Ind29


title: B_19_4-3-18

description: Sample name: H4.3/Ind18


title: B_13_4-3-12

description: Sample name: H4.3/Ind12


title: B_15_4-3-14

description: Sample name: H4.3/Ind14


title: B_16_4-3-15

description: Sample name: H4.3/Ind15


title: B_17_4-3-16

description: Sample name: H4.3/Ind16


title: B_14_4-3-13

description: Sample name: H4.3/Ind13


title: B_26_4-3-25

description: Sample name: H4.3/Ind25


title: B_11_4-3-10

description: Sample name: H4.3/Ind10


title: B_1_4-3-1

description: Sample name: H4.3/Ind1


title: B_12_4-3-11

description: Sample name: H4.3/Ind11


title: E_3-51_4-2-93

description: Sample name: H4.2/Ind93


title: E_3-53_4-2-95

description: Sample name: H4.2/Ind95


title: E_3-54_4-2-96

description: Sample name: H4.2/Ind96


title: E_3-50_4-2-92

description: Sample name: H4.2/Ind92


title: J_3-53_4-2-89

description: Sample name: H4.2/Ind89


title: J_3-49_4-2-85

description: Sample name: H4.2/Ind85


title: J_3-52_4-2-88

description: Sample name: H4.2/Ind88


title: J_3-50_4-2-86

description: Sample name: H4.2/Ind86


title: E_3-48_4-2-84

description: Sample name: H4.2/Ind84


title: E_3-49_4-2-91

description: Sample name: H4.2/Ind91


title: J_3-51_4-2-87

description: Sample name: H4.2/Ind87


title: E_3-46_4-2-83

description: Sample name: H4.2/Ind83


title: E_3-44_4-2-82

description: Sample name: H4.2/Ind82


title: E_3-43_4-2-81

description: Sample name: H4.2/Ind81


title: J_3-43_4-2-75

description: Sample name: H4.2/Ind75


title: J_3-46_4-2-77

description: Sample name: H4.2/Ind77


title: E_3-40_4-2-79

description: Sample name: H4.2/Ind79


title: E_3-52_4-2-94

description: Sample name: H4.2/Ind94


title: J_3-42_4-2-74

description: Sample name: H4.2/Ind74


title: J_3-40_4-2-73

description: Sample name: H4.2/Ind73


title: J_3-39_4-2-72

description: Sample name: H4.2/Ind72


title: J_3-38_4-2-71

description: Sample name: H4.2/Ind71


title: E_3-42_4-2-80

description: Sample name: H4.2/Ind80


title: J_4-42_4-4-75

description: Sample name: H4.4/Ind75


title: J_3-54_4-2-90

description: Sample name: H4.2/Ind90


title: J_3-37_4-2-70

description: Sample name: H4.2/Ind70


title: J_3-36_4-2-69

description: Sample name: H4.2/Ind69


title: J_3-35_4-2-68

description: Sample name: H4.2/Ind68


title: J_3-34_4-2-67

description: Sample name: H4.2/Ind67


title: J_4-56_4-4-5

description: Sample name: H4.4/Ind5


title: E_3-39_4-2-66

description: Sample name: H4.2/Ind66


title: E_3-38_4-2-65

description: Sample name: H4.2/Ind65


title: J_3-48_4-2-78

description: Sample name: H4.2/Ind78


title: J_3-44_4-2-76

description: Sample name: H4.2/Ind76


title: J_3-55_4-2-55

description: Sample name: H4.2/Ind55


title: J_3-59_4-2-59

description: Sample name: H4.2/Ind59


title: E_3-56_4-2-50

description: Sample name: H4.2/Ind50


title: E_3-60_4-2-54

description: Sample name: H4.2/Ind54


title: E_3-7_4-2-61

description: Sample name: H4.2/Ind61


title: E_3-57_4-2-51

description: Sample name: H4.2/Ind51


title: E_3-55_4-2-49

description: Sample name: H4.2/Ind49


title: J_3-57_4-2-57

description: Sample name: H4.2/Ind57


title: E_3-35_4-2-62

description: Sample name: H4.2/Ind62


title: J_4-37_4-4-71

description: Sample name: H4.4/Ind71


title: E_3-37_4-2-64

description: Sample name: H4.2/Ind64


title: E_3-59_4-2-53

description: Sample name: H4.2/Ind53


title: J_3-56_4-2-56

description: Sample name: H4.2/Ind56


title: E_3-58_4-2-52

description: Sample name: H4.2/Ind52


title: J_4-9_4-2-40

description: Sample name: H4.2/Ind40


title: J_3-58_4-2-58

description: Sample name: H4.2/Ind58


title: J_3-60_4-2-60

description: Sample name: H4.2/Ind60


title: E_3-36_4-2-63

description: Sample name: H4.2/Ind63


title: J_4-64_4-2-36

description: Sample name: H4.2/Ind36


title: J_4-29_4-2-34

description: Sample name: H4.2/Ind34


title: J_4-7_4-2-39

description: Sample name: H4.2/Ind39


title: J_4-9_4-2-33

description: Sample name: H4.2/Ind33


title: J_4-63_4-2-24

description: Sample name: H4.2/Ind24


title: J_4-60_4-2-21

description: Sample name: H4.2/Ind21


title: E_4-7_4-2-37

description: Sample name: H4.2/Ind37


title: J_4-7_4-2-32

description: Sample name: H4.2/Ind32


title: E_4-9_4-2-38

description: Sample name: H4.2/Ind38


title: J_4-61_4-2-22

description: Sample name: H4.2/Ind22


title: J_4-58_4-2-19

description: Sample name: H4.2/Ind19


title: J_3-3_4-1-8

description: Sample name: H4.1/Ind8


title: J_4-59_4-2-20

description: Sample name: H4.2/Ind20


title: E_3-34_4-1-61

description: Sample name: H4.1/Ind61


title: E_3-29_4-1-50

description: Sample name: H4.1/Ind50


title: WGA_4-1-70

description:
Sample name: H4.1/Ind70
For WGA samples, a genome devoid of DNA modifications was used to verify the efficiency of the bisulfite conversion reactions.


title: J_3-30_4-1-57

description: Sample name: H4.1/Ind57


title: J_3-28_4-1-55

description: Sample name: H4.1/Ind55


title: J_3-33_4-1-60

description: Sample name: H4.1/Ind60


title: E_3-30_4-1-51

description: Sample name: H4.1/Ind51


title: J_3-31_4-1-58

description: Sample name: H4.1/Ind58


title: E_3-32_4-1-53

description: Sample name: H4.1/Ind53


title: J_3-29_4-1-56

description: Sample name: H4.1/Ind56


title: J_3-32_4-1-59

description: Sample name: H4.1/Ind59


title: E_3-6_4-1-5

description: Sample name: H4.1/Ind5


title: E_3-28_4-1-49

description: Sample name: H4.1/Ind49


title: E_3-7_4-1-6

description: Sample name: H4.1/Ind6


title: E_3-33_4-1-54

description: Sample name: H4.1/Ind54


title: E_3-26_4-1-47

description: Sample name: H4.1/Ind47


title: E_3-25_4-1-46

description: Sample name: H4.1/Ind46


title: J_3-4_4-1-9

description: Sample name: H4.1/Ind9


title: E_3-31_4-1-52

description: Sample name: H4.1/Ind52


title: E_3-22_4-1-43

description: Sample name: H4.1/Ind43


title: E_3-24_4-1-45

description: Sample name: H4.1/Ind45


title: E_3-23_4-1-44

description: Sample name: H4.1/Ind44


title: J_3-1_4-1-7

description: Sample name: H4.1/Ind7


title: J_3-25_4-1-40

description: Sample name: H4.1/Ind40


title: J_3-27_4-1-42

description: Sample name: H4.1/Ind42


title: WGA_4-1-69

description:
Sample name: H4.1/Ind69
For WGA samples, a genome devoid of DNA modifications was used to verify the efficiency of the bisulfite conversion reactions.


title: E_3-5_4-1-4

description: Sample name: H4.1/Ind4


title: J_3-24_4-1-39

description: Sample name: H4.1/Ind39


title: J_3-23_4-1-38

description: Sample name: H4.1/Ind38


title: J_3-22_4-1-37

description: Sample name: H4.1/Ind37


title: E_3-21_4-1-36

description: Sample name: H4.1/Ind36


title: E_3-17_4-1-33

description: Sample name: H4.1/Ind33


title: E_3-16_4-1-32

description: Sample name: H4.1/Ind32


title: J_3-17_4-1-27

description: Sample name: H4.1/Ind27


title: J_3-20_4-1-29

description: Sample name: H4.1/Ind29


title: J_3-16_4-1-26

description: Sample name: H4.1/Ind26


title: J_3-19_4-1-28

description: Sample name: H4.1/Ind28


title: E_3-19_4-1-34

description: Sample name: H4.1/Ind34


title: J_3-15_4-1-25

description: Sample name: H4.1/Ind25


title: E_3-20_4-1-35

description: Sample name: H4.1/Ind35


title: J_4-33_4-2-35

description: Sample name: H4.2/Ind35


title: J_3-13_4-1-23

description: Sample name: H4.1/Ind23


title: J_3-14_4-1-24

description: Sample name: H4.1/Ind24


title: J_3-26_4-1-41

description: Sample name: H4.1/Ind41


title: E_3-15_4-1-31

description: Sample name: H4.1/Ind31


title: J_3-8_4-1-19

description: Sample name: H4.1/Ind19


title: E_3-3_4-1-2

description: Sample name: H4.1/Ind2


title: E_3-14_4-1-18

description: Sample name: H4.1/Ind18


title: J_3-9_4-1-20

description: Sample name: H4.1/Ind20


title: J_3-10_4-1-21

description: Sample name: H4.1/Ind21


title: J_3-11_4-1-22

description: Sample name: H4.1/Ind22


title: E_3-4_4-1-3

description: Sample name: H4.1/Ind3


title: E_3-10_4-1-15

description: Sample name: H4.1/Ind15


title: E_3-11_4-1-16

description: Sample name: H4.1/Ind16


title: E_3-13_4-1-17

description: Sample name: H4.1/Ind17


title: J_3-21_4-1-30

description: Sample name: H4.1/Ind30


title: E_3-27_4-1-48

description: Sample name: H4.1/Ind48


title: E_3-9_4-1-14

description: Sample name: H4.1/Ind14


title: E_3-8_4-1-13

description: Sample name: H4.1/Ind13


title: E_3-25_4-4-46

description: Sample name: H4.4/Ind46


title: J_3-7_4-1-12

description: Sample name: H4.1/Ind12


title: J_3-6_4-1-11

description: Sample name: H4.1/Ind11


title: J_4-51_3-2-90

description: Sample name: H3.2/Ind90


title: E_4-54_3-2-9

description: Sample name: H3.2/Ind9


title: E_4-50_3-2-95

description: Sample name: H3.2/Ind95


title: E_3-1_4-1-1

description: Sample name: H4.1/Ind1


title: E_4-52_3-2-7

description: Sample name: H3.2/Ind7


title: J_4-57_3-2-6

description: Sample name: H3.2/Ind6


title: E_4-7_3-2-37

description: Sample name: H3.2/Ind37


title: J_4-47_3-2-86

description: Sample name: H3.2/Ind86


title: J_4-64_3-2-31

description: Sample name: H3.2/Ind31


title: E_4-9_3-2-38

description: Sample name: H3.2/Ind38


title: E_4-64_3-2-30

description: Sample name: H3.2/Ind30


title: E_4-29_3-2-28

description: Sample name: H3.2/Ind28


title: E_4-33_3-2-29

description: Sample name: H3.2/Ind29


title: E_4-64_3-2-25

description: Sample name: H3.2/Ind25


title: E_4-7_3-2-26

description: Sample name: H3.2/Ind26


title: E_4-9_3-2-27

description: Sample name: H3.2/Ind27


title: E_4-63_3-2-18

description: Sample name: H3.2/Ind18


title: J_4-62_3-2-23

description: Sample name: H3.2/Ind23


title: E_4-61_3-2-16

description: Sample name: H3.2/Ind16


title: J_3-5_4-1-10

description: Sample name: H4.1/Ind10


title: E_4-57_3-2-12

description: Sample name: H3.2/Ind12


title: E_4-60_3-2-15

description: Sample name: H3.2/Ind15


title: E_4-59_3-2-14

description: Sample name: H3.2/Ind14


title: J_4-46_3-2-85

description: Sample name: H3.2/Ind85


title: E_4-50_3-1-95

description: Sample name: H3.1/Ind95


title: E_4-51_3-1-96

description: Sample name: H3.1/Ind96


title: E_4-48_3-1-93

description: Sample name: H3.1/Ind93


title: E_4-49_3-1-94

description: Sample name: H3.1/Ind94


title: E_4-47_3-1-92

description: Sample name: H3.1/Ind92


title: J_4-3_3-1-9

description: Sample name: H3.1/Ind9


title: E_4-44_3-1-83

description: Sample name: H3.1/Ind83


title: E_4-41_3-1-80

description: Sample name: H3.1/Ind80


title: E_4-45_3-1-84

description: Sample name: H3.1/Ind84


title: E_4-42_3-1-81

description: Sample name: H3.1/Ind81


title: J_4-2_3-1-8

description: Sample name: H3.1/Ind8


title: E_4-39_3-1-79

description: Sample name: H3.1/Ind79


title: E_4-62_3-2-17

description: Sample name: H3.2/Ind17


title: J_4-36_3-1-70

description: Sample name: H3.1/Ind70


title: E_4-38_3-1-66

description: Sample name: H3.1/Ind66


title: J_4-45_3-1-78

description: Sample name: H3.1/Ind78


title: E_4-37_3-1-65

description: Sample name: H3.1/Ind65


title: E_4-36_3-1-64

description: Sample name: H3.1/Ind64


title: E_4-58_3-2-13

description: Sample name: H3.2/Ind13


title: E_4-56_3-2-11

description: Sample name: H3.2/Ind11


title: E_4-32_3-1-61

description: Sample name: H3.1/Ind61


title: E_4-6_3-1-6

description: Sample name: H3.1/Ind6


title: E_4-30_3-1-53

description: Sample name: H3.1/Ind53


title: E_4-33_3-1-62

description: Sample name: H3.1/Ind62


title: E_4-31_3-1-54

description: Sample name: H3.1/Ind54


title: E_4-34_3-1-63

description: Sample name: H3.1/Ind63


title: J_4-52_3-2-1

description: Sample name: H3.2/Ind1


title: J_4-26_3-1-55

description: Sample name: H3.1/Ind55


title: E_4-29_3-1-52

description: Sample name: H3.1/Ind52


title: E_4-46_3-1-91

description: Sample name: H3.1/Ind91


title: E_4-27_3-1-50

description: Sample name: H3.1/Ind50


title: E_4-43_3-1-82

description: Sample name: H3.1/Ind82


title: E_4-23_3-1-46

description: Sample name: H3.1/Ind46


title: E_4-25_3-1-48

description: Sample name: H3.1/Ind48


title: E_4-28_3-1-51

description: Sample name: H3.1/Ind51


title: J_4-43_3-1-76

description: Sample name: H3.1/Ind76


title: E_4-24_3-1-47

description: Sample name: H3.1/Ind47


title: E_4-22_3-1-45

description: Sample name: H3.1/Ind45


title: E_4-26_3-1-49

description: Sample name: H3.1/Ind49


title: E_2-2-6-3_3-2-83

description: Sample name: M3.2/Ind83

tag: strain


title: J_2-1-60-3_3-2-81

description: Sample name: M3.2/Ind81


title: J_4-25_3-1-42

description: Sample name: H3.1/Ind42


title: E_4-20_3-1-43

description: Sample name: H3.1/Ind43


title: E_4-21_3-1-44

description: Sample name: H3.1/Ind44


title: WGA_3-2-82

description:
Sample name: M3.2/Ind82
For WGA samples, a genome devoid of DNA modifications was used to verify the efficiency of the bisulfite conversion reactions.


title: E_4-4_3-1-4

description: Sample name: H3.1/Ind4


title: J_4-21_3-1-38

description: Sample name: H3.1/Ind38


title: E_2-1-60-1_3-2-84

description: Sample name: M3.2/Ind84


title: J_2-1-60-2_3-2-80

description: Sample name: M3.2/Ind80


title: E_4-18_3-1-36

description: Sample name: H3.1/Ind36


title: E_4-17_3-1-35

description: Sample name: H3.1/Ind35


title: J_9-4_3-2-77

description: Sample name: M3.2/Ind77


title: E_6-10-2_3-2-74

description: Sample name: M3.2/Ind74


title: E_4-16_3-1-34

description: Sample name: H3.1/Ind34


title: E_4-5_3-1-5

description: Sample name: H3.1/Ind5


title: E_6-10-3_3-2-75

description: Sample name: M3.2/Ind75


title: E_4-15_3-1-33

description: Sample name: H3.1/Ind33


title: E_6-10-1_3-2-73

description: Sample name: M3.2/Ind73


title: E_4-14_3-1-32

description: Sample name: H3.1/Ind32


title: E_6-9-6_3-2-72

description: Sample name: M3.2/Ind72


title: E_4-13_3-1-31

description: Sample name: H3.1/Ind31


title: E_6-9-5_3-2-71

description: Sample name: M3.2/Ind71


title: J_4-15_3-1-27

description: Sample name: H3.1/Ind27


title: E_6-9-4_3-2-70

description: Sample name: M3.2/Ind70


title: E_60-7-3_3-2-69

description: Sample name: M3.2/Ind69


title: E_4-3_3-1-3

description: Sample name: H3.1/Ind3


title: J_4-16_3-1-28

description: Sample name: H3.1/Ind28


title: E_60-7-2_3-2-68

description: Sample name: M3.2/Ind68


title: J_4-13_3-1-25

description: Sample name: H3.1/Ind25


title: J_2-1-60-1_3-2-79

description: Sample name: M3.2/Ind79


title: E_60-7-1_3-2-67

description: Sample name: M3.2/Ind67


title: E_2-2-60-4_3-2-66

description: Sample name: M3.2/Ind66


title: E_4-11_3-1-17

description: Sample name: H3.1/Ind17


title: E_4-2_3-1-2

description: Sample name: H3.1/Ind2


title: E_6-9-2_3-2-64

description: Sample name: M3.2/Ind64


title: E_6-8-7_3-2-63

description: Sample name: M3.2/Ind63


title: E_4-12_3-1-18

description: Sample name: H3.1/Ind18


title: E_4-10_3-1-16

description: Sample name: H3.1/Ind16


title: E_4-9_3-1-15

description: Sample name: H3.1/Ind15


title: E_4-8_3-1-14

description: Sample name: H3.1/Ind14


title: E_6-8-6_3-2-62

description: Sample name: M3.2/Ind62


title: E_2-2-60-3_3-2-61

description: Sample name: M3.2/Ind61


title: E_2-2-60-2_3-2-60

description: Sample name: M3.2/Ind60


title: E_2-2-60-1_3-2-59

description: Sample name: M3.2/Ind59


title: E_4-7_3-1-13

description: Sample name: H3.1/Ind13


title: E_2-1-60-8_3-2-58

description: Sample name: M3.2/Ind58


title: E_4-1_3-1-1

description: Sample name: H3.1/Ind1


title: E_6-8-5_3-2-57

description: Sample name: M3.2/Ind57


title: J_4-6_3-1-12

description: Sample name: H3.1/Ind12


title: E_6-8-3_3-2-55

description: Sample name: M3.2/Ind55


title: E_2-1-60-3_3-2-52

description: Sample name: M3.2/Ind52


title: E_2-1-60-5_3-2-53

description: Sample name: M3.2/Ind53


title: E_6-8-4_3-2-56

description: Sample name: M3.2/Ind56


title: J_4-8_3-1-20

description: Sample name: H3.1/Ind20


title: E_6-8-2_3-2-54

description: Sample name: M3.2/Ind54


title: E_2-1-60-2_3-2-51

description: Sample name: M3.2/Ind51


title: WGA_1-2-46

description:
Sample name: H1.2/Ind46
For WGA samples, a genome devoid of DNA modifications was used to verify the efficiency of the bisulfite conversion reactions.


title: E_6-9-3_3-2-65

description: Sample name: M3.2/Ind65


title: S_LAC25_1-2-42

description: Sample name: H1.2/Ind42

source_name: Sperm

value: Sperm


title: E_2-2-6-3_3-2-49

description: Sample name: M3.2/Ind49


title: J_4-2_1-2-45

description: Sample name: H1.2/Ind45


title: S_21_1-2-2

description: Sample name: H1.2/Ind2


title: S_LAC10_1-1-34

description: Sample name: H1.1/Ind34


title: S_2_1-2-1

description: Sample name: H1.2/Ind1


title: S_LAC26_1-2-43

description: Sample name: H1.2/Ind43


title: S_LAC16_1-2-38

description: Sample name: H1.2/Ind38


title: J_4-1_1-2-44

description: Sample name: H1.2/Ind44


title: S_LAC23_1-2-41

description: Sample name: H1.2/Ind41


title: E_2-1-60-1_3-2-50

description: Sample name: M3.2/Ind50


title: S_LAC7_1-1-33

description: Sample name: H1.1/Ind33


title: S_LAC22_1-2-40

description: Sample name: H1.2/Ind40


title: S_LAC15_1-2-37

description: Sample name: H1.2/Ind37


title: S_22_1-1-27

description: Sample name: H1.1/Ind27


title: S_LAC13_1-1-36

description: Sample name: H1.1/Ind36


title: S_LAC21_1-2-39

description: Sample name: H1.2/Ind39


title: S_23_1-1-28

description: Sample name: H1.1/Ind28


title: S_LAC12_1-1-35

description: Sample name: H1.1/Ind35


title: S_21_1-1-26

description: Sample name: H1.1/Ind26


title: S_2_1-1-25

description: Sample name: H1.1/Ind25


title: S_LAC5_1-1-32

description: Sample name: H1.1/Ind32


title: DPY27 RNAi L1 rep4

city: Ann Arbor

first: Gyorgyi

last: Csankovszki

state: MI

address: 830 N. University Ave.

department: MCDB

institute: University of Michigan

data_processing:
Reads were trimmed for quality using the TrimGalore program from Babraham Bioinformatics and aligned to the C. elegans genome version WS235 with Tophat v 2.0.13. Default parameters allow up to 20 hits for each read. Gene expression was quantified using Cufflinks v2.2.1 with use of “rescue method” for multi-reads and supplying gene annotation for WS235. Gene count estimation was performed using HTSeq-count tool v0.6.0 in the default “union” mode.  Differential expression analysis was performed using DESeq2 v1.6.3 in R version 3.2.3. All analyses were performed which genes that had average expression level above 1 RPKM (reads per kilobase per million, as calculated by Cufflinks).
Genome_build: C. elegans genome version WS235
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, and values from DESeq2 (log2 fold change of (mutant/control) and p-values after adjustment for multiple test correction)

organism: Caenorhabditis elegans

source_name: L1 worms_DPY27 RNAi L1

growth_protocol: Worms were synchronized by bleaching gravid adults to isolate embryos and allowing worms to hatch overnight. Newly hatched L1 larval worms were plated and grown for 3 hours on NGM plates with OP50.

extract_protocol:
RNA was extracted and precipitated using the manufacturer's instructions. Total RNA was cleaned using the Qiagen RNeasy kit.
Non-stranded mRNA-seq libraries were prepared using TruSeq RNA Library Preperation Kit.

treatment_protocol: Packed larvae were resuspended in 10V of Trizol and frozen at -80C.

tag: strain/genotype

value: N2, DPY-27 RNAi

value: worms; packed larvae


title: cec-4, Vector RNAi L1 rep3

source_name: L1 worms_cec-4, Vector RNAi L1

value: RB2301, Vector RNAi


title: S_LAC4_1-1-31

description: Sample name: H1.1/Ind31


title: S_LAC2_1-1-30

description: Sample name: H1.1/Ind30


title: met-2 set-25, Vector RNAi L1 rep2

source_name: L1 worms_met-2 set-25, Vector RNAi L1

value: EKM99, Vector


title: atcep1 stage C

city: Beijing

first: dan

middle: dan

last: Zhang

address: No.35 Qinghua East Road, Haidian Distract

department: College of Biological Sciences and Biotechnology

institute: Beijing Forestry University

data_processing:
Raw reads were carried out data filtering and removed the adaptor sequences and/or low quality reads to obtain the clean reads (clean data).
The clean reads were mapped to the Arabidopsis reference genome (TAIR10) and reference genes using SOAP aligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
Reads Per kb per Million reads (RPKM) method were calculated using a protocol from Mortaiavi, et al., Nature Methods, 2008.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKMs.

source_name: bud, atcep1 mutant, stage 10-11

growth_protocol: Both the wild type (WT) and atcep1 mutant Arabidopsis plants were grown on soil mixture (3:1:1 mixture of peat moss-enriched soil: vermiculite: perlite) with 14 h light /10 h dark photoperiod at 23°C.

extract_protocol:
Arabidopsis buds at several development stages were flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
The 3ug total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000.

tag: ecotype/background

value: Columbia

value: atcep1 mutant

value: bud

tag: anther development stage


title: met-2 set-25, Vector RNAi L1 rep3


title: cec-4, Vector RNAi L1 rep1


title: N2, Vector RNAi L1 rep3

source_name: L1 worms_N2, Vector RNAi L1

value: N2, Vector RNAi


title: cec-4, Vector RNAi L1 rep2


title: atcep1 stage A

source_name: bud, atcep1 mutant, stage 5-6


title: S_LAC1_1-1-29

description: Sample name: H1.1/Ind29

value: Bisulfite-converted Padlock

value: M

tag: age


title: atcep1 stage B

source_name: bud, atcep1 mutant, stage 7-9

tag: tissue


title: DPY27 RNAi L1 rep1

tag: developmental stage


title: DPY27 RNAi L1 rep2


title: WT stage A

source_name: bud, WT, stage 5-6

tag: genotype/variation

value: wild type


title: WT stage C

source_name: bud, WT, stage 10-11


title: WT stage B

source_name: bud, WT, stage 7-9


title: N2, Vector RNAi L1 rep2


title: WT3

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

description: Liver tissue

data_processing:
Illumina pipeline version 1.8 used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: WT Liver

growth_protocol: RNA was isolated from flash frozen ground whole liver tissue.

extract_protocol:
RNA was isolated from flash frozen ground whole tissue following manufacturer’s instructions for Trizol (Invitrogen).
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.

tag: cell-type

value: Liver tissue

value: C57BL/6J x 129SvJ


title: N2, Vector RNAi L1 rep1


title: WT2

description: Liver tissue


title: M2_KO3

description: Liver tissue

source_name: PKM2 KO Liver


title: M2_KO2

description: Liver tissue