title: ATAC_L60_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D60 from early malignant lesions replicate#3


title: ATAC_L21_2

status: Public on May 17 2017

type: SRA

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: mouse splenocytes

library_source: genomic

data_processing:
Library strategy: ATAC-Seq
Base trimming and quality filtering using TrimGalore! v0.4.0, powered by CutAdapt v1.8.1 and FastQC v0.11.3 using paired and fastqc options
Alignment using Bowtie2 v2.2.5 using default parameter settings
conversion to bam, uniq, sort bam using SAMtools v0.1.18
peak calling using macs2 callpeak v2.1.0.20140616 on merged replicates per sample type, using p-value cutoff of 1e-2, no model, keep-dup=all, call-summits
IDR per sample to find reproducible peaks, create atlas of reproducible ATAC-seq peaks for both mouse and human
Counting of reads aligning to atlas peak regions using the summarizeOverlaps function of the R package GenomicAlignments v1.2.2 and GenomicRanges v1.18.4
Library-size normalized read counts per atlas peak were calculated using DESeq2 v1.6.3
Genome_build: mm10 for mus musculus data and hg38 for human samples
Supplementary_files_format_and_content: tab-delimited text file - columns: chromosome, peak start, peak end, gene symbol, gene refseq ID, peak type, DESeq2 size-factor normalized read count for peak

molecule: genomic DNA

organism: Mus musculus

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D21 from early malignant lesions replicate#2

extract_protocol:
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition happened at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47x106 paired reads were generated per sample.

tag: cd8 t cell status

value: TCR SV40-I transgenic CD8 T cells

tag: disease state

value: early malignant liver lesions


title: ATAC_L14_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D14 from early malignant lesions replicate#2


title: ATAC_L14_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D14 from early malignant lesions replicate#3


title: ATAC_L14_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D14 from early malignant lesions replicate#1


title: ATAC_L7_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D7 from early malignant lesions replicate#3


title: ATAC_L7_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D7 from early malignant lesions replicate#1


title: ATAC_L5_4

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D5 from early malignant lesions replicate#4


title: ATAC_L7_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D7 from early malignant lesions replicate#2


title: ATAC_L5_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D5 from early malignant lesions replicate#2


title: ATAC_L5_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D5 from early malignant lesions replicate#1


title: ATAC_L5_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D5 from early malignant lesions replicate#3


title: ATAC_M1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1/CD44+/CD62L+) central memory TCR SV40-I CD8 T cells replicate#1

value: acute Listeria infection


title: ATAC_M2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1/CD44+/CD62L+) central memory TCR SV40-I CD8 T cells replicate#2


title: ATAC_M3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1/CD44+/CD62L+) central memory TCR SV40-I CD8 T cells replicate#3


title: ATAC_L28_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D28 from early malignant lesions replicate#2


title: ATAC_E5_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) D5 effector TCR SV40-I CD8 T cells replicate#3


title: ATAC_E7_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) D7 effector TCR SV40-I CD8 T cells replicate#3


title: ATAC_E5_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) D5 effector TCR SV40-I CD8 T cells replicate#2


title: ATAC_N3

description: mouse splenocytes

source_name: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#3


title: ATAC_E5_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) D5 effector TCR SV40-I CD8 T cells replicate#1


title: ATAC_E7_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) D7 effector TCR SV40-I CD8 T cells replicate#2


title: ATAC_N1

description: mouse splenocytes

source_name: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#1


title: RNA_ML35_1

library_source: transcriptomic

data_processing:
Base trimming and quality filtering using TrimGalore! v0.4.0, powered by CutAdapt v1.8.1 and FastQC v0.11.3 using paired and fastqc options
Paired-end alignment using STAR v2.4.0f1 and default parameters
Conversion of sam to bam file and ordering of aligned reads using SAMtools v0.1.18
Counting of reads aligning to transcripts using the summarizeOverlaps function of the R package GenomicAlignments v1.2.2 and GenomicRanges v1.18.4
Library-size normalized read counts were calculated using DESeq2 v1.6.3
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing DESeq size-factor normalized counts per gene. First column indicates gene Entrez ID, second column indicates normalized count value

molecule: total RNA

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D35 from established tumors replicate#1

extract_protocol:
CD8 T cells were FACS-sorted straight into Trizol tube and stored at -80°C until all samples were collected. RNA from sorted cells was extracted using RNeasy mini kit (Qiagen) according to instructions provided by the manufacturer. After ribogreen quantification and quality control of Agilent BioAnalyzer, 6-15 ng of total RNA underwent amplification (12 cycles) using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing. 10ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 51 million paired reads were generated per sample and the percent of mRNA bases was 62.5% on average.
10ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).

tag: strain

value: established hepatocellular carcinoma


title: RNA_ML35_3

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D35 from established tumors replicate#3


title: RNA_ML35_2

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D35 from established tumors replicate#2


title: RNA_ML7_1

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors replicate#1


title: RNA_ML7_3

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors replicate#3


title: RNA_ML7_2

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors replicate#2


title: RNA_L60_1

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D60 from early malignant lesions replicate#1


title: RNA_L60_2

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D60 from early malignant lesions replicate#2


title: RNA_L35_3

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D35 from early malignant lesions replicate#3


title: RNA_L35_2

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D35 from early malignant lesions replicate#2


title: ATAC_Hum_PD1hi_2

organism: Homo sapiens

source_name: Sort-purified PD1hi CD8 T cells from melanoma patient 2

value: Tumor-infiltrating CD8 T cells

value: melanoma


title: TSC2_KO_RNA

city: Bethesda

first: Peng

last: Yang

state: Maryland

address: 6 Center Drive 6B-211

department: DDB

institute: NICHD/NIH

data_processing:
Illumina Casava software used for basecalling.
Fastq files were aligned by Bowtie2(v2.25) with default premeters to generate bam files.
Bam files were converted to tdf files by using IGVtools (2.3.78)
Genome_build: mm9
Supplementary_files_format_and_content: tdf files generated from IGVtools

source_name: Derived from zfp568-gfpflox/flox;RosaCreERT2 blastocysts embryos

extract_protocol:
RNA was prepared from cells or embryos using the RNeasy Plus Mini or Micro kit  (Qiagen) with on-column DNase digestion.
RNA-seq libraries were constructed according to Illumima protocol and sequenced with the Illumina Hiseq 2000. ChIP-seq libraries were constructied by using DNA SMART™ ChIPSeq Kit from Clontech

tag: tissue

value: TSC


title: TSC_KO_H3K9me3_ChIP


title: TSC_WT_H3K9me3_ChIP


title: RNA_L35_1

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D35 from early malignant lesions replicate#1


title: ATAC_Hum_PD1hi_3

source_name: Sort-purified PD1hi CD8 T cells from lung carcinoma patient 1

value: lung carcinoma


title: ATAC_N2

description: mouse splenocytes

source_name: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#2


title: ATAC_Hum_CM_3

source_name: Central Memory sort-purified CD8/CD45RO+/CD62L(hi) peripheral blood lymphocytes obtained from healthy donors

value: CD8 T cells from peripheral blood

value: healthy


title: ATAC_Hum_PD1hi_1

source_name: Sort-purified PD1hi CD8 T cells from melanoma patient 1


title: RNA_L28_2

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D28 from early malignant lesions replicate#2


title: RNA_L28_3

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D28 from early malignant lesions replicate#3


title: TSCrep_ZFP568_ChIP


title: RNA_L28_1

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D28 from early malignant lesions replicate#1


title: TSC_ZFP568_ChIP


title: ATAC_Hum_CM_1


title: TSC2_WT_RNA


title: TSC1_WT_RNA


title: RNA_L21_2

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D21 from early malignant lesions replicate#2


title: ATAC_Hum_CM_2


title: ATAC_Hum_EM_2

source_name: Effector Memory sort-purified CD8/CD45RO+/CD62L(low) peripheral blood lymphocytes obtained from healthy donors


title: RNA_L14_3

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D14 from early malignant lesions replicate#3


title: ESC_KO_ZFP568_ChIP

value: ESC


title: TSC1_KO_RNA


title: ATAC_Hum_EM_1


title: ESC_KO_H3K9me3_ChIP


title: RNA_L14_2

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D14 from early malignant lesions replicate#2


title: ESC_KAP1_ChIP


title: RNA_L21_1

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D21 from early malignant lesions replicate#1


title: ESC_WT_H3K9me3_ChIP


title: ATAC_Hum_N2

source_name: Naïve sort-purified CD8/CD45RA+ peripheral blood lymphocytes obtained from healthy donors


title: ATAC_Hum_N3


title: RNA_L21_3

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D21 from early malignant lesions replicate#3


title: RNA_L7_3

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D7 from early malignant lesions replicate#3


title: ESC_ZFP568_ChIP

source_name: Derived from zfp568-gfpflox/flox;RosaCreERT2 blastocysts embryos


title: ATAC_Hum_N1


title: RNA_L7_1

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D7 from early malignant lesions replicate#1


title: RNA_L7_2

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D7 from early malignant lesions replicate#2


title: ESCrep_ZFP568_ChIP


title: RNA_L5_3

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D5 from early malignant lesions replicate#3


title: ALL#7 CNS

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: ALL cells from CNS

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequence reads were mapped to hg19 reference genomes, downloaded on 25th April 2014, using Tophat v2.0.14. Calculation of gene expression value and normalization were performed by featureCounts and RUVseq.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized expressed gene counts of samples

source_name: ALL Pt#7 CNS cells

extract_protocol:
For samples of ALL#6 and #7, Total RNA was isolated by the RNeasy Kit (Qiagen, Valencia, CA), and cDNA libraries were generated with Ovation RNA-seq System V2 (NuGEN) according to the manufacturer’s instructions. For the sample of ALL#8, RNA extraction and cDNA synthesis of samples were perfomed with SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories, Inc. Mountain View, CA, USA) according to the manufacturer’s instructions. Sequencing libraries were constructed using the Nextera XT DNA Sample Prep kit (Illumina) and Nextera XT Index kit (Illumina).
For samples of ALL#6 and #7, the libraries were sequenced with the TruSeq SBS kit v3 and TruSeq PE Cluster kit v3 (Illumina) in 100-cycle paired-end mode of HiSeq 2500 (Illumina).   For the sample of ALL#8, The libraries were sequenced with the TruSeq SBS kit v3 and TruSeq SR Cluster kit v3 (Illumina) in 100-cycle Single-Read mode of HiSeq 2500 (Illumina).

tag: cell type

value: ALL cells

value: CNS

tag: patient id

tag: gender

value: female


title: ALL#8 CNS

description: ALL cells from CNS

source_name: ALL Pt#8 CNS cells

value: male


title: ATAC_Hum_EM_3


title: RNA_L5_2

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D5 from early malignant lesions replicate#2


title: ALL#8 BM

description: ALL cells from bone marrow

source_name: ALL Pt#8 BM cells

value: bone marrow


title: Set2-HTP_3

city: Grenoble

first: Camille

last: Sayou

address: 17 avenue de Martyrs

department: BGE UA13

country: France

institute: CEA, IRIG

description: Barcode (N is random nucleotide): NNNCGCTTAGC

data_processing:
Library strategy: CRAC
Demultiplexing: pyBarcodeFilter from pyCRAC (Webb et al, 2014) was used to split reads according to barcodes and clip the barcodes.
Removing 3’ adaptor: FLEXBAR (Dodt et al. 2012) was used to remove the 3’ sequencing adapters, trim low-quality positions from the 3’ end of reads and remove reads without a high-quality score (parameters –u 3 –q 30 –m 17 –ao 3).
Collapsing read: in addition of the barcode, the 5’ linkers contain a random 3 nt sequence, allowing PCR duplicates to be removed by collapsing identical sequences.
Removing low complexity reads: sequences with more than 80% of one nucleotide were excluded to avoid potential non-genome-encoded oligo(A) tails to map to A-rich regions of the genome (Tuck and Tollervey 2013).
Mapping: reads were aligned to the yeast genome (S. cerevisiae genome version EF4.74, from Ensembl) using novoalign from Novocraft (parameters -s 1 -r Random).
Collapsing mapped reads: to remove PCR duplicates that were not collapsed during preprocessing due to sequencing errors or differential trimming at the 3’ end, any reads with the same random tag in their 5’ linker and with 5’ ends mapping to the same genomic coordinate were collapsed (Tuck and Tollervey 2013).
Excluding non-RNAPII reads: reads mapping to RNAPI and RNAPIII transcripts (including novel transcripts described in Turowski et al. 2016) or originating from the mitochondrial genome were removed.
Calculating coverage: the coverage at each position along the genome was calculated and normalized to the library size (reads per million), as described in Milligan et al, 2016.
Genome_build: S. cerevisiae genome version EF4.74, from Ensembl
Supplementary_files_format_and_content: BigWig files contain information about the number of mapped and normalized reads at each position along the genome. For each dataset, there are two BigWig files, one for each strand.

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol under denaturing conditions. RNAs were partially digested.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose. RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Yeast cultures were irradiated with UV light, to fix protein-RNA interactions.

value: BY4741 Set2-HTP


title: BY4741_1

description: Barcode (N is random nucleotide): NNNTAAGC


title: BY4741_2


title: ALL#7 BM

description: ALL cells from bone marrow

source_name: ALL Pt#7 BM cells


title: ALL#6 CNS

description: ALL cells from CNS

source_name: ALL Pt#6 CNS cells


title: Set2-HTP_2

description: Barcode (N is random nucleotide): NNNAGAGC


title: ALL#6 BM

description: ALL cells from bone marrow

source_name: ALL Pt#6 BM cells


title: RNA_L5_1

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D5 from early malignant lesions replicate#1

value: TCR SV40-I transgenic CD8 T cells


title: RNA_M2

source_name: Sort-purified (CD8/Thy1.1/CD44+/CD62L+) central memory TCR SV40-I CD8 T cells replicate#2


title: Set2-HTP_1

description: Barcode (N is random nucleotide): NNNGACTTAGC


title: RNA_M3

source_name: Sort-purified (CD8/Thy1.1/CD44+/CD62L+) central memory TCR SV40-I CD8 T cells replicate#3


title: RNA_L14_1

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D14 from early malignant lesions replicate#1

value: early malignant liver lesions


title: Set1-HTP_4

value: BY4741 Set1-HTP


title: RNA_M1

source_name: Sort-purified (CD8/Thy1.1/CD44+/CD62L+) central memory TCR SV40-I CD8 T cells replicate#1

value: acute Listeria infection


title: RNA_E7_3

source_name: Sort-purified (CD8/Thy1.1) D7 effector TCR SV40-I CD8 T cells replicate#3


title: Set1-HTP_3

description: Barcode (N is random nucleotide): NNNTCTCTAGC


title: Set1-HTP_2


title: Hs688(A)T (primary cell line)

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
DNA from 7 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment was done using Bismark program.
UNIX scripts and our in house developed tool DMAP (Chatterjee et al 2012, Nucleic Acids Research) was used for post processing of the data
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .txt files describing methylation status of each filtered CpG sites.

source_name: primary melanoma cell line

extract_protocol:
Cells were grown under standard conditions (5% CO2, 37°C, humidified atmosphere). : DNA from the cell pellets were extracted using Pure link Genomic DNA mini kit (Invitrogen, Hilden, Germany) following the manufacturer’s protocol, with the modification of proteinase K treatment being performed overnight at 55°C.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 49bp run.

tag: cell line

value: primary melanoma cell line


title: RNA_E7_2

source_name: Sort-purified (CD8/Thy1.1) D7 effector TCR SV40-I CD8 T cells replicate#2


title: WM75 (primary cell line)


title: Set1-HTP_1

description: Barcode (N is random nucleotide): NNNACTCAGC


title: WM373 cell line  (metastatic cell line)

source_name: metastatic melanoma cell line

value: metastatic melanoma cell line


title: WM-266-4 cell line (metastatic cell line)


title: PTH-Set1_4

description: Barcode (N is random nucleotide): NNNATTAGC

value: BY4741 PTH-Set1


title: PTH-Set1dRRM2_1

value: BY4741 PTH-Set1deltaRRM2


title: PTH-Set1dRRM2_2

description: Barcode (N is random nucleotide): NNNGCGCAGC


title: RNA_E5_2

source_name: Sort-purified (CD8/Thy1.1) D5 effector TCR SV40-I CD8 T cells replicate#2


title: B1-1

city: Columbia

first: Alexander

last: Franz

state: MO

address: 303 Connaway Hall

department: Department of Veterinary Pathobiology

institute: University of Missouri

data_processing:
The raw sequences (fastq) were subjected to quality check by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The adapter removal and quality trimming of the raw reads were done using fqtrim (https://ccb.jhu.edu/software/fqtrim/). Read shorter than 30 nucleotides and quality score less than 25 were excluded from further analysis.
The trimmed reads generated were subjected to mapping to the Aedes aegypti reference genome AaegL3 using Hisat2 mapper
FeatureCounts was used to quantify transcript abundance in each sample using the gene annotation AaegL3.3 obtained from VectorBase (https://www.vectorbase.org/organisms/aedes-aegypti).
Differential expression (DE) analysis between sample groups were performed by edgeRrobust.
Genome_build: AaegL3
Supplementary_files_format_and_content: The processed data is read counts for each gene for all the 27 samples in a text format file.

organism: Aedes aegypti

source_name: midgut

growth_protocol: One week-old females of Ae. aegypti mosquitoes of the Higgs White Eye (HWE) strain were deprived of sugar for 24 h, and then fed for 1 h with a mixture of equal amount of CHIKV-infected cell culture or non-infected cell culture mixture (control) and 40% BSA or 2xPBS solution at 37°C using a single glass feeder per carton.  Fully engorged females were selected and reared in 1.9 L (64 oz.) cartons and offered raisins and water until the further analysis.

extract_protocol:
Total RNA was extracted from 15 midguts (= 1 sample) using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA samples were DNase-treated to remove potential contamination from genomic DNA. RNA purity and concentration were analyzed with a NanoDrop 1000 v 1.3.2 (Thermo Scientific, Wilmington, DE). The absence of RNA degradation was initially assessed by electrophoresis of 1 μg of RNA on a 1.0% agarose gel. Thereafter, the quality of each RNA sample was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with an RNA Nano Chip.
mRNA samples were further prepared for RNA-Seq analysis using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). First-strand cDNA synthesis produced single-stranded DNA copies from the fragmented RNA by reverse transcription. After second-strand cDNA synthesis, the double-stranded DNA underwent end-repair and the 3’ends were adenylated. Finally, universal adapters were ligated to the cDNA fragments and PCR was performed to produce the final sequencing library. These template molecules were used for cluster generation and sequencing on the Illumina NextSeq 500 instrument with multiple lanes and paired-end read (2 x 75 bases). Each treatment was analyzed as three independent biological replicates.

treatment_protocol: CHIKV infected  as treatment compared against uninfected Ae. aegypti HWE mosquitoes;  protein meal (BSA) or saline meal (PBS) fed compared with sugarfed Ae. aegypti HWE mosquitoes

tag: feeding protocol

value: Uninfected protein meal (BSA)

tag: time (postfeeding day of midgut sampling)

value: 1 day after feeding

value: pool of 15 dissected midguts


title: RNA_E5_3

source_name: Sort-purified (CD8/Thy1.1) D5 effector TCR SV40-I CD8 T cells replicate#3


title: PTH-Set1_3


title: P1i-2

value: CHIKV-infected saline meal (PBS)


title: WM-155 (primary cell line)


title: Mel-ST (melanocyte cell line)

source_name: melanocyte cell line

value: Mel-ST

value: melanocyte cell line


title: RNA_E5_1

source_name: Sort-purified (CD8/Thy1.1) D5 effector TCR SV40-I CD8 T cells replicate#1


title: PTH-Set1_2


title: RNA_N3

source_name: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#3


title: PTH-Set1_1

description: Barcode (N is random nucleotide): NNNTGGAGC


title: PTH-Set1dRRM2_3


title: B2i-1

value: CHIKV-infected protein meal (BSA)

value: 2 days after feeding


title: P2i-1


title: E8_KO2_RNA

source_name: E8.5 zfp568-gfpko/ko embryo

value: Embryo


title: B2i-2


title: E8_KO1_RNA


title: P2-3

value: Uninfected saline meal (PBS)


title: E8_WT2_RNA

source_name: E8.5   zfp568-gfpflox/flox embryo


title: B1-3


title: RNA_E7_1

source_name: Sort-purified (CD8/Thy1.1) D7 effector TCR SV40-I CD8 T cells replicate#1

value: TCR SV40-I transgenic CD8 T cells


title: RNA_N1

source_name: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#1


title: Hs688(B)T (metastatic cell line)


title: ESC_Mut2_ZFP568_ChIP

source_name: Mutation at binding site from ESC_WT

value: ESC


title: ESC_Mut2_H3K9me3_ChIP


title: ESC_Mut1_ZFP568_ChIP


title: S-1

value: Sugar fed


title: P1-3


title: B1i-3


title: ESC_Mut1_H3K9me3_ChIP


title: B1i-1


title: B1i-2


title: RNA_N2

source_name: Sort-purified (CD8/CD44low) naïve transgenic TCR SV40-I CD8 T cells replicate#2

value: acute Listeria infection


title: ESC_hybrid_KO2_RNA

source_name: Derived from CAST/Eij X C57BL/6 mice


title: ESC3_KO_RNA

source_name: Derived from zfp568-gfpflox/flox;RosaCreERT2 blastocysts embryos


title: ESC_hybrid_KO1_RNA


title: E8_WT1_RNA


title: ESC2_KO_RNA


title: ESC1_KO_RNA


title: ESC3_WT_RNA


title: P1i-1


title: P1-1


title: B2i-3


title: S-3


title: B1-2


title: ESC2_WT_RNA


title: P1i-3


title: ESC1_WT_RNA


title: B2-1


title: B2-3


title: P2-2


title: ESC_hybrid_WT_RNA


title: HSPC from hiPSC_RS7

city: Boston

first: Areum

last: Han

state: MA

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

data_processing:
Adaptor sequences were removed using a Cutadapt tool (Martin, 2011) allowing some mismatches (The specific parameters we used were -n 2 -e 0.1 –O 15 --quality-base=33).
The cleaned reads were aligned to the human genome/transcriptome (hg19 and corresponding UCSC gene model, hg19_UCSC_knownGene) using TopHat2 software (Kim et al., 2013).
To estimate expression levels for each gene, aligned reads per gene were counted using a htseq-count tool (Anders et al., 2015) on refGene gene model.
Counts were then normalized and converted to RPKM values (Reads Per Kilobase per Million) utilizing an edgeR package (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab-delimited text file includes RPKM values for each Sample.

source_name: HSPC from hiPSC

growth_protocol: Human iPSCs were differentiated with morphogens and hematopoietic cytokines according to Detadi 2015.

extract_protocol:
RNA was purified with RNeasy Micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Hemogenic endothelium was induced with lentiviral vectors encoding transcription factors, followed by transplantation to mouse models.

value: Hematopoietic stem/progenitor cells

tag: cell type derived from

value: human induced pluripotent stem cells


title: HSPC from CB_RS2 (single-cell RNA-seq)

description:
Single-cell RNA-seq
Profiling of same sample as GSM2214011 HSPC from CB_RS2  (bulk RNA-seq)

data_processing:
R2 reads were trimmed for adaptor sequence and poly Ts. Barcodes and UMI(Unique Molecular Identifier) were parsed out and used as cell identifiers and redundant reads indicators, respectively. R1 reads were mapped to human cDNA sequences using bowtie. Alignment results were filtered based on the indrop data processing protocol. We are reporting filtered UMI counts per cell and per gene.
Details on how to demultiplex the multiplexed fastq files:  see the README file and two barcode list files.
Genome_build: Homo_sapiens.GRCh38 cDNA
Supplementary_files_format_and_content: [.txt] tab deliminated text files with UMI filtered counts.  Each "bc#" column represents a single cell.

source_name: HSPC from CB

extract_protocol: RNA was purified and proccessed for indrop according to the protocol from Klein et al (Cell, 2015, doi:10.1016/j.cell.2015.04.044)

value: cord blood


title: HSPC from hiPSC_RS1 (single-cell RNA-seq)

description:
Single-cell RNA-seq
Profiling of same sample as GSM2214010 HSPC from hiPSC_RS1  (bulk RNA-seq)


title: B2-2

value: Uninfected protein meal (BSA)


title: P2i-3


title: P2i-2


title: P1-2

value: 1 day after feeding


title: HD rep 3

status: Public on May 16 2017

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

description:
60n8_BEC_A
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt

data_processing:
Reads were trimmed by base quality scores >20 and mapped to the hg19 genome with Tophat2.
Counts per gene were calculated by counting reads mapping to constitutive exons using HTSeq.
Counts for each gene were then analyzed with the R package DESeq2 to identify differentially expressed genes with a single comparison of HD versus non-disease. A 10% false discovery rate cutoff and log2 difference of 0.5 between non-diseased and HD conditions was used for significance.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt: Tab-delimited text file includes raw read count abundance measurements for each Sample.

source_name: iPSC-derived brain microvascular endothelial cells, HD

extract_protocol:
RNA was isolated from cell pellets with a Qiagen RNeasy Kit with QIAshredder homogenization.
RNA-Seq libraries were made with 1µg of RNA using the Illumina Tru-Seq v2 protocol. Libraries were sequenced on two lanes of the Hi-Seq 2500 at 75 bases using the rapid run protocol.

tag: disease status

value: Huntington's disease


title: CTL rep 2

description:
28n6_BEC_B
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt

source_name: iPSC-derived brain microvascular endothelial cells, control

value: Control


title: CTL rep 3

description:
33n1_BEC_A
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt

value: iPSC-derived brain microvascular endothelial cells


title: HD rep 5

description:
66n4_BEC_A
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: HD rep 8

description:
71n3_BEC_B
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: HSPC from CB_RS2


title: HE from hiPSC_RS3

source_name: HE from hiPSC

value: Hemogenic endothelial cells


title: HD rep 6

description:
66n4_BEC_B
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: S-2

source_name: midgut

value: pool of 15 dissected midguts


title: HD rep 4

description:
60n8_BEC_B
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: CTL rep 1

description:
28n6_BEC_A
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: HD rep 2

description:
109n1_BEC_B
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: Mov10_IP

city: Urbana

first: Stephanie

last: Ceman

state: IL

address: 601 S. Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois-Urbana Champaign

data_processing:
The libraries were pooled in equimolar concentration and sequenced on one lane on a HiSeq 2500 for 101 cycles from one end of the fragments with a HiSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
As all bases of all reads have quality scores greater than phred score 30, all raw reads were used to align against mouse genome mm10 using TopHat2 version 2.1.1 aligner with -g 2000 and all default parameters
Bioconductor package RIPSeeker version 3.3 was used to identify regions that are significantly enriched in Mov10_IP compared to Input samples
Bedtools intersect version 2.25.0 was used to find overlaps between regions identified by RIPSeeker and repeat elements and all mouse transcripts
Mouse genomic coordinates of repeatmasker database's repeat elements and RefSeq database's all mouse transcripts were obtained from UCSC genome browser table browser
Genome_build: mm10
Supplementary_files_format_and_content: GFF3 generated using RIPSeeker

source_name: brain

growth_protocol: the brains came from mice two days after birth (P2)

extract_protocol:
NA
standard Illumina prep

treatment_protocol: the brains were homogenized and immunoprecipitated

tag: fraction

value: Immunoprecipitated RNA


title: Input

value: input


title: HD rep 7

description:
71n3_BEC_A
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: CTL rep 4

description:
33n1_BEC_B
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: HD rep 1

description:
109n1_BEC_A
mRNA-Seq
Processed data file: HD iBMEC_RA_5DEC2014_gene_counts 24MAR2017.txt


title: P2-1

value: Uninfected saline meal (PBS)

value: 2 days after feeding


title: HE from hiPSC_RS4


title: HSPC from hiPSC_RS1


title: WT_UD_n_2

first: Joseph

last: Seimetz

state: Illinois

address: 506 South Mathews Ave.

department: Biochemistry

institute: University of Illinois Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
Insert distrubution calculated with Picard_1.119
FPKM values were generated and compared between sets of samples using CuffDiff_2.2.1
Gene Ontology was determined using DAVID_6.8
Genome_build: GRCm38 M8
Supplementary_files_format_and_content: CuffDiff output text file

growth_protocol: Cells were plated at a density of 200000 per well in 10% DMEM media.

extract_protocol:
Cells were dissociated and total RNA was extracted using TRIZOL reagent, followed by Phenol chloroform, checked for qulaity on 1% MOPS gel, cleaned using Zymoclean RNA concentrator Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”

treatment_protocol: 24hours after plating cells were either changed to fresh media or differentiated using retinoic acid in 2% Fetal Calf Serum containing media for 48hrs. Media was changed every day.

value: neuroblastoma cell line

tag: genotype/variation

value: wild type

tag: passages

tag: cell status

value: Undifferentiated


title: WT_D_n_2

value: differentiated with 20uM Retinoic Acid


title: WT_UD_n_1


title: Sample_HT1

city: Durham

first: Hongyu

last: Tian

address: B354 LSRC Research Drive

department: Department of Medicine

institute: Duke University

data_processing:
The flowcell was sequenced on a HiSeq 2500 V4 chemistry with 50bp Single read protocol.
Data was demultiplexed and Fastq files were generated using BcptoFastq 1.8.4 script provided by Illumina
RNA-SEQ reads (~54M per sample) were aligned to the UCSC hg19 reference genome using TopHat2.
The quantification results from htseq-count were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: hg19
Supplementary_files_format_and_content: normalized counts

source_name: Wild type PASMC

growth_protocol: Wild type and ENG-/- PASMC cell were purchased from the Cell Culture Facility at Duke University, and were grown in smooth muscle growth medium-2 (LONZA), supplemented with SingleQuots™ Kits (LONZA)

extract_protocol:
Total RNA was purified from NTC or ENG-/- PASMC cells using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with Agilent Tapestation 200 (Agilent Technologies) and Qubit 2.0 (ThermoFisher Scientific).
~250-500 ng RNA were used for library construction. The NGS libraries were constructed using the KAPA Stranded mRNA-Seq Kits (KapaBioSystems).

treatment_protocol: Endoglin-knockout cells were generated by stable transduction with lentivirus generated from pLentiCRISPRV2 constructs (Addgene Plasmid #52961) bearing the endoglin-targeting guide sequence (TGCCGACGACGCCATGACCC; HGLibA_15125) from the GeCKov2 library

value: PASMC vascular smooth muscle cells

value: WT

tag: crispr guide sequence

value: Non target control (NTC)


title: Sample_HT6

source_name: ENG-/- PASMC

value: ENG-/-

value: TGCCGACGACGCCATGACCC; HGLibA_15125


title: Sample_HT3


title: Sample_HT4


title: Sample_HT2


title: WT_D_n_1


title: Sample_HT5


title: KO_UD_n_2

source_name: Neuro-2a_MOV10 KO_undifferentiated

value: CRISPR-Cas Knockout lines for MOV10


title: input DNA for Gata6 ChIP-seq

city: London

first: Giacomo

last: Donati

address: Guy's Hospital, Great Maze Pond

country: United Kingdom

institute: King's College London

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using the BWA alignment program
Peak calling was performed with Homer (Heinz et al., 2010). The peaks detected by both antibodies were considered target regions.
Genome_build: mm9

source_name: primary keratinocytes_input

growth_protocol: Primary mouse keratinocytes were isolated from dorsal skin and cultured on confluent irradiated 3T3-J2 fibroblast feeders in FAD medium (DMEM: Ham’s F12, 3:1, 1.8 × 10−4  M adenine) supplemented with 10% FCS, hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), cholera toxin (8.4 ng/ml) and epidermal growth factor (10 ng/ml).

extract_protocol:
Lysates were clarified from sonicated nuclei and ∆NLef1-DNA complexes were isolated with antibody.
Immunoprecipitated DNA was prepared for sequencing as previously described (Schmidt et al., 2009). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200/300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Lentiviral virions used for infection of primary mouse keratinocytes were produced in HEK293T with the Trans-Lentiviral Packaging System in combination with Precision LentiORFs for Gata6 overexpression (Dharmacon).

tag: strain background

value: lentiviral (Gata6 overexpression) infected keratinocytes


title: Gata6_Ab2_ChIPSeq

source_name: primary keratinocytes_Gata6_ChIP-seq

tag: chip antibody

value: Gata6 (D61E4)

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody ref/lot info


title: KO_D_n_1

source_name: Neuro-2a_MOV10 KO_differentiated

tag: cell type


title: Negative_control(Flag Antibody) for Gata6 ChIP-seq

source_name: primary keratinocytes_Flag_ChIP-seq

value: Flag

value: Sigma

tag: chip antibody cat. #

tag: chip antibody lot. #


title: KO_D_n_2

tag: cell line


title: CFBE RPF replicate 2

city: Hamburg

first: Robert

last: Rauscher

address: Martin-Luther-King-Platz 6

country: Germany

institute: University Hamburg

description: Ribosome protected fragments

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 16
Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 16
Mapping to rRNA references using Bowtie, version 0.12.9, parameters -v 0
Genome mapping using reads unmapped to rRNA using Bowtie, version 0.12.9, parameters -l 16 -n 1 -e 50 -m 1 --best--strata. Additional information: CFTR was masked in the genome and a plasmid containing the CFTR gene was added
Read counting using htseq-count (HTSeq) version 0.6.0, parameters
Genome_build: GRCh37.73(Ensembl)
Supplementary_files_format_and_content: Tab separated file with to columns generated by htseq-counts tool. Column 1: Ensembl gene ID. Column 2: read counts

source_name: Homo sapiens

growth_protocol: Cystic Fibrosis Bronchial Epithelial cells were grown at 37°C to 80% confluency in Eagle's MEM.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA using the Ribo-Zero Gold rRNA Removal Kit (Illumina) and spiked with ERCC RNA Spike-In Mix(Thermo Fisher).
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009}

value: CFBE

tag: molecule type

value: Ribosome protected fragments


title: hyp2-3_rep3

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Library strategy: 5P-Seq
Read demultiplexed using Illumina BaseSpace servers. Illumina BaseSpace FASTQ Generation. Version: 1.0.0
For each read we trimmed the first 8 nt (UMI, unique molecular identifier) and align the rest to S. cerevisiae genome (version R64-1-1) using Hisat2 with default parameters (except limiting the maximum intron size to 2kb). Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI colapsed reads por positive and negative strand

growth_protocol: Saccharomyces cerevisiae haploid strains wild type BY4741 (MATa his3∆0 leu2∆0 met15∆0 ura3∆0) and the temperature-sensitive eIF5A mutants tif51A-1 (MATa ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 ssd1-d tif51A-1) and tif51A-3 (MATa ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 ssd1-d tif51A-3) were grown in liquid YPD (1% yeast extract, 2% peptone, 2% glucose) media at 25°C until exponential phase.

extract_protocol:
Cells were harvested and pellets were frozen in liquid nitrogen and kept at -80°C until further processing. Total RNA was extracted from yeast cells using phenol:chloroform extraction.
5PSeq methods was performed as previously described (PMID: 26820793) with minor modifications. 1µg of total RNA was used as input. After single-stranded RNA ligation, partial rRNA depletion was performed using mammalian RiboCop rRNA depletion kit (Lexogen). 5PSeq libraries were PRC amplified (18 cycles), pooled and size selected (300-500nt). Samples were sequenced using a NextSeq500 producing single-end 75 reads.

treatment_protocol: Cells were transferred to 37°C and were incubated for 4 h.

tag: strain


title: hyp2-3_rep2


title: hyp2-3_rep1


title: Gata6_Ab1_ChIPSeq

value: R&D Systems


title: hyp2-1_rep3


title: Laublab_ML2000_swarmer_1h_after_IPTG_withdrawal RNA

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

data_processing:
For analysis of DNA sequencing data, Hiseq 2500 Illumina short reads (40 bp) were mapped to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 using the following command:
bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-2014-bowtie --sam *.fastq
The Caulobacter NA1000 genome was divided into 4000 bins and mapped Illumina reads were allocated to their corresponding bins to quantify the number of reads in each genomic bin. For samples where the DSB was introduced at 780 kb, datasets were normalized so that the experimental and the control dataset have the same number of Illumina reads between genomic position 2800 kb and 3400 kb. This genomic region was chosen since it is far from the DSB and was not affected by AddAB-induced DNA degradation. For samples where DSB was introduced at 3042 kb, datasets were normalized to have the same number of Illumina reads between genomic position 600 kb and 1200 kb instead. The enrichment between experimental datasets (DSBs were induced) and control dataset (no DSBs) is represented as the ratio of read counts in each bin between the experiment and the control, smoothed using the Lowess function in R with the smoothing bandwidth set to 0.01, and plotted against the genomic positions.
For analysis of RNA-seq data, Hiseq 2500 Illumina short reads (40 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC-011916.1) using Bowtie 1 using the following command:
bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-2014-bowtie --sam *.fastq
The sequencing coverage was computed using BEDTools. The general feature format (gff) file for Caulobacter NA1000 was downloaded from NCBI (ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Caulobacter_crescentus_NA1000_uid32027/). The normalized value of reads per kb per million mapped reads (RPKPM) was calculated for each gene by a custom R script to enable comparison of gene expression within and between RNA-seq datasets. The enrichment between experimental datasets (DSBs were induced) and control dataset (no DSBs) is represented as the ratio of RPKPM of each gene between the experiment and the control and plotted against the genomic positions.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .txt: tab-delimited text file of nucleotide-resolution coverage from gDNA-seq or RNA-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus CB15N

growth_protocol: Cultures of Caulobacter were grown at 30oC in PYE and supplemented with antibiotics, as necessary, at appropriate concentrations. For induction of Plac-dnaA, IPTG was added to a final concentration of 0.5 mM. For induction of a DSB, cells were supplemented with 500 μM vanillate unless otherwise indicated. For DSB induction in non-replicating Caulobacter swarmer cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and DSBs were induced for 1 h by the addition of 500 μM vanillate.

extract_protocol:
DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen. RNA were extracted using Hot Trizol. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2000 sequencing platform

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) for 1 h. Cells were collected and snap-frozen before RNA extraction by Hot-Trizol

tag: developmental stage

value: swarmer cells (1.5 h after DnaA depletion and 1 h after synchronization)

tag: genotype

value: Plac_dnaA hfa:Plac_lacI


title: Laublab_ML2425_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate1

description: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_03821)::tetR; parSpMT1 site (after CCNA_03776)::specR; Pvan-I-SceI::chlorR; ΔrecA::gentR

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and DSBs were induced for 1 h by the addition of 500 μM vanillate. Cells were collected and snap-frozen before RNA extraction by Hot-Trizol

value: 1 h double-strand break induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_03821)::tetR; parSpMT1 site (after CCNA_03776)::specR; Pvan-I-SceI::chlorR; deltarecA::gentR


title: Laublab_ML2425_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate2


title: hyp2-1_rep2


title: Laublab_ML2471_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate2

description: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; ΔrecA::gentR

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; deltarecA::gentR


title: hyp2-1_rep1


title: KO_UD_n_1

value: neuroblastoma cell line

value: Undifferentiated


title: Laublab_ML2466_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate1

description: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; ΔaddAB::gentR

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; deltaaddAB::gentR


title: Laublab_ML2471_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate1


title: BY4741_rep3


title: Laublab_ML2465_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate2

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_03821)::tetR; parSpMT1 site (after CCNA_03776)::specR; Pvan-I-SceI::chlorR;


title: Laublab_ML2466_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate2


title: BY4741_rep2


title: Laublab_ML2464_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate2

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR;


title: CFBE RPF

description: Ribosome protected fragments


title: Laublab_ML2465_swarmer_4h_after_IPTG_withdrawal_and_van_induction

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and DSBs were induced for 4 h by the addition of 500 μM vanillate. Cells were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen.

value: 4 h double-strand break induction


title: Laublab_ML2465_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate1


title: Laublab_ML2464_swarmer_1h_after_IPTG_withdrawal_and_van_induction_replicate1


title: CFBE RPF replicate

description: Ribosome protected fragments


title: Laublab_ML2447_swarmer_1h_after_IPTG_withdrawal_and_van_induction

description: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; ΔrecA::gentR; PrecA-recA(K38A) (xyl locus)::kanR

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and DSBs were induced for 1 h by the addition of 500 μM vanillate. Cells were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen.

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; deltarecA::gentR; PrecA-recA(K38A) (xyl locus)::kanR


title: Laublab_ML2464_swarmer_1h_after_IPTG_withdrawal_and_van_induction_mungbean_treatment

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and DSBs were induced for 1 h by the addition of 500 μM vanillate. For Mung bean treatment, isolated genomic DNA was incubated at 30°C for 15 min with Mung bean nuclease (NEB) and the DNA was purified with a phenol-chloroform extraction. Cells were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen.

value: 1 h double-strand break induction+mung bean


title: Laublab_ML2464_asynchronous_cells

treatment_protocol: Mixed population of cells (OD ~0.1) were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen.

value: Mixed cell population


title: Laublab_ML2464_asynchronous_cells_1h_after_van_induction_500uMvanillate

treatment_protocol: Caulobacter cells were induced for 1 h by the addition of 500 μM vanillate. Cells were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen.

value: 1 h double-strand break induction (500uM van)


title: CBFβ-deficient naive CD8 CBF ChIP-Seq

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Histone Marks ChIP-Seq libraries, SICER (v1.1, Zang et al., Bioinformatics) was used to identify histone mark islands. In each library, islands were identified with false discovery rate (FDR) of less than 1E-4 and island-filtered tags were used for downstream analysis.
For CBFβ ChIP-Seq libraries, MACS (v1.4.2, Zhang et al., Genome Biol) was used for peak calling. We used the criteria of enrichment of four-fold or more, a P value of <1E-5 and false-discovery rate of <5% and thus identified CBFβ binding peaks.
Genome_build: mm9

source_name: CD8 T cells

extract_protocol:
CD8+ effector T cells were sort-purified on day 4 post-infection, the cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with antibodies against H3K4Me1, H3K4me3, H3K27me3, or H3K27Ac, which were then properly washed and immunoprecipitated DNA extracted. For ChIP-Seq of CBF, naive CD8 T cells and CD8+ effector T cells (sorted on day 8 post-infection) were isolated and immunoprecipated with an anti-CBF antiserum.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: Cbfb-/-

tag: tissue

value: Cbfb-/- naïve CD8 T Cells

tag: cell phenotype

value: CD8+, CD62L high, CD44 low to medium

value: CBFβ


title: Laublab_ML2471_swarmer_1h_after_IPTG_withdrawal_and_van_induction

value: 1 h double-strand break induction


title: Runx3-deficient CD8 Input

value: effector CD8 T cells


title: Laublab_ML2464_asynchronous_cells_1h_after_van_induction_2uMvanillate

treatment_protocol: Caulobacter cells were induced for 1 h by the addition of 2 μM vanillate. Cells were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen.

value: 1 h double-strand break induction (2uM van)


title: Runx3-deficient CD8 H3K27Me3 ChIP-Seq


title: Runx3-deficient CD8 H3K27Ac ChIP-Seq


title: Naïve CD8 CBF ChIP-Seq

value: wild type

value: WT naïve CD8 T Cells


title: Effector CD8 CBF ChIP-Seq

value: CD8+, KLRG1 high, IL-7Ra low.


title: Laublab_ML2644_swarmer_1h_after_IPTG_withdrawal_and_van_induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; lexA*::kanR


title: Runx3-deficient CD8 H3K4Me3 ChIP-Seq


title: Runx3-deficient CD8 H3K4Me1 ChIP-Seq


title: Laublab_ML2469_swarmer_1h_after_IPTG_withdrawal_and_van_induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; chiFor (after CCNA_00836)::gentR


title: T2SC_R3

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

data_processing:
FastQ adapter and Phred score (Q20) trimming using BBDuk
STAR (2.4.0j) aligner to mm37 genome, default except --seedSearchStartLmaxOverLread 0.5
Duplicates removed (Picard Tools MarkDuplicates, v1.105)
Read counts made with FeatureCounts (SubRead package), s=2
Genome_build: mm37
Supplementary_files_format_and_content: Read counts as per data processing step

source_name: Embryonic stem cells

growth_protocol: mESCs E14 were cultivated on gelatinized culture dishes in GMEM (SIGMA) supplemented with 10% (v/v) mESC certified FBS (Gibco), 100 U/ml penicillin and 100 U/ml streptomycin (Gibco), 50 uM Beta-Mercaptoethanol (SIGMA), 1:100 GlutaMAX (Gibco), 1:100 non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco) and 1000 U/ml  LIF (ESGRO). The cells were propagated every other day.

extract_protocol:
Total RNA was isolated using the QIAGEN RNeasy Mini Kit. In column DNase I digestion step was performed.
Illumina TruSeq Stranded
50bp Single End

treatment_protocol: Stable shRNA-mediated knockdown was achieved by lentiviral transduction of E14 mESCs with pLKO.1 targeting mouse Fam60a and Sin3a in three biological replicates. Control cells were generated in parallel by transduction of non-targeting pLKO.1 shScrambled. Cells were incubated with virus particles in the presence of 10 ug/ml Polybrene (Sigma) for 24 hours. After a recovery phase of 12 hours, cells were selected for several days with 2 ug/ml puromycin. Cells were propagated three times before harvested.

value: Embryonic stem cells

tag: age


title: T2SC_R1


title: T2SC_R2


title: Sin3a_R3


title: Fam60a_1_R3


title: Sin3a_R1


title: Laublab_ML2465_swarmer_2h_after_IPTG_withdrawal_and_van_induction

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and DSBs were induced for 2 h by the addition of 500 μM vanillate. Cells were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen.

value: 2 h double-strand break induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_03821)::tetR; parSpMT1 site (after CCNA_03776)::specR; Pvan-I-SceI::chlorR;


title: Wildtype CD8 Input


title: Fam60a_1_R2


title: CXZ01dgd

city: Hangzhou

first: cao

last: jiayi

address: 866 Yu Hang Tang Road

country: China

institute: Zhejiang University

description: processed data file: Supplementary Table S6 Targets of miRNAs detected by degradome sequenceing.xls

data_processing:
The single-end sequencing (36 bp) of the small RNA library was performed on an Illumina Hiseq2500 at the LC Science (Hangzhou, China). The raw sequences were filtered to remove the adapter sequences and contaminated reads. The retained mappable reads were further analyzed following the work flow by ATCG101-miR4.2 software (LC Science). The unique small RNA sequences were firstly mapped to known pre-miRNAs deposited in miRBase database (release 21.0) (http://www.mirbase.org/) by mapping program Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). After that, the reads matched to rRNA, tRNA, snRNA, snoRNA and other non-coding RNA sequences deposited in Rfam (http://rfam.janelia.org) and the repeat-Repbase (http://www.girinst.org/repbase.) were deducted. The remaining reads were mapped onto the reference genome (B. napus) by mapping program megablast (http://www.ncbi.nlm.nih.gov/blast/html/megablast.html) under default parameters. Sequences without mismatch to the genome were retained for miRNA prediction. Finally, new candidate miRNAs were identified by prediction of the secondary structures with Mfold program (http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form). The naming system of miRNAs identified in this study is as follows: The miRNA name is composed of the 1st known miR name in a cluster, an underscore, and a matching annotation: L-n means the miRNA_seq (detected) is n base less than known rep_miRSeq in the left side; R-n means the miRNA_seq (detected) is n base less than known rep_miRSeq in the right side; L+n means the miRNA_seq (detected) is n base more than known rep_miRSeq in the left side; R+n means the miRNA_seq (detected) is n base more than known rep_miRSeq in the right side; 2ss5TC13TA means 2 substitutin (ss), which are T to C at position 5 and T to A at position 13. If there is no matching annotation, the miRNA_seq (detected) is exactly the same as known rep_miRSeq. Newly discovered 5'/3' sequences are annotated as p5/p3 to distinguish from the reported 5'/3' sequences.
Identification and classification of categories of the sliced miRNA targets were processed according to the CleaveLand 3.0 software package (Addo-Quaye et al. 2009). The degradome sequences were used to search against unique genes of B. napus downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) for finding their potential target genes. All cleaved targets were sorted into five categories (Category 0 to 4). Briefly, Category 0 degradome tags correspond to the expected miRNA-mediated cleavage position, with abundance at a position equal to the maximum on the transcript, and exhibiting only one peak. Category 1 degradome tags are with abundance at a position equal to the maximum on the transcript, and forming more than one peak. Category 2 degradome tags are with abundance at a position higher than the median but less than the maximum on the transcript. Category 3 degradome tags are with abundance at the position equal to or less than the median for the transcript, and Category 4 we got only 1 raw read at the position of the transcript. Moreover, we also computationally predicted target genes of miRNAs by TargetFinder using a position-dependent, mispair penalty system as described (Allen et al, 2005). Penalties were assessed for mismatches, bulges, and gaps (+1 per position) and G:U pairs (+0.5 per position). Penalties were doubled if the mismatch, bulge, gap, or G:U pair occurred at positions 2 to 13 relative to the 5’ end of the miRNA. Only one single-nt bulge or single-nt gap was allowed. Based on a reference set of validated miRNA targets, only predicted targets with scores of four or less were considered reasonable.
Genome_build: Brassica_napus_v4.1; http://www.genoscope.cns.fr/brassicanapus/data/
Supplementary_files_format_and_content: Supplementary Table S2 Profiles of Brassica napus miRNAs.xls, miRNA sequence and expression data .Supplementary Table S6 Targets of miRNAs detected by degradome sequenceing.xls, miRNA target prediction results,target position and degradome fragments abundance on cleavage position

organism: Brassica napus

source_name: leaves, stems, roots and seeds

growth_protocol: B. napus plants were grown in growth cabinets at 22 ℃ to 25 ℃ with a 16/8-h day/night photoperiod.

extract_protocol:
Total RNA was isolated from each sample using an RNA Extraction Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions.
Small RNA libraries were generated from the mixture of samples using the Illumina TruSeq Small RNA Preparation kit (Illumina, San Diego, USA) according to the manufacturer’s guidelines.   Two degradome libraries were constructed following the methods described previously by German et al. (2008).
miRNA-Seq(CXZ_comp) and RNA-Seq (Parallel analysis of RNA ends (PARE),CXZ01dgd and CXZ02dgd)

treatment_protocol: B. napus leaves were inoculated with S. sclerotiorum mycelial plugs. Leaf discs of inoculated areas of 1 cm at diameter and those uninoculated tissue were collected.

value: leaves, stems, roots and seeds

tag: sample information

value: Mixture of equal amounts of total RNAs from leaves, stems, roots and seeds


title: Wildtype CD8 H3K27Me3 ChIP-Seq


title: Laublab_ML2464_swarmer_2h_after_IPTG_withdrawal_and_van_induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR;


title: Laublab_ML2470_swarmer_1h_after_IPTG_withdrawal_and_van_induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; chiRev (after CCNA_00836)::gentR


title: Laublab_ML2466_swarmer_1h_after_IPTG_withdrawal_and_van_induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; deltaaddAB::gentR


title: Runx3-deficient CD8 rep2

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample. Wig files are available for each sample.

extract_protocol:
CD8+ effector T cells were sort-purified and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol


title: Wildtype CD8 H3K4Me1 ChIP-Seq


title: Wildtype CD8 H3K4Me3 ChIP-Seq


title: Laublab_ML2465_swarmer_1h_after_IPTG_withdrawal_and_van_induction


title: Runx3-deficient CD8 rep1


title: Laublab_ML2464_swarmer_1h_after_IPTG_withdrawal_and_van_induction


title: Wildtype CD8 H3K27Ac ChIP-Seq


title: CXZ_comp

description: Leaf discs of inoculated areas of 1 cm at diameter at 12 hours post inoculation (hpi) and those uninoculated were collected

source_name: leaves

value: leaves

value: Mixture of total RNA from Sclerotinia sclerotiorum-inoculated and uninoculated leaves


title: Wildtype CD8 rep1

value: effector CD8 T cells


title: Laublab_ML2468_swarmer_1h_after_IPTG_withdrawal_and_van_induction

value: 1 h double-strand break induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; chiRev (after CCNA_00774)::gentR


title: Laublab_ML2000_swarmer_1h_after_IPTG_withdrawal DNA

treatment_protocol: Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) for 1 h. Cells were pelleted and genomic DNA was isolated using the DNeasy Blood and Tissue kit from Qiagen. DNA was sent for whole-genome Illumina sequencing (BioMicroCenter, MIT).

value: swarmer cells (1.5 h after DnaA depletion and 1 h after synchronization)

value: Plac_dnaA hfa:Plac_lacI


title: Laublab_ML2467_swarmer_1h_after_IPTG_withdrawal_and_van_induction

value: PlacI-lacI (hfaA locus); Plac-dnaA (dnaA locus); I-SceI site (after CCNA_00727)::tetR; parSpMT1 site (after CCNA_00747)::specR; Pvan-I-SceI::chlorR; chiFor (after CCNA_00774)::gentR


title: Sin3a_R2


title: Wildtype CD8 rep2

value: wild type

value: CD8+, KLRG1 high, IL-7Ra low.


title: CXZ02dgd

value: Total RNA from S. sclerotiorum-inoculated leaves sampled at 6 hpi


title: Whole fish

status: Public on May 15 2017

first: Marina

last: Venero Galanternik

address: 6 Center Drive Building 6B - Room 4B-412

department: NICHD

institute: NIH

description:
Processed data file: Raw Counts.txt
Processed data file: GFP_RFP.txt
Processed data file: GFP_Whole.txt
Wholefish_S4Aligned.sortedByCoord.out.bam
fish1_S9Aligned.sortedByCoord.out.bam
fish2_S10Aligned.sortedByCoord.out.bam
fish3_S11Aligned.sortedByCoord.out.bam

data_processing:
Illumina software for base calling.
Reads trimmed using trimmomatc and aligned using RNA-STAR.
Differential RNA expression was quantified by subread featureCounts and tested by DESeq2.
Genome_build: Zv10 (GRCz10, danRer10)
Supplementary_files_format_and_content: Raw Counts.txt: Tab-delimited text file includes the raw counts of the samples.
Supplementary_files_format_and_content: GFP_RFP.txt: Tab-delimited text file includes the comparisons between the GFP(+) and mCherry/RFP(+) cells.
Supplementary_files_format_and_content: GFP_Whole.txt: Tab-delimited text file includes the comparisons between the GFP(+) and whole fish cells.

organism: Danio rerio

source_name: Adult fish

extract_protocol:
Manual dissection of whole brain, trypsin mechanical dissociation and FACS sorting.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Ek

tag: genotype/variation

value: adult

tag: source tissue

value: Whole animal


title: Mrc1a-GFP(+)

description:
Processed data file: Raw Counts.txt
Processed data file: GFP_RFP.txt
Processed data file: GFP_Whole.txt
GFP1_S1Aligned.sortedByCoord.out.bam
GFP2_S2Aligned.sortedByCoord.out.bam
GFP3_S3Aligned.sortedByCoord.out.bam
GFP4_S4Aligned.sortedByCoord.out.bam

source_name: FGPs

value: fluorescent granular perithelial (FGP) cells

value: Brain


title: Fam60_1_R1

value: Embryonic stem cells


title: OX714F5

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

data_processing:
RNA-Seq:Short reads (51-bp) were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat6 with a supplied set of known RefSeq transcripts as the input.
RNA-Seq: Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
RNA-Seq: Expression values were quantified as read per kilobase of transcript length per million mapped reads (RPKM) based on the RefSeq gene model using the rpkmforgenes
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: RPKM values from RNA sequencing

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
From single FACS sorted cells, cDNA was generated according to Smart-seq2 protocol
Illumina sequenecing libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a protocol supplied by Fluidigm.
RNA-Seq samples were sequenced on Illumina HiSeq 2000

treatment_protocol: Cell populations isolated by FACS sorting from human bone marrow of CML patients or normal donors

tag: bcr-abl status

value: positive

tag: tumor stage

value: diagnosis

tag: phenotype


title: OX714E6

value: negative


title: OX714E8_merged


title: OX714E3


title: OX714F11


title: OX714F6


title: OX714E2


title: OX714E5


title: OX714F4


title: OX714E4


title: OX714F3


title: OX714E10


title: OX714D3


title: OX714D9


title: OX714D6


title: Kdrl-mCherry(+)

city: Bethesda

description:
Processed data file: Raw Counts.txt
Processed data file: GFP_RFP.txt
Processed data file: GFP_Whole.txt
RFP1_S5Aligned.sortedByCoord.out.bam
RFP2_S6Aligned.sortedByCoord.out.bam
RFP3_S7Aligned.sortedByCoord.out.bam
RFP4_S8Aligned.sortedByCoord.out.bam

source_name: Endothelial cells

tag: cell type

value: endothelial cells


title: OX714C9


title: OX714C8


title: OX714D7


title: OX714D5


title: OX714D4


title: OX714C3


title: OX714C11_merged


title: OX714D1


title: OX714C6


title: OX714C7


title: OX714D2


title: OX714B9


title: OX714B4


title: OX714C4


title: OX714A6


title: OX714A2


title: OX664H7_merged


title: OX714E9


title: OX664G9


title: OX714B6


title: OX714B8


title: OX664G7_merged


title: OX714B3


title: OX664G3_merged


title: OX714B2


title: OX714A5


title: OX714B1


title: OX714A4


title: OX714A7


title: OX714B5


title: OX714A3


title: OX714A1


title: OX664H8


title: OX664H5


title: OX664F4


title: OX664F3


title: OX664H2_merged


title: OX664G5


title: OX664G8


title: OX664F5


title: OX664G4


title: OX664E7


title: OX664E5


title: OX664D9


title: OX664D4


title: OX664D5


title: OX664G2


title: OX714A8_merged


title: OX664F9


title: OX664D3


title: OX664F7


title: OX664C5


title: OX664F8


title: OX664C3


title: OX664H3


title: OX664H4


title: OX664B5


title: OX664E8


title: OX664A8


title: OX664E4


title: OX664C4


title: OX664C9


title: OX664A6


title: OX664B8_merged


title: OX664A4


title: OX664B4


title: OX664A3


title: OX664B2


title: OX664B7


title: OX664A7_merged


title: OX2125F5


title: OX2125F7


title: OX664A5_merged


title: OX2125H11


title: OX2125F3


title: OX2125F10


title: OX2125F6


title: OX2125E8


title: OX664C7


title: OX2125E7


title: OX2125G10


title: OX2125F2


title: OX2125F11


title: OX2125E4


title: OX2125E2


title: OX2125E5


title: OX2125E12


title: OX2125E10


title: OX2125D7


title: OX2125D8


title: OX2125D6


title: OX2125H2


title: OX2125C9


title: OX2125D12


title: OX2125D10


title: OX2125F8


title: OX2125F12


title: OX2125C8


title: OX2125C7


title: OX2125C2


title: OX2125C12


title: OX2125C11


title: OX2125B2


title: OX2125C10


title: OX2125A7


title: OX2125B11


title: OX2125B6


title: OX2125A6


title: OX2125B8


title: OX2125B10


title: OX2125A2


title: OX2125A3


title: OX2125A11


title: OX2046H8


title: OX2046H7


title: OX2046H5


title: OX2046H2


title: OX2046H12


title: OX2046H3


title: OX2046H11


title: OX2046H10


title: OX2125B3


title: OX2046H4


title: OX2046H1


title: OX2046G9


title: OX2046H6


title: OX2046G8


title: OX2046G7


title: OX2046G6


title: OX2046G4


title: OX2046G3


title: OX2046G5


title: OX2046G12


title: OX2046G2


title: OX2046G10


title: OX2046G1


title: OX2046G11


title: OX2046F8


title: OX2046F9


title: OX2046F7


title: OX2046F6


title: OX2046F5


title: OX2046F4


title: OX2046F2


title: OX2046F11


title: OX2046F1


title: OX2046F10


title: OX2046H9


title: OX2046E9


title: OX2046E6


title: OX2046E8


title: OX2046E2


title: OX2046E12


title: OX2046E3


title: OX2046E5


title: OX2046D9


title: OX2046E10


title: OX2046E11


title: OX2046E1


title: OX2046D8


title: OX2046D2


title: OX2046D7


title: OX2046D6


title: OX2046D3


title: OX2046D5


title: OX2046D1


title: OX2046F12


title: OX2046D12


title: OX2046E4


title: OX2046D10


title: OX2046E7


title: OX2046C8


title: OX2046C12


title: OX2046C3


title: OX2046C11


title: OX2125A5


title: OX2046C5


title: OX2046C4


title: OX2046B7


title: OX2046C2


title: OX2046B6


title: OX2046C6


title: OX2046C10


title: OX2046C1


title: OX2046B9


title: OX2046B5


title: OX2046C9


title: OX2046B12


title: OX2046B11


title: OX2046B10


title: OX2046C7


title: OX2046A7


title: OX2046A8


title: OX2046D11


title: OX2046B1


title: OX2046B4


title: OX2046A9


title: OX2046A2


title: OX2038H8


title: OX2046A6


title: OX2046B3


title: OX2038H7


title: OX2046A3


title: OX2046A12


title: OX2046A10


title: OX2046A11


title: OX2046B8


title: OX2046A1


title: OX2038H6


title: OX2038H9


title: OX2046B2


title: OX2038H2


title: OX2046A5


title: OX2038H5


title: OX2038G9


title: OX2038G8


title: OX2038G6


title: OX2038H3


title: OX2038G7


title: OX2038H11


title: OX2038H1


title: OX2038H10


title: OX2046A4


title: OX2038H4


title: OX2038G3


title: OX2038F9


title: OX2038F8


title: OX2038G1


title: OX2038G5


title: OX2038F5


title: OX2038F4


title: OX2038F3


title: OX2038G12


title: OX2038F7


title: OX2038H12


title: OX2038G11


title: OX2038F6


title: OX2038F12


title: OX2038F11


title: OX2038F1


title: OX2038F2


title: OX2038F10


title: OX2038G2


title: OX2038E8


title: OX2038E7


title: OX2038E5


title: OX2038E9


title: OX2038E6


title: OX2038E3


title: OX2038E2


title: OX2038E11


title: OX2038E12


title: OX2038E10


title: OX2038D8


title: OX2038D9


title: OX2038D7


title: OX2038E1


title: OX2038D3


title: OX2038D6


title: OX2038D4


title: OX2038D5


title: OX2038D12


title: OX2038D10


title: OX2038C9


title: OX2038C4


title: OX2038C3


title: OX2038C8


title: OX2038C5


title: OX2038D1


title: OX2038E4


title: OX2038C6


title: OX2038C12


title: OX2038C10


title: OX2038C2


title: OX2038B5


title: OX2038B7


title: OX2038B6


title: OX2038C1


title: OX2038B4


title: OX2038B3


title: OX2038B2


title: OX2038B12


title: OX2038B1


title: OX2038B11


title: OX2038A8


title: OX2038B10


title: OX2038A7


title: OX2038A6


title: OX2038A5


title: OX2038A4


title: CML15_3mTKID10

data_processing:
RNA-Seq:Short reads (51-bp) were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat with a supplied set of known RefSeq transcripts as the input.
RNA-Seq: Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
RNA-Seq: Expression values were quantified as read per kilobase of transcript length per million mapped reads (RPKM) based on the RefSeq gene model using the rpkmforgenes
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: RPKM values from RNA sequencing

extract_protocol:
From single FACS sorted cells, cDNA was generated according to Smart-seq2 protocol
Illumina sequenecing libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a protocol supplied by Fluidigm.


title: OX2038A3


title: CML15_3mTKID9


title: OX2038B8


title: OX2038A12


title: OX2038A11


title: OX2038A10


title: CML15_3mTKIC8


title: OX2038G10


title: OX2038A2


title: CML15_3mTKIC1


title: OX2038A1


title: OX1931H9


title: CML15_3mTKIC9


title: OX1931H7


title: OX2038A9


title: OX1931H6


title: OX1931H8


title: OX1931H5


title: CML15_3mTKIC7


title: CML15_3mTKIA6


title: CML15_3mTKIB11


title: OX1931H2


title: CML15_3mTKID6


title: CML15_3mTKID5


title: CML15_3mTKIB4


title: OX1931H3


title: OX1931H11


title: CML15_3mTKIE1


title: CML15_3mTKIB5


title: CML15_3mTKIA11


title: OX1931H1


title: OX1931G8


title: CML15_3mTKIB10


title: OX1931G9


title: OX1931G6


title: CML15_3mTKIB9


title: OX1931G7


title: CML15_3mTKID1


title: CML15_3mTKIE5


title: CML15_3mTKID8


title: OX1931G5


title: CML15_3mTKIB2


title: OX1931G4


title: OX1931G3


title: CML15_3mTKIA10


title: CML15_3mTKIC11


title: OX1931G12


title: OX1931G2


title: CML15_3mTKIB6


title: CML15_3mTKIA8


title: OX1931H10


title: OX1931G10


title: OX1931G1


title: CML15_3mTKIB8


title: CML15_3mTKID11


title: CML15_3mTKIE4


title: OX1931F9


title: CML15_3mTKIA2


title: CML15_3mTKIC4


title: OX1931F7


title: CML22_6mTKID12


title: OX1931F5


title: CML15_3mTKIA12


title: OX1931F6


title: OX1931F8


title: OX1931F2


title: OX1931F4


title: CML22_3mTKIE12


title: CML15_3mTKIE6


title: CML22_6mTKIB7


title: OX1931F11


title: OX1931F10


title: CML22_6mTKIF4


title: CML22_6mTKIB10


title: OX1931F3


title: CML22_6mTKIH3


title: CML22_6mTKID11


title: CML22_6mTKIF7


title: CML22_6mTKIG4


title: OX1931E9


title: OX1931E8


title: OX1931G11


title: OX1931F1


title: OX1931E7


title: CML22_6mTKIB8


title: CML22_6mTKIB12


title: CML22_3mTKIE11


title: OX1931E6


title: CML22_6mTKIB9


title: CML22_6mTKIE7


title: OX1931E5


title: OX1931F12


title: OX1931E4


title: CML22_6mTKIA5


title: CML22_6mTKIB6


title: OX1931E3


title: OX1931E12


title: CML22_6mTKIF6


title: OX1931E2


title: CML22_6mTKIG7


title: OX1931E11


title: OX1931E1


title: CML22_6mTKIF11


title: CML22_3mTKIC2


title: OX1931D8


title: OX1931D7


title: CML22_3mTKIA10


title: OX1931D6


title: CML22_3mTKIC6


title: OX1931D5


title: CML22_3mTKIB12


title: CML22_3mTKIE1


title: OX1931D4


title: CML22_3mTKIB7


title: OX1931D3


title: OX1931D12


title: CML22_3mTKIB11


title: CML22_3mTKIA8


title: CML22_3mTKIA6


title: CML22_6mTKIG1


title: OX1931D11


title: CML22_3mTKIB8


title: OX1931E10


title: OX1931D1


title: CML22_3mTKIA2


title: CML22_3mTKID10


title: OX1931C7


title: CML22_3mTKIE2


title: CML22_3mTKIA9


title: OX1931D9


title: OX1931C8


title: OX1931C9


title: OX1931D10


title: OX1931C6


title: CML25_3mTKI_PL1H9


title: OX1931C4


title: CML25_3mTKI_PL1G10


title: CML25_3mTKI_PL2H1


title: OX1931C2


title: CML22_3mTKID11


title: OX1931C12


title: OX1931C5


title: CML25_3mTKI_PL1C8


title: CML25_3mTKI_PL1G2


title: CML25_3mTKI_PL2B10


title: CML25_3mTKI_PL2A6


title: CML25_3mTKI_PL2G5


title: OX1931C11


title: CML25_3mTKI_PL2F1


title: CML25_3mTKI_PL2B2


title: OX1931C10


title: OX1931B9


title: OX1931B8


title: OX1931B6


title: CML25_3mTKI_PL1A1


title: OX1931C1


title: CML25_3mTKI_PL2C4


title: CML25_3mTKI_PL2C9


title: OX1931B7


title: CML25_3mTKI_PL2A10


title: OX1931B5


title: OX1931B4


title: CML25_3mTKI_PL2F8


title: CML25_3mTKI_PL2F5


title: CML25_3mTKI_PL2H6


title: OX1931C3


title: OX1931B2


title: OX1931B12


title: CML25_3mTKI_PL2H10


title: CML25_3mTKI_PL2A11


title: OX1931B11


title: OX1931B10


title: CML25_3mTKI_PL2C6


title: CML25_3mTKI_PL2A3


title: OX1931B1


title: OX1931A9


title: OX1931A8


title: CML25_3mTKI_PL2H7


title: CML25_3mTKI_PL2E1


title: CML25_3mTKI_PL2C7


title: OX1931A7


title: OX1931A6


title: CML25_3mTKI_PL2G10


title: OX1931A5


title: OX1931A3


title: OX1931A2


title: CML25_3mTKI_PL2B6


title: OX1931B3


title: OX1931A12


title: CML25_3mTKI_PL2A4


title: CML25_3mTKI_PL2C2


title: CML25_3mTKI_PL2G4


title: OX1931A11


title: CML25_3mTKI_PL2D1


title: CML25_3mTKI_PL2B8


title: OX1931A10


title: OX1902H6


title: CML25_3mTKI_PL2A9


title: CML25_3mTKI_PL2E10


title: CML25_3mTKI_PL2H9


title: OX1931A1


title: CML25_3mTKI_PL2G11


title: OX1902H3


title: CML25_3mTKI_PL2B4


title: OX1902H2


title: OX1902H11


title: OX1931A4


title: CML25_3mTKI_PL2H8


title: OX1902H1


title: CML25_3mTKI_PL2A12


title: CML25_3mTKI_PL2D2


title: OX1902G5


title: CML25_3mTKI_PL2G7


title: OX1902G4


title: CML25_3mTKI_PL2E12


title: CML25_3mTKI_PL2B1


title: OX1902G3


title: OX1902G2


title: CML25_3mTKI_PL2B7


title: OX1902H4


title: OX1902G1


title: OX1902F4


title: OX1902F2


title: CML25_3mTKI_PL2D3


title: CML25_3mTKI_PL2H3


title: OX1902F1


title: CML25_3mTKI_PL2E11


title: CML25_3mTKI_PL2F11


title: OX1902E4


title: CML25_3mTKI_PL2F10


title: OX655_1yTKI_PL2H3


title: OX1902E2


title: OX1902G6


title: OX1902E1


title: OX1902G8


title: OX655_1yTKI_PL2B9


title: OX655_1yTKI_PL2A11


title: OX1902D4


title: OX1902D3


title: CML25_3mTKI_PL2D7


title: OX655_1yTKI_PL2H9


title: OX1902D12


title: OX655_1yTKI_PL2A9


title: CML25_3mTKI_PL2E5


title: OX655_1yTKI_PL3C8


title: OX655_1yTKI_PL1H10


title: OX1902D1


title: OX1902D2


title: OX655_1yTKI_PL2C11


title: OX655_1yTKI_PL2D9


title: OX1902C7


title: OX1902E7


title: OX1902C8


title: OX1902C3


title: OX1902C4


title: OX655_1yTKI_PL2F9


title: OX1902C2


title: OX655_1yTKI_PL2B5


title: OX1902C12


title: OX655_1yTKI_PL3D4


title: OX1902C1


title: OX1902B8


title: OX655_1yTKI_PL1F7


title: OX655_1yTKI_PL3B4


title: OX655_1yTKI_PL3G3


title: OX1902B6


title: OX1902B4


title: OX1902B5


title: OX655_1yTKI_PL2G4


title: OX1902B2


title: OX655_1yTKI_PL3C9


title: OX655_1yTKI_PL2F3


title: OX1902A5


title: OX1902B1


title: OX1902B3


title: OX655_1yTKI_PL3D8


title: OX655_1yTKI_PL3G11


title: OX655_1yTKI_PL3D10


title: OX1902A4


title: OX655_1yTKI_PL3E10


title: OX655_1yTKI_PL2A3


title: OX1902B12


title: OX655_1yTKI_PL3H6


title: OX655_1yTKI_PL2H4


title: OX1902A11


title: OX1902A2


title: CML656_6mTKI_PL2A11


title: CML656_6mTKI_PL3E7


title: OX1902A1


title: OX1674H8


title: CML656_6mTKI_PL2E7


title: CML656_6mTKI_PL1G4


title: CML_656_3mTKIA11


title: OX1674H7


title: OX1674H5


title: OX1674H6


title: CML_656_3mTKIB10


title: OX1674H4


title: CML_656_3mTKIC2


title: OX1674H12


title: CML_656_3mTKIC3


title: OX1674H3


title: OX1902A3


title: CML_656_3mTKIB2


title: CML_656_3mTKIB12


title: CML_656_3mTKIC1


title: CML_656_3mTKIA10


title: CML_656_3mTKIC5


title: OX1674H11


title: OX1674H2


title: OX655_1yTKI_PL3C5


title: OX1674G8


title: OX1674H1


title: CML656_6mTKI_PL3B12


title: CML656_6mTKI_PL3B7


title: OX1674G7


title: OX1674G6


title: OX1674G4


title: CML656_6mTKI_PL3D2


title: OX1674G5


title: OX1674G2


title: CML656_6mTKI_PL3B4


title: OX1674G3


title: CML656_6mTKI_PL3A12


title: OX1674G12


title: CML656_6mTKI_PL3D7


title: OX1674G10


title: OX1674G11


title: CML656_6mTKI_PL3C6


title: CML656_6mTKI_PL3C11


title: OX1674G1


title: CML656_6mTKI_PL3D11


title: CML656_6mTKI_PL3B11


title: CML656_6mTKI_PL3C8


title: OX1674F8


title: OX1674F9


title: CML656_6mTKI_PL3B6


title: CML656_6mTKI_PL3C9


title: CML656_6mTKI_PL3C4


title: CML656_6mTKI_PL3D12


title: OX1674F6


title: OX1674F2


title: CML656_6mTKI_PL3D1


title: OX1674F5


title: OX1674F4


title: OX1674F12


title: CML656_6mTKI_PL3E2


title: CML656_6mTKI_PL3C5


title: OX1674F11


title: OX1674F1


title: OX1674F10


title: CML656_6mTKI_PL3C10


title: CML656_6mTKI_PL3A1


title: OX1674F7


title: CML656_6mTKI_PL3C12


title: CML656_6mTKI_PL3A3


title: OX1674E8


title: OX1674E6


title: CML656_6mTKI_PL3B8


title: OX1674E5


title: OX1674E9


title: CML656_6mTKI_PL3B5


title: CML656_6mTKI_PL3D3


title: OX1674E4


title: OX1674E11


title: OX1674E7


title: OX1674E2


title: CML656_6mTKI_PL3C3


title: OX1674E10


title: CML656_6mTKI_PL3D5


title: CML656_6mTKI_PL3E6


title: OX1674E1


title: OX1674D9


title: CML656_6mTKI_PL3B9


title: CML656_6mTKI_PL3E10


title: CML_656_3mTKIB3


title: CML_656_3mTKIB11


title: OX1674D6


title: OX1674D8


title: CML656_6mTKI_PL3B3


title: OX1674D4


title: CML_656_3mTKIA6


title: CML_656_3mTKIA3


title: CML656_6mTKI_PL3E4


title: CML_656_3mTKIB7


title: CML_656_3mTKIB9


title: OX1674D11


title: CML_656_3mTKIC6


title: CML_656_3mTKIB1


title: OX1674D10


title: OX1674D1


title: OX1674C8


title: CML_656_3mTKIB8


title: CML_656_3mTKIC9


title: OX1674C9


title: CML_656_3mTKIA5


title: OX1674C6


title: OX1674C5


title: CML_656_3mTKIC4


title: OX1674C4


title: OX1674D5


title: OX1674C3


title: OX1674C11


title: CML940_3mTKIF11


title: OX1674D2


title: OX1674C10


title: OX1674D3


title: OX1674C1


title: CML940_3mTKIF2


title: CML940_3mTKIG6


title: CML_656_3mTKIB4


title: CML940_3mTKIF6


title: OX1674B9


title: OX1674B6


title: OX1674B5


title: CML940_3mTKIE5


title: OX1674B7


title: OX1071B11


title: CML940_3mTKIF9


title: OX1071A7


title: OX1674B3


title: OX1674B10


title: OX1071B10


title: OX1071B12


title: OX1674B1


title: OX1674A5


title: OX1674A4


title: OX1674A9


title: CML_656_3mTKIA1


title: OX1071C1


title: CML940_3mTKIE10


title: OX1071A8


title: OX1071D12


title: OX1674A7


title: OX1674A6


title: CML940_3mTKIE6


title: OX1674A3


title: OX1071C4


title: OX1674A2


title: OX1071B4


title: OX1071D9


title: OX1674B2


title: OX1071B9


title: OX1071A9


title: OX1674A11


title: OX1570H8


title: CML940_3mTKIE4


title: OX1071B7


title: OX1071A11


title: OX1570H6


title: OX1071D7


title: OX1071C6


title: OX1570H5


title: OX1570H2


title: OX1570H1


title: OX1071B6


title: OX1570G4


title: OX1071C5


title: OX1071A12


title: OX1570G9


title: OX1674A1


title: OX1071A10


title: OX1570G2


title: OX1570G12


title: OX1570G10


title: OX1570G1


title: OX1570F9


title: OX1071A5


title: OX1570F6


title: OX1083_PL1A10


title: OX1570F5


title: OX1083_PL1A3


title: OX1083_PL1D6


title: OX1083_PL1E4


title: OX1083_PL1A6


title: OX1083_PL1E8


title: OX1083_PL1E2


title: OX1570F11


title: OX1083_PL1C12


title: OX1570F3


title: OX1083_PL1D9


title: OX1570F4


title: OX1570F10


title: OX1071C3


title: OX1083_PL1B7


title: OX1570E7


title: OX1570E6


title: OX1083_PL1E3


title: OX1083_PL1D12


title: OX1570E5


title: OX1570D6


title: OX1570E11


title: OX1083_PL1A11


title: OX1570D9


title: OX1570D3


title: OX1083_PL1D11


title: OX1083_PL1A12


title: OX1570D10


title: OX1083_PL1A4


title: OX1570F12


title: OX1083_PL1D5


title: OX1083_PL1D10


title: OX1083_PL1C8


title: OX1570C2


title: OX1570E9


title: OX1083_PL1C2


title: OX1570C5


title: OX1570C12


title: OX1083_PL1A1


title: OX1570C10


title: OX1083_PL1A7


title: OX1083_PL1D4


title: OX1083_PL1D8


title: OX1570B9


title: OX1083_PL1B11


title: OX1570B7


title: OX1570C11


title: OX1528_PL1D4


title: OX1528_PL2B8


title: OX1083_PL1C5


title: OX1570B5


title: OX1570B6


title: OX1570B3


title: OX1570B12


title: OX1528_PL3H6


title: OX1570C7


title: OX1528_PL2A4


title: OX1528_PL2A9


title: OX1407H6_merged


title: OX1570A11


title: OX1570A5


title: OX1528_PL3D9


title: OX1528_PL2C10


title: OX1528_PL2B10


title: OX1528_PL2A2


title: OX1570A10


title: OX1407H3


title: OX1528_PL2A1


title: OX1528_PL2B9


title: OX1407G6


title: OX1407G5


title: OX1528_PL2B12


title: OX1528_PL2C9


title: OX1528_PL2A7


title: OX1528_PL2A3


title: OX1528_PL2B2


title: OX1407G3


title: OX1407G1


title: OX1407H5


title: OX1528_PL2A12


title: OX1528_PL2C5


title: OX1407F3


title: OX1407F6


title: OX1407F2


title: OX1407E6


title: OX1528_PL2C7


title: OX1528_PL2A10


title: OX1407E4


title: OX1407H2


title: OX1407E3


title: OX1407E5


title: OX1528_PL2C12


title: OX1407E1


title: OX1407D6


title: OX1528_PL2A8


title: OX1528_PL2C1


title: OX1528_PL2A6


title: OX1528_PL2B5


title: OX1407G2


title: OX1407G4


title: OX1407D5


title: OX1528_PL2D2


title: OX1528_PL2D1


title: OX1528_PL2B1


title: OX1528_PL2A5


title: OX1407D4


title: OX1407D3


title: OX1407C6


title: OX1705_PL1B9


title: OX1705_PL1A3


title: OX1407D1


title: OX1705_PL1B1


title: OX1528_PL2C6


title: OX1407C5


title: OX1705_PL1A5


title: OX1407C2


title: OX1407E2


title: OX1407C1


title: OX1705_PL1B8


title: OX1705_PL1B4


title: OX1407B6


title: OX1407B5


title: OX1705_PL1C1


title: OX1705_PL1C9


title: OX1407B4


title: OX1407B2


title: OX1705_PL1A2


title: OX1705_PL1A1


title: OX1705_PL1C7


title: OX1705_PL1B5


title: OX1705_PL1B6


title: OX1407B1


title: OX1407A5


title: OX1705_PL1A6


title: OX1407A3


title: OX1705_PL1B2


title: OX1705_PL1B10


title: OX1407A4_merged


title: OX1407A1_merged


title: OX1407A2_merged


title: OX1407C3


title: OX1705_PL1A10


title: OX1705_PL1B7


title: OX1705_PL1B12


title: OX1705_PL1A11


title: OX1302H9_merged


title: OX1302H7


title: OX1302H8


title: OX1705_PL1A4


title: OX1302H5


title: OX1705_PL1B11


title: OX2343_PL1B5


title: OX1302H3


title: OX2343_PL1G5


title: OX1302H10_merged


title: OX1407A6_merged


title: OX2343_PL1C1


title: OX1302H1_merged


title: OX2343_PL1C5


title: OX1302G9


title: OX2343_PL1C6


title: OX2343_PL1D4


title: OX1302G8


title: OX1302G5


title: OX1302G4_merged


title: OX1302G3


title: OX1302G7_merged


title: OX2343_PL1D5


title: OX2343_PL1D6


title: OX2343_PL1B7


title: OX2343_PL1E2


title: OX2343_PL1A4


title: OX1302G10_merged


title: OX2343_PL1A3


title: OX1302G11


title: OX2343_PL1B10


title: OX1302H2_merged


title: OX1302F9


title: OX2343_PL1D7


title: OX1302F8


title: OX2343_PL1C3


title: OX2343_PL1A2


title: OX1302F7


title: OX2343_PL1F2


title: OX2343_PL1H8


title: OX1302F3


title: OX2343_PL1G9


title: OX1302F5


title: OX2343_PL1F1


title: OX1302F2_merged


title: OX2343_PL1B3


title: OX1302F12


title: OX2343_PL1E11


title: OX1302G12_merged


title: OX1302F11


title: OX2343_PL1F7


title: OX1302F10_merged


title: OX2343_PL1H10


title: OX1302E9


title: OX2343_PL1H6


title: OX1302E3


title: OX1302E8


title: OX2343_PL1E9


title: OX2343_PL1F11


title: OX2343_PL1F6


title: OX2343_PL1C2


title: OX1302F4


title: OX1302E11


title: OX1302E2_merged


title: OX2343_PL1A5


title: OX1302G2


title: OX1302E10_merged


title: OX2343_PL1F5


title: OX1302E1


title: OX2343_PL1C9


title: OX1302D7


title: OX1302D8


title: OX2343_PL1B6


title: OX2343_PL1H1


title: OX2343_PL1G6


title: OX1302D2


title: OX2343_PL1G8


title: OX1302D11


title: OX1302D3


title: OX2343_PL1D11


title: OX1302D10


title: OX2343_PL1G10


title: OX1302E7


title: OX1302D1


title: OX2343_PL1B1


title: OX2343_PL1H4


title: OX1302C6


title: OX1302C7


title: OX1302C5_merged


title: OX2343_PL1F4


title: OX2343_PL1B11


title: OX2343_PL1H9


title: OX1302C2


title: OX2343_PL1E5


title: OX2343_PL1A7


title: OX1302C1


title: OX1302B8


title: OX2343_PL1E3


title: OX1302D5


title: OX1302B3


title: OX2343_PL1B4


title: OX2343_PL1D2


title: OX2343_PL1C8


title: OX1302B2_merged


title: OX1302B10


title: OX2343_PL1E10


title: OX2343_PL1A9


title: OX1302A6_merged


title: OX1302A4_merged


title: OX1302A7_merged


title: OX1302A5_merged


title: OX2343_PL1B9


title: OX1302C3_merged


title: OX2343_PL1A10


title: OX1302C11


title: OX2343_PL1C10


title: OX2343_PL1B12


title: OX1302A1_merged


title: OX2343_PL1F3


title: OX2343_PL1H2


title: OX1302A2_merged


title: OX1249H9


title: OX1302A3


title: OX2343_PL1E1


title: OX2343_PL1B2


title: OX1249H8


title: OX1249H7


title: OX2343_PL1D10


title: OX1249H4


title: OX1249H5_merged


title: OX2343_PL1G3


title: OX1249H2


title: OX2343_PL1G7


title: OX2343_PL1D9


title: OX1249H10


title: OX2343_PL1A12


title: OX1249G8


title: OX1249G9


title: OX1249G4


title: OX1249G3


title: OX2343_PL1D8


title: OX2343_PL1G11


title: OX1249G2


title: OX2343_PL1D1


title: OX2343_PL1G1


title: OX2343_PL1G2


title: OX2343_PL1G12


title: OX2343_PL1A11


title: OX1249G11


title: OX1249G12


title: OX1249G10


title: OX703_PL2B1


title: OX1249F9


title: OX703_PL2A2


title: OX2343_PL1C11


title: OX1249H11


title: OX703_PL2C8


title: OX703_PL2G1


title: OX1249F5


title: OX703_PL2F9


title: OX2343_PL1C7


title: OX1249F2_merged


title: OX1249F4


title: OX1249G7


title: OX703_PL2G10


title: OX1249F12


title: OX703_PL2C1


title: OX1249F11


title: OX703_PL2A1


title: OX703_PL2G9


title: OX703_PL2F2


title: OX703_PL2F5


title: OX1249E9


title: OX1249E5_merged


title: OX1249E8


title: OX1249E3


title: OX1249F10


title: OX703_PL2D2


title: OX703_PL2B11


title: OX703_PL2G5


title: OX1249E12


title: OX1249E10


title: OX703_PL2C7


title: OX1249E11


title: OX703_PL2C12


title: OX703_PL2D3


title: OX1249D9


title: OX703_PL2D9


title: OX703_PL2B5


title: OX1249D8


title: OX1249D7


title: OX1249D6_merged


title: OX703_PL2E12


title: OX703_PL2E6


title: OX1249D4


title: OX1249D5_merged


title: OX1249E6


title: OX703_PL2C2


title: OX1249D3_merged


title: OX1249D12


title: OX703_PL2D4


title: OX1249C9


title: OX750_PL1B12


title: OX750_PL1F9


title: OX1249D10


title: OX750_PL1A8


title: OX750_PL1C4


title: OX1249C7


title: OX1249C6_merged


title: OX1249C4


title: OX750_PL1B4


title: OX750_PL1D12


title: OX1249C3_merged


title: OX703_PL2E1


title: OX750_PL1A4


title: OX750_PL1B3


title: OX750_PL1G8


title: OX1249C11


title: OX1249C10


title: OX750_PL1B9


title: OX750_PL1H7


title: OX750_PL1B8


title: OX1249B8


title: OX1249C2_merged


title: OX1249B9


title: OX1249B7


title: OX750_PL1D9


title: OX1249C8


title: OX1249B10


title: OX1249A9


title: OX1249B4


title: OX750_PL1E7


title: OX750_PL1D7


title: OX1249B11


title: OX1249A8


title: OX1249A5


title: OX750_PL1C8


title: OX750_PL1A1


title: OX1249A4


title: OX750_PL1E6


title: OX750_PL1F4


title: OX750_PL1B1


title: OX1249A3_merged


title: OX1249A12


title: OX750_PL1F2


title: OX750_PL1E9


title: OX750_PL1F6


title: NBMG5

description: Normal donor 1991

value: normal


title: OX750_PL1F10


title: NBMG3

description: Normal donor 1991


title: OX750_PL1G11


title: OX750_PL1D8


title: OX750_PL1C11


title: NBMF5

description: Normal donor 1991


title: OX750_PL1B2


title: OX750_PL1F8


title: NBME5

description: Normal donor 1991


title: NBMD5

description: Normal donor 1991


title: NBME3

description: Normal donor 1991


title: OX750_PL1A9


title: OX1249A11


title: OX750_PL1E10


title: NBMC5

description: Normal donor 1991


title: NBMB5

description: Normal donor 1991


title: NBMA5

description: Normal donor 1991


title: OX1249A10


title: OX750_PL1F11


title: NBMH2

description: Normal donor 1991


title: OX750_PL1A12


title: NBMA3

description: Normal donor 1991


title: NBM_ERCCH5

description: Normal donor 1991_with_ERCC


title: NBMF2

description: Normal donor 1991


title: NBM_ERCCH4

description: Normal donor 1991_with_ERCC


title: OX750_PL1C10


title: OX750_PL1D1


title: OX750_PL1A10


title: OX750_PL1C3


title: OX750_PL1A6


title: NBME2

description: Normal donor 1991


title: OX750_PL1D10


title: NBM_ERCCH3

description: Normal donor 1991_with_ERCC


title: OX750_PL1A3


title: OX750_PL1B7


title: OX750_PL1G7


title: NBM_ERCCH1

description: Normal donor 1991_with_ERCC


title: OX750_PL1D3


title: OX750_PL1A2


title: NBM_ERCCG6

description: Normal donor 1991_with_ERCC


title: OX750_PL1E2


title: NBM_ERCCG5

description: Normal donor 1991_with_ERCC


title: OX750_PL1F3


title: NBM_ERCCG3

description: Normal donor 1991_with_ERCC


title: NBM_ERCCG2

description: Normal donor 1991_with_ERCC