title: M857-P010_C

status: Public on Nov 07 2019

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline54. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2. Duplicate reads were removed using SAMBLASTER before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5. To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0  to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K4me3, H3K27ac and H3K4me1 and MACS version 2.1 p-value threshold of 1e-5 were used to idenftify H3K27me3, H3K9me3 and H3K79me2 enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Melanoma Tumor Sample

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC).  ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

treatment_protocol:
Melanoma tumors were obtained from the Melcore tumor bank at MD Anderson Cancer Center.
Tissue was disassociated (50 mg of tissue; ~8 mg per histone modification antibody) manually in 2 mL of Hanks' Balanced Salt Solution (HBSS) using a sterile razor blade. Mince the tissue into 3 to 4 mm pieces for approximately 5 min in a sterile tissue culture dish. Transfer the tissue and HBSS solution into a dissociator tube and add another 8 mL of HBSS. Further disassociate the tissue using a dissociator until homogenized. For melanoma tumors, place the tubes in a dissociator and run the following cycles each one time in this order: h_tumor_01.01, h_tumor_02.01, h_tumor_03.01 and m_heart_02.01.

value: Tissue

tag: chip-antibody

value: H3K27ac Abcam ab4729


title: WT_1_ESC_D0_RNAseq

status: Public on Nov 12 2019

type: SRA

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

library_source: transcriptomic

data_processing:
Quality control of RNAseq reads were done using FastQC v0.11.2 , reads were trimmed using Trimmomatic v0.32 with settings  “ILLUMINACLIP:<TrueSeq3_PE_2>:2:30:10 HEADCROP:12 LEADING:22 SLIDINGWINDOW:4:22 MINLEN:25”
RNAseq reads were aligned to mm10 using HISAT v0.1.6.beta with --rna-strandness RF --minins 0 --maxins 1000  and a list of GENCODE M12 annotated splice sites was also provided.
Paired and uniquely mapped exonic reads for GENCODE M12 genes were counted using featureCounts from the R package Rsubread (1.32.1)
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: ChIPseq reads bigwig files were generated using bedtools v2.23.0  and UCSC Genome Browser Utility ‘bedGraphToBigWig’, the score represents strand-specific per-base genome coverage which was normalized to the library size
Supplementary_files_format_and_content: RIPseq reads bigwig files were generated using bamCoverage from deepTools (Ramírez et al., 2014), the score represents strand-specific per-base genome coverage which was normalized to the library size

molecule: total RNA

organism: Mus musculus

growth_protocol: ES cells were cultured on 0.2% gelatin coated plates in 2i/LIF containing medium.

extract_protocol:
Total RNA for RNAseq  was isolated using the RNeasy Mini Kit (Qiagen)
RNAseq libraries were prepared from 1 µg RNA using the TruSeq Stranded Total RNA library prep kit (Illumina) following rRNA depletion using Ribozero Gold (Illumina)

tag: cell line

tag: cell type

value: Embryonic stem cells

tag: genotype/variation

value: Wildtype


title: M857-P010_A

city: Houston

country: USA

molecule: genomic DNA

organism: Homo sapiens

value: H3K4me1 Abcam ab8895


title: M852-P008_A


title: WT BMDM 8h LPS 1

status: Public on Mar 24 2020

type: RNA

city: UNSW Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: UNSW Sydney

description: E05_KNI2057A5 WT1 LPS 8h

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Partek Genomics Suite software was used to analyse CEL files

label: biotin

source_name: WT bone marrow-derived macrophages

label_protocol: not provided

growth_protocol: Animals were housed in a specific pathogen-free environment at a constant ambient temperature of 22°C on a 12 h light dark cycle, with ad libitum access to standard chow food and water. Femora and tibiae were collected and flushed using cold sterile PBS then seeded into tissue culture dishes in 80% DMEM-F12 (containing 10% FCS and 1% penn-strep-glut) and 20% L929 conditioned media (containing M-CSF growth factor). BMDMs were grown over 7-10 days before treatment, with L929 media topped up every 2-3 days.

extract_protocol: Cells were lysed and homogenised in TRI reagent, and RNA isolated using phenol/chloroform extraction. RNA was then purified using a Qiagen RNeasy Mini Kit and eluted in RNase-free water.

treatment_protocol: Media was removed, cells washed with PBS then replaced with regular DMEM-F12 (10% FCS 1% PSG). 0 h samples were harvested for RNA extraction, and 8 h samples were treated with 100 ng/mL lipopolysaccharide (LPS) or vehicle (PBS). After 8 h these samples were harvested for RNA extractions.

tag: strain

value: FVB/NJ

tag: Sex

value: male

value: bone marrow-derived macrophages

value: WT


title: M852-P008_C


title: WT_2_ESC_D0_RNAseq


title: M762-P008_C


title: M807-P010_C


title: M822-P010_C


title: M762-P008_A


title: M807-P010_A


title: M749-P010_C


title: M749-P010_A


title: M721-P010_A


title: M721-P010_C


title: M642-P008_C


title: M642-P008_A


title: M822-P010_A


title: M399-P010_A


title: M399-P010_C


title: M357-P010_A


title: M357-P010_C


title: M409-P011_A


title: M527-P010_C


title: M527-P010_A


title: M409-P011_C


title: M306-P008_C


title: M306-P008_A


title: M305-P009_A


title: M305-P009_C


title: M263-P011_C


title: M275-P008_A


title: M275-P008_C


title: M263-P011_A


title: M233-P010_C


title: M233-P010_A


title: M137-P008_C


title: M137-P008_A


title: M035-P010_A


title: M028-P008_A


title: M035-P010_C


title: M028-P008_C


title: Sample 7_ES7_G4/p53 -/-

status: Public on Jun 25 2019

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

data_processing:
Illumina Casava1.8 software used for basecalling.
Adaptor trimming, read aligned to mirBase mouse miRNA sequences, miRNA quantification and normalization with miRDeep2 software
miRNAs with <=3 normalized count in ALL 11 samples were filtered out
Differential gene expression analysis using limma in R for 2-group comparisons
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-delimited text files include RPM (read per million) values for each sample

source_name: G4/p53 -/- _liver tissue

growth_protocol: Mice were euthanized and liver tissues were immediately processed to isolate total RNA

extract_protocol:
Total RNA was isolated from 50 mg liver tissue using Trizol followed by DNAs digestion and RNA easy column purification
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: G4 telomerase knockout mice with and without p53 (no treatment)

tag: strain background

value: Telomerase KO mice with short telomeres and lacking p53

tag: tissue

value: liver


title: Sample 12_ES11_G4/p53 -/-


title: Sample 10_ES9_G4/p53 -/-


title: Sample 8_ES8_G4/p53 -/-


title: Sample 4_ES4_G4/p53 +/+

source_name: G4/p53 +/+ _liver tissue

value: Telomerase KO mice with short telomeres and intact p53


title: Sample 6_ES6_G4/p53 -/-


title: Sample 2_ES2_G4/p53 +/+


title: Sample 11_ES10_G4/p53 -/-


title: 33E - lu2

status: Public on Dec 11 2018

description:
PDX of breast cancer tumor implanted in the mammary fat pad of a mouse and metastasized to the lung.
Processed data file: barcode.txt

data_processing:
We verified the quality of sequence reads using FastQC.
We removed reads from contaminating mouse cells by aligning them to the GRCm38 transcriptome using a GENCODE GTF using STAR.  Reads that aligned with at most 1 mismatch were discarded.
We aligned the reads to the human transcriptome using the hg19 assembly and a GTF of RefSeq genes.
Raw reads were used for post-analysis using R packages DESeq and EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of gene expression read counts for RefSeq protein coding transcriptome

source_name: PDX of breast cancer tumor

growth_protocol: Human tumors were engrafted into the mammary fat pads of NOD-SCID/gamma mice and allowed to metastasize to the lung.

extract_protocol:
To perform deep sequencing of RNA (RNA-seq), total RNA was isolated from tumors, treated with Dnase I, and depleted of cytoplasmic and mitochondrial ribosomal RNA using Ribo-Zero Gold.
TruSeq Stranded Total RNA after depletion of cytoplasmic and mitochondrial ribosomal RNA using Ribo-Zero Gold.  Libraries were sequenced on an Illumina HiSeq 4000 instrument.

tag: collection site

value: lung

tag: mouse

tag: barcoded

value: yes


title: 33E - lu5


title: 33E - lu4


title: 34B - lu7


title: 33E - lu1


title: 34B - li1

description:
PDX of breast cancer tumor implanted in the mammary fat pad of a mouse and metastasized to the liver
Processed data file: barcode.txt


title: 33E - lu3


title: ID235 HSC

status: Public on Apr 16 2019

city: Zurich

first: Slavica

last: Dimitrieva Janeva

state: Zurich

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH Zürich / University of Zurich

data_processing:
Generation of fastq files was done using bcl2fastq software version 2.19.0
Reads were trimmed with Trimmomatic version 0.33 (4 and 3 bases were hard-trimmed from the start and end respectively; adapter trimming was done at the end).
Trimmed reads were aligned to the Ensembl GRCh38 human reference genome and transcriptome with STAR version 2.5.1b.
Read quantification was done using the R/Bioconductor package Rsubread version 1.26.0.
Genome_build: Ensembl Human reference GRCh38 release 86
Supplementary_files_format_and_content: tab-delimited text file showing raw read counts for each sample (columns) and each gene (rows)

source_name: Blood

growth_protocol: Fresh human hematopoietic stem/progenitor cells were obtained from 5 healthy donors aged between 28 and 57 years old (average: 39.8); 4 males, 1 female; with informed consent and approval of the local ethics committee (KEK-ZH-Nr: 2015-0564, Clinical Hematology, University Hospital Zurich, Zurich Switzerland).

extract_protocol:
After mobilization with granulocyte-colony stimulating factor (G-CSF), stem-cell enriched mononuclear leukocytes were obtained via plasmapheresis from peripheral blood of donors for clinical stem cell transplantation (Clinical Hematology, University Hospital Zurich, Zurich Switzerland). Left-over material after clinical transplantation was enrichted for CD34+ stem/progenitor cells using immunomagnetic beads according to manufacturer instructions (CD34 MicroBead Kit; Miltenyi Biotec). Fluorescence-activated cell sorting and antibodies specific for CD2, CD3, CD4, CD7, CD8, CD14, CD19, CD56, CD10, CD11b, CD20, CD235a, CD34, CD38, CD123, CD45RA were used to isolate the various cell types (HSC, CMP, GMP, MEP). 10'000 cells of each subpopulations were sorted into RNeasy lysis buffer containing beta-mercaptoethanol. Total RNA was purified according to manufacturer instructions using the RNeasy Plus Micro Kit (Qiagen). The samples were of high enough quality for a poly-A tail based approach for RNA sequencing. RNA sequencing was performed as described in Picelli S. et al. Nature Protocols 2014 using the Illumina HiSeq 4000 sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stem-cell enriched mononuclear leukocytes were mobilized from the bone marrow using granulocyte-colony stimulating factor (G-CSF) (twice daily administrations over 4 days).

value: hematopoietic stem cells

tag: donor age

value: 29 years

tag: donor sex


title: 34B - lu6


title: 33E - MG

description:
PDX of breast cancer tumor implanted in the mammary fat pad of a mouse.
Processed data file: barcode.txt

value: mammary gland


title: ID234 HSC

value: 34 years


title: 34B - lu5


title: Sample 5_ES5_G4/p53 +/+


title: 34B - MG


title: 34D - MG


title: 34D - lu1


title: 33B - li5


title: 34D - lu2


title: Sample 3_ES3_G4/p53 +/+


title: 33B - li4


title: Sample 1_ES1_G4/p53 +/+


title: 33B - li3


title: 33B - lu6


title: 196C-lung3

description:
PDX of breast cancer tumor implanted in the mammary fat pad of a mouse and metastasized to the lung.
Processed data file: echeverria.txt

value: no


title: 197B-lung2


title: 33B - MG


title: 33B - lu7


title: 196B-MG

description:
PDX of breast cancer tumor implanted in the mammary fat pad of a mouse.
Processed data file: echeverria.txt


title: 33B - lu5


title: 196C-lung2


title: 196C-lung1


title: 196B-lung


title: WT scSVF Eos 3

status: Public on Apr 30 2019

hyb_protocol: For staining of SVF cells for FACS isolation, the following staining strategy was used: CD45-biotin (BD Pharmingen), Streptavidin-BV711 (BD Horizon), CD11b-FITC (BD Pharmingen), F4/80-PE/Cy7 (Biolegend) and SiglecF-BV421 (BD Horizon). Live cells were identified by the addition of TO-PRO-3 viability dye. Eosinophils were defined as live CD45+ CD11b+ F4/80+ SiglecF+ SSC hi cells. BD Influx was used for sorting cells.

scan_protocol: standard Affymetrix protocol

source_name: WT subcutaneous SVF eosinophils

label_protocol: standard Affymetrix protocol

growth_protocol: Animals were housed in a specific pathogen-free environment at a constant ambient temperature of 22°C on a 12 h light dark cycle, with ad libitum access to standard chow food and water

extract_protocol: Inguinal subcutaneous adipose tissue was dissected from 12-wk age- and litter-matched WT and KLF3 KO mice (n=3 per genotype). Adipose was digested using type II collagenase to yield the stromal vascular fraction (SVF), which was stained with fluorescently-conjugated antibodies to isolate eosinpohils (CD11b+ F4/80+ SiglecF+ SSC hi). RNA was extracted from isolated cells using a Qiagen RNeasy Micro Kit

treatment_protocol: No treatments were applied


title: spm13wb

status: Public on Apr 05 2018

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description: Illumina TruSeq RNA Sample Prep Kit

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.5.2_b with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --sjdbScore 1
counts were generated by featureCounts v1.5.1 with parameters -p -t exon -g gene_id -B -T8 -M -O --fraction
normalized log2-transformed count table was generated by the voom function from the R/Bioconductor limma package
mouse data was processed according to lexogen proprietary software
Genome_build: hg38/mm10
Supplementary_files_format_and_content: tab-delimited matrices including raw counts and log2-normalized counts for all samples.

source_name: whole brain

extract_protocol:
Total RNA was extracted from flow cytometry-sorted microglia cells using an RNeasy and AllPrep Micro Kit (Qiagen) and from whole brain tissue using RNeasy Lipid Tissue Mini kit (Qiagen), according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit was used with 60 ng of total RNA for the construction of sequencing libraries of 23 samples. Clontech SMARTer Stranded Total RNA-Seq Kit - Pico Input (Takara Bio, Japan) cDNA libraries were prepared for 16 samples starting with 500 pg of total RNA.
Human RNA libraries were prepared for sequencing using standard Illumina and Clontech protocols. Mouse  RNA samples were prepared with a Quantseq 3’mRNA-Seq kit. (Lexogen, USA)

value: brain

tag: age

tag: gender

value: M


title: spm14wb

description: Illumina TruSeq RNA Sample Prep Kit

value: F


title: spm11wb

description: Illumina TruSeq RNA Sample Prep Kit


title: 197B-lung1


title: 196C-MG


title: 197B-MG


title: spm15wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm25wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm28wb

description: Illumina TruSeq RNA Sample Prep Kit


title: KLF3 KO scSVF Eos 3

source_name: KLF3 KO subcutaneous SVF eosinophils

value: FVB/NJ


title: KLF3 KO scSVF Eos 1


title: spm33wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm30wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm5wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm35wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm6wb

description: Illumina TruSeq RNA Sample Prep Kit


title: KLF3 KO scSVF Eos 2


title: WT scSVF Eos 1


title: WT scSVF Eos 2


title: PyMT NET1 WT Rep 1

status: Public on May 23 2018

description: PyMT NET1 WT Rep 1

hyb_protocol: We incubated the cRNA with HYB buffer with the BeadChips at 58C for 17 hours and washed according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: We incubated each BeadChip with Cy3-Streptavidin for 10 min, dried, and then scanned on an Illumina BeadArray Scanner.

data_processing: The raw data were processed with IlluminaGenomeStudio.

source_name: Breast tumor from MMTV-PyMT in FVB mouse

label_protocol: Using the Ambion Illumina TotalPrep RNA Amplification kit (Ambion #IL1791), we reverse-transcribed 200 ng of total RNA using a T7 oligo-dT primer, used the resulting cDNA to synthesize the complement strand, purified, and in vitro transcribed biotinylated cRNA.

growth_protocol: Tumors developed spontaneously in a MMTV-PyMT model with either Net1-/- or Net1+/+.

extract_protocol: RNA from tumors was extracted using the EZNA Total RNA kit from Omega BioTek in accordance with the manufacturer's protocol.

treatment_protocol: After euthanasia, we isolated individual mammary tumors from separate mice.


title: PyMT NET1 KO Rep 1

description: PyMT NET1 KO Rep 1

value: KO


title: PyMT NET1 KO Rep 3

description: PyMT NET1 KO Rep 3


title: PyMT NET1 WT Rep 3

description: PyMT NET1 WT Rep 3


title: PyMT NET1 KO Rep 2

description: PyMT NET1 KO Rep 2


title: PyMT NET1 WT Rep 2

description: PyMT NET1 WT Rep 2


title: spm9wb

description: Illumina TruSeq RNA Sample Prep Kit


title: S12067

description: Illumina TruSeq RNA Sample Prep Kit

source_name: microglia

value: microglia


title: spm26wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm2wb

description: Illumina TruSeq RNA Sample Prep Kit


title: S12048

description: Illumina TruSeq RNA Sample Prep Kit


title: S13067

description: Illumina TruSeq RNA Sample Prep Kit


title: S14005

description: Illumina TruSeq RNA Sample Prep Kit


title: S12112

description: Illumina TruSeq RNA Sample Prep Kit


title: S1210100

description: Illumina TruSeq RNA Sample Prep Kit


title: spm36wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm18

description: Illumina TruSeq RNA Sample Prep Kit


title: S15018

description: Illumina TruSeq RNA Sample Prep Kit


title: spm10

description: Illumina TruSeq RNA Sample Prep Kit


title: spm12

description: Illumina TruSeq RNA Sample Prep Kit


title: spm27

description: Illumina TruSeq RNA Sample Prep Kit


title: spm20

description: Illumina TruSeq RNA Sample Prep Kit


title: spm22

description: Illumina TruSeq RNA Sample Prep Kit


title: spm24

description: Illumina TruSeq RNA Sample Prep Kit


title: spm21

description: Illumina TruSeq RNA Sample Prep Kit


title: spm19

description: Illumina TruSeq RNA Sample Prep Kit


title: spm8wb

description: Illumina TruSeq RNA Sample Prep Kit


title: spm31

description: Illumina TruSeq RNA Sample Prep Kit


title: spm34

description: Illumina TruSeq RNA Sample Prep Kit


title: spm32

description: Illumina TruSeq RNA Sample Prep Kit


title: spm37

description: Illumina TruSeq RNA Sample Prep Kit


title: spm11

description: Illumina TruSeq RNA Sample Prep Kit


title: spm01

description: Illumina TruSeq RNA Sample Prep Kit


title: spm23

description: Illumina TruSeq RNA Sample Prep Kit


title: spm14

description: Illumina TruSeq RNA Sample Prep Kit


title: spm15

description: Illumina TruSeq RNA Sample Prep Kit


title: spm26

description: Illumina TruSeq RNA Sample Prep Kit


title: Zfc3h1_KO_2_ESC_D0_RNAseq

value: Embryonic stem cells


title: spm25

description: Illumina TruSeq RNA Sample Prep Kit


title: spm28

description: Illumina TruSeq RNA Sample Prep Kit


title: spm33

description: Illumina TruSeq RNA Sample Prep Kit


title: spm35

description: Illumina TruSeq RNA Sample Prep Kit


title: spm36

description: Illumina TruSeq RNA Sample Prep Kit


title: spm04

description: Illumina TruSeq RNA Sample Prep Kit


title: spm05

description: Illumina TruSeq RNA Sample Prep Kit


title: spm30

description: Illumina TruSeq RNA Sample Prep Kit


title: spm06

description: Illumina TruSeq RNA Sample Prep Kit


title: spm08

description: Illumina TruSeq RNA Sample Prep Kit


title: spm09

description: Illumina TruSeq RNA Sample Prep Kit


title: T0_b RNAseq

status: Public on Nov 13 2017

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs)
STAR version 2.5.0a [1], with default parameters, was used for alignment on the reference genome (GRCm38 from Ensembl database)
Genes were counted using featureCounts version 1.4.6-p3 [2] from Subreads package (parameters: -t gene -s 0 -O)
Count data were analyzed using R version 3.3.1 and the Bioconductor package DESeq2 version 1.12.3]. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed without applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between T0, T3 and T5. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: GRCm38 from Ensembl database version 74
Supplementary_files_format_and_content: matrix of count from featurecounts

source_name: Skeletal muscle stem cells from Tg:Pax7-nGFP mice

extract_protocol:
Total RNA was exrtacted from fixed MuSCs using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE, Ambion, AM1975. Modification: cells were incubated at 50°C for 1h in digestion buffer plus Proteases. No 80°C incubation was performed as recommended by the manufacturer as this deteriorated RNA quality.
Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input Mammalian   following the manufacturer’s instructions (Clontech 635005). The quality of all libraries was checked with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen).
Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed with the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

treatment_protocol: T0: muscles fixed with 0.5% paraformaldehyde (PFA), 1h, 4°C. T3: MuSCs fixed with 0.5% PFA, 30min on ice after FACS-isolation. T5: MuSCs fixed with 0.5% PFA, 30min on ice after dissected muscles were incubated in DMEM at 37°C for 2h and then MuSCs isolated by FACS.

tag: muscle stem cells manipulation

value: in situ fixed MuSCs.

value: Pectoral, forelimb, and hindlimb muscles


title: T0_a RNAseq


title: T0_c RNAseq


title: n200 -4

status: Public on Apr 19 2017

city: Irvine

first: Ricardo

middle: Noel

last: Ramirez

state: California

address: 2300 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California Irvine

description: iMGL with no CD200 added

data_processing:
RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to Gencode version 24 gene annotations using RSEM (Li and Dewey, 2011).
FPKM files were generated per sample using RSEM with gene ENSEMBL ID's and common gene names
Genome_build: hg38

source_name: human iPS microglia

growth_protocol: Cultured in custom serum-free media and fully defined conditions stated in manuscript.

extract_protocol:
RNeasy Qiagen extraction for RNA
Cells were harvested and washed three times with DPBS (1X) and stored in RNAlater, RNA preservation solution. RNA was extracted from all cell types using using RNeasy Mini Kit (Qiagen) following manufacturer’s guidelines. RNA integrity (RIN) was measured for all samples using the Bioanalzyer Agilent 2100 series. All sequencing libraries analyzed were generated from RNA samples measuring a RIN score ≥ 9. The Illumina TruSeq mRNA stranded protocol was used to obtain poly-A mRNA from all samples. A total of 200 ng of isolated mRNA was used to construct RNA-seq libraries. Libraries were quantified and normalized using the Library Quantification Kit from Kapa Biosystems and sequenced as paired-end 100 bp reads on the Illumina HiSeq 2500 platform.

treatment_protocol: iPS-derived cells were differentiated as stated in manuscript. Primary samples were isoalted according as stated in manuscript.

tag: stimulus/treatment

tag: time (hours)

value: iMGL


title: n200 -2

description: iMGL with no CD200 added


title: WT MEF Gata1+Fli1 1 4 months

status: Public on Jan 11 2018

description: RNA from WT MEFs transduced with pMSCV-Hygro-Gata1 and pMSCV-Puro-Fli1 for 4 months

hyb_protocol: Standard for Affymetrix GeneChip® Mouse Gene 1.0 ST arrays

data_processing: Partek Genomics Suite

source_name: Fibroblast transfected with gata1 + fli1 4 months

label_protocol: Affymetrix protocol

growth_protocol: All cells were cultured in standard medium (Dulbecco’s Modified Eagle Medium (high glucose) supplemented with 10% heat-inactivated FCS and 1% penicillin/streptomycin/glutamine). Eighteen hours prior to infection, cells were seeded at 1.5x105 cells per 60 mm dish. At 48 hours after transfection, viral supernatants were filtered and added to fibroblast cells with polybrene (8 µg/mL) for 24 hours. Transduced cells were then maintained under selection in puromycin (2.5 µg/mL) or hygromycin (500 µg/mL), where appropriate. Additionally, after transduction, cells were cultured in medium supplemented with 50 ng/mL recombinant human TPO.

extract_protocol: Phenol chloroform extraction followed by Rneasy Mini Kit purification

treatment_protocol: See growth protocol

tag: time point

value: 4 months following transduction


title: WT MEF empty vector puro+hyg 1 7 months

description: RNA from WT MEFs transduced with pMSCV-Hygro and pMSCV-Puro for 7 months

scan_protocol: Standard for Affymetrix GeneChip® Mouse Gene 1.0 ST arrays

source_name: Empty transfected fibroblast 7 months

value: 7 months following transduction


title: DMSO replicate 1

status: Public on Sep 29 2017

city: Rochester

first: Paul

middle: L.

last: Boutz

state: NY

address: 601 Elmwood Ave.

department: Biochemistry & Biophysics

institute: University of Rochester School of Medicine

description:
DMSO-1
Poly(A)-selected RNA
Processed data file: Gene_Expression_With_Categories.xlsx
Processed data file: DI_and_Consensus_Coding_Isoform_Expression.xlsx
Processed data file: U87MG_DMSO_EPZ015666_DI_and_Consensus_Coding_Isoform_Annotation.gff3

data_processing:
Reads were mapped to hg19 with genome annotation based on Gencode v19 using STAR aligner version 2.4.1d (Dobin et al, 2013) with the following parameters: STAR --runMode alignReads --runThreadN 2 --genomeDir hg19 --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --outFilterType BySJout. For DI determination, reads were mapped to hg19 using Bowtie 1.0.1 (Langmead et al., 2009) with the parameters: bowtie -n 1 -l 30 -e 70 -t -p 2 -m 1 -S -X 500.
After custom genome annotation based on mapped reads, and filtering to remove low-abundance splice junctions, reads per intron were counted using Bedtools version 2.20.1 (Quinlan and Hall, 2010).
Custom scripts were used to identify detained introns by generating input for the program DESeq version 1.10.1 (Anders and Huber, 2010), which was used to calculate the ratio of observed to expected read counts per intron and the false-discovery rate adjusted p-value for each intron that was identified by read mapping after filtering low-abundance splice junctions, overlapping introns and introns spanning exons, and polyadenylation sites.
Custom scripts were used to generate consensus coding and DI-containing isoform annotations genome-wide, and the raw sequences or STAR mapped reads were used as input for RSEM/EBSeq version 1.2.26 (Li et al, 2010) and DESeq, respectively to perform differential expression analysis at the gene and isoform levels.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Gene_Expression_With_Categories.xlsx: Excel file includes total gene level differential expression analysis results.
Supplementary_files_format_and_content: DI_and_Consensus_Coding_Isoform_Expression.xlsx: Excel file includes total isoform level differential expression analysis results.
Supplementary_files_format_and_content: U87MG_DMSO_EPZ015666_DI_and_Consensus_Coding_Isoform_Annotation.gff3: Transcriptome annotation for DI and consensus coding isoforms.

source_name: U-87 MG cells, DMSO

growth_protocol: U-87 MG cells were grown in DMEM (Corning, #10-013-CV) media supplemented with 10% FBS.

extract_protocol:
RNA samples were extracted with the NucleoSpin RNAplus kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using the Illumina TruSeq kit according to manufacturer's protocol.

treatment_protocol: Samples labeled with "DMSO" were treated with the vehicle DMSO (10 ul per 10 ml tissue culture media) for 72h, samples labeled with "EPZ015666" were treated with EPZ015666 at a concentration of 10uM for 72 hours.

tag: cell line

value: U-87 MG

tag: treatment

value: DMSO

tag: concentration

value: 10 ul per 10 ml media

tag: incubation time


title: DMSO replicate 2

description:
DMSO-2
Poly(A)-selected RNA
Processed data file: Gene_Expression_With_Categories.xlsx
Processed data file: DI_and_Consensus_Coding_Isoform_Expression.xlsx
Processed data file: U87MG_DMSO_EPZ015666_DI_and_Consensus_Coding_Isoform_Annotation.gff3


title: DMSO replicate 3

description:
DMSO-3
Poly(A)-selected RNA
Processed data file: Gene_Expression_With_Categories.xlsx
Processed data file: DI_and_Consensus_Coding_Isoform_Expression.xlsx
Processed data file: U87MG_DMSO_EPZ015666_DI_and_Consensus_Coding_Isoform_Annotation.gff3


title: EPZ015666 replicate 3

description:
EPZ015666-3
Poly(A)-selected RNA
Processed data file: Gene_Expression_With_Categories.xlsx
Processed data file: DI_and_Consensus_Coding_Isoform_Expression.xlsx
Processed data file: U87MG_DMSO_EPZ015666_DI_and_Consensus_Coding_Isoform_Annotation.gff3

source_name: U-87 MG cells, EPZ015666

value: 10 uM


title: EPZ015666 replicate 1

description:
EPZ015666-1
Poly(A)-selected RNA
Processed data file: Gene_Expression_With_Categories.xlsx
Processed data file: DI_and_Consensus_Coding_Isoform_Expression.xlsx
Processed data file: U87MG_DMSO_EPZ015666_DI_and_Consensus_Coding_Isoform_Annotation.gff3


title: WT MEF empty vector puro+hyg 2 4 months

description: RNA from WT MEFs transduced with pMSCV-Hygro and pMSCV-Puro for 4 months

source_name: Empty transfected fibroblast 4 months


title: WT MEF Gata1+Fli1 2 4 months

source_name: Fibroblast transfected with gata1 + fli2 4 months


title: WT MEF Gata1+Fli1 1 7 months

description: RNA from WT MEFs transduced with pMSCV-Hygro-Gata1 and pMSCV-Puro-Fli1 for 7 months

source_name: Fibroblast transfected with gata1 + fli1 7 months


title: Aspergillus niger wild type grown on sugar beet pulp 2 hours, replicate 1

status: Public on Jan 29 2018

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

description:
SBP-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on sugar beet pulp.

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized to Affymetrix A. niger Genome GeneChips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Microarray data was analyzed using the Bioconductor tool package version 2.8 (http://www.bioconductor.org/) together with house-made Perl (version .5.0) and Python (version 3.0) scripts. Probe intensities were normalized for background by the robust multi-array average (RMA) method using the R statistical language and environment. This method makes use of only perfect match (PM) probes. Normalization was processed by the quantiles algorithm. The median polish summary method was used to calculate the gene expression values.

organism: Aspergillus niger

label_protocol: Biotin-labeled antisense cRNA was produced from 2 µg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: A. niger N402 wild type was pre-cultured in 1 L Erlenmeyer flasks in 250 mL complete medium (CM) supplemented with 2% D-fructose. The pre-cultures were inoculated with 10e6 spores/mL and incubated at 250 rpm for 16 h at 30°C.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: Mycelium was washed with MM and transferred for 2 h to 250 ml Erlenmeyer flasks containing 50 ml MM supplemented with 25 mM D-glucose, D-fructose, D-galactose, L-arabinose, D-xylose, D-mannose, D-galacturonic acid, L-rhamnose, Maltose, Sucrose, Ferulic acid or ferulic acid, or mixture of 25 mM L-rhamnose and 25 mM D-galacturonic acid, or 1% Inulin from chicory, Cellulose, Guar gum, Xyloglucan, Xylan (from beechwood), Polygalacturonic acid (from apples), Apple pectin, Galactan (from potato), Debranched 1,5-α-L-arabinan (from sugar beet), Rhamnogalacturonan I (from potato), Mannan (ivory nut), Citrus pulp, Sugar beet pulp or Soy bean hulls. The only exceptions were D-maltose cultures of N402 and ∆amyR strains that were incubated for 4 h. Mycelium was harvested by vacuum filtration, dried between towels and frozen in liquid nitrogen. While N402 liquid cultures were performed on all carbon sources listed before as well as on the mixture of L-rhamnose and D-galacturonic acid, the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX were grown on D-xylose, L-arabinose, maltose, L-rhamnose and D-galactose, respectively, and L-rhamnose and D-galacturonic acid. All cultures were performed as biological duplicates.

tag: strain

tag: genotype

value: cspA1 (wild type)

value: mycelium

value: 2 hours

tag: substrate

value: 1% sugar beet pulp


title: WT MEF empty vector puro+hyg 2 7 months


title: WT MEF Gata1+Fli1 2 7 months

source_name: Fibroblast transfected with gata1 + fli2 7 months


title: Aspergillus niger wild type grown on polygalacturonic acid 2 hours, replicate 2

description:
PGA-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on polygalacturonic acid.

tag: tissue

value: 1% polygalacturonic acid


title: Aspergillus niger wild type grown on sugar beet pulp 2 hours, replicate 2

description:
SBP-wt replicate 2
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on sugar beet pulp.


title: x2-2

data_processing:
RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to GENCODE version 24 gene annotations using RSEM (Li and Dewey, 2011).
FPKM files were generated per sample using RSEM with gene ENSEMBL ID's and common gene names.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKMs, ENSEMBL ID's and common gene names.

source_name: iPS microglia

extract_protocol:
Cells were harvested and washed three times with DPBS (1X) and stored in RNAlater, RNA preservation solution. RNA was extracted from all cell types using RNeasy Mini Kit (Qiagen) following manufacturer's guidelines. RNA integrity (RIN) was measured for all samples using the Bioanalyzer Agilent 2100 series.
All sequencing libraries analyzed were generated from RNA samples measuring a RIN score ≥ 9. The Illumina TruSeq mRNA stranded protocol was used to obtain poly-A mRNA from all samples. A total of 200 ng of isolated mRNA was used to construct RNA-seq libraries. Libraries were quantified and normalized using the Library Quantification Kit from Kapa Biosystems and sequenced as paired-end 100 bp reads on the Illumina HiSeq 2500 platform.

treatment_protocol: iPS-derived cells were differentiated as stated in manuscript. Primary samples were isolated as stated in manuscript.

tag: cell type


title: Aspergillus niger wild type grown on polygalacturonic acid 2 hours, replicate 1

description:
PGA-wt replicate 1
Wild type N402 cspA1
Gene expression data from A. niger wild type growing on polygalacturonic acid.


title: WT MEF empty vector puro+hyg 1 4 months


title: x2-1


title: x2-3


title: EPZ015666 replicate 2

description:
EPZ015666-2
Poly(A)-selected RNA
Processed data file: Gene_Expression_With_Categories.xlsx
Processed data file: DI_and_Consensus_Coding_Isoform_Expression.xlsx
Processed data file: U87MG_DMSO_EPZ015666_DI_and_Consensus_Coding_Isoform_Annotation.gff3


title: 7028X2


title: x2-4


title: 10318X2


title: spm29

description: Illumina TruSeq RNA Sample Prep Kit

value: M


title: n200 -3

description: iMGL with no CD200 added


title: lymphocytes_0Gy_rep40

status: Public on Jan 30 2017

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

hyb_protocol: RNA was hybridised to HT HG-U133+ PM GeneChip® arrays (Affymetrix, Santa Clara CA, USA) according to the manufacturer’s protocol.

scan_protocol: Scanning of the array was conducted by the MicroArray Department of the University of Amsterdam, and images were processed to obtain an intensity value for each oligonucleotide probe.

data_processing: Data were normalized and summarized to the probe set level using the robust multi-array average (RMA) method with default settings (function rma, package affy; version 1.44.0).

label_protocol: Biotin-labeled cRNA probes were generated according to the manufacturer’s protocol.

growth_protocol: Peripheral lymphocytes were isolated using Ficoll (Ficoll-Paque PLUS, GE Healthcare) gradient separation, and stored in liquid nitrogen.

extract_protocol: Isolation of RNA was executed 24h post radiation using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol. RIN value and RNA quality of both treated as untreated RNA was assessed with a BD Bioanalyzer.

treatment_protocol: Lymphocytes were cultured stimulated by phytohemagglutinin (concentration of 1μg/ml). After two weeks, half of the cells were irradiated at room temperature with 2Gy gamma rays from a 137Cs source, dose rate of approximately 0.5Gy/min and the other half of the cells was left untreated.

value: lymphocytes

tag: irradiation

tag: batch

tag: study

value: prospective


title: lymphocytes_0Gy_rep186


title: lymphocytes_2Gy_rep40


title: 3_HC_untreated

status: Public on Nov 02 2016

description:
HC-3
3. HC PBMC untreated

data_processing: The raw data were processed with IlluminaGenomeStudio with no background correction.  The data were log2 transformed and quantile normalized in BRBArrayTools.

source_name: 3. HC PBMC

growth_protocol: Healthy control PBMCs were plated in 6 well plates at density of 0.8-1x106 cells/well in RPMI supplemented with 10% FCS and 1% AA overnight prior to transduction. 6 hours after transduction with Lentivirus, cells were centrifuged and fresh media was added. Cells were collected after 72 hours.

extract_protocol: Cells were collected in RNeasy RLT buffer and RNA extracted with Qiagen’s RNeasy Mini Kits in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Cells were transduced with Lentivirus (carrying HLA-B35 or B8 or control virus)  using M.O.I.’s ranging from 0.1 to 1, mix of virus with 8 mg/ml Polybrene (Sigma) and RPMI was ass to cells for 6 hrs

value: blood

value: PBMC


title: 3_HC_2.5_B35_lentivirus

description:
2.5B35-3
3. HC PBMC treated with with 2.5 MOI of B35 lentivirus


title: 2_HC_untreated

description:
HC-2
2. HC PBMC untreated

source_name: 2. HC PBMC


title: TGFb

status: Public on Oct 29 2016

data_processing: The raw data were processed with the IlluminaExpressionFileCreator module in GenePattern.  The data were log2 transformed and quantile normalized.

source_name: Human mammary epithelial cells

label_protocol: Using the Ambion Illumina TotalPrep RNA Amplification kit (Ambion #IL1791), we reverse-transcribed 300 ng of total RNA using a T7 oligo-dT primer, used the resulting cDNA to synthesize the complement strand, purified, and in vitro transcribed biotinylated cRNA.

growth_protocol: HMLE cells were cultured in a 1:1 ratio of DME:F12 and MEBM+Bullet Kit.

extract_protocol: We extracted total RNA using Qiagen's RNeasy Mini Ki according to the manufacturer's protocol with DNAse digestion.

treatment_protocol: The cells were treated with either ectopic expression of Snail, TGF-beta, or DHA.

value: HMLE

tag: emt inducer

tag: tgfb (ng/ml)

tag: dha (um)


title: 3_HC_0.5_B35_lentivirus

description:
0.5 B35-3
3. HC PBMC treated with with 0.5 MOI of B35 lentivirus

tag: b35 vs b8

tag: b35 vs b8 pair

tag: b35 vs c

tag: b35 vs c pair


title: 2_HC_0.5_B35_lentivirus

description:
0.5 B35-2
2. HC PBMC treated with with 0.5 MOI of B35 lentivirus


title: 2_HC_0.5_control lentivirus

description:
0.5C-2
2. HC PBMC treated with 0.5 MOI of control Lentrivirus

value: C


title: 3_HC_0.5_control lentivirus

description:
0.5C-3
3. HC PBMC treated with 0.5 MOI of control Lentrivirus


title: lymphocytes_0Gy_rep39


title: ChIP-seq from limb (ENCLB782QDN)

status: Public on Jun 22 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR737QWV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 12.5 day mouse limb
experiment encode accession: ENCSR737QWV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR218CUA
encode release date: 2016-03-30
lab: Bing Ren, UCSD
library encode accession: ENCLB782QDN
size range: 300-500

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (12.5 days)

tag: antibody

value: limb

value: tissue

tag: description

value: Limb from 68 embryonic 12.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS313XRY at ENCODE; https://www.encodeproject.org/ENCBS313XRY/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Aire-KO MEChi

status: Public on Sep 23 2016

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

institute: INSERM _ Université de Nantes

data_processing:
Illumina HiSeq2000 sequencer
Sequenced reads were aligned to the mm9 genome using the STAR aligner (v2.3.0)
FPKM was calculated for each  gene annotates in the UCSC known genes table using RSEM
Genome_build: mm9
Supplementary_files_format_and_content: Text files include count numbers and FPKM values

source_name: medullary thymic epithelial cells

extract_protocol:
Total RNA was extracted by Trizol
non-directionnal TruSeq V3 RNA Sample Prep Kit on PolyA+ mRNA

treatment_protocol: MHC-II high mTECs were isolated from pools of three mice using a BD FACS Aria III cell sorter, following the typical isolation procedure

tag: tissue

value: thymus

tag: background strain

tag: cell type

value: medullary epithelial cells

tag: mhc level

value: HIGH

tag: genotype

value: Aire -/-


title: 1_HC_0.1_B8_lentivirus

description:
0.1B8-1
1. HC PBMC treated with with 0.1 MOI  of B8 lentivirus

source_name: 1. HC PBMC

value: blood

tag: b35 vs b8

tag: b35 vs b8 pair


title: 2_HC_0.5_B8_lentivirus

description:
0.5B8-2
2. HC PBMC treated with with 0.5 MOI  of B8 lentivirus

value: PBMC


title: lymphocytes_2Gy_rep41

value: lymphocytes

tag: irradiation

tag: batch

tag: study

value: prospective


title: 3_HC_2.5_control lentivirus

description:
2.5C-3
3. HC PBMC treated with 2.5 MOI of control Lentrivirus


title: Snail+DHA

tag: cell line

value: HMLE

tag: emt inducer

value: Snail

tag: tgfb (ng/ml)

tag: dha (um)


title: 1_HC_0.1_control lentivirus

description:
0.1C-1
1. HC PBMC treated with 0.1 MOI of control Lentrivirus

tag: b35 vs c

value: C

tag: b35 vs c pair


title: Snail


title: 1_HC_untreated

description:
HC-1
1. HC PBMC untreated


title: 1_HC_0.5_B35_lentivirus

description:
0.5B35-1
1. HC PBMC treated with with 0.5 MOI of B35 lentivirus


title: DHA


title: Vector


title: 3_HC_0.5_B8_lentivirus

description:
0.5B8-3
3. HC PBMC treated with with 0.5 MOI  of B8 lentivirus


title: TGFb+DHA


title: 3_HC_2.5_B8_lentivirus

description:
2.5B8-3
3. HC PBMC treated with with 2.5 MOI  of B8 lentivirus


title: 26I-0

status: Public on Mar 31 2016

data_processing:
TopHat v1.3.3 was used for aligning to the hg19 genome, assembling transcripts, and estimating abundance as FPKM values.
Missing values and values less than 1 were set to 1.
Values were logged with base 2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file contains log_2 FPKM values for each sample.

source_name: Transformed bronchial epithelial cells

growth_protocol: BEAS-2B cells were purchased from ATCC and cultured as instructed by the manufacturer.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) or RNeasy Mini Kit (QIAGEN) following the manufacturer's protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded and incubated for 1 day before transfection and/or TNF-a treatment.  For TNF-a stimulation, cells were cultured for 6h in medium containing 50 ng/ml of TNF-a.  Transfections of miRNA mimics and miRNA antagomir were carried out using lipofecatmine-RNAiMAX (Invitrogen) according to the manufacturer’s protocol.

tag: treatment

value: miR-26 antagomir

tag: stimulation


title: 26M-0

value: miR-26 mimic


title: 26CI-6

value: inhibitor control

value: TNFa, 6 hours


title: 26I-6


title: 26M-6


title: 26CI-0


title: 26CM-6

value: mimic control


title: 26CM-0


title: Ob_rep2

status: Public on Apr 28 2016

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

country: Japan

institute: The University of Tokyo

description:
Ob_Sp7-GFP2
HH_Osx_2

data_processing:
The raw reads were first subjected to pre-alignment Quality Assurance and Quality Control (QA/QC).
Any base below a Phred value of 20 was trimmed from either side of the read and reads shorter than 25 nt length were removed.
The processed reads were aligned by Tophat2-2.0.8 (Kim et al., 2013) to mm9 reference genome.
The mapping quality and coverage were checked by post-alignment QA/QC.
Aligned reads were quantified by an expectation maximization algorithm (Xing et al., 2006), followed by a normalization of mapped reads per kilo base length of transcript per million reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports abundance measurements

source_name: Primary osteoblast

growth_protocol: Primary osteoblasts were isolated P1 mouse calvaria and primary chondrocytes were isolated from P1 mouse rib cartilage

extract_protocol:
Primary osteoblasts were isolated by 1 unit/ml Liberase TM (05401119001, Roche). Primary chondrocytes were isolated by 2 mg/mL PRONASE Protease (53702, EMD Millipore Corporation)  and 0.2% Collagenase D (1088858; Roche Applied Science)
RNA libraries were constructed by Tru-Seq Illumina kit (RS-122-2001, illumina) with some modifications

value: GFP-sorted osteoblasts

tag: isolated from

value: calvaria

tag: strain

tag: age

value: Sp7 positive


title: Ob_rep1

description:
Ob_Sp7-GFP1
HH_Osx_1

tag: cell type

tag: genotype


title: ChIP-seq from liver (ENCLB087UEL)

description:
https://www.encodeproject.org/experiments/ENCSR136GMT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 12.5 day mouse liver
experiment encode accession: ENCSR136GMT
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR680ZSE
encode release date: 2016-03-30
lab: Bing Ren, UCSD
library encode accession: ENCLB087UEL
size range: 300-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (12.5 days)

tag: antibody

value: liver

value: tissue

tag: description

value: Liver from 88 embryonic 12.5 day mice

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS479VPX at ENCODE; https://www.encodeproject.org/ENCBS479VPX/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: spm13

description: Illumina TruSeq RNA Sample Prep Kit

source_name: microglia

tag: tissue

value: microglia

tag: gender

value: M


title: Wild type A.niger, zone4 biological rep2

status: Public on Mar 04 2016

first: miaomiao

last: Zhou

institute: centre of fungal biodiversity, Utrecht, KNAW

description: Gene expression data from A.niger wild type grow on sugar beet pulp for 5 days

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.

data_processing: Affymetrix CEL-data files were preprocessed by using the statistical language and environment R (R Development Core Team, 2007) version 2.6.1. The probe intensities were normalized for background by using the robust multiarray average method (Irizarry, 2003) by using only perfect match (PM) probes. Normalization was performed subsequently by using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

source_name: A.niger wild type grow on sugar_beet_pulp zone4

label_protocol: Biotin-labeled antisense cRNA was produced from 2 μg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: A. niger N402 (cspA1) (Bos et al. 1988) was grown at 30°C under constant light in water-saturated air. Colonies were grown as a sandwiched culture (Levin et al. 2007) in 9-cm petri dishes in a 0.2-mm thin layer of 1.25% agarose in between two perforated polycarbonate membranes (diameter, 76 mm; pore size, 0.1 m; Osmonics, GE Water Technologies, Trevose, PA) placed on top of solidified (1.5% agar) minimal medium (7) with 1% sugar beet pulp as a carbon source or in liquid minimum medium contained in a ring plate. Sandwiched cultures were inoculated with 1.5 l of spore suspension (108 spores l-1) and harvested after 6 days of growth.   A ring plate consists of a polycarbonate disc (9 cm in diameter, 1.2 cm thick) with six ring-shaped wells. The inner two rings are collectively called ring 1 because of their small volume, and the outer ring is called ring 5. The wells are separated by 0.1 cm and are 0.5 cm deep and 0.5 cm wide.

extract_protocol: Mycelium was ground using a microdismembrator (B. Braun GmBh, Melsungen, Germany), and RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. The RNA was purified using a Nucleospin RNA cleanup kit (Macherey-Nagel GmBh, Düren, Germany). The concentration of RNA was measured at A260. The quality of the RNA was analyzed with an Agilent 2100 bioanalyzer, using an RNA6000 LabChip kit (Agilent Technology, Palo Alto, CA).

treatment_protocol: Biotin-labeled antisense cRNA was generated by labeling 20 or 2 μg of total RNA with a BioArray high-yield RNA transcription labeling kit (ENZO) or an Affymetrix eukaryotic one-cycle target labeling and control reagent package, respectively. The quality of the cRNA was checked using the Agilent 2100 bioanalyzer. The labeled cRNA was hybridized to Affymetrix A. niger GeneChips (Affymetrix, Santa Clara, CA). The coding sequence of the annotated genome of CBS513.88 (Pel et al. 2007) was taken as the sequence template. Oligonucleotide probes were designed with 600-bp fragments, starting from the 3’ end of the gene. The probe sets consist of 12 pairs (match and mismatch) of 25-bp oligonucleotide probes, which are scattered across the chip. Arrays were hybridized with three independently obtained RNA samples of the peripheries of 5-day-old sandwiched cultures grown on sugar beet pulp.

value: Wild type N402

value: 5 days


title: Wild type A.niger, zone5 biological rep2

source_name: A.niger wild type grow on sugar_beet_pulp zone5


title: Wild type A.niger, zone3 biological rep2

source_name: A.niger wild type grow on sugar_beet_pulp zone3


title: Wild type A.niger, zone2 biological rep2

source_name: A.niger wild type grow on sugar_beet_pulp zone2


title: Wild type A.niger, zone1 biological rep1

source_name: A.niger wild type grow on sugar_beet_pulp zone1


title: Wild type A.niger, zone2 biological rep1


title: ETOH_DOX_24h_rep2

status: Public on Aug 20 2015

description: Total RNA hybridized onto an Illumina Human HT-12 gene expression microarray.

data_processing: The raw data were preprocessed on GenePattern using the IlluminaExpressionFileCreator module (no background subtraction was performed).

source_name: LNCaP cells with inducible shRNA directed against SH3YL1

growth_protocol: Cells were grown RPMI1640 phenol-red free supplemented with 10% charcoal-stripped FBS, 5% Non-essential amino acids, and 5% Sodium Pyruvate for 72 hours prior to first treatment.

extract_protocol: We extracted total RNA utilizing the BioRad RNA extraction kit according to manufacturer’s instructions.

treatment_protocol: Cells were treated with vehicle (EtOH), 100pM R1881 or 10nM R1881 for 24 or 72 hours +/- doxycycline

value: LNCaP


title: Wild type A.niger, zone5 biological rep1


title: ETOH_72h_rep2


title: Wild type A.niger, zone1 biological rep2


title: ETOH_DOX_24h_rep3


title: Wild type A.niger, zone4 biological rep1


title: ETOH_DOX_72h_rep2


title: ETOH_DOX_72h_rep3


title: ETOH_24h_rep3


title: R1881_10pm_DOX_24h_rep3


title: R1881_10pm_DOX_72h_rep3


title: Wild type A.niger, zone3 biological rep1


title: R1881_10pm_DOX_72h_rep2


title: ETOH_24h_rep2


title: R1881_10pm_DOX_24h_rep2


title: ETOH_24h_rep1


title: ETOH_DOX_72h_rep1


title: ETOH_DOX_24h_rep1


title: ETOH_72h_rep1


title: ETOH_72h_rep3


title: R1881_10pm_DOX_24h_rep1


title: R1881_10pm_DOX_72h_rep1


title: R1881_10pm_72h_rep2


title: R1881_10pm_72h_rep3


title: R1881_10pm_24h_rep2


title: R1881_10pm_24h_rep3


title: ITD1_Runx1_ChIP-Seq

status: Public on Jul 03 2015

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

description: Reanalysis of GSM722708

data_processing:
Base-calling (Illumina)
DNAse-seq reads were aligned to the hg18 genome assembly using Bowtie 1.00 to SAM output using --all --best --strata --v 2 -m 1 -S
Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011.
Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011
Peaks were called using CoCAS (Benoukraf et al. Bioinformatics 2009)
Genome_build: hg18
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011. Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. Nat Struct Mol Biol 2011. Peaks were called using CoCAS (Benoukraf et al. Bioinformatics 2009)

source_name: FLT3-ITD AML patient sample

growth_protocol: Patient and donor samples were obtained either from blood or bone marrow. Lymphoprep extraction of leukocytes was performed following 30 min no brake centrifugation. Enrichment for CD34 and CD117 were checked via FACS analysis. For CD14 samples, enricment for CD14 was controlled by FACS analysis. Where available, purification was performed using MACS columns following anti-CD34 bead conjugation to samples (anti-CD14 for CD14 samles).

extract_protocol:
Phenol-chloroform
Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer’s guidelines). Adenosine bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-minus), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers (sequences 5’- CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T).  The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 μl each sample on an Agilent Technologies 2100 Bioanalyser. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer. ETO, RUNX1, C/EBPα, PU.1, LMO2 ChIP and Kasumi-1 DNase I libraries were sequenced employing the Illumina Genome Analyzer GAIIx, by using 36 base pair single end reads.

treatment_protocol: Cells were resuspended in 10 ml of growing medium, and cross-linked with 1% formaldehyde (Pierce) for 10 min at RT. The cross-linking reaction was stopped by adding glycine to a final concentration of 0.4 M, followed by two washes with ice–cold PBS. Cells were resuspended in 10 ml of ice-cold ChIP buffer A (10 mM HEPES pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, proteinase inhibitor cocktail (Roche UK, Burgess Hill, UK) and 0.1 mM PMSF), incubated for 10 min at 4°C with rotation, and centrifuged 5 min at 500 x g at 4 °C. The pellet was resuspended in 10 ml of ice–cold ChIP buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, protease inhibitor cocktail and 0.1 mM PMSF), incubated for 10 min at 4 °C with rotation and centrifuged for 5 min at 500 x g at 4 °C. Cells were resuspended in 600 μl of ice-cold ChIP lysis buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.25% SDS, protease inhibitor cocktail and 0.1 mM PMSF), incubated 10 min on ice and sonicated at 5 °C using a Bioruptor™ (Diagenode, Liege, Belgium) to generate fragments an average length of 400-500 bp (10 min with 30 s “ON” and “OFF” cycles, power setting high). The lysates were centrifuged for 5 min at 16,000 x g at 4 °C and the supernatants were diluted with two volumes of ice-cold ChIP dilution buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 7.5% glycerol, protease inhibitor cocktail and 0.1 mM PMSF). For each IP, 15 μl of Dynabeads® protein G were pre–incubated with 50 μg BSA and 2 μg antibody against RUNX1 (Abcam, ab23980) for 2 h at 4 °C with rotation. The blocked antibody-bound protein G mix was added to 20–25 μg chromatin in a total volume of 500 μl diluted ChIP lysis buffer and incubated for 2 h at 4°C with rotation. After magnetic separation the beads were washed once with 1 ml wash buffer 1 (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with 1 ml wash buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 1 ml LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxycholate) and twice with 1 ml TE/NaCl buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). For each wash the beads were mixed with ice-cold washing buffers for 10 min at 4 °C. The immunoprecipitated DNA was eluted two times with 50 μl ChIP elution buffer (100 mM NaHCO3, 1% SDS) for 15 min at RT with shaking. At this step the input control (1% of the starting material) was included in the experimental procedure after first adjusting the final volume to 100 μl with ChIP elution buffer. The eluted DNA was incubated overnight at 65 °C in the presence of 50 μg proteinase K. The DNA was finally purified using Agencourt AMPure (Beckman Coulter) magnetic beads according to the manufacturer’s instructions, eluted with 50 μl x TE.


title: R1881_10pm_72h_rep1


title: R1881_10nm_DOX_72h_rep3


title: R1881_10nm_DOX_24h_rep3


title: R1881_10nm_DOX_24h_rep2


title: lymphocytes_2Gy_rep186

value: lymphocytes

tag: irradiation

tag: batch

tag: study

value: prospective


title: R1881_10nm_DOX_72h_rep2


title: R1881_10pm_24h_rep1


title: R1881_10nm_DOX_72h_rep1


title: R1881_10nm_72h_rep1


title: R1881_10nm_24h_rep1


title: R1881_10nm_72h_rep2


title: R1881_10nm_24h_rep2


title: R1881_10nm_DOX_24h_rep1


title: R1881_10nm_72h_rep3


title: R1881_10nm_24h_rep3


title: SAMPLE095

status: Public on May 26 2015

description: Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

data_processing: The raw data were exported from Illumina GenomeStudio (no background subtraction was performed).  The data were log2 transformed and normalized by quantiles using BRB-Array Tools.

source_name: skin biopsy

growth_protocol: A 3mm punch skin biopsy was obtained from the arm of study subjects.

extract_protocol: We extracted total RNA utilizing RNeasy Fibrous Tissue (Qiagen) according to manufacturer’s instructions.

treatment_protocol: The samples were put immediately in RNALater (Qiagen).

tag: patient

tag: group

value: Control

tag: gender (1=male)

tag: race

value: African American

tag: age at biopsy date


title: SAMPLE094

value: White


title: SAMPLE099


title: SAMPLE100

value: Latino


title: SAMPLE101


title: SAMPLE098


title: SAMPLE102


title: SAMPLE093

value: SSc

tag: diffuse vs limited

value: Dif

tag: antibody group

value: ACA

tag: on immunosurressive agents (1=yes)

tag: total skin score

tag: skin score at biopsy site

tag: affected (1=yes)


title: SAMPLE091


title: SAMPLE096


title: SAMPLE097


title: SAMPLE089


title: SAMPLE088

value: RNAP


title: SAMPLE090


title: SAMPLE092


title: SAMPLE084

tag: time point

value: Late


title: SAMPLE086


title: SAMPLE082

value: Early

value: Lim

tag: fvc less than 70

value: No ILD


title: SAMPLE087


title: Ob_rep3

description:
Ob_Sp7-GFP3
HH_Osx_3

tag: cell type

value: GFP-sorted osteoblasts

tag: isolated from

value: calvaria

tag: strain

tag: age

tag: genotype

value: Sp7 positive


title: SAMPLE085

tag: patient

tag: group


title: SAMPLE083

tag: gender (1=male)

tag: race


title: SAMPLE079

tag: age at biopsy date


title: SAMPLE080


title: SAMPLE081


title: SAMPLE075


title: SAMPLE074


title: SAMPLE073


title: SAMPLE071


title: SAMPLE077


title: SAMPLE070


title: SAMPLE078


title: SAMPLE067


title: MEChi

status: Public on May 25 2015

data_processing:
Illumina HiSeq2000 sequencer
Sequenced reads were casava-filtered for high-quality using the fastq_illumina_filter software
Paired-end reads were concatenated and trimmed to 50bp
Alignment to the mm9 genome was done using bowtie v1.0.0 with parameters --best
Read numbers were generated using intersectBed with parameters -f 1.0 followed by coverageBed part of the bedtools distribution
Genome_build: mm9
Supplementary_files_format_and_content: csv text files include read count numbers and RPKM values for each sample

source_name: MHC-II high mTECs

treatment_protocol: MHC-II low and MHC-II high mTECs were isolated from a pool of three B6 mice using a BD FACS Aria III cell sorter, following the typical isolation procedure

tag: strain background

tag: tissue

value: thymus

value: medullary epithelial cells

tag: mhc

value: MHC-II high


title: MEClo

source_name: MHC-II low mTECs

value: MHC-II low


title: SAMPLE064

value: Control


title: SAMPLE068

value: African American


title: SAMPLE076

value: Latino


title: SAMPLE066

value: White

tag: skin score at biopsy site


title: SAMPLE069


title: SAMPLE072


title: SAMPLE065


title: SAMPLE060


title: CIT584

status: Public on May 12 2015

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

hyb_protocol: Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45°C, 60 rpm on Human GeneChip HG-U133 Plus 2.0 arrays (Affymetrix).  The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v5_450.

scan_protocol: Scanner GeneChip 3000 7G ; Wavelenght : 570 nm, size pixel: 1.56 µm ; each chip is scanned once; Http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: RMA normalisation (Bioconductor R affy package) + ComBat (R sva package )

source_name: Frozen tissue of non tumoral colorectal mucosa

label_protocol: Biotinylated cRNA targets were prepared from 3.0 mg of total RNA, according to the GeneChip Expression Analysis Technical Manual : One-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: Samples stored at -80 C

extract_protocol: E3: total RNA was extracted using  Manual-Rneasy Micro (Qiagen)

treatment_protocol: Total RNA was performed according to the manufacturer's instructions.

tag: organism

value: Homo sapiens

tag: dataset

value: Non Tumoral

tag: Sex

value: Female

tag: age.at.diagnosis (year)

value: proximal

value: N

tag: os.delay (months)

value: pMMR

tag: dependancy sample


title: CIT581

value: Male

value: Y


title: SAMPLE061

tag: time point

value: Late

tag: total skin score


title: CIT577

value: dMMR


title: CIT579

value: FUFOL


title: SAMPLE062

tag: patient


title: CIT582

value: FOLFIRI


title: CIT572


title: CIT585


title: CIT583

value: distal


title: CIT573


title: CIT578


title: CIT580


title: CIT569


title: CIT574


title: CIT571


title: CIT568


title: SAMPLE063

tag: group

value: Control


title: Tumor biopsy FUNC-050

status: Public on Jan 05 2015

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0.

source_name: Prostate tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: A punch biopsy was collected from each patient at the time of surgery

extract_protocol: RNA was extracted with Rneasy MiniKit (Qiagen). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis. Biopsies with more than 75% malignant glands and less than 50% stroma in HE stained sections from the specimen were used further.

value: prostate tumor biopsy

tag: histology

value: Adeno carcinoma

tag: clinical t-stage (ct)

tag: lymph node metastasis status

tag: cohort

value: Investigation cohort


title: Tumor biopsy FUNC-052

tag: tissue


title: Tumor biopsy FUNC-047


title: CIT575

value: Homo sapiens


title: Tumor biopsy FUNC-036


title: Tumor biopsy FUNC-042


title: Tumor biopsy FUNC-045


title: CIT576

value: Non Tumoral


title: Tumor biopsy FUNC-049


title: Tumor biopsy FUNC-044


title: CIT567


title: Tumor biopsy FUNC-037


title: Tumor biopsy FUNC-048


title: Tumor biopsy FUNC-039


title: Tumor biopsy FUNC-034


title: Tumor biopsy FUNC-043


title: Tumor biopsy FUNC-051


title: Tumor biopsy FUNC-033


title: Tumor biopsy FUNC-038

value: Missing


title: CIT570

value: Female


title: Tumor biopsy FUNC-040


title: Tumor biopsy FUNC-053


title: Tumor biopsy FUNC-031


title: Tumor biopsy FUNC-032


title: Tumor biopsy FUNC-027


title: Tumor biopsy FUNC-030


title: Tumor biopsy FUNC-024


title: Tumor biopsy FUNC-035


title: Tumor biopsy FUNC-026


title: Tumor biopsy FUNC-016


title: Tumor biopsy FUNC-020


title: Tumor biopsy FUNC-014


title: Tumor biopsy FUNC-028


title: Tumor biopsy FUNC-023


title: Tumor biopsy FUNC-029


title: Tumor biopsy FUNC-013


title: Tumor biopsy FUNC-009


title: Tumor biopsy FUNC-018


title: Tumor biopsy FUNC-012


title: Tumor biopsy FUNC-005


title: Tumor biopsy FUNC-004


title: Tumor biopsy FUNC-006


title: Tumor biopsy FUNC-015


title: Tumor biopsy FUNC-021


title: Tumor biopsy FUNC-003


title: Tumor biopsy FUNC-008


title: 5491021015_K

status: Public on Aug 21 2013

data_processing: The raw data were exported from Illumina GenomeStudio (no background subtraction was performed).

growth_protocol: We cultured either human mammary epithelial cell lines, or collected RNA from human melanoma tissue.

extract_protocol: We extracted RNA using the Qiagen Rneasy kit according to manufacturer's instructions.

treatment_protocol: Cell lines were infected with adenovirus expression either GFP (control), E2F1, MYC, or Ras.

tag: cell type

value: Melanoma

tag: transfection

value: TL


title: 5491021054_C


title: 5491021020_H


title: 5491099062_G


title: Tumor biopsy FUNC-002


title: 5491021069_K


title: Tumor biopsy FUNC-001


title: 5491021015_J


title: 5491021067_D


title: 5491021054_L


title: 5491021054_B


title: 5491021067_J


title: 5491021015_I


title: 5491021067_B

value: Human Mammary Epithelial Cells

value: RAS


title: 5491021054_F


title: 5491021069_F


title: 5491099062_D


title: Tumor biopsy FUNC-019


title: 5491021067_I


title: 5491021069_C


title: 5491099062_F


title: 5491021067_C


title: 5491021015_F


title: 5491021069_E


title: 5491021067_H


title: 5491021069_I


title: 5491021067_A

value: MYC


title: 5491021020_E


title: 5491099062_L


title: 5491021054_G


title: 5491021020_F


title: 5491021054_K


title: 5491021054_E


title: 5491099062_K


title: 6991010082_D


title: 6991010082_F


title: 6991010018_J


title: 6991010018_F


title: 5491021069_J


title: 6991010018_I


title: 5491021020_G


title: 5491099062_E


title: 5491021054_A


title: 5491099062_C


title: 6991010082_C

value: GFP


title: 6991010018_D


title: 6991010082_B


title: 6991010082_J


title: 6991010082_G


title: 6991010082_A


title: 6991010018_E


title: 6991010018_C


title: 6991010018_H


title: 6991010082_K


title: 6991010082_H


title: 6991010018_L


title: 6991010082_E


title: 6991010082_I


title: 6991010018_A


title: 6991010018_B


title: E2F1-08

description: E2F1-transduced human mammary epithelial cells

hyb_protocol: A hybridization cocktail was prepared that contains the fragmented cRNA, probe array controls, BSA, and herring sperm DNA.  The cRNA is hybridized to the oligonucleotide probes on the array for 16 hours at 45C.

scan_protocol: Immediately following the hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the fluidic station and are then scanned on the GeneChip Scanner 3000 7G.

data_processing: RMA preprocessing using the Bioconductor toolkit.

source_name: Human Mammary Epithelial Cells

label_protocol: We performed an in vitro transcription reaction to produce biotin-labeled cRNA from the cDNA.

growth_protocol: HMEC cells were cultured in serum-free growth medium.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini kit.

treatment_protocol: Cells were transduced with adenovirus carrying GFP (control) or E2F1.


title: 5491021015_G


title: 6991010082_L


title: E2F1-09


title: E2F1-07


title: E2F1-10


title: E2F1-04


title: E2F1-01


title: GFP(E2F1)-12

description: GFP-transduced human mammary epithelial cells.


title: E2F1-03


title: E2F1-05


title: E2F1-02


title: GFP(E2F1)-07


title: 6991010018_K


title: GFP(E2F1)-08


title: GFP(E2F1)-10


title: E2F1-06


title: GFP(E2F1)-02


title: GFP(E2F1)-01


title: GFP(E2F1)-05


title: GFP(E2F1)-11


title: GFP(E2F1)-03


title: PATIENT59

status: Public on Jul 12 2013

description:
PATIENT59
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

tag: individual

value: skin biopsy

tag: gender [1 = male, 0 = female]

tag: on immunosuppressive agents [1 = yes, 0 = no]

tag: race

value: African American

tag: age

tag: antibody group

value: ATA

tag: fvc predicted

tag: fvc less than 70

value: No ILD

tag: dlco predicted


title: PATIENT56

description:
PATIENT56
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

value: Caucasian

value: ACA

tag: total skin score


title: PATIENT57

description:
PATIENT57
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT54

description:
PATIENT54
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

value: RNAP

value: ILD


title: PATIENT55

description:
PATIENT55
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

value: Hispanic

tag: skin score done by mdm


title: PATIENT58

description:
PATIENT58
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT53

description:
PATIENT53
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT50

description:
PATIENT50
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT52

description:
PATIENT52
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT51

description:
PATIENT51
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: GFP(E2F1)-06


title: 5491021015_H


title: PATIENT45

description:
PATIENT45
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT44

description:
PATIENT44
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT35

description:
PATIENT35
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT43

description:
PATIENT43
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT38

description:
PATIENT38
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT41

description:
PATIENT41
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT46

description:
PATIENT46
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT49

description:
PATIENT49
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT36

description:
PATIENT36
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT42

description:
PATIENT42
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT32

description:
PATIENT32
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT27

description:
PATIENT27
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT30

description:
PATIENT30
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT48

description:
PATIENT48
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT34

description:
PATIENT34
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT37

description:
PATIENT37
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT33

description:
PATIENT33
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT28

description:
PATIENT28
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT39

description:
PATIENT39
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT40

description:
PATIENT40
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT26

description:
PATIENT26
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT24

description:
PATIENT24
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

value: RNP


title: PATIENT23

description:
PATIENT23
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT31

description:
PATIENT31
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT25

description:
PATIENT25
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: 5491021069_D

description: Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT22

description:
PATIENT22
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT20

description:
PATIENT20
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT29

description:
PATIENT29
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT21

description:
PATIENT21
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT19

description:
PATIENT19
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT18

description:
PATIENT18
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

value: SE  Asian


title: PATIENT15

description:
PATIENT15
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT17

description:
PATIENT17
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT14

description:
PATIENT14
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT11

description:
PATIENT11
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT47

description:
PATIENT47
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT09

description:
PATIENT09
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT05

description:
PATIENT05
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT08

description:
PATIENT08
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: 6991010018_G


title: PATIENT12

description:
PATIENT12
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: PATIENT16

description:
PATIENT16
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: CIT561

status: Public on May 22 2013

description:
################
Mutation Details
################

ND: not determined
NA: Not applicable

When gene.mutation=M (mutated), than we have details in exon, protein and DNA.

gene.mutation=WT (wild type), the exon, protein and DNA columns are NA (not applicable).

BRAF.mutation.DNA means the CDS Mutation (http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=521)
And BRAF.mutation.Protein means the AA Mutation (http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=521)

source_name: Frozen tissue of primary colorectal Adenocarcinoma (validation)

extract_protocol: E1: total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), E2: total RNA was extracted using Manual-Cesium Chloride, E3: total RNA was extracted using  Manual-Rneasy Micro (Qiagen), E4: total RNA was extracted using Manual-Rneasy Mini (Qiagen), E5: total RNA was extracted using RNA NOW, E6: total RNA was extracted using  TriReagent & Manual-Rneasy Mini (Qiagen)

tag: organism

value: Homo sapiens

tag: dataset

value: validation

tag: Sex

value: Female

tag: age.at.diagnosis (year)

value: distal

value: N

tag: os.delay (months)

value: pMMR

value: M

value: WT

tag: dependancy sample

value: RNA NOW


title: PATIENT06

description:
PATIENT06
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

tag: individual

tag: tissue

value: skin biopsy

value: ATA


title: CIT565

value: proximal

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: PATIENT02

description:
PATIENT02
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

tag: gender [1 = male, 0 = female]

tag: on immunosuppressive agents [1 = yes, 0 = no]

value: African American

value: No ILD


title: PATIENT03

description:
PATIENT03
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

tag: race

value: Hispanic

tag: age

value: RNP


title: CIT562

value: Homo sapiens


title: CIT564

value: validation

value: Male

value: Y

value: FUFOL


title: PATIENT13

description:
PATIENT13
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

tag: antibody group

value: RNAP

tag: fvc predicted


title: CIT559

value: Female

value: distal

value: N

value: pMMR

value: M


title: CIT560

value: WT

value: RNA NOW


title: CIT555

value: proximal


title: CIT566

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: PATIENT07

description:
PATIENT07
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

value: skin biopsy

value: Caucasian

tag: fvc less than 70

value: No ILD

tag: dlco predicted


title: CIT552

value: Homo sapiens

value: validation


title: PATIENT01

description:
PATIENT01
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.

value: African American

value: ILD

tag: total skin score

tag: skin score done by mdm


title: PATIENT10

description:
PATIENT10
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: CIT557

tag: organism

tag: dataset

value: Male


title: PATIENT04

description:
PATIENT04
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.


title: CIT556

tag: Sex

tag: age.at.diagnosis (year)

value: Y

value: FOLFOX


title: CIT554

value: distal

value: N

tag: os.delay (months)

tag: dependancy sample


title: CIT553

value: Female

value: pMMR


title: CIT558

value: FUFOL

value: M

value: WT

value: RNA NOW


title: CIT551

value: proximal

value: dMMR


title: CIT563

value: Homo sapiens

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: CIT550

value: validation


title: CIT549


title: CIT548


title: CIT545


title: CIT537

value: Manual-Rneasy Micro (Qiagen)


title: CIT541

value: Manual-Rneasy Mini (Qiagen)


title: CIT540


title: CIT546

value: Male


title: CIT538


title: CIT543

value: Y


title: CIT536


title: CIT542

value: distal


title: CIT535

value: N


title: CIT533

value: Female


title: CIT526

value: pMMR


title: CIT524


title: CIT522


title: CIT530


title: CIT547


title: CIT528


title: CIT532


title: CIT518

value: FOLFOX


title: CIT527

value: M


title: CIT534

value: WT


title: CIT544

value: RNA NOW


title: CIT520


title: CIT529

value: proximal


title: CIT525


title: CIT521


title: CIT539

value: FUFOL


title: CIT516

value: Homo sapiens


title: CIT517


title: CIT512


title: CIT513


title: CIT505


title: CIT510


title: CIT504


title: CIT531


title: CIT514

value: dMMR


title: CIT507

value: validation


title: CIT515

value: Manual-Rneasy Micro (Qiagen)


title: CIT509


title: CIT502


title: CIT503


title: CIT498


title: CIT523


title: CIT493


title: CIT492


title: CIT495


title: CIT506


title: CIT499


title: CIT497


title: CIT500


title: CIT501


title: CIT494


title: CIT496


title: CIT489

value: Manual-Trizol


title: CIT488

value: Male

value: MX


title: CIT487

value: distal


title: CIT482

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: CIT483


title: CIT480

value: N


title: CIT479

value: Y

value: pMMR


title: CIT484

value: M


title: CIT481

value: Female

value: WT


title: CIT486


title: CIT490

value: proximal


title: CIT472


title: CIT468


title: CIT470


title: CIT469


title: CIT475


title: CIT477


title: CIT473


title: CIT476

value: FS


title: CIT471

value: Homo sapiens


title: CIT465


title: CIT474


title: CIT466


title: CIT508


title: CIT485


title: CIT478


title: CIT464


title: CIT467


title: CIT462


title: CIT461


title: CIT459


title: CIT457


title: CIT454

value: Manual-Rneasy Mini (Qiagen)


title: CIT458

value: validation


title: CIT453


title: CIT455


title: CIT456


title: CIT460


title: CIT463


title: CIT449


title: CIT452

value: FUFOL


title: CIT451


title: CIT448


title: CIT441

source_name: Frozen tissue of primary colorectal Adenocarcinoma (discovery)

value: discovery


title: CIT491

value: Male

value: dMMR

value: Manual-Trizol


title: CIT442

value: distal

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: CIT447

value: N


title: CIT445

value: pMMR


title: CIT444

value: Y

value: M


title: CIT443

value: Female

value: WT


title: CIT450


title: CIT446

value: proximal

value: FOLFIRI


title: CIT440

value: Homo sapiens


title: CIT439


title: CIT438


title: CIT511

value: validation

value: Manual-Rneasy Micro (Qiagen)


title: CIT519


title: CIT437

value: discovery


title: CIT433

value: Male

value: RNA NOW


title: CIT434

value: dMMR


title: CIT431

value: distal

value: Manual-Rneasy Mini (Qiagen)


title: CIT426

value: N


title: CIT427

value: pMMR


title: CIT436

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: CIT432

value: M


title: CIT423

value: Female

value: Y

value: FUFOL


title: CIT418

value: WT


title: CIT430

value: Homo sapiens

value: proximal


title: CIT413


title: CIT417


title: CIT421


title: CIT415

value: FOLFIRI


title: CIT422

value: discovery


title: CIT425

value: Male


title: CIT428


title: CIT411


title: CIT420


title: CIT424


title: CIT419


title: CIT414


title: CIT416


title: CIT429


title: CIT412


title: CIT408


title: CIT409


title: CIT410

value: FOLFOX


title: CIT402


title: CIT398


title: CIT406


title: CIT405


title: CIT403


title: CIT404


title: CIT397

value: dMMR


title: CIT395

value: distal


title: CIT400

value: Manual-Rneasy Mini (Qiagen)


title: CIT401

value: N


title: CIT396

value: pMMR


title: CIT391

value: Manual-Rneasy Micro (Qiagen)


title: CIT393

value: M


title: CIT394

value: Female


title: CIT392

value: Y


title: CIT407

value: FUFOL


title: CIT389

value: WT


title: CIT399

value: Homo sapiens


title: CIT386


title: CIT385


title: CIT384


title: CIT388


title: CIT383

value: proximal


title: CIT390


title: CIT381


title: CIT380


title: CIT382


title: CIT435

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: CIT387

value: discovery


title: CIT379

value: Male


title: CIT374


title: CIT377


title: CIT378


title: CIT375


title: CIT363


title: CIT369


title: CIT370


title: CIT362


title: CIT367


title: CIT373


title: CIT361


title: CIT364


title: CIT368


title: CIT360


title: CIT371


title: CIT366


title: CIT365


title: CIT376


title: CIT372


title: CIT359


title: CIT357


title: CIT352


title: CIT351


title: CIT356


title: CIT355


title: CIT349


title: CIT354


title: CIT358


title: CIT350


title: CIT348


title: CIT347


title: CIT353


title: CIT345


title: CIT342

value: Manual-Trizol


title: CIT339


title: CIT344

value: Tis


title: CIT340

value: distal

value: dMMR

value: codon 13 :GGC>GAC


title: CIT337

value: N

value: pMMR


title: CIT338

value: M


title: CIT343

value: Female

value: FOLFIRI


title: CIT334


title: CIT335

value: Y

value: FOLFOX


title: CIT336

value: Homo sapiens

value: WT


title: CIT333

value: proximal


title: CIT332

value: discovery


title: CIT341

value: Male


title: CIT346

value: Manual-Rneasy Micro (Qiagen)


title: CIT331

value: Manual-Trizol


title: CIT330


title: CIT326

value: distal


title: CIT329

value: dMMR


title: CIT325


title: CIT324


title: CIT327


title: CIT328


title: CIT323


title: CIT322


title: CIT320


title: CIT321


title: CIT316


title: CIT318


title: CIT317

value: Tis


title: CIT315

value: N


title: CIT313

value: pMMR


title: CIT319

value: M


title: CIT311


title: CIT310


title: CIT309

value: Female


title: CIT308


title: CIT314


title: CIT307


title: CIT306

value: MX


title: CIT312

value: Y

value: FUFOL


title: CIT305

value: Homo sapiens


title: CIT304

value: FOLFOX

value: WT


title: CIT301

value: discovery


title: CIT303


title: CIT298


title: CIT302


title: CIT296

value: proximal

value: FOLFIRI


title: CIT299

value: Manual-Trizol


title: CIT300

value: distal


title: CIT294

value: Male


title: CIT292


title: CIT293


title: CIT295


title: CIT289


title: CIT297


title: CIT290


title: CIT286


title: CIT291


title: CIT270

value: dMMR


title: CIT279


title: CIT274


title: CIT284


title: CIT282


title: CIT285

value: N


title: CIT287

value: pMMR


title: CIT281


title: CIT272

value: M


title: CIT267


title: CIT269


title: CIT277


title: CIT280


title: CIT266

value: Female


title: CIT264


title: CIT260

value: TriReagent & Manual-Rneasy Mini (Qiagen)


title: CIT288


title: CIT271

value: Y


title: CIT268


title: CIT278


title: CIT273


title: CIT259


title: CIT258


title: CIT263


title: CIT265


title: CIT262


title: CIT261


title: CIT275


title: CIT255


title: CIT251


title: CIT256

value: FS


title: CIT276

value: Homo sapiens


title: CIT243


title: CIT250


title: CIT252


title: CIT254

value: N+


title: CIT249

value: WT


title: CIT242

value: discovery


title: CIT246


title: CIT238


title: CIT245

value: proximal


title: CIT248


title: CIT244


title: CIT253


title: CIT240


title: CIT233


title: CIT234


title: CIT247


title: CIT239


title: CIT232


title: CIT241


title: CIT235


title: CIT237


title: CIT230


title: CIT231


title: CIT236


title: CIT227


title: CIT222


title: CIT223


title: CIT226


title: CIT225


title: CIT228


title: CIT220


title: CIT229


title: CIT217


title: CIT210


title: CIT224


title: CIT207


title: CIT202


title: CIT205


title: CIT208


title: CIT206


title: CIT211


title: CIT283


title: CIT203


title: CIT215


title: CIT218


title: CIT212


title: CIT214


title: CIT213


title: CIT221


title: CIT209


title: CIT204


title: CIT216


title: CIT219


title: CIT194


title: CIT195


title: CIT197


title: CIT200


title: CIT198


title: CIT201


title: CIT196


title: CIT189


title: CIT192


title: CIT199


title: CIT191


title: CIT188


title: CIT190


title: CIT186


title: CIT187


title: CIT179


title: CIT176

value: Manual-Rneasy Mini (Qiagen)


title: CIT175


title: CIT181


title: CIT174


title: CIT173


title: CIT193


title: CIT182


title: CIT178


title: CIT177


title: CIT180


title: CIT183


title: CIT185


title: CIT184


title: CIT257


title: CIT171


title: CIT162


title: CIT164


title: CIT169

value: FUFOL


title: CIT167


title: CIT149

value: distal


title: CIT165

value: Male


title: CIT160


title: CIT168


title: CIT161


title: CIT150


title: CIT157


title: CIT163


title: CIT166


title: CIT154


title: CIT151


title: CIT158


title: CIT148


title: CIT147


title: CIT144


title: CIT153


title: CIT156


title: CIT146


title: CIT145


title: CIT155


title: CIT172

value: FOLFOX


title: CIT143


title: CIT170

value: N


title: CIT152

value: pMMR


title: CIT140


title: CIT141

value: M


title: CIT142


title: CIT137

value: Female


title: CIT138


title: CIT128


title: CIT126

value: other


title: CIT131


title: CIT125


title: CIT134


title: CIT132


title: CIT127


title: CIT129


title: CIT133


title: CIT123

value: Y


title: CIT139


title: CIT119


title: CIT120


title: CIT117


title: CIT113


title: CIT114


title: CIT110


title: CIT121


title: CIT116


title: CIT124


title: CIT115


title: CIT130


title: CIT118


title: CIT107


title: CIT104


title: CIT136


title: CIT135


title: CIT109


title: CIT108

value: FOLFIRI


title: CIT102

value: Homo sapiens


title: CIT112


title: CIT099


title: CIT100


title: CIT106


title: CIT091


title: CIT101


title: CIT103


title: CIT098


title: CIT093


title: CIT159


title: CIT089


title: CIT090


title: CIT092


title: CIT088


title: CIT097


title: CIT086


title: CIT087


title: CIT096


title: CIT095


title: CIT085


title: CIT084


title: CIT080


title: CIT105


title: CIT111


title: CIT083


title: CIT081


title: CIT074

value: Manual-Cesium Chloride


title: CIT073

value: WT


title: CIT078

value: discovery


title: CIT079

value: proximal


title: CIT082

value: Manual-Rneasy Mini (Qiagen)


title: CIT070


title: CIT068


title: CIT077


title: CIT061


title: CIT060

value: dMMR

value: Manual-Trizol


title: CIT076


title: CIT094

value: distal


title: CIT072


title: CIT071


title: CIT059


title: CIT062


title: CIT069

value: Male


title: CIT065


title: CIT075

value: N


title: CIT063

value: pMMR