title: spermH01

description:
high_SCR;low_SCE
different lane for spermH01 whole genome bisufite sequencing

value: sperm

tag: breed

value: Holstein

value: adult


title: NIH3t3 Control

status: Public on Mar 20 2019

type: SRA

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

description: 3t3s_rsem.genes.expected_count.txt; 3t3s_rsem.genes.tpm.txt

library_source: transcriptomic

data_processing:
Ribosome footprint profiling data was mapped to mm10 version of the genome using RefSeq CDSs. Transcripts shorter that 100 nucleotides were filtered-out and 30 nucleotides were clipped form the start and end of each CDS, similarly to Ingolia (21). Ribosome footprint sequences were trimmed to maximal size of 34 and polyA sequences from the polyA tailing step were removes, such that footprints of lengths 22-34 were considered. FASTQ files were then filtered for rRNAs and tRNAs using STAR(22). Expression levels were quantified using RSEM (23) after mapping to clipped CDSs using Bowtie2(24) to produce transcript and gene level quantification TPM (Transcript Per Million) values.
Lowly expressed genes with an average TPM <2 across all samples were filtered out and  expression of all other genes was thresholded to a TPM of 4.
Genome_build: mm10
Supplementary_files_format_and_content: Samples' read counts and TPM values

molecule: total RNA

organism: Mus musculus

source_name: NIH 3T3

growth_protocol: Ribosome footprint profiling was performed as in Shalgi et al.  Molecular Cell, 2013 with the following modification: cells were grown and treated with Tg for the indicated times, then trypsinized, pelleted by 5 minutes at 1000RPM centrifugation, and flash frozen in LN2, without prior Cycloheximide treatment. Cycloheximide was also omitted from the buffers.

extract_protocol: RNAseq- RNAeasy for RNA extraction and standard illumina PE including size selection. Riboseq - RNA extraction and library prepration as described in Ingolia et al. Science, 2009

treatment_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: NIH 3T3

tag: genotype

value: WT

tag: treatment

value: Control


title: TOL4: 14196X4_170505_D00294_0319_BCAJ3JANXX

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

data_processing:
The quality of the reads was verified using FASTQC version 0.11.4
All reads were aligned to the nuclear genome (Neafsey et al., 2015; DOI: 10.1126/science.1258522)  and mitochondrial genome (GenBank accession: NC_028212) of An. arabiensis using HISAT2 (Kim et al., 2015; DOI: 10.1038/nmeth.3317) and the following options “--max-intronlen 75000 --rna-strandness RF --known-splicesite-infile splicesites.txt”. The “splicesites.txt” file was generated from the gene transfer format (GTF) files of the nuclear and mitochondrial genome of An. arabiensis using a script accompanying the HISAT2 software (hisat2_extract_splice_sites.py). The AaraD1.6 GTF file (13830 genes of which 13452 are protein coding genes, released 25 April 2017 at VectorBase, (https://www.vectorbase.org/organisms/anopheles-arabiensis/dongola/aarad16) was used for the nuclear genome, while the GTF file for the mitochondrial genome was generated from the GenBank file () using the bp_genbank2gff3.pl and gffread script included in the BioPerl (http://bioperl.org/) and Cufflinks package (Trapnell et al., 2012; DOI: 10.1038/nprot.2012.016), respectively. Resulting BAM files were subsequently sorted by read name using SAMtools version 1.5 (Li et al., 2009; DOI: 10.1093/bioinformatics/btp352).
Next, read counts per gene were obtained using the htseq-count script included in the HTSeq package, version 0.9.0 (Anders et al., 2015; DOI: 10.1093/bioinformatics/btu638), with the following settings “-i gene_id -t exon -f bam -s reverse” and the general feature format 3 (GFF3) version of the previously mentioned An. arabiensis GTF files.
Genome_build: AaraD1 (nuclear genome, release April 30, 2013, see https://www.vectorbase.org/organisms/anopheles-arabiensis/dongola/aarad1) and NC_028212.1 (mitochondrial genome, release November 17, 2015, see https://www.ncbi.nlm.nih.gov/nuccore/NC_028212.1/)
Supplementary_files_format_and_content: Tab-delimited text file includes read counts (HTSeq) for each sample

molecule: polyA RNA

organism: Anopheles arabiensis

source_name: complete organism

growth_protocol: Anopheles arabiensis larvae were collected in the South-West part of Ethiopia from a range of breeding sites: Asendabo (ASN), Chewaka (CHW) and Tolay (TOL). Larvae were reared to adults on site in rooms with standard conditions of 25 ±2oC and a relative humidity of 80 ± 10% for all three respective sites. Larvae were fed with dog biscuits and brewery yeast whereas adults were provided a 10% sucrose solution soaked into cotton pads (Gerberg et al., 1994, ISBN: 0960621083). Two laboratory strains served as a pesticide susceptible population: an Ethiopian strain (Sekoru (SEK)), previously described in Alemayehu et al. (2017, DOI: 10.1186/s13071-017-2342-y), and a strain from Mozambique (MOZ) previously described in Witzig et al. (2013, DOI: 10.1038/hdy.2012.112). Both laboratory strains were reared in a similar way as the three Ethiopian populations collected from the field.

extract_protocol:
3-5 days old non-blood-fed An. arabiensis female adult mosquitoes from each population (ASN, CHW or TOL) or strain (SEK, MOZ) were preserved in RNAlater (Ambion, Thermo Fischer Scientific) in a 1.5ml Eppendorf tube. All tubes were stored at -80 oC. Total  RNA was extracted from batches of ten female mosquitoes using RNAqueous®-4PCR Kit (Ambion, Thermo Fischer Scientific) protocol. RNA was treated with DNase1 treatment and DNase inactivation according to the instructions of the RNAqueous®-4PCR Kit. Four biological replicates were included for each population and each laboratory strain.
Illumina libraries were constructed with the TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina, USA)
RNAseq, libraries were sequenced on an Illumina HiSeq 2500 to generate strand-specific paired reads of 2 x 125 bp (High-Throughput Genomics Core of the Huntsman Cancer Institute, University of Utah, Utah, USA). Sequenced reads were trimmed by the sequencing facility.

treatment_protocol: The ASN, CHW and TOL populations were previously shown to be resistant against deltamethrin and DDT (Alemayehu et al., 2017, DOI: 10.1186/s13071-017-2342-y).

tag: Stage

value: 3-5 day old female adult, non-blood-fed

tag: strain/population

value: Tolay

tag: tissue

value: complete organism


title: Cortex_1

city: Freiburg

first: Dieter

middle: Henrik

last: Heiland

address: Breisacherstr. 64

department: Department of Neurosurgery

country: Germany

institute: Medical Center Freiburg

data_processing:
Basecalling by Albacore 2.0.1, Quality Control, Identification of Barcoded Samples by PoreChop
Alignment by MiniMap2
Nanopore Pipeline (www.github.com/heilandd/)
Postprocessing by DESeq2 and AutoPipe (Cran)
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files of counts per barcode

organism: Homo sapiens

source_name: Astrocytes Tissue

extract_protocol:
Astrocytes were extracted by HepaCAM-Immunopanning
Library was constructed by Nanopore cDNA sequencing Kit, SQK-PCS109

value: Astrocytes

tag: barcode


title: TOL3: 14196X3_170505_D00294_0319_BCAJ3JANXX


title: PERK WT Tg8hr MEF

description: MEFs_rsem.genes.expected_count.txt; MEFs_rsem.genes.tpm.txt

source_name: MEF

value: MEF


title: Control-2-Cy5

type: RNA

city: Moraga

first: Vidya

last: Chandrasekaran

address: 1928 Saint Mary's Road

department: Biology

country: USA

institute: Saint Mary's College of California

description: Control neurons, no dendrites.

hyb_protocol: Not provided

scan_protocol: The chips were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: The hybridization target signal was subtracted from the background signal and the data was normalized using the LOWESS (local weighted scatterplot smoothing method) on the background subtracted data. Each RNA sample was spiked with a known ratio of spike-in positive control 20-mer RNA as an external normalization control. Two-way ANOVA as performed to detect differences in miRNA expression between control and BMP-7 treated cells and the differences in gene expression over time. The p-value and power were calculated using a sample size of N=2 for the two biological replicates.

organism: Rattus norvegicus

source_name: E21 cultured rat SCG neurons under control conditions

label_protocol: The RNA sample was labeled with Cy5 - Single sample chips were labeled with Cy5.

growth_protocol: Sympathetic neurons from the superior cervical ganglia of E21 rat pups were dissociated and grown on poly-D-lysine coated plates in a defined media with 1:1 mixture of DMEM and F12 containing insulin, selenium, transferrin and Nerve growth factor.

extract_protocol: The total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA) per the manufacturer’s instructions.

treatment_protocol: On day 2 in culture, the neurons were treated with 2 microM Ara-C to eliminate non-neuronal cells. Following this, neurons were maintained in control media for 24 hours. Then culture wells were maintained in control media for 24 hours, BMP-7 at 50ng/mL for 6 hours or 24 hours, following which the cells were lysed to extract total RNA.

tag: strain/background

value: Sprague-Dawley

tag: developmental stage

tag: cell type

value: Cultured sympathetic neurons


title: BMP7-6h-1-Cy5

description: Cultured neurons treated with BMP-7 at 50 ng/mL for 6 hours.

value: BMP-7 50 ng/mL

tag: time


title: PERK WT Tg5hr MEF


title: Cortex_2


title: Ptrn1 KO rep3

city: San Antonio

first: Lizhen

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Barshop Institute

institute: Universality of Texas Health Science Center at San Antonio

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to ce10 genome assembly using STAR 2.5.2b with default parameters. Refseq transcripts were supplied in GTF format file.
featureCounts v1.5.1 was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2.
Genome_build: ce10
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

organism: Caenorhabditis elegans

source_name: Ptrn1 KO rep3

growth_protocol: The following 5 strains were cultured at 20 celsus degree: wild-type, efa-6(tm3124), hdac-6(ok3203), ptl-1(ok621) and ptrn-1(tm5597). Synchronized Day 1 young adult animals were collected for RNA-extraction.

extract_protocol:
RNA extraction was done using Trizol followed by Qiagen RNeasy kit
500ng of total RNA from each sample were used to construct RNA-seq libraries using KAPA RNA HyperPrep Kit with RiboErase (KK8483, KAPA Biosystems) following the manufacturer’s protocol.

treatment_protocol: When animals reached young adulthood, young adult animals were picked to fresh NGM plates with OP50 and allowed to lay eggs for 1 hour. The eggs were developed on regular NGM plates until L4 stage before transferred to plates containing FUDR. Adult Day 1 worms (three replicates for each strain) were collected for RNA extraction


title: Control-1-Cy5

description: Control neurons, no dendrites.


title: PERK WT Tg1hr MEF


title: SEK4: 14196X16_170512_D00455L_0055_BCAUU0ANXX

value: Sekoru


title: PERK -/- Control MEF

value: PERK -/-


title: SEK3: 14196X15_170512_D00455L_0055_BCAUU0ANXX


title: Ptrn1 KO rep1

source_name: Ptrn1 KO rep1


title: Ga13ΔM/ΔM_RANKL

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR
Transcripts Per Million(TPM) were calculated using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Bone Marrow Macrophages

growth_protocol: Bone marrow was flushed from femur and tibia and cultured with M-CSF for 3 days to get bone marrow macrophages.

extract_protocol:
RNA was harvested using RLT buffer from Rneasy RNA extraction kit. mRNA was purified by poly-A+ selection. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bone marrow macropahges were treated with RANKL for 5days.

tag: strain

value: Bone Marrow Macrophages

tag: agent

value: RANKL


title: TOL1: 14196X1_170505_D00294_0319_BCAJ3JANXX


title: Ptrn1 KO rep2

source_name: Ptrn1 KO rep2


title: Ga13ΔM/ΔM_Basal

value: control


title: Ptl1 KO rep3

source_name: Ptl1 KO rep3


title: Ptl1 KO rep2

source_name: Ptl1 KO rep2


title: SEK2: 14196X14_170512_D00455L_0055_BCAUU0ANXX


title: pooled_Vγ6

city: Hamburg

first: Immo

last: Prinz

address: Falkenried 94

department: Institute of Systems Immunology

institute: University medical center Hamburg Eppendorf

data_processing:
Sequencing libraries were demultiplexed to individual fastq files, than Cellranger v2.0 (10xGenomics) was used for alignment, annotation, and generation of barcode-gene matrices. Fastq files were mapped to the reference mouse genome mm10 (UCSC). Data from ambient RNA was trimmed based on nUMI-barcode saturation curve.
The R package Seurat v2.3 was used under R 3.5 for further data trimming, unsupervised clustering, and visualization(Butler et al., 2018). Briefly, to remove cells with poor quality, doublets and stressed cells, genes expressed on less than 10 cells and cells that have a gene number lower 400 or higher than 2500 were removed. Mitochondrial gene ratio was calculated to filter out cells with more than 8% mitochondrial genes(Ilicic et al., 2016). Next, the function ‘NormalizeData’ was used to normalize for differences on sequencing depth across single cells. Cell cycle score and cell phase were assigned to every single cell by the function ‘CellCycleScoring’ according to a gene list of known cell cycle markers (Kowalczyk et al., 2015). To reduce confounders, UMI number, percentage of mitochondrial genes and cell cycle scores were regressed out by the function ‘ScaleData’. Highly variable genes (hvg) were defined by ‘FindVariableGenes’ and used as input for principle component analysis (PCA). Using the PCElbowplot, we determined principle components (PCs)1 - 17 as statistically significant PCs which explained the most variance. Based on significant PCs and setting resolution = 0.4, unsupervised graph-based clustering was performed by ‘FindCluster’. Cells are embedded by tSNE plot. We executed ‘FindAllMarkers’ to identify differentially expressed genes (DEGs) among all genes, surface markers (Gene ontology ID: GO:0009986), or transcription factors (Riken Transcription Factor Database) by using wilcoxon rank sum test. We defined DEGs as average log2-fold change (logFC) ≥ 0.5, expressed in minimal percentage cells in at least 1 test group (min.pct) ≥ 20%, and adjust p-value ≤ 0.01.
For integrated analysis libraries of Vγ6pos /Vγ4neg thymus, Vγ6pos skin and Vγ6pos pLN samples were aggregated together and normalized by ‘cellranger aggr’ command provided by cellranger.
To further explorer Vγ6+ T cells, clusters with IL-17 committed gene signatures (Cd44+ Il23r+ Ccr2+ Cd27-) were subdivided as Vγ6+ T cell dataset, than we scaled and clustered this dataset as above.
To compare the transcriptome of skin Vγ4+ and Vγ6+ T cells, datasets of these two were integrated following the integrated analysis protocol from Seurat (Butler et al., 2018). Briefly, the top 1500 hvg from either were selected for canonical correlation analysis (CCA) by ‘RunCCA’ function in Seurat, which identified shared sources of variation across Vγ4 and Vγ6 datasets and combine them into one. CC1 – 10 were chosen for aligning into an integrated low-dimensional space (CCA.aligned). Based on CCA.aligned, we performed ‘FindCluster’ as above by a resolution = 0.6, then visualized the dataset by tSNE-map. DEGs were identified by ‘FindAllMarkers’ as above.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: genes.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: Vγ6 γδ T cells

extract_protocol:
After euthanasia, ears, thymi and peripheral lymph nodes (pLN; including superficial cervical, axillary, brachial and inguinal) were collected.    To isolate lymphocytes from ear skin, ears were split into dorsal and ventral layers, cut into small pieces, and digested in RPMI media supplemented with (2 mg/ml) collagenase IV (Worthington) and (187.5 µg/ml) DNaseI (Roche) for 75 minutes at 37°C under 1400 rpm of shaking. The digestion was terminated by 5mM EDTA. Digested ears repeatedly went through an 18G needle for further dissociating tissue structure and releasing cells. Subsequently cells were filtered (100 μM cell strainer (Falcon) and facilitated to density gradient centrifugation using 40% and 70% Percoll solutions. For downstream applications cells were re-suspended in MACS buffer (PBS with 3% FCS and 4mM EDTA).  Single cell suspensions from thymus and peripheral lymph nodes were obtained by filtering organs through nylon gaze. To enrich thymus samples γδ T cells, CD4+ and CD8+ T cells were depleted. For flow cytometric cell sorting of Vγ6+ T cells and subsequent single-cell RNA-seq library generation, CD4+ and/or CD8+ thymus cells were lysed via incubation with monoclonal anti-CD4 and anti-CD8β IgM (homemade), DNaseI (Roche) and Standard Rabbit Complement (Cedaralane) at 37°C for 30 minutes. Next, thymus cells were retrieved via density gradient centrifugation using Lympholyte M (Cederlane).
FACS-Aria II (BD Bioscience) was used for cell sorting of indicated cell populations into PBS/4mM EDTA/5%FCS. Sorted Vγ4+  and Vγ6+  γδTcells were diluted to ≤ 1000 cells/μL. Single cell sequencing libraries were generated using the Chromium™ Single Cell 3’ reagent kits v2 according to the manufactures protocol (10xGenomics). Indexed libraries were pooled, and paired-end sequencing was performed by Hiseq4000 (Illumina).

value: mixed sample (non-demultiplexed) [TcrdCreER (peripheral lymph node);  ACT-FLPe (Thymus); TcrdH2BeGFP (Ear skin)]

value: mixed sample (non-demultiplexed) [ear skin; Thymus; peripheral lymph node]

tag: age

value: mixed sample (non-demultiplexed) [8~10 weeks]


title: SEK1: 14196X13_170512_D00455L_0055_BCAUU0ANXX


title: WT_RANKL


title: NR rep4

city: Zhoushan

first: Jianhua

last: Liu

address: 1 Zheda Road, Lin-cheng street

country: China

institute: Ocean College, Zhejiang University

description: three days after medium shift to f/2 with nitrate

data_processing:
Using FastQC v0.11.2 to check the qualities of sequenced reads
Sequenced Reads were removed adaptor-like sequences of 12-nts at the 5’-end and low quality nucleotide with different length at the 3’-end using Trimmomatic v0.32
De novo assembly using Trinity v2.2.0 with processed reads (ALL biosamples) (--CPU 8  --KMER_SIZE 25)
Transcriptome were annotated by running BLASTX to 6 algal genomes (evalue < 1e-7) (-max_target_seqs 1 -outfmt 6 -evalue 1e-7)
Expression levels of EST were determined using Trinity-bundled perl script align_and_estimate_abundance.pl which utilizes RSEM to calculate TPM values (--est_method RSEM --aln_method bowtie2 --trinity_mode)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Nannochloropsis sp.

source_name: microalgae

growth_protocol: All the algal cells were grown in f/2 medium in glass flask with orbital shaking at 100 rpm, 25°C, under continuous illumination of 50 μM photon m-2 s-1.

extract_protocol:
Total RNA was extracted from sample cells using TRIzol Plus RNA Purification System (Invitrogen-Life Technologies Co., Carlsbad, CA, USA) according to manufacturer’s protocol, ribosomal RNA were removed prior to library construction.
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

treatment_protocol: Cells at log phase were subjected to medium shift to f/2 without nitrate and with nitrate. Cells three days after medium shift were collected for RNA-seq analysis.

value: PJ12 strain

value: log phase

tag: culture medium

value: f/2 medium


title: Ptl1 KO rep1

source_name: Ptl1 KO rep1


title: NR rep3


title: TOL2: 14196X2_170505_D00294_0319_BCAJ3JANXX

value: 3-5 day old female adult, non-blood-fed

value: Tolay

value: complete organism


title: WT_Basal


title: MO3.13_BC200-KO-2_RNAseq

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

description:
MO313.Ensembl.ensGene.exon.s2.raw.tsv.gz
MO313.Ensembl.ensGene.exon.s2.norm.tsv.gz

data_processing:
Read trimming was performed with Trimmomatic v0.35
Alignment was performed with STAR v2.3.0e (RNA-seq and small RNA-seq) or bowtie2 v.2.2.9 (ChIP-seq)
Reads were counted with featureCounts v1.5.0
Normalization and differential expression analysis (RNAseq and small RNAseq) were performed with DESeq2
ChIP-seq read counts were normalized to the median of total read counts and Pol III occupancy scores were calculated as the log2(IPread_count/Inputread_count)
Genome_build: hg19
Supplementary_files_format_and_content: For each dataset, raw and normalized counts per sample are provided in one file (tsv, csv or txt)

source_name: MO3.13 cell line

growth_protocol: HEK293 and MO3.13 cells were grown in DMEM supplemented with 10% FBS and 1% pen-strep

extract_protocol:
Total RNA extracted with Qiagen miRNeasy
NEBNext rRNA-depleted stranded library preparation

treatment_protocol: CRISPR-Cas9 editing was used to introduce POLR3A mutations or BC200 KO

tag: chip antibody


title: MOZ4: 14196X20_170512_D00455L_0055_BCAUU0ANXX

value: Mozambique


title: PERK WT Tg2hr MEF

value: MEF

value: WT


title: NR rep2


title: Hdac6 KO rep2

source_name: Hdac6 KO rep2


title: MOZ2: 14196X18_170512_D00455L_0055_BCAUU0ANXX


title: Hdac6 KO rep1

source_name: Hdac6 KO rep1


title: CGG_siTRA2

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

description:
Gene expression data from COS-7 cells
DexSeq.CGG_siTRA.vs.CGG.csv
DexSeq.CGG_siTRA.vs.CTL.csv
EventPointer.CGGsiTRA.vs.siTRA.csv
EventPointer.CGGTRA.vs.CGGsiTRA.csv

data_processing:
Trimming was made using cutadapt v1.14 with standard illumina adapters
Alignment was made using STAR_2.5.2
Pre-processing of bam files was made with python scripts “dexseq_prepare_annotation.py” and “dexseq_count.py” provided in the DEXSeq v 1.24.2
Statistical analysis of alternative splicing events was made with DEXSeq v 1.24.2. Results in DexSeq .csv files include counts for the samples in the contrast.
Statistical analysis of alternative splicing events was made with EventPointer  v1.0.0
Normalization of the count data. Counts are divided by the sizeFactors calculated using the "median ratio method" described by Equation 5 in  Anders and Huber (2010). Default method for DESeq2. Results are in CountsNorm.csv file.
Genome_build: GENCODE release27 (GRCh38.p10)
Supplementary_files_format_and_content: csv files containing the output of the DEXseq and EventPointer analysis.

organism: Chlorocebus sabaeus

source_name: kidney

extract_protocol:
RNA was extracted following Qiagen protocol including DNAse treatment
For library preparation with TruSeq total RNA-rRNA depletion (Illumina)

value: kidney

tag: condition

value: COS-7 cells transfected with CGG expansion at the 5'UTR FMR1 (60X) and with knockdown for TRA2A (cond4)


title: MOZ3: 14196X19_170512_D00455L_0055_BCAUU0ANXX

source_name: complete organism


title: NR rep1


title: siTRA2A-1+CGG (first round)

tag: cell line


title: CGG+siTRA2A-1(third round)


title: PERK WT Control MEF

tag: genotype

value: Control


title: Efa6 KO rep3

source_name: Efa6 KO rep3


title: MOZ1: 14196X17_170512_D00455L_0055_BCAUU0ANXX


title: CGG_TRA6

description:
Gene expression data from COS-7 cells
EventPointer.CGGTRA.vs.CGG.csv
EventPointer.CGGTRA.vs.CGGsiTRA.csv

value: COS-7 cells transfected with CGG expansion at the 5'UTR FMR1 (60X) and with overexpression of TRA2A (cond5)


title: ND rep3

description: three days after medium shift to f/2 without nitrate

value: f/2 medium-N


title: ND rep4


title: CHW4: 14196X12_170512_D00455L_0055_BCAUU0ANXX

value: Chewaka


title: Efa6 KO rep2

source_name: Efa6 KO rep2


title: ND rep2


title: CGG_TRA4


title: ND rep1


title: Efa6 KO rep1

source_name: Efa6 KO rep1


title: CGG_TRA3


title: MDA_MB_231 ERa Abcam Rep2

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description:
MDA_MB_231_2_ER_ABCam
processed data file: MDA_MB_231_ER_ABCam_peaks.narrowPeak.gz

library_source: genomic

data_processing:
Reads were mapped to hg38 genome using bwa version 0.7.12.
Aligned reads with the mapping quality less than 15 were filtered out.
The Bioconductor package GreyListChIP version 1.8.0 and the blacklist file for hg38 was downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz was used to identify regions for filtering.
For each antibody/input and cell type combination the 3 replicate filtered bams were merged after having reads marked as duplicates removed.
Peak calling was carried out using MACS2 version 2.1.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_peaks.narrowPeak: bed/text

molecule: genomic DNA

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin. MDA-MB-231 cells were grown in RPMI supplemented with 10% FBS, 2mM L-glutamine and 50 U/ml penicillin and 50 ug/ml streptomycin.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication (Bioruptor plus, Diagenode). Chromatin was immunoprecipitated over night using specific antibodies. Beads were washed six times in RIPA buffer and eluted from beads using SDS buffer. After RNase and proteinase K treatment, DNA was purified by phenol/chloroform extraction.
Libraries were prepared using the Thruplex kit (Illumina) according to the manufacturer's instructions.

value: Breast cancer cell line

tag: passages

value: anti-ERalpha (Abcam, ab3575)


title: Hdac6 KO rep3

source_name: Hdac6 KO rep3


title: CHW3: 14196X11_170512_D00455L_0055_BCAUU0ANXX

tag: Stage


title: Ctrl rep3

source_name: Ctrl rep3

value: wild type


title: CHW2: 14196X10_170505_D00294_0319_BCAJ3JANXX

tag: strain/population


title: Sample_Baboon_8623_highLDL_HCHF_RNA_seq_26

city: Winston-Salem

first: Genesio

last: Karere

state: NC

address: 1 medical center blvd

department: Internal Medicne

institute: Wake Forest Baptist Health Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
The sequencing output FASTQ files were analyzed using default settings of Partek Flow (Partek Inc., MO).
The sequence reads were aligned with STAR aligner v2.3.1j to baboon transcriptome (Ensembl PapAnu2 release 76).
To quantify the expression levels of transcripts, the mapped reads were normalized (reads assigned per kilobase of target per million mapped reads, RPKM) and quantified using Partek’s expectation maximization (EM) algorithm. Differential expression of genes was evaluated using Partek’s gene specific analysis (GSA).
Genome_build: Ensembl PapAnu2 release 76
Supplementary_files_format_and_content: fastq

organism: Papio hamadryas

source_name: WBC

growth_protocol: Baboon blood collected, buffy coat isolated and stored in -80 freezer.

extract_protocol:
Libraries were constructed with the Illumina Paired-End Cluster Generation Kitv4 (2x100bp)
RNA Seq; two files per run included

treatment_protocol: Total RNA siolated using Trizol and Quigen reagents.

tag: tissue

value: Blood

value: TGACCA


title: Ctrl rep2

source_name: Ctrl rep2


title: siTRA2

description:
Gene expression data from COS-7 cells
DexSeq.CTL.vs.SiTRA.csv
DexSeq.GFP_TRA.vs.siTRA.csv
EventPointer.CGGsiTRA.vs.siTRA.csv

value: COS-7 cells knockdown for TRA2A (cond3)


title: ASN4: 14196X8_170505_D00294_0319_BCAJ3JANXX

value: 3-5 day old female adult, non-blood-fed

value: Asendabo


title: Sample_Baboon_8024_lowLDL_HCHF_RNA_seq_2

description: Libraries were constructed with the Illumina Paired-End Cluster Generation Kitv4 (2x100bp)

tag: barcode


title: Ctrl rep1

source_name: Ctrl rep1


title: GFP_TRA4

description:
Gene expression data from COS-7 cells
DexSeq.CTL.vs.GFP_TRA.csv
DexSeq.GFP_TRA.vs.siTRA.csv
EventPointer.GFPTRA.vs.CTL.csv

value: COS-7 cells overexpressing TRA2A (cond2)


title: CHW1: 14196X9_170505_D00294_0319_BCAJ3JANXX

value: complete organism


title: siTRA1


title: Sample_Baboon_6910_lowLDL_HCHF_RNA_seq_8

value: AGTTCC


title: Sample_Baboon_8623_highLDL_chow_RNA_seq_25

value: CGATGT


title: GFP_TRA2

value: kidney


title: ASN2: 14196X6_170505_D00294_0319_BCAJ3JANXX


title: ASN1: 14196X5_170505_D00294_0319_BCAJ3JANXX


title: Sample_Baboon_8024_lowLDL_chow-RNA_seq_1


title: ASN3: 14196X7_170505_D00294_0319_BCAJ3JANXX


title: GFP_TRA1


title: Sample_Baboon_6265_lowLDL_HCHF_RNA_seq_14

value: TTAGGC


title: Sample_Baboon_6910_lowLDL_chow_RNA_seq_7

value: AGTCAA


title: CGG2

description:
Gene expression data from COS-7 cells
DexSeq.CGG_siTRA.vs.CGG.csv
EventPointer.CGG.vs.CTL.csv
EventPointer.CGGTRA.vs.CGG.csv

value: COS-7 cells transfected with CGG expansion at the 5'UTR FMR1 (60X) (cond1)


title: siTRA3


title: WT6h_1

city: Beijing

first: Yifan

last: Zhou

address: No. 30 Shuangqing Road

department: School of Medicine

institute: Tsinghua University

data_processing:
The software for base calling is BaseCallV1.6.0.19379
We use internal software SOAPnuke to filter reads, followed as: (1) Remove reads with adaptors;(2) Remove reads in which unknown bases(N) are more than 10%; (3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read).After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. The software for base calling is HISAT2 v2.0.4, -p8--phred64--sensitive-I 1-X 10000.
We filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.Then we assembled those clean reads into Unigenes, followed with Unigene functional annotation, SSR detection and calculate the Unigene expression levels and SNPs of each sample. Finally, we identify DEGs (differential expressed genes) between samples and do clustering analysis and functional annotations.
We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. Then, we calculate pearson correlation between all samples using cor, perform hierarchical clustering between all samples using hclust, perform PCA analysis with all samples using princomp, and draw the diagrams with ggplot2 with fuctions of R. Software information: Bowtie2 : Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Genome_build: NCBI_GRCm38.p5
Supplementary_files_format_and_content: The processed data files include FPKM values for all the samples.

source_name: Splenocytes

extract_protocol:
The spleen was collected and smashed on ice. Total RNA samples were harvested using Trizol reagent. We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution.
1. mRNA enrichment: Oligo dT Selection or rRNA depletion. 2. RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3. End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. 4. PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. 5. Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6.Sequencing on BGISEQ- 500 platform.

treatment_protocol: The wilde type and GdX-/Y mice were injected with LPS (20 mg/kg body weight, i.p.), and the spleen was collected at 90 min or 6 hrs after injection.

value: spleen

value: 8 weeks


title: CGG3


title: WT90min_1


title: WT6h_2


title: Sample_Baboon_6265_lowLDL_chow-RNA_seq_13

value: ATCACG


title: Sample_Baboon_1x4154_highLDL_chow_RNA_seq_37


title: CGG1


title: KO90min_2

value: GdX-/-


title: CTL3

description:
Gene expression data from COS-7 cells
DexSeq.CGG_siTRA.vs.CTL.csv
DexSeq.CTL.vs.GFP_TRA.csv
DexSeq.CTL.vs.SiTRA.csv
EventPointer.CGG.vs.CTL.csv
EventPointer.GFPTRA.vs.CTL.csv

value: Control COS-7


title: KO90min_1


title: CTL2


title: Sample_Baboon_1x3817_highLDL_chow_RNA_seq_31

value: Blood


title: Sample_Baboon_1x3817_highLDL_HCHF_RNA_seq_32


title: CTL1


title: KO6h_1


title: HC-1-exosome

status: Public on Mar 19 2019

city: Yaan

first: jideng

last: Ma

address: Xinkang road

institute: Sichuan Agricultural University(SICAU),

description: microRNA derived from seminal plasma exosomes of hemicastrated (HC) pigs

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp)
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM), then standardized by the formula log2 (RPM+1), which allowed unbiased comparison among samples.
Genome_build: Genome database:pig genome (assembly GCA_000003025.6); miRbase version: V21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

organism: Sus scrofa

growth_protocol: The experimental procedures used in this study were approved by the Institutional Animal Care and Use Committee of Sichuan Agricultural University. A total of 30 Yorkshire boars from 15 pairs of full sibs were used in this study. At the age of seven days, one pig from each pair was randomly selected to be hemicastrated (HC) under anesthesia, and another one remained intact as normal control (CT). All boars in hemicastration group (HC) were performed unilateral orchiectomy via a midline scrotal incision to remove unilateral (left) testis. Meanwhile, sham surgery performed in the control group (CT) at the same time. All boars were weaned at the age of 25 days, and transferred to a nursery and fed in same house. At the age of 60 days, each boar in HC and CT groups were fed in an independent house and all boars were fed diet of same nutritional level throughout this study until slaughter (10-month-old).

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000  Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: The ejaculates from each boar were collected using a manual collection method before slaughter, and only the spermatozoa-rich fractions of the ejaculates were collected and used in subsequent assays. Fresh semen were diluted in Beltsville Thawing Solution (1:1 volume) and shipped with gel packs (17 °C) to the laboratory. Diluted semen was placed in 50 mL Falcon tubes and centrifuged at 1000 × g for 20 min at 4 °C to separate sperm and seminal plasma. Sperm pellet were washed twice using Beltsville Thawing Solution (BTS) at 1000 × g for 20 min at 4 °C and treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H2O) for 40 min on ice to eliminate somatic cell contamination, after which the sperm be pelleted by centrifugation at 600 × g for 5 minutes and then immediately put into the liquid nitrogen until use. Seminal plasma exosomes were isolated by ultra-centrifugation and filtration according to a previously described method with some modifications. Briefly, the seminal plasma was centrifuged at 16,000 ×g for 1 h at 4°C to remove cell debris, next, the supernatant was successively filtered using 0.45 μm and 0.22 μm filters, and then centrifuged at 120,000 × g for 60 min at 4°C. The pellets were washed twice with buffer (30 mM TRIS, 130 mM NaCl, pH 7.6) followed by centrifugation at 120,000 × g for 60 min at 4°C. Finally, seminal plasma exosome pellet was then re-suspended in 250 μl nuclease free water and stored at −80 °C until use.

value: Yorkshire

value: seminal plasma


title: HC-2-exosome

source_name: microRNA derived from seminal plasma exosomes of hemicastrated (HC) pigs


title: CT-1-exosome

description: microRNA derived from seminal plasma exosomes of control (CT) pigs


title: CT-3-exosome

source_name: microRNA derived from seminal plasma exosomes of control (CT) pigs


title: HC-3-sperm

description: microRNA derived from sperm cells of hemicastrated (HC) pigs

value: sperm cells


title: CT-2-exosome


title: CT-1-sperm

description: microRNA derived from sperm cells of control (CT) pigs


title: HC-1-sperm

source_name: microRNA derived from sperm cells of hemicastrated (HC) pigs


title: CT-3-sperm

source_name: microRNA derived from sperm cells of control (CT) pigs


title: HC-2-sperm


title: CT-2-sperm


title: Sample_Baboon_1x4154_highLDL_HCHF_RNA_seq_38


title: hela.2.OE.vector.Input

city: Los Angeles

first: Ye

last: Wang

state: California

address: 611 Charles E Young Dr E

department: Bioinformatics

institute: UCLA

data_processing:
Library strategy: MeRIP-m6A-seq
Reads were trimmed by pair-end model of cutadapt (v1.18) software.
Trimmed reads were aligned to hg38 genome assembly by hisat2 (v2.1.0) software using the default parameter for pair-end model
Peakcalling were performed by R package exomepeak (v3.8), the enrichment fold threshold is 1, FDR threshold is 0.05, differential peaks were identified by diff model of exomepeak.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited xls files include peak coordination, enrichment, fdr, ensemble gene id. Change of enrichment and gene names are also included in sig_diff.xls

source_name: HeLa cells

growth_protocol: HeLa cell were cultured by DMEM medium(10% FBS) in 15cm dish under 37℃, 5%CO2

extract_protocol:
Total RNA was first extracted from HeLa cells by Trizol reagent, The polyA RNA was then purified with oligo d(T)25 magnetic beads
PolyA RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module. A portion of fragmented RNA was reserved as m6A input sample and the left was incubated with anti-m6A antibody and eluted to get the m6A IP. Both input and m6A IP samples were prepared for next-generation sequencing library by standard protocol of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: HeLa cells

value: none (input)


title: hela.3.OE.sfpq.Input


title: hela.3.OE.vector.Input


title: hela.2.OE.sfpq.Input


title: hela.2.OE.vector.IP

value: anti-m6A(Synaptic System,Polyclonal, rabbit,Cat. No. 202 003)


title: hela.1.OE.vector.Input


title: hela.1.OE.sfpq.IP


title: hela.1.OE.vector.IP


title: ChIP-seq_786-M1A_FLAG-EGFP_hg38

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

data_processing:
Fastq files were aligned to hg38 using Bowtie2.
Genomewide coverage was determined in 10bp windows and normalized to counts/million uniquely mapped reads.
Genomewide coverage data was converted to BigWig format.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files display counts/million uniquely mapped reads in 10bp windows.

source_name: 786-M1A cell line

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10min at room temperature, followed by 5 min quenching with 0.125M glycine. Cells were washed twice with PBS, the supernatant was aspirated and cell pellets were frozen in liquid nitrogen and stored at -80°C. 100µl of Protein A/G magnetic beads (Thermo 26162) were blocked with 0.5% BSA in PBS, followed by incubation with the antibody. Cross-linked cells were resuspendend and sonicated in lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, and 1% Triton X-100). Sonication was performed using Bioruptor (Diagenode) for 14 cycles (30’’ on/ 30’’ off) at max output to obtain fragments of 100-500bp. Sonicated lysates were cleared and incubated overnight at 4°C with antibody-bound magnetic beads. Beads were sequentially washed three times with low salt buffer (50mM HEPES pH7.5, 140mM NaCl, 1% Triton) and once with high salt buffer (50mM HEPES pH7.5, 500mM NaCl, 1% Triton). DNA was eluted in elution buffer (50mM NaHCO3, 1%SDS) and cross-links were reversed for 3h (65°C, 1000rpm shaking). DNA was purified using the QuickClean II PCR Extraction Kit (Genescript L00419-100) according to the manufacturer’s recommendations and eluted with 100µl H2O.
Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries with the KAPA Hyper Prep Kit (KR0961) Illumina platforms sample preparation protocol (v1.14). Briefly, DNA was end-repaired and A-tailed to produce end-repaired, 5’-phosphorylated, 3’-dA-tailed, dsDNA fragments. These 3’-dA-tailed library fragments were then ligated with dsDNA adapters with 3’dTMP overhangs. After adapter ligation, libraries were size selected to 150-350bp using AMPure XP reagent (Agencourt A63880) according to the protocol recommendations. Size selected libraries were amplified for 15 cycles using the KAPA HiFi HotStart ReadyMix. PCR libraries were pooled in equimolar concentrations and sequenced.

tag: cell line type

value: renal cancer cell line

tag: treatment

value: FLAG-EGFP

tag: target molecule

tag: antibody

value: F1804 Monoclonal Anti-Flag M2 Ab (Sigma)


title: CP21

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Serum exosome

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: Exosomes were isolated using the ExoQuick exosome precipitation kit and total RNA was extracted from cells using miRNesy mini kit (Qiagen).

tag: disease

value: patients with chronic pancreatitis

tag: gender

value: Female


title: CP20

tag: age


title: CP18

value: Male


title: hela.3.OE.sfpq.IP


title: hela.2.OE.sfpq.IP


title: hela.3.OE.vector.IP


title: CP16


title: CP19


title: AIP15

value: patients with type 1 autoimmune pancreatitis


title: CP12


title: AIP13


title: AIP14


title: CP15


title: AIP12


title: CP14


title: AIP6


title: CP13


title: AIP7


title: AIP5


title: hela.1.OE.sfpq.Input


title: KO19_3

data_processing:
Fastq files were mapped to the human transcriptome using Bowtie2, relative gene expression was determined using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: Gene level RSEM output files.

source_name: Del SE 3-19

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
RNA was extracted from 80% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bionalyzer 2100 instrument.
RNA-Seq libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen) following the manufacturer’s recommendations with 1μg of total RNA as the starting material. The size and quality of the final library products were assessed using the Agilent High Sensitivity DNA Kit (Agilent 5067-4626). Library concentration was determined using the KAPA Library Quantification Kit (KR0405). Libraries were pooled in equimolar concentrations and subjected to Illumina sequencing.

tag: cell type

value: 113kb SE deletion


title: HC16

value: healthy controls


title: AIP8


title: AIP10


title: AIP9


title: HC12


title: HC15


title: CP17


title: HC10


title: HC11


title: RaviLabHam.48: Global Elmo1-/-

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: GCF_000223135.1_CriGri_1.0_genomic
Supplementary_files_format_and_content: .XLS file with correct gene names, generated using DESeq2, with normalized read counts and differential expression statistics

source_name: Peritoneal macrophages (overnight culture)

growth_protocol: Macrophages were grown in X-VIVO 10 media supplemented with 1% Penicillin-Streptamycin-L-glutamine over-night.

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform

value: Global Elmo1-/-

value: Macrophages

value: Peritoneal macrophages


title: RaviLabHam.47: Global Elmo1-/-


title: RaviLabHam.46: Global Elmo1-/-


title: HC7


title: HC6


title: RaviLabHam.45: Global Elmo1-/-


title: RaviLabHam.42: Elmo1 WT

value: Elmo1 WT


title: RaviLabHam.43: Elmo1 WT


title: RaviLabHam.44: Elmo1 WT


title: RaviLabHam.38: Global Elmo1-/-

source_name: Purified from total bone marrow

value: Neutrophils

value: total bone marrow


title: RaviLabHam.36: Elmo1 WT


title: RaviLabHam.40: Global Elmo1-/-


title: RaviLabHam.41: Elmo1 WT


title: RaviLabHam.39: Global Elmo1-/-


title: RaviLabHam.37: Global Elmo1-/-


title: RaviLabHam.34: Elmo1 WT


title: RaviLabHam.35: Elmo1 WT


title: CAPZ_KO_rep3

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: CDN

data_processing:
Basecalls performed using bcl2fastq
Raw reads were aligned using STAR (version 2.5.3a; Dobin et al., 2013) to build version mm10 of the mouse genome
Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package (Liao et al., 2014) in R-3.3.1
Normalization and differential analysis were carried out using edgeR R package (Robinson et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing raw counts for each sample

source_name: CAPZ_KO_liver tissue

growth_protocol: Adult mice, between 8-10 weeks of age

extract_protocol:
Mice were euthanized and livers harvested after perfusion with cold 1XPBS to reduce blood contaminants. Livers were dissected in a petri dish with 1XPBS on ice, and a portion was snap-frozen in liquid nitrogen for extraction of mRNA. Total liver RNA extractions were performed using Trizol (Thermo) extraction. Contaminant DNA was removed by RNase free-DNase (Thermo).
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina), according to manufacturer’s instructions.

treatment_protocol: Mice received five consecutive daily i.p. injections of tamoxifen starting at 4-6 weeks of age to induce recombination of the Capzb-floxed alleles

tag: strain background

value: adult; between 8-10 weeks of age

tag: genotype/variation

value: CAPZ LKO

value: liver


title: CAPZ_KO_rep4

description: CDO


title: RaviLabHam.33: Elmo1 WT


title: Dark

city: Davis

first: Marie

last: Burns

state: CA

address: 1 Shields Ave

institute: University of California Davis

data_processing:
Fastq files were created using Cell Ranger v 2.0 (Chromium)
I1 reads are technical (sample index), R1 reads are biological (transcript), R2 reads are technical (cell barcode), and R3 reads are technical (unique molecular identifier).
Cell Ranger v 2.0 was used to align both samples to the 10x Genomics reference mm10 genome
Gene barcode matrices were generated using Cell Ranger v 2.0
Further processing, including filtering, PCA, clustering, and more was performed using the Seurat package in R
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain gene and barcode IDs, mtx files contain counts

source_name: CD11b+CD45+ cells

growth_protocol: Arr1-/- mice are bred and reared in darkness

extract_protocol:
Mice were euthanized and retinas were harvested. Retinas were placed in digestion buffer containing Collagenase A and Dnase I for 15 minutes at 37degreesC. After filtering and rinsing, cells were stained for fluorescence activated cell sorting. Cells were sorted on a MoFlo Astrios cell sorter (Beckman) and all alive cells both CD11b+ and CD45+ were collected. Cells were collected in cold DMEM supplemented with 10% FBS and kept on ice until library preparation.
Libraries were prepared for Illumina sequencing using the 10x Genomics system single cell 3' v1 chemistry (Chromium) according to manufacturers recommendations

treatment_protocol: Mice used in the "light" (degenerating) sample were exposed to constant ambient room lighting of approximately 200 lux for 48 hours prior to cell isolation

value: no light exposure

value: retina

tag: retinal health

value: control (healthy)

value: CD11b+CD45+ cells


title: CAPZ_KO_rep1

description: CDL


title: Light

tag: genotype

value: 48 continuous hours of ~200 lux light exposure

value: degenerating


title: CAPZ_KO_rep2

description: CDM


title: WT_rep4

description: CDK

source_name: WT_liver tissue

value: Wild type


title: HC9

value: healthy controls

value: Male


title: WT_rep3

description: CDJ


title: HC14

value: Female


title: HC8


title: WT_rep1

description: CDH


title: Baseline tumor tissue_Patient: 14332405

city: San Diego

first: Zhou

last: Zhu

address: 10646 Science Center Drive (CB4)

institute: Pfizer Worldwide Research & Development

description: Targeted RNA profiling by EdgeSeq Oncology BM Panel

data_processing:
The HTG EdgeSeq Parser was used for post-sequencing data processing.
Genome_build: hg19
Supplementary_files_format_and_content: Data are provided as raw counts and normalized.

source_name: breast cancer tissue (FFPE)

extract_protocol:
The EdgeSeq system used targeted capture sequencing to quantitate RNA expression levels of gene targets in FFPE tissues.
Library preparation was conducted by following the laboratory process and manufacturer protocols.

treatment_protocol: FFPE (formalin-fixed paraffin-embedded) tissues

value: baseline tumor tissue


title: Baseline tumor tissue_Patient: 15638008


title: Baseline tumor tissue_Patient: 11439374


title: Baseline tumor tissue_Patient: 17471382


title: Baseline tumor tissue_Patient: 14571365


title: Baseline tumor tissue_Patient: 15289806


title: Baseline tumor tissue_Patient: 9024333


title: Baseline tumor tissue_Patient: 14283787


title: Baseline tumor tissue_Patient: 13373115


title: Baseline tumor tissue_Patient: 15068922


title: Baseline tumor tissue_Patient: 11317748


title: Baseline tumor tissue_Patient: 12016682


title: Baseline tumor tissue_Patient: 14803677


title: Baseline tumor tissue_Patient: 17134502


title: Baseline tumor tissue_Patient: 9897006


title: Baseline tumor tissue_Patient: 8333307


title: Baseline tumor tissue_Patient: 9957343


title: Human cochlea

city: Kansas City

first: Hinrich

last: Staecker

state: KS

address: Rainbow Blvd.

department: Otolaryngology Head and Neck Surgery

institute: University of Kansas School of Medicine

description: RNA expression derived from Affymetrix console

hyb_protocol: Affymetrix HTA 2.0 array, performed at KUMC Microarray facility

scan_protocol: Affymetrix GeneChip Scanner 3000 7G using a single scan with default normalization

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HTA-2_0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: Healthy inner ear

label_protocol: Using an Affymetrix GeneChip WT Pico labelling kit, 50 ng of total RNA was TdT end labelled with biotin

extract_protocol: Total RNA was extracted with Trizol reagent (Thermofisher, cat #15596018) and purified by centrifuging with phase lock heavy gel (Tiagen, cat # WMS-2302830

value: basilar membrane, lateral wall, modiolus


title: Baseline tumor tissue_Patient: 8338892


title: Baseline tumor tissue_Patient: 13033296


title: WT_rep2

description: CDI


title: Baseline tumor tissue_Patient: 7666079


title: Baseline tumor tissue_Patient: 10246861


title: Baseline tumor tissue_Patient: 10236516


title: Baseline tumor tissue_Patient: 9867842


title: Baseline tumor tissue_Patient: 16031917


title: Baseline tumor tissue_Patient: 8795891


title: Baseline tumor tissue_Patient: 11918089


title: Baseline tumor tissue_Patient: 15937912


title: Baseline tumor tissue_Patient: 14803585


title: Baseline tumor tissue_Patient: 12696312


title: Baseline tumor tissue_Patient: 14117733


title: Baseline tumor tissue_Patient: 15528956


title: Baseline tumor tissue_Patient: 8907703


title: Baseline tumor tissue_Patient: 12138689


title: Baseline tumor tissue_Patient: 8427224


title: Baseline tumor tissue_Patient: 10645574


title: Baseline tumor tissue_Patient: 16499566


title: Baseline tumor tissue_Patient: 8380818


title: Baseline tumor tissue_Patient: 11303685


title: Baseline tumor tissue_Patient: 16491843


title: Baseline tumor tissue_Patient: 14540040


title: Baseline tumor tissue_Patient: 7814768


title: Baseline tumor tissue_Patient: 13085934


title: Baseline tumor tissue_Patient: 10659740


title: Baseline tumor tissue_Patient: 12679937


title: Baseline tumor tissue_Patient: 13184123


title: Baseline tumor tissue_Patient: 7448186


title: Baseline tumor tissue_Patient: 7009169


title: Baseline tumor tissue_Patient: 8503446


title: Baseline tumor tissue_Patient: 10547384


title: Baseline tumor tissue_Patient: 12392188


title: Baseline tumor tissue_Patient: 7028146


title: Baseline tumor tissue_Patient: 14370839


title: Baseline tumor tissue_Patient: 13217237


title: Baseline tumor tissue_Patient: 11022686


title: Baseline tumor tissue_Patient: 7980329


title: Baseline tumor tissue_Patient: 8397147


title: Baseline tumor tissue_Patient: 14684864


title: Baseline tumor tissue_Patient: 13235775


title: Baseline tumor tissue_Patient: 8681218


title: Baseline tumor tissue_Patient: 10915028


title: Baseline tumor tissue_Patient: 8238899


title: Baseline tumor tissue_Patient: 16241056


title: Baseline tumor tissue_Patient: 16765527


title: Baseline tumor tissue_Patient: 9750935


title: Baseline tumor tissue_Patient: 14097614


title: Baseline tumor tissue_Patient: 13151039


title: Baseline tumor tissue_Patient: 10658316


title: Baseline tumor tissue_Patient: 14905147


title: Baseline tumor tissue_Patient: 7622571


title: Baseline tumor tissue_Patient: 15165426


title: Baseline tumor tissue_Patient: 9735427


title: Baseline tumor tissue_Patient: 9806499


title: Baseline tumor tissue_Patient: 15632623


title: Baseline tumor tissue_Patient: 7515528


title: Baseline tumor tissue_Patient: 10266235


title: Baseline tumor tissue_Patient: 9432954


title: Baseline tumor tissue_Patient: 13470896


title: Baseline tumor tissue_Patient: 8103925


title: Baseline tumor tissue_Patient: 15516043


title: Baseline tumor tissue_Patient: 15741010


title: Baseline tumor tissue_Patient: 14182858


title: Baseline tumor tissue_Patient: 11723346


title: Baseline tumor tissue_Patient: 9614206


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title: Baseline tumor tissue_Patient: 11085155


title: Baseline tumor tissue_Patient: 16456024


title: Baseline tumor tissue_Patient: 11064539


title: Baseline tumor tissue_Patient: 13092075


title: Baseline tumor tissue_Patient: 6923644


title: Baseline tumor tissue_Patient: 11247989


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title: Baseline tumor tissue_Patient: 14591342


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title: Baseline tumor tissue_Patient: 7291082


title: Baseline tumor tissue_Patient: 9481814


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title: Baseline tumor tissue_Patient: 13421746


title: Baseline tumor tissue_Patient: 6418604


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title: Baseline tumor tissue_Patient: 15472273


title: Baseline tumor tissue_Patient: 8966418


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title: Baseline tumor tissue_Patient: 6347884


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title: Baseline tumor tissue_Patient: 14840625


title: Baseline tumor tissue_Patient: 7717203


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title: Baseline tumor tissue_Patient: 7064073


title: Baseline tumor tissue_Patient: 13892011


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title: Baseline tumor tissue_Patient: 12790177


title: Baseline tumor tissue_Patient: 15518170


title: Baseline tumor tissue_Patient: 13454872


title: Baseline tumor tissue_Patient: 7802836


title: Baseline tumor tissue_Patient: 6467218


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title: Baseline tumor tissue_Patient: 6357612


title: Baseline tumor tissue_Patient: 14452413


title: Baseline tumor tissue_Patient: 7317996


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title: Baseline tumor tissue_Patient: 11144218


title: Baseline tumor tissue_Patient: 15652456


title: Baseline tumor tissue_Patient: 15682969


title: Baseline tumor tissue_Patient: 16003565


title: Baseline tumor tissue_Patient: 12526020


title: Baseline tumor tissue_Patient: 14597670


title: Baseline tumor tissue_Patient: 9000225


title: Baseline tumor tissue_Patient: 13392322


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title: Baseline tumor tissue_Patient: 13875764


title: Baseline tumor tissue_Patient: 16212848


title: Baseline tumor tissue_Patient: 14603550


title: Baseline tumor tissue_Patient: 10930860


title: Baseline tumor tissue_Patient: 15186868


title: Baseline tumor tissue_Patient: 15478511


title: Baseline tumor tissue_Patient: 6240867


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title: Baseline tumor tissue_Patient: 16482299


title: Baseline tumor tissue_Patient: 11272450


title: Baseline tumor tissue_Patient: 12641687


title: Baseline tumor tissue_Patient: 10009291


title: Baseline tumor tissue_Patient: 14817129


title: Baseline tumor tissue_Patient: 13755340


title: Baseline tumor tissue_Patient: 12096405


title: Baseline tumor tissue_Patient: 14815779


title: Baseline tumor tissue_Patient: 11357561


title: Baseline tumor tissue_Patient: 10083362


title: Baseline tumor tissue_Patient: 9647231


title: Baseline tumor tissue_Patient: 12187283


title: Baseline tumor tissue_Patient: 13481231


title: Baseline tumor tissue_Patient: 9713194


title: Baseline tumor tissue_Patient: 6090137


title: Baseline tumor tissue_Patient: 8164265


title: Baseline tumor tissue_Patient: 6851839


title: Baseline tumor tissue_Patient: 12384548


title: Baseline tumor tissue_Patient: 11571190


title: Baseline tumor tissue_Patient: 9718923


title: Baseline tumor tissue_Patient: 13835633


title: Baseline tumor tissue_Patient: 8891377


title: Baseline tumor tissue_Patient: 10351535


title: Baseline tumor tissue_Patient: 13726368


title: Baseline tumor tissue_Patient: 11163096


title: Baseline tumor tissue_Patient: 9827010


title: Baseline tumor tissue_Patient: 12375363


title: Baseline tumor tissue_Patient: 9545826


title: Baseline tumor tissue_Patient: 8414524


title: Baseline tumor tissue_Patient: 14871523


title: Baseline tumor tissue_Patient: 10558951


title: Baseline tumor tissue_Patient: 6029590


title: Baseline tumor tissue_Patient: 9669204


title: Baseline tumor tissue_Patient: 15636625


title: Baseline tumor tissue_Patient: 9717874


title: Baseline tumor tissue_Patient: 9416636


title: Baseline tumor tissue_Patient: 7229673


title: Baseline tumor tissue_Patient: 6640532


title: Baseline tumor tissue_Patient: 13850702


title: Baseline tumor tissue_Patient: 7278435


title: Baseline tumor tissue_Patient: 7745089


title: Baseline tumor tissue_Patient: 5939244


title: Baseline tumor tissue_Patient: 9682262


title: Baseline tumor tissue_Patient: 11675985


title: Baseline tumor tissue_Patient: 8060702


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title: Baseline tumor tissue_Patient: 12216477


title: Baseline tumor tissue_Patient: 6098439


title: Baseline tumor tissue_Patient: 7148025


title: Baseline tumor tissue_Patient: 10862993


title: Baseline tumor tissue_Patient: 11785866


title: Baseline tumor tissue_Patient: 5922367


title: Baseline tumor tissue_Patient: 14812439


title: Baseline tumor tissue_Patient: 11044542


title: Baseline tumor tissue_Patient: 10535678


title: Baseline tumor tissue_Patient: 6291314


title: Baseline tumor tissue_Patient: 7826829


title: Baseline tumor tissue_Patient: 10212650


title: Baseline tumor tissue_Patient: 11183777


title: Baseline tumor tissue_Patient: 10713196


title: Baseline tumor tissue_Patient: 12185968


title: Baseline tumor tissue_Patient: 8252350


title: Baseline tumor tissue_Patient: 7580737


title: Baseline tumor tissue_Patient: 14110277


title: Baseline tumor tissue_Patient: 8565574


title: Baseline tumor tissue_Patient: 8870322


title: Baseline tumor tissue_Patient: 8463052


title: Baseline tumor tissue_Patient: 7862766


title: Baseline tumor tissue_Patient: 9252246


title: Baseline tumor tissue_Patient: 9841574


title: Baseline tumor tissue_Patient: 6180244


title: Baseline tumor tissue_Patient: 14408515


title: Baseline tumor tissue_Patient: 9518950


title: Baseline tumor tissue_Patient: 10193523


title: Baseline tumor tissue_Patient: 6214356


title: Baseline tumor tissue_Patient: 6669457


title: Baseline tumor tissue_Patient: 12707446


title: Baseline tumor tissue_Patient: 14413497


title: Baseline tumor tissue_Patient: 8702104


title: Baseline tumor tissue_Patient: 9559793


title: Baseline tumor tissue_Patient: 12870166


title: Baseline tumor tissue_Patient: 12046061


title: Baseline tumor tissue_Patient: 14414892


title: Baseline tumor tissue_Patient: 8322680


title: Baseline tumor tissue_Patient: 15754651


title: Baseline tumor tissue_Patient: 5600387


title: Baseline tumor tissue_Patient: 8252945


title: Baseline tumor tissue_Patient: 6749425


title: Baseline tumor tissue_Patient: 12686465


title: Baseline tumor tissue_Patient: 12385070


title: Baseline tumor tissue_Patient: 6230470


title: Baseline tumor tissue_Patient: 7234964


title: Baseline tumor tissue_Patient: 5907197


title: Baseline tumor tissue_Patient: 12813901


title: Baseline tumor tissue_Patient: 13834630


title: Baseline tumor tissue_Patient: 11926362


title: Baseline tumor tissue_Patient: 12448980


title: Baseline tumor tissue_Patient: 12305851


title: Baseline tumor tissue_Patient: 15705911


title: Baseline tumor tissue_Patient: 11949517


title: Baseline tumor tissue_Patient: 11520597


title: Baseline tumor tissue_Patient: 9778730


title: Baseline tumor tissue_Patient: 13350770


title: Baseline tumor tissue_Patient: 12595036


title: Baseline tumor tissue_Patient: 8440908


title: 99262

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
We used STAR-2.5.2 to align the reads to the mouse reference genome (mm10)
We then used HTSeq-0.6.1 to count the number of uniquely mapped reads for each gene using GENCODE (vM18)
The gene expression level was modeled using a negative binomial distribution and normalized in DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix text

growth_protocol: Primary keratinocytes were expanded in culture for 3 days prior to harvest

extract_protocol:
RNA was isolated using Mouse RiboPure-Blood RNA Isolation Kit (Thermo Fisher Scientific) for whole blood, TriPure Isolation Reagent (MilliporeSigma) for skin, and Buffer RLT (Qiagen) for keratinocytes per the manufacturer’s protocols
Library construction protocol: Stranded mRNA libraries were prepared using the TruSeq RNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 4000 sequencer

tag: strain

tag: animal tag

value: M


title: 99261

value: WT

value: F


title: 112579

source_name: blood


title: 99258


title: 99259


title: Baseline tumor tissue_Patient: 9682880


title: 99260


title: 99263


title: Baseline tumor tissue_Patient: 10612292


title: Baseline tumor tissue_Patient: 8030324


title: 112575


title: 112576


title: Baseline tumor tissue_Patient: 6312812


title: Baseline tumor tissue_Patient: 14880217


title: Baseline tumor tissue_Patient: 8154546


title: 112577


title: Baseline tumor tissue_Patient: 7348034


title: Baseline tumor tissue_Patient: 7279254


title: Baseline tumor tissue_Patient: 12583688


title: 112573


title: 112578


title: Baseline tumor tissue_Patient: 10098696


title: 112572


title: Baseline tumor tissue_Patient: 7519625


title: 112571


title: 112569


title: 112568


title: 112567


title: Baseline tumor tissue_Patient: 13399826


title: Baseline tumor tissue_Patient: 7697999


title: Baseline tumor tissue_Patient: 11022127


title: 112566


title: Baseline tumor tissue_Patient: 5566605


title: 112570


title: Baseline tumor tissue_Patient: 6973353


title: 112574


title: Baseline tumor tissue_Patient: 13125259


title: Baseline tumor tissue_Patient: 9006242


title: Baseline tumor tissue_Patient: 5794563


title: 112564


title: Baseline tumor tissue_Patient: 7244600


title: Baseline tumor tissue_Patient: 14412336


title: H3K9me3_ChIPSeq_RPE Exp2

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

data_processing:
Quality control of sequencing reads was performed using FastQC.
Reads were then aligned to the reference genome (mm10) obtained from the UCSC genome browser using BWA software v.0.7.5a.
Samples were filtered for regions blacklisted by the ENCODE project. Subsequently samples were deduplicated using SAMtools version 1.3.1.
Alignment coordinates were converted to BED format using BEDTools v.2.17 and peak calling was performed using SICER with customized parameters for each histone mark.
Genome_build: mm10
Supplementary_files_format_and_content: BED files were generated using SICER with customized parameters for each histone mark. The first column is the name of the chromosome; second - the starting position of the peak; third - the ending position of the peak; fourth - the name of the peak; fifth - the p-value of the peak

source_name: RPE

extract_protocol:
Freshly isolated RPE were cross-linked in 1% formaldehyde with 1X PBS. To stop the cross linking reaction, glycine was added to a final concentration of 0.125M. The chromatin was prepared using the True MicroChIP Kit (Diagenode Cat# C01010130). Chromatin was sheared using the Bioruptor® Pico sonication device (Diagenode Cat# B01060001). ChIP was performed using IP-Star® Compact Automated System (Diagenode Cat# B03000002) following the protocol of the aforementioned kit. Chromatin corresponding to 14,000-28,000 cells was immunoprecipitated using the antibodies.
Libraries were prepared from input and ChIP’d DNA (500 pg) using the MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Library amplification is assessed using the High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were then purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analyzed by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). When the proportion of fragments >500bp was too high, libraries were subjected to a double size selection using Agencourt® AMPure® XP (Beckman Coulter). Libraries were pooled and sequenced on an Illumina HiSeq 4000 with single-end reads of 50bp lengths, running HiSeq Control Software HD version 3.4.0.38.

value: retinal pigment epithelium (RPE)

tag: chip antibody

value: H3K9me3 (Diagenode Cat# C15410193)


title: H3K27me3_ChIPSeq_RPE Exp2

tag: tissue

value: H3K27me3 (Diagenode Cat# C15410195)


title: Baseline tumor tissue_Patient: 11130466


title: Baseline tumor tissue_Patient: 6422724


title: Baseline tumor tissue_Patient: 10102313


title: H3K4me3_ChIPSeq_RPE Exp2

value: H3K4me3 (Diagenode Cat# C15410003-50)


title: Baseline tumor tissue_Patient: 12404284


title: H3K27me3_ChIPSeq_RPE Exp1


title: Baseline tumor tissue_Patient: 10561227


title: Baseline tumor tissue_Patient: 9074974


title: H3K4me1_ChIPSeq_RPE Exp2

value: H3K4me1 (Diagenode Cat# C15410194)


title: H3K4me3_ChIPSeq_RPE Exp1


title: H3K4me1_ChIPSeq_RPE Exp1


title: H3K9me3_ChIPSeq_RPE Exp1


title: Baseline tumor tissue_Patient: 13538313


title: Baseline tumor tissue_Patient: 5424788


title: hepa_D2-rep3

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
B6_DBA_H3K4me3_hepatocyte_peak_associations.txt.gz
B6_DBA_H3K4me3_hepatocyte_peak_associations_reads.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-Seq reads were aligned to the mm10 or DBA/2J REL-1509 genome assembly using bwa v.0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
Genome_build: mm10
Supplementary_files_format_and_content: processed files are text files representing the position of an identified H3K4me3 peak in both mm10 and DBA/2J coordinates as identified by sequence homology. Large matrix of all H3K4me3 peaks and read counts for each of the four cell types. One file is the read counts and positions of DSBs in male germ cells represented by DMC1-associated ssDNA fragments

source_name: hepatocytes

growth_protocol: Crude isolation of germ cells was conducted from male mice at 14 days post-partum (dpp). Hepatocyte and cardiomyocyte isolation from female animals. Mouse embryonic stem cells were derived following protocol from Czechanski et al. 2014. Nature Protocols. For detailed protocol see publication

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection for all germ cell data or the KAPA hyper kit (Kapa Biosystems) for mESC, cardiomyocytes, and hepatocytes.

value: 8 weeks old

tag: ChIP


title: hepa_D2-rep2


title: 112565


title: Baseline tumor tissue_Patient: 15093241


title: Baseline tumor tissue_Patient: 8524784


title: input RPE DNA Exp2

value: none (input)


title: hepa_D2-rep1


title: input RPE DNA Exp1


title: Baseline tumor tissue_Patient: 10228368


title: hepa_D2-input

value: Input DNA


title: Baseline tumor tissue_Patient: 9533761


title: Baseline tumor tissue_Patient: 13826810


title: hepa_BXD87-rep3


title: hepa_BXD87-rep2


title: Baseline tumor tissue_Patient: 7912381


title: hepa_BXD87-rep1


title: Baseline tumor tissue_Patient: 8434002


title: Baseline tumor tissue_Patient: 9779025


title: Baseline tumor tissue_Patient: 12995760


title: hepa_BXD75-rep3


title: hepa_BXD75-rep2


title: Baseline tumor tissue_Patient: 9905568


title: Baseline tumor tissue_Patient: 11941643


title: hepa_BXD75-rep1


title: Baseline tumor tissue_Patient: 7137610


title: Baseline tumor tissue_Patient: 9979859


title: hepa_B6-rep3


title: hepa_B6-rep2


title: Baseline tumor tissue_Patient: 5683646


title: hepa_B6-rep1


title: Baseline tumor tissue_Patient: 9022773


title: hepa_B6-input


title: esc_D2-216-K4me3

description:
B6_DBA_H3K4me3_EScells_peak_associations.txt.gz
B6_DBA_H3K4me3_EScells_peak_associations_reads.txt.gz

source_name: mouse embryonic stem cells


title: esc_D2-203-rep3-K4me3


title: Baseline tumor tissue_Patient: 9700003


title: Baseline tumor tissue_Patient: 12305927


title: Baseline tumor tissue_Patient: 7556955


title: esc_D2-203-rep2-K4me3


title: Baseline tumor tissue_Patient: 12748382


title: esc_D2-203-rep1-input


title: Baseline tumor tissue_Patient: 13708409


title: Baseline tumor tissue_Patient: 6412808


title: esc_D2-173-K4me3


title: Baseline tumor tissue_Patient: 6661396


title: esc_BXD87-K-K4me3


title: Baseline tumor tissue_Patient: 6470737


title: esc_BXD87-C-input


title: esc_BXD87-I-K4me3


title: Baseline tumor tissue_Patient: 7458742


title: Baseline tumor tissue_Patient: 6380300


title: esc_BXD75-F-K4me3


title: esc_BXD75-N-K4me3


title: Baseline tumor tissue_Patient: 5603637


title: esc_B6-49-rep2-K4me3


title: esc_B6-49-rep1-input


title: esc_B6-49-rep3-K4me3


title: esc_BXD75-Q-K4me3


title: esc_BXD75-A-input


title: esc_D2-203-rep1-K4me3


title: esc_B6-49-rep1-K4me3


title: esc_BXD87-X-K4me3


title: esc_BXD75-Y-K4me3


title: esc_BXD75-A-K4me3


title: esc_BXD87-M-K4me3


title: cardio_D2-Input

description:
B6_DBA_H3K4me3_cardiomyocytes_peak_associations.txt.gz
B6_DBA_H3K4me3_cardiomyocytes_peak_reads.txt.gz

source_name: cardiomyocytes


title: esc_B6-139-K4me3


title: cardio_D2-Rep1


title: esc_B6-146-K4me3


title: cardio_BXD87-Rep2


title: cardio_D2-Rep3


title: cardio_BXD87-Rep3


title: cardio_D2-Rep2


title: esc_BXD87-C-K4me3


title: Yan4_S4

city: St Louis

first: Carolina

middle: B

last: Lopez

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
fastq files were aligned to self-developed algorithm VODKA to identify possbile copy-back defective viral genomes
Genome_build: RSV isolate NCBI accesion number KJ672447
Supplementary_files_format_and_content: output from VODKA: txt file contain the breakpoint position, sequences, length, READID, CIGAR score of all DVG junction reads.

source_name: pediatric patient H73

extract_protocol:
RNA samples from 2 RSV strain A infected pediatric samples were prepared as follows: RNA extracted from TRIzol reagents as manufacture's introduction.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: viral contents

value: RSV strain A Full-length (FL) genome and Defective Viral Genomes

tag: repeat

value: Replicate pool 2


title: cardio_BXD87-Input


title: Yan2_S2

value: Replicate pool 1


title: cardio_BXD75-Rep3


title: Yan3_S3

source_name: pediatric patient H4


title: cardio_BXD75-Rep2


title: Yan1_S1


title: MDA-MB-231-1833PF1502_rep3_RNA-seq

first: Joyce

middle: Marie

last: Slingerland

address: 1501 NW 10th Avenue

institute: University of Miami

data_processing:
Paired end sequencing was performed on Illumina NextSeq platform using 150 cycles 400M kit
Quality and adapter trimming was performed by Trimmomatic
Genome alignment was performed using STAR version 2.5.0b
Raw counts were calculated with featureCounts subread v1.5.0
Differentially expressed genes were then identified by DESeq2 version 1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: text file with counts or rpkm

growth_protocol: The cells are grown in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY, USA) with 10% fetal bovine serum, 1% glutamine, 1% sodium pyruvate (Invitrogen, Carlsbad, CA, USA), and 50 µg/ml gentamicin (Mediatech, Manassas, VA, USA) under the cell incubation conditions (5% CO2, 95% relative humidity, 37°C).

extract_protocol:
Total RNA was extracted from cell lines with a TRIzol reagent kit (Invitorogen), according to the manufacturer’s instructions.
The quality of total RNA isolated from the cell lines was measured using Bioanalyzer RNA Nano 6000 (Agilent Technologies, Santa Clara, CA, USA). Library preparation was performed by TruSeq Standed Total RNA Library Prep (Illumina, San Diego, USA), and the quality was confirmed using KAPA qPCR Library Quantification (Kapa Biosystems, Wilmington, MA, USA). Paired end sequencing was performed on Illumina 150 cycles 400M reads.

treatment_protocol: Cells were treated with the PI3K/mTOR dual kinase inhibitor at 250 nM PF-04691502 (PF1502) for 48 hours.

tag: cell line

value: derived from MDA-MB-231

value: cancer cells (PI3K inhibitor-treated line)

value: breast


title: cardio_BXD75-Rep1

tag: antibody


title: cardio_BXD75-Input


title: MDA-MB-231-1833PF1502_rep1_RNA-seq


title: cardio_B6-Rep2


title: MDA-MB-231-1833shp27_rep3_RNA-seq

value: cancer cells (p27 knockdown line)


title: cardio_B6-Rep1


title: cardio_B6-Rep3


title: MDA-MB-231-1833PF1502_rep2_RNA-seq


title: cardio_B6-Input


title: MDA-MB-231-1833shp27_rep2_RNA-seq


title: MDA-MB-231-1833_rep3_RNA-seq

value: cancer cells (a bone-tropic metastatic line)


title: MDA-MB-231-1833shp27_rep1_RNA-seq


title: MDA-MB-231p27CK-DD_rep3_RNA-seq

value: cancer cells (phosphomimetic p27 line)


title: MDA-MB-231-1833_rep1_RNA-seq


title: MDA-MB-231p27CK-DD_rep2_RNA-seq


title: MDA-MB-231_rep3_RNA-seq

value: cancer cells


title: MDA-MB-231_rep2_RNA-seq


title: MDA-MB-231p27CK-DD_rep1_RNA-seq


title: cardio_BXD87-Rep1


title: MDA-MB-231_rep1_RNA-seq


title: MDA-MB-231-1833shp27_p27_ChIPSeq-rep2

data_processing:
Basecalls performed using RTA version 2.4.11
ChIP-seq reads were aligned to the hg19 genome using bowtie 2.3.3.1
Quality and adapter trimming was performed by Trim Galore version 0.4.4
PCR duplicates were then marked and removed by Picard version 2.13
Peaks are called with MACS2 version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
ChIP assay was preformed by ChIP-IT High Sensitivity kit (Active Motif; 53040). After cells were crosslinked with 1% formaldehyde, the cells were lysed and sonicated. For the immunoprecipitation, sonicated samples were incubated with anti-cJun (Cell Signaling; 9165s) and p27 (Cell Signaling; 3686s) antibodies for overnight at 4°C. After elution DNA, the quality was measured using Bioanalyzer DNA HS (Agilent Technologies).
Libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit (NEB), and their quality was measured by High Sensitivity D1000 Screen Tape (Agilent Technologies). ChIP sequencing was performed on Illumina 75 cycles 400M reads.

value: p27 (Cell Signaling; 3686S)


title: MDA-MB-231-1833shp27_p27_ChIPSeq-rep1


title: parous_B29

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

institute: Fox Chase Cancer Center

description: gene expression

hyb_protocol: Hybridization was performed as described in the GeneChip Expression Analysis (701021 Rev.5) protocol from Affymetrix, following the instructions for 49 formta (standard)/64 format array.

scan_protocol: The scanner used was Affymetrix® GeneChip® Scanner 3000 and the software used was Command Console.

data_processing: The data were (1) RMA normalized; (2) filtered to exclude probesets present (P) in fewer than 25% of both parous & nulliparous samples; (3) batch normalized with ComBat (default parameters); (4) filtered to remove probesets with variance in the lowest quartile

source_name: Human breast biopsy

label_protocol: GeneChip Expression 3’-Amplification Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) was used for sample preparation following manufacturer's protocol.

extract_protocol: Total RNA from core needle biopsies specimens was isolated using the Qiagen Allprep RNA/DNA Mini Kit according to manufacturer's instructions (Qiagen, Alameda, CA, USA)

treatment_protocol: Core needle biopsies specimens was collected from the breast of premenopausal women free of any breast abnormality.  Samples were kept in RNA later.

tag: parity

value: parous

tag: batch

tag: years since last pregnancy


title: parous_B31

description: gene expression


title: MDA-MB-231-1833_p27_ChIPSeq-rep1

tag: cell type


title: parous_B30

description: gene expression


title: MDA-MB-231p27CK-DD_p27_ChIPSeq-rep2


title: MDA-MB-231_p27_ChIPSeq-rep2


title: MDA-MB-231-1833_rep2_RNA-seq


title: MDA-MB-231_p27_ChIPSeq-rep1


title: MDA-MB-231-1833shp27_cJun_ChIPSeq-rep2

value: cJun (Cell Signaling; 9165S)


title: MDA-MB-231-1833shp27_cJun_ChIPSeq-rep1


title: MDA-MB-231-1833_cJun_ChIPSeq-rep1


title: MDA-MB-231p27CK-DD_p27_ChIPSeq-rep1


title: MDA-MB-231p27CK-DD_cJun_ChIPSeq-rep2


title: MDA-MB-231-1833_p27_ChIPSeq-rep2


title: MDA-MB-231-1833_cJun_ChIPSeq-rep2


title: parous_B25

description: gene expression


title: nulliparous_B24

description: gene expression

value: nulliparous


title: parous_B28

description: gene expression


title: nulliparous_B22

description: gene expression


title: nulliparous_B23

description: gene expression


title: nulliparous_B20

description: gene expression


title: MDA-MB-231p27CK-DD_cJun_ChIPSeq-rep1


title: parous_B18

description: gene expression


title: parous_B17

description: gene expression


title: parous_B8

description: gene expression


title: parous_B26

description: gene expression


title: parous_B27

description: gene expression


title: parous_B21

description: gene expression


title: MDA-MB-231_cJun_ChIPSeq-rep1


title: MDA-MB-231_cJun_ChIPSeq-rep2


title: MDA-MB-231-1833shp27_Input DNA-rep2


title: MDA-MB-231-1833shp27_Input DNA-rep1


title: parous_B7

description: gene expression


title: nulliparous_B4

description: gene expression


title: parous_B9

description: gene expression


title: MDA-MB-231-1833_Input DNA-rep2


title: MDA-MB-231-1833_Input DNA-rep1


title: MDA-MB-231p27CK-DD_Input DNA-rep1


title: MDA-MB-231_Input DNA-rep2


title: nulliparous_B14

description: gene expression


title: parous_B3

description: gene expression


title: MDA-MB-231_Input DNA-rep1


title: parous_B5

description: gene expression


title: parous_B13

description: gene expression


title: parous_B16

description: gene expression


title: MDA-MB-231p27CK-DD_Input DNA-rep2


title: parous_B12

description: gene expression


title: nulliparous_B10

description: gene expression


title: nulliparous_B2

description: gene expression


title: parous_B131

description: gene expression


title: parous_B11

description: gene expression


title: parous_B130

description: gene expression


title: parous_B1

description: gene expression


title: parous_B98

description: gene expression


title: parous_B97

description: gene expression


title: nulliparous_B129

description: gene expression


title: parous_B128

description: gene expression


title: CP-317

city: Murcia

first: Angel

last: Esteban-Gil

state: Murcia

address: Campus de Ciencias de la Salud Carretera Buenavista s/n

department: Biomedical Informatics and Bioinformatics Platform

institute: Institute for Biomedical Research of Murcia (IMIB)

hyb_protocol: A 2000ng cRNA product was hybridized with Whole Human Genome Oligo Microarray Kit (Agilent p/n G4112F-014850_4x44k)

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol.

data_processing: Data extracted using Agilent Feature Extraction Software 10.7.1 following the Agilent grid template 014850_D_F_20100430 protocol GE1_107_Sep09 and the QC Metric Set GE1_QCMT_Sep09.  Agilent raw data were pre-processed using Agilent background correction, and quantile normalization was applied to obtain homogeneous scales in all samples.

source_name: Colorectal tissue

label_protocol: Total RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and fragment size distribution was analysed by RNA 6000 Pico Bioanalyzer assay (Agilent Technologies, Palo Alto, California USA). RNA 150ng was concentrated in a SpeedVac to a working dilution and used to produce Cyanine 3-CTP-labeled cRNA using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305) according to the ‘One-Color Microarray-Based Gene Expression Analysis’ protocol Version 6.0 (Agilent p/n G4140-90040). This method uses T7 RNA polymerase which simultaneously amplifies target material and incorporates cyanine 3- labelled CTP.

growth_protocol: The clinico-pathological features of the patients have been previously reported. Updated follow-up information was obtained from cancer registry files and approval for the study was granted by the Local Ethical Board. SACs were diagnosed on the basis of criteria proposed by Mäkinen et al., and hMSI-Hs according to prior established criteria (mucinous, signet-ring cell, and medullary carcinoma, tumor infiltrating and peritumoral lymphocytes, “Crohn-like” inflammatory response, poor differentiation, tumor heterogeneity, and “pushing” tumor border).

extract_protocol: A volume of approximately 10mm3 was extracted from each frozen tissue using the disposable sterile biopsy punch Acupunch 2mm (Acuderm Inc, Lauderdale, FL, USA). RNA was extracted following the manufacturer´s instructions (Qiagen, Hilden, Germany). Briefly, tissue was disrupted and homogenized in 700µl of Qiazol (Qiagen ref:1023537) using a Tissueruptor by Qiagen for 20 seconds. The homogenate was incubated at room temperature for 5 minutes. After adding 140µl of chloroform and centrifuging at 12,000xg for 15 minutes at 4ºC, 350µl of the aqueous phase was subjected to automatic total RNA extraction using the Qiacube equipment and the miRNeasy Mini Kit (ref:217004), both provided by Qiagen.

tag: age

tag: Sex

value: male

tag: tissue status

value: polyp


title: parous_B126

description: gene expression


title: parous_B99

description: gene expression


title: nulliparous_B127

description: gene expression


title: parous_B122

description: gene expression


title: CP-323

value: female


title: nulliparous_B132

description: gene expression


title: CP-43

value: tumoral


title: CP-29


title: CP-318


title: CP-172

value: normal


title: CP-163


title: CP-322


title: CP-309


title: CP-324


title: nulliparous_B121

description: gene expression


title: CP-319


title: nulliparous_B119

description: gene expression


title: CP-42


title: CP-321


title: parous_B118

description: gene expression


title: CP-308


title: parous_B120

description: gene expression


title: nulliparous_B116

description: gene expression


title: parous_B117

description: gene expression


title: CP-167


title: CP-314


title: CP-325


title: parous_B113

description: gene expression


title: CP-320


title: CP-27


title: nulliparous_B110

description: gene expression


title: parous_B115

description: gene expression


title: parous_B109

description: gene expression


title: CP-170


title: parous_B114

description: gene expression


title: parous_B108

description: gene expression


title: CP-7


title: CP-164


title: CP-313


title: parous_B105

description: gene expression


title: CP-47


title: parous_B103

description: gene expression


title: CP-307


title: nulliparous_B101

description: gene expression


title: CP-32


title: CP-40


title: CP-28


title: parous_B96

description: gene expression


title: parous_B102

description: gene expression


title: parous_B95

description: gene expression


title: CP-161


title: parous_B92

description: gene expression


title: CP-30


title: parous_B91

description: gene expression


title: parous_B93

description: gene expression


title: parous_B100

description: gene expression


title: parous_B94

description: gene expression


title: CP-3


title: parous_B104

description: gene expression


title: CP-18


title: CP-16


title: parous_B90

description: gene expression


title: nulliparous_B88

description: gene expression


title: CP-37


title: CP-52


title: parous_B89

description: gene expression


title: parous_B107

description: gene expression


title: parous_B87

description: gene expression


title: CP-316


title: CP-312


title: CP-168


title: CP-310


title: CP-48


title: CP-23


title: parous_B86

description: gene expression


title: nulliparous_B85

description: gene expression


title: nulliparous_B84

description: gene expression


title: parous_B81

description: gene expression


title: CP-39


title: parous_B83

description: gene expression


title: parous_B82

description: gene expression


title: nulliparous_B78

description: gene expression


title: CP-36


title: CP-162


title: CP-41


title: nulliparous_B77

description: gene expression


title: CP-311


title: parous_B76

description: gene expression


title: CP-44


title: CP-304


title: parous_B74

description: gene expression


title: CP-159


title: CP-12


title: CP-305


title: CP-33


title: CP-24


title: parous_B75

description: gene expression


title: CP-15


title: nulliparous_B73

description: gene expression


title: CP-315


title: nulliparous_B60

description: gene expression


title: C47i: TU-A130-TU130_TU130R

type: genomic

city: Otsu

first: Hiroyuki

last: Sugihara

state: Shiga

address: Seta, Tsukinowa-cho

department: Pathology

institute: Shiga University of Medical Science

description:
Grid: 021924_D_F_20090227
protocol: CGH_1105_Oct12
Feature Extraction software: 11.5.1.1

hyb_protocol: Labelled samples were hybridized on SurePrint G3 Human CGH Microarray 8x60K  (Agilent, GPL10152) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: Signal intensity extraction, and normalization were performed using the Agilent Feature Extraction software 11.5.1.1. Linear normalization method with default parameters (protocol CGH_1105_Oct12 and Grid: 021924_D_F_20090227)  was used in signal intensity extraction procedure.

source_name: invasive part of invasive colorectal cancer

label_protocol: 250ng DNA was labelled using the SureTag DNA Labeling Kit coupling method (Agilent – 5190-3400).

growth_protocol: Colorectal archival materials (including metastatic lymph nodes) from operative resection and endoscopic resection were selected in this study. Formalin-fixed paraffin embedded tissues (FFPE) of colorectal carcinomas from 48 patients from 2012 to 2017.

extract_protocol: The samples were obtained from 5-micrometer-thick tissue sections using a laser microdissection system (LMD6000, Leica Microsystems, Wetzlar, Germany). Each  sample was dissected from at least > 6mm2 area, in which neoplastic cells accounted for 90% of total cell count. These cells were then digested in 200 mg/ml proteinase K solution for 70±2 hours at 37ºC. Genome DNA was extracted with phenol-chloroform-isoamyl alcohol extraction method and further treated using the Maxtract high density extraction column(QIAGEN).Eluted DNA was assessed for purity using the Nanodrop-1000 and double stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer's instructions. GenomeDNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) Kit (SIGMA). For each WGA 100 ng (Nanodrop) or 10 ng (Qubit) of starting material was used. The amplified DNA product was purified using the GeneElute PCR Clean-Up Kit (SIGMA).

tag: excision year

tag: analysis year

tag: gender

value: M

tag: pathologic stage

source_name: corresponding non-neoplastic sample

value: corresponding non-neoplastic sample


title: C47ln: TU-A131-TU131_TU130R

tag: tissue

value: invasive part of invasive colorectal cancer


title: C48ln: TU-A133-TU133_TU132R


title: C48i: TU-A132-TU132_TU132R


title: C46i: TU-A128-TU128_TU128R


title: C46ln: TU-A129-TU129_TU128R


title: parous_B63

description: gene expression

value: breast


title: nulliparous_B58

description: gene expression


title: parous_B57

description: gene expression


title: CP-303


title: parous_B55

description: gene expression


title: C45ln: TU-A127-TU127_TU126R

value: F


title: parous_B61

description: gene expression


title: nulliparous_B56

description: gene expression


title: C45i: TU-A126-TU126_TU126R


title: parous_B62

description: gene expression


title: parous_B59

description: gene expression


title: C44ln: TU-A125-TU125_TU124R


title: C44i: TU-A124-TU124_TU124R


title: C43ln: TU-A123-TU123_TU122R


title: parous_B54

description: gene expression


title: parous_B52

description: gene expression


title: CP-6


title: parous_B51

description: gene expression


title: parous_B53

description: gene expression


title: C42ln: TU-A121-TU121_TU120R


title: C41ln: TU-A119-TU119_TU118R


title: parous_B49

description: gene expression


title: C42i: TU-A120-TU120_TU120R


title: C41i: TU-A118-TU118_TU118R


title: C20i: TU-A117-TU117_TU116R


title: nulliparous_B43

description: gene expression


title: nulliparous_B46

description: gene expression


title: parous_B45

description: gene expression


title: C40m: TU-A114-TU113_TU107R

source_name: intramucosal part of invasive colorectal cancer


title: C19m: TU-A115-TU114_TU107R

value: intramucosal part of invasive colorectal cancer


title: C40a: TU-A113-TU112_TU107R

source_name: adenoma part of invasive colorectal cancer


title: CP-302


title: C39i: TU-A112-TU111_TU107R


title: nulliparous_B40

description: gene expression


title: C43i: TU-A122-TU122_TU122R


title: parous_B39

description: gene expression


title: parous_B38

description: gene expression


title: C39a: TU-A110-TU109_TU107R

value: adenoma part of invasive colorectal cancer


title: parous_B37

description: gene expression


title: C38m: TU-A109-TU108_TU107R

value: Tis


title: C38a: TU-A108-TU107_TU107R


title: parous_B36

description: gene expression


title: C19i: TU-A116-TU115_TU107R


title: C37m: TU-A107-TU106_TU107R


title: C37a: TU-A106-TU105_TU107R


title: parous_B33

description: gene expression


title: parous_B44

description: gene expression


title: nulliparous_B34

description: gene expression


title: parous_B41

description: gene expression


title: C36a: TU-A104-TU103_TU107R


title: nulliparous_B106

description: gene expression


title: parous_B42

description: gene expression


title: C35m: TU-A103-TU102_TU103R


title: C39m: TU-A111-TU110_TU107R


title: C34m: TU-A101-TU100_TU099R


title: C36m: TU-A105-TU104_TU107R


title: C35a: TU-A102-TU101_TU103R


title: A1541_st_L80

description: gene expression

scan_protocol: The scanner used was Affymetrix® GeneChip® Scanner 3000 and the software used was Affymetrix GeneChip Command Console, v.3.2.

data_processing: The data were (1) RMA normalized; (2) For each subject a linear regression model was fitted across all genes. The gene expression values in the whole tissue were modeled as a linear function of the gene expression in epithelial and stromal tissues.

label_protocol: RNA amplification and labelling was performed using MessageAmpTM Premier RNA Amplification Kit (Life Technologies)

extract_protocol: The RNA extraction from the collected cells was performed using the Arcturus® PicoPure®RNA Isolation Kit (Life Technologies).

treatment_protocol: Core needle biopsies specimens was collected from the breast of premenopausal women free of any breast abnormality.  Laser capture microdissection was performed to select and capture all the epithelial tissue present in each section.  The tissue left on the slide was then scraped into a different tube and classified as stroma. RNA was also extracted from a second core biopsy, in which no LCM was performed

tag: subject id

tag: organ

value: stroma

tag: tissue abbrevation

value: st


title: C33a: TU-A98-TU097_TU097R


title: C32m: TU-A97-TU096_TU095R


title: A1533_st_L81

description: gene expression


title: A1478_wt_L78

description: gene expression

value: whole

value: wt


title: A1541_ep_L71

description: gene expression

value: epithelium

value: ep


title: A1497_wt_L62

description: gene expression


title: A1478_st_L60

description: gene expression


title: A1479_ep_L63

description: gene expression


title: A1541_wt_L57

description: gene expression


title: A1533_wt_L59

description: gene expression


title: A1489_st_L64

description: gene expression


title: C32a: TU-A96-TU095_TU095R


title: C31i: TU-A95-TU094_TU092R


title: C31a: TU-A93-TU092_TU092R


title: C31m: TU-A94-TU093_TU092R


title: A1478_ep_L56

description: gene expression


title: A1485_wt_L46

description: gene expression


title: C30m: TU-A92-TU091_TU090R


title: C33m: TU-A99-TU098_TU097R


title: C30a: TU-A91-TU090_TU090R


title: C34a: TU-A100-TU099_TU099R