title: Pool3_Index3_TTAGGC_L007_R1_001


title: H3K27me3 in Lgr5+Tspan8- rep1

status: Public on Feb 01 2017

type: SRA

city: Melbourne

first: Casey

last: Ah-Cann

state: Victoria

address: 1G Royal Parade, Parkville

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

library_source: genomic

data_processing:
Rsubread package (version 1.20.3, Liao et al. Bioinformatics, 2014) was used for read mapping and summarisation.
Sequenced reads were mapped using the align function with default parameters.
Gene-level summarisation was carried out using the featureCounts and in-built mm10 annotation.
Counts for H3K27me3 were summarised across the genebody.
Counts for H3K4me3 were summarised over the promoter region of genes.
Genome_build: mm10
Supplementary_files_format_and_content: Text files containing Entrez gene identifiers and counts were extracted from the output generated by Rsubread.

molecule: genomic DNA

organism: Mus musculus

source_name: FACS-sorted cells from mouse mammary gland

growth_protocol: Basal cells defined by Lgr5 and Tspan8 expression were directly isolated from the mammary glands of females.

extract_protocol:
Cells were lysed and the chromatin was sheared to a size range of 200 to 400 bp using Covaris M220 sonicator. Sheared chromatin was diluted and incubated at 4°C overnight with antibodies against Histone H3 trimethyl Lys4 (K4, Millipore #07-473), Histone H3 trimethyl Lys27.
ChIP samples were prepared and indexed for Illumina sequencing using the TruSeq DNA sample Prep Kit.

treatment_protocol: No treatment.

tag: sample

tag: subpopulation

tag: tissue

value: Mammary gland

tag: antibody

tag: antibody vendor/catalog

value: Millipore #07-449

tag: genetic background


title: S_No_37_ACAGTG_L001_R1_001

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

library_source: transcriptomic

data_processing:
bcl2fastq v1.8.4 used for Basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence ends and filtered by sequence size (<15) using PRINSEQ v0.20.3
Reads were mapped with the aligner segemehl with the -H 1 parameter enabled to the Nothobranchius furzeri genome published by Reichwald et al Cell 2015
Reads were counted using rnacounter with parameters -s -m raw
Genome_build: nfurzeri_genebuild_v1
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

molecule: total RNA

organism: Nothobranchius furzeri

source_name: Embryo

extract_protocol:
The organs of the fishes were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 30 Hz for 3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed thoroughly and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000 x g at 4°C for 20 min. The supernatant was removed and the pellet was washed with 80% Ethanol twice and air dried for 10 min. The RNA was resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80°C until use.
Sequencing procedure was done using Illumina methodology [Bentley et al, 2008]. Around 1 µg of total RNA was used for library preparation (Illumina, TruSeq™ small RNA Sample Prep Kit) using the manufacturer’s description.

tag: strain

value: Embryo

tag: age

value: two weeks postfertilization plus diapause


title: Pool3_Index1_ATCACG_L007_R1_001


title: Pool3_Index4_TGACCA_L007_R1_001


title: neutralizer controller 3

city: Cambridge

first: Xu

middle: G

last: Yu

state: Massachusetts

address: 400 Technology sqr

country: USA

institute: Ragon Institute of MGH, MIT and Harvard

description:
NT3
raw reads indexing length: 8

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline. STAR and RSEM were used to align to HG38 and to calculate the raw counts for genes, respectively.
Genome_build: HG38
Supplementary_files_format_and_content: raw counts

organism: Homo sapiens

source_name: dendritic cell

extract_protocol:
Total RNA was extracted using a commercial kit recommended for low numbers of cells (mirVanaTM Isolation Kit; Life TechnologiesTM)
According to Trombetta et al CPMB 2014
Whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2.

tag: phenotype

value: neutralizer controllers


title: MZM040324hpf_TAGCTT_L001_R1_001


title: Input control in Lgr5+Tspan8- rep2

value: none (input)


title: shWHSC1 H3K36me2 ChIPSeq

city: Shanghai

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq  500) were mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis
Tags were extended in silico (using Active Motif software) at their 3´-  ends to a length of 150-250 bp, depending on the average fragment length in the size selected  library (normally 200 bp). To identify the density of fragments (extended tags) along the genome,  the genome was divided into 32-nt bins and the number of fragments in each bin was determined.
Peaks were called using SICER.
Tag Normalization: tag number of all samples was reduced (by random sampling) to the number of tags present in the smallest sample.
"Active Regions" were used when comparing different amples.
Genome_build: hg19
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.

source_name: shWHSC1 H3K36me2 ChIPSeq

growth_protocol: RPMI1640 supplied with 10% fetal bovine serum.

extract_protocol:
The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K36me2( Millipore).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

tag: cell line

value: prostate; derived from metastatic site:bone

tag: chip antibody


title: MZM0403som_GATCAG_L001_R1_001


title: Input control in Lgr5+Tspan8hi rep2


title: neutralizer controller 2

description:
NT2
raw reads indexing length: 8


title: neutralizer controller 1

description:
NT1
raw reads indexing length: 8


title: non-neutralizer controller 4

description:
NN4
raw reads indexing length: 8

value: non-neutralizer controllers


title: JM97_3_TGACCA_L006_R1_001

source_name: Liver

value: mzm

value: Liver

value: 5 weeks


title: JM98_3_ACAGTG_L008_R1_001


title: input DNA

source_name: input DNA


title: JM96_1_TTAGGC_L003_R1_001

source_name: Brain

value: Brain


title: JM97_1_TGACCA_L005_R1_001


title: MDA MB-231 cell line treated with anacardic acid replicate 2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
Raw sequences were mapped to the hg19 genome assembly using tophat2 v2.0.13 generating alignments in bam format, using an Ensembl gene and transcript gtf as a guide.
Mapped reads were assembled according to the Ensembl hg19.gtf file using cufflinks v2.2.1.
Cufflinks assembles were merged using cuffmerge.
Differentially expressed genes were compared in four pairwise comparisions using cuffdiff v2.2.1.  The four comparisons include: MCF-7 AnActrt treatment vs. control; MDA MB-231 AnActrt treatment vs. control; MCF-7 AnActrt treatment and MDA MB-231 AnActrt treatment vs. MCF-7 control and MDA MB-231 control; and MCF-7 AnActrt treatment and MCF-7 control vs. MDA MB-231 AnActrt treatment and MDA MB-231 control.
The resulting mapped files from cufflinks were normalized and concatenated into a single tab-delimited gene matrix file using cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing cuffnorm normalized FPKM for each sample

source_name: MDA MB-231 cell line

growth_protocol: MCF-7 and MDA-MB-231 are maintained in a base growth medium Improved Minimum Essential Medium (IMEM) containing 5% Fetal Bovine Serum (FBS) and 1% Penecillin/Streptomycin. Cells are kept in an incuabtor at 37°C containing 5% CO2 for optimal growth.

extract_protocol:
After treatment medium is removed and a total RNA isolation kit from Exiqon was used to extract both mRNA and miRNA. The kit itseld includes the binding of RNA (mRNA and miRNA) to a spin column, followed by a series of washes for purification and finally elution.
RNA libraries were prepared for sequencing using standard Illumina protocols.  The Truseq Stranded mRNA kit was used to prepare mRNA libraries from 1ug total RNA.  Libraries were confirmed on the Agilent 2100 Bioanalyzer and quantitated using the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems and the ABI7900HT real-time PCR instrument.  76 cycle single read sequencing was performed with the 500 High-output v2 (75cycle) sequencing kit on the Illumina NextSeq500 instrument.

treatment_protocol: Prior to treatment, normal growth medium is replaced with phenol red-free starvation medium containg 5% dextran coated charcoal stripped fetal bovine serum (DCC-FBS) for 48 hours. Treatment includes addition of 13.5uM or 35uM Anacardic Acid dissolved in EtOH for MCF-7 or MDA-MB-231, respectively.

value: MDA MB-231


title: JM95_5_CACCGG_L005_R1_001

source_name: Skin

value: Skin


title: MDA MB-231 cell line control replicate 2


title: MDA MB-231 cell line treated with anacardic acid replicate 1


title: JM94_5_CAACTA_L004_R1_001


title: MDA MB-231 cell line control replicate 1


title: JM91_5_CTCAGA_L005_R1_001

value: 20 weeks


title: JM88_5_CTATAC_L004_R1_001


title: MCF-7 cell line treated with anacardic acid replicate 3

source_name: MCF-7 cell line


title: MCF-7 cell line treated with anacardic acid replicate 2


title: JM87_5_CTAGCT_L003_R1_001


title: JM86_1_CTTGTA_L006_R1_001


title: JM85_3_ATGTCA_L008_R1_001


title: MCF-7 cell line control replicate 3


title: control H3K36me2_ChIPSeq

source_name: control H3K36me2_ChIPSeq


title: MCF-7 cell line treated with anacardic acid replicate 1


title: MCF-7 cell line control replicate 1


title: MCF-7 cell line control replicate 2


title: JM84_5_CGGAAT_L002_R1_001


title: JM84_1_GGCTAC_L005_R1_001


title: GFP-ESCO2-ΔB (208-212)

city: Vienna

first: Heinz

last: Ekker

address: Dr. Bohrgasse 3

country: Austria

institute: VBCF

description: single aphidicolin arrest

data_processing:
Basecalling with Illumina RTA v1.18.61.0
Demultiplexing with BamIndexDecoder vV1.03-184-g590b59e-dirty
Alignment against genome hg19 with bowtie 0.12.5 parameters " -v 2 --best --strata --tryhard   -m 1"
Peak calling using BayesPeak_1.22.0 bin size 1000bp
Genome_build: hg19
Supplementary_files_format_and_content: BED files with called peaks

source_name: Roberts syndrome (vu1199-F SV40)

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 0.2 mM glutamine, penicillin, and streptomycin.

extract_protocol:
Samples were formaldehyde-crosslinked, lysed, sonicated, presipitated, and reverse crosslinked.
Illumina sample libraries were prepared according to NEB protocol E6040

treatment_protocol: Cells were arrested in G1/S phase with aphidicolin (1.2 μg/ml) for 24 hours.

value: GFP-trap beads (Chromotek, gta-200)


title: REH

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

data_processing:
Pipeline Casava version 1.8.2 was run to produce the reads.
Sequences were mapped with tophat 2.0.4 using the hg19 genome built with refSeq hg19 annotation file (-G).
Quantification of the refSeq genes was done using the alignment files and htseq-count [http://www-huber.embl.de/users/anders/HTSeq/doc/count.html] (htseq-count -t exon -m intersection-strict -i gene_id -s no -).
DESeq was used to normalize the data and detect differentially expressed genes for each of the sample types.
In addition, Cuffdiff 2 was run with the above tophat alignment files and the refSeq hg19 annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq.txt is a tab delimited file containing htseq gene quantification counts, DESeq normalized quantification counts and DESeq output containing mean expression,  fold changes and p value.
Supplementary_files_format_and_content: Cuffdiff2_gene_exp.diff.txt is one of the outputs of Cuffdiff2, it  is a tab delimited file  containing the results of differential expression testing between the samples, including  FPKM counts , fold change and p values.

source_name: cell line REH

growth_protocol: Regular RPMI medium with 10% fetal bovine serum

extract_protocol:
Total RNA and was isolated using TRI Reagent®, according to manufacturer instructions.
For each RNA sample, we prepared Illumina mRNA-seq libraries using the TruSeq RNA kit (version 1, rev A), using 1 μg of total RNA

treatment_protocol: Grown to sub confluency

tag: cell attribute

value: Precursor ALL lacking the t(4;11) abnormality

value: REH


title: JM82_3_AGTCAA_L007_R1_001


title: JM83_3_GTGGCC_L008_R1_001

value: 27 weeks


title: JM79_3_CTTGTA_L005_R1_001


title: JM79_1_TAGCTT_L003_R1_001


title: JM79_5_CCAACA_L001_R1_001


title: JM75_3_GGCTAC_L004_R1_001


title: JM74_3_GTGAAA_L006_R1_001


title: JM72_5_TACAGC_L006_R1_001


title: JM72_3_GTCCGC_L007_R1_001


title: CC-HL-E105-Wt-Mm-Rep1 part2

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description: Captured genomic DNA from 3C library

data_processing:
Frag profiles: Paired-end sequencing data from Capture-C experiments was mapped and cleaned from invalid di-tags and duplicates using the HiCUP pipeline v0.5.8 (Wingett et al. 2015) and Bowtie 2.2.6 (Langmead and Salzberg 2012). All sequencing data was mapped to mouse reference genome mm9. Viewpoint-specific contact profiles were generated from BAM files with custom Java code using htsjdk 1.139 (https://samtools.github.io/htsjdk/) for the processing of BAM files. A di-tag was considered only if one mate was located in an enriched viewpoint region while the other mapped to the non-enriched part of the genome. Contact profiles were generated for each viewpoint by counting the number reads per restriction fragment. Count data was binned into a regular grid of 1 kb intervals centered around the middle of the corresponding viewpoint region. The count value of each restriction fragment was assigned to the bin, which contains the fragment center.
Smoothed profiles: count data per fragments was combined from both replicates, binned, smoothed with a running window of 3 and 5 bins. To make contact profiles with different read densities comparable, each profile was scaled by the total contact count on the chromosome of the viewpoint (Sum of cis contacts/1000).
Peak calling: Scaled contact profiles were pooled across all samples and viewpoints to generate a simple, empirical background model, which incorporates the distance dependent decay of the contact frequency. The positioning of the grid around viewpoint center allows an overlay of all profiles by aligning their centers. Now, each 1 kb bin can be described by its offset relative to the viewpoint center and has the contact information from 6244 profiles (7 tissues/stages × 446 viewpoints × 2 replicates). The 99th and 95th percentile of the empirical distribution were used to derive an individual threshold for each bin. A spline function was used to smooth the resulting threshold line. To avoid the calling of spurious interactions due to a lower profile density at locations distant from the viewpoint, the threshold was set constant for all regions more than 0.5 Mb away from the viewpoint. A bin was selected as candidate region, when the contact value exceeds the threshold in both replicates. Within the candidate region the maximum value from the merged profile was used to determine the peak center. A region +-10 kb around the selected peak was excluded from the candidate region to suppress peaks nearby. The selection of maxima and exclusion of sub-peaks was repeated until no further candidates were left.
Enhancer calling: Putative enhancers were called based on the combination of three thresholds: the 95th percentile of the empirical background for the interaction strength, the 99th percentile for H3K27Ac and 95th percentile for H3K4me1. Percentiles of the histone modifications were computed based on genome wide distribution of mapped reads within 5 kb windows.
Genome_build: mm9
Supplementary_files_format_and_content: Bed and bedgraph files were generated in each sample for 446 different viewpoints and packed for each analysis into one archive.

source_name: Embryonic Limb Bud

growth_protocol: Limb bud sand midbrain were micro-dissected from mouse embryos

extract_protocol:
The 3C library was prepared according to (Hagege et al. 2007), i.e. crosslinking, cell lysis, DpnII digestion, ligation and de-crosslinking. Re-ligated products were then sheared using a covaris sonicator (Duty cycle: 10%, Intensity:5, Cycles per Burst: 200, Time: 6 cycles of 60 sec each, Set Mode: Frequency sweeping, Temperature: 4° to 7°C).
Adaptors were added to the sheared DNA and amplified. The adapted-ligated library was then hybridized to the custom-designed sure-select beads indexed for sequencing using an indexing PCR following Agilent instructions.

value: Hindlimb

tag: genotype

value: wild type


title: JM73_5_TCATTC_L005_R1_001


title: CC-HL-E105-Wt-Mm-Rep1 part1

description: Captured genomic DNA from 3C library


title: JM72_1_CCGTCC_L002_R1_001


title: JM69_3_GTAGAG_L005_R1_001


title: 60 minutes

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
Reads were normalized by dividing the read count of each gene by the total number of reads per cell and multiplying by 10000
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited normalized gene counts per cell
Supplementary_files_format_and_content: P1_Cold_*.txt: Files contain the barcodes of cells that correspond to the different cell types / clusters from cold active protease disassociated kidney tissue.

source_name: kidney

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Post natal day 1


title: JM62_1_AGTTCC_L008_R1_001


title: JM62_5_TAATCG_L002_R1_001


title: 15 minutes


title: JM66_1_ATGTCA_L001_R1_001


title: JM77_1_GTTTCG_L008_R1_001

value: 32 weeks


title: Cold active protease


title: JM84_3_AGTTCC_L006_R1_001


title: JM75_1_GATCAG_L002_R1_001


title: JM61_3_CCGTCC_L004_R1_001


title: SH11 RNA-Seq

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

description:
SH11 RNA-Seq Eμ-Myc lymphoma #1.2 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.2 JQ1 2 hours_2

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using TopHat/bowtie2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with HTSeq-Count from HTSeq using transcript annotation from Ensembl Release 73
The Voom-LIMMA workflow was used to normalize data and compute statistical significance of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing transcript counts for each Sample

source_name: Eμ-Myc lymphoma #1.2 cell line

growth_protocol: Cell lines grown in high-glucose Dulbecco's modified Eagle medium supplemented with 10% fetal calf serum, penicillin (100 U/mL), streptomycin (100mg/mL), 0.1mM L-Asparagine, and 50μM 2-mercaptoethanol

extract_protocol:
RNA was extracted using the Nucleospin® RNA extraction kit (Macherey-Nagel, Bethlehem, PA) as per the manufacturer's instructions.
cDNA libraries were prepared and then processed using TruSeq RNA library Prep Kit (Illumina)

treatment_protocol: Early passage cells were cultured in vitro in the presence of 250nM JQ1, or DMSO vehicle, for 2 hours

value: E<mu>-Myc lymphoma #1.2 cell line

tag: treatment

value: JQ1 treated (250nM)

tag: treatment period

value: 2 hours


title: JM55_5_GACGAC_L001_R1_001

value: mzm


title: JM66_5_TATAAT_L003_R1_001


title: SH10 RNA-Seq

description:
SH10 RNA-Seq Eμ-Myc lymphoma #1.2 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.2 DMSO 2 hours_2

value: DMSO vehicle treated


title: JM52_1_AGTCAA_L007_R1_001

value: Brain


title: JM50_1_GTGGCC_L007_R1_001


title: SH7 RNA-Seq

description:
SH7 RNA-Seq Eμ-Myc lymphoma #1.1 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.1 DMSO 2 hours_2

source_name: Eμ-Myc lymphoma #1.1 cell line

value: E<mu>-Myc lymphoma #1.1 cell line


title: SH1 RNA-Seq

description:
SH1 RNA-Seq Eμ-Myc lymphoma #1.1 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.1 DMSO 2 hours_1


title: 3Eu_Myc_exp1_Myc_JQ1_S42 ChIP-Seq

description: 3Eu_Myc_exp1_Myc_JQ1_S42 ChIP-Seq Eμ-Myc lymphoma #1 cell line

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (GRCm38/mm10) using bowtie (2.2.3)
Peak-calling was performed using MACS2.0.10
Genome_build: mm10
Supplementary_files_format_and_content: peaks files

source_name: Eμ-Myc lymphoma #1 cell line

growth_protocol: Cell lines were cultured in supplemented DMEM based media

extract_protocol:
Lysate were isolated from formaldehyde cross-linked cells and sonicated to release the chromatin, then immunoprecipitated using relevant antibodies.
For BRD4, RNA Polymerase II, IRF1, STAT1, H3K27Ac ChIP-Seq, indexed libraries were prepared using KAPA Hyper Prep Kit for Illumina platforms (Kapa Biosystems) and SeqCap Adapter Kit (Roche). For MYC ChIP-Seq, indexed libraries were prepared using Nugen Ovation Ultralow system (v2, Nugen protocol M01379v3).

treatment_protocol: Cell lines were cultured in the presence of 1000nM JQ1, or DMSO vehicle control. AT-3 were additionally grown in the presence or absence of recombinant mouse interferon-gamma (1ng/mL)

value: E<mu>-Myc lymphoma #1 cell line

tag: culture media

value: High-glucose Dulbecco's modified Eagle medium supplemented with 10% fetal calf serum, penicillin (100 U/mL), streptomycin (100mg/mL), 0.1mM L-Asparagine, and 50μM 2-mercaptoethanol

value: anti-MYC (ab32072, Abcam)


title: SH5 RNA-Seq

description:
SH5 RNA-Seq Eμ-Myc lymphoma #1.2 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.2 JQ1 2 hours_1


title: JM29_1_GTCCGC_L005_R1_001


title: SH2 RNA-Seq

description:
SH2 RNA-Seq Eμ-Myc lymphoma #1.1 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.1 JQ1 2 hours_1


title: JM27_1_GTAGAG_L003_R1_001


title: 2Eu_Myc_exp1_Myc_Veh_S41 ChIP-Seq

description: 2Eu_Myc_exp1_Myc_Veh_S41 ChIP-Seq Eμ-Myc lymphoma #1 cell line

value: DMSO vehicle


title: JM24_5_CGATGT_L005_R1_001

value: Skin

value: 39 weeks


title: JM1_5_TCCCGA_L006_R1_001


title: JM18_5_ATCACG_L005_R1_001


title: JM1_3_GTTTCG_L004_R1_001

value: Liver


title: SH4 RNA-Seq

description:
SH4 RNA-Seq Eμ-Myc lymphoma #1.2 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.2 DMSO 2 hours_1


title: JM1_1_CGTACG_L001_R1_001


title: EuMYC-Pol2-JQ1-2h ChIP-Seq

description: EuMYC-Pol2-JQ1-2h ChIP-Seq Eμ-Myc lymphoma #1 cell line

value: anti-RNA polymerase II (CTD4H8, Millipore)


title: 1Eu_Myc_exp1_input_S40 ChIP-Seq

description: 1Eu_Myc_exp1_input_S40 ChIP-Seq Eμ-Myc lymphoma #1 cell line


title: JM18_3_ACTGAT_L008_R1_001


title: JM18_1_ATCACG_L005_R1_001


title: JM15_5_TCGGCA_L006_R1_001


title: EuMYC-BRD4-Abcam-UT ChIP-Seq

description: EuMYC-BRD4-Abcam-UT ChIP-Seq Eμ-Myc lymphoma #1 cell line

value: anti-Brd4 (ab128874, Abcam)


title: EuMYC-Input ChIP-Seq

description: EuMYC-Input ChIP-Seq Eμ-Myc lymphoma #1 cell line


title: EuMYC-Pol2-UT ChIP-Seq

description: EuMYC-Pol2-UT ChIP-Seq Eμ-Myc lymphoma #1 cell line


title: EuMYC-BRD4-Abcam-JQ1-2h ChIP-Seq

description: EuMYC-BRD4-Abcam-JQ1-2h ChIP-Seq Eμ-Myc lymphoma #1 cell line


title: JM15_3_GGTAGC_L006_R1_001


title: 30 minutes

value: Post natal day 1


title: SH-AT3-8 3'RNA-Seq

description:
SH-AT3-8 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-8

data_processing:
Illumina Casava 1.8.2 software used for basecalling and low-quality reads (Q<30) were removed.
The RNA sequencing reads were trimmed at the 5' end using Cutadapt(v1.9)
Reads were mapped to the reference genome (hg19 for human and mm10 for mouse) using HISAT2.
Read Counting was performed usding featureCounts part of the subread v1.5.0 software package
Differential gene expression analysis was performed using Voom-LIMMA
Genome_build: hg19 for human (ALF1 cell line) and mm10 for mouse (AT-3 cell line)
Supplementary_files_format_and_content: tab-delimited text files containing transcript counts for each Sample

molecule: polyA RNA

source_name: AT-3 cell line

growth_protocol: AT-3 cells were grown in supplemented DMEM-based media (supplemented with 10% FCS, 100U/mL penicillin, 100mg/mL streptomycin). ALF1 cells were grown in supplemented Gibco RPMI-1640-based media (supplemented with 10% FCS, 100U/mL penicillin, 100mg/mL streptomycin).

extract_protocol:
RNA was extracted using the Nucleospin® RNA extraction kit (Macherey-Nagel, Bethlehem, PA) as per the manufacturer's instructions.
The QuantSeq 3'mRNA-Seq Library Prep Kit for Illumina (Lexogen) were used to generate libraries as per the manufacturers instructions, which were sequenced on the NextSeq (Illumina; 75bp PE).

treatment_protocol: Cell lines were cultured in vitro with 1000nM JQ1, 1ng/mL recombinant mouse (AT-3) or human (ALF1) interferon gamma, the combination of JQ1 and interferon-gamma, or DMSO vehicle control

value: AT-3 mammary tumor cell line

value: 1ng/mL recombinant mouse IFN-γ+1000nM JQ1


title: SH8 RNA-Seq

description:
SH8 RNA-Seq Eμ-Myc lymphoma #1.1 cell line
Hogg_EuMyc_RNAseq_countsmatrix.txt
Eu-Myc #1.1 JQ1 2 hours_2

value: JQ1 treated (250nM)

value: 2 hours


title: JM13_5_TCGAAG_L004_R1_001

value: mzm


title: JM31_1_GTGAAA_L006_R1_001

value: Brain

value: 32 weeks


title: SH-AT3-7 3'RNA-Seq

description:
SH-AT3-7 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-7

value: 1ng/mL recombinant mouse IFN-γ


title: JM12_3_CGTACG_L005_R1_001


title: JM15_1_GGTAGC_L003_R1_001


title: JM13_1_GAGTGG_L002_R1_001


title: SH-AT3-6 3'RNA-Seq

description:
SH-AT3-6 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-6


title: SH-AT3-5 3'RNA-Seq

description:
SH-AT3-5 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-5


title: SH-AT3-3 3'RNA-Seq

description:
SH-AT3-3 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-3


title: JM116_5_CATTTT_L006_R1_001

value: 12 weeks


title: JM110_5_CAGGCG_L003_R1_001


title: SH-AT3-2 3'RNA-Seq

description:
SH-AT3-2 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-2


title: JM115_3_TAGCTT_L008_R1_001


title: JM113_1_ACTTGA_L001_R1_001


title: SH-AT3-1 3'RNA-Seq

description:
SH-AT3-1 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-1


title: Sample_6_MMH6_WITHdox_rep3

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Removed reads with at least one "N" in the sequence from the raw FASTQ files.
Aligned FASTQ files using tophat-2.0.12 and bowtie2-2.2.3.
Counted gene hits using Bioconductor's summerizeOverlaps() function with "Intersection-Strict" mode.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts in CSV format annotated by UCSC known gene track on mm10.

source_name: cultured mouse myoblasts (C2C12)

growth_protocol: C2C12, mouse myoblasts (ATCC® CRL-1772™), were grown in DMEM (Gibco/Life Technologies) supplemented with 10% fetal bovine serum (Thermo Scientific) and 1% penicillin/streptomycin (Life Technologies) and 2.6ug/ml puromycin to select for cells carrying the transgene indicated.

extract_protocol:
Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).
RNA-seq libraries were pooled (14-plex) and clustered onto two flow cell lanes.

treatment_protocol: 2ug/ml doxycycline treatment for 36 hours

tag: genotype/variarion

value: DOXYCYCLINE


title: SH-AT3-4 3'RNA-Seq

description:
SH-AT3-4 3'RNA-Seq AT-3 cell line
Hogg_AT3_3mRNAseq_countsmatrix.txt
SH-AT3-4


title: Sample_5_MMH6_WITHdox_rep2


title: JM106_3_ACTTGA_L007_R1_001


title: JM105_5_CATGGC_L004_R1_001


title: JM107_1_GCCAAT_L007_R1_001


title: C2C12_MMH6_HA

data_processing:
Filtered out reads containing at least 'N' in sequence.
Aligned reads using BWA on genome build mm10.
Filtered low-quality reads (mapq score < 15).
Performed peak calling using MACS2 allowing 3 mismatch with mininum FDR=0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak

extract_protocol:
Briefly, ~6x10e7 cells were fixed in 1% formaldehyde for 11 minutes, quenched with glycine, lysed, and then sonicated to generate final DNA fragments of 150–600 bp. The soluble chromatin was diluted 1:10 and pre-cleared with protein A:G beads for 2 hours. Remaining chromatin was incubated with primary antibody overnight, then protein A:G beads were added for an additional 2 hours. Beads were washed and then de-crosslinked overnight.
ChIP-seq libraries were prepared from IP samples using an Ovation Ultralow Library System kit (NuGEN Technologies., San Carlos, CA, USA).
ChIP-seq libraries were pooled (12-plex) and clustered onto two flow cell lanes.

treatment_protocol: induced with 2ug/ml doxycycline treatment for 18 hours or uninduced for 18 hours, as indicated

value: anti-HA


title: Sample_2_MMH6_nodox_rep2


title: JM105_3_CAGATC_L005_R1_001


title: Sample_4_MMH6_WITHdox_rep1


title: JM107_3_GATCAG_L006_R1_001


title: JM105_1_ACAGTG_L006_R1_001


title: JM109_1_CAGATC_L008_R1_001


title: JM13_3_GAGTGG_L007_R1_001


title: Sample_3_MMH6_nodox_rep3


title: JM104_3_GCCAAT_L004_R1_001


title: wildtype spleen 4

city: Dallas

first: Theo

last: Ross

state: TX

address: 5323 Harry Hines Blvd.

department: Internal Medicine-Hem/Onc

institute: UT Southwestern Medical Center

description:
Sample name: X_17579_sp
expression data from spleens of mice 2-3 mo. of age

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
RNAseq reads aligned to mm10 using TopHat v2.0.12
Raw read counts generated using featureCounts (package subread v1.4.6)
Normalized read counts generated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt files that include raw and normalized read counts for each sample, normalized counts ar CPM i.e counts per million

source_name: Brca1+/+ spleen 4

growth_protocol: mice were fed normal diet per protocol specifications and housed in institutional animal resource facilities in specific patho-free conditions and were monitored regularly for evidence of disease and abnormal peripheral blood cell counts.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: 2-3 months


title: wildtype spleen 3

description:
Sample name: X_17365_sp
expression data from spleens of mice 2-3 mo. of age

source_name: Brca1+/+ spleen 3


title: JM109_5_CACTCA_L002_R1_001

value: Skin


title: JM104_5_CACGAT_L001_R1_001


title: C2C12_MMH6_488_489

value: MO488, MO489 (anti-hDUX4)


title: wildtype spleen 2

description:
Sample name: X_17364_sp
expression data from spleens of mice 2-3 mo. of age

source_name: Brca1+/+ spleen 2


title: mutant spleen 3

description:
Sample name: X_17050_sp
expression data from spleens of mice 2-3 mo. of age

source_name: Brca1∆/∆ enlarged spleen 3


title: JM103_3_TTAGGC_L007_R1_001

source_name: Liver

value: Liver

value: 5 weeks


title: JM103_1_CGATGT_L002_R1_001

source_name: Brain


title: JM102_5_ATTCCT_L002_R1_001

source_name: Skin


title: mutant spleen 2

description:
Sample name: X_16634_sp
expression data from spleens of mice 2-3 mo. of age

source_name: Brca1∆/∆ enlarged spleen 2


title: wildtype spleen 1

description:
Sample name: X_17363_sp
expression data from spleens of mice 2-3 mo. of age

source_name: Brca1+/+ spleen 1


title: JM101_3_CGATGT_L005_R1_001


title: Sample_mDUX_DOXY_IgG

description: Sample_mDUX_DOXY_A19:Sample_mDUX_DOXY_IgG_peaks.xls

data_processing:
Filtered out reads containing at least 'N' in sequence and trimed the as soon as 2 of 5 nucleotides has quality encoding less than “4” (phred score 20). Dropped reads that are less than 36nt.
Aligned reads using Subread on genome build mm10.
Filtered low-quality reads (mapq score < 15).
Performed peak calling using MACS2 allowing 3 mismatch with mininum FDR=0.01.
Genome_build: mm10

tag: genotype/variation

value: mDUX codon-altered

value: anti-IgG


title: Sample_2-hDUX4-WITHdoxy-MO

description: Sample_2-hDUX4-WITHdoxy-MO:Sample_1-hDUX4-WITHdoxy-HA_peaks.xls

value: HDUX4 codon-altered


title: Sample_1_MMH6_nodox_rep1


title: Sample_mDUX_DOXY_A19

value: A-19 (anti-mDUX)


title: JG73_1_CGTACG_L008_R1_001

value: grz

value: 14 weeks


title: JG7_5_GTCCGC_L002_R1_001


title: mutant spleen 1

description:
Sample name: X_15341_sp
expression data from spleens of mice 2-3 mo. of age

source_name: Brca1∆/∆ enlarged spleen 1


title: JM100_5_ATGAGC_L001_R1_001

value: mzm


title: Sample_mDUX_DOXY_S20

description: Sample_mDUX_DOXY_S20:Sample_mDUX_DOXY_IgG_peaks.xls

value: S-20 (anti-mDUX)


title: JM101_1_ATCACG_L001_R1_001

value: Brain


title: Sample_1-hDUX4-WITHdoxy-HA

value: DOXYCYCLINE

tag: anitbody


title: JM100_3_ATCACG_L004_R1_001

tag: tissue


title: JG72_1_GTTTCG_L007_R1_001


title: JG73_3_GTTTCG_L008_R1_001


title: JM103_5_CAAAAG_L003_R1_001


title: Sample_C2C12_mDUX_36h_15B_NODOX2

value: NO DOXYCYCLINE


title: JG71_3_ACTGAT_L004_R1_001


title: Sample_C2C12_mDUX_36h_15B_DOX3


title: JG70_5_ACTGAT_L005_R1_001


title: JG70_3_GGTAGC_L005_R1_001


title: JG70_1_ACTGAT_L007_R1_001


title: Sample_C2C12_mDUX_36h_15B_DOX2


title: Sample_C2C12_mDUX_36h_15B_NODOX3


title: Sample_C2C12_mDUX_36h_15B_DOX1


title: Sample_C2C12_mDUX_36h_15B_NODOX1


title: Sample_C2C12_Luc2A_36h_NODOX2

value: Luciferase


title: JG69_5_GGTAGC_L004_R1_001


title: JG69_1_GGTAGC_L002_R1_001


title: JG68_3_GAGTGG_L006_R1_001


title: Sample_C2C12_Luc2A_36h_DOX3


title: Sample_C2C12_Luc2A_36h_NODOX1


title: JG68_5_GAGTGG_L003_R1_001


title: JG67_5_CGTACG_L002_R1_001


title: Sample_C2C12_Luc2A_36h_DOX2


title: Sample_C2C12_Luc2A_36h_DOX1


title: Sample_C2C12_HDUX4_36h_9_NODOX2


title: JG66_1_GAGTGG_L001_R1_001


title: Sample_C2C12_HDUX4_36h_9_NODOX1


title: Sample_C2C12_HDUX4_36h_9_DOX3


title: JG67_3_CGTACG_L007_R1_001


title: JG65_5_TAGCTT_L005_R1_001

value: 7 weeks


title: Sample_C2C12_HDUX4_36h_9_DOX2


title: JG66_5_GTTTCG_L001_R1_001

value: Skin


title: Sample_C2C12_HDUX4_36h_9_DOX1


title: Healthy Donor 6 CD34+ non-targeting shRNA control RNA-seq

city: Bethesda

first: Jeffery

middle: L.

last: Miller

state: MD

address: 10 Center Drive Room 9N311

department: NIDDK

institute: NIH

data_processing:
The data were processed using RTA version 1.13.48 and CASAVA 1.8.2, The sequence reads were aligned to hg19 reference build using  Illumina’s Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) mapping algorithm.
Bam files were converted to Fastq using SamtoFastq.
FASTQ files were loaded into the public main Galaxy server (https://usegalaxy.org/) processed with FASTQ Masker (Galaxy Version 1.0.0) and loaded into TopHat (Galaxy Version 2.1.0) was then used as a gapped-read mapper to align RNA-Seq reads against the hg19 genome with Bowtie to generate the FPKM value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample generated using Galaxy

source_name: CD34+ cells transduced with Sigma non-targeting shRNA negative control (SHC002V)

growth_protocol: Human adult CD34+ cells were cultured in 21 days three phase serum free media as described in previous publication PMID: 23798711.

extract_protocol:
Qiagen miRNAeasy Kit
GLOBINclear Kit (Life Technologies), RiboZero GOLD (Illumina, San Diego, CA) then paired-end sequenced.

treatment_protocol: Briefly, cells were transduced with Sigma non-targeting shRNA negative control (SHC002V) Lentiviral particles on culture day 3.  After 24 hours, puromycin was added for 3 more days than transferred into phase 2 medium without puromycin for 7 more days as described in previouls publication PMID: 23798711.

value: CD34+ Cells

tag: time-point

value: Day 14 Culture


title: JG6_5_CCGTCC_L001_R1_001

value: 12 weeks


title: JG65_1_TAGCTT_L008_R1_001


title: JG64_5_GATCAG_L004_R1_001


title: Sample_C2C12_Luc2A_36h_NODOX3


title: Healthy Donor 4 CD34+ non-targeting shRNA control RNA-seq


title: 281

city: Boston

first: Chia-Ling

last: Wu

state: MA

address: 700Albany St

department: Whitaker Cardiovascular Institute

institute: Boston University

description:
Gastrocnemius muscle without muscle hypertrophy
281_L1.D704_1.fastq.gz
281_L1.D704_2.fastq.gz

data_processing:
To prepare reads for alignment, sequence adaptors were removed from sequences using Fastq-Mcf (code.google.com/p/ea-utils/wiki/FastqMcf).
Sequence reads were mapped to mm10 transcriptome using the “RSEM-calculate-expression” script in RNAseq by Expectation Maximization (RSEM) v1.1.13 program. For all the unaligned reads, they were aligned and annotated to the full genome using the alignment software BWA.
All 8 samples were normalized by upper quartile normalization. Differential expression analysis was performed using edge-R algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet of the normalized gene expression value of all 8 samples

source_name: Gastrocnemius

growth_protocol: Skeletal muscle-specific conditional Akt1 transgenic mice (DTG) were generated by mating of 1256[3Emut]Mck-rtTA [1] and TRE-myrAkt1 [2] transgenic mice as previously described [3].  All the mice were genotyped by PCR from tail DNA.  Mice were provided with chow and water ad libitum and housed in pairs on a fixed 12-h light/dark cycle in the Laboratory Animal Science Center at Boston University School of Medicine.

extract_protocol:
Mice were starved overnight before the day of sacrificing. Bilateral gastrocnemius muscles collected from anesthetized DTG and Mck-rtTA mice were weighed, snapped frozen in liquid nitrogen, and stored at -80°C until analysis. Total RNA was isolated using TRIzol Reagent (15596026, Life Technologies, Grand Island, NY) according to manufacturer’s instructions followed by DNase I clean-up using Qiagen (Valencia, CA) RNeasy Mini columns.
Total RNA was sent to Expression Analysis Inc (Quntile, Morrisville, NC) for library preparation and data anlaysis. mRNA library was prepared by Illumina TrueSeq stranded mRNA sample.  Eight library preparations were loaded on two lanes of the Illumina HiSeq 2000 machines (Illumina, San Diego, CA) for paired-end 50bp sequencing using the standard Illumina mRNA-seq protocol.
poly(A+)RNA-Seq

treatment_protocol: At the age of 4-month, male DTG mice were treated with 0.5mg/ml doxycycline (AB03550, American Bioanalytical) in drinking water for 2 weeks to induce skeletal muscle-specific Akt1 overexpression.  To eliminate the effect of doxycycline water on muscle metabolism, Mck-rtTA or Tre-myrAkt1 single transgenic littermates were used as controls and treated with Dox in the same manner as DTG mice.

value: Myo L8

value: Skeletal muscle

value: 4 month old

value: Single transgenic mice (1256[3Emut]Mck-rtTA+)


title: 307

description:
Gastrocnemius muscle without muscle hypertrophy
307_L8.D712_1.fastq.gz
307_L8.D712_2.fastq.gz


title: Sample_C2C12_HDUX4_36h_9_NODOX3

value: HDUX4 codon-altered


title: JG64_1_GATCAG_L007_R1_001

data_processing:
bcl2fastq v1.8.4 used for Basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence ends and filtered by sequence size (<15) using PRINSEQ v0.20.3
Reads were mapped with the aligner segemehl with the -H 1 parameter enabled to the Nothobranchius furzeri genome published by Reichwald et al Cell 2015
Reads were counted using rnacounter with parameters -s -m raw
Genome_build: nfurzeri_genebuild_v1
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

value: grz


title: 280

description:
Gastrocnemius muscle without muscle hypertrophy
280_L8.D702_1.fastq.gz
280_L8.D702_2.fastq.gz


title: JG62_3_ATGTCA_L004_R1_001

value: Liver

value: 10 weeks


title: 253

description:
Gastrocnemius muscle hypertrophy induced by 2 weeks of Ak1 overexpression
253_L1.D705_1.fastq.gz
253_L1.D705_2.fastq.gz

value: Double transgenic mice (1256[3Emut]Mck-rtTA+, TRE-myrAkt1+ )


title: Healthy Donor 2 CD34+ non-targeting shRNA control RNA-seq


title: JG65_3_TAGCTT_L004_R1_001


title: TKI08 3'RNA-Seq

description:
TKI08 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI08

source_name: ALF1 cell line

value: ALF1 plasma cell leukaemia cell line

value: 2 hours

value: 1ng/mL recombinant human IFN-γ+1000nM JQ1


title: Healthy Donor 1 CD34+ non-targeting shRNA control RNA-seq


title: JG62_1_GGCTAC_L001_R1_001

value: Brain


title: JG61_5_GGCTAC_L001_R1_001

value: Skin


title: 306

description:
Gastrocnemius muscle hypertrophy induced by 2 weeks of Ak1 overexpression
306_L8.D711_2.fastq.gz
306_L8.D711_1.fastq.gz


title: JG60_5_ATGTCA_L005_R1_001


title: TKI07 3'RNA-Seq

description:
TKI07 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI07

value: 1ng/mL recombinant human IFN-γ


title: 282

description:
Gastrocnemius muscle hypertrophy induced by 2 weeks of Ak1 overexpression
282_L8.D701_1.fastq.gz
282_L8.D701_2.fastq.gz


title: JG60_3_AGTTCC_L005_R1_001


title: Healthy Donor 5 CD34+ non-targeting shRNA control RNA-seq

value: CD34+ Cells

value: Day 14 Culture


title: 283

description:
Gastrocnemius muscle hypertrophy induced by 2 weeks of Ak1 overexpression
283_L1.D703_1.fastq.gz
283_L1.D703_2.fastq.gz

value: Myo L8


title: TKI05 3'RNA-Seq

description:
TKI05 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI05

value: DMSO vehicle


title: Apc(D716) p53(M/M) 2

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

country: Japan

institute: kanazawa university

data_processing:
HiSeq Control Software (HCS) v2.2.38 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using StrandNGS.
RPKMs (Reads per kilobase million)  of each gene in a reference gene annotation (mm10) were calculated using StrandNGS software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: Apc(D716) p53(M/M), tumor derived organoids

extract_protocol:
Total RNA was extracted using ISOGEN (Nippon Gene) and purified using Rneasy Mini Kit (Quiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestinal tumor-derived organoids

value: 15-20 weeks

value: Apc truncation mutation at 716 and LOH, p53 homozygous missense mutation R270H


title: JG60_1_ATGTCA_L001_R1_001

extract_protocol:
The organs of the fishes were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 30 Hz for 3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed thoroughly and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000 x g at 4°C for 20 min. The supernatant was removed and the pellet was washed with 80% Ethanol twice and air dried for 10 min. The RNA was resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80°C until use.
Sequencing procedure was done using Illumina methodology [Bentley et al, 2008]. Around 1 µg of total RNA was used for library preparation (Illumina, TruSeq™ small RNA Sample Prep Kit) using the manufacturer’s description.

value: grz


title: Apc(D716) p53(M/M) 1


title: JG5_5_GTGAAA_L003_R1_001

value: 12 weeks


title: TKI03 3'RNA-Seq

description:
TKI03 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI03


title: 255

description:
Gastrocnemius muscle without muscle hypertrophy
255_L1.D706_1.fastq.gz
255_L1.D706_2.fastq.gz

value: Skeletal muscle

value: 4 month old

value: Single transgenic mice (1256[3Emut]Mck-rtTA+)


title: JG64_3_GATCAG_L005_R1_001

value: Liver

value: 7 weeks


title: Healthy Donor 3 CD34+ non-targeting shRNA control RNA-seq


title: Apc(D716) p53(flox/flox) 2

source_name: Apc(D716) p53(flox/flox), tumor derived organoids

value: Apc truncation mutation at 716 and LOH, p53 homozygous null mutation


title: TKI04 3'RNA-Seq

description:
TKI04 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI04

value: ALF1 plasma cell leukaemia cell line

value: 2 hours

value: 1ng/mL recombinant human IFN-γ+1000nM JQ1


title: Apc(D716) p53(flox/flox) 1


title: JG59_3_AGTCAA_L006_R1_001

value: 10 weeks


title: TKI01 3'RNA-Seq

description:
TKI01 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI01


title: JG59_1_AGTTCC_L008_R1_001

value: Brain


title: TKI02 3'RNA-Seq

description:
TKI02 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI02


title: JG59_5_AGTTCC_L004_R1_001

value: Skin


title: Donor 5, CD34+ RNA-seq

description: Day 14 Culture

source_name: CD34+ Cells

treatment_protocol: No Treatment

value: cord blood

tag: cell type

value: CD34+ Erythroblasts

tag: subject

value: Healthy Donor 5


title: Donor 4, CD34+ RNA-seq

description: Day 14 Culture

value: Healthy Donor 4


title: JG58_1_AGTCAA_L007_R1_001

tag: strain

value: grz


title: JG58_3_CTTGTA_L007_R1_001

tag: age


title: Donor 6, CD34+ RNA-seq

description: Day 14 Culture

value: Healthy Donor 6


title: JG58_5_AGTCAA_L003_R1_001


title: Apc(D716) p53(+/+) 1

source_name: Apc(D716) p53(+/+), tumor derived organoids

value: intestinal tumor-derived organoids

value: 15-20 weeks

value: Apc truncation mutation at 716 and LOH


title: Apc(D716) p53(+/+) 2


title: Donor 2, CD34+ RNA-seq

description: Day 14 Culture

value: Healthy Donor 2


title: JG57_5_CTTGTA_L002_R1_001


title: TKI06 3'RNA-Seq

description:
TKI06 3'RNA-Seq ALF1 cell line
Hogg_ALF1_3mRNAseq_countsmatrix.txt
TKI06


title: Donor 3, CD34+ RNA-seq

description: Day 14 Culture

value: Healthy Donor 3


title: Donor 1, CD34+ RNA-seq

description: Day 14 Culture

value: Healthy Donor 1


title: JG57_1_CTTGTA_L002_R1_001


title: Donor 6

value: Day 14 Culture


title: JG55_5_ACTTGA_L003_R1_001

value: 7 weeks


title: H1-9_L001_14

city: Medford

middle: R

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

description:
Original raw file name: H1-9_S9_L001_R1_001_0014.fastq.gz
Original raw file name: H1-9_S9_L001_R2_001_0014.fastq.gz

data_processing:
Samples were run across four lanes on 3 different flow cells and reads for each sample were generated via the Illumina HiSeq 2500 (~25,000,000 reads per replicate, totalling ~100,000,000 per sample)
Fastq files are quality checked via FastQC (v0.10.1) and possessed Phred quality scores > 30 (i.e. less than 0.1% sequencing error)
We computed the read counts per gene using the HTSeq (v0.6.1p1) Python package. For spicesome analysis counts per exon bin were calculated using the dexseq_count.py Python script available through the DEXSeq (v1.12.2) R package.  Count normalization was carried out with weighted trimmed mean of M-values (TMM) using edgeR (v3.8.6) R package. Differential gene expression and splice variant analysis was carried out using the Limma (v3.22.7) R package.
Genome_build: mm10 (transcriptome); mm9 (splicesome)
Supplementary_files_format_and_content: Tab Delimited file of read counts per gene from HTSeq
Supplementary_files_format_and_content: Tab Delimited file of read counts per exon bin fromDEXSeq

source_name: Striatum

extract_protocol:
Control C57BL/6J (B6) and heterozygous Hnrnph1 KO (H) mice at about 50 - 80 days of age were decaptitate for brain retrieval. As mentioned before, 3mm striatal punches (left and right hemispheres) were pooled per mouse, and collected tissue was immediately places into RNAlater (QIAGEN) for 24 hours. After incubation, RNA was extracted via miRNeasy Mini Kit and quality was assessed by Bioanalyzer analysis.
RNA that was deemed high quality was send to the University of Chicago Genomics Core Facility for cDNA library preparation. Libraries were prepared according to Illumina's detailed instructions accompanying the Illumina TruSeq Stranded mRNA LT (100bp; paired-end reads).  The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols

tag: sampleID

tag: lane

tag: condition

tag: Sex

value: M

tag: cage

value: control

value: striatal hemispheres


title: H1-9_L002_14

description:
Original raw file name: H1-9_S9_L002_R1_001_0014.fastq.gz
Original raw file name: H1-9_S9_L002_R2_001_0014.fastq.gz


title: H1-8_L008_09

description:
Original raw file name: H1-8_S8_L008_R1_001_0009.fastq.gz
Original raw file name: H1-8_S8_L008_R2_001_0009.fastq.gz

value: H

value: F

value: Hnrnph1 heterozygous KO


title: JG57_3_GGCTAC_L008_R1_001

value: Liver

value: 10 weeks


title: JG55_3_ACTTGA_L006_R1_001

value: grz


title: H1-9_L008_09

description:
Original raw file name: H1-9_S9_L008_R1_001_0009.fastq.gz
Original raw file name: H1-9_S9_L008_R2_001_0009.fastq.gz


title: Donor 4


title: JG55_1_ACTTGA_L002_R1_001

value: Brain


title: H1-8_L002_14

description:
Original raw file name: H1-8_S8_L002_R1_001_0014.fastq.gz
Original raw file name: H1-8_S8_L002_R2_001_0014.fastq.gz


title: H1-8_L001_14

description:
Original raw file name: H1-8_S8_L001_R1_001_0014.fastq.gz
Original raw file name: H1-8_S8_L001_R2_001_0014.fastq.gz


title: H1-8_L001_12

description:
Original raw file name: H1-8_S8_L001_R1_001_0012.fastq.gz
Original raw file name: H1-8_S8_L001_R2_001_0012.fastq.gz


title: Donor 2


title: Nan-KLF1 Input DNA

first: Kevin

middle: Robert

last: Gillinder

address: 99 Commercial Road

department: Australian Centre for Blood Diseases

institute: Monash University

data_processing:
Base calling was performed with Torrent Suite v4.0.1
[ChIP-seq]
TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4 was used to map reads to the reference genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz)
Fragments mapping to the same position on the same strand were taken to be PCR duplicates and were subsequently discarded, retaining only unique alignments with the highest MAPQ score.
ChIP-seq peaks were called with MACS (v1.4.2) using uniquely mapped ChIP and input sequence alignments.
Significant peaks identified by MACS were further filtered and ranked based on >30 fold-enrichment compared to input, and a false-discovery rate <0.1%. Peaks overlapping regions identified as RNA repeats by the Repeatmasker software were ignored, yielding lists of high-confidence peaks for each sample.
Each peak summit was subsequently annotated with the genomic context, overlapping peaks and central KLF1 binding motif.
[RNA-seq]
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -N 4, --read-gap-length 4, --read-edit-dist 4, --read-realign-edit-dist 0, -a 5, -i 50, -g 6, --coverage-search, --microexon-search, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: mapall, -v, -Y, -u, -o 2, stage1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Alignments of less than 30 nt were discarded.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between replicate groups was performed with Cuffdiff2 using default parameters. A mean FPKM cutoff of 1.0 was required in at least one sample and only differentially expressed genes (DEGs) with >2 fold-change were reported.
Genome_build: mm9
Supplementary_files_format_and_content: Nan-KLF1_Annotated_Peaks.csv.gz is a tab-delimited annotated MACS peaks file
Supplementary_files_format_and_content: KLF1_Annotated_Peaks.csv.gz is a tab-delimited annotated MACS peaks file
Supplementary_files_format_and_content: K1-ER_K1-NanER_DEGs.csv.gz reports tab-delimited FPKM values and differential gene expression analysis
Supplementary_files_format_and_content: Nan_FL_DEGs.csv.gz reports tab-delimited FPKM values and differential gene expression analysis

source_name: K1-NanER Cells

growth_protocol: Erythroid cell lines were passaged (1:5) every 2-3 days in DMEM supplemented with 10% FBS, 1% Glutamine & 1% Penicillin-Streptomycin in a standard tissue culture incubator at 37 °C with 5% CO2

extract_protocol:
ChIP was performed as described (Hodge et al. A global role for EKLF in definitive and primitive erythropoiesis. Blood 2006). Three replicates were induced with 4-OHT (or ethanol control) and incubated for 3 hours before fixation with 1% formaldehyde. Chromatin was fragmented to approximately 200-400bp by sonication (Diagenode Bioruptor® for 15 minutes cycling between 30 seconds ‘ON’ and 30 seconds ‘OFF’), pre-cleared and immunoprecipitated with protein A sepharose beads (GE Healthcare).
Sequencing libraries were generated from 3 pooled replicates using the Ion Xpress™ Plus gDNA Fragment Library Preparation Kit following the Ion ChIP-Seq Library Preparation protocol.

treatment_protocol: Cells were induced through the addition of (Z)-4-Hydroxytamoxifen at a final concentration of 200 nM for 3 h.

value: KLF1 null erythroblasts (K1)

tag: transgene

tag: chip antibody


title: H1-7_L008_09

description:
Original raw file name: H1-7_S7_L008_R1_001_0009.fastq.gz
Original raw file name: H1-7_S7_L008_R2_001_0009.fastq.gz


title: Donor 3


title: Donor 1


title: Nan-KLF1 ChIP-seq

value: KLF1 Antibody

tag: chip antibody reference

value: Perkins, A. C., Sharpe, A. H. & Orkin, S. H. Lethal beta-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF. Nature 375, 318–322 (1995).


title: H1-9_L001_12

description:
Original raw file name: H1-9_S9_L001_R1_001_0012.fastq.gz
Original raw file name: H1-9_S9_L001_R2_001_0012.fastq.gz


title: JG53_3_CAGATC_L007_R1_001


title: H1-7_L002_14

description:
Original raw file name: H1-7_S7_L002_R1_001_0014.fastq.gz
Original raw file name: H1-7_S7_L002_R2_001_0014.fastq.gz


title: Donor 6 LIN28A OE

source_name: Donor 6 LIN28A OE

extract_protocol:
Qiagen miRNAeasy Kit
RiboGold Treated and paired-end sequenced.

treatment_protocol: Briefly, cells were transduced with either Empty Vector or LIN28A-OE Lentiviral particles on culture day 3.  After 24 hours, puromycin was added for 3 more days than transferred into phase 2 medium without puromycin for 7 more days as described in previouls publication PMID: 23798711.

value: CD34+ Cells

value: overexpressing LIN28A

tag: culture


title: H1-7_L001_14

description:
Original raw file name: H1-7_S7_L001_R1_001_0014.fastq.gz
Original raw file name: H1-7_S7_L001_R2_001_0014.fastq.gz

tag: genotype/variation


title: KLF1 Input DNA

source_name: K1-ER Cells


title: JG53_1_CAGATC_L001_R1_001


title: JG48_5_GCCAAT_L001_R1_001

value: Skin


title: H1-7_L001_12

description:
Original raw file name: H1-7_S7_L001_R1_001_0012.fastq.gz
Original raw file name: H1-7_S7_L001_R2_001_0012.fastq.gz


title: H1-6_L008_09

description:
Original raw file name: H1-6_S6_L008_R1_001_0009.fastq.gz
Original raw file name: H1-6_S6_L008_R2_001_0009.fastq.gz


title: Donor 5

value: Day 14 Culture


title: KLF1 ChIP-seq


title: Donor 5 LIN28A OE

source_name: Donor 5 LIN28A OE


title: H1-6_L002_14

description:
Original raw file name: H1-6_S6_L002_R1_001_0014.fastq.gz
Original raw file name: H1-6_S6_L002_R2_001_0014.fastq.gz

value: M


title: Donor 4 LIN28A OE

source_name: Donor 4 LIN28A OE


title: JG35_5_ATCACG_L001_R1_001

source_name: Skin

value: 5 weeks


title: JG53_5_CAGATC_L002_R1_001

value: 7 weeks


title: JG48_1_GCCAAT_L008_R1_001

source_name: Brain


title: H1-6_L001_12

description:
Original raw file name: H1-6_S6_L001_R1_001_0012.fastq.gz
Original raw file name: H1-6_S6_L001_R2_001_0012.fastq.gz

value: H

value: striatal hemispheres


title: H1-5_L008_09

description:
Original raw file name: H1-5_S5_L008_R1_001_0009.fastq.gz
Original raw file name: H1-5_S5_L008_R2_001_0009.fastq.gz

value: control


title: JG48_3_GCCAAT_L008_R1_001

source_name: Liver

value: Liver


title: H1-6_L001_14

description:
Original raw file name: H1-6_S6_L001_R1_001_0014.fastq.gz
Original raw file name: H1-6_S6_L001_R2_001_0014.fastq.gz

value: Hnrnph1 heterozygous KO


title: Donor 2 LIN28A OE

source_name: Donor 2 LIN28A OE


title: H1-5_L002_14

description:
Original raw file name: H1-5_S5_L002_R1_001_0014.fastq.gz
Original raw file name: H1-5_S5_L002_R2_001_0014.fastq.gz


title: Donor 1 LIN28A OE

source_name: Donor 1 LIN28A OE


title: JG35_1_TTAGGC_L001_R1_001

value: grz


title: Donor 6 Control

source_name: Donor 6 Control


title: JG25_5_CGATGT_L002_R1_001


title: JG25_3_CGATGT_L007_R1_001


title: H1-5_L001_14

description:
Original raw file name: H1-5_S5_L001_R1_001_0014.fastq.gz
Original raw file name: H1-5_S5_L001_R2_001_0014.fastq.gz


title: Donor 5 Control

source_name: Donor 5 Control


title: Donor 3 Control

source_name: Donor 3 Control


title: Donor 3 LIN28A OE

source_name: Donor 3 LIN28A OE


title: Donor 4 Control

source_name: Donor 4 Control


title: Donor 1 Control

source_name: Donor 1 Control


title: Donor 2 Control

source_name: Donor 2 Control


title: H1-5_L001_12

description:
Original raw file name: H1-5_S5_L001_R1_001_0012.fastq.gz
Original raw file name: H1-5_S5_L001_R2_001_0012.fastq.gz

source_name: Striatum


title: SC6

city: ROME

first: Claudio

last: Talora

address: Viale Regina ELENA 291

department: Molecular Medicine

country: Italy

institute: Sapienza University of ROME

data_processing:
Illumina Casava1.8.4 software used for basecalling
Sequenced reads were first analyzed with the FastQC tool and then trimmed for adaptor sequence removal using TrimGalore tool, with  a stringency value of 4 and minimum length of 20.
Mapping of reads to reference genome (hg19) was performed using STAR (version 2.3.0e). Only reads mapping uniquely on the genome were used for downstream anlysis.
Raw read counts were created using HTSeq with Ensembl GTF annotation. Only reads overlapping exon-features were counted. All reads mapping to features with the same identifier were summed. The "gene"-attribute was used as feature identifier. Only  genes with at least one count per million in at least three samples were kept for further analysis.
The edgeR package was used for Trimmed Mean of M-values (TMM) normalization and to compare expression levels of genes between lesional (SC2,SC4,SC6) and non-lesional (SC1,SC3,SC5) skin samples. We obtained fold-changes, p-values and adjusted p-values, after Benjamini-Hochberg correction for multiple testing.
Genome_build: hg19
Supplementary_files_format_and_content: A matrix table, tab-delimited text file, contains: Accession (the Ensembl Gene ID) and the raw read counts for each sample.

source_name: skin

extract_protocol:
Primary human keratinocytes were established from 4-mm punch biopsies derived from non-lesional and lesional skin of patients with Hailey-Hailey disease. Cells were maintained in modified low calcium medium (Clonetics; Cambrex Bio Science, Walkersville, MD, U.S.A.). At passages 2 cell were used for study purposes. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lesioanl

tag: diagnosis

value: Hailey-Hailey disease

value: skin

tag: genotype/atp2c1 mut*


title: JG23_3_ATCACG_L008_R1_001

last: Groth

institute: Leibniz Institute on Aging - FLI

tag: tissue


title: H1-4_L001_14

description:
Original raw file name: H1-4_S4_L001_R1_001_0014.fastq.gz
Original raw file name: H1-4_S4_L001_R2_001_0014.fastq.gz

value: F


title: JG25_1_CGATGT_L008_R1_001

value: Brain


title: H1-4_L001_12

description:
Original raw file name: H1-4_S4_L001_R1_001_0012.fastq.gz
Original raw file name: H1-4_S4_L001_R2_001_0012.fastq.gz


title: JG21_5_TTAGGC_L003_R1_001


title: JG35_3_TTAGGC_L006_R1_001


title: H1-4_L002_14

description:
Original raw file name: H1-4_S4_L002_R1_001_0014.fastq.gz
Original raw file name: H1-4_S4_L002_R2_001_0014.fastq.gz


title: JG23_1_ATCACG_L007_R1_001


title: H1-4_L008_09

description:
Original raw file name: H1-4_S4_L008_R1_001_0009.fastq.gz
Original raw file name: H1-4_S4_L008_R2_001_0009.fastq.gz


title: H1-3_L001_12

description:
Original raw file name: H1-3_S3_L001_R1_001_0012.fastq.gz
Original raw file name: H1-3_S3_L001_R2_001_0012.fastq.gz


title: JG21_1_TGACCA_L002_R1_001


title: SC4

value: lesional


title: JG20_1_ACAGTG_L007_R1_001


title: JG19_5_ACAGTG_L005_R1_001

value: Skin


title: SC1

value: non-lesional


title: H1-3_L001_14

description:
Original raw file name: H1-3_S3_L001_R1_001_0014.fastq.gz
Original raw file name: H1-3_S3_L001_R2_001_0014.fastq.gz


title: SC2


title: JG18_5_TGACCA_L004_R1_001


title: JG22_3_TGACCA_L005_R1_001


title: H1-2_L008_09

description:
Original raw file name: H1-2_S2_L008_R1_001_0009.fastq.gz
Original raw file name: H1-2_S2_L008_R2_001_0009.fastq.gz

value: M


title: s_N_PLUS_L_3

city: New York City

first: Carlos

last: Carmona-Fontaine

address: 31 Washigton Place

institute: New York University

data_processing:
rnaStar was used to map reads
BWA was used to re-map unmaped reads
HTSeq-counts was then used to generate count matrix
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file were each column represents one of the samples. Headers included

source_name: BMDMs

extract_protocol:
poly(A) RNA was isolated using Dynabeads mRNA DIRECT Micro Kit
Library preparation was performed according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies), with 16 cycles of PCR.
Samples were barcoded, template-positive Ion PI Ion Sphere Particles (ISPs) were prepared using the ion one touch system II and Ion PI Template OT2 200kit v2 Kit (Life Technologies). Enriched particles were sequenced on a Proton sequencing system using  200bp version 2 chemistry. An average of 40  million reads per sample were generated.

tag: cell type

value: bone marrow-derived macrophages

tag: passages

value: Primary culture (day 7)

tag: genetic background

tag: incubation

value: Normoxia

tag: treatment

value: 25mM NaLactate


title: SC5


title: JG17_3_ACAGTG_L004_R1_001

city: Jena

first: Marco

address: Beutenbergstraße 11

tag: strain

tag: age

value: 5 weeks


title: H1-3_L008_09

description:
Original raw file name: H1-3_S3_L008_R1_001_0009.fastq.gz
Original raw file name: H1-3_S3_L008_R2_001_0009.fastq.gz

tag: sampleID

tag: lane

tag: condition

tag: Sex

value: control

value: striatal hemispheres


title: H1-3_L002_14

description:
Original raw file name: H1-3_S3_L002_R1_001_0014.fastq.gz
Original raw file name: H1-3_S3_L002_R2_001_0014.fastq.gz

tag: cage


title: fat body IP, rep1

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description:
PolyA mRNA
Each biological replicate is a pool of 4 technical replicates.
Processed data file: FPKM_qval.txt

data_processing:
Reads were aligned with TopHat v2.0.6 to the reference genome BDGP 5.69.
Gene-level expression values were estimated using Cufflinks v2.0.2.
For pair-wise differential expression tests, q-values were calculated by Cuffdiff v2.0.2.
Genome_build: BDGP 5.69 (Release 5)
Supplementary_files_format_and_content: FPKM_qval.txt: Tab-delimited text file containing FPKM and q-values.

organism: Drosophila melanogaster

source_name: adult head fat body, IP

extract_protocol:
Ribosome affinity purification was adapted from Heiman et al., 2008 (PMID 19013281). Briefly, 1000 fly heads were homogenized with dounce homogenizer in ice-cold ribosome extraction buffer (10 mM HEPES pH 7.6,
150 mM KCl,
5 mM, MgCl2,
protease inhibitor cocktail (Roche), 0.5 mM DTT, 100 μg/ml cycloheximide (CHX) and 100 U/ml RNasIn (Promega)). After removing nuclei by centrifugation (2000G 10 min), ribosomes were released by adding NP-40 (final 1%) and DHPC (final 30 mM, Avanti Polar Lipids 850306P-200 mg). The lysate was cleared (13000G 10 min), and after taking an input sample, immuno-precipitation was performed in 4 technical replicates. For each, 2 µl goat anti-GFP antibody (Schauer et al., 2013) was added and incubated for 15 min, followed by adding 25 µl equilibrated Sepharose protein G beads for 45 min on ice with gently mixing every 10 min (GE Healthcare, Product code: 17-0618-01). The beads were washed quickly 3x with ribosome wash buffer (10 mM HEPES pH 7.6, 350 mM KCl, 5 mM MgCl2, 1% NP-40, protease inhibitor cocktail (Roche), 0.5 mM DTT, 100 μg/ml cycloheximide (CHX) and 100 U/ml RNasIn (Promega)). Finally, input and IP RNA was purified using RNeasy MinElute kit (Qiagen).
Sequencing libraries were prepared using Illumina polyA-mRNA library preparation methods in biological duplicates.
Paired-end, 100bp RNA-seq reads.

tag: strain/background

value: adult

value: head

value: fat body

tag: affinity purification

value: IP with GFP antibody


title: s_N_MINUS_L_3

value: 25mM NaCL


title: s_N_PLUS_L_2


title: JG14_5_GTGGCC_L004_R1_001

value: grz

value: 12 weeks


title: s_N_PLUS_L_1


title: JG15_1_CCGTCC_L002_R1_001

value: Brain


title: fat body IP, rep2

tag: genotype/variation


title: H1-2_L001_12

description:
Original raw file name: H1-2_S2_L001_R1_001_0012.fastq.gz
Original raw file name: H1-2_S2_L001_R2_001_0012.fastq.gz

value: H

value: Hnrnph1 heterozygous KO


title: JG15_3_CCGTCC_L008_R1_001

value: Liver


title: SC3

value: non-lesional

tag: diagnosis

value: Hailey-Hailey disease

value: skin

tag: genotype/atp2c1 mut*


title: H1-2_L001_14

description:
Original raw file name: H1-2_S2_L001_R1_001_0014.fastq.gz
Original raw file name: H1-2_S2_L001_R2_001_0014.fastq.gz

value: M

tag: tissue


title: glia IP, rep2

source_name: adult head glia, IP

tag: cell type

value: glia


title: fat body Input, rep2

source_name: adult head fat body, input

value: Input


title: JG14_1_GTGGCC_L002_R1_001

source_name: Brain


title: s_H_PLUS_L_3

value: bone marrow-derived macrophages

tag: passages

value: Primary culture (day 7)

tag: genetic background

value: Hypoxia

value: 25mM NaLactate


title: H1-16_L002_14

description:
Original raw file name: H1-16_S16_L002_R1_001_0014.fastq.gz
Original raw file name: H1-16_S16_L002_R2_001_0014.fastq.gz

value: F

value: striatal hemispheres


title: s_N_MINUS_L_2

tag: incubation

value: Normoxia

tag: treatment

value: 25mM NaCL


title: H1-16_L001_14

description:
Original raw file name: H1-16_S16_L001_R1_001_0014.fastq.gz
Original raw file name: H1-16_S16_L001_R2_001_0014.fastq.gz

value: H

tag: strain


title: fat body Input, rep1

tag: age

value: adult

value: head

value: fat body


title: JG14_3_GTGGCC_L004_R1_001

source_name: Liver

value: grz

value: Liver

value: 12 weeks


title: s_N_MINUS_L_1


title: H1-16_L008_09

description:
Original raw file name: H1-16_S16_L008_R1_001_0009.fastq.gz
Original raw file name: H1-16_S16_L008_R2_001_0009.fastq.gz

tag: sampleID

tag: lane

value: Hnrnph1 heterozygous KO


title: glia IP, rep1

value: glia

value: IP with GFP antibody


title: s_H_PLUS_L_1

value: bone marrow-derived macrophages

value: Primary culture (day 7)


title: s_H_MINUS_L_2

value: Hypoxia


title: H1-2_L002_14

description:
Original raw file name: H1-2_S2_L002_R1_001_0014.fastq.gz
Original raw file name: H1-2_S2_L002_R2_001_0014.fastq.gz

tag: condition

tag: Sex

value: M


title: H1-16_L001_12

description:
Original raw file name: H1-16_S16_L001_R1_001_0012.fastq.gz
Original raw file name: H1-16_S16_L001_R2_001_0012.fastq.gz

value: F

tag: cage

value: striatal hemispheres


title: H1-15_L008_09

description:
Original raw file name: H1-15_S15_L008_R1_001_0009.fastq.gz
Original raw file name: H1-15_S15_L008_R2_001_0009.fastq.gz

value: control


title: H1-15_L001_14

description:
Original raw file name: H1-15_S15_L001_R1_001_0014.fastq.gz
Original raw file name: H1-15_S15_L001_R2_001_0014.fastq.gz


title: JG13_5_GTAGAG_L006_R1_001

source_name: Skin

value: Skin


title: s_H_PLUS_L_2

value: 25mM NaLactate


title: glia Input, rep2

source_name: adult head glia, input

tag: strain/background

value: adult

value: head

tag: affinity purification

value: Input


title: JG13_3_GTGAAA_L005_R1_001

value: grz

value: Liver


title: neuron Input, rep1

source_name: adult head neurons, input

tag: genotype/variation

value: neurons


title: JG10_1_GTAGAG_L007_R1_001

value: Brain

value: 12 weeks


title: s_H_MINUS_L_3

value: bone marrow-derived macrophages

value: 25mM NaCL


title: JG13_1_GTGAAA_L001_R1_001


title: glia Input, rep1

value: glia


title: K1-NanER 4sU-RNA-seq Rep 2

city: Melbourne

description:
K1-ER_K1-NanER_DEGs.csv.gz
4sU-RNA

source_name: K1-NanER Clone X

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Life Technologies, #15596026) according to the manufacturer’s instructions with manually dissociated cells washed in 1 ml DPBS (Gibco™, #14190-136). Extracted RNA was subsequently treated with DNase I (New England Biolabs, #M0303L) to remove residual gDNA contamination. Isolation of 4sU-RNA was performed essentially as previously described (Rabani et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 2011) with minor modifications. Purified RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce; #21341) and isolated using µMacs Streptavidin Kit (Miltenyi; #130-074-101). 4sU-enriched RNA was then purified with RNeasy MinElute Spin Columns (Qiagen; #74204).
Purified 4sU-labelled RNA was used with the Ion Total RNA-Seq Kit v2 (Life Technologies; #4479789) to prepare libraries for sequencing on the Ion Proton™ System.

treatment_protocol: Cells were induced through the addition of (Z)-4-Hydroxytamoxifen at a final concentration of 200 nM and newly transcribed RNA labeled with 500 μM 4sU for 1 h.

value: KLF1 null erythroblasts (K1)

tag: transgene


title: neuron IP, rep2

source_name: adult head neurons, IP

tag: tissue

value: IP with GFP antibody


title: Animal 3: right salivary gland

city: Cambridge

first: David

last: Molnar

address: Tennis Court Road

department: Genetics / Systems Biology Centre

country: United Kingdom

institute: University of Cambridge

data_processing:
Adaptor trimming.
genome alignment (dm6) using STAR.
Transcript abundance estimation with Cufflinks.
Adaptor localisation and phasing for termini using R
Genomic coverage track generation using BEDtools
Genome_build: dm6
Supplementary_files_format_and_content: .bw: genome coverage, all reads, without strand information, bigWig format.
Supplementary_files_format_and_content: *_3p_weighted.bed.bb: position of transcription start sites on the plus strand, per-gene-relative-densities of start sites for each position, bigBED format.
Supplementary_files_format_and_content: *_3m_weighted.bed.bb: position of transcription start sites on the minus strand, per-gene-relative-densities of start sites for each postion, bigBED format.
Supplementary_files_format_and_content: *_5p_weighted.bed.bb: position of transcription stop sites on the plus strand, per-gene-relative-densities of stop sites for each position, bigBED format.
Supplementary_files_format_and_content: *_5m_weighted.bed.bb: position of transcription stop sites on the minus strand, per-gene-relative-densities of stop sites for each postion, bigBED format.

source_name: right salivary gland

growth_protocol: Cornmeal-yeast at 21˚C, eggs colelcted on apple agar with yeast.

extract_protocol:
Dissection, lysis, reverse transcription, SMART amplification, qPCR testing.
Multiplexed with TruSeq primers.

tag: developmental stage

value: Oregon-R

tag: genotype

value: wild type

value: right salivary gland

tag: replicate


title: K1-NanER 4sU-RNA-seq Rep 1

description:
K1-ER_K1-NanER_DEGs.csv.gz
4sU-RNA

source_name: K1-NanER Clone B

tag: cell type


title: Animal 2: right salivary gland


title: JG11_3_GTCCGC_L006_R1_001


title: H1-15_L002_14

first: Eric

description:
Original raw file name: H1-15_S15_L002_R1_001_0014.fastq.gz
Original raw file name: H1-15_S15_L002_R2_001_0014.fastq.gz

value: F

value: control

value: striatal hemispheres


title: neuron IP, rep1

value: adult

value: head


title: JG11_1_GTCCGC_L008_R1_001

value: grz


title: JG10_3_GTAGAG_L007_R1_001

value: Liver


title: H1-14_L001_12

description:
Original raw file name: H1-14_S14_L001_R1_001_0012.fastq.gz
Original raw file name: H1-14_S14_L001_R2_001_0012.fastq.gz

value: H

value: M

value: Hnrnph1 heterozygous KO


title: H1-13_L008_09

description:
Original raw file name: H1-13_S13_L008_R1_001_0009.fastq.gz
Original raw file name: H1-13_S13_L008_R2_001_0009.fastq.gz


title: neuron Input, rep2

value: neurons

value: Input


title: H1-15_L001_12

description:
Original raw file name: H1-15_S15_L001_R1_001_0012.fastq.gz
Original raw file name: H1-15_S15_L001_R2_001_0012.fastq.gz


title: K1 4sU-RNA-seq Rep 2

description:
K1-ER_K1-NanER_DEGs.csv.gz
4sU-RNA

source_name: K1 Parental Cells

value: KLF1 null erythroblasts (K1)


title: H1-13_L002_14

description:
Original raw file name: H1-13_S13_L002_R1_001_0014.fastq.gz
Original raw file name: H1-13_S13_L002_R2_001_0014.fastq.gz


title: K1 4sU-RNA-seq Rep 1

description:
K1-ER_K1-NanER_DEGs.csv.gz
4sU-RNA


title: H1-14_L002_14

description:
Original raw file name: H1-14_S14_L002_R1_001_0014.fastq.gz
Original raw file name: H1-14_S14_L002_R2_001_0014.fastq.gz


title: H1-14_L008_09

description:
Original raw file name: H1-14_S14_L008_R1_001_0009.fastq.gz
Original raw file name: H1-14_S14_L008_R2_001_0009.fastq.gz


title: 48h-2_miRNA

city: Grand Forks

first: Archana

last: Dhasarathy

state: North Dakota

address: 501 N Columbia Rd.

institute: University of North Dakota

data_processing:
Sequences were trimmed using Cutadapt v1.6
Sequences were aligned to hg19 genome using Bowtie v1.1.1 as part of the mapper module of MirDeep v2.0.0.5
Sequences were assigned the miRNAs using the quantifier module of MirDeep v2.0.0.5
Differential expression analysis was performed using edgeR v3.10.2
Genome_build: hg19
Supplementary_files_format_and_content: comma separated text file that contains count data for all samples

source_name: Astrocytes

extract_protocol:
RNA extraction protocol not provided.
Library construction protocol not provided.

value: astrocytes

tag: time point

value: 48 hours

tag: infection status

value: Borrelia burdorferi infected


title: H1-13_L001_14

description:
Original raw file name: H1-13_S13_L001_R1_001_0014.fastq.gz
Original raw file name: H1-13_S13_L001_R2_001_0014.fastq.gz

source_name: Striatum

tag: strain


title: 24h-2_miRNA

value: 24 hours


title: Animal 2: left salivary gland

source_name: left salivary gland

value: Oregon-R

value: wild type

value: left salivary gland


title: H1-14_L001_14

description:
Original raw file name: H1-14_S14_L001_R1_001_0014.fastq.gz
Original raw file name: H1-14_S14_L001_R2_001_0014.fastq.gz

tag: sampleID

value: striatal hemispheres


title: 48h-1_miRNA


title: 24h-1_miRNA


title: s_H_MINUS_L_1

source_name: BMDMs

value: bone marrow-derived macrophages

tag: passages

value: Primary culture (day 7)

tag: genetic background

tag: incubation

value: Hypoxia

tag: treatment

value: 25mM NaCL


title: Animal 1: right salivary gland

value: right salivary gland


title: H1-12_L008_09

description:
Original raw file name: H1-12_S12_L008_R1_001_0009.fastq.gz
Original raw file name: H1-12_S12_L008_R2_001_0009.fastq.gz

tag: lane

tag: condition

value: H

tag: Sex

value: F

tag: cage

value: Hnrnph1 heterozygous KO


title: K1-ER 4sU-RNA-seq Rep 2

description:
K1-ER_K1-NanER_DEGs.csv.gz
4sU-RNA

source_name: K1-ER Clone C

value: KLF1 null erythroblasts (K1)

tag: transgene


title: Animal 2: Malpighian tubules

source_name: Malpighian tubules

tag: developmental stage

tag: tissue

value: Malpighian tubules


title: H1-12_L002_14

description:
Original raw file name: H1-12_S12_L002_R1_001_0014.fastq.gz
Original raw file name: H1-12_S12_L002_R2_001_0014.fastq.gz

tag: genotype/variation


title: K1-ER 4sU-RNA-seq Rep 1

description:
K1-ER_K1-NanER_DEGs.csv.gz
4sU-RNA

source_name: K1-ER Clone A

tag: cell type


title: Animal 3: left salivary gland

tag: genotype

tag: replicate


title: Animal 1: left salivary gland

tag: strain


title: Untreated-1_miRNA

value: astrocytes

tag: time point

tag: infection status

value: uninfected control


title: Animal 2: ventral nerve cord

source_name: ventral nerve cord

value: ventral nerve cord


title: H1-12_L001_12

description:
Original raw file name: H1-12_S12_L001_R1_001_0012.fastq.gz
Original raw file name: H1-12_S12_L001_R2_001_0012.fastq.gz

tag: sampleID


title: H1-13_L001_12

description:
Original raw file name: H1-13_S13_L001_R1_001_0012.fastq.gz
Original raw file name: H1-13_S13_L001_R2_001_0012.fastq.gz

value: M

value: control


title: H1-12_L001_14

description:
Original raw file name: H1-12_S12_L001_R1_001_0014.fastq.gz
Original raw file name: H1-12_S12_L001_R2_001_0014.fastq.gz


title: Untreated-2_miRNA

value: 24 hours


title: H1-11_L002_14

description:
Original raw file name: H1-11_S11_L002_R1_001_0014.fastq.gz
Original raw file name: H1-11_S11_L002_R2_001_0014.fastq.gz

value: striatal hemispheres


title: Animal 3: ventral nerve cord

value: Oregon-R

value: wild type


title: Animal 3: hindgut

source_name: hindgut

value: hindgut


title: H1-11_L001_12

description:
Original raw file name: H1-11_S11_L001_R1_001_0012.fastq.gz
Original raw file name: H1-11_S11_L001_R2_001_0012.fastq.gz


title: Animal 1: ventral nerve cord


title: H1-11_L008_09

description:
Original raw file name: H1-11_S11_L008_R1_001_0009.fastq.gz
Original raw file name: H1-11_S11_L008_R2_001_0009.fastq.gz


title: H1-11_L001_14

description:
Original raw file name: H1-11_S11_L001_R1_001_0014.fastq.gz
Original raw file name: H1-11_S11_L001_R2_001_0014.fastq.gz


title: Animal 3: Malpighian tubules


title: Animal 1: hindgut


title: Animal 1: posterior midgut

source_name: posterior midgut

value: posterior midgut


title: Animal 2: posterior midgut


title: Animal 1: Malpighian tubules


title: H1-10_L001_12

description:
Original raw file name: H1-10_S10_L001_R1_001_0012.fastq.gz
Original raw file name: H1-10_S10_L001_R2_001_0012.fastq.gz


title: H1-10_L002_14

description:
Original raw file name: H1-10_S10_L002_R1_001_0014.fastq.gz
Original raw file name: H1-10_S10_L002_R2_001_0014.fastq.gz


title: Animal 3: posterior midgut


title: H1-1_L008_09

description:
Original raw file name: H1-1_S1_L008_R1_001_0009.fastq.gz
Original raw file name: H1-1_S1_L008_R2_001_0009.fastq.gz


title: H1-10_L008_09

description:
Original raw file name: H1-10_S10_L008_R1_001_0009.fastq.gz
Original raw file name: H1-10_S10_L008_R2_001_0009.fastq.gz


title: Animal 1: anterior midgut

source_name: anterior midgut

value: anterior midgut


title: P2_CGATGT_L004_R1_001

organism: Iconisemion striatum

source_name: Brain

value: "Aquarienstamm"

value: Brain

tag: age

value: lifespan class 1


title: Animal 3: foregut

source_name: foregut

value: foregut


title: 57_ACTTGA_L005_R1_001

organism: Nothobranchius pienaari

value: lifespan class 4


title: Animal 2: foregut


title: H1-10_L001_14

description:
Original raw file name: H1-10_S10_L001_R1_001_0014.fastq.gz
Original raw file name: H1-10_S10_L001_R2_001_0014.fastq.gz

value: H

value: Hnrnph1 heterozygous KO


title: Animal 3: anterior midgut


title: Animal 2: anterior midgut


title: Animal 2: hindgut


title: H1-1_L002_14

description:
Original raw file name: H1-1_S1_L002_R1_001_0014.fastq.gz
Original raw file name: H1-1_S1_L002_R2_001_0014.fastq.gz


title: H1-1_L001_14

description:
Original raw file name: H1-1_S1_L001_R1_001_0014.fastq.gz
Original raw file name: H1-1_S1_L001_R2_001_0014.fastq.gz


title: B3_ACAGTG_L004_R1_001

organism: Nothobranchius rachovii

value: Beira 96

value: lifespan class 3


title: oxygen limited without nitrate

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

data_processing:
Illumina MiSeq Real-time analysis (RTA) used for basecalling.
Sequenced reads were trimmed for low-quality sequence, then mapped to CP000814 using bowtie v1.1.2 within Geneious v9.1 parameters -n 2 -l 28 -q -p 4  --best --strata
Geneious software was used to calculate the normalized transcripts per million (TPM) and to compare expression levels between the control growth condition (microaerophilic) and experimental conditions (oxygen limited+ nitrate, and oxygen limited).
Genome_build: CP000814.1
Supplementary_files_format_and_content: comma-delimited text files include TPM, Raw transcript count, FPKM, RPKM

organism: Campylobacter jejuni

source_name: monoculture

growth_protocol: Campylobacter precultures were diluted to an OD550 of 0.05 and grown either microaerophilic (5% O2, 8% CO2, 8% H2) or under oxygen-limited conditions (0.3% O2, 8% CO2, 8% H2), with or without addition of 10 mM nitrate to mid-log phase.

extract_protocol:
Total RNA was extracted from  mid-log phase cultures with the RNA-BeeTM kit (Tel-Test, Inc) according to the manufacturer’s specifications. . Subsequently, RNA was treated with RNAse-free DNAseI (Thermo) according to the instructions of the manufacturer.
Ribozero Magnetic Kit for-gram negative bacteria (Illumina) following manufacturer’s instructions using following the 5ug RNA procedure and option 1 (Ethanol precipitation), except using 1/8th reaction volumes/amounts. Illumina libraries were prepared using the KAPA stranded RNA-seq kit (Kapa Biosystems, Wilmington, MA), following manufacturer’s instructions to produce ~300bp fragments. Standard desalting TruSeq LT primers were ordered from Integrated DNA Technologies (Coralville, IA) and used at 50-100nM final concentration based on starting RNA amount. The PCR step was reduced to 6 cycles. Libraries were quantified using the KAPA Library Quantification Kit (Kapa), except with 10 µl volume and 90 sec annealing/extension PCR. Libraries were pooled and normalized to 4 nM. Pooled libraries were re-quantified by ddPCR on a QX200 system (Bio-Rad), using the Illumina TruSeq ddPCR Library Quantification Kit and following manufacturer’s protocols. The libraries were sequenced in two 2x76bp paired end v3 runs on a MiSeq instrument (Illumina) at 13.5 pM, following manufacturer's protocols.


title: 74_GATCAG_L005_R1_001

organism: Nothobranchius kuhntae


title: P1_ATCACG_L004_R1_001


title: B2_TGACCA_L004_R1_001

organism: Nothobranchius kadleci


title: H1-1_L001_12

description:
Original raw file name: H1-1_S1_L001_R1_001_0012.fastq.gz
Original raw file name: H1-1_S1_L001_R2_001_0012.fastq.gz

value: M

value: control


title: B1_TTAGGC_L004_R1_001


title: microaerophilic


title: Dark_MM_RNA-Seq

city: Iksan-si

first: Yong

middle: Hoon

last: Lee

state: Jeollabuk do

address: 79, Gobong-ro, Madong

department: Division of Biotechnology

country: South Korea

institute: Chonbuk National University

data_processing:
Sequenced using Illumina HiSeq 2500
Data analysis was performed with bowtie and Inhouse script
Differential gene expression analysis was performed with CLRNASeq software from ChunLab Inc., South Korea
Genome_build: http://www.ncbi.nlm.nih.gov/assembly/GCF_000517305.1/
Supplementary_files_format_and_content: text files with normalized values and raw read counts.

organism: Pseudomonas cichorii JBC1

source_name: Pseudomonas cichorii JBC1_dark

growth_protocol: Pseudomonas cichorii JBC1 was cultured in LB media at 30°C

extract_protocol:
RNA was extracted using TRI reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pseudomonas cichorii JBC1 was cultured in minimal media and incubated under green light and dark condition at 30°C with shaking for 12 hours.


title: 75_TAGCTT_L005_R1_001

department: Core Facility - Next Generation Sequencing


title: Animal 1: foregut

treatment_protocol: No treatment.


title: 56_CAGATC_L005_R1_001


title: ATR WT_tumor 3

status: Public on Jan 31 2017

city: Irvine

first: Anand

last: Ganesan

address: 836 Health Science Rd

department: Dermatology

institute: University of California, Irvine

description:
ATR +/+ is equivalent to ATR WT.
processed data column: wt4.counts

data_processing:
Paired-end sequencing reads were analyzed for quality using the Fastqc program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and aligned to the mouse reference genome version mm10 using the Tophat alignment software (version 2.0.12). Tophat2 parameters include -T –G mm10.gtf -o [SampleName]_thout
The edgeR library of the R statistical environment was used for differential gene expression analysis of mapped read counts.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values files include log fold change (logFC), log counts per million (logCPM), p-value (Pvalue), FDR, counts for all samples. Values for all genes are included.

source_name: ATR WT_tumor

extract_protocol:
Skin samples were homogenized using the Precellys24 high-throughput tissue homogenizer in hard tissue homogenizing reinforced tubes that contain 2.8 mm ceramic beads. RNA was extracted using the Rneasy Firous Tissue Mini Kit according to the manufacturer's instructions.
Library construction was performed according to the Illumina TruSeq RNA v2 protocol. Briefly, the input quantity for total RNA was 1g and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented for four minutes. First strand synthesis used random primers and reverse transcriptase to make cDNA. After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.

tag: strain background

value: ATR +/+; Braf CA/+; Pten fl/+; Cre +

value: tumor


title: ATR WT_tumor 2

description:
ATR +/+ is equivalent to ATR WT.
processed data column: wt3.counts


title: 28_CTTGTA_L005_R1_001

organism: Nothobranchius korthausae

value: lifespan class 2


title: oxygen limited with nitrate

value: wild type


title: ATR mD/mD_tumor 4

description:
ATR fl/fl is equivalent to ATR mD/mD where a portion of the ATR kinase domain is deleted.
processed data column: ko5.counts

source_name: ATR mD/mD_tumor

value: ATR fl/fl; Braf CA/+; Pten fl/+; Cre +


title: ATR mD/mD_tumor 2

description:
ATR fl/fl is equivalent to ATR mD/mD where a portion of the ATR kinase domain is deleted.
processed data column: ko3.counts


title: ATR mD/mD_tumor 3

description:
ATR fl/fl is equivalent to ATR mD/mD where a portion of the ATR kinase domain is deleted.
processed data column: ko4.counts


title: ATR mD/mD_tumor 1

description:
ATR fl/fl is equivalent to ATR mD/mD where a portion of the ATR kinase domain is deleted.
processed data column: ko2.counts


title: Control Rep4

city: Edmonton

first: Qiumin

last: Tan

state: Alberta

address: 6-16 Medical Sciences Building

department: Cell Biology

country: Canada

institute: University of Alberta

data_processing:
Illumina HiSeq 2500 software used for basecalling
Raw reads were first groomed by removing 15bp from the 5'-ends with random base concentration, then mapped to mm10 using TopHat v2.0.9
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under the exons of the gene (union of all the exons of the gene). This read counts obtained are analogous to the expression level of the gene.
Using the obtained read counts, differential gene analyses were carried out using the DESeq2 package in the R environment.
Genome_build: mm10
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: Brain Otp-lineage cells

growth_protocol: standard animal house conditions

extract_protocol:
Mice were euthanized under anesthesia and the hypothalamus and medial amygdala were quickly dissected over ice. RNA was extracted following published protocols on translating ribosome affinity purification (TRAP). Isolated RNA was submitted to the Genomic and RNA Profiling Core at Baylor College of Medicine. Sample quality checks using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100 were conducted.
Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.

value: hypothalamus and medial amygdala Otp+ cells

value: Otp-Cre; ROSAfsTRAP


title: KO Rep3

value: Otp-Cre; Cicflox/flox; ROSAfsTRAP


title: Control Rep3


title: Green_MM_RNA-Seq

source_name: Pseudomonas cichorii JBC1_green light


title: Control Rep2


title: KO Rep2


title: ATR WT_tumor 4

description:
ATR +/+ is equivalent to ATR WT.
processed data column: wt5.counts


title: ATR WT_tumor 1

description:
ATR +/+ is equivalent to ATR WT.
processed data column: wt2.counts


title: B4_GCCAAT_L004_R1_001

value: Beira 97

value: Brain


title: ATR mD/mD 3

description: ATR fl/fl is equivalent to ATR mD/mD where a portion of the ATR kinase domain is deleted. This sample is referred to as "c3_r3" in the processed data file

source_name: ATR mutant mouse nevi

value: ATR fl/fl; Braf CA/+; Cre +

value: skin


title: ATR mD/mD 2

description: ATR fl/fl is equivalent to ATR mD/mD where a portion of the ATR kinase domain is deleted. This sample is referred to as "c3_r2" in the processed data file


title: ATR mD/mD 1

description: ATR fl/fl is equivalent to ATR mD/mD where a portion of the ATR kinase domain is deleted. This sample is referred to as "c3_r1" in the processed data file


title: ATR WT 1

description: ATR +/+ is equivalent to ATR WT. This sample is referred to as "c2_r1" in the procesessed data file.

source_name: ATR wild type

value: ATR +/+; Braf CA/+; Cre +


title: LCMV Clone13 D8 CD8 T cell  rep 1

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Library strategy: ATAC-seq
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using the HOMER package v4.8.2.
Peak files from each sample were merged using the HOMER mergePeaks function into a single file.  Next, for each peak the raw read counts and reads per million normalized counts were annotated for all samples.
Genome_build: mm9
Supplementary_files_format_and_content: HOMER annotation file containing raw read counts and log2rpm values for all peaks.

source_name: Early chronic infection CD8 T cell

extract_protocol:
At the indicated time points naïve or antigen-specific CD8 T cells were isolated by FACS using the sorting markers described.
Cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed using the Illumina Nextera Kit by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: Wt mice were infected with either LCMV Armstrong (2x105 PFU IP) or LCMV Clone-13 (2x106 PFU IV).

value: female

tag: sorting markers

value: CD8+ CD44+ CD62L-  gp33/gp276/np396 tetramer+

tag: infection

value: LCMV Clone-13 2x106 PFU IV

tag: time post-infection (days)

tag: tissue source

value: spleen

value: virus-specific CD8 T cell


title: LCMV Armstrong D30 CD8 T cell rep 1

source_name: Acute infection memory CD8 T cell

tag: Sex

value: LCMV Armstrong 2x105 PFU IP


title: LCMV Armstrong D8 CD8 T cell rep 3

source_name: Peak acute infection CD8 T cell

value: male


title: LCMV Armstrong D8 CD8 T cell rep 2


title: LCMV Armstrong D4 CD8 T cell rep 2

source_name: Early acute infection CD8 T cell


title: LCMV Armstrong D4 CD8 T cell rep 1


title: Naïve CD8 T cell rep 3

source_name: Naïve CD8 T cell

value: CD8 T cells


title: Naïve CD8 T cell rep 1


title: ATR WT 2

description: ATR +/+ is equivalent to ATR WT. This sample is referred to as "c2_r2" in the procesessed data file.


title: LCMV Clone13 D28 CD8 T cell  rep 1

source_name: Late chronic infection CD8 T cell


title: KO Rep4


title: 26_GGCTAC_L005_R1_001

value: "Aquarienstamm"

value: lifespan class 2


title: MAQCB_2

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

data_processing:
Tophat-Cufflinks (Bowtie2 v2.1.0 Tophat v2.0.10 Cufflinks v2.1.1) all standard parameters
Tophat-HTSeq v0.5.4 all standard parameters
Kallisto v0.42.1 all standard parameters
Salmon v0.6.0 all standard parameters
Genome_build: Ensembl GRCh37, release 75
Supplementary_files_format_and_content: txt files

source_name: Human Brain Reference RNA, Thermo Fisher Scientific

extract_protocol:
Extracted by respectively Agilent Technologies and Thermo Fisher Scientific
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: Human Brain Reference RNA from Thermo Fisher Scientific


title: MAQCB_1


title: Control Rep1

tag: tissue

value: hypothalamus and medial amygdala Otp+ cells

value: Otp-Cre; ROSAfsTRAP


title: LCMV Clone13 D28 CD8 T cell  rep 2


title: KO Rep1

value: Otp-Cre; Cicflox/flox; ROSAfsTRAP


title: MAQCA_1

source_name: Universal Human Reference RNA, Agilent Technologies

value: Universal Human Reference RNA from Agilent Technologies