title: Sample_29_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt


title: Sample_6_longRNA

status: Public on Sep 06 2019

type: SRA

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

country: USA

institute: Mount Sinai School of Medicine

description:
Sperm_RNAseq
RPKMgenomic.txt

library_source: transcriptomic

data_processing:
For long RNA samples, paired-end reads were trimmed of adaptors and low-quality bases using Trimmomatic (version 0.36) [217], using default parameters (2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15), and requiring a minimum read length of 50 bp (MINLEN:50). The TruSeq Universal adaptor (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) was used as input to Trimmomatic.
For long RNA samples, trimmed paired and unpaired reads were aligned to the consensus human ribosomal RNA (GenBank: U13369.1) using HISAT2 (version 2.0.6) and the non-default parameters (-p10 --max-seeds 30 -k 2), then aligned to the human genome (hg38) and exogenous RNA spike-in sequences, using the same HISAT2 parameters. Reads without alignments in either U13369.1, the human genome (hg38), or an exogenous RNA were further assessed for alignments to repeat sequences (RepBase, February 2017 release), using HISAT2, with the following parameters (-p10 --no-spliced-alignment --max-seeds 10 -k 3). Reads without alignments in either U13369.1, hg38, an exogenous RNA, or RepBase were aligned to bacterial and viral genomes using Kraken (version 0.10.5-beta) and Jellyfish (version 1.1.10), implementing the full Kraken library and filtering alignments with a threshold of 0.15. Read alignments to the human genome, exogenous RNAs, and U13369.1 were processed to remove duplicated reads using Picardtools MarkDuplicates (version 1.129).
For long RNA samples, RNA element (RE) discovery algorithm (REDa) was applied to genomic read alignments, and expression in Reads Per Kilobase per Million (RPKM) for the RE loci was calculated. Due to the use of REs, rather than whole transcripts, Paired-end read alignments were treated as individual (single) reads, and the common FPKM value was replace by RPKM. Depending on a read pair’s insert size and RE length, this approach ran the risk of inflating the read count for a given RE. To mitigate this risk, read counts were assessed for the forward and reverse reads separately, with the read count from single (non-paired due to mate loss during quality control) reads were added to the forward and reverse read counts. The averaged read count between the forward and reverse reads were then used for generating the RPKM values.
For small RNA libraries, reads were trimmed of adaptors and low-quality bases, followed by removal of reads smaller than 13 bp. sncRNAbench (version 10.14) was used for assigning reads to small RNA species and repeat classes, followed by a custom code for generating normalized expression values (RPM- Reads Per Million).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files include RPKM values for long RNA libraries and RPM values for small RNA libraries

molecule: total RNA

organism: Homo sapiens

source_name: Ejaculated spermatozoa

extract_protocol:
Sperm samples were brought up to 1ml volume with PureSperm Buffer (Nidacon) and laid onto a 50% PureSperm (Nidacon) gradient, then centrifuged at 300xg for 20 minutes. The pellet was removed and washed in PureSperm Buffer. Each sample was added to a 2ml tube containing 500ul RLT buffer (Qiagen) with 7.5ul BME (14.3M), 100mg 0.2mm nuclease free SS beads. The sample were homogenized, 500ul Qiazol (Qiagen) added and homogenized again. 200ul chloroform (0.124M) was added and samples shaken by hand then centrifuged at 12,000xg for 20 minutes at 4⁰C and the upper aqueous layer removed. RNA was isolated from the aqueous layer using a customized Qiacube (Qiagen) protocol. RNA samples were treated with 4U Turbo DNase (Ambion) for 20 minutes at room temperature.  Samples were tested for DNA contamination by RT-PCR and intron spanning PRM1 primers. Samples still containing DNA were treated a second time and tested again by RT-PCR. The RNA samples void of DNA were quantified with a fluorescent assay as described. An aliquot of RNA (5 ng or 10 ng) of each sample was used to make cDNA with SuperScript III RT (Invitrogen). The cDNAs were used as template for RT-PCR with intron spanning PRM1 primers providing verification of RNA.
Two nanograms of RNA per sample was used with the Seqplex (Sigma-Aldrich) amplification kit prior to library construction. Fifty nanograms of Seqplex cDNA product was used with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing at a concentration of 2 nM per sample. All samples were subject to paired-end sequencing using either the NextSeq 500 (Illumina) sequencer, HiSeq 2500 (Illumina) sequencer or the HiSeq 4000 (Illumina) sequencer. One nanogram of small RNA per sample was used with the NEXTflex Small RNA-Seq Kit v2 (Bioo Scientific) to create sequencing libraries. Complete barcoded libraries were quantified and pooled for sequencing. Samples were subject to paired-end sequencing using the MiSeq (Illumina) sequencer.

tag: cell type

value: spermatozoa

tag: study subject

tag: visit number

tag: visit type

value: Baseline

tag: dbp level

tag: rna fraction

value: long RNA


title: HC25_LNv_ZT10

city: Evanston

first: Ravi

last: Allada

state: IL

address: 2205 Tech Drive

department: Neurobiology

institute: Northwestern University

data_processing:
Sequence reads were processed to calculate TPM and estimated counts by kallisto.
TPM values were used as input for booteJTK to identify cycling genes.
Genome_build: dmel-all-transcript-r6.14
Supplementary_files_format_and_content: PDF_abundance_transcripts.csv: This is a summary file for transcript abundance for all the conditions and time points for which raw data files are deposited.
Supplementary_files_format_and_content: PDF_all.cmn_eJTKprep_10-2017.xlsx: This is a summary file for gene level TPM for all the conditions and time points for which raw data files are deposited.
Supplementary_files_format_and_content: SUMMARY_LNv_BeJTK_results_10-04-17.xlsx: This results from booteJTK for HC25 and 3 conditions data.

organism: Drosophila melanogaster

source_name: LNv neurons

growth_protocol: Flies were raised at standard 1.5x sucrose-yeast (SY) food at 25°C, 1.5xSY at 18°C, or 0.5xSY at 25°C.

extract_protocol:
Fly brains were dissected at certain time points and processed as previously described (Kula-Eversole et al., 2010; Nagoshi et al., 2010). RNA from FACS sorted LNvs were extracted with PicoPure Kits. We synthesized 1st and 2nd strand cDNA from RNA first with Superscript III and DNA polymerase. Then we amplified the RNA by synthesizing more RNA from the cDNA template with T7 RNA polymerase. After the second round of cDNA synthesis from amplified RNA, the cDNA was submitted to HGAC at the University of Chicago for library preparation and sequencing.
Library construction and sequencing followed the protocol at HGAC at University of Chicago.

tag: strain/background

tag: genotype/variation

value: WT

tag: gender

value: Female

value: LNv neurons

tag: condition

tag: time point


title: HC25_LNv_ZT08


title: Blood_trained_A1_1_6_rep1

type: RNA

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

description: blood-borne miRNA sequencing

hyb_protocol: Agilent protocols.

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized and log2 transformed.

label: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

source_name: Peripheral blood, trained, A1, 1_6, replicate 1

label_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

extract_protocol: Whole blood samples were collected in PAXGene Blood RNA Tubes (BD Biosciences). Total RNA including miRNAs was isolated using the PAXGene Blood miRNA kit (Qiagen) according to manufacturers recommendations.

tag: tissue

value: whole blood

value: male

tag: age

tag: participant

tag: timepoint

tag: rin-value

tag: cho-first-round(y/n)

value: y


title: Sample_9_longRNA

description:
Sperm_RNAseq
RPKMgenomic.txt

tag: cell type


title: Blood_untrained_E1_1_5_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood untrained, E1, 1_5, replicate 1


title: Blood_trained_A2_1_4_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A2, 1_4, replicate 1

value: female


title: HC25_LNv_ZT06


title: HC25_LNv_ZT04


title: Trim24-KO-IL-4_ChIPSeq

city: Shanghai

first: Tao

last: Yu

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Chinese Academy of Science

library_source: genomic

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are 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 are used in the subsequent analysis.
tags are 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 is divided into 32-nt bins and the number of fragments in each bin is determined.
The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Peritoneal Macrophage

growth_protocol: 4% thioglycolate was intraperitoneally injected into WT and Trim24 myliod-cells-conditional knockout mice, 4 days later, mice were sacrificed, and the peritoneal cavity was lavaged with DMEM medium. Macrophages were allowed to adhere for 4 h, washed with fresh medium to remove unattached cells and starved with DMEM containing 0.5% FBS.

extract_protocol:
The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against Stat6.
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: Stimulated for 1 hour with IL-4

tag: strain

tag: chip antibody

value: Stat6 ( Cell Signaling Technology, Cat#5397)

tag: treatment

value: Stimulated for 1 h with IL-4


title: Blood_untrained_E2_1_3_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E2, 1_3, replicate 1


title: PianpKO amygdala biological rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Gene expression data of Pianp-deficient murine amygdala.
Amygdala_KO_156

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: PianpKO biological rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Pianptm1a(KOMP)Wtsi mice were crossed with B6N.Cg-Tg(ACTFLPe)9205Dym/CjDswJ mice to generate Pianp floxed mice (FL). These mice were further bred with B6.C-Tg(CMV-cre)1Cgn/J mice to generate constitutive knockout mice, denoted as PianpKO (KO).

extract_protocol: Total RNA was extracted from dissected brain region tissue using the RNeasy Mini Kit (Qiagen).

treatment_protocol: The whole brain from experimentally naive male mice was cut coronally and manually microdissected into the respective regions using brain punches. Allen mouse brain atlas (version 2, 2011, https://www.brain-map.org/) was used for identification of the different brain areas.

value: Amygdala

tag: genotype

value: KO


title: Input DNA

value: Input


title: Blood_trained_A1_1_2_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, trained, A1, 1_2, replicate 1


title: PianpKO amygdala biological rep1

description:
Gene expression data of Pianp-deficient murine amygdala.
Amygdala_KO_155

source_name: PianpKO biological rep1


title: WT-IL-4_ChIPSeq


title: KO_LGMP_3

status: Public on Sep 05 2019

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were mapped to mm10 using STAR, version 2.5.3a, with settings: “alignSJoverhangMin” 8; “alignSJDBoverhangMin” 1; “outFilterMismatchNmax” 999; “alignIntronMin” 20; “alignIntronMax” 1000000; “alignMatesGapMax” 1000000; “twopassMode” Basic; “sjdbOverhang” 100.
FPKM and differential gene expression were calculated with DESeq2 (version 1.18.1) and Ensembl 84 as the reference.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited (TSV) file containing a matrix of FPKM values for all samples

source_name: KO Leukemic GMP cells

extract_protocol:
Cell were sorted into Trizol and RNA were extracted using RNeasy MiniElute Cleanup kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.
cDNA libraries were generated using the Smart-seq2 protocol. Sequencing libraries were generated from 250 pg of amplified cDNA using Nextera XT kit according to the manufacturer's instructions. Barcoded libraries were purified and sequenced on a NextSeq 500 platform.

treatment_protocol: L-GMP cells were isolated from AMPK WT and KO mice.

value: Prkaa1 and Prkaa2 double knockout

value: Leukemic GMP cells


title: Blood_untrained_E1_1_1_rep1

description: blood-borne miRNA sequencing

source_name: Peripheral blood, untrained, E1, 1_1, replicate 1


title: WT_LGMP_2

source_name: WT Leukemic GMP cells

value: wild type


title: KO_LGMP_1


title: KO_LGMP_2


title: WT_LGMP_1


title: PianpKO amygdala biological rep3

description:
Gene expression data of Pianp-deficient murine amygdala.
Amygdala_KO_157

source_name: PianpKO biological rep3


title: PianpKO amygdala biological rep4

description:
Gene expression data of Pianp-deficient murine amygdala.
Amygdala_KO_165

source_name: PianpKO biological rep4


title: Control amygdala biological rep5

description:
Gene expression data of control murine amygdala.
Amygdala_FL_122

source_name: Control biological rep5

value: FL


title: Control amygdala biological rep3

description:
Gene expression data of control murine amygdala.
Amygdala_FL_112

source_name: Control biological rep3


title: Control amygdala biological rep1

description:
Gene expression data of control murine amygdala.
Amygdala_FL_110

source_name: Control biological rep1


title: Control amygdala biological rep2

description:
Gene expression data of control murine amygdala.
Amygdala_FL_111

source_name: Control biological rep2


title: HiC in AdnpKO mESC, biological replicate 2, technical replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument. Some samples were sequenced on multiple independent lanes and raw fastq files need to be pooled prior to mapping. These are indicated with "a" and "b" in the file name.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
ChIPseq: Sequenced reads were aligned using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within ).
Hi-C: Raw reads were filtered and aligned using HiC-Pro 2.9.0 (Servant et al., 2015). Further analysis was performed using the R package GENOVA.
4C: Raw reads were mapped using the 4C-mapping pipeline from the de Wit lab (https://github.com/deWitLab/4C_mapping). Mapped reads were further processed using peak_C from the de Wit lab (https://github.com/deWitLab/peakC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools). Bed files containing peak positions were generated from the .narrowPeak output file from MACS2. HiC allValidPairs files were generated by HiC-Pro 2.9.0. 4C wig files for replicates were generated from the filtered_reads output from peak_C by adding a wiggle file header.

source_name: embryonic stem (ES) cells

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
In situ HiC was performed according to Rao et al, 2015. For details see Kaaij et al, 2019.
HiC libraries were generated according to Rao et al, 2015. For details see Kaaij et al, 2019.

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/6

value: Adnp KO


title: HiC in AdnpKO mESC, biological replicate 1, technical replicate 1


title: HiC in AdnpKO mESC, biological replicate 1, technical replicate 2


title: HiC in AdnpKO mESC, biological replicate 2, technical replicate 1


title: HC25_LNv_ZT02

source_name: LNv neurons

tag: strain/background

value: WT

value: Female

value: LNv neurons


title: HiC in wt mESC, biological replicate 1, technical replicate 1

value: wt


title: HiC in wt mESC, biological replicate 1, technical replicate 2


title: HiC in wt mESC, biological replicate 2, technical replicate 2


title: HiC in wt mESC, biological replicate 2, technical replicate 1


title: U937 IRF2KO_pIRF2-RNAseq-replicate3

city: Lyon

first: Thomas

last: Henry

address: 21 avenue Tony Garnier

department: CIRI

country: France

institute: INSERM

data_processing:
Base Calling with RTA2 run with default parameters: "The NextSeq 500 uses an implementation of Real-Time Analysis (RTA) software called RTA2. RTA2 runs on the instrument computer and extracts intensities from images, performs base calling, and assigns a quality score to the base call."
Reads were filtered / timmed with fastx 0.0.14 with parameters: fastx_trimmer -v -f 9 -l 75 | fastq_quality_trimmer -v -t 20 -l 1 | fastq_quality_filter -v -q 30 -p 75
tRNA and rRNA treads where filtered out by mapping on a tRNA / rRNA mini-genome with Bowtie 2.3.3 with parameters bowtie2 -t --fast -p 16 -x /<path>/human_rRNA_tRNA_index | samtools view -b -f 4 | bedtools bamtofastq -i
Reads were mapped with Tophat 2.1.1 with parameters: --library-type fr-firststrand --b2-sensitive -i 30 -m 1 -g 10 --max-coverage-intron 1000000 -G <path>/gencode.v23.chr_patch_hapl_scaff.annotation_appris_principal.gtf
Mapped reads were counted with HTSeq-count  0.9.1 with parameters : -f sam -s reverse -a 10 -t exon -i gene_id -m union
Genome_build: hg38
Supplementary_files_format_and_content: An Excel .xlsx file containing a matrix of raw counts, as provided by HTSeq-count, for all samples.

source_name: U937 IRF2KO-pIRF2

extract_protocol:
RNA was extracted using RNA extraction kit (Macherey Nagel)
SENSE mRNASeq Library Prep Kit V2 (Lexogen)

tag: cell line

value: U937 human monocyte cell line


title: U937 IRF2KO_pIRF2-RNAseq-replicate1


title: U937 IRF2KO_pIRF2-RNAseq-replicate2


title: U937 IRF2KO_RNAseq-replicate2

source_name: U937 IRF2KO


title: Lung Biopsy, PF, VUILD48

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 N. Fifth Street

department: Integrated Cancer genomics division

institute: Translational Genomics Research Institute

data_processing:
Indivual sample reads were input into Cellranger 3.0.2 using reference hg38
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger output format with all samples aggregated together, includes celltype metadata

source_name: Lung Biopsy

extract_protocol:
Custom tissue dissociation
10X 5' Gene Expression (GEX) Library Construction

tag: disease state

value: pulmonary fibrosis (PF)

value: Lung Biopsy


title: U937 IRF2KO_RNAseq-replicate3


title: Keratinocyte-cocultured CVG1 with shCtrl

city: PITTSBURGH

first: Yulong

last: Bai

state: Pennsylvania

address: Public Health Building, 130 De Soto St,, 3121

department: Human Genetics

institute: University of Pittsburgh

description: CVG-1 cells transduced with shCtrl were cocultred with primary human keratinocytes

data_processing:
The reads were aligned to a concatenation of the human and MCV transcriptomes and quantified using CellRanger (version 3.0.0). The human transcriptome was generated based on genome asembly GRCh38.87. The MCV transcriptome was generated from the reverse-genetics plasmids.
Scater package was used to implement cell-wise cleaning. we used library size, the proportion of expressed genes, and mitochondrial proportion as the internal controls by assuming that most cells were in normal condition and their RNAs were well sequenced and quantified. Cells (85 cells) with log-transformed library size 2 median absolute deviations (MADs) below the median and cells (112 cells) with log-transformed number of expressed genes 2 MADs below median were identified as low quality and filtered out. Cells (1,746 cells) with a mitochondrial proportion 2 MADs higher than the median were identified as broken or dead and removed.
For gene-wise filtering, we kept genes that are expressed (UMI > 1) in at least 1% of all cells. After the filtering, the expression matrix was reduced to hold 11,851 genes and 25,836 cells.
Differential expression analysis was implemented using MAST approach in Seurat package. We considered genes with Benjamini-Hochberg-adjusted p-values of less than 0.01 as differentially expressed genes. Further, we selected genes that have more than or equal to 0.15 log2 fold change between the average expression of two groups to be further considered as genes with fold changes.
Genome_build: GRCh38.87
Supplementary_files_format_and_content: h5 files generated by CellRanger (version 3.0.0) including the filtered count matrix

molecule: polyA RNA

source_name: Kerainocyte and Merkel cell carcinoma cells with control shRNA

growth_protocol: The MCC cell line CVG-1 was cocultured with keratinocytes in the keratinocyte serum-free medium (ThermoFisher)

extract_protocol:
To prepare cDNAs for single cell transcriptome analysis, Single nuclei are stained using trypan blue for visualization, counting and viability assessment using the Countess II Automated Cell Counter and diluted as needed to a final concentration of 700-1200 nuclei/μL in 1x PBS + 0.04% BSA.  A minimum of two reproducible counts with SD <25% are required before droplet preparation and <5% of input should be viable cells. Nuclei are added to a master mix containing reverse transcription reagents and primer, and are then transferred to the ChromiumChip with gel beads and partitioning oil for the preparation of nanoliter-scale Gel Bead-In-Emulsions (GEMs). The emulsion undergoes reverse transcription to produce cDNA with a cellular 10X barcode and UMI, and is recovered with Dynabeads MyOne SILANE magnetic beads according to the manufacturer's directions.  Subsequently, the cDNA undergoes 8-14 cycles of amplification before clean-up using SPRIselect Reagent (Beckman).  Total cDNA yield is calculated following a quality assessment (High Sensitivity D5000 ScreenTape, Agilent) and fluorometric quantitation (Qubit).
Libraries are constructed by enzymatic fragmentation, end repair, and A-tailing according to the manufacturer's instructions.  A double-sided SPRIselect Reagent (Beckman) clean up prepares samples for adapter ligation and another round of magnetic bead clean-up before sample indexing PCR for 5-16 cycles, depending on the cDNA input for library construction. A further double-sided size selection produces libraries of 400-600bp, which are quantified for paired-end sequencing (26bp x 98bp) using a NextSeq 500 System.

treatment_protocol: CVG-1 cells were trasduced with shpanT that targets entire Merkel cell polyoamvirus T antigen transcripts or with control shRNA (shCtrl) prior to keratinocyte coculture.

value: Merkel cell carcinoma cell line CVG-1 cocultured with keratinocytes

tag: shRNA  transduced into mcc cells

value: shCtrl control shRNA


title: Keratinocyte-cocultured CVG1 with shpanT

description: CVG-1 cells transduced with shpanT were cocultred with primary human keratinocytes

source_name: Kerainocyte and Merkel cell carcinoma cells with shpanT that targets viral T antigen

value: shpanT that targets  pan viral T antigen transcripts


title: U937 WT_RNAseq-replicate2


title: U937 IRF2KO_RNAseq-replicate1


title: aES3 IGF2-KO hep rep3

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Human androgenetic ESCs aES3 differentiated into hepatocytes, IGF2-KO technical replicate 3

data_processing:
Reads were aligned to the human reference genome (GRCh38/hg38) using STAR (version 2.5) allowing up to 3 mismatches
Gene expression levels were calculated as normalized read counts using HTSeq (version 0.6.1p1) and DESeq2 (version 1.14.1) and analyzed as regularized logarithm (rlog) values
Genome_build: Ensembl/GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text file includes rlog values for each sample

source_name: Hepatic cells from human androgenetic ESCs aES3 IGF2-KO rep3

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen) or NucleoSpin RNA Plus Kit (Macherey-Nagel). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (RIN > 8)
Libraries were prepared using Illumina TruSeq RNA Library Prep Kit

value: aES3 IGF2-KO

tag: passage

value: Hepatocyte-differentiated


title: aES3 IGF2-KO hep rep2

description: Human androgenetic ESCs aES3 differentiated into hepatocytes, IGF2-KO technical replicate 2

source_name: Hepatic cells from human androgenetic ESCs aES3 IGF2-KO rep2


title: aES3 IGF2-KO hep rep1

description: Human androgenetic ESCs aES3 differentiated into hepatocytes, IGF2-KO technical replicate 1

source_name: Hepatic cells from human androgenetic ESCs aES3 IGF2-KO rep1


title: aES1 IGF2-KO hep rep1

description: Human androgenetic ESCs aES1 differentiated into hepatocytes, IGF2-KO technical replicate 1

source_name: Hepatic cells from human androgenetic ESCs aES1 IGF2-KO rep1

value: aES1 IGF2-KO


title: aES3 WT hep rep3

description: Human androgenetic ESCs aES3 differentiated into hepatocytes, WT technical replicate 3

source_name: Hepatic cells from human androgenetic ESCs aES3 WT rep3

value: aES3 WT


title: aES1 IGF2-KO hep rep2

description: Human androgenetic ESCs aES1 differentiated into hepatocytes, IGF2-KO technical replicate 2

source_name: Hepatic cells from human androgenetic ESCs aES1 IGF2-KO rep2


title: aES1 IGF2-KO hep rep3

description: Human androgenetic ESCs aES1 differentiated into hepatocytes, IGF2-KO technical replicate 3

source_name: Hepatic cells from human androgenetic ESCs aES1 IGF2-KO rep3


title: aES3 WT hep rep2

description: Human androgenetic ESCs aES3 differentiated into hepatocytes, WT technical replicate 2

source_name: Hepatic cells from human androgenetic ESCs aES3 WT rep2


title: Lung Biopsy, PF, VUILD54

tag: tissue


title: aES1 WT hep rep2

description: Human androgenetic ESCs aES1 differentiated into hepatocytes, WT technical replicate 2

source_name: Hepatic cells from human androgenetic ESCs aES1 WT rep2

value: aES1 WT


title: aES3 WT hep rep1

description: Human androgenetic ESCs aES3 differentiated into hepatocytes, WT technical replicate 1

source_name: Hepatic cells from human androgenetic ESCs aES3 WT rep1


title: aES1 WT hep rep3

description: Human androgenetic ESCs aES1 differentiated into hepatocytes, WT technical replicate 3

source_name: Hepatic cells from human androgenetic ESCs aES1 WT rep3


title: aES1 WT hep rep1

description: Human androgenetic ESCs aES1 differentiated into hepatocytes, WT technical replicate 1

source_name: Hepatic cells from human androgenetic ESCs aES1 WT rep1


title: CU-ES5 hep

description: Human bi-parental ESCs CU-ES5 differentiated into hepatocytes

source_name: Hepatic cells from human bi-parental ESCs CU-ES5


title: U937 WT_RNAseq-replicate3


title: HuES14 hep

description: Human bi-parental ESCs HuES14 differentiated into hepatocytes

source_name: Hepatic cells from human bi-parental ESCs HuES14


title: CU-ES4 hep

description: Human bi-parental ESCs CU-ES4 differentiated into hepatocytes

source_name: Hepatic cells from human bi-parental ESCs CU-ES4


title: hnRNPG_PC_d2_S3

city: Chicago

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
PAR-CLIP of hnRNP-G
merged_sorted_parclip.bed

data_processing:
RNA-Seq data was mapped using the STAR computer program version 2.5.3a (PMID 23104886) .
Soft-clipped bases were removed using bamutils' "removeclipping" function version 0.5.7-32a2e98 (PMID 25883319).
BAM files were re-converted into FASTQ files using bedtools' "bamtofastq" function version 2.17.0 (PMID 20110278).
FASTQ files re-mapped using bowtie1 (PMID 19261174), using PARalyzer suggested parameters: -p 28 -v 2 -m 10 --best --strata.
PARalyzer version 1.1 (PMID 21851591) was used to convert aligned reads into PAR-CLIP sites, following default C-to-T detection parameters.
genome build: GRCH37/hg19
processed data files format and content: BED file of PAR-CLIP sites

growth_protocol: Embryonic kidney cell line HEK293T (CRL-11268) were obtained from American Type Culture Collection (ATCC) and were cultured under standard conditions

extract_protocol:
NEBNext multiplex small RNA library preparation kit (NEB, E7300S)
For chromatin PAR-CLIP, chromatin extraction was performed based on a published protocol (Brugiolo et. al., Nucleic Acids Research, 2017, 45(18):10452–65). The chromatin pellet from 3* 15 cm of HEK293T cells was solublized 900 µL chromatin extraction buffer (20 mM Tris-Cl [pH 7.5], 100 mM KCl, 2 mM MgCl2, 2.5 mM CaCl2, 0.3 M sucrose, and 0.1% v/v Triton X-100, 1% protease and phosphatase inhibitor) with 5 U/mL Micrococcal Nuclease (N3755, Sigma) by shaking at 4 ºC for 2 hours. The immunoprecipitation was performed with 5 ug of rabbit anti-hnRNPG antibody (Ab190352, abcam) overnight and 100 uL Protein A beads (10002D, Thermo) for another 4 hours at 4ºC. Co-immunoprecipitated RNA fragments were then washed, end-repaired on-beads, size-selected by SDS-PAGE, and released by Protease K digestion. RNA was purified by Acid-Phenol:Chloroform extraction and overnight ethanol precipitation. For ChIP-seq, we followed the protocol of ChIP-IT® Express kit (53008, Active motif) with Spike-in normalization strategy. The chromatin samples were sheared by sonication into 200-500 bp in size. For each immunoprecipitation reaction, 20 ug of the sample chromatin, 5 ug of the antibody, 10 ng of Spike-in chromatin (53083, Active motif), and 1 ug of Spike-in antibody (61686, Active Motif) were used. After washing, reverse crosslinking, and treatment with RNase A and Protease K, the DNA was purifed by with DNA Clean & Concentrator-5 (D4013, Zymo research).

treatment_protocol: The Cells were fed with 200 µM 4-Thiouridine (T4905, Sigma) for 14 hours and crosslinked twice with 0.15 J/cm2 365 nm UV light before collection

tag: par-clip antibody


title: U937 WT_RNAseq-replicate1


title: hnRNPG_PC_d1_S2

value: rabbit anti-hnRNPG antibody (Ab190352, abcam)


title: aES3 hep

description: Human androgenetic ESCs aES3 differentiated into hepatocytes

source_name: Hepatic cells from human androgenetic ESCs aES3


title: hnRNPG_PC_d2_S1


title: hnRNPG_PC_d2_S2


title: aES5 hep

description: Human androgenetic ESCs aES5 differentiated into hepatocytes

source_name: Hepatic cells from human androgenetic ESCs aES5


title: pES6 hep

description: Human parthenogenetic ESCs pES6 differentiated into hepatocytes

source_name: Hepatic cells from human parthenogenetic ESCs pES6


title: pES10 hep

description: Human parthenogenetic ESCs pES10 differentiated into hepatocytes

source_name: Hepatic cells from human parthenogenetic ESCs pES10


title: aES1 hep

description: Human androgenetic ESCs aES1 differentiated into hepatocytes

source_name: Hepatic cells from human androgenetic ESCs aES1


title: pES12 hep

description: Human parthenogenetic ESCs pES12 differentiated into hepatocytes

source_name: Hepatic cells from human parthenogenetic ESCs pES12


title: CU-ES5 TR

description: Human bi-parental ESCs CU-ES5 differentiated into trophoblast cells

source_name: Trophoblast cells from human bi-parental ESCs CU-ES5

value: Trophoblast-differentiated


title: HuES14 TR

description: Human bi-parental ESCs HuES14 differentiated into trophoblast cells

source_name: Trophoblast cells from human bi-parental ESCs HuES14


title: CU-ES4 TR

description: Human bi-parental ESCs CU-ES4 differentiated into trophoblast cells

source_name: Trophoblast cells from human bi-parental ESCs CU-ES4


title: pES12 TR

description: Human parthenogenetic ESCs pES12 differentiated into trophoblast cells

source_name: Trophoblast cells from human parthenogenetic ESCs pES12


title: hnRNPG_PC_d1_S3


title: aES3 TR

description: Human androgenetic ESCs aES3 differentiated into trophoblast cells

source_name: Trophoblast cells from human androgenetic ESCs aES3


title: pES6 TR

description: Human parthenogenetic ESCs pES6 differentiated into trophoblast cells

source_name: Trophoblast cells from human parthenogenetic ESCs pES6


title: aES5 TR

description: Human androgenetic ESCs aES5 differentiated into trophoblast cells

source_name: Trophoblast cells from human androgenetic ESCs aES5


title: pES10 TR

description: Human parthenogenetic ESCs pES10 differentiated into trophoblast cells

source_name: Trophoblast cells from human parthenogenetic ESCs pES10


title: aES1 TR

description: Human androgenetic ESCs aES1 differentiated into trophoblast cells

source_name: Trophoblast cells from human androgenetic ESCs aES1


title: CU-ES4 T

description: Teratoma cells derived from human bi-parental ESCs CU-ES4

source_name: Teratoma from human bi-parental ESCs CU-ES4

value: Teratoma


title: pES12 T2

description: Teratoma cells derived from human parthenogenetic ESCs pES12, biological replicate 2

source_name: Teratoma from human parthenogenetic ESCs pES12 rep2


title: hnRNPG_PC_d1_S1

description:
PAR-CLIP of hnRNP-G
merged_sorted_parclip.bed


title: pES12 T1

description: Teratoma cells derived from human parthenogenetic ESCs pES12, biological replicate 1

source_name: Teratoma from human parthenogenetic ESCs pES12 rep1


title: pES10 T

description: Teratoma cells derived from human parthenogenetic ESCs pES10

source_name: Teratoma from human parthenogenetic ESCs pES10


title: aES5 T

description: Teratoma cells derived from human androgenetic ESCs aES5

source_name: Teratoma from human androgenetic ESCs aES5


title: aES1 T

description: Teratoma cells derived from human androgenetic ESCs aES1

source_name: Teratoma from human androgenetic ESCs aES1


title: CU-ES5

description: Human bi-parental ESCs CU-ES5

source_name: Human bi-parental ESCs CU-ES5

value: ESC


title: CU-ES4

description: Human bi-parental ESCs CU-ES4

source_name: Human bi-parental ESCs CU-ES4


title: aES7

description: Human androgenetic ESCs aES7

source_name: Human androgenetic ESCs aES7


title: aES1 rep2

description: Human androgenetic ESCs aES1, biological replicate 2

source_name: Human androgenetic ESCs aES1 rep2


title: aES3 rep1

description: Human androgenetic ESCs aES3, biological replicate 1

source_name: Human androgenetic ESCs aES3 rep1


title: aES5 rep1

description: Human androgenetic ESCs aES5, biological replicate 1

source_name: Human androgenetic ESCs aES5 rep1


title: aES3 rep2

description: Human androgenetic ESCs aES3, biological replicate 2

source_name: Human androgenetic ESCs aES3 rep2


title: aES1 rep1

description: Human androgenetic ESCs aES1, biological replicate 1

source_name: Human androgenetic ESCs aES1 rep1


title: aES3 T

description: Teratoma cells derived from human androgenetic ESCs aES3

source_name: Teratoma from human androgenetic ESCs aES3


title: aES5 rep2

description: Human androgenetic ESCs aES5, biological replicate 2

source_name: Human androgenetic ESCs aES5 rep2


title: aES9

description: Human androgenetic ESCs aES9

source_name: Human androgenetic ESCs aES9


title: aES8

description: Human androgenetic ESCs aES8

source_name: Human androgenetic ESCs aES8


title: Dataset 1_MS-5 cultured alone Technical Replicate 2

city: London

first: Dominique

last: Bonnet

state: London

address: 1 Midland Rd

country: United Kingdom

institute: Francis Crick Institute

description: Dataset 1_MS-5 cultured alone

hyb_protocol: The hybridisation cocktail was prepared using the NuGEN Cocktail PICR v1.0 protocol. This hybridisation cocktail protocol is derived from the NuGEN FL-Ovation cDNA Biotin Module v2 user guide. The  NuGEN hybridisation v1.0  protocol was followed for hybridising labelled DNA  to standard GeneChips with 11 micron feature size. This hybridisation protocol is derived from the NuGEN FL-Ovation cDNA Biotin Module v2 user guide and the Affymetrix GeneChip Expression Analysis Technical Manual

scan_protocol: Scanning was performed using the Affymetrix GeneChip scanner 3000 with autoloader running AGCC software.

data_processing: Microarray data was analysed using limma and affy packages on the R environment (R version 3.5.1). Raw CEL files were uploaded with the ReadAffy function and RMA normalization was then performed. A differentially expression statistical analysis was consequently performed in which we set up the experimental design including conditions and batch effect as factors. Differentially expressed genes were then obtained by contrasting the different conditions using the makeContrast function. Given the linear model fit, the statistics were computed by empirical Bayes moderation of the standard errors with the eBayes function.

source_name: Dataset 1_MS-5 cultured alone

label_protocol: The RNA was amplified using the WT-Ovation Pico target prep v1.0 protocol which was derived from the NuGEN WT-Ovation Pico RNA Amplification system  and the NuGEN FL-Ovation cDNA Biotin Module v2

growth_protocol: MS5 MSCs are grown in alpha-MEM with nucleosides and penicillin/streptomycin. MS5 are seeded at 70 % confluency 48h prior to the assay (see treatment protocol)

extract_protocol: RNA extraction was performed using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions

treatment_protocol: At day 0 the MS5 media is replaced with AML patient samples, AML cell lines or human cord blood CD34+ cells resuspended in  H5100 Myelocult from STEM CELL TECHNOLOGIES. For MS5 cultured alone the media is replaced with H5100 Myelocult from STEM CELL TECHNOLOGIES.

value: Bone marrow mesenchymal stroma cells

tag: co-culture

value: alone


title: Dataset 1_MS-5 co-cultured with AML cell line FUJIOKA Technical Replicate 1

value: AML cell line


title: Dataset 1_MS-5 co-cultured with AML cell line THP1 Technical Replicate 1


title: Dataset 2_MS-5 cultured alone Technical Replicate 1

description: Dataset 2_MS-5 cultured alone

source_name: Dataset 2_MS-5 cultured alone


title: Dataset 1_MS-5 co-cultured with AML cell line Kasumi-1 Technical Replicate 2


title: Dataset 2_MS-5 co-cultured with human CB CD34+ Technical Replicate 1

value: human CB CD34+


title: Dataset 1_MS-5 co-cultured with AML cell line FUJIOKA Technical Replicate 2


title: Dataset 1_MS-5 co-cultured with AML cell line THP1 Technical Replicate 2


title: Dataset 1_MS-5 co-cultured with AML cell line KG1 Technical Replicate 1


title: Dataset 2_MS-5 co-cultured with human CB CD34+ Technical Replicate 2


title: Dataset 1_MS-5 co-cultured with AML cell line HL60 Technical Replicate 1


title: Dataset 2_MS-5 cultured alone Technical Replicate 2

description: Dataset 2_MS-5 cultured alone


title: Dataset 2_MS-5 co-cultured with AML patient AML8 TechnicalReplicate 3

value: AML patient cells


title: Dataset 2_MS-5 co-cultured with AML patient AML7 Technical Replicate 3


title: Dataset 1_MS-5 co-cultured with AML cell line NB4 Technical Replicate 1


title: Dataset 1_MS-5 cultured alone Technical Replicate 1

description: Dataset 1_MS-5 cultured alone


title: Dataset 2_MS-5 cultured alone Technical Replicate 3

description: Dataset 2_MS-5 cultured alone


title: Dataset 1_MS-5 co-cultured with AML cell line Kasumi-1 Technical Replicate 1


title: Dataset 1_MS-5 co-cultured with AML cell line U937 Technical Replicate 1


title: Dataset 1_MS-5 co-cultured with AML cell line U937 Technical Replicate 2


title: Dataset 1_MS-5 co-cultured with AML cell line KG1 Technical Replicate 2


title: Dataset 2_MS-5 co-cultured with human CB CD34+ Technical Replicate 3


title: Dataset 2_MS-5 co-cultured with AML patient AML8 Technical Replicate 2


title: Dataset 1_MS-5 co-cultured with AML cell line NB4 Technical Replicate 2


title: Dataset 2_MS-5 co-cultured with AML patient AML8 Technical Replicate 1


title: Dataset 2_MS-5 co-cultured with AML patient AML7 Technical Replicate 2


title: Dataset 2_MS-5 co-cultured with AML patient AML7 Technical Replicate 1


title: Dataset 1_MS-5 co-cultured with AML cell line HL60 Technical Replicate 2


title: WT_LGMP_3

source_name: WT Leukemic GMP cells

value: wild type

value: Leukemic GMP cells


title: PWD752

city: Bath

first: Katy

last: Morgan

address: Milner Centre for Evolutionary Biology

department: Department of Biology and Biochemistry

institute: University of Bath

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing:
A total of 499 samples were analyzed. Raw microarray data was taken from two previous studies (Turner et al. 2014 and Turner and Harr, 2014). The raw microarray data was normalized using the quantile method and batch corrected using Combat (Johnson et al. 2007).
quantile

source_name: testis gene expression

label_protocol: standard Agilent protocol

extract_protocol: none provided by the submitter

tag: hybrid category

value: Musculus

tag: fertility (lf - low fertility)

value: Pure

tag: batch

value: A


title: PWD623


title: PWD1405


title: PWD753


title: PWD1185


title: FP185

value: C


title: FP175

value: HZ

value: N


title: PWD622


title: FP111


title: FP011


title: FP165


title: PWD621


title: PWD624


title: FP020


title: FP035


title: FP211


title: FP005


title: FP215


title: FP009


title: FP121


title: FP160


title: FP104


title: FP173


title: FP181


title: FP021


title: FP067


title: FP038


title: FP244


title: FP007_1.txt


title: FP147


title: FP162


title: FP030


title: FP062


title: FP088


title: FP192


title: FP015_1.txt


title: FP167


title: FP099


title: FP076


title: FP081


title: FP141


title: FP161


title: FP150


title: FP164


title: FP013


title: FP142


title: FP194


title: FP072


title: FP077

value: LF


title: FP068


title: FP138


title: FP069


title: FP074


title: FP039


title: FP152


title: FP110


title: FP106


title: FP233


title: FP130


title: FP087


title: FP082


title: FP028_2.txt


title: FP154


title: FP131_1.txt


title: FP197


title: FP135


title: FP144


title: FP036


title: FP199


title: FP193


title: FP245


title: FP131_2.txt


title: FP064


title: FP117


title: FP044


title: FP184


title: FP096


title: FP046


title: FP179


title: FP028_1.txt


title: FP170


title: FP091


title: FP048


title: FP042


title: FP115


title: FP176


title: FP153


title: FP156


title: FP101


title: FP136


title: FP171


title: FP089


title: FP045


title: FP103


title: FP169


title: FP114


title: FP166


title: FP092


title: FP008

value: F


title: FP123


title: FP113


title: FP083


title: FP112


title: FP018


title: FP022


title: FP124


title: FP079


title: FP109


title: FP016


title: FP127


title: FP250


title: FP143


title: FP249


title: FP060


title: FP183


title: FP049


title: FP070


title: FP140


title: FP041


title: FP107


title: FP090


title: FP200


title: FP017


title: FP037


title: FP019


title: FP058


title: FP189


title: FP053


title: FP004_1.txt


title: FP128


title: FP191


title: FP195


title: FP186


title: FP116


title: FP145


title: FP086


title: FP061


title: FP075


title: FP137


title: FP149


title: FP059


title: FP012


title: FP055


title: FP084


title: FP026_1.txt


title: FP033


title: FP126


title: FP094


title: FP054


title: FP080


title: FP177


title: FP196


title: FP151


title: FP102


title: FP172


title: FP188


title: FP120


title: FP100


title: FP002


title: FP098


title: FP029


title: FP071


title: FP146


title: FP240


title: FP043


title: FP158


title: FP065


title: FP214


title: FP095


title: FP119


title: FP093


title: FP108


title: FP225


title: FP025


title: FP006


title: FP050


title: FP132


title: FP190


title: FP230


title: FP066


title: FP032


title: FP182


title: F2WP693


title: F2WP732


title: FP133


title: FP236


title: F2WP355


title: FP125


title: F2WP1746


title: F2WP358


title: FP163


title: FP198


title: F2WP345


title: FP051


title: F2WP1023


title: F2WP1520


title: F2WP584


title: F2WP1377


title: F2WP1084


title: F2WP1762


title: F2WP737


title: F2WP599


title: F2WP1603


title: F2WP731


title: F2WP1483


title: F2WP1784


title: F2WP1511


title: F2WP346


title: F2WP831


title: F2WP591


title: F2WP1524


title: F2WP608


title: F2WP1378


title: F2WP1253


title: F2WP653


title: F2WP1683


title: F2WP1009


title: F2WP630


title: F2WP487


title: F2WP1434


title: F2WP1041


title: F2WP667


title: F2WP1215


title: F2WP1546


title: F2WP1623


title: F2WP664


title: F2WP739


title: F2WP1767


title: F2PW441


title: F2WP1586


title: F2WP489


title: F2WP1155


title: F2WP1213


title: F2PW783


title: F2PW540


title: F2WP1157


title: F2WP835


title: F2PW539


title: F2WP948


title: F2WP396


title: F2WP1411


title: F2WP416


title: F2WP1480


title: F2WP1479


title: F2WP1302


title: F2WP592


title: F2WP1706


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title: F2WP1545


title: F2WP1117


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title: F2WP972


title: F2WP963


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title: F2PW642


title: F2WP491


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title: F2WP600


title: F2WP1481


title: F2WP1415


title: F2WP498


title: F2WP395


title: F2WP718


title: F2WP687


title: F2WP493


title: F2WP1544


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title: F2WP513


title: F2WP1466


title: F2WP744


title: F2WP851


title: F2WP920


title: F2WP499


title: F2WP428


title: F2WP334


title: F2WP950


title: F2WP767


title: F2WP1785


title: F2WP729


title: F2WP846


title: F2WP426


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title: F2WP834


title: F2WP1472


title: F2WP691


title: F2WP1713


title: F2WP830


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title: F2WP1523


title: F2WP606


title: F2WP659


title: F2WP1482


title: F2WP921


title: F2WP924


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title: F2WP500


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title: F2WP829


title: F2WP719


title: F2WP657


title: F2WP918


title: F2WP741


title: F2WP839


title: WSB1486

value: Domesticus


title: F2WP833


title: WSB1487


title: F2WP825


title: F2WP730


title: WSB1325


title: WSB1224


title: F2WP743


title: FP180


title: WSB1175


title: WSB1391


title: WSB1488


title: WSB1174


title: FP187


title: FP078


title: F2WP673


title: Modern Human (I1583) Reconstructed Methylome

first: David

last: Gokhman

address: Givat Ram, Safra Campus

description:
Reconstructed DNA methylation
Full DNA methylation maps were reconstructed from the genomes of ancient individuals, based on the asymmetry of post-mortem deamination in methylated vs. unmethylated cytosines. Genomes were aligned to hg19. Pre-mortem substitutions were removed in single-stranded libraries based on the G->A ratio in the opposite strand. In double-stranded libraries, pre-mortem substitutions were removed using a threshold of 0.25 for the C->T ratio. A sliding window of 25 CpGs was used to smooth the signal and account for stochasticity in deamination.

data_processing:
Sequence quality was evaluated using FastQC software v0.11.2. TRIMMOMATIC v.0-32 was used to filter low quality bases with the following parameters: -phred33 LEADING:30 TRAILING:30 MAXINFO:70:0.9 MINLEN:70. Paired-end sequencing reads were mapped to bisulfite converted human or chimpanzee (hg19, panTro4) reference genome using Bismark v0.14.3 and bowtie2 v2.2.4 not allowing multiple alignments and using the following parameters: --bowtie2 --non_bs_mm --old_flag -p 4. Potential PCR duplicates were removed using Bismark’s deduplicate_bismark_alignment_output.pl Perl program. Bismark’s bismark_methylation_extractor script was used to produce methylation calls with the following parameters: -p --no_overlap --comprehensive --merge_non_CpG --no_header --bedGraph --multicore 2 --cytosine_report. Examination of the M-bias plots led us to ignore the first 5 bp of both reads in human samples. Custom scripts were used to summarize methylation levels at CpG sites based on the frequencies of methylated and unmethylated mapped reads on both strands.
Reconstruction of ancient methylation maps was done as described previously by Gokhman et al. 2014. C->T ratio was computed for every CpG position along the hg19 (GRCh37) human genome assembly, for each of the hominins, as previously described. In all genomes, a fixed sliding window of 25 CpGs was set for the smoothing of the C->T ratio. This allowed for an unbiased scanning of differentially methylated regions (DMRs) that is not affected by the size of the window. C->T ratios were translated to methylation percentages using linear transformation based on two points - mean C->T ratio in completely unmethylated CpG positions (0% methylation, hereinafter mu0), and mean C->T ratio in completely methylated CpG positions (100% methylation, hereinafter μ100). Positions where C->T ratio > μ100 were given the μ100 values. For genomes that were extracted from bones, the modern osteoblast RRBS map was used as reference to compute the mean C->T ratio at each of these positions. For genomes that were extracted from teeth, there was no available modern reference methylation map, and therefore, we transformed the C->T ratio into methylation percentage based on the assumption that the genome-wide mean methylation is similar to bone tissue, and thus, the genome-wide mean genomic C->T ratio represents the C->T ratio of 80% methylation. In these genomes, μ0 was set to 0, and μ100 was set to 1.25 x mean genome-wide C->T ratio.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedGraph

source_name: Bone

extract_protocol: DNA was extracted from bones using QIAamp® DNA Investigator kit (56504, Qiagen). Bones were cut to thin slices (0.2-0.5 mm) and then thoroughly washed (X5) with PBS, to clean samples from blood. Bones were crushed with mortar and pestle in liquid nitrogen and 100 mg bone powder was taken to extract DNA according to the protocol "Isolation of Total DNA from Bones and Teeth" of the DNA Investigator kit.

value: Bone


title: FP034


title: Modern Human (La Brana 1) Reconstructed Methylome

source_name: Tooth

value: Tooth


title: FP052


title: Modern Human Bone WGBS 2

description:
WGBS
Whole-genome bisulfite sequencing (WGBS) was done on DNA extracted from present-day human bones.

data_processing:
Sequence quality was evaluated using FastQC software v0.11.2. TRIMMOMATIC v.0-32 was used to filter low quality bases with the following parameters: -phred33 LEADING:30 TRAILING:30 MAXINFO:70:0.9 MINLEN:70. Paired-end sequencing reads were mapped to bisulfite converted human or chimpanzee (hg19, panTro4) reference genome using Bismark v0.14.3 and bowtie2 v2.2.4 not allowing multiple alignments and using the following parameters: --bowtie2 --non_bs_mm --old_flag -p 4. Potential PCR duplicates were removed using Bismark’s deduplicate_bismark_alignment_output.pl Perl program. Bismark’s bismark_methylation_extractor script was used to produce methylation calls with the following parameters: -p --no_overlap --comprehensive --merge_non_CpG --no_header --bedGraph --multicore 2 --cytosine_report. Examination of the M-bias plots led us to ignore the first 5 bp of both reads in human samples. Custom scripts were used to summarize methylation levels at CpG sites based on the frequencies of methylated and unmethylated mapped reads on both strands.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedGraph


title: N_G0213

city: Changchun

first: Mengqi

last: Cui

address: 5368 Renmin Street

institute: National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
then mapped to hg19 whole genome using  Tophat2 and Hisat2, Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks and Stringtie software, then differentially expressed genes were found using Cuffdiff and Ballgown.
Genome_build: hg19
Supplementary_files_format_and_content: Tophat-Cufflinks-Cuffdiff was used to produce the FPKM data in the processed data files, summarized across all samples per tissue type (paracancerous (N) or liver cancer (T)).

source_name: liver

extract_protocol:
Liver tissue was removed and flash frozen on dry ice, and RNA was harvested using Trizol reagent,for each sample, 10g of total RNA was used for RNA-seq library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: paracancerous liver

tag: patient id


title: N_G0228


title: T_G0224

value: liver cancer


title: T_G0218


title: T_G0164


title: T_G0213


title: N_G0164


title: N_G0218


title: N_G0267


title: N_G0224


title: B_7_3

city: Columbus

first: John

last: Gunn

state: Ohio

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

description: processed data file: AllData_160223_GUNN_RNASeq_Results.xlsx

data_processing:
Each sample was aligned to the GRCm38.p4 assembly of the Mus musculus reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.24/) using version 2.5.0c of the RNA-Seq aligner STAR.
Features were identified from the GFF file that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count.
Differentially expressed features were calculated using DESeq2.
Genome_build: NCBI GRCm38.p4
Supplementary_files_format_and_content: AllData_160223_GUNN_RNASeq_Results.xlsx: Excel spreadsheet containing normalized read counts for each sample and differential expression data for each feature.

source_name: mouse gallbladders

extract_protocol:
rRNA was removed from 1500 ng with Epidemiology rRNA removal kit (Illumina, CA).
Libraries were constructed from first strand cDNA using ScriptSeq v2  (Illumina, CA).

tag: strain

tag: Sex

value: Male

value: Gallbladder

value: PBS control

tag: time point

value: 7 DPI


title: B_7_2

tag: treatment


title: Modern Human Bone WGBS 1


title: T_G0267


title: T_G0228


title: FP056

value: Pure


title: B_7_1


title: B_21_6

value: 21 DPI


title: A_21_2

value: Salmonella infected


title: B_21_5


title: B_21_4


title: A_7_2


title: A_21_3


title: A_7_1


title: B_21_1


title: p53−/−MEFs treatment with doxorubicin

city: Suita

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: p53−/−MEFs treatment with doxorubicin

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Data were analyzed using the bioinformatics software GeneSpring 13.0 (Agilent)

source_name: mouse embryonic fibroblasts (MEFs)

label_protocol: 200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was and purified using NucleoSpin RNA kit (Takara).

tag: genotype/variation

tag: agent

value: doxorubicin


title: dKOTreg_#1

city: La Jolla

first: Bi-Huei

last: Yang

address: 9500 Gilman Dr

institute: UCSD

data_processing:
used STAR to map raw data
normalization using Cuffdiff
Genome_build: GRCm38 genome
Supplementary_files_format_and_content: excel with fpkm

source_name: dKOTreg

growth_protocol: Foxp3cre/wtTcf7wt/wtLef1wt/wt and Foxp3cre/wtTcf7fl/flLef1fl/fl mice were bred in house under SPF condition

extract_protocol:
QIAGEN RNeasy Plus Mini Kit
Illumina TruSeq® Stranded mRNA LT - Set A

treatment_protocol: CD4 enrichment by MACS, cell sorted by FACS

tag: strain background

value: dKOTreg

value: spleen + lymph nodes

tag: cell type

value: lymphocytes


title: dKOTreg_#2


title: WTTreg_#2

source_name: WTTreg

value: wild type


title: p53−/−MEFs treatment without doxorubicin


title: FP014

value: Domesticus

value: C


title: WTTreg_#1


title: CD62L-TCF1-_#2

source_name: lymphocytes

growth_protocol: Foxp3Thy1.1Tcf7GFP reporter mice were bred in house under SPF condition

tag: genotype

value: Treg

tag: cell markers


title: CD62L-TCF1+_#2

tag: tissue


title: Hs766T_shARHGEF10

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data were normalised using quantile normalisation and log2 transformation,background correction with the lumi package in R

source_name: Pancreatic cancer cell line, ARHGEF10 knockdown

label_protocol: Standard Illumina protocol

growth_protocol: Transduced cell lines were grown under standard cell culture conditions in Dulbecco's Modified Eagle Media supplemented with 10% fetal bovine serum and 1ug/ ml puromycin for selection

extract_protocol: RNA was extracted from cultured cells with QIAGEN RNeasy mini kit according to the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment was applied to the cells prior to extraction

tag: disease

value: pancreatic adenocarcinoma

value: pancreas

value: epithelial

tag: cell line


title: A_21_1

value: Male

value: Gallbladder


title: MiaPACA2_EV

source_name: Pancreatic cancer cell line, empty vector control


title: A_7_3

value: 7 DPI


title: FP040

tag: hybrid category

value: Pure


title: p53+/+MEFs treatment without doxorubicin

value: wild-type


title: CD62L-TCF1-_#1


title: NYSCF2

source_name: Human bi-parental ESCs NYSCF2

extract_protocol:
RNA was isolated using the Total RNA Purification Micro Kit (Norgen). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples
Libraries were prepared using Illumina TruSeq RNA Library Prep Kit

tag: passage

value: ESC


title: CD62L+TCF1+_#2


title: CD62L-TCF1+_#1


title: CD62L+TCF1+_#1


title: pES6

source_name: Human parthenogenetic ESCs pES6


title: OVCA420 2.5 uM cisplatin-16 hr

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

description: Gene expression data from cisplatin treated cell line

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GenChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: OVCA420 2.5 uM cisplatin-16 hr

label_protocol: Biotinylated cRNA were prepared using MessageAmp Premier RNA Amplication Kit (ThermoFisher) according to the manufacturer's protocol with 100ng total RNA as starting material.

growth_protocol: A2780 ovarian cancer cells were grown in RPMI media containing 10% fetal bovine serum, 100 U/ml penicillin, and 100µg/ml streptomycin (Sigma-Aldrich, St. Louis, MO) in a humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Ambion, Austin, TX).

treatment_protocol: When cells reached 70% confluency, cisplatin was added to a final concentration of 5μM or 10μM for different time points - 30 minutes, 1 hour, 2 hours, and 16 hours.

value: p53 mutant

value: ovarian cancer cell line


title: OVCA420 5 uM cisplatin-16 hr

source_name: OVCA420 5 uM cisplatin-16 hr


title: OVCA420 untreated

description: Gene expression data from untreated cell line

source_name: OVCA420 untreated


title: p53+/+MEFs treatment with doxorubicin

description: p53+/+MEFs treatment with doxorubicin

value: doxorubicin


title: MiaPACA2_ARHGEF10

source_name: Pancreatic cancer cell line, ARHGEF10 overexpressing


title: Patient NP17, pre-treatment primary tumor sample, location 2

type: genomic

city: Ann Arbor

first: Karin

last: Hardiman

state: Michigan

address: 2922F Taubman Center

department: General Surgery

institute: University of Michigan

description: fresh frozen

hyb_protocol: Arrays were hybridized overnight (17 hrs). Then the arrays were washed with SSPE-based wash buffers and stained by stacking layers of streptavidin-phycoerithrin and biotinylated antistreptavidin antibody using parallel GeneChip Fluidics 450 stations.

scan_protocol: Oncoscan v3 scanning script, GeneChip Scanner 3000 7G, AGCC software

data_processing:
CEL files are combined by Affymetrix OncoScan Console v.1.1.0 software (ThermoFisher, Waltham, Massachusetts) to generate OSCHP files, which are analyzed by Nexus Copy Number v7.5 (Biodiscovry, El Segundo, California) using their SNP-FASST2 segmentation algorithm.
Probe intensity data at 50-100kb resolution across a set of 891 cancer genes and 300-400kb across the rest of the genome are generated, resulting in a median Log2 Ratio and a median B-allele frequency (BAF) measurement for each genomic segment.

source_name: Rectal cancer pre-treatment tumor NP17, primary , location 2

label_protocol: Samples were labeled with biotin according to the Affymetrix protocol for Oncoscan (P/N 703175 Rev. 1).

extract_protocol: DNA was extracted, using the Allprep mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: For radiation treatment samples, a combination 5-flourouracil (or the oral equivalent, xeloda) and radiation 5 days per week for 6 weeks for a total of 50.4 Gray (Gy) followed by a 6-10 week waiting period and then proctectomy

tag: gender

value: female

value: rectal


title: Patient NP16, pre-treatment primary tumor sample, location 3

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP16, primary , location 3


title: Patient NP16, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP16, primary


title: Patient NP19, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP19, primary

value: Xeloda


title: Patient NP18, pre-treatment primary tumor sample, location 2

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP18, primary , location 2


title: Patient NP17, pre-treatment primary tumor sample, location 1

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP17, primary , location 1


title: Patient NP18, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP18, primary


title: Patient NP19, pre-treatment primary tumor sample, location 2

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP19, primary , location 2


title: Patient NP18, pre-treatment primary tumor sample, location 3

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP18, primary , location 3


title: Patient NP16, pre-treatment primary tumor sample, location 2

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP16, primary , location 2


title: Patient NP14, pre-treatment primary tumor sample, location 1

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP14, primary , location 1

value: male


title: Patient NP12, pre-treatment primary tumor sample, location 1

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP12, primary , location 1


title: Patient NP12, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP12, primary


title: Patient NP14, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP14, primary


title: Patient NP11, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP11, primary


title: Patient NP19, pre-treatment primary tumor sample, location 3

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP19, primary , location 3


title: Patient NP11, pre-treatment primary tumor sample, location 4

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP11, primary , location 4


title: Patient NP17, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP17, primary


title: Hs766T_shGFP

source_name: Pancreatic cancer cell line,  knockdown control


title: Patient NP10, pre-treatment primary tumor sample, location 4

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP10, primary , location 4


title: Patient NP10, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP10, primary


title: Patient NP10, pre-treatment primary tumor sample, location 3

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP10, primary , location 3


title: Patient NP11, pre-treatment primary tumor sample, location 3

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP11, primary , location 3


title: Patient NP10, pre-treatment primary tumor sample, location 2

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP10, primary , location 2


title: Patient NP04, pre-treatment primary tumor sample, location 1

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP04, primary , location 1


title: Patient NP10, pre-treatment primary tumor sample, location 1

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP10, primary , location 1


title: Patient NP11, pre-treatment primary tumor sample, location 1

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP11, primary , location 1


title: Patient NP01, pre-treatment primary tumor sample, location 3

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP01, primary , location 3

value: Stage IV


title: 29991_WSDT

city: Beaverton

first: Cecily

middle: Vauna

last: Bishop

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive & Developmental Sciences

institute: Oregon National Primate Research Center

description:
Periovulatory Follicle RNA
processed.rawCounts.txt

data_processing:
adapters and low quality bases trimmed with Trimmomatic
trimmed reads aligned to Mmul8 reference genome with STAR (v020201), using Ensembl release 87 annotation. Two-pass mode was used.
Number of reads aligned to each gene calculated via STAR, using the --quantMode GeneCounts parameter. Total Unstranded counts were used.
Genome_build: Mmul8 from Ensembl
Supplementary_files_format_and_content: tab delimited text file containing the raw counts for each gene (Ensembl Gene ID) in each sample

organism: Macaca mulatta

source_name: Luteinized Granulosa Cell Total RNA

extract_protocol:
Promega ReliaPrep™ Cell RNA Miniprep System
Illumina TruSeq RNA Sample Prep v2 kit, resulting in a non-directional, polyA+ selected library

treatment_protocol: Rhesus macaques were treated using a 2-by-2 factorial design (n=10/treatment) near onset of menarche  with implants containing either cholesterol (C) or testosterone (T; 4-5 fold increase above C) and a standard or “Western-style” diet alone (WSD), or in combination (T+WSD). Following ~3.5 years of treatment, females underwent controlled ovulation (COv; n=7-10/treatment) cycles, and contents of the naturally-selected periovulatory follicle were aspirated.

tag: oocyte

value: Degenerating

tag: diet

value: WSD

tag: steroid

value: T

tag: treatment group

value: WSD+T


title: 30630_T

value: Chow

value: Chow+T


title: Patient NP01, pre-treatment primary tumor sample, location 2

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP01, primary , location 2


title: 30503_WSDT

value: MI


title: 30435_T

value: MII


title: 30019_WSDT


title: 30625_WSDC

value: C

value: WSD+C


title: 30511_WSDC


title: 29273_WSDC


title: 30237_WSDC


title: Patient NP04, pre-treatment primary tumor sample, location 2

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP04, primary , location 2


title: Patient NP01, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP01, primary

value: FOLFOX/Xeloda


title: 29901_1_WSDT


title: 30598_C

value: Chow+C


title: Patient NP01, pre-treatment primary tumor sample, location 1

description: fresh frozen

source_name: Rectal cancer pre-treatment tumor NP01, primary , location 1


title: 29809_T

value: GV


title: 30628_T


title: 30618_WSDC


title: TRA00038988: 20 FoxOTKO

city: Boston

first: Hui

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Mouse Muscle RNA-seq by Illumina HiSeq 2500

data_processing:
Reads were aligned to the mouse genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: Muscle

extract_protocol:
RNA was extracted from a mixture of powdered Quad and gastrocnemius muscles using Trizol reagent (Invitrogen).
Stranded cDNA libraries with unique index tags for each sample (48 multiplexed) were made using a directional RNA-seq kit (Wafergen).

value: KO

tag: drug

value: Muscle


title: TRA00038989: 21 STZFoxOTlox

value: Lox

value: STZ


title: TRA00038987: 19 FoxOTlox


title: 30420_WSDT


title: 30466_C


title: 29906_C


title: 30707_C


title: 29696_WSDT


title: TRA00038897: 10 FoxOTKO


title: TRA00038896: 9 FoxOTlox


title: TRA00038929: 14 STZFoxOTlox


title: TRA00038928: 13 FoxOTKO


title: TRA00038950: 17 STZFoxOTlox


title: TRA00038930: 15 STZFoxOTKO


title: TRA00038899: 11 STZFoxOTKO


title: TRA00038949: 16 FoxOTKO


title: Patient NP04, post-treatment primary tumor sample

description: FFPE

source_name: Rectal cancer post-treatment tumor NP04, primary

value: male

value: Xeloda

value: rectal


title: TRA00038951: 18 STZFoxOTKO


title: TRA00038900: 12 STZFoxOTKO


title: MSC_Stanniocalcin_3

description:
Normalized data.txt
MSC_Stanniocalcin_3

data_processing:
Raw reads were quality and adapter trimmed using cutadapt-1.9.1 prior to alignment. Reads were then aligned and quantified using RSEM- 1.3.0/STAR-2.5.2 against the human genome GRCh38 and annotation release 86, both from Ensembl. FPKM (Fragments Per Kilobase Million) and TPM (Transcripts Per Kilobase Million) values were also generated using RSEM/STAR. RNAseq data was analysed using Deseq2 package on the R environment (R version 3.5.1). Raw counts were uploaded and a Deseq object was created taking into account conditions and pool of donors as batch effect on the experimental design. Normalization was then performed using the DESeq function. Regularized log transformation was done with rlog function. Pairwise comparisons were then performed with the contrast function from which differentially expressed genes between different conditions were obtained.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: MSC

growth_protocol: Prior to co-culture MSCs were cultured at sub-confluency in alpha-MEM with nucleotides with 10 % fetal bovine serum and penicillin/streptomycine. 48h before the co-culture the MSCs were seeded at 70 % confluncy. Cord blood HSPCs from three independent donors were co-cultured with MSCs with myelocult H5100 with penicillin/streptomycine (STEM CELL TECHNOLOGIES) supplemented with 100 ng/ml STC1 (Biovendor) or PBS as control.

extract_protocol:
CB HSPCs, HPCs and MSCs were FACS-sorted directly into TRI Reagent and RNA was isolated using the Direct-zol RNA microprep kit from Zymo Research according to the manufacturer's instructions
RNA libraries were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (cat number E6420S) according to the manufacturer's instructions

value: Bone marrow

tag: phenotype

tag: treatment

value: Stanniocalcin 1


title: MSC_vehicle_2

description:
Normalized data.txt
MSC_Vehicle_2

value: Vehicle (PBS)


title: MSC_Stanniocalcin_1

description:
Normalized data.txt
MSC_Stanniocalcin_1


title: MSC_Stanniocalcin_2

description:
Normalized data.txt
MSC_Stanniocalcin_2


title: MSC_vehicle_3

description:
Normalized data.txt
MSC_Vehicle_3


title: HPCs_Stanniocalcin_Donor 3

description:
Normalized data.txt
HPCs_Stanniocalcin_5

source_name: HPCs

tag: donor

value: Cord blood


title: TRA00038439: 8 STZFoxOTKO


title: MSC_vehicle_1

description:
Normalized data.txt
MSC_Vehicle_1


title: HPCs_Stanniocalcin_Donor 1

description:
Normalized data.txt
HPCs_Stanniocalcin_3


title: HPCs_Stanniocalcin_Donor 2

description:
Normalized data.txt
HPCs_Stanniocalcin_4


title: TRA00038438: 7 STZFoxOTlox


title: HPCs_Vehicle_Donor 3

description:
Normalized data.txt
HPCs_Vehicle_5


title: HPCs_Vehicle_Donor 1

description:
Normalized data.txt
HPCs_Vehicle_3


title: TRA00038422: 4 STZFoxOTKO


title: TRA00038436: 5 FoxOTlox


title: TRA00038421: 3 STZFoxOTlox


title: HSPCs_Stanniocalcin_Donor 3

description:
Normalized data.txt
HSC_Stanniocalcin_5

source_name: HSPCs


title: TRA00038420: 2 FoxOTKO


title: HSPCs_Stanniocalcin_Donor 2

description:
Normalized data.txt
HSC_Stanniocalcin_4


title: TRA00038437: 6 FoxOTKO


title: HPCs_Vehicle_Donor 2

description:
Normalized data.txt
HPCs_Vehicle_4


title: HSPCs_Stanniocalcin_Donor 1

description:
Normalized data.txt
HSC_Stanniocalcin_3


title: TRA00038419: 1 FoxOTlox


title: HSPCs_Vehicle_Donor 3

description:
Normalized data.txt
HSC_Vehicle_5


title: WT Immobilized Set2 Rep 4

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed by means of a pipeline that used FastQC, to asses read quality, and Cutadapt 1.7.1 to trim sequencing reads, eliminating Illumina adaptor remains, and to discard reads that were shorter than 30 bp.
The resulting reads were mapped against the mouse transcriptome (GRCm38, release 76; aug2014 archive) and quantified using RSEM v1.2.20.
Data were normalized using Voom with the Bioconductor package EdgeR-limma
Genome_build: GRCm38, release 76
Supplementary_files_format_and_content: tab-delimited text files include Voom-normalized counts per million reads sequenced

source_name: Tibialis anterior muscle

extract_protocol:
Tibialis anterior muscleswere removed, flash frozen on dry ice, and RNA was harvested using the combination of QIAzol Lysis Reagent and RNAeasy minikit columns (Qiagen) following the manufacturer’s instructions.
cDNA library preparation and amplification were performed from 200 ng total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina.  RNAseq was performed in two sets. Sets are indicated in the sample and file names (Set1 and Set2).
RNAseq using Illumina Hiseq 2500

tag: strain

value: Skeletal muscle

tag: age

value: 4 months

value: wild type

tag: Sex


title: WT Immobilized Set2 Rep 3

tag: tissue

tag: genotype


title: 4SPII KT

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: samples are part of same experiment as GSE49039

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 2.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA (as implemented in the XPS package of Bioconductor). As we prefer at least 5 samples for proper functioning of the quantile normalization subroutine, we RMA-processed the samples together with the samples from companion study GSE49039. Reported values are on log2-scale.

source_name: thymus CD8β-CD4+CD3+ CD27- CD1+ CD69+cells

label_protocol: RNA concentration was determined with the Qubit RNA Assay using the Qubit 2.0 Fluorometer (Life Technologies), RNA purity was determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

extract_protocol: miRNAeasy kit (Qiagen), following manufacturers instructions

treatment_protocol: No treatment applied.

value: child

value: thymus


title: WT Immobilized Set2 Rep 2


title: HSPCs_Vehicle_Donor 2

description:
Normalized data.txt
HSC_Vehicle_4


title: TCRbDP

source_name: coculture TCRβ transduced (NGFR+) CD8β+CD4+ TCRαβ+  CD1a+ CD27- postnatal thymic CD34+ cells

growth_protocol: Cultured cells were cultured in alphaMEM supplemented with SCF, flt3  and interleukin-7.

value: in vitro culture from thymus stem cells


title: US8_P: dsDNA stimulated HA-US8 HFF cells

city: seoul

first: areum

last: park

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: immune

hyb_protocol: We washed the hybridized arrays, stained them using a GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using GCS3000 Scanner (Affymetrix).

source_name: dsDNA stimulated HA-US8 HFF cells

label_protocol: Approximately 5.5 µg of labeled DNA target was hybridized to the Affymetrix GeneChip Human Gene ST 2.0 ST Array at 45°C for 16 h.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HFF cells expressing empty vector, HA-US7, or HA-US8 were transfected with 500 ng/ml dsDNA for 12 h

value: human foreskin fibroblast (HFF) cells


title: HSPCs_Vehicle_Donor 1

description:
Normalized data.txt
HSC_Vehicle_3


title: Mock_M: no stimulated empty vector HFF cells

source_name: no stimulated empty vector HFF cells


title: Pax7Lo

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

data_processing:
Cell Ranger version 1.3.1 (10x Genomics) to process raw sequencing data
Seurat suite version 2.0.0 for downstream analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count value for each Sample

source_name: Satellite cells

extract_protocol:
Cellular suspensions of Pax7Hi, Pax7Mi and Pax7Lo were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell gel bead-in emulsions (GEMs), respectively. GEM-reverse transcriptions (GEM-RTs) were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific). After RT, GEMs were harvested and the cDNAs were amplified and cleaned up with the SPRIselect Reagent Kit (Beckman Coulter)
Indexed sequencing libraries were constructed using the Chromium Single-Cell 30 Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup.

value: tibialis anterior muscle

value: 3 month

tag: cell population


title: Pax7Hi


title: Aged-TA-rep3

data_processing:
Data filtering: Illumina bcl2fastq v2.19 software used for basecalling.
Alignment: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using  tophat with parameters -p 4 --rg-platform-unit Illumina  -r 200 --mate-std-dev 100 --no-coverage-search --microexon-search
Counts and differential expression was estimated using DESeq2 (Love et. al., 2014).
Genome_build: mm9

source_name: Skeletal muscle

extract_protocol:
Total RNA was extracted from skeletal muscles using the TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TA muscle

value: 18 month


title: CCS 135

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to UCSC human genome build GRCh38
Gene counts were obtained using featureCounts on GENCODE V26 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: genecounts_20190903.txt

source_name: Control Inferior Turbinate

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted by double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenolchloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA), followed by Qiagen RNeasy Micro clean-up (Qiagen, Hilden, Germany).
cDNA libraries were prepared with 2 ng total RNA input and 1 μl of a 1:50,000 dilution of ERCC RNA Spike-in Controls (Ambion®, Thermo Fisher Scientific, Waltham, MA, USA) using the SMARTSeq v2 protocol with the following modifications: 1) 20 μM template switch oligos, and 2) 250 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA).
The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on Perkin Elmer Labchip GX system (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed PE sequencing run of 2x151 cycles on Illumina HiSeq 4000 platform (30 samples/lane).

treatment_protocol: Not applicable

value: Control Inferior Turbinate


title: CCY 1


title: CCY 27


title: CCY 20


title: Pax7Mi


title: Aged-TA-rep2


title: CCS 133


title: WT Denervated Set2 Rep 4

value: male


title: WT Immobilized Set2 Rep 1


title: WT Denervated Set2 Rep 1


title: WT Denervated Set2 Rep 3


title: WT Denervated Set2 Rep 2


title: Aged-TA-rep1


title: US7_P: dsDNA stimulated HA-US7 HFF cells

source_name: dsDNA stimulated HA-US7 HFF cells


title: WT Basal Set2 Rep 4


title: Young-TA-rep2


title: CCS 132


title: WT Basal Set2 Rep 3


title: Young-TA-rep1


title: Mock_P: dsDNA stimulated empty vector HFF cells

source_name: dsDNA stimulated empty vector HFF cells


title: WT Basal Set2 Rep 2


title: WT Basal Set2 Rep 1


title: CC 212


title: H4K8ac_KO_LGMP_1

city: Houston

first: Daisuke

last: Nakada

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were trimmed for quality using Trimmomatic (version 0.36)
Trimmed reads were aligned to mm10 using bowtie2 (version 2.2.6)
bedGraph files were generated using deepTools (version 3.1.0; bamCoverage)
Peak calling, enhancer, and super-enhancer predictions were performed using HOMER (version 4.10)
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.

source_name: KO LGMP cells

extract_protocol:
50,000 WT or KO L-GMP cells were sorted and treated with Mnase, histone-DNA complexes were isolated with antibody
ChIP DNA was purified for end repair, adapter ligation, and amplification using a NEB Ultra II library preparation kit following the manufacturer’s protocols (New England BioLabs, Ipswich, MA)

tag: chip-antibody

value: H4K8ac (#2594, CST, Danvers, MA)

value: Prkaa1 and Prkaa2 double knockout

tag: cell type

value: leukemia-GMP


title: H4K8ac_KO_LGMP_2


title: H4K8ac_WT_LGMP_3

source_name: WT LGMP cells


title: CC 213


title: H4K8ac_KO_LGMP_3


title: Young-TA-rep3


title: CC 211


title: Sesn1 KO Immobilized Set2 Rep 4


title: H4K8ac_WT_LGMP_2


title: H3K27ac_KO_LGMP_3

value: H3K27ac (D5E4, #8173, CST, Danvers, MA)


title: H4K8ac_WT_LGMP_1


title: CC 205


title: Sesn1 KO Immobilized Set2 Rep 3

value: Skeletal muscle


title: H3K27ac_KO_LGMP_2


title: CC 203


title: H3K27ac_KO_LGMP_1


title: TCRaDP

source_name: coculture TCRα transduced (GFP+) CD8β+CD4+ TCRαβ+   CD1a+ CD27- postnatal thymic CD34+ cells


title: CC 202


title: H3K27ac_WT_LGMP_3


title: H3K27ac_WT_LGMP_2


title: CC 111


title: H3K27ac_WT_LGMP_1


title: H3K9ac_KO_LGMP_3

value: H3K9ac (C5B11, #9649, CST, Danvers, MA)


title: H3K9ac_KO_LGMP_2


title: Sesn1 KO Basal Set2 Rep 4

value: 4 months


title: CC 110


title: Sesn1 KO Immobilized Set2 Rep 1


title: H3K9ac_KO_LGMP_1


title: Sesn1 KO Basal Set2 Rep 3


title: aES3 T

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

institute: The Hebrew University of Jerusalem

scan_protocol: HumanMethylation450 BeadChips were scanned with Illumina's iScan System

data_processing: IDAT files were processed and normalized by subset-quantile within array normalization (SWAN) using the R package ChAMP (version 2.4.0)

label: Cy5 and Cy3

source_name: Teratoma derived from human androgenetic ESCs aES3

extract_protocol: Genomic DNA was isolated with GenElute Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) or High Pure PCR Template Preparation Kit (Roche) and bisulfite converted with EZ DNA Methylation Kit (Zymo Research) according to the manufacturer's protocol

tag: cell line

tag: passage

value: Teratoma


title: CC 109


title: H3K9ac_WT_LGMP_2

value: wild type


title: Sperm A

source_name: Human sperm A

value: Sperm


title: Input_KO_LGMP_2


title: CC 107


title: H3K9ac_WT_LGMP_3


title: Input_KO_LGMP_1


title: WT Immobilized Set1 Rep 3


title: aES1

source_name: Human androgenetic ESCs aES1

value: ESC


title: aES3

source_name: Human androgenetic ESCs aES3


title: CU-ES4

source_name: Human bi-parental ESCs CU-ES4


title: Input_WT_LGMP_3


title: aES1 T

source_name: Teratoma derived from human androgenetic ESCs aES1


title: pES10 T

source_name: Teratoma derived from human parthenogenetic ESCs pES10


title: CC 108


title: H3K9ac_WT_LGMP_1


title: Input_KO_LGMP_3


title: Sesn1 KO Basal Set2 Rep 1

source_name: Tibialis anterior muscle


title: CC 106


title: Input_WT_LGMP_2


title: CU-ES5

source_name: Human bi-parental ESCs CU-ES5


title: Input_WT_LGMP_1


title: WT Immobilized Set1 Rep 2


title: CC 105


title: Sperm F

source_name: Human sperm F


title: pES10 rep1

source_name: Human parthenogenetic ESCs pES10, biological replicate 1


title: Sesn1 KO Immobilized Set2 Rep 2


title: aES5

source_name: Human androgenetic ESCs aES5


title: WT Immobilized Set1 Rep 1


title: CC 104

source_name: Control Inferior Turbinate


title: WT Basal Set1 Rep 4


title: CC 103


title: Sperm D

source_name: Human sperm D


title: WT Basal Set1 Rep 3


title: CC 102


title: Chimpanzee Bone RRBS

address: Givat Ram, Safra Campus

description: RRBS

data_processing:
Sequence quality was evaluated using FastQC software v0.11.2. TRIMMOMATIC v.0-32 was used to filter low quality bases with the following parameters: -phred33 LEADING:30 TRAILING:30 MAXINFO:70:0.9 MINLEN:70. Paired-end sequencing reads were mapped to bisulfite converted human or chimpanzee (hg19, panTro4) reference genome using Bismark v0.14.3 and bowtie2 v2.2.4 not allowing multiple alignments and using the following parameters: --bowtie2 --non_bs_mm --old_flag -p 4. Potential PCR duplicates were removed using Bismark’s deduplicate_bismark_alignment_output.pl Perl program. Bismark’s bismark_methylation_extractor script was used to produce methylation calls with the following parameters: -p --no_overlap --comprehensive --merge_non_CpG --no_header --bedGraph --multicore 2 --cytosine_report. Examination of the M-bias plots led us to ignore the first 5 bp of both reads in human samples. Custom scripts were used to summarize methylation levels at CpG sites based on the frequencies of methylated and unmethylated mapped reads on both strands.
Genome_build: panTro4 (Pan_troglodytes-2.1.4)
Supplementary_files_format_and_content: bedGraph

organism: Pan troglodytes

source_name: Bone

extract_protocol:
DNA was extracted from bones using QIAamp® DNA Investigator kit (56504, Qiagen). Bones were cut to thin slices (0.2-0.5 mm) and then thoroughly washed (X5) with PBS, to clean samples from blood. Bones were crushed with mortar and pestle in liquid nitrogen and 100 mg bone powder was taken to extract DNA according to the protocol "Isolation of Total DNA from Bones and Teeth" of the DNA Investigator kit.
RRBS libraries were generated according to Boyle et al. Briefly, 100-200 genomic DNA was digested with MspI, subsequently the digested DNA fragments were end-repaired and adenylated in the same reaction. After ligated with methylated adapters, samples with different adapters were pooled together and subjected to bisulfite conversion using the EpiTect Bisulfite kit (QIAGen) per the manufacturer's recommendations with the following modification: after first bisulfite conversion, the converted DNA was treated with sodium bisulfite again to guarantee that conversation rates were no less than 99%. Two-third of bisulfite-converted DNA was PCR amplified and final RRBS libraries were sequenced in an Illumina HiSeq 2000 sequencer.

value: Bone


title: CC 101


title: pES7

source_name: Human parthenogenetic ESCs pES7


title: WT Basal Set1 Rep 2


title: WT Basal Set1 Rep 1


title: PY 304

source_name: Nasal Polyp Tissue

value: Nasal Polyp Tissue


title: CU-ES4 T

source_name: Teratoma derived from human bi-parental ESCs CU-ES4


title: H99-vivo Sample 116

city: Durham

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

data_processing:
The quality filtering and adaptor trimming were performed using Cutadapt (v 1.12).
Paired-read alignment for RNA-seq data was carried out against the gene set for C. neoformans var. grubii H99 (CNA3)  excluding non-coding RNAs and mitochondria genes, using STAR (v 2.5.3a).
The expected read count for each gene was computed based on a maximum likelihood estimate, derived from an Expectation Maximization algorithm in RSEM (v1.2.31).
The expected count data were then converted to counts per million (CPM) and normalized by adjusting with the effective library size via the calcNormFactors function implemented in edgeR (v. 3.16.5).
The DEGs were determined by using the negative binomial generalized linear models with quasi-likelihood tests (glmQLFit and glmQLFTest functions in the edgeR package).
Genome_build: CNA3 (GCA_000149245.3)
Supplementary_files_format_and_content: Tab-delimited text files containing expected counts of all genes for all samples.
Supplementary_files_format_and_content: Tab-delimited text files containing FDR P-values of differential gene expression test for each comparison.
Supplementary_files_format_and_content: Tab-delimited text files containing the Log fold-changes of differential gene expression test for each comparison.

organism: Cryptococcus neoformans

source_name: yeast cell

growth_protocol: The strains were extracted from five different culture conditions for 24 hours including growth in yeast extrace-peptone-dextrose (YPD), starvation-low-iron medium (SLIM) and Pigeon Guano (PG) medium, macrophages, and rabbit cerebrospinal fluid

extract_protocol:
These lyophilized samples were treated with Trizol and total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions.
Library preparation was prepared by shearing the RNA and adapted for Illumina sequencing using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA).

tag: isolate

value: VNI

tag: source

value: Clinic

tag: condition

value: rabbit cerebrospinal fluid

tag: repeat

value: Rep 1


title: Bt85-vivo Sample 114

value: VNBI


title: CHC193-vivo Sample 118