title: WT3CRB

city: Dublin

first: Albert

last: Sanfeliu

address: Trinity Translational Medicine Institute, St James's Hospital, James's Street

department: Psychiatry

country: Ireland

institute: Trinity College Dublin

data_processing:
Reads were aligned to the Ensembl GRCm38 mouse genome construct using Hisat2 with default parameters
Count tables were generated using Stringtie, using the –e and –B options (simplified protocol) and the rest of parameters on default. The output of Stringtie was processed with the script prepDE.py provided by the developers
Genome_build: GRCm38
Supplementary_files_format_and_content: Csv file consisting of a matrix of raw counts for each sample at the gene level. Counts are associated to Ensembl Ids and MGI gene names

source_name: Cerebellum

extract_protocol:
Cerebellum was dissected, frozen in dry ice and stored at -80ºC until extraction. RNA was extracted and purified using the miRNeasy Mini Kit (Qiagen - iD: 217004).  RNA integrity and concentration were measured using a Bioanalyzer; only samples with a RIN > 7 were used.
Libraries were prepared using a NEBNext Ultra Directonal RNA Library Prep Kit for Illumina (New England Biolabs - #E7760), along with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs - #E7490S) and the NEBNext Multiplex Oligos for illumina (New England Biolabs - #E7335S).

value: WT

value: Cerebellum

value: 7 weeks


title: WT1BL

status: Public on Apr 29 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Blood

extract_protocol:
Blood was extracted by cardiac suction and stored in  RNAprotect Animal Blood Tubes (Qiagen - ID: 76544). RNA qas extracted and purified using the Rneasy Protect Animal Blood Kit (Qiagen - ID: 73224). Globin mRNA was depleted using the Mouse/rat GLOBINclear Kit (Ambion - AM1981). RNA integrity and concentration were measured using a Bioanalyzer; only samples with a RIN > 7 were used.
Libraries were prepared using a NEBNext Ultra Directonal RNA Library Prep Kit for Illumina (New England Biolabs - #E7760), along with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs - #E7490S) and the NEBNext Multiplex Oligos for illumina (New England Biolabs - #E7335S).

tag: strain

tag: genotype

tag: tissue

value: Blood

tag: age


title: WT3BL


title: NULL3CRB


title: NULL2CRB


title: NULL1BL


title: NULL2BL


title: WT2BL


title: 125S: EXOME of homo sapiens, recipient liver

type: genomic

city: Shanghai

first: Yuan

last: Liu

state: Shanghai

address: No.277 Chongqingnan Road, Huangpu Distict,Shanghai

country: China

institute: Shanghai Jiaotong University school of medicine

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.113 BeadChip.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: Illumina MiSeq® System

data_processing: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium ® Human Exome-12 v1.2 BeadChip (Illumina).

label: cy3, cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: recipient liver

label_protocol: 600ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Both donor and recipient genomic DNA were extracted from liver tissues (stored at -80°C) using an AllPrep DNA/RNA Mini Kit

value: recipient liver

tag: gender

value: female


title: 118S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.106 BeadChip.

value: male


title: 119S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.107 BeadChip.


title: 123S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.111 BeadChip.


title: NULL1CRB


title: 117S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.105 BeadChip.


title: WT1CRB


title: WT2CRB


title: NULL3BL


title: ES Pcgf2/4-/- rep2

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

data_processing:
bcl2fastq v2 for basecalling
Adaptors and the last nucleotide (the number 51) were removed and reads where mapped to mm9 using: 1. tophat (v2.1.1) with parameters --no-coverage-search --library-type fr-unstranded (RNA-seq) and 2. bowtie v1.2.2 with default parameters without allowing for multi-mapping (-m 1) (ChIP-seq).
PCR duplicates were removed using picard tools (1.62)
For RNA-seq, read counts per gene were calculated using Htseq-count (v0.7.2) with parameters -q -t exon --stranded=no --mode=intersection-nonempty using the mm9 Refseq gtf from UCSC. Genes with 0 counts in all samples were removed and differential analysis was performed using DESeq2 (v3.7) with default parameters.
For ChIP-seq, peaks were called using MACS2 v2.1.1 with parameters -g mm --nomodel -p 1e-10 –B
Genome_build: mm9
Supplementary_files_format_and_content: NarrowPeak: Peaks called by MACS2 with -log10(pvalue) >= 10^5; DESeq output file: Results of differential expression analyses performed with DESeq2; GeneCounts: output from Htseq-count containing the number of counts per gene.

molecule: polyA RNA

source_name: Mouse Embryonic Stem Cells

growth_protocol: All ESC lines (E14 and derivatives) were grown in a 0.1% gelatin-coated dish in GMEM supplemented with 15% FBS (Euroclone), 2 mM L-glutamine, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 0.1 mM non- essential amino acids, 1 mM sodium pyruvate, 50 µm -mercaptoethanol (Gibco), leukemia inhibitory factor, 3 µm GSK3β inhibitor (CHIR99021, STEMCELL Technologies), 1 µm MEK1/2 Inhibitor (PD0325901, STEMCELL Technologies). For knockdown experiments, cells were transduced with 5 µg/mL polybrene and lentivirus particles delivering pLKO.1 vector expressing specific shRNAs for 16 hr; cells were then puromycin-selected (2 µg/mL) and grown for 72 hr prior harvesting.

extract_protocol:
ChIP assays were carried out as described previously (Ferrari et al., 2014) . Briefly, 1% formaldehyde cross- linked chromatin (1 mg) was fragmented by sonication to an average size of 300–600 bp and incubated overnight in IP Buffer (33 mM Tris-HCl, pH 8, 100 mM NaCl, 5 mM EDTA, 0.2% NaN 3 , 0.33% SDS, 1% Triton X-100) at 4ºC with 1–8 µg of the indicated antibodies, followed by incubation for 2–4 hr with protein A sepharose beads (GE Healthcare). Beads were washed three times with 150 washing buffer (20 mM Tris/HCl, pH 8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1 % Triton X-100), once with 500 wash buffer (20 mM Tris/HCl, pH 8, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), and re-suspended in 120 µl of de-crosslinking solution (0.1 M NaHCO3, 1% SDS). For ChIP-seq, column-purified DNA from a ChIP experiment was quantified using the Qubit dsDNA HS Assay Kit (Thermo Scientific, Q32854) and 10 ng DNA were processed at IEO NGS core unit employing an automated platform (Beckman Coulter) with the Illumina ChIP-seq sample prep kit (IP-102-1001) and multiplexing oligonucleotide kit (PE400-1001). DNA libraries were quality-checked and quantified on an automated sample processing workstation (Caliper Life Sciences) and used for cluster generation and sequencing by the HiSeq 2000 (Illumina) and 50 bp read length. For PCGF1 ChIP, chromatin was crosslinked for 50 min at RT with 2 mM EGS (Sigma) and then for 10 min with 1% formaldehyde. For histone modifications, quantitative ChIP experiments were performed relative to a reference exogenous genome (ChIP-Rx) (Orlando et al., 2014) . For this, a total of 5% of Drosophila chromatin from S2 cell line, with a sheared size of 200–300 bp, was added to each ChIP reaction.
RNA-seq was performed with minor modifications according to the SMART-seq2 protocol (Picelli et al., 2014) . Briefly, poly-A containing mRNA molecules from 2 g of total extracted RNA were copied into first- strand cDNA by reverse transcription and template-switching using oligo(dT) primers and an LNA- containing template-switching oligo (TSO); resulting cDNA was pre-amplified, purified, and tagmented with in-house produced Tn5 transposase. cDNA fragments generated after tagmentation were gap-repaired, amplified by PCR, and cleaned to obtain the final cDNA library.

treatment_protocol: To generate stable Pcgf KO cell lines, 10 µg pX459 2.0 plasmids (Addgene) encoding Cas9 and sgRNAs were transfected using Lipofectamine 2000 (Invitrogen), according to the manufacturer´s instruction. Puromycin selection was performed for 30 hr at 2 µg/ml, 2000 cells were seeded into a 15-cm dish, and clones were isolated 10 days later. Clones were screened by PCR for genomic DNA, and Western Blot for protein lysates. PCR from positive clones were Sanger-sequenced to confirm genome editing. For double- or triple KO cell lines, single KO clones were subjected to genome editing following the same procedure. The Ring1A –/– ;Ring1B fl/fl ;Rosa26::CreERT2 conditional mESC line was described previously (Endoh et al., 2008)

tag: cell line

tag: chip antibody


title: ES Pcgf3/5/6-/- rep2


title: ES Pcgf3/5-/- rep2


title: ES Pcgf3/5/6-/- rep1


title: ES WT rep2

value: wild-type


title: ES Pcgf1/2/4-/- rep2


title: 111S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.100 BeadChip.


title: 114S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.102 BeadChip.


title: 109S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.99 BeadChip.


title: 116S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.104 BeadChip.


title: ES Pcgf6-/- rep2


title: ES Pcgf1-/- rep2


title: 108S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.98 BeadChip.


title: Pcgf6_shCtr_ChIPseq

library_source: genomic

value: shCtr


title: ES Pcgf3/5-/- rep1


title: ES Pcgf1-/- rep1


title: Usf1_wild-type_ChIPseq


title: ES Pcgf6-/- rep1


title: ES Pcgf2/4-/- rep1


title: 115S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.103 BeadChip.


title: ES Pcgf1/2/4-/- rep1


title: ES WT rep1


title: 55G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.167 BeadChip.

source_name: donor liver

value: donor liver


title: 113S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.101 BeadChip.


title: 62G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.174 BeadChip.


title: Wdr5_wild-type_ChIPseq


title: Pcgf3_shCtr_ChIPseq


title: Pcgf3_shUsf1_ChIPseq


title: 107S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.97 BeadChip.


title: 106S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.96 BeadChip.


title: Pcgf3_shUsf2ChIPseq


title: Pcgf6_shE2F6_ChIPseq


title: Pcgf6_shE2F6-MGAdHLH_ChIPseq


title: Pcgf6_shMGA_ChIPseq

value: shMGA


title: Pcgf6_shMGAdHLH_ChIPseq

value: shMGAdHLH


title: 105S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.95 BeadChip.


title: 104S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.94 BeadChip.


title: 101S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.93 BeadChip.


title: H2AK119Ub1_Pcgf3/5/6-/-_ChIPseq


title: H3K27me3_Pcgf3/5/6-/-_ChIPseq


title: 100S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.92 BeadChip.


title: Suz12_Pcgf3/5/6-/-_ChIPseq


title: Ring1b_Pcgf3/5/6-/-_ChIPseq


title: Ring1b_Pcgf1/2/4-/-_rep2_ChIPseq


title: 97S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.90 BeadChip.


title: Pcgf3_Ring1a/b-/-_ChIPseq


title: Pcgf6_Ring1a/b-/-_ChIPseq


title: 95S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.88 BeadChip.


title: H3K27me3_Pcgf1/2/4-/-_ChIPseq


title: H2AK119Ub1_Pcgf1/2/4-/-_ChIPseq


title: 96S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.89 BeadChip.


title: Suz12_Pcgf1/2/4-/-_ChIPseq


title: H2AK119Ub1_Pcgf1/2/4-/-_rep2_ChIPseq


title: Pcgf2_Ring1a/b-/-_ChIPseq


title: Pcgf3_Ring1a-/-_Ring1bfl_ChIPseq


title: 94S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.87 BeadChip.


title: 99S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.91 BeadChip.


title: 92S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.85 BeadChip.


title: Pcgf1_Ezh1/2-/-_ChIPseq


title: Pcgf2_Ring1a-/-_Ring1bfl_ChIPseq


title: Pcgf1_Ring1a-/-_Ring1bfl_ChIPseq


title: Pcgf2_Ezh1/2-/-_ChIPseq


title: H2AK119Ub1_Pcgf6-/-_ChIPseq


title: Pcgf1_Ring1a/b-/-_ChIPseq


title: Pcgf6_Ring1a-/-_Ring1bfl_ChIPseq


title: H2AK119Ub1_Pcgf2/4-/-_ChIPseq


title: 90S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.83 BeadChip.


title: H2AK119Ub1_wild-type_ChIPseq


title: H2AK119Ub1_Pcgf1-/-_ChIPseq


title: 57G: EXOME of homo sapiens, donor liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.169 BeadChip.


title: 88S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.81 BeadChip.


title: Ring1b_Pcgf1/2/4-/-_ChIPseq


title: H3K4m3_Pcgf6-/-_ChIPseq


title: 89S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.82 BeadChip.


title: H3K36m3_Pcgf6-/-_ChIPseq


title: H3K4m3_wild-type_ChIPseq


title: H3K4m3_Pcgf3/5-/-_ChIPseq


title: H3K36m3_Pcgf3/5-/-_ChIPseq


title: H3K4m3_Pcgf2/4-/-_ChIPseq


title: H3K4m3_Pcgf1-/-_ChIPseq


title: 93S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.86 BeadChip.


title: 86S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.79 BeadChip.


title: H3K36m3_Pcgf2/4-/-_ChIPseq


title: H3K36m3_Pcgf1-/-_ChIPseq


title: 91S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.84 BeadChip.


title: 83S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.78 BeadChip.


title: 82S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.77 BeadChip.


title: H3K36m3_wild-type_ChIPseq


title: 87S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.80 BeadChip.


title: H3K27m3_Pcgf2/4-/-_ChIPseq


title: H3K27m3_Pcgf3/5-/-_ChIPseq


title: 80S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.76 BeadChip.


title: H3K27m3_Pcgf6-/-_ChIPseq


title: H3K27m3_wild-type_ChIPseq


title: Suz12_Pcgf6-/-_ChIPseq


title: H3K27m3_Pcgf1-/-_ChIPseq


title: Suz12_Pcgf3/5-/-_ChIPseq


title: 78S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.74 BeadChip.


title: 79S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.75 BeadChip.


title: Suz12_Pcgf2/4-/-_ChIPseq


title: Suz12_wild-type_ChIPseq


title: Ring1b_Pcgf6-/-_ChIPseq


title: 76S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.72 BeadChip.


title: 77S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.73 BeadChip.


title: 75S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.71 BeadChip.


title: Ring1b_Pcgf1-/-_ChIPseq


title: Ring1b_Pcgf2/4-/-_ChIPseq


title: Ring1b_Pcgf3/5-/-_ChIPseq


title: 74S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.70 BeadChip.


title: Ring1b_wild-type_ChIPseq


title: H2AK119Ub1_Pcgf3/5-/-_ChIPseq


title: Pcgf6_Pcgf3/5-/-_ChIPseq


title: Pcgf6_Pcgf6-/-_ChIPseq


title: 73S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.69 BeadChip.


title: Pcgf6_Pcgf2/4-/-_ChIPseq


title: 72S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.68 BeadChip.


title: Pcgf6_Pcgf1-/-_ChIPseq


title: Pcgf6_wild type_ChIPseq

value: wild type


title: 71S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.67 BeadChip.


title: 70S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.66 BeadChip.


title: 69S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.65 BeadChip.


title: Pcgf3_Pcgf3/5-/-_ChIPseq


title: Pcgf3_wild-type_ChIPseq


title: Pcgf2_Pcgf6-/-_ChIPseq


title: 66S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.63 BeadChip.


title: Pcgf2_Pcgf2/4-/-_ChIPseq


title: Pcgf2_Pcgf1-/-_ChIPseq


title: Pcgf2_wild-type_ChIPseq


title: Pcgf1_Pcgf3/5-/-_ChIPseq


title: Pcgf3_Pcgf1-/-_ChIPseq


title: 65S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.62 BeadChip.


title: 64S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.61 BeadChip.


title: Contusion SCI, Replicate 6

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Rattus norvegicus reference genome assembly (Rn6) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (Rn6 version 93).
The annotation file was parsed to exclude mitochondria genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 24,613 gene locations.
Genome_build: rn6
Supplementary_files_format_and_content: Expression data tracks in UCSC Genome Browser bigwig format were generated for each sample.

organism: Rattus norvegicus

source_name: dorsal root ganglion

growth_protocol: All rats were housed initially in standard cages and maintained in a continuous 12h-light/dark cycle. Tap water and a standard rodent diet were available to all rats ad libitum.

extract_protocol:
Animals were perfused with PBS supplemented with 20% RNAlater (Ambion, Life Technologies). T11-L4 bilateral DRGs were retrieved from both sides of the spinal column and collected in QIAzol (Qiagen). Total RNA from each sample was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) and Set B (Cat# RS-122-2102) with poly-A enrichment.

treatment_protocol: Animals were given either T2 complete transection SCI, T2 contusion SCI, or no SCI. A subset of contused SCI animals were exposed to either swimming or shallow water walking exercise.

tag: injury type

value: T2 Contusion

tag: weeks after injury?

value: Sprague Dawley


title: Contusion SCI, Replicate 5


title: Contusion SCI, Replicate 4


title: Input_E14_wild-type_ChIPseq

value: input


title: Suz12_Pcgf1-/-_ChIPseq


title: 63S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.60 BeadChip.


title: 61S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.58 BeadChip.


title: 62S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.59 BeadChip.


title: Pcgf2_Pcgf3/5-/-_ChIPseq


title: 67S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.64 BeadChip.


title: Contusion SCI, Replicate 3


title: Pcgf1_wild-type_ChIPseq


title: Pcgf1_Pcgf6-/-_ChIPseq


title: Pcgf1_Pcgf1-/-_ChIPseq


title: 59S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.56 BeadChip.


title: Pcgf1_Pcgf2/4-/-_ChIPseq


title: No SCI, Replicate 4

value: No SCI


title: Contusion SCI, Replicate 1


title: No SCI, Replicate 2


title: No SCI, Replicate 1


title: 57S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.54 BeadChip.


title: Complete transection SCI, Replicate 4

value: T2 Complete transection


title: Complete transection SCI, Replicate 3


title: Complete transection SCI, Replicate 2


title: Pcgf3_Pcgf6-/-_ChIPseq


title: 56S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.53 BeadChip.


title: Complete transection SCI, Replicate 1


title: Contusion SCI + SWW, Replicate 5


title: No SCI, Replicate 3


title: 54S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.51 BeadChip.


title: Contusion SCI + SWW, Replicate 4


title: Contusion SCI + SWW, Replicate 2


title: Contusion SCI + SWW, Replicate 3


title: Contusion SCI, Replicate 2


title: 53S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.50 BeadChip.


title: Contusion SCI + SWW, Replicate 1


title: Contusion SCI + SWIM, Replicate 4


title: Contusion SCI + SWIM, Replicate 5


title: 52S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.49 BeadChip.


title: 58S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.55 BeadChip.


title: Contusion SCI + SWIM, Replicate 2


title: Contusion SCI + SWIM, Replicate 1


title: 50S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.47 BeadChip.


title: 51S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.48 BeadChip.


title: 60S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.57 BeadChip.


title: 48S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.46 BeadChip.


title: SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 5

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Rattus norvegicus reference genome assembly (Rn6) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq using Ensembl annotations (Rn6 version 93).
The annotation file was parsed to exclude mitochondria genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 24,613 gene locations.
Genome_build: rn6
Supplementary_files_format_and_content: Expression data tracks in UCSC Genome Browser bigwig format were generated for each sample. GeneMatrix_RawCounts_ALL.txt includes gene counts for all samples and is available on the series record.

source_name: No Injury + Standard Cage

growth_protocol: All animal procedures were performed in accordance with the Public Health Service Policy on Humane Care and Use of Laboratory Animals (Institute of Laboratory Animal Resources, National Research Council, 1996) and the University of Louisville Institutional Animal Care and Use Committee. Female Sprague Dawley rats of body weight 235-249 g were obtained from Sprague Dawley, Inc. (Indianapolis, IN). All rats were housed in standard cages and subjected to a 12h-light/dark cycle. Tap water and a standard rodent diet were available to all rats ad libitum.

extract_protocol:
Animals were sacrificed at 11.5 weeks post-SCI or equivalent uninjured age with a ketamine overdose. The transection injury group was sacrificed  8.5 weeks post-SCI. Hearts were arrested in diastole with an injection of 3M KCl. Animals were perfused with PBS supplemented with 20% RNAlater (Ambion, Life Technologies, Carlsbad, CA). Liver tissue was collected and equal amounts of tissue (200 mg) were processed for RNA isolation using Trizol (Qiagen, Germantown, MD) using standard procedures. Total RNA from each sample was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) and Set B (Cat# RS-122-2102) with poly-A enrichment.

treatment_protocol: All rats were initially gentled for two weeks. Animals were anaesthetized with pentobarbital (50 mg/kg, IP) and given prophylactic antibiotics (gentamicin sulphate, 15 mg/kg, SC) prior to surgery and again 3 and 5 days post-injury. For animals in the contusion injury groups, a single level laminectomy was performed at the T2 vertebrae before receiving a moderately-severe contusion injury (25 g-cm SCI) at the T2 spinal cord level using the NYU Impactor. For animals in the transection injury group, a single level laminectomy was performed at the T2 vertebrae before receiving a complete transection of the spinal cord at T2. All injured animals received buprenorphine (0.1 mg/kg, SC) twice a day for three days. Manual bladder expression was performed twice daily for each animal until reflexive voiding returned.   After recovery, animals in the SCI Cage Size groups were housed two/cage in standard cages (22” x 12.5” x 8”), tiny cages (7.5” x 8.5” x 8”), to restrict their movement, or large cages (16” x 20” x 8” ), to allow for greater movement for the duration of the study. The subjects were randomized into three groups: No SCI+Standard, CONT SCI+Tiny, and CONT SCI+Large. For animals in the SCI+Activity groups, this involved housing animals two/cage in standard cages (22” x 12.5” x 8”) or tiny cages (7.5” x 8.5” x 8”, to restrict their activity) for the duration of the study. The subjects were randomized into five groups: No SCI, TX SCI, CONT SCI, CONT SCI + swimming (SWIM), and CONT SCI + shallow water walking (SWW).  Swimming and shallow water walking (three five minute bouts separated by a short break twice/day) began 10 days post-injury and was conducted 5 consecutive days/week for 8 weeks. These 15 minutes sessions were separated with an hour break in between.

tag: Sex

value: Sprague-Dawley

value: liver

tag: initial age

value: 8-9 weeks (weight-based estimate)

tag: days after injury

tag: sci level


title: SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 4


title: 47S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.45 BeadChip.

value: recipient liver


title: SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 1

value: female


title: SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 2


title: SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 5

source_name: Contusion SCI + Tiny Cage

value: Contusion SCI

tag: age at injury

value: 11.5 weeks post injury

value: Level T2


title: 45S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.44 BeadChip.

value: male


title: SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 4


title: 43S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.42 BeadChip.


title: SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 3


title: 44S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.43 BeadChip.


title: 42S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.41 BeadChip.


title: Pcgf3_Pcgf2/4-/-_ChIPseq


title: Contusion SCI + SWIM, Replicate 3


title: SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 2


title: SCI+In-Cage Activity Group, Contusion SCI + Tiny Cage, Replicate 1


title: 41S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.40 BeadChip.


title: SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 2

source_name: Contusion SCI + Large Cage


title: SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 3


title: SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 4


title: SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 4


title: SCI+In-Cage Activity Group, No SCI + Standard Cage, Replicate 3


title: 40S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.39 BeadChip.


title: SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 1


title: SCI+In-Cage Acitivity Group, Contusion SCI + Large Cage, Replicate 5


title: 39S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.38 BeadChip.


title: SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 2


title: SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 3


title: 38S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.37 BeadChip.


title: SCI+Exercise Group, Contusion SCI + Tiny Cage, Replicate 1


title: 37S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.36 BeadChip.


title: NL87Cp

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic was used for cleaning.
R package “QuasR” was used for the read alignment to human genome (hg19) followed by the counting at gene level.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

source_name: parietal cortex

extract_protocol:
Tissues were homogenized into Trizol Reagent (Thermo Fisher Scientific), and aqueous phase was collected after phase separation by adding chloroform. Further RNA purification was performed using Direct-zol™ RNA MiniPrep Plus (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: parietal cortex

tag: disease state

value: healthy control


title: 36S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.35 BeadChip.


title: NL89IC

source_name: internal capsule

value: internal capsule


title: NL88H

source_name: hippocampus

value: hippocampus


title: SCI+Exercise Group, No SCI + Tiny Cage, Replicate 2

source_name: No Injury + Tiny Cage


title: SCI+Exercise Group, No SCI + Tiny Cage, Replicate 3


title: NL86CF

source_name: frontal cortex

value: frontal cortex


title: SCI+Exercise Group, No SCI + Tiny Cage, Replicate 4


title: 34S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.33 BeadChip.


title: SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 3

source_name: Complete transection SCI + Tiny Cage

value: Complete transection SCI

value: 8.5 weeks post injury


title: SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 4


title: 35S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.34 BeadChip.


title: SCI+Exercise Group, No SCI + Tiny Cage, Replicate 1


title: NL82H


title: NL80CF


title: NL81Cp


title: 32S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.31 BeadChip.


title: 55S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.52 BeadChip.


title: SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 1


title: 30S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.29 BeadChip.


title: SCI+Exercise Group, Complete Transection + Tiny Cage, Replicate 2


title: NL79CC

source_name: corpus callosum

value: corpus callosum


title: 33S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.32 BeadChip.


title: SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 5

source_name: Contusion SCI + Sww + Tiny Cage

value: Sprague-Dawley


title: 31S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.30 BeadChip.


title: 29S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.28 BeadChip.


title: SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 4

value: liver


title: NL77IC


title: SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 2

value: 8-9 weeks (weight-based estimate)


title: NL76H


title: 28S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.27 BeadChip.

value: recipient liver


title: NL83IC


title: 27S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.26 BeadChip.


title: SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 1

value: female


title: NL75Cp


title: NL74CF


title: 25S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.24 BeadChip.


title: SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 5

source_name: Contusion SCI + Swim + Tiny Cage

value: Contusion SCI


title: SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 4

value: 11.5 weeks post injury


title: 24S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.23 BeadChip.


title: NL73CC


title: 23S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.22 BeadChip.


title: NL71IC


title: SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 3

value: Level T2


title: NL70H


title: SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 1


title: NL68CF


title: SCI+Exercise Group, Contusion SCI + SWW + Tiny Cage, Replicate 3


title: NL69Cp


title: 26S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.25 BeadChip.

value: male


title: ΔHel-C_rep1

city: Tokyo

first: Shigeki

last: Hirakata

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Adapter-trimmed reads equal to or longer than 18 nucleotides in length were mapped against the Drosophila genome (BDGP Release 6 + ISO1 MT/dm6) with FlyBase gene model (Release 6.21) using STAR (Dobin et al., 2013). Uniquely mapped reads with up to two mismatches were used for further analysis.
Reads mapped to transposons and genes were counted using HTSeq (Anders et al., 2015). For transposon annotation, the annotation file of repeat sequences was obtained from RepeatMasker (dm6 – Apr 2006 – RepeatMasker open-4.0.6 – Dfam 2.0) and transposons were extracted without distinction between I-int and LTR. Reads mapped to exons of coding genes but not overlapping with repeat sequences, tRNAs, rRNAs, snRNAs, snoRNAs, pseudo genes, ncRNAs, and pre-miRNAs were counted as genic piRNAs using annotation files obtained from RepeatMasker (for repeat sequences) and FlyBase (for the other features). Merged reads of biological duplicates were normalized to one million mapped reads.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-deliminated text files include normalized count of reads mapped to each genes in sense orientation and transposons in antisense orientation.

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells (OSC)

growth_protocol: Cells were grown at 26 degrees on OSC medium as described previously (Saito et al., 2009).

extract_protocol:
Piwi-piRNA complexes were isolated with antibody as described previously (Saito et al., 2010).
RNAs of 23−30 nucleotides in length were eluted from the gels and cloned manually based on the manufacturer’s instructions for the TruSeq Small RNA Sample Prep Kit (Illumina), as previously described (Sumiyoshi et al., 2016).

treatment_protocol: Transfection of plasmids and siRNAs was performed using a Nucleofector 2b device as described previously (Yashiro et al., 2018).

tag: cell type

value: Ovarian Somatic Cells (OSC)

tag: plasmid

value: Yb delta-Hel-C

tag: antibody

value: Flag (Medical & Biological Laboratories, M185-3L)

tag: sirna

value: siYb


title: ΔHel-C_rep2


title: 21S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.20 BeadChip.

source_name: recipient liver

tag: tissue


title: 22S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.21 BeadChip.

tag: age


title: NL65IC

value: internal capsule

value: healthy control


title: WT_Yb_rep_2

value: Yb WT


title: NL67CC

value: corpus callosum


title: 17S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.17 BeadChip.

tag: gender


title: 15S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.15 BeadChip.


title: NL63Cp

value: parietal cortex


title: SCI+Exercise Group, Contusion SCI + Swim + Tiny Cage, Replicate 2

tag: strain

value: Sprague-Dawley

value: liver


title: NL62CF

value: frontal cortex


title: 14S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.14 BeadChip.

value: recipient liver


title: 13S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.13 BeadChip.


title: 20S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.19 BeadChip.


title: MS59IC

value: MS


title: 18S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.18 BeadChip.

value: female


title: MS58H

value: hippocampus


title: NL61CC


title: 11S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.11 BeadChip.


title: NL64H


title: WT_Yb_rep_1


title: 16S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.16 BeadChip.

value: male


title: 9S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.9 BeadChip.


title: MS57Cp


title: MS56CF


title: MS55CC


title: 8S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.8 BeadChip.


title: Testis_RR_rep19

type: RNA

city: Bergen

last: Crespo

address: Nordnesgaten 50

department: Reproduction and Developmental Biology

country: Norway

institute: Institute of Marine Research

description: Gene expression after exposure to a restricted ration

hyb_protocol: Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing and scanning

scan_protocol: Standard parameters (5 µm and 20 bits; DNA Microarray Scanner, Agilent Technologies)

data_processing: Data were then collected with Feature Extraction software (version 10.7.1.1; Agilent Technologies), log2-transformed and submitted to a quantile normalization, Normalized and filtered data were imported into GeneSpring GX version 11.0.2 (Agilent Technologies)

organism: Salmo salar

label_protocol: For each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (> 0.825 µg cRNA) and specific activity (> 6 pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with NanoDrop, and 600 ng of each Cy3-cRNA was fragmented and hybridized on a different subarray

extract_protocol: Testicular tissue was homogenized in 2 mL tubes containing Trizol reagent from the iPrep Trizol Plus RNA Kit (Invitrogen, Carlsbad, California, USA) and zirconium oxide beads in a Precellys 24 Homogenizer (Bertin, Villeurbanne, France). Subsequently, total RNA was extracted in an iPrep Purification Instrument (Invitrogen), according to the manufacturer's instructions. Total RNA yield was determined using a NanoDrop ND-1000 spectrophotometer (Labtech, Palaiseau, France) and RNA integrity was checked with an Agilent Bioanalyzer (Agilent Technologies, Massy, France)

value: Testis

tag: ration

value: Normal


title: Testis_RR_rep21


title: MS53IC


title: 6S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.7 BeadChip.


title: NL85CC


title: MS52H


title: 12S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.12 BeadChip.


title: Testis_RR_rep18


title: Testis_RR_rep17


title: Testis_RR_rep14


title: Testis_RR_rep16


title: Testis_RR_rep15


title: MS51Cp


title: 10S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.10 BeadChip.


title: 5S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.6 BeadChip.


title: 4S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.5 BeadChip.


title: H3K79me2 ChIP-seq on 5d cultured HSPC with MLLT3 shRNA virus (#93), sample1

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

data_processing:
Alignment: Bowtie2 v2.2.5
Coverage file: Bamcoverage, Deeptools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig tracks for each of the samples

source_name: human FL CD34+CD38-/lowCD90+GFP+

growth_protocol: Fetal Liver is mechanically disrupted. CD34+ cells are magnetically separated. cells are infected with MLLT3_OE lentivitus or control and cultured for 4 weeks on OP9M2. K562 cultured in IMDM w 10%FBS, P/S/G

extract_protocol:
Cells are crosslinked 10' in 1%formaldehide, lysed and sonicated. The indicated mark is immunoprecipitated overnaight, and enriched by magnetical isolation. IP fraction is eluted and decrosslinked.
Ovation Ultralow v2 (Nugen)

treatment_protocol: lentivirus infection with MLLT3 overexpression or empty vector. lentivirus infection with MLLT3 shRNA (#93) or empty shRNA (LKO) vector. Treatment with DMSO or EPZ-5676 500nM

value: FL-HSPC

tag: chip antibody

value: Abcam, ab3594


title: H3K79me2 ChIP-seq on 10d cultured HSPC with MLLT3 virus, and treated with EPZ-5676


title: Testis_RR_rep13


title: H3K79me2 ChIP-seq on 5d cultured HSPC with MLLT3 shRNA virus (#93), sample2


title: MS50CF


title: MS49CC


title: 3S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.4 BeadChip.


title: Testis_RR_rep20


title: MS47IC

value: internal capsule


title: 2S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.3 BeadChip.


title: H3K79me2 ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample5


title: 1S: EXOME of homo sapiens, recipient liver

description: Genomic DNA extracted from donor and recipient liver was genotyped using Infinium® Human Exome-12 v1.2 BeadChip.


title: H3K79me2 ChIP-seq on 10d cultured HSPC with MLLT3 virus, and treated with DMSO


title: Testis_RR_rep10


title: MS46H


title: MS45Cp


title: Testis_RR_rep11


title: H3K79me2 ChIP-seq on 5d cultured HSPC with CTR shRNA virus, sample2


title: MS44CF


title: H3K79me2 ChIP-seq on 5d cultured HSPC with CTR shRNA virus, sample1


title: NT-LW-TE

city: Guangzhou

first: Xiaoyan

last: He

address: No.483 Wushan Road, Tianhe District

institute: South China Agricultural University

data_processing:
Paired-end clean reads were aligned to the porcine reference genome using Hisat2 v2.0.4.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using DESeq or DEGSeq.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for differentially expressed genes of all samples

organism: Sus scrofa

source_name: embryos

growth_protocol: Cloned embryos were cultured in the PZM3 medium in a low-oxygen humidified atmosphere containing 5% CO2, 5% O2, and 90% N2 at 38.5°C. In vivo matured oocytes and embryos were collected immediately after rushing out of the sows with DPBS. Morphologically normal embryos with few fragments were selected for RNA-seq.

extract_protocol:
cDNA was generated and amplified with the SMART-Seq® v4 Ultra Low Input RNA Kit for Sequencing.
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit.

value: Laiwu

tag: developmental stage

value: pre-implantation

tag: method

value: nuclear transfer


title: NT-LW-MO


title: NT-LW-IT


title: Testis_RR_rep12


title: Testis_RR_rep7


title: Testis_RR_rep8


title: MS41IC


title: MLLT3 ChIP-seq on K562

source_name: ATCC

value: Genetex, GTX102835


title: Input for MLLT3 ChIP-seq on K562

value: none (input)


title: Testis_RR_rep9


title: H3K9cr ChIP-seq on uncultured HSPC

source_name: human FL CD34+CD38-/lowCD90+

value: PTM, #PTM-516


title: NT-LW-8C


title: H3K79me2 ChIP-seq on 4w cultured HSPC with MLLT3 virus, sample4


title: MS43CC

value: corpus callosum


title: MS40H


title: NT-LW-2C


title: MS39Cp

value: parietal cortex


title: H3K27ac ChIP-seq on uncultured HSPC

value: Active Motif, #39133


title: Testis_RR_rep5


title: Testis_RR_rep4


title: NT-LW-1C


title: Testis_RR_rep6


title: Testis_RR_rep3


title: NT-LW-4C


title: H3K79me2 ChIP-seq on 10d cultured HSPC with CTR virus, and treated with EPZ-5676


title: NT-D-OC1

source_name: oocytes

value: Duroc


title: NT-D-TE


title: H3K79me2 ChIP-seq on 10d cultured HSPC with CTR virus, and treated with DMSO


title: H3K79me2 ChIP-seq on 4w cultured HSPC with CTR virus, sample5


title: Testis_RR_rep2


title: Testis_RR_rep1


title: MS35IC

value: MS


title: MS37CC


title: NT-D-MO


title: Testis_NR_rep16

description: Gene expression after exposure to a normal ration


title: MS34H

value: hippocampus


title: MS33Cp


title: H3K79me2 ChIP-seq on 4w cultured HSPC with CTR virus, sample4


title: MS32CF

value: frontal cortex


title: MS38CF


title: NT-D-8C1


title: C58 wt sucrose+NH4_rep2-1

city: Gif-sur-Yvette

first: Almudena

last: González Mula

state: Ile-de France

address: 1 Avenue de la Terrasse

country: France

institute: CNRS

data_processing:
Libraries were sequenced on a NextSeq 500 instrument (Illumina, CA, USA) at the I2BC platform (Gif-sur-Yvette, France) using the 75-cycles NextSeq 500 High Output Kit
The generated data were demultiplexed using bcl2fastq2 v2.15.0 software (Illumina, San Diego, USA)
The quality of the data was checked with the software FastQC 0.10.1 from Babraham Bioinformatics, Cambridge, UK). The Illumina 3′-adapter was trimmed using Cutadapt-1.3 (Python community), and only reads with a minimal length of 10 nucleotides were kept.
After the trimming step, the data were mapped using BWA-0.7.4 (Li and Durbin, 2010) with a seed length of 32 to the appropriate reference genome of A. tumefaciens C58.
The DESeq2 package (version 1.12.4, (Love et al., 2014)) was used to analyze the differential expression of genes between sucrose+NH4 and GHB and GABA mediums. The cutoff chosen for differentially expressed genes (DEG) are a False Discovery Rate (FDR) < 0.01 and a log2 fold change > 2.
Genome_build: NC_003062.2; NC_003063.2; NC_003064.2; NC_003065.3
Supplementary_files_format_and_content: tab-delimited text files include number of reads for each sample

organism: Agrobacterium tumefaciens

source_name: bacterial cells

growth_protocol: An overnight culture of A. tumefaciens C58 was grown in AB medium supplemented with sucrose and ammonium chloride.

extract_protocol:
Exponential phase cultures were centrifuged and total RNA was extracted using the MasterPure™ Complete DNA and RNA Purification Kit according to the supplier’s instructions.
RNA-Seq libraries were constructed using the Ribo-Zero and ScriptSeq-V2 kits (Illumina)

treatment_protocol: This culture was washed twice with NaCl 0.8% and served to inoculate three replicates of AB medium with sucrose or GHB as carbon source and NH4 or GABA as nitrogen source

tag: Stage

value: exponential phase culture

tag: agent

tag: genotype

value: wild type


title: Testis_NR_rep15

value: Testis

value: Normal


title: C58 wt sucrose+NH4_rep3-1


title: NT-D-2C


title: MS31CC


title: Testis_NR_rep13


title: C58 wt sucrose+NH4_rep1-1


title: NT-D-4C1


title: Testis_NR_rep14


title: wildtype_2

city: Clemson

first: Zhicheng

last: Dou

state: South Carolina

address: 190 Collings Street

department: Biological Sciences

institute: Clemson University

description:
WT_2
Type I RH∆ku80∆hxg clone

data_processing:
Basecalls performed by bcl2fastq
Sequenced reads were trimmed for low quality bases and adaptor sequence using trimmomatic version 0.36 with recommended parameters.
Gsnap was used to align reads to the reference genome.
Subread's featureCounts was used to call features using ToxoDB-34_TgondiiGT1.gff
BioConductor's edgeR was used to filter and normalize the data and complete the differential gene expression analyses.
Genome_build: ToxoDB-34_TgondiiGT1_Genome (http://toxodb.org/toxo/)
Supplementary_files_format_and_content: tab-delimited text file including raw counts per sample for each gene in reference.

organism: Toxoplasma gondii

source_name: wildtype

growth_protocol: Parasites were grown in human foreskin fibroblasts for two days, scraped, syringed, and filter-purfied.

extract_protocol:
Total RNA was extracted by using Zymo Direct-zol RNA miniprep plus kit (R2072).
Libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA USA) and input RNA normalized to 200 ng per sample.

value: Type I RH{delta}ku80{delta}hxg clone

value: tachyzoite


title: C58 wt sucrose+GABA_rep3

value: sucrose+GABA


title: NT-D-IT1

value: pre-implantation

value: nuclear transfer


title: Testis_NR_rep11


title: C58 wt sucrose+GABA_rep2


title: NT-D-1C


title: IV-D-OC1

value: in vivo


title: IV-D-TE


title: C58 wt sucrose+GABA_rep1


title: crt-ko_1

description:
crt_1
TgCRT KO derived from RH∆ku80∆hxg clone

source_name: crt-ko

value: TgCRT KO derived from RH{delta}ku80{delta}hxg clone


title: C58 wt GHB+NH4_rep3


title: IV-D-IT1


title: Testis_NR_rep12


title: IV-D-MO


title: C58 wt GHB+NH4_rep2


title: C58 wt GHB+NH4_rep1


title: wildtype_1

description:
WT_1
Type I RH∆ku80∆hxg clone


title: IV-D-8C1


title: Testis_NR_rep8


title: Testis_NR_rep7


title: C58 wt sucrose+NH4_rep3


title: crt-ko_2

description:
crt_2
TgCRT KO derived from RH∆ku80∆hxg clone


title: A375 sgLNK-1

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
RNA-seq aligned to hg19 genome and UCSC reference transcript using STAR (version 2.4.0).
Expression analysis performed by Featurecounts (version 1.5.0).
Bigwig generated after normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

extract_protocol:
RNA was harvested using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

treatment_protocol: A375 cells were growth until 90% confluent, and then either treated with or without IFNG  (400 U/ml)  for 24 hours.

tag: cell line

value: Human melanoma cell line

tag: genotype/variation

value: LNK knockdown-1 cells

tag: treatment

value: untreated


title: IV-D-4C1

value: Duroc


title: A375 sgLNK-2

value: LNK knockdown-2 cells


title: A375 sgLNK-1 + IFNG

value: interferon gamma


title: IV-D-2C


title: A375 + IFNG

value: control cells


title: C58 wt sucrose+NH4_rep1

value: exponential phase culture

value: wild type


title: A375 sgLNK-2 + IFNG


title: Testis_NR_rep4

value: Testis

value: Normal


title: Testis_NR_rep10


title: A375


title: Testis_NR_rep6


title: IV-D-1C


title: HZ-S1

status: Public on Apr 28 2019

city: Durham

first: Hongyuan

last: Zhang

state: NC

address: 450 Research Drive

department: Orthopaedic Surgery / Cell Biology

institute: Duke University

data_processing:
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.
Reads were mapped to the GRCm38v75 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool
Reads were kept for subsequent analysis if they mapped to a single genomic location
Gene counts were compiled using the HTSeq tool
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment
Genome_build: GRCm38v75
Supplementary_files_format_and_content: excel data including lgFC, FDR and normalized expession levels

source_name: Col2a1Cre_primary sternal chondrocytes

extract_protocol:
Sterna was digested by protenase and collagenase IV. After wash, chondrocytes were collected by centrifugation. RNA was extracted using QIAGEN Rneasy kit.
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit.

tag: strain background

value: embryonic day 18.5

tag: cell type

value: Primary sternal chondrocytes


title: HZ-S2

source_name: Idh1 fl/+_primary sternal chondrocytes

value: Idh1 fl/+


title: HZ-S4


title: HZ-S5


title: C58 wt sucrose+NH4_rep2


title: Testis_NR_rep3


title: HZ-S8


title: Testis_NR_rep2


title: HZ-S7

source_name: Col2a1Cre;Idh1 fl/+_primary sternal chondrocytes

value: Col2a1Cre;Idh1 fl/+


title: Testis_NR_rep5


title: HZ-S3


title: Testis_NR_rep1


title: 1 ppm PFOS R2

city: Barcelona

first: Rubén

middle: Francisco

last: Martínez López

state: Cataluña

address: Carrer Jordi Girona, 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

data_processing:
Real Time Analysis (RTA 1.13.48) software was used for basecalling and the quality scoring of the run.
Generation of FASTQ sequence files was carried out with CASAVA software.
RNA-seq reads were aligned to the GRCz10 genome reference using STAR version 2.5.1b
Genes annotated in GRCz10.84 were quantified using RSEM version 1.2.28 with default parameters
Differential expression analysis between all PFOS conditions was performed with the DESeq2 (v.1.10.1) R package with the Likelihood ratio test option (Li and Dewey, 2011; Love et al., 2014)
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads values (normalized counts) for each sample.

organism: Danio rerio

source_name: Whole larvae

growth_protocol: Zebrafish (Danio rerio) embryos were obtained by natural mating following standard procedures. At 2 hours post fertilization (hpf), eggs were collected, rinsed and fertilized viable eggs were transferred to embryo water (90 µg/ml of Instant Ocean -Aquarium Systems, Sarrebourg, France-, 0.58 mM CaSO4·2H2O, dissolved in reverse osmosis purified water) and kept under standard conditions (28.5 ºC and 12L:12D photoperiod).

extract_protocol:
ZF embryos were taken in an Eppendorf (10 larvae per replicate) and flash frozen on dry ice. Total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA). Then, total RNA was assayed for quantity and quality using Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent Technologies).
Libraries for RNA-Seq were prepared from total RNA using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems) with minor modifications. Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads and 500 ng of total RNA as the input material, the mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters (Illumina) were added by ligation. The ligation product was enriched through 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2x76bp. We generated on average 39 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina) following the manufacturer’s protocol.

treatment_protocol: The exposure of the larvae was driven through the water: perfluorooctanesulfonate potassium salt (PFOS, Sigma-Aldrich, St. Louis, MO, USA) stock solutions (15, 150 and 500 mg·L-1) were prepared in DMSO and stored at -20 °C. During the exposure period, fresh working solutions were prepared everyday by dissolving the stock solutions in fish water, with a final concentration of DMSO of 0.2% (v/v). The final PFOS working concentrations were: 0 (control), 0.03, 0.3 and 1 mg·L-1.

value: 5 days post fertilization

value: eleutheroembryo

tag: condition

value: 1 ppm PFOS

tag: exposure time

value: from 2 to 5 dpf

tag: nº larvae/replicate


title: 1 ppm PFOS R3

tag: age


title: 1 ppm PFOS R1


title: 0.3 ppm PFOS R3

value: 0.3 ppm PFOS


title: 0.3 ppm PFOS R2


title: 0.3 ppm PFOS R1


title: HZ-S6


title: 0.03 ppm PFOS R3

value: 0.03 ppm PFOS


title: 0.03 ppm PFOS R1


title: Control R2

value: Control


title: Control R3


title: 0.03 ppm PFOS R2


title: Testis_NR_rep9

tag: tissue


title: Control R1


title: A375FlagPI3KWT-DT-7d

status: Public on Apr 27 2019

city: Chapel Hill

first: Evan

last: DuBose

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC Chapel Hill

description:
A375FlagPI3K-DT-7d_S9
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR 2.4..2a
reads were translated to transcriptome coordinates using Salmon 0.60
Isoform data were collated to single gene IDs using the R package biomaRt, and abundance estimates were upper quartile normalized using R
Genome_build: hg38
Supplementary_files_format_and_content: Processed files (.xlsx) contain normalized transcript abundance estimates, organized by official gene symbol.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
2 µg total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.

tag: cell line background

value: human BRAFV600E mutant melanoma cell line

value: PI3K WT overexpression

tag: culture media

value: DMEM supplemented with 5% FBS, 1% penicillin-streptomycin

tag: library preparation kit

value: Illumina TruSeq RNA library kit v2


title: 2_KO5-DT-24h

description:
2_KO5-DT-24h_S8
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized

value: PTEN-null


title: 2_A375WT-DMSO

description:
2_A375-DMSO_S1
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized

value: wild type


title: 2_KO5-DMSO

description:
2_KO5-DMSO_S7
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: A375Flag-PI3Kmut-DT-24h

description:
A375Flag-PI3Kmut-DT-24h_S11
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized

value: PI3K H1047R mutant overexpression


title: 2_A375WT-DT-24h

description:
2_A375-DT-24h_S2
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: 3_KO11-DT-7d

description:
KO11-DT-7d_S6
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: 2_KO11-DT-7d

description:
2_KO11-DT-7d_S12
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: 3_A375WT-DMSO

description:
3_A375-DMSO_S1
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: A375Flag-PI3Kmut-DMSO

description:
A375Flag-PI3Kmut-DMSO_S10
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: 3_A375WT-DT-7d

description:
3_A375-DT-7d_S3
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: A375Flag-PI3Kmut-DT-7d

description:
A375Flag-PI3Kmut-DT-7d_S12
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: A375FlagPI3KWT-DMSO

description:
A375FlagPI3K-DMSO_S7
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: 2_KO11-DMSO

description:
2_KO11-DMSO_S10
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: 2_KO5-DT-7d

description:
2_KO5-DT-7d_S9
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: 3_A375WT-DT-24h

description:
3_A375-DT-24h_S2
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: 3_KO11-DMSO

description:
KO11-DMSO_S4
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: KO11-DT-7d

description:
KO11-DT-7d_S12
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: KO11-DMSO

description:
KO11-DMSO_S10
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: KO5-DT-7d

description:
KO5-DT-7d_S9
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: 2_KO11-DT-24h

description:
2_KO11-DT-24h_S11
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: KO11-DT-24h

description:
KO11-DT-24h_S11
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: KO5-DMSO

description:
KO5-DMSO_S7
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: 3_KO11-DT-24h

description:
KO11-DT-24h_S5
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: A375WT-DT-7d

description:
A375-DT-7d_S3
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: 2_A375WT-DT-7d

description:
2_A375-DT-7d_S3
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: A375FlagPI3KWT-DT-24h

description:
A375FlagPI3K-DT-24h_S8
processed data file: 180801_A375WT_PTEN KO11_Pi3KWT_PI3Kmut_normalized


title: KO5-DT-24h

description:
KO5-DT-24h_S8
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: A375WT-DT-24h

description:
A375-DT-24h_S2
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized


title: Bait44_CoW1

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

data_processing:
The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (4C fragment ends), using custom Perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on homo sapiens hg19.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle tracks (win1) contain uniquely mapped reads at 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located. Scores represent the number of reads mapping to a DpnII restriction fragment end.
Supplementary_files_format_and_content: Wiggle tracks (win21) are wiggle files modified from the win1 wiggle files, with a running mean window of 21 4C fragments, to achieve a more robust and reproducible output to view in genome browsers.

source_name: Circle of Willis blood vessel

extract_protocol:
The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics (PMID 17033623)), remain unchanged. Homogenized tissue is cross-linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme treatment (Csp6I). After a second re-ligation step, the sample is purified and a 4C PCR is performed.
4C PCR

treatment_protocol: Tissue frozen in liquid nitrogen and homogenized using a Mixer Mill MM 400 tissue disrupter (Retsch GmbH) and then cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

value: Circle of Willis

tag: sample id

tag: gender

value: Female

tag: Cause of death

value: Heart failure

tag: post mortem delay

value: 6:35 hours

tag: experiment type

tag: bait number


title: Bait36_CoW1


title: Bait18_CoW1


title: Bait5_CoW1


title: Bait22_CoW1


title: Bait34_CoW1


title: Bait14_CoW1


title: Bait21_CoW2

value: 8:00 hours


title: Bait27_CoW1


title: Bait10_CoW1


title: Bait12_CoW1


title: Bait35_CoW1


title: Bait23_CoW2


title: Bait4_CoW1


title: A375WT-DMSO

description:
A375-DMSO_S1
processed data file: 160901_171023_A375 WT and PTEN KO5_KO11_2 reps normalized

tag: genotype/variation


title: Bait11_CoW1


title: Z-EL35-replicate1

city: beijing

first: LEI

last: SUN

institute: BEIJING ACADEMY OF FORESTRY AND POMOLOGY SCIENCES

description: RNA-seq of vitis:19

data_processing:
We use internal software SOAPnuke to filter reads, followed as:       1) Remove reads with adaptors;       2) Remove reads in which unknown bases(N) are more than 55%;       3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 51% in a read).       After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. For HISAT which is much faster, sensitive and high accuracy analysis software.
We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with  RSEM .  RSEM  is a software package for estimating gene and isoform expression levels from RNA-Seq data
Genome_build: The V2 reference genome of V. vinifera (http://genomes.cribi.unipd.it/grape/).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Vitis vinifera

source_name: grape

extract_protocol:
The extraction of total RNA from the berries was carried out by a Plant RNA extraction kit (Aidlab Biotechnologies, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Zaomeiguixiang

value: fruit

tag: developmental stage

tag: replicate


title: Y-EL38-replicate2

description: RNA-seq of vitis:17

value: Italia


title: Z-EL36-replicate1

description: RNA-seq of vitis:22


title: Z-EL35-replicate3

description: RNA-seq of vitis:21


title: Z-EL36-replicate3

description: RNA-seq of vitis:24


title: Z-EL38-replicate1

description: RNA-seq of vitis:25


title: Z-EL35-replicate2

description: RNA-seq of vitis:20


title: Y-EL38-replicate1

description: RNA-seq of vitis:16


title: Y-EL38-replicate3

description: RNA-seq of vitis:18


title: Z-EL38-replicate2

description: RNA-seq of vitis:26


title: Bait19_CoW1


title: Bait29_CoW1


title: Z-EL38-replicate3

description: RNA-seq of vitis:27


title: Z-EL36-replicate2

description: RNA-seq of vitis:23


title: Y-EL36-replicate3

description: RNA-seq of vitis:15


title: Y-EL36-replicate2

description: RNA-seq of vitis:14


title: Y-EL35-replicate3

description: RNA-seq of vitis:12


title: Y-EL36-replicate1

description: RNA-seq of vitis:13


title: Y-EL35-replicate2

description: RNA-seq of vitis:11


title: X-EL38-replicate2

description: RNA-seq of vitis:8

value: Xiangfei


title: Y-EL35-replicate1

description: RNA-seq of vitis:10


title: X-EL36-replicate2

description: RNA-seq of vitis:5


title: X-EL35-replicate2

description: RNA-seq of vitis:2


title: X-EL36-replicate1

description: RNA-seq of vitis:4


title: X-EL35-replicate1

description: RNA-seq of vitis:1


title: X-EL35-replicate3

description: RNA-seq of vitis:3


title: Bait43_CoW1


title: Bait46_CoW1


title: Bait45_CoW1


title: Bait40_CoW1


title: Bait39_CoW1


title: X-EL38-replicate1

description: RNA-seq of vitis:7


title: Bait32_CoW1


title: Bait33_CoW1


title: Bait30_CoW1


title: Bait28_CoW1


title: X-EL36-replicate3

description: RNA-seq of vitis:6


title: X-EL38-replicate3

description: RNA-seq of vitis:9


title: Parental MCF7 cells 2

city: Copenhagen

first: Mikkel

last: Rohde

address: Strandboulevarden 49

country: Denmark

institute: Danish Cancer Society

data_processing:
sequencing and basecalling performed by BGI, Hong-Kong, on a Illumina high-seq 2000 system
mapping to the human genomic reference sequence and quantification of reads was performed on CLC Genomic Workbench software
Genome_build: HG38
Supplementary_files_format_and_content: Gene name and expression level in RPKM. Excel file format.

source_name: Breast cancer cell line

growth_protocol: Cells were grown in DMEM + 6% FCS

extract_protocol:
RNA was isolated using Trizol reagent
Illumina standard RNA library protocol

tag: acquired resistance

tag: cell line

value: Parental MCF7


title: Parental MCF7 cells 1


title: CAD resistant MCF7 cells 2

value: 6microM siramesine

value: CAD resistant MCF7


title: CAD resistant MCF7 cells 3


title: CAD resistant MCF7 cells 1


title: Bait24_CoW1

tag: age


title: Bait25_CoW1

tag: tissue


title: Bait23_CoW1


title: Bait20_CoW1


title: Bait16_CoW2


title: Bait15_CoW1


title: Bait17_CoW2


title: Bait16_CoW1


title: Bait42_CoW1


title: Bait13_CoW1


title: Bait9_CoW2


title: Bait6_CoW2


title: Bait9_CoW1


title: Bait2_CoW2


title: Bait3_CoW2


title: Bait31_CoW1


title: Bait3_CoW1


title: Bait26_CoW1


title: Bait21_CoW1


title: Bait13_CoW2


title: Bait15_CoW2


title: retina_142 P28 hyperoxia

city: Krakow

first: Anna

last: Madetko-Talowska

state: Krakow

address: Wielicka 265

department: Medical Genetics Chair of Pediatriics

country: Poland

institute: jagiellonian university medical College

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis — Low Input Quick Amp Labeling ver.6.5

scan_protocol: SureScan Microarray Scanner (Agilent, Santa Clara, USA)

data_processing: Feature Extraction Software (Agilent, Santa Clara, USA).

source_name: Murine retina

extract_protocol: RNeasy Micro Kit (Qiagen, Hilden, Germany)

treatment_protocol: mice were stabled and bred at 24°C on a 12:12 light/dark cycle; on postnatal day 7 (P7) pups were assigned within the litters (P12, P17, P28);  each litter was then randomized either to hyperoxia (75% oxygen) or normoxia (21% oxygen)

value: day 28

tag: strain

tag: oxygen status

value: hyperoxia

source_name: Universal Mouse Reference RNA (Agilent)

tag: sample type

value: reference


title: retina_85 P28 normoxia

label_protocol: Two-Color Microarray-Based Gene Expression Analysis — Low Input Quick Amp Labeling ver.6.5

value: normoxia


title: retina_122 P28 hyperoxia


title: retina_132 P28 hyperoxia


title: retina_69 P28 normoxia


title: retina_112 P28 normoxia


title: retina_75 P28 normoxia


title: retina_49 P28 hyperoxia


title: retina_18 P28 hyperoxia


title: retina_232 P28 normoxia


title: retina_108 P28 normoxia


title: retina_89 P28 normoxia


title: retina_41 P28 normoxia


title: retina_208 P28 normoxia


title: retina_32 P28 hyperoxia


title: retina_37 P28 normoxia


title: retina_100 P28 hyperoxia


title: retina_138 P28 hyperoxia


title: retina_116 P28 hyperoxia


title: retina_204 P28 normoxia


title: retina_5 P28 normoxia


title: retina_45 P28 hyperoxia


title: retina_22 P28 hyperoxia


title: retina_236 P28 normoxia


title: retina_65 P28 normoxia


title: retina_274 P17 normoxia

value: day 17


title: retina_96 P28 hyperoxia


title: retina_284 P17 normoxia


title: retina_28 P28 hyperoxia


title: retina_279 P17 normoxia


title: donor 4 hypoxia

city: Moscow

first: Natalia

last: Kalinina

address: 27-1, Lomonosovsky av

country: Russia

institute: Lomonosov Moscow State University

description:
donor 4 hypoxia
opyt1-N4.AVG_Signal
SAMPLE 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalised using rank-invariant normalization. The file normalized_data.txt includes only normalized data for probes with p value < 0.01.  The complete normalized data set was not available.

label: standard

label_protocol: Standard Illumina labeling protocol

growth_protocol: ADSCs were isolated from donor's adipose tissue using enzyme digest and cultured for 3-4 passages in Mesenchymal Stem Cell growth medium (HyClone)

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen, cat #K0221)

treatment_protocol: 48 hrs of incubation in 1% of O2

value: adipose tissue

tag: cell type

value: adipose tissue derived stromal cells (ADSC)

tag: donor


title: donor 3 hypoxia

description:
donor 3 hypoxia
opyt1-N3.AVG_Signal
SAMPLE 6


title: donor 2 hypoxia

description:
donor 2 hypoxia
opyt1-N2.AVG_Signal
SAMPLE 4


title: donor 2 control

description:
donor 2 control
kontr1-N2.AVG_Signal
SAMPLE 3


title: donor 1 control

description:
donor 1 control
kontr1-N1.AVG_Signal
SAMPLE 1


title: donor 3 control

description:
donor 3 control
kontr1-N3.AVG_Signal
SAMPLE 5


title: retina_202 P17 normoxia


title: retina_254 P17 normoxia


title: retina_256 P17 normoxia


title: retina_195 P17 hyperoxia


title: donor 4 control

description:
donor 4 control
kontr1-N4.AVG_Signal
SAMPLE 7


title: retina_76 P17 normoxia


title: retina_192 P17 hyperoxia


title: retina_185 P17 hyperoxia


title: donor 1 hypoxia

description:
donor 1 hypoxia
opyt1-N1.AVG_Signal
SAMPLE 2


title: retina_259 P17 normoxia


title: retina_190 P17 hyperoxia


title: retina_182 P17 hyperoxia


title: retina_115 P17 hyperoxia


title: retina_8 P17 normoxia


title: retina_210 P17 hyperoxia


title: retina_29 P17 hyperoxia


title: retina_155 P17 hyperoxia


title: retina_205 P17 normoxia


title: retina_123 P17 hyperoxia


title: retina_84 P17 normoxia


title: IPAH Patient SPH753JW5029

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

hyb_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) Log(2) Signal Intensity

label: biotin

source_name: Pulmonary Artery

extract_protocol: RNA was extracted from tissue samples using a Qiagen RNEasy kit

treatment_protocol: Untreated fresh human samples

tag: diagnosis

value: IPAH

value: pulmonary artery


title: retina_175 P17 hyperoxia


title: retina_133 P17 hyperoxia


title: retina_21 P17 hyperoxia


title: Human peripheral blood mononuclear cells, ALF, rep12

city: EDINBURGH

first: Kenneth

last: Simpson

address: SCRM building, 5 Little France Drive

department: MRC Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: 3ug of fragmented, biotin-labelled cDNA was hybridised to the Affymetrix Human Gene 2.1 ST array plate in the Gene Titan using the Affymetrix standard protocols.

scan_protocol: Array plates were scanned immediately after hybridization, wash and staining using the Affymetrix hyb wash stain kit. The built in scanner on the  Affymetrix GeneTitan was used at its default settings.

data_processing: Expression data were read and processed using the Oligo package (v1.26.6) of Bioconductor. RMA background correction and quantile normalisation were applied. QC checks were carried out by examining intensity distributions both before and after pre-processing.

label_protocol: The RNA sample concentration and integrity were assessed using Agilent TapeStation and Nanodrop. Only samples with sufficient RNA and a RIN value >7 were used for labelling. The total RNA was labelled using the WT Expression Kit (Invitrogen P/N 4411974) to produce single stranded cDNA which could be labelled using the Affymetrix Terminal Labelling Kit (Affymetrix P/N 900652).

extract_protocol: RNA was extracted from frozen monocyte pellets using micro-RNAesy Kits (Qiagen) and reverse transcribed using Quantitect reverse transcription kit (Qiagen).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by density centrifugation using Histopaque (Sigma Aldrich). Monocytes were isolated using pan-monocyte isolation microbeads (Miltenyi).

tag: patient outcome

value: acute liver failure

tag: survival

value: dead or transplanted

tag: overdose type

value: mixed

value: peripheral blood mononuclear cells


title: IPAH Patient SPH703NA3085

scan_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual)


title: Human peripheral blood mononuclear cells, ALF, rep10


title: retina_272 P12 normoxia

value: day 12


title: retina_282 P12 normoxia


title: IPAH Patient SPH461LF2565

label_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual)


title: Human peripheral blood mononuclear cells, ALF, rep6

value: spontaneously survived

value: non-staggered


title: Human peripheral blood mononuclear cells, ALF, rep9


title: IPAH Patient SPH728CK5002


title: Human peripheral blood mononuclear cells, ALF, rep7


title: Human peripheral blood mononuclear cells, ALF, rep8


title: Human peripheral blood mononuclear cells, ALF, rep11


title: Human peripheral blood mononuclear cells, ALF, rep5


title: Human peripheral blood mononuclear cells, ALF, rep1


title: Human peripheral blood mononuclear cells, ALF, rep4


title: Control NC13

value: Control


title: retina_271 P12 normoxia


title: Human peripheral blood mononuclear cells, ALF, rep3

value: staggered


title: Human peripheral blood mononuclear cells, ALF, rep2


title: Control NC63


title: retina_233 P12 normoxia


title: Control GM82D


title: Control NC69


title: Human peripheral blood mononuclear cells, ALI, rep4

value: acute liver injury


title: Human peripheral blood mononuclear cells, ALI, rep3


title: retina_207 P12 normoxia

value: reference


title: Human peripheral blood mononuclear cells, ALI, rep2


title: retina_267 P12 normoxia

value: normoxia


title: Human peripheral blood mononuclear cells, control, rep4

value: control


title: Human peripheral blood mononuclear cells, ALI, rep1


title: retina_148 P12 normoxia


title: CTEPH patient 1109

source_name: pulmonary arteries surrounding thrombus

value: CTEPH

value: pulmonary arteries surrounding thrombus


title: Human peripheral blood mononuclear cells, control, rep3


title: Human peripheral blood mononuclear cells, control, rep2


title: Human peripheral blood mononuclear cells, control, rep5


title: retina_252 P12 normoxia


title: CTEPH patient 1104


title: Human peripheral blood mononuclear cells, ALI, rep7


title: CTEPH patient 949


title: retina_2 P12 normoxia


title: retina_200 P12 normoxia


title: retina_82 P12 normoxia


title: CTEPH patient 948


title: CTEPH patient 943


title: CTEPH patient 925


title: CTEPH patient 947


title: retina_90 P12 normoxia


title: retina_221 P12 hyperoxia

value: hyperoxia


title: CTEPH patient 963


title: CTEPH patient 1112


title: Human peripheral blood mononuclear cells, control, rep1


title: CTEPH patient 936


title: retina_146 P17 normoxia

value: day 17


title: CTEPH patient 924


title: retina_183 P12 hyperoxia


title: retina_228 P12 hyperoxia


title: retina_177 P12 hyperoxia


title: DAP10 rep1

city: Beijing

first: Yan

last: Long

state: China

address: Zhongguancun South street No.12

institute: Chinese Academy of Agricultural Sciences

data_processing:
Illumina High-seq 2500 software used for basecalling.
raw sequence data were transformed into raw reads by base calling. Several steps were used for clean data identification, including the removal of adapter sequences, reads in which unknown bases exceeded 10%, and low-quality sequences.
Clean data were mapped to the flax reference genome (https://phytozome.jgi.doe.gov/pz/portal.html). Then, the FPKM(Fragments Per Kilobase Of Exon Per Million Fragments Mapped) method was applied to calculate gene expression levels based on the number of reads mapped to the reference sequence. A heatmap of gene expression profiles was constructed using Mev 4.0 software with Pearson’s correction and complete linkage clustering.
Genome_build: Linum usitatissimum v1.0(https://phytozome.jgi.doe.gov/pz/portal.html)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ..

organism: Linum usitatissimum

source_name: Heiya No.14

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, 15596–026) according to the manufacturer’s instructions.
RNA samples of high quality were used to construct transcriptome sequence libraries with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s instructions.

value: seed


title: DAP20 rep2


title: DAP30 rep2


title: CTEPH patient 345


title: DAP10 rep2


title: DAP30 rep1


title: retina_179 P12 hyperoxia


title: retina_173 P12 hyperoxia


title: DAP20 rep1


title: DAP5 rep2


title: CTEPH patient 920


title: retina_188 P12 hyperoxia


title: retina_113 P12 hyperoxia


title: CTEPH patient 921


title: retina_23 P12 hyperoxia


title: retina_31 P12 hyperoxia


title: DAP5 rep1


title: WT AM

city: Seoul

first: Yeon Duk

last: Woo

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University, College of Medicine

description: Gene expression data from lung derived alveolar macrophages from Lysm-cre

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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: Lysm-Cre lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were raised under Specific Pathgen Condition. Mice between ages of 8~10 weeks were used for the following experiment

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

treatment_protocol: Lung derived alveolar macrophages were sorted via flow-cytometry followed by immediate treatment with Trizol

tag: cell

value: Alveolar macrophages

tag: genotype/variation

value: Lysm-Cre


title: KO AM

description: Gene expression data from lung derived alveolar macrophages from Lysm-creSsu72fl/fl

source_name: Lysm-CreSsu72fl/fl lung


title: Mutant No. 6 [MA1002M_0088123]

first: Chulwoo

last: Park

address: Anam

institute: Korea univ.

data_processing:
Quality-filtered reads were aligned to the reference genome sequence using Bowtie2.
The abundance of relative transcript was shown by reads per kilobase of the exon sequence per million mapped sequence reads (RPKM) defined as total exon reads / (mapped reads in millions × exon length in kilobases).
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_004758605.1
Supplementary_files_format_and_content: RPKM

organism: Deinococcus metallilatus

source_name: Automobile air-conditioning system

growth_protocol: Both strains were cultured in TYG media until 24 h with agitation (220 rpm. 30 ℃)

extract_protocol:
Total RNA was isolated from 10 ml of cells using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer's instructions
Libraries for Illumina sequencing were constructed with the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA, USA) following the manufacturer's protocol.

tag: strain background

value: mutant generated by UV-mutagenesis

tag: growth stage

value: exponential phase (24 h)


title: Wild type strain [MA1002W_0088122]

value: wild type


title: retina_153 P12 hyperoxia

value: day 12


title: retina_197 P12 hyperoxia


title: mouse_65 P28 normoxia

status: Public on Apr 26 2019

source_name: Murine blood MNC

treatment_protocol: mice were stabled and bred at 24°C on a 12:12 light/dark cycle; on postnatal day 7 (P7) pups were assigned .within the litters (P12, P17, P28);  each litter was then randomized either to hyperoxia (75% oxygen) or normoxia (21% oxygen)

value: day 28


title: mouse_45 P28 hyperoxia


title: mouse_96 P28 hyperoxia


title: mouse_32 P28 hyperoxia


title: mouse_112 P28 normoxia


title: mouse_69 P28 normoxia


title: mouse_256 P17 normoxia


title: mouse_284 P17 normoxia


title: mouse_28 P28 hyperoxia


title: mouse_138 P28 hyperoxia


title: mouse_116 P28 hyperoxia


title: mouse_274 P17 normoxia


title: mouse_89 P28 normoxia


title: mouse_122 P28 hyperoxia


title: mouse_37 P28 normoxia


title: mouse_41 P28 normoxia


title: mouse_142 P28 hyperoxia


title: mouse_75 P28 normoxia


title: mouse_254 P17 normoxia


title: mouse_204 P28 normoxia


title: mouse_85 P28 normoxia


title: mouse_239 P17 normoxia


title: mouse_279 P17 normoxia


title: mouse_49 P28 hyperoxia


title: mouse_205 P17 normoxia


title: retina_46 P12 hyperoxia


title: mouse_100 P28 hyperoxia


title: mouse_108 P28 normoxia


title: mouse_264 P17 normoxia


title: mouse_208 P28 normoxia


title: mouse_76 P17 normoxia


title: mouse_84 P17 normoxia


title: mouse_210 P17 hyperoxia


title: mouse_115 P17 hyperoxia


title: mouse_228 P12 normoxia


title: mouse_221 P12 normoxia


title: mouse_190 P17 hyperoxia


title: mouse_123 P17 hyperoxia


title: mouse_146 P17 normoxia


title: mouse_175 P17 hyperoxia


title: mouse_48 P17 hyperoxia


title: mouse_192 P17 hyperoxia


title: mouse_202 P17 normoxia


title: mouse_195 P17 hyperoxia


title: mouse_228 P12 hyperoxia


title: mouse_185 P17 hyperoxia


title: mouse_183 P12 normoxia


title: mouse_221 P12 hyperoxia


title: mouse_173 P12 normoxia


title: mouse_188 P12 normoxia


title: mouse_133 P17 hyperoxia


title: mouse_182 P17 hyperoxia


title: mouse_153 P12 normoxia


title: mouse_90 P12 normoxia


title: mouse_167 P12 normoxia


title: mouse_29 P17 hyperoxia


title: mouse_179 P12 normoxia


title: mouse_197 P12 normoxia


title: mouse_197 P12 hyperoxia


title: mouse_177 P12 normoxia


title: Batch 3-5C_Day 9

first: Yifang

last: Liu

address: Haidian District

institute: Peking University

data_processing:
To compare gene expression proﬁle between paired-end and single-end libraries, we take only the read1 from our generated sequencing paired-end reads.
The read1 and the downloaded single-end read were trimmed to the same 40bp length by using Cutadapt.
The expression values for each sample were quantified by Salmon.
Genome_build: hg19 for human
Supplementary_files_format_and_content: expression values for each sample

source_name: primary human hepatocyte

extract_protocol:
Total RNA from each sample was isolated using RNeasy Micro Kit (50) (Qiagen).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: human hepatocytes were cultured in different conditions for a few weeks and then collected for RNA extraction.

tag: tissue/cell type

value: primary human hepatocyte

tag: treatment

value: Cultured under 5C condition for 9 days

tag: batch number

value: Batch 3


title: Batch 3-Sandwich_Day 20

value: Cultured under sandwich condition for 20 days


title: Batch 3-5C_Day 20

value: Cultured under 5C condition for 20 days


title: Batch 3-Null_Day 20

value: Cultured under Null condition for 20 days


title: Batch 3-DMSO_Day 20

value: Cultured under DMSO condition for 20 days


title: Batch 3-Sandwich_Day 9

value: Cultured under sandwich condition for 9 days


title: Batch 3-DMSO_Day 9

value: Cultured under DMSO condition for 9 days


title: Batch 3-Null_Day 9

value: Cultured under Null condition for 9 days


title: Batch 2-5C_Day 30

value: Cultured under 5C condition for 30 days

value: Batch 2


title: Batch 1-DMSO_Day 27

value: Cultured under DMSO condition for 27 days

value: Batch 1


title: Batch 1-Null_Day 27

value: Cultured under Null condition for 27 days


title: Batch 1-5C_Day 40

value: Cultured under 5C condition for 40 days


title: Batch 1-DMSO_Day 40

value: Cultured under DMSO condition for 40 days


title: Batch 2-DMSO_Day 30

value: primary human hepatocyte

value: Cultured under DMSO condition for 30 days


title: Batch 1-Sandwich_Day 27

value: Cultured under sandwich condition for 27 days


title: Batch 1-Null_Day 40

value: Cultured under Null condition for 40 days


title: Batch 1-5C_Day 27

value: Cultured under 5C condition for 27 days


title: Batch 1-Sandwich_Day 40

value: Cultured under sandwich condition for 40 days


title: Batch 2-Null_Day 30

value: Cultured under Null condition for 30 days


title: Batch 1-Sandwich_Day 20

value: Cultured under sandwich condition for 20 days


title: Batch 1-Null_Day 20

value: Cultured under Null condition for 20 days


title: Batch 1-5C_Day 20

value: Cultured under 5C condition for 20 days


title: Batch 3-Adult liver tissue

source_name: human adult liver tissue

value: human adult liver tissue

value: fresh isolated

value: Batch 3


title: Batch 2-Adult liver tissue

value: Batch 2


title: Batch 1-Adult liver tissue

value: Batch 1