title: O_W0D0_O7_Unprotected


title: O_W0D7_O6_Protected

status: Public on Jun 28 2021

type: SRA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

library_source: transcriptomic

data_processing:
Quality of mRNA-seq reads were assessed using FastQC version 0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Both rhesus globin and ribosomal sequences were filtered via alignments with Bowtie v2.1.0.
Adapters were digitally removed using cutadapt, version 1.8.3.
Mapping was performed using STAR v2.4.0h1 .
Cene counts were generated using HTSeq-count v0.6.1p1.
Genome_build: Macaque mulatta genome Mmul1 (https://support.illumina.com/sequencing/sequencingsoftware/igenome.html )
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
Whole blood was collected from RM in PAXgene RNA tubes (PreAnalytiX) following the manufacturer's procedures. (PreAnalytiX). RNA was isolated using PAXgene Blood miRNA  kits (Qiagen) following the protocol provided with the kit that included an on-column DNase treatment.
Illumina TruSeq® Stranded mRNA HT kit

tag: group

value: O

value: Oral

tag: phase

value: Prime

tag: outcome

value: Protected


title: RH4_DMSO_6h_T

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
adaptor trimming and QC: fastqc v0.11.7
reads alignment: Hisat2 v2.1.0 with options “--rna-strandness RF --fr”
BAM generation and index: Samtools v1.9
Mapping QC: Qualimap v2.2.1
read fragment count at the gene level: featurecounts v1.6.3 with the options “-p -B -O -M --fraction”
differential gene expression: DESeq2 v3.7
Genome_build: GRCH38
Supplementary_files_format_and_content: final expression level of genes in text file format

organism: Homo sapiens

extract_protocol:
Total RNAs were extracted by RNeasy Plus Mini Kit (Qiagen).
Truseq Stranded Total RNA Library

treatment_protocol: RH4 cells were treated with the ACBI1 or DMSO for the indicated time before harvest of total RNA

tag: cell line

tag: diagnosis

value: rhabdomyosarcoma

tag: treatment

value: DMSO control for 6 hours

tag: genotype

value: wild type

tag: antibody


title: RH4_DMSO_24h_rep3_T

value: DMSO control for 24 hours


title: [Cappable-seq] B. anthracis 34F2 ΔatxA #2 enriched

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

country: Japan

institute: Hokkaido University

data_processing:
Library strategy: Cappable-seq
[ChIP-seq] Sequence reads were applied for adapter trimming and quality filtering using Trim Galore! version 0.6.4_dev with the option "-a GATCGGAAGAGCACACGT", followed by mapping to the genome sequence of B. anthracis Ames ancestor strain (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17. The mapping data was applied for R package csaw 1.22.1 with 158 bp of fragment length and 50 bp of window width.
[Cappable-seq] For the analysis of sequence reads, adapter sequence was removed using cutadapt 2.1 with the option "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", followed by mapping to the genome sequence of B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using Bowtie2 2.3.5 with the option "-L 16". Coverage of the first base of mapped reads was calculated for each position with considering strands.
[3´-RACE] Reads were mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-backtrack 0.7.17.
[RNA-seq] Reads were trimmed using Trim Galore! 0.6.4_dev with the option "-a AGATCGGAAGAGA", mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17, and tag counted with htseq-count.

organism: Bacillus anthracis

source_name: B. anthracis 34F2 ΔatxA

growth_protocol: A colony of the strain grew on BHI plate at 37°C for overnight was inoculated into NBY medium supplemented with 8% NaHCO3, followed by shaking at 37°C under 15% CO2 for 3 h. 100-fold diluted in NBY medium supplemented with NaHCO3 and cultured at 37°C under 15% CO2 for 3 h.

extract_protocol:
[ChIP-seq] Cells were pelleted and treated with 1% formaldehyde for for crosslinking. 250 mM glycine was added for quenching. After pelleting and resuspension in lysis buffer with cOmplete Mini Protease Inhibitor Cocktail, the samples were sonicated using Covaris S2. Supernatants were combined with Anti-FLAG M2 affinity gel for enrichment, followed by wash and protease K treatment at 65°C. [Cappable-seq] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. After removing DNA with DNA-free DNA removal kit, RNA samples followed the protocol described before (Ettwiller et al, BMC Genomics 17:199, 2016) [3´-RACE] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. DNA was removed with DNA-free DNA removal kit. [RNA-seq] RNA was extracted using TRIzol after incubating the pellet with 2% SDS. DNA was removed with DNA-free DNA removal kit. rRNA was depleted by the protocol described before (Culviner et al, mBio, 2020), followed by fragmentation with the treatment with a divalent cation and heat.
[ChIP-seq] Library was constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina. [Cappable-seq, 3´-RACE, and RNA-seq] Library was constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina.

tag: strain

value: B. anthracis 34F2 {delta}atxA


title: RH4_DMSO_48h_T

value: DMSO control for 48 hours


title: RH4_ACBI1_250nM_24h_rep3_T

value: ACBI1 at 250nM for 24 hours


title: RH4_ACBI1_250nM_6h_T

value: ACBI1 at 250nM for 6 hours


title: RH4_ACBI1_250nM_48h_T

value: ACBI1 at 250nM for 48 hours


title: O_W0D3_O6_Protected


title: RH4_ACBI1_1000nM_6h_T

value: ACBI1 at 1000nM for 6 hours


title: RH4_ACBI1_250nM_24h_rep2_T


title: [Cappable-seq] B. anthracis 34F2 ΔatxA #1 enriched


title: O_W0D1_O6_Protected


title: RH4_ACBI1_1000nM_48h_T

value: ACBI1 at 1000nM for 48 hours


title: [Cappable-seq] B. anthracis 34F2 ΔatxA #3 unenriched


title: RH4_ACBI1_1000nM_24h_rep2_T

value: ACBI1 at 1000nM for 24 hours


title: RH4_DMSO_24h_rep2_T


title: O_W18D0_O6_Protected

value: Boost


title: O_W88D0_O5_Protected

value: O


title: [Cappable-seq] B. anthracis 34F2 ΔatxA #2 unenriched


title: K562_Rep3_Input

city: Cambridge

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

country: United Kingdom

institute: AstraZeneca

description: input

library_source: genomic

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/sblab-bioinformatics/cmpp/
Genome_build: hg19
Supplementary_files_format_and_content: Data was processed jointly with G4 ChIP-seq data in K562 available in GSE107690

molecule: genomic DNA

source_name: K562 cell line

growth_protocol: Mycoplasma-free human chronic myelogenous leukemia K562 cells (CCL-243) were purchased from ATCC, grown in RPMI1640 (Glutamine plus, Life Technologies) supplemented with 10% of fetal bovine serum (Life Technologies) at 37°C in 5% CO2. Cells were periodically tested for mycoplasma contamination and identity confirmed by STR typing.

extract_protocol:
K562 cells  were cross-linked using  2 mM disuccinimidyl glutarate for 30min then in 1% formaldehyde for 10 min at room temperature. Chromatin was isolated using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117) und sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 150-400 bp.
ChIPed DNA was subjected library preparation using a NEBNext Ultra DNA Library Prep Kit for Illumina (NE Biolabs) following the manufacturer’s protocol . Final products were sequenced by Illumina Nextseq 500 platform.  For further details see methods section in the associated manuscript.


title: K562_Rep3_SMARCA4

description: G4 ChIP-seq


title: O_W0D0_O6_Protected

value: Oral


title: K562_Rep2_Input

description: input


title: O_W18D7_O5_Protected


title: #9-S-ASC-2

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17
Raw sequencing reads were aligned to Ensembl release 84 (GRCh38 assembly) using the HISAT2 2.1.0 pipeline
Counts were summarized per gene using the summarizeOverlaps function in the GenomicsAlignment R package
Gene counts were normalized to reads per million and log2 transformed
Genome_build: GRCH38
Supplementary_files_format_and_content: count text files

source_name: CRC sphere cells

growth_protocol: Cells were grown in serum-free stem cell medium (SCM) supplemented with EGF and b-FGF

extract_protocol:
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the samples
mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation were measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's protocols. A concentration of 1.6 pM of DNA was used. NextSeq control software 2.0.2 was used.

treatment_protocol: Colorectal cancer cells were starved from EGF and b-FGF for 24 hours and then treated with with conditioned medium from subcutaneous (S-ASCs) or visceral (V-ASCs) adipose stromal cells, or control medium, for 48 hours. RNA was then collected using Trizol.

value: S-ASC conditioned medium


title: O_W18D3_O5_Protected

value: Protected


title: [Cappable-seq] B. anthracis 34F2 WT #2 enriched

source_name: B. anthracis 34F2 WT

value: B. anthracis 34F2 WT


title: #9-control-2

value: Control medium


title: #9-V-ASC-1

value: V-ASC conditioned medium


title: [Cappable-seq] B. anthracis 34F2 WT #3 enriched


title: #9-V-ASC-2


title: O_W18D0_O5_Protected


title: RH4_ACBI1_1000nM_24h_rep3_T

value: rhabdomyosarcoma

value: wild type


title: [Cappable-seq] B. anthracis 34F2 WT #1 enriched


title: #9-S-ASC-1


title: [Cappable-seq] B. anthracis 34F2 WT #3 unenriched


title: #9-control-1


title: [Cappable-seq] B. anthracis 34F2 ΔatxA #1 unenriched

value: B. anthracis 34F2 {delta}atxA


title: O_W0D7_O5_Protected

value: Prime


title: #8-V-ASC-2


title: #8-S-ASC-2


title: O_W0D3_O5_Protected


title: [Cappable-seq] B. anthracis 34F2 WT #2 unenriched


title: #8-control-2


title: K562_Rep2_SMARCA4

description: G4 ChIP-seq


title: K562_Rep1_Input

description: input


title: #8-V-ASC-1


title: [Cappable-seq] B. anthracis 34F2 WT #1 unenriched


title: #8-S-ASC-1


title: O_W18D1_O5_Protected


title: K562_Rep1_SMARCA4

description: G4 ChIP-seq


title: O_W0D1_O5_Protected


title: O_W0D0_O5_Protected


title: WT totalRNA Replicate 3 Lane 4

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
totalRNA
WT totalRNA Replicate 3 Lane 4 Read 1
S12_L004_R1

data_processing:
Read pairs were aligned against the human reference genome hg38 using STAR with default options.
Read counts at Entrez gene level were generated with the featureCounts function from the Rsubread package version 1.28.1 using options annot.inbuilt='hg38',isPairedEnd=TRUE,requireBothEndsMapped=TRUE,checkFragLength=TRUE
Genome_build: hg38
Supplementary_files_format_and_content: Excel XLSX with featureCounts gene level quantification per sample

source_name: HEK293T cells

growth_protocol: Cells growing in 175 cm2 flasks in DMEM Full Media at 37 ºC/5 % CO2 were trypsinised and plated in three 10 cm Petri dishes. Each dish contained 1x107 cells. 24 hours after plating cells were collected and RNA extracted for polysome profilling analyses

extract_protocol:
Cells in each Petri dish were treated with 7 mL of 100 μg/mL CHX in DMEM Full Media at 37 ºC/5 % CO2 for 3 minutes. Cells were then washed with 4 mL of ice-cold PBS containing 100 μg/mL CHX (PBS/CHX). PBS/CHX was removed and cells were harvested by scrapping the Petri dish and were placed in pre-chilled 1.5 mL RNase-free Eppendorf tubes and were kept on ice at all times. Harvested cells from all three Petri dishes were combined to generate a single cell lysate. Cells were centrifuged at 1000 xg for 5 minutes at 4 ºC and the supernatant was discarded. Cell pellets were gently washed (one pipette “up and down” stroke) with 1 mL PBS/CHX, and were centrifuged at 1000 xg for 5 minutes at 4 ºC. Supernatant was removed and cell pellets were re-suspended (five pipette strokes) in 500 μL “Polysome extraction buffer” (PEB) (20 mM Tris pH 7.4, 100 mM KCl, 10 mM MgCl2, 0.5 % NP-40, 2 mM DTT, 100 μg/mL CHX, 100 U/mL RNasin (N2615, Promega), 1x PIC). Cells were incubated on ice for 10 minutes, vortexing briefly every 2 minutes. Cell lysate was then centrifuged at maximum speed for 10 minutes at 4 ºC and supernatant (approximately 600 μL) was recovered. 10 % of this lysate was used for total RNA extraction, and the rest was used to obtain polysome profiles. RNA was extracted with TRIzol LS (Cat Number 10296010)
Library preparations were prepared using the TruSeq mRNA library preparation kit (single indexes set A; 20020492, Illumina), following manufacturer’s recommendations. The 12 libraries were indexed, pooled, and then sequenced in a NextSeq Flow Cell machine as 2 x 150bp paired-end reads

value: WT

tag: replicate

tag: time


title: [ChIP-seq] B. anthracis 34F2 AtxA-1xFLAG #3 enriched

data_processing:
[ChIP-seq] Sequence reads were applied for adapter trimming and quality filtering using Trim Galore! version 0.6.4_dev with the option "-a GATCGGAAGAGCACACGT", followed by mapping to the genome sequence of B. anthracis Ames ancestor strain (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17. The mapping data was applied for R package csaw 1.22.1 with 158 bp of fragment length and 50 bp of window width.
[Cappable-seq] For the analysis of sequence reads, adapter sequence was removed using cutadapt 2.1 with the option "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", followed by mapping to the genome sequence of B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using Bowtie2 2.3.5 with the option "-L 16". Coverage of the first base of mapped reads was calculated for each position with considering strands.
[3´-RACE] Reads were mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-backtrack 0.7.17.
[RNA-seq] Reads were trimmed using Trim Galore! 0.6.4_dev with the option "-a AGATCGGAAGAGA", mapped to B. anthracis Ames ancestor (RefSeq assembly accession no. GCF_000008445.1 with manual modification for sequence difference in xrrC) using BWA-mem 0.7.17, and tag counted with htseq-count.

source_name: B. anthracis 34F2 AtxA-1xFLAG

value: B. anthracis 34F2 AtxA-1xFLAG

tag: chip antibody

value: Anti-FLAG M2 affinity gel


title: [ChIP-seq] B. anthracis 34F2 AtxA-1xFLAG #2 enriched


title: O_W88D0_O4_Protected


title: WT totalRNA Replicate 3 Lane 2

description:
totalRNA
WT totalRNA Replicate 3 Lane 2 Read 1
S12_L002_R1


title: WT totalRNA Replicate 3 Lane 3

description:
totalRNA
WT totalRNA Replicate 3 Lane 3 Read 1
S12_L003_R1


title: #8-control-1


title: WT totalRNA Replicate 3 Lane 1

description:
totalRNA
WT totalRNA Replicate 3 Lane 1 Read 1
S12_L001_R1


title: O_W18D7_O4_Protected


title: WT hightranslRNA Replicate 3 Lane 4

description:
hightranslRNA
WT hightranslRNA Replicate 3 Lane 4 Read 1
S11_L004_R1


title: [ChIP-seq] B. anthracis 34F2 AtxA-1xFLAG #1 enriched


title: O_W18D3_O4_Protected


title: [ChIP-seq] B. anthracis 34F2 WT #3 enriched


title: O_W18D1_O4_Protected


title: O_W18D0_O4_Protected


title: [ChIP-seq] B. anthracis 34F2 WT #2 enriched


title: [ChIP-seq] B. anthracis 34F2 WT #1 enriched


title: O_W0D7_O4_Protected


title: WT hightranslRNA Replicate 3 Lane 3

description:
hightranslRNA
WT hightranslRNA Replicate 3 Lane 3 Read 1
S11_L003_R1


title: WT hightranslRNA Replicate 3 Lane 2

description:
hightranslRNA
WT hightranslRNA Replicate 3 Lane 2 Read 1
S11_L002_R1


title: Treatment_Cu_3

city: Nan Jing

first: Qian

last: Gao

address: No 1, Weigang

country: China

institute: Nanjing Agricultural University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the susScr11 reference genome using tophat2 (v2.0.13).
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: susScr11 (Sscrofa11.1)
Supplementary_files_format_and_content: raw_expression.csv: Comma-separated matrix table with FPKMs for every gene and every sample.

organism: Sus scrofa

source_name: porcine oocyte

extract_protocol:
The cell was lysed and the RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

tag: Sex

value: Female

tag: cell type

value: Oocytes

tag: Stage

value: Metaphase II

value: Copper


title: Control_Cu_2

value: Control


title: O_W0D3_O4_Protected

value: O

value: Oral


title: WT totalRNA Replicate 2 Lane 1

description:
totalRNA
WT totalRNA Replicate 2 Lane 1 Read 1
S10_L001_R1


title: WT totalRNA Replicate 2 Lane 2

description:
totalRNA
WT totalRNA Replicate 2 Lane 2 Read 1
S10_L002_R1


title: WT hightranslRNA Replicate 3 Lane 1

description:
hightranslRNA
WT hightranslRNA Replicate 3 Lane 1 Read 1
S11_L001_R1


title: WT totalRNA Replicate 2 Lane 3

description:
totalRNA
WT totalRNA Replicate 2 Lane 3 Read 1
S10_L003_R1


title: WT hightranslRNA Replicate 2 Lane 3

description:
hightranslRNA
WT hightranslRNA Replicate 2 Lane 3 Read 1
S9_L003_R1


title: WT totalRNA Replicate 2 Lane 4

description:
totalRNA
WT totalRNA Replicate 2 Lane 4 Read 1
S10_L004_R1


title: WT hightranslRNA Replicate 2 Lane 1

description:
hightranslRNA
WT hightranslRNA Replicate 2 Lane 1 Read 1
S9_L001_R1


title: WT totalRNA Replicate 1 Lane 4

description:
totalRNA
WT totalRNA Replicate 1 Lane 4 Read 1
S8_L004_R1


title: WT hightranslRNA Replicate 2 Lane 2

description:
hightranslRNA
WT hightranslRNA Replicate 2 Lane 2 Read 1
S9_L002_R1


title: Control_Cu_1


title: O_W0D1_O4_Protected

value: Protected


title: O_W0D0_O4_Protected


title: WT totalRNA Replicate 1 Lane 2

description:
totalRNA
WT totalRNA Replicate 1 Lane 2 Read 1
S8_L002_R1


title: O_W88D0_O3_Unprotected

value: Unprotected


title: WT totalRNA Replicate 1 Lane 3

description:
totalRNA
WT totalRNA Replicate 1 Lane 3 Read 1
S8_L003_R1


title: WT hightranslRNA Replicate 1 Lane 4

description:
hightranslRNA
WT hightranslRNA Replicate 1 Lane 4 Read 1
S7_L004_R1


title: WT hightranslRNA Replicate 2 Lane 4

description:
hightranslRNA
WT hightranslRNA Replicate 2 Lane 4 Read 1
S9_L004_R1


title: WT hightranslRNA Replicate 1 Lane 3

description:
hightranslRNA
WT hightranslRNA Replicate 1 Lane 3 Read 1
S7_L003_R1


title: O_W18D7_O3_Unprotected

value: Boost


title: O_W88D0_O8_Protected


title: WT hightranslRNA Replicate 1 Lane 2

description:
hightranslRNA
WT hightranslRNA Replicate 1 Lane 2 Read 1
S7_L002_R1


title: WT totalRNA Replicate 1 Lane 1

description:
totalRNA
WT totalRNA Replicate 1 Lane 1 Read 1
S8_L001_R1


title: KO totalRNA Replicate 3 Lane 4

description:
totalRNA
KO totalRNA Replicate 3 Lane 4 Read 1
S6_L004_R1

value: KO


title: O_W18D1_O3_Unprotected


title: O_W18D3_O3_Unprotected


title: KO totalRNA Replicate 3 Lane 2

description:
totalRNA
KO totalRNA Replicate 3 Lane 2 Read 1
S6_L002_R1


title: KO totalRNA Replicate 3 Lane 1

description:
totalRNA
KO totalRNA Replicate 3 Lane 1 Read 1
S6_L001_R1


title: WT hightranslRNA Replicate 1 Lane 1

description:
hightranslRNA
WT hightranslRNA Replicate 1 Lane 1 Read 1
S7_L001_R1


title: O_W18D0_O3_Unprotected


title: KO totalRNA Replicate 3 Lane 3

description:
totalRNA
KO totalRNA Replicate 3 Lane 3 Read 1
S6_L003_R1


title: KO hightranslRNA Replicate 3 Lane 4

description:
hightranslRNA
KO hightranslRNA Replicate 3 Lane 4 Read 1
S5_L004_R1


title: KO hightranslRNA Replicate 3 Lane 2

description:
hightranslRNA
KO hightranslRNA Replicate 3 Lane 2 Read 1
S5_L002_R1


title: KO hightranslRNA Replicate 3 Lane 3

description:
hightranslRNA
KO hightranslRNA Replicate 3 Lane 3 Read 1
S5_L003_R1


title: KO hightranslRNA Replicate 3 Lane 1

description:
hightranslRNA
KO hightranslRNA Replicate 3 Lane 1 Read 1
S5_L001_R1


title: KO totalRNA Replicate 2 Lane 4

description:
totalRNA
KO totalRNA Replicate 2 Lane 4 Read 1
S4_L004_R1


title: O_W0D1_O3_Unprotected


title: KO totalRNA Replicate 2 Lane 2

description:
totalRNA
KO totalRNA Replicate 2 Lane 2 Read 1
S4_L002_R1


title: KO totalRNA Replicate 2 Lane 1

description:
totalRNA
KO totalRNA Replicate 2 Lane 1 Read 1
S4_L001_R1


title: KO totalRNA Replicate 2 Lane 3

description:
totalRNA
KO totalRNA Replicate 2 Lane 3 Read 1
S4_L003_R1


title: O_W0D0_O3_Unprotected


title: O_W0D3_O3_Unprotected


title: KO hightranslRNA Replicate 2 Lane 4

description:
hightranslRNA
KO hightranslRNA Replicate 2 Lane 4 Read 1
S3_L004_R1


title: O_W0D7_O3_Unprotected


title: Huh7.5.1_HCV_triamcinolone_0.058uM_rep1

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

label: biotin

source_name: Huh7.5.1, HCV, triamcinolone

growth_protocol: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif) were cultured in DMEM with 1% DMSO for 10 days.

extract_protocol: Cells were washed with PBS and lysed with 5 µl of iScript™ RT-qPCR Sample Preparation Reagent (Bio-rad, Hercules, California).

treatment_protocol: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif) were exposed to mock or HCV Jc1 clone, then treated with various drugs to measure modulation of Prognostic Liver Signature genes.

tag: exposure with etiological agent

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

tag: duration with etiological agent

value: 10 days

tag: intervention

value: Triamcinolone (58 nanoM)

tag: duration of intervention

value: 3 days


title: Huh7.5.1_HCV_triamcinolone_0.058uM_rep3

scan_protocol: Refer to the NanoString nCounter Assay System Manual.

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)


title: Huh7.5.1_HCV_triamcinolone_0.058uM_rep2

label_protocol: Refer to the NanoString nCounter Assay System Manual.


title: KO hightranslRNA Replicate 2 Lane 1

description:
hightranslRNA
KO hightranslRNA Replicate 2 Lane 1 Read 1
S3_L001_R1


title: KO hightranslRNA Replicate 2 Lane 3

description:
hightranslRNA
KO hightranslRNA Replicate 2 Lane 3 Read 1
S3_L003_R1


title: KO hightranslRNA Replicate 2 Lane 2

description:
hightranslRNA
KO hightranslRNA Replicate 2 Lane 2 Read 1
S3_L002_R1


title: KO totalRNA Replicate 1 Lane 4

description:
totalRNA
KO totalRNA Replicate 1 Lane 4 Read 1
S2_L004_R1


title: Huh7.5.1_HCV_tolnaftate_10uM_rep3

source_name: Huh7.5.1, HCV, tolnaftate

value: Tolnaftate (10 microM)


title: O_W18D7_O2_Protected

tag: group

tag: phase

tag: outcome


title: glioblastoma tissue 3 in TIVA group

city: Beijing

first: Yi

last: An

address: Changchun Street No.45

institute: xuanwu Hospital

description: Gene expression data from glioblastoma tissue treated with propofol and remifentanil (TIVA group).

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

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: All of the glioblastoma specimens were obtained from the glioblastoma resection and stored at -80℃.

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

treatment_protocol: The glioblastoma tissue were all acquired from craniotomy glioma resection which performed under general anesthesia. Besides propofol and sevolurane, other anesthetics used in this study were exactly the same. The operations were performed by the same neurosurgeon and patients who received a combination of propofol and sevoflurane intraoperative were eliminated from this trial.

tag: tissue

value: glioblastoma


title: glioblastoma tissue 1 in INHA group

description: Gene expression data from glioblastoma tissue treated with sevoflurane and remifentanil (INHA group).


title: glioblastoma tissue 2 in TIVA group

source_name: glioblastoma tissue treated with propofol


title: glioblastoma tissue 1 in TIVA group


title: glioblastoma tissue 3 in INHA group

source_name: glioblastoma tissue treated with sevoflurane


title: NSC Cell line H3K79me2 ChIP

first: Ayush

middle: T

last: Raman

state: MA

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

description: PRC2 WT

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Model based analysis of ChIP-seq (MACS) version 1.4.2 and macs2  peak calling algorithm with a p-value threshold of 1e-5 to identify histone mark enrichment over “input” background
deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed peak file, bigwig

source_name: Normal Schwann cell

growth_protocol: Cells were cultured in DMEM, 10% Fetal Bovine Serum (FBS), 1% Penicillin/Streptomycin at 37c, 5% CO2.

extract_protocol:
Cells were crosslinked with both 0.75% formaldehyde and glycine. Chromatin was sheared to 200-700 bp using a Diagenode Bioruptor.
DNA were end-repaired, adapter-ligated using NEBNext Ultra II DNA library prep kit from Illumina and sequenced by Illumina HiSeq2000 at SR-36.

treatment_protocol: Cells did not undergo any treatment.

value: Peripheral nerve

tag: chip-antibody

value: H3K79me2 Abcam ab3594

tag: genotype

value: PRC2 WT


title: O_W18D3_O2_Protected


title: Huh7.5.1_HCV_tolnaftate_10uM_rep1

tag: cell line


title: Huh7.5.1_HCV_tolnaftate_10uM_rep2


title: KO hightranslRNA Replicate 1 Lane 4

description:
hightranslRNA
KO hightranslRNA Replicate 1 Lane 4 Read 1
S1_L004_R1

tag: replicate


title: O_W18D1_O2_Protected


title: KO totalRNA Replicate 1 Lane 2

description:
totalRNA
KO totalRNA Replicate 1 Lane 2 Read 1
S2_L002_R1

tag: time


title: Huh7.5.1_HCV_tivozanib_0.5uM_rep2

source_name: Huh7.5.1, HCV, tivozanib

value: Tivozanib (0.5 microM)


title: KO totalRNA Replicate 1 Lane 3

description:
totalRNA
KO totalRNA Replicate 1 Lane 3 Read 1
S2_L003_R1


title: O_W88D0_O2_Protected

value: O


title: O_W0D7_O2_Protected

value: Oral

value: Prime


title: KO hightranslRNA Replicate 1 Lane 1

description:
hightranslRNA
KO hightranslRNA Replicate 1 Lane 1 Read 1
S1_L001_R1


title: KO hightranslRNA Replicate 1 Lane 2

description:
hightranslRNA
KO hightranslRNA Replicate 1 Lane 2 Read 1
S1_L002_R1


title: Scx-Flag input-3

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

institute: CINCINNATI CHILDREN'S HOSPITAL

description: Scx ChIPseq Input_vs_ChIP

data_processing:
ChIP-seq reads were aligned to UCSC mouse genome mm10 using STAR aligner (ver. 2.7.4) [1]. To match the sequencing depth across samples, aligned reads were down-sampled to 30 million. After deduplication, peaks were called for each Scx ChIP-seq data using Homer (ver. 4.11) [2] against a matching input sample. To identify reproducible and unified Scx peaks, we performed differential analysis comparing Scx samples versus input samples. First, Scx peaks from the three biological replicates were pooled and merged into a preliminary peak set. Second, read count were measured in all the Scx samples and input samples within the peak set. Finally, exact test was performed using edgeR [3] comparing Scx and input samples. Final Scx peaks were defined by log2 fold-change (log2FC) over input > 2 and FDR < 0.01. De novo motif search within the Scx peaks were performed using Homer.
mm10
excel file, list of all peaks

organism: Mus musculus

source_name: forelimb cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with anti-FLAG antibody.
Sequencing libraries were generated using Rubicon ThruPLEX DNA sequencing kit (Rubicon Genomics, Ann Arbor MI).

tag: age

tag: antibody

value: none input


title: Huh7.5.1_HCV_tivozanib_0.5uM_rep1

tag: cell type


title: Scx-Flag ChIP-3

description: Scx ChIPseq Input_vs_ChIP

value: anti-FLAG


title: Huh7.5.1_HCV_tivozanib_0.5uM_rep3


title: glioblastoma tissue 2 in INHA group


title: KO totalRNA Replicate 1 Lane 1

description:
totalRNA
KO totalRNA Replicate 1 Lane 1 Read 1
S2_L001_R1

value: KO


title: Scx-Flag input-2

description: Scx ChIPseq Input_vs_ChIP


title: KO hightranslRNA Replicate 1 Lane 3

description:
hightranslRNA
KO hightranslRNA Replicate 1 Lane 3 Read 1
S1_L003_R1


title: Huh7.5.1_HCV_TG-101348_0.1uM_rep3

value: HCV Jc1 infection (TCID50/mL=10^6/mL)


title: Huh7.5.1_HCV_TG-101348_0.1uM_rep2

value: 10 days


title: Scx-Flag ChIP-2

description: Scx ChIPseq Input_vs_ChIP


title: Scx-Flag input-1

description: Scx ChIPseq Input_vs_ChIP


title: Scx-Flag ChIP-1

description: Scx ChIPseq Input_vs_ChIP


title: O_W0D1_O2_Protected

value: Protected


title: E15.5 Scx-RNAseq mutant2

data_processing:
RNA-seq reads were aligned as described in ChIP-seq data analysis. Read counts for each genes were measured using featureCount in subread packcage (ver. 1.6.2) [4]. To avoid sex-specific bias in the analysis, genes in chrY were discarded. Also, we used RUVseq (RUVs, k=1) [5] to account for sex-specific contribution to the gene expression profiles and to identify sex-independent gene expression changes upon Scx deletion. Differential gene expression analysis was performed using DESeq2 [6]. Differentially expressed genes were identified by FDR < 0.05. Gene ontology analysis was performed using EnrichR [7]. Hierarchical clustering was performed using the differential genes using 1 – Pearson correlation coefficient of log-transformed gene expression level (FPKM) as a dissimilarity measure under Ward’s criterion. Clustering heatmap was visualized in z-score.
mm10
excel file, list of all transcription entities

source_name: GFP+ forelimb cells

extract_protocol:
E15.5 forelimb samples were freshly dissected,digested with trypsin-EDTA solution at 37°C for 4 minutes. After inactivation of trypsin with DMEM containing 10% FBS, cells were dissociated by pipetting. The dissociated cells were resuspended in PBS with 2% FBS and 10 mM EDTA, and filtered through a 40 μm nylon cell strainer, GFP+ cells were isolated using BD FACSAria II. RNA was extracted by Qiagen RNeasy Micro kit.
Sequencing libraries were generated by using Illumina Nextera DNA Sample Prep kit.

value: no


title: E15.5 Scx-RNAseq mutant3


title: O_W18D0_O2_Protected

value: Boost


title: O_W0D0_O2_Protected


title: O_W88D0_O1_Unprotected

value: Unprotected


title: P. mume Daqiandi flower buds_OVB3

city: Nanjing

first: Shahid

last: Iqbal

state: Jiangsu

address: Nanjing, China

institute: Nanjing Agriculture University

description: OVB3 FPKM

data_processing:
After sequencing, millions of raw reads (FASTQ format) were obtained and filtered to eliminate the low quality reads and adopter sequences containing >10% unknown nucleotide (N) and 50 % bases of quality value < 5 using the software SOAPnuke (v 1.4.0)
Bowtie2 software (v 2.2.5) (Langmead and Salzberg, 2012) was used to map the high quality reads to the P. mume reference genome (https://www.ncbi.nlm.nih.gov/genome/?term=prunus%20mume) and the expression level of the genes and transcript were calculated using RSEM (v 1.2.8)  (Li and Dewey, 2011).
DEGseq software, an R package was used to analyze the differentially expressed genes from transcriptomic data (Wang et al., 2009)
To identify the transcription factor related to transcriptome sequencing, all the identified unigenes were mapped to PlantTFDB (http://plntfdb.bio.uni-potsdam.de/v3.0/) using HMMER (v 3.0)
GO analysis was performed with a fold change >2 and FDR threshold < 0.01 as a significant enrichment using the phyper function in the R software. For pathway analysis, all the identified DEGs were mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) with a p-value < 0.05 accomplished standard of Bonferroni method (Bland and Altman, 1995) to identify the significantly enriched pathway.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=prunus%20mume
Supplementary_files_format_and_content: RSEM calculated values for all transcripts

organism: Prunus mume

growth_protocol: All plants were grown at National Field Gene Bank for ‘Prunus mume’ located in Nanjing, Jiangsu Province, China

extract_protocol:
All the samples were ground into powder form in liquid nitrogen and total RNA was extracted from the pistil of three stages using the method described by (Wu et al., 2019)
The sequencing libraries were prepared using TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) following the manufacturer’s protocol.
The transcriptome sequencing was performed in triplicate using BGISEQ-500 platform by Beijing Genomic institute (B.G.I), China.

tag: cultivar

value: Daqiandi

tag: pistil abortion stage

value: ovary browning (OVB)

value: pistils of flower buds


title: Huh7.5.1_HCV_selumetinib_0.5uM_rep3

source_name: Huh7.5.1, HCV, selumetinib

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

tag: exposure with etiological agent

tag: duration with etiological agent

value: Selumetinib (0.5 microM)

value: 3 days


title: E15.5 Scx-RNAseq mutant1


title: Huh7.5.1_HCV_TG-101348_0.1uM_rep1

tag: intervention

tag: duration of intervention


title: O_W18D7_O1_Unprotected

source_name: Whole blood

tag: group

value: O

value: Oral

tag: phase


title: O_W0D3_O2_Protected

value: Prime

tag: outcome


title: P. mume Daqiandi flower buds_OVB2

description: OVB2 FPKM

tag: tissue


title: E15.5 Scx-RNAseq control3


title: O_W18D3_O1_Unprotected


title: Huh7.5.1_HCV_selumetinib_0.5uM_rep2


title: Huh7.5.1_HCV_selumetinib_0.5uM_rep1


title: P. mume Daqiandi flower buds_STIB3

description: STLB3 FPKM

value: stigma browning (STIB)


title: Huh7.5.1_HCV_rolipram_10uM_rep3

source_name: Huh7.5.1, HCV, rolipram

value: Rolipram (10 microM)


title: O_W18D0_O1_Unprotected


title: O_W18D1_O1_Unprotected


title: P. mume Daqiandi flower buds_STIB2

description: STLB2 FPKM


title: Huh7.5.1_HCV_rolipram_10uM_rep2

value: HCV Jc1 infection (TCID50/mL=10^6/mL)


title: 4M mLN Trm 4

city: Iowa City

first: John

last: Harty

state: Iowa

address: 25 S. Grand Ave, 1020 ML, University of Iowa

institute: University of Iowa

data_processing:
The sequence reads quality was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and were aligned to the mouse genome version mm10 using STAR aligner.
Differentially expressed genes were identified using Partek GS software and genes with significant changes were filtered using adjusted p- value of 0.05 as threshold
Genome_build: mm10
Supplementary_files_format_and_content: ANOVA All genes SMA RNASeq.csv

source_name: Mediastinal Lymph Node

extract_protocol:
Freshly sorted 1M or 4M P14s were (as indicated above) were re-suspended in TRIzol and RNA was 757 purified using a RNAeasy kit (Qiagen) according to the manufacturer’s protocol. RNA was assessed for purity and quality using an Agilent 2100 Bioanalyzer.
RNA seq was performed using the single cell/low input library kit (NEB), full-length cDNAs were sequenced on the Illumina HiSeq 2500 High760 output platform using 2x150 Paired-end Libraries.

treatment_protocol: B6 mice containing CD90.1 congenic Primary (1M) or Quarternary (4M) Memory P14 cells at 23-30 days post Intranasal Influenza (PR8-GP33) infection were IV labeled with CD45.2-BV450 3 minutes prior to sacrifice. Pooled splenocytes (6-10 samples/sort) or Mediastinal Lymph Nodes (15-25 samples/sort) were isolated, processed through a 70uM cell strainer, stained with APC-labeled -CD19, -NK1.1 and -CD4 and CD103-PE, CD69-PE-CY7, CD90.1-PerCP-eFluor710, Live/Dead-e780. Samples were negatively enriched with aAPC-beads and Macs columns, resuspended in MACS buffer with DNAse for subsequent sorting. Populations of IV- CD69-/CD103- (Tcirculating) and IV- CD69+/CD103+ (Tms) were sort purified and resuspended in TRIzol.

tag: mosue strain

tag: pathogen

value: Influenza

tag: treatment

value: Mediastinal Lymph Node


title: 4M mLN Trm 1


title: P. mume Daqiandi flower buds_STIB1

description: STLB1 FPKM


title: O_W0D3_O1_Unprotected


title: P. mume Daqiandi flower buds_STYB3

description: STYB3 FPKM

value: style browning (STYB)


title: O_W0D7_O1_Unprotected


title: 4M mLN DN 2


title: Huh7.5.1_HCV_rolipram_10uM_rep1

tag: cell line

value: 10 days


title: O_W0D1_O1_Unprotected

value: Unprotected


title: Huh7.5.1_HCV_resveratrol_10uM_rep3

source_name: Huh7.5.1, HCV, resveratrol

value: Resveratrol (10 microM)


title: P. mume Daqiandi flower buds_STYB2

description: STYB2 FPKM

value: Daqiandi


title: O_W0D0_O1_Unprotected


title: P. mume Daqiandi flower buds_STYB1

description: STYB1 FPKM

value: pistils of flower buds


title: P. mume Daqiandi flower buds_OVB1

description: OVB1 FPKM

value: ovary browning (OVB)


title: Huh7.5.1_HCV_resveratrol_10uM_rep1

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)


title: E15.5 Scx-RNAseq control2

tag: age

value: no


title: E15.5 Scx-RNAseq control1

tag: antibody


title: Huh7.5.1_HCV_primidone_10uM_rep3

source_name: Huh7.5.1, HCV, primidone

tag: cell type

value: Primidone (10 microM)

value: 3 days


title: 1M mLN Trm 1


title: Vcamp-luxR-Rep_3_TEX_neg

city: Bloomington

first: Julia

middle: C

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping (READemption 0.3.0)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalization (READemption 0.3.0)
Genome_build: CP030788, CP030789, CP030790
Supplementary_files_format_and_content: Tab-delimited text files containing counts of mapped reads overlapping with each of the annotated features. Each file has eight columns - Reference, source, feature type, start position, end position, strand, feature attributes and count of mapped reads overlapping with that feature.

organism: Vibrio campbellii

source_name: Bacterial lysate

growth_protocol: Cells were grown at 30°C in LM media to an OD600 of 1.0

extract_protocol:
Trizol Reagent followed by Dnase I treatment
For Illumina sequencing  of cDNA molecules, the libraries were constructed by vertis Biotechnology AG, Germany. The cDNA libraries were sequenced using a NextSeq 500 machine (Illumina) in single-read mode

treatment_protocol: When indicated (pos) samples were treated with Terminator Exonucleae (TEX; epicentre)

tag: strain

tag: genotype

value: {delta}luxR (CAS196)


title: Huh7.5.1_HCV_primidone_10uM_rep2

tag: exposure with etiological agent


title: Vcamp-luxR-Rep_3_TEX_pos


title: 1M mLN DN 2


title: Huh7.5.1_HCV_primidone_10uM_rep1

tag: duration with etiological agent


title: Huh7.5.1_HCV_resveratrol_10uM_rep2

tag: intervention


title: Vcamp-luxR-Rep_2_TEX_neg


title: 4M mLN DN 1


title: 1M mLN DN 1


title: Vcamp-luxR-Rep_2_TEX_pos


title: 4M Tcirc 3

source_name: Spleen

value: Spleen


title: Vcamp-luxR-Rep_1_TEX_neg


title: 1M mLN Trm 2


title: Huh7.5.1_HCV_pralidoxime_10uM_rep3

source_name: Huh7.5.1, HCV, pralidoxime

value: Pralidoxime (10 microM)

tag: duration of intervention


title: Huh7.5.1_HCV_pralidoxime_10uM_rep2

value: HCV Jc1 infection (TCID50/mL=10^6/mL)


title: Huh7.5.1_HCV_pioglitazone_1uM_rep3

source_name: Huh7.5.1, HCV, pioglitazone

value: Pioglitazone (1 microM)


title: Huh7.5.1_HCV_pralidoxime_10uM_rep1


title: Vcamp-luxR-Rep_1_TEX_pos


title: Vcamp-WT-Rep_3_TEX_neg

value: WT (CAS107)


title: 4M Tcirc 1

value: Influenza


title: Huh7.5.1_HCV_pioglitazone_1uM_rep2

value: 10 days


title: 1M Tcirc 2


title: Vcamp-WT-Rep_3_TEX_pos


title: 4M Tcirc 2


title: Vcamp-WT-Rep_2_TEX_neg


title: 1M Tcirc 1


title: Huh7.5.1_HCV_pioglitazone_1uM_rep1


title: Huh7.5.1_HCV_pimozide_1uM_rep3

source_name: Huh7.5.1, HCV, pimozide

value: Pimozide (1 microM)


title: Huh7.5.1_HCV_pimozide_1uM_rep2


title: 1M Tcirc 3


title: Vcamp-WT-Rep_2_TEX_pos


title: H1foo_ChIPseq_rep2

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

institute: Okayama University of Science

data_processing:
In this study, all of data processing for ChIP-seq was performed by using Galaxy platform (https://usegalaxy.org/).
Same fastq files were concatenated by using program “Concatenate datasets tail-to-head (Galaxy Version 1.0.0)”
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie (version 1.1.2).
Peaks were called using MACS (ver 1.0.1) with the following setting: Tag size (100), Band width (125), Pvalue cutoff for peak detection (1e-5).
Genome_build: mm10
Supplementary_files_format_and_content: Bed files were generated using MACS (ver1.0.1) with the following setting: Extend tag from its middle point to a wigextend size fragment (-1), Resolution for saving wiggle files (10).

source_name: mouse  embryonic stem cells

growth_protocol: Mouse embryonic stem cells overexpressing H1foo-GFP were maintained according to previous report (Koji Hayakawa 1, Jun Ohgane, Satoshi Tanaka, Shintaro Yagi, Kunio Shiota. Oocyte-specific linker histone H1foo is an epigenomic modulator that decondenses chromatin and impairs pluripotency. Epigenetics. 2012 Sep;7(9):1029-36.)

extract_protocol:
ChIP-enriched DNA was obtaind by using ChIP-IT Express Enzymatic (Active Motif, 53009) and H1foo specific antibody.
The libraries for ChIP-seq were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504) according to the manufacturer's instructions.

value: embryonic stem cells overexpressing mouse H1foo

value: H1foo (rabbit polyclonal antibody, prepared in-house)


title: AE4_ChIPseq_rep2

source_name: mouse embryonic stem cells

value: AE4 (mouse monoclonal antibody, Santa Cruz, sc-8030)


title: Vcamp-WT-Rep_1_TEX_neg


title: Vcamp-WT-Rep_1_TEX_pos


title: AE4_ChIPseq_rep1


title: Huh7.5.1_HCV_pimozide_1uM_rep1


title: CWR22Rv1_-R_H3K27me3

city: Hsinchu

first: Sheng-Chieh

last: Hsu

address: No. 101, Section 2, Kuang-Fu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to UCSC hg38 using BWA
Peak calling was performed using SICER.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: bedgraph

growth_protocol: All cells were maintained in RPMI 1640 supplemented with 100 U/ml penicillin/streptomycin and 10% FBS before experiments.

extract_protocol:
Cells were fixed with formaldehye, and chromatin was extracted with Magna ChIP™ A/G (Millipore). Chromatin was sheared with a Bioruptor Plus sonicator and isolated with antibodies.
Libraries were prepared using a KAPA Hyper Prep Kit according to the instructions.

treatment_protocol: For the control (+R) group, cells were maintained in the same culture medium for 48 h. For the arginine-deprived (-R) group, ADI-PEG20 (0.2 mg/ml) was added to deplete the arginine in the medium.

tag: chip antibody

value: H3K27me3 (Active Motif, 39155)


title: Huh7.5.1_HCV_pimasertib_0.5uM_rep3

source_name: Huh7.5.1, HCV, pimasertib

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

value: Pimasertib (0.5 microM)


title: H1foo_ChIPseq_rep1


title: Huh7.5.1_HCV_pimasertib_0.5uM_rep1


title: CWR22Rv1_+R_H3K27me3

source_name: CWR22Rv1_ADI-PEG20 for 48 h

value: ADI-PEG20 for 48 h


title: Huh7.5.1_HCV_pimasertib_0.5uM_rep2

value: 3 days


title: Huh7.5.1_HCV_PD-0325901_0.01uM_rep3


title: CWR22Rv1_-R_H3K9me3

value: H3K9me3 (Active Motif, 39765)


title: adult Leydig cells S3

city: Genève

first: Serge

last: Nef

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description:
Sex: XY
bulk RNA sequencing Leydig cells
FLcs_vs_ALCs_DESEq2_results.csv

data_processing:
Reads were demultiplexed with Casava (v1.8.2)
Mapped with GemTools (v1.7.1)
Read counts and RPKM gene expression quantifications were calculated with an in-house pipeline based on Gencode annotation GRCm38 (v4)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: counts and rpkm matrices
Supplementary_files_format_and_content: rMATS (splicing events) output

source_name: testis

extract_protocol:
Tissues were enzymatically dissociated with Trysine-EDTA and then filtered (70µm). The single cell solution is then sorted by fluorescent-active cell sorting to obtain a solution of alive and single Nr5a1-GFP+ cells. RNA was extracted from these cells with RNeasy Mini kit (Qiagen).
Sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Gold (Ribo-Zero), with 3 replicates by condition.
Sequencing with Illumina HiSeq 2500 (50 bp, paired-end)

value: Nr5a1 Tg

tag: Stage

tag: replicate

tag: Sex

value: Male


title: CWR22Rv1_+R_H3K9me3


title: Huh7.5.1_HCV_PD-0325901_0.01uM_rep2

value: HCV Jc1 infection (TCID50/mL=10^6/mL)


title: adult Leydig cells S1


title: adult Leydig cells S2


title: Huh7.5.1_HCV_PD-0325901_0.01uM_rep1


title: Huh7.5.1_HCV_oxetacaine_10uM_rep3

source_name: Huh7.5.1, HCV, oxetacaine

value: Oxetacaine (10 microM)


title: fetal Leydig cells S3


title: CWR22Rv1_-R_Input


title: CWR22Rv1_+R_Input


title: fetal Leydig cells S1


title: fetal Leydig cells S2


title: CHLA06_Technical_Replicate1

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Atypical Teratoid Rhabdoid Tumor (ATRT)

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software was used for basecalling and deplexing. Post deplexing, quality of the sequence data generated was inspected using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) followed by use of the Trimmomatic tool (http://www.usadellab.org/cms/?page=trimmomatic) to clip away adaptor sequence, 5' bias, and/or low quality sequence that might be present. Surviving read pairs were then mapped against the current instance of the human genome (ftp.ensembl.org/pub/release-82/fasta/homo_sapiens/dna/) two separate times using the "RNA-Seq" tool found within the CLCbio Genomics Workbench (www.clcbio.com) under default parameters. For the first mapping, expression for ensembl annotated transcripts (ftp.ensembl.org/pub/release-82/gtf/homo_sapiens/Homo_sapiens.GRCh38.82.chr.gtf.gz) was specified to be enumerated in TPM (Transcript Per Million) units. For the second mapping, expression was specified to also be enumerated in TPM units but this time for RepeatMasker "LTR" annotated features (http://www.repeatmasker.org/). These enumerated values were then imported into R (cran.r-project.org) and analyzed separately by mapping. To start, TPM units were pedestalled by 2, Log2 transformed, filtered to remove transcripts/features not having at least one transformed value >1, then quantile normalized. Post normalization, quality of the data was challenged and confirmed by Tukey box plot, covariance-based PCA scatter plot, and Pearson correlation heat map. To remove noise-biased expression, lowess modeling was performed across libraries (CV ~ mean expression) and the resulting fit inspected for the lowest expression value where the linear relationship between CV and mean expression was observed to be grossly lost. Expression values for a transcript/feature less than this value were subsequently construed to be noise-biased and floored to equal this value. Transcripts/Features not having at least one library with an expression greater than this value were then discarded as not detected. Expression for transcripts/features not discarded between libraries representing technical replicates were also collapsed using the max observed value per transcript/feature respectively. Where after, relationships across libraries were evaluated using expression for transcripts/features via clustered heat map (heatmap.2) and circos plot (RCircos).
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Tab-delimited text files containing TPM expression counts for ensembl annotated transcripts and RepeatMasker "LTR" annotated features.

source_name: CHLA 06

growth_protocol: Cells were grown under conditions recommended by ATCC (www.atcc.org); in DMEM:F12 Medium (ATCC 30-2006) with 20 ng/mL human recombinant EGF, 20 ng/mL human recombinant basic FGF, and B-27 Supplement (Invitrogen, Cat. No.17504) to a final concentration of 2% (v/v).

extract_protocol:
Total RNA was extracted using the RNeasy plus kit (Qiagen, USA) according to the manufacturer’s instruction.
Libraries were prepared and sequenced at NISC (www.nisc.nih.gov). The Illumina TruSeq Stranded Total RNA protocol was used in accordance with manufacturers instructions (Illumina, San Diego, CA). Stranded 125bp paired-end (Illumina HiSeq 2500).

tag: tissue

value: Atypical Teratoid Rhabdoid Tumor

value: CHLA 06

tag: technical replicate

value: Yes


title: CHLA06_Technical_Replicate2

description: Atypical Teratoid Rhabdoid Tumor (ATRT)


title: Huh7.5.1_HCV_oxetacaine_10uM_rep1

value: 10 days


title: Huh7.5.1_HCV_orteronel_40uM_rep3

source_name: Huh7.5.1, HCV, orteronel

value: Orteronel (40 microM)


title: Mutant_E13.5OFT_replicate3 [SL203090]

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description: C9CUFANXX_s7_*_TruseqHTDual_D706-TruseqHTDual_D506_SL203090

data_processing:
The raw FASTQ files were split into files containing 4,000,000 reads and checked for quality using the FASTX-Toolkit1 (version 0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/). The reads were filtered (removing sequences that did not pass Illumina's quality filter) and trimmed based on the quality results (3 nucleotides at the left end of the R1 reads)
Then, sequence alignment was performed using TopHat (v2.1.0) to mouse genome version mm10 (ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/mm10).
Following the alignment to the mouse genome,  BAM files were merged on a per-sample basis. Generation of BAM files was performed by OceanRidge Biosciences.
Aligned bam files are used to count the number of reads mapping to exons in each transcript using the GenomicAlignments (version 1.22.1) package in R to generate a gene-count matrix.
Differential expression was evaluated from this gene-count matrix using the DESeq2 package (version 1.26.0) using the standard differential expression analysis pipeline (without log fold change shrinkage method) in R.
Genome_build: mouse genome version mm10 (ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/mm10).
Supplementary_files_format_and_content: xlsx, Differential expression analysis output from DESeq2

source_name: Mutant_E13.5_Outlfow tract

extract_protocol:
E13.5 embryos were collected in an RNase-free environment. A blunt cut at the base of the OFT, below the conal cushions, was used to collect the OFT tissues from each embryo. The OFT were snap frozen until genotyping had been completed using tissue from the remaining embryo. Following genotyping of the embryos, three OFTs were pooled in 1 ml Trizol to form one biological replicate. Three biological replicates of the mutant embryos and three biological replicates of the wild type embryos were used for the final RNA-Seq analysis (i.e. 3 OFTs per sample submitted, 18 total OFTs). Total RNA was collected following tissue homogenization using TissueLyser II (Qiagen) and chloroform-isopropanol extraction and purification and isolated using the Total RNA Purification kit (Norgen Biotek Corp, 17200).
RNA-Seq was performed at OceanRidge Biosciences as previously described. RNA TruSeq Stranded Total RNA LT with Ribo-Zero Gold Set A kit (Illumina, RS-122-2301) was used to generate libraries.
Libraries were sequenced using Illumina HiSeq 2500 to generate paired-end 50 bp reads.

tag: developmental stage

value: Notch1-het; Nos3- null

value: Embryonic cardiac outflow tract


title: Mutant_E13.5OFT_replicate2 [SL203089]

description: C9CUFANXX_s7_*_TruseqHTDual_D705-TruseqHTDual_D505_SL203089


title: Mutant_E13.5OFT_replicate1 [SL203088]

description: C9CUFANXX_s7_*_TruseqHTDual_D706-TruseqHTDual_D504_SL203088


title: Huh7.5.1_HCV_orteronel_40uM_rep2

tag: cell line


title: Huh7.5.1_HCV_oxetacaine_10uM_rep2


title: CHLA04_Technical_Replicate2

description: Atypical Teratoid Rhabdoid Tumor (ATRT)

source_name: CHLA 04

value: CHLA 04


title: Control_E13.5OFT_replicate3 [SL203087]

description: C9CUFANXX_s7_*_TruseqHTDual_D706-TruseqHTDual_D502_SL203086

source_name: Control_E13.5_Outlfow tract

value: wildtype


title: CHLA02

description: Atypical Teratoid Rhabdoid Tumor (ATRT)

source_name: CHLA 02

value: CHLA 02

value: No


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 23

type: genomic

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

institute: Health Research Institute of Santiago (IDIS)

description:
LMS23
Invasive tumor front (ITF) of uterine leiomyosarcoma

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (Illumina) using standard Infinium HD FFPE Methylation Protocol (Illumina).

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing: Methylation module (1.9.0) of GenomeStudio software (V2011.1)

label: Cy5 and Cy3

source_name: Uterine leiomyosarcoma 23

label_protocol: Standard Infinium HD FFPE Methylation Protocol from Illumina

extract_protocol: Genomic DNA was isolated from FFPE tissue sections of microdissected invasive tumor front (ITF) of uterine adenocarcinomas and leiomyosarcomas using the AllPrep DNA/RNA FFPE Kit (Qiagen) and following the manufacturer’s instructions.

tag: gender

value: Female

tag: sample

tag: sample type

value: Formalin-fixed paraffin-embedded (FFPE)

tag: disease state

value: Uterine leiomyosarcoma


title: Huh7.5.1_HCV_orteronel_40uM_rep1

tag: cell type

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

value: 3 days


title: Control_E13.5OFT_replicate2 [SL203086]

description: C9CUFANXX_s7_*_TruseqHTDual_D705-TruseqHTDual_D503_SL203087

tag: genotype


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 20

description:
LMS20
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 20


title: CHLA04_Technical_Replicate1

city: Bethesda

description: Atypical Teratoid Rhabdoid Tumor (ATRT)


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 19

description:
LMS19
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 19


title: Invasive tumor front (ITF) of uterine adenocarcinoma 41a

description:
CE41a
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 41a

value: Uterine adenocarcinoma


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 16

description:
LMS16
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 16


title: Huh7.5.1_HCV_nizatidine_10uM_rep3

source_name: Huh7.5.1, HCV, nizatidine

tag: exposure with etiological agent

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

tag: duration with etiological agent

value: Nizatidine (10 microM)


title: CHLA05

description: Atypical Teratoid Rhabdoid Tumor (ATRT)

source_name: CHLA 05

value: Atypical Teratoid Rhabdoid Tumor

value: CHLA 05


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 21

description:
LMS21
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 21


title: Invasive tumor front (ITF) of uterine adenocarcinoma 39

description:
CE39
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 39


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 15

description:
LMS15
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 15


title: Huh7.5.1_HCV_nizatidine_10uM_rep2

value: 10 days

tag: intervention

tag: duration of intervention


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 13

description:
LMS13
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 13


title: Piwi-MatKD_2_rep3_SmallRNA [THU_rep3]

city: New Haven

first: Haifan

last: Lin

state: Connecticut

address: 10 Amistad Street

institute: Yale University

data_processing:
For Total RNA-Seq: reads were mapped to D. melanogaster Berkeley Drosophila Genome Project (BDGP) release 6, and counted at transposable element and gene features, defined by gene annotation in BDGP6.28, using TETools
For Small RNA-Seq: Adapter sequence (TGGAATTCTCGGGTGCCAAGG) was trimmed from reads using CutAdapt. rRNA, miRNA, tRNA, and siRNA (according to FlyBase annotation, and including exogenous siRNAs being expressed by our RNAi lines) were filtered out, and remaining sequences were then mapped to the Drosophila genome using Bowtie (1.2.2) to create the list of putative piRNAs. To identify putative piRNA target genes on non-transposon mRNAs, these putative piRNAs were mapped using Bowtie (1.2.2) to the transcribed sequences (sequence release 6, annotation release 25; dmel-all-gene-r6.26.fasta retrieved from FlyBase) of all D. melanogastar genes, excluding transposons. Mapping required the piRNA read to be antisense to the mRNA and allowed up to 3 mismatches in the first 24 nucleotides. Featurecounts was used to count the number of piRNA reads that aligned to each mRNA, weighted for the number of mapping locations for each read.
Genome_build: BDGP6.28
Supplementary_files_format_and_content: text file contains weighted piRNA counts at each non-transposon gene in Drosophila (generated from Bowtie and Featurecounts), all replicates of all three genotypes (Small RNA-seq)
Supplementary_files_format_and_content: CSV file contains RNA-seq counts at each transposon and non-transposon gene in Drosophila (generated from TETools), all replicates of all three genotypes

organism: Drosophila melanogaster

source_name: Piwi-MatKD_2_whole embryo

growth_protocol: Approximately 100 females (UAS-shRNA) and 20 males (MAT-GAL4) were mater together in embryo collection cages with grape juice plates at 25 degrees C for at least 2 days prior to embryo collection. Embryos were collected on grape juice plates for 0-1.5h and immediately harvested for RNA extraction.

extract_protocol:
Total RNA extracted using TRIzol, then small (20-30nt) RNAs extracted by size selection on 15% polyacrylamide gel
TRIzol extraction from whole embryos, standard protocol following manufacturer's instructions
RNA-seq (stranded) or Small RNA-seq; Illumina TruSeq Small RNA Library Prep Kit or Illumina TruSeq Stranded mRNA Library Prep kits
For small RNA-seq raw data, only Read 1 analyzed and submitted because read is so short that Read 2 is the reverse complement of Read 1

tag: maternal genotype

tag: paternal genotype

value: 0-1.5h embryo

tag: molecule subtype

value: 20-30 nucleotide RNA


title: Piwi-MatKD_2_rep2_SmallRNA [THU_rep2]

tag: tissue


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 5

description:
LMS5
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 5


title: 1379

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

data_processing:
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.74
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

source_name: Sperm

extract_protocol:
Sperm pellets were thawed and pretreated overnight at 37°C with a lysis buffer containing EDTA, Tris, Sarkosyl, dithiothreitol (DTT) and proteinase K. The lysate was used for DNA isolation with DNeasy Blood & Tissue Kit (QIAGEN, Germany) according to  the manufacturer’s protocol
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published protocols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, ~500ng of  DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplification.

treatment_protocol: Mthfr heterozygote (+/-) mice were mated in order to obtain an F1 generation of both wildtype (WT) and mutant (-/-) mice.  Upon sexual maturity, these F1 generation mice were mated with +/- mice to obtain the F2 generation of WT and -/- mice. An external cohort of mice (Mat_Def_colony) was also examined, where maternal- and paternal-deficient Mthfr mice were mated to obtain Mthfr -/- male mice.  Mice were sacrificed and sperm was collected from the paired caudal epididymides, washed and a 0.45% solution of NaCl and sperm pellets frozen a -80C.

value: Sperm

tag: strain

value: Mthfr -/-

tag: generation/colony


title: Huh7.5.1_HCV_nizatidine_10uM_rep1

tag: cell line


title: Piwi-MatKD_2_rep1_SmallRNA [THU_rep1]


title: Invasive tumor front (ITF) of uterine adenocarcinoma 34

description:
CE34
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 34

tag: gender


title: Huh7.5.1_mock-infected_untreated_rep3

source_name: Huh7.5.1, mock-infected, untreated

value: Mock infection


title: Piwi-MatKD_1_rep3_SmallRNA [37483_rep3]

source_name: Piwi-MatKD_1_whole embryo


title: 1361


title: Huh7.5.1_mock-infected_untreated_rep2


title: Invasive tumor front (ITF) of uterine adenocarcinoma 40

description:
CE40
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 40

tag: sample


title: Piwi-MatKD_1_rep2_SmallRNA [37483_rep2]


title: 1251


title: Huh7.5.1_mock-infected_untreated_rep1


title: Piwi-MatKD_1_rep1_SmallRNA [37483_rep1]


title: 1378


title: 1127


title: Invasive tumor front (ITF) of uterine adenocarcinoma 30

description:
CE30
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 30

tag: sample type


title: Control_E13.5OFT_replicate1 [SL203085]

description: C9CUFANXX_s7_*_TruseqHTDual_D705-TruseqHTDual_D501_SL203085

source_name: Control_E13.5_Outlfow tract

tag: developmental stage

value: wildtype

value: Embryonic cardiac outflow tract


title: GFP-MatKD_rep3_SmallRNA [41550_rep3]

source_name: GFP-MatKD_whole embryo


title: PBS_3_62

data_processing:
Adaptor sequences from raw sequencing reads were trimmed using trimmomatic (v0.36) prior to alignment. These reads were aligned to refence genome (rn4) using STAR 2-pass alignment procedure. Read counts were normalized for library size by Count Per Million (CPM) method, followed by trimmed mean of M-values (TMM) using edgeR R package. These normalized counts were log-transformed by log2(x+1). Genes with no expression in at least 50% of all samples or coefficient of variation (CV) less than 0.01 were filtered out.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited .txt file including normalized expression values (TMM) for each sample

organism: Rattus norvegicus

source_name: liver tissue

extract_protocol:
RNA was isolated using the RNeasy Mini kit (Qiagen), and cDNA was synthesized using the SuperScript III First-Strand Synthesis SuperMix Kit (Invitrogen) following manufacturer’s instructions.
Poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol.

treatment_protocol: 8-week-old male Wistar rats received weekly intraperitoneal injections of low-dose (50 mg/kg) diethylnitrosamine (DEN) to induce liver cirrhosis and cancer or PBS as control. After 12 weeks, DEN-treated cirrhotic rats were randomly assigned to receive vehicle or 15 mg/kg nizatidine by oral gavage daily for 6 weeks. Livers were harvested and total RNA was isolated for transcriptome profiling.

value: Wistar

tag: Sex

value: male

tag: disease status

value: healthy (PBS-treated)

tag: drug treatment

value: liver


title: Huh7.5.1_HCV_MK-2206_1uM_rep3

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

extract_protocol: Cells were washed with PBS and lysed with 5 µl of iScript™ RT-qPCR Sample Preparation Reagent (Bio-rad, Hercules, California).

tag: cell type

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

tag: exposure with etiological agent

tag: duration with etiological agent

value: MK-2206 (1 microM)

value: 3 days


title: 888

tag: genotype


title: PBS_2_61


title: Invasive tumor front (ITF) of uterine adenocarcinoma 32

description:
CE32
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 32

value: Female

value: Formalin-fixed paraffin-embedded (FFPE)

tag: disease state

value: Uterine adenocarcinoma


title: Huh7.5.1_HCV_MK-2206_1uM_rep2

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: 10 days

tag: intervention

tag: duration of intervention


title: Invasive tumor front (ITF) of uterine adenocarcinoma 35

description:
CE35
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 35


title: Invasive tumor front (ITF) of uterine leiomyosarcoma 7

description:
LMS7
Invasive tumor front (ITF) of uterine leiomyosarcoma

source_name: Uterine leiomyosarcoma 7

value: Uterine leiomyosarcoma


title: GFP-MatKD_rep2_SmallRNA [41550_rep2]

tag: maternal genotype

tag: paternal genotype

tag: tissue

value: 0-1.5h embryo

tag: molecule subtype

value: 20-30 nucleotide RNA


title: Invasive tumor front (ITF) of uterine adenocarcinoma 26

description:
CE26
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 26

tag: gender

tag: sample


title: Invasive tumor front (ITF) of uterine adenocarcinoma 29

description:
CE29
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 29

tag: sample type


title: Huh7.5.1_HCV_MK-2206_1uM_rep1

tag: cell line


title: 1413

value: Sperm

tag: strain

value: Mthfr +/+

tag: generation/colony


title: PBS_1_60

value: Wistar

tag: Sex

tag: disease status

tag: drug treatment


title: GFP-MatKD_rep1_SmallRNA [41550_rep1]


title: NIZ_1_559

value: male

value: cirrhosis (DEN-treated)

value: Nizatidine


title: Piwi-MatKD_2_rep3_RNA [THUT_rep3]

extract_protocol:
Total RNA extracted using TRIzol
TRIzol extraction from whole embryos, standard protocol following manufacturer's instructions
RNA-seq (stranded) or Small RNA-seq; Illumina TruSeq Small RNA Library Prep Kit or Illumina TruSeq Stranded mRNA Library Prep kits
For small RNA-seq raw data, only Read 1 analyzed and submitted because read is so short that Read 2 is the reverse complement of Read 1


title: 1411

tag: cell type

tag: genotype


title: 1337


title: NIZ_2_560

value: liver


title: Huh7.5.1_HCV_isoliquiritigenin_10uM_rep2

source_name: Huh7.5.1, HCV, isoliquiritigenin

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

tag: exposure with etiological agent

tag: duration with etiological agent

tag: intervention

value: Isoliquiritigenin (10 microM)


title: Piwi-MatKD_2_rep2_RNA [THUT_rep2]

source_name: Piwi-MatKD_2_whole embryo

tag: maternal genotype

tag: paternal genotype


title: Huh7.5.1_HCV_untreated_rep3

source_name: Huh7.5.1, HCV, untreated

tag: duration of intervention


title: DEN_3_463

value: Vehicle

tag: tissue


title: Huh7.5.1_HCV_isoliquiritigenin_10uM_rep1

value: 3 days


title: Piwi-MatKD_1_rep3_RNA [37483T_rep3]


title: Mut_G2_L8-A

source_name: Sperm

value: Mthfr -/-


title: Piwi-MatKD_2_rep1_RNA [THUT_rep1]


title: Mut_G2_L2-C


title: Huh7.5.1_HCV_isoliquiritigenin_10uM_rep3

value: HCV Jc1 infection (TCID50/mL=10^6/mL)


title: Huh7.5.1_HCV_untreated_rep2

value: 10 days


title: NIZ_3_564


title: Invasive tumor front (ITF) of uterine adenocarcinoma 25

description:
CE25
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 25

tag: gender

value: Female

tag: sample

value: Formalin-fixed paraffin-embedded (FFPE)

tag: disease state

value: Uterine adenocarcinoma


title: Invasive tumor front (ITF) of uterine adenocarcinoma 28

description:
CE28
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 28

tag: sample type


title: DEN_2_457

tag: strain


title: Piwi-MatKD_1_rep2_RNA [37483T_rep2]

source_name: Piwi-MatKD_1_whole embryo

value: 0-1.5h embryo


title: Invasive tumor front (ITF) of uterine adenocarcinoma 23

description:
CE23
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 23


title: DEN_1_255

tag: Sex


title: Mut_G2_L16-G

value: Sperm

tag: generation/colony


title: Invasive tumor front (ITF) of uterine adenocarcinoma 21

description:
CE21
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 21


title: Piwi-MatKD_1_rep1_RNA [37483T_rep1]


title: Huh7.5.1_HCV_untreated_rep5

tag: cell line


title: Invasive tumor front (ITF) of uterine adenocarcinoma 24

description:
CE24
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 24


title: 1336

tag: cell type

value: Mthfr +/+


title: Mut_G2_L16-E

tag: genotype


title: GFP-MatKD_rep3_RNA [41550T_rep3]

source_name: GFP-MatKD_whole embryo


title: GFP-MatKD_rep2_RNA [41550T_rep2]


title: intronless_gfp::his-61, wago-9_WM770

city: Worcester

first: Craig

last: Mello

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: UMass Med School/HHMI

description:
RNS-9-61_S16_L003
processed file mapped to gfp_intless_his61_index_1_17_21

data_processing:
Remove adapters with cutadapt: cutadapt -a AGATCGGAAG file, filter out reads shorter than 14 bp
align reads to transgenic sequences using bowtie2
normalize by the the total number of reads aligned to the genome (WS272) and transcriptome (WBcel235.cDNA), to 1 million reads
filter only antisense, 22 nucleotide long reads starting with nucleotide guanine (22G-RNAs)
Genome_build: WS272
Supplementary_files_format_and_content: csv files contaitning 22G read ("seq"), raw reads ("raw_reads"), parts per million value ("ppm"), alignment position of the guanine ("G_position"), name of the transgenic reference sequence ("ref_seq_name")

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Synchronous population of worms were grown on 150mm NGM plates on OP-50.

extract_protocol: Worms were treated with trizol. For input libraries, the extracted RNA was subjected to mirVana enrichment for small RNAs, before library construction. Libraries were constructed by dephosphorylating g and b phosphates of 22G-RNAs using homemade 5' polyphosphatase PIR-1, ligating 3' adaptor linker using T4 RNA ligase 2 (NEB), ligating 5' adaptor linker using T4 RNA ligase 1(NEB), converting RNA to cDNA using Superscript III (Thermo Fischer Scientific), and then amplified by PCR.

value: wago-9(ne4872) III; his-61(ne4847[intronless gfp::his-61]) IV

value: whole worm

tag: molecule

value: total small RNA


title: Huh7.5.1_HCV_untreated_rep4

tag: exposure with etiological agent

tag: duration with etiological agent


title: intronless_gfp::his-61, nrde-4_WM773

description:
RNS-6-16_S45_L008
processed file mapped to gfp_intless_his61_index_1_17_21

value: nrde-4(ne4679), his-61(ne4874[intronless gfp::his-61]) IV


title: Mut_G1_P3-4C


title: Huh7.5.1_HCV_untreated_rep6

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

tag: intervention


title: Mut_G1_P3-4-EG


title: Huh7.5.1_HCV_untreated_rep1


title: intronless_oma-1::gfp, oma-1_deletion_WM769

description:
RNS-7-43_S15_L003
processed file mapped to oma-1_gfp_intless_index_1_17_21

value: neSi75[oma-1*::gfp* (intronless); Cbr-unc-119(+)] II; unc-119(ed9) III; oma-1(ne4864[full deletion starts upstream of CDS and ends after 3' UTR]) IV


title: GFP-MatKD_rep1_RNA [41550T_rep1]

tag: maternal genotype

tag: paternal genotype


title: Salt-ΔDS complemented-Rep2

city: Stanford

first: Yanniv

last: Dorone

address: 371 Jane Stanford Way

institute: Stanford University

description: DSvsWTcomplementedSalt.xls

data_processing:
Reads were mapped with HISAT2 to the Arabidopsis thaliana TAIR10 reference genome using the Galaxy (Version 2.1.0+galaxy5) web platform.
The resulting BAM files were then analyzed on R using the DESeq2 and TxDB.Athaliana.BioMart.plantsmart28 (Bioconductor) packages. Genes with padj<0.05 were considered differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel

organism: Arabidopsis thaliana

source_name: Seeds imbibed in 220mM NaCl

growth_protocol: For imbibed and salt: dry seeds were sown onto separate agar plates of MS medium conditions with either 0 or 220mM NaCl and cold-stratified for 5 days at 4˚C in the dark. All plates were subsequently transferred to and held in a growth cabinet (Percival) for 4 hours under light (130 μmol.m−2.s−1) and 22˚C.

extract_protocol:
DNA-free total RNA was extracted from seeds and siliques as described in Meng & Feldman (2010). The extraction buffer utilized 0.5% β-mercaptoethanol.
Library preparation (250-300 bp insert cDNA library) was conduced by Novogene Corporation Inc.

treatment_protocol: RNA-seq analysis was carried out on six conditions: 1) dry ΔDS seeds; 2) dry +WT seeds; 3) imbibed ΔDS seeds; 4) imbibed +WT seeds; 5) ΔDS seeds imbibed with 220 mM NaCl; and 6)+WT seeds imbibed with 220 mM NaCl.

tag: genotype/variation

value: [delta]DS

tag: treatment

value: 5 days on MS media supplemented with 220mM NaCl in the dark at 4C, 4h in light conditions at 22C


title: Huh7.5.1_HCV_erlotinib_0.1uM_rep3

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

source_name: Huh7.5.1, HCV, erlotinib

value: Erlotinib (0.1 microM)

tag: duration of intervention

value: 3 days


title: intronless_gfp::his-61, prg-1_WM753

description:
RNS-6-2_S42_L008
processed file mapped to gfp_intless_his61_index_1_17_21

value: prg-1(ne4766[null]) I; his-61(ne4851[intronless gfp::his-61]) IV

tag: tissue


title: Salt-ΔDS complemented-Rep1

description: DSvsWTcomplementedSalt.xls


title: Wt_G2_L13-C


title: Mut_G1_3-9-BF

value: Mthfr -/-


title: Mut_G1_3-11-C


title: Imbibed-ΔDS complemented-Rep3

description: DSvsWTcomplementedImbibed.xls

source_name: Imbibed seeds

value: 5 days on MS media in the dark at 4C, 4h in light conditions at 22C


title: Huh7.5.1_HCV_erlotinib_0.1uM_rep2

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: 10 days


title: Huh7.5.1_HCV_erlotinib_0.1uM_rep1


title: intronless_gfp::his-61, rde-3_WM750

description:
RNS-6-4_S44_L008
processed file mapped to gfp_intless_his61_index_1_17_21

value: rde-3(ne4848[null]) I; his-61(ne4847[intronless gfp::his-61]) IV


title: Invasive tumor front (ITF) of uterine adenocarcinoma 22

description:
CE22
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 22

tag: gender

value: Female

tag: sample

tag: sample type

value: Formalin-fixed paraffin-embedded (FFPE)

tag: disease state

value: Uterine adenocarcinoma


title: Wt_G2_L14C

value: Sperm

tag: strain

value: Mthfr +/+

tag: generation/colony


title: Invasive tumor front (ITF) of uterine adenocarcinoma 19

description:
CE19
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 19


title: Huh7.5.1_HCV_dorzolamide_10uM_rep3

source_name: Huh7.5.1, HCV, dorzolamide

tag: cell line

tag: cell type

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

value: Dorzolamide (10 microM)


title: Wt_G1_3-9-G

tag: genotype


title: Huh7.5.1_HCV_dorzolamide_10uM_rep2

tag: exposure with etiological agent

tag: duration with etiological agent


title: intronless_gfp::his-61_WM749

description:
RNS-6-22_S41_L008
processed file mapped to gfp_intless_his61_index_1_17_21

value: whole worm

tag: molecule

value: total small RNA


title: Huh7.5.1_HCV_dorzolamide_10uM_rep1

tag: intervention


title: Invasive tumor front (ITF) of uterine adenocarcinoma 20

description:
CE20
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 20


title: intronless_oma-1*, prg-1_WM747

description:
RNS-5-17_S28_L007
processed file mapped to oma-1_intless_flag_11_21_2020

value: prg-1(ne4844[null]) I; oma-1(ne4845[intronless oma-1::3xFLAG]) IV


title: Imbibed-ΔDS complemented-Rep2

description: DSvsWTcomplementedImbibed.xls

tag: genotype/variation

value: [delta]DS


title: Invasive tumor front (ITF) of uterine adenocarcinoma 16

description:
CE16
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 16


title: Huh7.5.1_HCV_dilazep_1uM_rep3

source_name: Huh7.5.1, HCV, dilazep

value: Dilazep (1 microM)

value: 3 days


title: Invasive tumor front (ITF) of uterine adenocarcinoma 6

description:
CE6
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 6


title: ovarian cells_S144

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing:
Checked the quality control of reads data by FastQC
The reads data mapped and quantified as TPM using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: Plain txt file for illumina RNA-seq data, each file contain 5 column, the first column represents gene name, the second column represents the total length of genes, the third column represents the effective legnth of genes, the fourth column represents the TPM of genes and the fifth column represents the number of reads.

molecule: polyA RNA

source_name: ovarian cells_S144

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
The ovaries were digested in 500 µl HBSS supplemented with 0.25% trypsin, 1 mM ethylenediaminetetracetic acid (EDTA), and 0.01% DNase I and incubated at 37℃ for 10 min with gentle agitation. To stop the digestion, 500 µl HBSS (plus 10% FBS) was added and the cell suspensions were centrifuged at 400g for 5min at 4℃. After aspirating the supernatant completely, the cells were resuspended in 500 µl HBSS and transferred under the microscope.The collected oocyte were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor).The lysis solution also contains free dNTPs and tailed oligo-dT oligonucleotides (30-nt poly-dT stretch and a 25-nt universal 5′ anchor sequence) that are prepared of the Reverse Trianscription reaction on polyadenylated RNA sequences.
We used tagmentation to quickly and efficiently construct sequencing libraries from the amplified cDNA. The fragments in the tagmented DNA library have an average size that ranges from 200 to 300 bp and then purified for Illimina. The quantity of the libraries was assessed and defined by qPCR, respectively. All samples were sequenced using HiSeq XTen (Illumina) with paired-end 125-bp sequencing.

treatment_protocol: Newborn female pups from the same litter were collected immediately after delivery and ovaries (n=5) were harvested by carefully removing oviducts and ovarian bursa in calcium- and magnesium-free Hanks balanced salt solution (HBSS).

value: ovary

tag: age


title: ovarian cells_S145

source_name: ovarian cells_S145


title: Dry-ΔDS complemented-Rep2

description: DSvsWTcomplementedDry.xls

source_name: Dry seeds

tag: treatment

value: No


title: gfp::his-61_WM748

description:
RNS-6-24_S40_L008
processed file mapped to gfp_intless_his61_index_1_17_21

tag: tissue


title: intronless_oma-1::gfp_WM767

description:
RNS-8-46_S18_L004
processed file mapped to oma-1_gfp_intless_index_1_17_21

value: neSi74[oma-1*::gfp* (intronless); Cbr-unc-119(+)] II; unc-119(ed9) III


title: Salt-WT complemented-Rep3

description: DSvsWTcomplementedSalt.xls

value: WT

value: 5 days on MS media supplemented with 220mM NaCl in the dark at 4C, 4h in light conditions at 22C


title: Imbibed-ΔDS complemented-Rep1

description: DSvsWTcomplementedImbibed.xls

value: 5 days on MS media in the dark at 4C, 4h in light conditions at 22C


title: ovarian cells_S143

source_name: ovarian cells_S143


title: Dry-ΔDS complemented-Rep3

description: DSvsWTcomplementedDry.xls


title: ovarian cells_S142

source_name: ovarian cells_S142


title: intronless_oma-1*_WM782

description:
RNS-9-59_S3_L003
processed file mapped to oma-1_intless_flag_11_21_2020


title: restored_oma-1::3xflag_WM781

description:
RNS-9-328_S4_L003
processed file mapped to oma-1_intless_flag_11_21_2020

value: oma-1(ne4868[restored original intron-containing oma-1::3xFLAG]) IV


title: Dry-ΔDS complemented-Rep1

description: DSvsWTcomplementedDry.xls


title: Huh7.5.1_HCV_dilazep_1uM_rep2

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: 10 days

tag: duration of intervention


title: Invasive tumor front (ITF) of uterine adenocarcinoma 2

description:
CE2
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 2

tag: gender

value: Female

tag: sample

value: Formalin-fixed paraffin-embedded (FFPE)

value: Uterine adenocarcinoma


title: Invasive tumor front (ITF) of uterine adenocarcinoma 9

description:
CE9
Invasive tumor front (ITF) of uterine adenocarcinoma

source_name: Uterine adenocarcinoma 9

tag: sample type

tag: disease state


title: intronless_oma-1*, rde-3_WM784

description:
RNS-5-23_S29_L007
processed file mapped to oma-1_intless_flag_11_21_2020

source_name: whole worm

value: rde-3(ne4871[null]) I; oma-1(ne4869[intronless oma-1::3xFLAG]) IV

value: whole worm

value: total small RNA


title: ovarian cells_S141

source_name: ovarian cells_S141

tag: strain


title: intronless_cdk-1*::gfp*, rde-3_WM734

description:
rns2-2
processed file mapped to cdk-1_gfp_intless_index_10_8_20.txt

value: rde-3(ne3370) I; neSi71[cdk-1*::gfp*(intronless); Cbr-unc-119(+)] II


title: Huh7.5.1_HCV_clomifene_1uM_rep2

source_name: Huh7.5.1, HCV, clomifene

tag: cell line

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)

value: Clomifene citrate (1 microM)

value: 3 days


title: Huh7.5.1_HCV_clomifene_1uM_rep3

tag: cell type


title: Salt-WT complemented-Rep2

description: DSvsWTcomplementedSalt.xls

source_name: Seeds imbibed in 220mM NaCl


title: intronless_cdk-1*::gfp*_WM730

description:
rns2-5
processed file mapped to cdk-1_gfp_intless_index_10_8_20.txt

tag: genotype

value: neSi71[cdk-1*::gfp* (intronless); Cbr-unc-119(+)] II; unc-119(ed9) III


title: intronless_cdk-1*::gfp*, prg-1_WM737

description:
rns2-4
processed file mapped to cdk-1_gfp_intless_index_10_8_20.txt

value: prg-1(tm872); neSi73[cdk-1*::gfp* (intronless); Cbr-unc-119(+)] II; unc-119(ed9) III


title: cdk-1::gfp_WM242

description:
rns2-6
processed file mapped to cdk-1_gfp_intless_index_10_8_20.txt

value: neSi12[cdk-1::gfp; Cbr-unc-119(+)] II; unc-119(ed9) III


title: Salt-WT complemented-Rep1

description: DSvsWTcomplementedSalt.xls

value: WT

value: 5 days on MS media supplemented with 220mM NaCl in the dark at 4C, 4h in light conditions at 22C


title: ovarian cells_S140

source_name: ovarian cells_S140

value: ovary


title: Huh7.5.1_HCV_dilazep_1uM_rep1

tag: exposure with etiological agent

value: HCV Jc1 infection (TCID50/mL=10^6/mL)

value: 10 days

value: Dilazep (1 microM)


title: Huh7.5.1_HCV_CI-1040_1uM_rep2

tag: duration with etiological agent

value: CI-1040 (1 microM)


title: Huh7.5.1_HCV_CI-1040_1uM_rep3


title: Imbibed-WT complemented-Rep3

description: DSvsWTcomplementedImbibed.xls

source_name: Imbibed seeds

value: 5 days on MS media in the dark at 4C, 4h in light conditions at 22C


title: Huh7.5.1_HCV_clomifene_1uM_rep1


title: ovarian cells_S138

source_name: ovarian cells_S138


title: ovarian cells_S139

source_name: ovarian cells_S139


title: ovarian cells_S137

source_name: ovarian cells_S137


title: ovarian cells_S136

source_name: ovarian cells_S136


title: Imbibed-WT complemented-Rep1

description: DSvsWTcomplementedImbibed.xls


title: Imbibed-WT complemented-Rep2

description: DSvsWTcomplementedImbibed.xls


title: ovarian cells_S135

source_name: ovarian cells_S135


title: Huh7.5.1_HCV_CI-1040_1uM_rep1


title: Dry-WT complemented-Rep3

description: DSvsWTcomplementedDry.xls

value: No


title: Dry-WT complemented-Rep2

description: DSvsWTcomplementedDry.xls


title: Huh7.5.1_HCV_cediranib_0.5uM_rep3

source_name: Huh7.5.1, HCV, cediranib

value: Cediranib (0.5 microM)


title: Huh7.5.1_HCV_cediranib_0.5uM_rep2


title: ovarian cells_S134

source_name: ovarian cells_S134


title: Huh7.5.1_HCV_cediranib_0.5uM_rep1


title: Dry-WT complemented-Rep1

description: DSvsWTcomplementedDry.xls

source_name: Dry seeds


title: ovarian cells_S133

source_name: ovarian cells_S133


title: Huh7.5.1_HCV_captopril_5uM_rep3

description: Capto 5-3

source_name: Huh7.5.1, HCV, captopril

value: Captopril (5 microM)


title: ovarian cells_S131

source_name: ovarian cells_S131


title: ovarian cells_S132

source_name: ovarian cells_S132


title: Salt-floe1-1-Rep1

treatment_protocol: RNA-seq analysis was carried out on six conditions: 1) dry floe1-1 seeds; 2) dry Col-0 seeds; 3) imbibed floe1-1 seeds; 4) imbibed Col-0 seeds; 5) floe1-1 seeds imbibed with 220 mM NaCl; and 6) Col-0 seeds imbibed with 220 mM NaCl.


title: Salt-floe1-1-Rep3


title: ovarian cells_S146

source_name: ovarian cells_S146


title: Salt-floe1-1-Rep2


title: Imbibed-floe1-1-Rep3


title: Huh7.5.1_HCV_captopril_5uM_rep2

description: Capto 5-2

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)


title: Huh7.5.1_HCV_captopril_5uM_rep1

description: Capto 5-1


title: Imbibed-floe1-1-Rep2


title: 6 months Post-treatment [200742440054_C]

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with preprocessCore in R

source_name: PBMCs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Qiazole reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease

value: metastatic renal cell carcinoma (mRCC)

tag: time point

value: 6 months Post-treatment


title: Huh7.5.1_HCV_captopril_1uM_rep3

city: Dallas

description: Capto 1-3

tag: intervention

value: Captopril (1 microM)

value: 3 days


title: Pre-treatment [200742440054_A]

value: Pre-treatment


title: ovarian cells_S130

city: Beijing

source_name: ovarian cells_S130

tag: age


title: ovarian cells_S128

source_name: ovarian cells_S128


title: 3 months Post-treatment [200742440052_K]

value: 3 months Post-treatment


title: Pre-treatment [200742440052_J]


title: Huh7.5.1_HCV_captopril_1uM_rep2

description: Capto 1-2


title: 6 months Post-treatment [200742440052_L]


title: 3 months Post-treatment [200742440054_B]


title: 6 months Post-treatment [200742440052_H]


title: 3 months Post-treatment [200742440052_G]


title: 3 months Post-treatment [200742440052_F]


title: Huh7.5.1_HCV_captopril_1uM_rep1

description: Capto 1-1


title: Imbibed-floe1-1-Rep1

source_name: Imbibed seeds

tag: treatment


title: ovarian cells_S127

source_name: ovarian cells_S127

tag: tissue


title: Dry-floe1-1-Rep3


title: ovarian cells_S129

source_name: ovarian cells_S129


title: Pre-treatment [200742440052_E]


title: ovarian cells_S126

source_name: ovarian cells_S126


title: ovarian cells_S125

source_name: ovarian cells_S125


title: 6 months Post-treatment [200742440052_C]


title: ovarian cells_S124

source_name: ovarian cells_S124


title: Huh7.5.1_HCV_brefeldin-a_0.1uM_rep2

source_name: Huh7.5.1, HCV, brefeldin-a

value: Brefeldin a (0.1 microM)

tag: duration of intervention


title: Dry-floe1-1-Rep1


title: Salt-Col0-Rep3

source_name: Seeds imbibed in 220mM NaCl

value: 5 days on MS media supplemented with 220mM NaCl in the dark at 4C, 4h in light conditions at 22C


title: Huh7.5.1_HCV_brefeldin-a_0.1uM_rep3

value: HCV Jc1 infection (TCID50/mL=10^6/mL)


title: Salt-Col0-Rep2


title: ovarian cells_S123

source_name: ovarian cells_S123

value: ovary


title: Salt-Col0-Rep1


title: Salt-ΔDS complemented-Rep3

description: DSvsWTcomplementedSalt.xls

tag: genotype/variation

value: [delta]DS


title: ovarian cells_S122

source_name: ovarian cells_S122


title: Dry-floe1-1-Rep2

source_name: Dry seeds


title: Patient3_Pioglitazone

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

growth_protocol: Huh7.5.1 cells, HepG2 cells, and clinical liver tissue slices were cultured in DMEM with 1% DMSO for 2 to 10 days.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: DMSO-differentiated Huh7.5.1 cells, HepG2-NTCP cells, Huh7.5.1-NTCP cells or clinical liver tissue slices were exposed to mock, HCV, HBV, or EtOH, and treated with interferon, direct-acting anti-HCVs, erlotinib, pioglitazone, or metformin or co-culture with hepatic stellate cell line, LX2. Cells/tissues were harvested for RNA isolation and gene expression profiling by NanoString assay.

value: Tissue

value: Cryptogenic

value: Pioglitazone (10 microM)

value: 2 days

value: liver


title: Patient3_DMSO

scan_protocol: Refer to the NanoString nCounter Assay System Manual

value: DMSO


title: EtOH_40mM_3

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: Cell (Huh7.5.1dif)

value: EtOH (40 mM)

value: 10 days


title: EtOH_40mM_2

value: 3 days


title: ovarian cells_S121

source_name: ovarian cells_S121


title: Imbibed-Col0-Rep3

value: 5 days on MS media in the dark at 4C, 4h in light conditions at 22C


title: Huh7.5.1_HCV_brefeldin-a_0.1uM_rep1

value: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif)


title: ovarian cells_S120

source_name: ovarian cells_S120


title: Imbibed-Col0-Rep2


title: EtOH_40mM_1


title: Pre-treatment [200742440052_A]

value: metastatic renal cell carcinoma (mRCC)

value: Pre-treatment


title: 3 months Post-treatment [200742440049_K]

value: 3 months Post-treatment


title: 6 months Post-treatment [200742440049_L]

value: 6 months Post-treatment


title: EtOH_20mM_3

value: EtOH (20 mM)


title: 3 months Post-treatment [200742440052_B]


title: 6 months Post-treatment [200742440049_J]


title: 3 months Post-treatment [200742440049_I]


title: Imbibed-Col0-Rep1


title: Pre-treatment [200742440049_H]


title: ovarian cells_S118

source_name: ovarian cells_S118

value: ovary


title: EtOH_20mM_2


title: 6 months Post-treatment [200742440049_G]

source_name: PBMCs


title: Dry-Col0-Rep2

value: No


title: ovarian cells_S117

source_name: ovarian cells_S117


title: 3 months Post-treatment [200742440049_F]


title: EtOH_20mM_1


title: ovarian cells_S115

source_name: ovarian cells_S115


title: Control_to_EtOH_3


title: NSC-p5 RNA-seq

city: Cambridge

first: Ayush

last: Raman

address: 75 Ames St

institute: Broad Institute of MIT and Harvard

description: PRC2 WT

data_processing:
The quality of raw reads was assessed using FastQC (Andrews, 2010). The average per base quality score across all the files were greater than 32 and had passed all the major tests.
The raw reads were aligned to the Homo sapiens genome (hg19) using STAR v2.4.2a (Dobin et al., 2013). The mappability of unique reads on average was ~82%. The raw counts were computed using quantMode function in STAR.
The obtained read counts are analogous to the expression level of each gene across all the samples. The differential expression analysis was done using DESeq2 (Love et al., 2014a). Genes with raw mean reads greater than 10 were used for normalization and differential gene expression analysis using DESeq2 package in R. Wald test defined in the DESeq function of the package was used for differential expression analysis and shrunken log fold-changes (i.e., obtaining reliable variance estimates by pooling information across all the genes) were used for further analysis. Principal Component Analysis (PCA), hierarchical clustering plots (hclust) and XY plots between replicates of same genotypes were used to examine for nominal amounts of non-technical variation and other latent factors. PCA, hclust and bar plots were generated using ggplot2 (Wickham). All the heatmaps of differentially expressed genes were generated using pheatmap package (Kolde, 2012) in R environment.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files; raw counts file output from STAR and Diff Expressed Genes using DESeq2

source_name: Normal Schwann cells

growth_protocol: MPNST cells were grown in DMEM with 10% FBS. NSC, MPNST4970, MPNST181 were grown in Schwann cell medium and transferred to 10% DMEM 24 hrs before harvesting for RNA.

extract_protocol:
RNA was isolated from cultured cells using TRIzol (Cat# 10296010 Invitrogen) and purified using the RNeasy Mini Kit (Cat# 74106 Qiagen, Valencia, CA, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal control cells

value: Normal Schwann cells

value: PRC2 WT


title: Control_to_EtOH_2


title: ovarian cells_S114

source_name: ovarian cells_S114


title: Control_to_EtOH_1


title: Pre-treatment [200742440049_E]


title: ovarian cells_S113

source_name: ovarian cells_S113


title: Dry-Col0-Rep3


title: shALDOA-rep3

city: Guangzhou

first: Yi

last: Niu

address: No.2, Zhishan Garden, No.132, East Outer Ring Road

institute: Sun Yat-sen University

description: Gene changes in ALDOA-KD cells.xlsx

data_processing:
Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelson, T., Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., et al. (2014). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87.
Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd. TopHat2 and HTSeq are used for RNAseq data analysis
Genome_build: genome-wide CRISPR/Cas9 KO sgRNA library; hg38
Supplementary_files_format_and_content: Matrix table with  gene foldchange for every gene

growth_protocol: The HCC cells are cultured in 20% O2 and 1% O2 to mimic normoxia and hypoxia

extract_protocol:
genome-wide CRISPR/Cas9 knockout library HepG2 cells are collected,and genome DNA was harvested and sgRNAs were amplified with PCR.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA library preparation is performed by using NEBNext UltraDirectional RNA Library Prep Kit for Illumina (E7420L).

treatment_protocol: genome-wide CRISPR/Cas9 knockout library HepG2 cells are cultured in normoxia and hypoxia. shCtrl and shALDOA HepG2 cells are cultured in hypoxia

value: HCC cells


title: Pre-treatment [200742440049_A]


title: shALDOA-rep2

description: Gene changes in ALDOA-KD cells.xlsx


title: shALDOA-rep1

description: Gene changes in ALDOA-KD cells.xlsx