title: Nrf1-KO control rep2

description:
Immortalized
SR11


title: Nrf1-KO carfilzomib 6 hour rep3

status: Public on May 21 2020

type: SRA

city: Richmond

first: Senthil

last: Radhakrishnan

state: VA

address: 1101 E Marshall St

country: USA

institute: Virginia Commonwealth University

description:
Immortalized
SR15

library_source: transcriptomic

data_processing:
RNA Express workflow from Illumina Basespace website was used
The steps consist of: Alignment of reads with STAR aligner, assignment of aligned reads to genes, and differential gene expression with DESeq2
Supplementary_files_format_and_content: DeSeq2 results in csv format

molecule: total RNA

organism: Mus musculus

source_name: NIH-3T3 cell line

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS at 37 degree C in a humidified CO2 incubator

extract_protocol:
Qiagen RNAeasy kit was used for extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO (vehicle) or 200 nM carfilzomib

tag: cell type

value: Fibroblasts

tag: genotype

tag: agent

value: 200 nM carfilzomib

tag: time point

value: 6 hour


title: WT carfilzomib 24 hour rep2

description:
Immortalized
SR8

value: wild-type

value: 24 hour


title: WT carfilzomib 24 hour rep1

description:
Immortalized
SR7


title: WT carfilzomib 24 hour rep3

description:
Immortalized
SR9


title: Nrf1-KO control rep1

description:
Immortalized
SR10

value: DMSO


title: WD

city: La Jolla

first: Klaus

last: Ley

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Aortic leukocytes from WD-fed mice

data_processing:
FASTQ files were processed with the Cellranger count pipeline (10x Genomics), which uses STAR to align the reads to mm10 mouse reference transcriptome. Default settings were used throughout all samples. A single cell gene expression matrix was obtained as output and further used in down-stream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output of filtered gene matrix with barcodes and features files

source_name: Aorta

extract_protocol:
Leukocytes from atherosclerotic aortas were extracted by enzymatic digestion and stained with an antibody-cocktail for flow cytometry. Viable leukocytes were identified as CD45+ viability-dye-negative cells and sorted into PBS. After sorting, cells were washed, resuspended, and up to 10,000 sorted leukocytes were loaded and partitioned into Gel Bead In-Emulsions (GEM) according to the protocol by 10x Genomics. For each condition (CD and WD), cells from 10 individual aortas were pooled for one GEM preparation.
ScRNAseq libraries were prepared using the Single Cell 3’ Solution v2 Reagent Kit (10xGenomics). GEM reverse transcription was performed by the SimpliAmp thermal cycler (Thermo Fisher Scientific) running the following program: 53° C for 45 minutes and 85° C for 5 minutes; held at 4° C. Following reverse transcription, GEMs were broken, and single-strand cDNA was purified with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNA was amplified with the SimpliAmp thermal cycler: 98° C for 3 minutes, 12 cycles of 98° C for 15 seconds, 67° C for 20 seconds, 72° C 60 seconds; 72° C for 1 minute, and held at 4° C. Subsequently, cDNA was cleaned up using the SPRIselect reagent kit (Beckman Coulter), quantified, and quality controlled with the Agilent Bioanalyzer High Sensitivity Kit. Indexed sequencing libraries were prepared by Single Cell 3’ Solution v2 Reagent Kit’s components: (1) enzymatic fragmentation, (2) end repair, (3) A-tailing, (4) adaptor ligation, (5) post ligation cleanup with the SRPIselect reagent kit, and (6) sample index PCR using the SimpliAmp thermal cycler at 98° C for 45 seconds, 10 cycles of 98° C for 20 seconds, 54° C for 30 seconds, 72° C for 20 seconds; 72° C for 1 minute, and held at 4° C. The SPRIselect reagent kit was used for post sample index double-sided size selection, and the library was quality controlled post construction using the Agilent Bioanalyzer High Sensitivity Kit and Agilent Bioanalyzer high sensitivity chip. The library was quantified post construction by quantitative PCR (Kapa DNA Quantification Kit for Illumina platforms). The constructed libraries were loaded at 13 pM on a HiSeq2500 Rapid Run using a HiSeq Rapid Cluster Kit V2- Paired End (PE), and a HiSeq Rapid SBS Kit V2. A 26-base-pair Read 1 was used to sequence the cell barcode and UMI, an 8 bp i7 index read was used to sequence the sample index, and a 98 bp Read 2 was used to sequence the transcript on an Illumina HiSeq4000 using paired-end sequencing with dual indexing.

tag: strain

value: ApoE-/-

tag: diet

value: WD-fed mice

tag: tissue

value: Aorta

value: Aortic leukocytes


title: WT carfilzomib 6 hour rep3

description:
Immortalized
SR6


title: WT carfilzomib 6 hour rep2

description:
Immortalized
SR5


title: S3F

city: Madison

first: Cynthia

middle: A

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample as well as WGCNA data.

organism: Rattus norvegicus

source_name: Periaqueductal gray, brainstem

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Long Evans

value: Periaqueductal gray, brainstem

tag: age

value: 8 months

value: WT

tag: Sex

value: Female


title: 200544710056_L

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software v3.8

label: biotin

organism: Homo sapiens

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina Gene Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: disease state

value: head and neck squamous cell carcinoma

value: T-without


title: 200544710056_K

value: M


title: 200544710056_I


title: WT control rep2

description:
Immortalized
SR2

value: Fibroblasts


title: WT control rep3

description:
Immortalized
SR3


title: 200544710056_H


title: 200544710056_F


title: WT control rep1

description:
Immortalized
SR1


title: Bahd1-WT Embryo rep2

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome (GRCm38 from Ensembl database)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1)
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. Genes, whose sum of all samples counts was less than 10, were filtered out. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed.
Genome_build: GRCm38 from Ensembl database version 92
Supplementary_files_format_and_content: Embryo_KO_WT_brain_counts_table.txt

source_name: brain

extract_protocol:
Total RNA was extracted with RNeasy kit (Qiagen) from biological replicates according to the manufacturer's instructions. (Note: the procedure removes RNA smaller than 200 nucleotides). RNA samples were treated with Turbo DNase-free kit (Invitrogen) to remove residual DNA and were quality checked (Bioanalyser Agilent). Illumina TruSeq RNA Sample Prep Kit (Illumina, #RS-122-9004DOC) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Knock-out of the Bahd1 gene

value: brain

tag: developmental stage

value: embryo


title: Bahd1-KO Embryo rep3


title: Bahd1-KO Embryo rep2


title: 200544710056_G

value: T-with


title: 200544710056_J


title: Bahd1-WT Embryo rep1


title: Bahd1-KO Embryo rep1


title: Bahd1-WT Embryo rep3


title: Bahd1-WT Adult rep3_rc

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome (GRCm38 from Ensembl database)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1)
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. Genes, whose sum of all samples counts was less than 10, were filtered out. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed.
Genome_build: GRCm38 from Ensembl database version 92
Supplementary_files_format_and_content: Adult_KO_WT_brain_counts_table.txt

extract_protocol:
Brains were dissected and cut sagitally. Halves of the brain were frozen in RNAlater and further processed for Total RNA extraction, with RNeasy kit (Qiagen) according to the manufacturer's instructions. (Note: the procedureremoves RNA smaller than 200 nucleotides). RNA samples were treated with Turbo DNase-free kit (Invitrogen) to remove residual DNA and were quality checked (Bioanalyser Agilent). Illumina TruSeq RNA Sample Prep Kit (Illumina, #RS-122-9004DOC) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult

value: about 70 weeks old


title: WT carfilzomib 6 hour rep1

description:
Immortalized
SR4

value: wild-type

value: 200 nM carfilzomib

value: 6 hour


title: Bahd1-WT Adult rep2_rc


title: 200544710056_B


title: 200544710056_A


title: 200544710054_E


title: Bahd1-WT Adult rep1_rc


title: Bahd1-KO Adult rep3_rc


title: 200544710031_I


title: 200544710031_H


title: 200544710031_J


title: 200544710031_K


title: 200544710054_D


title: 200544710056_D


title: Bahd1-KO Adult rep1_rc


title: 200544710031_L


title: Sorghum leaf

city: Huntsville

first: Alex

last: Harkess

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: PARE

data_processing:
PARE-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 20 nucleotides.
Supplementary_files_format_and_content: Tag counts

organism: Sorghum bicolor

source_name: leaf

extract_protocol:
Trizol RNA
The library construction is based on a PARE protocol modified by Sandra Mathioni and used the Illumina TruSeq sRNA Indexes for the 3 prime adapter. The PARE library was constructed by Sandra Mathioni at the Donald Danforth Plant Science Center and sequenced on an Illumina HiSeq 2500 at the University of Delaware.
PARE-end

tag: sample type

value: Sorghum leaf


title: Sorghum spikelet <0.5 mm anthers

description: PARE

source_name: spikelet

value: Sorghum spikelet <0.5 mm anthers


title: Sorghum spikelet 0.5-1.2 mm anthers

description: PARE

value: Sorghum spikelet 0.5-1.2 mm anthers


title: Sorghum spikelet >1.2 mm

description: PARE

value: Sorghum spikelet >1.2 mm


title: 200544710031_G


title: Bahd1-KO Adult rep2_rc


title: 200544710031_E


title: 200544710031_C


title: 200544710031_D


title: 200544710031_A


title: 200544630061_K


title: 200544630061_L


title: 200544630061_J


title: EcN-NG-sta1

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Total RNA without ribosomal RNA
probiotics, generally recognized as safe (GRAS status)

data_processing:
(1) The quality of the sequence reads obtained from RNA-seq was checked by FastQC.
(2) The sequence reads were aligned to the reference genome using bowtie2.
(3) The Cufflink package (http://cufflinks.cbcb.umd.edu/) was run to obtain transcriptomic data.
Genome_build: The genome sequence of E. coli Nissle 1917 strain has been uploaded to Genbank (CP007799.1).
Supplementary_files_format_and_content: gtf, Reads Per Kilobase of exon per Megabase of library size (RPKM) values for each gene

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: Samples at the exponential growth phase were harvested at optical density at 600nm (OD600 ) 0.6-0.8, and samples at the stationary growth phase were harvested at OD600 1.2.

extract_protocol:
Total RNA including small RNAs was extracted by using an RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Then, the ribosomal RNAs were removed from the total RNA using the Ribo-Zero rRNA Removal Kit for Gram-negative bacteria (Illumina, San Diego, CA, USA).
The strand-specific RNA-seq library was constructed using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina platforms (Kapa Biosystems, Inc., Wilmington, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: The cells were treated with RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany).

value: Nissle 1917

value: wildtype

tag: growth phase

value: stationary

tag: treatment

value: normal gravity (NG)


title: EcN-MG-sta2

value: MG


title: EcN-MG-sta1


title: 200544710031_B

value: head and neck squamous cell carcinoma

value: M


title: EcN-NG-exp1

value: exponential


title: EcN-NG-exp2


title: EcN-MG-exp2


title: EcN-MG-exp1


title: EcN-NG-sta2


title: 200544630061_F

value: T-without


title: 200544710054_C


title: PC9 cells, day14_rep1_med

city: Cambridge

first: Yaara

last: Oren

state: Massachusetts

address: 415 Main street cambridge

institute: Broad institute

data_processing:
Reads were aligned ,samples were aggregated and expression quantified using the 10x pipeline cell ranger-2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-separated values file. Each column is a cell Id and each row is a gene.  For cell IDs, the number after the dash refers to sample type where 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 map to samples "0","3_rep1","3_rep2","7_rep1", "7_rep2", "14_rep1_high", "14_rep1_med", "14_rep1_low","14_rep2_high", "14_rep2_med", "14_rep2_low", respectively.

source_name: PC9  human cancer cell line

extract_protocol:
DissociateCells were washed, trypsinized, passed through a 40μM cell strainer, centrifuged at 400g, and resuspended at a concentration of 1,000 cells/μL in PBS + 0.5% BSA.
Single cells were processed through the Chromium Single Cell 3′ Solution platform using the Chromium Single Cell 3’ Gel Bead, Chip and Library Kits (10X Genomics), as per the manufacturer’s protocol.

treatment_protocol: Lung cancer PC9 cells were treated with osimertinib (300nM) and harvested before treatment, after 3,7, and 14 days of continuous drug treatment. At day 14 prior to sequencing, cells were sorted to three groups based on mCherry expression:cycling (low), moderate cyclers (med) and non-cycling (high)

tag: cell line

value: PC9 Lung cancer cell line

value: osimertinib

tag: time

tag: mcherry expression

value: med


title: PC9 cells, day14_rep2_med


title: PC9 cells, day14_rep1_low

value: low


title: 200544630061_A

value: T-with


title: PC9 cells, day14_rep2_high

value: high


title: 200544630061_H


title: 200544630061_I


title: 200544630025_J


title: PC9 cells, day3_rep2


title: PC9 cells, day7_rep2


title: 200544630061_C


title: PC9 cells, day14_rep1_high


title: PC9 cells, day7_rep1


title: PC9 cells, day14_rep2_low


title: PC9 cells, day3_rep1


title: PC9 cells, day0

value: control


title: 200544630061_G


title: 200544630061_D


title: 200544630012_L


title: 200544630025_F


title: 200544630012_I


title: 200544630012_E


title: 200544630061_E


title: 200544630025_K


title: 200544630012_J


title: 200544630012_K


title: 200544630025_C


title: 200544630012_D


title: 200544630012_C


title: DP78

city: Chongqing

first: Xue

last: Wei

address: 10# Changjiangzhilu

country: China

institute: Daping Hospital,  Army Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/） using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment.
Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Genome_build: hg18
Supplementary_files_format_and_content: read counts, rpkm

source_name: glioma tissue

growth_protocol: Tumor samples were maintained in liquid nitrogen prior to extract preparation.

extract_protocol:
Total RNAs were extracted from samples using TRIzol (Invitrogen) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina) with PE150 model.

value: glioblastoma

tag: who grade

value: IV

tag: group

value: xenograft-forming group


title: 200544630012_B


title: DP66

value: anaplastic oligodendroglioma

value: III

value: nonxenograft-forming group


title: DP72


title: DP69


title: DP70


title: DP74


title: DP63


title: DP64


title: DP62


title: DP58

value: anaplastic astrocytoma


title: 200536980068_F

value: head and neck squamous cell carcinoma


title: Typhimurium rep 3

city: Ithaca

first: Alexa

middle: Robyn

last: Cohn

state: NY

address: 411 Tower Rd

department: Food Science

institute: Cornell University

description: 10310_5515_87456_HH2YTBGX9_AC9-4084-1017_CATTTT

data_processing:
Basecalls were performed using BWA
RNA-seq reads were aligned to their respective assembled genomes, i.e. S. Cerro reads were aligned to the S. Cerro FSL R8-2349 genome, using featureCounts
Reads were normalized using limma+voom and differential expression was determine with cut-offs of log2FC > |2| and p < 0.05
Genome_build: PRJNA187545 (Cerro),  PRJNA627875 (Javiana), GCA_000022165.1 (Typhimurium)
Supplementary_files_format_and_content: tab delimited files contain normalized transcript abundances for each sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella enterica

growth_protocol: Samples were grown to late exponential phase in LB at 37C

extract_protocol:
RNA protect was added to samples, followed by a 5 minute incubation at room temperature and cell collection. Collected cells were treated with lysozyme and proteinase K, followed by phase extraction with TRI Reagent
Total RNA was DNA depleted using Turbo DNase, followed by rRNA depletion using Illumina RiboZero Bacterial Kit. 100 ng rRNA-depleted RNA was used as input for library prep with the NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: No treatment

tag: strain/isolate

value: ATCC 14028S

value: late exponential phase

tag: molecule subtype

value: rRNA-depleted RNA


title: Typhimurium rep 2

description: 10310_5515_87459_HH2YTBGX9_AC8-4084-1010_TCGGCA


title: Typhimurium rep 1

description: 10310_5515_87455_HH2YTBGX9_AC7-4084-1005_CACTCA


title: DP52


title: 200536980068_H

value: M


title: 200536980068_G


title: 200544630012_A


title: 200536980068_E


title: 200536980068_D


title: 200536980068_I

value: T-without


title: DP51


title: 200536980068_B


title: 200536980068_A


title: 200536980004_L


title: 200536980004_I


title: 200536980004_G


title: DP57


title: DP53


title: DP44


title: DP43

value: anaplastic oligoastrocytoma


title: 200536980004_A

value: T-with


title: PEA1 siTRAP1 2

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

institute: University of Naples “Federico II”

description: replicate 2

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol using HiScan system

data_processing: The data were normalized using neqc() quantile normalization with limma in R

source_name: PEA1 cells

label_protocol: Standard Illumina label protocol

growth_protocol: PEA1 cells were grown in RPMI 1640 media with 10% fetal bovine serum, glutamine and Normocin (Invivogen) at 37°C, 5% CO2 on 10-cm dishes until were approximately 85% confluent

extract_protocol: Total RNA was extracted using a standard acid guanidinium thiocyanate-phenol-chloroform extraction protocol

treatment_protocol: Cells were transfected with siRNAs targeting TRAP1 (Qiagen cat. no. SI00115150) or a nontargeting control siRNA (Qiagen; cat. no. SI03650318) using HiPerFect Transfection Reagent (Qiagen) according to manufacturer's protocol.

tag: cell type

value: Ovarian cancer cells

tag: knockdown

value: TRAP1-directed siRNA


title: DP45

tag: tissue


title: 200536980004_B


title: DP41


title: 200536850030_L


title: PEA1 siNeg 3

description: replicate 3

value: control siRNA


title: DP42

value: glioblastoma

value: IV


title: PEA1 siNeg 2

description: replicate 2


title: activated_CD8bm1-1

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

hyb_protocol: hybridized 17h using the standard Affymetrix protocol

scan_protocol: Arrays were scanned by Affymetrix 3000-7G scanner controlled by Affymetrix Genechip Command Console.

data_processing:
CEL files were imported into Partek Genomics Suite (Partek, Inc., St. Louis, Mo). RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: T cell clone

label_protocol: Affymetrix WT Plus using 100ng of total RNA

growth_protocol: RPMI 1640 media supplemented with 10% FBS, glutamax I, 5x10-5M 2 mercaptoethanol

extract_protocol: QIAGEN RNeasy

treatment_protocol: Immobilized 145-2c11 antibody (0.5 ug/ml in PBS overnight) adsorbed to tissue culture plates

tag: phenotype

value: allo CD8

value: activated


title: 200536850030_J


title: PEA1 siTRAP1 1

description: replicate 1


title: activated_CD8bm1-2


title: DP40

value: xenograft-forming group


title: activated_CD8bm1-3


title: PEA1 siNeg 1

description: replicate 1


title: activated_CD8bm1-4


title: DP37


title: 200536850030_H


title: 200536850030_I


title: activated_8uvmo-3-4


title: activated_8uvmo-3-3


title: DP31

value: nonxenograft-forming group


title: activated_8uvmo-2-4


title: 200536850030_G

value: head and neck squamous cell carcinoma


title: activated_8uvmo-3-2


title: EV-SKOV3 1

city: Changsha

first: Guanming

last: Deng

state: Hunan

address: 283 Tongzipo Road, Yuelu District

department: Gynecologic Oncology

institute: Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: SKOV3 cells

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, HyClone, USA) supplemented with 10% fetal bovine serum (FBS, BI, Israel) and 1% penicillin-streptomycin solution (HyClone, USA) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: EV-SKOV3 3


title: EV-SKOV3 2


title: activated_8uvmo-3-1


title: 200536850030_F


title: activated_8uvmo-2-3


title: activated_8uvmo-2-2


title: activated_8uvmo-2-1


title: activated_sAG3-4


title: 200536850030_E


title: 200536850030_C


title: 200536850030_D


title: activated_sAG3-2


title: activated_sAG3-1


title: activated_sAG1-3


title: activated_sAG3-3


title: 200536850030_B


title: ESRP1-SKOV3 3


title: WT1 27_50.9

city: Canberra

first: Patrick

last: Buerger

address: Clunies Ross St, S1.03, Bldg 101,

country: Australia

institute: CSIRO

data_processing:
QC with FastQC
Alignment to Reference genome with STAR, version 2.5.3.
Gene expression in R with Limma, version 3.36.5
Genome_build: Genome reference name host [Acropora tenuis], website http://aten.reefgenomics.org/download/  Genome reference name symbiont [Symbiodinium goreaui], website http://symbs.reefgenomics.org/download/
Supplementary_files_format_and_content: Text file, Gene expression matrix, STAR

organism:
Acropora tenuis
Cladocopium goreaui

source_name: Coral larvae in symbiosis with Symbiodiniaceae

extract_protocol:
Quick-RNA MiniPrep Kit (Zymo)
Illumina TruSeq Stranded mRNA v2; 2x 100 bp, NovaSeq 6000

tag: symbiont

value: Cladocopium goreaui

tag: strain

value: wild-type

tag: growth temperature


title: activated_sAG1-4


title: activated_sAG1-2


title: 200536850030_A

tag: disease state


title: activated_sAG1-1


title: dormant_CD8bm1-4

value: dormant


title: WT1 27_50.8

value: Coral larvae in symbiosis with Symbiodiniaceae


title: WT1 27_50.7


title: S3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
GRCh38
TXT file contain counts for each sample

extract_protocol:
Tumor tissue were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SKOV3 cells

value: Ovarian adenocarcinoma


title: dormant_CD8bm1-1


title: dormant_CD8bm1-3


title: dormant_CD8bm1-2


title: WT1 27_50.6


title: S2


title: dormant_8uvmo-3-4


title: WT1 27_50.5


title: dormant_8uvmo-3-2


title: dormant_8uvmo-3-3


title: WT1 27_50.1


title: S1


title: SS8 27_40.8

value: heat selected


title: 57

city: Solna

first: Staffan

last: Holmin

state: Non US/Canada

address: Visionsgatan 4, J5:20

country: Sweden

institute: Karolinska Institutet

data_processing:
TrimGalore for trimming reads
STAR for mapping reads to genome
featureCounts for counting genes
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: count matrix of reads mapped to genes

organism: Sus scrofa

source_name: Skeletal muscle_Baseline

extract_protocol:
RNAdvance Tissue kit with modifications: Reduce reagent volumes by dividing with 13. Use vortexing + centrifugation to homogenize samples.
SMARTer® Stranded Total RNA-Seq Kit v1

tag: pigid

value: Skeletal muscle

tag: sample type

tag: timepoint

value: Baseline


title: dormant_8uvmo-2-4


title: 56

source_name: Left heart ventricle_Conventional EMB_Follow-up

value: Left heart ventricle

value: Conventional EMB

value: Follow-up


title: dormant_8uvmo-2-3


title: dormant_8uvmo-3-1


title: SS8 27_40.9

tag: treatment


title: ESRP1-SKOV3 1

value: Ovarian cancer cells


title: dormant_8uvmo-2-2


title: 55


title: dormant_sAg1-3


title: SS8 27_40.7


title: cdk9as_htb1kr_3mb_pol2_r2

city: Bronx

first: PABITRA

middle: K

last: PARUA

address: 1300 Morris Park Avenue, Forchheimer 236, Molecular Pharmacology

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
ChIP-seq: Paired-end (40-nt reads) sequencing was performed on an Illumina NextSeq 500.
ChIP-seq: ‘FastQC Read Quality Reports’ (Galaxy Version 0.72) and ‘Trimmomatic Flexible Read Trimming Tool’ (Galaxy Version 0.36.6) were used to check quality of the sequencing reads and for barcode trimming, respectively.
ChIP-seq: Trimmed sequencing reads were aligned to the S. pombe genome (Schizosaccharomyces_pombe_1.1) using Bowtie2 in Galaxy (Galaxy Version 2.3.4.2). Normalization of the aligned reads was done using ‘bamCoverage’ (Galaxy Version 3.1.2.0.0) by 1) computing and applying scaling factor obtained using aligned sequencing reads of the spike-in reference genome (Saccharomyces cerevisiae, for spike-in samples) and 2) by computing RPKM (reads per kilobase per million) (for the samples without spike-in control).
ChIP-seq: Aligned sequences of each biological replicate were processed separately to identify enriched binding sites using MACS2 callpeak program (Galaxy Version 2.1.1.20160309.6). The resulting bedgraph files were converted to bigwig using ‘Wig/BedGraph-to-bigWig converter’ (Galaxy Version 1.1.1), replicates were combined using ‘Concatenate datasets’ (Galaxy Version 1.0.0).
ChIP-seq: Matrix was computed using ‘computeMatrix’ (Galaxy v.2.3.6.0) in DeepTools to prepare data for plotting heat maps and/or profiles of given regions. The genome-wide distributions, heat maps and metagene plots were created using ‘plotHeatmap’ (Galaxy Version 3.1.2.0.1) and ‘plotProfile’ (Galaxy Version 3.1.2.0.0) tools, respectively. The phospho-over-total signal ratios (log2-ratio) were calculated using ‘bigwigCompare’ (Galaxy Version 3.1.2.0.0).
Genome_build: ChIP-seq: S. pombe: ASM294v2.
Genome_build: ChIP-seq: Spike-in control Saccharomyces cerevisiae (April 2011, sacCer3)
Supplementary_files_format_and_content: ChIP-seq: processed files are in bigWig format (n = 2 biological replicates combined). There are 8-bigWig files in total. .

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: ChIP-seq: S. pombe cultures were grown in YES media till OD600 ~ 0.4.

extract_protocol:
ChIP-seq: After HCHO-crosslinking (15 min at 25°C), protein extract was prepared using Mini-bead beater (Biospec; 30 sec "ON" and 30 sec "OFF"). Lysates were precleared with Protein A agarose beads and used for IP with respective antibodies.
ChIP-seq: Preparation of multiplexed ChIP-seq libraries from purified immunoprecipitated chromatin and sequencing were performed as described. In brief, the NEBNext Ultra II DNA Library Preparation kit (E7103S) was used to generate libraries using 5-10 ng of input or immunoprecipitated DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina (Set 1, E7335 and Set 2, E7500)).

tag: strain genotype/variation

tag: temperature °c

tag: 3-mb-pp1 [μm]

tag: treatment time [min]

tag: antibody

value: Anti-RNA Pol II Rpb1 antibody (BioLegend # 664912)

tag: assay

value: ChIP-seq


title: 54

source_name: Left heart ventricle_Micro-EMB_Baseline

value: Micro-EMB


title: dormant_sAg3-2

tag: group


title: SS8 27_40.6

tag: tissue


title: dormant_sAg3-3

tag: phenotype


title: cdk9as_htb1kr_3mb_pol2_r1


title: 53


title: dormant_sAg1-2


title: dormant_sAg1-1


title: dormant_sAg3-1


title: SS8 27_40.5

tag: symbiont


title: cdk9as_htb1kr_3mb_myc_r1

value: Anti-cMyc antibody (BioLegend # 626802)


title: 52


title: dormant_8uvmo-2-1


title: cdk9as_htb1kr_dmso_pol2_r2

value: DMSO


title: 51

source_name: Whole blood_Baseline

value: Whole blood

value: Blood


title: cdk9as_htb1kr_dmso_myc_r2


title: cdk9as_htb1kr_dmso_pol2_r1


title: 50


title: cdk9as_htb1kr_dmso_myc_r1


title: SS5 27_25.9

value: Coral larvae in symbiosis with Symbiodiniaceae

value: Cladocopium goreaui

tag: strain


title: cdk9as_3mb_pol2_r1

source_name: cdk9as::KanMx pst2-myc::NatMx

value: cdk9as::KanMx pst2-myc::NatMx


title: cdk9as_htb1kr_3mb_myc_r2


title: cdk9as_3mb_myc_r2


title: 49


title: cdk9as_dmso_pol2_r2


title: SS5 27_25.6

value: heat selected

tag: growth temperature


title: 48

value: Skeletal muscle


title: SS5 27_25.5


title: cdk9as_dmso_pol2_r1


title: 47


title: cdk9as_htb1kr_dmso_input_r2


title: cdk9as_dmso_myc_r1


title: 45

value: Baseline


title: cdk9as_dmso_myc_r2


title: cdk9as_htb1kr_dmso_input_r1


title: cdk9as_3mb_pol2_r2


title: ESRP1-SKOV3 2

tag: cell type


title: SS3 27_14.8


title: SS5 27_25.7


title: 44

tag: pigid

value: Left heart ventricle


title: SS5 27_25.8


title: SS3 27_14.6


title: 43

tag: sample type


title: SS3 27_14.7


title: 41

tag: timepoint


title: cdk9as_3mb_myc_r1

tag: treatment


title: SS3 27_14.5


title: YY1683 oma-1 rep2

city: Boston

first: Scott

last: Kennedy

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
22G siRNAs
small RNA-seq

data_processing:
Select reads starting with the last 4 nucleotides of the 5’ adapters (either AGCG or CGTC) by custom python script.
Trim the 3’ adapter (CTGTAGGCACCATCAATAGATCGGAAGAGCAC) using cutadapt v1.14.
Trim the in-line portion of the 5’ adapter using cutadapt v1.14.
Align reads to the C. elegans genome using tophat v2.1.1 with corresponding annotation file (unique map and perfect match).
Count reads mapping to each gene using featureCounts v1.6.0.
Genome_build: WBcel235
Supplementary_files_format_and_content: .txt format generated by featureCounts.

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Animals grown on HT115 bacteria expressing L4440 or oma-1 dsRNA at 20C.

extract_protocol:
Young adults were washed with M9 twice, flash frozen in liquid nitrogen, extract with Trizol reagent. 20ug total RNAs were resolved by RNA Urea gel and small RNAs of ~18-35nt were selected from the gel.
Small RNAs were cloned using a 5′ monophosphate independent small RNA protocol as previously described (Gent et al. 2009).

tag: genotype

tag: age

value: Day1 gravid adults

value: whole body


title: N2 oma-1 rep2

description:
22G siRNAs
small RNA-seq

value: wild type


title: N2 L4440 rep2

description:
22G siRNAs
small RNA-seq


title: YY1683 L4440 rep2

description:
22G siRNAs
small RNA-seq


title: SS3 27_14.4


title: YY1683 oma-1 rep1

description:
22G siRNAs
small RNA-seq


title: 6-ergo-1-small-RNA-3

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using Cutadapt(Martin, 2011) and mapped to the C. elegans genome, WS258, using HISAT2(Kim, Langmead, & Salzberg, 2015) and the transcriptome using Salmon(Patro, Duggal, Love, Irizarry, & Kingsford, 2017). Data analysis was done using R, Excel, and custom Python scripts. Reads per million were plotted along the WS258 genome using Integrative Genomics Viewer 2.3.68(Robinson et al., 2011). Gene ontology analysis was performed using the Enrichment Analysis Tool on WormBase(Angeles-Albores, RY, Chan, & Sternberg, 2016). Gene enrichment analysis was performed using reference gene lists from WormExp(Yang et al., 2016).
Genome_build: WS258
Supplementary_files_format_and_content: tab-delimited text files including total reads mapping to each gene

source_name: ergo-1-whole animal

growth_protocol: Synchronized L1s of ergo-1(tm1860) and prg-1(n4357) worms were plated on enriched peptone plates and cultured at 20°C and 25°C.

extract_protocol:
8,000 animals per sample were harvested as adults (~68hrs at 20°C and ~48hrs at 25°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
Small RNA library preparation. Small RNAs (18- to 30- nt) were size selected on denaturing 15% polyacrylamide gels (Criterion 3450091) from total RNA samples. Libraries were prepared as previously described(Montgomery et al., 2012). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit. Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.

tag: Stage

value: Day 1 Adult

tag: molecule subtype

value: size selected RNA from total RNA


title: SS3 27_14.3


title: 5-ergo-1-small-RNA-2


title: 38

source_name: Left heart ventricle_Conventional EMB_Baseline

value: Conventional EMB


title: 3-prg-1-small-RNA-3

source_name: prg-1-whole animal


title: Mutant, 24 h, rep3

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätsstraße 150

department: Microbial Biology

country: Germany

institute: Ruhr University Bochum

description:
gene_expression_DUF1127.FPKM.xls
d3_24h_vs_WT_24h.genes.DEA.xls

data_processing:
Adapter sequences and raw reads of low quality were removed through in-house scripts by Novogene.
Clean paired-end reads were mapped via HISAT2 software.
Novel genes were using the Cufflinks Reference Annotation Based Transcript (RABT) assembly method.
The read numbers that were mapped for each gene were counted via HTSeq. FPKM (Fragments Per Kilobase of exon model per Million reads mapped) values were calculated.
A differential expression analysis was performed between two groups (three biological replicates each) using the DESeq2 R package. P values were adjusted via Banjamini.Hochberg procedure for determination of the False Discovery Rate. An adjusted p value below 0.05 was cosidered to describe a significantly differentially expressed gene.
Genome_build: ASM9202v1; small RNA genes were added from Wilms et al. (2012, DOI: 10.4161/rna.17212), Lee et al. (2013, DOI: 10.1371/journal.pone.0070720) and from Möller et al. (2014, DOI: 10.1371/journal.pone.0110427)
Supplementary_files_format_and_content: Files include FPKM values calculated from the three biological replicates, the binary logarithm of the fold change of each gene in the mutant and the corresponding p values.

organism: Agrobacterium fabrum str. C58

source_name: Agrobacterium fabrum C58 ∆L4 ∆atu1667 ∆atu8161 total RNA

growth_protocol: Cells were grown at 30 °C in YEB medium. Samples were taken at an optical density (600 nm) of 0.5, of 1.5 and after 24 h.

extract_protocol:
RNA was extracted via hot-phenol method as described in Wilms et al. (2012, DOI: 10.4161/rna.17212). Samples were treated with RNase-free DNase.
RNA libraries were prepared by Novogene. 1 µg of RNA was used. Sequencing libraries were generated with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to manufacturer's instructions. Index codes were added to attribute sequences to each sample. Fragmentation was done with divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5x) at elevated temperature. First strand synthesis was carried out with random hexamer primers and M-MuLV reverse transcriptase. Second strand was synthesized with DNA polymerase I and RNase H. Blunt ends were created from overhangs via exonuclease/polymerase activites. DNA 3' ends were adenylated and NEBNext Adaptors with hairpin loop were ligated. Fragments were purified with the AMPure XP system (Backman Cooulter, USA). The cDNA was incubated at 37 °C for 15 min with 3 µl USER Enzyme (NEB, USA) and then at 95 °C for 5 min.The subsequent PCR was done with Phusion High-Fidelity DNA polymerase, Universail PCR primers and Index (X) Primer. The PCR products were purified via AMPure XP system and the quality was assured via Agilent Bioanalyzer 2100.

value: delta_L4; delta_atu1667; delta_atu8161

tag: od

value: at 24 hours


title: 2-prg-1-small-RNA-2


title: YY1683 L4440 rep1

description:
22G siRNAs
small RNA-seq


title: N2 oma-1 rep1

description:
22G siRNAs
small RNA-seq


title: Mutant, 24 h, rep2


title: 37

value: Micro-EMB

value: Follow-up


title: 4-ergo-1-small-RNA-1


title: 36


title: N2 L4440 rep1

description:
22G siRNAs
small RNA-seq


title: 40


title: 39


title: 35


title: 1uM inorganic asenic treated #1 [iAs1_S61]

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

description:
iAs1_S61_L006
processed data file: miRquant_RPMMM.csv

data_processing:
Small RNA-seq samples were processed using miRquant2.0 and normalized counts were determined using DESeq2
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: rn6
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the reads per million mapped to miRs (RPMMM) for small RNA-seq or DESeq2 normalized counts for RNA-seq for each of the samples.

source_name: rat insulinoma cells_1uM inorganic asenic

growth_protocol: Cells were seeded 1 million/well in a 12-well plate 24 hours prior to exposure

extract_protocol:
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
RNA was isolated using Norgen Total RNA Purification kit.
See description column in Samples section

treatment_protocol: Cells were treated for 24 hours prior to RNA isolation.

value: liver

value: rat insulinoma cells

value: 1uM inorganic asenic

value: small RNA


title: 1uM inorganic asenic treated #2 [iAs2_S62]

description:
iAs2_S62_L006
processed data file: miRquant_RPMMM.csv


title: 25uM manganese treated #1 [Mn1_S67]

description:
Mn1_S67_L006
processed data file: miRquant_RPMMM.csv

source_name: rat insulinoma cells_25uM manganese

value: 25uM manganese


title: 5uM cadmium treated #3 [Cd3_S66]

description:
Cd3_S66_L006
processed data file: miRquant_RPMMM.csv

source_name: rat insulinoma cells_5uM cadmium

value: 5uM cadmium


title: 34

value: Left heart ventricle


title: 33

value: Baseline


title: 25uM manganese treated #2 [Mn2_S68]

description:
Mn2_S68_L006
processed data file: miRquant_RPMMM.csv


title: 5uM cadmium treated #2 [Cd2_S65]

description:
Cd2_S65_L006
processed data file: miRquant_RPMMM.csv


title: Untreated #3 [C3_S60]

description:
C3_S60_L006
processed data file: miRquant_RPMMM.csv

source_name: rat insulinoma cells_untreated

value: untreated


title: Untreated #2 [C2_S59]

description:
C2_S59_L006
processed data file: miRquant_RPMMM.csv


title: 32


title: 1-prg-1-small-RNA-1


title: Untreated #1 [C1_S58]

description:
C1_S58_L006
processed data file: miRquant_RPMMM.csv


title: Mutant, OD 1.5, rep3

description:
gene_expression_DUF1127.FPKM.xls
d3_15_vs_WT_15.genes.DEA.xls


title: 31

value: Skeletal muscle


title: Cerro rep 3

description: 10310_5515_87454_HH2YTBGX9_AC6-2349-0821_CACGAT

organism: Salmonella enterica subsp. enterica serovar Cerro

source_name: Salmonella enterica

tag: strain/isolate

tag: growth phase

value: late exponential phase

value: rRNA-depleted RNA


title: 25uM manganese treated #3 [Mn3_S69]

description:
Mn3_S69_L006
processed data file: miRquant_RPMMM.csv

tag: tissue


title: Mutant, 24 h, rep1


title: 30


title: Cerro rep 2

description: 10310_5515_87453_HH2YTBGX9_AC5-2349-0820_CAAAAG


title: Mutant, OD 1.5, rep1


title: Mutant, OD 1.5, rep2


title: 5uM cadmium treated #1 [Cd1_S64]

description:
Cd1_S64_L006
processed data file: miRquant_RPMMM.csv


title: 29


title: Cerro rep 1

description: 10310_5515_87452_HH2YTBGX9_AC4-2349-0818_ATGAGC


title: WT, OD 1.5, rep3

source_name: Agrobacterium fabrum C58 total RNA

value: wild type


title: WT, OD 1.5, rep2


title: WT, OD 1.5, rep1


title: Mutant, OD 0.5, rep3

description:
gene_expression_DUF1127.FPKM.xls
d3_05_vs_WT_05.genes.DEA.xls

value: delta_L4; delta_atu1667; delta_atu8161


title: 26


title: Mutant, OD 0.5, rep2


title: 24


title: Mutant, OD 0.5, rep1


title: H2Bub1_rep2

data_processing:
ChIP-seq: Paired-end sequencing (50-nt reads) was performed on an Illumina HiSeq 2000 (Genome Quebec Innovation Centre, McGill University).
ChIP-seq: Quality control and adapter trimming of the FASTQ (raw sequencing files) files were done in Galaxy using FastQC Read Quality reports (Galaxy Version 0.69) and trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.36.3) respectively.
ChIP-seq: After adaptor trimming and quality control, processed FASTQ files were aligned to the S. pombe genome using Bowtie2 (Galaxy Version 2.2.6.2).
ChIP-seq: Aligned sequences of each biological replicate were fed into MACS2 (Galaxy Version 2.1.1.20160309.0) to call peaks from alignment results. Generated “bedgraph treatment” files were converted into bigwig using “Wig/BedGraph-to-bigWig converter” (Galaxy Version 1.1.0), concatenated (Galaxy Version 1.0.1) to combine replicates of each sample, subtracted IgG reads from each and processed using computeMatrix (Galaxy Version 2.3.6.0) in DeepTools to prepare data for plotting a heatmap and/ or a profile of given regions.
Genome_build: ChIP-seq: S. pombe: ASM294v2.
Supplementary_files_format_and_content: ChIP-seq: processed files are in bigWig format. There are 6-bigWig files in total. 3 for H2B and 3 for H2Bub1 including two biological replicates.

extract_protocol:
ChIP-seq: After HCHO-crosslinking (15 min at 25°C) protein extract was prepared using Mini-beadbeater (Biospec; 30 sec "ON" and 30 sec "OFF"). Lysates were precleared with Protein A agarose beads and used for IP with respective antibodies.
ChIP-seq: Multiplexed ChIP-seq libraries were prepared using the Illumina TruSeq DNA Sample Preparation kit v2 with 75 ng of input or IP DNA and barcode adaptors.

tag: strain genotype/variation

tag: temperature °c

tag: chip antibody

value: Histone H2BK120ub1 antibody (Active Motif # 39623)


title: H2Bub1_rep1


title: 23

value: Conventional EMB


title: 28

value: Whole blood

value: Blood


title: WT, OD 0.5, rep3


title: 22

value: Micro-EMB

value: Follow-up


title: 25


title: WT, OD 0.5, rep2


title: H2B_rep2

value: Anti-FLAG® M2 antibody (SIGMA # F3165)


title: 21


title: 1uM inorganic asenic treated #3 [iAs3_S63]

description:
iAs3_S63_L006
processed data file: miRquant_RPMMM.csv

tag: strain

value: liver

value: rat insulinoma cells

value: 1uM inorganic asenic

value: small RNA


title: H2B_rep1


title: 27

value: Baseline


title: 20


title: Javiana rep 3

description: 10310_5515_87451_HH2YTBGX9_AC3-0395-0808_GGTAGC

organism: Salmonella enterica subsp. enterica serovar Javiana


title: Input_rep2

source_name: Input


title: WT, OD 0.5, rep1


title: 19

value: Left heart ventricle


title: Javiana rep 2

description: 10310_5515_87458_HH2YTBGX9_AC2-0395-0803_ACTGAT

value: late exponential phase


title: 18


title: iTreg ZFP36L2

city: Chiba

first: Sohei

last: Makita

state: Chiba

address: 1-8-1 inohana chuo-ku

country: Japan

institute: Chiba university

data_processing:
Illumina Casava1.8.2 software used for basecalling.
RNA-seq libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent).   Sequencing was performed on an Illumina HiSeq1500 using a HiSeq Rapid SBSkit v2 (Illumina) in a 50-base single-end mode.
mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: CD4 positive T cells

extract_protocol:
Total RNA was isolated by using an RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Foxp3hCD2 mice on a BALB/c background

value: After naïve CD4+ T cells of Foxp3hCD2 mice were stimulated with anti-CD3/anti-CD28 mAb under neutral conditions for 24 hours, cells were infected with retroviruses of MIG-Zfp36l2 or MIG, and cultured under iTreg-inducing conditions for three days.

value: CD4 positive T cells


title: SS5 27_25.1

source_name: Coral larvae in symbiosis with Symbiodiniaceae

tag: symbiont

value: Cladocopium goreaui

value: heat selected

tag: growth temperature


title: 17

tag: pigid

tag: sample type


title: iTreg Mock

tag: treatment


title: Input_rep1


title: 16

source_name: Left heart ventricle_Micro-EMB_Baseline

tag: timepoint


title: neut ZFP36L2

value: After naïve CD4+ T cells were stimulated with anti-CD3/anti-CD28 mAb under neutral conditions for 24 hours, cells were infected with retroviruses of MSCV-IRES-GFP-Zfp36l2 (MIG-Zfp36l2) or MIG, and cultured under neutral conditions for three days.


title: Javiana rep 1

description: 10355_5515_87733_HH3JMBGX9_AC1-0395-0623_ATGTCA

value: rRNA-depleted RNA


title: 15

value: Micro-EMB


title: neut Mock


title: 42 IgMlow

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from IgD+, IgMlow, CD27+ B cells.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Clariom D Human Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing:
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.52.0), using R version 3.3.2 and the Brainarray clariomdhumanhsentrezgcdf R package (version 21.0.0).
Brainarray Entrez Gene CDF, version 21.0.0, Human Clariom D

source_name: Sorted B cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: RNA was extracted using RNeasy Micro kit (Qiagen, Hiden, NRW) according to the manufacturer's protocol.

treatment_protocol: Sorted cells of healthy donors were collected in cold TRIzol.

tag: cell type

value: Sorted B cells

tag: volunteer

tag: cell population

value: IgMlow


title: 42 IgMhigh

description: Gene expression data from IgD+, IgMhigh, CD27+ B cells.

value: IgMhigh


title: 13


title: 42 Naive

description: Gene expression data from IgD+, IgM+, CD27- B cells.

value: Naive


title: S5F

city: Madison

first: Cynthia

last: Kelm-Nelson

address: 1300 University Avenue, 416 Medical Sciences Center

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample as well as WGCNA data.

source_name: Periaqueductal gray, brainstem

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Long Evans

value: Periaqueductal gray, brainstem

tag: age

value: 8 months

tag: genotype

tag: Sex

value: Female


title: Liver cancer 2

city: shanghai

first: Yan

last: Liu

state: Shanghai

address: 800 Xiangyin Road, Shanghai 200433

department: The Department of Medical Genetics

institute: Second Military Medical University, Shanghai 200433, China

hyb_protocol: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2. Equilibrate water bath to 60°C. 3. For 8*60K array, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:cyanine 3-labeled, linearly amplified cRNA 0.6ug,10X Blocking Agent 5ul,Nuclease-free water ×ul,25X Fragmentation Buffer 1ul.4.Mix well but gently on a vortex mixer. 5. Incubate at 60°C for exactly 30 minutes to fragment RNA. 6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.7.Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer;  mixing on a vortex mixer introduces bubbles. 8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9. Place sample on ice and load onto the array as soon as possible.10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense”manner.12.Slowly place an array “active side” down onto the SureHyb gasket slide, so that the  “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that thesandwich-pair is properly aligned.13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.14. Hand-tighten the clamp onto the chamber.15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17. Hybridize at 65°C for 17 hours.

scan_protocol: 1. Assemble the slides into an slide holder. 2. Place assembled slide holders into scanner carousel. 3. Verify scan settings for one-color scans. Scan region:Scan Area (61 x 21.6 mm);Scan resolution (μm): 5;5μm scanning mode: Single Pass;eXtended Dynamic range:(selected);Dye channel:Green;Green PMT: XDR Hi 100% ,XDR Lo 10%. 4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Extract data using Agilent Feature Extraction Software. Software:Agilent Feature Extraction.  Procedure:  1. Open the Agilent Feature Extraction (FE) software.2. Add the images (.tif) to be extracted to the FE Project.3. Set FE Project Properties.4. Check the Extraction Set Configuration.5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.6. Select Project > Start Extracting and export data to txt.

source_name: Liver cancer

label_protocol: Using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442).Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.Add 1.2 μL of T7 Promoter Primer.Use nuclease-free water to bring the total reaction volume to 11.5 μL.Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.Place the reactions on ice and incubate for 5 minutes.Immediately prior to use, gently mix the components including 5×First Strand Buffer,0.1M DTT and 10mM dNTP mix etc. in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.Incubate samples at 40°C in a circulating water bath for 2 hours.Move samples to a 65°C circulating water bath and incubate for 15 minutes.Move samples to ice. Incubate for 5 minutes.Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.Immediately prior to use, gently mix the components including T7 RNA Polymerase and Cyanine-3-CTP etc. in the order indicated for the Transcription Master Mix by pipetting at room temperature.Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: using the Biopulverizer(biospec) and the Mini-Bead-Beater-16(biospec) to make tissues into the homogenized samples, and then incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol® Reagent (Invitrogen life technologies). Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.

tag: tissue

value: Liver cancer

value: one-year-old


title: 12

value: Left heart ventricle

value: Conventional EMB

value: Baseline


title: 42 Switch

description: Gene expression data from IgD-, IgM-, CD27+ B cells.

value: Switch


title: 11


title: Liver cancer 3


title: 41 IgMlow


title: GenomicDNA_Control_Control_C8

type: genomic

city: DIJON

first: Yannis

last: Duffourd

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

institute: Inserm U1231

description: Control sample

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Human Methylation BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: R 3.6.0, Normalisation by SWAN Method from Minfi v1.32,  DMP detection using DMPFinder from limma v3_42.0, DMR detection using DMRCate v2.2.0

label: Cy5 and Cy3

source_name: Buccal smear

label_protocol: Standard Illumina Protocol.

extract_protocol: genomic DNA was extracted and purified from smear samples using Qiagen Gentra Puregene Blood Kit Kit according to standard instructions

tag: gender

value: Male

value: Control


title: 14

source_name: Whole blood_Baseline

value: Whole blood

value: Blood


title: 41 IgMonly

description: Gene expression data from IgD-, IgM+, CD27+ B cells.

value: Sorted B cells

value: IgMonly


title: GenomicDNA_ICSI_Global_60

description: ICSI Global sample

value: ICSI

value: Global


title: GenomicDNA_FIV_Global_49

description: FIV Global sample

value: FIV


title: 41 IgMhigh

value: IgMhigh


title: GenomicDNA_ICSI_Global_59

description: ICSI Global sample

value: Female


title: 10

value: Micro-EMB


title: Adult liver 3

source_name: Adult liver

value: Adult liver


title: GenomicDNA_Control_Control_C2

description: Control sample


title: GenomicDNA_Control_Control_C9

description: Control sample


title: GenomicDNA_FIV_Global_27

description: FIV Global sample


title: Liver cancer 1

value: Liver cancer

value: one-year-old


title: GenomicDNA_FIV_Global_38

description: FIV Global sample


title: GenomicDNA_FIV_Global_11

description: FIV Global sample


title: 9

value: Left heart ventricle

value: Baseline


title: Adult liver 2


title: GenomicDNA_FIV_SSM_37

description: FIV SSM sample

value: Male

value: SSM


title: GenomicDNA_FIV_Global_3

description: FIV Global sample


title: 8

value: Follow-up


title: GenomicDNA_FIV_Global_51

description: FIV Global sample


title: 41 Naive

value: Naive


title: GenomicDNA_ICSI_SSM_24

description: ICSI SSM sample


title: Adult liver 1


title: 7


title: GenomicDNA_Control_Control_C19

description: Control sample

value: Control


title: GenomicDNA_ICSI_SSM_67

description: ICSI SSM sample


title: GenomicDNA_ICSI_Global_12

description: ICSI Global sample


title: 40 IgMlow

value: Sorted B cells

value: IgMlow


title: GenomicDNA_ICSI_Global_1

description: ICSI Global sample

value: ICSI

value: Global


title: 5

value: Whole blood

value: Blood


title: Fetal liver 3

source_name: Fetal liver

value: Fetal liver

value: 17.5-day-old embryonic


title: Fetal liver 2


title: GenomicDNA_ICSI_Global_46

description: ICSI Global sample

value: Female


title: Fetal liver 1


title: GenomicDNA_Control_Control_C1

description: Control sample


title: 3

source_name: Left heart ventricle_Conventional EMB_Follow-up

value: Conventional EMB


title: 4

value: Left heart ventricle

value: Micro-EMB


title: 6

source_name: Left heart ventricle_Conventional EMB_Baseline

value: Baseline


title: 41 Switch

value: Switch


title: GenomicDNA_FIV_SSM_58

description: FIV SSM sample

value: Male

value: FIV

value: SSM


title: H838-12D-3

city: Tapei

first: Peishan

last: Hung

state: State...

address: NO.1 JEN AI ROAD SECTION 1 TAIPEI 100 TAIWAN R.O.C.

country: Taiwan

institute: Graduate Institute of Oncology

description: Gene expression data from H838 KRAS G12D cells

hyb_protocol: 11 ug labeled samples were hybridized to Clariom D chip at 45℃ for 16.5 hours.

scan_protocol: The wash and staining were performed by Fluidic Station-450 and the the Clariom D chip were scanned with Affymetrix GeneChip Scanner 7G.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.4 and the SST-RMA method. These files in turn are used with the Affymetrix Transcriptome Analysis Console (TAC) Software to produce the differential expression tables and charts.

source_name: H838 cancer cell KRAS G12D -3

label_protocol: 300 ng total RNA were used for cDNA synthesis, labeled by in vitro transcription followed by fragmentation following the manufactory’s suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: cell were growth in RPMI1640+10%FBS+L-glutamine+1% PSA

extract_protocol: The extraction of total RNA was performed according to the NucleoSpin® RNA kit (Macherey-Nagel) manufacturer's instructions.

tag: disease state

value: adenocarcinoma

value: H838 KRAS G12D cells


title: 39 IgMhigh

value: Sorted B cells

value: IgMhigh


title: 39 IgMlow

value: IgMlow


title: 39 IgMonly

value: IgMonly


title: 1

source_name: Skeletal muscle_Baseline

value: Skeletal muscle


title: GenomicDNA_ICSI_Global_36

description: ICSI Global sample

value: ICSI

value: Global


title: 39 Switch


title: S87[SK+Flag]

city: Singapore

first: Xiaolin

last: Wu

state: Singapore

address: 1 CREATE Way

country: Singapore

institute: Singapore-MIT Alliance for Research and Technology (SMART)

data_processing:
Reads were then removed adapter by cutadapt
Clean reads were aligned to the corresponding genome using Bowtie 2 with the default option
Peak calling was performed using CisGenome with parameters “window statistic >=5 and p-value <= e-6” using two-sample analysis mode
Bam files were converted to a .tdf format for visualization separately at forward and reverse strand in the GenomeView
Genome_build: CP008925.1
Supplementary_files_format_and_content: TDF file from BAM using igvtools count. By default includes duplicates

organism: Salmonella enterica

source_name: bacteria

growth_protocol: S. enterica 87 expressing Salmonella DndBCDE strains were grown in Luria-Bertani (LB) broth at 37 °C.

extract_protocol:
Samples were then reversed cross-linking with Proteinase K at 65°C, and protein binding DNA was purified by DNA purification kit (Qiagen).
NEB NEBNext® UltraTM II DNA Library Prep Kit for Illumina was used for library preparation.

treatment_protocol: Briefly, bacteria were fixed with formaldehyde (1%) for 30 min, stopped crosslink with glycine (250 mM) for 15 min and sheared through Covaris sonication to an average DNA size of 200 bp. About 10ul anti-Flag antibody (Sigma) was added to each cell lysate following by overnight incubation at 4° C.  Protein G agarose (Thermo Fisher) was used for further pull-down.

value: Salmonella enterica serovar Cerro 87

tag: chip antibody

value: Anti Flag :Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich

value: S. enterica 87 [pBluescriptSK(+)+Flag]

tag: role

value: Tag not fused to protein control


title: XTG103[DndBCDE]

tag: strain

value: No tag control


title: 39 Naive

value: Naive


title: H838-12V-3

description: Gene expression data from H838 KRAS G12V cells

source_name: H838 cancer cell KRAS G12V -3

value: H838 KRAS G12V cells


title: GenomicDNA_ICSI_Global_10

description: ICSI SSM sample

value: Male


title: WT_rep4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Primary isolated cells, AEC II

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: Mice (Black/6) were grown under standard conditions.

extract_protocol: miRNeasy Mini Kit

tag: genotype/variation

value: wild-type mouse


title: GenomicDNA_Control_Control_C7

description: Control sample

value: Control


title: CCSPrtTAtetOmiR154_rep4

value: mutant mouse overexpressing miR-154


title: H838-3

description: Gene expression data from H838 cells

source_name: H838 cancer cell -3

value: adenocarcinoma

value: H838 cells


title: H838-12D-2

source_name: H838 cancer cell KRAS G12D -2

value: H838 KRAS G12D cells


title: XTG103[Flag-DndE]

value: ChIP


title: H838-12V-2

source_name: H838 cancer cell KRAS G12V -2


title: XTG103[Flag-DndE]-mock

value: No antibody control


title: H838-2

description: Gene expression data from H838 cells

source_name: H838 cancer cell -2


title: WT_rep3


title: XTG103[Flag-DndD]


title: KO-Light

city: Lubbock

first: Degeng Wang

last: Wang

state: TX

address: 1207 Gilbert Drive

department: Environmental Toxicology

institute: Texas Tech University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  and then mapped to hg19 whole genome using STAR
Read counts was calculated with htseq-count for each gene.
Genome_build: HG19
Supplementary_files_format_and_content: Tab-delimitted text file containing read count values for each Sample

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

tag: cell line

value: Dicer1 knockout

tag: polysome subfraction

value: light (9mer or less)


title: GenomicDNA_FIV_SSM_23

description: FIV SSM sample

value: FIV

value: SSM


title: XTG103[Flag-DndD]-mock

value: Salmonella enterica serovar Cerro 87


title: XTG103[Flag-DndC]-mock


title: WT_rep2


title: CCSPrtTAtetOmiR154_rep3


title: H838-1

description: Gene expression data from H838 cells

source_name: H838 cancer cell -1


title: CCSPrtTAtetOmiR154_rep2


title: CCSPrtTAtetOmiR154_rep1


title: WT-Light

value: wild type


title: XTG103[Flag-DndC]

value: Anti Flag :Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich


title: E.coliJW3350[pJTU1238]

data_processing:
Raw reads were then cleaned by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle)
clean reads were aligned to the E.coli K12 BW25113 genome using Bowtie 2.
The quantification of gene expression was carried out by RSEM in the form of FPKM (Fragments Per Kilobase Million)
edgeR was used for gene differentially expression analysis
Genome_build: NZ_CP009273.1
Supplementary_files_format_and_content: tab-delimited text files include read counts,FPKM values and annotations for each Sample.

organism: Escherichia coli K-12

growth_protocol: E. coli K12 expressing Salmonella DndBCDE strains were grown in Luria-Bertani (LB) at 37 °C.

extract_protocol:
Briefly, the total RNA was extracted by TRIzol® Reagent (Invitrogen), and the ribosome RNA was removed by a Ribo-Zero Magnetic kit (EpiCentre).
Illumina TruseqTM RNA sample prep kit was used for the RNA-Seq library preparation

treatment_protocol: The strains grows to log phase in Luria-Bertani (LB) at 37 °C without treatment.

tag: grow phase

value: log

value: delta dam mutant

tag: expression


title: S87[Flag]

tag: serovar

value: Cerro 87

value: S. enterica 87 [pACYC184+Flag]

value: Tag not fused to protein control


title: H838-12V-1

source_name: H838 cancer cell KRAS G12V -1

value: adenocarcinoma

tag: cell type

value: H838 KRAS G12V cells


title: E.coliJW3350[pBluescriptSK+]

value: pBluescriptSK+


title: WXL1[DndBCDE]

value: No tag control


title: WT_rep1

value: wild-type mouse


title: RNA 1uM inorganic asenic treated #5 [1C52]

institute: Cornell University

description:
1C52_1_TAATGCGC-GGCTCTGA_S24_L004
processed data file: DESeq2_normalized_counts.csv

source_name: rat insulinoma cells_1uM inorganic asenic

extract_protocol:
Libraries were prepared according to the Kapa mRNA Library Kit
RNA was isolated using Norgen Total RNA Purification kit.
See description column in Samples section

value: liver

value: rat insulinoma cells

tag: treatment

value: 1uM inorganic asenic


title: DT_3 (Drought-stressed)

city: Uvalde

first: Vijay

last: Joshi

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

description: Treatment

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Citrullus_lanatus whole genome using hisat2-2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts
Differeantial expression analysis with DEseq2
Genome_build: Citrullus_lanatus _WCG_V2
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

organism: Citrullus lanatus

source_name: Leaf of cultivar Crimson Sweet

growth_protocol: Approximately 8-weeks old seedlings of the variety Crimson Sweet were transplanted to ten heavy-duty round nursery pots. Before transplanting, all pots were filled with the same weight (~ 22lb) of soil-less media Absorb-N-Dry (Balcones Minerals Corporation, TX), saturated completely with water and left overnight for drainage.  The weighs of each pot was recorded to establish initial water content. All pots were applied with standard fertilizer mix to avoid nutritional imbalance (Peters Professional Mix 20:20:20). Decagon 5TE moisture sensors (Decagon Devices, Inc. WA, USA) were inserted at a depth of 6 inches and connected to the EM 50 data loggers for recording, monitoring, and downloading the information of the percent volumetric water content (VWC) per pot. The 5TE sensor uses an electromagnetic field to measure the dielectric permittivity of the surrounding medium. The sensor supplies a 70 MHz oscillating wave to the sensor prongs that charges according to the dielectric of the material. The stored charge is proportional to soil VWC. The control (well-watered) pots were frequently watered to maintain 95±5% of relative water content while for drought stress treatment the pots were subjected to stress by withholding watering 28 days (81 days old plant) after transplanting to maintain the soil moisture at 35±5% as per VWC data using daily readings recorded from the data loggers.  Samples for RNA sequencing were collected 8 days after inititation of drought stress

extract_protocol:
The flash-frozen leaf samples collected 8 Days after initiattion of drought stress treatment (89 days old plants)  from three independent plants along with control (well-irrigated) plants were used for RNA-Seq analysis. Total RNA was extracted using a Quick-RNA™ Miniprep Kit (Zymo Research Corporation, Irvine, CA ) as per the manufacturer’s protocol and treated with DNase1 (Zymo Research Corporation, Irvine, CA ).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time point

value: 8 days after initiation of drought stress

tag: protocol

value: Drought-stressed

tag: cultivar

value: Crimson Sweet


title: GenomicDNA_ICSI_Global_35

description: ICSI Global sample

source_name: Buccal smear

value: Female

value: ICSI

value: Global


title: DT_2 (Drought-stressed)

description: Treatment


title: RNA 1uM inorganic asenic treated #4 [1B513]

description:
1B52_1_CTGAAGCT-GGCTCTGA_S20_L004
processed data file: DESeq2_normalized_counts.csv

tag: tissue


title: KO-Heavy

value: Dicer1 knockout

value: heavy (10mer or more)


title: WXL1[Flag-DndE]-mock

value: Cerro 87

tag: genotype

value: No antibody control


title: GenomicDNA_FIV_Global_42

description: FIV Global sample

tag: gender

value: FIV


title: GenomicDNA_ICSI_Global_57

description: ICSI Global sample

value: Male


title: H838-12D-1

source_name: H838 cancer cell KRAS G12D -1

tag: disease state

value: adenocarcinoma

value: H838 KRAS G12D cells


title: DT_1 (Drought-stressed)

description: Treatment


title: WXL1[Flag-DndE]

tag: chip antibody

value: Anti Flag :Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich

tag: role

value: ChIP


title: RNA 1uM inorganic asenic treated #3 [1B52]

description:
1B513_ATTCAGAA-GGCTCTGA_S21_L004
processed data file: DESeq2_normalized_counts.csv

tag: strain

value: liver

value: rat insulinoma cells

value: 1uM inorganic asenic


title: WXL1[Flag-DndD]-mock


title: RNA 1uM inorganic asenic treated #2 [1A922]

description:
1A922_GAGATTCC-GGCTCTGA_S22_L004
processed data file: DESeq2_normalized_counts.csv


title: WXL1[Flag-DndD]


title: CT1_3 (Control)

description: Control

value: 8 days after initiation of drought stress

value: Control

value: Crimson Sweet


title: RNA 1uM inorganic asenic treated #1 [1A52]

description:
1A52_1_GAATTCGT-GGCTCTGA_S23_L004
processed data file: DESeq2_normalized_counts.csv


title: GenomicDNA_Control_Control_C14

description: Control sample

value: Female


title: WT-Heavy

tag: cell line

tag: genotype/variation

value: wild type


title: WXL1[Flag-DndC]-mock


title: GenomicDNA_ICSI_Global_9

description: ICSI Global sample

value: ICSI

value: Global


title: CT1_1 (Control)

description: Control


title: RNA Untreated #4 [0C922]

description:
0C922_CGCTCATT-GGCTCTGA_S19_L003
processed data file: DESeq2_normalized_counts.csv

source_name: rat insulinoma cells_untreated

value: untreated


title: WXL1[Flag-DndC]

value: Cerro 87


title: GenomicDNA_FIV_SSM_55

description: FIV SSM sample

value: FIV

value: SSM


title: RNA Untreated #3 [0C513]

description:
0C52_1_TAATGCGC-CCTATCCT_S15_L003
processed data file: DESeq2_normalized_counts.csv


title: GenomicDNA_ICSI_SSM_65

description: ICSI SSM sample


title: shew_180min2

city: Gdansk

first: Pawel

last: Olszewski

address: Debinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdansk

data_processing:
Raw reads filtering using fastp; fastpv 0.20.1
Aligment and differential expression analysis with Rockhopper; Rockhopper v2.03
Genome_build: Shewanella baltica OS185 NC_009665.1
Supplementary_files_format_and_content: Wig files generated by Rockhopper software. Scores represent normalized counts.
Supplementary_files_format_and_content: Rockhopper results table containing raw counts, normalized counts, fold change calculations and p values.

organism: Shewanella baltica

source_name: bacterial culture

extract_protocol:
RNA was extracted with Qiagen RNA Isolation kit according to the manufacturer's protocol.
RNA depleted of ribosomal RNA with Ribo-Zero rRNA removal Kit Bacteria (Illumina). Library prepared with TruSeq Stranded Total RNA Sample Prep Kit (Illumina).

value: 180 minutes at 8C


title: E.coli JW3350[pJTU1980]-ctrl

data_processing:
Library strategy: nick-seq
Sequencing results were processed on the Galaxy web platform (https://usegalaxy.org/). Initially, the paired end reads were pre-processed by trim galore to remove adapters and the first 3 bp on the 5’ of read 1 were also trimmed.
All the reads were aligned to the corresponding genome using Bowtie 2.
A custom method for peak calling of sequencing data was developed with BamTools, BEDTools and Rstudio. Briefly, the bam results were filtered based on R1 (selected for nick translation data) or R2 (selected for 3’ capture data). The 5’ coverage (experiment sample) or full coverage (controls) on each position were calculated based on the filtered bam result by BEDTools(positive and negative strand separately)
The coverage of positionN (sample)/ coverage of positionN-1(sample), coverage of positionN(sample)/ coverage of positionN+1(sample) and coverage of positionN(sample)/ coverage of positionN(control)  ratio was calculated on each position and the positions with all the three ratios above 5 were regarded as strong signals.
Genome_build: CP009273.1 and CP008925.1
Supplementary_files_format_and_content: tabular files were generated by BEDTools containing the 5’ coverage (experiment sample) or full coverage (controls) on each position (positive and negative strand separately)

source_name: E.coli k12 JW3350

growth_protocol: S. enterica 87 and E. coli K12 expressing Salmonella DndBCDE strains were grown in Luria-Bertani (LB) at 37 °C.

extract_protocol:
Nick conversion of DNA PT sites by Ioline cleavage. 40 μl of the blocked DNA was added with 5 μl dibasic Sodium phosphate buffer (500mM, pH 9.0) and 2 μl of Iodine solution (0.1N, FLUKA). After incubate at 65°C for 5 minutes and cool down slowly to 4°C, the reaction product was purified by DyeEX column (QIAGEN) to remove salts and Iodine. The purified product was treated with rSAP by adding 5 μl of NEBcutsmart buffer and 1 μl of rSAP to remove any 3' end phosphate left from iodine cleavage.  After incubation at 37 °C for 20 min and 75 °C for another 10 min, the product was kept on ice for the following step.
Illumina library preparation was performed by the Clontech SMART ChIp-seq kit (Clontech) by following the manufacturer’s protocol. 12 cycles were used in the final step of PCR amplification. The PCR product from each sample was combined with its corresponding negative control and then size selected using AMPure XP beads (NEB). The purified library was submitted to Illumina HiSeq PE150 instrument for 75 bp paired-end sequencing.

treatment_protocol:
Fragmentation of genomic DNA.  To ensure a relatively random fragmentation of genomic DNA, 1 μg of the extracted DNA was digested separately by three DNA endonuclease combinations: NciI; HindIII and XhoI; SalI, XbaI and NdeI. RNase A was also added to each digestion mixture to remove any trace of contaminated RNA. After digestion, the digested products were purified by Qiagen PCR purification Kit. The three purified DNA sample were mixed together for the following blocking step.
Blocking of pre-existing strand break sites. Reaction mixture (40 μl) containing 4 μl of reaction buffer (NEBcutsmart buffer); 1 μl of Shrimp Alkaline Phosphatase (rSAP, NEB), 1 μg of template genomic DNA was incubated at 37 °C for 30 min to remove any pre-existing strand breaks with 3' end phosphate, then 70°C for 10min to inactivate rSAP. After cool down the reaction product to room temperature, add 2 μl of ddNTPs (2.5 mM each, TriLink) and 1 μl of DNA polymerase I (10 U, NEB), incubate at 37 °C for 40 min to block any pre-existing strand break sites. Then 1 μl of Shrimp Alkaline Phosphatase (rSAP, NEB) was added to the reaction mixture, incubate at 37 °C for another 30 min to degrade the excess ddNTPs. Reaction was terminated by heat-inactivation of rSAP and DNA polymerase I at 75 °C for 10 min. The reaction product was ready for one of the following nick creation or conversion procedure after de-salts by DyeEx column (QIAGEN)

value: negative control

value: {delta}dam mutant [DndBCDE]


title: S87[FN-Flag]

value: Anti Flag :Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich

value: S. enterica 87 [pFlag]

value: Tag not fused to protein control


title: shew_180min1


title: GenomicDNA_ICSI_SSM_18

description: ICSI SSM sample


title: RNA Untreated #2 [0C52]

description:
0C513_TCCGGAGA-GGCTCTGA_S16_L003
processed data file: DESeq2_normalized_counts.csv

value: liver

value: rat insulinoma cells


title: shew_90min2

value: 90 minutes at 8C


title: RNA Untreated #1 [0A52]

description:
0A52_1_CTGAAGCT-CCTATCCT_S18_L003
processed data file: DESeq2_normalized_counts.csv


title: GenomicDNA_Control_Control_C13

description: Control sample

value: Male

value: Control


title: E.coli JW3350[pJTU1238]-ctrl


title: E.coli JW3350[pJTU1980]-iodine

value: iodine

value: experiment sample


title: Neurog>lacZ rep 2

city: Atlanta

first: Alberto

last: Stolfi

state: GA

address: 950 Atlantic Dr

department: School of Biological Sciences

institute: Georgia Institute of Technology

description: [ngnz2] NgnOE-Allsamples-counts.dedup.xlsx

data_processing:
FASTQ files were processed by STAR 2.5.2b and mapped to the C. robusta genome
Output bam files were processed using Rsubread/featureCounts with the parameter “ignoreDup=TRUE” to remove the read duplications resulting from library amplification.
All reads after duplication removal that mapped to the exons of KyotoHoya (KH) gene models were counted for differential expression analysis.
Differential expression beween Neurog>Neurog and Neurog>lacZ, and between Neurog>Neurog::WRPW and Neurog>lacZ was measured by EdgeR.
processed data identifiers can be searched at ANISEED: https://www.aniseed.cnrs.fr/ and GHOST:  http://ghost.zool.kyoto-u.ac.jp/SearchGenomekh.html
Genome_build: KyotoHoya, Satou et al. 2008

organism: Ciona robusta

source_name: FACS-isolated cells

growth_protocol: Ciona robusta embryos grown in filtered buffered artificial sea water

extract_protocol:
RNAqueous-Micro (ThermoFisher)
SMART-seq v4 ultra low input RNA kit

treatment_protocol: Dissociation using calcium/magnesium-free sea water + trypsin, FACS using BD FacsAria I

value: BTN lineage cells labeled with Neurog>BFP or RFP

value: 9.5 hours post-fertilization, 20°C

tag: replicate

value: "Control" overexpression of lacZ


title: shew_90min1


title: YF11[Flag-DndC]-3-mock

source_name: bacteria

value: Cerro 87

value: No antibody control


title: GenomicDNA_FIV_Global_63

description: FIV Global sample

value: Female

value: FIV

value: Global


title: GenomicDNA_Control_Control_C6

description: Control sample


title: GenomicDNA_ICSI_SSM_17

description: ICSI SSM sample

value: ICSI

value: SSM


title: YF11[Flag-DndC]-3

value: Anti Flag :Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich

value: ChIP


title: Neurog>Neurog::WRPW rep 2

description: [ngnngnw2] NgnOE-Allsamples-counts.dedup.xlsx

value: Overexpression of dominant-interfering Neurog:WRPW


title: shew_control

value: growth at 20C


title: CT1_2 (Control)

description: Control

value: 8 days after initiation of drought stress

value: Control

value: Crimson Sweet


title: GenomicDNA_FIV_SSM_41

description: FIV SSM sample

value: Male


title: E.coli BW25113[pJTU1980]-ctrl

source_name: E.coli K12 BW25113

value: negative control

value: wildtype [DndBCDE]


title: E.coli JW3350[pJTU1238]-iodine

value: iodine

value: experiment sample

value: {delta}dam mutant [DndBCDE]


title: GenomicDNA_ICSI_Global_31

description: ICSI Global sample


title: Neurog>Neurog rep 2

description: [ngnngn2] NgnOE-Allsamples-counts.dedup.xlsx

value: BTN lineage cells labeled with Neurog>BFP or RFP

value: 9.5 hours post-fertilization, 20°C

value: Neurogenin overexpression


title: YF11[Flag-DndC]-2

value: Cerro 87


title: E.coli BW25113[pJTU1980]-iodine


title: YF11[Flag-DndC]-2-ctrl

source_name: Salmonella enterica serovar Cerro 87

value: {delta}dndC [pFlag-DndC]


title: YF11[Flag-DndC]-2-mock

value: No antibody control


title: YF11[Flag-DndC]-2-iodine


title: E.coli BW25113[pJTU1238]-ctrl


title: YF11[Flag-DndC]-1-mock


title: YF11[Flag-DndC]-1-ctrl


title: Neurog>Neurog::WRPW rep 1

description: [ngnngnw1] NgnOE-Allsamples-counts.dedup.xlsx

value: Overexpression of dominant-interfering Neurog:WRPW


title: YF11[Flag-DndC]-1

value: Anti Flag :Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich

value: ChIP


title: Neurog>lacZ rep 1

description: [ngnz1] NgnOE-Allsamples-counts.dedup.xlsx

value: "Control" overexpression of lacZ


title: GenomicDNA_Control_Control_C10

description: Control sample

value: Female

value: Control


title: E.coli BW25113[pJTU1238]-iodine


title: YF11[Flag-DndC]-1-iodine


title: GenomicDNA_FIV_Global_8

description: FIV Global sample

value: FIV

value: Global


title: E.coliBW25113[pBluescriptSK+]

organism: Escherichia coli BW25113

tag: grow phase

value: log

value: wildtype

tag: expression

value: pBluescriptSK+


title: Neurog>Neurog rep 1

description: [ngnngn1] NgnOE-Allsamples-counts.dedup.xlsx

value: BTN lineage cells labeled with Neurog>BFP or RFP


title: pig Oocyte BSseq

status: Public on May 20 2020

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence reads had the first 9 base pairs clipped off the 5' end to remove the 9N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.4, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 9). The remaining sequences were then aligned to the respective genomes in single-end mode using Bismark (v0.19.1; parameters: --pbat). The cow Oocyte data was processed as single-cell data: it was trimmed and aligned in the same manner but with the following parameters (v0.19.1; --non_directional). Methylation calls were extracted after duplicate sequences had been excluded.
Genome_build: Pig: Sscrofa11.1
Genome_build: Cow: UMD3.1
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: Oocyte

extract_protocol:
For pig, in vitro maturation (IVM) of oocytes was performed as previously described (Coy et al., 2010). Semen samples were collected by the gloved hand method from fertility-tested boars. Spermatozoa and oocytes were cocultured at 38.5°C under 5% CO2 in air saturated of humidity and 18 hours post insemination (hpi) the putative zygotes were washed and transferred to embryo culture medium. At 48, 72, 120 and 168 hpi, pools of forty 2-4 cell embryos, twenty 8-16 cell embryos, ten morula and single expanded blastocyst were selected, washed in PBS and ZP digested by 0.5% w/v pronase in PBS. Finally, embryos were washed three times in PBS and snap frozen in liquid nitrogen until further processing. For cow, non-lactating and non-pregnant cows  were used as oocyte donors. Ultrasound evaluation was performed in order to assess the size of follicle(s) or to count the number of puncturable follicles. Ovum pick up was performed on ≥ 15mm of diameter follicles. For single cell oocyte collection affter aspiration oocytes were collected under a stereomicroscope, washed in Dulbecco’s Phosphate buffered (without calcium nor magnesium, PBS) supplemented with 0.5% polyvinyl alcohol (wt/v). Cumulus cells were removed with gentle pipetting and treatment with hyaluronidase. Zona pellucida was removed using pronase. Oocytes were put in 5µl of RLT buffer, immediately frozen in liquid nitrogen and stored at -80ºC until processing for sc-BS seq. For embryo production, immature cumulus-oocyte complexes (COCs) were obtained by aspirating follicles (2-8 mm) from the ovaries of matured heifers and cows collected at slaughter house from local abattoirs. COCs were matured in four-well dishes in TCM-199 maturation medium, supplemented with 10% (v/v) fetal calf serum (FCS) and 10 ng/ml epidermal growth factor (EGF) in 4 well dishes in groups of 50 COCs per well at 38.5°C under an atmosphere of 5% CO2 in air with maximum humidity (Rizos et al., 2002).  After 24h of maturation, a representative number of the in vitro matured COCs were suspended in 100 μL of PBS without calcium nor magnesium supplemented with 1% BSA and their cumulus cells (CCs) completely removed by pipetting. Matured oocytes were in vitro fertilized (IVF). IVF was performed as described previously (Lopera-Vasquez et al., 2015)  The remaining matured oocytes were in vitro fertilized (IVF) for embryo production. IVF was performed as described previously (Lopera-Vasquez et al., 2015).
sample lysis: an individual sample (oocyte, 2-4, 8-16 cell, morula pools or individual blastocyst) was lysed for 1 hr in 1% SDS with proteinase K (1ul, 20 mg/mL) at 37C. Alternatively, either bull and boar sperm DNA was extracted from ejaculates of two biological individuals. Cells were lysed in the lysis buffer containing 10% SDS with proteinase K, 20 mM Tris, 10 mM DTT, 10 mM EDTA, 150 mM NaCl, 10 mM KCl for 2 hours at 50C. Further, DNA was purified with phenol:chloroform at 1:1 ratio and precipitated with equal volume of isopropanol. DNA pellet was washed with 70% ethanol, air dried and dissolved in EB buffer. DNA concentration was measured using Nanodrop and 10 ng was used for bisulfite conversion and PBAT library preparation as described below
Post bisulfite adapter tagging (PBAT) as  described in Muira et al (2012, PMID: 22649061) with few modifications (Canovas et al, 2017) (PMID: 28134613). Alternatively, for sc-BS-seq (single cow oocytes) protocol described by Smallwood et al, 2014 was used.

tag: cell type

value: Oocyte


title: pig Blastocyst BSseq

source_name: Blastocyst

value: Blastocyst


title: GenomicDNA_FIV_Global_61

description: FIV Global sample

organism: Homo sapiens

value: Male


title: GenomicDNA_Control_Control_C4

description: Control sample


title: pig 8-16 cells BSseq

source_name: 8-16 cell embryo

value: 8-16 cell embryo


title: pig Oocyte

data_processing:
Raw sequence reads were trimmed using Trim Galore (v0.6.4) to remove adapter contamination and reads with poor quality (Phred score cutoff 20); HISAT2 (v2.1.0) was used to align the reads in a splice aware manner. Data were passed through an additional filter of having a MAPQ score of 20 or more before quantitation.
The RNA-Seq pipeline of  Seqmonk was used to quantify mRNA features. Similar transcripts were merged. Log transformed (log2FPM)
Genome_build: Pig: Sscrofa11.1
Genome_build: Cow: UMD3.1
Supplementary_files_format_and_content: The RNA-Seq reports are tab-delimited and show annotated gene coordinates and their log2(FPM) values as follows: col 1: <gene name>, col2: <Chromosome>, col 3:  <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.

source_name: oocyte

extract_protocol:
ARCTURUS® PicoPure® RNA Isolation Kit (KIT0204, Life Technologies) was used to extract the RNA
Libraries were generated using Ovation RNA-Seq System V2 (NuGEN, Cat. 7102-08) for low amount of starting material and further amplified with NEB Next DNA Library Prep Master Mix for Illumina for 8 PCR cycles (NEB, Cat. E6040S)

value: oocyte


title: pig Sperm BSseq

source_name: Sperm

value: Sperm


title: pig Blastocyst


title: pig 2-4 cells

source_name: 2-4 cell embryo

value: 2-4 cell embryo


title: pig 8-16 cells


title: pig Morula BSseq

source_name: Morula

value: Morula


title: GenomicDNA_FIV_SSM_40

description: FIV SSM sample

value: SSM


title: GenomicDNA_ICSI_Global_53

description: ICSI Global sample

value: ICSI


title: pig 2-4 cells BSseq


title: PDTALL8 model, OMP52M51 resistant, mouse #1

city: Padova

first: Valentina

last: Agnusdei

state: PD

address: Via Gattamelata, 64

institute: Istituto Oncologico Veneto

description: Gene expression data from T-ALL cells recovered from mice treated with OMP52M51 until progression

hyb_protocol: Following fragmentation, 5.2 μg of fragmented and labeled ss-DNA were hybridized for 16 hr at 45°C on GeneChip HTA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: Affymetrix Expression Console.  Data were preprocessed following the RMA procedure using quantile normalization

source_name: human T-ALL cells derived from murine infiltrated spleen

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent KIT, 2013, Affymetrix).

growth_protocol: T-ALL cells were intravenously injected in NOD mice and leukemia growth was monitored by blood drawings and flow cytometric analysis

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

treatment_protocol: Leukemia bearing mice were intraperitoneally treated with the humanized anti-human Notch1 mAb OMP52M51 or control antibody (Rituximab) until progression of disease or in acute treatment (4 days before sacrifice). Both antibodies were administrated weekly at 20mg/Kg.

value: T-acute lymphoblastic leukemia cells

tag: treatment

value: Treated with Notch1 mAb OMP52M51 until progression


title: YF11[NoTag-DndC]

tag: serovar

value: Cerro 87

value: Anti Flag :Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804– Sigma Aldrich

value: No tag control


title: PDTALL8 model, control group, mouse #1

description: Gene expression data from T-ALL cells recovered from mice treated with Ctrl Ab

value: Control antibody


title: GenomicDNA_ICSI_Global_16

description: ICSI Global sample

source_name: Buccal smear

value: Female

value: Global


title: PDTALL8 model, OMP52M51 resistant, mouse #3


title: PDTALL8 model, OMP52M51 resistant, mouse #2


title: PDTALL19 model, acute treated with OMP52M51, mouse #2

description: Gene expression data from T-ALL cells recovered from mice acute treated with OMP52M51

value: Acute treated with Notch1 mAb OMP52M51


title: PDTALL19 model, acute treated with OMP52M51, mouse #1


title: GenomicDNA_ICSI_SSM_7

description: ICSI SSM sample


title: PDTALL19 model, acute treated with OMP52M51, mouse #3


title: PDTALL19 model, acute treated with OMP52M51, mouse #4