title: Tumor, mouse C4M4

city: Seattle

first: Kristin

middle: Gail

last: Anderson

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: Gene expression data from tumor, mouse C4M4

hyb_protocol: RNA samples were processed using the Clariom D Pico mouse Assay.

scan_protocol: standard Affymetrix protocol

data_processing: Arrays were analyzed using SST-RMA algorithm in the Affymetrix Transcriptome Analysis Console (TAC) Software. All samples passed the quality control criteria given by Affymetrix. Probes with less than two arrays above the 95th percentile of the antigenomic background probes were filtered out. Here, we provide the CHP files with the SST-RMA normalization.

label: biotin

source_name: Tumor

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted from fresh frozen ID8VEGF tumors using the Qiagen RNeasy Plus Mini RNA isolation kit (cat: 74134).

tag: mouseid

tag: well

tag: samplesource

value: Customer

tag: sampletype

value: Mouse RNA

tag: condition


title: Tumor, mouse C4M5

status: Public on Aug 22 2019

type: RNA

country: USA

description: Gene expression data from tumor, mouse C4M5

molecule: total RNA

organism: Mus musculus

tag: gender

value: Female

value: Tumor


title: 8017340

type: genomic

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

hyb_protocol: One fraction was bisulfite converted and analyzed by hybridization to the Illumina Epic Array. The second fraction was first glucosylated to protect the 5hmC using the TAB-array kit (WiseGene, Lnc.,Chicago, IL), followed by bisulfite treatment and hybridization to the EPIC arrays

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

tag: sample id

tag: tissue type

value: Adjacent

tag: subject id

tag: organism

value: Homo sapiens

tag: age

tag: tab


title: 7016892


title: p35_3

city: Bunkyo-ku

first: Natsuki

last: Shinoda

state: Tokyo

address: 7-3-1 Hongo

department: Department of Genetics, Faculty of Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent GE blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 custom microarray 8x60K (G4102A, #040871) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner using AgilentG3_GX_1Color_HighSensitivity.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 040871_D_F_20120511) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were quantile-normalized using R software. If the number of probes labelled as gIsWellAboveBG  were less than 5 among 15 samples, the probes were removed (filtered) using R software.

organism: Drosophila melanogaster

source_name: wing imaginal disc expressing p35 under the control of C10-Gal4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000c Spectrophotometer.

growth_protocol: Flies were kept at 25℃ on standard diet.

extract_protocol: Total RNA was extracted from 20 wing imaginal discs of female wandering 3rd larvae by using QIAzol Lysis Reagent (QIAGEN), followed by purification using RNeasy Plus Micro Kit (QIAGEN).

tag: genotype


title: 7044672


title: O1_TA_Hi_23 [scBS-seq]

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
BS-Seq sequences were trimmed with Trim Galore (v0.5.0; Cutadapt v1.15) in single-end mode with the options --clip_r1 6. Trimmed sequences were mapped to the mouse GRCm38 genome in single-end, --non_direcional mode using Bismark (Krueger and Andrews, 2011) (v0.20.0); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.cov: Bismark coverage files: 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: Tibialis anterior muscles

extract_protocol:
We prepared scM&T-seq libraries by isolating mRNA on magnetic beads and separating from the single-cell lysate prior to reverse transcription and amplification using Smartseq2 but with 25 PCR cycles.
scM&T-seq (C. Angermueller et al., 2016)

treatment_protocol: Mice were sacrificed by cervical dislocation. Tibialis anterior muscles were dissected and placed into cold DMEM (ThermoFisher, 31966). Muscles were then chopped and put into a 15 ml Falcon tube containing 10 ml of DMEM, 0.08% collagenase D (Sigma, 11 088 882 001), 0.1% trypsin (ThermoFisher, 15090), 10 µg/ml DNaseI (Sigma, 11284932) at 37°C under gentle agitation for 25 min. Digests were allowed to stand for 5 min at room temperature and the supernatants were collected on 5 ml of foetal bovine serum (FBS; Gibco) on ice. The digestion was repeated 3 times until complete digestion of the muscle. The supernatants were filtered through a 70-µm cell strainer (Miltenyi, 130-098-462). Cells were spun for 15 min at 515g at 4°C and the pellets were resuspended in 1 ml freezing medium (10% DMSO (Sigma, D2438) in foetal calf serum (FCS, Invitrogen)) for long term storage in liquid nitrogen. Before FACS isolation, samples were thawed in 50 ml of cold DMEM, spun for 15 min at 515g at 4°C. Pellets were resuspended in 300 µl of DMEM 2% FCS 1 µg/mL propidium iodide (Calbiochem, 537060) and filtered through a 40-µm cell strainer (BD Falcon, 352235). Viable cells were isolated based on size, granulosity and GFP expression level (top 10% nGFPHi cells) using a MoFlo Astrios cell sorter (Beckmann Coulter). Single cells were collected in 2.5 µL cold RLT Plus buffer (Qiagen, 1053393) containing 1U/µL RNase inhibitor (Ambion, AM2694) in 96 well-plates (LoBind Eppendorf, 0030129504), flash-frozen on dry ice and stored at -80°C.

tag: strain

tag: cell type

value: Muscle stem cells

value: 24 months

tag: mouse id


title: O1_TA_Hi_22 [scBS-seq]


title: p35_5


title: O1_TA_Hi_24 [scBS-seq]


title: R1_T36_3

city: San Antonio

first: Yufeng

last: Wang

state: TX

address: One UTSA Circle

institute: University of Texas at San Antonio

description:
raw.counts.txt
edgeR.output.csv

library_source: transcriptomic

data_processing:
the RNA-Sequencing reads were processed using the CLC Genomics Workbench 10.0 (QIAGEN). Quality-trimming and adapter-trimming were performed using default parameters.
Reads were mapped to the C. albicans strain SC5314 reference genome (assembly 21)
The uniquely mapped reads were used as the raw expression value, followed by the trimmed mean of M-values (TMM) normalization to eliminate RNA composition bias
Differential gene expression profiling was carried out using the edgeR package implemented in R. The Benjamini and Hochberg false discovery rate (FDR) procedure was used for multiple hypothesis testing correction.
Genome_build: C. albicans strain SC5314 reference genome (assembly 21)
Supplementary_files_format_and_content: txt files show raw counts and statistics for each sample

molecule: polyA RNA

organism: Candida albicans

source_name: Fungi

growth_protocol: The wild type C. albicans strain SC5314 was utilized for these studies. Cell stocks were stored at -80 °C and propagated by streaking onto yeast extract peptone dextrose (YPD) agar plates (1% (wt/vol) yeast extract, 2% (wt/vol) peptone, 2% (wt/vol) dextrose and 1.5% agar), and incubated overnight at 30 °C. From these, a loopful of cells was inoculated into flasks (150 ml) containing 25 ml of YPD liquid media in an orbital shaker at 180 r.p.m. and grown overnight for 14-16 h at 30 °C. Under these conditions, C. albicans grows as a budding yeast.

extract_protocol:
5μg total RNA was used for mRNA isolation using Dynabeads OligodT (Invitrogen, Carlsbad, CA), then about 30-50ng isolated mRNA was used for mRNA-Sequencing library preparation by following the BIOO Scientific NEXTflex Directional RNA-seq kit (dUTP-based) sample preparation guide. First, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic Dynabeads. Then, the mRNA was fragmented into small pieces using divalent cautions under elevated temperature (95 °C for 10 mins). The cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H and an end repair process consisting on the addition of a single ‘A’ base, which is then followed by ligation of the adapters. The products were purified and enriched by PCR to create the final RNA sequencing library. Directionality was retained by adding dUTP during the second strand synthesis step and subsequent cleavage of the uridine containing strand using Uracil DNA Glycosylase. The RNA sequencing libraries were then subjected to quantification process, pooled for cBot amplification and subsequent 100bp paired end sequencing run with Illumina HiSeq 2000 platform. After the sequencing run, demultiplexing with CASAVA was employed to generate the fastq file for each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C. albicans SC5314 strain was grown overnight, then washed with PBS and used to inoculate YPD containing 10% fetal bovine serum (FBS) at a 1:30 dilution and incubated at 37 °C for 90 minutes in the presence or absence of compound 9029936 at 5 uM.

value: wild type

tag: growth phase

value: filament-inducing conditions

tag: treatment

value: compound 9029936


title: R1_T36_2

description:
raw.counts.txt
edgeR.output.csv


title: R1_T36_1

description:
raw.counts.txt
edgeR.output.csv


title: LacZ_4

source_name: wing imaginal disc expressing LacZ under the control of C10-Gal4

value: C10 > LacZ


title: Tumor, mouse C4M1

description: Gene expression data from tumor, mouse C4M1

tag: mouseid

tag: well


title: 9113918


title: R1_Ctl_3

description:
raw.counts.txt
edgeR.output.csv

value: untreated


title: p35_1


title: O1_TA_Hi_21 [scBS-seq]


title: O1_TA_Hi_20 [scBS-seq]


title: p35_4


title: GFP_5

source_name: wing imaginal disc expressing GFP under the control of C10-Gal4

value: C10 > GFP


title: LacZ_1


title: R1_Ctl_2

description:
raw.counts.txt
edgeR.output.csv


title: p35_2


title: LacZ_5


title: LacZ_2


title: R1_Ctl_1

description:
raw.counts.txt
edgeR.output.csv


title: GFP_1


title: GFP_3


title: O1_TA_Hi_18 [scBS-seq]


title: LacZ_3


title: GFP_4


title: O1_TA_Hi_19 [scBS-seq]


title: GFP_2


title: O1_TA_Hi_1 [scBS-seq]


title: SH3GL2-1

city: Tyler

first: Santanu

last: Dasgupta

state: Texas

department: Cellular and Molecular Biology

institute: UT Health Science Center at Tyler

description: gene expression data of SH3GL2 transfected SUM159 cells

hyb_protocol: After fragmentation of the cRNA, hybridization was carried for 16 hours at 45 ºC with 60 rpm rotation in Affymetrix Hybridization oven

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

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

label: Biotin

source_name: SUM159 transfected with SH3GL2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: SUM159 cells were grown in ATCC recommended medium

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

treatment_protocol: Cells were stably transfected with empty vector and SH3GL2 insert (in pcDNA 3.1 vector)

tag: cell line

value: breast cancer cell line SUM159

value: SH3GL2 overexpression


title: SH3GL2-2


title: EMPTY VECTOR3

description: gene expression data of empty vector transfected SUM159 cells

source_name: SUM159 transfected with empty vector

value: control


title: EMPTY VECTOR1


title: EMPTY VECTOR2


title: O1_TA_Hi_15 [scBS-seq]


title: O1_TA_Hi_16 [scBS-seq]


title: 6005043

value: Male


title: O1_TA_Hi_17 [scBS-seq]


title: O1_TA_Hi_14 [scBS-seq]


title: SH3GL2-3


title: O1_TA_Hi_11 [scBS-seq]


title: O1_TA_Hi_10 [scBS-seq]


title: O1_TA_Hi_13 [scBS-seq]


title: peripheric NK cells_Hypoxic-cultured 3 days_3

city: Hefei

first: Xiaohu

last: Zheng

state: Anhui

address: Huang Shan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

hyb_protocol: Cy3-labeled cDNA were hybridized to Agilent Whole Human Genome Microarray (4*44K) Design ID 014850.

scan_protocol: Fluorescence was detected using the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Images were analyzed using Feature Extraction software (version V9.1.3, Agilent Technologies).

source_name: NK cells from blood, hypoxic cultured 3 days

label_protocol: RNA was amplified and labeling of CTP with cyanine-3 (cy3) was done with Agilent one-color labeling kits (Agilent Technologies).

extract_protocol: Cells were suspended in TRIzol and total RNA was extracted with an RNeasy MiniKit (Qiagen, Hilden, Germany).

treatment_protocol: NK cells were purifed from HCC patients and normal donors. Hypoxic NK cells were kept in <1% O2 balanced with N2 in hypoxystation, whereas normoxic NK cells were cultured in 20% O2 conditions for 3 days.

tag: tissue

value: blood

tag: disease state

value: healthy donor

value: NK cells

value: hypoxic culture


title: peripheric NK cells_Hypoxic-cultured 3 days_2

tag: gender

value: Female


title: peripheric NK cells_Normal-cultured 3 days_2

source_name: NK cells from blood, normal cultured 3 days

value: normal culture


title: peripheric NK cells_Normal-cultured 3 days_3


title: ZCP9

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads obtained from PFC were mapped to mm10 using HISAT2 (Kim et al., 2015).
Counts of reads mapped to genes were obtained using HTSeq-count (Anders et al., 2015) against Ensembl v90 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text file generated using HTSeq-count

source_name: Prefrontal cortex neurons

growth_protocol: C57BL/6J mice were euthanized 24 hours after final behavior via cervical dislocation. In order to acquire only infected tissue within prefrontal cortex (PFC), microdissection was performed under a fluorescent microscope. Brain slices containing PFC were either visualized on blade and punched directly or suspended in cold phosphate buffered saline (PBS) prior to tissue dissection. PFC was collected as either a single midline 12- gauge punch or bilateral 14-gauge punches, which varied according to virus spread. However, only PFC was included in dissections. Mice were excluded from analysis when the PFC was not correctly targeted. Dissected tissue was immediately frozen on dry ice.

extract_protocol:
Total RNA was isolated from frozen dissected PFC tissue using QIAzol lysis reagent and purified using the miRNAeasy mini kit (Qiagen). For RNA being utilized for RNA-seq, RNA integrity (RIN) was assayed using an Aligent 2100 Bioanalyzer (Aligent, Santa Clara CA).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA). Briefly, mRNA was polyA selected from the total RNA pool. mRNA was then fragmented and converted to cDNA with reverse transcriptase followed by cDNA size selection and purification with AMPure XP beads (Beckman Coulter, Brea CA). To identify eachsample, strand-specific adapters were ligated to adenylated 3’ ends and an additional size selection step was performed. The cDNA library was then amplified using polymerase chain reaction. During this step, barcodes of six base pairs were added to the adaptors. Library quality and concentration was measured by the Bioanalyzer before sequencing.

tag: sgrna

tag: over-expression

value: Zfp189 + GFP

value: Control


title: peripheric NK cells_Normal_1

source_name: NK cells from blood


title: peripheric NK cells_Hypoxic-cultured 3 days_1


title: peripheric NK cells_Normal-cultured 3 days_1


title: O1_TA_Hi_12 [scBS-seq]

value: Muscle stem cells

value: 24 months


title: Targeted_Bisulfite_GSK343_rep2

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

data_processing:
The targeted bisulfite sequencing library were aligned to Homo sapiens (hg19) using Bowtie2.
Genome_build: hg19
Supplementary_files_format_and_content: After deduplication (deduplicate_bismark), methylation levels (bismark_methylation_extractor) were estimated using bismark tools with default parameters.

source_name: Neuroblastoma

growth_protocol: SH-SY5Y (Korean Cell Line Bank, 22266) were maintained in DMEM/F12 (Gibco, 11320033) supplemented with 10% fetal bovine serum (Welgene, S001-01) and Penicillin/Streptomycin (Lonza, 17-602E) at 5% CO2 in 37°C.

extract_protocol:
SH-SY5Y cells were washed with 10ml of PBS and genomic DNA were prepared using AccuPrep Genomic DNA Extraction Kit (Bioneer, K-0332).
Targeted Bisulfite-Seq library were prepared using the SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies). Briefly, 3μg of genomic DNA per sample was fragmented to median size of 150bp, repaired, and ligated with adapters. The prepared gDNA library was hybridized using SureSelectXT methyl-Seq capture reagent, followed by bisulfite conversion using EZ DNA Methylation-Gold kit (ZymoResearch, Cat #D5005). After desulphonation, the sequence-modified, target-enriched library were amplified and uniquely indexed by PCR. The indexed libraries were pooled and multiplexed into 4 separate lanes using 100 bp paired-end sequencing (Illumina HiSeq2500).

treatment_protocol: SH-SY5Y cells (density of 0.5~0.6 x 106 cells/ml) were treated with either DMSO or 5 uM GSK343 (an inhibitor of H3K27me3-specific HMTase) for 72hours.

value: Neuroblastoma


title: Reactivated

city: Xiamen

first: Shuangbo

last: Kong

state: Fujian

address: Xiangan south Rd

institute: Xiamen University

description: Reactivated blastocyst

data_processing:
Single-end 50-bp reads were mapped to the mouse reference genome GRCm38 using SOLiDTM System Analysis Pipeline Tool (Corona Lite: https://solidsoftwaretools.com/corona).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Natue Methods, 2008.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: blastocyst

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen).
Sequencing libraries were generated using SOLiD™ Total RNA-Seq Kit for ABI (ThermoFisher) following the manufacturer’s recommendations.

treatment_protocol: Female mice were ovariectomized on the morning of D4 (0800-1000 h) of pregnancy and injected daily with progesterone (2 mg per mouse) from D5-7. Dormant blastocysts were collected by flushing the uteri with Chatot-Ziomek-Bavister (CZB) medium in the morning of D8. For reactivating and reactivated blastocysts, progesterone-primed implantation-delayed pregnant mice were killed 6h and 12h after E2 injection on D7, respectively. Total RNA was isolated using the RNeasy mini kit (Qiagen). Ribosomal RNA was removed by the guidance of ribo-minus RNA-sequencing method. Sequencing libraries were generated using SOLiD™ Total RNA-Seq Kit for ABI (ThermoFisher) following the manufacturer’s recommendations, and sequenced on an ABI SOLiD sequencing platform at Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Science (Beijing, China), and finally 50 bp single-end reads were obtained. Blastocysts were washed six times in the same medium, rapidly frozen with liquid nitrogen and stored at -80°C until used for RNA extraction. More than 3000 blastocysts of each were collected for the RNA sequence analysis.

value: blastocyst

tag: Sex


title: Reactivating

description: Reactivating blastocyst

tag: age


title: Dormant

description: Dormant blastocyst


title: peripheric NK cells_HCC_1

value: Hepatocellular carcinoma patient


title: Normal liver NK cells-_Benign patient_1

source_name: NK cells from normal tissue,replicate 1

value: liver

value: normal


title: peripheric NK cells_Normal_2


title: peripheric NK cells_HCC_2


title: Targeted_Bisulfite_GSK343_rep1


title: Tumor adjacent NK cells_HCC_1

source_name: NK cells from tumor adjacent normal tissue,replicate 1

value: matched tumor adjacent normal liver tissue


title: Tumor edge NK cells_HCC_1,2

source_name: NK cells from tumor edge tissue

value: Male

value: Hepatocellular carcinoma tissue


title: Normal liver NK cells-_Benign patient_2

source_name: NK cells from normal tissue,replicate 2


title: Tumor adjacent NK cells_HCC_2

source_name: NK cells from tumor adjacent normal tissue,replicate 2


title: Intratumor NK cells_HCC_1,2

source_name: NK cells from tumor tissue


title: ZCP8


title: Dhx37001 (sgDhx37_1)

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
Bulk mRNA-seq fastq files were processed by kallisto (Bray et al., 2016), with the settings --rf-stranded –b 100. Differential expression analysis was then performed using Sleuth (Pimentel et al., 2017). Significant differentially expressed genes were defined by a Benjamini-Hochberg adjusted p-value < 0.05. Differentially expressed genes were used for DAVID gene ontology analysis (Huang et al., 2009). The full dataset was also used for GSEA (Subramanian et al., 2005). Motif enrichment analysis in the promoters of differentially expressed genes was performed using Pscan (Zambelli et al., 2009), using a -450 to +50 bp interval and the TRANSFAC database.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized TPM matrix for all samples

source_name: CD8 T cells, transduced with AAV-sgDhx37

extract_protocol:
Cells were washed with PBS and incubated with TRIzol for 5 minutes at RT. RNA was purified via PureLink RNA mini kit from Invitrogen.
TruSeq strand-specific kit

value: C57BL/6J, OT-1; Cas9

value: CD8 T cells

tag: genotype/variation

value: transduced with AAV-sgDhx37


title: Dhx37003 (sgDhx37_3)


title: Targeted_Bisulfite_DMSO_rep2

value: DMSO


title: ZCP7

tag: genotype


title: Targeted_Bisulfite_DMSO_rep1


title: ZCP1

tag: strain


title: NTC004 (Vector_4)

description: AAV-Vector

source_name: CD8 T cells, transduced with AAV-Vector

value: transduced with AAV-Vector


title: Dhx37004 (sgDhx37_4)


title: 6005014

tag: sample id

tag: tissue type

value: Tumor

tag: subject id

tag: organism

value: Homo sapiens

value: Female

tag: tab


title: 6005010

value: Adjacent


title: GCP7

value: GFP

value: Control


title: 6005046


title: Dhx37002 (sgDhx37_2)


title: MB231.CTL.3

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

data_processing:
FASTQ files were trimmed with autoadapt
rsem-calculate-expression --star --star-gzipped-read-file --output-genome-bam -p 12 --paired-end
Genome_build: hg19
Supplementary_files_format_and_content: tab separated value

source_name: Breast Cancer Cell Line

growth_protocol: A549 and MDA-MB-231 cells were cultured in DMEM+10% FBS.

extract_protocol:
Total cell RNA was extracted when cells were ~80% confluent in 2D culture and on day 4 in 3D culture using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: The cell were transfected either a control siRNA or three distinct Bloom-specific siRNAs in A549 cells or one Bloom-specific siRNA in MDA-MB-231 cells.

tag: cell type

value: Breast Cancer

value: Breast

value: control


title: MB231.CTL.2

tag: cell line


title: GCP6


title: NTC002 (Vector_2)

description: AAV-Vector

tag: tissue


title: NTC001 (Vector_1)

description: AAV-Vector


title: NTC003 (Vector_3)

description: AAV-Vector


title: KPI4

city: Jacksonville

first: Alan

last: Fields

address: 4500 San Pablo Road

institute: Mayo Clinic Jacksonville

data_processing:
Base-calling is performed using Illumina’s RTA version 1.18.64.
RNA-seq reads were aligned to the mm10 genome assembly using TopHat v2.1 and bowtie v1.1.2 with the following options: --keep-fasta-order, --keep-tmp, --no-coverage-search, --bowtie1, --library-type fr-unstranded, --max-multihits 20, --solexa1.3-quals, --fusion-search, --fusion-ignore-chromosomes chrM, --fusion-min-dist 50000
Gene counts are generated by FeatureCounts using the gene definitions files from Ensembl v78. Option "-O" within FeatureCounts is used to account for the expression derived from regions shared by multiple genomic features.
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated.
Genome_build: mm10

source_name: lung adenocarcinoma cells

extract_protocol:
Total RNA was extracted using the RNAeasy Plus mini Kit (Qiagen, Valencia, CA). Quality of RNA  samples was determined using an Agilent Bioanalyzer and only samples with  RINs >9.0 were used for genomic sequencing analysis. Sequencing was carried out  at Mayo Clinic Advanced Genomic Technology Center at Rochester, MN.
RNA libraries were prepared using 120 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA).   Libraries were sequenced at 50-80 million read pairs per sample following Illumina’s standard protocol using the Illumina cBot and Paired end cluster kit version 3. The flow cells were sequenced as 101 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HCS 2.2.58 data collection software. Base-calling is performed using Illumina’s RTA version 1.18.64.

value: spheroid cultured tumor cells

value: lung

value: Kras-G12D/p53 KO/Prkci KO


title: GCP4


title: KPI5


title: KPI6


title: KPI3


title: MB231.CTL.1


title: MB231.BLM.siRNA1.3


title: KPI2


title: GCP2


title: KPI1


title: d9_Zfp189

value: Zfp189 + GFP

value: Defeat


title: KP5

value: Kras-G12D/p53 KO


title: KP4


title: MB231.BLM.siRNA1.1


title: d6_Zfp189


title: MB231.BLM.siRNA1.2


title: ZCP4


title: KP6


title: A549.CTL.2

source_name: Lung Cancer Cell Line

value: Lung Cancer

value: Lung


title: d66_Zfp189


title: A549.CTL.3


title: KP2


title: d52_GFP


title: d61_GFP


title: A549.BLM.siRNA3.3


title: d45_Zfp189


title: A549.BLM.siRNA3.2


title: run2675: HSP47_3_17526

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Upon induction of Postn gene expression, and tamoxifen administration, expression of Cre-recombinase is turned on, Cre/LoxP-dependent recombination of Hsp47 gene occurs, and eGFP reporter allele is recombined.

data_processing:
AltAnalyze version 2.1.2
Quantification following pseudoalignment as transcript per million values
Using AltAnalyze version 2.1.2 (Emig, Salomonis 2010), gene expression values were quantified as transcript per million values from the paired-end FASTQ files following pseudoalignment and quantification with Kallisto (Ensembl 72 reference for mm10). Gene-level TPMs were summed from the transcript TPMs and differential expression analyses performed using the default emperical Bayes moderated t-test p<0.05 (non-adjusted) with a fold>2.
Genome_build: Ensembl 72 reference for mm 10
Supplementary_files_format_and_content: Txt

source_name: Cardiac fibroblasts

growth_protocol: All genetically-modified mouse lines utilized in this study have been previously described in the literature: these include lines containing a knock-in of a MerCreMer cDNA into either the Postn genomic loci (1), the Rosa26 reporter mice (R26eGFP) purchased from Jackson laboratories (Stock# 012429), and LoxP-targeted Hsp47 mice (3). Mice were administered pharmaceutical grade tamoxifen (100 mg/kg body weight, i.p.) dissolved in 95% peanut oil/ 5% ethanol twice  coupled with continuous feeding of tamoxifen-citrate chow (40 mg/kg body weight, Envigo - TD.130860) until termination of experiment. Eight to ten week-old control and HSP47-deficient mice were subjected to pressure overload by TAC surgery; effectiveness of the procedure was verified by Doppler echocardiography, via measurement of pressure-gradients across the aortic constriction.  Four weeks after TAC surgery interstitial cells were isolated from cardiac ventricles, as previously described (1). Flow cytometry analysis was performed on these cells using a Becton Dickinson FACSCanto II running FACSDiva software; for sorting of fibroblasts from Postn expressing lineages, endogenous eGFP fluorescence expressed by the recombined reporter allele was utilized. Count of GFP+ cells was normalized to number of CD31+ cells to ensure similar digestion of samples and to eliminate differences in total counts resulting from sample preparation variability.  1. Kanisicak O, et al. Genetic lineage tracing defines myofibroblast origin and function in the injured heart. Nat Commun. 2016;7:12260.  2. Acharya A, et al. Efficient inducible Cre-mediated recombination in Tcf21 cell lineages in the heart and kidney. Genesis. 2011;49:870-7.  3. Masago Y, Hosoya A, Kawasaki K, Kawano S, Nasu A, Toguchida J, et al. The molecular chaperone Hsp47 is essential for cartilage and endochondral bone formation. J Cell Sci. 2012;125(Pt 5):1118-28.

extract_protocol:
Total RNA was extracted from fibroblasts. RNA quality and yield were determined using Agilent Bioanalyzer and submitted for RNA-seq analysis.
Total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1 ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10 min. NT Buffer was then added to neutralize the samples. Libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min.  The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocol.

treatment_protocol: GFP+ fibroblasts were flow-sorted directly into Qiazol for lysis and RNA isolation.

value: Cardiac fibroblasts

tag: genetic modification

value: MerCreMer cDNA in periostin (Postn) genomic locus; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus; Hsp47flox/flox

value: Fibroblasts are CRE+, GFP+, and HSP47-deficient


title: KP3


title: run2675: HSP47_2_17525


title: HMEC-1 exposed to preeclamptic trophoblast debris_rep3

city: AUCKLAND

first: Larry

last: Chamley

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

hyb_protocol: Following fragmentation, 10 µg of aRNA were hybridized for 16 hr at 45C on GeneChip PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing:
The statistical software program R was used to analyse the results. The data was pre-processed and normalised using RMA from the R package affy. The package limma was used to check for differential expression, and an empirical Bayes method used to moderate the t-statistic. The Benjamini-Hochberg method was used to adjust the p-values for multiple testing
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.0.38

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip 3’IVT Express Kit, Affymetrix).

growth_protocol: HMEC-1 was grown in MCDB 131 medium supplemented with 10% FBS, 1% L-glutamine and 1% Penicillin/Streptomycin at 37°C until 80% confluent

extract_protocol: Total RNA was extraced and purified by Trizol and PureLink® RNA Mini Kit according to the manufacturer's instructions.

treatment_protocol: Trophoblastic debris was added into the HMEC-1 cells culture at the final concentration of 60 µg total protein per mL for 21 hours.

value: Human microvascular endothelial cells (HMEC-1)

tag: treated with

value: preeclamptic trophoblast debris for 21 hrs


title: A549.BLM.siRNA3.1


title: d23_GFP

tag: sgrna

value: GFP


title: A549.CTL.1


title: run1739: Con_HK4_16113

description: Upon induction of Postn gene expression, and tamoxifen administration, expression of Cre-recombinase is turned on, and eGFP reporter allele is recombined.

value: MerCreMer cDNA in periostin (Postn) genomic locus; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus

value: Fibroblasts are CRE+ and GFP+


title: KP1


title: HMEC-1_untreated_rep3

value: none (untreated)


title: run2675: HK_2_17527


title: A549.BLM.siRNA2.3


title: d34_GFP

tag: over-expression


title: HMEC-1 exposed to control trophobalst debris_rep3

value: control trophobalst debris for 21 hrs


title: d21_GFP


title: run1739: Con_HK3_16112


title: A549.BLM.siRNA2.2


title: HMEC-1_untreated_rep2


title: HMEC-1 exposed to control trophobalst debris_rep2


title: HMEC-1 exposed to preeclamptic trophoblast debris_rep2


title: d49_Zfp189


title: A549.BLM.siRNA2.1


title: 9G

value: non-targeted

value: Control


title: HMEC-1 exposed to control trophobalst debris_rep1


title: run2675: HSP47_1_17524


title: 9E


title: mdt-15(tm2182) 15oC rep3

city: Daejeon

first: Seung-Jae

middle: V

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

data_processing:
The BCL (base calls) binary is converted into FASTQ utilizing illumina package  bcl2fastq (v2.17.1.14).
Sequenced reads were trimmed for adaptor sequence, then mapped to C. elegans genome (ce11) using HISAT2 (v.2.0.5), StringTie (v.1.3.3), and Ballgown (v.2.0.0) methods.
R packages limma (v.3.24.15) and edgeR (v.3.10.5) were used for analyzing differentially expressed genes (DEG).
Genome_build: ce11

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans mdt-15 mutant at 15oC

growth_protocol: Caenorhabditis elegans strains were grown on OP50-seeded NGM plates at 25oC or 15oC

extract_protocol:
Total RNA from synchronized day 1 adult worms was extracted by using RNA Isoplus (Takara, Shiga, Japan)
Three independent biological repeats were used for analysis. cDNA library was prepared and cDNA sequencing was performed by using a HiSeq 4000 platform (MACROGEN, South Korea). Paired-end reads were aligned to the C. elegans genome ce11, and analyzed by using HISAT2 (v.2.0.5), StringTie (v.1.3.3), and Ballgown (v.2.0.0) methods (56). R packages limma (v.3.24.15) (57) and edgeR (v.3.10.5) (58) were used for analyzing differentially expressed genes (DEG), and genes whose expression was not detected (counts per million (cpm) < 1) were excluded

value: Whole body

tag: developmental stage

value: Day 1 adult


title: Wild-type 15oC rep3

source_name: Caenorhabditis elegans wild-type at 15oC

value: Bristol N2


title: A549.BLM.siRNA1.3

value: Lung Cancer


title: 9D

source_name: Prefrontal cortex neurons

value: CRE-motif

value: Defeat


title: A549.BLM.siRNA1.2

value: Lung


title: TIME55

city: Halle (Saale)

first: Julia

last: Schumann

address: Franzosenweg 1a

country: Germany

institute: University Medicine Halle (Saale)

description: DHA supplemented/cytokine stimulated

data_processing:
Basecalls and Demultiplexing was performed using CASAVA version 1.4
Raw reads were adapter trimmed with cutadapt version 1.9.1. Only adapter trimmed reads between 15 and 27 bp lengthwere considered processed miRNAs and selected for alignment.
small RNA seq reads were aligned to the GRCm38/GRCh38 genome assembly using Bowtie2 version 2.2.7 allowing 1 mismatch and alignment to multiple targets
Reads were annotated by intersecting genome coordinates of known miRNAs from miRBase version 21  using Bedtools version 2.25.0
Reads were counted using the R/Bioconductor programming environment by application of the ShortRead library and the table function together with the miRNA name in the annotation
Count normalisation was done using the R/Bioconductor packages DESeq2 and EdgeR
Genome_build: GRCm38 (RAW264.7 samples) or GRCh38 (TIME samples)
Supplementary_files_format_and_content: Processed data files contain raw counts, DESeq and EdgeR normalised counts as labelled

source_name: TIME

growth_protocol: Cells were cultured according to ATCC recommendations

extract_protocol:
Total RNA extraction was performed based on TRIZOL according to the Manufacturer`s standard protocol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA Prep kit v2. Size restriction (140-165bp), purification, and quantification of barcoded libraries were performed using the Library quantification kit - Illumina/Universal. For cluster generation up to 10 libraries per were factored using an Illumina cBot.

treatment_protocol: The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling either 72 h (RAW264.7) or 144 h (TIME). Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of either LPS (1 µg/mL; from E. coli serotype 0111:B4) for cell line RAW264.7 or the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml for cell line TIME.

value: endothelial cell

value: TIME

tag: treatment

value: DHA supplemented/cytokine stimulated


title: TIME52

description: DHA supplemented/cytokine stimulated


title: mdt-15(tm2182) 15oC rep2

tag: genotype/variation


title: A549.BLM.siRNA1.1

tag: genotype


title: CHL1-S4

city: Parkville

first: Karen

last: Sheppard

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Center

description:
CHL1-S4_S11
processed data file: CHL1_CHL1AR991_repeat_count_AbuHammad_et_al.csv

data_processing:
Illumina CASAVA 1.8.2 was used for base calling and quality control was performed using RNA-SeQC v1.1.7
Adapters were trimmed using Cutadapt v1.7
Reads were mapped to the human reference genome (hg19v67 ) using TopHat2
HTSeq v0.5  was used to count the number of reads per gene
Limma-Voom method was applied for data normalisation and differential gene expression analysis
Genome_build: hg19v67
Supplementary_files_format_and_content: csv file includes normalized counts for each sample

source_name: CHL1 cell line

growth_protocol: A375AR and CHL1AR991 cells were grown in fully supplemented RPMI medium containing gardually increasing concentrations of palbociclib, once resistance developed, cells were maintained in fully supplemented RPMI medium containing 4  μΜ palbociclib. Control cells were grown in fully supplemented RPMI medium

extract_protocol:
Total RNA was extracted RNeasy Mini Kit as per manufacturer's instructions
RNA libraries were prepared for sequencing according to standard Illumina protocols (TruSeq RNA Sample Preparation Guide v2 Guide)

treatment_protocol: prior to RNA extraction cells were grown in palbociclib - free medium for 72 hr

tag: tissue source

value: Melanoma

tag: replicate

value: Replicate 3

value: No treatment


title: CHL1-S3

description:
CHL1-S3_S9
processed data file: CHL1_CHL1AR991_repeat_count_AbuHammad_et_al.csv

value: Replicate 2


title: HMEC-1_untreated_rep1

value: Human microvascular endothelial cells (HMEC-1)

value: none (untreated)


title: ILTV-PP2-2

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Genome_build: The reference genome and annnotation is download form http://ftp.ensembl.org/pub/release-73/fasta/gallus_gallus/dna/.
Supplementary_files_format_and_content: FPKM

organism: Gallus gallus

growth_protocol: LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Seperated single-cell samples were treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LMH cells were infected with ILTV at MOI 0.1 in the presence or absence of PP1 or PP2 treatment

value: Chick embryo liver

value: LMH


title: ILTV-PP2-3


title: ILTV-PP2-4


title: HMEC-1 exposed to preeclamptic trophoblast debris_rep1-2

value: preeclamptic trophoblast debris for 21 hrs


title: TIME43

description: AA supplemented/cytokine stimulated

value: AA supplemented/cytokine stimulated


title: HMEC-1 exposed to preeclamptic trophoblast debris_rep1-1


title: CHL1-S2

description:
CHL1-S2_S7
processed data file: CHL1_CHL1AR991_repeat_count_AbuHammad_et_al.csv

value: Replicate 1


title: CHL1AR991-S4

description:
CHL1AR991-S4_S12
processed data file: CHL1_CHL1AR991_repeat_count_AbuHammad_et_al.csv

source_name: CHL1AR991 cell line

value: increasing concentrations of palbociclib for 3 months


title: TIME50

description: DHA supplemented/cytokine stimulated


title: mdt-15(tm2182) 25oC rep2

source_name: Caenorhabditis elegans mdt-15 mutant at 25oC

value: Whole body

value: Day 1 adult


title: TIME41

description: AA supplemented/cytokine stimulated

value: endothelial cell


title: TIME37

description: AA supplemented/cytokine stimulated

value: TIME


title: ILTV-PP2-1


title: Wild-type 15oC rep2

value: Bristol N2


title: ILTV-PP1-4


title: Wild-type 25oC rep2

source_name: Caenorhabditis elegans wild-type at 25oC


title: CHL1AR991-S2

description:
CHL1AR991-S2_S8
processed data file: CHL1_CHL1AR991_repeat_count_AbuHammad_et_al.csv

value: Melanoma


title: TIME35

description: unsupplemented/cytokine stimulated

value: unsupplemented/cytokine stimulated


title: mdt-15(tm2182) 25oC rep3


title: Wild-type 25oC rep3


title: TIME32

description: unsupplemented/cytokine stimulated


title: ILTV-PP1-3


title: mdt-15(tm2182) 15oC rep1


title: ILTV-PP1-2


title: Wild-type 15oC rep1


title: mdt-15(tm2182) 25oC rep1


title: ILTV-PP1-1


title: TIME27

description: AA supplemented/unstimulated

value: AA supplemented/unstimulated


title: A375-S3

description:
A375-S3_S3
processed data file: A375_A375AR991_repeat_count_AbuHammad_et_al.csv

source_name: A375 cell line

value: Replicate 2

value: No treatment


title: Wild-type 25oC rep1


title: TIME30

description: unsupplemented/cytokine stimulated


title: A375-S4

description:
A375-S4_S5
processed data file: A375_A375AR991_repeat_count_AbuHammad_et_al.csv

value: Replicate 3


title: ILTV-DMSO-3

value: Chick embryo liver


title: ILTV-DMSO-4

value: LMH


title: A375-S2

description:
A375-S2_S1
processed data file: A375_A375AR991_repeat_count_AbuHammad_et_al.csv


title: A375AR991-S4

description:
A375AR991-S4_S6
processed data file: A375_A375AR991_repeat_count_AbuHammad_et_al.csv

source_name: A375AR991 cell line

value: increasing concentrations of palbociclib for 7 months


title: ILTV-DMSO-2


title: ILTV-DMSO-1


title: CHL1AR991-S3

description:
CHL1AR991-S3_S10
processed data file: CHL1_CHL1AR991_repeat_count_AbuHammad_et_al.csv


title: TIME16

description: DHA supplemented/unstimulated

value: DHA supplemented/unstimulated


title: A375AR991-S3

description:
A375AR991-S3_S4
processed data file: A375_A375AR991_repeat_count_AbuHammad_et_al.csv


title: TIME23

description: AA supplemented/unstimulated


title: Control-PP2-4


title: TIME13

description: DHA supplemented/unstimulated


title: TIME10

description: DHA supplemented/unstimulated


title: Control-PP2-2


title: Control-PP2-3


title: OB_M_4

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) Reads were trimmed using trim_galore v0.4.3 with the --rrbs flag.
2) Trimmed reads were mapped to hg38 and methylation levels estimated using Bismark v0.18.1 and Bowtie2 on default settings
3) The SNPs (dbSNP build 150) with major allele frequency 0.95 at most in autosomal chromosomes were filtered out
4) The missing values in CpG sites was kNN imputed for both methylation and unmethylation matrix, separately (R package: impute v1.56.0)
5) The CpG sites were aggregated into probe regions comprising minimum 20 CpG sites close to each other no more than 100 bp in at least 95% of the samples by using BiSeq v1.22.0
6) CpG probes with coverage larger than 10 times the 95-percentile of coverage in each sample are filtered out
7) Differential methylation analysis was performed with edgeR v3.24.0 using gender as a covariate
Genome_build: hg38
Supplementary_files_format_and_content: Tab-seperated text files (txt) with methylated (_Me) and unmethylated (_Un) CpG counts. imputed_methylationMatrix.txt.gz contains the count matrix from data processing step 4 and raw_methylationMatrix.txt.gz contains the count matrix from data processing step 3. Coverage (cov) files contain the coverage per sample data processing step 2. Excel file (xlsx) contains the clinical data relevant to each sample. Note: Samples GD_B_1, GD_B_2, GD_B_5, GD_B_6, GD_M_5 were removed from the txt files as they were not included in the final analysis due to low coverage and high NA content.

source_name: Whole blood

extract_protocol:
Blood from mothers were taken from a fasting blood sample collected in T3. Blood from infants were sampled with a neonatal heel prick 48h after birth. Blood from both mother and infant was collected in EDTA tubes and stored at -80°C.   Genomic DNA was extracted from whole blood using DNeasy Blood and Tissue Kit (QIAGEN, Germany) according to the manufacturer’s protocol. Yield and quality was assessed by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Denmark ) and NanoDrop (Thermo Fisher Scientific).
Multiplexed reduced representation bisulfite sequencing (RRBS) was performed as previously described. Briefly, genomic DNA was incubated with Msp1 (NEB, Germany) restriction enzyme overnight for fragmentation. Adenylation was performed using dNTP (NEB) and Klenow fragment (NEB) followed by an AMpure Bead clean-up (Beckman Coulter, Denmark) and ligation to TruSeq adapters (Illumina). Twelve ligated samples were pooled and subjected to bisulfite conversion using EZ DNA Methylation Kit (Zymo Research, Germany). The library pool was amplified by PCR (2 min 95 °C (30 s 95 °C, 30 s 65 °C; 45 s 72 °C) × 20 cycles; 7 min 72 °C) with PfuTurbo Hotstart DNA polymerase (Agilent, Denmark). PCR products were purified using the AMPure Bead clean-up. Libraries were sequenced on a HiSeq 2500 (Illumina) at the Danish National High-Throughput DNA Sequencing Centre, on a 50 bp single-end sequencing mode.

tag: mother/newborn

value: Mother

tag: group

value: Obese

tag: lineage

tag: Sex

value: Female


title: OB_M_3


title: TIME7

description: unsupplemented/unstimulated

tag: cell type

value: unsupplemented/unstimulated


title: OB_M_2


title: TIME4

description: unsupplemented/unstimulated

value: endothelial cell

tag: cell line


title: Control-PP2-1

tag: tissue


title: LE_M_7

value: Lean


title: A375AR991-S2

description:
A375AR991-S2_S2
processed data file: A375_A375AR991_repeat_count_AbuHammad_et_al.csv

value: Replicate 1


title: TIME1

description: unsupplemented/unstimulated

value: TIME


title: Control-PP1-3


title: WGC091223_Group B (LV from CMNKO mice; B_18)

city: DALLAS

first: Zhao

middle: V.

address: 6000 Harry Hines Blvd

institute: UT southwestern medical center

data_processing:
Sequencing was carried out on a HiSeq X Ten (Illumia)
Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <13.
The clean reads were then aligned to mouse genome
Genome_build: mm8
Supplementary_files_format_and_content: two excel files include expression values for each sample and the list of genes whose expressions are significantly different between A and B group.

source_name: Group B (LV from CMNKO mice)

growth_protocol: Mice used in this study were  housed in a specific pathogen free (SPF) facility.

extract_protocol:
Total RNA was extracted by Trizol reagent. And then check RNA quality.
TruSeq technology

tag: strain background

tag: age

value: 2 months old

value: cardiomyocyte-specific NCoR1 knockout (CMNKO)

value: Heart

tag: tissue subype

value: Left ventricular


title: LE_M_8


title: WGC091582_Group A (LV from LC mice; A_26)

source_name: Group A (LV from LC mice)

value: littermate control (LC)


title: LE_M_5


title: Control-PP1-4

value: Chick embryo liver


title: WGC091221_Group B (LV from CMNKO mice; B_16)


title: WGC091222_Group B (LV from CMNKO mice; B_17)


title: Control-PP1-2

value: LMH


title: Control-DMSO-3


title: Control-PP1-1


title: TIME19

description: AA supplemented/unstimulated

value: AA supplemented/unstimulated


title: CN-LB9.0

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

description:
CN_Lauryl betaine 9.0 μg/mL
CN_TPM.xlsx

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using tophat2 with '--very-sensitive' option.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, retrieved counts were normalized as TPM (Transcripts Per Kilobase Million) values.
Genome_build: C. neoformans var. grubii H99 (GCA_000149245.3), M. restricta KCTC 27527 (GCA_003290485.1)
Supplementary_files_format_and_content: Normalized TPM and fold change values were listed as a xlsx format for each organism.

organism: Cryptococcus neoformans H99

source_name: Clinical isolate

growth_protocol: M. restricta cells were cultured on mDixon agar medium at 34˚C for 12 hours. C. neoformans cells were cultured in YPD medium at 30˚C for 3 hours.

extract_protocol:
Total RNA was extracted using RiboPure Yeast RNA extraction kit (Ambion, Cat#AM1926).
Sequencing libraries for RNA-seq were constructed using the TruSeq Stranded Total RNA Kit (Cat No. 20020596, Illumina, USA) following the manufacturer’s instructions.

treatment_protocol: mDixon medium containing 3 mg/mL of lauryl betaine at 34˚C for 12 hours. YPD medium containing 4.5 μg/mL or 9.0 μg/mL of lauryl betaine at 30˚C for 3 hours.

value: treated by lauryl betaine 9.0 μg/mL


title: LE_M_6

value: Mother


title: WGC091581_Group A (LV from LC mice; A_25)


title: LE_M_4


title: LE_M_3


title: Control-DMSO-4


title: WGC091220_Group A (LV from LC mice; A_15)


title: Control-DMSO-2


title: LE_M_2


title: Control-DMSO-1


title: OB_M_1

value: Obese


title: LE_M_1

value: Female


title: CD34+ BM donor 12

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Sequencing was performed on an Illumina HiSeq 1000 using single-end sequencing at a target depth of 20 million reads per sample.
For gene expression quantification, pseudo-alignment of the RNA-Seq reads was performed using the software Kallisto in AltAnalyze. For splicing analyses, BAM files from STAR aligned reads were analyzed using the MultiPath-PSI algorithm in AltAnalyze version 2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited-text

source_name: Healthy donor CD34+ Bone Marrow

extract_protocol:
RNA was processed from young adult healthy CD34+ bone marrow. The total RNA was extracted by using mirVana miRNA Isolation Kit (Lifetech, Grand Island, NY) with total RNA extraction protocol. In brief, freshly prepared cells were immediately lyzed by Lysis/Binding Buffer, treated with Homogenate Additive, and followed by Acid-Phenol:Chloroform extraction according to the standard protocol. The supernatant was mixed with ethanol and passed through Filter Cartridge. The bound RNA was then washed and eluted. The RNA concentration was measured by Nanodrop (Thermo Scientific, Wilmington, DE) and its integrity was determined by Bioanalyzer (Agilent, Santa Clara, CA).
Using PrepX mRNA Library kit (WaferGen) and Apollo 324 NGS automatic library prep system, the depleted or isolated RNA was RNase III fragmented, adaptor-ligated and Superscript III reverse transcriptase (Lifetech, Grand Island, NY) converted into cDNA, followed by automatic purification using Agencourt  AMPure XP beads (Beckman Coulter, Indianapolis IN). Next, using the universal (SR) and index-specific primer with limited PCR cycle number (~13), sample-specific index was added to each ligated cDNA sample and the amplified library was enriched by AMPure XP beads purification with the final elution volume of 16 µl.

tag: disease state

value: healthy donor

value: CD34+ sorted bone marrow progenitors

tag: donor age (years)

value: M

tag: ethnicity

value: Caucasian


title: Lung Treg

city: San Francisco

first: Jarish

last: Cohen

state: CA

address: 513 Parnassus Avenue

department: Dermatology

institute: University of California, San Francisco

data_processing:
Fastq files generated from bcl files and analzyed by Cell Ranger (lung v 3.0.2; skin v 2.1.1) with default parameters to generate filtered feature matrices
Genome_build: mm10
Supplementary_files_format_and_content: processed data files are the cellranger output filtered feature bc matrix files

source_name: lung

extract_protocol:
collagenase digested skin and lung were FACS purified and sorted for Foxp3-expressing Tregs (GFP+ CD4+ CD3+ CD45+ cells)
10x Single Cell 3' v2 chemistry

tag: strain

value: Foxp3-GFP C57Bl/6 (Tachilla strain)


title: Skin Treg

source_name: back skin

value: Foxp3-CreERT2GFP C57Bl/6


title: CD34+ BM donor 11


title: ILC_ST2_neg_CD127_neg_Rep1

city: La Jolla

first: Taylor

last: Doherty

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
020_TaDo_ReDo_RNA_15_1_H5
5 ng totRNA > SmartSeq2 RNA-seq

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Alternaria alternata extract challenged murine lung

growth_protocol: Mice were challenged with PBS or 50μg of Alternaria alternata (Alternaria) extract (Greer, NC) daily for 4 times over 10 days and euthanized 24 hours after the last challenge for lung tissue harvest. lung single-cell suspensions were counted on a Novocyte flow cytometer (Acea Biosciences) and prepared for staining by washing with a solution of 2% FBS and 0.01% sodium azide in PBS.  Cells were incubated with a monoclonal antibody to CD16/CD32 for 10 minutes at 4oC to block Fc receptors and then stained for 30 minutes at 4oC with various combinations of antibodies to surface markers.  All antibodies were purchased from BioLegend unless otherwise noted.  In order to identify eosinophils (defined as CD45+Siglec-F+CD11c−), BAL and lung cells were stained with PerCP conjugated anti-CD45.2, PE conjugated anti–Siglec-F (BD), and FITC conjugated anti-CD11c.

extract_protocol:
ILC RNA was extracted using RNA Easy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.  Prior to RNA seq library preparation, Samples were quantified as described previously (Rosales et al, 2018) and quality of RNA assessed by Fragment Analyzer (Advance Analytical). All samples had a RNA integrity number (RIN)  > 7.5.
Purified total RNA (≈5 ng) was amplified following the Smart-seq2 protocol (Picelli et al, 2013, Rosales et al, 2018). Briefly, mRNA was captured using poly-dT oligos and directly reverse-transcribed into full-length cDNA using the described template-switching oligo. cDNA was amplified by PCR for 15 cycles and purified using AMPure XP magnetic bead (0.9:1 (vol:vol) ratio, Beckman Coulter).  From this step, for each sample, 1 ng of cDNA was used to prepare a standard NextEra XT sequencing library (NextEra XT DNA library prep kit and index kits; Illumina).  Barcoded Illumina sequencing libraries (NextEra; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter).  Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability.  Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR preamplification cycles, and fragment library size.  None of the samples failed quality controls.
libraries were pooled at equimolar concentration, loaded and sequenced on the Illumina Sequencing platform (HiSeq2500, or NovaSeq6000).  Libraries were sequenced to obtain more than 10 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina) mapping uniquely to mRNA reference.

treatment_protocol: Lungs were digested using Mouse Lung Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s protocol and subsequently filtered with a 40um cell strainer. Lung single-cell suspensions were counted on a Novocyte flow cytometer (Acea Biosciences) and prepared for staining by washing with a solution of 2% FBS and 0.01% sodium azide in PBS.  Cells were incubated with a monoclonal antibody to CD16/CD32 for 10 minutes at 4˚C to block Fc receptors and then stained for 30 minutes at 4˚C with various combinations of antibodies to surface markers.  All antibodies were purchased from BioLegend unless otherwise noted. In order to identify ILCs (defined as CD45.2+lineage−Thy1.2+ lymphocyte-sized cells) and conventional ILC2s (defined as CD45.2+lineage−Thy1.2+ST2+CD127+ lymphocyte-sized cells), lung cells were stained with: FITC conjugated Lineage Cocktail (anti-CD3e, anti-GR-1, anti-CD11b, anti-B220, anti-Ter119), anti-CD11c, anti-NK1.1, anti-CD5, anti-FcεR1, anti-TCR, and anti-TCRγδ; PerCP conjugated anti-CD45.2; eFluor 450 conjugated anti-Thy1.2 (ThermoFisher); APC conjugated anti-ST2; and PE-Cy7 conjugated anti-CD127.

tag: cell subtype

tag: background

value: Lung

value: Innate lymphoid cells (ILC)


title: GD_M_7

value: GDM


title: CD34+ BM donor 10


title: CD34+ BM donor 9


title: ILC_ST2_pos_CD127_neg_Rep1

description:
018_TaDo_ReDo_RNA_13_1_F5
5 ng totRNA > SmartSeq2 RNA-seq


title: ILC_ST2_neg_CD127_pos_Rep1

description:
019_TaDo_ReDo_RNA_14_1_G5
5 ng totRNA > SmartSeq2 RNA-seq


title: ILC_ST2_pos_CD127_pos_Rep1

description:
017_TaDo_ReDo_RNA_7_1_E5
5 ng totRNA > SmartSeq2 RNA-seq


title: GD_M_5


title: GD_M_4


title: CN-LB4.5

description:
CN_Lauryl betaine 4.5 μg/mL
CN_TPM.xlsx

tag: treatment

value: treated by lauryl betaine 4.5 μg/mL


title: CD34+ BM donor 8


title: CD34+ BM donor 6

value: F


title: CD34+ BM donor 7


title: CN-WT

description:
CN_control
CN_TPM.xlsx

value: C. neoformans control


title: zpdN_over_Bsub_LB_exp

city: Bloomington

first: Daniel

middle: B

last: Kearns

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

description: Overnight cultures were diluted to OD590 0.0003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.1. At which point zpdN expression was induced with 1 mM IPTG and cells were collected one hour later.

data_processing:
the 3’ linker sequences were stripped.
Bowtie v. 1.2.1.1 (options -v 1 -k 1) was used for sequence alignment to the reference genome NC 000964.3 (B. subtilis chromosome) and KF365913.1 (B. subtilis plasmid pBS32)
To deal with non-template addition during reverse transcription, reads with a mismatch at their 5’ end had their 5’ end re-assigned to the immediate next downstream position.
The 5’ and 3’ ends of mapped reads between 15 and 45 nt in sizes were counted separately at genomic positions to produce wig files.
The wig files were normalized per million non-rRNA and non-tRNA reads for each sample. Shadows were removed from wig files first by identifying the position of peaks and then by reducing the other end of the aligned reads by the peak’s enrichment factor to produce the final normalized and shadow removed wig files.
Genome_build: NC 000964.3 (B. subtilis chromosome) and KF365913.1 (B. subtilis plasmid pBS32)
Supplementary_files_format_and_content: wig

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

extract_protocol:
RNA was extracted using Trizol (ThermoFisher) and cleaned up and DNase treated using RNAeasy kit (QIAGEN)
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

value: subspecies 3610

tag: growth medium

value: LB

tag: genotype


title: DzpdN_MMC_Bsub_LB_exp

description: Overnight cultures were diluted to OD590 0.0003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.1. At which point 1 ug/ml MMC was added and cells were harvested 2 hours later.

value: zpdN


title: GD_M_3

tag: mother/newborn

value: Mother

tag: group

tag: lineage


title: RKN resistant control

city: Salinas

first: Pawan

last: Kumar

address: 1636 E Alisal Street

institute: USDA-ARS

description: RNA-Seq

data_processing:
The qualities of the raw reads were checked using FastQC program
Low-quality bases and adapter sequences from paired reads were trimmed using the Trimmomatic v0.30 program
Trimmed reads were mapped to the G. hirsutum reference genome using HISAT2 v2.1.0
Genome_build: Gossypium hirsutum (assembly ASM98774v1)

organism: Gossypium hirsutum

source_name: Roots

extract_protocol:
Whole intact root system from inoculated and un-inoculated M120 and C201 plants were carefully removed from the potting-mix at 12 and 30 DAI, washed with de-ionized water, dried with sterilized paper towels and immediately frozen in liquid nitrogen. Frozen roots were stored at -80 °C until RNA extraction
All libraries were constructed using the NEBNext Ultra RNA library Prep Kit for Illumina (New England BioLabs Inc.) following the manufacturers protocol.  The NEBNext Multiplex Oligos for Illumina (Index Primers Set 2, New England BioLabs Inc.) containing adaptors and primers were used to label libraries facilitating pooling.

treatment_protocol: Replicated set of cDNA libraries were constructed from M120 and C201 plants at 12, 30 DAI and untreated plants.

value: root

value: resistant


title: GD_M_8

tag: Sex

value: Female


title: WT_MMC_Bsub_LB_exp

value: WT


title: CD34+ BM donor 5

value: healthy donor

tag: cell type

value: CD34+ sorted bone marrow progenitors

value: Caucasian


title: RKN resistant at 30 DAI

description: RNA-Seq

tag: tissue


title: GD_M_1


title: GD_M_2


title: RKN resistant at 12 DAI

description: RNA-Seq

tag: age


title: OB_M_8

value: Obese


title: WT_Bsub_LB_exp

description: Overnight cultures were diluted to OD590 0.0003 in 25 mL fresh media. The culture was kept in a 125 mL flask at 37C with aeration (180 rpm) until OD590 reached 0.1.


title: CD34+ BM donor 3


title: RKN susceptable control

description: RNA-Seq

value: susceptible


title: TMAO, biological rep1

city: Boston

first: Sudha

last: Biddinger

state: MA

address: 3 Blackfan Cir

institute: boston children's hospital

description: Gene expression data

hyb_protocol: After fragmentation, cRNAs were hybridized on the Array, washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data was processed using the open-source Bioconductor packages, affy and limma.

organism: Rattus norvegicus

source_name: Primary rat hepatocytes

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

growth_protocol: Cells were suspended in William’s E medium supplemented with penicillin-streptomycin, 100 nM glutamine and 10% FBS, and placed into six-well plates that were pre-coated with rat tail collagen I.

extract_protocol: RNA was extracted by Trizol according to the manufacturer's instructions.

treatment_protocol: Cells were treated with TMAO (50 μM) for 30 h or left untreated as control.

tag: gender

value: Male

value: Sprague-Dawley

value: Eight-week-old

value: Primary rat hepatocytes


title: TMAO, biological rep3

description: Gene expression data


title: Control, biological rep1

description: Gene expression data


title: TMAO, biological rep2

description: Gene expression data


title: Control, biological rep2

description: Gene expression data


title: OB_M_7


title: CD11bGD3

city: Nanjing

first: Yuqing

last: Wu

address: 101 Longmian Road

institute: Nanjing Medical University

data_processing:
Basecalls performed using BGISEQ-500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p5 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Data were filtered using SOAPnuke version v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: CD11b+ macrophages_GD

growth_protocol: Macrophage and CD4+T cells were isolated from spleens of WT and Gsdmd-/- mice with CD11b and CD4 microbeads (Stem Cell), respectively.

extract_protocol:
RNA isolation were performed on a BGISEQ-500 (Beijing Genomic Institution, BGI)
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: WT and Gsdmd-/- mice were immunized with myelin oligodendrocyte glycoprotein (MOG35–55) peptide and pertussis toxin to induce EAE mice model

tag: genotype/variation

value: Gsdmd-/-

value: 8 weeks

value: spleen

value: CD11b+ macrophages


title: CD34+ BM donor 2

tag: disease state

tag: donor age (years)

value: F


title: OB_M_6

value: Mother


title: RKN susceptable at 30 DAI

description: RNA-Seq

value: root


title: CD11bGD2

tag: strain


title: CD11bGD1


title: Control, biological rep3

description: Gene expression data


title: RKN susceptable at 12 DAI

description: RNA-Seq


title: CD11bWT3

source_name: CD11b+ macrophages_WT

value: wild type


title: OB_M_5

value: Female


title: CD34+ BM donor 4

value: healthy donor

value: CD34+ sorted bone marrow progenitors

value: M

tag: ethnicity


title: OB_B_4

value: Baby

value: Obese


title: CD11bWT2


title: NP-5573

city: Fraiburgo

first: cecilia

middle: constantino

last: rocha

state: SC

address: ivan a de souza, 133

department: Animal Reproduction

country: Brazil

institute: Universidade de São Paulo

data_processing:
GLM analisys
Genome: Bos_taurus/NCBI/ARS-UCD1.2/sequence
Pregnant VS Non pregnant
maping with STAR
Genome_build: DE analysis using edegR

organism: Bos indicus

source_name: Bos taurus indicus

extract_protocol:
RNA was harvest using Rneasy mini kit (Quiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: pregnancy status

value: Non-Pregnant

value: Blood

value: peripheral blood mononuclear cells (PBMC)


title: 9859_Low_ASI_Chicory_Diet_Testis

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

institute: Technical University of Denmark

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmomatic v.0.33 - trimming for bad reads by standard parameters: PE -phred33 \ ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Cutadapt v.1.8.1 - trimming for adapter sequences: -a TACACTCTTTCCCTACACGACGCTCTTCCGATCT -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -a GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT -A AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \ -e 0.1 -O 5 -m 15 --minimum-length 1 STAR aligner v. 020201 - aligned by parameters: --runThreadN 10 --outFilterMultimapNmax 3 --outFilterMismatchNmax 8 --readFilesCommand zcat --outSAMunmapped Within --outReadsUnmapped Fastx >> output.log
samtools v. 1.3.1 by parameters: view -h -F 1792
HT-seq count v. 0.6.0 - genes counted by parameters: -m intersection-nonempty -s reverse -r pos -f sam -a 10 -t exon
Genome_build: Sus scrofa 10.2.87
Supplementary_files_format_and_content: HT-seq count file (.txt) - raw gene counts

organism: Sus scrofa

growth_protocol: Male pigs, Crossbred Duroc X Landrace/Yorkshire slaughtered at around 100 kg weight

extract_protocol:
Qiagen RNA Minikit
TruSeq stranded mRNA (Illumina, San Diego, USA) kit following instructions of the manufacturer

treatment_protocol: Fed either a control or chicory (15%) additive. All androstenone, skatole and indole concentrations measured by spectrophotometry.

tag: breed

value: Danish crossbred Duroc X Landrace/Yorkshire

value: male

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)

tag: indole concentration (mg/kg)

tag: estimated breeding values of sire for androstenone

tag: carcass weight (kg)

tag: sow id

tag: diet (control or chicory additive (15%))

value: Chicory

value: testis


title: 8095_High_ASI_Chicory_Diet_Testis

tag: Sex

tag: group

tag: tissue


title: NP-5602

tag: cell type


title: OB_B_3

tag: mother/newborn

tag: lineage

value: Male


title: NP-5606


title: CD11bWT1

tag: strain

tag: genotype/variation

tag: age

value: 8 weeks

value: spleen

value: CD11b+ macrophages


title: NP-5514

tag: pregnancy status


title: OB_B_2


title: 8086_Low_ASI_Chicory_Diet_Testis

tag: breed

tag: androstenone concentration (mg/kg)


title: OB_B_1


title: CD4GD2

source_name: CD4+ T cells_GD

value: Gsdmd-/-

value: CD4+ T cells


title: CD4GD3


title: CD34+ BM donor 1

city: Cincinnati

tag: disease state

value: healthy donor

value: CD34+ sorted bone marrow progenitors

tag: donor age (years)

value: F

tag: ethnicity

value: Caucasian


title: NP-5748

value: Non-Pregnant


title: 8080_Low_ASI_Chicory_Diet_Testis

tag: skatole concentration (mg/kg)

tag: indole concentration (mg/kg)

tag: estimated breeding values of sire for androstenone

tag: carcass weight (kg)

tag: sow id


title: LE_B_7

value: Baby

tag: group

value: Lean

tag: Sex

value: Female


title: LE_B_8

tag: mother/newborn

tag: lineage


title: CD4WT3

source_name: CD4+ T cells_WT

tag: strain

tag: genotype/variation

value: wild type

tag: tissue

tag: cell type


title: CD4GD1

tag: age


title: 8079_Low_ASI_Chicory_Diet_Testis

tag: breed

value: Danish crossbred Duroc X Landrace/Yorkshire

value: male

tag: androstenone concentration (mg/kg)

tag: diet (control or chicory additive (15%))

value: Chicory


title: 9867_High_ASI_Control_Diet_Testis

tag: skatole concentration (mg/kg)

value: Control

value: testis


title: P-5682

tag: pregnancy status

value: Pregnant

value: Blood

value: peripheral blood mononuclear cells (PBMC)


title: LE_B_6


title: CD4WT2

value: 8 weeks

value: spleen

value: CD4+ T cells


title: P-5611


title: 8078_High_ASI_Chicory_Diet_Testis

tag: indole concentration (mg/kg)

tag: estimated breeding values of sire for androstenone


title: LE_B_5

value: Male


title: CD4WT1


title: 8094_Low_ASI_Control_Diet_Testis

tag: carcass weight (kg)

tag: sow id


title: 8077_Low_ASI_Chicory_Diet_Testis

tag: Sex

tag: group


title: NP-5487

value: Non-Pregnant


title: P-5777


title: P-5623


title: P-5593


title: 7869_High_ASI_Control_Diet_Testis


title: LE_B_3

tag: mother/newborn

value: Baby

tag: lineage


title: 7864_Low_ASI_Control_Diet_Testis


title: LE_B_1

value: Lean


title: MR-LB3.0

description:
MR_Lauryl betaine 3.0 mg/mL
MR_TPM.xlsx

organism: Malassezia restricta

tag: strain

tag: treatment

value: treated by lauryl betaine 3.0 mg/mL


title: P-5846

tag: tissue

tag: cell type


title: 7863_High_ASI_Control_Diet_Testis

tag: breed


title: MR-WT

description:
MR_control
MR_TPM.xlsx

value: M. restricta control


title: GD_M_6

value: Mother

value: GDM

value: Female


title: 7858_High_ASI_Control_Diet_Testis

value: Danish crossbred Duroc X Landrace/Yorkshire

value: male

tag: androstenone concentration (mg/kg)

value: Control


title: GD_B_7


title: 9874 Low_ASI-Control

hyb_protocol: a service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/

data_processing: Genome studio, GenCall Version = 6.3.0. The Final Report from GenomeStudio was converted into PLINK files by the software SNPConvert (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003493/) and loaded into PLINK software (v. 1.90b3.44)

source_name: Loin muscle

growth_protocol: Danish crossbred Duroc x Landrace/Yorkshire male pigs (n=48) were slaughtered at 100 kg. Loin muscle samples were collected by punch biopsies, genomic DNA was extracted by Qiagen DNA Minikit and subjected to NEOGEN GeneSeek GGP 80K Porchine Bead Chip

extract_protocol: Punch biopsy at slaughterhouse and Qiagen DNA Minikit

treatment_protocol: Danish Landrace males pigs were categorised into low, medium and high summarised EBVs of skatole and human nose scores, derived from the sires of each pig.

tag: gender

tag: estimated breeding value from sire (androstenone)


title: LE_B_4


title: 9867 High_ASI-Control

scan_protocol: a service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/

tag: skatole concentration (mg/kg)


title: 8072_Low_ASI_Chicory_Diet_Testis

tag: indole concentration (mg/kg)

tag: diet (control or chicory additive (15%))

value: Chicory

value: testis


title: 7005_High_ASI_Control_Diet_Testis

tag: estimated breeding values of sire for androstenone

tag: carcass weight (kg)


title: GD_B_6

tag: Sex


title: GD_B_5

tag: group


title: LE_B_2

tag: mother/newborn


title: 5995_Low_ASI_Chicory_Diet_Testis

tag: sow id


title: 9859 Low_ASI-Chicory

label_protocol: a service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/


title: Primary ovarian tumor, patient 5

city: Seattle

first: Kristin

last: Anderson

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description: Gene expression data from primary ovarian tumor, patient 5

hyb_protocol: RNA samples were processed using the Clariom D Pico human Assay.

scan_protocol: standard Illumina protocol

data_processing: Arrays were analyzed using SST-RMA algorithm in the Affymetrix Transcriptome Analysis Console (TAC) Software. All samples passed the quality control criteria given by Affymetrix. Probes with less than two arrays above the 95th percentile of the antigenomic background probes were filtered out. Here, we provide the CHP files with the SST-RMA normalization.

source_name: Primary Ovarian Tumor

label_protocol: standard Illumina protocol

extract_protocol: RNA was extracted from fresh frozen primary human HGSOC, metastatic HGSOC, or adjacent normal tissue from patients using the Qiagen RNeasy Plus Mini RNA isolation kit (cat: 74134).

tag: patientid

tag: well

tag: samplesource

value: Customer

tag: sampletype

value: Fresh Frozen

value: Primary Ovarian Tumor


title: Omentum metastatic tumor, patient 4

description: Gene expression data from omentum metastatic tumor, patient 4

source_name: Omentum Metastatic Tumor

tag: tissue

value: Omentum Metastatic Tumor


title: Normal fallopian tube, patient 5

description: Gene expression data from normal fallopian tube, patient 5

source_name: Normal Fallopian Tube

value: Normal Fallopian Tube


title: GD_B_4

source_name: Whole blood

value: Baby

tag: lineage


title: Primary ovarian tumor, patient 4

description: Gene expression data from primary ovarian tumor, patient 4


title: Normal fallopian tube, patient 4

description: Gene expression data from normal fallopian tube, patient 4


title: GD_B_8

value: Male


title: 5991_High_ASI_Control_Diet_Testis

tag: breed

tag: androstenone concentration (mg/kg)


title: 7859_High_ASI_Control_Diet_Testis

tag: skatole concentration (mg/kg)


title: GD_B_3


title: Primary ovarian tumor, patient 3

description: Gene expression data from primary ovarian tumor, patient 3


title: 8094 Low_ASI-Control

tag: gender

tag: indole concentration (mg/kg)

tag: estimated breeding value from sire (androstenone)


title: 5990_High_ASI_Control_Diet_Testis

tag: estimated breeding values of sire for androstenone

tag: carcass weight (kg)

tag: diet (control or chicory additive (15%))


title: GD_B_2

tag: mother/newborn

tag: group

tag: Sex


title: 5986_Low_ASI_Control_Diet_Testis

tag: sow id


title: 8093 Low_ASI-Control


title: 8090 High_ASI-Chicory


title: GD_B_1


title: OB_B_8

value: Obese


title: 8095 High_ASI-Chicory


title: Normal fallopian tube, patient 3

description: Gene expression data from normal fallopian tube, patient 3

tag: patientid

tag: well

tag: samplesource


title: Omentum metastatic tumor, patient 3

description: Gene expression data from omentum metastatic tumor, patient 3

tag: sampletype

tag: tissue


title: 8085 Low_ASI-Control

tag: androstenone concentration (mg/kg)


title: 5988_Low_ASI_Control_Diet_Testis

tag: breed

tag: skatole concentration (mg/kg)


title: 5983_Low_ASI_Chicory_Diet_Testis

tag: indole concentration (mg/kg)


title: 5982_Low_ASI_Control_Diet_Testis


title: 8083 Low_ASI-Chicory

tag: gender

tag: estimated breeding value from sire (androstenone)


title: 5985_High_ASI_Chicory_Diet_Testis

tag: estimated breeding values of sire for androstenone

tag: carcass weight (kg)


title: siMondoA_rep3_RNA-seq

city: Philadelphia

first: Byungyong

last: Ahn

state: Pennsylvania

address: 3400 Civic Center Blvd Bldg 421

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

description: Gene expression data

data_processing:
reads alignment by STAR 2.5.0c with parameters "--runMode alignReads --genomeLoad LoadAndKeep NoSharedMemory --runThreadN 4 --genomeDir %s --readFilesIn %s --readFilesCommand zcat --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 --outFileNamePrefix %s" with "--genomeDir" for your reference genome, "--readFilesIn" for your input raw data and "--outFileNamePrefix" for the output prefix
sorting and indexing by samtools 1.3.1
reads counting by bedtools 2.26.0 with parameters "multicov -split -D -bams"
reas count arragement by paste in python 2.7.12
reads normalization by edgeR 3.20.9
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Primary skeletal myotube

growth_protocol: Primary human skeletal myoblasts are cultured in low glucose DMEM supplemented with 10% fetal bovine serum. When the cells reach 80-90% confluency, the cells are switched to differentiation media composed of alpha-MEM with 2% fetal bovine serum. This media is replaced every other day.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) following the manufacturers' protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA against MondoA or control was transfected on day 6 following differentiaiton. The cells were harvested 3days after transfection.

tag: cell type

value: Primary human myocytes

tag: passages

tag: genotype

value: MondoA KD


title: 8080 Low_ASI-Chicory

tag: group

tag: sow id


title: 5980_High_ASI_Chicory_Diet_Testis

tag: Sex

tag: diet (control or chicory additive (15%))


title: Primary ovarian tumor, patient 2

state: WA

description: Gene expression data from primary ovarian tumor, patient 2

tag: patientid

tag: well

tag: samplesource

tag: sampletype


title: Normal ovary, patient 2

description: Gene expression data from normal ovary, patient 2

source_name: Normal Ovary

tag: tissue

value: Normal Ovary


title: Abdominal implant metastatic tumor, patient 2

description: Gene expression data from abdominal implant metastatic tumor, patient 2

source_name: Abdominal Implant Metastatic Tumor

value: Abdominal Implant Metastatic Tumor


title: Omentum metastatic tumor, patient 1

description: Gene expression data from omentum metastatic tumor, patient 1


title: Primary ovarian tumor, patient 1

description: Gene expression data from primary ovarian tumor, patient 1


title: 5976_Low_ASI_Control_Diet_Testis

tag: breed

value: Danish crossbred Duroc X Landrace/Yorkshire

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)

tag: indole concentration (mg/kg)


title: 8079 Low_ASI-Chicory

tag: gender

tag: estimated breeding value from sire (androstenone)

tag: carcass weight (kg)


title: Normal fallopian tube, patient 1

description: Gene expression data from normal fallopian tube, patient 1


title: 8078 High_ASI-Chicory


title: 8086 Low_ASI-Chicory


title: 5974_High_ASI_Chicory_Diet_Testis

value: male

tag: estimated breeding values of sire for androstenone


title: OB_B_7

tag: mother/newborn

tag: group

tag: lineage


title: OB_B_6

tag: Sex


title: Hip_circR-3

city: Shijiazhuang

first: Lei

last: Wang

address: Hebei Medical University, No. 361, Zhongshan East Road, Chang'an District

institute: Heibei Medical University

hyb_protocol: Hybridization solution (50 μl) was dispensed into the gasket slide and assembled to a mouse circRNA microarray (8x15K, Arraystar) slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.The hybridized arrays were washed and fixed.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
The scanned images were imported into Agilent Feature Extraction software for raw data extraction. After quantile normalization of the raw databy using the R software limma package, and then low intensity filtering was performed. The expression profiles of circRNAs in the hippocampus tissues of Nrf2 (+/+) and Nrf2 (-/-) mice were obtained.
To compare the profile differences in the hippocampus tissues between Nrf2 (+/+) and Nrf2 (-/-) mice, the fold change between these groups for each circRNA was computed. Finally, circRNAs with p<0.05 and fold change > 1.5 were identified as meaningful.

source_name: Mouse hippocampus

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA by utilizing a random priming method with an Arraystar Super RNA Labelling Kit (Arraystar, Inc). The ﬂuorophore-labelled cRNA was purified with an RNeasy Mini Kit (Qiagen, Germany). 1 μg of each labelled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heating the mixture at 60°C for 30 min, and finally, 25 μl 2 × Hybridization buffer was added to dilute the labelled cRNA.

extract_protocol: Hippocampus tissues of each mouse were obtained from surgery, and immediately homogenized for the extraction of total RNA. Sample labelling and array hybridization were performed based on the manufacturer’s protocol. Briefly, total RNA was digested with RNaseR (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs,

tag: strain

value: ICR

tag: age

value: 3-4 months

tag: genotype

value: Nrf2 gene knockout

value: hippocampus

tag: molecule subtype

value: circular RNA


title: Hip_circR-1

tag: tissue


title: Hip_circR-2


title: 8077 Low_ASI-Chicory

tag: sow id


title: siMondoA_rep1_RNA-seq

description: Gene expression data

tag: cell type

tag: passages


title: 5973_High_ASI_Chicory_Diet_Testis

tag: breed

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)

tag: indole concentration (mg/kg)

tag: diet (control or chicory additive (15%))

value: Chicory

value: testis


title: siControl_rep3_RNA-seq

description: Gene expression data

value: control


title: siMondoA_rep2_RNA-seq

description: Gene expression data


title: 3923_Low_ASI_Control_Diet_Testis

tag: estimated breeding values of sire for androstenone

tag: carcass weight (kg)

value: Control


title: 8074 Low_ASI-Control

tag: gender

value: Male

tag: group

tag: estimated breeding value from sire (androstenone)


title: Hip_circR+2

tag: strain

tag: age

tag: Sex

value: Wild type


title: siControl_rep2_RNA-seq

description: Gene expression data

value: Primary human myocytes

tag: genotype


title: 3920_High_ASI_Chicory_Diet_Testis

tag: sow id

tag: tissue


title: siControl_rep1_RNA-seq

description: Gene expression data

tag: cell type

tag: passages


title: 3918_High_ASI_Control_Diet_Testis

tag: breed

tag: androstenone concentration (mg/kg)


title: 8073 High_ASI-Chicory

tag: skatole concentration (mg/kg)

tag: indole concentration (mg/kg)


title: Hip_circR+1

tag: molecule subtype


title: OB_B_5

tag: mother/newborn

value: Baby

value: Obese

tag: lineage


title: 8072 Low_ASI-Chicory

tag: gender

tag: group

tag: carcass weight (kg)


title: WT translatome Rep 1, no CHX

city: Stanford

first: Kevin

middle: C.

last: Stein

state: California

address: Clark Center E200, 318 Campus Drive

institute: Stanford University

data_processing:
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer.
Ribosomal RNA reads were removed by alignment using Bowtie v1.0.0.
Remaining reads were aligned using Bowtie  v1.0.0 (parameters "-y -a -m 1 -v 2 --norc --best --strata") to a library of open reading frames that excluded dubious ORFs and ORFs that overlapped with other genes.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Genome_build: sacCer3 R64-1-1
Supplementary_files_format_and_content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.

organism: Saccharomyces cerevisiae

source_name: WT translatome, no CHX

growth_protocol: Yeast were grown at 30°C in YPD until mid-log phase, followed by harvesting using fast filtration and flash freezing in liquid nitrogen.

extract_protocol:
Following cell lysis, samples were digested with RNase I and ribosomal pellets were isolated by ultracentrifugation using a sucrose cushion (or sucrose gradient for WT translatome samples). As indicated, TRiC- or Ssb-bound ribosomes were immunoprecipitated, followed by RNA extraction.
RNA fragments in the range of 24-35 nucleotides were gel purified. After dephosphorylation, a DNA linker (CTGTAGGCACCATCAAT) was ligated to the 3' end of the RNA footprints, which were then reverse transcribed into cDNA, and circularized. Depletion of rRNA was performed using the Ribo-Zero Gold kit (Illumina) before linker ligation, or using biotinylated subtraction oligonucleotides after circularization for WT translatome libraries. Libraries were then barcoded during PCR amplification and sent for sequencing.

tag: strain

tag: genotype/variation

value: wild-type

value: Ribosome protected mRNA


title: atp2 mutant TRiC total Rep 2

source_name: atp2 mutant TRiC total

tag: treatment

value: Cells were treated with 100 µg/mL cycloheximide (CHX) and immediately harvested using fast filtration.


title: 8071 High_ASI-Chicory

tag: estimated breeding value from sire (androstenone)

tag: sow id


title: 7869 High_ASI-Control


title: atp2 mutant TRiC total Rep 1


title: 9859_Low_ASI_Chicory_Diet_Liver

value: Danish crossbred Duroc X Landrace/Yorkshire

tag: Sex

value: male

tag: estimated breeding values of sire for androstenone

tag: diet (control or chicory additive (15%))

tag: tissue

value: liver


title: 9867_High_ASI_Control_Diet_Liver

tag: breed

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)


title: MDA231-Par VEC rep2

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

institute: KAIST

data_processing:
RNA-Seq reads were aligned to the human reference genome (NCBI 37, hg19) using the spliced read aligner TopHat version 1.4.0 (1).
The bam files from TopHat were assembled using Cufflinks
The individual transcript assemblies from multiple RNA-Seq libraries are assembled into one master transcriptome using Cuffmerge
using Cuffdiff comparisons of expression levels of genes from the different conditions was performed
Genome_build: hg19

source_name: Breast cancer cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; JR Scientific, Woodland, CA) for 2 days.

extract_protocol:
Total RNAs were isolated using Qiazol (Qiagen, Valencia, CA) followed by chloroform extraction.
Total RNAs were subjected to enrichment of polyA+ RNA using Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). Strand-specific RNA-seq libraries were prepared from the polyA+ RNA. The RNA-seq libraries were sequenced using single-end methodology with a length of 50 nt (SE50) (two replicates each) using an Illumina HiSeq 2500.

tag: cell type

value: MDA-MB-231 parental

tag: passage

tag: genotype

value: vector control


title: 7864 Low_ASI-Control

tag: gender

tag: group

tag: indole concentration (mg/kg)


title: 7863 High_ASI-Control

tag: carcass weight (kg)


title: 3908_High_ASI_Control_Diet_Testis


title: MDA231-Par VEC rep1


title: MDA231-LM2 shG14 rep2

value: Lung metastatic derivative of MDA-MB-231

value: GALNT14 knockdown


title: Hip_circR+3

tag: strain

value: ICR

tag: age

value: 3-4 months

value: hippocampus

tag: molecule subtype

value: circular RNA


title: Ssb total puromycin Rep 2

source_name: Ssb total puromycin

tag: genotype/variation

tag: treatment

value: Lysis buffer supplemented with 5 mM puromycin.


title: 8094_Low_ASI_Control_Diet_Liver

tag: Sex

tag: estimated breeding values of sire for androstenone

tag: sow id

tag: diet (control or chicory additive (15%))

value: Control


title: 7859 High_ASI-Control

value: Male

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)

tag: estimated breeding value from sire (androstenone)


title: Ssb total puromycin Rep 1

value: wild-type


title: 7858 High_ASI-Control


title: MDA231-Par WT rep2

tag: cell type

tag: passage

tag: genotype

value: GALNT14 over-expression


title: 8086_Low_ASI_Chicory_Diet_Liver

tag: breed

tag: group

tag: indole concentration (mg/kg)

value: Chicory

tag: tissue


title: MDA231-Par WT rep1


title: MDA231-LM2 shCntr rep2

value: nontargeting shRNA


title: MDA231-LM2 shG14 rep1


title: 7852 Low_ASI-Control

tag: gender

tag: carcass weight (kg)


title: 8080_Low_ASI_Chicory_Diet_Liver

value: Danish crossbred Duroc X Landrace/Yorkshire

value: male


title: Ssb-bound puromycin Rep 2

source_name: Ssb-bound puromycin

tag: strain

tag: genotype/variation

tag: treatment

tag: molecule subtype

value: Ribosome protected mRNA


title: MDA231-LM2 shCntr rep1


title: atp2 mutant TRiC-bound Rep 1

source_name: atp2 mutant TRiC-bound

value: Cells were treated with 100 µg/mL cycloheximide (CHX) and immediately harvested using fast filtration.


title: Ssb-bound puromycin Rep 1


title: 8079_Low_ASI_Chicory_Diet_Liver

tag: Sex

tag: estimated breeding values of sire for androstenone

tag: sow id

tag: diet (control or chicory additive (15%))

value: liver


title: atp2 mutant TRiC-bound Rep 2


title: 8078_High_ASI_Chicory_Diet_Liver

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)


title: 8095_High_ASI_Chicory_Diet_Liver


title: Ssb total Rep 2

source_name: Ssb total


title: 7005 High_ASI-Control

tag: estimated breeding value from sire (androstenone)


title: Oil and Pathogen Liver 2

city: Ocean Springs

first: Maria

middle: L

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

data_processing:
Bases called using Illumina CASAVA software
Read quality assessed using Illumina FastQC software; adpater trimming performed using Trimomatic software
Reads were aligned to Larimichthys crocea genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany).
Gene expression (Transcripts per million --TPM) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany)
Genome_build: Larimichthys crocea genome (NCBI genome ID 12197)
Supplementary_files_format_and_content: CSV text files including TPM expression values

organism: Sciaenops ocellatus

source_name: Liver

growth_protocol: All organisms were kept at 15 ppt salinity, 24 degrees C, and dissolved oxygen greater than 6 ppm

extract_protocol:
Qiagen RNeasy kit using manufacturer's protocols
Illumina TruSeq Stranded mRNA kit to construct polyA libraries

treatment_protocol: Oil-exposed organisms were subject to exposure for the duration of the experiment.  Pathogen-exposed fish were exposed to V. anguillarum for 1 hour 24 hours before experiment termination.

value: Liver

tag: oil treatment

tag: pathogen treatment


title: 7850 Low_ASI-Chicory

source_name: Loin muscle

tag: group

tag: indole concentration (mg/kg)


title: Oil and Pathogen Liver 3

tag: tissue


title: 5995 Low_ASI-Chicory

tag: gender

tag: carcass weight (kg)


title: 8072_Low_ASI_Chicory_Diet_Liver

tag: breed


title: Oil and Pathogen Liver 1


title: WT translatome Rep 2, no CHX

tag: strain

tag: genotype/variation


title: 7869_High_ASI_Control_Diet_Liver

tag: Sex


title: Ssb-bound Rep 2

source_name: Ssb-bound

tag: treatment

tag: molecule subtype


title: 5990 High_ASI-Control

tag: sow id


title: Pathogen Only Liver 3

value: 0 ug/L


title: 5989 High_ASI-Chicory

tag: androstenone concentration (mg/kg)


title: 5988 Low_ASI-Control

tag: skatole concentration (mg/kg)


title: 7864_Low_ASI_Control_Diet_Liver

tag: estimated breeding values of sire for androstenone

tag: diet (control or chicory additive (15%))


title: TRiC total puromycin Rep 2

source_name: TRiC total puromycin


title: 7863_High_ASI_Control_Diet_Liver


title: Pathogen Only Liver 1

tag: oil treatment

tag: pathogen treatment


title: 5995_Low_ASI_Chicory_Diet_Liver

tag: group

tag: indole concentration (mg/kg)


title: 7005_High_ASI_Control_Diet_Liver

tag: tissue


title: Pathogen Only Liver 2


title: TRiC total puromycin Rep 1


title: Ssb-bound Rep 1


title: 5986 Low_ASI-Control

tag: gender

tag: estimated breeding value from sire (androstenone)

tag: carcass weight (kg)


title: Oil Only Liver 3

value: 0 cfu/mL


title: Ssb total Rep 1

tag: strain

tag: genotype/variation


title: TRiC-bound puromycin Rep 1

source_name: TRiC-bound puromycin

tag: treatment


title: TRiC-bound puromycin Rep 2

tag: molecule subtype


title: Oil Only Liver 1


title: 5991_High_ASI_Control_Diet_Liver

tag: breed

tag: Sex

tag: sow id


title: Oil Only Liver 2


title: 5985 High_ASI-Chicory

tag: androstenone concentration (mg/kg)

tag: skatole concentration (mg/kg)