title: Q107_UREA


title: 58TX

status: Public on Sep 18 2019

type: genomic

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description:
processed data file:
Plate_1_Full_Data_Table.txt

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned on iScan

data_processing:
no data processing was applied
Processed data files include: Genotype: AA,AB,BB,or NC (no call). The first 10 columns of  *Full_Data_Table.txt files contain info about probes, processed values start at 11th column.

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA).

extract_protocol: Genomic DNA was extracted from whole blood treated with EDTA using a QIAamp DNA Mini Kit

tag: tissue

value: blood

tag: patient diagnosis

value: breast cancer

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: Q107_CONTROL

type: SRA

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

country: USA

institute: University of Kentucky

library_source: transcriptomic

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between samples from the control and urea groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.1 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: normalized abundance measurements- Cufflink Gene.FPKM.Tracking

molecule: total RNA

organism: Equus caballus

source_name: Uterus

extract_protocol:
Total cellular RNA was extracted from endometrial samples using TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer’s recommendations. After extraction, RNA concentration and quality were analyzed using a NanoDrop DP-1000 spectrophotometer (Agilent Technologies, Palo Alto, CA) and a Bioanalyzer® (Agilent, Santa Clara, CA). All samples had a 260/280 ratio > 2.0 and RNA integrity number (RIN) > 8 (8.95±0.4, mean ± SEM). A total of 1 μg of RNA was treated with DNase I (Ambion Inc., Austin, TX) for 30 minutes at 37℃ to remove genomic DNA according to manufacturer’s instructions.
The extracted RNA (1ng), was used for library preparation and RNA Sequencing. Paired-end reads with 150 nucleotides in length were produced. The RNAseq libraries were prepared with Illumina's TruSeq Stranded mRNAseq Sample Prep kit (Illumina, San Diego, CA). Read 1 aligns to the antisense strand and Read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.  The lane produced a total of 700 million reads. Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

treatment_protocol: Mares received a urea-treatment or control infusion (n = 7 mares/group) in a crossover design. The intervening estrous cycle was skipped and served as a washout cycle. Mares received 2500 IU of human chorionic gonadotropin (hCG) (Chorulon; Intervet, Millsboro, DE) intravenously when they had a follicle of at least 35 mm in diameter and pronounced uterine edema. Animals were scanned daily by ultrasound for ovulation detection (Day 0 = ovulation) and infusions were initiated at Day 7 of diestrus (D7). On the day of infusion, both jugular veins were catheterized using. Treatment consisted of a loading dose of 0.03 g/kg of urea (Sigma-Aldrich Company, St. Louis, MO) diluted in 100 mL of saline solution (Hospira, Inc, Lake Forest, IL) (15 g of urea for a 500 kg horse) to achieve a rapid increase in urea concentrations, and control mares received 100 mL of saline solution. Subsequently, mares received a bolus injection of urea (0.03 g/kg/hr) diluted in 15 mL of saline solution every 30 minutes over 6 hours (90 g of urea during 6 hours for a 500 kg horse). The control group received the same amount of saline solution as the urea group, 100 mL of saline solution as a loading dose and 15 mL of saline solution every 30 minutes over 6 hours. A uterine biopsy was collected from the base of the uterine horn.

value: Endometrium

tag: treatment

value: control


title: ChIPseq.s2.input_6

city: Planegg-Martinsried

first: Christian

last: Albig

address: Großhaderner Strasse 9

department: Biomedical Center

country: Germany

institute: Ludwig-Maximilians-University Munich

library_source: genomic

data_processing:
Sequence reads were aligned to the D. melanogaster release 6 reference genome (BDGP6) using Bowtie (Langmead et al., 2009) version 1.1.2 (parameter –m 1).
To generate bigWig files, reads were extended to 150 bp and per base normalized genome coverage vectors were calculated as described in (Villa et al., 2016) and raw per base genome coverage vectors were generated by summing up all reads and normalizing to million mapped reads (rpm).
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files with coverage

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2‑DRSC (DGRC stock # 181), Kc167 (DGRC stock # 1) cells were cultured in Schneider’s Drosophila Medium (Thermo Fisher), supplemented with 10% heat-inactivated Fetal Bovine Serum (Sigma‑Aldrich), 100 units/mL penicillin and 0.1 mg/mL streptomycin (Sigma‑Aldrich) at 26°C.

extract_protocol:
ChIP-seq was performed on MNase digested chromatin as described previously (Straub et al., 2008 and Kasinathan et al., 2013) with some modifications. Cells were fixed in 1% formaldehyde for 1 min at 26°C, followed by quenching with 125 mM glycine and washing with PBS. Nuclei were released by resuspending in TM2+ with NP-40. MNase digestion was performed in TM2+IC using 4U MNase (Sigma Aldrich, resuspended in EX50 (Bonte & Becker, 1999)) in the presence of CaCl2 for 13 min at 37 °C. Reaction was stopped with EGTA and Triton-X-100, SDS, NaDOC and NaCl was added to final concentration as in RIPA Buffer. MNase digested chromatin was incubated for 1 h at 4°C while slight agitation and chromatin was solubilized by passing ten times through 27 G needle and centrifuged for 30 min at 15,000 g at 4°C. 100 µL soluble chromatin was pre‑cleared with 3 µL (6 µL 50% slurry) Protein A:Protein G (1:1) beads (GE Healthcare) and supernatant was directly used for immunoprecipitation by adding antibody to 200 µL chromatin adjusted to 500 µL with RIPA and incubated for 16 h at 4°C. 100 µL supernatant was added to 3 µL (6 µL 50% slurry) Protein A:Protein G beads (1:1) and icubated for 4 h at 4°C. Beads were washed five times with RIPA. For DNA recovery, beads were resuspended in 6.7 bed volumes TE Buffer (10 mM Tris/HCl pH 8.0, 1 mM EDTA), RNA was digested with 50 µg/mL RNaseA (Sigma‑Aldrich) for 30 min at 37°C, and protein was digested with 0.5 µg/mL Proteinase K (Sigma‑Aldrich) supplemented with 0.5% (v/v) SDS for 16 h at 65°C. DNA was purified with 1.8x AMPure XP beads (Beckmann Coulter).
Libraries were prepared with NEBNext ChIP‑Seq Library Perp Kit for Illumina (NEB).

tag: cell line

tag: gender

value: male

tag: antibody

value: none (Input)


title: K131_UREA

value: urea


title: ChIPseq.s2.input_4


title: 10TX


title: aortic_control_rep1

type: RNA

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

hyb_protocol: Labeled miRNAs were hybridized to Agilent G3 Human miRNA Microarray (G4872A) overnight at 55°C. After hybridization, microarrays were washed, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent high-resolution Scanner (G2565C) using one color scan setting for 8x60k array slides (Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent) using default parameters. Data was normlised using RMA (Robust Microarray Analysis).

source_name: aortic media from healthy control 1

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng RNA using miRNA Complete Labeling and Hyb kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using miRVana kit (Life technologies), according to provider recommendations. Concentration of RNA samples were checked using a Nanodrop spectrophotometer.

treatment_protocol: Aortic media were recovered from aortic biopsies and directly frozen at -80°C for long term storage. Aortic media were thawed and approximatively 45 mg of aortic media were crushed in Lysis Binding Buffer (Ambion) and frozen at -80°C for storage before RNA extraction.

value: aortic media

tag: disease state

value: healthy control


title: ChIPseq.s2.input_5


title: K131_CONTROL

tag: tissue


title: Q108_UREA


title: 132TX

tag: patient diagnosis


title: 111TX

tag: (z)-4-oh-tam + 3-oh-tam


title: ChIPseq.s2.h3k36me3_3


title: ChIPseq.s2.h3k36me3_4


title: 96TX

tag: (z)-endoxifen + 3-oh-ndm-tam


title: 81TX

tag: tamoxifen


title: 28TX

tag: ndm-tam


title: ChIPseq.kc.msl3_3

source_name: Kc cells

value: Kc

value: female

value: MSL3 (GP)


title: K130_UREA


title: ChIPseq.s2.input_3


title: 57TX

tag: (e)-endoxifen


title: K130_CONTROL


title: 43TX

tag: tam-n-oxide


title: 72_total_rep2

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: GeneChip® 3' IVT Express kit (cat. # 901229) was used for hybridization, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affimetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

label: biotin

organism: Arabidopsis thaliana

label_protocol: RNA was processed and cRNA synthesized according to the 3’ GeneChips OneCycle kit.

growth_protocol: For the monosomal and polysomal RNA analyses Col-0 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006).

extract_protocol: The total RNA and polysomal RNA were purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from freshly harvested, dry seeds of three biological replicates of each genotype.

tag: ecotype

tag: protocol

value: 72 hours imbibed seedlings

value: seedling

tag: rna fraction

value: Total RNA


title: 26TX

tag: tam-n-gluc

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: 72_total_rep1


title: 72_total_rep3


title: ChIPseq.kc.msl3_2

tag: cell line

tag: gender

tag: antibody


title: ChIPseq.kc.h3k36me3_3


title: ChIPseq.kc.input_3


title: 72_polysome_rep3

tag: tissue

value: Polysomal RNA


title: Adult_Sham_Flu_12hr_2

city: Philadelphia

first: Alison

middle: J

last: Carey

state: PA

address: 245 N 15th Street Room 18119

department: Pediatrics

institute: Drexel Univeristy

hyb_protocol: Hybridized according to manufactorer's protcol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to manufactorer's protcol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

data_processing: Raw counts from the nCounter system were normalized to housekeeping and control probe counts using DESeq2, and subsequent analyses used DESeq2 for differential expression analysis.

organism: Mus musculus

source_name: Whole Lung

label_protocol: Labeled according to manufactorer's protcol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: Total RNA was extracted using Trizol Reagent and cleaned up using Qiagen RNeasy Clean Up Kit according to manufacturers protocol.

treatment_protocol: Neonates were treated on day of life 1 and 2 intranasally  with 1e6 CFU of Lactobacillus rhamnosus GG and Instranasally Infected with TCID50 0.04 PR8 Influenza A virus.

tag: age

value: Adult

tag: lgg treatment

value: No

tag: influenza a infection

value: Yes


title: Adult_Sham_Flu_12hr_3


title: Adult_Sham_Flu_12hr_1


title: Neonate_LGG_Flu_12hr_2

value: Neonate


title: 131TX

value: blood

tag: patient diagnosis

value: breast cancer

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam


title: 72_polysome_rep2

tag: ecotype

tag: protocol

tag: rna fraction


title: Neonate_LGG_Flu_12hr_1


title: 72_monosome_rep3

value: Monosomal RNA


title: 72_monosome_rep1


title: RNAseq.s2.jil8.batch2

data_processing:
Sequence reads were aligned to the D. melanogaster release 6 reference genome (BDGP6) using STAR (Dobin et al., 2013) version 2.6.0 (parameters --quantMode TranscriptomeSAM GeneCounts, --outFilterMultimapNmax 1).
Gene quantification was performed using RSEM (Li and Dewey, 2011) version 1.3.0 (parameters –bam, --paired-end, --forward-prob 0).
Genome_build: BDGP6
Supplementary_files_format_and_content: tsv with reads per gene

extract_protocol:
2 million S2 cells or Kc cells after RNAi treatment were resuspended in Trizol and RNA was purified using the RNeasy Mini Kit (QIAGEN).
1 µg of purified total RNA’s was used for rRNA depletion using Ribo-Zero Gold rRNA Removal Kit (Illumnia, MRZG 12324) or NEBNext rRNA Depletion Kit (NEB, E6310). Library preparation was done according to the manufacturer’s instructions with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760).

treatment_protocol: For RNAi against target genes in S2 and Kc cells for RNA-seq, cells were washed with serum‑free medium and 10 µg dsRNA per 10^6 cells at a concentration of 10 µg/mL in serum‑free medium (10^6 cells in 6‑well plate) was added, incubated for 10 min at room temperature (RT) with slight agitation and further 50 min at 26°C. Two volumes of complete growth medium were added and cells were incubated for 3 days at 26°C. At day 3, cells were split, and reseeded and retreated as at day 1. Cells were incubated for further 4 days at 26°C.

value: male

tag: treatment

value: jil-1 RNAi


title: Neonate_LGG_Flu_12hr_3


title: 110TX

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: Dry_total_rep3

value: Dry seeds

tag: tissue

value: seed


title: 72_polysome_rep1


title: 8TX


title: Dry_total_rep2


title: Neonate_Sham_Flu_12hr_3

tag: age

tag: lgg treatment

tag: influenza a infection


title: 95TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam


title: RNAseq.s2.jil4.batch1

tag: cell line

tag: gender


title: RNAseq.s2.jil9.batch2


title: Neonate_Sham_Flu_12hr_2


title: Neonate_Sham_Flu_12hr_1


title: 56TX

tag: tamoxifen

tag: ndm-tam


title: Neonate_Sham_Mock_12hr_3


title: Dry_total_rep1

tag: ecotype

tag: protocol

tag: rna fraction


title: Dry_polysome_rep3


title: RNAseq.s2.ctrl9.batch2

tag: treatment

value: control RNAi


title: Neonate_Sham_Mock_12hr_2


title: 42TX

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam


title: 24TX

tag: tissue

tag: z-endoxifen ratio


title: Dry_monosome_rep3


title: RNAseq.s2.ctrl8.batch2


title: Zheng_12_S48

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description:
Wart tissue sample from intravenously-infected rabbit.
limma_DEG_Ectopic-Vein_all_genes.txt
limma_DEG_Vein-Control_all_genes.txt

data_processing:
Samples were pooled and sequenced on one HiSeq run using Illumina TruSeq Stranded Total RNA Kit RS-122-2201.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the hg19 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Supplementary_files_format_and_content: Tab-delimited text files are limma-voom normalized differential expression output.

organism: Oryctolagus cuniculus

source_name: wart tissue

growth_protocol: Eight adult (4 males and 4 females) outbred New Zealand white rabbits.

extract_protocol:
The total RNA was isolated using TriPure Reagent (Millipore-Sigma, Part No. 11667165001) and DNase-treated on column using RNeasy Mini Kit (Qiagen, Part No. 74104).
TruSeq Stranded Total RNA Kit (Illumina; RS-122-2201)

treatment_protocol: The rabbits were infected by pre-scarification protocol on the back skin, followed by either cutaneous or intravenous inoculation of virus innocullum.

tag: disease stage

value: Tumor

tag: gender/animal/site

tag: route if infection

value: intravenous


title: RNAseq.s2.jil5.batch1

tag: cell line

tag: gender


title: RNAseq.s2.ctrl5.batch1


title: Zheng_11_S47


title: 5TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam


title: Neonate_LGG_Flu_3

tag: age

tag: lgg treatment

tag: influenza a infection


title: 80TX

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam


title: Dry_polysome_rep1

tag: ecotype

tag: protocol

tag: tissue

tag: rna fraction


title: Dry_polysome_rep2


title: Dry_monosome_rep2


title: RNAseq.s2.jil11.batch3

tag: cell line

tag: gender

tag: treatment


title: 72_monosome_rep2

value: 72 hours imbibed seedlings

value: seedling


title: RNAseq.s2.ctrl4.batch1


title: Zheng_9_S45

tag: disease stage

tag: gender/animal/site

tag: route if infection


title: 130TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: Neonate_LGG_Flu_2

tag: age

tag: lgg treatment

tag: influenza a infection


title: 109TX

tag: tissue

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam


title: Zheng_8_S44

description:
Wart tissue sample from cutaneously-infected rabbit.
limma_DEG_Ectopic-Control_all_genes.txt
limma_DEG_Ectopic-Vein_all_genes.txt

tag: disease stage

tag: gender/animal/site

value: cutaneous


title: RNAseq.s2.ctrl11.batch3

tag: cell line

tag: gender

tag: treatment


title: RNAseq.kc.jil4.batch2

value: Kc

value: female


title: Zheng_7_S43

tag: route if infection


title: 94TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam


title: Neonate_Sham_Mock_12hr_1

tag: age

tag: lgg treatment

value: No

tag: influenza a infection


title: 76TX

tag: tissue

tag: (e)-endoxifen

tag: tam-n-oxide

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: Neonate_LGG_Flu_1

value: Neonate

value: Yes


title: Zheng_6_S42

tag: disease stage

tag: gender/animal/site


title: 54TX

value: blood

value: breast cancer

tag: tam-n-gluc

tag: (e)-a-oh-tam


title: Zheng_4_S40

description:
Skin sample from Control rabbit.
limma_DEG_Ectopic-Control_all_genes.txt
limma_DEG_Vein-Control_all_genes.txt

source_name: normal skin tissue

value: Normal

tag: route if infection

value: control (mock)


title: RNAseq.kc.jil3.batch2

tag: cell line

tag: gender

tag: treatment

value: jil-1 RNAi


title: Neonate_LGG_Mock_3


title: 41TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam


title: Dry_monosome_rep1

tag: ecotype

tag: protocol

value: Dry seeds

tag: tissue

value: seed

tag: rna fraction

value: Monosomal RNA


title: RNAseq.kc.jil1.batch1


title: Zheng_3_S39

tag: disease stage


title: RNAseq.kc.ctrl4.batch2

value: control RNAi


title: Zheng_2_S38

tag: gender/animal/site


title: RNAseq.kc.jil2.batch1


title: Neonate_Sham_Flu_24hr_3

tag: age

tag: lgg treatment

tag: influenza a infection


title: Neonate_LGG_Mock_2


title: Neonate_LGG_Mock_1


title: 23TX

tag: (e)-endoxifen

tag: tam-n-oxide

tag: tam-n-gluc

tag: (e)-a-oh-tam

tag: (z)-a-oh-tam

tag: z-endoxifen ratio


title: RNAseq.kc.ctrl3.batch2

tag: cell line

tag: gender

tag: treatment


title: 3TX

tag: patient diagnosis

tag: (z)-4-oh-tam + 3-oh-tam

tag: (z)-endoxifen + 3-oh-ndm-tam

tag: tamoxifen

tag: ndm-tam


title: Neonate_Sham_Flu_24hr_2

tag: age


title: Zheng_1_S37

tag: disease stage

tag: gender/animal/site

tag: route if infection


title: RNAseq.kc.ctrl2.batch1


title: Neonate_Sham_Flu_24hr_1

tag: lgg treatment

tag: influenza a infection


title: TD49-treated Gills

city: nanjing

first: Cheng

last: Chi

address: weigang road

country: China

institute: Nanjing Agricultural University

description:
Bay scallop
processed data file: Control-VS-TD49-0.64-48.PossionDis_Method.GeneDiffExp.xls

data_processing:
The library preparation and Illumina sequencing were performed by Beijing Genomics Institute (BGI) (Hongkong, China). For cluster generation, the qualified and quantified libraries were firstly amplified within the flow cell on the cBot instrument (HiSeq® 4000 PE Cluster Kit, Illumina). For paired-end sequencing, the clustered flow cell was then loaded onto the HiSeq 4000 Sequencer (HiSeq® 4000 SBS Kit, Illumina) with 100bp which was recommended read lengths.
The resulting sequences assembled using Trinity (version: v2.0.6; parameters: --min_contig_length 150 --CPU 8 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stder) was referred to as transcripts.
Gene family clustering was then carried out using TGICL (version: v2.0.6; parameters: -l 40 -c 10 -v 25 -O '-repeat_stringency 0.90 -minmatch 35 -minscore 35') to obtain the final unigenes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: CN-Unigene.fa, TD49-Unigene.fa
Supplementary_files_format_and_content: Excel files includes RPKM values for each group.
Supplementary_files_format_and_content: Fasta files include unigene sequences for each group.

organism: Argopecten irradians

source_name: gill

extract_protocol:
Gills were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA integrity was measured using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Bay scallops were exposed to Thiazolidinedione derivatives 49 at a concentration of 0.64 μM for 48 h.

tag: tissue

value: Gill

value: Thiazolidinedione derivatives 49


title: B2 vs C2

city: Nanjing

first: Dongliang

last: Yang

state: Jiangsu

address: 9 wenyuan road, xianlin

department: Institute of Advanced Materials

institute: Nanjing University of Posts and Telecommunications

description:
Biological replicate 2 of 2. Hyphae growth of C. albicans was induced in YPD medium supplement  with 5% FBS and treated with 150 μM ethyl alcohol (control group)
Biological replicate 2 of 2. Hyphae growth of C. albicans was induced in YPD medium supplement  with 5% FBS and treated with 150 μM BDSF (experiment group)

hyb_protocol: Scanned on  a LuxScan 10 KA confocal laser scanner

scan_protocol: Images were quantified using  LuxScan3.0 software

data_processing: LOWESS normalized, background subtracted data obtained from  processed Red signal/processed Green signal. Agilent software was used.

organism: Candida albicans SC5314

source_name: C. albicans treated with 150 μM ethyl alcohol: Control Replicate 2 (C2)

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

extract_protocol: Total RNA extracted using  EASYspin Yeast Kit (Aidlab)

treatment_protocol: Hyphae growth of C. albicans was induced in YPD medium supplement  with 5% FBS and 150 μM BDSF, while control group was treated with 150 μM ethyl alcohol

tag: strain

source_name: C. albicans treated with 150 μM BDSF: Experiment Replicate 2 (B2)


title: Control Gills

value: Control


title: RNAseq.kc.ctrl1.batch1

value: Kc


title: B1 vs C1

description:
Biological replicate 1 of 2. Hyphae growth of C. albicans was induced in YPD medium supplement  with 5% FBS and treated with 150 μM ethyl alcohol (control group)
Biological replicate 1 of 2. Hyphae growth of C. albicans was induced in YPD medium supplement  with 5% FBS and treated with 150 μM BDSF (experiment group)

source_name: C. albicans treated with 150 μM ethyl alcohol: Control Replicate 1 (C1)

source_name: C. albicans treated with 150 μM BDSF: Experiment Replicate 1 (B1)


title: Neonate_Sham_Mock_24hr_3


title: HEK293T, HELZ-null replicate 1 for RNA-seq

status: Public on Sep 17 2019

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

data_processing:
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis

growth_protocol: 6.4x10^6 cells of HEK293T WT or HELZ-null cells were plated on 15 cm dishes 24 hrs before harvesting.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: HELZ-null


title: HEK293T, HELZ-null replicate 2 for RNA-seq

tag: cell line


title: HEK293T, Wild-type replicate 2 for RNA-seq

value: Wild-type


title: Neonate_Sham_Mock_24hr_2

value: Neonate

value: No


title: T18 hypoxia rep1

city: Belvaux

first: Elisabeth

last: Letellier

address: 6, Avenue du Swing

department: Life Sciences Research Unit

institute: University of Luxembourg

description:
miRNA expression intensities
T18_H1

hyb_protocol: Labeling reaction was checked by an Elosa QC Assay before performing hybridization. GeneChip Eukaryotic Poly-A RNA Controls and Control Oligonucleotide B2 (Affymetrix, High Wycombe, United Kingdom) were added to the hybridization mix. 130µl of the hybridization cocktail were injected onto the arrays.

scan_protocol: Arrays were incubated at 48°C, 60 rpm for 16 hours. Then arrays were stained and washed with the GeneChip® Hybridization Wash and Stain kit (Affymetrix, High Wycombe, United Kingdom) using the Fluidic script FS450_0002. GeneChip® miRNA Array v4.0 st (Affymetrix, High Wycombe, United Kingdom) were performed according to manufacturers user guide FlashTag Biotin HSR RNA  Labeling Kit For Affymetrix® GeneChip® miRNA Arrays P/N 703095 Rev3

data_processing:
The data were imported, normalized and summarized to transcript cluster level using Partek GS software. We used GC RMA method with quantile normalization.
log2 GC-RMA data; miRNAs for which none of the replicates was >5, the miRNA was considered "not expressed" and removed from the analysis

source_name: hypoxic patient T18 TICs

label_protocol: 300ng of total RNA were subjected to a Poly (A) tailing with a PAP Enzyme, a Biotin Labeling was performed with a T4 DNA Ligase using the FlashTagTM Biotin RNA Labeling kit (Affymetrix, High Wycombe, United Kingdom).

growth_protocol: Sphere cultures were maintained in serum-free medium containing growth factors

extract_protocol: Total RNA was extracted with Qiazol, using the miRNeasy extraction kit (Qiagen), following the user manual

treatment_protocol: Normoxia (incubator): 72h at 21% O2, Hypoxia (incubator): 72h at 1% O2

value: colorectal cancer

tag: culture type

value: patient-derived sphere culture

tag: patient

value: hypoxia


title: T18 hypoxia rep3

description:
miRNA expression intensities
T18_H3

tag: treatment


title: T18 normoxia rep3

description:
miRNA expression intensities
T18_N3

source_name: normoxic patient T18 TICs

value: normoxia


title: T18 hypoxia rep2

description:
miRNA expression intensities
T18_H2


title: T6 hypoxia rep4

description:
miRNA expression intensities
T6_H4

source_name: hypoxic patient T6 TICs


title: Neonate_Sham_Mock_24hr_1


title: HEK293T, Wild-type replicate 1 for RNA-seq


title: T18 normoxia rep2

description:
miRNA expression intensities
T18_N2


title: T6 hypoxia rep2

description:
miRNA expression intensities
T6_H2


title: T18 normoxia rep1

description:
miRNA expression intensities
T18_N1


title: T6 normoxia rep4

description:
miRNA expression intensities
T6_N4

source_name: normoxic patient T6 TICs


title: T6 hypoxia rep1

description:
miRNA expression intensities
T6_H1


title: T6 hypoxia rep3

description:
miRNA expression intensities
T6_H3


title: T6 normoxia rep1

description:
miRNA expression intensities
T6_N1


title: T6 normoxia rep2

description:
miRNA expression intensities
T6_N2


title: RNA-seq E12.5 replicate 3

city: Wako

first: Koh

last: Onimaru

state: Saitama

address: 312 Information Science Building, 2-1 Hirosawa

country: Japan

institute: Center for Biosystems Dynamics Research

description:
replicate 3
mouse_limb_average_TPM_expression_data_with_gene_symbol.txt
mouse_limb_TPM_expression_data_with_gene_symbol.txt

data_processing:
Basecalling with Illumina RTA 1.18.64
Short reads were aligned to curated, non-redundant genes in GCF_000001635.26_GRCm38.p6_rna.fna for mouse samples and a transcriptome assemble for bamboo shark samples using RSEM with bowtie2 (bowtie2 options: –no-mixed --no-discordant --gbar 1000 --end-to-end -k 200).
Transcripts per million (TPM) were calculated using RSEM and a perl script in Trinity software.
Genome_build: mm10 or a transcritopme assembly
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each species.

source_name: forelimb bud at E12.5

extract_protocol:
RNeasy Mini plus kit
Described in the SAMPLES section
Using >100 μg of each of the RNA samples, strand-specific single-end RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Cat. No. RS-122-2101 and/or RS-122-2102 ). For purification, we applied 1.8x (after end repair) and 1.0x (after PCR) volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880). The optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be XXXX cycles for mouse limb buds and XXX cycles for bamboo shark fin buds. The quality of the libraries was checked by Agilent 4200 TapeStation.

value: forelimb bud


title: RNA-seq E11.5 replicate 3

source_name: forelimb bud at E11.5


title: RNA-seq E12.5 replicate 1

description:
replicate 1
mouse_limb_average_TPM_expression_data_with_gene_symbol.txt
mouse_limb_TPM_expression_data_with_gene_symbol.txt


title: RNA-seq E12.5 replicate 2

description:
replicate 2
mouse_limb_average_TPM_expression_data_with_gene_symbol.txt
mouse_limb_TPM_expression_data_with_gene_symbol.txt


title: RNA-seq E11.5 replicate 1


title: RNA-seq E10.5 replicate 1

source_name: forelimb bud at E10.5


title: RNA-seq E10.5 replicate 3


title: RNA-seq E09.5 replicate 3

source_name: forelimb bud at E09.5

extract_protocol:
RNeasy Micro plus kit
Described in the SAMPLES section
Using >100 μg of each of the RNA samples, strand-specific single-end RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Cat. No. RS-122-2101 and/or RS-122-2102 ). For purification, we applied 1.8x (after end repair) and 1.0x (after PCR) volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880). The optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be XXXX cycles for mouse limb buds and XXX cycles for bamboo shark fin buds. The quality of the libraries was checked by Agilent 4200 TapeStation.


title: RNA-seq E09.5 replicate 2


title: RNA-seq E09.5 replicate 1


title: T6 normoxia rep3

description:
miRNA expression intensities
T6_N3


title: IG_DMR_KO_placenta_RNA seq_2

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

description: Placenta obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletion of IG-DMR

data_processing:
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.1.1). The gene expression levels were calculated by Cufflinks (version 2.1.1). The expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited txt files for RNA seq including FPKM values for each gene

source_name: Placenta

extract_protocol:
For blastocyst, to separate ICM and TE from E3.5 embryos(Liu et al., 2016), blastocysts were broken using micromanipulator and washed three times in HCZB. The zona pellucidae of blastocysts were digested with 0.5% pronase E (Sigma) for 10-15 mins and washed three times again in HCZB. The embryos were then incubated in Ca2+-free CZB for 30 mins in 37 ℃, and the ICM and TE were separated into single cells by gently pipetting using a pipette with a diameter of 40–60 μm. Each sample was obtained about 10 cells from one embryo for amplification according the cell shape. For placenta, total RNA was isolated from mouse placentae using Dynabeads™ mRNA DIRECT™ Purification Kit (Thermo Scientific™).
For blastocyst, the cDNA library were prepared by SPAPK DNA Sample Pre Kit (Enzymatics) for sequencing using an Illumina HiSeq X Ten sequenator. For placenta, RNA-seq library were prepared by VAHTS mRNA-seq V3 Library Prep Kit for Illumina® (Vazyme), and then applied for deep sequencing on Illumina NovaSeq6000 platform.

value: placenta tissue

value: C57BL/6 X F1

tag: development stage


title: DKO_placenta_RNA seq_3

description: Placenta obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR


title: H19_13kb_KO_placenta_RNA seq_2

description: Placenta obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletion of h19-DMR and H19 gene (13Kb)

value: Deletions of  H19 gene body and H19-DMR (chr7:149761078-149774522)


title: IG_DMR_KO_placenta_RNA seq_1


title: H19_13kb_KO_placenta_RNA seq_1


title: WT_placenta_RNA seq_3

description: Placenta obtained by Intracytoplasmic wt  androgenetic haploid ESC injection

value: wild type


title: ICSI_placenta_RNA seq_3

description: Placenta obtained by Intracytoplasmic sperm injection (ICSI)


title: DKO_placenta_RNA seq_1


title: H19_13kb_KO_placenta_RNA seq_3


title: IG_DMR_KO_placenta_RNA seq_3


title: untreated

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

institute: University of Münster

data_processing:
Raw sequence reads were quality checked using quality control tool FastQC.
Read mapping was performed by bowtie2 (https://bioinformatics.readthedocs.io/en/latest/bowtie2/) using the raw fastq data files. Option ‘--very-sensitive-local’ was set to carry out soft trimming and highest sensitivity.
Expression values for coding genes were calculated from read count data using the Transcript Per Million (TPM) method (doi:10.1007/s12064-012-0162-3). A cutoff of at least 10 TPM was used to determine genes that were assumed as expressed. TPM values below the cutoff were adjusted to 10 for calculation of the corresponding fold changes.
Genome_build: CP000243
Supplementary_files_format_and_content: Excel files including TPM values for each sample

organism: Escherichia coli

source_name: urine

growth_protocol: 1 CFU of agar grown UPEC strain UTI89 was inoculated into 5 mL of pooled human urine and incubated overnight (~15 h) without shaking. 1 mL of the urine grown bacterial suspension was transferred to 200 mL of pooled human urine from the untreated volunteers (Tag 0) or after treatment with cranberry extract (Tag 8). These cultures were incubated at 37 °C for 2 h to reach the mid-logarithmic phase.

extract_protocol:
The suspension was centrifuged (5 min, 4 °C) and the bacterial pellet was resuspended in 35 µL lysis buffer (lysozyme in TE buffer, 85 mg/mL). After 10 min incubation at RT and gentle vortexing every 10 sec, 1 mL TRizol ® (Thermo Fisher Scientific) was added and the isolation process was continued according to the manufacturer's protocol. 10 µg of isolated total RNA were used for DNA digestion, using the Turbo DNase (Turbo-DNA-free™ Kit, Thermo Fisher Scientific) according to the manufacturer's instructions.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3' adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified (11 PCR cycles) to about 10-20 ng/µl using a high fidelity DNA polymerase. The TruSeq barcode sequences AGGATAGG or TCAGAGCC, which are part of the 5' TruSeq sequencing adapter were used. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: 1 mL of the bacterial culture with an OD600 of 1 was mixed with 0.125 mL of stop solution (95 % ethanol, 5 % phenol).

value: strain UTI89

tag: agent

value: untreated


title: DKO_placenta_RNA seq_2


title: WT_placenta_RNA seq_1


title: RNA-seq E11.5 replicate 2


title: cranberry-treated

value: cranberry-treated


title: RNA-seq E10.5 replicate 2


title: ICSI_placenta_RNA seq_1


title: ATAC-seq E11.5 replicate 2

data_processing:
Basecalling with Illumina RTA 1.18.64
Short reads were aligned to mouse mm10 genome using bwa with mem option.
Peaks were called using MACS2 version 2.1.1 (options: --nomodel --shift -100 --extsize 200 -f BAMPE -g mm -B -q 0.01).
Coverage files were generated using bamCoverage command in deepTools (options: --normalizeUsing BPM --effectiveGenomeSize 2652783500 -e).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
For sampling, mouse forelimb buds of each stage were dissected and treated with collagenase for 10 min at RT. Then, cells were dissociated into single-cell suspensions by pipetting and 40 μm mesh filter (Funakoshi, Cat. No. HT-AMS-14002), and frozen in CryoStor® media (Stemcell technologies Cat. No. ST07930) with Mr. Frosty™ (Thermo Scientific, Cat. No. 5100-0001) at −80°C for overnight
Stored cells were melted in 38 °C water bus, and spun down at 500 g for 5min at 4 °C, which was followed by a wash using 50 μl of cold PBS once and centrifugation at 500g for 5 min. Ten thousands of cells per sample were collected without distinguishing dead cells, and lysed using 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1 % IGEPAL CA-630). Immediately after lysis, cells were spun at 1000 g for 10 min at 4 °C, and the supernatant was discarded. For transposition reaction, cells were re-suspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water), and incubated for 30 min at 37 °C. For control, 50 ng control genome DNA was also transposed. The reaction mix was purified using DNA Clean & Concentrator-5 (zymo, Cat. No. D4004) by adding 350 μl of DNA binding buffer, and eluted in 10 μl. After 5 cycle pre PCR amplification, the optimal number of PCR cycles was determined by a preliminary PCR using KAPA Library Amplification Kit (KAPA, Cat. No. KK2702) and estimated to be 4 cycles. The PCR products were purified using 1.8x volumes of Agencourt AMPure XP (Beckman Coulter, Cat. No. A63880).


title: ICSI_placenta_RNA seq_2


title: ATAC-seq E12.5 replicate 3


title: ATAC-seq E12.5 replicate 2


title: ATAC-seq E11.5 replicate 3


title: ATAC-seq input

source_name: mouse genome

value: mouse genome


title: ChIPseq.kc.msl3_1

source_name: Kc cells

value: Kc

tag: gender

value: female

tag: antibody

value: MSL3 (GP)


title: ATAC-seq E11.5 replicate 1

tag: age


title: WT_placenta_RNA seq_2


title: ATAC-seq E10.5 replicate 3


title: ATAC-seq E10.5 replicate 2


title: ATAC-seq E10.5 replicate 1


title: DKO_TE_RNA seq_4

description:
TE obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-TE4

source_name: Trophectoderm

value: TE cells


title: DKO_TE_RNA seq_5

description:
TE obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-TE5


title: ATAC-seq E09.5 replicate 2


title: ATAC-seq E09.5 replicate 3


title: DKO_TE_RNA seq_2

description:
TE obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-TE2


title: DKO_TE_RNA seq_3

description:
TE obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-TE3


title: ATAC-seq E09.5 replicate 1


title: WT_TE_RNA seq_1

description:
TE obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-TE1


title: DKO_TE_RNA seq_1

description:
TE obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-TE1


title: WT_TE_RNA seq_3

description:
TE obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-TE3


title: WT_TE_RNA seq_4

description:
TE obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-TE4


title: WT_TE_RNA seq_2

description:
TE obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-TE2


title: WT_TE_RNA seq_5

description:
TE obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-TE5


title: ATAC-seq E12.5 replicate 1


title: ICSI_TE_RNA seq_4

description:
TE obtained by Intracytoplasmic sperm injection (ICSI)
C-TE4


title: ICSI_TE_RNA seq_3

description:
TE obtained by Intracytoplasmic sperm injection (ICSI)
C-TE3


title: ICSI_TE_RNA seq_5

description:
TE obtained by Intracytoplasmic sperm injection (ICSI)
C-TE5


title: ICSI_TE_RNA seq_2

description:
TE obtained by Intracytoplasmic sperm injection (ICSI)
C-TE2


title: ICSI_TE_RNA seq_1

description:
TE obtained by Intracytoplasmic sperm injection (ICSI)
C-TE1


title: DKO_ICM_RNA seq_5

description:
ICM obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-ICM5

source_name: Inner cell mass

value: ICM cells


title: DKO_ICM_RNA seq_1

description:
ICM obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-ICM1


title: DKO_ICM_RNA seq_3

description:
ICM obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-ICM3


title: DKO_ICM_RNA seq_4

description:
ICM obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-ICM4


title: WT_ICM_RNA seq_5

description:
ICM obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-ICM5


title: WT_ICM_RNA seq_3

description:
ICM obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-ICM3


title: WT_ICM_RNA seq_1

description:
ICM obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-ICM1


title: ICSI_ICM_RNA seq_5

description:
ICM obtained by Intracytoplasmic sperm injection (ICSI)
C-ICM5


title: ICSI_ICM_RNA seq_4

description:
ICM obtained by Intracytoplasmic sperm injection (ICSI)
C-ICM4


title: ICSI_ICM_RNA seq_2

description:
ICM obtained by Intracytoplasmic sperm injection (ICSI)
C-ICM2


title: ICSI_ICM_RNA seq_3

description:
ICM obtained by Intracytoplasmic sperm injection (ICSI)
C-ICM3


title: ICSI_ICM_RNA seq_1

description:
ICM obtained by Intracytoplasmic sperm injection (ICSI)
C-ICM1


title: DKO_ICM_RNA seq_2

description:
ICM obtained by Intracytoplasmic injection of androgenetic haploid ESC with deletions of h19-DMR and IG-DMR
D-ICM2


title: WT_ICM_RNA seq_4

description:
ICM obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-ICM4


title: WT_ICM_RNA seq_2

description:
ICM obtained by Intracytoplasmic wt  androgenetic haploid ESC injection
W-ICM2


title: Buccal swab, 9343114108_R06C01

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, color-correction)

label: Cy5 and Cy3

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Buccal epithelial swabs were collected using MasterAmp Buccal Swabs (Epicentre Biotechnologies). DNA was extracted using Isohelix Buccal DNA Isolation Kits (Cell Projects) then purified and concentrated using DNA Clean & Concentrator (Zymo Research). Genomic DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

tag: cell type

value: buccal epithelial cells

value: M


title: Buccal swab, 9343114108_R04C02

value: F


title: Buccal swab, 9343114108_R05C02


title: Buccal swab, 9343114108_R04C01


title: Buccal swab, 9343114108_R02C02


title: Buccal swab, 9343114093_R01C02


title: Buccal swab, 9343114108_R01C02


title: Buccal swab, 9343114108_R01C01


title: Buccal swab, 9343114108_R03C02


title: BW25113

city: Tianjin

first: Tingli

last: Xue

address: Weijin Road No.92

institute: Tianjin University

data_processing:
Illumina HiSeq 4000TM platform used for sequencing
The processed reads were mapped to the BW25113 (LOCUS NZ_CP009273) genome assembly using Bowtie2 with reference annotation
The differentially expression genes (DEGs) between two samples were analyzed by DESeq package (v1.24.0)
Gene Ontology (GO) functional categories based on GOSeq (v1.22) and top GO (v2.22)
Genome_build: BW25113 (LOCUS NZ_CP009273)

source_name: bacteria

growth_protocol: Strains BW25113 and DTrob was incubated in 50 mL LB containing 0.75% (v/v) butanol for 9.5 hours ,OD600 = 0.6 – 1.1.

extract_protocol:
The 3 mL cultures were harvested and washed using ice-cold PBS. And then cells were used to extracted Total RNA by TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
The cDNA library preparation using standard Illumina protocols

tag: genotype/variation

value: Wild type


title: Buccal swab, 9343114093_R01C01


title: Buccal swab, 9343114108_R03C01


title: Buccal swab, 9343114093_R06C02


title: Q2: Queen Pool 2 (RNA-seq)

city: Dunedin

first: Peter

middle: Kenneth

last: Dearden

address: 710 Cumberland St

department: Department of Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
The sequencing was done using the Illumina HiSeq2500 technology, generating 49 bp reads.
The Illumina Genome Analyzer Pipeline Version 1.5 software was used to qualify reads based on the quality scores assigned to each base call. The qualified reads were exported to the CLC Genomic Workbench for the RNA-Seq algorithm followed by Expression analysis.
Low quality reads were discarded.  High quality reads were mapped to the Amel_4.5 genome using the RNA-seq algorthim implemented in CLC genomics Create fusion gene table = No, Create report = Yes, Create list of unmapped reads = Yes, Additional downstream bases = 500, Exon discovery = Yes, Minimum read count fusion gene table = 5, Minimum length of putative exons = 50, Minimum number of reads = 10, Maximum number of mismatches (short reads) = 2, Organism type = Eukaryote, Use annotations for gene and transcript identification = Yes, Expression level possible values: Genes, Transcripts = Genes, Use strand specific assembly = No, Unspecific match limit = 10, Additional upstream bases = 500, Use colorspace encoding = No, Minimum exon coverage fraction = 0.2, Minimum length fraction (long reads) = 0.9, Minimum similarity fraction (long reads) = 0.8, Expression value = Read Per Kilobase of exon Model value.
Data was normalized using the quantile method  and data was transformed by adding a constant of 1.
Differential gene expression was determined using Baggerleys test with a false discovery rate correction
Genome_build: Apis mellifera Amel_4.5
Supplementary_files_format_and_content: comma separated files (CSV) include RPKM values for each Sample and associated statistics

organism: Apis mellifera

source_name: Queen

growth_protocol: Apis mellifera were obtained from Betta Bees Research Limited and cultured using standard techniques in Dunedin, New Zealand. Honeybees were housed in wooden Langstroth hives or wooden nucleus boxes at three sites around Dunedin.  Queen tissue was obtained from young queens (~12 months old) that were active egg layers heading colonies. All queen-right worker bees were obtained from standard hive with a laying queen.  Queen-less worker bees were obtained by removing frames with brood and bees from queen-right hives and placing into a standard nucleus box.  Queen cells were destroyed and colonies were regularly surveyed for the presence of worker laid eggs. Ovaries were dissected from queen-less worker bees 2 - 4 weeks after establishing a queen-less hive; a sufficient period for brood to have emerged and worker laid eggs to be detected.

extract_protocol:
Total RNA was extracted using TRIZOL (Invitogen) and purified with RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bees were chilled lightly to anesthetise and ovaries were dissected, visually scored for level of ovary activity, and immediately frozen on dry ice

value: ovary

tag: ovary score

tag: Sex


title: Buccal swab, 9343114079_R06C01


title: Buccal swab, 9343114079_R01C02


title: Buccal swab, 9343114093_R04C01


title: Buccal swab, 9343114079_R04C02


title: Q1: Queen Pool 1 (RNA-seq)


title: Buccal swab, 9343114093_R05C01


title: AW2: Active Pool 2 (RNA-seq)

source_name: Queen-less worker


title: Buccal swab, 9343114093_R06C01


title: Buccal swab, 9343114093_R02C01


title: Buccal swab, 9343114093_R03C01


title: AW1: Active Pool 1 (RNA-seq)


title: W2: Worker Pool 2 (RNA-seq)

source_name: Queen-right worker


title: DT900

value: rob gene mutated strain


title: Buccal swab, 9343114079_R05C02


title: Buccal swab, 9343114093_R03C02


title: Buccal swab, 9343114093_R04C02


title: W1: Worker Pool 1 (RNA-seq)


title: Q2: Queen 2 (ChIP-seq)

description: H3K27me3 ChIP DNA

data_processing:
The sequencing was done using the Illumina HiSeq2500 technology, generating 49 bp reads.
The Illumina Genome Analyzer Pipeline Version 1.5 software was used to qualify reads based on the quality scores assigned to each base call.
Low quality reads were discarded.  All honeybee genome sequences (v4.5) in fasta format were obtained with the corresponding gff3 file from the NCBI FTP genome directory available at ftp://ftp.ncbi.nih.gov/genomes/Apis_mellifera. Bowtie (version 1.0) was then used to map the raw sequencing reads in fastq format to the honeybee reference genome version 4.5 using default parameters. The SAM (sequence alignment/map) format was converted to BAM (binary alignment/map) format using samtools (v 1.5).
The MACS version 2  (version 2.1.1.20160309) peak calling program was used to identify regions of the genome where H3K27me3 was significantly enriched in the treatment group compared to the input control. MACS2 was run using broad peak calling with an extension size of 147.  Unique peaks were identified using bedtools intersect (version v2.19.0) and differential peaks were identified using ChIPcomp (version 3.7) which allows differential peaks to be identified taking into account the biological replicates.
Genome_build: Apis mellifera Amel_4.5

extract_protocol:
Tissue was homogenized first using a 22 gauge hypodermic needle and syringe in PBS and then transferred to a dounce homogeniser for 20 strokes of the B pestle. The chromatin extraction, shearing and immunoprecipitation was performed using the Magnify ChIP Kit (Invitrogen). The chromatin was sheared using the Covaris AFA Technology. ChIP experiments were repeated in triplicate and pooled for sequencing (~1 ng/μl). Biological duplicates were created for queen ovary, active worker ovary and worker ovary. DNA for each ChIP reaction for each sample was combined and then air-dried in the speed vac and resuspended in Elution Buffer. The size and concentration of the ChIP DNA was determined with the Agilent 2100 Bioanalyser and the high sensitivity DNA kit. ChIP DNA was sequenced on an Illumina HiSeq 2000 (service provided by Beijing Genomics Institute).
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols by BGI

treatment_protocol: Bees were chilled lightly to anesthetise and ovaries were dissected, visually scored for level of ovary activity, and chromatin extracted from fresh tissue


title: Buccal swab, 9343114093_R05C02


title: QI: Queen input (ChIP-seq)

description: Input chromatin DNA


title: Q1: Queen 1 (ChIP-seq)

description: H3K27me3 ChIP DNA


title: Buccal swab, 9343114079_R02C02


title: Buccal swab, 9343114093_R02C02


title: Buccal swab, 9343114079_R06C02


title: WI: Queen-right input (ChIP-seq)

description: Input chromatin DNA


title: Buccal swab, 9343114079_R03C02


title: W2: Queen-right worker 2 (ChIP-seq)

description: H3K27me3 ChIP DNA


title: W1: Queen-right worker 1 (ChIP-seq)

description: H3K27me3 ChIP DNA


title: AI: Queen-less worker input (ChIP-seq)

description: Input chromatin DNA


title: A2: Queen-less worker 2 (ChIP-seq)

description: H3K27me3 ChIP DNA


title: Buccal swab, 9343114079_R03C01


title: A1: Queen-less worker 1 (ChIP-seq)

description: H3K27me3 ChIP DNA


title: input DNA

city: Charlestown, MA

first: Raz

last: Ben-Yair

state: MA

address: 13th st.

department: CVRC

institute: MGH

data_processing:
ChIP libraries were indexed, pooled, and sequenced on Illumina NextSeq-500 sequencers at the Broad Institute sequencing center. Reads were aligned by the Broad Genomics Platform with BWA (Li and Durbin 2009, v0.7.10) using default parameters against the Danio rerio danRer7 genome assembly ((bwa v. :0.5.9-tpx; bwa aln -q 5 -l 32 -k 2
out1.sai fastq_1 file; bwa aln -q 5 -l 32 -k 2 out2.sai fastq_2 file; bwa sampe -T -P -f
out_sam_paired.sam Danio_rerio.fasta out1.sai out2.sai fastq_1 _fastq_2). H3K4me3-
associated read peaks were called using MACS2 using the following parameters: Macs2
callpeak -t sample.bam -c WCE.bam -f BAM -g 1.5e9 -B -p 1e-3 --to-large --nomodel -
-broad --extsize 147). Quality scores of bam files were adjusted using the CleanSam
utility version 2.18.11, and files were converted to fastq and aligned against the GRCz10
Zebrafish genome assembly using bowtie2 v. 2.3.2 with default parameters, and -p 8.
Mapped reads were marked with PICARD v. 2.8.1 MarkDuplicates function with
parameters MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000
SORTING_COLLECTION_SIZE_RATIO=0.25
REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag
REMOVE_DUPLICATES=false ASSUME_SORTED=false
DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES
PROGRAM_RECORD_ID=MarkDuplicates
PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized
capture of last three ':' separated fields as numeric values>
OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false
VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
GA4GH_CLIENT_SECRETS=client_secrets.json PN:MarkDuplicates . The resulting
bam files were sorted and filtered with samtools to exclude sam flags 1796. Read count tables were generated using bedtools v. 2.26.0 (Quinlan et al. 2010) multicov -p utility versus a .bed file containing promoter regions spanning 2Kb up and downstream of each TSS (based on ENSEMBL release 89). Differential isoform expression was estimated with DESeq2 (Love et al 2014) to obtain log2
fold-change data and significance levels (p-values) between uninjured and 5 dpa
samples. IGVtools utility 'count' was used on aligned bam files to compute the average alignment over 200 base windows across the genome and generate binary tiled data (.tdf) files (Thorvaldsdottir et al. 2013).
Genome_build: danRer10
Supplementary_files_format_and_content: csv files are a DEseq2 estimations of changes in read density across 4-kb windows centered on annotated TSSs (danRer10/ENSEMBL 89) between experimental groups.
Supplementary_files_format_and_content: tdf files are binary tiled data files of aligned ChIP-Seq data from the IGVtools count utility that contain average alignment counts across the genome and can viewed in the IGV genome browser.

organism: Danio rerio

source_name: Cardiac ventricle tissue

extract_protocol: Cell purification protocol: The apical third of ventricles from 1-1.5 year old fish were extracted and dissociated into single cell suspensions using the murine neonatal heart dissociation kit (Miltenyi). Cardiomyocytes were strained on a 10 micrometer nylon mesh while other cell types in the flowthrough were discarded. The strainer with the attached cells was then processed as a cell pellet, including 30 minute fixation in methanol-free formaldehyde (1% final concentration) and washing with sterile PBS containing protease inhibitors. Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. Libraries were prepared on a BRAVO automated liquid handling platform (Agilent) as previously described (Busby M. et al., 2016).

value: heart ventricle

value: enriched cardiomyocytes

tag: experimental batch

value: mixed

value: TuAB

tag: chip antibody


title: Buccal swab, 9343114079_R04C01


title: H3K27me3_ChIPSeq_resected_rep3

tag: tissue

value: 5 days post ventricular apex resection

tag: strain

value: H3K27me3 (Cell Signaling C36B11)


title: H3K27me3_ChIPSeq_resected_rep2


title: Buccal swab, 9343114079_R05C01


title: Buccal swab, 9343114108_R02C01


title: H3K27me3_ChIPSeq_resected_rep1


title: H3K27me3_ChIPSeq_uninjured_rep3

value: uninjured


title: Buccal swab, 9343114076_R06C02


title: H3K27me3_ChIPSeq_uninjured_rep2


title: Buccal swab, 9343114079_R02C01


title: Buccal swab, 9343114079_R01C01


title: H3K27me3_ChIPSeq_uninjured_rep1


title: H3K4me3_ChIPSeq_resected_rep3

value: H3K4me3 (Cell Signaling C42D8 )


title: H3K4me3_ChIPSeq_resected_rep2

extract_protocol: The apical third of ventricles from 1-1.5 year old fish were extracted and dissociated into single cell suspensions using the murine neonatal heart dissociation kit (Miltenyi). Cardiomyocytes were strained on a 10 micrometer nylon mesh while other cell types in the flowthrough were discarded. The strainer with the attached cells was then processed as a cell pellet, including 30 minute fixation in methanol-free formaldehyde (1% final concentration) and washing with sterile PBS containing protease inhibitors. Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. Libraries were prepared on a BRAVO automated liquid handling platform (Agilent) as previously described (Busby M. et al., 2016).


title: Buccal swab, 9343114076_R03C02


title: H3K4me3_ChIPSeq_resected_rep1


title: H3K4me3_ChIPSeq_uninjured_rep2


title: Buccal swab, 9343114076_R05C02


title: H3K4me3_ChIPSeq_uninjured_rep1


title: Buccal swab, 9343114076_R02C02


title: Buccal swab, 9343114076_R04C01


title: Buccal swab, 9343114076_R01C02


title: Buccal swab, 9343114076_R03C01


title: Buccal swab, 9341679042_R03C02


title: Buccal swab, 9341679042_R05C02


title: H3K4me3_ChIPSeq_uninjured_rep3


title: Buccal swab, 9341679042_R01C02


title: Buccal swab, 9343114076_R02C01


title: Buccal swab, 9341679042_R06C01


title: Buccal swab, 9343114076_R06C01


title: Buccal swab, 9343114076_R01C01


title: Buccal swab, 9341679042_R03C01


title: Buccal swab, 9341679042_R02C01


title: Tunica albuginea_rep3

city: Adelaide

first: Katja

last: Hummitzsch

state: SA

address: Level 5, North Tce/George Street

department: Obstetrics& Gynaecology

country: Australia

institute: The University of Adelaide

description: Gene expression data from ovarian stroma

hyb_protocol: Hybridization to bovine gene 1.0 ST Arrays (Affymetrix) was performed according to Affymetrix protocols at the Ramaciotti Centre for Genomics.

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

data_processing: The data were analysed in Partek Genomics Suite (v6.5) using RMA (Robust Multi Array Algorithm, Irizarry et al 2003) background corrrection with quantile normalization, mean probe set summarization and adjustment for GC content.

organism: Bos taurus

source_name: ovarian follcular thecal tissue

label_protocol: cDNA was fragmented and labelled using the Encore Biotin Module kit (NuGEN) and used to hybridise against each array.

growth_protocol: Bovine ovaries (one per animal) were collected at a local abattoir from non-pregnant Bos taurus cows.

extract_protocol: Total RNA was extracted from thecal samples using RNeasy mini kits (Qiagen). Total RNA was extracted from the laser-dissected samples using the RNAqueous®-Micro Kit (Cat# AM1931, Thermo Fisher Scientific) procedure for LCM. All samples were treated with DNase I. And all samples were then amplified and cDNA generated with the Ovation® Pico WTA System V2 (NuGEN, San Carlos, CA, USA) from an original amount of 5 μL each of 100–200 pg/μL per  sample.

treatment_protocol: For laser capture and microarray analyses of pre-theca, interstitium and tunica albuginea, strips of ovarian cortex were cut from each ovary and placed surface-side down into cryomolds containing optimal cutting temperature (OCT) compound, frozen on dry ice and stored at −80°C. 10 μm thick serial sections were placed onto room temperature PET (polyethylene terephthalate) membrane frame slides, then fixed with 70% ethanol and stained with cresyl violet. During laser-microdissection excised samples were collected into 25 μL of Ambion lysis solution for RNA isolation (Invitrogen).

tag: compartment

value: ovarian tunica albuginea


title: Tunica albuginea_rep4


title: Buccal swab, 9341679042_R06C02


title: Buccal swab, 9341679042_R01C01


title: Tunica albuginea_rep2


title: Buccal swab, 9341679039_R04C02


title: Buccal swab, 9341679039_R06C02


title: Buccal swab, 9341679039_R05C02


title: Buccal swab, 9341679039_R03C01


title: Buccal swab, 9341679042_R04C01


title: Tunica albuginea_rep1


title: Buccal swab, 9341679039_R04C01


title: Buccal swab, 9341679039_R06C01


title: Buccal swab, 9341679037_R06C02


title: Buccal swab, 9341679039_R02C02


title: Buccal swab, 9341679042_R04C02


title: Buccal swab, 9341679037_R04C02


title: Buccal swab, 9341679037_R03C02


title: Buccal swab, 9341679039_R02C01


title: Buccal swab, 9341679042_R05C01


title: Buccal swab, 9341679042_R02C02


title: Buccal swab, 9343114076_R05C01


title: Stroma close to follicle_rep2

value: ovarian stroma close to follicle


title: Buccal swab, 9341679037_R05C01


title: Stroma close to follicle_rep3


title: Buccal swab, 9341679039_R03C02


title: Buccal swab, 9341679039_R01C02


title: Theca_small healthy follicle_rep5

value: ovarian follicular theca


title: Stroma close to follicle_rep4


title: Theca_small healthy follicle_rep6


title: Stroma close to follicle_rep1


title: Interstitial stroma_rep2

value: ovarian interstitial stroma


title: Buccal swab, 9341679037_R01C02

value: buccal epithelial cells

value: M


title: Buccal swab, 9341679037_R04C01


title: Buccal swab, 9341679037_R05C02

value: F


title: Theca_small healthy follicle_rep4

value: ovary


title: T51 miR-215 TICs 3

description: gene expression intensities

scan_protocol: Arrays were incubated at 48°C, 60 rpm for 16 hours. Then arrays were stained and washed with the GeneChip® Hybridization Wash and Stain kit (Affymetrix, High Wycombe, United Kingdom) using the Fluidic script FS450_0002. GeneChip® Affymetrix Human Gene 2.0 ST Array (Affymetrix, High Wycombe, United Kingdom) were performed according to manufacturers user guide FlashTag Biotin HSR RNA  Labeling Kit For Affymetrix® Human Gene 2.0 ST Arrays

data_processing: The data were imported, normalized and summarized to transcript cluster level using Partek GS software. We used GC RMA method with quantile normalization.

source_name: T51 miR-215 TICs

treatment_protocol: Lentiviral transduction of miR-215-expression or corresponding control vector via ready-to-use lentiviral particles (Biosettia)

value: colorectal cancer

tag: culture type

value: patient-derived sphere culture

value: miR-215 vector

tag: vector

value: LV miR-215 expression (Biosettia)


title: T51 miR-215 TICs 2

description: gene expression intensities

tag: patient

tag: treatment


title: T51 miR-215 TICs 1

description: gene expression intensities


title: Theca_small healthy follicle_rep3


title: Buccal swab, 9341679039_R01C01


title: Interstitial stroma_rep4


title: T51 control TICs 3

description: gene expression intensities

source_name: T51 Ctrl TICs

value: Ctrl vector

value: LV control (Biosettia)


title: Theca_small healthy follicle_rep1


title: T51 control TICs 1

description: gene expression intensities


title: Theca_small healthy follicle_rep2


title: Interstitial stroma_rep3


title: T51 control TICs 2

description: gene expression intensities


title: Buccal swab, 9341679037_R03C01


title: Interstitial stroma_rep1


title: Buccal swab, 9341679037_R02C02


title: Tr_Pos_2

city: Rotterdam

first: Qiuwei

last: Pan

address: Wytemaweg 80

institute: Erasmus University Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Perform alignments with HISAT2 to the reference. HISAT2 uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons.
Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used. In RNA-seq, FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, is the most common method of estimating gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments. HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode. The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.
Genome_build: mm8
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

source_name: liver cancer organoid cells

extract_protocol:
Intact sorted cells can be stored in 6μl Lysis Buffer from SMART-Seq™ v4 kit, after the volume measurement, fresh cells are cracked with SMARTSeq
The cDNA samples were sheared by the Covaris system, and then the sheared fragments is end-repaired, A-tailed, and ligated to sequencing adaptors. A size selection of about 200 bp is performed before the PCR enrichment

value: Liver cancer

tag: genotype


title: Tr_Pos_1


title: Tr_Pos_3


title: Tr_Neg_3


title: Tr_Neg_1


title: Tr_Neg_2


title: Buccal swab, 9341679037_R02C01

tag: gender


title: Co_Pos_2


title: Buccal swab, 9341679037_R01C01


title: Co_Pos_3


title: Buccal swab, 9341679033_R03C01


title: Buccal swab, 9341679033_R05C02


title: Co_Pos_1


title: Buccal swab, 9341679100_R03C02


title: Buccal swab, 9341679033_R06C01


title: Buccal swab, 9341679100_R05C02


title: Buccal swab, 9341679033_R04C02


title: Co_Neg_2


title: Co_Neg_3


title: Co_Neg_1


title: Buccal swab, 9341679033_R02C02


title: Buccal swab, 9341679033_R02C01


title: Buccal swab, 9341679100_R06C02


title: Buccal swab, 9341679033_R06C02


title: Buccal swab, 9341679100_R06C01


title: Buccal swab, 9341679100_R02C02


title: Buccal swab, 9341679033_R05C01


title: RNA_seq_SAL_rep6

city: La Jolla

first: Chi-Yu

last: Lai

state: California

address: 10010 North Torrey Pines Road

institute: Salk Institute

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq were performed as described in Amodeo and Lai et al., 2019
Adapters were trimmed using Trim Galore v0.4.0
Trimmed reads were aligned to the mm10 genome using STAR version STAR_2.5.1b
Gene counts were estimated using quantmode in STAR version STAR_2.5.1b
Gene expression levels in TPMs were estimated using RSEM v1.2.31
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using RSEM v1.2.31

source_name: whole tissue from frontal cortex

growth_protocol: Male C57BL/6J mice were singly housed for 3 consecutive days. On the fourth day two, 10-week old female mice were introduced to the age-matched males and left undisturbed for three days. After three days females were singly housed for the remainder of pregnancy. Control mice received 0.9% saline injections. Dams (n=11), were left undisturbed until 5 days after birth of offspring. Pups remained with mothers until weaning on postnatal day (PD24) and then were group housed by sex and prenatal group

extract_protocol:
The frontal cortices of MIA offspring were harvested on PD 189 for RNA-Seq analysis (Poly(I:C) = 9 and vehicle = 8). Animals were anesthetized with isoflurane and decapitated. The brain was immediately extracted and whole frontal cortex was obtained by slicing the adult brains coronally at Bregma 1 mm, and dissecting the frontal cortical tissue, being careful to avoid contamination with olfactory or putamen regions. Finally, the frontal cortex was flash frozen on dry ice and stored at -80oC. Total RNA was then extracted by using RNeasy Mini kit with DNAse I treatment (Qiagen 74104).
Strand-specific cDNA libraries were constructed by selecting poly-adenylated mRNA transcripts using Truseq Stranded mRNA LT kit (Illumina, RS-122-2101 and RS-122-2102). Libraries were deeply sequenced using Illumina HiSeq 2500, generating 25 million reads (100 bp, single end sequencing).

treatment_protocol: Dams were checked daily for the presence of a seminal plug and then recorded as gestational day (G) 0.5. On G12.5 female mice received an intraperitoneal (ip) injection of 20 mg/kg Poly(I:C) acid potassium salt (P9582, Lot number 034M4086V, Sigma-Aldrich, St. Louis, MO) in 0.9% saline.

value: brian

value: postnatal 189 days

value: Saline

value: male


title: RNA_seq_SAL_rep5


title: RNA_seq_SAL_rep7


title: RNA_seq_SAL_rep4


title: RNA_seq_SAL_rep3


title: Buccal swab, 9341679033_R03C02


title: Buccal swab, 9341679100_R04C01


title: Buccal swab, 9341679091_R05C02


title: RNA_seq_SAL_rep1


title: Buccal swab, 9341679100_R04C02


title: Buccal swab, 9341679100_R03C01


title: RNA_seq_PIC_rep9


title: RNA_seq_SAL_rep8


title: RNA_seq_SAL_rep2


title: Buccal swab, 9341679100_R02C01


title: RNA_seq_PIC_rep7


title: Buccal swab, 9341679100_R01C01


title: Buccal swab, 9341679100_R01C02


title: Buccal swab, 9341679091_R04C02


title: RNA_seq_PIC_rep6


title: RNA_seq_PIC_rep4


title: RNA_seq_PIC_rep5


title: Buccal swab, 9341679033_R01C01


title: Buccal swab, 9341679091_R06C02


title: RNA_seq_PIC_rep3


title: Buccal swab, 9341679091_R02C02


title: RNA_seq_PIC_rep8


title: Buccal swab, 9341679090_R06C02


title: RNA_seq_PIC_rep2


title: RNA_seq_PIC_rep1


title: Buccal swab, 9341679091_R06C01


title: B6 WT 3 [997]

city: Austin

first: Joseph

middle: D

last: Dekker

state: TX

address: 2506 Speedway Blvd, NMS 1.264

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
cDNA was analyzed by deep sequencing using Illumina sequencing technology.
FASTQ files were aligned to the mouse genome (mm9, NCBI Build 37) using TopHat2
Gene expression profiles for the individual samples were calculated with Cufflinks as RPKM values
Cd19cre; Foxp1 samples were normalized to controls and statistical analysis was performed using Cuffdiff
Genome_build: mm9, NCBI Build 37
Supplementary_files_format_and_content: FPKM

source_name: B6 WT_CD43- splenocytes

extract_protocol:
Cells were magentically sorted by CD43 depletion, and total RNA was collected and converted to cDNA by standard procesures
Library preparation employed the Nextera DNA Library Preparation kit from Illumina (San Diego, CA)

tag: strain background

value: wild type

value: CD43- splenocytes


title: Buccal swab, 9341679091_R05C01

value: buccal epithelial cells

tag: age


title: B6 WT 2 [995]

tag: cell type


title: Buccal swab, 9341679091_R02C01


title: CD19cre cKO 4 [994]

source_name: CD19creFoxp1 cKO_CD43- splenocytes

tag: genotype/variation

value: CD19creFoxp1 cKO


title: Buccal swab, 9341679100_R05C01

value: F


title: Buccal swab, 9341679091_R03C01


title: CD19cre cKO 3 [547]


title: Buccal swab, 9341679091_R04C01

value: M


title: Buccal swab, 9341679090_R05C02


title: Buccal swab, 9341679091_R03C02


title: CD19cre cKO 2 [546]


title: B6 WT 1 [545]


title: CD19cre cKO 1 [000]


title: Illumina.UNT_9576

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

description:
re-analysis of GSM2599715
FINAL_master_list_of_gene_counts_MIN.sense.Truseq.txt.gz

data_processing:
RNA-Seq data were aligned to the mouse genome build mm9 by GSNAP.v2018-07-04.
Data were normalized at the gene-level, using a resampling strategy, the code is available at https://github.com/itmat/Normalization (-v0.8.5b-beta)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: Liver

growth_protocol: Twelve-week old male C57/B6J mice were acquired from Jackson Labs.

extract_protocol:
Mice were sacrificed and liver samples were dissected and snap-frozen in liquid nitrogen. RNA was extracted from the liver tissue using TRIzol and Qiagen Rneasy Kit, according to manufacturers’ protocols.
Illumina TruSeq: Total RNA from each liver sample was prepared for sequencing using the Illumina: TruSeq Stranded mRNA Sample Preparation Kit. 200 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 2500. Depths of 16-34 million paired-end 125 bp reads were generated for each sample. (GSE98562)    Takara Bio SMARTer: Total RNA from each liver sample was prepared for sequencing using the Takara Bio SMARTer: SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. 1.7-2.6 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 4000. Depths of 30-44 million paired-end 150 bp reads were generated for each sample. The libraries were reproduced to repeat the experiment and ensure reproducibility.    Takara Bio SMART-Seq: Total RNA from each liver sample was prepared for sequencing using the Takara Bio SMART-Seq: SMART-Seq® v4 Ultra® Low Input RNA Kit. 0.8-1.3 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 4000. Depths of 15-30 million paired-end 150 bp reads were generated for each sample.

treatment_protocol: Four hours prior to tissue collection, mice were treated with either 20 µg/Kg of IL-1B or saline.

value: saline

value: Twelve-week


title: Illumina.UNT_9575

description:
re-analysis of GSM2599713
FINAL_master_list_of_gene_counts_MIN.sense.Truseq.txt.gz


title: Illumina.ILB_9582

description:
re-analysis of GSM2599727
FINAL_master_list_of_gene_counts_MIN.sense.Truseq.txt.gz

value: IL-1 Beta


title: Illumina.ILB_9583

description:
re-analysis of GSM2599729
FINAL_master_list_of_gene_counts_MIN.sense.Truseq.txt.gz


title: Buccal swab, 9341679091_R01C01


title: Buccal swab, 9341679090_R04C01


title: Buccal swab, 9341679090_R01C02


title: Illumina.ILB_9579

description:
re-analysis of GSM2599725
FINAL_master_list_of_gene_counts_MIN.sense.Truseq.txt.gz


title: Buccal swab, 9341679090_R06C01


title: Buccal swab, 9341679090_R02C02


title: bmpSb_2

city: Houston

first: Aryeh

last: Warmflash

address: 6100 Main St

institute: Rice University

data_processing:
Reads were aligned to the genome using STAR-2.6.1d software with the 2-pass procedure
STAR output was quantified using RSEM-1.3.1.  Alignment and quantification were performed separately for each replicate.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Excel file with Fragments per kilobase per transcript per million (FPKM) values obtained from RSEM for each replicate in each sample.

source_name: BMP+SB treated hESCs

growth_protocol: hESCs were grown in the chemically defined medium mTeSR1 in tissue culture dishes and kept at 370C, 5% CO2

extract_protocol:
Total RNA was extracted with Invitrogen RNAqueous Micro Kit.
Illumina paired end 150

treatment_protocol: hESCs in Sample1 were kept in mTeSR1 for 48h in the growth conditions. hESCs in Samples 2, 3 and 4 were also kept in mTeSR1 but treated with 10ng/ml BMP4, 10ng/ml BMP4 + 4μM IWP2,  and 10ng/ml BMP4 + 10μM SB431542 respectively for 48h.

value: hESCs


title: bmpSb_1


title: Buccal swab, 9341679090_R03C01


title: Buccal swab, 9341679090_R03C02


title: Buccal swab, 9341679090_R04C02


title: Buccal swab, 9341679090_R01C01


title: bmpIwp2_2

source_name: BMP+IWP2 treated hESCs


title: Buccal swab, 9341679090_R05C01


title: Buccal swab, 9341679088_R06C02


title: Buccal swab, 9341679088_R02C02


title: bmp_2

source_name: BMP-treated hESCs


title: Buccal swab, 9341679088_R01C02

source_name: buccal swab genomic DNA


title: media_2

source_name: pluripotent hESCs


title: Buccal swab, 9341679090_R02C01


title: media_1


title: RNAseq_CS_rep100

city: Koto-ku

first: Osamu

last: Gotoh

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation For Cancer Research

data_processing:
Illumina Casava1.8.2 software used for basecalling
Sequenced reads were mapped to hg19 using bowtie2-2.2.3.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using RSEM-1.3.0.
Rsem.genes.results file has columns named TPM and FPKM. Each columns represent Transcripts Per Million mapped reads and Fragments Per Kilobase of transcript and Million mapped reads for each gene.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

source_name: ovarian carcinosarcoma

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen).
Stranded mRNA HT Sample Prep Kit (Illumina) was used with 200 ng of total RNA for the construction of sequencing libraries.

tag: anatomical site

value: ovary

value: female


title: Buccal swab, 9341679088_R04C01


title: RNAseq_CS_rep99

tag: Sex


title: Buccal swab, 9341679088_R04C02


title: RNAseq_CS_rep98


title: Buccal swab, 9341679088_R03C01


title: Buccal swab, 9341679088_R05C01


title: RNAseq_CS_rep97


title: RNAseq_CS_rep96


title: Buccal swab, 9341679088_R01C01


title: RNAseq_CS_rep95


title: Illumina.UNT_9574

description:
re-analysis of GSM2599711
FINAL_master_list_of_gene_counts_MIN.sense.Truseq.txt.gz


title: Buccal swab, 9343114058_R05C02


title: RNAseq_CS_rep94


title: Buccal swab, 9343114058_R06C01


title: Buccal swab, 9343114058_R01C02


title: RNAseq_CS_rep92


title: Buccal swab, 9343114058_R05C01


title: RNAseq_CS_rep91


title: Buccal swab, 9341679088_R05C02


title: Buccal swab, 9343114058_R02C02


title: RNAseq_CS_rep90


title: Buccal swab, 9343114058_R04C01


title: Buccal swab, 9343114058_R01C01


title: Buccal swab, 9341679088_R03C02


title: Buccal swab, 9343114058_R03C01


title: RNAseq_CS_rep88


title: bmpIwp2_1


title: Buccal swab, 9343114028_R04C02


title: Buccal swab, 9343114028_R06C02


title: RNAseq_CS_rep86

source_name: uterin carcinosarcoma

value: uterus


title: RNAseq_CS_rep85


title: Buccal swab, 9343114028_R03C02


title: RNAseq_CS_rep87


title: RNAseq_CS_rep84


title: Buccal swab, 9343114028_R05C02


title: bmp_1


title: RNAseq_CS_rep83


title: RNAseq_CS_rep89


title: Buccal swab, 9343114028_R02C02


title: RNAseq_CS_rep82


title: Buccal swab, 9343114028_R05C01


title: RNAseq_CS_rep81


title: RNAseq_CS_rep80


title: Buccal swab, 9343114028_R06C01


title: Buccal swab, 9343114028_R03C01


title: Buccal swab, 9343114058_R04C02


title: Buccal swab, 9343114058_R03C02


title: RNAseq_CS_rep78


title: RNAseq_CS_rep79


title: RNAseq_CS_rep75


title: RNAseq_CS_rep77


title: RNAseq_CS_rep76


title: RNAseq_CS_rep93


title: Buccal swab, 9343114028_R01C01


title: Buccal swab, 9343114028_R02C01


title: Buccal swab, 9343114025_R06C02


title: RNAseq_CS_rep74


title: Buccal swab, 9343114025_R05C02


title: Buccal swab, 9343114028_R04C01


title: RNAseq_CS_rep73


title: RNAseq_CS_rep72


title: RNAseq_CS_rep71


title: RNAseq_CS_rep70


title: RNAseq_CS_rep68


title: RNAseq_CS_rep67


title: RNAseq_CS_rep69


title: RNAseq_CS_rep66


title: RNAseq_CS_rep65


title: Buccal swab, 9343114028_R01C02


title: Buccal swab, 9343114025_R03C02


title: RNAseq_CS_rep63


title: Buccal swab, 9343114058_R02C01


title: Buccal swab, 9343114013_R03C02


title: Buccal swab, 9343114025_R04C01


title: RNAseq_CS_rep62


title: Buccal swab, 9343114013_R05C02


title: Buccal swab, 9343114013_R04C02


title: RNAseq_CS_rep61


title: Buccal swab, 9343114025_R01C02


title: Buccal swab, 9343114013_R04C01


title: RNAseq_CS_rep60


title: Buccal swab, 9343114025_R05C01


title: Buccal swab, 9343114025_R02C01


title: RNAseq_CS_rep59


title: Buccal swab, 9343114025_R03C01


title: Buccal swab, 9343114013_R02C02


title: Buccal swab, 9343114013_R01C02


title: RNAseq_CS_rep64


title: Buccal swab, 9343114025_R01C01


title: Buccal swab, 9343114013_R06C01


title: Buccal swab, 9343114013_R03C01


title: Buccal swab, 9343114025_R04C02


title: RNAseq_CS_rep56


title: RNAseq_CS_rep53


title: RNAseq_CS_rep54


title: RNAseq_CS_rep55


title: RNAseq_CS_rep52


title: RNAseq_CS_rep51


title: RNAseq_CS_rep50


title: Buccal swab, 9343114013_R01C01


title: Buccal swab, 101130760108_R03C02

extract_protocol: Genomic DNA was extracted using the Gentra Puregene Buccal Cell Kit (Qiagen #158845) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research).


title: Buccal swab, 101130760109_R03C01


title: RNAseq_CS_rep47


title: Buccal swab, 101130760108_R05C02


title: RNAseq_CS_rep48


title: Buccal swab, 101130760108_R06C02


title: RNAseq_CS_rep46


title: Buccal swab, 9343114025_R02C02


title: Buccal swab, 101130760109_R05C01


title: Buccal swab, 101130760108_R02C01


title: RNAseq_CS_rep57


title: RNAseq_CS_rep44


title: Buccal swab, 101130760108_R03C01


title: Buccal swab, 101130760108_R02C02


title: Buccal swab, 9343114013_R05C01


title: Buccal swab, 101130760041_R05C02


title: RNAseq_CS_rep58


title: RNAseq_CS_rep41


title: Buccal swab, 101130760108_R04C01


title: Buccal swab, 101130760041_R04C02


title: Buccal swab, 101130760041_R04C01


title: RNAseq_CS_rep49


title: RNAseq_CS_rep40


title: RNAseq_CS_rep39


title: Buccal swab, 101130760041_R05C01


title: Buccal swab, 101130760041_R06C01


title: Buccal swab, 101130760040_R06C02


title: Buccal swab, 101130760108_R06C01


title: Buccal swab, 101130760109_R06C01


title: Buccal swab, 9343114013_R02C01


title: RNAseq_CS_rep36


title: RNAseq_CS_rep45


title: Buccal swab, 101130760041_R01C01


title: RNAseq_CS_rep43


title: RNAseq_CS_rep34


title: Buccal swab, 101130760041_R02C01


title: RNAseq_CS_rep33


title: RNAseq_CS_rep35


title: RNAseq_CS_rep32


title: Buccal swab, 101130760040_R02C02


title: RNAseq_CS_rep38


title: RNAseq_CS_rep29


title: Buccal swab, 101130760040_R06C01


title: RNAseq_CS_rep30


title: RNAseq_CS_rep31


title: Buccal swab, 101130760041_R02C02


title: Buccal swab, 101130760040_R04C02


title: RNAseq_CS_rep28


title: Buccal swab, 101130760040_R05C02


title: RNAseq_CS_rep27


title: RNAseq_CS_rep26


title: RNAseq_CS_rep42


title: Buccal swab, 101130760040_R05C01


title: RNAseq_CS_rep25


title: RNAseq_CS_rep37


title: RNAseq_CS_rep24


title: Buccal swab, 101130760040_R02C01


title: RNAseq_CS_rep23


title: RNAseq_CS_rep22


title: Buccal swab, 101130760039_R01C02


title: Buccal swab, 101130760040_R04C01


title: RNAseq_CS_rep20


title: Buccal swab, 101130760041_R01C02


title: RNAseq_CS_rep17


title: RNAseq_CS_rep21


title: Buccal swab, 101130760039_R02C02


title: RNAseq_CS_rep19


title: RNAseq_CS_rep16


title: Buccal swab, 101130760039_R06C02


title: Buccal swab, 101130760039_R03C02


title: RNAseq_CS_rep15


title: Buccal swab, 101130760039_R05C01


title: RNAseq_CS_rep13


title: Buccal swab, 101130760039_R06C01


title: Buccal swab, 101130760030_R01C01


title: Buccal swab, 101130760039_R05C02


title: Buccal swab, 101130760019_R03C02


title: RNAseq_CS_rep12


title: RNAseq_CS_rep14


title: Buccal swab, 101130760030_R03C02


title: Buccal swab, 101130760030_R04C02


title: RNAseq_CS_rep11


title: Buccal swab, 101130760030_R05C02


title: RNAseq_CS_rep9


title: RNAseq_CS_rep8


title: RNAseq_CS_rep7


title: Buccal swab, 101130760019_R06C02


title: Buccal swab, 101130760030_R02C02


title: Buccal swab, 100973330058_R02C01


title: Buccal swab, 100973330058_R06C02


title: Buccal swab, 101130760030_R04C01


title: RNAseq_CS_rep4


title: Buccal swab, 100973330058_R03C01


title: RNAseq_CS_rep3


title: RNAseq_CS_rep18


title: Buccal swab, 101130760019_R02C02


title: RNAseq_CS_rep2


title: Buccal swab, 101130760019_R01C01


title: Buccal swab, 100973330058_R05C02


title: Buccal swab, 100973330058_R04C02


title: RNAseq_CS_rep6


title: Buccal swab, 100973330053_R03C02


title: Buccal swab, 100973330058_R02C02


title: Buccal swab, 100973330053_R06C01


title: RNAseq_CS_rep10


title: Buccal swab, 100973330053_R04C02


title: Buccal swab, 100973330053_R05C02


title: RNAseq_CS_rep5


title: Buccal swab, 101130760030_R01C02


title: Buccal swab, 100973330053_R04C01


title: Buccal swab, 100973330052_R02C02


title: CFPAC1.HNF1BKO.H3K27Ac.Rep1

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: Chromatin IP against H3K27ac

data_processing:
Reads were pre-processing (filtering, quality trimming and adapter clipping) using Trimmomatic (version 0.38),  then single-end 50-bp reads were aligned to human genome build GRCh38/hg38 using Bowtie2 v2.2.6 with “–very-sensitive” preset of parameters. Reads that did not align to nuclear genome or aligned to mitocondrial genome were removed. PCR duplicates were removed using samtools.
Peak calling was performed using MACS2 (version 2.1.0.20150731) with the “--nomodel”, “--extsize 200” and “--qvalue 0.05” flags and arguments. Each IP was compared to input DNA.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.narrowPeak, list of the peaks called by MACS2

growth_protocol: IMDM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

extract_protocol: ChIP lysates were generated from 50x10^6 cells. Cells were either fixed in 1% formaldehyde for 10min (for FOXA2, HOXB8, JUNB and FOXA3 ChiP-seq) or with a double cross-linking protocol consisting in 45 minutes of 2 mM DSG followed by 10 minutes in 1% formaldehyde for FOS ChIP-seq.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

treatment_protocol: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961) carring the expression of wt Cas9 and a guide RNA targeting HNF1B gene

tag: cell line

value: CFPAC1 genome-edited clonal cell line

value: Pancreatic Ductal Adenocarcinoma (PDAC) cell line

tag: antibody

value: Anti-H3K27ac (Abcam ab4729 Lot. GR3187597-1)


title: Buccal swab, 100973330031_R05C02


title: Buccal swab, 100973330031_R03C02


title: Buccal swab, 100973330053_R06C02


title: Buccal swab, 100973330052_R01C02


title: Buccal swab, 100973330052_R01C01


title: Buccal swab, 100973330052_R06C02


title: CFPAC1.HNF1BWT.H3K27Ac.Rep2

description: Chromatin IP against H3K27ac

treatment_protocol: Isolation of clonal cell line by dilution of CFPAC1 cells infected with lentiCRIPSv2 plasmid (Addgene #52961)

value: CFPAC1 clonal cell line


title: Buccal swab, 101130760044_R06C02


title: Buccal swab, 101130760044_R06C01


title: Buccal swab, 100973330052_R04C01


title: CFPAC1.HNF1BWT.H3K27Ac.Rep1

description: Chromatin IP against H3K27ac


title: Buccal swab, 101130760044_R05C01


title: Buccal swab, 100973330031_R06C01


title: Buccal swab, 101130760044_R03C02


title: Buccal swab, 100973330031_R02C02


title: Buccal swab, 100973330052_R06C01


title: Buccal swab, 101130760044_R03C01


title: Buccal swab, 100973330031_R01C01


title: CFPAC1.HNF1BKO.ChIP.FOXA2

description: Chromatin IP against FOXA2

value: Anti-FOXA2 (Antibody sc-6554 Lot. A0715)


title: Buccal swab, 101130760033_R04C02


title: Buccal swab, 101130760044_R04C02


title: Buccal swab, 101130760033_R03C02


title: Buccal swab, 100973330053_R01C02


title: CFPAC1.HNF1BKO.H3K27Ac.Rep2

description: Chromatin IP against H3K27ac


title: CFPAC1.ChIP.FOXA2.Rep1

description: Chromatin IP against FOXA2


title: PANC1.ChIP.FOXA2.Rep1

description: Chromatin IP against FOXA2

growth_protocol: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep

value: original PANC1 cell line


title: CFPAC1.ChIP.FOS

description: Chromatin IP against FOS

value: original CFPAC1 cell line

value: Anti-FOS (Antibody Sigma HPA018531 - Lot E106326)


title: CFPAC1.ChIP.JUNB

description: Chromatin IP against JUNB

value: Anti-JUNB (Antibody sc73X Lot K0311)


title: RNAseq_CS_rep1


title: inducible DNp63-expressing LK2 cells with doxycycline_replicate1 [OE_3]

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing reads were aligned to the human reference genome hg19/GRCh37 using Tophat (v2.1).
Read counts per RefGene symbol on the USCS database was estimated using the htseq-count function in SAMtools.
The read counts were normalized using DEseq2 normalization algorithm.
Genome_build: hg19/GRCh37 RefGene
Supplementary_files_format_and_content: Text files

growth_protocol: LK2 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.

treatment_protocol: For inducible DNp63-expressing LK2 cells, cells were treated with or without 2 μg/ml doxycycline for 6 days.

value: lung squamous cell carcinoma (LUSC) cell lines

tag: doxycycline treatment

value: Yes


title: inducible DNp63-expressing LK2 cells with doxycycline_replicate2 [OE_4]


title: CFPAC1.WT.ChIP.FOXA2

description: Chromatin IP against FOXA2

treatment_protocol: Isolation of clonal cell line by dilution of CFPAC1 cells electroporated with plasmid pSpCas9-2A-GFP (px458; Addgene #48138)


title: inducible DNp63-expressing LK2 cells without doxycycline_replicate2 [CTRL_4]

value: No


title: DNp63-overexpressed LK2 cells_2 [OE_2]

source_name: DNp63-overexpressed LK2 cells


title: DNp63-overexpressed LK2 cells_1 [OE_1]


title: GFP-overexpressed LK2 cells_2 [CTRL_2]

source_name: GFP-overexpressed LK2 cells


title: inducible DNp63-expressing LK2 cells without doxycycline_replicate1 [CTRL_3]


title: Buccal swab, 101130760033_R04C01

value: buccal epithelial cells

value: F


title: Brn2 MNase ChIP input for NCI-H520

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
Peaks were identified by MACS
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: BED

growth_protocol: Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
For H3K27ac, Sox2 and p63 ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies. For Brn2 ChIP, cells were cross-linked with disuccinimidyl glutarate and formaldehyde. Nuclei were extracted, digested with micrococcal nuclease and sonicated. Then, histone-DNA complexes were isolated with ant-Brn2 antibody.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 500 with paired-end 75bp reads.

tag: chip antibody


title: GFP-overexpressed LK2 cells_1 [CTRL_1]


title: Buccal swab, 101130760033_R01C02


title: Brn2 MNase ChIP input for LK2


title: Buccal swab, 101130760033_R02C01


title: Buccal swab, 101130760033_R01C01


title: Brn2 MNase ChIP for NCI-H520

value: Brn2 (Cell Signaling, #12137)


title: Buccal swab, 100973330053_R02C02

value: M


title: Buccal swab, 101130760026_R06C02