title: Duodenum tissue 35 days group 2 replicate 1

city: BAREILLY

first: ANAND

last: PRAKASH

state: UTTAR PRADESH

address: IZATNAGAR

department: CARI

country: India

institute: ICAR

description: Differential gene expression in coloured broilers divergently selected for RFI

hyb_protocol: For chip hybridization, 1.65 μg of Cy3 labelled cRNAs was fragmented at 60 °C for 30 min in a reaction volume of 55 μl containing 25× Agilent Fragmentation buffer and 10×Agilent Gene Expression Blocking agent. On completion, 55 μl of 2×HI-RPM hybridization buffer (Agilent) was added. Out of total volume, 100 μl of samples were hybridized on chicken (V2) Gene Expression Microarray 4x44K for 17 h at 65 °C in a rotating hybridization chamber (Agilent). Following hybridization, microarray slides were washed with Gene Expression wash buffer 1 (Agilent) for 1 min at room temperature and with Gene Expression wash buffer 2 (prewarmed at 37 °C for overnight) at 37 °C for 1 min.

scan_protocol: The slides were scanned with an Agilent SureScan Microarray Scanner. The scanned images were analysed with Agilent Feature Extraction Software 11.0.1.

data_processing: Data generated were analysed by GeneSpring software version 13.0. Paired t-test (p < = 0.05, logFold change (FC)> = 2.0) was used to find differentially expressed genes.

organism: Gallus gallus

source_name: Duodenum tissue of 35 days old low FE broiler

label_protocol: A 200 ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled cRNA for hybridization. One-Color Low input Quick Amp labelling Kit (Agilent) was used for labeling followed by cleaning using RNeasy column purification kit (Qiagen). Dye integration and cRNA concentration were determined with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Each of experimental chicks were housed in individual cages fixed with individual feeder and waterer to provide feed and water ad libitum. In each of the cage 100 W bulbs were used to provide adequate temperature. The cages were housed in brooder house of experimental broiler farm (EBF) to maintain brooding temperature inside the cages. RFI trial was conducted for 35 days. Each chick were provided standard quality of starter ration up to 4 week and thereafter, finisher ration was given.

extract_protocol: Total RNA was extracted using the RNeasy microarray Tissue mini Kit (Qiagen, USA) following manufacturers instruction. 50 mg of tissue was taken and was homogenized in QIAzol lysis reagent followed by chloroform extraction. After several washings with RW1 and RPE buffer, the flow through was discarded and the RNA was eluted in RNAse free water. The samples belonging to the same group were then diluted to the same concentration and pooled together prior to library construction. As a final step, RNA integrity was assessed using a 2100 Bio-analzyer (Agilent, Foster City, CA).

value: Duodenum

value: Both Female

tag: age

value: 35 days old


title: Liver tissue 35 days group 2 replicate 1

status: Public on Jul 12 2018

type: RNA

molecule: total RNA

source_name: Liver tissue of 35 days old low FE broiler

tag: tissue

value: Liver

tag: gender

tag: rfi

value: low


title: Duodenum tissue 35 days group 1 replicate 2

source_name: Duodenum tissue of 35 days old high FE broiler


title: Duodenum tissue 35 days group 1 replicate 1


title: Duodenum tissue 35 days group 2 replicate 2

value: 1 Male and 1 Female


title: Liver tissue 35 days group 1 replicate 2

source_name: Liver tissue of 35 days old high FE broiler

value: high


title: Liver tissue 35 days group 1 replicate 1


title: Liver tissue 35 days group 2 replicate 2


title: ChIPseq_H2B_Dot1OE_NKI6151_2

type: SRA

city: Amsterdam

first: Tessy

last: Korthout

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: The Netherlands Cancer Institute

library_source: genomic

data_processing:
mapping of the reads to reference genome
filter for mapping quality < 37
merge BAM files of replicate samples
extend each read with 150 bp
normalize for sequencing depth
convert to bigwig
Genome_build: R64-2-1
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in YEPD.

extract_protocol:
Cells were cross-linked for 20 min with of the volume of freshly prepared Fix Solution containing 1% formaldehyde. Cells were washed once in cold TBS with 0.2 mM PMSF and lysed by bead beating in 200 μl breaking buffer with Zirconia/silica beads. The lysate was washed twice in FA buffer and sonicated using the Bioruptor PICO for 10 min.
Libraries were prepared using the KAPA HTP Library Preparation Kit (Illumina), using Illumina-provided adapters at 200nM. After eleven PCR cycles, cleanup and pooling was as described above. After 11 PCR cycles, a size selection cleanup was performed using 0.5X Agencourt AMPure XP PCR Purification beads to get rid of large fragments due to crosslinking DNA. The supernatant of the 0.5X cleanup was used to catch the smaller fragments; this supernatant was cleaned up 2 times with 1X beads to remove primers present in the libraries.

tag: genetic background strain

tag: strain

tag: genotype

tag: chip antibody

value: H2B, Active Motif, Catalog# 39238, Lot# 03108001


title: ChIPseq_H2B_Dot1OE_NKI6151_1


title: STOMP sample 6-0191-03

type: genomic

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array at 50C for 17 hours according to the manufacturer's instructions. DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array at 50C for 17 hours according to the manufacturer's instructions.

scan_protocol: The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000. The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
To achieve comprehensive CNV calling, we used three separate algorithms to detect CNVs; Birdsuite, iPattern, and Genotyping Console. CNVs were considered stringent calls if detected by two or more of the algorithms used. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
Genotype Call (SNP call): AA, AB, BB, and NoCall
To achieve comprehensive CNV calling, we used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs14. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
Genotype Call (SNP call): AA, AB, BB, and NoCall

label: biotin

organism: Homo sapiens

source_name: whole blood

label_protocol:
As per manufacturer (Affymetrix)
As per manufacturer (Affymetrix)

growth_protocol:
DNA was extracted from whole blood.
Cell lines were grown according to standard conditions.

extract_protocol: Lymphocyte isolation by the Ficoll separation procedure followed by cryopreservation and storage in liquid nitrogen and cell lines were established using EBV-transformation.

value: Male

tag: ethnicity

value: whole blood

tag: diagnosis

value: pediatric obesity


title: Small RNAs from ovaries of EY03241 transgenic strain, technical rep2

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

library_source: transcriptomic

data_processing:
The reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect matching.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the raw counts of clipped read occurrences in each library.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogen) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

value: ovaries

tag: strain/background

tag: technical replicate


title: PB1438Pop5

city: Atlanta

first: Greg

last: Gibson

state: GA

address: 950 Atlantic Dr. NW

department: Biological Sciences

country: USA

institute: Georgia Institute of Technology

data_processing:
Paired end 100bp reads were mapped to hg38, using Tophat2 to generate bam files
HTseq (version) was then used to assess read counts at the gene level in each gene
The mapped libraries were then normalized accounting for differences in size and dispersion using the default parameters of EdgeR for gene abundance levels)
Read counts were converted to the log base 2 scale and principal component variance analysis (PCVA) in JMP-Genomics (version 8.0) was used to assess the contributions of Individual, Batch, Cell Population, and Tissue to the weighted average variance explained by the first 3 PCs
Since Batch explained 53% of the variance, in order to maximize the contrasts across the populations, we elected to use remove the batch effect using the SNM (supervised normalization of microarray) method 54 with Cell Population as the Biological variable and Batch as the adjustment variable with the Rm=True option
Genome_build: hg38
Supplementary_files_format_and_content: CSV file containing log2 of normalized read counts (expression values).

source_name: ASC, Pop5

growth_protocol: FACS-based purified ASCs

extract_protocol:
RNA was purified using QIAGEN Micro RNEasy columns, and RNA quality assessed using Agilent Bioanalyzer
2 ng of total RNA was used as input for mRNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit, according to manufacturer’s instructions. Amplified mRNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits

tag: samplenum

tag: samplename

tag: individual

tag: cellpopulation

tag: cell type

value: Antibody Secreting Cell

value: Peripheral Blood

tag: batch


title: Small RNAs from ovaries of EY03241 transgenic strain, technical rep1

tag: tissue


title: Sendai-iPS-Edom-iPS-31_P40

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

description:
7539308071_R03C02
Edom9-derived iPS cslls

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

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

tag: gender

value: Female

value: inducible pluripotent stem cells (iPSCs)

tag: disease state

value: normal

tag: vector type

value: Sendai virus


title: Genotyping data for sample 6-0287-03

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software

hyb_protocol: Standard Illumina protocol for Omni2.5M Beadchip

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina 2.5M platform we used iPattern, PennCNV, QuantiSNP, and CNVPartition.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label: Standard Illumina protocol

source_name: genomic DNA extracted from whole blood

extract_protocol: DNA was extracted from whole blood.


title: Genotyping data for sample 6-0286-03

scan_protocol: Standard Illumina protocol for Omni2.5M Beadchip


title: ChIPseq_H2Bub_WT_NKI6061_1

tag: genetic background strain

tag: strain

value: WT

value: H2Bub, developed by our lab from clone H2Bub1B3F12/A9


title: Genotyping data for sample 6-0283-03

label_protocol: Standard Illumina protocol for Omni2.5M Beadchip


title: Genotyping data for sample 6-0282-03


title: Genotyping data for sample 6-0281-03


title: Genotyping data for sample 6-0288-03


title: N402Barcode_701-520

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

data_processing:
Read alignment, STAR, 2.5.0a,  –outSAMstrandField intronMotif --runThreadN {threads} --outFileNamePrefix {wdir} --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outReadsUnmapped Fastx --clip3pAdapterSeq CTGTCTCTTATACACATCT --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1; gene count, htseq-count, 0.10.0, -s no -t exon -r pos -f bam -i Parent -m intersection-strict
Genome_build: schistosoma_mansoni.PRJEA36577.WBPS9.genomic.fa.gz. See text file on Series record with full link to genome.
Supplementary_files_format_and_content: Comma-separated values of normalized gene count (tpm) matrix where rows are genes and columns are sample names.

molecule: polyA RNA

organism: Schistosoma mansoni

source_name: Schistosoma mansoni stem cells

extract_protocol:
Smart-seq2 protocol, which lysed cells with Triton X-100
Nextera XT DNA

value: stem cells

tag: mouse strain with s. mansoni

value: Swiss  Webster NR-21963

tag: worm age

value: 2.5 weeks


title: N402Barcode_710-513


title: N402Barcode_715-521


title: N402Barcode_726-505


title: PB1131Pop2

source_name: ASC, Pop2


title: N402Barcode_710-522


title: N402Barcode_711-520


title: Genotyping data for sample 6-0279-03

tag: diagnosis


title: Genotyping data for sample 6-0270-03


title: Genotyping data for sample 6-0263-03


title: Genotyping data for sample 6-0260-03


title: N402Barcode_715-505


title: N402Barcode_704-502


title: N402Barcode_702-521


title: N402Barcode_718-502


title: Genotyping data for sample 6-0257-03


title: Genotyping data for sample 6-0253-03


title: Genotyping data for sample 6-0280-03


title: N402Barcode_712-510


title: Genotyping data for sample 6-0197-03


title: Genotyping data for sample 6-0250-03


title: Genotyping data for sample 6-0237-03


title: Genotyping data for sample 6-0212-03


title: Genotyping data for sample 6-0246-03


title: N402Barcode_712-522


title: ChIPseq_H2B_ubp8KO_NKI4656_2

tag: genotype

tag: chip antibody


title: Genotyping data for sample 6-0247-03


title: N402Barcode_704-507


title: Genotyping data for sample 6-0248-03


title: N402Barcode_727-510


title: N402Barcode_703-518


title: N402Barcode_702-503


title: N402Barcode_723-518


title: N402Barcode_726-518


title: Genotyping data for sample 6-0253-04


title: ChIPseq_H2B_ubp8KO_NKI4656_1


title: N402Barcode_703-508


title: Genotyping data for sample 6-0323-003


title: N402Barcode_727-515


title: Genotyping data for sample 6-0321-003


title: Genotyping data for sample 6-0325-003


title: N402Barcode_718-508


title: N402Barcode_707-507


title: Genotyping data for sample 6-0324-003


title: N402Barcode_720-508


title: Genotyping data for sample 6-0320-003


title: N402Barcode_727-502


title: N402Barcode_718-511


title: N402Barcode_727-520


title: Genotyping data for sample 6-0319-003


title: N402Barcode_702-516


title: Genotyping data for sample 6-0317-003


title: Genotyping data for sample 6-0316-003


title: Genotyping data for sample 6-0312-003


title: N402Barcode_727-508


title: N402Barcode_707-508


title: N402Barcode_701-516


title: N402Barcode_716-505


title: N402Barcode_711-508


title: N402Barcode_715-513


title: N402Barcode_703-502


title: N402Barcode_722-503


title: N402Barcode_702-506


title: N402Barcode_718-506


title: IB4 - Poly-A selected

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Reads were aligned to the human and EBV gneomes using STAR version 2.5
Backsplice and forward splice junctions were called using find_circ version 1.2
Genome_build: hg38 and EBV_Akata_inverted
Supplementary_files_format_and_content: Backsplice and forward splice counts in BED format

source_name: B-cell lymphoma

extract_protocol:
RNA was harvested using Trizol.
1 ug of RNA was input into the Illumina TruSeq RNA Sample Prep Kit v2 (Cat# RS-122-2001) to construct the sequencing libraries.

tag: protocol

value: Poly-A selected

value: B-cell lymphoma

tag: rna type

value: Total cellular RNA

tag: cell line

tag: treatment


title: JY - Cytoplasmic RNA - RNase R treated

value: RNase R treated

value: Cytoplasmic RNA

value: JY


title: JY - Poly-A selected


title: N402Barcode_721-517

tag: cell type


title: YCCEL1 - RNase R treated

source_name: Gastric carcinoma

value: Gastric carcinoma


title: Mutu III - Poly-A selected

value: Mutu III


title: Sav I - Poly-A selected

value: Sav I


title: N402Barcode_715-520


title: SNU719 - RNase R treated


title: Mutu I (induced) - Poly-A selected

value: Mutu I

value: Induced with 10 ug/ml of anti-IgM for 48 hours


title: Mutu I (uninduced) - Poly-A selected

value: Uninduced (Ctl)


title: N402Barcode_714-506


title: N402Barcode_711-505


title: N402Barcode_724-502


title: Jijoye - RNase R treated

value: Jijoye


title: Mutu III - RNase R treated


title: JY - Nuclear RNA - RNase R treated

value: Nuclear RNA


title: N402Barcode_705-516

value: stem cells


title: N402Barcode_728-522

value: Swiss  Webster NR-21963


title: IB4 - RNase R treated


title: Genotyping data for sample 6-0308-03

value: Female

value: whole blood

value: pediatric obesity


title: Jijoye - Poly-A selected

value: Poly-A selected

value: B-cell lymphoma

value: Total cellular RNA


title: N402Barcode_701-522

value: 2.5 weeks


title: N402Barcode_723-522


title: JY - Total RNA - RNase R treated

value: RNase R treated

value: JY


title: N402Barcode_721-502


title: Akata (induced) - Cytoplasmic RNA - RNase R treated

value: Cytoplasmic RNA

value: Akata

value: Induced with 10 ug/ml of anti-IgG for 24 hours


title: Mutu I (uninduced) - RNase R treated

value: Mutu I

value: Uninduced (Ctl)


title: N402Barcode_719-521


title: Akata (induced) - Nuclear RNA - RNase R treated

value: Nuclear RNA


title: Akata (uninduced) - Nuclear RNA - RNase R treated


title: N402Barcode_701-507

value: stem cells


title: N402Barcode_707-502

value: Swiss  Webster NR-21963


title: Akata (induced) -Total RNA - RNase R treated


title: Akata (uninduced) - Total RNA - RNase R treated


title: Akata (uninduced) - Cytoplasmic RNA - RNase R treated


title: N402Barcode_707-516


title: N402Barcode_706-507


title: N402Barcode_722-515


title: N402Barcode_728-511


title: N402Barcode_712-517


title: N402Barcode_721-510


title: N402Barcode_722-522


title: N402Barcode_724-517


title: Sav I - RNase R treated

value: Sav I


title: Mutu I (induced) - RNase R treated

value: Induced with 10 ug/ml of anti-IgM for 48 hours


title: N402Barcode_711-506


title: N402Barcode_720-518


title: N402Barcode_714-502


title: N402Barcode_727-517


title: N402Barcode_711-503


title: N402Barcode_723-521


title: N402Barcode_711-517


title: N402Barcode_721-515


title: N402Barcode_701-502


title: N402Barcode_728-513


title: N402Barcode_711-515


title: N402Barcode_719-520


title: N402Barcode_723-505


title: DNA/protein_biological rep3

city: Warsaw

first: Barbara

last: Kalenik

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description: Gene expression data from spleen of chicken immunized once with DNA vaccine and once with protein vaccine.

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45 degrees Cent. on Affymetrix ChiGene-1_1-st-v1microarrays, following by washing and staining in the Gene Atlas System following standard manufacturer's instructions.        scan protocol  GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

scan_protocol: The chips were scanned using the Affymetrix Gene Atlas Scanner.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 beta software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

source_name: Chicken immunized once with DNA vaccine and once with protein vaccine.

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 100 ng total RNA by the sequential use of the Ambion® WT Expression Kit and the Affymetrix GeneChip® WT Terminal Labelling Kit according to the manufacturer’s protocols.

growth_protocol: Broiler chickens Ross 308 were purchased from a commercialbrooder on the day of hatching and maintained at an experimentalpoultry house in standard bedding conditions.

extract_protocol: Whole spleens were homogenised in Buffer RLT Plus (Qiagen) with the ULTRA-TURRAX Tube Disperser (IKA, Germany). According to the manufacturer’s protocol, 700 μl of the lysate was used for RNA isolation with RNeasy Plus Mini Kit (Qiagen) with on-column DNase digestion followed by DNase digestion using TURBO DNase kit (Ambion) to eliminate DNA contamination.

treatment_protocol: Chickens were divided into four groups: 'pCI/pCI' group was a negative control; 'Protein/protein' group was vaccinated twice with Pichia-produced  hemagglutinin (HA) protein from H5N1 virus; 'DNA/DNA' group was vaccinated twice with HA DNA on pCI vector and 'DNA/protein' group gained one dose of HA DNA  on pCI vector and one dose of Pichia-produced HA protein. The DNA vaccine was applied with Lipofectin (Invitrogen, Germany) carrier in a final volume of 100 μl via intramuscular injection, while the protein (recombinant H5 HA) was delivered with alhydrogel adjuvant in a final volume of 200 μl via subcutaneous injection. The empty pCI vector (Promega, Poland) was used as a negative control. 8-day-old chickens were primed, 22-day-old chickens were boosted and 29-day-old chickens were sacrificed. The spleens were collected one week after the booster and stored in RNAlater solution (Ambion).

value: spleen

value: Broiler chicken Ross 308

value: DNA (1x) and protein (1x) vaccine


title: N402Barcode_727-511


title: N402Barcode_718-522


title: N402Barcode_721-511


title: DNA/DNA_biological rep1

description: Gene expression data from spleen of chicken immunized twice with DNA vaccine.

source_name: Chicken immunized twice with DNA vaccine.

value: DNA vaccine (2x)


title: Protein/protein_biological rep3

description: Gene expression data from spleen of chicken immunized twice with protein vaccine.

source_name: Chicken immunized twice with protein vaccine.

value: protein vaccine (2x)


title: N402Barcode_707-517

value: 2.5 weeks


title: Protein/protein_biological rep4


title: DNA/protein_biological rep1


title: pCI/pCI_biological rep2

description: Gene expression data from spleen of chicken immunized twice with empty vector pCI.

source_name: Chicken immunized twice with empty vector pCI.

value: empty pCI vector (2x)


title: DNA/protein_biological rep2


title: N402Barcode_712-505


title: Protein/protein_biological rep2


title: N402Barcode_719-505


title: Protein/protein_biological rep1


title: N402Barcode_712-515


title: KLF2/KLF4 DKO ESC RNA-seq rep5

first: Amy

last: Chen

address: 279 Campus Drive West

data_processing:
Reads were trimmed to remove adapter sequences using cutadapt and mapped to the genome (mm10) with STAR. Reads mapping to exons were then counted using featureCounts.
Differential expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: text file with exon counts

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: All cells were grown in Knockout DMEM with 15%FBS, Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).

extract_protocol:
RNA was extracted using a standard Trizol extraction protocol.
600 ng of total RNA was used as input for the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: ESCs

tag: cell line of origin

value: V6.5 ESCs

value: KLF2/KLF4 DKO

value: Lif 2i


title: N402Barcode_719-511


title: KLF2/KLF4 DKO ESC RNA-seq rep4


title: KLF2/KLF4 DKO ESC RNA-seq rep3


title: N402Barcode_712-511


title: pCI/pCI_biological rep1

tag: tissue


title: N402Barcode_720-510


title: KLF2/KLF4 DKO ESC RNA-seq rep2


title: Wildtype ESC RNA-seq rep4

value: wildtype


title: N402Barcode_724-508


title: DNA/DNA_biological rep2


title: KLF2/KLF4 DKO ESC RNA-seq rep1


title: Wildtype ESC RNA-seq rep3


title: N402Barcode_718-510


title: Wildtype ESC RNA-seq rep2


title: N402Barcode_716-517


title: N402Barcode_703-511


title: WT EpiLC RNA-seq rep3

data_processing:
Reads were trimmed to remove adapter sequences using cutadapt and mapped to the genome (mm10) with STAR. Reads mapping to exons were then counted using featureCounts.
Differential expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: text file with exon read counts.

source_name: epiblast-like cells

extract_protocol:
RNA was extracted using a standard Trizol extraction protocol. rRNA was depleted using the Ribo-Zero Gold kit (Illumina).
~ 100 ng of rRNA depleted RNA was used as input for the Kapa Stranded RNA-Seq kit (Kapa).

value: EpiLCs

value: -Lif -2i day 3


title: Wildtype ESC RNA-seq rep1


title: WT EpiLC RNA-seq rep2


title: N402Barcode_718-507

value: stem cells

value: Swiss  Webster NR-21963


title: N402Barcode_716-503


title: N402Barcode_712-520


title: N402Barcode_728-505


title: WT ESC RNA-seq rep3


title: N402Barcode_726-510


title: WT EpiLC RNA-seq rep1


title: WT ESC RNA-seq rep2


title: N402Barcode_704-513


title: N402Barcode_716-521


title: N402Barcode_716-508


title: N402Barcode_703-513


title: N402Barcode_716-502


title: N402Barcode_710-508


title: N402Barcode_701-510


title: N402Barcode_710-511


title: N402Barcode_706-505


title: N402Barcode_728-517


title: N402Barcode_711-518


title: N402Barcode_704-520


title: N402Barcode_701-506


title: N402Barcode_704-517


title: N402Barcode_718-517


title: N402Barcode_707-520


title: N402Barcode_722-505


title: N402Barcode_710-517


title: N402Barcode_719-507


title: N402Barcode_706-520


title: N402Barcode_710-518


title: N402Barcode_710-520


title: N402Barcode_727-505


title: N402Barcode_703-522


title: N402Barcode_716-511


title: N402Barcode_701-508


title: N402Barcode_723-511


title: N402Barcode_710-516


title: N402Barcode_712-502


title: N402Barcode_728-518


title: N402Barcode_704-522


title: N402Barcode_715-510


title: N402Barcode_726-513


title: N402Barcode_727-521


title: N402Barcode_712-503


title: N402Barcode_724-518


title: N402Barcode_712-518


title: N402Barcode_705-517


title: N402Barcode_714-515


title: N402Barcode_706-521


title: N402Barcode_711-513


title: N402Barcode_711-521


title: N402Barcode_706-516


title: N402Barcode_716-522


title: N402Barcode_710-510


title: N402Barcode_724-515


title: N402Barcode_726-517


title: N402Barcode_705-520


title: N402Barcode_724-506


title: N402Barcode_723-503


title: N402Barcode_718-518


title: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3(Dox-)_Replicate2 Bisulfite-Seq

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

description: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3 doxycycline-inducuble negative Replicate 2

data_processing:
Use BSMAP-2.90 to align bisulfite-treated sequencing reads to the human genome hg19 of bisulfite treated data
Use the medule Bsratio to compute the methylation ratio of single base level
Genome_build: hg19
Supplementary_files_format_and_content: Text output of bsmap utility methratio.py; chromosome, coordinate (1-based), strand, sequence context (2nt upstream to 2nt downstream in Watson strand direction), methylation ratio, number of effective total C+T counts on this locus, number of total C counts on this locus, number of total C+T counts on this locus, number of total G counts on this locus of reverse strand, number of total G+A counts on this locus of reverse strand, lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion, upper bound of 95% confidence interval

growth_protocol: Human embryonic kidney cell line (HEK293T) were incubated in DMEM media with 10 % fetal bovine serum (FBS) and 1 % penicillin/streptomycin (P/S) at 5 % CO2 and 37°C incubator. HEK293T cells were transfected with dCas9-SunTag-DNMT3A vectors using Lipofectamine 3000 (Life Technologies) and co-transfected with pMD2.G (Addgene # 12259) and psPAX2 (Addgene # 12260). Lentiviral particles were collected in forty-eight hours and seventy-two hours after transfection. 4X PEG (32 % PEG6000, 0.4 M NaCl and 0.04 M HEPES) was added to precipitate viral particles in 4°C overnight. Viral particles were then centrifuge in 1500g for 45 minutes and resuspended in X-VIVO 15 media (Lonza).

extract_protocol:
DNA extraction by Purelink extraction kit
Bisulfite treated DNA was made into library with Illumina TruSeq DNA sample preparation kit

treatment_protocol: Genomic DNA of dCas9-SunTag-DNMT3A treated cells was extracted by purelink mini kit (Invitrogen) and bisulfite converted by epitect bisulfite kit (Qiagen). Promoter (chr2:172,950,395-172,950,785)  and gene-body (chr2:172,951,180-172,951,400) regions of DLX1, and promoter (chr2:105,470,350-10,470,850)  and gene-body (chr2:105,471,850-105,472,350) regions of POU3F3 were amplified from bisulfite-treated DNA by PCR using the following program. First, samples were heat activated with 95°C for 5 minutes, then kept 95°C for 30 seconds, then 60°C for 2 minutes and 30 seconds and decreased 0.2°C every cycle, 72°C for 2 minutes and 30 seconds and repeated from second step for 40 cycles, finally, elongated in 72°C for 10 minutes. Bisulfite PCR primers used for promoter (P) and gene-body (E) of DLX1: DLX1-P-F 5’- GGGAAGTAGAGGAGAGAAAGTTTTA -3’, DLX1-P-R 5’- CTCTCCTCTCTTCTCTTTCTCTC -3’, DLX1-E-F: 5’- ATTTTTTTT GTAAAGGTAGGAGTTGAG -3’, DLX1-E-R 5’- AACACATACACACAATAACA CCC -3’. Bisulfite PCR products were run in 2 % agarose gel electrophoresis, excised and extracted using gel extraction kit (Qiagen). DNA concentration of gel-extracted products was measured using qubit dsDNA HS assay kit (Life technologies) and adjusted to 0.2 ng/μl for Nextera libraries preparation. Nextera libraries preparation was based on manufacturer’s instruction (Illumina).

value: embryonic semi-differentiated kidley cells


title: N402Barcode_707-510


title: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3(Dox+)_Replicate1 Bisulfite-Seq

description: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3 doxycycline-inducuble positive Replicate1


title: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3(Dox+)_Replicate2 Bisulfite-Seq

description: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3 doxycycline-inducuble positive Replicate 2


title: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3(Dox-)_Replicate1  Bisulfite-Seq

description: idCas9SunTag+iscFvDNMT3A_E756A+sgDLX1+sgPOU3F3 doxycycline-inducuble negative Replicate 1


title: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3(Dox+)_Replicate2 Bisulfite-Seq

description: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3 doxycycline-inducuble positive Replicate 2


title: N402Barcode_712-508


title: N402Barcode_711-511


title: N402Barcode_716-515


title: N402Barcode_720-515


title: NSR_2: nsra/b RNAseq

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

data_processing:
Mapping of reads to TAIR10 genome was performed using tophat2.0.9 allowing segment-mismatches of 2 and segment-length equal to 20.
(Li and Dewey, 2011). Read were counted using SummarizeOverlap function from the GenomicRange R package (Lawrence et al., 2013) using strand specific and Union mode.
Genome_build: Genome_build: TAIR10.22

organism: Arabidopsis thaliana

source_name: nsra nsrb double mutant (Mock)

growth_protocol: Plants were grown in a long day (16h light/ 8h dark) on solid half-strength MS (Duchefa biochemie, M0222) medium. Plantlets were collected at 15 days.

extract_protocol:
Plantlets were collected, frozen in liquid nitrogen and grind. RNA was extracted using Qiagen RNeasy® Plant kit according to the supplier’s instructions (QIAGEN S.A, France) including the DNAse treatment. RNA libraries were prepared for sequencing using standard Illumina protocols.
TruSeq Stranded mRNA SamplePrep Guide 15031047_D protocol (Illumina®, California, U.S.A.). The RNA-seq samples have been sequenced in paired-end (PE) with a sizing of 260 bp and a read length of 100.

treatment_protocol: 14 days old plantlets were transfer to a mock medium (solid half-strength MS) for 24 hours.

value: plantlets

value: nsra/nsrb double mutant


title: NSR_3: nsra/b RNAseq


title: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3(Dox+)_Replicate1 Bisulfite-Seq

description: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3 doxycycline-inducuble positive Replicate1


title: N402Barcode_721-506


title: N402Barcode_727-506


title: N402Barcode_723-513


title: NSR_1: nsra/b RNAseq


title: WT_3: Col0_RNAseq

source_name: Col-0 (Mock)

value: wild type


title: N402Barcode_719-506


title: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3(Dox-)_Replicate2 Bisulfite-Seq

description: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3 doxycycline-inducuble negative Replicate 2


title: N402Barcode_721-513


title: N402Barcode_716-518


title: idCas9SunTag+sgDLX1+sgPOU3F3(Dox+)_Replicate2 Bisulfite-Seq

description: idCas9SunTag+sgDLX1+sgPOU3F3 doxycycline-inducuble positive Replicate 2


title: N402Barcode_722-517


title: WT ESC RNA-seq rep1


title: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3(Dox-)_Replicate1  Bisulfite-Seq

description: idCas9SunTag+iscFvDNMT3A+sgDLX1+sgPOU3F3 doxycycline-inducuble negative Replicate 1


title: N402Barcode_705-511


title: N402Barcode_720-505


title: N402Barcode_704-511


title: idCas9SunTag+sgDLX1+sgPOU3F3(Dox-)_Replicate2 Bisulfite-Seq

description: idCas9SunTag+sgDLX1+sgPOU3F3 doxycycline-inducuble negative Replicate 2


title: WT_2: Col0_RNAseq


title: idCas9SunTag+sgDLX1+sgPOU3F3(Dox-)_Replicate1  Bisulfite-Seq

description: idCas9SunTag+sgDLX1+sgPOU3F3 doxycycline-inducuble negative Replicate 1


title: N402Barcode_711-522


title: N402Barcode_721-518


title: WT_1: Col0_RNAseq


title: N402Barcode_724-520


title: N402Barcode_723-516


title: N402Barcode_728-516


title: idCas9SunTag+sgDLX1+sgPOU3F3(Dox+)_Replicate1 Bisulfite-Seq

description: idCas9SunTag+sgDLX1+sgPOU3F3 doxycycline-inducuble positive Replicate1


title: N402Barcode_714-507


title: N402Barcode_704-516


title: N402Barcode_721-521


title: N402Barcode_723-508


title: I1-TNF

city: Herlev

last: Li

address: Rebæk Søpark

department: Gastroenterology

country: Denmark

institute: Herlev Hospital, University of Copenhagen

data_processing:
Raw reads were firstly aligned to Human 7rRNA sequence including 28S (NR_003287.2), 18S (NR_003286.2), 5S 8(NR_023379.1), and 5.8S (NR_003285.2) using SOAP2. The mapped reads were filtered using customs’ script
The low quality reads were filtered using SOAPnuke. Then clean reads were mapped to the reference transcript (Gencode, V19 ) via bowtie2
abundances of each gene  were counted using the RSEM
Genome_build: hg19

source_name: Human intestinal organoids

growth_protocol: The organoids were cultured in growth medium consisting of Ad-Df+++, B27 supplement, N2 supplement, N-acetylcysteine, A-83-01, SB202190, nicotinamide, recombinant epidermal growth factor, Noggin, and R-spondin 1–conditioned medium (10×) and Wnt3a-conditioned medium (2×), both produced in-house.

extract_protocol:
Lyse organoids using the RP buffer from the RNA purification kit (Macherey-Nagel, Düren, Germany). Remove the media and lyse directly in the well, and proceed directly with the RNA extraction.
Library was constructed using Illumina PE150 (Q30≥80%).

treatment_protocol: Intestinal organoids were cultured for 4 days and treated with TNF (10 ng/ml), with or without supplementation of PGE2 (1 µM), or treated with PGE2 alone for 48 h.

value: Human colonic epithelial stem cells

tag: passage


title: J2-TNF+PGE2


title: J1-TNF+PGE2


title: N402Barcode_726-507


title: N402Barcode_724-507


title: N402Barcode_722-520


title: I3-TNF


title: I2-TNF


title: B2-PGE2


title: N402Barcode_720-520


title: N402Barcode_719-513


title: N402Barcode_703-510


title: N402Barcode_712-506


title: N402Barcode_715-507


title: N402Barcode_720-506


title: J3-TNF+PGE2


title: N402Barcode_720-516


title: B3-PGE2


title: B1-PGE2


title: N402Barcode_703-516


title: N402Barcode_707-503


title: N402Barcode_726-522


title: N402Barcode_728-503


title: A3-Ctrl


title: N402Barcode_701-503


title: N402Barcode_701-518


title: decidua_recurrent spontaneous abortion_rep3

city: Nanjing

first: Mingming

last: Yu

address: NO.818 Tianyuan East Road, Jiangning District

department: School of public health

country: China

institute: Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  whole genome using tophat with default parameters
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using a protocol from Cole Trapnell  et al., Nature Protocols volume 7, pages 562–578 (2012).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: decidua samples from recurrent spontaneous abortion patients

extract_protocol:
RNA was extracted by RNeasy Kits (Qiagen, Hilden, NRW, Germany) and treated with DNase I (Thermo Fisher Scientific, Wilmington, DE, USA) according to standard protocols. RNA-sequencing was done in Genesky using TruSeq Stranded mRNA Library Preparation (Genesky, Shanghai, China). Briefly, intact RNA was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: decidua

tag: Stage

value: Twelve weeks before pregnancy

tag: age

value: 25 years old


title: N402Barcode_721-508

value: 2.5 weeks


title: N402Barcode_715-511


title: A2-Ctrl


title: N402Barcode_714-518


title: A1-Ctrl


title: N402Barcode_728-508


title: N402Barcode_720-507


title: N402Barcode_705-505


title: N402Barcode_724-510


title: decidua_induced abortion_rep2

source_name: decidua sample from induced abortion patients

value: 23 years old


title: decidua_recurrent spontaneous abortion_rep1

value: 24 years old


title: N402Barcode_707-505


title: N402Barcode_716-506


title: decidua_induced abortion_rep3


title: N402Barcode_714-517


title: N402Barcode_701-517


title: N402Barcode_715-508


title: N402Barcode_714-510


title: N402Barcode_706-522


title: N402Barcode_711-502


title: decidua_recurrent spontaneous abortion_rep2


title: N402Barcode_728-520


title: N402Barcode_707-515


title: N402Barcode_702-515


title: N402Barcode_702-520


title: N402Barcode_703-507


title: N402Barcode_704-510


title: N402Barcode_712-521


title: N402Barcode_715-518


title: N402Barcode_716-507


title: N402Barcode_727-522


title: N402Barcode_723-502


title: N402Barcode_701-515


title: N402Barcode_702-511


title: N402Barcode_720-517


title: N402Barcode_716-510


title: N402Barcode_720-503


title: N402Barcode_722-513


title: decidua_induced abortion_rep1


title: N402Barcode_705-510


title: N402Barcode_705-508


title: N402Barcode_728-507


title: d42 Bb CD25-

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 h at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000

data_processing: Data were analyszed using GeneSpring GX10.0 software the Transcriptome Analysis Console 4.0 (Affmetrix) applying RMA probe summarization algorithm and quantile normalization

source_name: Sorted CD4+CD25- T cells from pooled splenocytes 42 days post Bordetella bronchiseptica infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed under specific pathogen free conditions. Bordetella bronchiseptica was grown on Bordet-Gengou agar plates

extract_protocol: RNA was isolated using the RNeasy Mini from Qiagen company according to manufacturer recommendations

treatment_protocol: Mice were intranasally infected with 5x10^5 bacteria. Mice were sacrificed with CO2 inhalation, splenocytes were isolated, stained with fluorescently conjugated antibodies and FACS sorted on a FACS  Aria II device (BD) for CD4+CD25+ and CD4+CD25- T cells.

value: BALB/c

value: splenocytes

tag: agent

value: Bordetella bronchiseptica

tag: days post infection

tag: cell population

value: CD4+CD25- T cells


title: N402Barcode_705-522

value: stem cells

tag: mouse strain with s. mansoni

tag: worm age


title: N402Barcode_719-517

value: Swiss  Webster NR-21963


title: d42 Bb CD25+

source_name: Sorted CD4+CD25+ T cells from pooled splenocytes 42 days post Bordetella bronchiseptica infection

tag: strain

value: CD4+CD25+ T cells


title: d7 Bb CD25-

source_name: Sorted CD4+CD25- T cells from pooled splenocytes 7 days post Bordetella bronchiseptica infection


title: d42 uninf CD25+

source_name: Sorted CD4+CD25+ T cells from pooled splenocytes of uninfected age-matched mice

value: none (uninfected)


title: d42 uninf CD25-

source_name: Sorted CD4+CD25- T cells from pooled splenocytes of uninfected age-matched mice


title: d7 uninf CD25+

source_name: Sorted CD4+CD25+ T cells from pooled splenocytes of uninfected mice


title: d7 Bb CD25+

source_name: Sorted CD4+CD25+ T cells from pooled splenocytes 7 days post Bordetella bronchiseptica infection


title: N402Barcode_726-521

source_name: Schistosoma mansoni stem cells


title: N402Barcode_715-503


title: d7 uninf CD25-

source_name: Sorted CD4+CD25- T cells from pooled splenocytes of uninfected mice


title: N402Barcode_714-516


title: N402Barcode_712-513


title: N402Barcode_704-515


title: N402Barcode_728-510


title: N402Barcode_707-506


title: N402Barcode_701-505


title: N402Barcode_721-503


title: N402Barcode_726-511


title: N402Barcode_703-520


title: N402Barcode_702-508


title: N402Barcode_728-521


title: N402Barcode_724-505


title: Tet2KO_Sham

city: Shanghai

first: Hao

last: Wang

address: 180 Fenglin Road

institute: Fudan University

description: RNA was pooled from three mice

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

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7G.

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

source_name: Kidney, Sham

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Manual Target Preparation for GeneChip® 3' Expression Arrays, 2013, Affymetrix).

growth_protocol: Mice were housed in specific-pathogen-free (SPF) condition.

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

treatment_protocol: Mice were subjecte to sham surgery or 60 min renal ischemia followed by 24 hours' reperfusion.

tag: gender

value: Male

tag: genotype

value: Sham


title: WT_Sham

description: RNA was pooled from three mice

value: WT


title: Tet2KO_IR

description: RNA was pooled from three mice

source_name: Kidney, Ischemia reperfusion

value: IR


title: N402Barcode_707-521


title: N402Barcode_710-521


title: WT_IR

description: RNA was pooled from three mice


title: imMKCL(CL-7) day4, dish

city: Kyoto

first: Koji

last: Eto

address: 53 Kawahara-cho, Shogoin Kawahara-cho, Sakyo-ku

department: CiRA

institute: Kyoto University

description: Dish

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Human Gene 2.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG.

data_processing: Human Gene 2.0 ST arrays were normalized using RMA16 implemented in the GeneSpring (Agilent).

source_name: gene off day4 imMKCL CL-7(dish culture)

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) were used according to Affymetrix protocol.

growth_protocol: ImMKCL was cultured in IMDM supplemented with 5% human plasma, 50 ng/mL SCF, 200 ng/mL TA-316, 15 µM KP-457, 0.5 µM GNF-351, and 0.5 µM Y39983  for 4 days under dish or VerMES culture condition.

extract_protocol: RNA was isolated with miRNeasy mini kit (QIAGEN).

treatment_protocol: ImMKCL was lysed with QIAzol(QIAGEN).

value: ImMKCL

value: mature megakaryocyte

tag: culture condition

value: dish


title: N402Barcode_705-521

value: 2.5 weeks


title: imMKCL(CL-7) day4, VerMES

description: VerMES

source_name: gene off day4 imMKCL CL-7(VerMES culture)

tag: cell line

value: VerMES


title: N402Barcode_729-502


title: N402Barcode_719-503


title: N402Barcode_702-510


title: N402Barcode_706-503


title: N402Barcode_702-505


title: N402Barcode_718-513


title: N402Barcode_701-511


title: N402Barcode_727-507


title: N402Barcode_703-503


title: N402Barcode_704-506


title: N402Barcode_715-515


title: N402Barcode_721-516


title: N402Barcode_718-520


title: N402Barcode_705-507


title: N402Barcode_722-516


title: N402Barcode_706-511


title: OG1RF PL Rep2

city: Minneapolis

first: Gary

middle: M

last: Dunny

state: MN

address: 689 23rd Avenue S.E.

department: Department of Microbiology and Immunology

institute: University of Minnesota

description:
Wild-type
Growth conditions: BHI
Gakaxy73, OG1RF vs D983_PL

data_processing:
Illumina RNAseq library creation and sequencing, using paired-end HiSeq 2500 (50 bp and 125 bp), HiSeq (100 bp) and MiSeqv3 (75 bp) platform, were performed at the University of Minnesota Genomics Center (UMGC). The fastq CASAVA (version 1.8 Illumina) sequence files were de-multiplexed and deposited in Minnesota Supercomputer Institute (MSI, University of Minnesota).
Sequence analysis on paired end reads were carried out using Galaxy maintained by MSI. The fastq CASAVA 1.8 files were converted to CASAVA 1.7 and assessed for quality using FastQC Read and Quality Reports. (The libraries run on the HiSeq instrument were run on two lanes (technical replicates) for each condition.  The fastq files collected were combined to create a single output file for each condition using the MSI text manipulation tool, concatenate datasets, prior to converting to CASAVA 1.7.)
FASTQ Quality Trimmer by sliding window and cutadapt were used to remove the 3’ends of raw sequencing reads that had a Phred quality score <20 and to remove adapter sequences, respectively.
FASTQ interlacer and FASTQ de-interlacer or resync: Paired-end resynchronization (MSI tool) were used on the trimmed fastqsanger files to remove any unmatched paired end reads followed by mapping to the OG1RF reference genome (NC_017316.1/CP002621.1) using Bowtie for Illumina.
The Bowtie SAM files were sorted by chromosome and start position using Picard Sortsam.
For each condition, Cufflinks was used to assemble the transcripts and determine expression levels (FPKM).   The generated gtf files created for biological replicates, for the conditions to be compared, were assembled using Cuffmerge.
Cuffdiff was used to determine significant differences in transcriptional expression between culture conditions with the False Discovery Rate at 0.05.
Genome_build: NC_017316.1/CP002621.1
Supplementary_files_format_and_content: tabular file includes FPKM values, fold change and statistical analysis for Galaxy33, OG1RF R6_R7_D983_R4_R5 PLvsBIO
Supplementary_files_format_and_content: tabular file includes FPKM values, fold change and statistical analysis for Galaxy73,  OG1RF vs D983_PL

organism: Enterococcus faecalis

source_name: bacterial cellular RNA

growth_protocol:
E. faecalis biofilm and planktonic cells were obtained from CDC Biofilm Reactors (CBR) that were set-up as previously described (Dale et al., npj Biofilms Microbiomes, 2017). Briefly, OG1RF and ΔahrC were streaked on BHI plates containing rifampicin and fusidic acid.  For each reactor, an overnight M9-YE culture was inoculated with three colonies and grown at 37°C.  A CBR containing full strength M9-YE was inoculated with 2 ml of an overnight culture at a cell density of 1.4 x 109-2.8 x 109 and incubated with stirring at 37°C for 4 h to allow for bacterial attachment. M9-YE (10%) was then pumped through reactor for additional 2 h.  Next, biofilm cells from 24 polycarbonate coupons (BioSurface Technologies Corp., Bozeman, MT) and eight Aclar fluoropolymer strips (Electron Microscopy Sciences, Hatfield, PA) from the reactors were washed, treated with RNAprotect (Qiagen) and vortexed as described in Dale et al, (2017).  Three milliliters of planktonic cells were treated with RNAprotect, pelleted and stored with the biofilm cells at -80°C.  Two biological replicates were run for each strain.  To recover sufficient RNA from ΔahrC, two reactors were pooled for each replicate. For one of the OG1RF replicates, two reactors were also pooled.
Planktonic cells from OG1RF and ΔahrC were also acquired from liquid cultures grown in BHI.  Overnight cultures were diluted 1:100 in BHI medium and grown under static conditions until optical density 600 nm reached 0.600-0.650 at 37°C. Three milliliters of cells from each culture were treated with RNAprotect (Qiagen) according to the manufacturer’s protocol.  Cells were pelleted and stored at -80°C. Two biological replicates were run for each strain.

extract_protocol:
Planktonic and biofilm cell pellets, were thawed and resuspended in 200 µl Tris/EDTA/ mutanolysin/lysozyme solution (10 mM Tris [pH 8.0], 1.0 mM EDTA [pH 8.0], mutanolysin (500 U/ml), lysozyme (30 mg/ml)) and incubated at 37⁰C for 10 minutes. To the resuspensions, 700 µl of Buffer RLT (Qiagen RNeasy Mini Kit) with 10 µl β-ME was added and vortexed to mix. RNA was then purified using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. Total RNA from biological replicates were treated with TURBO DNase (Ambion /ThermoScientific, Waltham, MA) using the rigorous protocol according to the manufacturer’s instructions. DNase was removed from treated samples using the RNA Clean & Concentrator-25 (Zymo Research). mRNA was enriched by rRNA removal using the MICROBExpress Bacterial mRNA Purification Kit (Ambion/ThermoScientific) according to the manufacturer’s instructions.
University of Minnesota Genomic Center (UMGC) performed QC and library preparation.  mRNA quantified using fluorimetry (RiboGreen assay) and RNA integrity assessed using capillary electrophoresis (e.g., Agilent BioAnalyzer 2100), generating an RNA Integrity Number (RIN). For a sample to pass QC, mass must be ≥ 1 ug, with a RIN > 8.  Library created using TruSeq RNA V2 kit.  Briefly, cDNA was generated using reverse transcriptase, fragmented and blunt-ended, and ligated to indexed (barcoded) adapters. The RNA library was gel size selected to generate inserts of ~200 bp.

tag: strain/genotype

tag: sample type

value: Planktonic (PL)


title: N402Barcode_706-510

tag: cell type


title: N402Barcode_714-508


title: N402Barcode_719-510


title: N402Barcode_705-518


title: N402Barcode_723-507


title: N402Barcode_710-515


title: N402Barcode_710-505


title: N402Barcode_728-515


title: N402Barcode_704-508


title: N402Barcode_714-505


title: N402Barcode_722-510


title: N402Barcode_719-516


title: D983 PL Rep2

description:
Mutant
Growth conditions: BHI
Gakaxy73, OG1RF vs D983_PL

value: delta-ahrC


title: CC053d5_4

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Eye blood was collected in RNAprotect animal blood tubes (Qiagen) and immediately stored at -20 °C for at least 5 days. Blood RNA was isolated with the RNeasy protect animal blood kit (Qiagen). RNA concentration was measured with the NanoDrop (Thermo Scientific).

treatment_protocol: The CC strains (CC001, CC002, CC003, CC004, CC005, CC006, CC019, CC036, CC041, CC051 and CC053) were obtained from the University of North Carolina (Chapel Hill, NC) and bred in our animal facility. All mice were maintained under specific pathogen-free conditions and according to the German animal welfare law. Female, 8- to 12-week-old mice were anesthetized by intra-peritoneal injection with Ketamine/Xylazine (100 mg/ml Ketamine and 20 mg/ml Xylazine) in sterile natrium chloride solution. The doses were adjusted to the individual body weight using 200 µl/20 g body weight. Mice were then intra-nasally infected with 20 µl virus solution (10 FFU). Body weight was monitored daily as percentage of initial weight at the day of the infection. Mice that lost more than 30% of their body weight had to be euthanized for ethical reasons and were scored as dead.

value: female

value: 8-12 weeks

tag: tissue

value: blood

tag: infection status

value: infected

tag: infection severity

value: severe

tag: infection day


title: N402Barcode_728-502

value: stem cells

value: Swiss  Webster NR-21963


title: N402Barcode_707-511


title: N402Barcode_718-503


title: CC053cd3_6

tag: age

value: mock

value: control


title: CC053d5_2


title: CC053d5_3


title: CC053d3_3


title: N402Barcode_714-503


title: N402Barcode_706-506


title: N402Barcode_718-516


title: CC053d3_4


title: CC053d3_5


title: N402Barcode_711-510


title: CC053cd3_4


title: CC053cd3_5


title: CC051d8_2


title: N402Barcode_701-521


title: CC051d8_5


title: N402Barcode_710-507


title: CC051d5_5


title: N402Barcode_705-506


title: CC051d5_4


title: N402Barcode_726-503


title: N402Barcode_711-516


title: N402Barcode_720-522


title: N402Barcode_710-503


title: N402Barcode_723-520


title: N402Barcode_711-507


title: N402Barcode_715-517


title: N402Barcode_703-515


title: N402Barcode_724-516


title: N402Barcode_722-502


title: N402Barcode_707-522


title: N402Barcode_715-516


title: CC051d8_4


title: CC051d5_1


title: N402Barcode_704-518


title: N402Barcode_721-522


title: N402Barcode_714-513


title: CC051d3_3


title: N402Barcode_714-520


title: N402Barcode_712-507


title: CC051d3_2


title: N402Barcode_705-502


title: N402Barcode_706-513


title: CC051d3_1


title: N402Barcode_723-506


title: CC051cd3_3


title: CC041d8_6


title: N402Barcode_707-513


title: N402Barcode_720-502


title: N402Barcode_721-520


title: N402Barcode_729-513


title: N402Barcode_726-506


title: N402Barcode_721-505


title: N402Barcode_727-513


title: N402Barcode_706-508


title: N402Barcode_703-521


title: N402Barcode_702-522


title: N402Barcode_703-506


title: N402Barcode_718-521


title: N402Barcode_723-510


title: CC051cd3_2


title: N402Barcode_702-502


title: CC041d5_6


title: N402Barcode_706-502


title: N402Barcode_724-521


title: CC041d8_3


title: CC041d8_1


title: N402Barcode_710-502


title: CC041d5_5


title: CC051cd3_5


title: CC041d5_4


title: CC041d3_3


title: CC041d3_4


title: CC041d3_6


title: CC041d3_5


title: CC041cd3_7


title: CC041cd3_3


title: CC041cd3_2


title: N402Barcode_719-515


title: N402Barcode_710-506


title: N402Barcode_727-518


title: N402Barcode_705-515


title: N402Barcode_726-515


title: N402Barcode_720-511


title: N402Barcode_714-521


title: N402Barcode_704-521


title: N402Barcode_706-518


title: N402Barcode_722-511


title: N402Barcode_703-517


title: N402Barcode_721-507


title: N402Barcode_726-508


title: N402Barcode_726-502


title: N402Barcode_726-516


title: CC036d5_5


title: N402Barcode_702-517


title: N402Barcode_719-508


title: N402Barcode_718-515


title: CC041cd3_1


title: CC036d3_5


title: CC036d5_1


title: CC036d3_6


title: CC036d3_4


title: CC036d5_3


title: N402Barcode_719-518


title: N402Barcode_722-508


title: N402Barcode_720-521


title: N402Barcode_724-503


title: CC036cd3_3


title: N402Barcode_722-521


title: N402Barcode_714-522


title: N402Barcode_714-511


title: N402Barcode_707-518


title: N402Barcode_702-518


title: N402Barcode_716-520


title: N402Barcode_704-505


title: N402Barcode_703-505


title: CC036cd3_1


title: CC019d8_3


title: N402Barcode_720-513


title: N402Barcode_704-503


title: N402Barcode_701-513


title: N402Barcode_719-502


title: N402Barcode_724-522


title: N402Barcode_715-506


title: N402Barcode_723-515


title: CC036cd3_2


title: N402Barcode_726-520


title: CC019d5_6


title: CC019d5_5


title: CC019d8_1


title: CC019d5_3


title: CC019d5_4


title: CC019d8_4


title: N402Barcode_715-522


title: CC019d5_2


title: N402Barcode_702-507


title: N402Barcode_727-516


title: N402Barcode_716-513


title: N402Barcode_722-507


title: N402Barcode_706-517


title: N402Barcode_718-505


title: N402Barcode_705-503


title: N402Barcode_715-502


title: N402Barcode_724-513


title: N402Barcode_712-516


title: CC019d3_1


title: N402Barcode_727-503


title: N402Barcode_702-513


title: CC019d3_2


title: N402Barcode_724-511


title: CC019d3_3


title: N402Barcode_706-515


title: N402Barcode_728-506


title: CC019cd3_3


title: N402Barcode_716-516


title: N402Barcode_722-506


title: CC019cd3_1


title: N402Barcode_723-517


title: N402Barcode_705-513


title: CC019cd3_2


title: N402Barcode_719-522


title: CC006d5_4


title: CC006d5_1


title: CC006d5_2


title: CC006d3_5


title: CC006d3_4


title: CC006d3_2


title: S1236-00510

city: Belfast

first: Suneil

last: Jain

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

hyb_protocol: Labelled cDNA was combined with dimethyl sulfoxide, hybridization buffer and nuclease free water and hybridised onto a Prostate Disease Specific Array (ThermoFisher) for 18hrs at 40oC.  Following hybridization, all arrays were washed using buffers of varying salt concentrations and stained with streptavidin-phycoerythrin conjugate (SAPE) .    All reaction components are contained within the hybridization, wash and stain kit (ThermoFisher).

scan_protocol: The arrays were scanned on the GeneChip scanner system (Thermofisher) using an epiflourescent, confocal microscope.  A solid-state laser contained within the GeneChip system was used to excite fluorophores bound to the hybridized cDNA molecules. The fluorescent values were firstly converted into an electronic signal and then to a numerical value representing the fluorescent intensity.

data_processing: CEL file intensities have been normalised to probeset level using Robust Multichip Average (RMA) consisting background adjustment, quantile normalisation and summarisation pre-processing (Bolstad et al, 2003).

label: Biotin

source_name: Primary Prostate Cancer

label_protocol: 3.5 µg of cDNA was first enzymatically fragmented by DNase at 37oC for 30min followed by labelling with a terminal deoxynucleotidyl transferase (TdT) and biotin at 37oC for 60min.  All reaction components are contained within the  Encore Biotin Module (NuGEN Inc).

extract_protocol: From each specimen, 4x5 micron FFPE sections were macrodissected using the most dominant Gleason as identified by a central pathologist.  Samples were all extracted using the Roche HighPure Extraction Kit.

value: Primary Prostate Cancer

tag: patient age (years)

tag: psa (ng/ml)

tag: t-stage

value: Unknown

tag: gleason grade

tag: bcr event (1=yes, 0=no)

tag: follow-up time (bcr, months)

tag: met event (1=yes, 0=no)

tag: follow-up time (met, months)


title: CC006cd3_6

tag: strain

tag: gender


title: S1236-00505


title: S1236-00500


title: S1236-00493


title: S1236-00491


title: S1236-00492


title: S1236-00508


title: CC005d8_3

value: resistant


title: S1236-00479


title: CC006cd3_5


title: CC006cd3_3


title: S1236-00482


title: S1236-00476


title: S1236-00488


title: S1236-00489


title: CC005d8_2


title: S1236-00494


title: S1236-00477


title: S1236-00483


title: CC005d5_3


title: S1236-00503


title: S1236-00485


title: S1236-00470


title: CC005d8_1


title: S1236-00473


title: S1236-00469


title: CC005d5_2


title: S1236-00465


title: S1236-00467


title: CC005d3_3


title: CC005d3_2


title: CC005d5_1


title: CC005cd3_2


title: CC005d3_1


title: S1236-00453


title: S1236-00461


title: S1236-00439


title: CC004d5_5


title: CC005cd3_1


title: S1236-00436


title: CC004d5_6


title: CC004d5_4


title: CC005cd3_3


title: S1236-00451


title: S1236-00456


title: S1236-00447


title: S1236-00446


title: S1236-00445


title: S1236-00440


title: S1236-00458


title: S1236-00450


title: S1236-00442


title: S1236-00422


title: S1236-00462


title: S1236-00435


title: S1236-00429


title: S1236-00424


title: S1236-00431


title: CC004d3_3


title: S1236-00428


title: S1236-00421


title: CC004d3_2


title: S1236-00420


title: CC004cd3_4


title: S1236-00410


title: CC004cd3_3


title: CC004cd3_2


title: S1236-00405


title: S1236-00403


title: S1236-00401


title: CC003d8_4


title: S1236-00412


title: S1236-00419


title: S1236-00404


title: S1236-00397


title: CC003d8_5


title: CC003d8_2


title: CC003d8_3


title: S1236-00402


title: S1236-00390


title: S1236-00389


title: CC003d8_1


title: S1236-00391


title: S1236-00385


title: S1236-00383


title: S1236-00386


title: S1236-00393


title: S1236-00377


title: CC003d5_5


title: CC003d5_4


title: S1236-00370


title: CC003d5_3


title: S1236-00408


title: S1236-00382


title: S1236-00369


title: S1236-00367


title: CC004d3_1


title: S1236-00364


title: S1236-00374


title: S1236-00363


title: S1236-00360


title: CC003d3_6


title: CC003d3_5


title: CC003d3_4


title: S1236-00368


title: S1236-00358


title: CC003cd3_6


title: CC002d8_5


title: CC002d8_4


title: S1236-00334


title: S1236-00350


title: S1236-00353


title: S1236-00351


title: S1236-00349


title: S1236-00331


title: S1236-00338


title: CC003cd3_4


title: CC002d8_3


title: CC003cd3_5


title: S1236-00347


title: S1236-00344


title: S1236-00321


title: S1236-00327


title: S1236-00318


title: CC002d5_7


title: S1236-00315


title: S1236-00319


title: CC002d3_4


title: S1236-00324


title: CC002d5_6


title: CC002d5_2


title: CC002d3_3


title: S1236-00416


title: CC002d3_2


title: CC002cd3_5


title: S1236-00312


title: CC002cd3_4


title: CC002cd3_3


title: S1236-00357


title: S1236-00307


title: S1236-00303


title: S1236-00295


title: S1236-00298


title: S1236-00354


title: S1236-00305


title: S1236-00302


title: S1236-00292


title: S1236-00313


title: S1236-00297


title: S1236-00288


title: S1236-00284


title: CC001d8_1


title: CC001d8_6


title: S1236-00291


title: CC001d8_5


title: S1236-00274


title: S1236-00277


title: S1236-00286


title: S1236-00280


title: CC001d8_2


title: S1236-00268


title: S1236-00267


title: S1236-00266


title: CC001d5_1


title: CC001d3_3


title: S1236-00262


title: CC001d5_2


title: S1236-00275


title: S1236-00271


title: S1236-00263


title: CC001d5_3


title: S1236-00257


title: S1236-00259


title: S1236-00261


title: S1236-00256


title: S1236-00255


title: S1236-00340


title: S1236-00333


title: CC001cd3_3


title: S1236-00253


title: S1236-00246


title: CC001cd3_2


title: S1236-00249


title: CC001d3_2


title: S1236-00240


title: RNA-seq_GFPday9R2

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

description:
GFPD9R2
genes_ntc_expression_eSox.txt

data_processing:
fastqc
The mouse transcriptome index was generated by RSEM with bowtie 2 and then the raw reads were aligned to the transcriptome index
Per-gene read counts were calculated using RSEM GC normalized using EDAseq
Genes with mean read counts over all traits and replicates of less than 20 were discarded leading to a final set of ~14,000 genes
DESeq2 for differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene counts

growth_protocol: OG2MEF cells were transduced twice by pMX-Oc4, Klf4 and or cMYC along with Sox2 or top eSox candidates form DERBYSeq screen.  Viruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the media was switched to DMEM with serum+Lif+Vitmain-C  (mES) reprogramming medium. The mES media switch day was defined as day 0 and cells were cultured until iPScs are generated.

extract_protocol:
Total RNA was prepared with TRIzol
TruSeq Nano RNA sample prep kit (Illumina) was used for library constructions.

value: OG2 MEF

tag: protocol

value: reprogramming cells

tag: day of reprogramming


title: RNA-seq_GFPday6R2

description:
GFPD6R2
genes_ntc_expression_eSox.txt

tag: cell type


title: S1236-00236

tag: tissue


title: S1236-00227


title: RNA-seq_GFPday6R1

description:
GFPD6R1
genes_ntc_expression_eSox.txt


title: RNA-seq_GFPday9R1

description:
GFPD9R1
genes_ntc_expression_eSox.txt


title: S1236-00225


title: S1236-00247


title: S1236-00242


title: S1236-00229


title: S1236-00234


title: S1236-00237


title: CC001d3_1

tag: infection status

tag: infection severity


title: RNA-seq_GFPday3R2

description:
GFPD3R2
genes_ntc_expression_eSox.txt


title: S1236-00226


title: CC001cd3_1

tag: age

tag: infection day


title: S1236-00219

tag: patient age (years)

tag: psa (ng/ml)


title: S1236-00232

tag: t-stage

tag: gleason grade


title: RNA-seq_GFPday3R1

description:
GFPD3R1
genes_ntc_expression_eSox.txt


title: S1236-00215

tag: bcr event (1=yes, 0=no)

tag: follow-up time (bcr, months)


title: S1236-00213

tag: met event (1=yes, 0=no)

tag: follow-up time (met, months)


title: S1236-00223


title: RNA-seq_eSox17WHC-iPSCR1

description:
WHC_IPScA
genes_ntc_expression_eSox.txt

value: iPSC cells


title: RNA-seq_eSox17WHC-iPSCR2

description:
WHC_IPScB
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox17FNV-iPSCR2

description:
FNV_IPScB
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox17FNV-iPSCR1

description:
FNV_IPScA
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox2NRR-iPSCR2

description:
NRR_IPScB
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox2NRR-iPSCR1

description:
NRR_IPScA
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox17FNVday9R1

description:
FNVD9R1
genes_ntc_expression_eSox.txt


title: S1236-00199


title: S1236-00202


title: S1236-00197


title: S1236-00200


title: S1236-00203


title: S1236-00210


title: S1236-00205


title: RNA-seq_eSox17FNVday9R2

description:
FNVD9R2
genes_ntc_expression_eSox.txt


title: S1236-00251


title: S1236-00195


title: S1236-00189


title: S1236-00181


title: S1236-00183


title: S1236-00212


title: S1236-00191


title: S1236-00186


title: S1236-00187


title: S1236-00207


title: RNA-seq_eSox2NRRday9R2

description:
NRRD9R2
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox2NRRday9R1

description:
NRRD9R1
genes_ntc_expression_eSox.txt


title: RNA-seq_Sox17day9R2

description:
Sox17D9R2
wildtype Sox17
genes_ntc_expression_eSox.txt


title: S1236-00169


title: S1236-00173


title: S1236-00170


title: S1236-00174


title: S1236-00172


title: RNA-seq_Sox2day9R2

description:
Sox2D9R2
wildtype Sox2
genes_ntc_expression_eSox.txt


title: S1236-00167


title: S1236-00171


title: S1236-00168


title: RNA-seq_eSox17FNVday6R2

description:
FNVD6R2
genes_ntc_expression_eSox.txt


title: RNA-seq_Sox2day9R1

description:
Sox2D9R1
wildtype Sox2
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox17FNVday6R1

description:
FNVD6R1
genes_ntc_expression_eSox.txt


title: S1236-00164


title: RNA-seq_eSox2NRRday6R2

description:
NRRD6R2
genes_ntc_expression_eSox.txt


title: RNA-seq_Sox17day9R1

description:
Sox17D9R1
wildtype Sox17
genes_ntc_expression_eSox.txt


title: S1236-00160


title: S1236-00159


title: S1236-00158


title: S1236-00156


title: RNA-seq_eSox2NRRday6R1

description:
NRRD6R1
genes_ntc_expression_eSox.txt


title: RNA-seq_Sox17day6R1

description:
Sox17D6R1
wildtype Sox17
genes_ntc_expression_eSox.txt


title: RNA-seq_Sox2day6R2

description:
Sox2D6R2
wildtype Sox2
genes_ntc_expression_eSox.txt


title: RNA-seq_Sox17day6R2

description:
Sox17D6R2
wildtype Sox17
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox17FNVday3R2

description:
FNVD3R2
genes_ntc_expression_eSox.txt


title: RNA-seq_eSox17FNVday3R1

description:
FNVD3R1
genes_ntc_expression_eSox.txt


title: S1236-00151


title: RNA-seq_eSox2NRRday3R2

description:
NRRD3R2
genes_ntc_expression_eSox.txt


title: RNA sequencing from IGG IP 2

data_processing:
Mapping of reads to TAIR10 genome was performed using tophat2.0.9 allowing segment-mismatches of 2 and segment-length equal to 20.
Read were counted using SummarizeOverlap function from the GenomicRange R package (Lawrence et al., 2013) using strand specific and Union mode.
Genome_build: Genome_build: TAIR10.22
Supplementary_files_format_and_content: tab-delimited text files include raw read values for each Sample; normalized?

source_name: RNA sequencing from IGG IP

extract_protocol:
Plantlets were collected, frozen in liquid nitrogen and grind.NSRa protein tagged with HA was immunoprecipitated from the nrsa mutant background expressing the pNSRa:NSRa-HA  construct (Bardou et al., 2014). Briefly, 10 day old seedlings treated with 100 nM NAA for 24 hours were irradiated three times with UV using a UV crosslinker CL-508 (Uvitec) at 0.400 J/cm2. Plants were ground in liquid nitrogen and RNA-IP was performed as in Sorenson and Bailey-Serres (Sorenson and Bailey-Serres, 2014) with the following modification : immunoprecipitation (IP) was performed in duplicate using anti mouse HA-7 monoclonal antibody (Sigma) and the negative IP (Mock) was done using anti mouse IgG (Millipore). RNA was eluted from the beads with 50U proteinase K (RNase grade, Invitrogen) in 2 μl of RNase inhibitor at 55°C for 1 hr in wash buffer and extracted using Trizol according to manufacturer instructions. A tenth of the input fraction was saved for RNA extraction. RNA was extracted using TRIZOL according to manufacturer instructions
RNA were depleted of rRNA using the plant leaf ribozero kit (Illumina) and libraries were prepared using the Illumina TruSeq Stranded mRNA library prep kit according to the manufacturer instruction but omitting the polyA RNA purification step and sequenced on a NextSeq500 sequencer (Illumina) using single-end 75 bp reads mode.

treatment_protocol: 14 days old plantlets were transfered to a 1µM NAA (solid half-strength MS) for 24 hours.

tag: genotype/variation

value: 14 days old plantlets

tag: rip antibody

value: anti mouse IgG (Millipore)

tag: molecule subtype

value: rRNA depleted RNA


title: S1236-00153


title: S1236-00146


title: S1236-00149


title: RNA-seq_Sox2day6R1

description:
Sox2D6R1
wildtype Sox2
genes_ntc_expression_eSox.txt

tag: cell type

tag: protocol

tag: day of reprogramming


title: S1236-00152

tag: tissue


title: S1236-00150


title: RNA-seq_eSox2NRRday3R1

description:
NRRD3R1
genes_ntc_expression_eSox.txt


title: S1236-00144


title: S1236-00140


title: S1236-00147


title: S1236-00128


title: S1236-00132


title: S1236-00129


title: S1236-00127


title: S1236-00123


title: S1236-00125


title: RNA sequencing from anti HA IP 2

source_name: RNA sequencing from anti HA IP

value: anti mouse HA-7 monoclonal antibody (Sigma)


title: S1236-00120


title: S1236-00115


title: S1236-00142


title: S1236-00109


title: S1236-00136


title: S1236-00121


title: S1236-00119


title: RNA sequencing from anti HA IP 1


title: RNA-seq_Sox17day3R1

description:
Sox17D3R1
wildtype Sox17
genes_ntc_expression_eSox.txt


title: S1236-00107


title: S1236-00114


title: RNA sequencing from IGG IP 1


title: RNA-seq_Sox2day3R2

description:
Sox2D3R2
wildtype Sox2
genes_ntc_expression_eSox.txt


title: RNA sequencing from RIP input 2

source_name: RNA sequencing from RIP input


title: S1236-00104


title: RNA-seq_Sox2day3R1

description:
Sox2D3R1
wildtype Sox2
genes_ntc_expression_eSox.txt


title: RNA-seq_Sox17day3R2

description:
Sox17D3R2
wildtype Sox17
genes_ntc_expression_eSox.txt


title: S1236-00103


title: RNA sequencing from RIP input 1


title: Input_day6

data_processing:
fastqc
Read were aligned to mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive –end-to-end -nomixed
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read was retained.
Samtools was used to discard reads with mapping quality < 10
MAC2 Peaks were called with options --call-summits --to-large -p 0.0001 –bdg options.
For each binding location, the read coverage for all libraries was calculated using the bedtools multicov function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed followed by bedGraphToBigWig.

extract_protocol:
Reprogramming cells (7.5-10 x 106 cells per sample were collected by trypsinization at day 3 and 6 days post transduction and washed twice with PBS (Gibco). Cells were resuspended in PBS at a density of 5 x 105/mL and then chemically crosslinked by the addition of 1% formaldehyde for 10 min at room temperature with gentle rotation. Crosslinking was stopped by the addition of glycine to a final concentration of 125 mM for 5 min at room temperature. Cells were washed twice with 10 mL cold PBS and lysed in 10 mL Lysis Buffer 1 (150 mM NaCl, 0.5% NP40; 1 mM EDTA, 10% glycerol, 0.25% triton-X100, freshly added complete proteinase inhibitor cocktail in 15 mL tubes at 4°C for 10 min with gentle rocking. The lysate was centrifuged for 10 min at 1350 x g at 4°C. The supernatant was discarded and the pellet was resuspended in 10 mL lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, protease inhibitor) incubated at 4°C for 10 min. The procedure was repeated using 10 mL lysis buffer 3 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, protease inhibitor) and 10 min rocking at RT. Nuclei were collected by centrifugation and washed twice with sonication buffer (10 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, protease inhibitor) and finally suspended in sonication buffer. Samples were sonicated using a Covaris S220 machine with settings to obtain DNA fragments with a length from 150 to 500 bp using microTUBEs (130 μL) for 5 cycles of 30 sec ON and 60 sec OFF using default settings recommended for microTUBEs. 10% Triton-X100 was added and the lysate was centrifuged at high speed (20000 x g for 10 min at 4°C). 1/10 of the supernatant was stored as input control. ChIP was performed in an automated fashion using the IP-Star compacted automated system (Diagenode) using 6 g ChIP-grade antibodies  and 50 l protein G Dynabeads (Invitrogen). The coupling time for beads and antibody was 5 hours followed by incubation with lysate for 15 hours at 4°C. Automated wash steps of 10 minutes at 4°C were performed in the following order: low salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 150 mM NaCl) , high salt buffer (20 mM Tris-HCl pH 8.0, 0.1% SDS 1% TritonX-100, 2 mM EDTA, 500 mM NaCl), LiCl buffer (500 mM LiCl, 50 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% NP-40, 0.5% Na-deoxycholate), TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) with final elution in 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS buffer. The eluted chromatin and input samples were reverse‐crosslinked by overnight incubation at 65°C. Samples were treated with RNaseA (0.2 mg/ml final concentration) at 37°C for 2h followed by proteinase K (0.2 g/ml final conc.) at 55°C for 3 hours. DNA was extracted by phenol:chloroform:isoamyl alcohol (25:24:1) and phase separated using heavy phase-lock tubes (TianGen) by centrifugation at 10000 rpm for 10 min at RT and precipitated with 100% ethanol with 20 μg/μl glycogen as co-precipitant. The precipitate was washed with 80% ethanol and finally eluted in 20ul water. DNA concentration was determined using Qubit dsDNA HS assay kit.
The libraries were generated using the Trueseq Nano DNA kit (Illumina)

tag: antibody

value: none (input)


title: Input_day3


title: ChIP-seq_eSox17FNV_day6

value: Sox17 Antibody (Novus biologicals, catalog number AF1924)


title: ChIP-seq_eSox17FNV_day3


title: ChIP-seq_Sox17_day6


title: ChIP-seq_Sox17_day3


title: S1236-00099


title: S1236-00098


title: S1236-00097


title: S1236-00091


title: S1236-00093


title: S1236-00089


title: S1236-00086


title: S1236-00083


title: S1236-00084


title: S1236-00073


title: S1236-00088


title: S1236-00081


title: S1236-00079


title: S1236-00090


title: S1236-00072


title: S1236-00077


title: S1236-00070


title: S1236-00069


title: S1236-00066


title: S1236-00068


title: NA12878-4 450K

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: minfi_1.20.2 with Illumina background correction and subset within array normalization probe normalization

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

tag: gender

value: Female

tag: cell line

value: EBV-transformed lymphoblastoid cell line


title: S1236-00061

tag: patient age (years)

tag: psa (ng/ml)


title: S1236-00062

tag: t-stage

tag: gleason grade


title: brain_Sham operated_4 (mRNA)

city: Bunkyo-ku

first: Ayako

last: Takuma

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

hyb_protocol: cRNA 15µg were flagmentated, and hybridized for 16hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized using the statistical software R, and the qFARMS method.

organism: Rattus norvegicus

source_name: brain extracted from Sham treated rats

label_protocol: Biotin-labeled cRNA was synthesized from 100ng total RNA according to the manufacture's protocol.

growth_protocol: The rats had free access to food and water, and were kept in a 12 hour light/dark cycle.

extract_protocol: Total RNA was extracted from the brain sample using TRIzol Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol. The extracted total RNA was cleaned up with RNeasy Mini Kit (QIAGEN).

treatment_protocol: The rats were subjected to operation, and the left hemisphere of the brain was extracted 24hr after the reperfusion.

value: male

tag: age

value: 8 weeks old

tag: stress

value: Sham

value: brain


title: S1236-00060

value: Primary Prostate Cancer

tag: bcr event (1=yes, 0=no)

tag: follow-up time (bcr, months)

tag: met event (1=yes, 0=no)

tag: follow-up time (met, months)


title: S1236-00059


title: brain_Sham operated_3 (mRNA)


title: S1236-00056


title: brain_Sham operated_2 (mRNA)


title: brain_Sham operated_5 (mRNA)


title: brain_Sham operated_1 (mRNA)


title: S1236-00052


title: IMR-90-4 450K

tag: cell type

value: Fetal lung fibroblast


title: IMR-90-3 450K


title: S1236-00049


title: brain_MCAO operated_7 (mRNA)

source_name: brain extracted from MCAO treated rats

value: Middle Cerebral Artery Occlusion


title: brain_MCAO operated_6 (mRNA)


title: S1236-00045


title: S1236-00054


title: brain_MCAO operated_5 (mRNA)


title: NA12878 450K


title: S1236-00047

value: Unknown


title: NA12878-3 450K


title: S1236-00040


title: brain_MCAO operated_3 (mRNA)


title: S1236-00042


title: NA12878-2 450K


title: brain_MCAO operated_2 (mRNA)


title: IMR-90 450K


title: S1236-00037


title: SL139394: IgG_Control_4

city: Charlottesville

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

data_processing:
Basecalls performed using CASAVA
Data were aligned to the mm9 genome using STAR version 3.0
Aligned reads were counted against genes from the UCSC mm9 annotation using the featureCounts from the SubRead package
Data were normalized for library size using the DESeq2 median ration normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R
Genome_build: mm9
Supplementary_files_format_and_content: Counts of reads aligning to genes from the mm9 annotation as output from featureCounts

source_name: Atherosclerosis lesion

extract_protocol:
BCA were removed and flash frozen and RNA was harvested using standar Trizol reagent/protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were maintened in a Western Diet for 18 weeks

value: Atherosclerosis lesion

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)

tag: strain

tag: treatment

value: IgG

tag: diet

value: Western Diet


title: SL139396: IL1_AB_4

tag: tissue


title: SL139393: IgG_Control_3


title: SL139392: IL1_AB_2


title: NA12878-4 EPIC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

tag: gender


title: brain_MCAO operated_1 (mRNA)


title: SL139391: IL1_AB_1


title: SL139390: IgG_Control_2


title: S1236-00033


title: SL139389: IgG_Control_1


title: S1236-00028


title: S1236-00027


title: S1236-00025


title: S1236-00032


title: S1236-00029


title: NA12878-2 EPIC

tag: cell line


title: IMR-90-2 EPIC


title: SL139395: IL1_AB_3


title: STOMP sample 6-0302-03

city: Toronto

first: Stephen

last: Scherer

address: 686 Bay Street

institute: The Hospital for Sick Children

data_processing:
To achieve comprehensive CNV calling, we used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs14. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
Genotype Call (SNP call): AA, AB, BB, and NoCall
To achieve comprehensive CNV calling, we used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs14. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.
Genotype Call (SNP call): AA, AB, BB, and NoCall

source_name: whole blood

growth_protocol:
DNA was extracted from whole blood..
Cell lines were grown according to standard conditions.

extract_protocol: Lymphocyte isolation by the Ficoll separation procedure followed by cryopreservation and storage in liquid nitrogen and cell lines were established using EBV-transformation.

tag: ethnicity

value: whole blood

tag: diagnosis

value: pediatric obesity


title: STOMP sample 6-0299-03


title: NA12878 EPIC


title: S1236-00023

tag: patient age (years)

tag: psa (ng/ml)

tag: t-stage


title: IMR-90-2 450K


title: S1236-00010

tag: gleason grade


title: S1236-00021

tag: bcr event (1=yes, 0=no)


title: S1236-00039

tag: follow-up time (bcr, months)


title: S1236-00018

tag: met event (1=yes, 0=no)


title: S1236-00011

tag: follow-up time (met, months)


title: S1236-00035


title: S1236-00007


title: S1236-00008


title: S1236-00001


title: S1236-00004


title: S1236-00014


title: S1236-00016


title: NA12878-3 EPIC

tag: cell type


title: S1236-00006


title: IMR-90 EPIC


title: STOMP sample 6-0301-03

value: Male


title: CSF_TREATED_REP4

city: Durham

first: Dorothy

last: Sipkins

state: NC

address: 905S La Salle Street

department: Hematological Malignancies and Cell Therapy

institute: Duke University

description: NALM6 human ALL cells isolated from SCID mice after control/PI3Kd treatment

hyb_protocol: Hybridization targets were prepared with the Affymetrix WT Plus Kit (Affymetrix, Santa Clara, CA) and Affymetrix GeneChip WT Terminal Labeling Kit (included with Affy WT Plus)  from total RNA, hybridized to GeneChip® Human Clariom D arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

scan_protocol: Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20

data_processing: Total RNA isolated from BM and CSF was sent for gene expression profiling using the Clariom D Human microarrays (Affymetrix, Santa Clara, USA) at the Duke Center for Genomic and Computational Biology. Raw cell intensity data was imported in to Expression Console (Affymetrix, Santa Clara, USA) and BM arrays (vehicle and GS-649443 samples), and CSF arrays (vehicle and GS-649443) were normalized using the RMA algorithm. Gene level differential expression analysis was performed using the Transcript Analysis Console (v3.1.0.5: Affymetrix, Santa Clara, USA) and ANOVA statistical analysis performed on the BM and CSF arrays separately. Transcripts identified to be differentially regulated in the BM, or CSF samples by ±1.5-fold with a p-value <0.05 were carried forward for pathway analysis.

source_name: cerebrospinal fluid, treated with PI3Kd treated

label_protocol: Affymetrix WT Plus Kit (PN 902280) and GeneChip WT Terminal Labeling Kit (PN 900670)

growth_protocol: NALM6 cells were engrated in SCID mice, which were treated with control/PI3Kd until animals reached clinical endpoint.

extract_protocol: Mouse femurs were collected and BM cells were aspirated with RPMI1640 containing 10% FBS. Murine spleen tissues were homogenized in RPMI1640 containing 10% FBS. The spine was removed from mice, cut into columns and aspirated with RPMI1640 containing 10% FBS to collect CSF cells. The BM, spleen and CSF cells were passed through 70 μm filters, washed with PBS and treated with ACK lysis buffer.RNA was extracted using RNAeasy kit (Qiagen, Germantown, MD) and total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

treatment_protocol: Mice were dosed twice a day with 2 mg/kg PI3Kd

value: Cerebrospinal Fluid

value: PI3Kd inhibitor


title: STOMP sample 6-0208-03


title: CSF_TREATED_REP1


title: D983 PL Rep1

tag: strain/genotype

value: delta-ahrC

tag: sample type

value: Planktonic (PL)


title: CSF_TREATED_REP3

tag: treatment


title: CSF_CONTROL_REP6

source_name: cerebrospinal fluid, control

tag: tissue

value: Control


title: CSF_CONTROL_REP5


title: brain_MCAO operated_4 (mRNA)

tag: gender

value: male

tag: age

value: 8 weeks old

tag: stress

value: brain


title: CSF_TREATED_REP2


title: S30um-3

city: QingDao

first: Zhang

middle: Rui

last: Qian

state: ShanDong

address: Great Wall Road

institute: Qingdao Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 2.1.0 with default parameters
Count gene expression using htseq with default parameters
Genome_build: ASM130575v1
Supplementary_files_format_and_content: tab-delimited text files include gene expression count for each Sample

organism: Equus asinus africanus

source_name: ovary granulosa cell

growth_protocol: Donkey granulosa cells (dGCs) were aspirated from the antral follicles using a 10 ml syringe

extract_protocol:
Total RNA was extracted from the cultured GCs by the use of an RNAprep pure MicroKit in line with the manufacturer’s instruction (Aidlab, RN07, Beijing, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ZEA was added to the cultured medium at final concentrations of the 10 µM or 30 µM, then the cells were incubated with ZEA for 72 h. The control and 10 μM ZEA group added the same dose of DMSO to 30 μM ZEA group for accuracy.

value: 30 um Zearalenone

value: Granulosa cell

value: Ovary


title: OG1RF PL Rep1


title: CSF_CONTROL_REP4


title: CSF_CONTROL_REP3


title: dMLL3/4 RNAi Drosophila pre-ZGA embryos; bio. rep. 1

city: Oeiras

first: Jorg

middle: D

last: Becker

address: Rua da Quinta Grande No 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

description:
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
dMLL3/4RNAi_1

hyb_protocol: 3.5µg of the amplified, fragmented and labeled ss-cDNA were prepared in a 150µl hybridization cocktail (containing hybridization controls) and 120µl were used for the hybridization

scan_protocol: The array strips were subsequently washed, double-stained and scanned. The hybridization, washing and scanning were done on an Affymetrix GeneAtlas System.

data_processing: The 4 scanned arrays were analyzed with Affymetrix Expression Console software using RMA to obtain expression values.

source_name: Drosophila embryos before nuclear cycle 9 (maternal transcripts)

label_protocol: Total RNA was processed for hybridization onto Drosophila Gene 1.1 ST Array Strip using a GeneChip WT PLUS Reagent Kit and a GeneAtlas Hybridization, Wash and Stain Kit for WT Array Strips according to manufacturer’s instructions. Briefly, 100ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Poly-A RNA Control Kit) were reverse transcribed for synthesis of single-stranded cDNA. After a second-strand synthesis, the obtained double-stranded cDNA was used as template for an in vitro transcription (IVT) reaction to generate amplified cRNA. Fifteen micrograms of purified cRNA were then used for a second cycle of single-strand cDNA synthesis, after which 5.5 μg of ss-cDNA was fragmented and end-labeled.

growth_protocol: Egg laying cages with 40 females and approximately 20 males were maintained at 25ºC for 48 hours prior to analysis. Embryos were collected in apple juice agar plates (up to 30 minutes after egg laying) and immediately processed.

extract_protocol: Total RNA was extracted using the PureLink RNA Mini Kit (Ambion).

treatment_protocol: Embryos were dechorionated with 50% bleach and manually selected under the dissecting scope for the absence of pole cells and cortical nuclei.

value: dechorionated embryos

tag: cross

value: F1 from Bloomington stock no. 36916 crossed to nos-GAL4

value: embryos younger than nuclear cycle 9, i.e. before pole cells budding

tag: genotype

value: dMLL3/4 depleted


title: Control Drosophila pre-ZGA embryos; bio. rep. 1

description:
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
ControlRNAi_1

value: F1 from Bloomington stock no. 35785 crossed to nos-GAL4

value: control


title: dMLL3/4 RNAi Drosophila pre-ZGA embryos; bio. rep. 2

description:
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
dMLL3/4RNAi_2


title: Control Drosophila pre-ZGA embryos; bio. rep. 2

description:
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
ControlRNAi_2


title: R5Delta983BIO Rep2

description:
Mutant
Growth conditions: M9-YE, CBR
Galaxy33, OG1RF R6_R7_D983_R4_R5 PLvsBIO

value: Biofilm (BIO)


title: IMR-90-3 EPIC

value: Female

tag: cell line

value: Fetal lung fibroblast


title: S30um-2


title: S30um-1


title: CSF_CONTROL_REP2

value: Cerebrospinal Fluid


title: BM_TREATED_REP4

source_name: bone marrow, treated with PI3Kd inhibitor

value: Bone Marrow

value: PI3Kd inhibitor


title: HUVECs_H7

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

institute: Medical University of Gdansk

description:
H7_ACAGTG
H5_S8-READs

data_processing:
Qiagen’s Geneglobe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances
Only miRNA with 2 fold changes verus normoxic control in at least one experimental condition were considered
The analyses of the differential expression of small RNAs between the control (normoxia) and the experimental samples were performed with geNorm (Gene Globe Software)
Genome_build: hg19
Supplementary_files_format_and_content: reads per sample; fold-change

source_name: HUVECs

growth_protocol: Primary HUVECs (passages 2-6 were used) pooled from 10 independent donors that were obtained from Cellworks (UK, division of Catalog Medsystems Ltd) and maintained until passage five in EGM-2 BulletKit™ medium (Lonza). Cells were split either into 6-well plates or 10 cm dishes and allowed to grow to 70-80% confluence prior to the start of the experiments.

extract_protocol:
Total RNA containing the microRNA fraction was isolated using miRNeasy kit (Qiagen) according to the manufacturer’s protocol.
MiRNA sequencing libraries were prepared using QIAseq miRNA library kit (Qiagen) following the manufacturer’s instructions and followed by sequencing on an Illumina NextSeq instrument. Using Qiagen’s Geneglobe Software, sequencing reads were aligned to the human reference genome assembly (hg19) followed by transcript assembly and estimation of the relative abundances

treatment_protocol: Hypoxia was induced in a CO2/O2 incubator  for hypoxia research (Tri-gas Binder CB150). Briefly, cells were cultured in 35 mm cm dishes at 0.9% O2 for the time periods specified. Control cells were maintained in normoxic conditions in the same incubator and harvested at the specified times. Cells maintained in cyclic hypoxia were cultured at 0.9% O2 for 1 hour and then in normoxia for 36 minutes for the specified number of cycles (1 h 36 min per cycle).

value: primary endothelial cells 10 donors pool

tag: passages

tag: exposed to

value: 14h and 24 min of hypoxia (0.9% O2)

tag: molecule subtype

value: miRNA


title: BM_TREATED_REP3


title: BM_TREATED_REP6


title: S10um-3

value: 10 um Zearalenone

value: Granulosa cell


title: HUVECs_H5

description:
H5_TGACCA
H2_S7-READs

value: 8h of hypoxia (0.9% O2)


title: R4Delta983PL Rep1

value: delta-ahrC

value: Planktonic (PL)


title: S10um-2

value: Ovary


title: R5Delta983PL Rep2


title: HUVECs_H2

description:
H2_CGATGT
H0_S6-READs

value: 3h and 12 min of hypoxia (0.9% O2)


title: S10um-1


title: R7OG1RFBIO Rep2

description:
Wild-type
Growth conditions: M9-YE, CBR
Galaxy33, OG1RF R6_R7_D983_R4_R5 PLvsBIO


title: R4Delta983BIO Rep1


title: STOMP sample 6-0303-03

tag: ethnicity

value: whole blood

tag: diagnosis

value: pediatric obesity


title: BM_TREATED_REP5


title: BM_TREATED_REP2


title: R6OG1RFBIO Rep1

value: Biofilm (BIO)


title: R7OG1RFPL Rep2


title: CSF_CONTROL_REP1

value: Control


title: BM_TREATED_REP1


title: HUVECs_C9

description:
C9_CAACTA
C9_S14-READs

value: 9 cycles of hypoxia (1h hypoxia 0.9% O2 and 36 min reoxygenation)


title: R6OG1RFPL Rep1