title: Patient 11 4195

description:
4195
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 10 4194

status: Public on Oct 26 2018

type: genomic

city: Cantanhede

first: Helena

last: Vazao

address: Biocant Park Nucleo4, 4A

department: HeartGenetics

country: Portugal

institute: HeartGenetics

description:
4194
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

hyb_protocol: Not applicable

scan_protocol: The status of 171 mutations (by the reading of 61 positions) in 6 genes (OncoAlvo® Panel) was assessed using a high-throughput DNA Microchip platform, the iPLEX® system (Agena Bioscience, Inc). This array platform allows an optimal genetic analysis by combining the benefits of accurate primer extension chemistry with MALDI-TOF mass spectrometry. The different masses of each generated PCR product are then converted into mutational status information.

data_processing: The processed data (attached as 14 .txt files) were generated by software computing analysis. The processing was made by normalizing the peak intensity (converted into fraction of mutant alleles) of each genetic variant of each sample by the peak intensity of the correspondent variant of the average of 96 baseline samples. As the baseline samples serve as the minimum threshold, the computer software does not give a processed data file for them; thus, there are no processed data .txt files for these 96 samples. The processed data files only show the positive results.

molecule: genomic DNA

organism: Homo sapiens

source_name: metastatic colorectal carcinoma

label_protocol: Not applicable

growth_protocol: FFPE human colon adenocarcinoma.

extract_protocol: A commercial kit was used to perform DNA extraction and purification from FFPE colon adenocarcinoma. DNA concentration and quality were evaluated with MultiskanGo spectrophotometer (Thermo Scientific).

treatment_protocol: No treatment applied.

tag: tissue

value: FFPE colon adenocarcinoma


title: AFF4_SW1271_rep2

type: SRA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

description: ChiP-seq AFF4

library_source: genomic

data_processing:
ChIP-seq was done according to a previously published protocol (Liang et al., 2015). Briefly, cells were crosslinked with 1% paraformaldehyde for 10 min and were quenched with glycine for 5 min at room temperature. Fixed chromatin was sonicated with a Covaris Focused-ultrasonicator for 6 minutes and immunoprecipitated with the indicated antibody. Libraries were prepared with the HTP Library Preparation Kit for Illumina (KAPA Biosystems) and sequenced on a NextSeq 500. ChIP-seq reads were aligned to the Drosophila genome (UCSC dm3) or human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm). Peaks were called using MACS (model based analysis of ChIP-Seq) (Zhang et al., 2008) version 1.4.2 using default parameters. Ensembl version 75 transcripts were chosen with the highest total coverage from the annotated TSS to 200 nt downstream for protein coding genes that also have a refseq identifier, were at least 2 kb long, and 2 kb away from the nearest gene. For pausing indexes, the promoter region was defined as -200 bp upstream to 400 bp downstream, and the body region was the remainder of the entire gene body. The ratio of the average coverage (r.p.m) of the promoter over the average coverage of the gene body was then taken to be the Pausing Index. ECDF plots were made in R version 3.3.3 using the ecdf function. P-values were calculated with a one-sided Kolmogorov-Smirnov test. Heatmaps tables were made for the indicated windows around the TSS or TES using the average coverage (r.p.m) in 25bp & 50bp bins (50bp bins for 50kb downstream of the TSS). Meta gene tables were made by approximating the coverage across all genes to the same length. All ChIP-seq heatmaps were sorted by the decreasing coverage in indicated windows by the control sample and visualized using JavaTreeView version 1.6.4 (Saldanha, 2004). Average profile plots were made by averaging the coverage for all genes using colMeans in R.
PRO-seq was performed according to the previously published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 µM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5’ RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp. After sequencing, adaptors were removed with cutadapt version 1.14 (Martin, 2011). Reads were trimmed from the 3prime end to 36bp with removing low quality bases using Trimmomatic version 0.33 (Bolger et al., 2014) requiring a minimal read length of 16nt. Reads were then mapped to the human genome (UCSC hg19) using Bowtie version 1.1.2 (Langmead et al., 2009). Only uniquely mapped reads with up to 2 mismatches in the entire read were used for further analysis. Read where then converted to single nucleotide 3prime BigWig strand specific tracks by taking 5prime positions of the read (using bedtools genomecov version 2.17 (Quinlan and Hall, 2010) with options -strand -bg -5. Strands were then swapped to give the correct orientation with the 5prime end now becoming the 3prime end of the read (Mahat et al., 2016a). PRO-seq genome browser track examples show coverage of the entire length of the read for easier visualization. For the Pol II-selected genes described above, we found the site of maximum coverage, in the region from the annotated TSS to 500bp downstream, to which we assign the pausing site. Heatmap tables were made as described above but instead centering at this calculated pausing site.
4sU-seq reads were aligned to the human genome (UCSC hg19). Alignments were processed with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 50 bp read. The resulting reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million, rpm) for each strand. Genes used for calculating elongation rates were required to have an observed transcription start site with 4sU RNA signals, a minimum gene length of 50 kb and must be at least 2kb away from the transcription start site of another gene. Genes were further filtered for activity/coverage by filtering on the reads-per-million count within each gene body (+400 to TES) in our untreated, wildtype data. Thus, the read coverage must be present at levels above background (RPM > 1). Elongation rates were calculated in two ways. 1. Advancing waves were identified using a three state Hidden Markov Model (HMM) that was previously developed and implemented on GRO-seq data from a human cell line (Danko et al., 2013). 2. Peaks were called with SICER version 1.1 (Zang et al., 2009) with the following options --windowSize 150 --fragSize 150 --gapSize 3 with strand separated reads over input. These strand-specific peaks were filtered for an FDR < 0.01. Peaks were merged together if there was a gap less than 2kb. Peaks were then overlapped with TSS’s of genes on the same strand that were greater than 50kb. The distance traveled was calculated from the TSS to the 3’ end of the merged peak and the elongation rate in kb/min was calculated using the time after release.
Total RNA-seq reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic version 0.33 (Bolger et al., 2014) and then aligned to the human genome (UCSC hg19, using Tophat version 2.1.0) with the following options -no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --num-threads 10 --max-multihits 20 then post filtering for uniquely mapped reads using the NH flag. Protein coding genes from Ensembl version 75 that also had a refseq identifier were only considered for analysis. Raw read counts were normalized to r.p.m. per sample and then displayed in the UCSC genome browser as bigWig-formatted coverage tracks. Exonic reads were assigned to specific genes from Ensembl release 75 using Bioconductor package GenomicRanges countOverlaps. We used the R Bioconductor package edgeR, version 3.12.0 to fit the data to a negative binomial generalized log–linear model and estimate a dispersion parameter. We used an adjusted P value threshold of 0.001 and a log2 r.p.m cut off of 3 to identify genes significantly differentially expressed in one experimental condition relative to another. GO term analysis was done using Metascape
Genome_build: hg19, dm3
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

growth_protocol: HEK293T (ATCC), HCT116 (ATCC), Flag-AFF1 and Flag-AFF4 stable cell lines were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, catalog No. F6178, Sigma). NCI-H2171 [H2171] (ATCC CRL-5929) and SW1271 (ATCC CRL-2177) small cell lung cancer cells were maintained in RPMI-1640 and DMEM/F12 medium supplemented with 20% FBS. The Jurkat J-Lat full-length cells (6.3) (Cat # 9846) were provided by the NIH AIDS Reagent Program and cultured in RPMI-1640 medium with 10% FBS. Drosophila S2 cells were maintained in Schneider's medium. The wild-type Pol II, slow Pol II (R749H) and fast Pol II (E1126G) mutant HEK293T cell lines (Fong et al., 2014) were provided by Dr. David Bentley (University of Colorado School of Medicine) and cultured in DMEM with 10% FBS.  After induction with doxycycline (2.0 μg/mL) for 16 hr, speed-mutant cells were treated with α-amanitin (2.5 μg/mL, Sigma) for 42 hr prior to ChIP-seq analysis.

extract_protocol:
Total RNA was extracted using Trizol and QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit
PRO-seq was performed according to the previously published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 μM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5’ RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp.
4sU-seq Cell Labeling with 4sU, RNA Extraction and Fragmentation 20-50 million cells were treated with flavopiridol for 1 hour and washed with PBS twice. The cells were labeled in media with 500 μM 4-thiouridine (4sU, Sigma-Aldrich, St. Louis, MO, USA.) and harvested through centrifugation for 3 min at 3,000 rpm. RNA was extracted with 4 mL Trizol (Invitrogen) and 5 μL 20 mg/mL glycogen. The extracted RNA was further fragmented by base hydrolysis in 0.2 M NaOH on ice for 18 min, neutralized by adding 1x volume of 1 M Tris-HCl pH 6.8 and precipitated with isopropanol.

treatment_protocol: Treatment withKL-1 or KL-2 inhibitors was administrated only once

tag: cell type

value: small cell lung cancer

tag: mutation

value: No MYC amplifcation

tag: antibody

value: homemade AFF4NT


title: AFF4_SW1271_rep1

description: ChiP-seq AFF4


title: Patient 9 4193

description:
4193
Raw data file: G1156558.xml
Processed data file: G1156558_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: AFF4_H2171_rep2

description: ChiP-seq AFF4

value: MYC amplifcation


title: SAMP8, 9 months_rep2

type: RNA

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

description:
Senescent-Accelerated Prone Mouse 8
SAMPLE 11

data_processing:
miRNAs was measured in a CFX384 Touch Real-Time PCR Detection System through SYBR-green-based real time PCR.
The mean of the relative gene expression of the small non-coding RNAs SNORD68, SNORD72, SNORD95 and SNORD96A was used to normalize the results since they presented similar expression levels between groups and the lowest Standard Deviations (SD) among all of the housekeepings proposed.
Fold Change (target gene signal normalized to housekeeping genes; e.g., 2ΔCt, Where -ΔCt = -(Ct_Target- Ct_Mean_Housekeeping_genes)

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: SAMP8, 9 months

label_protocol: SYBR Green-labeling according to manufacturer's protocol.

growth_protocol: RNA from the hippocampus of SAMR1 and SAMP8 mice were converted to cDNA through a reverse trancription reaction using miScript II RT Kit (Qiagen, Hilden Germany) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted employing the mirVana RNA Isolation kit (Applied Biosystems) according to the manufacturer's instructions. The yield, purity, and quality of the samples were determined by at A260/280 ratio in a NanoDrop ND-1000 apparatus (Thermo Scientific).

treatment_protocol: Hippocampus extraction from mice, microRNA extraction with mirVana kit to obtain microRNAs, RT-PCR with Thermofisher.

tag: condition

value: Senescent-Accelerated Prone

tag: age

value: 9 months

value: Hippocampus


title: SAMP8, 9 months_rep3

description:
Senescent-Accelerated Prone Mouse 8
SAMPLE 12


title: Patient 8 4192

description:
4192
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: SAMP8, 9 months_rep1

description:
Senescent-Accelerated Prone Mouse 8
SAMPLE 10


title: AFF4_H2171_rep1

description: ChiP-seq AFF4


title: ELL2_H2171_rep2

description: ChiP-seq ELL2

value: homemade ELL2


title: SAMR1, 9 months_rep3

description:
Senescent-Accelerated Resistant Mouse 1
SAMPLE 9

source_name: SAMR1, 9 months

value: Senescent-Accelerated Resistant


title: AFF1_SW1271_rep2

description: ChiP-seq AFF1

value: homemade AFF1CT


title: Patient 7 4191

description:
4191
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: SAMR1, 9 months_rep2

description:
Senescent-Accelerated Resistant Mouse 1
SAMPLE 8


title: AFF1_SW1271_rep1

description: ChiP-seq AFF1


title: SAMR1, 9 months_rep1

description:
Senescent-Accelerated Resistant Mouse 1
SAMPLE 7


title: Patient 5 4185

description:
4185
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: d5_R2

city: Worcester

first: Guangping

last: Gao

state: Massachusetts

address: Albert Sherman Center (AS6-2011)

department: Gene Therapy Center

institute: University of Massachusetts, Medial School

description: 5 days post-treatment

data_processing:
Data were normalized to the top 100 most highly expressed miRNAs in each sample, and the average ± 2 SD of six internal negative control probes were used to determine background detection threshold. We computed the mean expression values of each miRNA across our cohort to filter for expressed miRNAs,
A threshold cutoff-point of 1.0 was selected based on background detection threshold. Values exceeding this cutoff-point were considered to be indicative of relevant miRNA expression.

label: biotinylated capture probe and color coded reporter probe pairs

molecule: polyA RNA

source_name: cornea

label_protocol: Labeling was performed according to the manufacturer's instructions.

extract_protocol: A total of 100 ng of RNA was extracted from whole mouse corneas. Four corneas were pooled into one sample

value: cornea

value: 6-8 week old

tag: gender

value: female

tag: strain


title: d5_R1

description: 5 days post-treatment


title: AFF1_H2171_rep2

description: ChiP-seq AFF1


title: SAMP8, 2 months_rep2

description:
Senescent-Accelerated Prone Mouse 8
SAMPLE 5

source_name: SAMP8, 2 months

value: 2 months


title: Kidney at Colistin 0mg/kg for 7d, biological rep1

city: Daejeon

first: Jung-Hwa

last: Oh

address: 141 Gajeong-ro, Yuseong

country: South Korea

institute: Korea Institue of Toxicology

description: Gene expression data from kidney in CMS-treated rat (0 mg/kg, vehicle)

hyb_protocol: The microarrays were hybridized at 45°C at 60 rpm for 16 h. The microarrays were stained and washed using a Fluidics Station 450 system (Affymetrix).

scan_protocol: A GeneChip® Scanner 3000 (Affymetrix) was used to scan the microarrays. The reproducibility of the microarray experiments was confirmed using well-defined quality control criteria according to the manufacturer’s instructions.

data_processing: To perform preprocessing and statistical analysis of the microarray data, CHIP data was obtained using Expression Console. Normalization was performed using RMA quantile median normalization.

label: biotin

organism: Rattus norvegicus

source_name: Sprague–Dawley rat kidney from CMS-treated group (0 mg/kg)

label_protocol: cDNA synthesis, cRNA synthesis, biotin labeling, cRNA purification, and fragmentation were performed according to the manufacturer’s instructions (Affymetrix).

growth_protocol: Sprague–Dawley rats (8 weeks old) were purchased from Orient Bio Co. (Seongnam, Korea) and acclimated for 1 week prior to the experiment. All rats were housed under standard laboratory conditions on a 12 h light/dark cycle, under controlled temperature (23°C ± 3°C) and humidity (50% ± 20%).

extract_protocol: At sacrifice, the whole right kidney was extracted and frozen immediately in liquid nitrogen. Frozen samples were homogenized with a TissueLyser (Qiagen, Hilden, Germany) and total RNA was purified using an RNeasy® Mini Kit (Qiagen) according to the manufacturer’s instructions. The concentration and quality of total RNA were determined using a NanoDrop™ spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the RNA integrity was measured using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Colistin methanesulfonate sodium was purchased from Samchundang Pharm (Seoul, Korea), diluted with 0.9% saline (Dai Han Pharm, Co., Ansan, Korea), and administered (0, 25, and 50 mg/kg body weight). Each Sprague–Dawley rat was injected with a vehicle control or CMS via intraperitoneal injection daily for 7 d.

value: Sprague-Dawley

value: kidney

tag: treatment

value: control

tag: dose

tag: treatment outcome

value: no lesion


title: Kidney at Colistin 0mg/kg for 7d, biological rep2


title: Patient 4 4184

description:
4184
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma


title: SAMP8, 2 months_rep1

description:
Senescent-Accelerated Prone Mouse 8
SAMPLE 4


title: AFF1_H2171_rep1

description: ChiP-seq AFF1

value: small cell lung cancer


title: Patient 3 4183

description:
4183
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Kidney at Colistin 25mg/kg for 7d, biological rep1

description: Gene expression data from kidney in CMS-treated rat (25 mg/kg)

source_name: Sprague–Dawley rat kidney from CMS-treated group (25 mg/kg)

value: Colistin

value: tubular basophilia and dilated tubules


title: SAMR1, 2 months_rep2

description:
Senescent-Accelerated Resistant Mouse 1
SAMPLE 2

source_name: SAMR1, 2 months


title: SAMR1, 2 months_rep3

description:
Senescent-Accelerated Resistant Mouse 1
SAMPLE 3


title: Patient 1 4181

description:
4181
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Patient 6 4187

description:
4187
Raw data file: G1116205.xml
Processed data file: G1116205_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Fascin scRNAseq

city: Atlanta

first: Alberto

last: Stolfi

state: Georgia

address: 950 Atlantic Dr

department: School of Biological Sciences

institute: Georgia Institute of Technology

library_source: transcriptomic

data_processing:
Single-cell data processing (fastq generation, alignment, counting, etc) was performed using CellRanger version 2.0.0
Fastq files were generated using “cellranger mkfastq” with default arguments
Counting was done by “cellranger count” using KyotoHoya (KH) gene models, with default arguments except “--force-cells=3000”
For bulk RNA-seq, raw fastq files were first processed by STAR 2.5.2b and mapped to the Ciona robusta (formerly Ciona intestinalis type A) genome
The output bam files were then processed using Rsubread/featureCounts with the parameter "ignoreDup=TRUE" to remove reads duplication caused by library amplification
After duplication removal, the reads which mapped to the exons of KyotoHoya (KH) gene models were counted for downstream differential expression analysis
Differential expression between TH+ and Fascin+ replicates was measured by EdgeR (https://osf.io/vjq95/?view_only=18df57e03275448d88c9dd78611f7cfc)
Genome_build: Genome used was Ciona intestinalis (KH2012, Ghost Database) (Dehal et al., 2002; Satou et al., 2008). Gene model used was KyotoHoya (KH) gene model (Satou et al., 2008)
Supplementary_files_format_and_content:
[scRNAseq]  Gene-barcode matrices and per-molecule information for all molecules in HDF5 format and molecule information (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/overview)
[bulk RNAseq]  raw counts file (processed data)

organism: Ciona robusta

source_name: FACS-isolated cells

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

extract_protocol: single-cell RNAseq (10X Genomics Chromium Single Cell 3' kit v2 chemistry).  *n02* libraries contain the mapping reads while *n01* libraries contain UMI and cellular barcode reads (barcode: the first 16 bases of R1; UMI: the following 10 bases).

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

value: brain

value: Fascin>tagRFP+ cells (brain + contaminants)

tag: developmental stage

value: 20 hours post-fertilization, 18C


title: SAMR1, 2 months_rep1

description:
Senescent-Accelerated Resistant Mouse 1
SAMPLE 1

value: Senescent-Accelerated Resistant

value: Hippocampus


title: SAMP8, 2 months_rep3

description:
Senescent-Accelerated Prone Mouse 8
SAMPLE 6

value: Senescent-Accelerated Prone


title: Kidney at Colistin 50mg/kg for 7d, biological rep1

description: Gene expression data from kidney in CMS-treated rat (50 mg/kg)

source_name: Sprague–Dawley rat kidney from CMS-treated group (50 mg/kg)

value: cell necrosis, tubular degeneration/dilatation, and eosinophilic casts


title: 4h_STM-D23580_D2_292141

status: Public on Oct 25 2018

city: Oxford

first: Anna

last: Aulicino

state: Oxfordshire

address: Headley Way, Headington

department: Human Immunology Unit, WIMM

country: United Kingdom

institute: University of Oxford

data_processing:
Alignment to concatenated Homo_sapiens.GRCh38.dna.primary_assembly.fa and ERCC92.fa sequences using HISAT2 (version 2.0.3b),
Read count assigned to annotated features in concatenated Homo_sapiens.GRCh38.86.chr.gtf and ThermoFisher ERCC92.gtf using featureCounts (subread version 1.5.0-p2).
Genome_build: Homo_sapiens.GRCh38, ERCC92
Supplementary_files_format_and_content: Tabulated read counts.

source_name: Monocyte-derived dendritic cells

growth_protocol: Leukocyte Reduction System cones were obtained from the UK National Blood Centre with informed consent following local ethical guidelines. Blood was diluted in Phosphate-Buffered Saline (PBS) and layered on a standard density gradient (LymphoprepTM). Peripheral Blood Mononuclear Cells (PBMC) were collected from the interface and washed in PBS at 4 C. Monocytes were obtained by magnetic positive selection, using the human anti-CD14+ MicroBeads (Miltenyi Biotec, Germany) according to the manufacturer’s protocol.  Freshly isolated monocytes were differentiated into Dendritic Cells (MoDCs)  in the presence of 40 ng/mL of recombinant human (rh) Granulocyte Macrophage-Colony-Stimulating Factor (GM-CSF; Peprotech) and 40 ng/mL rh Interleukin-4 (IL-4; Peprotech).

extract_protocol:
5'000 live cells were sorted in eppendorf containig 10uL of PBS. RNA was extracted with Qiagen RNeasy Micro kit and 1 uL of RNA was added to 4uL of lysis buffer (0.4% Triton, 2U/uL RNase inhibitor (Clonotech, Takara), 7.5uM oligo dT (Biomers) and 10mM dNTP [supplemented with ERCC spike-in 1:10,000,000] (Invitrogen)) and processed as for single cells.
Nextera XT DNA sample preparation kit with the dual index strategy

treatment_protocol: DCs were infected with S. Tyhpimurium strain LT2 or D23580 at a MOI of 10 or left uninfected for 2h, 4h or 6h before sorting.

tag: infection

tag: status

value: Infected

tag: time

tag: well


title: 4h_Mock_D2_289105

value: Mock

value: Uninfected


title: 6h_STM-D23580_D3_296189

value: Exposed


title: 2h_STM-D23580_D3_294165


title: 4h_STM-D23580_D3_295177


title: 4h_STM-LT2_D2_290117


title: 4h_STM-LT2_D2_291129


title: 4h_STM-D23580_D2_293153


title: Patient 59 4264

description:
4264
Raw data file: G1116574.xml
Processed data file: G1116574_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.


title: Kidney at Colistin 25mg/kg for 7d, biological rep3

value: Sprague-Dawley

value: kidney


title: 4h_STM-D23580_D3_287176


title: 6h_STM-D23580_D3_288188


title: Kidney at Colistin 25mg/kg for 7d, biological rep2


title: Kidney at Colistin 0mg/kg for 7d, biological rep3

value: control

value: no lesion


title: Kidney at Colistin 50mg/kg for 7d, biological rep3

value: Colistin


title: 2h_STM-D23580_D2_285152


title: 2h_STM-LT2_D2_283128


title: Patient 2 4182

description:
4182
Raw data file: G1104129.xml
Processed data file: G1104129_processed.txt
Besides all these 457 samples genotyping, another 96 non-mutated control samples were analysed to define the basal threshold. All testing samples were normalized using that threshold.

value: FFPE colon adenocarcinoma


title: 2h_STM-D23580_D2_284140


title: 2h_STM-LT2_D2_282116


title: Kidney at Colistin 50mg/kg for 7d, biological rep2


title: 6h_STM-LT2_D3_280187


title: 2h_Mock_D2_281104


title: 4h_STM-LT2_D3_279175


title: 2h_STM-LT2_D3_278163


title: 6h_STM-D23580_D1_276139


title: 6h_STM-LT2_D1_275127


title: 2h_STM-D23580_D3_286164


title: 6h_STM-LT2_D1_274115


title: 2h_STM-LT2_D3_270162


title: 4h_STM-LT2_D1_267126


title: 6h_Mock_D1_273103


title: 6h_Mock_D3_264185


title: 4h_Mock_D3_263173


title: 2h_STM-D23580_D1_261149


title: 6h_STM-D23580_D2_204142


title: 4h_STM-LT2_D3_271174


title: 6h_STM-LT2_D2_203130


title: 2h_Mock_D3_262161


title: 4h_Mock_D1_265102


title: 6h_STM-LT2_D2_202118


title: 2h_STM-D23580_D1_260137


title: 6h_STM-D23580_D2_205154


title: 6h_STM-D23580_D1_277151


title: 6h_Mock_D2_201106


title: 4h_STM-D23580_D1_268138


title: 4h_Mock_uninfected_256207

extract_protocol:
Live single cells were sorted into 96-well plates filled with 4uL of lysis buffer (0.4% Triton, 2U/uL RNase inhibitor (Clonotech, Takara), 7.5uM oligo dT (Biomers) and 10mM dNTP [supplemented with ERCC spike-in 1:10,000,000] (Invitrogen))
Nextera XT DNA sample preparation kit with the dual index strategy

value: uninfected

tag: plate

tag: lane


title: 6h_Mock_uninfected_256208


title: 6h_LT2_infected_256206

value: infected


title: 2h_Mock_D1_257101


title: 6h_LT2_infected_256205


title: 4h_STM-D23580_D1_269150


title: 2h_STM-LT2_D1_258113


title: 4h_D23580_infected_256204


title: 4h_D23580_infected_256203


title: 4h_STM-LT2_D1_266114


title: 6h_STM-LT2_D3_272186


title: 2h_LT2_infected_256202


title: 4h_Mock_uninfected_255207


title: 6h_Mock_uninfected_255208


title: 6h_LT2_infected_255206


title: 6h_LT2_infected_255205


title: 2h_LT2_infected_255202


title: 4h_D23580_infected_255203


title: 2h_STM-LT2_D1_259125


title: 6h_Mock_uninfected_254208


title: 4h_D23580_infected_255204


title: 6h_LT2_infected_254206


title: 6h_LT2_infected_254205


title: 4h_D23580_infected_254204


title: 4h_Mock_BULK_253207

value: BULK


title: 6h_Mock_uninfected_253208


title: 2h_LT2_infected_254201


title: 2h_LT2_infected_254202


title: 4h_D23580_infected_253203


title: 2h_LT2_infected_253201


title: 4h_D23580_infected_254203


title: 6h_LT2_infected_253206


title: 4h_Mock_uninfected_254207


title: 6h_Mock_uninfected_252208


title: 2h_Mock_uninfected_252207


title: 6h_LT2_infected_253205


title: 2h_LT2_infected_253202


title: 2h_LT2_infected_256201


title: 6h_LT2_infected_252206


title: 2h_LT2_infected_255201


title: 6h_LT2_exposed_252205

value: exposed


title: 4h_D23580_infected_252204


title: 4h_D23580_exposed_252203


title: 2h_LT2_infected_252202


title: 6h_Mock_uninfected_251208


title: 2h_Mock_uninfected_251207


title: 2h_LT2_exposed_252201


title: 4h_D23580_infected_251204


title: 6h_LT2_exposed_251205


title: 4h_D23580_infected_253204


title: 6h_LT2_infected_251206


title: 4h_D23580_exposed_251203


title: 2h_LT2_exposed_251201


title: 2h_LT2_infected_251202


title: 6h_LT2_infected_250206


title: 6h_Mock_uninfected_250208


title: 2h_Mock_uninfected_250207


title: 4h_D23580_exposed_250203


title: 4h_D23580_infected_250204


title: 6h_LT2_exposed_250205


title: 2h_LT2_infected_250202


title: 2h_LT2_exposed_250201


title: 6h_Mock_BULK_249208


title: 6h_LT2_infected_249206


title: 2h_LT2_exposed_249201


title: 2h_LT2_infected_249202


title: 4h_Mock_uninfected_232208


title: 2h_Mock_uninfected_249207


title: 6h_LT2_exposed_232206


title: 6h_LT2_exposed_232205


title: 4h_D23580_exposed_249203


title: 4h_D23580_infected_249204


title: 2h_LT2_exposed_232202


title: 2h_Mock_uninfected_232207


title: 2h_Mock_uninfected_231207


title: 6h_LT2_exposed_231206


title: 6h_LT2_exposed_231205


title: 2h_LT2_exposed_232201


title: 6h_LT2_exposed_249205


title: 4h_D23580_exposed_231203


title: 4h_D23580_exposed_231204


title: 2h_Mock_uninfected_230207


title: 6h_LT2_exposed_230206


title: 2h_LT2_exposed_230202


title: 4h_D23580_exposed_230204


title: 4h_D23580_exposed_230203


title: 6h_LT2_exposed_230205


title: 4h_D23580_exposed_232203


title: 4h_D23580_exposed_232204


title: 4h_Mock_uninfected_231208


title: 4h_Mock_uninfected_229208


title: 2h_Mock_BULK_229207


title: 2h_LT2_exposed_230201


title: 6h_LT2_exposed_229206


title: 4h_Mock_uninfected_230208


title: 2h_LT2_exposed_229202


title: 6h_Mock_uninfected_228231


title: 6h_D23580_infected_228229


title: 2h_LT2_exposed_229201


title: 2h_LT2_exposed_231201


title: 2h_D23580_infected_228225


title: 4h_D23580_exposed_229204


title: 6h_D23580_infected_228230


title: 6h_LT2_exposed_229205


title: 4h_LT2_infected_228228


title: 2h_LT2_exposed_231202


title: 4h_D23580_exposed_229203


title: 2h_D23580_infected_228226


title: 6h_Mock_uninfected_227231


title: 6h_D23580_infected_227230


title: 6h_D23580_infected_227229


title: 4h_LT2_infected_227228


title: 4h_LT2_infected_227227


title: 6h_Mock_uninfected_227232


title: 2h_D23580_infected_227225


title: 2h_D23580_infected_227226


title: Blank_Blank_Blank_228232

value: Blank


title: 4h_LT2_infected_228227


title: 6h_Mock_uninfected_226232


title: 6h_Mock_uninfected_226231


title: 6h_D23580_infected_226229


title: 6h_D23580_infected_226230


title: 4h_LT2_infected_226227


title: 2h_D23580_infected_226226


title: 4h_LT2_infected_226228


title: 6h_Mock_uninfected_225231


title: 2h_D23580_infected_226225


title: 4h_LT2_infected_225227


title: 4h_LT2_infected_225228


title: 2h_D23580_infected_225226


title: 6h_D23580_infected_225230


title: 4h_LT2_infected_208228


title: 6h_D23580_exposed_208229


title: 2h_D23580_infected_225225


title: 6h_Mock_uninfected_225232


title: 6h_Mock_uninfected_208232


title: 6h_D23580_infected_225229


title: 6h_Mock_uninfected_207231


title: 2h_D23580_infected_208226


title: 6h_Mock_uninfected_208231


title: 2h_D23580_exposed_208225


title: 6h_Mock_uninfected_207232


title: 6h_D23580_infected_207230


title: 6h_D23580_exposed_207229


title: 4h_LT2_infected_207228


title: 2h_D23580_infected_207226


title: 2h_D23580_exposed_207225


title: 4h_LT2_exposed_207227


title: 6h_Mock_uninfected_206231


title: 6h_Mock_uninfected_206232


title: 6h_D23580_infected_208230


title: 6h_D23580_infected_206230


title: 6h_D23580_exposed_206229


title: 4h_LT2_infected_206228


title: 4h_LT2_exposed_206227


title: 6h_Mock_uninfected_205232


title: 2h_D23580_exposed_206225


title: 4h_LT2_exposed_208227


title: 6h_D23580_exposed_205229


title: 4h_LT2_infected_205228


title: 6h_Mock_uninfected_205231


title: 6h_Mock_uninfected_204232


title: 4h_LT2_exposed_205227


title: 6h_Mock_uninfected_204231


title: 2h_D23580_infected_206226


title: 2h_D23580_infected_205226


title: 2h_D23580_exposed_205225


title: 4h_LT2_exposed_204228


title: 6h_D23580_exposed_204229


title: 6h_D23580_exposed_204230


title: 4h_LT2_exposed_204227


title: 2h_D23580_exposed_204225


title: 2h_D23580_exposed_204226


title: 6h_Mock_uninfected_203232


title: 6h_Mock_uninfected_203231


title: 6h_D23580_exposed_203230


title: 6h_D23580_infected_205230


title: 6h_D23580_exposed_203229


title: 4h_LT2_exposed_203228


title: 4h_LT2_exposed_203227


title: 2h_D23580_exposed_203226


title: 6h_Mock_uninfected_202232


title: 6h_Mock_uninfected_202231


title: 2h_D23580_exposed_203225


title: 6h_D23580_exposed_202230


title: 6h_D23580_exposed_202229


title: 4h_LT2_exposed_202228


title: 4h_LT2_exposed_202227


title: 2h_D23580_exposed_202226


title: 6h_Mock_uninfected_201231


title: 2h_D23580_exposed_202225


title: 6h_Mock_uninfected_201232


title: 4h_LT2_exposed_201228


title: 6h_D23580_exposed_201229


title: 6h_D23580_exposed_201230


title: 4h_LT2_exposed_201227


title: 2h_D23580_exposed_201225


title: Pineo-113FH_P2

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: PDOX

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

tag: material

value: Frozen

tag: tumor subgroup

value: PB


title: PBT-08FH_P2


title: PBT-06FH_P5


title: PBT-08FH_ht

source_name: human tumor


title: PBT-05FH_P5


title: PBT-08FH_P5


title: PBT-07FH_P5


title: PBT-04FHTC_P12

source_name: cell line


title: PBT-04FH_ht

value: FFPE


title: PBT-06FH_ht


title: PBT-04FH_P5


title: PBT-07FH_ht


title: 2h_D23580_exposed_201226


title: PBT-05FH_ht


title: PBT-04FH_P2


title: PBT-07FH_P2


title: PBT-02FH_P1


title: PBT-02FH_ht


title: PBT-06FH_P2


title: 4h_Mock_uninfected_256231

value: Mock


title: 6h_LT2_infected_256230


title: 4h_Mock_uninfected_256232


title: PBT-05FHTC_P13


title: PBT-02FH_P5


title: PBT-05FH_P2


title: 6h_LT2_infected_256229


title: 2h_LT2_infected_256226


title: PBT-01FH_P2


title: 4h_D23580_infected_256227


title: 4h_Mock_uninfected_255232


title: Med-813FH_P1


title: PBT-01FH_ht


title: 2h_LT2_infected_256225


title: PBT-03FH_P1


title: 6h_LT2_infected_255230


title: 4h_Mock_uninfected_255231


title: Med-913FH_ht


title: 6h_LT2_infected_255229


title: 4h_D23580_infected_255228


title: Med-913FH_P1


title: 2h_LT2_infected_255225


title: 4h_Mock_uninfected_254232


title: 6h_LT2_infected_254230


title: 4h_Mock_uninfected_254231


title: 6h_LT2_infected_254229


title: Med-610FH_P4


title: 4h_D23580_infected_254228


title: 4h_D23580_infected_256228


title: Med-411FH_P5


title: 4h_D23580_infected_255227


title: Med-610FH_P2


title: 2h_LT2_infected_254226


title: Med-314FH_P2


title: 4h_Mock_uninfected_253232


title: Med-813FH_P5


title: Med-314FH_P4


title: 6h_LT2_infected_253230


title: Med-211FH_P4


title: Med-610FH_ht


title: 2h_LT2_infected_254225


title: Med-411FH_P2


title: Med-2312FH_ht


title: Med-2312FH_P5


title: Med-2312FH_P2


title: 4h_Mock_uninfected_253231


title: 2h_LT2_infected_255226


title: 6h_LT2_infected_253229


title: 4h_D23580_infected_254227


title: 2h_LT2_infected_253226


title: Med-211FH_ht


title: 2h_LT2_infected_253225


title: 4h_D23580_infected_253227


title: Med-211FH_P2


title: Med-2112FH_P2-2


title: Med-210FH_P2


title: Med-210FH_P5


title: Med-1911FH_P2


title: Med-210FH_ht


title: 4h_Mock_uninfected_252231


title: 4h_D23580_infected_253228


title: 4h_Mock_uninfected_252232


title: Med-314FH_ht


title: 6h_LT2_infected_252230


title: Med-1712FH_P1


title: 2h_LT2_infected_252226


title: 4h_D23580_infected_252228


title: Med-1712FH_P4


title: 2h_LT2_exposed_252225


title: 4h_D23580_exposed_252227


title: 6h_LT2_exposed_252229


title: Med-2112FH_ht


title: 4h_Mock_uninfected_251232


title: 4h_Mock_uninfected_251231


title: Med-1911FH_ht


title: 6h_LT2_exposed_251229


title: 4h_D23580_infected_251228


title: 4h_D23580_exposed_251227


title: Med-1512FH_P5


title: 2h_LT2_infected_251226


title: 2h_LT2_exposed_251225


title: Med-1512FH_P2


title: 6h_LT2_infected_251230


title: 4h_Mock_uninfected_250232


title: 4h_Mock_uninfected_250231


title: Med-114FH_ht


title: Med-113FH_P1


title: Med-114FH_P5


title: 6h_LT2_exposed_250229


title: GBM-611FH_P1


title: 4h_D23580_infected_250228


title: Med-113FH_P5


title: 4h_D23580_exposed_250227


title: GBM-311FH_P5


title: 2h_LT2_infected_250226


title: Med-114FH_P2


title: GBM-611FH_P4


title: 2h_LT2_exposed_250225


title: GBM-311FH_ht


title: GBM-511FHTC_P6


title: EPD-710FH_ht


title: EPD-613FH_P2


title: Med-1911FH_P4


title: Med-113FH_ht


title: EPD-210FHTC_P3


title: NBL-V9

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: After washing and scanning, resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.

data_processing: Data normalization was done in R (version 3.5.1) using the quantile algorithm from Bioconductor package ‘preprocessCore’ (version  1.42.0). A reference dataset of 476 normalized 44K microarrays (see PMID:20676065) was used as target distribution.

source_name: tumor sample

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: 30-60mg of snap-frozen neuroblastoma specimen was cryo-sliced and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). With few exceptions, only samples with an RNA Integrity Number >7.5 were taken for further analysis.

treatment_protocol: All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.

tag: age [days]

tag: stage [inss]

tag: mycn status

value: not amplified

tag: tert rearrangement


title: EPD-210FH_P5


title: EPD-210FH_ht


title: 4h_Mock_uninfected_249232


title: 4h_Mock_uninfected_249231


title: 6h_LT2_infected_249230


title: 6h_LT2_exposed_249229


title: NBL-V7


title: 4h_D23580_infected_249228


title: 4h_D23580_exposed_249227


title: EPD-210FH_P2


title: 6h_LT2_infected_250230


title: GBM-311FH_P2


title: 2h_LT2_infected_249226


title: NBL-V8


title: 2h_LT2_exposed_249225


title: NBL-V6


title: GBM-110FHTC_P5


title: NBL-V4


title: ATRT-312FH_ht


title: NBL-V20


title: NBL-V3


title: ATRT-311FHTC_P6


title: 4h_Mock_uninfected_232232


title: 6h_LT2_exposed_232230


title: NBL-V5


title: ATRT-312FH_P4


title: 4h_D23580_exposed_232228


title: 4h_D23580_exposed_232227


title: ATRT-310FHTC_P4


title: NBL-V17


title: NBL-V15


title: 2h_LT2_exposed_232226


title: NBL-V19


title: NBL-V18


title: NBL-V2


title: ATRT-310FH_cP10


title: Med-1712FH_ht


title: NBL-V14


title: 2h_LT2_exposed_232225


title: NBL-V16


title: EPD-613FH_P4


title: 4h_Mock_uninfected_231231


title: 6h_LT2_exposed_231230


title: 4h_D23580_exposed_231228


title: 6h_LT2_exposed_231229


title: 4h_Mock_uninfected_231232


title: ATRT-312FH_P2


title: NBL-V12


title: NBL-V11


title: 4h_D23580_exposed_231227


title: NBL-T99

value: amplified


title: NBL-V1


title: NBL-T98


title: NBL-V10


title: EPD-710FH_P1


title: 4h_Mock_uninfected_230232


title: 2h_LT2_exposed_231225


title: 4h_Mock_uninfected_230231


title: 6h_LT2_exposed_230229


title: 6h_LT2_exposed_230230


title: 4h_D23580_exposed_230228


title: 4h_D23580_exposed_230227


title: 2h_LT2_exposed_231226


title: 2h_LT2_exposed_230225


title: NBL-T96


title: 2h_LT2_exposed_230226


title: NBL-T91


title: NBL-T95


title: NBL-T92


title: NBL-T90


title: 4h_Mock_uninfected_229232


title: NBL-T94


title: NBL-T9


title: NBL-T93


title: 4h_Mock_uninfected_229231


title: NBL-T88


title: 4h_D23580_exposed_229228


title: 4h_D23580_BULK_229227


title: 2h_LT2_exposed_229226


title: NBL-T97


title: 2h_LT2_BULK_229225


title: NBL-T89


title: 6h_LT2_exposed_229230


title: NBL-T85


title: NBL-T83


title: NBL-T86


title: NBL-T81


title: 6h_LT2_BULK_229229


title: NBL-T84


title: 2h_Mock_uninfected_228207


title: oocyte_IV_RNA_seq

city: Beijing

first: Bingjie

last: Zhang

state: Beijing

address: 30 Shuangqing Rd

country: China

institute: Tsinghua University

data_processing:
RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) with following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic.
All STAR ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM).
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level
Genome_build: danRer7
Supplementary_files_format_and_content: Bigwig for ChIP-seq and RNA-seq tracks, gene expression table for RNA-seq data

organism: Danio rerio

source_name: oocyte

growth_protocol: The wild type Tu female strain were raised as standard protocol.

extract_protocol:
Total RNA of oocytes were purified using RNeasy Mini kit (QIAGEN, 74104) as recommended protocols
5 ug RNA was DNase I (Fermentas, Cat # EN0521) treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly-A tailed mRNA was collected using DynabeadsTM mRNA purification kit (Invitrogen, Cat # 61006). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat # E6186A) at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers (Invitrogen, Cat # 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat # 10812014), MgCl2, DTT, dNTP, dUTP, RNase H (Fermentas, Cat # EN0202), E. coli DNA ligase (NEB, Cat # M0205S) and DNA polymerase I (NEB, Cat # M0209S). DNA was purified after 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat # N808-0096) at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase (NEB, Cat # M0530L). The amplified DNA was size selected using AMPure Beads for 200-500 bp DNA fragments.

treatment_protocol: The ovaries of adult female were isolated and transferred into specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). Then stage I-V oocytes were separated from the ovary with tweezers under microscope according to their morphology, and the surrounding follicle cells were detached gently as much as possible.

value: stage IV

tag: cell type

value: metaphase I oocyte

tag: strain

value: Tu


title: 6h_D23580_infected_228206


title: NBL-T87


title: oocyte_II_RNA_seq

value: stage II

value: S-phase oocyte


title: 6h_D23580_infected_228205


title: Blank_Blank_Blank_228208


title: NBL-T79


title: NBL-T82


title: NBL-T78


title: NBL-T74


title: 4h_LT2_infected_228204


title: oocyte_I_RNA_seq

value: stage I

value: G1-phase oocyte


title: NBL-T75


title: NBL-T77


title: 4h_Mock_uninfected_232231

value: uninfected


title: 256cell_DNMT1_control_H3K27ac_rep1

description: processed data file: 256cell_DNMT1_control_H3K27ac_rep1.bw

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with standard control MOs. And about 45 hrs later, the females mated with wild type Tu males to produce embryos

extract_protocol:
The ChIP procedure (STAR ChIP-seq) was based on a previously described method with modifications to adapt it for zebrafish embryos (Gilfillan et al., 2012; Zhang et al., 2016). For oocyte and embryo samples, yolk was firstly removed as described above. After centrifuge, cell pellet was lysed in 40 µl lysis buffer (0.5% NP-40, 0.5% Tween, 0.1% SDS and proteinase inhibitor) with pipetting up and down several times. 0.1 unit of MNase (Sigma, Cat # N3755) was added for chromatin digestion at 37℃ for 5 min. The reaction was then terminated by adding 1 µl 0.5 M EGTA. IP sample was incubated with 1 µg H3K4me3 antibody (Homemade), 2 µg H3K27ac antibody (Active Motif, Cat # 39133), 2 µg H3K27me3 antibody (Active Motif, Cat # 61017), or 2 µg H3K36me3 antibody (Active Motif, Cat # 61021), overnight with rotation at 4℃. In the next day, the sample was incubated with 300 µg protein A or protein G dynabeads (Life technologies, Cat # 10001D or 10003D) for 2 hrs with rotation at 4℃. The beads were washed 5 times in 150 µl RIPA buffer and once in 150 µl LiCl buffer. After washing, spin tubes briefly and remove the supernatant. For each IP sample, resuspend beads with 27 µl ddH2O and 1 µl 10x Ex-Taq buffer (TaKaRa). 1 µl proteinase K (Roche, Cat # 10910000) was then added and the mix was incubated at 55℃ for 90 min to elute DNA from beads. The supernatant was then transferred to a new tube and the proteinase K was inactivated at 72℃ for 40 min. 1 µl rSAP (NEB, Cat # M0371) was then added to dephosphorylate 3’ end of DNA at 37℃ for 1 h. rSAP was inactivated at 65℃ for 10 min. The resulting sample was subjected to TELP library preparation as previously described (Peng et al., 2015).
The resulting sample is ready for TELP library preparation (Peng et al., 2015).

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with control MO were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 256-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of 256-cell stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.

value: Tu X AB

value: embryo

tag: antibody

value: Active Motif, Cat # 39133


title: 256cell_H3K27ac_rep2_seq1

description: processed data file: 256cell_H3K27ac_rep2.bw

growth_protocol: The wild type AB females mated with wild type Tu males to produce embryos naturally.

treatment_protocol: In order to obtain a large number of synchronously developing embryos, embryos were acquired via in vitro fertilization using standard procedures. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 256-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: 2h_D23580_infected_228202

value: infected


title: 2h_D23580_infected_228201


title: 256cell_H3K36me3_rep1_seq2

description: processed data file: 256cell_H3K36me3_rep1.bw

value: Active Motif, Cat # 61021


title: NBL-T73


title: NBL-T8


title: NBL-T71


title: NBL-T72


title: NBL-T70


title: NBL-T7


title: NBL-T68


title: 4h_LT2_infected_228203


title: 2h_Mock_uninfected_227208


title: 256cell_H3K36me3_rep2

description: processed data file: 256cell_H3K36me3_rep2.bw


title: NBL-T67


title: 2h_Mock_uninfected_227207


title: 4cell_H3K27ac_seq1

description: processed data file: 4cell_H3K27ac.bw

treatment_protocol: In order to obtain a large number of synchronously developing embryos, embryos were acquired via in vitro fertilization using standard procedures. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 4-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: 6h_D23580_infected_227206


title: 4cell_RNA_seq_rep1

description:
processed data file: 4cell_RNA_seq_rep1_str2.bw
processed data file: 4cell_RNA_seq_rep1_str1.bw
processed data file: 4cell_RNA_seq_rep1_genes_fpkm.txt

extract_protocol:
Total RNA were purified using RNeasy Mini kit (QIAGEN, 74104) as recommended protocols
5 μg RNA was DNase I (Fermentas, Cat # EN0521) treated at 37℃ for 1 h. RNA was then purified using AMPure beads. Poly-A tailed mRNA was collected using DynabeadsTM mRNA purification kit (Invitrogen, Cat # 61006). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat # E6186A) at 95℃ for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers (Invitrogen, Cat # 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat # 10812014), MgCl2, DTT, dNTP, dUTP, RNase H (Fermentas, Cat # EN0202), E. coli DNA ligase (NEB, Cat # M0205S) and DNA polymerase I (NEB, Cat # M0209S). DNA was purified after 2 hrs incubation on thermomixer at 16℃. Synthesized cDNA was subjected to library preparation. DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat # N808-0096) at 37℃ for 1 hour followed by DNA amplification using Phusion HF DNA polymerase (NEB, Cat # M0530L). The amplified DNA was size selected using AMPure Beads for 200-500 bp DNA fragments.


title: 6h_D23580_infected_227205


title: NBL-T66


title: NBL-T65


title: NBL-T64


title: dome_amanitin_H3K27ac_rep1

description: processed data file: dome_amanitin_H3K27ac_rep1.bw

source_name: dome

treatment_protocol: The α-amanitin (Sigma, Cat # A2263) was microinjected into naturally fertilized 1-cell stage embryos, according to commonly used zebrafish microinjection protocol. After injection, embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃. The dose of α-amanitin was 0.2 ng per embryo.

value: dome


title: 6h_LT2_exposed_232229

value: exposed


title: NBL-T69

value: not amplified


title: NBL-T63


title: 4h_LT2_infected_227204


title: NBL-T62

value: amplified


title: NBL-T61


title: NBL-T60


title: dome_amanitin_H3K4me3_rep2

description: processed data file: dome_amanitin_H3K4me3_rep2.bw

value: Homemade


title: 2h_D23580_infected_227202


title: dome_amanitin_H3K27me3_rep1

description: processed data file: dome_amanitin_H3K27me3_rep1.bw

value: Active Motif, Cat # 61017


title: NBL-T6


title: 4h_LT2_infected_227203


title: 2h_D23580_infected_227201


title: dome_amanitin_RNA_seq

description:
processed data file: dome_amanitin_RNA_seq_str2.bw
processed data file: dome_amanitin_RNA_seq_str1.bw
processed data file: dome_amanitin_RNA_seq_genes_fpkm.txt


title: dome_control_MO_RNA_seq_rep2_seq1

description:
processed data file: dome_control_MO_RNA_seq_rep2_str2.bw
processed data file: dome_control_MO_RNA_seq_rep2_str1.bw
processed data file: dome_control_MO_rep2_genes_fpkm.txt

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with three HATs MOs. And about 42 hrs later, the females mated with wild type Tu males to produce embryos naturally.

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with control MO were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: 2h_Mock_uninfected_226208

value: Mock


title: NBL-T56


title: NBL-T57


title: NBL-T58


title: NBL-T59


title: 2h_Mock_uninfected_226207


title: dome_H3K27ac_rep1_seq1

description: processed data file: dome_H3K27ac_rep1.bw

treatment_protocol: In order to obtain a large number of synchronously developing embryos, embryos were acquired via in vitro fertilization using standard procedures. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: NBL-V13


title: NBL-T53


title: NBL-T55


title: NBL-T52


title: NBL-T51


title: 6h_D23580_infected_226206


title: dome_H3K27me3_rep1_seq1

description: processed data file: dome_H3K27me3_rep1.bw


title: 6h_D23580_infected_226205


title: dome_H3K27me3_rep2

description: processed data file: dome_H3K27me3_rep2.bw


title: NBL-T5


title: NBL-T49


title: 4h_LT2_infected_226204


title: dome_H3K27ac_rep2

description: processed data file: dome_H3K27ac_rep2.bw


title: NBL-T50


title: dome_H3K4me3_rep1_seq2

description: processed data file: dome_H3K4me3_rep1.bw


title: dome_H3K4me3_rep1_seq1


title: dome_H3K4me3_rep2_seq1

description: processed data file: dome_H3K4me3_rep2.bw


title: 2h_D23580_infected_226202


title: 2h_D23580_infected_226201


title: NBL-T54


title: NBL-T48


title: NBL-T47


title: dome_TKD_MO_RNA_seq_rep2_seq1

description:
processed data file: dome_TKD_MO_RNA_seq_rep2_str2.bw
processed data file: dome_TKD_MO_RNA_seq_rep2_str1.bw
processed data file: dome_TKD_MO_rep2_genes_fpkm.txt

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with HATs MOs were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the dome stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of dome stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.


title: NBL-T46


title: NBL-T45


title: NBL-T44


title: NBL-T43


title: NBL-T41


title: 2h_Mock_uninfected_225207


title: NBL-T40


title: 4h_LT2_infected_226203


title: oocyte_H3K27ac_rep1_seq1

description: processed data file: oocyte_H3K27ac_rep1.bw

growth_protocol: The wild type AB female strain were raised as standard protocol.

treatment_protocol: Unfertilized oocytes were collected with spoon by squeezing sexual maturation female fish gently. Oocytes were placed in ΔHank’s buffer (Hank’s buffer without Ca2+ and Mg2+) with 1% (wt/vol) BSA (Solarbio, Cat # A8020) to avoid activation until enough oocytes were collected. Dechorionation treatment by pronase diluted in ΔHank’s buffer for 15 min at 28.5℃ was conducted to keep oocytes from activation for a longer time. For each batch of about 500 dechorionated oocytes, 1 ml ice-cold 1% BSA ΔHank’s buffer was added. Oocytes were deyolked by repeatedly blowing with a 200 µl pipette and cell pellets were collected by spinning down at 5000 rpm for 5 min at 4℃.

value: AB

value: metaphase II oocyte

value: stage V


title: NBL-T39


title: NBL-T4


title: NBL-T42


title: 2h_Mock_uninfected_225208


title: NBL-T37


title: NBL-T36


title: NBL-T38


title: oocyte_III_RNA_seq

value: stage III

value: prophase I oocyte

value: Tu


title: oocyte_H3K27me3_rep1

description: processed data file: oocyte_H3K27me3_rep1.bw


title: 6h_D23580_infected_225206


title: NBL-T35


title: 6h_D23580_infected_225205


title: oocyte_H3K27ac_rep2

description: processed data file: oocyte_H3K27ac_rep2.bw


title: oocyte_H3K27me3_rep2

description: processed data file: oocyte_H3K27me3_rep2.bw


title: muscle_H3K36me3

description: processed data file: muscle_H3K36me3.bw

source_name: muscle

treatment_protocol: An wild type adult AB fish was euthanized with tricaine, and skeletal muscle was dissected carefully from trunk region after skin elimination by tweezers.

value: muscle cell

value: adult


title: 4h_LT2_infected_225204

value: infected


title: 4h_LT2_infected_225203


title: oocyte_H3K36me3_rep1

description: processed data file: oocyte_H3K36me3_rep1.bw

value: Active Motif, Cat # 61021


title: NBL-T33


title: NBL-T76


title: NBL-T31


title: oocyte_H3K4me3_rep1_seq1

description: processed data file: oocyte_H3K4me3_rep1.bw


title: 2h_D23580_infected_225202


title: NBL-T34


title: 2h_D23580_infected_225201


title: NBL-T29


title: oocyte_RNA_seq_rep2

description:
processed data file: oocyte_RNA_seq_rep2_str2.bw
processed data file: oocyte_RNA_seq_rep2_str1.bw
processed data file: oocyte_RNA_seq_rep2_genes_fpkm.txt


title: NBL-T3


title: 2h_Mock_uninfected_208208

value: uninfected


title: sperm_H3K27me3_rep1_seq1

description: processed data file: sperm_H3K27me3_rep1.bw

source_name: sperm

growth_protocol: The wild type Tu male strain were raised as standard protocol.

extract_protocol:
The procedures is adopted from a previous paper (Wu et al., 2011). Sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. The pellet was resuspended and washed with 1 ml PBS/ 1mM PMSF once. The sperm pellet was then treated with 1ml 0.05% lysosphatidylcholine in PBS on ice for 10 min. After washing with 1 ml PBS/1 mM PMSF twice, sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. Sperm were lysed in 91 µl PND buffer (0.1% NP-40, 1 mM DTT in PBS) and 5 µl 20 mM CaCl2. 10 units of MNase were then added to digest chromotin for 5 min at 37℃. 5 µl 0.5 M EGTA was used to stop the reaction. 150 µl release buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.4% Triton X-100, 5 mM EGTA) was then added at 37℃ for 10 min. After spinning down at 12000 rpm for 10 min at 4℃ the supernatant was transferred to a new tube. The rest procedure followed the STAR ChIP-seq protocol.
The resulting sample is ready for TELP library preparation (Peng et al., 2015).

treatment_protocol: Sperm were released by squeezing sexual matured male fish gently under anesthesia and collected with capillary tube. Sperm from several males were pooled in ice-cold, full-strength Hank's buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, 1.3 mM CaCl2 and 1.0 mM MgSO4).

value: mature sperm

value: spermatozoa


title: 2h_Mock_uninfected_208207


title: NBL-T27

value: not amplified


title: sperm_H3K27me3_rep2_seq1

description: processed data file: sperm_H3K27me3_rep2.bw

extract_protocol: The procedures is adopted from a previous paper (Wu et al., 2011). Sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. The pellet was resuspended and washed with 1 ml PBS/ 1mM PMSF once. The sperm pellet was then treated with 1ml 0.05% lysosphatidylcholine in PBS on ice for 10 min. After washing with 1 ml PBS/1 mM PMSF twice, sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. Sperm were lysed in 91 µl PND buffer (0.1% NP-40, 1 mM DTT in PBS) and 5 µl 20 mM CaCl2. 10 units of MNase were then added to digest chromotin for 5 min at 37℃. 5 µl 0.5 M EGTA was used to stop the reaction. 150 µl release buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.4% Triton X-100, 5 mM EGTA) was then added at 37℃ for 10 min. After spinning down at 12000 rpm for 10 min at 4℃ the supernatant was transferred to a new tube. The rest procedure followed the STAR ChIP-seq protocol.


title: NBL-T28


title: NBL-T25


title: 6h_D23580_infected_208206


title: NBL-T80


title: NBL-T30


title: NBL-T23


title: 6h_D23580_exposed_208205

value: exposed


title: NBL-T26


title: sperm_H3K4me3_rep1_seq1

description: processed data file: sperm_H3K4me3_rep1.bw

extract_protocol:
The procedures is adopted from a previous paper (Wu et al., 2011). Sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. The pellet was resuspended and washed with 1 ml PBS/ 1mM PMSF once. The sperm pellet was then treated with 1ml 0.05% lysophosphatidylcholine in PBS on ice for 10 min. After washing with 1 ml PBS/1 mM PMSF twice, sperm were collected by spinning down at 8000 rpm for 5 min at 4℃. Sperm were lysed in 91 µl PND buffer (0.1% NP-40, 1 mM DTT in PBS) and 5 µl 20 mM CaCl2. 10 units of MNase were then added to digest chromotin for 5 min at 37℃. 5 µl 0.5 M EGTA was used to stop the reaction. 150 µl release buffer (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.4% Triton X-100, 5 mM EGTA) was then added at 37℃ for 10 min. After spinning down at 12000 rpm for 10 min at 4℃ the supernatant was transferred to a new tube. The rest procedure followed the STAR ChIP-seq protocol.
The resulting sample is ready for TELP library preparation (Peng et al., 2015).

value: Homemade


title: 4h_LT2_infected_208204


title: 4h_LT2_exposed_208203


title: 2h_D23580_infected_208202


title: sperm_H3K36me3_rep1

description: processed data file: sperm_H3K36me3_rep1.bw


title: NBL-T21


title: NBL-T15


title: 2h_Mock_uninfected_207208

value: Mock


title: NBL-T18


title: NBL-T17


title: NBL-T16


title: NBL-T2


title: NBL-T24


title: NBL-T14


title: NBL-T20


title: NBL-T22


title: NBL-T112


title: NBL-T111

value: amplified


title: NBL-T12


title: 2h_D23580_exposed_208201


title: NBL-T13


title: NBL-T110


title: 2h_Mock_uninfected_207207


title: NBL-T19


title: NBL-T109


title: NBL-T108


title: 6h_D23580_infected_207206


title: 6h_D23580_exposed_207205


title: NBL-T107


title: 4h_LT2_infected_207204


title: 4h_LT2_exposed_207203


title: 2h_D23580_infected_207202


title: NBL-T105


title: gdTCR+ non stimulated

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

description:
gd ns
Gene expression data from purified gdTCR+ cells non stimulated

hyb_protocol: Hybridization was done on a GeneChip Human Transcriptome 2.0 array from Affymetrix

scan_protocol: Scan was performed with an Affymetrix GeneChip Scanner 3000 7G and the Affymetrix GeneChip Command Console

data_processing: Data was processed with Affymetrix Expression Console and Transcription Analysis Console softwares

label: Biotin

source_name: gdTCR+ non stimulated

label_protocol: Labeling was performed with the GeneChip WT PLUS Reagent Kit from Affymetrix

growth_protocol: CD19+, CD8+, CD4+, gdTCR+ and CD56+ cells were purified by MACS or sorting and kept in culture in RPMI supplemented with 10% FCS

extract_protocol: mRNA was extracted with the ZR RNA PicroPrep kit from Zymo Research

treatment_protocol: Cells were treated for 6 hours with IL-12 (20ng/ml) or IL-23 (100ng/ml)

value: gdTCR+ cells purified by sorting

tag: agent

value: control


title: NBL-T103


title: NBL-T104


title: CD56+ IL-23 stimulated

description:
NK IL23
Gene expression data from purified CD56+ cells stimulated with IL-23

source_name: CD56+ IL-23 stimulated

value: CD56+ cells MACS purifed from PBMCs


title: CD56+ non stimulated

description:
NK ns
Gene expression data from purified CD56+ cells non stimulated

source_name: CD56+ non stimulated


title: NBL-T11


title: CD4+ IL-12 stimulated

description:
CD4 IL12
Gene expression data from purified CD4+ cells stimulated with IL-12

source_name: CD4+ IL-12 stimulated

value: CD4+ cells MACS purifed from PBMCs


title: CD56+ IL-12 stimulated

description:
NK IL12
Gene expression data from purified CD56+ cells stimulated with IL-12

source_name: CD56+ IL-12 stimulated


title: NBL-T101


title: NBL-T106


title: gdTCR+ IL-12 stimulated

description:
gd IL12
Gene expression data from purified gdTCR+ cells stimulated with IL-12

source_name: gdTCR+ IL-12 stimulated


title: 2h_Mock_uninfected_206208


title: CD8+ IL-12 stimulated

description:
CD8 IL12
Gene expression data from purified CD8+ cells stimulated with IL-12

source_name: CD8+ IL-12 stimulated

value: CD8+ cells MACS purifed from PBMCs


title: gdTCR+ IL-23 stimulated

description:
gd IL23
Gene expression data from purified gdTCR+ cells stimulated with IL-23

source_name: gdTCR+ IL-23 stimulated


title: NBL-T102


title: CD4+ IL-23 stimulated

description:
CD4 IL23
Gene expression data from purified CD4+ cells stimulated with IL-23

source_name: CD4+ IL-23 stimulated


title: CD8+ IL-23 stimulated

description:
CD8 IL23
Gene expression data from purified CD8+ cells stimulated with IL-23

source_name: CD8+ IL-23 stimulated


title: 2h_Mock_uninfected_206207

source_name: Monocyte-derived dendritic cells


title: NBL-T10


title: NBL94


title: NBL96


title: CD8+ non stimulated

description:
CD8 ns
Gene expression data from purified CD8+ cells non stimulated

source_name: CD8+ non stimulated


title: NBL91

source_name: tumor sample


title: NBL-T100


title: NBL-T1


title: CD4+ non stimulated

description:
CD4 ns
Gene expression data from purified CD4+ cells non stimulated

source_name: CD4+ non stimulated


title: 4h_LT2_infected_206204


title: NBL77


title: NBL78


title: 4h_LT2_exposed_206203


title: NBL83


title: 6h_D23580_infected_206206


title: NBL360


title: CD19+ IL-23 stimulated

description:
B IL23
Gene expression data from purified CD19+ cells stimulated with IL-23

source_name: CD19+ IL-23 stimulated

value: CD19+ cells MACS purifed from PBMCs


title: NBL69


title: NBL341


title: NBL376


title: NBL80


title: CD31posCD144neg day 10 with CK replicate 2

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

data_processing:
Basecall files generated from NextSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq (version 2.17.1.14). Lane-wise alignment was performed by bowtie2 (version 2.2.1) to ensembl human reference genome (GRCh37.75) with default parameters. SAM files from bowtie2 alignment were converted to BAM files by samtools (v0.1.19). Parameters for samtools SAM to BAM conversion: -q 10 -f 2 -F 260. The expression levels of 57,773 annotated features were determined by using the featureCounts function from the Bioconductor package Rsubread (version 1.13.13).
Genome_build: Human (Ensembl GRCh37.7)

source_name: hESC-EB hematopoietic differentiation

growth_protocol: Man-5 human ES cell lines grown and differentiated as in Kennedy M et al. 2012

extract_protocol:
RNA was extracted using the Qiagen RNAeasy micro kit.
Indexed total RNA libraries were prepared using 10ng of Total RNA, a 4 minute fragmentation time, and 12 cycles of amplification in the Clontech SMARTer Stranded Total RNA-Seq Kit-Pico input ( Cat No: 635009). Libraries were quantified by qPCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems Inc. Cat No: KK4835). Single end 75bp sequencing was carried out by clustering 1.8 pM of the pooled libraries on a NextSeq 500 sequencer (Illumina inc.)

treatment_protocol: no treatments

value: hESC-EB hematopoietic differentiation

tag: passage

value: 25-30 passages

tag: sorted

tag: sort stage

value: day 10 EB differentiation


title: NBL346


title: 2h_D23580_infected_206202

tag: infection

tag: status

value: infected

tag: time


title: CD19+ IL-12 stimulated

description:
B IL12
Gene expression data from purified CD19+ cells stimulated with IL-12

source_name: CD19+ IL-12 stimulated


title: CRISPR library uninfected control cells

city: Dallas

first: John

last: Schoggins

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description:
Brunello_500x_A04
CRISPR-transduced Huh7.5 cells, uninfected.
PCR amplicon
Liver
processed data file: JS.count.txt

data_processing:
Bcl files were demultiplexed using bcl2fastq (v2.20).
sgRNA sequences were trimmed using an inhouse script.
Enriched genes and normalized read counts were identified via MAGeCK (v0.5.4), Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens.
Genome_build: Human CRISPR Knockout Pooled Library (Brunello).
Supplementary_files_format_and_content: JS.count.txt: Tab-delimited text file that includes the raw counts for each sgRNA.

growth_protocol: Human Huh7.5 cells were grown in DMEM supplemented with 10% FBS, 1X non-essential amino acids, and selected for lentivirus transduction with 4 ug/mL puromycin.

extract_protocol:
Genomic DNA was extracted by phenol:chloroform:isoamyl alcohol and purified by ethanol precipitation.
Six to ten micrograms of total genomic DNA were used per PCR reaction with barcoded primers to produce a CRISPR amplicon library for each sample. Amplicon library samples were purified with AmpureXP beads and tested for purity by Agilent Bioanalyzer and qPCR with sequencing specific primers. Samples were quantified by Qubit, pooled, then sequenced on an Illumina NextSeq 500.

treatment_protocol: Huh7.5 cells were treated with CRISPR-library lentivirus for 2 days, then selected with media containing 4 ug/mL puromycin for 3 days. Cells were plated into 15cm dishes, then infected the next morning with YFV-17D-venus for 24hrs. The infected cells were harvested and prepared for flow cytometry. By FACS, GFP-positive gated cells were collected, pelleted, and lysed for genomic DNA extraction.

tag: cell line

tag: crispr library

value: Brunello human library

tag: treatment

value: uninfected


title: 6h_D23580_exposed_206205

tag: plate

tag: lane

tag: well


title: CD31posCD144neg day 10 with CK replicate 1


title: GFP-positive YFV-infected CRISPR library cells

description:
IFN_screen_GFP_A07
CRISPR-transduced Huh7.5 cells, infected with YFV-17D-venus, and sorted by FACS.
PCR amplicon
Liver
processed data file: JS.count.txt

value: IFN-alpha


title: CD19+ non stimulated

description:
B ns
Gene expression data from purified CD19+ cells non stimulated

source_name: CD19+ non stimulated


title: CD31posCD144neg day 10 no CK replicate 2


title: 2h_D23580_exposed_206201

value: exposed


title: NBL320

tag: age [days]

tag: stage [inss]

tag: mycn status

value: not amplified

tag: tert rearrangement


title: NBL335


title: NBL34


title: 2h_Mock_uninfected_205208

value: Mock


title: NBL-T32


title: NBL333


title: NBL322

value: amplified


title: NBL332


title: NBL319


title: 6h_D23580_infected_205206


title: CD31posCD144pos day 10 with CK replicate 2

tag: cell type


title: NBL311


title: CD31posCD144pos day 10 with CK replicate 1

tag: passage


title: 6h_D23580_exposed_205205


title: 2h_Mock_uninfected_205207


title: NBL313


title: CD31posCD144pos day 10 no CK replicate 1

tag: sorted


title: NBL278


title: CD31posCD144neg day 10 no CK replicate 1

tag: sort stage


title: 2h_D23580_exposed_207201

tag: infection


title: CD31posCD144pos day 8 with CK replicate 2

value: day 8 EB differentiation


title: 4h_LT2_infected_205204

tag: status


title: NBL296


title: 4h_LT2_exposed_205203

tag: time


title: 2h_D23580_infected_205202


title: CD31posCD144pos day 8 with CK replicate 1


title: NBL237


title: NBL309


title: CD31posCD144pos day 10 no CK replicate 2


title: NBL221


title: NBL226


title: NBL272


title: NBL305


title: 2h_D23580_exposed_205201


title: CD31posCD144pos day 8 no CK replicate 2


title: NBL196


title: NBL208


title: NBL198


title: 2h_Mock_uninfected_204208


title: CD31posCD144pos day 8 no CK replicate 1


title: 2h_Mock_uninfected_204207


title: CD31posCD144pos day 6 replicate 2

value: day 6 EB differentation


title: 6h_D23580_exposed_204206


title: CD31posCD144pos day 6 replicate 1


title: 6h_D23580_exposed_204205


title: NBL177


title: NBL171


title: 4h_LT2_exposed_204203


title: NBL173


title: 4h_LT2_exposed_204204


title: NBL178


title: NBL195


title: GW_EV_3

city: San Francisco

first: Ni-Ting

last: Chiou

address: 513 Parnassus Ave

institute: University of San Francisco

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (mm10).
The mapped reads were then intersected with gene annotation (Ensemble GRCm38 release 91) supplemented with the tRNA fragment (tRF) bed files modified from tRNA annotation in the Genomic tRNA Database (Lowe and Eddy, 1997)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample.

source_name: CD4+ T cells

growth_protocol: DMEM high-glucose media with supplements as described in previous publications was used for all T cells cultures

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
small RNA libraries were prepared as previous publication with modifications.

treatment_protocol: T cells were stimulated for 3 days in the presence of the nSMase inhibitor, GW4869 for EV release. EVs were isolated from cell culture media as described.

tag: tissue

value: spleen and lymph nodes

tag: strain

value: CD4+ T cells


title: GW_EV_1


title: GW_EV_2


title: NBL139


title: NBL165


title: GW_CEL_3

treatment_protocol: T cells were stimulated for 3 days in the presence of the nSMase inhibitor, GW4869.


title: NBL133

treatment_protocol: All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.


title: NBL135


title: 2h_D23580_exposed_204201

treatment_protocol: DCs were infected with S. Tyhpimurium strain LT2 or D23580 at a MOI of 10 or left uninfected for 2h, 4h or 6h before sorting.


title: NBL118


title: NBL134


title: GW_CEL_2


title: NBL109


title: NBL114


title: NBL115


title: NBL105


title: NBL129


title: 2h_Mock_uninfected_203208


title: 2h_D23580_exposed_204202


title: NBL124


title: NBL108


title: GW_CEL_1


title: DM_EV_3

treatment_protocol: T cells were stimulated for 3 days in the presence of the control vehicle DMSO for EV release. EVs were isolated from cell culture media as described.


title: NBL112


title: 6h_D23580_exposed_203206


title: NBL103


title: DM_EV_2


title: 2h_Mock_uninfected_203207


title: NBL102


title: 4h_LT2_exposed_203204


title: DM_CEL_3

treatment_protocol: T cells were stimulated for 3 days in the presence of the control vehicle DMSO.


title: DM_EV_1


title: DM_CEL_2


title: 4h_LT2_exposed_203203


title: 2h_D23580_exposed_203202


title: NBL89

extract_protocol: 30-60mg of snap-frozen neuroblastoma specimen was cryo-sliced and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.

tag: disease

value: neuroblastoma tumor

tag: apb


title: NBL92


title: NBL90


title: NBL97


title: NBL99


title: 6h_D23580_exposed_203205

tag: plate

tag: lane


title: DM_CEL_1


title: NBL87

tag: age [days]


title: NBL82

tag: stage [inss]


title: 2h_D23580_exposed_203201

tag: well


title: S_EV_3

treatment_protocol: T cells were stimulated for 3 days with plate-bound anti-CD3 (2ug/ml) and anti-CD28 (5ug/ml)-containing media for EV release. EVs were isolated from cell culture media as described.


title: 2h_Mock_uninfected_202208


title: NBL81

tag: mycn status

tag: tert rearrangement


title: S_EV_2

tag: cell type


title: NBL86


title: NBL101


title: 2h_Mock_uninfected_202207


title: NBL74


title: NBL8


title: NBL75


title: NBL76


title: NBL85


title: 6h_D23580_exposed_202206


title: NBL93


title: NBL72


title: NBL71


title: S_CEL_3

treatment_protocol: T cells were stimulated for 3 days with plate-bound anti-CD3 (2ug/ml) and anti-CD28 (5ug/ml)-containing media.


title: NBL70


title: S_CEL_2


title: 2h_D23580_exposed_202202


title: 6h_D23580_exposed_202205


title: S_EV_1


title: R_EV_3

treatment_protocol: T cells were stimulated for 2 days followed by expansion for 1 days and then rested in IL2-contaning media for 2 days for EV release. EVs were isolated from cell culture media as described.


title: S_CEL_1


title: 4h_LT2_exposed_202204


title: NBL7


title: 4h_LT2_exposed_202203


title: 2h_D23580_exposed_202201


title: R_EV_2


title: NBL66


title: NBL62


title: 2h_Mock_uninfected_201208


title: NBL53


title: NBL52


title: NBL60


title: NBL54


title: NBL61


title: R_CEL_3

treatment_protocol: T cells were stimulated for 2 days followed by expansion for 1 days and then rested in IL2-contaning media for 2 days.


title: NBL51


title: NBL6


title: NBL50


title: NBL5


title: NBL59


title: R_CEL_2


title: 2h_Mock_uninfected_201207


title: R_CEL_1


title: NBL49


title: R_EV_1


title: 6h_D23580_BULK_201205

value: BULK


title: 6h_D23580_exposed_201206


title: 4h_LT2_exposed_201204


title: 4h_LT2_BULK_201203


title: 2h_D23580_exposed_201202


title: NBL47


title: NBL45


title: NBL40


title: NBL44


title: NBL41


title: NBL42


title: NBL48


title: NBL392


title: NBL390


title: 2h_D23580_BULK_201201


title: NBL389


title: NBL386


title: NBL39


title: NBL391


title: NBL4


title: NBL385


title: NBL395


title: NBL380


title: NBL383


title: NBL374


title: NBL378


title: NBL375


title: NBL370


title: NBL377


title: NBL373


title: HUVEC BCE 2.0

city: Hirosaki

first: Kayo

last: Horie

address: 66-1 Hon-cho

country: Japan

institute: Hirosaki university

description: HUVEC blackcurrant

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.

source_name: HFDPC blackcurrant

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: HUVEC were purchased from TAKARA BIO INC. The HFDPC were routinely cultured in phenol red-free follicle dermal papilla cell growth medium at 37ºC in 5% CO2.

extract_protocol: Total RNA was extracted by using the RNeasy mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: Then medium replace with phenol red-free follicle dermal papilla cell basal medium with or without BCE (2.0μg/ml). After the cells were incubated for 24 h at 37 °C 5% CO2.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: treatment

value: blackcurrant extract (BCE) 2.0μg/ml


title: NBL369


title: NBL37


title: NBL387


title: NBL38


title: HUVEC BCE 0

description: HUVEC control

source_name: HFDPC control

value: none (control)


title: NBL365


title: NBL367


title: NBL364


title: NBL368


title: NBL36


title: NBL355


title: NBL359


title: NBL358


title: NBL353


title: NBL363


title: NBL352


title: NBL357


title: NBL350


title: NBL361


title: NBL342


title: NBL340


title: NBL351


title: NBL347


title: NBL339


title: NBL356


title: NBL33


title: NBL336


title: NBL344


title: NBL330


title: NBL327


title: H12-4 (re-analyzed)

first: James

last: Krueger

state: NY

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: standard Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: normal skin

label_protocol: Affymetrix double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

value: normal skin

tag: amplification

value: Double

tag: material

value: bulk biopsy


title: NBL329


title: NBL325


title: NBL328


title: NBL323


title: H13-4 (re-analyzed)


title: H14-4 (re-analyzed)


title: H11-4 (re-analyzed)


title: NBL31


title: NBL32


title: NBL315


title: 5_normal (re-analyzed)


title: NBL310


title: H23 (re-analyzed)

source_name: dysplastic nevus

value: dysplastic nevus

value: sliced section


title: H21 (re-analyzed)


title: NBL307

value: not amplified


title: NBL295


title: NBL312


title: H69 (re-analyzed)


title: H10-4 (re-analyzed)


title: NBL301


title: NBL298


title: H67 (re-analyzed)


title: H19 (re-analyzed)


title: NBL300


title: NBL303


title: H18 (re-analyzed)


title: NBL308


title: NBL294


title: NBL3


title: NBL293


title: NBL292


title: NBL304


title: NBL297


title: H17 (re-analyzed)


title: NBL291


title: H60 (re-analyzed)

source_name: common nevus

value: common nevus


title: NBL285

value: amplified


title: NBL284


title: NBL289


title: NBL288


title: H59 (re-analyzed)


title: NBL283


title: NBL282


title: NBL281


title: mole-2 (re-analyzed)


title: NBL379


title: NBL280


title: NBL274


title: NBL277


title: mole-1 (re-analyzed)


title: NBL28


title: H15 (re-analyzed)


title: NBL266


title: NBL271


title: NBL270


title: PBT-04FHTC_P12

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
MAS5.0 normalized data
For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: cell line

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

tag: tumor subgroup


title: NBL275


title: ATRT-310FHTC_P4


title: PBT-07FH_ht

source_name: human tumor


title: NBL268


title: NBL279


title: NBL26


title: NBL259


title: Med-113FH_P5

source_name: PDOX


title: NBL258


title: NBL263


title: Med-210FH_P5


title: Med-113FH_P1


title: NBL257


title: NBL261


title: NBL253


title: GBM-110FHTC_P5


title: NBL250


title: Pineo-113FH_P2

value: PB


title: NBL255


title: Med-913FH_ht


title: NBL248


title: NBL245


title: NBL239


title: Med-113FH_ht


title: NBL238


title: NBL233


title: NBL227


title: NBL244


title: NBL229


title: Med-114FH_ht


title: Med-813FH_P1


title: ATRT-310FH_cP10


title: NBL236


title: NBL234


title: NBL243


title: Med-411FH_P2


title: Med-1911FH_ht


title: NBL235


title: NBL230


title: NBL246


title: NBL241


title: PBT-06FH_P2


title: Med-913FH_P1


title: Med-314FH_P2


title: NBL225


title: NBL232


title: NBL220


title: NBL222


title: NBL216


title: PBT-08FH_P2


title: NBL22


title: NBL224


title: NBL211


title: NBL191


title: NBL206


title: Med-2312FH_P2


title: NBL21


title: NBL214


title: NBL202


title: NBL194


title: NBL192


title: Med-1512FH_P2


title: NBL19


title: PBT-07FH_P2


title: NBL200


title: NBL217


title: NBL193


title: GBM-611FH_P1


title: EPD-613FH_P2


title: Med-114FH_P2


title: Med-210FH_P2


title: NBL2


title: NBL185


title: EPD-210FH_P2


title: ATRT-312FH_P2


title: NBL180


title: NBL188


title: NBL170


title: NBL17


title: NBL163


title: PBT-03FH_P1


title: Med-211FH_ht


title: EPD-210FHTC_P3


title: NBL169


title: PBT-01FH_P2


title: NBL154


title: NBL159


title: ATRT-311FHTC_P6


title: NBL158


title: NBL16


title: NBL156


title: GBM-511FHTC_P6


title: NBL172


title: NBL162


title: NBL153


title: NBL167


title: Med-1911FH_P2


title: NBL152


title: pigmented at E13.5, biological rep1

first: Lena

last: Iwai-Takekoshi

address: 3227 Broadway, Room L3-043, Quad 3C

department: Pathology and Cell Biology

institute: Columbia University

description: Gene expression data from embryonic retinal pigment epithelium (whole eye region)

hyb_protocol: Following fragmentation, cRNA was hybridized for 16hr on Mouse Genome 430 2.0 Array chips

scan_protocol: Arrays were scanned according to the Affymetrix protocol

data_processing: Affymetrix Expression Console (1.1) was used for RMA and quantile normalization of all microarray data

source_name: Pigmented RPE at E13.5

label_protocol: Biotinylated cRNA were prepared usingl GeneChip 3'IVT Expression Kit (Affymetrix) from 100ng total RNA.

growth_protocol: E13.5 embryos were harvested from pregnant females housed in a barrier facility in a timed pregnancy colony. Conception is assumed to take place at approximently midnight, and E0.5 refers to the day on which the vaginal plug was detected.

extract_protocol: RNA extraction was performed using Rneasy Plus Mini Kit (QIAGEN) according to the manufacture's instructions.

treatment_protocol: E13.5 embryos were removed from pregnant females under anesthesia and decapitated in PBS over ice. The head was immersed in PBS and the eyecup were removed to isolate RPE. The corniea, the lens and the neural retina were detached from the eyecup and extraocular tissue was removed. The isolated RPE was pooled into ice-cold RNAprotect cell reagent (QIAGEN) and processed according to the manufacture's instructions.

tag: genotype

value: control (pigmented)

value: retinal pigmented epithelium

tag: age

value: E13.5 embryos


title: NBL155

value: neuroblastoma tumor


title: pigmented at E13.5, biological rep3

tag: tissue


title: albino at E13.5, biological rep3

source_name: Albino RPE at E13.5

value: albino


title: albino at E13.5, biological rep2


title: NBL151

source_name: tumor sample

tag: disease


title: DSC8days_1

city: West Haven

first: Kalle

middle: T

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the human (GRCh37.69) cDNA builds using Tophat2 version 2.0.5
Number of times reads overlapped with known features (gene counts) was counted using HTSeq
Transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: GRCh37.69
Supplementary_files_format_and_content: ESF_DSC3days_DSC8days_HTseqcounts_TPMs.txt is a tab limited text file that contains the HTseq read counts and transcripts per million (TPM) values for the samples

source_name: decidual stromal cells

extract_protocol:
Cell cultures were treated with trypsin and detached from flasks, and RNA was isolated using the RNeasy Mini or Midi RNA extraction kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: 8 days in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: NBL150

tag: apb


title: PBT-05FH_P5


title: DSC8days_2


title: pigmented at E13.5, biological rep2


title: DSC3days_2

value: 3 days in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: NBL147


title: DSC3days_1


title: NBL128


title: NBL140


title: PBT-02FH_P1


title: NBL144


title: NBL125


title: albino at E13.5, biological rep1


title: EPD-710FH_P1


title: ESF_3

source_name: endometrial stromal fibroblasts

value: endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: GBM-611FH_P4


title: Med-610FH_P4


title: ESF_2


title: NBL148


title: NBL123


title: NBL132


title: EPD-710FH_ht


title: NBL12


title: NBL113


title: NBL10


title: NBL107


title: PB58 6hrs rep1

city: Tampa

first: Rays

last: Jiang

state: FL

address: 4202 E Fowler Ave

department: Department of Global Health

institute: University of South Florida College of Public Health

data_processing:
Reads were aligned to 3D7 reference release 27 using HISAT2 version 2.0.4
Raw counts were obtained using FeatureCounts Version 1.50.0-p3
Transcripts were assembled using Cufflinks Version 2.2.1
FPKM (Fragments per kilobase per million mapped reads) values calculated using Cuffnorm Version 2.2.1 using the classic-fpkm setting and normalization was performed by strain and time point
Genome_build: Plasmodium falciparum 3D7 Version 28
Supplementary_files_format_and_content: Accession number and either the gene counts or the gene FPKM

organism: Plasmodium falciparum

growth_protocol: Standard culture conditions

extract_protocol:
When a culture reached a harvest time point the parasites were separated from the red blood cells with 0.015% saponin at room temperature for 5 minutes. The parasites were then pelleted and washed three times in 10 mL room temperature PBS and the samples were stored at -80 oC in 1 mL TRIzol reagent (Fisher Scientific, Hampton, NH) until extraction. For extraction 200 μl of chloroform was added and the samples vortexed vigorously for 15 seconds and then incubated at room temperature for up to 5 minutes. The samples were then spun down at 12000xg (10800 rpm) at 4oC for 10 minutes and the supernatant discarded. 1 ML of 75% ethanol was added and then the samples spun down at 10000xg (9800 rpm) for 5 minutes. The resulting supernatant was discarded and the pellet briefly allowed to dry and the pellet dissolved in 20-50 μl of DEPC-treated water while being incubated at 55oC for 10-15 minutes.
0.5 μg-1.0 μg of RNA samples were prepped for sequencing using the Illumina TruSeq Stranded mRNA Kit. Library quantification was measured by qPCR and TapeStation (Agilent Technologies).  Sequencing was performed on an Illumina MiSeq using 300-cycle V2 MiSeq reagent kit (Illumina).

treatment_protocol: synchonzied by 3 rounds of sorbitol synchronization. The time points collected were 6, 24, 38, and 48 hours. Time zero was defined as the time when the synchronized culture was half late schizonts and half early rings

tag: strain

tag: genotype/variation

value: Isogenic K13 mutant of NF54

value: whole organism


title: PB58 48hrs rep2


title: PB58 6hrs rep3


title: NBL100

tag: age [days]

tag: stage [inss]


title: NBL116

tag: mycn status


title: PB58 6hrs rep2


title: PB58 48hrs rep1


title: NBL11

tag: tert rearrangement


title: NBL130


title: ATRT-312FH_ht


title: oocyte_H3K4me1_rep2

source_name: oocyte

treatment_protocol: Unfertilized oocytes were collected with spoon by squeezing sexual maturation female fish gently. Oocytes were placed in ΔHank’s buffer (Hank’s buffer without Ca2+ and Mg2+) with 1% (wt/vol) BSA (Solarbio, Cat # A8020) to avoid activation until enough oocytes were collected. Dechorionation treatment by pronase diluted in ΔHank’s buffer for 15 min at 28.5℃ was conducted to keep oocytes from activation for a longer time. For each batch of about 500 dechorionated oocytes, 1 ml ice-cold 1% BSA ΔHank’s buffer was added. Oocytes were deyolked by repeatedly blowing with a 200 µl pipette and cell pellets were collected by spinning down at 5000 rpm for 5 min at 4℃.

tag: antibody

value: Active Motif , Cat # 39297

tag: developmental stage

value: stage V

tag: cell type

value: metaphase II oocyte

value: AB


title: EPD-210FH_P5


title: PB58 38hrs rep3


title: PBT-01FH_ht


title: PB58 38hrs rep2


title: Med-1712FH_P1


title: Med-2112FH_ht


title: Med-2112FH_P2-2


title: Med-1712FH_ht


title: PBT-04FH_P2


title: oocyte_H3K4me1_rep1


title: NBL1

value: not amplified


title: Med-211FH_P2


title: Med-210FH_ht


title: NBL106


title: PB58 26hrs rep2


title: 256cell_DNMT1_KD_H3K27ac_rep2

description: processed data file: 256cell_DNMT1_KD_H3K27ac_rep2.bw

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with dnmt1 MOs. And about 43 hrs later, the females mated with wild type Tu males to produce embryos naturally.

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with dnmt1 MO were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 256-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of 256-cell stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.

value: Tu X AB

value: embryo

value: Active Motif, Cat # 39133


title: 256cell_DNMT1_KD_H3K27ac_rep1

description: processed data file: 256cell_DNMT1_KD_H3K27ac_rep1.bw

growth_protocol: The operated AB females were transferred into fish water containing tricaine (Sigma), penicillin and streptomycin (HyClone, SV30010) after OMIS with dnmt1 MOs. And about 44 hrs later, the females mated with wild type Tu males to produce embryos naturally.


title: 256cell_DNMT1_control_H3K27ac_rep2

description: processed data file: 256cell_DNMT1_control_H3K27ac_rep2.bw

treatment_protocol: Following OMIS and embryo collection, embryos derived from OMIS with control MO were identified by co-injected rhodamine B dye. Then these embryos were grown in fresh Holtfreter solution (0.05 g/L KCl, 0.1 g/L CaCl2, 0.025 g/L NaHCO3, 3.5 g/L NaCl, pH 7.0) at 28.5℃ around the 256-cell stage and dechorionated by pronase for 15 min at 28.5℃.  At last the cell pellets of 256-cell stage embryos were collected by spinning down at 5000 rpm for 5 min at 4℃.