title: HCCPER095: Peruvian, HCC, Patient, 095

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 095,Age: 30,Gender: Male,HBV: Positive,mtDNA haplotypes: A

value: Patient 095

value: Male


title: HCCPER047: Peruvian, HCC, Patient, 047

status: Public on Jan 31 2021

type: RNA

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

country: France

institute: CRCT

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 047, Age: 78, Gender: Female, HBV: Positive, mtDNA haplotypes: C

hyb_protocol: 5.5 μg of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45C on GeneChip™ Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using the limma software standard pipeline (R package) and normalized using Robust Multichip Average (RMA) algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peruvian patient with hepatocellular carcinoma (HCC)

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA, according to the standard Affymetrix protocol (Manual Target Prepartion for GeneChip Whole Transcription Expression Array, 20013, Affymetrix).

extract_protocol: Total RNA was extracted using TRI Reagent® (Sigma-Aldrich), according to the manufacturer's instructions.

treatment_protocol: Sampling protocol: About 50 mg of HCC, as well as NTL from tumor-free margins of the resected surgical pieces, were harvested, flash-frozen in liquid nitrogen, and kept at -150°C for long-term storage.

tag: patient diagnosis

value: hepatocellular carcinoma (HCC)

tag: tissue

tag: subject id

value: Patient 047

tag: age

tag: gender

value: Female

tag: hbv status

value: Positive

tag: mtdna haplotype

value: C


title: HCCPER068: Peruvian, HCC, Patient, 068

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 068, Age: 44, Gender: Female, HBV: Positive, mtDNA haplotypes: B

value: Patient 068

value: B


title: HCCPER054: Peruvian, HCC, Patient, 054

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 054, Age: 46, Gender: Female, HBV: Positive, mtDNA haplotypes: D

value: Patient 054

value: D


title: HCCPER016: Peruvian, HCC, Patient, 016

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 016, Age: 74, Gender: Female, HBV: Positive, mtDNA haplotypes: B

value: Patient 016


title: HCCPER083: Peruvian, HCC, Patient, 083

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 083,Age: 73,Gender: Male,HBV: Negative,mtDNA haplotypes: B

value: Patient 083

value: Negative


title: HCCPER070: Peruvian, HCC, Patient, 070

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 070, Age: 64, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Patient 070


title: HCCPER026: Peruvian, HCC, Patient, 026

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 026, Age: 36, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Patient 026


title: HCCPER088: Peruvian, HCC, Patient, 088

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 088,Age: 67,Gender: Male,HBV: Positive,mtDNA haplotypes: B

value: Patient 088


title: HCCPER015: Peruvian, HCC, Patient, 015

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 015, Age: 32, Gender: Female, HBV: Positive, mtDNA haplotypes: B

value: Patient 015


title: HCCPER004: Peruvian, HCC, Patient, 004

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 004, Age: 70, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Patient 004

value: Male


title: HCCPER013: Peruvian, HCC, Patient, 013

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 013, Age: 68, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: hepatocellular carcinoma (HCC)

value: Patient 013


title: HCCPER011: Peruvian, HCC, Patient, 011

description: subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 011, Age: 17, Gender: Male, HBV: Positive, mtDNA haplotypes: B

value: Patient 011

value: Positive


title: Polistes_worker_2

type: SRA

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

library_source: transcriptomic

data_processing:
Trinity used to assemble a de novo transcriptome
RSEM used to calculate normalised gene counts per Trinity transcript
Supplementary_files_format_and_content: Trinity fasta transcriptome files (.fnn) and tab-delimited RSEM files for each queen/worker which include TPM/FPKM and expected count for each sample.

organism: Polistes canadensis

source_name: Whole brain

extract_protocol:
All wasps were collected directly from their nests during the daytime, placed immediately into RNAlater (Ambion, Invitrogen) and stored at -20°C until further use. Total RNA was extracted using the RNeasy Universal Plus Mini kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

tag: caste

value: Worker

value: whole brain


title: Polistes_queen_3

value: Queen


title: H1155_Empty_1

city: Tianjin

first: Zhe

last: LIU

address: 22 Qixiangtai Road

department: Department of Immunology

country: China

institute: TIanjin Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.0
FeatureCounts v1.5 and stringtie v1.3 for RNA quantification and qualification
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SCLC cell

extract_protocol:
totoal RNAs from H1155 empty-1/2/3  and H1155-PAX5.KO-1/2/3 were extracted by Trizol Reagent according to the manufacturer`s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: H1155 were transfected with 305 empty or PAX5 KO lentivirus for 8h per day and change with normal medium, repeat 4 days.

tag: cell line

value: Lung

tag: transfection

value: wild type


title: B23-Rep2-Kutluay_H522-MOI1-96hpi

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

country: USA

institute: Washington University School of Medicine

data_processing:
Salmon v1.1.0 was used for quantification of RNA data.
Salmon indexes were constructed for both hg38, Gencode v27; as well as Sars-CoV2 based on reference genome NC_045512.2_cds_YP_009724389.1_1.
The R tximport package was used for per gene aggregation of human transcripts based quantification from Salmon, using Gencode v27 as well.

growth_protocol: H522 cells were grown in RPMI-10%FBS media.

extract_protocol:
RNA was exctracted by Trizol following manufacturer's instructions.
Extracted RNA was subjected to Illumina stranded mRNA prep. Libraries were sequenced using Illumina NextSeq following the manufacturer's protocols.

treatment_protocol: Cells were infected with SARS-CoV-2 at an MOI of 0.015, 0.6, 0.25 or 1 pfu/cell and RNA was extracted from cells at 4, 24, 48, 72 and 96 hpi.

tag: treatment

tag: moi

tag: batch

value: B

tag: sample prep

value: RNA-seq


title: Polistes_queen_2


title: B21-Rep2-Kutluay_H522-MOI1-4hpi


title: B15-Rep2-Kutluay_H522-MOI0-25-4hpi


title: B20-Rep2-Kutluay_H522-MOI1-48hpi


title: B22-Rep2-Kutluay_H522-MOI1-72hpi


title: B14-Rep2-Kutluay_H522-MOI0-25-48hpi


title: B18-Rep2-Kutluay_H522-MOI0-25-mock

value: mock


title: E292K 3

city: Palmerston North

first: Jasna

last: Rakonjac

address: Riddet Road

department: Institute of Fundamental Science

country: New Zealand

institute: Massey University

description: pIV-E292K biological replicate 3

data_processing:
Illumina CASAVA v 1.8 was used for base-calling
FastQCv0.10.0 was used for quality analysis
Removal of poor quality reads and illumina primers using Trimmomatic v0.30 with parameters ILLUMINACLIP TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:40
Alignment to reference genes obtained from Ensembl Bacteria (assemley: GCA_000022345.1.20) using Bowtie2 v2.1.0 and parameters -p14 -1 -2 -nofw
read count libraries formed using mapcount.pl (http://mpcox.github.io/mapcount)
removal of rRNA and tRNA genes from count libraries. Initial data exploration using R: Prior to differential gene expression analysis, the raw count data was filtered to remove genes with <10 counts in all samples. The coefficient of variation (CV) is defined as the ratio of the standard deviation to the mean and can be used as a measure of variability across a set of samples or replicates. Biological variation within sample replicates (i.e. from cultures bearing the same plasmid) was constrained by removing genes whose counts had a coefficient of variation >0.7, improving the validity of tests by removing unreliable data. Differentially expressed genes should show a high level of variability between three different strains (not producing pIV, producing wild-type pIV and producing pIV E292K mutant). Therefore, genes with a coefficient of variation <0.3 across all samples (regardless of which plasmid they bear) were removed.
Differential Expression analysis using R package DESeq2 v1.6
Genome_build: GCA_000022345.1
Supplementary_files_format_and_content: tab-delimited files for each sample generated using mapcount.pl, Scores represent read counts per gene (9 files).

organism: Escherichia coli K-12

source_name: bacterial liquid culture_expressing pIV-E292K

growth_protocol: Overnight cultures started from individual colonies were diluted 100-fold into 2xYT, supplemented with 25 μg/mL chloramphenicol and grown at 37°C with shaking, gene expression from plasmids was induced at OD600 = 0.2 by addition of 1 mM IPTG, 10 mL of culture was harvested 1 hr post-induction for RNA extraction

extract_protocol:
Overnight cultures started from three independent colonies of each of three E. coli K1508-derived strains, containing either (i) pGZ119EH; (ii) pPMR132; (iii) pPMR132-E292K, were used to inoculate 20 mL cultures (altogether 9 cultures). At OD600 =0.2, 1 mM IPTG was added to induce the tac promoter of the expression cassette in the plasmids. One hour post-induction, 10 mL of culture was immediately harvested by centrifugation (10 min, 4000 x g at 4°C). Supernatant was aspirated and the pellet suspended in 1 mL resuspension buffer (20 mM NaOAc pH 5.5, 1 mM EDTA; prewashed with phenol:chloroform). An equal volume of cold acid phenol:chloroform (1:1 mix) was added together with acid-washed glass beads (Sigma-Aldrich) to assist cell disruption by vortexing. The aqueous phase was separated by centrifugation (5 min, 13000 x g, 4°C) and washed again in phenol:chloroform, then with phenol and finally chloroform before precipitating nucleic acids by addition of 1/10 volume of 3 M sodium acetate (pH 5.5 and 2.5 volumes of 95% ethanol (molecular biology grade, Merck), overnight at -80°C. Precipitate was collected by centrifugation (30 min, 13000 RCF, 4°C). Pellets were air-dried and suspended in DEPC-treated de-ionised water (Milli Q) containing 1 U/μL Superase-In RNAse Inhibitor (Ambion). Genomic DNA was removed by DNAse digest (30 min at room temperature) using TURBO DNAse I (Ambion) and repurified by phenol:chloroform as described above. The quantity and quality of extracted RNA was determined by spectrophotometry. Furthermore, capillary electrophoresis (Bioanalyser 2100, Agilent) was used to determine the ratio of 16S to 23S bands and rule out the skew of RNAs towards shorter lengths as a measure of RNA integrity. The quality score assigned based on the electrophoresis profile is expressed as RNA integrity number (RIN) and determined using the Bioanalyser 2100 software; score between 8 and 10 is considered to be acceptable for transcriptomic analysis. Samples with RIN >8.5), were submitted to Ambry Genetics (Los Angeles, USA) for RNA sequencing.
RNA sequencing libraries were prepared by Ambry Genetics (Los Angeles, USA). First, ribosomal RNA was depleted from the total RNA samples using the Ribo-Zero rRNA depletion kit (EpiCentre), then directional 100 bp, paired-end RNA sequencing libraries were prepared using the TruSeq stranded sample preparation kit version 2 (Illumina, CA, USA), allowing differentiation of sense from antisense transcripts. These libraries were then sequenced on two lanes of an Illumina HiSeq 2000.

treatment_protocol: gene expression from plasmids induced by addition of 1 mM IPTG when culture OD600 reached 0.2

tag: strain

value: MC4100, {delta}lamB106

tag: plasmid

tag: expressed gene

value: expresses mutation of gIV (G937→A) encoding pIV containing E292→K missense mutation.


title: H1155_Empty_2


title: E292K 2

description: pIV-E292K biological replicate 2


title: wildtype 1

description: wildtype pIV biological replicate 1

source_name: bacterial liquid culture_expressing wildtype pIV

value: Derivative of pGZ119EH; expresses gIV wild-type under the control of tac promoter


title: E292K 1

description: pIV-E292K biological replicate 1


title: Polistes_queen_1


title: wildtype 2

description: wildtype pIV biological replicate 2


title: B19-Rep2-Kutluay_H522-MOI1-24hpi


title: B16-Rep2-Kutluay_H522-MOI0-25-72hpi


title: B24-Rep2-Kutluay_H522-MOI1-mock


title: B11-Rep2-Kutluay_H522-MOI0-06-96hpi


title: B17-Rep2-Kutluay_H522-MOI0-25-96hpi


title: B13-Rep2-Kutluay_H522-MOI0-25-24hpi


title: vector 2

description: vector control biological replicate 2

source_name: bacterial liquid culture_expressing vector

value: CmR marker and ColD origin of replication; protein expression cassette driven by the tac promoter.


title: vector 3

description: vector control biological replicate 3


title: B10-Rep2-Kutluay_H522-MOI0-06-72hpi


title: vector 1

description: vector control biological replicate 1


title: wildtype 3

description: wildtype pIV biological replicate 3


title: B12-Rep2-Kutluay_H522-MOI0-06-mock


title: B4-Rep2-Kutluay_H522-MOI0-015-72hpi


title: B3-Rep2-Kutluay_H522-MOI0-015-4hpi


title: B2-Rep2-Kutluay_H522-MOI0-015-48hpi


title: B6-Rep2-Kutluay_H522-MOI0-015-mock


title: A22-Rep1-Kutluay_H522-MOI1-72hpi

value: A


title: A23-Rep1-Kutluay_H522-MOI1-96hpi


title: A19-Rep1-Kutluay_H522-MOI1-24hpi


title: A21-Rep1-Kutluay_H522-MOI1-4hpi


title: Healthy 3, B cells

first: Jo

last: Spencer

state: Kent

address: Guy’s Hospital Campus

institute: King's College London

description: 5' Gene expression libraries and CITE-seq

data_processing:
Processing of sequencing results to generate transcript matrices was performed using the 10X Genomics Cell Ranger count v3.1.0 pipeline with default settings, using GRCh38 reference for alignment and Ensembl 93 (GRCh38-3.0.0) for gene quantification.
Seurat v3.1.1 was used for splitting cells by hash, quality control for each sample and integration of the three samples into a single dataset.
Seurat v3.1.1 was also used for normalization, dimensionality reduction, clustering and differential gene expression.
Slingshot 1.61 was used to infer trajectories
Genome_build: GRCh38
Supplementary_files_format_and_content: tar.gz files contain the filtered_feature_bc_matrix folder for each sample output from cellranger, containing barcodes, features and matrix files

source_name: Blood

growth_protocol: Lymphocytes were isolated from blood using Ficoll Hypaque centrifugation.

extract_protocol:
Labelled cells were loaded into 10x Genomics platform.
5' gene expression libraries were constructed following the manusfacturer's protocols.

treatment_protocol: CD19+ cells were sorted by FACS. Cells were also labelled using oligonucleotide tagged 'CITE-seq' antibodies and washed.

tag: disease state

value: Healthy

tag: Sex

value: Female

tag: cell type

value: B cells from blood


title: A20-Rep1-Kutluay_H522-MOI1-48hpi


title: Healthy 1, B cells


title: B8-Rep2-Kutluay_H522-MOI0-06-48hpi


title: B7-Rep2-Kutluay_H522-MOI0-06-24hpi


title: B9-Rep2-Kutluay_H522-MOI0-06-4hpi


title: A17-Rep1-Kutluay_H522-MOI0-25-96hpi


title: B5-Rep2-Kutluay_H522-MOI0-015-96hpi


title: B1-Rep2-Kutluay_H522-MOI0-015-24hpi


title: A16-Rep1-Kutluay_H522-MOI0-25-72hpi


title: P7731_A

city: Herston

first: Georgia

last: Trench

state: QLD

address: 300 Herston Rd

department: Cancer Genetics

country: Australia

institute: QIMR Berghofer Medical Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised to the baseline of the mean of all samples and then filtered using an Illumina detection score of ≥ 0.95 (p-value ≤ 0.05) and an average raw signal of ≥ 150 using GeneSpring v11.5.1 (Agilent Technologies).

source_name: Cell line

label_protocol: Biotinylated RNA was generated using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to manufacturer's instructions.

growth_protocol: P7731 cells were maintained in RPMI1640 + 10% FBS.

extract_protocol: RNA from P7731 cells was extracted using the RNeasy “animal cells spin” protocol (Qiagen) according to manufacturer’s instructions.  Primary tumour and MEC RNA was extracted with TriReagent (SIGMA) and isopropanal precipitated.

value: breast cancer cells

tag: tissue source

value: ER-/PR-/HER2- bone metastasis from a breast cancer patient

value: carcinoma


title: primary_B

source_name: right breast

tag: tissue type

value: primary tumour

value: breast

value: invasive ductal carcinoma


title: normal MEC_A

source_name: mammary epithelial

value: normal mammary epithelial cells

value: normal


title: P7731_B


title: normal MEC_B


title: RPMI, 24h, donor H

city: Nijmegen

first: Mariolina

last: Bruno

address: Geert Grooteplein Zuid 10

department: Experimental Internal Medicine

country: Netherlands

institute: Radboudumc

data_processing:
The RNA sequencing analysis of this dataset was performed as previously described (Li et al., 2016). Briefly, sequencing reads were mapped to the human genome using STAR (version 2.3.0) (Dobin et al., 2013). The aligner was provided with a file containing junctions from Ensembl GRCh37.71. Htseq-count of the Python package HTSeq (version 0.5.4p3) was used (the HTSeq package, http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) to quantify the read counts per gene based on annotation version GRCh37.71, using the default union-counting mode. Raw count matrix was saved in a single raw_counts_collected.csv, which contains all the raw counts per sample of all the conditions
Given the absence of sample replicates, PBMC donors were considered biological replicates. After quality control 2 donors stimulated for 4h and three donors stimulated for 24h with R. oryzae needed to be excluded from the analysis. Differentially expressed genes were identified by statistics analysis using DESeq2 package from bioconductor (Love et al., 2014). The statistically significant threshold (FDR P ≤ 0.05 and Fold Change ≥ 2) was applied.
Genome_build: GRCh37.71
Supplementary_files_format_and_content: CSV file containing expression values in counts for each gene. The column names are the identifier of samples. Files are generated by HTSeq-count.

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

extract_protocol:
After incubation, the supernatant was removed and the cells were lysed.
RNA was isolated using the mirVANA RNA isolation kit (Applied Biosystems) according to the protocol supplied by the manufacturer. RNAseq libraries were prepared from 1 µg RNA using the TruSeq RNA sample preparation kit v2 (Illumina) according to the manufacturer’s instructions, and these libraries were subsequently sequenced on a HiSeq 2500 sequencer (Illumina) using paired-end sequencing of 2 x 50 bp, upon pooling of 10 samples per lane.

treatment_protocol: 1x10^7 PBMCs were stimulated in 6 well plates with 1x10^7/mL A. fumigatus (Ku80, PFA fixed) 1x10^6/mL C. albicans (UC820, heat killed), 1x10^7/mL R. oryzae (RA 99-880, PFA fixed), or were left unstimulated for 4h or 24h at 37°C with 5% CO2. A

tag: time

tag: stimulus

value: RPMI

tag: donor

value: H

value: PBMCs


title: RPMI, 24h, donor G

value: G


title: normal MEC_C


title: A13-Rep1-Kutluay_H522-MOI0-25-24hpi

tag: cell line

value: RNA-seq


title: A24-Rep1-Kutluay_H522-MOI1-mock

value: mock

value: A


title: A14-Rep1-Kutluay_H522-MOI0-25-48hpi


title: RPMI, 24h, donor E

value: E


title: A18-Rep1-Kutluay_H522-MOI0-25-mock


title: RPMI, 24h, donor C

value: C


title: RPMI, 24h, donor B

value: B


title: A8-Rep1-Kutluay_H522-MOI0-06-48hpi


title: A11-Rep1-Kutluay_H522-MOI0-06-96hpi


title: A10-Rep1-Kutluay_H522-MOI0-06-72hpi


title: RPMI, 4h, donor H


title: RPMI, 24h, donor A


title: RPMI, 24h, donor F

value: F


title: RPMI, 4h, donor F


title: RPMI, 24h, donor D

value: D


title: A15-Rep1-Kutluay_H522-MOI0-25-4hpi


title: P7731_C

value: breast cancer cells

value: ER-/PR-/HER2- bone metastasis from a breast cancer patient

value: carcinoma


title: RPMI, 4h, donor E


title: RPMI, 4h, donor D


title: A7-Rep1-Kutluay_H522-MOI0-06-24hpi


title: Healthy 2, B cells

value: Healthy

value: Female

value: B cells from blood


title: A5-Rep1-Kutluay_H522-MOI0-015-96hpi


title: RPMI, 4h, donor B

value: RPMI


title: A3-Rep1-Kutluay_H522-MOI0-015-4hpi


title: RPMI, 4h, donor C

value: PBMCs


title: RPMI, 4h, donor A


title: A1-Rep1-Kutluay_H522-MOI0-015-24hpi


title: Rhizopus-oryzae, 24h, donor H

value: Rhizopus-oryzae

value: H


title: A2-Rep1-Kutluay_H522-MOI0-015-48hpi

value: RNA-seq


title: RPMI, 4h, donor G

value: G


title: Rhizopus-oryzae, 24h, donor F


title: A6-Rep1-Kutluay_H522-MOI0-015-mock

value: mock

value: A


title: Rhizopus-oryzae, 24h, donor G


title: Rhizopus-oryzae, 24h, donor D


title: Pooled 1 B cells

description: 5' Gene expression libraries

data_processing:
Pre-processing of sequencing results to generate transcript matrices was performed using the 10x Genomics Cell Ranger pipeline with default settings (v2.1.1) and aligning to the GRCh38 genome build.
Seurat v3.1 was used for splitting cells by hash, quality control for each sample and integration of the three samples into a single dataset.
Seurat v3.1 was also used for normalisation, dimensionality reduction, clustering and differential gene expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: gzip files contain the filtered_feature_bc_matrix folder for each sample output from cellranger, containing barcodes, features and matrix files

extract_protocol:
Pooled cells from 5 donors were loaded onto 10x Genomics platform.
5' gene expression libraries were constructed following the manufacturers protocols.

treatment_protocol: CD19+ cells that were either IgMhi or IgMlo were sorted by FACS.

tag: disease

value: IgMhi Transitional B cells

value: Cells from 5 donors pooled


title: Rhizopus-oryzae, 24h, donor C

value: C


title: Pooled 2 B cells

description: 5' Gene expression libraries

value: IgMlo Transitional B cells


title: A9-Rep1-Kutluay_H522-MOI0-06-4hpi

tag: treatment


title: Rhizopus-oryzae, 24h, donor B

value: B


title: SRSF2-ASXL1-NRAS-FLT3-3_ATACseq

city: New York

first: Eirini

last: Papapetrou

address: One Gustave L. Levy Place Box 1044A

institute: Icahn School of Medicine

library_source: genomic

data_processing:
RNA alignment: STAR alignment tool; v2.5.3a
RNA analysis: R v3.5.0; DESeq2 v1.16.1
ATAC alignment: Bowtie 2 alignment tool; v2.3.3.1
ATAC peak calling: MACS2 v2.1.1
IDR v2.0.3
Genome_build: hg19
Supplementary_files_format_and_content: RNA: DESeq2-normalized count matrix
Supplementary_files_format_and_content: ATAC: DESeq2-normalized count matrix and peak description file

molecule: genomic DNA

source_name: iPSC

growth_protocol: For hematopoietic differentiation,spin EBs were prepared and cultured in APEL medium, as describedbyNg et al. (2008, PMID: 18451785)

extract_protocol:
50,000 MACS-sorted CD45+ cells from two to three clones of P, A, SA, SAR and SARF cells were processed as follows: nuclei were isolated by lysing with 50 ul of ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and washing with 1 ml of ATAC wash buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20).
Cell lysates were spun to obtain nuclear pellets, which were subjected to transposase reaction using the Illumina Nextera DNA Sample Preparation Kit according to the manufacturer’s instructions. The final libraries were quantified using the Agilent BioAnalyzer. Sequencing of 75 nucleotide-long paired-end reads was performed in a NextSeq-500 (Illumina).

value: iPS-derived hematopoietic progenitor cells

tag: cell genotype

value: SRSF2(WT/P95L), ASXL1(WT/pE635fs*15), NRAS(WT/G12D), FLT3(WT/ITD)


title: A12-Rep1-Kutluay_H522-MOI0-06-mock

tag: moi

tag: batch


title: Rhizopus-oryzae, 24h, donor A


title: SRSF2-ASXL1-NRAS-FLT3-2_ATACseq


title: SRSF2-ASXL1-NRAS-FLT3-1_ATACseq


title: A4-Rep1-Kutluay_H522-MOI0-015-72hpi

tag: sample prep


title: SRSF2-ASXL1-NRAS-3_ATACseq


title: SRSF2-ASXL1-NRAS-2_ATACseq


title: SRSF2-ASXL1-2_ATACseq

value: SRSF2(WT/P95L), ASXL1(WT/pE635fs*23)


title: Rhizopus-oryzae, 4h, donor H


title: SRSF2-ASXL1-1_ATACseq


title: SRSF2-ASXL1-NRAS-1_ATACseq


title: SRSF2-ASXL1-NRAS-FLT3-3_RNAseq

extract_protocol:
Magnetic cell sorting of CD45+ cells was performed using the MACS cell separation microbeads and reagents (Miltenyi Biotec). Total RNA was extracted with the RNeasy mini kit (Qiagen).
PolyA-tailed mRNA was selected with beads from 1μg total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). cDNAs were generated using random hexamers and ligated to barcoded Illumina adaptors with the NEXTflex Rapid Directional RNA-Seq Library Prep Kit (Bioo Scientific). Sequencing of 75 nucleotide-long single-end reads was performed in a NextSeq-500 (Illumina).


title: Parental-2_ATACseq

value: Wildtype


title: ASXL1-2_ATACseq


title: Parental-1_ATACseq


title: ASXL1-3_ATACseq


title: Parental-3_ATACseq


title: Rhizopus-oryzae, 4h, donor B


title: Aspergillus-fumigatus, 24h, donor H

value: Aspergillus-fumigatus


title: Aspergillus-fumigatus, 24h, donor A

value: PBMCs


title: Aspergillus-fumigatus, 24h, donor E

value: E


title: Aspergillus-fumigatus, 24h, donor F

value: F


title: Rhizopus-oryzae, 4h, donor F

value: Rhizopus-oryzae


title: Rhizopus-oryzae, 4h, donor D

value: D


title: Aspergillus-fumigatus, 24h, donor B


title: Aspergillus-fumigatus, 24h, donor D


title: Rhizopus-oryzae, 4h, donor C


title: Rhizopus-oryzae, 4h, donor A


title: Rhizopus-oryzae, 4h, donor G

value: G


title: SRSF2-ASXL1-NRAS-FLT3-2_RNAseq


title: Aspergillus-fumigatus, 4h, donor H

value: H


title: Aspergillus-fumigatus, 24h, donor G


title: Aspergillus-fumigatus, 4h, donor G


title: Rhizopus-oryzae, 4h, donor E


title: Aspergillus-fumigatus, 24h, donor C


title: SRSF2-ASXL1-NRAS-FLT3-1_RNAseq


title: Parental-2_RNAseq


title: SRSF2-ASXL1-NRAS-3_RNAseq


title: SRSF2-ASXL1-1_RNAseq


title: SRSF2-ASXL1-NRAS-1_RNAseq


title: ASXL1-3_RNAseq


title: ASXL1-2_RNAseq


title: Parental-1_RNAseq


title: SRSF2-ASXL1-2_RNAseq


title: SRSF2-ASXL1-NRAS-2_RNAseq


title: Parental-3_RNAseq


title: Aspergillus-fumigatus, 4h, donor C


title: Candida-albicans, 4h, donor C

value: Candida-albicans


title: Aspergillus-fumigatus, 4h, donor E


title: Aspergillus-fumigatus, 4h, donor F


title: TT-seq_CtrAMO1h_rep2

city: Göttingen

first: Sara

middle: Patricia

last: Monteiro Martins

address: Fassberg 11

department: Molecular Biology

country: Germany

institute: MPI for biophysical chemistry

description: 4sU-labeled RNA

data_processing:
TT-seq and RNA-seq: Paired-end 75 and 150 bp reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated with Pladienolide B (Pla-B) and two replicates treated with a control solvent (DMSO). Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016)
mNET-seq: Paired-end 42 bp reads with additional 6 bp of barcodes were obtained for each of the samples. Reads were trimmed for adapter content with Cutadapt (1.18, RRID:SCR_011841) (Martin, 2011) with -O 12 -m 25 -a TGGAATTCTCGG -A GATCGTCGGACT. mNET-seq data was normalized using S. cerevisiae RNA spike-ins. To this end, a combined genome was generated using the Ensemble genome assembly for both human hg38 (GRCh38) and S. cerevisiae (R64-1-1), against which the reads were mapped using STAR (2.6.0, RRID:SCR_015899) (Dobin et al., 2013). Around 80% and 20% of reads mapped to the human and S. cerevisiae genomes, respectively. Bam files were filtered with Samtools (1.3.1, RRID:SCR_002105) (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (0.6.1.p1, RRID:SCR_005514) (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Antisense bias ratio was determined using positions in regions without antisense annotation with a coverage of at least 100 according to the defined major isoforms. Data was normalized using added S. cerevisiae RNA spike-ins. mNETs-seq coverage was normalized with a median of ratios method (Love et al., 2014) using the antisense corrected counts for S. cerevisiae transcripts with an RPK of 100 or higher in two summarized replicates of mNET-seq solvent control (DMSO).
ChIP-seq: Paired-end 42 or 75 bp reads with additional 6 bp of barcodes were obtained for each of the samples. Reads were aligned using Bowtie 2 (2.3.5, RRID:SCR_005476) (Langmead and Salzberg, 2012) to both human hg38 (GRCh38) and D. melanogaster (BDGP6.28). Bam files were filtered with Samtools (1.3.1, RRID:SCR_002105) (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. ChIP-seq coverages were obtained from piled-up counts for every genomic position, using physical coverage, that is, counting both sequenced bases covered by reads and unsequenced bases spanned between proper mate-pair reads. Data was normalized using added D. melanogaster RNA spike-ins. Normalization factors were obtained by dividing the total D. melanogaster read counts for each sample by the total read counts of the sample with the lowest read counts. ChIP-seq coverages were divided by the respective normalization factors.
Major isoform annotation: Salmon (0.13.1, RRID:SCR_017036) (Patro et al., 2017) was used in order to select the major isoforms present in our dataset. RNA-seq samples for 1 h DMSO or 1 uM Pla-B treatments were mapped against curated RefSeq annotated protein-coding isoforms (UCSC RefSeq GRCh38, downloaded in April 2019). For each gene, the major isoform was determined as the one with maximum mean Transcripts Per Million (TPM) value across all RNA-seq samples. Major isoforms were excluded from further analysis if they represented less than 70 % of the gene isoforms based on the calculated mean TPM value. Additionally, major isoforms associated with overlapping genes as well as isoforms located on chromosomes X, Y and M were discarded from further analysis. The final major isoform annotation includes 6,694 isoforms containing 65,976 exons and 59,282 introns.  A total of 5,535 major transcript isoforms of protein-coding genes with RPK >= 50 of TT-seq solvent control (DMSO) were included in the analysis.
Intronless genes annotation: Intronless genes were defined as RefSeq annotated genes comprising one single isoform with one single exon. To avoid effects from neighboring intron-containing genes, only intronless genes at least 1 kb distant from the neighboring intron-containing annotated transcripts (strand independent) were included in the analysis. Moreover, because a long 3Â´ UTR has been recently reported to be alternatively spliced in an intronless gene (FranÃ§ois et al., 2018), only intronless genes with UTRs <= 100 bp were included. A total of 51 expressed protein-coding intronless genes were included in the analysis.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig coverage files

source_name: K562 erythroleukemia cells

growth_protocol: Human K562 cells were obtained from DSMZ (DSMZ no.: ACC-10) and cultured in antibiotic-free RPMI 1640 medium (Thermo Fisher Scientific, 31870–074) supplemented with 10% heat-inactivated fetal bovine serum (Thermo Fisher Scientific, 10500–064) and 2 mM GlutaMAX (Thermo Fisher Scientific, 35050087) at 37 ̊C and 5% CO2. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen, rep-pt1). K562 cells were authenticated at the DSMZ Identification Service according to standards for STR profiling (ASN-0002). Biological replicates were grown independently.

extract_protocol: Ovation Universal RNA-Seq System (NuGEN)

treatment_protocol: Cells at a confluency of 300.000 cell/mL were treated with DMSO (1:20.000 dilution, Sigma, D2438) as solvent control or with 1 μM Pladienolide-B from a DMSO-resuspended 20 mM stock (1:20.000 dilution, Santa Cruz, sc-391691).

tag: method protocol

value: TT-seq, RNA-seq (Schwalb et al, 2016; Wachutka et al., 2019)

tag: treatment condition

value: 43 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_U2AMO1h_rep1

description: 4sU-labeled RNA

value: 44 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_U2AMO1h_rep2

description: 4sU-labeled RNA

value: 45 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: Aspergillus-fumigatus, 4h, donor B

value: B


title: Candida-albicans, 24h, donor H


title: Candida-albicans, 24h, donor G


title: Aspergillus-fumigatus, 4h, donor A

value: A


title: TT-seq_SSA1h_rep2

description: 4sU-labeled RNA

value: 41 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_CtrAMO1h_rep1

description: 4sU-labeled RNA

value: 42 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_SSA1h_rep1

description: 4sU-labeled RNA

value: 40 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: Candida-albicans, 24h, donor F

value: PBMCs


title: Candida-albicans, 24h, donor D


title: Candida-albicans, 24h, donor E

value: E


title: Candida-albicans, 24h, donor C

value: C


title: TT-seq_DMSO1h_rep2_SSAcontrol

description: 4sU-labeled RNA

value: 39 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_DMSO1h_rep1_SSAcontrol

description: 4sU-labeled RNA

value: 38 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: Candida-albicans, 24h, donor A


title: TT-seq_DMSO1h_rep1_PlaB100nMcontrol

description: 4sU-labeled RNA

value: 37 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_Pla-B100nM1h_rep2

description: 4sU-labeled RNA


title: TT-seq_DMSO1h_rep2_PlaB100nMcontrol

description: 4sU-labeled RNA


title: Candida-albicans, 24h, donor B


title: Jurkat cells - H3K9me3 - CXCL12 (SDF)-treated

city: Madrid

first: Javier

last: Redondo-Muñoz

state: Madrid

address: Ramiro de Maeztu,9

department: Molecular Biomedicine

country: Spain

institute: CIB-CSIC

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human/mouse genome (hg19) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak calling was done with the SICER script (SICER v1.1; FDR 1E-10, gap=600).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with peak data
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: Jurkat cells were stimulated or not with CXCL12 (100 ng/ml) for 15 min.

value: Jurkat

tag: chip antibody

value: H3K9me3 (ActiveMotif, Cat 39161, Lot 2)

value: treated with CXCL12 (SDF) for 15 minutes


title: Jurkat cells - H3K9me3 - Control

value: untreated


title: Jurkat cells - H3K9me3 - Input


title: primary_A

description: Primary _Tumour_A

value: primary tumour

value: breast

tag: disease state

value: invasive ductal carcinoma


title: Bulk RNA-seq dataset: SKMEL28 9-day dabrafenib-treated replicate #2

city: Stony Brook

first: Frank

middle: Vincent

last: Celeste

state: NY

address: 101 Nicolls Road

department: Pathology

institute: Stony Brook University

data_processing:
For the single-cell RNA-seq datasets: *I1_001.fastq.gz: contains the 8 nt sample index, *R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt), *R2_001.fastq.gz: contains the 150 nt RNA sequence. Single Cell sequencing data were pre-processed by cellranger 3.0.1 from 10X Genomics using default settings. Downstream analysis was performed by Seurat 3.0
For the bulk RNA-seq datasets: Salmon (Release 1.2.1) was used to generate a list of genome targets (decoys) with the human genome assembly (GRCh38). Index files were generated by concatenating transcriptome (GRCh38 cDNA) and genome (GRCh38 DNA) reference files. RNA-seq reads were pseudo-aligned to the reference index with Salmon (Release 1.2.1). Gene-level counts were prepared for differential expression analysis with tximport (Release 1.14.2). Differential expression was measured using DESeq2 (Release 1.26.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets: barcodes.tsv, features.tsv, matrix.mtx
For the bulk RNA-seq datasets: .txt files containing abundance values

source_name: Cutaneous melanoma cell line

growth_protocol: Clonal SK-MEL-28 cells were cultured on TC-treated plates in MEM with 5% FBS supplemented with antibiotics and antimycotics. Cells were plated and allowed to attach 24 hours prior to drug treatment.

extract_protocol:
For the single-cell RNA-seq datasets: Cells for each sample set were pooled from three 100 mm tissue culture plates, following drug treatment for the indicated time.Cells were detached with TrypLE and a single cell suspension of viable cells was prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.  For the bulk RNA-seq datasets: Cell plating was staggered such that RNA from 3-day treated, 9-day treated, and untreated control samples was extracted from cells simultaneously, using RNeasy Mini Kit (QIAGEN) protocol and reagents.
For the single-cell RNA-seq datasets: Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.  For the bulk RNA-seq datasets: Library preparation was performed using the KAPA mRNA HyperPrep Kit. An Agilent Bioanalyzer was used to verify the RNA concentration and assess RNA sample quality.

treatment_protocol: 9 days prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar dabrafenib.Drug media was replaced every 3 days.

value: dabrafenib

tag: time point

value: Day 9


title: Bulk RNA-seq dataset: SKMEL28 9-day dabrafenib-treated replicate #3


title: Bulk RNA-seq dataset: SKMEL28 9-day dabrafenib-treated #1


title: Candida-albicans, 4h, donor G

value: Candida-albicans

value: G

tag: cell type


title: Candida-albicans, 4h, donor D

value: D

value: PBMCs


title: Candida-albicans, 4h, donor E

value: E


title: Bulk RNA-seq dataset: SKMEL28 3-day dabrafenib-treated replicate #3

treatment_protocol: 3 days prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar dabrafenib.

value: Day 3


title: Bulk RNA-seq dataset: SKMEL28 3-day dabrafenib-treated replicate #2


title: Aspergillus-fumigatus, 4h, donor D

value: Aspergillus-fumigatus


title: TT-seq_Pla-B100nM1h_rep1

description: 4sU-labeled RNA

value: TT-seq, RNA-seq (Schwalb et al, 2016; Wachutka et al., 2019)

value: 37 °C, 1 μM Pla-B for 1h, 500μM 4sU (Carbosynth) labeling during the last 10 minutes.


title: Candida-albicans, 4h, donor A

value: A


title: Candida-albicans, 4h, donor H

value: H


title: Bulk RNA-seq dataset: SKMEL28 untreated replicate #3

treatment_protocol: 3 days prior to sample collection, regular growth media was removed and replaced with fresh regular growth media.

value: untreated

value: Day 0


title: Bulk RNA-seq dataset: SKMEL28 untreated replicate #2


title: Bulk RNA-seq dataset: SKMEL28 3-day dabrafenib-treated replicate #1


title: Bulk RNA-seq dataset: SKMEL28 untreated replicate #1


title: Candida-albicans, 4h, donor B

value: B


title: MDA-MB-231 GATA3-flag G->E cells - GATA3_rep2

city: Boston

first: Collin

last: Tokheim

state: MA

address: 3 Blackfan Circle, CLS 11007

department: Data Science

institute: Dana-Farber Cancer Institute

data_processing:
The Sentieon Bwa-mem aligner was used to map reads to the hg38 reference genome (https://support.sentieon.com/manual/)
ChIP-seq peak calling was then performed using MACS2 v2.1.4 (Zhang et al., 2008), with the following parameters: “-SPMR -B -q 0.01 –keep-dup 1”
Mapped reads were then down sampled to 4 million for subsequent quality control analysis using the ChiLin pipeline (Qin et al., 2016). Quality control consisted of five metrics (Table S5): 1) the average read quality according to FastQC (Andrews, 2010); 2) the fraction of uniquely mapped reads; 3) a PCR bottleneck coefficient, which is the fraction of locations with one uniquely mapped read; 4) fraction of reads in peaks according to MACS2 (Zhang et al., 2008) (more, the better); 5) overlap of peaks with DNA hypersensitivity sites. All samples were of adequate quality.
Only peaks with at least 5fold enrichment by MACS2 (v2.1.4)  were utilized for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig scores represent signal per million reads from MACS2
Peak files are bed files.

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cells were seeded (typically 4-5 × 10e6 cells)  into a 150 mm petri dish with DMEM Complete Medium. Cells will be harvested on day 3.

extract_protocol:
Lysates were clarified from sonicated nuclei and GATA3-DNA complexes were pulled down with antibody.
Libraries were prepared according toTAKARA's instructions accompanying Smarter Thruplex DNAseq Kit. Briefly, in the first step, Template Preparation, the DNA is repaired and yields molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5' ends are ligated with high efficiency to the 5' end of the genomic DNA, leaving a nick at the 3' end. The adaptors can not ligate to each other and do not have single-strand tails, both of which contribute to non-specific background found with many other NGS preparations. In the final step, the 3' ends of the genomic DNA are extended to complete library synthesis, and Illumina-compatible indexes are added through a high-fidelity amplification. Any remaining free adaptors are destroyed. Hands-on time and the risk of contamination are minimized by using a single tube and eliminating intermediate purifications.

treatment_protocol: No treatment

value: triple-negative breast cancer cells

tag: genotype

value: GATA3-flag G->E


title: MDA-MB-231 GATA3-flag A->M cells - GATA3_rep1

value: GATA3-flag A->M


title: MDA-MB-231 GATA3-flag G->E cells - GATA3_rep1


title: MDA-MB-231 GATA3-flag A->M cells - GATA3_rep2


title: MDA-MB-231 GATA3-flag cells - GATA3_rep1

value: GATA3-flag wildtype


title: MDA-MB-231 empty vector cells - GATA3_rep2

value: empty vector


title: Bulk RNA-seq dataset: PC9 9-day gefitinib-treated replicate #3

source_name: Lung adenocarcinoma cell line derived from metastatic site (lymph node)

growth_protocol: Clonal PC-9 cells were cultured on TC-treated plates in RPMI with 5% FBS supplemented with antibiotics and antimycotics. Cells were plated and allowed to attach 24 hours prior to drug treatment.

treatment_protocol: 9 days prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar gefitinib.Drug media was replaced every 3 days.

value: gefitinib

value: Day 9


title: MDA-MB-231 empty vector cells - GATA3_rep1


title: MDA-MB-231 GATA3-flag cells - GATA3_rep2


title: MDA-MB-231 GATA3 G->E cells - GATA3_rep2

value: GATA3 G->E


title: Bulk RNA-seq dataset: PC9 9-day gefitinib-treated replicate #2


title: MDA-MB-231 GATA3 A->M cells - GATA3_rep2

value: GATA3 A->M


title: MDA-MB-231 GATA3 G->E cells - GATA3_rep1


title: Bulk RNA-seq dataset: PC9 3-day gefitinib-treated replicate #3

treatment_protocol: 3 days prior to sample collection, regular growth media was removed and replaced with fresh regular growth media containing 5 micromolar gefitinib.

value: Day 3


title: Bulk RNA-seq dataset: PC9 9-day gefitinib-treated #1


title: MDA-MB-231 GATA3 A->M cells - GATA3_rep1


title: MDA-MB-231 GATA3 wildtype cells - GATA3_rep2

value: GATA3 wildtype


title: Bulk RNA-seq dataset: PC9 3-day gefitinib-treated replicate #1


title: MDA-MB-231 GATA3 wildtype cells - GATA3_rep1


title: Bulk RNA-seq dataset: PC9 3-day gefitinib-treated replicate #2


title: CD33KO_shPTPN6_6

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and base call file conversion.
Sequenced reads were corrected for low-quality sequence, then mapped to hs38 whole genome with the ensembl gene annotation version 97 using STAR v2.7.3a with standard parameters and --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3
Read count generation was performed using featureCounts/Subread v2.0.0 ignoring multimapping reads.
One sample from the group CD33-/- shPTPN6 (CD33KO_shPTPN6_2) was removed from further analysis due to very low overall counts.
Differentially expression analysis was performed with R v3.6.1 in RStudio v1.2.1335 using the DESeq2 package v1.26.0  with the contrasts either WT versus CD33KO (factor genotypes) or shCTRL versus shPTPN6 (factor treatment). The log2-fold change (log2FC) shrinkage was performed using apeglm to preserve large effects of true positives [v1.8.0 (Zhu, Ibrahim, and Love 2019)].
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: THP1 Macrophages

growth_protocol: THP1 monocytes were cultured in cell culture flasks with 5 % CO2 at 37 °C. The medium for maintaining THP1 monocytes consisted of RPMI (Gibco), 100 μM penicillin/streptomycin (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 1 % human N2-supplement (Gibco) and 1 % heat-inactivated chicken serum (Gibco). For differentiation of THP1 monocytes into adherent macrophages, the monocytes were incubated with 10 ng/ml PMA (Sigma-Aldrich) in cell culture plates for 48 hours, and then the attached THP1 cells were washed three times with medium to remove residual PMA. Subsequently, THP1 cells were cultured in medium without PMA for another 48 hours for further maturation towards macrophage phenotype.

extract_protocol:
Cells were collected in 1 ml QIAzol (QIAGEN) and RNA was isolated according to the RNeasy Mini Kit (QIAGEN) according to manufacturer´s instructions.
Library preparation was performed using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) with an input of 100 ng total RNA according to manufacturer's instructions.

treatment_protocol: Knockdown of PTPTN6/SHP1 was achieved via viral transduction of THP1 cells with a pLKO.1 plasmid (TRCN0000006887, Open Biosystems) containing a short hairpin RNA (shRNA) against the target sequence (5’-CGACATGCTCATGGAGAACAT-3’). pLKO.1 empty vector was used as control vector (Open Biosystems). Production of viral particles was performed by transfection of HEK-293FT cells (Invitrogen) with 5 µg of packaging and PTPN6 knockdown or empty vector control plasmids according to manufacturer’s instructions. The supernatant containing viral particles was collected 48 hours after transfection. Wild type (WT) and CD33 /  THP1 cells were incubated with the solution containing viral particles with either PTPN6 knockdown (shPTPN6) or empty vector control (shCTRL) plasmids for 24 hours followed by a medium change and a 48 hours resting phase. Subsequently, treatment with 1 µg/ml puromycin for selecting transduced monocytes was performed.

value: CD33 knockout

value: THP1 monocytes

value: knockdown of PTPN6 using shRNA


title: Bulk RNA-seq dataset: PC9 untreated replicate #2

value: untreated


title: Bulk RNA-seq dataset: PC9 untreated replicate #3

value: Day 0


title: Bulk RNA-seq dataset: PC9 untreated replicate #1


title: T47D_coculture_repl_3

first: Eugen

last: Dhimolea

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_T47D_Co_C_ED5520_S12_R1_001

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Differential gene expression analysis for the RNA-seq data using the bioconductor DEseq2 package
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Breast cancer cell line

growth_protocol: The breast cancer cells were grown in matrigel alone or together with HS5 bone marrow stromal cells in DMEM/10% FBS for 8 days.

extract_protocol:
The gel was enzymatically disintegrated and the separation of tumor and stromal cell subpopulations was performed using mesenchymal cells depletion microbeads. Next, the RNA was extracted from the tumor cells using RNA extraction kit (Qiagen), The lysates were supplemented with ERCC RNA spike-in mix to adjust for the cell number and analyzed by RNA sequencing using Illumina NextSeq 500 Next Gen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture setting

value: co-culture with HS5


title: T47D_coculture_repl_2

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_T47D_Co_B_ED5520_S11_R1_001


title: T47D_monoculture_repl_3

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_T47Dmono_C_ED5520_S9_R1_001

value: mono-culture


title: T47D_monoculture_repl_2

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_T47Dmono_B_ED5520_S8_R1_001


title: T47D_coculture_repl_1

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_T47D_Co_A_ED5520_S10_R1_001


title: T47D_monoculture_repl_1

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_T47Dmono_A_ED5520_S7_R1_001


title: CD33KO_shPTPN6_5


title: ZR751_coculture_repl_2

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_ZR75-1_Co_B_ED5520_S17_R1_001


title: ZR751_coculture_repl_1

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_ZR75-1_Co_A_ED5520_S16_R1_001


title: CD33KO_shPTPN6_4


title: CD33KO_shCTRL_3

value: shRNA Control plasmid


title: CD33KO_shCTRL_2


title: CD33KO_shCTRL_1


title: CD33KO_shPTPN6_1


title: CD33KO_shCTRL_4


title: CD33KO_shPTPN6_3


title: ZR751_monoculture_repl_3

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_ZR75-1mono_C_ED5520_S15_R1_001


title: CD33KO_shCTRL_5


title: CD33KO_shCTRL_6


title: CD33KO_shPTPN6_2


title: WT_shPTPN6_6

value: wild type


title: ZR751_monoculture_repl_2

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_ZR75-1mono_B_ED5520_S14_R1_001


title: ZR751_monoculture_repl_1

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_ZR75-1mono_A_ED5520_S13_R1_001


title: WT_shPTPN6_5


title: WT_shPTPN6_4


title: Candida-albicans, 4h, donor F

tag: time

tag: stimulus

value: Candida-albicans

value: F

value: PBMCs


title: MCF7_coculture_repl_3

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_MCF7_Co_C_ED5520_S6_R1_001

tag: cell line


title: WT_shPTPN6_3


title: ZR751_coculture_repl_3

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_ZR75-1_Co_C_ED5520_S18_R1_001


title: MCF7_coculture_repl_2

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_MCF7_Co_B_ED5520_S5_R1_001


title: MCF7_coculture_repl_1

description:
breast cancer cells isolated from 3D co-culture
20180516_3D_MCF7_Co_A_ED5520_S4_R1_001


title: WT_shPTPN6_1


title: MCF7_monoculture_repl_2

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_MCF7-1mono_B_ED5520_S2_R1_001


title: WT_shPTPN6_2


title: WT_shCTRL_6


title: MCF7_monoculture_repl_3

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_MCF7-1mono_C_ED5520_S3_R1_001


title: MCF7_monoculture_repl_1

description:
breast cancer cells isolated from 3D mono-culture
20180516_3D_MCF7-1mono_A_ED5520_S1_R1_001


title: TT-seq_PlaB4h_rep1

description: 4sU-labeled RNA

value: TT-seq, RNA-seq (Schwalb et al, 2016; Wachutka et al., 2019)

value: 37 C, 1 uM Pla-B for 4h, 500uM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_DMSO4h_rep2

description: 4sU-labeled RNA

value: 37 C, DMSO for 4h, 500uM 4sU (Carbosynth) labeling during the last 10 minutes.


title: RNA-seq_PlaB1h_rep2

description: Total fragmented RNA

value: 37 C, 1 uM Pla-B for 1h, 500uM 4sU (Carbosynth) labeling during the last 10 minutes.


title: WT_shCTRL_3


title: WT_shCTRL_4


title: WT_shCTRL_1


title: WT_shCTRL_5


title: TT-seq_PlaB4h_rep2

description: 4sU-labeled RNA


title: TT-seq_DMSO4h_rep1

description: 4sU-labeled RNA


title: WT_shCTRL_2


title: Y) NLS-AURKA c3

city: Morgantown

first: Elena

last: Pugacheva

state: WV

address: 44 Medical Center Drive

department: Biochemistry

institute: West Virginia University

description: Pugacheva Y

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmoatic (Bioinformatics. 2014 Aug 1; 30(15): 2114–2120. ) package will be used to remove adapter sequences.
Hisat2 (https://ccb.jhu.edu/software/hisat2) aligner was used for alignment, and Samtools (http://www.htslib.org/) for marking duplicates, sorting, and indexing, and Partek Genomic Suite (PGS, MO, USA) for differential expressions before generation of gene list for downstream functional analysis such as pathways using Ingenuity Pathway Analysis (IPA, Qiagen, USA).
Group-wise comparison was performed and FDR p value correction by Benjamini Hochberg methods ( Benjamini, Y., Hochberg, Y. JRSS, B, 57, 289-300. 1995) was used before gene list was generated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

growth_protocol: MDA-MB-231 (ATCC) cells were grown on tissue culture treated plastic dishes in full growth media (MEM with glutamine and sodium pyruvate, 10% FBS-HI, 1%AA, 5%CO2, 37C, normoxia)

extract_protocol:
RNA was extracted from 1x10^6 cells using RNeasy Mini kit (Qiagen)
RNA-Seq libraries were constructed from 500ng of total RNA using the KAPA mRNA Hyper Prep Kit- Biosciences with Illumina compatible adapters

treatment_protocol: The cells were continously grown in the presence of 0.1-1mg/ml doxycyline to express exogenouse AURKA cDNA under control rtTA responsive promoter.

value: MDA-MB-231 cells

tag: passages

tag: genotype/variation

value: MDA-MB-231Luc pLUTZ mRFP MUT1 NLS AURKA sgAURKA1 c3


title: Z) NLS-AURKA c3

description: Pugacheva Z


title: RNA-seq_PlaB1h_rep1

description: Total fragmented RNA


title: X) NLS-AURKA c2

description: Pugacheva X

value: MDA-MB-231Luc pLUTZ mRFP MUT1 NLS AURKA sgAURKA1 c2


title: RNA-seq_DMSO1h_rep1

description: Total fragmented RNA

value: 37 C, DMSO for 1h, 500uM 4sU (Carbosynth) labeling during the last 10 minutes.


title: RNA-seq_DMSO1h_rep2

description: Total fragmented RNA


title: H) NLS-AURKA c2

description: Pugacheva H


title: TT-seq_PlaB1h_rep2_150bp

description: 4sU-labeled RNA


title: V) NES-AURKA c2

description: Pugacheva V

value: MDA-MB-231Luc pLUTZ mRFP MUT2 NES AURKA sgAURKA2 c2


title: TT-seq_DMSO1h_rep2_150bp

description: 4sU-labeled RNA


title: A) NES-AURKA c2

description: Pugacheva A


title: TT-seq_PlaB1h_rep2_75bp

description: 4sU-labeled RNA


title: TT-seq_DMSO1h_rep1_150bp

description: 4sU-labeled RNA


title: W) NLS-AURKA c2

description: Pugacheva W


title: TT-seq_PlaB1h_rep1_75bp

description: 4sU-labeled RNA


title: T) NES-AURKA c1

description: Pugacheva T

value: MDA-MB-231Luc pLUTZ mRFP MUT2 NES AURKA sgAURKA2 c1


title: S) NES-AURKA c1

description: Pugacheva S


title: TT-seq_DMSO1h_rep2_75bp

description: 4sU-labeled RNA


title: B) NLS-AURKA c3

description: Pugacheva B


title: O) WT-AURKA c1

description: Pugacheva O

value: MDA-MB-231Luc pLUTZ mRFP MUT2 WT AURKA sgAURKA2 c1


title: R) WT-AURKA c2

description: Pugacheva R

value: MDA-MB-231Luc pLUTZ mRFP MUT2 WT AURKA sgAURKA2 c2


title: Q) WT-AURKA c2

description: Pugacheva Q


title: P) WT-AURKA c1

description: Pugacheva P


title: M) NLS-Empty SgCon

description: Pugacheva M

value: MDA-MB-231Luc pLUTZ mRFP NLS empty sgCon


title: F) NES-AURKA c1

description: Pugacheva F


title: TT-seq_DMSO1h_rep1_75bp

description: 4sU-labeled RNA


title: TT-seq_PlaB1h_rep1_150bp

description: 4sU-labeled RNA


title: G) NLS-Empty SgCon

description: Pugacheva G


title: E) Empty SgCon

description: Pugacheva E

value: MDA-MB-231Luc pLUTZ mRFP empty sgCon


title: C) NES-Empty SgCon

description: Pugacheva C

value: MDA-MB-231Luc pLUTZ mRFP NES empty sgCon


title: I) Empty SgCon

description: Pugacheva I


title: K) NES-Empty SgCon

description: Pugacheva K


title: N) NLS-Empty SgCon

description: Pugacheva N


title: MYB+/+_CD43+ve_day12rep2

city: Guangzhou

first: ZAHIR

last: SHAH

state: Guangdong

address: 190 Kaiyuan avenue, Haungpu district, Guangzhou, China

department: Stem Cells and Regenerative Medicines

institute: GIBH,CAS, China

data_processing:
Samples were checked with FastQC software with no considerable issues found. Reads were trimmed and filtered with BBduk tool from the Bbmap package (used parameters: qtrim=rl trimq=20 maq=20 minlen=50). This procedure keeps 94.98-97.02% bases and 98.64-99.8% reads per sample.
Trimmed reads were mapped to the GRCh38 human genome with Gencode v.24 gene annotation (Harrow 2012) using the --quantMode GeneCounts option of the STAR v.2.5.3ab software (Dobin 2013). After removing of ~15,000 pseudogenes and 552 rRNA genes the STAR output tallies raw read per gene counts, that is total read counts for each of 46,214 transcripts, 19,844 of them representing protein-coding genes. According to the STAR manual, “with --quantMode GeneCounts option STAR will count number reads per gene while mapping. EdgeR was used to convert raw read per gene counts to CPM (counts per million reads) matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: mRNA expression raw counts
Supplementary_files_format_and_content: mRNA expression counts per million reads
Supplementary_files_format_and_content: description of genes_ntc_expression_raw_cpm_GEO.txt file

source_name: in vitro hematopoietic cells

growth_protocol: hESC cells–derived hematopoietic cells were routinely generated using EBs-based hematopoietci development in our established serum-free and cytokine-free hematopoietic system (un-published), with initial mesodermal patterning by BMP4 and VEGF supplimentations.

extract_protocol:
Differentiated cells were harvested at different time points, filtered and incubated with cell surface markers on ice. The washed cells were collected into Trizol reagent directly from Aria II-cell sorter.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hESC-derived hematopoietic progenitors

tag: passage

tag: day of differentiation

value: Day 12

value: MYB+/+


title: MYB+/+_CD43+ve_day12rep3


title: MYB+/+_CD43+ve_day12rep1


title: MYB+/+_CD43-ve_day12rep3


title: MYB+/+_CD43-ve_day12rep2


title: MYB+/+_CD43-ve_day12rep1


title: D) WT-AURKA c1

description: Pugacheva D


title: L) NES-Empty SgCon

description: Pugacheva L


title: 7 h_Cu_rep3

city: Durham

first: Katherine

middle: J.

last: Franz

state: NC

address: 2103 French Science Center, 124 Science Dr., Box 90346

department: Chemistry

institute: Duke University

data_processing:
The raw reads were trimmed by Cutadapt (v 1.12) for quality filtering and adaptor removal.
The paired-reads were aligned to the transcriptome of Candida albicans SC5314 (GCF_000182965.3) by using STAR (v 2.5.3)
After the normalization, the read counts of all genes for each sample were then estimated with RSEM (v2.20).
The gene count data was converted to counts per million (CPM) and normalized by adjusting with the effective library size via the 'calcNormFactors' function implemented in the R package edgeR (v. 3.26.7)
The significant DEGs, comparing to NT condition, were determined by using the negative binomial generalized linear models with quasi-likelihood tests ('glmQLFTest'functions in the edgeR package) with FDR p-values of less than 0.05.
Genome_build: We also carried out GO term and KEGG pathway enrichment for DEGs in each cluster by using Fisher's Exact Test with multiple testing correction of FDR threshold 0.05.

organism: Candida albicans

source_name: Candida albicans yeast cells

growth_protocol: C. albicans cells were streaked onto a YPD agar plate from a frozen glycerol stock and incubated at 30 °C for 24 h. A single colony was used to inoculate liquid YPD growth medium (10 mL), and this culture was incubated overnight (~18 h) at 30 °C with shaking at 200 rpm. The overnight culture of C. albicans in YPD medium was inoculated into fresh YPD medium at an OD600 of 0.3 and this subculture was allowed to grow for 3 h at 30 °C with shaking at 200 rpm prior to treatment.

extract_protocol:
Total RNA was isolated from frozen pellets using a Qiagen RNeasy Mini Kit, and DNase was treated with a Turbo DNA-free kit (Roche) according to the manufacturer’s instructions. RNaseZap RNase Decontamination Solution (Invitrogen) was used on all materials and surfaces to preserve RNA integrity.
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit. In brief, mRNA transcripts were first captured using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed using random priming. During the second strand synthesis, the cDNA:RNA hybrid was converted into double-stranded cDNA (dscDNA) and dUTP incorporated into the second cDNA strand, effectively marking the second strand. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. The strand marked with dUTP was not amplified, allowing strand-specificity sequencing. Libraries are typically indexed using a dual indexing approach allowing for multiple libraries to be pooled and sequenced on the same sequencing lane on a NovaSeq 6000 Illumina sequencing platform. Before pooling and sequencing, fragment length distribution and library quality were first assessed on a Fragment Analyzer. All libraries were then pooled in equimolar ratio and sequenced.

treatment_protocol: Cultures were either left untreated or treated with CuSO4 (10 µM), fluconazole (50 µM), or both CuSO4 and fluconazole. Cells were harvested at 0, 0.25, 0.67, 1, 3, 5, and 7 h, flash frozen in liquid nitrogen, and stored at −80 °C prior to processing.

tag: strain

tag: treatment

value: 10 µM CuSO4

tag: timepoint

value: 7 h


title: 7 h_Both_rep3

value: 10 µM CuSO4 + 50 µM fluconazole


title: 7 h_untreated_rep3

value: untreated


title: 7 h_Flu_rep3

value: 50 µM fluconazole


title: 7 h_Both_rep2


title: J) Empty SgCon

description: Pugacheva J

value: MDA-MB-231 cells


title: 7 h_Flu_rep2


title: 7 h_Cu_rep2


title: H. burtonii YPD + 1M NaCl 30 min #2

city: Seoul

first: Dong Wook

last: Lee

address: 84, Heukseok-ro, Dongjak-gu

country: South Korea

institute: Chung-Ang university

description:
TN1805R3570--ATGTCAGA
Hb_30min_2
EXP:KJJ43_Nacl_30min_2:FPKM

data_processing:
Illumina Casava 1.8.2 software used for basecalling
The quality check were performed using the Fastqc tool (v 0.11.8)
Clean reads were mapped into the draft genome of Hyphopichia burtnoii and Hyphopichia pseudoburtnoii using Tophat (v 2.1.1)
The gene expression levels were then estimated using Cufflinks (v 2.2.1) based on the gene annotations.
Genome_build: Reference sequences of H. burtnoii (GCA_001661395.1) and H. pseudoburtnoii (GCA_003856775.1)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Hyphopichia burtonii

source_name: H. burtonii YPD + 1M NaCl 30 min

growth_protocol: WT H. burtonii and H. pseudoburtonii were inoculated at OD600 = 0.6 to 2.0 in YPD broth

extract_protocol:
total RNA was extracted be de novo RNA preparation method, we are going to publish this protocol
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After reached OD600 = 2.0, harvest 0 min samples, add same volume of YPD+2M NaCl broth to YPD broth. Aftef 5, 15, 30 min later, harvest each samples

tag: isolation source

value: Nuruk

tag: mutant status

value: WT

value: YPD + 1M NaCl 30 min


title: 7 h_untreated_rep2


title: 5 h_Both_rep3

value: 5 h


title: 7 h_Cu_rep1


title: 7 h_Both_rep1


title: H. burtonii YPD + 1M NaCl 30 min #1

description:
TN1805R3569--AGTTCCGT
Hb_30min_1
EXP:KJJ43_Nacl_30min_1:FPKM


title: 5 h_Both_rep2


title: 7 h_untreated_rep1


title: 5 h_Flu_rep3


title: 5 h_untreated_rep3


title: 5 h_Cu_rep3


title: 7 h_Flu_rep1


title: 5 h_Flu_rep2


title: H. burtonii YPD + 1M NaCl 5 min #1

description:
TN1805R3565--TAGCTTAT
Hb_5min_1
EXP:KJJ43_Nacl_5min_1:FPKM

source_name: H. burtonii YPD + 1M NaCl 5 min

value: YPD + 1M NaCl 5 min


title: H. burtonii YPD + 1M NaCl 5 min #2

description:
TN1805R3566--GGCTACAT
Hb_5min_2
EXP:KJJ43_Nacl_5min_2:FPKM


title: H. burtonii YPD + 1M NaCl 15 min #1

description:
TN1805R3567--CTTGTAAT
Hb_15min_1
EXP:KJJ43_Nacl_15min_1:FPKM

source_name: H. burtonii YPD + 1M NaCl 15 min

value: YPD + 1M NaCl 15 min


title: H. burtonii YPD + 1M NaCl 0 min #2

description:
TN1805R3564--GATCAGAT
Hb_0min_2
EXP:KJJ43_Nacl_0min_2:FPKM

source_name: H. burtonii YPD + 1M NaCl 0 min

value: YPD + 1M NaCl 0 min


title: 5 h_Cu_rep2


title: H. burtonii YPD + 1M NaCl 0 min #1

description:
TN1805R3563--ACTTGAAT
Hb_0min_1
EXP:KJJ43_Nacl_0min_1:FPKM


title: 5 h_untreated_rep2


title: H. burtonii YPD + 1M NaCl 15 min #2

description:
TN1805R3568--AGTCAACA
Hb_15min_2
EXP:KJJ43_Nacl_15min_2:FPKM


title: 5 h_Both_rep1


title: 5 h_Flu_rep1


title: 5 h_untreated_rep1


title: 3 h_Cu_rep3

value: 3 h


title: 3 h_Flu_rep3


title: 3 h_untreated_rep3


title: 3 h_Both_rep3


title: 3 h_Both_rep2


title: Panicle, Control_N22_2

city: New Delhi

first: Amitha Mithra

last: Sevanthi

address: LBS Centre, Pusa Campus

country: India

institute: ICAR - National Institute for Plant Biotechnology

description: The panicles were collected from the main tillers of the respective genotype which were raised in the open field facility adjacent to the high temperature stress phenotyping facility.

hyb_protocol: Affymatrix Genechip Rice Genome array was used for hybridization. The array was filled with 200µl of 1X hybridization buffer through septa on the back of the array and incubated for 10 min at 45 °C with rotation (60 rpm). Meanwhile, the hybridization cocktail was heated to 99 °C for 5 mins in dry bath incubator followed by incubation at 45 °C for 5 min. After 10 min incubation, the buffer solution was replaced with hybridization cocktail. The probe array was placed into hybridization oven 640 (Affymatrix, Santa Clara, CA, USA) and incubated at 45 °C with 60 rpm for 16 h. The Affymatrix fluidics station 450 was used to wash and stain the probe arrays. It is operated using GCOS. For initialization of the fluidics station, priming was done to ensure that the lines of the fluidics station were filled with proper buffers (Gene Chip wash buffer A and Gene Chip wash buffer B). The inlets of buffer were filled with buffer and ‘‘Prime_450’’ protocol was run for each module. The fluidics station was used for washing and staining after 15 min of priming.  After 16 h of hybridization, the chips were removed from the hybridization oven and hybridization cocktail of the probe array was replaced with 250 µl of wash buffer A and kept at 4 °C. Before starting the washing and staining protocol, the probe arrays were brought to room temperature. The probe array were put in respective modules and the protocol ‘‘EuKGE-WS2V5_450’’ was run for each module. When the programme prompeted ‘‘Load Vials -1-2-3’’, MCT with 600 µl stain cocktail 1 solution was loaded in sample holder, the anti-stretavidin biotinylated antibody solution (stain Cocktail 2) was loaded in sample holder 2 whereas Array holding Buffer was kept in sample holder 3.

scan_protocol: The Affymetrix® Gene Chip® Scanner 3000 was used for scanning. Each of the two septa on the probe array was covered by tough-tags TM (Sigma, USA) to prevent leakage from the cartridge during scanning. The probe arrays were loaded on the scanner, scanned and viewed. The shutdown protocol, ‘‘Shutdown_450”, was run on fluidics station modules and then it was switched off.

data_processing: The data were processed by using R open source software. The normalization done by GC-RMA method using gcrma package in R. The default parameters were considered while doing normalization.

label: Biotin

organism: Oryza sativa

label_protocol: aRNA was labelled with Biotin using the in-vitro transcription (IVT) express kit

growth_protocol: The Nagina22 and IR64 genotypes were direct sown in temperature controlled phenotyping facility at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India for exposing to high temperature at flowering stage. The plant to plant distance of 15 cm and row to row distance of 20 cm was maintained. The structure was kept open from initial sowing stage to until flowering stage, wherein rice plant received environmental conditions as prevailing in the outside. For control experiment, plants were raised outside of the facility were plant experienced natural environment throughout life cycle.

extract_protocol: Total RNA from 8 days heat stressed and controlled plant (Unstressed) panicles from the rice cultivars (Nagina22 and IR64) were isolated following Promega’s SV total RNA isolation system. The sample was processed as per standard manufacture’s procedure.

treatment_protocol: The heat stress was imposed on rice genotypes IR64 (Susceptible) and Nagina22 (Heat Tolerant) during flowering time and the temperature was fixed 5°C above the ambient  temperature for 8 continuous days including night time. After Treatment, panicles were collected from main tiller and dipped in Liquid nitogen and used for downstream work.

tag: cultivar

tag: stress

value: Control

tag: tissue

value: Panicle


title: 5 h_Cu_rep1


title: Panicle, HS_N22_3

description: The heat stress was imposed on plants during flowering time. The panicles merging from the main tillers were tagged once they entered booting and the temperature was fixed 5°C above the ambient temperature for 8 continuous days including night time  after which the samples were collected.

value: HS


title: Panicle, HS_IR64_2


title: Panicle, Control_N22_3


title: DNTLX3+_rep1

city: Marseille

first: Mohamed

last: BELHOCINE

address: 163, Avenue de Luminy

institute: INSERM

description: Gene expression data from DN-TLX3+ Cell

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing:
The data was normalized and analyzed by
The data analysis was performed with R version2.9.0 using the “Affy” package from Bioconductor. The probe intensities were log2 transformed and normalized using RMA method.

organism: Mus musculus

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: Thymi from 4- to 6-week old C57Bl/6 mice were extracted and mechanistically disrupted on a 75-µm nylon cell strainer (BD Bioscience). CD4-CD8- Double-negative (DN) thymocytes were purified by the depletion of CD4+CD8+ double positive (DP) cells; and of CD4+CD8- and CD4-CD8+ single positive (SP) cells using the AutoMACS system (Miltenyi Biotec). Single-cell suspensions of thymocytes were stained with magnetic bead-conjugated anti-CD4 and anti-CD8 antibodies (Miltenyi Biotec) at 4°C for 15 min, and then sorted in AutoMACS. For maximum purity, sorting of DN cells was performed using a FACS Aria sorter (BD Biosciences). Sorted DN cells to be transduced with pMSCV-GFP or pMSCV-GFP-TLX3 retroviral vectors were resuspended in vector supernatants in the presence of 10µg/ml polybrene and spinoculated for 2 hours at 3500 rpm.

extract_protocol: RNA extraction was performed as described previously in Dadi, S. et al. Cancer Cell - 2012.

treatment_protocol: Transduced thymocytes were seeded in 6-well plates in co-culture with OP9-DL1 γ-irradiated cells for further T-cell differentiation in vitro during 4-5 weeks. The differentiation medium (referred to as IL-7/Flt3L medium) consisted of α-MEM medium supplemented with 10% FCS, 50µM 2-ME, 2 mM glutamine, 10 mM HEPES (pH 7.5), 1 mM sodium pyruvate, 100 U/ml penicillin, 0.1mg/ml streptomycin, 10µg/ml gentamicin, 1% supernatant of rIL-7-secreting J558L cells, and 2.5% supernatant of rFlt3L-producing SP2.0 cells. All cells were maintained at 37°C in a humidified incubator 5% CO2.

tag: model

value: Tumoral


title: Panicle, HS_N22_1


title: Panicle, Control_N22_1


title: Panicle, HS_N22_2


title: RAG-/-_rep3

description: Gene expression data from RAG-/- Cell

source_name: RAG-/- Cell


title: 3 h_Cu_rep2

value: 10 µM CuSO4


title: DNTLX3+_rep2

description: Gene expression data from DN-TLX3+ Cell


title: Panicle, Control_IR64_1


title: RAG-/-_rep2

description: Gene expression data from RAG-/- Cell


title: DNTLX3+_rep3

description: Gene expression data from DN-TLX3+ Cell


title: Panicle, Control_IR64_2


title: Panicle, Control_IR64_3


title: 3 h_untreated_rep2


title: Panicle, HS_IR64_1


title: 3 h_Flu_rep2


title: Panicle, HS_IR64_3


title: NPEC2-BMI SLCs

city: GuangZhou

first: CONG

last: Sun

address: No.651, DongFengDong road, YueXiu district

institute: Sun Yat-sen University Cancer Center

description: gene expression of NPEC2-BMI SLCs

hyb_protocol: 875ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 55μL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Microarrays for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NPEC2-BMI cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 4ug RNA using the QIAGEN RNeasy® Mini Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the QIAGEN RNeasy® Mini Kit following the manufacturer's recommendations.The protocol includes the synthesis of cDNA, label and purify the cRNA with aaUTP. Then cRNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: 5 × 104 or 5 × 105 NPECs BMI1 cells were seeded at 48 well plates and cultured 36 h.The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2 and cells were cultured with KSF medium. Cells at 5 × 104 density turned to grow as MLCs, while cells at 5 × 105 density grew as SLCs.Then the SLCs  were infected with EBV at MOI of ～300.

tag: Stage

value: grew as SLCs


title: NPEC2-BMI MLCs

description: gene expression of NPEC2-BMI MLCs

value: grew as MLCs


title: 3 h_Both_rep1

value: 10 µM CuSO4 + 50 µM fluconazole


title: NPEC1-BMI SLCs

description: gene expression of NPEC1-BMI SLCs

source_name: NPEC1-BMI cell line


title: NPEC1-BMI MLCs

description: gene expression of NPEC1-BMI MLCs


title: 3 h_Flu_rep1

value: 50 µM fluconazole


title: 3 h_Cu_rep1


title: 3 h_untreated_rep1

value: untreated


title: RAG-/-_rep1

description: Gene expression data from RAG-/- Cell


title: NPEC2-BMI SLCs EBV infected

description: gene expression of NPEC2-BMI SLCs EBV infected

value: grew as SLCs and EBV infected


title: 1 h_Cu_rep3

value: 1 h


title: 1 h_Flu_rep3


title: NPEC1-BMI SLCs EBV infected

description: gene expression of NPEC1-BMI SLCs EBV infected


title: 1 h_untreated_rep3


title: 9256320054_J_CD4_Tcell

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

institute: Case Western Reserve University

description:
HIV Infected
9256320054_J

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: PBMCs from the RV217 Asian and African cohort subjects were collected and cryopreserved. CD4+ T cells were sorted by flow cytometry from thawed PBMCs without any growth in vitro.

extract_protocol: CD4 T cell subsets were sorted in 2x buffer for RNA extraction. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software. Analysis of the genome array output data was conducted using the R statistical language and the Limma statistical package from Bioconductor.

treatment_protocol: Sorting of CD4 T cells was performed in a resting state without any prior treatment or experimental manipulation

tag: subject

tag: diagnosis

value: HIV Infected

value: setPoint

tag: cell type

value: CD4 Tcell

tag: region

value: Africa


title: 9256320054_F_CD4_Tcell

description:
HIV Infected
9256320054_F


title: 9256320054_A_CD4_Tcell

description:
HIV Infected
9256320054_A

value: Asia


title: 9256320054_K_CD4_Tcell

description:
HIV Infected
9256320054_K


title: 1 h_Both_rep3


title: 9256320033_D_CD4_Tcell

description:
HIV Infected
9256320033_D


title: 9256320033_A_CD4_Tcell

description:
HIV Infected
9256320033_A

value: baseline


title: 9256320054_B_CD4_Tcell

description:
HIV Infected
9256320054_B


title: 9256320037_L_CD4_Tcell

description:
HIV Infected
9256320037_L


title: 9256320032_J_CD4_Tcell

description:
HIV Infected
9256320032_J


title: 9256320033_J_CD4_Tcell

description:
HIV Infected
9256320033_J


title: 9256320033_C_CD4_Tcell

description:
HIV Infected
9256320033_C


title: 9256320032_H_CD4_Tcell

description:
HIV Infected
9256320032_H


title: 9256320032_L_CD4_Tcell

description:
HIV Infected
9256320032_L


title: 9256320037_C_CD4_Tcell

description:
HIV Infected
9256320037_C


title: 9256320032_A_CD4_Tcell

description:
HIV Infected
9256320032_A


title: 9256320031_H_CD4_Tcell

description:
HIV Infected
9256320031_H


title: 9256320033_B_CD4_Tcell

description:
HIV Infected
9256320033_B


title: 1 h_Cu_rep2


title: 1 h_Both_rep2


title: 1 h_Flu_rep2


title: 1 h_untreated_rep2


title: 9256320037_I_CD4_Tcell

description:
HIV Infected
9256320037_I


title: 9256320032_I_CD4_Tcell

description:
HIV Infected
9256320032_I


title: 1 h_Both_rep1


title: 1 h_Flu_rep1


title: 0.67 h_Both_rep3


title: 1 h_Cu_rep1


title: 0.67 h_Flu_rep3


title: 1 h_untreated_rep1


title: 9256320032_B_CD4_Tcell

description:
HIV Infected
9256320032_B


title: U) NES-AURKA c2

description: Pugacheva U

tag: cell line

value: MDA-MB-231 cells

tag: passages

tag: genotype/variation

value: MDA-MB-231Luc pLUTZ mRFP MUT2 NES AURKA sgAURKA2 c2


title: 9252621086_G_CD4_Tcell

description:
HIV Infected
9252621086_G


title: 9256320031_A_CD4_Tcell

description:
HIV Infected
9256320031_A


title: 9252621086_J_CD4_Tcell

description:
HIV Infected
9252621086_J


title: 9252621082_I_CD4_Tcell

description:
HIV Infected
9252621082_I


title: 9252621072_E_CD4_Tcell

description:
HIV Infected
9252621072_E


title: 9256320031_G_CD4_Tcell

description:
HIV Infected
9256320031_G


title: 9252621082_E_CD4_Tcell

description:
HIV Infected
9252621082_E


title: 0.67 h_untreated_rep3

tag: strain


title: 9256320031_E_CD4_Tcell

description:
HIV Infected
9256320031_E


title: 0.67 h_Both_rep2

tag: treatment


title: 9252621086_A_CD4_Tcell

description:
HIV Infected
9252621086_A

tag: timepoint


title: 9252621067_L_CD4_Tcell

description:
HIV Infected
9252621067_L


title: 0.67 h_Flu_rep2


title: 0.67 h_Cu_rep3


title: 9252621072_A_CD4_Tcell

description:
HIV Infected
9252621072_A


title: 9231092145_K_CD4_Tcell

description:
HIV Infected
9231092145_K


title: 9231092145_G_CD4_Tcell

description:
HIV Infected
9231092145_G


title: 9252621086_C_CD4_Tcell

description:
HIV Infected
9252621086_C


title: 220_S38

city: New Haven

first: Nathan

middle: L

last: Price

state: CT

address: 10 Amistad St Rm 320

department: CMED

institute: Yale University

data_processing:
Base calling was done on Illumina HiSeq 2500 platform.
Reads were trimmed for quality using customs Perl scripts.
Alignment was carried out using TopHat2 with default parameters.
Transcript estimation and differential gene-expression was carried out using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Liver

extract_protocol:
Total RNA from the liver of WT and liver specific miR-33 knockout animals was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen). The purity and integrity of total RNA sample was verified using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina).
RNA libraries were performed TrueSeq Small RNA Library preparation (Illumina) and were sequenced for 45 cycles on Illumina HiSeq 2000 platformm (1 x 75bp read length). The reads obtained from the sequencer are trimmed for quality using in-house developed scripts.  The trimmed reads are aligned to the reference genome using TopHat2.  The transcript abundances and differences calculated using cuffdiff.  The results were plotted using R and cummeRbund using in-house developed scripts.

treatment_protocol: Livers were removed from chow diet and high fat diet fed wildtype or liver specific miR-33 knockout mice, snap frozen with liquid nitrogen, and stored at -80 C.

tag: diet

value: Chow diet

tag: genotype

value: Wildtype


title: 215_S34

value: miR-33 Liver knockout


title: 214_S33


title: 217_S36


title: 0.67 h_Cu_rep2

value: 10 µM CuSO4


title: 219_S37


title: 9231092145_E_CD4_Tcell

description:
HIV Infected
9231092145_E


title: 0.67 h_untreated_rep2


title: 216_S35


title: 9231092145_I_CD4_Tcell

description:
HIV Infected
9231092145_I


title: 9231092099_J_CD4_Tcell

description:
HIV Infected
9231092099_J


title: 4986_S31

value: HFD


title: 9252621072_C_CD4_Tcell

description:
HIV Infected
9252621072_C


title: 213_S32


title: 4961_S29


title: 4960_S28


title: 4959_S27


title: 9231092145_J_CD4_Tcell

description:
HIV Infected
9231092145_J


title: 9231092099_G_CD4_Tcell

description:
HIV Infected
9231092099_G


title: 9252621082_B_CD4_Tcell

description:
HIV Infected
9252621082_B


title: 4985_S30


title: 0.67 h_Flu_rep1

value: 50 µM fluconazole


title: 0.67 h_Cu_rep1


title: 4935_S23


title: 4958_S26


title: 4938_S24


title: 4957_S25


title: 0.25 h_Both_rep3

value: 10 µM CuSO4 + 50 µM fluconazole


title: 0.67 h_Both_rep1


title: 0.25 h_Cu_rep3


title: 0.25 h_Cu_rep2


title: 0.25 h_untreated_rep3

value: untreated


title: 0.25 h_Both_rep2


title: 0.25 h_Flu_rep2


title: 0.67 h_untreated_rep1


title: 0.25 h_Cu_rep1


title: 0.25 h_Flu_rep1


title: 0.25 h_untreated_rep2


title: 0.25 h_Both_rep1


title: 0.25 h_untreated_rep1


title: sample24: testis 3-41-5

city: Davis

first: Trish

last: Berger

address: One Shields Avenue

department: Animal Science

institute: University of California

data_processing:
Illumina files (Vincent J. Coates Genomics Sequencing Laboratory) were imported into CLC Genomics Workbench 11 software.
QC report for each index inspected and reads trimmed from each index.
Reads were mapped in CLC Genomics Workbench 11 software to Sus Scrofa 11.1 reference genome.
Data normalization (within software) was reads per kilobase per million mapped reads (RPKM).
Experiments (comparisons between treatments at an age) were set up within the CLC Genomics Workbench software.
Genome_build: Sus scrofa 11.1 (Ensembl)
Supplementary_files_format_and_content: Excel files containing RPKM value and other parameters for each gene for each sample

organism: Sus scrofa

source_name: testis

growth_protocol: Animals were managed consistent with normal pig production practices, transitioned to a starter diet, and weaned at 3 1/2 weeks of age.

extract_protocol:
RNA was extracted with Trizol reagent.
Libraries were constructed using TruSeq RNA kits (Illumina) with initial step being isolation of the polyA mRNA using oligo-dT magnetic beads.

treatment_protocol: Animals were orally dosed with either the letrozole treatment or the canola oil vehicle weekly.

value: testis

value: letrozole

tag: age

value: 5 weeks

tag: genetic bkgd

value: PIC


title: 0 h_untreated_rep3

value: 0 h


title: sample23: testis 8-41-6

tag: tissue

value: vehicle

value: 3 weeks


title: 0.25 h_Flu_rep3


title: sample22: testis 6-39-11


title: 0 h_untreated_rep2


title: sample21: testis 7-39-12


title: blood_203281980028_R04C01

type: genomic

city: Tuebingen

first: Vanessa

last: Nieratschker

address: Calwerstr. 14

department: Department of Psychiatry and Psychotherapy

institute: University of Tuebingen

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

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

data_processing: For background and dye bias correction, the preprocessNoob() function from the minfi package was applied. Additionally, we excluded 59 single nucleotide polymorphism (SNP) probes, 19,632 sex chromosome probes, 53,315 cross-reactive and polymorphic probes, 4,081 poorly performing probes (i.e. probes with a beadcount < 3 in 5% of the samples and probes with a detection p-value > 0.05 in at least 1% of the samples), and 98,983 known invariant probes (inter-quantile range (IQR, 0.1 - 0.9) < 0.02). To adjust for the bias originating from the two different bead types present on the BeadChip array, Beta-Mixture Quantile (BMIQ) normalization was performed . To reduce batch effects of different runs, chips and rows, the ComBat() function was applied. The estimateCellCounts.wmln() function from the wateRmelon package was used to estimate the relative proportions of monocytes, granulocytes, CD4+ and CD8+ T cells, B cells and natural killer cells. Adjustment for cell type composition was done by using the statistical estimates in a regression-based approach.

label: Cy3 and Cy5

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the QIAamp Blood Maxi Kit (Qiagen, Hilden, GER) according to manufacturer’s instructions

tag: Sex

value: F

tag: sad

value: yes

tag: ela

value: no


title: blood_203281980028_R06C01


title: blood_203281980028_R05C01


title: blood_203281980017_R07C01


title: blood_203281980028_R03C01


title: blood_203281980017_R05C01

value: M


title: blood_203281980017_R02C01


title: blood_203281980028_R08C01


title: blood_203281980017_R01C01


title: blood_203281980017_R08C01


title: blood_203281980028_R07C01


title: blood_203281980017_R06C01


title: 0 h_untreated_rep1


title: blood_203281980028_R02C01


title: sample20: testis 21-15-11


title: blood_203273630272_R03C01


title: blood_203273630272_R07C01


title: blood_203273630272_R06C01


title: blood_203281980017_R04C01


title: blood_203273630272_R08C01


title: blood_203281980028_R01C01


title: blood_203273630272_R05C01


title: sample18: testis 1-14-6


title: sample15: testis 25-41-10


title: sample19: testis 20-15-10


title: sample17: testis 8-14-9


title: blood_203273630272_R01C01


title: blood_203273630272_R02C01


title: blood_203273630266_R07C01


title: sample14: testis 4-39-9


title: blood_203273630266_R06C01


title: blood_203281980017_R03C01


title: blood_203273630272_R04C01


title: sample12: testis 11-15-9


title: blood_203273630266_R04C01


title: sample16: testis 23-41-9


title: sample10: testis 9-14-10


title: blood_203273630266_R05C01


title: RBPJ_KD rep2

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Reads were trimmed to remove the bases with low quality and adapter sequences
The trimmed reads were assigned directly to transcripts and counted with Salmon software
Gene expression level was quantified and normolized by Salmon(v0.14.1)
Differentially expressed genes between NC and KD group were selected by DESeq2
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Text files include normalized counts by DESeq2 for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: embryo

extract_protocol:
Total RNA extraction was performed using Picopure RNA isolation kit (Life Technologies, Grand Island, NY, USA) based on the manufacturer's manual. Before RNA isolation, equal amount of GFP and RFP mRNA were added to each group as a spike-in control.
mRNAs separation was achieved using oligo(dT)25 beads. Sequencing libraries were constructed with NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the instruction. In brief, mRNAs were fragmented followed by reverse transcription. The cDNA library underwent end repair, poly(A)-tailing, adaptor ligation, and PCR amplification for 12–15 cycles to prepare sequencing libraries.

value: embryo

tag: developmental stage

value: Late morula (D6 after IVF)

tag: knockdown

value: RBPJ


title: sample9: testis 3-14-7


title: blood_203273630266_R03C01


title: sample8: testis 27-41-11

value: 2 weeks


title: blood_203273630266_R02C01


title: RBPJ_KD rep1


title: blood_203273630235_R02C01


title: NOTCH1_KD rep2


title: sample7: testis 22-41-8


title: blood_203273630223_R07C01


title: blood_203273630223_R06C01


title: blood_203273630266_R01C01


title: blood_203273630235_R06C01


title: NOTCH1_KD rep1


title: blood_203273630235_R01C01


title: NC rep2

value: control


title: sample6: testis 12-39-13


title: sample4: testis 1-15-7


title: sample11: testis 10-15-8


title: blood_203273630235_R03C01


title: NC rep1


title: blood_203273630235_R04C01


title: blood_203273630223_R02C01


title: sample13: testis 5-39-10


title: sample5: testis 2-39-8


title: blood_203273630223_R08C01


title: sample2: testis 14-14-8


title: SAMPLE 4_GFP(high)

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

institute: University of Cologne

hyb_protocol: Agilent miRNA labeling and hybridization Kit

scan_protocol: Agilent G2505C scanner

data_processing: Genespring 14.9, Normalization: Shift to 75 percentile

source_name: wound

extract_protocol: Trizol for RNA isolation

value: wound

tag: cell type

value: myofibroblast

tag: molecule subtype

value: miRNA


title: sample1: testis 13-14-5

value: testis


title: SAMPLE 3_GFP(high)

label_protocol: Agilent miRNA labeling and hybridization Kit