title: 82_Borzoi_HC_Female

description:
82
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:HC

value: Female


title: MSC from healthy bone marrow donor 28

status: Public on Dec 01 2020

type: RNA

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by using the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO).  Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MSC from healthy bone marrow donor

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

growth_protocol: BM-MSCs were obtained as previously described (Guilloton F, Blood 2012).

extract_protocol: RNA extraction was  performed using RNEasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: MSC were expanded from bone marrow mononuclear cells until passage 1 in aphaMEM+10%FBS+FGF2 (1ng/mL)

tag: status

value: Healthy donor

tag: tissue

value: Bone marrow

tag: cell type

value: In vitro expanded bone marrow mesenchymal stroma cells


title: MSC from healthy bone marrow donor 30


title: GT75_W8_T

type: SRA

city: Manchester

first: Ardeshir

last: Bayat

address: Oxford Road

country: United Kingdom

institute: University of Manchester

library_source: transcriptomic

data_processing:
Raw image data file from high-throughput sequencing (Illumina PE150 Nova-Seq) was transformed to Sequenced Reads by CASAVA v1.8 base recognition (Base Calling)
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR v2.5) software.
Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.  The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
For samples with biological replicates, differential expression analysis of two conditions/groups was performed using the DESeq2 R package providing statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Genome_build: Ensembl version Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: Processed data is in Excel format including differential expression analysis data

source_name: Human skin

extract_protocol:
Tissue biopsies were homogenised in 300μL of RLT buffer (Qiagen, GmbH, Helden, Germany) mixed with β-mercaptoethanol (Sigma-Aldrich, St Louis, MO) (10μl β-mercaptoethanol/ml RLT buffer) using 5-mm stainless steel beads and a Qiagen TissueLyser II (Qiagen GmbH) at 30 oscillations/second for 10 minutes. RNA was extracted using RNeasy Tissue Mini Kits (Qiagen GmbH). Eluted RNA quantity and purity was assessed using NanoDrop ND-100 v3.0.1 spectrophotometer (NanoDrop Technologies, Wilmington, DE), Agarose gel electrophoresis and Agilent 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human skin

tag: wound/scar time point and group

value: Week 8

tag: egcg treated/placebo

value: Treatment

tag: group allocation


title: 86_Poodle Standard_Acute_GDV_Male

type: genomic

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

country: USA

institute: Translational Genomic Research Institute

description:
86
Canis familiaris

hyb_protocol: SNP array genotyping was performed on samples using the Illumina CanineHD Whole-Genome Genotyping BeadChip arrays including 173,662 SNPs located on autosomes and sex chromosomes.

scan_protocol: Arrays were scanned.

data_processing: Genotype calling of SNPs as well as data visualization were performed with GenomeStudio v2.0 and exported to PLINK format using the CanFam3.1.75 genome assembly to retrieve chromosomal coordinates. SNP array data imputation was conducted using a phased genotype reference dataset of 365 dogs from multiple breeds genotyped by whole-genome sequencing. The reference dataset was filtered excluding sex chromosomes, removing insertion/deletions, non-PASS variants, and variants with more than two alleles. The SNP array dataset of all 241 dogs on our study (target dataset) was filtered excluding sex chromosomes and duplicate variants, including variants with: minor allele frequency (MAF) ≥ 0.005, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. The resulting dataset was subjected to principal component analysis (PCA) in PLINK v1.9 to identify outliers and dogs whose PCA clustering would differ from the owner-identified breed information. We computed the relatedness PIHAT metric using PLINK v1.9 for each pair of samples aiming to identify duplicated samples (PIHAT=1.0). Outliers, duplicated and misclassified samples were removed from the dataset. Reference and target datasets were compared using the Conform-gt software, keeping only variants shared between the target and the reference dataset. Finally, the genotypes were imputed with the software Beagle v5, using the recombination rate map reference, default settings and effective population size = 200. After imputation, variants were filtered with dosage R2 (DR2)< 0.4, ultimately including only with MAF ≥ 0.05, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. Gene annotation of SNPs was performed with R-BiomartTv2.40.4 using the dog genome reference CanFam3.1.

label: biotin/dinitrophenyl

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Peripheral blood

label_protocol: Extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labeled nucleotide. C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl-labeled. Signal amplification of the incorporated label further improves the overall signal-to-noise ratio of the assay.

extract_protocol: Peripheral blood samples were collected from all animals with DNA extracted by Qiagen DNeasy Blood and Tissue kit or Qiagen Genomic DNA Midi Kit (Qiagen Inc., Hilden, Germany # 69504, # 51183). DNA was quantified by Qubit with the Qubit Broad Range dsDNA assay kit (Life Technologies, Carlsbad, CA, USA #Q32853). DNA quality was determined by DNA Integrity Number on an Agilent 4400 Tapestation (Agilent, Santa Clara, CA, USA #G2991AA).

tag: breed

value: Poodle Standard

tag: status (hc = healthy control, gdv

value: gastric dilatation-volvulus:Acute_GDV

tag: Sex

value: Male

value: Peripheral blood


title: iNeuron.rna_seq.LHX8_NGN3.day6.rep2

city: Durham

first: Charles

last: Gersbach

state: NC

address: 101 Science Drive

department: Biomedical Engineering

institute: Duke University

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest human reference genome (GRCh38) using the aligner STAR (Langmead et al., 2009)
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 running on R.
Genome_build: hg38
Supplementary_files_format_and_content: Comma separated value file with TPM gene counts

source_name: TUBB3-2A-mCherry iPSC

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and 100 ng of RNA was used to develop RNA-seq libraries.
RNA-sequencing libraries were prepared using the Truseq Stranded mRNA kit (Illumina) according to the manufacturer’s protocol.

value: induced pluripotent stem cell

tag: genotype

tag: treatment

value: TetO-NGN3 + TetO-LHX8


title: 81_Borzoi_HC_Female

description:
81
Canis familiaris


title: MSC from healthy bone marrow donor 27


title: iNeuron.rna_seq.LHX8_NGN3.day6.rep1


title: iNeuron.rna_seq.E2F7_NGN3.day6.rep1

value: TetO-NGN3 + TetO-E2F7


title: MSC from healthy bone marrow donor 26


title: GT75_W8_P

value: Placebo


title: 80_Borzoi_HC_Female

description:
80
Canis familiaris

value: Borzoi


title: 84_Golden Retriever_Acute_GDV_Male

description:
84
Canis familiaris

value: Golden Retriever


title: MSC from healthy bone marrow donor 25


title: iNeuron.rna_seq.NGN3_only.day6.rep3


title: MSC from healthy bone marrow donor 24


title: MSC from healthy bone marrow donor 23


title: GT75_W4_T

value: Week 4


title: iNeuron.rna_seq.NGN3_only.day6.rep2


title: GT75_W4_P


title: iNeuron.rna_seq.NGN3_only.day6.rep1


title: 79_Borzoi_HC_Male

description:
79
Canis familiaris

value: gastric dilatation-volvulus:HC


title: 77_Borzoi_HC_Male

description:
77
Canis familiaris


title: iPSC.rna_seq.Ctrl.day6.rep3

value: Untreated


title: 78_Borzoi_HC_Male

description:
78
Canis familiaris


title: 76_Borzoi_HC_Female

description:
76
Canis familiaris

value: Female


title: GT100_W8_P

value: Human skin


title: GT75_DO_T

value: Day 0

value: Untreated (T)


title: GT75_DO_P

value: Untreated (P)


title: iPSC.rna_seq.Ctrl.day6.rep2


title: 73_Borzoi_HC_Female

description:
73
Canis familiaris


title: iPSC.rna_seq.Ctrl.day6.rep1


title: GT100_W4_P


title: MSC from FL 37

source_name: MSC from FL

value: FL patient

value: Bone marrow

value: In vitro expanded bone marrow mesenchymal stroma cells


title: GT100_W8_T

value: Week 8

value: Treatment


title: MSC from FL 36


title: MSC from FL 38


title: MSC from FL 35


title: MSC from FL 34


title: MSC from FL 33


title: GT100_W4_T


title: A375 p53-/- replicate 1

city: Dallas

first: John

middle: M

last: Abrams

state: TX

address: 5323 Harry Hines Blvd

department: Cell Biology

institute: University of Texas Southwestern Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were preprocessed to remove adapters and low quality sequences before alignment to the hg38 assembly of the human genome using the STAR aligner.
Duplicate reads were identified with Picard. HTseq counts table was used as input to perform normalization and differential gene expression analysis with Deseq2.  CPM normalized bigwig files were created with Deeptools.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: normalized gene expression

source_name: A375 p53-/- replicate 1

growth_protocol: A375 Cells were grown in DMEM.

extract_protocol:
RNA was extracted using Trizol and purified following the manufacturer's instructions.  RNA was treated with TruboDNAse.  Sequencing libraries were prepared from 1ug of purified RNA using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7750S) and the NEB polyadenlyated mRNA enrichment kit (NEB #E7490S)
RNA libraries were prepared for sequencing using standard NEBNext Ultra II Directional Library Prep Kit protocol.

value: crispr cas9 p53 knockout

tag: cell line


title: A375 parental WT replicate 2

source_name: A375 parental WT replicate 2

value: parental p53 Wild Type


title: GT100_DO_U 2

value: Uninjured (Treatment 2)


title: cvpA library grown in LB

city: Boston

first: Matthew

middle: K

last: Waldor

state: MA

address: 181 Longwood Avenue

department: Microbiology

institute: Harvard Medical School

description: processed file: fitness_in_doc.txt

library_source: genomic

data_processing:
Library strategy: Tn-Seq, TIS
Reads were trimmed of transposon and adapter sequences in CLC Genomics Workbench
Reads were mapped to EHEC genome (chromosome NZ_CP008957.1, plasmid NZ_CP008958.1) using Bowtie, allowing for no mismatches
Data was processed using the ARTIST pipeline. Code available in Pritchard 2014 Plos Genetics 10(11):e1004782
Genome_build: chromosome NZ_CP008957.1, plasmid NZ_CP008958.1
Supplementary_files_format_and_content: matrix of ARTIST pipeline output

organism: Escherichia coli O157:H7 str. EDL933

source_name: Enterohemorrhagic E. coli (EHEC) colonies

growth_protocol: libraries were created on LB Kanamycin 50ug/mL plates at 37C

extract_protocol:
gDNA was isolated using Wizard Genomic DNA extraction kit
transposon-containing fragments were amplified with custom primers using PCR

treatment_protocol: for selection, libraries were grown for 1 hour in liquid LB culture at 37C and then plated on either LB Kan 50 ug/mL or LB plates containing 1% DOC and Kan 50 ug/mL

value: cvpA deletion

value: grown on LB plates


title: cvpA library grown in 1% DOC

description: processed file: fitness_in_doc.txt

value: grown on LB plates containing 1% deoxycholate (DOC)


title: A549-CRISPR cells_PA14_rep3

city: Grenoble

first: Vincent

last: Deruelle

address: 17 avenue des Martyrs

institute: CEA Grenoble

description: gRNA amplification

data_processing:
Sequencing reads were de-multiplexed by the CNRS platform of Orsay (Institut de Biologie Intégrative de la Cellule) by using the barcodes. The trimmed reads were used to map gRNA sequences to the TKOv3 library in order to define a read count for each gRNA of each sample. Then data were processed and analyzed using the web-based analysis platform, CRISPR-AnalyzeR. Count data were filtered and normalized, and sgRNA sequences and genes were ranked by MAGeCK method. The adjusted p-values were analyzed according to MAGeCK method to identify overrepresented genes targeted by gRNAs in outpools compared to input.
Genome_build: TKOv3 library
Supplementary_files_format_and_content: text files include the occurrence of each sgRNA indexes in TKOv3 library for all samples. The excel file includes a summary of Illumina reads and sgRNA counts for individual samples. Number of Illumina reads after analysis and sgRNAs counts (≥10 reads) are shown

source_name: Adenocarcinomic human alveolar basal epithelial cells

growth_protocol: Toronto human knockout pooled library (TKOv3) was obtained from Addgene ((#90294). Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and were grown at 37°C with 5% CO2. A549 cells were infected with lentiviruses containing the TKOv3 library. First, the lentiviral concentration was established by serial dilutions of lentivirus on A549 cells containing 8 µg.mL-1 polybrene and treated or not treated with 2 µg.mL-1 puromycin. The virus volume that gave 30% survival with puromycin selection vs. without puromycin was chosen for library construction. Then, 50.106 trypsinized A549 cells (calculated for 200-fold TKOv3 library coverage) were prepared in DMEM containing 10% FBS, supplemented with 8 µg.mL-1 polybrene. Cells were incubated with lentiviral particles at MOI of 0.3. After 24 hours of incubation, media were replaced with DMEM containing 10% FBS supplemented with 2 µg.mL-1 puromycin and cells were additionally incubated for 48 h to select transfected cells.

extract_protocol:
After three rounds of infection, the surviving populations were expanded to obtain 20.106 cells. Uninfected A549-CRISPR cells were expanded similarly. Each cell population was subjected to genomic DNA (gDNA) extraction with a QIAamp DNA Blood Maxi kit (Qiagen).
A one-step PCR was carried out to enrich and amplify gRNAs from the gDNA of selected cell populations with Illumina TruSeq adapters and a unique barcode of two 8-bp index required for Illumina sequencing. The resulting amplicons were gel extracted, quantified and sequenced using a NextSeq 500 (Illumina).

treatment_protocol: A549 cells were transduced with TKOv3 lentiviral library and infected with PA14 (ExoU+ strain) for 90 min at MOI of 10. To stop the infection, cells were trypsinized after washing and reseeded in DMEM supplemented with 10% FBS and 20 µg.mL-1 polymixin B. The surviving population was expanded and evaluated daily to monitor the recovery of cells. The day after the seeding, 90 µg.mL-1 gentamicin was also added in the medium to prevent proliferation of polymyxin-resistant bacteria. When surviving cells reached 70-80% confluence, they were subjected to a second and a third round of infection with PA14, allowing the repetition of the procedure.

value: Adenocarcinomic human alveolar basal epithelial cell line

value: Infected with PA14 (ExoU+ strain)


title: GT70_W8_T

value: Human skin


title: WT library grown in LB

description: processed file: fitness_in_doc.txt

value: WT


title: MSC from FL 31


title: GT100_DO_U 1

value: Day 0

value: Uninjured (Placebo 1)


title: A549-CRISPR cells_PA14_rep1

description: gRNA amplification


title: blood-6Month-ScoreB-patientMV200514

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 microarray (8X60K, Design 039494  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 46 out of 57 microarrays or with a minimal weight of 6 per group (timePoint combined with MADRS score) from at least one experimental group. At this step, 33129 spots out of 62976 were selected. The mean signal of the 30 first samples and 27 last ones were substracted to individuals signals to correct the batch effect of the 2 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 27202 rows each corresponding to a unique ProbeName (provided as data Matrix).

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Total RNA was extracted with the PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France) according to the manufacturer's protocol. Total RNA quality was assessed and its concentration was measured using RNA Nano chips onto a Bioanalyser 2100 (Agilent, Boeblingen, Germany).

treatment_protocol: 5ml venous blood were collected from the 57 patients, using vacuum tubes which included a reagent that immediately stabilized intracellular RNA (PAXgene blood RNA system, PreAnalytiX GmbH, Hombrechtikon, Switzerland). The samples were kept at room temperature for 8 h as required for stabilizing RNA and then at -20°C until RNA extraction.

tag: patient

tag: time

tag: MADRS

value: B

value: Venous blood


title: A375 parental WT replicate 1

source_name: A375 parental WT replicate 1


title: blood-0Month-ScoreB-patientMV200514


title: blood-6Month-ScoreA-patientMLL261113

value: A


title: blood-0Month-ScoreA-patientMLL261113


title: GT70_W4_T

value: Week 4


title: MSC from FL 32

value: FL patient

value: Bone marrow

value: In vitro expanded bone marrow mesenchymal stroma cells


title: blood-6Month-ScoreB-patientPH100614


title: A549-CRISPR cells_PA14_rep2

description: gRNA amplification


title: GT70_W8_P

value: Week 8

value: Placebo


title: WT library grown in 1% DOC

description: processed file: fitness_in_doc.txt


title: HCT116 miR-200High rep2 - Exp.2

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis was performed using DESeq2 with DMSO samples for each cellline as the respective control
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

growth_protocol: HCT116 (ATCC) cells were cultured in McCoy’s 5A media (Sigma) supplemented with 10% FBS (Sigma), 1%Pen/Strep (Sigma) and 1%L-Glutamine (Sigma).  Cells were grown at 37°C in a 5% CO 2 incubator.

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 were transiently transfected with PEI and a miR-200b/c activity sensor plasmid that allows to differentiate by fluorescence and FACS sort the cells with lowest and highest expression/activity

value: colon cancer

tag: mir-200b/c activity

value: sorted high


title: blood-0Month-ScoreB-patientPH100614


title: cvpA library

description: processed file: synthetic_fitness.txt

value: cvpA deletion


title: Uninfected A549-CRISPR cells

description: gRNA amplification

value: Adenocarcinomic human alveolar basal epithelial cell line

value: Uninfected


title: DAP-bHLH38

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description:
Sample 20
Protein-DNA interaction

data_processing:
Library strategy: DAP-seq
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Genome_build: Arabidopsis TAIR10 genome (Ensemble Release 42)
Genome_build: Solanum lycopersicum SL4.0 assembly, ITAG4.0 annotation
Genome_build: Marchantia polymnorpha MpTak1v5 version
Supplementary_files_format_and_content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4

organism: Arabidopsis thaliana

source_name: 10 days-old seedlings

growth_protocol: 10 days-old seedlings grown in MS medium

extract_protocol:
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.

tag: protein

tag: gene id

tag: protein expression

value: E.coli expressed


title: blood-6Month-ScoreB-patientPM120914

tag: tissue


title: Input AthDNAc

description:
Sample 21
Input-DNA for samples 12-20

value: Input-DNA for samples 12-20

value: Input DNA


title: GT70_W4_P

value: Human skin

tag: wound/scar time point and group


title: HCT116 miR-200High rep1 - Exp.2


title: DAP-bHLH18

description:
Sample 19
Protein-DNA interaction


title: HCT116 miR-200Low rep1 - Exp.2

value: sorted low


title: blood-0Month-ScoreB-patientPM120914

value: B

value: Venous blood


title: GT69_W8_T

tag: egcg treated/placebo

value: Treatment


title: GT69_W8_P

tag: group allocation


title: GT70_DO_U 2

value: Day 0

value: Uninjured (Treatment 2)


title: DAP-PIF5

description:
Sample 17
Protein-DNA interaction


title: HCT116 miR-200High rep2 - Exp.1


title: GT70_DO_U 1

value: Uninjured (Placebo 1)


title: GT82_D_P

value: Untreated (P)


title: HCT116 miR-200Low rep2- Exp.2

value: colon cancer


title: GT82_W4_P

value: Week 4

value: Placebo


title: HCT116 miR-200High rep1 - Exp.1

value: sorted high


title: blood-0Month-ScoreA-patientBB080414

value: A


title: DAP-bHLH11

description:
Sample 18
Protein-DNA interaction

value: E.coli expressed


title: WT library

description: processed file: synthetic_fitness.txt

value: WT


title: GT69_W4_T


title: GT69_W4_P


title: DAP-PIF4

description:
Sample 16
Protein-DNA interaction


title: HCT116 miR-200Low rep2- Exp.1


title: blood-0Month-ScoreA-patientPP120315


title: DAP-bHLH66

description:
Sample 15
Protein-DNA interaction


title: GT69_DO_U 2


title: HCT116 miR-200Low rep1 - Exp.1


title: GT69_DO_U 1


title: DAP-bHLH92

description:
Sample 14
Protein-DNA interaction


title: DAP-bHLH99

description:
Sample 13
Protein-DNA interaction


title: 4564-007

city: Leiden

first: Roel

last: Bijkerk

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

description:
T0
7

data_processing:
Reads were mapped to miRbase 20
TPM is the unit used to measure expression in this NGS experiment. The number of reads for a particular microRNA is divided by the total number of mapped reads and multiplied by 1 million (Tags Per Million ).
The differential expression analysis is done using the EdgeR statistical software package (Bioconductor, http://www.bioconductor.org/).
For normalization the trimmed mean of M-values method was used based on log-fold and absolute gene wise changes in expression levels between samples (TMM normalization).
Genome_build: miRbase 20, human
Supplementary_files_format_and_content: excel file including TPM values for each group including differential expression between t0 and t12

source_name: plasma

extract_protocol:
RNA was harvested from plasma samples using Trizol reagent.
plasma RNA was converted into microRNA NGS libraries using NEBNEXT library generation kit (New England Biolabs Inc.) according to the manufacturer’s instructions. Each individual RNA sample had adaptors ligated to its 3’ and 5’ ends and converted into cDNA. Then the cDNA was pre-amplified with specific primers containing sample specific indexes. After 18 cycle pre-PCR the libraries were purified on QiaQuick columns and the insert efficiency evaluated by Bioanalyzer 2100 instrument on high sensitivity DNA chip (Agilent Inc.). The miRNA cDNA libraries were size fractionated on a LabChip XT (Caliper Inc.) and a band representing adaptors and 15-40 bp insert excised using the manufacturer’s instructions. Samples were then quantified using qPCR and concentration standards. Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar concentrations. The library pool(s) were finally quantified again with qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flow cell before sequencing using v3 sequencing methodology according to the manufacturer’s instructions (Illumina Inc.). Samples were sequenced on the Illumina NextSeq 500 system.

treatment_protocol: Transwomen received oral treatment with a daily dose of both 50 mg cyproteroneacetate (CPA) (Androcur®, Bayer) and 4 mg Estradiol Valerate (Progynova®, Bayer) or 100 µg/24h transdermal estradiol (Systen®, Janssen-Cilag) twice a week, as previously described (van Velzen et al., 2019). Paired plasma samples were obtained at the start of treatment and after one year of daily estrogen suppletion

value: pooled plasma of 4 patients

tag: time point

value: start of treatment


title: 4564-008

description:
T0
8


title: blood-6Month-ScoreA-patientBB080414


title: blood-0Month-ScoreA-patientCPP281113


title: blood-6Month-ScoreA-patientNR180314


title: DAP-bHLH115

description:
Sample 12
Protein-DNA interaction


title: GT96_W8_P

value: Human skin

value: Week 8


title: GT96_W4_T


title: blood-0Month-ScoreA-patientNR180314

value: Venous blood


title: blood-6Month-ScoreA-patientCPP281113


title: HaP53

city: Lanzhou

first: Quan-Sheng

last: Qiu

state: Gansu

address: 222 South Tianshui Road

department: MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences

country: China

institute: Lanzhou University

data_processing:
Sequencing, assembly, and annotation of the reference transcriptome
The cDNA libraries for 3 biological replicates prepared from NEB Next Ultra RNA Library Prep Kit for Illumina were sequenced with paired-end sequencing on an Illumina HiSeq 2500 platform (Novogene, China). An average of 56 and 59 million 125nt long reads were obtained for control groups and 5% PEG-treated group, respectively. Reads with more than 10% Ns or more than 50% Q<=5 bases were removed from the raw data after quality check.
For the de novo transcriptome assembly, RNA-seq reads from control and 5% PEG treatment group were pooled separately. Two independent assemblies for control and 5% PEG treatment group were performed with Trinity v2.2.0 (Grabherr et al., 2011)with default settings except for setting --min_kmer_cov to 5 and --group_pairs_distance to 300. After removing contaminants, artefacts, contigs with low read support and redundancy from each assemblies, those two assemblies were merged to get a reference transcriptome. All assembled transcript contigs in the merged transcriptome assembly showing > 95% sequence identity over > 70% of the total length were clustered using CD-HIT-EST v4.6(Li and Godzik, 2006). We selected a representative transcript containing the longest continuous open reading frames (ORFs) predicted by TransDecoder v2.0.1 (https://transdecoder.github.io/) for each cluster to generate a non-redundant H.ammodendron transcriptome.
Annotation was based on best BLASTN hits found in TAIR10 Arabidopsis gene model sequence, National Center for Biotechnology Information (NCBI) plant 'refseq_rna' database (June 2016), as well as the non-redundant (nr) database (June 2016), with 10-5 as the e-value cut-off. Non-plant hits were also removed by performing BLAST against NCBI non-plant database refseqRNA (June 2016).
Assembly assessment
Quantitative assessment of assembly completeness was performed using Core Eukaryotic Genes Mapping Approach (CEGMA)(Parra et al., 2007) and Benchmarking Universal Single-Copy Orthologs (BUSCO) v1.22 (Sim?o et al., 2015) with the default settings. Modified python script and early plant release datasets were used upon request from the author of BUSCO.
Genome_build: reference sequence used for read alignment.
Supplementary_files_format_and_content: Count file  were generated from the control and treatment group

organism: Haloxylon ammodendron

growth_protocol: The seeds were placed on the filterpaper and cultured with 1/2 Hoagland solution (PhytoTechnology Laboratories, H353). The Petri dishes were placed in a greenhouse for 3 days at 22 ℃ with a 16-h-light/8-h-dark photoperiod.

extract_protocol:
Total RNA was isolated with TRIZOL reagent (Invitrogen) from the PEG treatment and control seedlings.
The cDNA libraries for 3 biological replicates prepared from NEB RNA Library Prep Kit for Illumina were sequenced with paired-end sequencing on an Illumina HiSeq 2500 platform

treatment_protocol: After germination, the seedlings were subjected to drought stress with 5% PEG 6000 (Merck) (in 1/2 Hoagland solution) for 7 days.

value: whole seedlings

tag: age

value: 10 days

value: wild type


title: blood-0Month-ScoreA-patientLB141114


title: 4564-005

description:
T12
5

value: after one year


title: blood-0Month-ScoreA-patientDD101214


title: HaP52


title: GT96_W4_P


title: blood-6Month-ScoreA-patientLB141114


title: 4564-004

description:
T12
4


title: GT96_W8_T

value: Treatment


title: HaP51


title: blood-6Month-ScoreA-patientDD101214


title: GT96_DO_U 1

value: Day 0

value: Uninjured (Placebo 1)


title: blood-0Month-ScoreB-patientMA021214

value: B


title: HaP03


title: GT95_W8_T


title: 4564-001

description:
T0
1


title: 4564-006

description:
T12
6


title: HaP02


title: GT95_W8_P

value: Placebo


title: blood-0Month-ScoreB-patientJMV220115


title: blood-0Month-ScoreB-patientNC130214


title: blood-0Month-ScoreA-patientSB221013

value: A


title: blood-6Month-ScoreB-patientNC130214


title: 4564-002

description:
T0
2


title: HaP01


title: GT95_W4_T

value: Week 4


title: GT96_DO_U 2

value: Uninjured (Treatment 2)


title: VEH3

city: Utrecht

first: Bart

last: Westendorp

address: Uppsalalaan 8

department: Molecular Health Sciences

institute: Utrecht University

description:
genotype/variation: FUCCI-cells +/- E2F7/8 deletion
Row I-P contain vehicle-treated RPE-FUCCI cells

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters.
The mapped reads were counted using STAR. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Further processing was done using Seurat v3. Cells expressing <1000 or>10000 genes, <4000 Unique Molecular Identifier (UMI) counts, and >30 percent mitochondrial genes were filtered out. Next, data were normalized and scaled with the SCTransform method.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: logNormalize_data_180cells.csv: Comma-separated file containing normalized UMI counts.
Supplementary_files_format_and_content: metadata_180cells.csv: Comma-separated metadata file with cell IDs, fluorescence microscopy data, genotype, treatment, and other experimental parameters.
Supplementary_files_format_and_content: celseq2_bc.csv: Comma-separated file containing barcodes with corresponding well IDs.

source_name: RPE1-hTERT cell line

growth_protocol: DMEM + FBS, normal growth conditions in vitro.

extract_protocol:
Cells were sorted into 5µl Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by an automated version of the previously described CEL-Seq2 technique.
Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: NCS 200 ng/mL was added to the cells 24 or 48 prior to harvesting; vehicle-treated cells received only DMSO 24h prior to harvesting.

tag: genotype/variation

value: mixed sample (non-demultiplexed)

value: vehicle-treated


title: VEH2

description:
genotype/variation: FUCCI-cells +/- E2F7/8 deletion
Row B-H contain vehicle-treated RPE-FUCCI cells

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters.
The mapped reads were counted using STAR. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 6bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Further processing was done using Seurat v3. Cells expressing <1000 or>10000 genes, <4000 Unique Molecular Identifier (UMI) counts, and >30 percent mitochondrial genes were filtered out. Next, data were normalized and scaled with the SCTransform method.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: logNormalize_data_180cells.csv: Comma-separated file containing normalized UMI counts.
Supplementary_files_format_and_content: metadata_180cells.csv: Comma-separated metadata file with cell IDs, fluorescence microscopy data, genotype, treatment, and other experimental parameters.
Supplementary_files_format_and_content: celseq2_bc.csv: Comma-separated file containing barcodes with corresponding well IDs.


title: CFK1 OE_line2 WGBS

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

data_processing:
Bisulfite reads were aligned to the TAIR10 genome using the BSMAP. Number of methylated and un-methylated reads were obtained form methratio.py (from BSMAP). Only cytosine with reads coverage >=5 were used to calculate methylation ratios. Methylation ratios at each cytosine were converted to bedGraph files using awk and to bigWig files using the UCSC executable script "bedGraphToBigWig". DMRs were called with Fisher's exact test and also R package MethylKit. The overlapped ones were regarded as DMRs and used for subsequent analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Methratio output files  were converted to bedGraph via custom awk scripts and bedGraph files were converted to BigWig files via the UCSC "bedGraphToBigWig" executable script.

source_name: 3-week old flower tissue

growth_protocol: Plants were grown on 1/2X MS agar (0.7%) for 10 days under constant light condition and then transferred to soil under long day conditions (16hrs light/8hrs dark). After three weeks of growth from seedlings, flower tissue was harvested and frozen in liquid nitrogen for DNA extraction for sequencing.

extract_protocol:
DNA extracted using  Qiagen DNeasy Plant Mini Kit (catalog # 69104)
Bisulfite-seq were prepared as Pignatta, D. et al Bio-Protocols 2015.

value: flower

value: 3-week old

value: Columbia-0 background with CFK1-FLAG transgene


title: CFK1 OE_line1 WGBS


title: NCS24+VEH1

description:
genotype/variation: FUCCI-cells +/- E2F7/8 deletion
treatment: vehicle-treated, or 24h after 200 ng/mL neocarzinostatin
Well IDs C1 through I24 contain 24h NCS-treated RPE-FUCCI cells; well IDs M1 through P24 contain vehicle treated cells


title: GT95_DO_U 2

value: Human skin


title: drm2 WGBS

value: Columbia-0 background with DRM2 T-DNA insertion mutation


title: NCS48

description:
genotype/variation: FUCCI-cells +/- E2F7/8 deletion
Row J-M contains 48h NCS-treated RPE-FUCCI cells

value: 48h after 200 ng/mL neocarzinostatin


title: GT95_DO_U 1


title: Col-0 WGBS

value: wild-type Columbia-0


title: GT65_W8_T

value: Week 8

value: Treatment


title: A375 p53-/- replicate 2

source_name: A375 p53-/- replicate 2

tag: genotype

value: crispr cas9 p53 knockout


title: MCF-7, HCM2

city: Ithaca

first: Gerlinde

last: Van de Walle

state: NY

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: 5 x MCF7 files

data_processing:
reads were trimmed to remove adaptor and low-quality bases with cutadapt v1.8.3, aligned with TopHat 2.1.1
trimmed reads were analyzed for differential gene expression using cuffdiff v2.2.1 2.2.1 using Ensembl annotations
transcript abundance was measured in fragments per kilo base (kb) of exon per million fragments mapped (FPKM)
genome build: hg19
Supplementary_files_format_and_content: processed with Cuffdiff
Supplementary_files_format_and_content: DIFF
Supplementary_files_format_and_content: READ_GROUP_TRACKING

source_name: ATCC

growth_protocol: cells were cultured according to ATCC instructions

extract_protocol:
RNA was extracted with TRIzol reagent following manufacturer’s recommendations
RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit using 500 ng total RNA followed by polyA+ enrichment

treatment_protocol: cells were treated with self conditioned medium (control) or conditioned medium from equine mammosphere derived epithelial cells

value: mammary gland; breast

tag: cell type

value: epithelial-like

tag: agent

value: test, horse MDEC conditioned medium


title: MCF-7, OCM2

description: 5 x MCF7 files

value: control, own conditioned medium

tag: cell line


title: GT65_W8_P

value: Placebo


title: blood-6Month-ScoreB-patientJMV220115

tag: patient

tag: time

value: B

value: Venous blood


title: Msc1_wt Rep2

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

data_processing:
BWA (Li, 2010 #9905;Li, 2009 #9908) or BOWTIE2 (Langmead, 2012 #9901) was used to map ChIP-seq reads onto the S. pombe genome assembly EF2 (ASM294v2) or modified genome assembly generated based on ASM294v2, where centromere 2 was replaced with sequence from centromere 1 to mimic (cc2∆::cc1) and to include pHCC2 plasmid sequence.
Indexed, sorted bam files were created for each dataset using SAMtools (Li, 2009 #9907).
The program bamCoverage from the deepTools suite version 2.5.3 (Ramirez, 2016 #9919) or BEDtools (Quinlan, 2014 #9916;Quinlan, 2010 #9917) was used to create bigwig files from the mapped bam files and scaled using reads per kilobase of transcript per million mapped reads [RPKM]
SeqPlots (Stempor, 2016 #9923) was used to plot the occupancy over transcription start sites [TSS] as annotated in PomBase.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Genome_build: S. pombe +pHCC2 genome (see pombe.ASM294v2.20.cc2_D.gtf.gz, pombe_cc2D_pHcc2.bed.gz, pombe_cc2_D_pHetcc2.ann.gz, pombe_cc2_D_pHetcc2.fa.gz)
Supplementary_files_format_and_content: bigWig

organism: Schizosaccharomyces pombe

growth_protocol: S.pombe strains were grown in YES media. ~150x107 cells were harvested from o/n cultures and processed for ChIP

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) for 15 min at room temperature and lysed using a bead beater (Biospec Products). Cell lysates were sonicated in a Bioruptor (Diagenode) (30/40 min, 30 s On and 30 s Off at ‘High’ (200W) position). For CENP-ACnp1 ChIPs, anti-CENP-ACnp1 serum was used with Protein G sephrose beads (Roche). For all other ChIPs, Protein G Dynabeads (Life Technologies) were used along with anti-Myc 9B11 (Cell Signaling) or anti-Flag M2 antibody (Sigma), as appropriate. Immunoprecipitated DNA was recovered using Qiagen Min-Elute PCR purification kit.
ChIP-seq libraries were generated using an Illumina-based protocol with custom reagents using NEXTFlex-96 DNA Barcodes (Bioo Scientific). Briefly, immunoprecipitated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina adapters, which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA fragments were size-selected using AmpureXP beads to remove excess adapters and adapter-modified DNA fragments were enriched by PCR amplification with Illumina primers for 12 cycles. The purified ChIP-seq libraries thus generated were validated and subsequently captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500/ HiSeq4000 system following the manufacturer's protocols.

value: wt

tag: antibody

value: anti-Flag (Sigma - Cat# F1804)

tag: expressing


title: MCF-7, HCM1

description: 5 x MCF7 files


title: T01

city: Guiyang

first: Huiqing

last: Yan

state: Guizhou

address: Guizhou Normal University

department: School of Life Science

institute: Guizhou Normal University

data_processing:
De novo assembly was performed using the Trinity assembly program with default settings based on the de Bruijn graph algorithm. Clean reads were first broken into shorter fragments (K-mers) and then assembled into longer fragments named contigs. The overlapping reads were mapped back to the corresponding contigs. Based on the paired-end reads,ifferent contigs from the same transcripts were identified, and the distances among these contigs were calculated. These contigs were further assembled using Trinity to obtain sequences that were no longer defined as unigenes. The assembled genome was used as the genom
Bowtie2 and RSEM (RNA-Seq by Expectation-Maximization)were used to map clean reads to the assembled transcriptome and evaluate the abundance of each transcript,respectively.
To compare the expression levels of transcripts in the different samples, FPKM fragments per kilobase of ranscript per million mapped reads) was used to normalize the gene expression according to the formula: FPKM = (106 × C × 103)/NL. C represents the number of reads uniquely aligned to a certain unigene, N indicates the total number of reads uniquely aligned to all unigenes, and L is the base number of this unigene.
Genome_build: FASTA included on the series record.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mangifera indica

source_name: mango leaf

extract_protocol:
The total RNA of mango flower, leaf and fruit were extracted using TAKARA Trizol Reagent according to the protocol of manufacture.
The total RNA was treated with RNase-free DNase I to eliminate DNA contamination.The enrichment of mRNA was performed with Oligo (dT)-attached magnetic beads,and fragmentation was performed using divalent cations under high temperature in NEBNext First Strand Synthesis Reaction Buffer (5×) to randomly interrupt mRNA. The first-strand cDNA chain was synthesized by random hexamers and M-MuLV Reverse Transcriptase (RNase H) with the mRNA template. Subsequently, the second-strand cDNA chain was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. The the double stranded cDNA was purified using AMPure XP beads. Following end-pair and single nucleotide A (adenine) addition for the purified cDNA, adapters were used to distinguish the different samples by selection with AMPure XP beads for PCR amplification, following which the cDNA library was obtained.

value: wild type

value: leaf

value: tender leaf


title: MCF-7, OCM1

description: 5 x MCF7 files


title: GT65_W4_P

data_processing:
Raw image data file from high-throughput sequencing (Illumina PE150 Nova-Seq) was transformed to Sequenced Reads by CASAVA v1.8 base recognition (Base Calling)
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR v2.5) software.
Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.  The filtering process is as follows:  (1) Discard reads with adaptor contamination.  (2) Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%).  (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read.
For samples with biological replicates, differential expression analysis of two conditions/groups was performed using the DESeq2 R package providing statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Genome_build: Ensembl version Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: Processed data is in Excel format including differential expression analysis data

value: Human skin

value: Week 4


title: Swr1_wt Rep2

value: anti-myc (9B11 - Cell Signaling, Cat# 2276)


title: MDA-MB-231, OCM2

description: 5 x 231 files

value: epithelial


title: T02

source_name: mango fruit

value: fruit

value: mature fruit


title: GT65_DO_U 1

source_name: Human skin

value: Day 0

value: Uninjured (Placebo 1)


title: blood-6Month-ScoreB-patientAC030215

tag: MADRS


title: blood-0Month-ScoreB-patientSM070415


title: GT65_W4_T

value: Treatment


title: Swr1_wt Rep1


title: blood-6Month-ScoreB-patientSM070415


title: MDA-MB-231, HCM1

description: 5 x 231 files

value: mammary gland; breast

value: test, horse MDEC conditioned medium


title: blood-0Month-ScoreB-patientAC030215

value: B

value: Venous blood


title: blood-0Month-ScoreA-patientKP261113

value: A


title: MDA-MB-231, OCM1

description: 5 x 231 files

value: control, own conditioned medium


title: C172

city: Shenzhen

first: Zheng

last: Zhang

state: Guangdong

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

description: Single-cell RNAseq

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 3’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, filtered gene-barcode matrix of all samples was integrated with Seurat v3 to remove batch effect across different samples(Stuart et al., 2019). In parameter settings, the first 50 dimensions of CCA and PCA were used.
The filtered gene-barcode matrix was first normalized using ‘LogNormalize’ methods in Seurat v3 with default parameters. The top 2, 000 variable genes were then identified using ‘vst’ method in Seurat FindVariableFeatures function. Variables nCount_RNA and percent.mito were regressed out in the scaling step and principal component analysis (PCA) was performed using the top 2, 000 variable genes. Then Uniform Manifold Approximation and Projection (UMAP) was performed on the top 50 principal components for visualizing the cells. Meanwhile, graph-based clustering was performed on the PCA-reduced data for clustering analysis with Seurat v3, the resolution was set 1.0 to get a finer result.
MAST in Seurat v3 was used to perform differential gene expression analysis(Finak et al., 2015). For each cluster, differentially-expressed genes (DEGs) were generated relative to all of the other cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count

molecule: polyA RNA

source_name: lung tissue

extract_protocol: The scRNA-Seq libraries were prepared with Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics; PN-1000075, PN-1000073 and PN-120262) following the user guide provided. Briefly, Gel bead in Emulsion (GEM) are generated by combining barcoded Gel Beads, a Master Mix containing 20,000 cells, and Partitioning Oil onto Chromium Chip B. Reverse transcription (RT) takes place inside each GEM, after which cDNAs are pooled for amplification and library construction in bulk. Finished library molecules consist of Illumina adapters and sample indices, allowing pooling and sequencing of multiple libraries on a next-generation short read sequencer.

tag: organ

value: lung

tag: Sex

value: male

tag: patient group

value: Severe COVID-19

tag: cell subsets

value: Total cell

tag: sars-cov-2 status

value: negative


title: H2A.ZPht1_msc1∆ Rep4

value: anti-myc (9B11 - Cell Signaling, Cat# 2276)


title: Msc1_wt Rep1

value: wt

value: anti-Flag (Sigma - Cat# F1804)


title: C170

description: Single-cell RNAseq


title: blood-6Month-ScoreA-patientKP261113

tag: tissue


title: MDA-MB-231, HCM2

description: 5 x 231 files

value: epithelial


title: H2A.ZPht1_msc1∆ Rep3


title: blood-0Month-ScoreA-patientVF200115


title: blood-6Month-ScoreA-patientVF200115


title: blood-0Month-ScoreA-patientTDC270115


title: GT65_DO_U 2

city: Manchester

first: Ardeshir

last: Bayat

address: Oxford Road

institute: University of Manchester

extract_protocol:
Tissue biopsies were homogenised in 300μL of RLT buffer (Qiagen, GmbH, Helden, Germany) mixed with β-mercaptoethanol (Sigma-Aldrich, St Louis, MO) (10μl β-mercaptoethanol/ml RLT buffer) using 5-mm stainless steel beads and a Qiagen TissueLyser II (Qiagen GmbH) at 30 oscillations/second for 10 minutes. RNA was extracted using RNeasy Tissue Mini Kits (Qiagen GmbH). Eluted RNA quantity and purity was assessed using NanoDrop ND-100 v3.0.1 spectrophotometer (NanoDrop Technologies, Wilmington, DE), Agarose gel electrophoresis and Agilent 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human skin

tag: wound/scar time point and group

value: Day 0

tag: egcg treated/placebo

value: Uninjured (Treatment 2)

tag: group allocation


title: C168

description: Single-cell RNAseq


title: blood-0Month-ScoreB-patientSS150414


title: H2A.ZPht1_msc1∆ Rep2

tag: genotype


title: C166

description: Single-cell RNAseq


title: TRIM8_NC2

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

data_processing:
An average of 46M paired-end 75bp reads per sample were generated by Illumina NextSeq500 sequencer
Raw data in FASTQ format were transferred from the SUNYMAC core facility server
Sequencing quality was accessed by FastQC v0.11.7 program, low-quality bases and reads were filtered from raw reads by Trimmomatic v0.36 with a Phred score cutoff of 30
The trimmed reads were mapped to Gencode GRCh38.p12 Release 29 human reference genome using STAR aligner v2.6.0c.
Reads mapped to genes were summarized by featureCounts program in subread v1.6.1. Genes were filtered by CPM (count-per-million) ≥ 1 in at least 2 samples, and data were normalized to effective library size by edgeR v3.22.3 program.
Genome_build: Gencode GRCh38.p12 Release 29 human reference genome
Supplementary_files_format_and_content: Normalized gene counts for each sample in log2 scale

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells (NPCs) were maintained in Neural Progenitor Medium (StemCell Technologies, #05833)

extract_protocol:
Total RNA was extracted from cells using the miRNeasy Mini Kit (217004, Qiagen) and treated with DNAase.
450ng RNA per sample was used for library preparation with Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Kit following manufacturer protocols

treatment_protocol: NPCs were infected with POU3F2 or TRIM8  ShRNA Lentivirus (Origene，# TL310273V, #TL300821V), After 72 h viral infection, cells were treated with puromycin (1µg/ml) to generate mixed NPCs expressing specific gene sequences

tag: cell type

value: iPSCs-derived Neural progenitor cells

tag: passage

value: TRIM8 control

tag: gender

value: Male


title: blood-0Month-ScoreB-patientAG121114

tag: patient

tag: time

value: B

value: Venous blood


title: H2A.ZPht1_msc1∆ Rep1

tag: antibody

tag: expressing


title: blood-6Month-ScoreB-patientAG121114

tag: MADRS


title: blood-6Month-ScoreA-patientAE170614

value: A


title: TRIM8_NC1


title: H2A.ZPht1_swr1∆ Rep4


title: Con rep2 RRBS

city: Beijing

first: Jiao

last: Fan

address: Fuxing road

institute: 301 hospital

data_processing:
We used Trim Galore to remove poor-quality bases and adaptor sequences from raw sequencing reads and obtained the cleaned data.
Bismark  was used to map the cleaned data to the Homo sapiens (human) genome assembly GRCh38.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files for each samples

source_name: intestine

extract_protocol:
Genomic DNA was extracted from the intestine sample and subjected to RRBS library preparation.
Libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: small intestinal atresia

value: intestine


title: Con rep1 RRBS


title: NEC rep2 RRBS

value: stage III acute NEC


title: H2A.ZPht1_swr1∆ Rep2


title: TRIM8_NC3


title: TRIM8_KD2

value: TRIM8 knockdown


title: NEC rep1 RRBS


title: TRIM8_KD1


title: blood-0Month-ScoreA-patientAE170614


title: H2A.ZPht1_swr1∆ Rep1

value: anti-myc (9B11 - Cell Signaling, Cat# 2276)


title: POU3F2_NC3

value: POU3F2 control


title: H2A.ZPht1_wt Rep4

value: wt


title: SRI37240 10 uM ribosome profiling C

city: Baltimore

first: Rachel

last: Green

state: MD

address: 725 N Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
5 prime ends of reads were trimmed using seqtk removing 4 nucleotides of degenerate RT primer sequence (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG)
Linker sequence (NNNNNNCACTCGGGCACCAAGGAC) was trimmed using Skewer
reads aligning to non-coding RNA sequences including rRNA and tRNA were depleted using STAR
remaining reads were aligned to the human genome using STAR
Genome_build: GRCh38 (hg38), Gencode release 30
Supplementary_files_format_and_content: Count tables for ribosome profiling and RNA-seq samples

source_name: HEK293T_SRI37240 10 uM ribosome profiling

growth_protocol: Cells were grown in DMEM with 10% FBS to ~75% confluency before harvest

extract_protocol:
Cells were lysed on ice in the presence of cycloheximide. Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation.
For ribosome profiling, fragments ranging from 15-34 nt were gel purified. Upon dephosphorylation of sample RNA, the linker was ligated and this product and rRNA was depleted using Ribo-Zero Gold from Illumina. This was followed by reverse transcription and gel purification. Libraries were then circularized, PCR-amplified, and gel-purified cDNA was submitted for sequencing.

treatment_protocol: Drugs were added to cells and treated for 24 hours

tag: cell line

tag: treatment

tag: concentration

value: 10 uM

tag: duration

value: 24 hours

tag: adapter

value: NNNNNNCACTCGGGCACCAAGGAC

tag: molecule subtype

value: Ribosome Protected mRNA (15-35 nt)


title: H2A.ZPht1_swr1∆ Rep3


title: POU3F2_NC2

value: iPSCs-derived Neural progenitor cells


title: H2A.ZPht1_wt Rep3


title: SRI37240 10 uM ribosome profiling B


title: TRIM8_KD3


title: blood-0Month-ScoreA-patientCN220714

tag: tissue


title: POU3F2_NC1

tag: genotype


title: SRI37240 10 uM ribosome profiling A


title: POU3F2_KD3

tag: cell type

value: POU3F2 knockdown


title: H2A.ZPht1_wt Rep2


title: blood-0Month-ScoreB-patientSB091214


title: G418 500 ug/mL ribosome profiling C

source_name: HEK293T_G418 500 ug/mL ribosome profiling

value: 500 ug/mL


title: blood-6Month-ScoreB-patientSB091214

value: B


title: POU3F2_KD2

tag: passage

value: Male


title: G418 500 ug/mL ribosome profiling B


title: blood-6Month-ScoreB-patientMC261113

value: Venous blood


title: msc1∆_CENP-ACnp1

value: anti-Cnp1 (sheep)


title: H2A.ZPht1_wt Rep1


title: POU3F2_KD1

tag: gender


title: swr1∆_CENP-ACnp1


title: wt_CENP-ACnp1_2


title: DMSO ribosome profiling B

source_name: HEK293T_DMSO ribosome profiling

value: DMSO


title: MM1S cells with KRAS knockdown, replicate 3

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

data_processing:
Base calling and demultiplexing was performed with bcl2fastq v2.18.0.12.
Residual adapter sequences present in sequencing reads were removed with Cutadapt version 1.12.
Reads were aligned to the human reference sequence GENCODE v24 using STAR version 2.5.2b using the --quantMode parameter setting to output read couts per gene.
a strand specific library preparation protocol generated reads specific for the minus strand. The read counts from column 4 of each processe data file was used for the analysis.
Genome_build: GENCODE v24
Supplementary_files_format_and_content: Count tables were assembled from STAR --quantMode output in R (v3.3.1); scores represent raw read counts per gene.
read counts per gene ID (column 1) without strand specificity (column 2), specific for the plus strand (column 3) and specific for the minus strand (column 4) [https://www.biostars.org/p/218995/]

source_name: MM1S cells with KRAS knockdown

growth_protocol: Cells were grown in FCS+Pen/Strep supplemented growth medium at 37°C and 5% CO2.

extract_protocol:
RNA was isolated using the NucleoSpin RNA-Kit (no. 740955.250; Macherey-Nagel, Düren, Germany).
RNA sequencing libraries were prepared with the TruSeq stranded mRNA kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with empty pSUPER vector or with pSUPER-derived vectors expressing shRNAs against RALA and KRAS.

value: multiple myeloma cell line

tag: genotype/variation

value: KRAS knockdown

tag: rin (rna integrity number)


title: pht1∆_CENP-ACnp1

tag: antibody


title: MM1S cells with RAL knockdown, replicate 3

data_processing:
Base calling and demultiplexing was performed with bcl2fastq v2.18.0.12.
Residual adapter sequences present in sequencing reads were removed with Cutadapt version 1.12.
Reads were aligned to the human reference sequence GENCODE v24 using STAR version 2.5.2b using the --quantMode parameter setting to output read couts per gene.
a strand specific library preparation protocol generated reads specific for the minus strand. The read counts from column 4 of each processe data file was used for the analysis.
Genome_build: GENCODE v24
Supplementary_files_format_and_content: Count tables were assembled from STAR --quantMode output in R (v3.3.1); scores represent raw read counts per gene.

source_name: MM1S cells with RAL knockdown

value: RAL knockdown


title: blood-6Month-ScoreA-patientCN220714

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 46 out of 57 microarrays or with a minimal weight of 6 per group (timePoint combined with MADRS score) from at least one experimental group. At this step, 33129 spots out of 62976 were selected. The mean signal of the 30 first samples and 27 last ones were substracted to individuals signals to correct the batch effect of the 2 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 27202 rows each corresponding to a unique ProbeName (provided as data Matrix).

tag: patient

tag: time

value: A


title: blood-6Month-ScoreA-patientGMD170315

tag: MADRS


title: blood-0Month-ScoreB-patientSM260215


title: DMSO ribosome profiling A

tag: cell line


title: G418 500 ug/mL ribosome profiling A

tag: treatment


title: MM1S cells with RAL knockdown, replicate 2


title: ste11_nontreated_s6

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

country: Canada

institute: Western University

data_processing:
RNA sequencing reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1(MARTIN 2011) with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`). Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (PERTEA et al. 2015) which returned gene abundances for each sample. We imported gene abundances into R and conducted differential analysis of gene count data using the DESeq2 R package (Love et al. 2014).
Genome_build: C. albicans SC5314 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files

organism: Candida albicans

source_name: opaque cells

extract_protocol:
Total RNA isolation was performed as previously described (Tebbji et al, PloSGenetics 2014)
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit

treatment_protocol: growth in SC-GlcNac medium and untreated

value: opaque cells

value: ste11 mutant

value: untreated


title: ste11_nontreated_s5


title: blood-0Month-ScoreB-patientMC261113

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

institute: INRAE

extract_protocol: Total RNA was extracted with the PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France) according to the manufacturer's protocol. Total RNA quality was assessed and its concentration was measured using RNA Nano chips onto a Bioanalyser 2100 (Agilent, Boeblingen, Germany).


title: MM1S cells with KRAS knockdown, replicate 2


title: Input 8H

first: Lora

last: Boteva

state: City of Edinburgh, Midlothian

address: Crewe Road

department: Institute of Genetics and Molecular Medicine

description: Input  DNA from  control HCT116 cells, 8 hours post release from G1/S

data_processing:
Fastq files were aligned to hg 19 using Bowtie 2
PCR duplicate removal, file sorting and indexing was performed with Samtools 1.2
Bam files were generated and read density in 1000 bp windows across the genome were calculated using the "multicov" option in Bedtools 2.25
Normalised FPKM values were generated for each window in R
FPKM values for genomic input for the corresponding cell cycle stage was subtracted
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files containing FPKM values normalised for genomic input in 1kb windows only for chromosomes 2 and 4. Genome-wide data were not produced as part of this study as the focus was on chr 2 and 4.

source_name: Input  from  control HCT116 cells, 8 hours post release from G1/S

growth_protocol: HCT116 (ATCC CCL-247) were cultured in DMEM-F12 supplemented with, 3 mM glutamine, 15 mM HEPES, 10% FBS, penicillin (100 U ml−1), streptomycin (100 μg ml−1) and phenol red (8.1 mg l−1).

extract_protocol:
Synchronised HCT116 cells were cross-linked first with 1 mM disuccinimidyl suberate (DSS, sigma) for 40 minutes and then with 1% formaldehyde for 20 minutes at room temperature, and then incubate in 200 mM glycine for 5 min to quench reactive DSS and formaldehyde. Cells were scraped, flash-frozen and stored at -20 °C. Cell pellets were lysed in 100 µl SDS Lysis buffer (50 mM Tris-HCl [pH 7.5], 10 mM EDTA, and 1% SDS) and added ChIP dilution buffer (50 mM Tris-HCl [pH7.5], 167 mM NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate, and protease inhibitor cocktail complete EDTA-free (Roche)) before sonication (Soni-prep sonicator for 20 cycles [40 seconds on, 20 seconds off]). Samples were then spun at 13000 rpm for 15 minutes at 4 °C, supernatant was collected and 10% of the supernatant volume was saved as an input. Immunoprecipitation was performed with Dynabeads protein G beads (Invitogen) coupled to an anti-SMC2 antibody provided by Kumiko Samejima. Samples were mixed with beads and incubated at 4 °C for 4 hours with rotation and washed sequentially with RIPA-150 mM NaCl and RIPA-500 mM NaCl (50 mM Tris-HCl [p8.0H], 150/500 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, and 0.1% sodium deoxycholate) and TE, then added direct elution buffer (10 mM Tris-HCl [pH8.0], 300 mM NaCl, 5 mM EDTA, and 0.5% SDS) before overnight at 65 °C to reverse cross-linking. Samples were treated with 5/200 units/ml RNaseA/T1 (Ambion) and 250 µg/ml proteinase K. DNA was extracted from the input and ChIP samples via phenol/chloroform precipitation.
Libraries were prepared with a NEBNext® Ultra II™ DNA Library Prep Kit for Illumina (NEB), according to manufacturer’s instructions and sample uniquely barcoded using NEBNext Multiplex oligo for Illumina (NEB). Samples were quantified using Qubit using a High Sensitivity reagents. Libraries were analysed by Edinburgh Genomics at the University of Edinburgh, UK, who performed quality control and sequencing using an Illumina NovaSeq, 100 base paired-end reads.

treatment_protocol: Cells were synchronised at the G1/S boundary by treatment with 5mg/ml aphidicolin for 24 hours. In addition, some samples were treated with a low dose of aphidicolin (0.4 microM) post release.

tag: cell cycle

value: late S

tag: condition

value: input DNA

tag: chip antibody

value: none (input)


title: Input 10H

description: Input  DNA from  control HCT116 cells, 10 hours post release from G1/S

source_name: Input  from  control HCT116 cells, 10 hours post release from G1/S


title: blood-6Month-ScoreA-patientDC160914


title: blood-0Month-ScoreA-patientDC160914


title: DMSO ribosome profiling C

tag: concentration

tag: duration

value: 24 hours

tag: adapter

value: NNNNNNCACTCGGGCACCAAGGAC

tag: molecule subtype

value: Ribosome Protected mRNA (15-35 nt)


title: 4564-003

description:
T12
3

data_processing:
Reads were mapped to miRbase 20
TPM is the unit used to measure expression in this NGS experiment. The number of reads for a particular microRNA is divided by the total number of mapped reads and multiplied by 1 million (Tags Per Million ).
The differential expression analysis is done using the EdgeR statistical software package (Bioconductor, http://www.bioconductor.org/).
For normalization the trimmed mean of M-values method was used based on log-fold and absolute gene wise changes in expression levels between samples (TMM normalization).
Genome_build: miRbase 20, human
Supplementary_files_format_and_content: excel file including TPM values for each group including differential expression between t0 and t12

source_name: plasma

tag: tissue

value: pooled plasma of 4 patients

tag: time point

value: after one year


title: blood-0Month-ScoreA-patientMP220714

value: Venous blood


title: blood-0Month-ScoreA-patientGMD170315


title: MM1S cells with empty vector, replicate 3

source_name: MM1S cells with empty vector

tag: cell type

tag: genotype/variation

value: control


title: MM1S cells with empty vector, replicate 2

value: multiple myeloma cell line

tag: rin (rna integrity number)


title: blood-0Month-ScoreB-patientJA021214

tag: patient

value: B


title: Input 4H

description: Input DNA  from  control HCT116 cells, 4 hours post release from G1/S

source_name: Input  from  control HCT116 cells, 4 hours post release from G1/S

value: early S


title: blood-0Month-ScoreA-patientJDF280314

tag: time

value: A


title: MM1S cells with RAL knockdown, replicate 1

value: RAL knockdown


title: wt_treated_s4

treatment_protocol: growth in SC-GlcNac medium and treated with α-pheromone

value: opaque cells

tag: genotype

value: wild type

value: α-pheromone


title: wt_treated_s3


title: GT95_W4_P

value: Human skin

tag: wound/scar time point and group

value: Week 4

tag: egcg treated/placebo

value: Placebo

tag: group allocation


title: APH rep2 10h

description: SMC2 ChIP in aphidicolin-treated HCT116 cells, 10 hours post release from G1/S, replicate 2

tag: cell line

tag: cell cycle

tag: condition

value: APH-treated


title: APH rep 2 8h

description: SMC2 ChIP in aphidicolin-treated HCT116 cells, 8 hours post release from G1/S, replicate 2

value: late S

tag: chip antibody


title: MM1S cells with KRAS knockdown, replicate 1

value: KRAS knockdown


title: wt_nontreated_s2

tag: treatment

value: untreated


title: APH rep 2 4h

description: SMC2 ChIP in aphidicolin-treated HCT116 cells, 4 hours post release from G1/S, replicate 2


title: blood-6Month-ScoreB-patientTP100414

tag: MADRS

value: Venous blood


title: wt_nontreated_s1


title: Sin3B RNAi knockdown replicate 3

city: Kansas City

first: Gaye

middle: L

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic version 0.36
Reads were mapped to genome using Hisat2 version 2.1.0
Read counts were calculated with htseq-count
FPKM values were calculated with DESeq2 version 1.20.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count .csv file and FPKM .csv file

source_name: HEK293T cells with Sin3B RNAi knockdown

growth_protocol: HEK293T cells were cultured in DMEM + 10 % FBS + GlutaMAX™ Supplement at 37 °C and 5 % CO2.

extract_protocol:
HEK293T total RNA was isolated using TRIzol™ Reagent. Isolates were DNAseI treated, then extracted with TRIzol™ Reagent a second time.
Illumina TruSeq RNA library prep kit
poly-A stranded RNA-Seq

treatment_protocol: HEK293T cells were transfected with Ambion Silencer™ Select siRNAs at final concentrations of 10 nM with Lipofectamine™ RNAiMAX Transfection Reagent for 36 h. Cells were transfected with Control siRNA


title: Sin3B RNAi knockdown replicate 2


title: IP VSV infected RNA1 Hela

city: CHICAGO

first: Zijie

state: IL

department: Chemistry

institute: University of Chicago

description: m6A enriched mRNA

data_processing:
Seequencing reads were aligned to VSV reference genome by Hisat2
m6A peak calling was performed using R package m6Amonster

organism: Vesicular stomatitis virus

source_name: Hela cells

growth_protocol: HeLa (ATCC CCL-2) cell lines were purchased from the American Type Culture Collection (Manassas, VA) and were grown in Dulbecco's modified Eagle's medium (DMEM; Life Technologies) supplemented with 10% FBS.

extract_protocol:
TRIzol (Invitrogen) + polyT beads(thermo fisher)
Kapa hyper RNA library kit
MeRIP-seq

treatment_protocol: VSV was propagated and titered in HeLa cells. To prepare purified rgVSV, 20 T150 flasks of HeLa cells were infected by rgVSV at an MOI of 0.1, and cell culture supernatants harvested at 48 or 72 h post-infection were clarified by centrifugation at 10,000 ×g for 30 min.

tag: group

value: VSV infected


title: APH rep 1 8h

description: SMC2 ChIP in aphidicolin-treated HCT116 cells, 8 hours post release from G1/S, replicate 1


title: APH rep 1 4h

description: SMC2 ChIP in aphidicolin-treated HCT116 cells, 4 hours post release from G1/S, replicate 1


title: IP VSV genome RNA2 Hela

description: m6A enriched mRNA

value: viral genome


title: IP VSV infected RNA2 Hela

description: m6A enriched mRNA


title: blood-0Month-ScoreA-patientCB291013

tag: tissue


title: blood-6Month-ScoreA-patientCB291013


title: Sin3B RNAi knockdown replicate 1


title: blood-0Month-ScoreB-patientTP100414

value: B


title: Sin3A RNAi knockdown replicate 3

source_name: HEK293T cells with Sin3A RNAi knockdown


title: Sin3A RNAi knockdown replicate 2


title: IP VSV genome RNA1 Hela

description: m6A enriched mRNA


title: Control rep2 10h

description: SMC2 ChIP in control HCT116 cells, 10 hours post release from G1/S, replciate 2

value: control


title: Control rep 2 8h

description: SMC2 ChIP in control HCT116 cells, 8 hours post release from G1/S, replicate 2


title: Input VSV infected RNA2 Hela

description: mRNA


title: Sin3A RNAi knockdown replicate 1


title: Control rep 2 4h

description: SMC2 ChIP in control HCT116 cells, 4 hours post release from G1/S, replciate 2

value: early S


title: MM1S cells with empty vector, replicate 1

tag: cell type

value: multiple myeloma cell line


title: Control replicate 3

source_name: HEK293T cells


title: Input VSV genome RNA2 Hela

description: virus RNA


title: APH rep 1 10h

description: SMC2 ChIP in aphidicolin-treated HCT116 cells, 10 hours post release from G1/S, replicate 1


title: Control rep 1 8h

description: SMC2 ChIP in control HCT116 cells, 8 hours post release from G1/S, replciate 1


title: Input VSV genome RNA1 Hela

description: virus RNA


title: Control replicate 2


title: Control rep 1 10h

description: SMC2 ChIP in control HCT116 cells, 10 hours post release from G1/S, replciate 1


title: Control replicate 1


title: Input VSV infected RNA1 Hela

description: mRNA


title: Control rep 1 4h

description: SMC2 ChIP in control HCT116 cells, 4 hours post release from G1/S, replicate 1


title: W1_vs_RM114

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to microarrays in 8x15k format, custom made by Agilent (Design ID: 032565) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized log2 ratio data from biological replicates and technical replicates (dye swap) were averaged and the statistical significance (p-value) was calculated.

organism: Aspergillus nidulans

source_name: mycelium

label_protocol: Samples of total RNA (5μg) were labeled with QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.

growth_protocol: 100 ml of minimal medium (MM-S) supplemented with 0.3 mM methionine and 0.0005 mg/ml pyridoxine in 300-ml Erlenmeyer flasks was inoculated with 2-5x108 conidia collected with 2-3 ml of 0,01% Tween-80 from fresh (48-72h, 37oC) solid complete medium cultures. Mycelia were grown for 18-19 h at 30oC in orbital shaker set to 200 rpm up to approximately 0.8 g of wet weight. Mycelia were then harvested by filtration, washed with distilled water, dried on filter paper, weighed, frozen in liquid nitrogen and kept at –80oC.

extract_protocol: 300 mg of mycelia were powdered in liquid nitrogen and total RNA was isolated using TRI Reagent (Molecular Research Center) according to the manufacturer’s protocol. RNA was further purified by precipitation with lithium chloride added to a final concentration of 3.42 M. Purified RNA was stored at -80°C.

tag: strain

value: W1 (yA2; pyroA4; veA1)

value: RM114 (yA2; metR1; pyroA4; veA1)


title: AOP-1 1 36h exp3

status: Public on Nov 30 2020

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

institute: University of Liverpool

hyb_protocol: Standard Agilent One-Colour Analysis

scan_protocol: Standard Agilent One-Colour Analysis

data_processing: We normalised and analysed our data using the statistical programming environment R (R Core Team, 2016).  The two different normalisation approaches were: 1) quantile normalisation (‘normalize.quantiles’ function from the preprocessCore package) and 2) cyclic loess normalisation against their respective experimental and developmental stage control (‘normalizeWithinArrays’ function in the limma package).  The expression level of each gene, within each treatment group and time point, are normalised against their corresponding aquarium water control group gene.  We did not normalise gene expression along the IPR treatment to tap water, because chemicals contained within it could mask residual genomic effects along the advanced treatment process.  Loess normalization takes into account the effect of development on the molecular response, and in doing so will emphasize the effect of treatment. We used principal component analysis (PCA) to reduce the overall dimensionality of data and for visualization purposes. We analysed differential gene expression using the Significance Analysis for Microarrays (SAM) methodology as implemented in the samr package (Tusher et al., 2001).

organism: Danio rerio

label_protocol: For the microarray, we used a One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling kit supplied by Agilent Technologies, with a final concentration of 75 ng/µl total RNA. Broadly, the procedure includes the following steps; cDNA synthesis, cRNA synthesis and amplification, cRNA purification, preparation of hybridization sample, 17 hour hybridisation (65°C), wash, scan and feature extraction (Agilent, 2014).

growth_protocol: We sourced adult zebrafish (Danio rerio) (Tübingen strain) of breeding age from University College London (UCL, UK). Following a quarantine period of two weeks in static renewal tanks, we separated the fish according to sex, and placed them into 10 litre flow-through tanks maintained at 26-28°C in a dedicated room with a photoperiod of 14h Light: 10 h Dark.  We fed the fish 3 times a day; twice with flake food (King British Tropical flake food, Lillicos, Surrey) and once with adult brine shrimp (Tropical Marine Centre, Gamma irradiated). Our aquarium water is dechlorinated carbon-filtered (5 and 10 µm) tap water fed from header tanks at a flow rate of 20 litres/hour. All tubing (flow-line, air-lines, siphon and the attached grids) are made of medical grade silicon (VWR, UK).

extract_protocol: We extracted RNA using the RNeasy Mini Kit (QIAGEN, USA) following the manufacturer's generic protocol for the preparation of RNA from tissue (QIAGEN, 2012) with modifications for use with fish embryos. Briefly, we removed the embryos from the -80°C freezer and defrosted them on ice, after which we removed the RNAlater® using a pipette. We then homogenised the embryos using 350 µl Buffer RLT (containing 10 µl β-mercaptoethanol/ml of buffer) by repeatedly drawing up and dispensing the mix using a 1ml syringe. To prevent the filter from blocking, we passed the resulting lysate 10 times through a blunt 20-gauge needle (0.9 mm diameter) and used “On-Column DNase Digestion with the RNase-Free DNase Set” (as detailed in the protocol) to recover the RNA.  Finally, we eluted the RNA from the column with 36 µl RNase-free water.  We quantified RNA yield using a Thermo Scientific NanoDrop™ 1000 Spectrophotometer and visualised the RNA purity and quality by gel electrophoresis (1.5% agarose gel with ethidium bromide).

treatment_protocol: To investigate temporal changes in gene transcriptional responses, we randomly allocated 50 embryos to 200 ml of IPR water (or control waters) in 300 ml glass crystallising dishes and used a glass petri dish as a lid. We incubated the dishes at 28°C in large fish tanks receiving a flow of heated water from the header tanks. Every IPR product water (FE, MF, AOP1, RO, AOP2, FP) and the controls (aquarium water and Brunel University London tap water) consisted of six independent sampling time-points (at 8, 12, 16, 24, 36 and 48 hours post fertilisation), carried out in duplicates, resulting in 96 dishes for each experiment.  We sampled embryos throughout development in order to capture biological effects that might happen transiently during embryogenesis, and that might be of relevance to abnormalities seen.   At each time point, we photographed one ‘normal’ embryo from each dish and counted and removed any dead embryos. We photographed and documented any abnormal embryos in order to increase the sample size for abnormality data, and preserved these individually in RNAlater® (0.6 ml/embryo). Finally, we pooled the remaining ‘normal’ looking embryos and preserved them together in 1.4 ml of RNAlater®. We carried out three independent exposures over a period of approximately one month.

tag: hours

tag: date


title: Final 1 48h exp3

value: FINAL


title: AOP-2 2 36h exp2


title: MF 1 48h exp3

value: MF


title: Tap 1 8h exp2

value: TAP


title: Tap 1 36h exp3


title: RAW 1 36h exp3

value: RAW


title: AOP-2 1 36h exp3


title: RO 1 36h exp3

value: RO


title: AOP-1 1 48h exp3


title: Control 1 36h exp3

value: Control


title: AOP-2 1 48h exp3


title: Control 1 48h exp3


title: MF 1 36h exp3


title: Final 1 36h exp3


title: AOP-1 1 24h exp3


title: Tap 1 48h exp3


title: Tap 1 24h exp3


title: RAW 1 16h exp3


title: Final 1 24h exp3


title: AOP-1 1 24h exp2


title: RAW 1 24h exp3


title: RO 1 48h exp3


title: AOP-2 1 24h exp3


title: RO 1 24h exp3


title: MF 1 24h exp3


title: MF 1 16h exp3


title: MF 1 8h exp3


title: Tap 1 12h exp3


title: wt_CENP-ACnp1

data_processing:
BWA (Li, 2010 #9905;Li, 2009 #9908) or BOWTIE2 (Langmead, 2012 #9901) was used to map ChIP-seq reads onto the S. pombe genome assembly EF2 (ASM294v2) or modified genome assembly generated based on ASM294v2, where centromere 2 was replaced with sequence from centromere 1 to mimic (cc2∆::cc1) and to include pHCC2 plasmid sequence.
Indexed, sorted bam files were created for each dataset using SAMtools (Li, 2009 #9907).
The program bamCoverage from the deepTools suite version 2.5.3 (Ramirez, 2016 #9919) or BEDtools (Quinlan, 2014 #9916;Quinlan, 2010 #9917) was used to create bigwig files from the mapped bam files and scaled using reads per kilobase of transcript per million mapped reads [RPKM]
SeqPlots (Stempor, 2016 #9923) was used to plot the occupancy over transcription start sites [TSS] as annotated in PomBase.
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Genome_build: S. pombe +pHCC2 genome (see pombe.ASM294v2.20.cc2_D.gtf.gz, pombe_cc2D_pHcc2.bed.gz, pombe_cc2_D_pHetcc2.ann.gz, pombe_cc2_D_pHetcc2.fa.gz)
Supplementary_files_format_and_content: bigWig

value: wt

tag: antibody

value: anti-Cnp1 (sheep)


title: AOP-1 1 16h exp3


title: Final 1 16h exp3


title: AOP-1 1 12h exp3


title: AOP-1 1 8h exp3


title: Tap 1 8h exp3


title: MF 1 48h exp2


title: Final 1 48h exp2


title: Control 1 12h exp3


title: AOP-2 1 12h exp3


title: RO 1 8h exp3


title: RO 1 16h exp3


title: Control 1 8h exp3


title: AOP-2 1 16h exp3


title: RAW 1 8h exp3


title: MF 1 12h exp3


title: Final 1 12h exp3


title: Control 1 48h exp2


title: RAW 1 24h exp2


title: RO 2 36h exp2


title: AOP-2 1 48h exp2


title: Tap 1 16h exp3


title: MF 1 36h exp2


title: MF 1 24h exp2


title: AOP-1 1 36h exp2


title: Control 1 36h exp2


title: Tap 1 48h exp2


title: GT91_W4_P

source_name: Human skin

value: Human skin

value: Week 4

value: Placebo


title: AOP-1 1 8h exp2


title: AOP-2 1 24h exp2


title: AOP-2 1 8h exp2


title: Final 1 8h exp2


title: MF 1 48h exp1


title: Tap 1 12h exp2


title: Control 1 24h exp2


title: Tap 1 24h exp2


title: RO 1 16h exp2


title: Final 1 24h exp2


title: MF 1 12h exp2


title: Control 1 8h exp2


title: RAW 1 12h exp2


title: AOP-1 1 48h exp1


title: AOP-1 1 12h exp2


title: RO 1 48h exp1


title: MF 1 16h exp2


title: RAW 1 36h exp1


title: RAW 1 48h exp1


title: Control 1 16h exp2


title: Final 1 16h exp2


title: RO 1 8h exp2


title: AOP-2 1 12h exp2


title: RAW 1 16h exp2


title: Tap 1 16h exp2


title: Final 1 12h exp2


title: RAW 1 8h exp2


title: Control 1 48h exp1


title: Control 1 12h exp2


title: MF 1 36h exp1


title: AOP-1 1 36h exp1


title: RO 1 36h exp1


title: MF 1 24h exp1


title: Tap 1 24h exp1


title: Control 1 16h exp1


title: Control 1 24h exp1


title: AOP-1 1 24h exp1


title: Tap 1 36h exp1


title: RO 1 16h exp1


title: Control 1 36h exp1


title: Control 1 24h exp3


title: AOP-1 1 16h exp1


title: control 12h exp1


title: RAW 1 12h exp1


title: RAW 1 16h exp1


title: RO 2 8h exp1


title: MF 2 8h exp1


title: RAW 1 48h exp3


title: tap1 12h exp1


title: RAW 1 12h exp3


title: Control 1 16h exp3


title: RO 1 12h exp3


title: Tap 2 8h exp1


title: AOP-2 1 8h exp3


title: AOP1-2 8h exp1


title: RAW 2 8h exp1


title: ro1 12h exp1


title: Final 1 8h exp3


title: RO 1 48h exp2


title: RO 1 24h exp1


title: LNCaP Negative Control_Replicate 2

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Basecalls performed in BaseSpace
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2, with default parameters.
Reads were filtered using minimum MAPQ quality score of 15.
Peaks were called using MACS with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated in Galaxy

source_name: Prostate cancer cell line

growth_protocol: LNCaP cells were grown in RPMI+10%FBS.

extract_protocol:
After 72 hours, cells were fixed with formaldehyde. Nuclear pellets were sonicated on ice for 10 cycles (30 sec on, 30 sec off) using a Diagenode Bioruptor. Lysates were immunoprecipitated with 4 ug FOXA1 antibody (Abcam 23738)  which had been pre-coupled to Protein G Dynabeads (Life Technologies, 10004D). DNA was purified using a PCR purification kit (Qiagen) and eluted in 100 µl.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Prep Kit

treatment_protocol: LNCaP cells were transfected with 50nM miR-194 mimic or negative control in suspension

value: Prostate cancer cell line LNCaP

value: LNCaP Negative Control

value: Abcam Anti-FOXA1 ab23738


title: LNCaP Negative Control_Replicate 1


title: LNCaP miR-194_Replicate 3

value: LNCaP miR-194


title: AOP-1 1 48h exp2


title: LNCaP Negative Control_Pooled Input


title: LNCaP miR-194_Replicate 2


title: LNCaP Negative Control_Replicate 3


title: AOP-1 1 16h exp2


title: RO 1 24h exp2


title: RAW 1 36h exp2


title: LNCaP miR-194_Pooled Input


title: RO 1 12h exp2


title: LNCaP miR-194_Replicate 1


title: aop1-1 12h exp1


title: Engineered Human Kidney Organoids (scRNA-seq)

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

data_processing:
Demultiplexing, alignment to the homo sapiens (hg38) genome and quantification was performed using 10X Genomics Cell Ranger (v3.0.1)
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix. Gene x Cells UMI count matrix

source_name: Human Kidney Organoid

extract_protocol:
Cells were thawed and centrifuged at 1,500 RPM for 5 minutes. After that, cells were stained with sytox blue (Thermofisher) and sorted by FACS to remove the nonviable cells, generating a single cell suspension with greater than 90% viability analyzed using the cellometer K2 (Nexcelom Biocience).
Libraries were prepared using the Chromium Single Cell 3ʹ GEM, v3, (PN-1000075, 10X genomics) following the manufacturer´s instructions and sequenced with a NEXTseq500 (R1:28, R2: 55, i7:8) up to 30.000 reads per cell.
single cell 3' RNA-seq

value: kidney organoids

tag: 10x barcode

value: 10X Barcode G3


title: RAW 1 48h exp2


title: Control 2 8h exp1


title: AOP-2 1 16h exp2


title: Tap 1 36h exp2


title: Tap 1 48h exp1


title: Tap 1 16h exp1


title: RAW 1 24h exp1


title: MF 1 16h exp1


title: Final 1 36h exp2

value: FINAL


title: MF 1 8h exp2

value: MF


title: U3065MG-C271_R3_42d_IL: Malignant glioma clone U3065MG-C271 42 days IL1beta stimulation, replicate serie 3

city: Uppsala

first: Bo

last: Segerman

address: Dag Hammarskjolds v 20

country: Sweden

institute: Uppsala University

hyb_protocol: GeneChip® Human Transcriptome Array 2.0 were hybridized for 16 hours in a 45°C incubator. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were washed and stained using the Fluidics Station 450

scan_protocol: scanned using the GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Affymetrix® Expression Console™ Software using Affymetrix default analysis settings with the Robust Multiarray Averaging (RMA) algorithm.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: adherent cultures on laminin-coated dishes using neural stem cell media

extract_protocol: RNeasy Plus Mini Kit, QIAGEN

treatment_protocol: 10 ng/ml IL1beta (Peprotech)

value: Malignant glioma clone


title: U3065MG-C271_R3_29d_CTR: Malignant glioma clone U3065MG-C271 29 days control, replicate serie 3

value: Untreated


title: MF 1 12h exp1


title: U3065MG-C271_R3_29d_IL: Malignant glioma clone U3065MG-C271 29 days IL1beta stimulation, replicate serie 3


title: U3065MG-C271_R2_14d_IL: Malignant glioma clone U3065MG-C271 14 days IL1beta stimulation, replicate serie 2


title: U3065MG-C271_R2_11d_CTR: Malignant glioma clone U3065MG-C271 11 days control, replicate serie 2


title: U3065MG-C271_R3_13d_CTR: Malignant glioma clone U3065MG-C271 13 days control, replicate serie 3


title: U3065MG-C271_R2_28d_CTR: Malignant glioma clone U3065MG-C271 28 days control, replicate serie 2


title: U3065MG-C271_R1_1d_IL: Malignant glioma clone U3065MG-C271 1 day IL1beta stimulation, replicate serie 1


title: Mir155KO_BMDM_LPS_IL10_rep2

city: Dublin 2

first: Claire

middle: E

last: McCoy

address: 123 St Stephen's Green

country: Ireland

institute: Royal College of Surgeons in Ireland

hyb_protocol: cDNA was hybridised onto the Affymetrix mouse 430 2.0 array in accordance with the NuGEN guidelines for hybrdisation onto Affymetrix GeneChip arrays

scan_protocol: The array was scanned using probe level intensity measurements (CEL files), background corrected, normalised and summarised as expression measurement

data_processing: The data were processed with R/Bioconductor using the affy package and the rma function with default settings. Subsequent statistical analyses were performed using the limma package.

organism: Mus musculus

source_name: Mir155 knockout bone marrow derived macrophages treated with LPS and IL10

label_protocol: RNA was amplified using NUGEN ovation RNA amplification system. cDNA was fragmented, labelled and hysridised using the NuGEN encore biotin Module

growth_protocol: bone marrow was extracted from the femurs of C57Bl/6 wild-type (n=2) and miR-155 KO animals (n=2) and stored in liquid nitrogen until later use. Cells were thawed and differentiated into BMDM using L929 (15%) conditioned media for 7 days.

extract_protocol: RNA was extracted using Applied Biosystems Rneasy kit

treatment_protocol: BMDM were stimulated with LPS (100 ng/ml) alone for 24 hours or pre-treated with IL-10 (20 ng/ml) for 5 minutes prior to the addition of LPS

value: bone marrow derived macrophages

tag: genotype/variation

value: miR-155 knockout

tag: replicate

tag: gender

value: male


title: Mir155KO_BMDM_LPS_rep2

source_name: Mir155 knockout bone marrow derived macrophages treated with LPS

value: LPS


title: U3065MG-C271_R2_11d_IL: Malignant glioma clone U3065MG-C271 11 days IL1beta stimulation, replicate serie 2


title: hAstroCtr3: Human Astrocytes 13 days control, replicate 3

source_name: Human Astrocytes 13 days control

growth_protocol: Astrocyte media (AM) supplemented with 2% fetal calf serum and 1% astrocyte growth supplement (ScienCell)

value: Astrocytes


title: U3065MG-C271_R1_1d_CTR: Malignant glioma clone U3065MG-C271 1 day control, replicate serie 1


title: U3065MG-C271_R2_14d_CTR: Malignant glioma clone U3065MG-C271 14 days control, replicate serie 2


title: U3065MG-C271_R1_21d_CTR: Malignant glioma clone U3065MG-C271 21 days control, replicate serie 1


title: Mir155KO_BMDM_LPS_rep1


title: Mir155KO_BMDM_LPS_IL10_rep1


title: hAstroCtr1: Human Astrocytes 12 days control, replicate 1

source_name: Human Astrocytes 12 days control


title: hAstroCtr2: Human Astrocytes 13 days control, replicate 2


title: U3065MG-C271_R3_13d_IL: Malignant glioma clone U3065MG-C271 13 days IL1beta stimulation, replicate serie 3


title: hAstroStim3: Human Astrocytes 13 days IL1beta stimulation, replicate 3


title: hAstroStim1: Human Astrocytes 12 days IL1beta stimulation, replicate 1


title: U3065MG-C271_R1_21d_IL: Malignant glioma clone U3065MG-C271 21 days IL1beta stimulation, replicate serie 1


title: U3065MG-C271_R2_28d_IL: Malignant glioma clone U3065MG-C271 28 days IL1beta stimulation, replicate serie 2


title: U3065MG-C271_R3_42d_CTR: Malignant glioma clone U3065MG-C271 42 days control, replicate serie 3


title: U3065MG-C271_R2_1d_IL: Malignant glioma clone U3065MG-C271 1 day IL1beta stimulation, replicate serie 2


title: U3065MG-C271_R2_1d_CTR: Malignant glioma clone U3065MG-C271 1 day control, replicate serie 2


title: WT_BMDM_LPS_IL10_rep2

source_name: Wild-type bone marrow derived macrophages treated with LPS and IL10

value: Wild-type

value: female