title: Bo_ChIP-seq_input

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

data_processing:
The ChIP-seq reads of B. rapa and B. oleracea were aligned to the corresponding reference genome using Bowtie2 v2.3.453,
Only read pairs with high-quality alignments (mapping quality > 30) were kept.
the mapped reads were binned and normalized with deepTools2 (v. 3.1.2)61 bamCompare using a bin size of 10 bp.
then  calculated the log2 ratio of ChIP versus input as the histone signal
Genome_build: Brassica. rapa(chiifu_V3); Brassica oleracea (TO1000)
Supplementary_files_format_and_content: bigwig

organism: Brassica oleracea

source_name: leaves

extract_protocol:
Two grams of young leaves per accession was cross-linked with 1% formaldehyde in a vacuum for 15 min. The formaldehyde was quenched by adding 2.5 mL of 2 M glycine, and vacuum infiltration was continued for 5 min.The extracted chromatin of these crosslinked tissue samples was sonicated to 100-300 bp. With protein G beads, the proteins of interest were pulled down by adding a specific antibody
The ChIP libraries were constructed following the protocol of the NEXTflex® Rapid DNA-Seq Kit and sequenced on Illumina HiSeq X-Ten with the PE 150 method.

value: 30 days

tag: developmental stage

value: five-leaf stage

tag: cultivar

value: leaves


title: DDT8B [S204]

status: Public on Jun 06 2019

type: SRA

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

country: USA

institute: University of North Carolina at Charlotte

library_source: transcriptomic

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

molecule: total RNA

organism: Nematostella vectensis

source_name: dark:dark_time point 8_whole organism

growth_protocol: Animals were maintained as described in Hand et al. (1994)

extract_protocol:
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: Animals were experimentally exposed to either light:dark (LD) or dark:dark (DD) conditions for 1 month, then sampled every 4 hours for 1 day (24 hours), then in the LD treatment, the light cycle was removed and animals were continually sampled from both LD and DD for 2 more days (44 more hours)

tag: genome

value: Putnam et al. (2007)

tag: light

value: dark cycling timepoint:dark:dark, time point 8, replicate B

tag: age

value: adult


title: RNA-Seq_CD8SP-WT_S1

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description:
Truseq kit
RNA-Seq_CD8SP_EomesTGvsWT_CP20M.csv
RNA-Seq_CD8SP_EomesTGvsWT_DifferentialAnalysisResults.xlsx

data_processing:
reads were filtered using FastX 0.0.13 and ShortRead 1.16.3, polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type) were removed
reads were aligned to the reference genome mm10 using Tophat v2.0.13 with the following parameters: --library-type fr-firststrand --min-intron-length 50 --max-intron-length 500000 --no-coverage-search --no-mixed --read-realign-edit-dist 3
reads from the alignment that are non-primary mappings or have a mapping quality ≤20 were removed
read counts were estimated using featureCounts v1.4.6 with the following parameters: -Q 0 -s 2 -t exon -g gene_id and genes that have less than 1 counts-per-million were removed
raw read  counts were normalised with the EDASeq package and FPKM values were obtained
differential expression analysis was performed with edgeR 3.4.0 package by applying a corrected p value FDR<0.05 and absolute log2-ratio larger than 1.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing raw read counts and FPKM normalized counts (TIM vs Naive) and  tab-delimited text files containing normalized read counts (such as total read count=20M)  for each sample and gene and differential analysis results (EomesTG vs WT)

organism: Mus musculus

source_name: Thymus

extract_protocol:
RNA from 106 sorted CD8SP populations was extracted using RNeasy Plus Mini kit according to manufacturer’s instructions
RNA library was prepared using Truseq Ribo zero gold kit for TIM and Naive, and Truseq kit for CD8SP WT and CD8SP EomesTg following manufacturer's instruction.

tag: cell type

value: Thymocytes

tag: Stage

value: CD8SP WT

tag: strain

tag: genotype

value: wild type


title: 143B_E9_treated_rep3: RNA Seq

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

data_processing:
The FASTX-Toolkit v0.0.13 was used to remove adapter sequences and trim reads with the quality cutoff of 20, excluding any reads shorter than 25bp. ChIP-seq reads were aligned to hg19 with Bowtie 2 v2.0.649, searching for multiple alignments but reporting the one with the best mapping quality score. PCR duplicates were removed using SAMtools 1.2. Peaks were detected with MACS2 2.1.1.20160309 with an input DNA sample as control, scaling the input dataset to match the read depth of the ChIP dataset. MACS2 peaks with a q-value of greater than 0.001 and overlapping ENCODE blacklisted regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were filtered out. BigWIGs were generated with DeepTools v3.0.1-2-2fa58e8 and normalized to 1x average coverage (RPGC option)
Cutadapt v1.14 was used to trim 3’ adapters, discarding trimmed reads shorter than 20bp. Sickle v1.33 was then used to trim reads with the quality cutoff of 20. RNA-Seq reads were aligned to hg19 assembly plus ERCC RNA Spike-In DNA sequences with STAR v2.5.3a. Cufflinks v2.0.2 was run with genomic bias correction to quantify the levels of transcripts in the hg19 reFLAT annotations file as well as the ERCC transcripts file. Scatter plots of ERCC transcript FPKMs versus their expected concentrations in the spike-in mix were constructed to aid in quality control assessment of the data. The FPKM table was then floored to the background noise level of 0.3. Differential expression analysis between E9-treated and untreated samples was performed by calculating the fold change of mean E9 FPKM over mean DMSO FPKM.
After removing adapter sequences using cutadapt v1.8.1,1 the DNA FASTQ files were aligned to the hg19 reference genome using BWA-mem (v0.7.17-r1188).2,3 The aligned files were then indexed and had PCR duplicates removed using samtools (v0.1.18).4 Each BAM file underwent base quality score recalibration using GATK(v4.0.1.1).5
Refseq hg19 genes underwent the following filtering steps prior to use in downstream analyses for each pair of treated and untreated samples to ensure 1-to-1 mapping of genes to TSS’s: 1:Retrieve RNA-Pol RPKM within 1KB of each TSS and calculate the minimum of E9 and DMSO RPKMs. In case of the same gene with multiple TSS’s, only retain the gene record with the max RNA-Pol RPKM minimum. 2:In case of multiple genes with the same TSS, calculate the minimum FPKM between E9 and DSMO for each gene and only retain the gene with the max FPKM minimum
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq and whole genome sequencing WIG tracks were generated with deeptools v3.1.3 and normalized with the RPGC option

molecule: polyA RNA

organism: Homo sapiens

source_name: highly metastatic osteosarcoma cell line

growth_protocol: Human osteosarcoma cell lines (MG63.3-GFP, 143B-GFP) were grown in DMEM 1x (Gibco, 11965-092) supplemented with 10% FBS (Corning, 35-010-CV) and 1% penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol.
ChIP-Seq libraries were prepared as previously described (Schmidt et al. 2009). For RNA-seq, Total RNA was treated with DNase I (Invitrogen, Carlsbad, CA). RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, Foster City, CA) and analyzed on an Agilent Bioanalyzer 2100 for integrity. PolyA+ RNA was isolated using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol. For Whole Genome Sequencing, PCR-free libraries were prepared from MG63.3-GFP and 143B-GFP cells using TruSeq DNA PCR-Free High Throughput Library Prep Kit (Illumina, 20015963) and following the manufacturer’s instructions.

treatment_protocol: For ChIP-seq and RNA-seq, 143B-GFP and MG63.3-GFP cells were treated for 6 hours with E9 at 200nM or DMSO. Cells prepared for ChIP-seq were crosslinked with formalin.

tag: tissue

tag: cell line

tag: chip antibody


title: CD4_w0__R259_K9691: CD4 before treatment 5

city: sinjuku-ku

first: Masaru

last: Takeshita

state: Tokyo

address: 35 shinanomachi

department: Division of Rheumatology

country: Japan

institute: Keio University

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: CD4 T cell

extract_protocol:
Total RNA from were extracted using RNeasy Micro kit (Qiagen).
0.2 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit. Then cDNA is amplified using Ion AmpliSeq™ technology. After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 75 pM and pooled equally, with eighteen individual samples per pool.

treatment_protocol: Frozen peripheral mononuclear cells were thawed, and CD4 and CD8 T cell were purified using FACS Aria Ⅲ.

tag: diagnosis

value: rheumatoid arthritis

value: CD4 T cell

tag: gender

value: F


title: DDT8C [S205]

value: dark cycling timepoint:dark:dark, time point 8, replicate C


title: DDT8A [S203]

value: dark cycling timepoint:dark:dark, time point 8, replicate A


title: LDT8D [S202]

source_name: light:dark_time point 8_whole organism

value: dark cycling timepoint:light:dark, time point 8, replicate D


title: 143B_E9_treated_rep2: RNA Seq

value: highly metastatic osteosarcoma cell line


title: Bo_H3K4me3

country: Germany

library_source: genomic

molecule: genomic DNA

value: H3K4me3 (Abcam; ab8580)


title: CD4_w0__R254_K9756: CD4 before treatment 4


title: Br_ChIP-seq_input

organism: Brassica rapa

value: 30 days

value: Chiifu


title: 143B_E9_treated_rep1: RNA Seq


title: LDT8C [S201]

value: dark cycling timepoint:light:dark, time point 8, replicate C


title: CD4_w24__R104_K9215: CD4 after treatment 3


title: 143B_DMSO_treated_rep3: RNA Seq


title: 143B_DMSO_treated_rep2: RNA Seq


title: CD4_w24__R087_K5779: CD4 after treatment 2


title: LDT8A [S199]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 8, replicate A


title: Br_H3K27me3

value: five-leaf stage

value: leaves


title: LDT8B [S200]

value: dark cycling timepoint:light:dark, time point 8, replicate B

value: adult


title: CD4_w0__R104_K8115: CD4 before treatment 3

value: rheumatoid arthritis


title: MG63-3_DMSO_treated_rep1: RNA Seq


title: Br_H3K9ac


title: 143B_DMSO_treated_rep1: RNA Seq


title: Bo_H3K9ac


title: Br_H3K4me3


title: CD4_w0__R087_K8710: CD4 before treatment 2

value: CD4 T cell


title: DDT7D [S198]

source_name: dark:dark_time point 7_whole organism

value: dark cycling timepoint:dark:dark, time point 7, replicate D


title: CITE-Seq HTO: BM-MNC

city: Seattle

first: Andrew

last: Butler

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

description: other

data_processing:
CITE-seq RNA reads were mapped to the human genome (GRCh38). Transcripts were quanitfied using CellRanger v2.1.0
ADT and HTO antibody counts were quantified using CITE-seq-count (https://github.com/Hoohm/CITE-seq-Count)
Cells were demultiplexed after normalization via a centered log ratio transformation using the HTOdemux function in Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data provided as a TSV expression matrix where the rows correspond to genes and the columns to either a particular replicate for the bulk data, or single cells for the single-cell data

molecule: other

source_name: Bone Marrow Mononuclear Cells

growth_protocol: For both bulk and scRNA-seq experiments: BM MNCs were thawed in 37C water bath. RPMI +10% FBS media was added drop-wise to the thawed cells. Cells were spun down and resuspended in PBS 1X. Cell  viability was quantified using trypan blue.

extract_protocol:
For the bulk experiment:  CD4-/CD8+/CD3+CD69+ and  CD4-/CD8+/CD3+CD69- cells were sorted into wells containing RLT lysis buffer using a SONY SH800 sorter. RNA was isolated by performing a 2X Ampure bead cleanup. RNA was resuspended into RT mix and cDNA synthesis and amplification was performed as described in dx.doi.org/10.17504/protocols.io.nkgdctw. Briefly, we used a modified version of Smart Seq 2 protocol that allows for sequencing of the 3' end of each transcript.
For the scRNA/CITE-seq experiment: a panel of 25 antibodies (ADTs) was used to stain the cells according to the CITE-seq protocol. To identify cell doublets, we split cells into 10 aliquots and stained each aliquot with a unique hashing (HTOs) antibody.  Samples were washed and recombined and load on a 10genomics chip. 3prime 10x genomics Version 2 was ran and the manufacturers protocols was followed for cDNA library generation. To recover HTOs and ADTs we followed the CITE-seq protocol found here: https://cite-seq.com/protocol/
CITE-seq (10x genomics 3prime Version 2)

value: bone marrow


title: Bo_H3K27me3


title: CD4_w24__R254_K9246: CD4 after treatment 4

value: F


title: DDT7C [S197]

value: dark cycling timepoint:dark:dark, time point 7, replicate C


title: DDT7B [S196]

value: dark cycling timepoint:dark:dark, time point 7, replicate B


title: CD4_w24__R084_K7821: CD4 after treatment 1

value: M


title: CITE-Seq ADT: BM-MNC

description: other


title: CD4_w0__R084_K9656: CD4 before treatment 1


title: Ssr4_3

city: Hangzhou

first: wei

last: shao

state: zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

country: China

institute: zhejiang university

description: Replicate 3 of library ∆Ssr4

data_processing:
Illumina Novaseq  used for sequencing
Raw reads were filtered before downstream analysis to decrease data noise. The reads with adaptor sequence and with over 10% unknown bases. Low quality reads which contains over 50% low quality bases were also removed. After filtering, the remaining reads are called “clean reads” and stored as FASTQ format.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with DESeq software.
Screening of differentially expressed genes in paired library of WT/disruption mutant. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Table including ID, Gene name,FPKM values, FDR-value, log2(fold change), Regulated(up or down).

organism: Beauveria bassiana ARSEF 2860

growth_protocol: Conidia suspension (100 ml, 1 ´ 107 conidia ml-1) of WT and Δssr4 of Beauveria bassiana were inoculated on the SDAY plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar), respectively, and incubated at 25 °C for 96 h.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates.

value: ARSEF 2860

tag: genotype/variation

value: ssr4 mutant

value: mycelia


title: Ssr4_2

description: Replicate 2 of library ∆Ssr4


title: Ssr4_1

description: Replicate 1 of library ∆Ssr4


title: DDT7A [S195]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 7, replicate A


title: CITE-Seq RNA: BM-MNC


title: CD8_w24__R103_K7583: CD8 after treatment 6

source_name: CD8 T cell

value: CD8 T cell


title: PARE_Nt_S_rep3

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
Library strategy: PARE
For these small RNA libraries, raw files resulting from 2 separate runs were processed and concatenated to produce a single processed file.
Read quality control using FastQC.
Adaptor trimming and chopping using Trimmomatic.
Genome alignment using Bowtie and TN90 Nicotiana tabacum genome.
Sequences are then formatted to tag-count format.
Genome_build: N. tabacum TN90 (Sierro et al. 2014)
Supplementary_files_format_and_content: *_chopped.txt: Tab-delimited text files; Final trimmed and cropped output file in tag-count format.

organism: Nicotiana tabacum

source_name: BY-2 cell suspension, S phase

growth_protocol: Cells were weekly subcultured in liquid MS medium supplemented with KH2PO4 (200mg/L), myo-inositol (100mg/L), thiamin (1mg/L), 2,4-D(0,2mg/L) and sucrose (30g/L). Cells were kept in the dark, on a shaker at 180 RPM.

extract_protocol:
Cells were vacuum filtered and frozen in liquid nitrogen. After mechanical grinding, RNA was extracted using Trizol/chloroform protocol.
PARE libraries were constructed following the published protocol Zhai et al., 2014.

treatment_protocol: Cells were synchronized using aphidicolin following the published protocol from Nagata et al. 1992.

value: Tobacco BY-2

tag: expression

value: GFP-fused AGO1

tag: growth type

value: suspension

tag: cell cycle phase

value: S

tag: replicate


title: WT_3

description: Replicate 3 of library WT

source_name: WT

value: 4 days


title: PARE_Nt_S_rep2


title: CD8_w24__R259_K9021: CD8 after treatment 4

value: rheumatoid arthritis


title: CD8_w0__R103_K5705: CD8 before treatment 5


title: WT_2

description: Replicate 2 of library WT


title: LDT7C [S193]

source_name: light:dark_time point 7_whole organism

tag: genome

value: dark cycling timepoint:light:dark, time point 7, replicate C

value: adult


title: CD8_w0__R259_K9691: CD8 before treatment 4

value: F


title: LDT7B [S192]

tag: light

value: dark cycling timepoint:light:dark, time point 7, replicate B


title: WT_1

description: Replicate 1 of library WT


title: PARE_Nt_M_rep3

source_name: BY-2 cell suspension, M phase

value: M


title: PARE_Nt_S_rep1


title: PARE_Nt_M_rep2


title: CD8_w24__R254_K9246: CD8 after treatment 3

tag: age


title: RNA-seq_MO DP-R1hi rep2

city: Oxford

first: Florian

last: Bonkhofer

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: Oxford University

description: double positive *runx1*-high   mCherry+Citrinehigh with runx1 morpholino injection

data_processing:
Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol.
Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32).
Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1).
To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads (QC-passed reads count) has been obtain using Samtools mapping statistics (flagstat tool).
RAW data files represent the trimmed sequencing reads in separated lanes.
Genome_build: Zv10
Supplementary_files_format_and_content: Wt-DP-R1hi_Wt-DP-R1lo  Differential analysis between Wt DP-R1hi and Wt DP-R1lo cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene_id,  Counts Per Million, gene_name, end value of each sample, log FC (wt/mo), P value and FDR value.
Supplementary_files_format_and_content: Wt-DP-R1hi_MO-DP-R1hi Differential analysis between Wt DP-R1hi and MO DP-R1hi cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene_id,  Counts Per Million, gene_name, end value of each sample, log FC (wt/mo), P value and FDR value.
Supplementary_files_format_and_content: Wt-DN_MO-DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains  edgeR normalisation and GLM estimation of dispersion. The file contains gene_id,  Counts Per Million, gene_name, end value of each sample, log FC (wt/mo), P value and FDR value.

organism: Danio rerio

source_name: haemogenic endothelium

growth_protocol: TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos, were raised to 28-30 hpf.

extract_protocol:
whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034).
High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). 2.2 ng of total RNA was used for to generate SMARTer libraries for low-input RNA.

treatment_protocol: double transgenic embryos were collected, batches were split in half and were either injected or non-injected with a runx1-morpholino

tag: cell isolation

value: FACS isolated cells

value: haemogenic endothelium

value: runx1-morpholino injected


title: DDT6D [S190]

source_name: dark:dark_time point 6_whole organism

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 6, replicate D


title: CD8_w0__R254_K9756: CD8 before treatment 3

value: CD8 T cell


title: PARE_Nt_M_rep1

value: Tobacco BY-2


title: DDT6C [S189]

value: dark cycling timepoint:dark:dark, time point 6, replicate C


title: LDT7D [S194]

value: dark cycling timepoint:light:dark, time point 7, replicate D


title: CD8_w24__R087_K5779: CD8 after treatment 2


title: DDT6B [S188]

value: dark cycling timepoint:dark:dark, time point 6, replicate B


title: PARE_Nt_G2_rep3

source_name: BY-2 cell suspension, G2 phase

value: GFP-fused AGO1

value: suspension


title: RNA-seq_MO DP-R1hi rep1


title: RNA-seq_MO DN rep3

description: mCherry-Citrine- with runx1 morpholino injection

source_name: non-endothelial tissue

value: non-endothelial tissue


title: PARE_Nt_G2_rep2


title: RNA-seq_MO DN rep2


title: DDT6A [S187]

value: dark cycling timepoint:dark:dark, time point 6, replicate A

value: adult


title: CD8_w24__R084_K7821: CD8 after treatment 1

value: rheumatoid arthritis


title: RNA-seq_MO DN rep1


title: CD8_w0__R084_K9656: CD8 before treatment 1

value: M


title: LDT7A [S191]

value: dark cycling timepoint:light:dark, time point 7, replicate A


title: LDT6D [S186]

source_name: light:dark_time point 6_whole organism

value: dark cycling timepoint:light:dark, time point 6, replicate D


title: PARE_Nt_G2_rep1


title: RNA-seq_MO DP-R1hi rep3

value: FACS isolated cells

value: haemogenic endothelium

value: runx1-morpholino injected


title: PARE_Nt_G1_rep3

source_name: BY-2 cell suspension, G1 phase


title: RNA-seq_Wt DP-R1hi rep2

description: double positive *runx1*-high   mCherry+Citrinehigh

value: non-injected


title: PARE_Nt_G1_rep1

value: Tobacco BY-2


title: LDT6B [S184]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 6, replicate B


title: PARE_Nt_G1_rep2


title: LDT6C [S185]

value: dark cycling timepoint:light:dark, time point 6, replicate C


title: RNA-seq_Wt DP-R1hi rep3


title: RNA-seq_Wt DP-R1hi rep1


title: AGO1IP_10G1_rep5

description:
Small RNA-seq
AGO1 IP RNA

data_processing:
For these small RNA libraries, raw files resulting from 2 separate runs were processed and concatenated to produce a single processed file.
Read quality control using FastQC.
Adaptor trimming and chopping using Trimmomatic.
Genome alignment using Bowtie and TN90 Nicotiana tabacum genome.
Sequences are then formatted to tag-count format.
Genome_build: N. tabacum TN90 (Sierro et al. 2014)
Supplementary_files_format_and_content: *_chopped.txt: Tab-delimited text files; Final trimmed and cropped output file in tag-count format.

source_name: BY-2 cell suspension, G1 phase, AGO1 IP

extract_protocol:
Cells were vacuum filtered and frozen in liquid nitrogen. After mechanical grinding, RNA was extracted using Trizol/chloroform protocol.
Small RNA libraries were constructed following Illumina TruSeq Small RNA Library Preparation Kit.

value: GFP-fused AGO1

tag: rip antibody

value: VHH anti-GFP (Chromotek, Ref:gtm-20)


title: CD8_w0__R087_K8710: CD8 before treatment 2

value: CD8 T cell

value: F


title: AGO1IP_7M_rep5

description:
Small RNA-seq
AGO1 IP RNA

source_name: BY-2 cell suspension, M phase, AGO1 IP

value: suspension


title: RNA-seq_Wt DP-R1med rep3

description: double positive *runx1*-medium   mCherry+Citrinemed

source_name: aortic endothelium

value: aortic endothelium


title: DDT5D [S182]

source_name: dark:dark_time point 5_whole organism

value: dark cycling timepoint:dark:dark, time point 5, replicate D

value: adult


title: RNA-seq_Wt DP-R1med rep2


title: DDT5C [S181]

value: dark cycling timepoint:dark:dark, time point 5, replicate C


title: RNA-seq_Wt DP-R1med rep1

value: FACS isolated cells


title: DDT5B [S180]

value: dark cycling timepoint:dark:dark, time point 5, replicate B


title: DDT5A [S179]

value: dark cycling timepoint:dark:dark, time point 5, replicate A


title: AGO1IP_1S_rep5

description:
Small RNA-seq
AGO1 IP RNA

source_name: BY-2 cell suspension, S phase, AGO1 IP

value: S


title: AGO1IP_10G1_rep4

description:
Small RNA-seq
AGO1 IP RNA

value: Tobacco BY-2


title: LDT5D [S178]

source_name: light:dark_time point 5_whole organism

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 5, replicate D


title: RNA-seq_Wt DP-R1lo rep2

description: double positive *runx1*-low   mCherry+Citrinelow

value: non-injected


title: LDT5C [S177]

value: dark cycling timepoint:light:dark, time point 5, replicate C


title: AGO1IP_3G2_rep4

description:
Small RNA-seq
AGO1 IP RNA

source_name: BY-2 cell suspension, G2 phase, AGO1 IP

value: GFP-fused AGO1

value: VHH anti-GFP (Chromotek, Ref:gtm-20)


title: LDT6A [S183]

value: dark cycling timepoint:light:dark, time point 6, replicate A


title: AGO1IP_7M_rep4

description:
Small RNA-seq
AGO1 IP RNA

value: suspension

value: M


title: RNA-seq_Wt SP-kdrl rep2

description: single positive-*kdrl*  mCherry+Citrine-

source_name: non-aortic endothelioum (NAE)

value: non-aortic endothelioum (NAE)


title: RNA-seq_Wt SP-kdrl rep3


title: AGO1IP_1S_rep4

description:
Small RNA-seq
AGO1 IP RNA


title: AGO1IP_3G2_rep5

description:
Small RNA-seq
AGO1 IP RNA


title: RNA-seq_Wt SP-kdrl rep1


title: tRNA_10G1_rep5

description: Small RNA-seq


title: LDT5A [S175]

value: dark cycling timepoint:light:dark, time point 5, replicate A

value: adult


title: DDT4C [S173]

source_name: dark:dark_time point 4_whole organism

value: dark cycling timepoint:dark:dark, time point 4, replicate C


title: RNA-seq_Wt DP-R1lo rep3

value: FACS isolated cells

value: aortic endothelium


title: DDT4D [S174]

value: dark cycling timepoint:dark:dark, time point 4, replicate D


title: RNA-seq_Wt DN rep3

description: mCherry-Citrine-

value: non-endothelial tissue


title: LDT5B [S176]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 5, replicate B


title: DDT4B [S172]

value: dark cycling timepoint:dark:dark, time point 4, replicate B


title: RNA-seq_Wt DP-R1lo rep1

value: non-injected


title: RNA-seq_Wt DN rep2

description: mCherry-Citrine-


title: tRNA_3G2_rep5

description: Small RNA-seq

value: Tobacco BY-2

value: GFP-fused AGO1


title: tRNA_1S_rep5

description: Small RNA-seq

source_name: BY-2 cell suspension, S phase

value: S


title: tRNA_10G1_rep4

description: Small RNA-seq

value: suspension


title: DDT4A [S171]

value: dark cycling timepoint:dark:dark, time point 4, replicate A


title: ChIPseq of Sox3 in zebrafish wild type embryos at 80epi

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Reads were aligned using Bowtie
Peaks were called using MACS2 software with default parameters
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: Called peaks in narrowPeak format

source_name: Whole embryo

growth_protocol: Embryos were cultivated at 28°C in E3 medium until desired developmental stage

extract_protocol:
Embryos were fixed in 1% paraformaldehide and quenched with 0.125M Glycine. Nuclei were extracted and lysed, and chromatin sonicated in a Covaris M220 sonicator to an average of 300bp fragments. Sonicated chromatin was divided in 6 aliquots and incubated overnight at 4ºC with 2µg of antibody per aliquiot. Immunoprecipitated chromatin was then incubated with magnetic beads, washed, TAGmented with Tn5 transposase (Schmidl et al., 2015) and eluted from beads. Then, chromatin was decrosslinked and DNA was purified using Minelute kit (Qiagen)
Preparation of ChIPmentation libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

tag: antibody

tag: developmental stage

value: 80% epiboly

value: WT


title: tRNA_7M_rep5

description: Small RNA-seq

source_name: BY-2 cell suspension, M phase

value: M


title: LDT4D [S170]

source_name: light:dark_time point 4_whole organism

value: dark cycling timepoint:light:dark, time point 4, replicate D

value: adult


title: LDT4C [S169]

value: dark cycling timepoint:light:dark, time point 4, replicate C


title: ChIPseq of Sox3 in zebrafish wild type embryos at 36hpf, replicate 2

tag: genotype


title: ChIPseq of Sox3 in zebrafish wild type embryos at 36hpf, replicate 1


title: tRNA_3G2_rep4

description: Small RNA-seq

source_name: BY-2 cell suspension, G2 phase

tag: cell line


title: ChIPseq of Sox3 in zebrafish tp63 mutant embryos at 36hpf, replicate 2


title: RNA-seq_Wt DN rep1

description: mCherry-Citrine-

source_name: non-endothelial tissue

value: FACS isolated cells

tag: tissue


title: LDT4A [S167]

value: dark cycling timepoint:light:dark, time point 4, replicate A


title: tRNA_1S_rep4

description: Small RNA-seq


title: R + Enz  Illumina TruSeq Stranded mRNA [S18_MDV]

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Sequence reads were trimmed using Cutadapt v1.8.3 (TruSeq adapters and qual 20)
Trimmed reads were aligned to reference using HISAT v 2.1.0.
Expression values of genes were calculated using HTSeq v0.9.0.
Supplementary_files_format_and_content: CSV file contains CPM values of genes.

source_name: LNCaP

growth_protocol: Cells were cultured in RPMI-1640 medium with 10% FBS (Atlanta Biologicals) and 2 mM L-glutamine (Corning), 100 U/ml penicillin (Corning), and 100 mg/ml streptomycin (Corning). 3x105 cells were plated in 6-well plates, with 2ml medium/each well.

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen) according to manufacturer’s protocol.
Library Prepreration was preformed using the TruSeq Stranded mRNA Sample Preperation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Cells were starved with 5% androgen-depleted medium for 24 hours, then treated with ethanol/1 nM R1881 and DMSO/IMTPPE (10 mM)/(-)-JJ-450 (10 mM)/enzalutamide (10 mM)/ (+)-JJ-450 (25 mM) for additional 24 hours prior to total RNA isolation.

tag: cell type

value: prostate epithelial

tag: passages

tag: agent

value: androgen and enzalutamide

value: LNCaP

value: Derived from metastatic site:left supraclavicular lymph node


title: AGO1IP_10G1_rep3

description:
Small RNA-seq
AGO1 IP RNA

value: Tobacco BY-2

tag: expression

value: VHH anti-GFP (Chromotek, Ref:gtm-20)


title: ChIPseq of Sox3 in zebrafish tp63 mutant embryos at 36hpf, replicate 1


title: R + Enz  Illumina TruSeq Stranded mRNA [S17_MDV]


title: DDT3D [S166]

source_name: dark:dark_time point 3_whole organism

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 3, replicate D


title: AGO1IP_7M_rep3

description:
Small RNA-seq
AGO1 IP RNA

value: GFP-fused AGO1

tag: growth type

value: suspension


title: DDT3C [S165]

value: dark cycling timepoint:dark:dark, time point 3, replicate C


title: ChIPseq of Sox3 in zebrafish wild type embryos at 24hpf

value: WT


title: AGO1IP_3G2_rep3

description:
Small RNA-seq
AGO1 IP RNA

tag: cell cycle phase


title: R + Enz  Illumina TruSeq Stranded mRNA [S16_MDV]


title: tRNA_7M_rep4

description: Small RNA-seq

value: M

tag: replicate


title: DDT3B [S164]

tag: genome

value: dark cycling timepoint:dark:dark, time point 3, replicate B

value: adult


title: ChIPseq of p63 in zebrafish wild type embryos at 80epi, replicate 2

value: 80% epiboly


title: R + (-) 450 Illumina TruSeq Stranded mRNA [S15_Minus450]

value: androgen and JJ-(-)450


title: AGO1IP_1S_rep3

description:
Small RNA-seq
AGO1 IP RNA

value: S


title: LDT4B [S168]

tag: light

value: dark cycling timepoint:light:dark, time point 4, replicate B


title: R + (-) 450 Illumina TruSeq Stranded mRNA [S14_Minus450]

value: prostate epithelial

value: LNCaP


title: DDT3A [S163]

value: dark cycling timepoint:dark:dark, time point 3, replicate A

tag: age


title: LDT3D [S162]

source_name: light:dark_time point 3_whole organism

value: dark cycling timepoint:light:dark, time point 3, replicate D


title: AGO1IP_10G1_rep2

description:
Small RNA-seq
AGO1 IP RNA

source_name: BY-2 cell suspension, G1 phase, AGO1 IP

value: Tobacco BY-2

value: VHH anti-GFP (Chromotek, Ref:gtm-20)


title: R + (-) 450 Illumina TruSeq Stranded mRNA [S13_Minus450]

value: Derived from metastatic site:left supraclavicular lymph node


title: AGO1IP_7M_rep2

description:
Small RNA-seq
AGO1 IP RNA

source_name: BY-2 cell suspension, M phase, AGO1 IP

value: GFP-fused AGO1

value: suspension


title: ChIPseq of p63 in zebrafish wild type embryos at 36hpf, replicate 2

value: WT


title: LDT3C [S161]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 3, replicate C


title: ChIPseq of p63 in zebrafish wild type embryos at 36hpf, replicate 1


title: AGO1IP_3G2_rep2

description:
Small RNA-seq
AGO1 IP RNA


title: LDT3B [S160]

value: dark cycling timepoint:light:dark, time point 3, replicate B

value: adult


title: R + (+) 450 Illumina TruSeq Stranded mRNA [S12_Plus450]

value: androgen and JJ-(+)-450


title: ChIPseq of p63 in zebrafish wild type embryos at 24hpf, replicate 2


title: ChIPseq of p63 in zebrafish wild type embryos at 80epi, replicate 1

value: 80% epiboly


title: R + (+) 450 Illumina TruSeq Stranded mRNA [S11_Plus450]


title: LDT3A [S159]

value: dark cycling timepoint:light:dark, time point 3, replicate A


title: AGO1IP_1S_rep2

description:
Small RNA-seq
AGO1 IP RNA

value: S


title: R + (+) 450 Illumina TruSeq Stranded mRNA [S10_Plus450]

value: prostate epithelial

value: LNCaP


title: DDT2D [S158]

source_name: dark:dark_time point 2_whole organism

value: dark cycling timepoint:dark:dark, time point 2, replicate D


title: AGO1IP_10G1_rep1

description:
Small RNA-seq
AGO1 IP RNA

value: Tobacco BY-2


title: ATACseq in zebrafish wild type embryos at 8som, replicate 2

description:
ATAC_seq
ATACseq_zebra_WT_8som_IDR_Peaks.bed

data_processing:
Alignment: reads were aligned against reference genome using Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: BED files with peaks called using Irreproducibility Discovery Rate (IDR) framework

source_name: whole embryo

extract_protocol:
Wild type or mutant embryos were dechorionated, deyolked and lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

value: 8 somites


title: R + IMTPPE Illumina TruSeq Stranded mRNA [S9_10]

value: androgen and IMTPPE

value: Derived from metastatic site:left supraclavicular lymph node


title: ATACseq in zebrafish wild type embryos at 8som, replicate 1


title: DDT2B [S156]

value: dark cycling timepoint:dark:dark, time point 2, replicate B


title: AGO1IP_1S_rep1

description:
Small RNA-seq
AGO1 IP RNA

source_name: BY-2 cell suspension, S phase, AGO1 IP

value: GFP-fused AGO1

value: suspension

value: VHH anti-GFP (Chromotek, Ref:gtm-20)


title: ATACseq in zebrafish tp63 mutant embryos at 8som, replicate 2

description:
ATAC_seq
ATACseq_zebra_p63mut_8som_IDR_Peaks.bed


title: AGO1IP_7M_rep1

description:
Small RNA-seq
AGO1 IP RNA

value: M


title: DDT2C [S157]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 2, replicate C

value: adult


title: ATACseq in zebrafish tp63 mutant embryos at 8som, replicate 1


title: AGO1IP_3G2_rep1

description:
Small RNA-seq
AGO1 IP RNA

source_name: BY-2 cell suspension, G2 phase, AGO1 IP


title: DDT2A [S155]

value: dark cycling timepoint:dark:dark, time point 2, replicate A


title: R + IMTPPE Illumina TruSeq Stranded mRNA [S7_10]


title: R (Androgen)  Illumina TruSeq Stranded mRNA [S5_R]

value: androgen


title: totalRNA_10G1_rep3

description: Cells were synchonized using aphidicolin

data_processing:
For these RNA libraries, raw files resulting from 2 separate runs were processed and concatenated to produce a single processed file
Read quality control usinf FastQC
Adaptor trimming and chopping using Trimmomatic
Genome alignment unig HiSat2 and TN90 Nicotiana tabacum genome
sequeces are then formated to tag-count format
Genome_build: Nicotiana tabacum genome version 4 (Edwards et al., 2017)
Supplementary_files_format_and_content: Final trimmed and cropped output file in tag-count format

source_name: cell suspension

growth_protocol: Cells were weekly subcultured  in liquid MS medium supplemented with KH2PO4 (200mg/L), myo-inositol (100mg/L), thiamin (1mg/L), 2,4-D(0,2mg/L) and sucrose ( 30g/L). Cells are kept in the dark, on a shacker at 180 RPM.

extract_protocol:
Cells were vacuum filtered and frozen in liquid nitrogen.  After mechanical grinding, RNA was extracted using Trizol/chloroform protocol.
RNA libraries were constructed following Illumina TruSeq Stranded mRNA Library Preparation Kit.

treatment_protocol: Cells were synchronized  following the published protocol from Nagata et al 1992.

tag: cell  line


title: R (Androgen)  Illumina TruSeq Stranded mRNA [S6_R]

value: prostate epithelial


title: R + IMTPPE Illumina TruSeq Stranded mRNA [S8_10]

value: LNCaP


title: LDT2D [S154]

source_name: light:dark_time point 2_whole organism

value: dark cycling timepoint:light:dark, time point 2, replicate D


title: tRNA_10G1_rep3

description: Small RNA-seq

source_name: BY-2 cell suspension, G1 phase

value: Tobacco BY-2


title: ChIPseq of p63 in zebrafish wild type embryos at 24hpf, replicate 1

source_name: Whole embryo

value: WT


title: totalRNA_7M_rep3


title: Control Illumina TruSeq Stranded mRNA [S3_C]

value: vehicle


title: LDT2B [S152]

value: dark cycling timepoint:light:dark, time point 2, replicate B


title: tRNA_3G2_rep3

description: Small RNA-seq


title: tRNA_7M_rep3

description: Small RNA-seq

source_name: BY-2 cell suspension, M phase


title: LDT2C [S153]

value: dark cycling timepoint:light:dark, time point 2, replicate C


title: R (Androgen)  Illumina TruSeq Stranded mRNA [S4_R]

value: Derived from metastatic site:left supraclavicular lymph node


title: tRNA_1S_rep3

description: Small RNA-seq

source_name: BY-2 cell suspension, S phase

value: GFP-fused AGO1

value: suspension

value: S


title: Control Illumina TruSeq Stranded mRNA [S2_C]


title: totalRNA_1S_rep3


title: LDT2A [S151]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 2, replicate A


title: tRNA_10G1_rep2

description: Small RNA-seq


title: totalRNA_10G1_rep2


title: Control Illumina TruSeq Stranded mRNA [S1_C]


title: tRNA_7M_rep2

description: Small RNA-seq

value: M


title: totalRNA_7M_rep2


title: DDT1C [S149]

source_name: dark:dark_time point 1_whole organism

value: dark cycling timepoint:dark:dark, time point 1, replicate C

value: adult


title: DDT1B [S148]

value: dark cycling timepoint:dark:dark, time point 1, replicate B


title: tRNA_3G2_rep2

description: Small RNA-seq

source_name: BY-2 cell suspension, G2 phase


title: totalRNA_3G2_rep2


title: RNAseq in zebrafish wild type embryos at 36hpf replicate 2

data_processing:
Reads were aligned against reference genome using STAR software, and reads per gene were counted using htseq-count script from HTSeq tools software package
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: Individual counts files (reads per gene)

extract_protocol: RNA was extracted using TRIsure (Bioline) and treated with TURBO DNA free kit (Invitrogen)


title: tRNA_1S_rep2

description: Small RNA-seq


title: totalRNA_1S_rep2


title: DDT1A [S147]

value: dark cycling timepoint:dark:dark, time point 1, replicate A


title: RNAseq in zebrafish wild type embryos at 36hpf replicate 1


title: totalRNA_3G2_rep3


title: LDT1D [S146]

source_name: light:dark_time point 1_whole organism

value: dark cycling timepoint:light:dark, time point 1, replicate D


title: totalRNA_10G1_rep1


title: LDT1C [S145]

value: dark cycling timepoint:light:dark, time point 1, replicate C


title: tRNA_3G2_rep1

description: Small RNA-seq

value: Tobacco BY-2


title: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3


title: tRNA_7M_rep1

description: Small RNA-seq


title: DDT1D [S150]

value: dark cycling timepoint:dark:dark, time point 1, replicate D


title: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2


title: LDT1B [S144]

value: dark cycling timepoint:light:dark, time point 1, replicate B


title: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1


title: totalRNA_7M_rep1


title: totalRNA_3G2_rep1


title: RNAseq in zebrafish wild type embryos at 36hpf replicate 3

value: WT


title: tRNA_1S_rep1

description: Small RNA-seq


title: LDT1A [S143]

value: dark cycling timepoint:light:dark, time point 1, replicate A


title: tRNA_10G1_rep1

description: Small RNA-seq

value: GFP-fused AGO1


title: Org 21

status: Public on Jun 05 2019

city: Boston

first: Amanda

middle: Joy

last: Kedaigle

state: MA

address: 1325 Boylston St

department: Systems Biology - Molecular Innovation

institute: Decibel Therapeutics

description:
processed data file:
expression_PGP1.6mon.batch3.txt.gz

data_processing:
The Cell Ranger 2.0.1 pipeline (10X Genomics) was used to align reads from RNA-seq to the GRCh38 human reference genome and produce the associated cell by gene count matrix.
Unique Molecular Identifier (UMI) counts were analyzed using the Seurat R package v2.3.4. Cells expressing a minimum of 500 genes were kept, and UMI counts were normalized for each cell by the total expression, multiplied by 1 million, and log-transformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files contain matrices of normalized and log-transformed UMI counts for each gene in each cell. In cell names, "_X1_" indicates which organoid the cell was derived from within that batch.

source_name: PGP1_human brain organoid

growth_protocol: To generate dorsally patterned forebrain organoids, we modified the method previously described in Kadoshima et al, PNAS, 2013. We eliminated the need for growth under 40% O2, the need for cell aggregates to be periodically bisected, and the use of high O2 penetration dishes, by adapting the cultures to growth in spinner-flask bioreactors. Specifically, on day 0, feeder-free cultured human PSCs, 80-90% confluent, were dissociated to single cells with Accutase (Gibco), and 9,000 cells per well were reaggregated in ultra-low cell-adhesion 96-well plates with V-bottomed conical wells (sBio PrimeSurface plate; Sumitomo Bakelite) in Glasgow-MEM (Gibco) with 20% Knockout Serum Replacement (Gibco), 0.1 mM Minimum Essential Medium non-essential amino acids (MEM-NEAA) (Gibco), 1 mM pyruvate (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 100 U/mL penicillin, and 100 μg/mL streptomycin (Corning). From day 0 to day 6, ROCK inhibitor Y-27632 (Millipore) was added to the medium at a final concentration of 20 μM. From day 0 to day 18, Wnt inhibitor IWR1 (Calbiochem) and TGFβ inhibitor SB431542 (Stem Cell Technologies) were added at a concentration of 3 μM and 5 μM, respectively. From day 18, the floating aggregates were cultured in ultra-low attachment culture dishes (Corning) under orbital agitation (70 rpm) in DMEM/F12 medium (Gibco) with 2mM Glutamax (Gibco), 1% N2 (Gibco), 1% Chemically Defined Lipid Concentrate (Gibco), 0.25 μg/mL fungizone (Gibco), 100 U/mL penicillin, and 100 μg/mL streptomycin (Corning). On day 35, cell aggregates were transferred to spinner-flask bioreactors (Corning) and maintained at 56 rpm, and media was supplemented with 10% fetal bovine serum (FBS) (GE-Healthcare), 5 μg/mL heparin (Sigma) and 1% Matrigel (Corning). From day 70, the concentration of Matrigel was increased to 2%, and B27 supplement containing vitamin A (Gibco) was added to the medium

extract_protocol:
Individual brain organoids were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington Biochemical). Dissociated cells were resuspended in ice-cold PBS containing 0.04% BSA (Sigma) at a concentration of 1000 cells/μL, and approximately 17,400 cells per channel were loaded onto a Chromium™ Single Cell 3' Chip (10X Genomics, PN-120236) and processed through the Chromium Controller to generate single-cell GEMs (Gel Beads in Emulsion).
Single-cell RNA-Seq libraries were prepared with the Chromium™ Single Cell 3' Library & Gel Bead Kit v2 (10X Genomics, PN-120237). Libraries from different samples were pooled based on molar concentrations and sequenced on NextSeq 500 instrument (Illumina) with 26 bases for read 1, 57 bases for read 2 and 8 bases for Index 1.

value: 6 months

tag: protocol

value: Dorsally patterned


title: Org 20


title: Org 18

description:
processed data file:
expression_PGP1.6mon.txt.gz


title: Org 19


title: Org 9

description:
processed data file:
expression_HUES66.3mon.txt.gz

source_name: HUES66_human brain organoid

value: 3 months


title: Org 8


title: Org 17


title: Org 12

description:
processed data file:
expression_11a.6mon.txt.gz

source_name: 11a_human brain organoid


title: Org 13

description:
processed data file:
expression_GM.6mon.txt.gz

source_name: GM8330_human brain organoid


title: Org 16


title: Org 10


title: Org 15


title: Org 11


title: Org 14


title: Org 1

description:
processed data file:
expression_PGP1.3mon.txt.gz


title: Org 6

description:
processed data file:
expression_PGP1.3mon.batch2.txt.gz


title: totalRNA_1S_rep1

value: S


title: Org 4


title: Org 3


title: Org 2


title: iBMEC_no_coculture_3

city: Los Angeles

first: Michael

last: Workman

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

description:
RNA isolated with Qiagen RNeasy Micro Kit
iBMECs_CocultureSamples_Salmon_GeneCounts.csv

data_processing:
Demultiplexing and conversion of raw sequencing data to FASTQ was performed with Illumina bcl2fastq software
FastQC was used to assess sequence quality and reads were aligned to the GRCh38 genome assembly (GENCODE 28) using Salmon version 0.11.3
Gene-level read counts were quantified with Salmon
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are formatted as comma-separated values containing gene-level read counts generated using Salmon v0.11.3

source_name: iPSC-derived brain microvascular endothelial cells grown in PDMS tissue chip

growth_protocol: iPSCs were passaged onto Matrigel in mTeSR1 medium for 2–3 days of expansion then switched to unconditioned medium lacking bFGF for 6 days. Human endothelial serum-free medium (hESFM; Life Technologies) supplemented with 20 ng/ml bFGF, all-trans retinoic acid (RA, 10 uM; Sigma) and 1% platelet-poor plasma derived bovine serum (Biomedical Technologies, Inc.) was then added for 2 days. After which, cells were incubated with Accutase for 35 min, gently dissociated and seeded onto the ‘blood side’ of the chip coated with a mixture of collagen IV (320 mg/ml; Sigma) and fibronectin (80 mg/ml; Sigma). iBMECs were subsequently grown in endothelial cell medium (ECM) without bFGF and RA.

extract_protocol:
Total RNA was isolated from cells using Invitrogen PureLink RNA Mini Kit or Qiagen RNeasy Micro Kit as descibed in Sample description following the manufacturer's protocol.
RNA libraries were generated using Takara SMART-Seq v4 Ultra Low Input RNA Kit and prepared for sequencing using standard Illumina protocols

tag: culture


title: iBMEC_no_coculture_1

value: iPSC-derived brain microvascular endothelial cell


title: iBMEC_cocultured_iNeural_2

value: iPSC-derived neural progenitor cells


title: iBMEC_cocultured_iNeural_1


title: iBMEC_no_coculture_2


title: iBMEC_cocultured_AP_3

value: primary human astrocytes and pericytes


title: iBMEC_cocultured_AP_2


title: Org 7


title: iBMEC_2.4dyn_3

description:
RNA isolated with Invitrogen PureLink RNA Mini Kit
iBMECs_ShearSamples_Salmon_GeneCounts.csv

tag: shear stress range


title: iBMEC_2.4dyn_2


title: iBMEC_2.4dyn_1


title: iBMEC_0.5dyn_3


title: iBMEC_0.01dyn_2


title: iBMEC_0dyn_Static_1


title: Org 5


title: iBMEC_0dyn_Static_3


title: iBMEC_0.01dyn_1


title: iBMEC_0dyn_Static_2


title: iBMEC_0.5dyn_1


title: iBMEC_0.5dyn_2


title: iBMEC_cocultured_iNeural_3


title: ECT-O_7

city: Leuven

first: Matteo

last: Boretto

address: Herestraat 49

institute: KU Leuven

description: ECT-O

data_processing:
Raw reads were subjected to quality control
Sequence reads were pre-processed to remove adaptors and filter low-quality reads
high-quality reads were aligned to the human reference genome using Hisat2 v2.1.0
Mapping reads were summarized as the reads count table by featureCounts v1.5.3
Differnetial expression analysis was performed using the DESeq2 v1.32.0 package of Bioconductor
Genome_build: hg19
Supplementary_files_format_and_content: .xls, differetial expression analysis results generated by the DESeq2 package

source_name: organoids derived from ectopic endometrium (endometriotic lesion)

growth_protocol: organoids were cultured with human endometrial organoid medium (see reference) and passaged every 10-14 days

extract_protocol:
RNA was isolated using the Rneasy micro kit (Qiagen)
library prep was performed using the NEBNext Ultra DNA Library prep kit (Illumina)

value: endometrial organoids

tag: patient diagnosis

value: endometriosis

value: 2 to 4

tag: medium

value: Human endometrial organoid medium

tag: tissue condition


title: ECT-O_9

description: ECT-O

tag: tissue


title: ECT-O_4

description: ECT-O

tag: passages


title: ECT-O_13

description: ECT-O


title: EUT-O_7

description: EUT-O

source_name: organoids derived from eutopic endometrium (endometrium of people with endometriosis)

value: eutopic endometrium (endometrium of patients with endometriosis)


title: ECT-O_6

description: ECT-O


title: EM-O_3

description: EM-O

source_name: organoids derived from healthy endometrium

value: healthy

value: healthy endometrium


title: ECT-O_11

description: ECT-O


title: EUT-O_6

description: EUT-O


title: iBMEC_cocultured_AP_1

tag: cell type

tag: cell line


title: EUT-O_3

description: EUT-O


title: EM-O_1

description: EM-O


title: EUT-O_4

description: EUT-O


title: EM-O_4

description: EM-O


title: iBMEC_0.01dyn_3


title: EM-O_2

description: EM-O


title: ECT-O_3

description: ECT-O


title: medium-chain (MC) high-fat diets Livers rep5

first: Edward

middle: V

last: Prochownik

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

data_processing:
Raw sequencing reads were quality checked for potential sequencing issues and contaminants using FastQC (Babraham Bioinformatics, Inc, Cambridge, UK.). Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and PRINSEQ (http://prinseq.sourceforge. net/manual.html). Reads with a remaining length of less than 20 bp after trimming were discarded. Paired end reads were mapped to the mouse genome (m10) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) in a strand specific manner. Read coverage on forward and reverse strands for genome browser visualization was computed using SAMtools, BEDtools, and UCSC Genome Browser utilities. Pairwise differential expression was quantified using Cuffdiff and DESeq [4, 5]. Cufflinks was used to determine FPKM levels for each gene from the TopHat alignment and was used as input for Cuffdiff. Significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05. DESeq was utilized
for raw read counts, which were calculated by HTSeq based on the STAR alignment (http://www-huber.embl.de/users /anders/HTSeq/doc/count.html). Read counts were then normalized across all samples and significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: cufflinks.tar.gz contains cufflinks output (genes.fpkm_tracking, isoforms.fpkm_tracking, transcripts.gtf) files

source_name: medium-chain (MC) high-fat diets Livers

extract_protocol:
Total RNAs were extracted using Qiagen RNeasy columns (Valencia, CA). Each RNA sample was assessed for quality and quantity using a Qubit 2.0 fluorometer and Agilent Bioanalyzer TapeStation 2200. The Sample preparation was replicated using Illumina TruSeq Stranded mRNA kit (San Diego, CA). mRNA was used to generate poly-A+ libraries using oligo-dT beads following 2 rounds of poly-A selection.
mRNA was fragmented to an average length of 260 nt by magnesium-catalyzed hydrolysis at 940C and then converted into cDNA by random priming. cDNA 3’ ends were adenylated, followed by adaptor ligation and a 9-cycle PCR to enrich DNA fragments. cDNA libraries were then validated using KAPA Biosystems (Wilmington, MA) primer premix kit with Illumina-compatible DNA primers on the Qubit 2.0 fluorometer and Tapestation 2200 systems described above. Libraries were diluted in 0.1% Tween 20 to concentrations of 2 nM for stabilization. The cDNA libraries were then pooled to final concentrations of 2.5 pM.

tag: strain

value: F1 from FVB/N-Tg(tetO-MYC)36aBop/J x B6.Cg-Tg[Cebpb-tTA]5Bjd/J

tag: treatment

value: medium-chain (MC) high-fat diets

value: Liver

tag: tissue subtype

value: liver tisuue

tag: genotyping

value: tet-o-myc negative


title: medium-chain (MC) high-fat diets Livers rep2


title: medium-chain (MC) high-fat diets Livers rep1


title: medium-chain (MC) high-fat diets Livers rep3


title: medium-chain (MC) high-fat diets Tumors rep5

source_name: medium-chain (MC) high-fat diets Tumors

value: hepatocellular carcinoma

value: tet-o-myc positive


title: long-chain (LC) high-fat diets Tumors rep5

source_name: long-chain (LC) high-fat diets Tumors

value: long-chain (LC) high-fat diets


title: long-chain (LC) high-fat diets Tumors rep4


title: medium-chain (MC) high-fat diets Tumors rep1


title: medium-chain (MC) high-fat diets Tumors rep3


title: long-chain (LC) high-fat diets Tumors rep2


title: long-chain (LC) high-fat diets Liver rep4

source_name: long-chain (LC) high-fat diets Liver


title: long-chain (LC) high-fat diets Tumors rep1


title: medium-chain (MC) high-fat diets Livers rep4


title: medium-chain (MC) high-fat diets Tumors rep4


title: long-chain (LC) high-fat diets Tumors rep3


title: long-chain (LC) high-fat diets Liver rep5


title: long-chain (LC) high-fat diets Liver rep3


title: Normal diets Tumors rep4

source_name: Normal diets Tumors

value: Normal diets


title: long-chain (LC) high-fat diets Liver rep2


title: Normal diets Tumors rep3


title: Normal diets Liver rep4

source_name: Normal diets Liver


title: long-chain (LC) high-fat diets Liver rep1


title: Normal diets Tumors rep1


title: Normal diets Liver rep3


title: Normal diets Liver rep5


title: Normal diets Tumors rep2


title: Normal diets Liver rep2


title: Normal diets Liver rep1


title: medium-chain (MC) high-fat diets Tumors rep2


title: Lung Epithelium rep2

first: Mattia

last: Lion

address: Simches Research Center 185 Cambridge Street, CPZN7250

department: Department of Molecular Biology

institute: Massachusetts General Hospital

description: processed data file: MACC_LungEp.rep.set._bin300.gn.wig

data_processing:
Fragments were aligned to mouse mm10 genome assembly using Bowtie v.0.12.9 aligner with the following settings ( -I=50, -X=500, -m=10, -k=1 )
Fragments that were mapped at same genomic position at high frequency (above z-score=7) were filtered (Kharchenco et al. 2018).
QC: fragment length density, nucleosomal periodicity plot & hierarchical clustering of replicates.
Genome-wide MACC profiles were computed as described in (Mieczkowski et al. 2016), using the heaviest and lightest MNase concentrations.
Genome-wide nucleosome position was computed as described in (Mieczkowski & Tolstorukov 2018).
Generating average profiles (chromatin accessibility & nucleosome positioning) around RSS.
A permutation test was performed to assess the significance of accessibility at antigen receptor loci. Accessibility values at Antigen receptor loci were compared to those at randomly chosen genomic regions with similar length using a Wilcoxon test (significance level of 0.05).
Genome_build: mm10 (GRCm38): mouse genome assembly
Supplementary_files_format_and_content: Wig files contains MACC scores.

source_name: lung

growth_protocol: All animal procedures were performed according to NIH guidelines and approved by the Committee on Animal Care at Massachusetts General Hospital and Harvard University.

extract_protocol:
Cells were collected after cell sorting and nuclei were extracted. Nuclei were counted and subjected to digestion with titrated amounts of MNase enzyme for 5 minutes at 37°C. MNase-digested samples were treated with RNase A for 1 h at 37°C and incubated with proteinase K and 1% SDS overnight at 60°C. Digested DNA was cleaned up using Agencourt AMPure XP beads and visualized on either Agilent Bioanalyzer or Agilent TapeStation.
Libraries were prepared for each individual titration point using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs) and barcoded using NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1&2, New England Biolabs). Number of PCR cycles was calculated using a real-time qPCR-based approach (Bowman et al. 2013). Four barcoded titration libraries were pooled in one sample and paired-end 50-cycle sequencing in an Illumina HiSeq 2500 instrument was performed.

treatment_protocol: No treatment.

tag: strain/background

tag: genotype

value: Wild type

value: 4-6 weeks

value: Lung Epithelium

value: MNase digestion


title: Small pre-B rep2

description: processed data file: MACC_SpreB.rep.set._bin300.gn.wig

source_name: bone marrow

tag: age

value: Small pre-B


title: Lung Epithelium rep1


title: Small pre-B rep1


title: Large pre-B rep1

description: processed data file: MACC_LpreB.rep.set._bin300.gn.wig

value: Large pre-B


title: Large pre-B rep2


title: BLP rep1

description: processed data file: MACC_BLP.rep.set._bin300.gn.wig

value: BLP


title: HSC rep2

description: processed data file: MACC_HSC.rep.set._bin300.gn.wig

value: HSC


title: BLP rep2


title: pro-B rep1

description: processed data file: MACC_proB.rep.set._bin300.gn.wig

value: pro-B


title: LMPP rep1

description: processed data file: MACC_LMPP.rep.set._bin300.gn.wig

value: LMPP


title: ALP rep1

description: processed data file: MACC_ALP.rep.set._bin300.gn.wig

value: ALP


title: ALP rep2


title: DD010_A223

city: Cold Spring Harbor

first: Dannielle

last: Engle

state: NY

address: 1 Bungtown Road, Cold Spring Harbor Laboratory

institute: Cold Spring Harbor Laboratory

data_processing:
Transcript abundances were estimated by Kallisto 0.43.1
Transcript abundances were aggregated to gene abundances by tximport 1.6 (Bioconductor 3.6)
Differential gene expression was estimated by DESeq2 1.18.1 (Bioconductor 3.6) at 10% FDR using timepoint and treatment contrasts 4h vs 0h neg, 24h vs 0h neg, 24h vs 4h neg, 4h vs 0h pos, 24h vs 0h pos, and 24h vs 4h pos (neg = untreated, pos = dox treated)
Raw counts were normalized using transcripts per million (TPM) and DESeq's variance-stabilizing transformation (VST).  All three quantifications are provided.
Genome_build: GRCm38
Supplementary_files_format_and_content: Transcript abundances in tab-separated text files

source_name: Normal pancreas ductal organoids, genetic negative

growth_protocol: Normal pancreas organoids were grown embedded in growth factor reduced Matrigel overlaid with liquid media: Advanced DMEM/F-12, 10mM HEPES pH 7.2-7.5, Penicillin/Strptomycin, GlutaMAX, 0.5uM A 83-01, 0.05ug/ml mEGF, 0.1ug/ml hFGF-10. 0.02ug/ml hGastrin 1, 0.1ug/ml mNoggin, 1.25mM N-acetylcysteine, 10mMNicotinamide, 10% R-Spondin 1 Conditioned Medium, B27 Supplement

extract_protocol:
Liquid medium was removed from the organoid-containing Matrigel mounds. 500ul of Trizol was added to the wells and triturated to dissolve the organoids and Matrigel. Trizol was stored at -80C before RNA isolation was performed using the RNAeasy PLUS kit according the the manufacturer's instructions. RNA samples with a RIN value of 9.8 - 10 were used.
Performed by the JP Sulzberger Columbia Genome Center: protocol 133, Ribo-zero 60M PE100. Ribosomal RNA was depleted using the Ribo-zero kit and libraries prepared using the Illumina TruSeq RNA prep kit.

treatment_protocol: 24 hours prior to the harvest, Organoid media was refreshd. 1ug/ml of Doxycycline was added at the appropriate timepoints such that all samples were ready for harvest simultaneously.

tag: genotype/variation

value: genetic negative

tag: dox treatment (hours)

value: normal pancreas ductal organoids


title: DD015_A225

source_name: Normal pancreas ductal organoids, CA19-9 inducible

value: CA19-9 inducible


title: DD011_A223


title: DD007_A220


title: DD006_A218


title: DD013_A225


title: HSC rep1


title: DD005_A218


title: DD012_A223


title: DD004_A218


title: DD008_A220


title: DD003_A217


title: DD002_A217


title: LMPP rep2


title: Ox-48h-2

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

description: with ox-LDL

data_processing:
miRDeep2 software was used for base-calling. The raw reads were subjected to a series of additional strict filters (such as removing low-quality reads, repeated sequences, and adaptor sequences), and the filtered data called clean data. The clean reads were compared against the Rfam databases to remove known classes of mouse RNAs (i.e. rRNA, tRNA, snRNA, and snoRNA). Then the remaining sequences were mapped to a reference mouse genome (assembly GRCm38.p5) with loose matches (± 1bp) to analyze their expression and distribution. All mappable reads were aligned with the mouse pre-miRNAs in miRBase 21.0 with only one mismatch to identify mouse known miRNAs.
To identify the DE miRNAs, miRNA expression in 6 librarieswas normalized to obtain the expression of transcripts per million
Genome_build: Genome database:mouse genome (assembly GRCm38.p5); miRbase version: V21.0
Supplementary_files_format_and_content: identified miRNAs in each library with reads and normalized data

source_name: RAW 264.7 cells

extract_protocol:
The total RNA was harvested using Trizol reagent.
The integrity of total RNA was determined by the Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA) with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 17 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 14 to 36 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

tag: Sex

value: male

value: macrophages


title: DD001_A217


title: DD014_A225


title: Ox-48h-3

description: with ox-LDL


title: pro-B rep2


title: Control-2

description: without treatment


title: Ox-48h-1

description: with ox-LDL


title: DD009_A220


title: Control-1

description: without treatment


title: S.elongatus_Z-COTE_5h_rep1

type: RNA

city: METZ

first: Bénédicte

last: SOHM

address: 8 rue du Gal Delestraint

country: France

institute: CNRS

description: S.elongatus PCC7942, Z-COTE exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 1

hyb_protocol: For each sample, 825 ng of cRNA with a specific activity of at least 15 pmol of Cy3 per µg of cRNA (according to the manufacturer’s protocol) was hybridized in presence of GE Hybridization Buffer HI-RPM (Agilent) on an Agilent custom design microarray (8×15 K slide format, design ID: 020846 from Vijayan et col. 2009, PNAS) 17h at 60°C in a rotation oven (Agilent). Slides were washed successively 1 min in GE wash buffer 1 and 2 (Agilent) and dried by centrifugation.

scan_protocol: Microarray was scanned at 5 µm resolution with GenePix 4100 A (Molecular Devices, CA, USA).

data_processing: Image analysis was performed with GenePix Pro 7 software (Molecular Device), background was defined with the “Local features background median” method.  Lowess normalization was applied in R (version 3.3.0) with the LIMMA software package (version 2.16.5). Spots corresponding to Synechococcus elongatus were extracted.  Four probes for each gene were spoted on the array. Mean signal of the four probes were calculated.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

label_protocol: Total RNA was reverse transcribed, amplified, and labeled with cyanine 3 (Cy3) using the low Input Quick Amp WT labeling kit (Agilent, CA, USA). No Spike-In RNA was used. The labeled cRNA (antisense) was then purified with the RNeasy mini spin columns (Qiagen). Quantification and measure of incorporation level of Cy3 were done with a NanoDrop ND-1000 (Thermo Scientific, DE, USA).  The labeled cRNA was fragmented with Agilent fragmentation buffer 30 min at 60°C and RNA fragmentation was checked on BioAnalyzer.

growth_protocol: Synechococcus elongatus PCC 7942 (ATCC  33912) cells were grown in BG11 medium under constant temperature (20°C), rotary agitation (100 rpm) and with a circadian period (16:8).

extract_protocol: Cells were broken in TRIzol® (Thermo Fisher) with 4 round of freeze/heat at 70°C and total RNA was extracted with TRIzol/chloroform extraction and isopropanol precipitation. DNA contamination was removed with DNAse I digestion (Sigma) and RNA was clean up with RNeasy kit (Qiagen). RNA quantity and purity were verified by optical density measurements (OD 260 nm; OD ratio 260/280 and 260/230 respectively) and RNA integrity was checked using Bioanalyzer 2100 (Agilent, CA, USA).

treatment_protocol: Cells in exponential phase of growth (OD730nm =  0.24) were harvested by centrifugation (7,500 × g, 6 min) and washed once with sterile EPA Very Soft Water. The OD730nm was adjusted to 0.27 (3.10E8 cells/mL) and this cell suspension was split up into aliquot of 31.5 mL and exposed to Z-COTE, Z-COTE HP1 or ZnCl2 at final concentration of 5 mg/L , with 4 replicates for each condition. The cells were exposed during 5 h at 20 °C under 100 rpm agitation and continuous light.

tag: incubation medium

value: EPA Very Soft Water (pH 6.4± 0.3) + 5 mg/L Z-COTE

tag: incubation condition

value: 5 h, 20°C,  100 rpm agitation,  continuous light


title: Control-3

description: without treatment


title: S.elongatus_Z-COTE_5h_rep4

description: S.elongatus PCC7942, Z-COTE exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 4


title: S.elongatus_Z-COTE_5h_rep3

description: S.elongatus PCC7942, Z-COTE exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 3


title: S.elongatus_ZnCl2_5h_rep1

description: S.elongatus PCC7942, ZnCl2 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 1

value: EPA Very Soft Water (pH 6.4± 0.3) + 5 mg/L ZnCl2


title: S.elongatus_ZnCl2_5h_rep2

description: S.elongatus PCC7942, ZnCl2 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 2


title: S.elongatus_Z-COTE_5h_rep2

description: S.elongatus PCC7942, Z-COTE exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 2


title: S.elongatus_Z-COTEHP1_5h_rep4

description: S.elongatus PCC7942, Z-COTE HP1 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 4

value: EPA Very Soft Water (pH 6.4± 0.3) + 5 mg/l Z-COTE HP1


title: S.elongatus_ZnCl2_5h_rep4

description: S.elongatus PCC7942, ZnCl2 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 4


title: S.elongatus_Z-COTEHP1_5h_rep3

description: S.elongatus PCC7942, Z-COTE HP1 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 3


title: 2.5 NP 1

city: London

first: Matthew

middle: A

last: Veras

state: ON

address: 1151 Richmond St.

country: Canada

institute: Western University

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Command Console v3.2.4 using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

source_name: Pool of all lumbar and thoracic NP tissues from 2.5 month mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in standard cages and maintained on a 12 hr light/dark cycle, with rodent chow and water available ad libitum

extract_protocol: Extraction of total RNA with the Aurum Totoal RNA Fatty and Fibrous Tissue Kit was performed according to the manufacturer's instructions.

treatment_protocol: The notochord-specific NotoCre/WT mouse strain (derived on a CD1(ICR) background) was mated to the conditional ROSA26 (R26) mT/mG reporter mouse (Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J; 129X1/SyJ background).

value: Mixed (Black 6/CD1)

value: thoracic and lumbar nucleus pulposus

value: 2.5 months


title: 21 NP 2

source_name: Pool of all lumbar and thoracic NP tissues from 21 month mouse

value: 21 months


title: S.elongatus_Z-COTEHP1_5h_rep2

description: S.elongatus PCC7942, Z-COTE HP1 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 2


title: S.elongatus_Z-COTEHP1_5h_rep1

description: S.elongatus PCC7942, Z-COTE HP1 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 1


title: 6 NP 2

source_name: Pool of all lumbar and thoracic NP tissues from 6 month mouse

value: 6 months


title: 21 NP 3


title: 2.5 NP 2


title: S.elongatus_control_5h_rep1

description: S.elongatus PCC7942, control culture, 5h, 20 °C, light, 100 rpm, replicate 1

value: EPA Very Soft Water (pH 6.4± 0.3)


title: S.elongatus_control_5h_rep3

description: S.elongatus PCC7942, control culture, 5h, 20 °C, light, 100 rpm, replicate 3


title: S.elongatus_control_5h_rep4

description: S.elongatus PCC7942, control culture, 5h, 20 °C, light, 100 rpm, replicate 4


title: S.elongatus_control_5h_rep2

description: S.elongatus PCC7942, control culture, 5h, 20 °C, light, 100 rpm, replicate 2


title: 21 NP 1


title: S.elongatus_ZnCl2_5h_rep3

description: S.elongatus PCC7942, ZnCl2 exposed culture (5mg/L), 5h, 20 °C, light, 100 rpm, replicate 3


title: 6 NP 1


title: 2.5 NP 3


title: pILC3  donor:  c

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: R/Bioconductor, limma rma

source_name: PB pILC3

label_protocol: Briefly, PB and cord blood was enriched for ILCs by immunomagnetic cell sorting, using a negative selection of CD3, CD14, CD16 and CD19 with Mojosort magnetic cell separation system (BioLegend, San Diego, CA, USA) Tonsillar mononuclear cells were depleted of CD3 and CD19 cells by MACS depletion. The cells suspensions were stained with antibodies against Lineage (CD1a, CD3, CD4, CD5, CD14, CD19, CD16, CD34, CD94, CD123, BDCA2, TCRαβ, TCRγδ, FcER1α), CD45, CD161, CD127, CD117, CRTH2, KLRG1, NKp44, NKp46, CD56 and IL-1R1. Cells were sorted on a FACSAria, purity of the sorted cells in all experiments was >99%.

extract_protocol: Buffy coats were provided by the blood bank (Sanquin, Amsterdam). Tonsils were obtained from routine tonsillectomies and tissue collection was done at the Academic Medical Center (AMC), Onze Lieve Vrouwe Gasthuis (OLVG) hospital (Amsterdam, The Netherlands). Inflamed nasal polyps were obtained from chronic rhinosinusitis patients during surgery and umbilical cord blood was collected at the AMC. The collection and use of all human samples was approved by the Medical Ethical Committee of the AMC and with informed consent. Peripheral blood and umbilical cord blood mononuclear cells were isolated by Ficoll-Hypaque density gradient (Lymphoprep; Axis-Shield). Tonsil tissue was cut in fine pieces and mechanically disrupted using the Stomacher 80 Biomaster. Cell suspensions were filtered through a 70- µm cell strainer. Nasal tissues were manually cut into fine pieces and digested for 45 min at 37°C with Liberase TM (125 µg/mL) and DNase I (50 U/mL). Cell suspensions were filtered through a 70 µm cell strainer. Mononuclear cells were then isolated by Ficoll-Hypaque density gradient. Subsequently, ILCs were isolated as described previously .

tag: donor

value: c

value: Peripheral Blood


title: ILC2  donor:  c

source_name: PB ILC2

tag: tissue


title: pILC3  donor:  d

value: d


title: ILC2  donor:  b

value: b


title: ILC2  donor:  a

value: a


title: pILC3  donor:  b


title: pILC2  donor:  d

source_name: PB pILC2


title: pILC2  donor:  b


title: glioblastoma cancer stem cells H10

city: Memphis

first: Doug

last: Green

state: Tn

address: 262 Danny Thomas Pl

department: Immunology

institute: St. Jude Children's Research Hospital

data_processing:
Trimmomatic – 0.35 – Paired reads were trimmed using the following parameters: SLIDINGWINDOW:4:20 MINLEN:36 LEADING:20 TRAILING:20
Reads were aligned using Star 2.5.0b - runMode = alignReads, quantMode = GeneCount, outSAMstrandField = intronMotif
Htseq-count – parameters: -r  = pos,  -i = gene_id, -a = 10,  --stranded=no,  -f = bam
Genome_build: GRCh38
Supplementary_files_format_and_content: glio_chrom_instability_normalized_expression_matrix.tsv

source_name: glioblastoma cancer stem cells

growth_protocol: Cells were grown in serum-free culture conditions as described in Pollard et al, Cell Stem Cell, 568-580, 2009.

extract_protocol:
Single cells were caputured, lysed, and cDNA prepared using the C1 Single Cell Auto Prep system from Fluidigm.
Single Cell RNA seq libraries were prepared for sequencing using Illumina Nextera XT DNA sample prep kit as per the C1-RNA seq protocol.

treatment_protocol: The cells were dissociated, filter strain with 40µm, resuspended in the serum free culture medium.

value: glioblastoma cancer stem cells

tag: grade

value: Grade IV

tag: type

value: aneuploid


title: glioblastoma cancer stem cells H09

tag: cell type

tag: cell line


title: glioblastoma cancer stem cells H06


title: glioblastoma cancer stem cells H05


title: glioblastoma cancer stem cells H12


title: glioblastoma cancer stem cells H08


title: ILC2  donor:  779


title: pILC3  donor:  806


title: pILC2  donor:  779


title: pILC3  donor:  807


title: pILC2  donor:  c


title: pILC3  donor:  779


title: glioblastoma cancer stem cells H04


title: glioblastoma cancer stem cells H02


title: glioblastoma cancer stem cells H03


title: T44posILC3  donor:  11

source_name: Tonsil NKp44+ ILC3

value: NKp44+ ILC3

value: Tonsil


title: pILC2  donor:  807


title: pILC2  donor:  806


title: T44negILC3  donor:  11

source_name: Tonsil NKp44- ILC3

value: NKp44- ILC3


title: glioblastoma cancer stem cells G11


title: T44negILC3  donor:  3


title: ILC2  donor:  806


title: T44negILC3  donor:  8


title: ILC2  donor:  807


title: T44posILC3  donor:  8


title: T44posILC3  donor:  3


title: glioblastoma cancer stem cells G10


title: glioblastoma cancer stem cells G08


title: glioblastoma cancer stem cells G07


title: glioblastoma cancer stem cells G05


title: glioblastoma cancer stem cells F11


title: glioblastoma cancer stem cells G02


title: glioblastoma cancer stem cells F12


title: glioblastoma cancer stem cells F10


title: glioblastoma cancer stem cells G03


title: glioblastoma cancer stem cells G06


title: glioblastoma cancer stem cells F05


title: Rice-Shoot-SALT3

first: Liangbo

last: Fu

state: Zhejiang

address: Yuhangtang Road 866

department: college of agriculture and biotechnology

institute: Zhejiang University

data_processing:
The cDNA fragments were amplified and enriched by PCR and purified with adapters ligated at both ends using Illumina TruSeqTM RNA Sample Preparation Kit (Illumina, San Diego, CA).
PCR products were loaded onto Illumina HiSeq2500 platform (Illumina, San Diego, CA) for 2×100 bp pair-ends sequencing.
Raw reads were trimmed by removing adaptor sequences, empty reads and low quality reads (Q<30 and length<50 bp) to get clean data.
Sequence annotation was performed using Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) based on the released reference genome of barley cv. Morex and rice cv. Nipponbare from Ensembl Genomes 2013 (http://plants.ensembl.org/index.html).
Transcript abundance of each gene was normalized by the fragments per kilo-base per million fragments mapped reads (FPKM) method,The ratio of [FPKM (treatment)]/[FPKM (control)] was calculated as the change fold for each gene. Differentially expressed genes (DEGs) were identified by following criterion: fold>2 and false discovery rate (FDR) <0.001. GO annotation and KEGG analysis were done using Blast2GO software version 3.2 (https://www.blast2go.com) based on the sequences of DEGs.
Genome_build: reference genome of barley cv. Morex and rice cv. Nipponbare from Ensembl Genomes 2013 (http://plants.ensembl.org/index.html)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

growth_protocol: Seeds of Tibetan wild barley accession XZ26 and Japonica rice cultivar Nipponbare were disinfected for 30 min with 2% H2O2, rinsed 5 times using distilled water and transferred onto moist filter paper in a germination box, then placed in a growth chamber (22/18 °C, day/night) in dark. After germination, the uniform seedlings of barley and rice were transplanted into 15 L black plastic containers filled with hydroponic solution as described by Fu et al (2018). All seedlings were grown in a controlled growth room at 26 °C of 14 h day/20 °C of 10 h night, with fluorescent lamps at 250 μmol m−2 s−1.

extract_protocol:
After 7 d of salt treatments, fresh roots and the latest completely expanded leaves of barley (XZ26) and rice (Nipponbare) were sampled from both salt treatment and control, and immediately stored in liquid nitrogen for further transcriptomic analysis. Three biological replicates were done. Total RNA was extracted from approximately 0.1 g fresh tissues using the TRIzol Reagent (Invitrogen, Carlsbad, CA), and then was purified by the RNeasy Mini Kit (Qiagen, Germantown, MD). The concentration of total RNA was determined by Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA).
The RNA library construction, sequencing and data processing were performed as described by Wang et al (2016). Briefly, mRNA enrichment was obtained from total RNA by poly-T oligo-attached magnetic beads and randomly fragmented into small pieces. Double-stranded cDNA was synthesized using mRNA fragments with random hexamer-primers. The cDNA fragments were amplified and enriched by PCR and purified with adapters ligated at both ends using Illumina TruSeqTM RNA Sample Preparation Kit (Illumina, San Diego, CA). Then, PCR products were loaded onto Illumina HiSeq2500 platform (Illumina, San Diego, CA) for 2×100 bp pair-ends sequencing. Raw reads were trimmed by removing adaptor sequences, empty reads and low quality reads (Q<30 and length<50 bp) to get clean data. Sequence annotation was performed using Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) based on the released reference genome of barley cv. Morex and rice cv. Nipponbare from Ensembl Genomes 2013 (http://plants.ensembl.org/index.html). For gene expression analysis, transcript abundance of each gene was normalized by the fragments per kilo-base per million fragments mapped reads (FPKM) method (Li et al., 2018). The ratio of [FPKM (treatment)]/[FPKM (control)] was calculated as the change fold for each gene. Differentially expressed genes (DEGs) were identified by following criterion: fold>2 and false discovery rate (FDR) <0.001. GO annotation and KEGG analysis were done using Blast2GO software version 3.2 (https://www.blast2go.com) based on the sequences of DEGs.

treatment_protocol: Salt treatment was initiated to barley and rice plants by increasing 50 mM NaCl a day to reach a final concentration at 100 mM in the hydroponics. The solution without NaCl addition was used as the control.

tag: developmental stage

value: seedling stage

tag: passages

tag: cultivar

value: Nipponbare

value: Shoot

tag: treatment

value: SALT (100 mM NaCl)


title: glioblastoma cancer stem cells F03


title: glioblastoma cancer stem cells F02


title: Rice-Shoot-SALT2


title: Rice-Shoot-SALT1


title: glioblastoma cancer stem cells F08


title: Rice-Shoot-CK2

value: CK (0 mM NaCl)


title: glioblastoma cancer stem cells F07


title: glioblastoma cancer stem cells E07


title: Rice-Shoot-CK1


title: glioblastoma cancer stem cells E08


title: Rice-Root-SALT3

value: Root


title: glioblastoma cancer stem cells G04


title: Rice-Shoot-CK3


title: glioblastoma cancer stem cells E10


title: glioblastoma cancer stem cells E06


title: glioblastoma cancer stem cells E05


title: Rice-Root-SALT1


title: glioblastoma cancer stem cells F09


title: Rice-Root-CK3


title: glioblastoma cancer stem cells E04


title: Rice-Root-CK2


title: Rice-Root-CK1


title: glioblastoma cancer stem cells E11


title: glioblastoma cancer stem cells E01


title: glioblastoma cancer stem cells E02


title: glioblastoma cancer stem cells D11


title: Rice-Root-SALT2


title: glioblastoma cancer stem cells E09


title: rde-4_25C_whole_worm_R3

city: Tel Aviv

first: Itai

middle: Antoine

last: Toker

address: Haim levanon St.

department: Neurobiology

country: Israel

institute: Tel Aviv University

data_processing:
Adapter trimming - cutadapt
Quality examination - fastQC
Alignment - Butter
Filter-20-23 bp
Counting - HTseq_count
Comparisons - DESeq2
Genome_build: WS220/ce10
Supplementary_files_format_and_content: HTseq_count output files

organism: Caenorhabditis elegans

growth_protocol: 20C (or25C when noted), fed on E.coli OP-50 bacteria

extract_protocol:
TRIZOL
NEBNext® Multiplex Small RNA Library Prep Set for Illumina® or TruSeq Small RNA Library Prep Kit, Nextera XT DNA Library Preparation Kit for mRNA

treatment_protocol: Transgenic expression

tag: strain

value: BFF 12

value: Whole animal

tag: temperature


title: F3_Psng-1_rde-4_SC_Whole_Worms_R1

tag: generation

value: F3 of heterozygote BFF16

tag: genotype/variation


title: rde-4_25C_whole_worm_R2


title: F3_Psng-1_rde-4_SC_Whole_Worms_R2


title: glioblastoma cancer stem cells D08


title: glioblastoma cancer stem cells D09


title: glioblastoma cancer stem cells D10


title: N2_25C_whole_worm_R2

source_name: N2 wild-type

value: N2 Bristol Isolate

value: N2 wild-type


title: HC_Prgef-1_rde-4_F3_R2

value: F3 of BFF15


title: N2_25C_whole_worm_R1


title: glioblastoma cancer stem cells D04

value: glioblastoma cancer stem cells

value: Grade IV


title: glioblastoma cancer stem cells D06

value: aneuploid


title: glioblastoma cancer stem cells D03


title: glioblastoma cancer stem cells D05


title: N2_25C_whole_worm_R3


title: glioblastoma cancer stem cells D07


title: glioblastoma cancer stem cells D02


title: HC_Prgef-1_rde-4_F1_R3

value: F1 of BFF15


title: rde-4_25C_whole_worm_R1


title: HC_Prgef-1_rde-4_F3_R1


title: glioblastoma cancer stem cells C12


title: glioblastoma cancer stem cells E03


title: HC_Prgef-1_rde-4_F1_R2


title: HC_Prgef-1_rde-4_P0_R3

value: BFF 15


title: glioblastoma cancer stem cells C09


title: HC_Prgef-1_rde-4_F1_R1


title: glioblastoma cancer stem cells C07


title: HC_Prgef-1_rde-4_P0_R2


title: rde-4_whole_worm_R11


title: HC_Prgef-1_rde-4_P0_R1


title: glioblastoma cancer stem cells D12


title: glioblastoma cancer stem cells C06


title: HC_Prgef-1_rde-4_F3_R3


title: glioblastoma cancer stem cells C05


title: glioblastoma cancer stem cells C11


title: glioblastoma cancer stem cells C04


title: HC_Psng-1_rde-4_P0_R6

value: BFF 14


title: rde-4_whole_worm_R10


title: rde-4_whole_worm_R9


title: rde-4_whole_worm_R8


title: glioblastoma cancer stem cells B08


title: glioblastoma cancer stem cells C01


title: glioblastoma cancer stem cells C03


title: glioblastoma cancer stem cells B09


title: EZH2 inhibitor treated

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
raw data was transformed to raw reads by CASAVA and stored in FASTQ files
adaptor sequences were trimmed and low quality reads containg >10% N were removed
sequence reads were mapped by STAR using a two-step mapping
FPKM (fragments per kilobase of transcript sequence per million basepairs) were calculated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: SUM-149 EZH2 inhibitor treated

growth_protocol: SUM-149 cells were mixed with Matrigel at 1:1 ratio and injected into mammary fat pads of Nu/Nu female mice.

extract_protocol:
Total RNAs were isolated from tumor cells treated with vehicle or CDK2 inhibitor and EZH2 inhibitor by using the RNeasy® Mini Kit (QIAGEN). RNAseq was performed in NOVOGENE (UC Davis)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SUM-149 xenograft mouse model was treated with CDK2 inhibitor (dinaciclib) and EZH2 inhibitor (EPZ6438) for 10 days and tumor tissues were collected.

tag: source cell line

value: breast cancer cell line

tag: sample type

value: xenograft mouse model

value: EZH2 inhibitor (EPZ6438) for 10 days


title: HC_Psng-1_rde-4_P0_R4


title: HC_Psng-1_rde-4_P0_R5


title: glioblastoma cancer stem cells B07


title: rde-4_whole_worm_R7


title: CDK2 inhibitor treated

source_name: SUM-149 CDK2 inhibitor treated

value: CDK2 inhibitor (dinaciclib) for 10 days


title: glioblastoma cancer stem cells B06


title: rde-4_whole_worm_R6


title: glioblastoma cancer stem cells B03


title: Vehicle control

description: Vehicle

source_name: SUM-149 mock treated

value: Vehicle control


title: glioblastoma cancer stem cells B02


title: Psng-1_rde-4_SC_whole_worm_R2

value: BFF 16


title: glioblastoma cancer stem cells B01


title: Psng-1_rde-4_SC_whole_worm_R3

value: Whole animal


title: glioblastoma cancer stem cells A12


title: Psng-1_rde-4_SC_whole_worm_R1


title: glioblastoma cancer stem cells A11


title: N2_whole_worm_R3

value: wild-type


title: rde-4_whole_worm_R2

source_name: rde-4 (ne299) mutant

value: BFF 12

value: rde-4 (ne299) mutant


title: glioblastoma cancer stem cells A07


title: Control_5

city: marseille

first: Amira

last: Ben Amara

address: 27  Boulevard Leï Roue

institute: IHU-CRCM

description: SAMPLE 21

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis, Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours,

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner  G2505C, Image analysis and correction of intra-array signals were performed with the Feature Extraction Software10,7,3,1 (Agilent Technologies),

data_processing: Microarray data analysis was performed using the GeneSpring software, Raw data were filtered and normalized, unsupervised and supervised analyses were done using hierarchical clustering, principal composant analysis (PCA) and the signicantly modulated genes using GeneSpring Software (Agilent Technologies), Genes were considered to be differentially expressed when fold change (FC) was  FC ≥ 2 with p-value (p) was p < 0,001 in at least one of the 3 pair combination. Gene Ontology (GO) annotations attributed to biological processes and corrected p ≤ 0,001 (Bonferroni correction) allow us to identify the biological functions that were modulated,

source_name: Healthy control

label_protocol: In brief, 300 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies

growth_protocol: RNAs were extracted from whole blood (PAXgene tubes, Qiagen, Courtaboeuf, France) with PAXgene kit with a DNase I treatment to eliminate DNA contaminants and according to the recommendations of the manufacturer (Qiagen, Courtaboeuf, France)

extract_protocol: RNA was extracted using an PAXgene kit (Qiagen, Courtaboeuf, France), The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France), The RNA was eluted in 30 µl of water and stored at -80°C,

treatment_protocol: Whole blood prelevment was realized on PAXgene tubes where RNAs extraction were performed

tag: subject status

value: Healthy control

value: Whole blood

tag: sample group id


title: rde-4_whole_worm_R3

tag: tissue


title: N2_whole_worm_R2

value: N2 Bristol Isolate


title: Control_4

description: SAMPLE 20


title: glioblastoma cancer stem cells A06

value: glioblastoma cancer stem cells

tag: grade

value: Grade IV

value: aneuploid


title: Control_2

description: SAMPLE 18


title: PQF_5

description: SAMPLE 13

source_name: Persistent Q fever patient

value: Persistent Q fever


title: PQF_6

description: SAMPLE 14


title: PQF_2

description: SAMPLE 10


title: Control_3

description: SAMPLE 19


title: Control_1

description: SAMPLE 17


title: glioblastoma cancer stem cells A10

tag: type


title: AQF_5

description: SAMPLE 5

source_name: Acute Q Fever patient

value: Acute Q fever


title: rde-4_whole_worm_R1


title: AQF_6

description: SAMPLE 6


title: glioblastoma cancer stem cells A08

tag: cell type


title: N2_whole_worm_R1


title: glioblastoma cancer stem cells A05

tag: cell line


title: PQF_8

description: SAMPLE 16


title: PQF_7

description: SAMPLE 15


title: glioblastoma cancer stem cells A04


title: PQF_3

description: SAMPLE 11


title: PQF_1

description: SAMPLE 9


title: AQF_8

description: SAMPLE 8


title: PQF_4

description: SAMPLE 12


title: AQF_4

description: SAMPLE 4


title: glioblastoma cancer stem cells A03


title: glioblastoma cancer stem cells A02