title: 776DV-tmH3K9-bio-rep-2-tech-rep-1


title: RMB3791

status: Public on Sep 01 2021

type: SRA

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

description: Liver total cells, B6, no treatment

library_source: transcriptomic

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38_M13 from GENCODE using RSEM program version 1.3.0 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program.
TPM (Transcripts Per Million) table were generated by RSEM 1.3.0.
Genome_build: GRCm38_M13
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: liver NPCs

growth_protocol: C57BL/6 were housed in SPF conditions and organs were harvested when mice were 8 wk-old

extract_protocol:
Liver digested by collagenase/DNAse for 30 mins
Smartseq2

treatment_protocol: Cells form 3 mice were independently prepared and pooled before the sorting

tag: sorting

value: sorted alive CD45+ CD3- CD19- CD49b- Ly6G- CD64+ F4/80+ cells

tag: strain

tag: kit

value: Smart Seq -Nextera XT v2

tag: cell type

value: liver macrophages


title: 776DV-mmH3K20-bio-rep-1-tech-rep-2

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

country: USA

institute: University of North Dakota Genomics Core

library_source: genomic

data_processing:
Preliminary quality control analysis of FastQ files was performed using FastQC v.0.11.2.
The three prime adapters were trimmed from the reads using scythe v0.981. Quality trimming was carried out using sickle v1.33.
To remove contaminating cellular reads, reads aligning to African green monkey (Chlorocebus sabeus1.1) or human (hg19) genomes were removed.
Duplicate fragments were removed using the Picard Tools (Broad) Mark Duplicates function.
Bam files were filtered to contain only fragments between 100-150bp using an awk script.
Replicate bam files were merged together using samtools v1.3.1.
Bedgraphs normalized to 1x Coverage were generated from filtered, deduplicated reads using Deeptools v2.5.4.
Genome_build: GCA_000837645.1 (ViralProj14024)
Supplementary_files_format_and_content: *_depthNorm.bedgraph: BedGraphs normalized to 1x Coverage were generated from deduplicated reads using Deeptools v2.5.4.

molecule: genomic DNA

organism: Betapolyomavirus macacae

extract_protocol:
The samples obtained from ChIP analyses were first purified using Zymo Research ChIP DNA Clean and Concentrator columns according to the supplied protocol.
Libraries were prepared using the New England Biolabs Next UltraII kit according to the protocol supplied with the kit with one exception. All reagent volumes were reduced by half for the preparation of libraries with no apparent effect on library quality or quantity.

tag: strain/background

tag: genotype/variation

value: WT

tag: time

tag: virion

value: Yes

tag: gradient

tag: chip antibody


title: RMB3788

description: Liver total cells, B6, no treatment


title: RMB3798

description: Liver total cells, B6, no treatment


title: RMB3792

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K4-bio-rep-2-tech-rep-1

value: No


title: RMB3789

description: Liver total cells, B6, no treatment


title: RMB3780

description: Liver total cells, B6, no treatment


title: RMB3778

description: Liver total cells, B6, no treatment


title: RMB3779

description: Liver total cells, B6, no treatment


title: 776DV-mmH3K9-bio-rep-4-tech-rep-1


title: RMB3776

description: Liver total cells, B6, no treatment


title: RMB3782

description: Liver total cells, B6, no treatment


title: RMB3781

description: Liver total cells, B6, no treatment


title: RMB3787

description: Liver total cells, B6, no treatment


title: 776-48h-tmH3K4-bio-rep-1-tech-rep-1


title: 776DV-HH4-bio-rep-2-tech-rep-1


title: 776-48h-dmH3K4-bio-rep-1-tech-rep-1


title: RMB3783

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-bio-rep-7-tech-rep-1


title: RMB3771

description: Liver total cells, B6, no treatment


title: RMB3772

description: Liver total cells, B6, no treatment


title: 776DV-HH4-bio-rep-1-tech-rep-1


title: RMB3777

description: Liver total cells, B6, no treatment


title: 776-48h-HH3-bio-rep-1-tech-rep-1


title: 776DV-HH3-bio-rep-1-tech-rep-1


title: 776-48h-HH3-bio-rep-1-tech-rep-2


title: RMB3773

description: Liver total cells, B6, no treatment


title: 776DV-HH3-bio-rep-2-tech-rep-1


title: RMB3768

description: Liver total cells, B6, no treatment


title: 776-48h-RNA-P2-bio-rep-1-tech-rep-2


title: 776-48h-dmH3K9-bio-rep-1-tech-rep-1


title: RMB3785

description: Liver total cells, B6, no treatment


title: 776DV-mmH3K9-bio-rep-3-tech-rep-2


title: 776-48h-HH4-bio-rep-1-tech-rep-1


title: 776DV-tmH3K9-bio-rep-1-tech-rep-1


title: RMB3774

description: Liver total cells, B6, no treatment


title: 776-48h-tmH3K9-bio-rep-1-tech-rep-1


title: RMB3775

description: Liver total cells, B6, no treatment


title: RMB3760

description: Liver total cells, B6, no treatment


title: RMB3759

description: Liver total cells, B6, no treatment


title: 776-48h-RNA-P2-bio-rep-1-tech-rep-1


title: 776DV-mmH3K9-bio-rep-2-tech-rep-1


title: 776-48h-mmH3K9-bio-rep-2-tech-rep-1


title: 776-48h-mmH3K9-bio-rep-4-tech-rep-1


title: RMB3763

description: Liver total cells, B6, no treatment


title: RMB3769

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-bio-rep-5-tech-rep-1


title: RMB3758

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-bio-rep-6-tech-rep-1


title: RMB3766

description: Liver total cells, B6, no treatment


title: RMB3757

description: Liver total cells, B6, no treatment


title: RMB3767

description: Liver total cells, B6, no treatment


title: RMB3765

description: Liver total cells, B6, no treatment


title: RMB3762

description: Liver total cells, B6, no treatment


title: RMB3756

description: Liver total cells, B6, no treatment


title: RMB3770

description: Liver total cells, B6, no treatment


title: RMB3764

description: Liver total cells, B6, no treatment


title: 776DV-mmH3K9-bio-rep-3-tech-rep-1


title: fndc-1 KO rep3

city: Rush

first: keith

last: nehrke

state: NY

address: 1514 Rush Scottsville Rd

department: Medicine

institute: University of Rochester Medical Center

description:
F3
Raw_gene_counts_matrix.txt

data_processing:
Data Formatting: bcltofastq-2.19.0
Data Cleaning: Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment: STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1: subread-1.6.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification2: subread-1.6.1, featurecounts, -M -s 2 -t exon -g gene_name
Genome_build: WBcel235
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

organism: Caenorhabditis elegans

source_name: worm

growth_protocol: Non-stress standard conditions.

extract_protocol:
OP50 were removed, using liquid nitrogen to flash freeze samples, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA.

tag: genotype

tag: age

value: 1 day adult

tag: tissue

value: whole worm


title: 776DV-mmH3K9-bio-rep-1-tech-rep-1


title: RMB3753

description: Liver total cells, B6, no treatment


title: RMB3748

description: Liver total cells, B6, no treatment


title: RMB3752

description: Liver total cells, B6, no treatment


title: double KO rep4

description:
AF4
Raw_gene_counts_matrix.txt


title: double KO rep3

description:
AF3
Raw_gene_counts_matrix.txt


title: RMB3747

description: Liver total cells, B6, no treatment


title: 776-48h-mmH3K9-bio-rep-3-tech-rep-1


title: double KO rep1

description:
AF1
Raw_gene_counts_matrix.txt


title: RMB3746

description: Liver total cells, B6, no treatment


title: RMB3761

description: Liver total cells, B6, no treatment


title: N2 rep5

description:
N5
Raw_gene_counts_matrix.txt

value: wild type


title: 776-48h-mmH3K9-bio-rep-1-tech-rep-1


title: RMB3743

description: Liver total cells, B6, no treatment


title: double KO rep5

description:
AF5
Raw_gene_counts_matrix.txt


title: double KO rep2

description:
AF2
Raw_gene_counts_matrix.txt


title: 776-48h-mmH3K4-bio-rep-1-tech-rep-1


title: fndc-1 KO rep2

description:
F2
Raw_gene_counts_matrix.txt


title: RMB3749

description: Liver total cells, B6, no treatment


title: fndc-1 KO rep4

description:
F4
Raw_gene_counts_matrix.txt


title: AtKAI2OE_+KAR2_rep3

city: Toronto

first: Zhenhua

last: Xu

state: ON

address: 25 Willcocks St.

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
illumina RTA2.0 was used to the primary data process including base calling and imaging
Raw reads for each sample was trimmed and filtered using htStream (v1.3.0), including the following commands and parameters:  hts_CutTrim -b 1 | hts_QWindowTrim | hts_NTrimmer | hts_LengthFilter -n -m 25
Splice sites and exons were extracted using HISAT2 (v2.1.0) provided python script, extract_splice_sites.py and extract_exons.py, respectively
hisat2-build was used to build Arabidopsis thalina TAIR10 genome HISAT2 index
Cleam reads were mapped to Arabidopsis thaliana TAIR10 genome using HISAT2 (v2.1.0), with the parameter -p 4 --dta
Unmapped and multi-loci mapped reads were removed using Samtools (v1.10), with the following command:  samtools view -@ 4 -h -F 260 | samtools sort -@ 4
Transcript assemble for each sample was performed using StringTie (v2.1.3) against Arabidopsis thaliana Araport11 annotation with default parameters. Transcriptome assembles from each sample were merged using stringTie --merge
A customized python script, stringtieGeneIdReplace2.py (https://github.com/maplexuci/stringtie_gene_id_replacement) was written to replace the StringTie default 'MSTRG'-tagged gene_id with the TAIR10 gene locus name in order to facilitate the comparisons of genes and transcripts between different samples
A StringTie provided python script, prepDE.py, was used to extract the read counts matrix
R package, DESeq2 (v1.18.1) was used to generate normalized counts and to identify the differentially express genes between various comparisons
Genome_build: TAIR10
Supplementary_files_format_and_content: csv files include normalized read counts for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. File name: Raw_count_matrix.csv

organism: Arabidopsis thaliana

source_name: seed

growth_protocol: Seeds were spreaded on medium under 0.3 µM m-2 s-1 light condition and imbibed in dark at 4˚ C for 4 days, then germinated in the dark at room temperature for 24 hours.

extract_protocol:
Seeds were collected and flash frozen in liquid nitrogen for each treatment with 3 biological replicates. Total RNA were extracted using mini hot phenol RNA extraction protocol (Mylne, J.S. et al. (2011) Nature Chemical Biology 7, 257-259), treated with DNaseI and purified using Monarch® RNA Cleanup Kit
Libraries were constructed using a standard protocol of NEB Ultra II Directional library construction kit.
Stranded Whole-Transcriptome Sequencing

treatment_protocol: Medium contains either 0 or 0.5 μM KAR2 for the corresponding samples.

value: whole seeds

tag: ecotype

value: AtKAI2 overexpression

tag: time point

value: Dark germination for 24 hours

tag: treatment

value: 0.5 μM KAR2


title: N2 rep4

description:
N4
Raw_gene_counts_matrix.txt


title: RMB3739

description: Liver total cells, B6, no treatment


title: AtKAI2OE_+KAR2_rep1


title: AtKAI2OE_control_rep3

value: 0 μM KAR2


title: AtKAI2OE_control_rep2


title: RMB3755

description: Liver total cells, B6, no treatment


title: RMB3737

description: Liver total cells, B6, no treatment


title: RMB3736

description: Liver total cells, B6, no treatment


title: RMB3754

description: Liver total cells, B6, no treatment


title: Ara-1_control_rep3

value: Wile type


title: fndc-1 KO rep1

description:
F1
Raw_gene_counts_matrix.txt


title: fndc-1 KO rep5

description:
F5
Raw_gene_counts_matrix.txt


title: RMB3735

description: Liver total cells, B6, no treatment


title: Ara-1_control_rep2


title: RMB3742

description: Liver total cells, B6, no treatment


title: RMB3745

description: Liver total cells, B6, no treatment


title: RMB3740

description: Liver total cells, B6, no treatment


title: RMB3734

description: Liver total cells, B6, no treatment


title: RMB3750

description: Liver total cells, B6, no treatment


title: RMB3751

description: Liver total cells, B6, no treatment


title: RMB3741

description: Liver total cells, B6, no treatment


title: RMB3738

description: Liver total cells, B6, no treatment


title: N2 rep1

description:
N1
Raw_gene_counts_matrix.txt


title: N2 rep2

description:
N2
Raw_gene_counts_matrix.txt


title: N2 rep3

description:
N3
Raw_gene_counts_matrix.txt


title: RMB3732

description: Liver total cells, B6, no treatment


title: RMB3744

description: Liver total cells, B6, no treatment


title: RMB3729

description: Liver total cells, B6, no treatment


title: WT_vehicle_vehicle_b2_p3_G08

first: Fan

last: Lee

address: 31 Biopolis Way, The NANOS, #06-01

institute: Institute of Bioengineerng and Nanotechnology

description: WT pilot combined FINAL.csv

data_processing:
Data processing was performed by BioSpyder Technologies Inc.
Illumina Casava1.7 software used for base-calling
No filtering was done since aligning to known sequence
Reads were aligned using the STAR aligner 2.5.3a allowing 2 bp mismatches and not allowing indels. The softclipping option is turned on.
The Tempo-SeqR package was used to generate read counts matrix
Genome_build: rn6
Supplementary_files_format_and_content: Read counts matrix (row = treatment; column = gene)

organism: Rattus norvegicus

source_name: liver

growth_protocol: Freshly isolated hepatocytes were maintained in collagen sandwich at 25,000 cells/well in a 96-well plate with William’s medium E containing 1 mg/mL BSA, 0.5 µg/mL insulin, 2 mM L-glutamine, 100 nM dexamethasone, 10 ng/mL EGF, 100 μg/mL streptomycin and 100 U/mL penicillin.

extract_protocol:
After 24 h of chemical treatment, the spent medium was removed and the wells were washed with 100 µL of PBS twice. Cells were lysed by adding 20 µL of 1X TempO-Seq lysis buffer (BioSpyder) in PBS. The cell lysates were shipped frozen on dry ice to to BioSpyder Technologies, Inc. (Carlsbad, CA, USA), where libraries were prepared directly from the cell lysates and RNA-seq was performed.
2 μL of sample lysate was hybridized with detector oligos from the TempO-Seq rat surrogate (ST) or whole-transcriptome (WT) assay, with 1 h hybridization period for the ST assay and overnight for the WT assay. After ligation and nuclease digestion, the ligated products were added into an amplification mix with sample-specific PCR primer pairs which include the standard Illumina adaptor and a sample-specific barcode sequence. Amplicons were pooled and purified using a PCR clean-up kit (Macherey-Nagel, Mountain View, CA, United States).

treatment_protocol: Chemical treatments were performed in culture medium containing 0.5 % DMSO for 24 h.

value: Wistar

tag: gender

value: Male

value: hepatocytes

tag: tempo-seq assay

value: rat whole transcriptome assay

tag: chemical

value: vehicle

tag: dose (um)


title: RMB3731

description: Liver total cells, B6, no treatment

tag: sorting

value: sorted alive CD45+ CD3- CD19- CD49b- Ly6G- CD64+ F4/80+ cells

tag: strain

tag: kit

value: Smart Seq -Nextera XT v2

tag: cell type

value: liver macrophages


title: Ara-1_control_rep1


title: WT_Chloramphenicol_450_b2_p3_G04

description: WT pilot combined FINAL.csv

value: Chloramphenicol


title: RMB3728

description: Liver total cells, B6, no treatment


title: WT_Chloramphenicol_18_b2_p3_G05

description: WT pilot combined FINAL.csv


title: WT_Chloramphenicol_450_b2_p3_G06

description: WT pilot combined FINAL.csv


title: RMB3727

description: Liver total cells, B6, no treatment


title: WT_Chloramphenicol_450_b2_p3_G02

description: WT pilot combined FINAL.csv


title: WT_Chloramphenicol_18_b2_p3_G03

description: WT pilot combined FINAL.csv


title: RMB3723

description: Liver total cells, B6, no treatment


title: RMB3725

description: Liver total cells, B6, no treatment


title: AtKAI2OE_control_rep1


title: WT_vehicle_vehicle_b2_p3_G09

description: WT pilot combined FINAL.csv


title: WT_vehicle_vehicle_b2_p3_F10

description: WT pilot combined FINAL.csv


title: RMB3733

description: Liver total cells, B6, no treatment


title: WT_Chloramphenicol_18_b2_p3_G07

description: WT pilot combined FINAL.csv


title: AtKAI2OE_+KAR2_rep2


title: WT_media_media_b2_p3_G10

description: WT pilot combined FINAL.csv

value: media


title: RMB3730

description: Liver total cells, B6, no treatment


title: WT_media_media_b2_p3_G11

description: WT pilot combined FINAL.csv


title: RMB3724

description: Liver total cells, B6, no treatment


title: RMB3721

description: Liver total cells, B6, no treatment


title: WT_Sulfasalazine_100_b2_p3_F06

description: WT pilot combined FINAL.csv

value: Sulfasalazine


title: RMB3718

description: Liver total cells, B6, no treatment


title: RMB3726

description: Liver total cells, B6, no treatment


title: WT_Sulfasalazine_4_b2_p3_F07

description: WT pilot combined FINAL.csv


title: WT_Indomethacin_12_b2_p3_E07

description: WT pilot combined FINAL.csv

value: Indomethacin


title: WT_Sulfasalazine_4_b2_p3_F03

description: WT pilot combined FINAL.csv


title: RMB3717

description: Liver total cells, B6, no treatment


title: WT_Sulfasalazine_100_b2_p3_F02

description: WT pilot combined FINAL.csv


title: WT_Indomethacin_300_b2_p3_E06

description: WT pilot combined FINAL.csv


title: RMB3722

description: Liver total cells, B6, no treatment


title: RMB3713

description: Liver total cells, B6, no treatment


title: WT_Sulfasalazine_4_b2_p3_F05

description: WT pilot combined FINAL.csv


title: RMB3719

description: Liver total cells, B6, no treatment


title: RMB3720

description: Liver total cells, B6, no treatment


title: cKO - CNP-Cre; TDP-43 homozygous conditional knockout mouse, ID-2748

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

institute: National University of Singapore

data_processing:
Sequenced reads filtered for low quality reads with skewer 0.2.2. (-Q 5)
The RNA-Seq reads were aligned and quantified using Kallisto v.0.44.0 with standard parameters and 100 bootstraps
Sleuth v.0.30.0 was used to quantify abundance
Genome_build: GRCm38 ENSEMBL 94
Supplementary_files_format_and_content: csv file with gene abundance for all samples

source_name: Sciatic Nerve

extract_protocol:
Sciatic nerves were removed from 21-day old mice and flash frozen under liquid nitrogen. The RNA was harvested using Trizol reagent
RNA-Seq libraries were contructed using the Illumina TruSeq Sample Prep Kit

value: Sciatic Nerve

value: M

value: Cnp-Cre; Tardbp-fl/fl

tag: library preparation

value: Illumina TruSeq RNA Sample Prep Kit


title: WT_media_media_b2_p3_F11

description: WT pilot combined FINAL.csv


title: RMB3712

description: Liver total cells, B6, no treatment


title: RMB3715

description: Liver total cells, B6, no treatment


title: RMB3711

description: Liver total cells, B6, no treatment


title: WT_Indomethacin_12_b2_p3_E05

description: WT pilot combined FINAL.csv


title: WT_Sulfasalazine_100_b2_p3_F04

description: WT pilot combined FINAL.csv


title: WT_Indomethacin_12_b2_p3_E03

description: WT pilot combined FINAL.csv


title: RMB3714

description: Liver total cells, B6, no treatment


title: WT_Acetaminophen_10000_b2_p3_D06

description: WT pilot combined FINAL.csv

value: Acetaminophen


title: WT_Acetaminophen_400_b2_p3_D03

description: WT pilot combined FINAL.csv

value: Wistar


title: WT_WY14643_8_b2_p3_C07

description: WT pilot combined FINAL.csv

value: Male


title: Control - TDP-43 floxed mouse, ID-2743

value: F

value: Tardbp-fl/fl


title: WT_Acetaminophen_400_b2_p3_D07

description: WT pilot combined FINAL.csv

value: hepatocytes

value: rat whole transcriptome assay


title: WT_Acetaminophen_10000_b2_p3_D02

description: WT pilot combined FINAL.csv


title: WT_Indomethacin_300_b2_p3_E04

description: WT pilot combined FINAL.csv


title: cHet - CNP-Cre; TDP-43 hemizygous conditional knockout mouse, ID-2742


title: cKO - CNP-Cre; TDP-43 homozygous conditional knockout mouse, ID-2747

value: Cnp-Cre; Tardbp-fl/+


title: RMB3716

description: Liver total cells, B6, no treatment

value: sorted alive CD45+ CD3- CD19- CD49b- Ly6G- CD64+ F4/80+ cells

value: Smart Seq -Nextera XT v2

value: liver macrophages


title: CTX GM, rep1

city: Neuherberg

first: Pawel

last: Smialowski

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Sample 2  replicate 1

data_processing:
RSEM
Genome_build: mm9 USCS 2014
Supplementary_files_format_and_content: RSEM file

source_name: Cerebral cortex grey matter

growth_protocol: Homozygous mice carrying Rpl22HA floxed/floxed were crossed with GlastCreERT2 *eGFP mice to induce selectively Hemaglutinin (HA)-tagged ribosomal protein Rpl22 labelling in astrocytes, .

extract_protocol:
mRNA transcripts were isolated from the tissue as described before (Sanz et al., 2009). RNA purification was performed using RNeasy Micro Kit (Qiagen 74004).
cDNA was prepared from the isolated RNA using Ovation RNA-Seq System v2 (NuGEN 7102).  Amplified cDNA was fragmented and libraries were prepared using IonXpress plus gDNA & Amplificon Library Preparation kit (4471269, 4471252, 4471250). Samples were barcoded during the library preparation with sample specific indices. Equimolar ratio of each sample was then pooled and sequencd on an Ion Proton Sequencer.

treatment_protocol: Recombination was induced by administration of Tamoxifen at the age of 9 weeks, both sexes were used. Tamoxifen (Sigma-Aldrich) was dissolved in corn oil (Sigma-Aldrich) to a final solution concentration of 40 mg ml−1 and delivered by oral gavage three times once every 48 hours (0,4 mg per g of body weight). Material from 3 mice was pooled per replicate: diencephalon (without the region around the third ventricle), cortical grey matter (meninges and white matter removed).

tag: mouse line

value: Slc1a3tm1(cre/ERT2)Mgoe * B6N.129-Rpl22 tm1.1Psam/J * FVB.B6-Tg(CAG-cat,-EGFP)1Rbns/KrnzJ

value: Slc1a3 +/- GFP+ Rpl22HA fl/fl

value: 3 months

value: cortical grey matter

value: astrocytes


title: WT_Indomethacin_300_b2_p3_E02

description: WT pilot combined FINAL.csv

value: Indomethacin


title: WT_Ketoconazole_0.6_b2_p3_B07

description: WT pilot combined FINAL.csv

value: Ketoconazole


title: WT_WY14643_200_b2_p3_C04

description: WT pilot combined FINAL.csv

value: Wistar


title: WT_WY14643_200_b2_p3_C02

description: WT pilot combined FINAL.csv

value: Male


title: cHet - CNP-Cre; TDP-43 hemizygous conditional knockout mouse, ID-2745

value: Sciatic Nerve

value: F

value: Illumina TruSeq RNA Sample Prep Kit


title: cKO - CNP-Cre; TDP-43 homozygous conditional knockout mouse, ID-2744


title: WT_Ketoconazole_15_b2_p3_B06

description: WT pilot combined FINAL.csv

value: hepatocytes

value: rat whole transcriptome assay


title: WT_WY14643_8_b2_p3_C05

description: WT pilot combined FINAL.csv


title: WT_Ketoconazole_0.6_b2_p3_B05

description: WT pilot combined FINAL.csv


title: DIE, rep3

description: Sample 1  replicate 3

source_name: Diencephalon

value: diencephalon


title: WT_Acetaminophen_400_b2_p3_D05

description: WT pilot combined FINAL.csv

value: Acetaminophen


title: iPSC34.3_51_cNT

city: Leuven

first: Kian

middle: Peng

last: Koh

state: Select...

address: Herestraat 49, O&N IV - box 804

country: Belgium

institute: KULeuven

description:
sequencing_3rd batch
biological replicate_2

data_processing:
Illumina Casava2.18 software used for basecalling and demultiplexing
Index-trimmed single-end 50bp reads were aligned to the mouse reference genome (mm10) by using Hisat2 (v2.1.0)
Gene-level read count matrix was summarized from mapped reads by using featureCounts (v1.5.3; http://bioinf.wehi.edu.au/featureCounts/)
Count matrix was imported into the R Bioconductor DESeq2 package (v1.18.1) for differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: text file provide count information

molecule: polyA RNA

source_name: non-targeted iPSC34.3 clonal line

growth_protocol: iPSCs were cultured in KSR for 14 passages and transfected with Cas9 ribonucleoprotein, sgRNA targeting Tet1, and ssODN and treated for 12h with HRD enhancer. Colonies were picked and expanded for 4 passages in KSR medium and expanded on MEFs. iPSCs were removed from feeders and RNA was extracted

extract_protocol:
RNA was purified using TRIzol (Cat.#15596026,Invitrogen) and RNeasy mini kit (Cat#74004, Qiagen).
300 ng of RNA was used for library preparation using the KAPA stranded mRNA-seq kit (Cat#07692193001, Roche) according to the manufacturer’s instructions (V5.17). KAPA single-indexed adapters (Cat#08005699001, Roche) were added to the A-tailed cDNA for library amplification with 14 cycles of PCR. The final library was purified by using Agencourt AMPure XP beads (Cat#A63881, Beckman Coulter) to size select fragments of 200-300 bp.
stranded RNA-seq

tag: Stage

value: Terminal iPSC clonal line at passage 14 + 4

value: wt/wt;GFP/wt

value: male


title: iPSC34.3_52_cNT

description:
sequencing_3rd batch
biological replicate_3

tag: genotype


title: DIE (scRNA-seq)

data_processing:
CellRanger 3.0.2
Genome_build: mm9 USCS 2014
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

growth_protocol: Brains from 9 three months old Aldh1l1-eGFP mice of both sexes were dissected out prior cell isolation.

extract_protocol:
Sorted cells were eluted and resuspended in PBS to reach a final concentration of 1000 cells /µl.
17000 cells were processed using the Single Cell 3’ Reagent Kits V2 from 10x Genomics according to the manufacturer instructions. After GEM generation and barcoding, post GEM-RT cleanup, cDNA amplification and library construction, cDNA was diluted to 5nM in EB buffer. Illumina sequencing libraries were sequenced on one lane with a HiSeq 4000 system (100bp sequencing, 50k row reads per cell) after quality assessment with the Bioanalyzer.

treatment_protocol: Diencephalic astrocytes were isolated by ACSA-2 (Anti-ACSA-2 MicroBead Kit, mouse; Miltenyi Biotec) magnetic associated cell separation as described before (Batiuk et al., 2017).

value: FVB

tag: age

value: 3 months


title: cHet - CNP-Cre; TDP-43 hemizygous conditional knockout mouse, ID-2750

tag: tissue

value: M

value: Cnp-Cre; Tardbp-fl/+


title: iPSC34.3_33_cKO

source_name: TET1 Cas9 KO iPSC34.3 clonal line

value: wt/wt;GFP/wt - Tet1 Cas9 mut/mut


title: WT_Acetaminophen_10000_b2_p3_D04

description: WT pilot combined FINAL.csv

value: Wistar


title: Control - TDP-43 floxed mouse, ID-2746

value: Tardbp-fl/fl


title: CTX GM, rep3

description: Sample 2  replicate 3

value: Slc1a3tm1(cre/ERT2)Mgoe * B6N.129-Rpl22 tm1.1Psam/J * FVB.B6-Tg(CAG-cat,-EGFP)1Rbns/KrnzJ

value: Slc1a3 +/- GFP+ Rpl22HA fl/fl

value: cortical grey matter

value: astrocytes


title: WT_vehicle_vehicle_b2_p2_G09

description: WT pilot combined FINAL.csv

value: Male

value: hepatocytes

value: rat whole transcriptome assay

value: vehicle


title: DIE, rep1

description: Sample 1  replicate 1

value: diencephalon


title: WT_Ranitidine_160_b2_p2_G07

description: WT pilot combined FINAL.csv

value: Ranitidine


title: Control - TDP-43 floxed mouse, ID-2754

value: Sciatic Nerve

value: Illumina TruSeq RNA Sample Prep Kit


title: iPSC27_KO3

data_processing:
Shallow run was performed on 10 samples (~3-fold genome coverage) and eight of them, sample 1 to 8, were sequenced in full depth (total ~20 fold coverage). Bisulfite conversion rates ranged from 98.3-99.3% and oxidation conversion rates from 93.0-95.5% based on internal spike-in controls of the TrueMethyl kit.
Quality trimming of reads included removal of presumed adapter sequences using GenomeScan in-house tool AdapterTrim v2, low complexity trimming according to TrueMethyl kit instructions to eliminate most Adaptase tails, and filtering using QualityTrim v2 to remove bases with phred scores below Q30 and reads shorter than 36 bp (both pairs in paired-end reads). Resulting quality-trimmed reads averaged 129.4 ± 2.3 bp with phred scores 39.1 ± 0.2 (mean ± SD) across all samples.
Read pair duplicates (8.0-15.9%) were removed using the deduplication program provided by Bismark, resulting in final read pairs in the range of 93.3-101.9 million.
Reads were aligned to UCSC mm10 reference sequence using Bismark v0.19.0 with default settings, yielding mapping rates of 61.5-67.8% across all samples. Methylation calls at all covered Cs were extracted with Bismark extraction to calculate global methylation percentages. Methylation levels at individual Cs were calculated by Bismark using thresholds set with a minimum coverage of 10 and a maximum coverage with a percentile of 99, as recommended by the Methylkit package.
Genome_build: mm10

source_name: TET1 KO iPSC clonal line, experiment 2

growth_protocol: 1x105 to 3x106 cells in each reprogramming intermediate fraction ( mCherry+ and mCherry+/GFP+) were sorted. iPSC samples were passaged 6-7 times on feeders in KSR media, then feeder-depleted and harvested for genomic DNA.

extract_protocol:
DNA was isolated by using DNeasy Blood & Tissue Kit (Cat# 69504, Qiagen).
200 ng of DNA was subjected to oxidative bisulfite sequencing (OxBS) by using TrueMethyl Whole Genome kit v3.1 (CEGX) according to the oxBS mode only pipeline. λ-DNA was added to the input as 0.5% of total DNA amount for calculation of BS conversion rates.

value: Terminal iPSC clonal line at passage 6-7

value: mut/mut;GFP/wt

value: male


title: WT_Ranitidine_4000_b2_p2_G06

description: WT pilot combined FINAL.csv

value: Wistar


title: WT_WY14643_8_b2_p3_C03

description: WT pilot combined FINAL.csv


title: DIE, rep2

description: Sample 1  replicate 2

value: 3 months


title: WT_Ranitidine_4000_b2_p2_G04

description: WT pilot combined FINAL.csv


title: 73E6_d0MEF

source_name: Day 0 mouse embryonic fibroblasts

value: B6- Tet1tm1.1Koh x B6;129S4-Pou5f1tm2Jae/J

value: Parental mouse embryonic fibroblast

value: Tg(mCherry)/wt; Tg(GFP)/wt


title: iPSC34.3_14_cKO

description:
sequencing_3rd batch
biological replicate_1

value: Terminal iPSC clonal line at passage 14 + 4

value: wt/wt;GFP/wt - Tet1 Cas9 mut/mut


title: WT_Ranitidine_4000_b2_p2_G02

description: WT pilot combined FINAL.csv

value: Male

value: hepatocytes


title: 65E1_d14ChGFP

source_name: Day 14 naivex2 mCherry+/GFP+

value: B6; 129S4-Tg(Tet1-mCherry)B37Koh x B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J

value: Stage V reprogramming intermediate


title: WT_media_media_b2_p2_F11

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay

value: media


title: CTX GM, rep2

description: Sample 2  replicate 2

value: Slc1a3tm1(cre/ERT2)Mgoe * B6N.129-Rpl22 tm1.1Psam/J * FVB.B6-Tg(CAG-cat,-EGFP)1Rbns/KrnzJ

value: Slc1a3 +/- GFP+ Rpl22HA fl/fl

value: cortical grey matter

value: astrocytes


title: 73E8_d10ChGFP

source_name: Day 10 totalx2 mCherry+/GFP+

value: Stage II reprogramming intermediate

value: male


title: 65E1_d12Ch

source_name: Day 12 naivex2 mCherry+/GFP-

value: Stage III reprogramming intermediate


title: iPSC34_KO7

source_name: TET1 KO iPSC clonal line, experiment 1

value: Terminal iPSC clonal line at passage 6-7

value: mut/mut;GFP/wt


title: iPSC34.3_49_cNT

value: Terminal iPSC clonal line at passage 14 + 4

value: wt/wt;GFP/wt


title: 73E8_d10Ch

source_name: Day 10 totalx2 mCherry+/GFP-

value: B6- Tet1tm1.1Koh x B6;129S4-Pou5f1tm2Jae/J

value: Stage I reprogramming intermediate

value: Tg(mCherry)/wt; Tg(GFP)/wt


title: WT_WY14643_200_b2_p3_C06

description: WT pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes


title: WT_Ketoconazole_15_b2_p3_B04

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay

value: Ketoconazole


title: WT_media_media_b2_p2_G10

description: WT pilot combined FINAL.csv

value: media


title: WT_Ketoconazole_15_b2_p3_B02

description: WT pilot combined FINAL.csv


title: iPSC34_WT1

source_name: wild-type iPSC clonal line, experiment 1


title: WT_Ranitidine_160_b2_p2_G03

description: WT pilot combined FINAL.csv

value: Ranitidine


title: iPSC27_WT5

source_name: wild-type iPSC clonal line, experiment 2


title: iPSC34.3_30_cKO

value: wt/wt;GFP/wt - Tet1 Cas9 mut/mut


title: ATAC-seq_Melanoma_p14_WT_119-2_1

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
ATAC-seq of mouse melanoma cell, clone 119, biological replicate 2.
processed data file: melanoma_stat3_peaks.raw_coverage.csv

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences.
Reads were mapped to mm10 genome using bowtie2 v2.2.4 with the –very-sensitive parameter.
Duplicate reads were marked and removed with picard tools version 1.118.
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair created.
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair.
Supplementary_files_format_and_content: narrowPeak files contain peaks called by MACS2.
Supplementary_files_format_and_content: melanoma_stat3_peaks.raw_coverage.csv: Comma-separated text file with raw read counts per sample per regulatory element.

source_name: Melanoma cell line

growth_protocol: Mouse melanoma cell lines were established from primary lymph node single cell suspensions from diseased mice with cutaneous melanoma onset around 25-30 weeks of age. Multiple individual primary pools of cell lines per Stat3fl and Stat3∆ melanoma cell genotype were generated, upon which we selected two pools each for further detailed analysis.

extract_protocol:
Duplicates of two different STAT3fl and STAT3∆ cell lines were used for the assay. A volume containing 50.000 cells were harvested with the aid of an automated cell counter (TC20 Bio-Rad) and spun at 500g for 5 minutes at 4°C in PBS.
After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 µl 2xTD buffer, 2 µl TDE1 (Illumina), and 10.25 µl nuclease-free water, 0.25 µl 1% Digitonin (Sigma)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 12 µl, 1 µl of the eluted DNA was used in a quantitative PCR reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA and concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers.

value: Melanoma cell line

tag: genotype/variation

value: Wild type

tag: clone

tag: biological replicate


title: WT_Caffeine_10000_b2_p2_F04

description: WT pilot combined FINAL.csv

tag: gender

value: Caffeine


title: ATAC-seq_Melanoma_p68_WT_73-1_1

description:
ATAC-seq of mouse melanoma cell, clone 73, biological replicate 1.
processed data file: melanoma_stat3_peaks.raw_coverage.csv


title: ATAC-seq_Melanoma_p44_STAT3_KO_113-2_1

description:
ATAC-seq of mouse melanoma cell with STAT3 knockout, clone 113, biological replicate 2.
processed data file: melanoma_stat3_peaks.raw_coverage.csv

value: STAT3 knockout


title: WT_Ketoconazole_0.6_b2_p3_B03

description: WT pilot combined FINAL.csv

tag: tempo-seq assay


title: WT_Doxorubicin_0.08_b2_p2_F09

description: WT pilot combined FINAL.csv

tag: chemical

value: Doxorubicin


title: ATAC-seq_Melanoma_p68_WT_73-2_1

description:
ATAC-seq of mouse melanoma cell, clone 73, biological replicate 2.
processed data file: melanoma_stat3_peaks.raw_coverage.csv


title: WT_Ranitidine_160_b2_p2_G05

description: WT pilot combined FINAL.csv

tag: dose (um)


title: 65E1_d12ChGFP

source_name: Day 12 naivex2 mCherry+/GFP+

value: B6; 129S4-Tg(Tet1-mCherry)B37Koh x B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J

value: Stage IV reprogramming intermediate

value: male


title: WT_Caffeine_10000_b2_p2_F06

description: WT pilot combined FINAL.csv

source_name: liver


title: WT_Caffeine_400_b2_p2_F07

description: WT pilot combined FINAL.csv


title: WT_Doxorubicin_2_b2_p2_F08

description: WT pilot combined FINAL.csv


title: ATAC-seq_Melanoma_p44_STAT3_KO_113-1_1

description:
ATAC-seq of mouse melanoma cell with STAT3 knockout, clone 113, biological replicate 1.
processed data file: melanoma_stat3_peaks.raw_coverage.csv


title: WT_Doxorubicin_0.08_b2_p2_E11

description: WT pilot combined FINAL.csv


title: WT_media_media_b2_p2_G11

description: WT pilot combined FINAL.csv


title: ATAC-seq_Melanoma_p18_STAT3_KO_112-2_1

description:
ATAC-seq of mouse melanoma cell with STAT3 knockout, clone 112, biological replicate 2.
processed data file: melanoma_stat3_peaks.raw_coverage.csv


title: ATAC-seq_Melanoma_p14_WT_119-1_1

description:
ATAC-seq of mouse melanoma cell, clone 119, biological replicate 1.
processed data file: melanoma_stat3_peaks.raw_coverage.csv


title: ATAC-seq_Melanoma_p18_STAT3_KO_112-1_1

description:
ATAC-seq of mouse melanoma cell with STAT3 knockout, clone 112, biological replicate 1.
processed data file: melanoma_stat3_peaks.raw_coverage.csv


title: WT_Caffeine_400_b2_p2_F03

description: WT pilot combined FINAL.csv


title: WT_Doxorubicin_2_b2_p2_E10

description: WT pilot combined FINAL.csv


title: WT_Caffeine_400_b2_p2_F05

description: WT pilot combined FINAL.csv


title: WT_Caffeine_10000_b2_p2_F02

description: WT pilot combined FINAL.csv


title: WT_Doxorubicin_0.08_b2_p2_E09

description: WT pilot combined FINAL.csv


title: WT_vehicle_vehicle_b2_p2_F10

description: WT pilot combined FINAL.csv

value: vehicle


title: WT_Doxorubicin_2_b2_p2_E08

description: WT pilot combined FINAL.csv

value: Wistar


title: WT_Diclofenac_16_b2_p2_E07

description: WT pilot combined FINAL.csv

value: Male

value: Diclofenac


title: WT_vehicle_vehicle_b2_p2_G08

description: WT pilot combined FINAL.csv

value: hepatocytes

value: rat whole transcriptome assay


title: WT_Diclofenac_400_b2_p2_E06

description: WT pilot combined FINAL.csv


title: WT_Diclofenac_16_b2_p2_E05

description: WT pilot combined FINAL.csv


title: WT_Diclofenac_16_b2_p2_E03

description: WT pilot combined FINAL.csv


title: WT_Diclofenac_400_b2_p2_E04

description: WT pilot combined FINAL.csv


title: WT_Simvastatin_2.4_b2_p2_D11

description: WT pilot combined FINAL.csv

value: Simvastatin


title: WT_Simvastatin_2.4_b2_p2_D09

description: WT pilot combined FINAL.csv


title: WT_Simvastatin_60_b2_p2_D10

description: WT pilot combined FINAL.csv


title: WT_Diclofenac_400_b2_p2_E02

description: WT pilot combined FINAL.csv


title: mRNA expression

city: Nanjing

first: Yan

last: Zeng

address: No.1, Weigang

country: China

institute: Nanjing Agricultural University

data_processing:
Basecalls performed using CASAVA.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome using HISAT2. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
BLASTN was used to compare reads with the sRNA, tRNA, snRNA and snoRNA of rfam database (Nawrocki et al., Nucleic Acids Research, 2015). Mirdeep2 was used to compare miRNA with reference genome, identify new miRNA and analyze miRNA expression.
Genome_build: reference sequence used for read alignment.
Supplementary_files_format_and_content: tab-delimited text files include FPKM or RPM values for each Sample.

organism: Drosophila melanogaster

source_name: adult

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: sample type

value: mRNA


title: miRNA expression

value: miRNA


title: WT_Valproic_400_b2_p2_D07

description: WT pilot combined FINAL.csv

tag: strain

value: Valproic


title: WT_Simvastatin_60_b2_p2_D08

description: WT pilot combined FINAL.csv


title: WT_Valproic_10000_b2_p2_D06

description: WT pilot combined FINAL.csv


title: Shoot Est Rep3 [CLE3]

type: RNA

city: Tokyo

first: Dichao

last: Ma

address: 1-1-1 Yayoi, Bunkyo-ku

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

description: Gene expression data from shoots of estradiol inducible CLE3 overexpressing Arabidopsis that roots were treated with estradiol

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

label: bintin

source_name: Estradiol inducible CLE3 overexpressing Arabidopsis that roots were treated with DMSO

label_protocol: Sense-strand DNA target preparation was performed in combination with Ambion WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix).

growth_protocol: Surface sterilized Arabidopsis seeds were sown on half Murashige and Skoog medium and vertically cultured at 22°C under continuous white light (25–30 μmol m−2 s-−1) for 7 days.

extract_protocol: Total RNAs used in transcriptional analyses were prepared using RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: Roots of 7-day-old estradiol inducible CLE3 overexpressing plants were treated with 5 mM β-estradiol for 24 h. After the 24-h induction, roots and shoots of plants were sampled separately and used for microarray analysis.

value: Shoots

value: 7-day-old seedlings


title: Shoot DMSO Rep2 [CLE3]

description: Gene expression data from shoots of estradiol inducible CLE3 overexpressing Arabidopsis that roots were treated with DMSO


title: Shoot Est Rep2 [CLE3]


title: WT_Valproic_10000_b2_p2_D02

description: WT pilot combined FINAL.csv


title: Root Est Rep2 [CLE3]

description: Gene expression data from roots of estradiol inducible CLE3 overexpressing Arabidopsis that roots were treated with estradiol

source_name: Estradiol inducible CLE3 overexpressing Arabidopsis that roots were treated with estradiol

value: Roots


title: Root DMSO Rep1 [CLE3]

description: Gene expression data from roots of estradiol inducible CLE3 overexpressing Arabidopsis that roots were treated with DMSO


title: WT_Simvastatin_2.4_b2_p2_C11

description: WT pilot combined FINAL.csv


title: Root Est Rep1 [CLE3]


title: Root DMSO Rep3 [CLE3]


title: Shoot DMSO Rep1 [CLE3]


title: Root Est Rep3 [CLE3]


title: Shoot DMSO Rep3 [CLE3]


title: WT_Naproxen_80_b2_p2_C09

description: WT pilot combined FINAL.csv

value: Naproxen


title: WT_Simvastatin_60_b2_p2_C10

description: WT pilot combined FINAL.csv


title: WT_Naproxen_2000_b2_p2_C08

description: WT pilot combined FINAL.csv


title: WT_Isoniazid_400_b2_p2_C07

description: WT pilot combined FINAL.csv

value: Isoniazid


title: Root DMSO Rep2 [CLE3]


title: WT_Valproic_400_b2_p2_D05

description: WT pilot combined FINAL.csv


title: Shoot Est Rep1 [CLE3]


title: WT_Isoniazid_400_b2_p2_C05

description: WT pilot combined FINAL.csv


title: WT_Isoniazid_400_b2_p2_C03

description: WT pilot combined FINAL.csv


title: WT_Isoniazid_10000_b2_p2_C04

description: WT pilot combined FINAL.csv


title: WT_Naproxen_80_b2_p2_B11

description: WT pilot combined FINAL.csv


title: WT_Naproxen_80_b2_p2_B09

description: WT pilot combined FINAL.csv


title: WT_Naproxen_2000_b2_p2_B08

description: WT pilot combined FINAL.csv


title: WT_Isoniazid_10000_b2_p2_C02

description: WT pilot combined FINAL.csv


title: WT_Naproxen_2000_b2_p2_B10

description: WT pilot combined FINAL.csv


title: WT_Valproic_10000_b2_p2_D04

description: WT pilot combined FINAL.csv


title: WT_Valproic_400_b2_p2_D03

description: WT pilot combined FINAL.csv


title: ST_media_media_b2_p3_G11

description: ST pilot combined FINAL.csv

value: S1500+ rat surrogate assay

value: media


title: ST_vehicle_vehicle_b2_p3_G09

description: ST pilot combined FINAL.csv

value: vehicle


title: ST_media_media_b2_p3_G10

description: ST pilot combined FINAL.csv

value: Wistar


title: ST_vehicle_vehicle_b2_p3_G08

description: ST pilot combined FINAL.csv

value: Male


title: ST_Chloramphenicol_18_b2_p3_G07

description: ST pilot combined FINAL.csv

value: Chloramphenicol


title: whole blood_Healthy_70

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to transcriptome GRCh38 version using salmon
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample and Matrix table with raw mRNA counts for every mRNA and every sample

organism: Homo sapiens

source_name: whole blood

extract_protocol:
RNA was isolated using the miRNeasy Serum/Plasma Advanced Kit (50) (cat# 217204) according to the manufacturers’ recommendation (QIAGEN).
The library preparation was done using the QIAseq RNA Library Kit (QIAGEN). A total of 5ul total RNA was converted into RNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR, the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

tag: tb-status

value: not TB

tag: hiv status

value: not infected

tag: pregnancy status

value: not pregnant not postpartum


title: whole blood_Healthy_73


title: WT_Isoniazid_10000_b2_p2_C06

description: WT pilot combined FINAL.csv

tag: cell type

value: hepatocytes

value: rat whole transcriptome assay


title: ST_Chloramphenicol_450_b2_p3_G06

description: ST pilot combined FINAL.csv


title: ST_Chloramphenicol_18_b2_p3_G05

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_71


title: whole blood_Healthy_72


title: ST_Chloramphenicol_450_b2_p3_G04

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_68


title: ST_Sulfasalazine_4_b2_p3_F07

description: ST pilot combined FINAL.csv

value: Sulfasalazine


title: ST_Chloramphenicol_450_b2_p3_G02

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_69


title: ST_Sulfasalazine_100_b2_p3_F06

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_67


title: whole blood_Healthy_66


title: whole blood_Healthy_65


title: ST_media_media_b2_p3_F11

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_64


title: whole blood_Healthy_62


title: ST_Sulfasalazine_100_b2_p3_F04

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_63


title: ST_vehicle_vehicle_b2_p3_F10

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_61


title: ST_Sulfasalazine_4_b2_p3_F03

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_59


title: ST_Sulfasalazine_100_b2_p3_F02

description: ST pilot combined FINAL.csv


title: ST_Chloramphenicol_18_b2_p3_G03

description: ST pilot combined FINAL.csv


title: ST_Indomethacin_12_b2_p3_E07

description: ST pilot combined FINAL.csv

value: Indomethacin


title: ST_Indomethacin_300_b2_p3_E04

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_58


title: ST_Indomethacin_12_b2_p3_E05

description: ST pilot combined FINAL.csv


title: whole blood_Healthy_60


title: whole blood_Postpartum_TB_56

value: TB infected

value: HIV infected

value: Postpartum


title: whole blood_Postpartum_TB_53


title: ST_Indomethacin_300_b2_p3_E02

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_TB_55

value: Pregnant


title: ST_Acetaminophen_400_b2_p3_D07

description: ST pilot combined FINAL.csv

value: S1500+ rat surrogate assay

value: Acetaminophen


title: whole blood_Pregnant_TB_52


title: whole blood_Pregnant_control_54


title: whole blood_Postpartum_TB_51


title: ST_Acetaminophen_10000_b2_p3_D04

description: ST pilot combined FINAL.csv


title: ST_Indomethacin_12_b2_p3_E03

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_49


title: ST_WY14643_8_b2_p3_C07

description: ST pilot combined FINAL.csv


title: ST_Sulfasalazine_4_b2_p3_F05

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_TB_48


title: ST_Acetaminophen_400_b2_p3_D05

description: ST pilot combined FINAL.csv


title: ST_Acetaminophen_10000_b2_p3_D02

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_TB_45


title: whole blood_Pregnant_TB_47


title: whole blood_Healthy_57


title: ST_WY14643_200_b2_p3_C06

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_43


title: ST_WY14643_200_b2_p3_C04

description: ST pilot combined FINAL.csv


title: ST_WY14643_8_b2_p3_C05

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_44


title: ST_WY14643_8_b2_p3_C03

description: ST pilot combined FINAL.csv


title: ST_Acetaminophen_10000_b2_p3_D06

description: ST pilot combined FINAL.csv


title: ST_Indomethacin_300_b2_p3_E06

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_TB_50


title: whole blood_Postpartum_TB_41


title: whole blood_Pregnant_control_42


title: ST_WY14643_200_b2_p3_C02

description: ST pilot combined FINAL.csv


title: ST_Acetaminophen_400_b2_p3_D03

description: ST pilot combined FINAL.csv


title: ST_Ketoconazole_15_b2_p3_B06

description: ST pilot combined FINAL.csv

value: Ketoconazole


title: whole blood_Pregnant_TB_40


title: whole blood_Pregnant_TB_37


title: ST_media_media_b2_p2_G11

description: ST pilot combined FINAL.csv

value: Wistar

value: media


title: whole blood_Postpartum_TB_36


title: whole blood_Pregnant_control_39


title: ST_Ketoconazole_15_b2_p3_B04

description: ST pilot combined FINAL.csv

value: Male


title: whole blood_Postpartum_TB_38


title: ST_Ketoconazole_0.6_b2_p3_B03

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_TB_35


title: ST_Ketoconazole_15_b2_p3_B02

description: ST pilot combined FINAL.csv


title: ST_media_media_b2_p2_G10

description: ST pilot combined FINAL.csv


title: ST_Ketoconazole_0.6_b2_p3_B07

description: ST pilot combined FINAL.csv


title: ST_vehicle_vehicle_b2_p2_G09

description: ST pilot combined FINAL.csv

value: vehicle


title: whole blood_Pregnant_control_46

value: not TB


title: whole blood_Postpartum_control_33


title: whole blood_Pregnant_control_32


title: ST_Ketoconazole_0.6_b2_p3_B05

description: ST pilot combined FINAL.csv


title: ST_Ranitidine_160_b2_p2_G05

description: ST pilot combined FINAL.csv

value: Ranitidine


title: whole blood_Pregnant_control_30


title: ST_Ranitidine_4000_b2_p2_G06

description: ST pilot combined FINAL.csv

value: hepatocytes


title: ST_Ranitidine_160_b2_p2_G07

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_control_29


title: whole blood_Postpartum_control_31


title: ST_Ranitidine_4000_b2_p2_G04

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_28


title: ST_Ranitidine_160_b2_p2_G03

description: ST pilot combined FINAL.csv


title: ST_Ranitidine_4000_b2_p2_G02

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_26


title: ST_media_media_b2_p2_F11

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_control_27


title: ST_Doxorubicin_0.08_b2_p2_F09

description: ST pilot combined FINAL.csv

value: Doxorubicin


title: ST_vehicle_vehicle_b2_p2_F10

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_24


title: whole blood_Postpartum_control_23


title: whole blood_Pregnant_control_22


title: ST_Caffeine_400_b2_p2_F07

description: ST pilot combined FINAL.csv

value: Caffeine


title: whole blood_Pregnant_control_34


title: ST_Doxorubicin_2_b2_p2_F08

description: ST pilot combined FINAL.csv


title: ST_vehicle_vehicle_b2_p2_G08

description: ST pilot combined FINAL.csv


title: ST_Caffeine_10000_b2_p2_F06

description: ST pilot combined FINAL.csv


title: ST_Caffeine_10000_b2_p2_F04

description: ST pilot combined FINAL.csv


title: ST_Caffeine_400_b2_p2_F05

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_control_19


title: whole blood_Pregnant_control_20


title: ST_Caffeine_400_b2_p2_F03

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_18


title: ST_Doxorubicin_0.08_b2_p2_E11

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_16


title: whole blood_Postpartum_control_17


title: ST_Doxorubicin_2_b2_p2_E10

description: ST pilot combined FINAL.csv


title: ST_Caffeine_10000_b2_p2_F02

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_control_15


title: whole blood_Postpartum_control_25


title: ST_Doxorubicin_0.08_b2_p2_E09

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_control_11


title: whole blood_Pregnant_control_12


title: ST_Diclofenac_400_b2_p2_E06

description: ST pilot combined FINAL.csv

value: Diclofenac


title: ST_Doxorubicin_2_b2_p2_E08

description: ST pilot combined FINAL.csv


title: ST_Diclofenac_16_b2_p2_E07

description: ST pilot combined FINAL.csv


title: whole blood_Pregnant_control_10


title: ST_Diclofenac_16_b2_p2_E05

description: ST pilot combined FINAL.csv


title: ST_Diclofenac_400_b2_p2_E04

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_control_21


title: whole blood_Pregnant_control_8


title: whole blood_Pregnant_control_7


title: whole blood_Pregnant_control_6


title: whole blood_Pregnant_control_14


title: ST_Diclofenac_400_b2_p2_E02

description: ST pilot combined FINAL.csv


title: ST_Simvastatin_60_b2_p2_D10

description: ST pilot combined FINAL.csv

value: Simvastatin


title: whole blood_Postpartum_control_13

value: HIV infected


title: whole blood_Postpartum_control_5

value: Postpartum


title: ST_Simvastatin_2.4_b2_p2_D11

description: ST pilot combined FINAL.csv


title: ST_Simvastatin_2.4_b2_p2_D09

description: ST pilot combined FINAL.csv


title: whole blood_Postpartum_control_3


title: whole blood_Pregnant_control_4

value: Pregnant


title: ST_Simvastatin_60_b2_p2_D08

description: ST pilot combined FINAL.csv

value: S1500+ rat surrogate assay


title: whole blood_Pregnant_control_1


title: ST_Diclofenac_16_b2_p2_E03

description: ST pilot combined FINAL.csv


title: ST_Valproic_10000_b2_p2_D06

description: ST pilot combined FINAL.csv

value: Valproic


title: whole blood_Postpartum_control_9


title: ST_Valproic_10000_b2_p2_D02

description: ST pilot combined FINAL.csv


title: ICH9-A

city: Tianjin

first: Qiang

last: Liu

state: Tianjin

address: No.154 Anshan Road, Heping District

department: Neurology

institute: Tianjin Medical University General Hospital

description: Peri-hematomal edema tissue collected 6h after intracerebral hemorrhage.

data_processing:
For data quality control, the sequencing data was filtered with SOAPnuke (v1.5.2)(43) by: 1) Removing reads containing sequencing adapter; 2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; 3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome (the Human Genome 19) using HISAT2 (v2.0.4).
The clean reads were assembled separately using the Trinity method for each library. Gene expression were measured by counting the number of reads for each gene and were normalized to Reads Per Kilobase of transcript per Million mapped reads (FPKM). To compare gene expression variation between two samples, an analysis method based on Poisson distribution was used as previously reported (45) and the false discovery rate (FDR) was preset as less than 0.05 at the beginning of the statistics. Except gene’s FDR value, we also calculated the fold changes in gene expression between samples based on their FPKM value. The smaller the FDR value and (or) the greater the multiple of difference, which indicates that the expression difference of the gene is more significant. In our analysis, differentially expressed genes (DEGs) between two samples are defined as genes with FDR ≤ 0.001 and the fold difference is more than 2 times.
To take insight to the change of brain phenotype, gene ontology (GO) analysis was performed at https://david.ncifcrf.gov/ after loading DEGs list between two groups. Gene ontology terms with Benjamini and Hochberg (BH) corrected p-value < 0.05 were considered significant.
Genome_build: Gene identity was determined by alignment against the Human Genome 19 Reference.
Supplementary_files_format_and_content: All_Gene_FPKM_of_ICH9-A.xls: Excel file includes FPKM values for each gene in sample.

source_name: Brain tissue

extract_protocol:
The total RNA of peri-hematomal tissues from 11 patient with ICH was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s protocol and RNA integrity was measured. Magnetic beads with Oligo (dT) are used to isolate mRNA (for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). 1-5 μg of total RNA was removed ribosomal RNA. The quality of RNA (ribosomal RNA 28s:18s > 1.7) for brain tissue was performed the further transcriptome analysis. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments.
cDNA is synthesized using the mRNA fragments as templates. Strand-specific RNA-seq data was generated. During the QC steps, Agilent 2100 Bioanalyzer and Applied Biosystems StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.
Library preparation was established using the Illumina TruSeq Stranded kit and sequenced on an Illumina Hiseq 4000 sequencer. Libraries were barcoded and sequenced in one lane, thus avoiding lane effects, to obtain 100 bp paired end reads. An average of 30 million reads were obtained for each sample.

treatment_protocol: The peri-hematomal brain tissue adherent to removed clot from ICH patients undergoing hemorrhage evacuation during craniotomy surgery was carefully isolated and immediately put and maintained in ice-cold saline prior to transportation and further operations. Rinsed of blood was performed with ice-cold saline and verified under microscope. The tissue was stored in frozen liquid nitrogen and the process from tissue isolation to freezing is less than 1 hour for each sample. The typical size of micro-dissected brain parenchyma was 100-200 mg for RNA sequencing assay.

tag: diagnosis

value: Intracerebral hemorrhage

value: Peri-hematomal tissue from basal ganglia areas

value: 48 years


title: BL12, BL12 (TCR-seq)

city: Stanford

first: Bomi

address: 1291 Welch Road

institute: Stanford University

description:
TCR-seq library: BL12
Single cells
BL12_filtered_contig_annotations.csv

data_processing:
Library strategy: TCR-seq
cellranger 4.0 count function to generate count matrix
Genome_build: hg38
Supplementary_files_format_and_content:
Feature Barcode Matrix Format is HDF5 format which used as the top level for matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
annotation csv file contains one contig, consensus, or clonotype per row

source_name: Pancreas

growth_protocol: Pancreatic immune cells were isolated from fresh pancreatic tissues of donors or patients who underwent total pancreatectomy within 24-36 hours. There was no growth process.

extract_protocol:
To enrich immune cells from human pancreatic tissues, pancreatic tissues were enzymically digested as described in the previous study. After removing red blood cells with RBC lysis buffer (Sigma, R7757), the recovered cells were then washed again with RPMI buffer that contained 10% BCS and suspended in the recovery cell culture freezing medium (Gibco, #12648-010) to be stored in -80 ºC freezer and liquid nitrogen. To isolate pure leukocytes for the single-cell sequencing analyses, the frozen single cells were thawed and washed twice with RPMI containing 10% FBS. The recovered cells were resuspended in HBSS containing 2% BCS and stained with Live/Dead marker (BioLegend, Zombie Aqua, #423102) and anti-CD45 antibody (BioLegend, PerCP-Cy5.5, #304028) for FACS.
Library generation for feature barcoding, gene expression, and V(D)J TCRs was performed using the 10x Chromium Single Cell reagent kits. Following library generation, sequencing was performed on an Illumina HiSeq 4000 (2 x75bp).

treatment_protocol: Isolated cells were frozen and stored in -80 degree and liquid nitrigen. Thawed single cells were sorted for live CD45+ cells and underwent feature antibody staining and single cell sequencing procedure. There was no specific treatment or stimulation to cells.

tag: disease

value: Chronic pancreatitis (Idiopathic)

tag: genetic mutations

value: Female

value: Pancreas

value: Immune cells


title: ST_Valproic_10000_b2_p2_D04

description: ST pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes


title: ST_Valproic_400_b2_p2_D05

description: ST pilot combined FINAL.csv


title: ICH6-A

description: Peri-hematomal edema tissue collected 5h after intracerebral hemorrhage.

data_processing:
For data quality control, the sequencing data was filtered with SOAPnuke (v1.5.2)(43) by: 1) Removing reads containing sequencing adapter; 2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; 3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome (the Human Genome 19) using HISAT2 (v2.0.4).
The clean reads were assembled separately using the Trinity method for each library. Gene expression were measured by counting the number of reads for each gene and were normalized to Reads Per Kilobase of transcript per Million mapped reads (FPKM). To compare gene expression variation between two samples, an analysis method based on Poisson distribution was used as previously reported (45) and the false discovery rate (FDR) was preset as less than 0.05 at the beginning of the statistics. Except gene’s FDR value, we also calculated the fold changes in gene expression between samples based on their FPKM value. The smaller the FDR value and (or) the greater the multiple of difference, which indicates that the expression difference of the gene is more significant. In our analysis, differentially expressed genes (DEGs) between two samples are defined as genes with FDR ≤ 0.001 and the fold difference is more than 2 times.
To take insight to the change of brain phenotype, gene ontology (GO) analysis was performed at https://david.ncifcrf.gov/ after loading DEGs list between two groups. Gene ontology terms with Benjamini and Hochberg (BH) corrected p-value < 0.05 were considered significant.
Genome_build: Gene identity was determined by alignment against the Human Genome 19 Reference.
Supplementary_files_format_and_content: Gene_FPKM_of_ICH6-A.xls: Excel file includes FPKM values for each gene in sample.

tag: tissue

tag: age

value: 56 years


title: whole blood_Pregnant_control_2

value: not TB


title: BL11, BL11 (TCR-seq)

description:
TCR-seq library: BL11
Single cells
BL11_filtered_contig_annotations.csv


title: ST_Simvastatin_2.4_b2_p2_C11

description: ST pilot combined FINAL.csv

value: Simvastatin


title: BL10, BL10 (TCR-seq)

description:
TCR-seq library: BL10
Single cells
BL10_filtered_contig_annotations.csv


title: ST_Valproic_400_b2_p2_D03

description: ST pilot combined FINAL.csv


title: BL8, BL8 (TCR-seq)

description:
TCR-seq library: BL8
Single cells
BL8_filtered_contig_annotations.csv


title: BL9, BL9 (TCR-seq)

description:
TCR-seq library: BL9
Single cells
BL9_filtered_contig_annotations.csv


title: ST_Naproxen_80_b2_p2_C09

description: ST pilot combined FINAL.csv

value: Naproxen


title: ST_Simvastatin_60_b2_p2_C10

description: ST pilot combined FINAL.csv


title: BL7, BL7 (TCR-seq)

description:
TCR-seq library: BL7
Single cells
BL7_filtered_contig_annotations.csv


title: ST_Naproxen_2000_b2_p2_C08

description: ST pilot combined FINAL.csv


title: ST_Isoniazid_400_b2_p2_C07

description: ST pilot combined FINAL.csv

value: Isoniazid


title: ST_Isoniazid_10000_b2_p2_C06

description: ST pilot combined FINAL.csv

value: S1500+ rat surrogate assay


title: ST_Valproic_400_b2_p2_D07

description: ST pilot combined FINAL.csv

value: Valproic


title: BL4, BL4 (TCR-seq)

description:
TCR-seq library: BL4
Single cells
BL4_filtered_contig_annotations.csv

value: Chronic pancreatitis (Hereditary)


title: BL5, BL5 (TCR-seq)

description:
TCR-seq library: BL5
Single cells
BL5_filtered_contig_annotations.csv

value: PRSS1, CFTR


title: BL6, BL6 (TCR-seq)

description:
TCR-seq library: BL6
Single cells
BL6_filtered_contig_annotations.csv


title: ST_Isoniazid_400_b2_p2_C05

description: ST pilot combined FINAL.csv


title: BL3, BL3 (TCR-seq)

description:
TCR-seq library: BL3
Single cells
BL3_filtered_contig_annotations.csv

value: PRSS1, CFTR, SPINK1


title: ST_Isoniazid_10000_b2_p2_C04

description: ST pilot combined FINAL.csv


title: BL2, BL2 (TCR-seq)

description:
TCR-seq library: BL2
Single cells
BL2_filtered_contig_annotations.csv


title: BL11, Idio3 (CITE-seq)

description:
CITE-seq library: BL11
Single cells
BL11_filtered_feature_bc_matrix.h5

data_processing:
Library strategy: CITE-seq
cellranger 4.0 count function to generate count matrix
Genome_build: hg38
Supplementary_files_format_and_content:
Feature Barcode Matrix Format is HDF5 format which used as the top level for matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
annotation csv file contains one contig, consensus, or clonotype per row

molecule: other

value: Chronic pancreatitis (Idiopathic)


title: ST_Isoniazid_10000_b2_p2_C02

description: ST pilot combined FINAL.csv


title: ST_Naproxen_80_b2_p2_B11

description: ST pilot combined FINAL.csv


title: BL9, Idio1 (CITE-seq)

description:
CITE-seq library: BL9
Single cells
BL9_filtered_feature_bc_matrix.h5

value: Female


title: BL1, BL1 (TCR-seq)

description:
TCR-seq library: BL1
Single cells
BL1_filtered_contig_annotations.csv

value: Pancreas


title: ST_Isoniazid_400_b2_p2_C03

description: ST pilot combined FINAL.csv


title: ST_Naproxen_80_b2_p2_B09

description: ST pilot combined FINAL.csv


title: BL8, Ctl3 (CITE-seq)

description:
CITE-seq library: BL8
Single cells
BL8_filtered_feature_bc_matrix.h5

value: Immune cells


title: ST_Naproxen_2000_b2_p2_B08

description: ST pilot combined FINAL.csv

value: Wistar


title: BL7, Ctl2 (CITE-seq)

description:
CITE-seq library: BL7
Single cells
BL7_filtered_feature_bc_matrix.h5


title: ST_Naproxen_2000_b2_p2_B10

description: ST pilot combined FINAL.csv

value: Male


title: WT_Chloramphenicol_18_b1_p5_G07

description: WT pilot combined FINAL.csv

value: hepatocytes

value: rat whole transcriptome assay

value: Chloramphenicol


title: BL6, Ctl1 (CITE-seq)

description:
CITE-seq library: BL6
Single cells
BL6_filtered_feature_bc_matrix.h5


title: WT_Chloramphenicol_450_b1_p5_G06

description: WT pilot combined FINAL.csv


title: BL5, Her1 (CITE-seq)

description:
CITE-seq library: BL5
Single cells
BL5_filtered_feature_bc_matrix.h5


title: WT_Chloramphenicol_450_b1_p5_G04

description: WT pilot combined FINAL.csv


title: BL4, Her1 (CITE-seq)

description:
CITE-seq library: BL4
Single cells
BL4_filtered_feature_bc_matrix.h5


title: WT_Chloramphenicol_450_b1_p5_G02

description: WT pilot combined FINAL.csv


title: WT_Chloramphenicol_18_b1_p5_G03

description: WT pilot combined FINAL.csv


title: BL3, Her1 (CITE-seq)

description:
CITE-seq library: BL3
Single cells
BL3_filtered_feature_bc_matrix.h5


title: WT_Sulfasalazine_4_b1_p5_F07

description: WT pilot combined FINAL.csv

value: Sulfasalazine


title: Muscle M8A

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description: Paired End

data_processing:
SOAPnuke v.1.5.2 was used to filter reads with adapters, reads with unknown bases more than 10%, low quality reads (the percentage of base which quality is lesser than 15 is greater than 50% in a read)
HiSat2 used for allignment using mm10 build and GRCm38 GTF file. FeatureCounts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Genome_build: mm10

source_name: Muscle

growth_protocol: Animals were grown at Jackson labs

extract_protocol:
The poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: No treatments were applied

value: Muscle

tag: genotype

value: Mecp2 -/-

tag: Sex

value: male


title: WT_Sulfasalazine_4_b1_p5_F05

description: WT pilot combined FINAL.csv

tag: gender


title: Muscle M10A

description: Paired End


title: Muscle M9A

description: Paired End


title: WT_Sulfasalazine_100_b1_p5_F06

description: WT pilot combined FINAL.csv

tag: tempo-seq assay


title: BL2, Her1 (CITE-seq)

description:
CITE-seq library: BL2
Single cells
BL2_filtered_feature_bc_matrix.h5


title: WT_Sulfasalazine_100_b1_p5_F04

description: WT pilot combined FINAL.csv

tag: chemical


title: Muscle M7A

description: Paired End


title: BL12, Idio4 (scRNA-seq)

description:
scRNA-seq library: BL12
Single cells
BL12_filtered_feature_bc_matrix.h5


title: BL11, Idio3 (scRNA-seq)

description:
scRNA-seq library: BL11
Single cells
BL11_filtered_feature_bc_matrix.h5


title: HFS

first: Hao

last: Wu

address: No.190 Jiaoyuan Road, Hongqiao District

department: Department of Cardiology

institute: Tianjin Union Medical Center

description: Gene expression data form mouse heart with dapagliflozin treatment group

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: Mouse in the experimental group after dapagliflozin treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 10-week-old C57BL/6 male mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

treatment_protocol: Wild-type C57BL/6 male mice (10-week old) were subjected to abdominal aortic constriction (AAC). In the sham group, the silk was removed without ligation. In the treatment group, after the establishment of AAC model, dapagliflozin was administered in the drinking water at a dose of 25 mg/kg/d for 12 weeks

value: heart

tag: treatment

value: dapagliflozin treatment group


title: Muscle M6A

description: Paired End


title: WT_Sulfasalazine_4_b1_p5_F03

description: WT pilot combined FINAL.csv

tag: dose (um)


title: NC

description: Gene expression data from mouse heart with control group

source_name: mouse in the control group

tag: strain

value: control group


title: Mouse kidney intraperitoneally administered with LPS and Stx_72h_2

city: Fukushima

first: Yohei

last: Kume

state: Fukushima

address: 1, Hikarigaoka

department: Pediatrics

institute: Fukushima Medical University

hyb_protocol: Following labeling, 5.2 ug of cDNA were hybridized for 16 hr at 45 degree C on Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G system.

data_processing: The data analysis were used Transcriptome Analysis Console Ver.4.0.  Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (SST-RMA),  Expression Analysis was perfoermed using ebayes ANOVA.

source_name: Kidney samples obtained 72 hours after intraperitoneal administration of LPS and Stx

label_protocol: The fragmented 5.2 μg of single-stranded cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent that is covalently linked to biotin. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

growth_protocol: Animal experiments involved 8-10-wk-old male inbred C57BL/6 mice (NIHON SLC, Shizuoka, Japan).  Mice were maintained on a 12-h light-dark cycle with free access to water and standard chow diet.

extract_protocol: Kidney samples were obtained 6 hours and 72 hours after intraperitoneal administration of LPS and Stx, and 72 hours after saline administration in the control group. The kidneys were collected after inhalation anesthesia with sevoflurane and washed with PBS. For RNA analysis, it was treated with RNA later at 4°C overnight and then stored at -80°C.Kidney samples were obtained 6 hours and 72 hours after intraperitoneal administration of LPS and Stx, and 72 hours after saline administration in the control group. The kidneys were collected after inhalation anesthesia with sevoflurane and washed with PBS. For RNA analysis, it was treated with RNA later at 4°C overnight and then stored at -80°C.

treatment_protocol: LPS (300 μg/kg, 10.0 mL/kg) and Stx (225 ng/kg, 10.0 mL/kg) were intraperitoneally administered to 8-10 week old mice. In the control group, physiological saline (10 ml/kg) was intraperitoneally administered. In each case, daily body weight and condition were observed after administration.

tag: srain

value: kidney


title: HF

description: Gene expression data form mouse heart with AAC-induced group

source_name: AAC-induced heart failure mouse

value: AAC-induced group


title: Muscle M5A

description: Paired End

value: Control


title: Mouse kidney intraperitoneally administered with LPS and Stx_72h_3


title: WT_Sulfasalazine_100_b1_p5_F02

description: WT pilot combined FINAL.csv

data_processing:
Data processing was performed by BioSpyder Technologies Inc.
Illumina Casava1.7 software used for base-calling
No filtering was done since aligning to known sequence
Reads were aligned using the STAR aligner 2.5.3a allowing 2 bp mismatches and not allowing indels. The softclipping option is turned on.
The Tempo-SeqR package was used to generate read counts matrix
Genome_build: rn6
Supplementary_files_format_and_content: Read counts matrix (row = treatment; column = gene)


title: WT_Chloramphenicol_18_b1_p5_G05

description: WT pilot combined FINAL.csv


title: WT_Indomethacin_12_b1_p5_E07

description: WT pilot combined FINAL.csv

value: Indomethacin


title: BL1, Her1 (CITE-seq)

description:
CITE-seq library: BL1
Single cells
BL1_filtered_feature_bc_matrix.h5

value: Chronic pancreatitis (Hereditary)

value: Pancreas

value: Immune cells


title: BL9, Idio1 (scRNA-seq)

description:
scRNA-seq library: BL9
Single cells
BL9_filtered_feature_bc_matrix.h5

value: Chronic pancreatitis (Idiopathic)

value: Female


title: Mouse kidney intraperitoneally administered with LPS and Stx_72h_4


title: Mouse kidney intraperitoneally administered with LPS and Stx_72h_1


title: BL10, Idio2 (scRNA-seq)

description:
scRNA-seq library: BL10
Single cells
BL10_filtered_feature_bc_matrix.h5


title: Muscle M4A

description: Paired End


title: Control kidney_5

source_name: Control kidney (72 hours after saline administration)


title: BL8, Ctl3 (scRNA-seq)

description:
scRNA-seq library: BL8
Single cells
BL8_filtered_feature_bc_matrix.h5


title: WT_Indomethacin_300_b1_p5_E06

description: WT pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes

value: rat whole transcriptome assay


title: Muscle M2A

description: Paired End

value: Muscle

value: male


title: BL7, Ctl2 (scRNA-seq)

description:
scRNA-seq library: BL7
Single cells
BL7_filtered_feature_bc_matrix.h5


title: WT_Indomethacin_12_b1_p5_E05

description: WT pilot combined FINAL.csv


title: Control kidney_3


title: Liver L10A

description: Paired End

source_name: Liver

value: Liver

value: Mecp2 -/-


title: BL6, Ctl1 (scRNA-seq)

description:
scRNA-seq library: BL6
Single cells
BL6_filtered_feature_bc_matrix.h5


title: Control kidney_2

value: kidney


title: BL5, Her1 (scRNA-seq)

description:
scRNA-seq library: BL5
Single cells
BL5_filtered_feature_bc_matrix.h5

value: PRSS1, CFTR


title: WT_Indomethacin_12_b1_p5_E03

description: WT pilot combined FINAL.csv


title: Liver L9A

description: Paired End


title: WT_Indomethacin_300_b1_p5_E02

description: WT pilot combined FINAL.csv


title: Control kidney_1


title: Muscle M3A

description: Paired End

value: Control


title: BL4, Her1 (scRNA-seq)

description:
scRNA-seq library: BL4
Single cells
BL4_filtered_feature_bc_matrix.h5


title: WT_Acetaminophen_400_b1_p5_D07

description: WT pilot combined FINAL.csv

value: Acetaminophen


title: Muscle M1A

description: Paired End


title: Liver L8A

description: Paired End


title: BL3, Her1 (scRNA-seq)

description:
scRNA-seq library: BL3
Single cells
BL3_filtered_feature_bc_matrix.h5

value: Chronic pancreatitis (Hereditary)

value: PRSS1, CFTR, SPINK1


title: WT_Indomethacin_300_b1_p5_E04

description: WT pilot combined FINAL.csv

value: Indomethacin


title: WT_Acetaminophen_10000_b1_p5_D06

description: WT pilot combined FINAL.csv


title: BL2, Her1 (scRNA-seq)

description:
scRNA-seq library: BL2
Single cells
BL2_filtered_feature_bc_matrix.h5

value: Pancreas

value: Immune cells


title: Liver L7A

description: Paired End


title: BL1, Her1 (scRNA-seq)

description:
scRNA-seq library: BL1
Single cells
BL1_filtered_feature_bc_matrix.h5


title: Liver L6A

description: Paired End


title: Mouse kidney intraperitoneally administered with LPS and Stx_6h_2

source_name: Kidney samples obtained 6 hours after intraperitoneal administration of LPS and Stx


title: WT_Acetaminophen_400_b1_p5_D05

description: WT pilot combined FINAL.csv

value: Wistar


title: Liver L5A

description: Paired End


title: WT_Acetaminophen_10000_b1_p5_D04

description: WT pilot combined FINAL.csv

value: Male


title: Liver L4A

description: Paired End


title: Mouse kidney intraperitoneally administered with LPS and Stx_6h_4


title: WT_Acetaminophen_10000_b1_p5_D02

description: WT pilot combined FINAL.csv

value: hepatocytes


title: Mouse kidney intraperitoneally administered with LPS and Stx_6h_3


title: WT_Acetaminophen_400_b1_p5_D03

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay


title: C0009L0

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

country: France

institute: Assistance Publique des Hôpitaux de Paris

data_processing:
Fastq files produced after RNA-seq sequencing have been processed by in-house CNRGH (Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France ) tools in order to assess quality of raw and genomic-aligned nucleotides
Quality control was performed on a random selection of 2 x 10 million reads, including the following steps: removal of adapters and poor-quality sequences to evaluate the % of usable reads (use of trimmomatic); alignment on the reference genome (Hisat2) as well as on the transcriptome and rRNAs (Bowtie2)
Use of rseqc and picardTools to evaluate the % of mapping on the genome and transcriptome, the % of duplicate sequences, the % of rRNA and the total number of usable sequences
Fastq files were aligned against the human GRCh38 genome assembly using STAR-2.6.0 according to author’s procedure (Dobin et al. 2016)
Genome_build: human GRCh38 genome assembly
Supplementary_files_format_and_content: table count

source_name: PBMC

extract_protocol:
Promega Maxwell® technology (simply RNA tissue kit, AS1340)
Libraries have been prepared using the "TruSeq Stranded Total RNA Gold” Kit from Illumina

tag: individual

value: Recipient

tag: couple number

value: M

value: PBMC

tag: cohort

value: National multicentric cohort

tag: outcome related


title: C0006J7

value: F

tag: cell type


title: Mouse kidney intraperitoneally administered with LPS and Stx_6h_1

value: male

value: kidney


title: C0006KX


title: C0006IJ


title: CD4+ T cells expressing oncogenic Vav1 (lymph node) rep1

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description:
9.ONCO2.LN
Gene expression data from lymph node.

hyb_protocol: Clariom S arrays (Affymetrix) under standard conditions.

scan_protocol: Standard Affymetrix protocol.

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.6.3).

source_name: Lymph node (oncogenic Vav1)

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: This experiment has been done with animals.

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

treatment_protocol: CD4+ T cells were transduced with either GFP or oncogenic Vav1.

tag: genotype/variation

value: WT + Oncogenic Vav1

value: Lymph node CD4+ T cells


title: Liver L3A

description: Paired End

tag: tissue

value: Liver

value: Control


title: C0006LZ

tag: age


title: CD4+ T cells expressing oncogenic Vav1 (lymph node) rep2

description:
10.ONCO3.LN
Gene expression data from lymph node.


title: Kidney K10A

description: Paired End

source_name: Kidney

value: Kidney

tag: genotype

value: Mecp2 -/-


title: WT_WY14643_200_b1_p5_C06

description: WT pilot combined FINAL.csv

source_name: liver

extract_protocol:
After 24 h of chemical treatment, the spent medium was removed and the wells were washed with 100 µL of PBS twice. Cells were lysed by adding 20 µL of 1X TempO-Seq lysis buffer (BioSpyder) in PBS. The cell lysates were shipped frozen on dry ice to to BioSpyder Technologies, Inc. (Carlsbad, CA, USA), where libraries were prepared directly from the cell lysates and RNA-seq was performed.
2 μL of sample lysate was hybridized with detector oligos from the TempO-Seq rat surrogate (ST) or whole-transcriptome (WT) assay, with 1 h hybridization period for the ST assay and overnight for the WT assay. After ligation and nuclease digestion, the ligated products were added into an amplification mix with sample-specific PCR primer pairs which include the standard Illumina adaptor and a sample-specific barcode sequence. Amplicons were pooled and purified using a PCR clean-up kit (Macherey-Nagel, Mountain View, CA, United States).

value: Wistar


title: WT_WY14643_200_b1_p5_C04

description: WT pilot combined FINAL.csv

value: Male


title: CD4+ T cells expressing oncogenic Vav1 (spleen) rep4

description:
6.ONCO4.BZ
Gene expression data from spleen.

source_name: Spleen (oncogenic Vav1)

value: Spleen CD4+ T cells


title: CD4+ T cells expressing oncogenic Vav1 (spleen) rep2

description:
4.ONCO2.BZ
Gene expression data from spleen.


title: Kidney K8A

description: Paired End

tag: Sex


title: CD4+ T cells expressing oncogenic Vav1 (spleen) rep1

description:
3.ONCO1.BZ
Gene expression data from spleen.


title: CD4+ T cells expressing GFP (spleen) rep2

description:
2.CTL4.BZ
Gene expression data from spleen.

source_name: Spleen (control)

value: WT + GFP


title: CD4+ T cells expressing GFP (lymph node) rep1

description:
7.CTL1.LN
Gene expression data from lymph node.

source_name: Lymph node (control)


title: WT_WY14643_8_b1_p5_C03

description: WT pilot combined FINAL.csv

tag: gender

value: hepatocytes

value: rat whole transcriptome assay


title: WT_WY14643_8_b1_p5_C05

description: WT pilot combined FINAL.csv

tag: tempo-seq assay


title: Liver L1A

description: Paired End


title: WT_Ketoconazole_0.6_b1_p5_B07

description: WT pilot combined FINAL.csv

tag: chemical

value: Ketoconazole


title: mouse_submandibular_glands_KO03

city: Mizuho

first: Taiki

last: Mori

address: 1851 Hozumi

institute: Asahi University School of Dentistry

description: RMA expression value derived from Transcriptome Analysis Console software

hyb_protocol: Samples were hybridized using GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific) at 45°C, 16 h (60 rpm)  on Clariom™ Assay for mouse and washed using GeneChip™ Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Thermo Fisher Scientific)

data_processing: Raw data were processed with the Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) for background correction and normalization. Data analysis and statistical evaluations were also performed with the Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) according to the manufacturer’s instructions.

source_name: Submandibular glands in mouse

label_protocol: Single-stranded cDNA was generated from GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific).

extract_protocol: RNA was isolated from submandibular glands with the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: 10 weeks old

value: NOD.B6-Myd88−/− mouse

value: female


title: CD4+ T cells expressing GFP (lymph node) rep2

description:
8.CTL2.LN
Gene expression data from lymph node.


title: WT_WY14643_8_b1_p5_C07

city: Singapore

description: WT pilot combined FINAL.csv


title: Kidney K9A

description: Paired End

value: male


title: C0006JD

value: Recipient

value: M

value: PBMC

value: National multicentric cohort


title: C0006J5

value: F


title: Kidney K4A

description: Paired End

value: Kidney

value: Control


title: Kidney K3A

description: Paired End


title: C0006LD


title: C0006JF


title: Liver L2A

description: Paired End

value: Liver


title: CD4+ T cells expressing oncogenic Vav1 (spleen) rep3

description:
5.ONCO3.BZ
Gene expression data from spleen.

value: WT + Oncogenic Vav1

value: Spleen CD4+ T cells


title: WT_WY14643_200_b1_p5_C02

description: WT pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes


title: Kidney K6A

description: Paired End

value: Mecp2 -/-


title: C0009LP


title: WT_Ketoconazole_0.6_b1_p5_B03

description: WT pilot combined FINAL.csv

value: rat whole transcriptome assay

value: Ketoconazole


title: C0009K2


title: Kidney K5A

description: Paired End

value: male


title: mouse_submandibular_glands_KO02

value: 10 weeks old

value: NOD.B6-Myd88−/− mouse

value: female


title: C0006JB

value: Recipient

value: M

value: PBMC

value: National multicentric cohort


title: C0006M1


title: WT_Ketoconazole_15_b1_p5_B06

description: WT pilot combined FINAL.csv


title: WT_Ketoconazole_15_b1_p5_B02

description: WT pilot combined FINAL.csv


title: Hippocampus H10A

description: Paired End

source_name: Hippocampus

value: Hippocampus


title: C0009K4


title: WT_Ketoconazole_15_b1_p5_B04

description: WT pilot combined FINAL.csv


title: Hippocampus H9A

description: Paired End


title: C0006LV

value: F


title: WT_vehicle_vehicle_b1_p4_G10

description: WT pilot combined FINAL.csv

value: vehicle


title: Hippocampus H8A

description: Paired End


title: CD4+ T cells expressing GFP (spleen) rep1

description:
1.CTL2.BZ
Gene expression data from spleen.

value: WT + GFP

value: Spleen CD4+ T cells


title: mouse_submandibular_glands_WT03

value: NOD.B6-Myd88+/+ mouse


title: mouse_submandibular_glands_WT01


title: mouse_submandibular_glands_WT02


title: Kidney K1A

description: Paired End

value: Kidney

value: Control


title: Blood of normal control_rep3

city: Xi'an City

first: Xuzhao

last: Bian

state: Shaanxi Province

address: No.28 Xianning West Road, Beilin District

department: School of Public Health

institute: Xi’an Jiaotong University

description: gene expression of normal child

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.

scan_protocol: After hybridization, slides were scanned on the Agilent, Microarray Scanner (Agilent technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies,Santa Clara, CA, US). Raw data were normalized by Quantile algorithm,R package “limma”. The microarray experiments were performed by following the protocol of Agilent technologies Inc at Sinotech Genomics Corporation

source_name: Peripheral Blood of control, replicate 3

label_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA samples of each group were then used to generate biotinylated cRNA targets for the Sino Human ceRNA array V3.0

extract_protocol: Plasma was isolated by centrifugation, followed by total RNA extraction using TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA).

treatment_protocol: Whole blood sample (5ml per patient) was collected in Na2EDTA tubes

value: whole blood

tag: disease

value: healthy


title: Kidney K2A

description: Paired End

value: male


title: WT_vehicle_vehicle_b1_p4_G11

first: Fan

address: 31 Biopolis Way, The NANOS, #06-01

institute: Institute of Bioengineerng and Nanotechnology

description: WT pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes

value: rat whole transcriptome assay

tag: dose (um)


title: Hippocampus H7A

description: Paired End

tag: strain

value: Mecp2 -/-


title: Blood of normal control_rep4

description: gene expression of normal child

source_name: Peripheral Blood of control, replicate 4


title: WT_Ketoconazole_0.6_b1_p5_B05

description: WT pilot combined FINAL.csv

value: Ketoconazole


title: C0006J3

value: Recipient

value: M

value: PBMC

value: National multicentric cohort


title: Kidney K7A

description: Paired End


title: WT_Doxorubicin_0.08_b1_p4_G09

description: WT pilot combined FINAL.csv

value: Doxorubicin


title: C0006K9


title: C0009L6

value: F


title: Blood of normal control_rep1

description: gene expression of normal child

source_name: Peripheral Blood of control, replicate 1


title: mouse_submandibular_glands_KO01

value: 10 weeks old

value: NOD.B6-Myd88−/− mouse

value: female


title: WT_Doxorubicin_2_b1_p4_G08

description: WT pilot combined FINAL.csv


title: C0006J1


title: C0009KK


title: WT_Ranitidine_160_b1_p4_G07

description: WT pilot combined FINAL.csv

value: Ranitidine


title: C0006IX


title: Blood of normal control_rep2

description: gene expression of normal child

source_name: Peripheral Blood of control, replicate 2

value: whole blood

value: healthy


title: Hippocampus H5A

description: Paired End

value: Hippocampus

value: Control

value: male


title: Blood of normal control_rep5

description: gene expression of normal child

source_name: Peripheral Blood of control, replicate 5


title: Blood of CP patient_rep5

description: gene expression of CP child

source_name: Peripheral Blood of CP, replicate 5

value: cerebral palsy


title: Hippocampus H4A

description: Paired End


title: Hippocampus H3A

description: Paired End


title: C0006KV


title: Hippocampus H6A

description: Paired End

value: Mecp2 -/-


title: WT_Ranitidine_4000_b1_p4_G06

description: WT pilot combined FINAL.csv

value: Wistar

value: Male

value: hepatocytes

value: rat whole transcriptome assay


title: WT_Ranitidine_4000_b1_p4_G04

description: WT pilot combined FINAL.csv


title: WT_Ranitidine_160_b1_p4_G05

description: WT pilot combined FINAL.csv


title: C0009L5

value: Recipient

value: M

value: PBMC

value: National multicentric cohort


title: Blood of CP patient_rep3

description: gene expression of CP child

source_name: Peripheral Blood of CP, replicate 3


title: WT_Ranitidine_160_b1_p4_G03

description: WT pilot combined FINAL.csv


title: C0006LP


title: -G12h_1

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

institute: Shenzhen University

data_processing:
Raw reads were trimmed and clipped with SeqPrep and Sickle
De novo transcriptome assembly was performed with Trinity software
RSEM software was used to calculate gene expression levels from RNA-seq data
Supplementary_files_format_and_content: matrix table include TPM values for each Sample

organism: Nitzschia laevis

source_name: microalgae

growth_protocol: All cultures were grown in LDM medium in the 250-mL column (3-cm diameter) photoreactor with aeration of 1.5% CO2 enriched air. And continuous illumination at 40 μmol photons m-2 s-1 was applied. Cells were pre-cultivated under autotrophic conditions without glucose at 25 °C.

extract_protocol:
Total RNA was extracted using the plant RNA extraction kit (TaKaRa, Tokyo, Japan), and contaminating DNA was removed with RNase-free DNase I. The assessment of RNA concentration and quality was performed by Nano-Drop (ND1000 UV–Vis spectrophotometer; NanoDrop Technologies) and Agilent 2100 Bio analyzer (Agilent Technologies, Inc.).
Poly-A containing mRNA molecules were purified, fragmented and copied into cDNA, then subsequent ligation of the adapter was performed. The products were purified and enriched with PCR amplification. The PCR yield was quantified by QuantiFluor® dsDNA System, and samples were pooled together to form the final library. The pooled samples were subject to cluster generation and sequenced using an Illumina HiSeq.

treatment_protocol: To apply trophic transition, cells from autotrophic cultures were inoculated into LDM medium with addition of 5g/L glucose (+G). Cultures in autotrophic conditions were maintained as control (-G). RNA sequencing (RNA-seq) experiment was performed on 18 samples collected at 3 h, 6 h and 12 h after inoculation in treated medium with glucose addition (+G) and control group (-G) respectively.

value: UTEX 2047


title: Hippocampus H2A

description: Paired End


title: C0006JL

source_name: PBMC


title: WT_vehicle_vehicle_b1_p4_F11

last: Lee

description: WT pilot combined FINAL.csv

value: vehicle


title: Dorsal Striatum D9A

description: Paired End

source_name: Dorsal Striatum

value: Dorsal Striatum


title: Blood of CP patient_rep4

description: gene expression of CP child

source_name: Peripheral Blood of CP, replicate 4

value: whole blood


title: C0006K3


title: -G12h_2


title: Hippocampus H1A

description: Paired End

value: Hippocampus


title: WT_media_media_b1_p4_F10

description: WT pilot combined FINAL.csv

source_name: liver

value: media


title: -G6h_3


title: -G6h_2


title: -G12h_3


title: Dorsal Striatum D8A

description: Paired End

value: male


title: Dorsal Striatum D10A

description: Paired End


title: -G6h_1


title: C0006JP


title: Blood of CP patient_rep1

description: gene expression of CP child

source_name: Peripheral Blood of CP, replicate 1

value: cerebral palsy


title: C0006IH

value: F


title: C0009LS


title: WT_Ranitidine_4000_b1_p4_G02

description: WT pilot combined FINAL.csv

value: Wistar

value: Ranitidine


title: Blood of CP patient_rep2

description: gene expression of CP child

source_name: Peripheral Blood of CP, replicate 2


title: -G3h_2


title: -G3h_3


title: Dorsal Striatum D6A

description: Paired End

value: Mecp2 -/-


title: Dorsal Striatum D7A

description: Paired End


title: C0006LN


title: Dorsal Striatum D5A

description: Paired End

value: Control


title: WT_Caffeine_10000_b1_p4_F06

description: WT pilot combined FINAL.csv

value: Male

value: hepatocytes

value: rat whole transcriptome assay

value: Caffeine


title: +G12h_3

value: UTEX 2047


title: WT_Caffeine_400_b1_p4_F05

description: WT pilot combined FINAL.csv


title: C0009K0

value: Recipient

value: M

value: PBMC

value: National multicentric cohort


title: WT_Caffeine_400_b1_p4_F07

description: WT pilot combined FINAL.csv