title: D19_VCM_rep3

city: Amsterdam

first: Alexandra

last: Wiesinger

state: Amsterdam

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: late ventricular cardiomyocytes at day 19 of differentiation

data_processing:
Libraries were sequenced on NextSeq500 using 1x75 bp read length kit
Mapping was performed using BWA-MEM against the (human) genome assembly GRCh38 (hg38). Count matrices were generated using MapAndGo, filtering reads with a minimum quality score of 60 and no alternative hits.
Genome_build: hg38
Supplementary_files_format_and_content: transcript counts as .tsv files

growth_protocol: hiPSCs were maintained in mTeSR medium on growth factor reduced Matrigel

extract_protocol:
Cells at different stages during differentiation were singularzed and FACS sorted into 384-well plates (Muraro et al, 2016)
Preparation of single-cell libraries was performed using the CEL-Seq2 protocol (Muraro et al. 2016; Hashimshony et al., 2016)

treatment_protocol: Differentiation of hiPSCs towards MESP1+ mesoderm was initiated by activating Activin/Nodal, BMP and WNT signaling (Devalla et al., 2015; Devalla et al., 2016). To steer mesoderm towards a cardiomyocyte fate, WNT signaling was inhibited using XAV 939 for 96 hours, which resulted in predominantly ventricular-like cardiomyocytes (VCM). To direct mesoderm towards SANCM, we treated cultures with BMP4, RA, WNT inhibitor (XAV 939), TGFbR1/ALK5 inhibitor (SB431542) and FGF inhibitor (PD173074) for 48 hours (Protze et al., 2017).

value: hiPSC derived ventricular cardiomyocytes

tag: genotype

value: wild type

tag: timepoint


title: VM-CUB-1_LAK31

status: Public on Sep 01 2022

type: SRA

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

library_source: genomic

data_processing:
Mapping was done against the Homo sapiens (hg38) (May 25, 2017) genome sequence.
For each sample peak values, average peak values were mapped against genome position. Shrunken logarithmic fold changes were calculated for treated sample in comparison to DMSO solvent control.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-Seq_HDACi_in_urological_malignancies.xlsx

molecule: genomic DNA

organism: Homo sapiens

source_name: urothelial carcinoma

growth_protocol: 2102EP cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin); VM-CUB-1, Caki-1 and DU-145 were cultivated in RMPI medium (10% FCS, 1% Penicillin / Streptomycin).

extract_protocol:
Cells were harvested and shock frozen, extraction was performed by Active Motif (1. Prepare nuclei. To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed-angle centrifuge and carefully pipetted away from the pellet after centrifugations. 2. Transpose and purify. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit).
Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (Supplementary Table 1), using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.
During the ATAC-seq protocol, we chose to avoid a size-selection step to maximize the library complexity. The sequenced insert size is a distribution between 40 bp and 1 kb with a mean of ∼120 bp. From the bioanalyzer and gels we observed fragments >2 kb, which would make Qubit and other mass-based quantitation methods hard to interpret. For this reason we quantified our libraries using qPCR-based methods.

treatment_protocol: Cells were treated with corresponding EC50 values of LAK31, MZ-1, Romidepsin or Quisinostat for 16 h.

tag: cell line

tag: treatment


title: R4

city: Glasgow

first: Katherine

last: West

address: University of Glasgow

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

description:
EPZ6438
Chip sample

data_processing:
RNA-seq reads were aligned with HiSat2
Transcripts were assembled with Stringtie
DESeq2 was used to compare all drug treated samples with control samples, for each cell line
ChIP-seq reads were aligned with Bowtie2
ChIP-seq peaks were called with MACS2 using the broad peak setting, FDR 0.05.
Bigwig files were generated using bamcoverage
Genome_build: Hg38
Supplementary_files_format_and_content: RNA-seq processed data files are the normalised counts output from DESeq2, comparing the three drugs with the control.
Supplementary_files_format_and_content: ChIP-seq processed datafiles are the bigwig and MACS peak files.

source_name: glioblastoma stem cell line

growth_protocol: Cells were grown on Matrigel coated plates in AdDMEM F12 medium supplemented with 20ng/ml EGF, 10ng/ml bFGF,1% B27, 0.5% N2, 4ng/μl Heparin, and  L-Glutamine (Fael Al-Mayhani et al., 2009, Gomez-Roman et al., 2017)

extract_protocol:
RNA was purified using Qiagen Rneasy kit with DNase I treatment. Chromatin was formaldehyde crosslinked, purified, sonicated and subject to ChIP using antibodies to H3K27me3 or H3K4me3.
RNAseq library prep and sequencing was performed by BGI genomics. ChIP-seq library prep and sequencing was performed by Novagen.
paired end RNA-seq and paired end ChIP-seq.

treatment_protocol: Cells were incubated with 2 μM of GSK343, UNC1999, EPZ6438 or DMSO for 5 days

tag: antibody


title: D19_VCM_rep2

library_source: transcriptomic

molecule: polyA RNA

tag: cell type


title: genomic DNA from saliva sample 118

type: genomic

city: Maastricht

first: Rebekka

middle: Maria

last: Koeck

address: Maastricht UMC+

department: Clinical Genetics

institute: Maastricht University Medical Centre

description:
K-SICM saliva sample
I-033

hyb_protocol: bisulphite converted DNA (EpiTect - Qiagen) was hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: The raw data were processed in R using the RnBeads package. SWAN normalisation was carried out before greedycut (p-value threshold 0.05) filtering was applied to remove poor quality sites and samples. Further filtering was carried out to remove sites (i) on the sex chromosomes, (ii) near single nucleotide polymorphisms, (iii) with missing values in more than 5% of samples, (iv) sites not in a CpG context. Samples were also excluded if their predicted sex, predicted using the sEsst package, did not match the recorded sex. The values presented are methylation beta values.

label: Cy5 and Cy3

source_name: saliva sample 118

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from saliva samples using the Saliva DNA Collection, Preservation and Isolation Kit (Norgen Biotek, Canada) according to the manufacturer's instructions.

tag: culturemedium

value: K-SICM

tag: Sex

value: Male

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: genomic DNA from saliva sample 119

description:
G3 saliva sample
I-138

source_name: saliva sample 119

value: Female


title: genomic DNA from saliva sample 120

description:
G3 saliva sample
I-087

source_name: saliva sample 120


title: 2102EP_LAK31

source_name: non-seminoma germ cell tumor, embryonal carcinoma


title: genomic DNA from saliva sample 117

description:
G3 saliva sample
I-068

source_name: saliva sample 117


title: D19_VCM_rep1


title: D19_SANCM_rep3

description: late SAN cardiomyocytes at day 19 of differentiation

value: hiPSC derived sinoatrial node cardiomyocytes


title: genomic DNA from saliva sample 113

description:
K-SICM saliva sample
I-021

source_name: saliva sample 113


title: genomic DNA from saliva sample 114

description:
K-SICM saliva sample
I-018

source_name: saliva sample 114


title: genomic DNA from saliva sample 115

description:
K-SICM saliva sample
I-106

source_name: saliva sample 115


title: genomic DNA from saliva sample 112

description:
G3 saliva sample
I-080

source_name: saliva sample 112


title: D19_SANCM_rep2


title: genomic DNA from saliva sample 111

description:
K-SICM saliva sample
I-041

source_name: saliva sample 111


title: genomic DNA from saliva sample 109

description:
G3 saliva sample
I-098

source_name: saliva sample 109


title: D19_SANCM_rep1


title: genomic DNA from saliva sample 108

description:
K-SICM saliva sample
I-084

source_name: saliva sample 108


title: D10_rep2

description: early SAN cardiomyocytes at day 10 of differentiation

value: Day 10


title: D10_rep1


title: genomic DNA from saliva sample 105

description:
G3 saliva sample
I-052

source_name: saliva sample 105


title: genomic DNA from saliva sample 106

description:
K-SICM saliva sample
I-066

source_name: saliva sample 106


title: genomic DNA from saliva sample 101

description:
G3 saliva sample
I-088

source_name: saliva sample 101


title: genomic DNA from saliva sample 116

description:
G3 saliva sample
I-024

source_name: saliva sample 116


title: genomic DNA from saliva sample 104

description:
K-SICM saliva sample
I-042

source_name: saliva sample 104


title: genomic DNA from saliva sample 102

description:
G3 saliva sample
I-082

source_name: saliva sample 102


title: D6_rep1

description: 48 hours after treatment with RA, BMP4, ALK5 inhibitor, FGF inhibitor, WNT inhibitor

value: Day 6


title: genomic DNA from saliva sample 100

description:
G3 saliva sample
I-129

source_name: saliva sample 100


title: genomic DNA from saliva sample 98

description:
K-SICM saliva sample
I-105

source_name: saliva sample 98


title: sib_D7_3

city: Wuhan

first: Ruilin

last: Zhang

address: 185 Donghu Road

country: China

institute: Wuhan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 whole genome using Hisat2 v2.0.5
Genome_build: GRCz11
Supplementary_files_format_and_content: excel files include FPKM for each sample

molecule: total RNA

organism: Danio rerio

source_name: whole larva

growth_protocol: zebrafish were raised and maintained under standard conditions

extract_protocol:
Whole larval total RNA samples were harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: whole larva

tag: strain

value: AB

tag: age

value: 7 days post fertilization

value: ercc2/xpd+/+ & ercc2/xpd+/-


title: genomic DNA from saliva sample 99

description:
G3 saliva sample
I-090

source_name: saliva sample 99


title: D5_rep2

description: 24 hours after treatment with RA, BMP4, ALK5 inhibitor, FGF inhibitor, WNT inhibitor

value: Day 5


title: Group 10 Weakly Adherent

city: La Jolla

last: Birmingham

state: Ca

address: 2880, Torrey Pines Scenic Drive

department: Bioengineering

country: USA

institute: University of California San Diego

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt
Quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build hg19 using STAR
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression (RLE) using DESeq2 R library
Read Distribution percentages, heatmaps, and sample plots were generated as part of the QC step using RSeQC. DEseq2 was also used to calculate fold changes and p-values.
Assembly: hg19
Supplementary files format and content: text files with Relative Log Expression (RLE) values for each sample

organism: Mus musculus

source_name: Primary tumor

growth_protocol: Grown in DMEM+10%FBS+5% Penstrep in a T75 flask at 1E6 confluency, media changed every 2 days

extract_protocol:
Tumors were removed from mice, disociated into single cells, then bulk mRNA performed on the cells
RNA quality was assessed using TapeStation (Agilent), RNA libraries were prepared using the Illumina TruSeq Stranded RNA, High Throughput Library Prep Kit and sequenced using the Illumina HiSeq 4000 system to generate 50 bp single-end reads.

treatment_protocol: Sheared at 10 dyn/cm2 (weakly adherent cells), 50 dyn/cm2 (strongly adherent cells), or no shear (unsorted cells)

value: Primary tumor

tag: mouse strain

value: Nod/Skid

value: MDAMB231 GFP+ Luc+

tag: adhesion profile

value: Weakly adherent


title: genomic DNA from saliva sample 97

description:
K-SICM saliva sample
I-004

source_name: saliva sample 97


title: Group 9 Weakly Adherent


title: D5_rep1

tag: genotype

tag: timepoint


title: genomic DNA from saliva sample 107

description:
G3 saliva sample
I-062

source_name: saliva sample 107


title: genomic DNA from saliva sample 103

description:
G3 saliva sample
I-055

source_name: saliva sample 103


title: genomic DNA from saliva sample 110

description:
G3 saliva sample
I-121

source_name: saliva sample 110


title: hiPSC_rep2

description: hiPSC prior to differentiation

source_name: hiPSC

value: human induced pluripotent stem cell

value: Day 0


title: D4_rep2

description: cardiac mesoderm induced with Activin A, BMP4 and CHIR

value: hiPSC derived cardiac mesoderm

value: wild type

value: Day 4


title: D6_rep2

value: hiPSC derived sinoatrial node cardiomyocytes


title: sib_D7_2


title: sib_D7_1


title: genomic DNA from saliva sample 96

description:
K-SICM saliva sample
I-029

source_name: saliva sample 96

value: K-SICM

value: Female


title: D4_rep1


title: Group 9 Unsorted

value: Unsorted


title: sib_D5_3

value: whole larva

value: AB

value: 5 days post fertilization


title: Group 7-8 Weakly Adherent


title: genomic DNA from saliva sample 95

description:
K-SICM saliva sample
I-010

source_name: saliva sample 95

value: Male


title: hiPSC_rep1

description: hiPSC prior to differentiation


title: Group 9 Strongly Adherent

value: Primary tumor

value: Strongly adherent


title: genomic DNA from saliva sample 93

description:
K-SICM saliva sample
I-039

source_name: saliva sample 93


title: genomic DNA from saliva sample 94

description:
K-SICM saliva sample
I-092

source_name: saliva sample 94


title: UiMPC_10_P9

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
Reads were aligned to  hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using  RSEM
The gene expression was normalized using EDAseq on a basis of GC-content. RNA-seq data was expressed in units of GC-normalized tag counts.
Genome_build: hg38

source_name: UiPSM Passage9

growth_protocol: Specific culture media for each cell type

extract_protocol:
Purified total RNA was capture with magnetic bead with oligo-polyA, interrupt and reverse-transcribed into cDNA using the VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme), purified using VAHTS DNA Clean Beads (N411, Vazyme).
cDNAs ligated adapters and amplified libraries using the amplification mix (NR611, Vazyme). Finally, sequencing the cDNAs library to obtain 150bp paired-end reads.

treatment_protocol: Extracted RNA using phenolic chloroform after pretreatment with Trizol

value: UiPSM Passage9


title: sib_D5_2

value: ercc2/xpd+/+ & ercc2/xpd+/-


title: KO_D7_2

value: 7 days post fertilization

value: ercc2/xpd -/-


title: UiMPC_8_P1

source_name: UiPSM Passage1

value: UiPSM Passage1


title: Group 7-8 Unsorted

value: Nod/Skid

value: MDAMB231 GFP+ Luc+


title: UiMPC_10_P1


title: genomic DNA from saliva sample 92

description:
K-SICM saliva sample
I-054

source_name: saliva sample 92


title: UiMPC_8_P9


title: Group 6 Unsorted


title: s26

city: Prague

first: Jiri

last: Baloun

address: Na Slupi 450/4

department: Department of experimental rheumatology

country: Czech Republic

institute: Institute of Rheumatology

data_processing:
Count-based miRNA expression data were generated by the Chimira (Vitsios et al, Bioinformatics, 2015) tool from FASTQ files.
All sequences were adapter trimmed and mapped against miRBase v22 allowing up to two mismatches per sequence.
Raw reads were analysed by DESeq2 method
Genome_build: miRBase v22
Supplementary_files_format_and_content: tab-delimited text file containing miRNAs mapped in ech sample and its read count

source_name: Human serum

extract_protocol:
Circulating miRNAs were isolated from the serum using the NucleoSpin miRNA Plasma, Mini kit for circulating miRNA (Macherey-Nagel) according to the manufacturer`s protocol. Libraries for sequencing were prepared from 10.5 µL of isolated miRNAs using a NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific) according to the manufacturer`s protocol.
small RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human serum

tag: before/after ovariectomy

value: after

tag: ID

tag: menopause

value: yes

tag: estrogen treatment


title: sib_D5_1


title: genomic DNA from saliva sample 91

description:
G3 saliva sample
I-115

source_name: saliva sample 91

tag: culturemedium

tag: Sex

value: Female


title: KO_D7_1

source_name: whole larva

value: whole larva


title: Group 6 Strongly Adherent

tag: cell type


title: 20180502.UiMPC.10.P18

source_name: UiPSM Passage18

value: UiPSM Passage18


title: genomic DNA from saliva sample 90

description:
G3 saliva sample
I-017

source_name: saliva sample 90

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem


title: KO_D7_3

tag: tissue

value: AB


title: KO_D5_3

tag: strain

value: 5 days post fertilization


title: genomic DNA from saliva sample 88

description:
G3 saliva sample
I-081

source_name: saliva sample 88

tag: allergicproblems

tag: batch


title: genomic DNA from saliva sample 89

description:
G3 saliva sample
I-064

source_name: saliva sample 89


title: 20180502.UiMPC.8.P18


title: Group 6 Weakly Adherent

source_name: Primary tumor

value: Primary tumor

tag: mouse strain

tag: adhesion profile

value: Weakly adherent


title: genomic DNA from saliva sample 87

description:
G3 saliva sample
I-102

source_name: saliva sample 87

value: Male


title: Group 5 Weakly Adherent


title: Group 5 Unsorted

value: Unsorted


title: KO_D5_1

tag: age

tag: genotype


title: KO_D5_2


title: Hela_DNMDP_tRNA_Rep2

city: Cambridge

first: Stephanie

last: Hoyt

state: MA

address: 415 Main St

department: Cancer Program

institute: Broad Institute of MIT and Harvard

description: tRNA

data_processing:
Sequencing reads were 5’, 3’-adaptor trimmed and filtered reads (length < 18nt or length > 40nt) with cutadapt.
Reads were aligned to cytoplasmic mature-tRNA sequences from GtRNAdb and the mitochondrial tRNA sequences from mitotRNAdb using BWA software (0.7.12-r1039).
The tRNAs expression profiling was calculated based on uniquely mapped reads.
For tRNA alignment, the maximum mismatch was 2.
Genome_build: Genomic tRNA Database (GtRNAdb); mitotRNAdb
Supplementary_files_format_and_content: Text files include counts per million (CPM) values per sample

source_name: Hela cell line

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37°C in 5% CO2.

extract_protocol:
Total RNA was purified and cleaned up using Trizol reagents (Invitrogen) and RNA Clean & Concentrator-25 (Zymo Research) following the manufacturer's protocol. 60-100 nt tRNA was extracted on a urea-polyacrylamide gel.
Purified tRNA was demethylated by ALKBH5 demethylase and fragmented by alkaline hydrolysis. For end-repair of the partially hydrolyzed tRNA fragments, RNA was sequentially treated with calf intestinal phosphatase and then T4 polynucleotide kinase. RNA-seq libraries were prepared using NEBNext® Multiplex Small RNA Library kit and sequenced on Illumina NextSeq 500 instrument with a single read 50 bp.
tRNA-seq

treatment_protocol: HeLa cells were treated with DMSO or 1 µM DNMDP for 18 hours.

tag: treatment

value: treated with DNMDP for 18 hours


title: RNA CRS T015N

type: RNA

city: Honolulu

first: Yurii

last: Shvetsov

state: HI

address: 701 Ilalo St

department: Cancer Center

institute: University of Hawaii

description: Gene expression data from FFPE tumor or normal tissue

hyb_protocol: In a rotating chamber, 5.5 μg of fragmented and labeled ss-cDNA were hybridized to the Clariom D Human Array for 16 h at 45 °C.

scan_protocol: The hybridized arrays were scanned on the Affymetrix GeneChip Array Scanner 3000-7G.

data_processing: Generated CEL files were normalized and differential gene expression was investigated using the TAC software.

label: biotin

source_name: CRS015 matched set, non-sepsis sample, tumor tissue

label_protocol: A combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) was used to fragment ssDNA, which was afterwards labelled with biotin (WT Terminal Labelling Kit, Thermo Fisher Scientific).

extract_protocol: Samples were prepared for microarray hybridization as described in the Thermo Fisher Scientific GeneChip Whole Transcript (WT) Expression manual using the WT Pico Reagent Kit.

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: non-sepsis sample

value: tumor tissue

tag: age group

value: 40-44 years

tag: ethnicity

value: Japanese

tag: tumor stage

value: Regional

tag: tumor grade

value: Moderately differentiated; Grade II

tag: chemotherapy (y/n)

value: Yes

tag: radiation treatment (y/n)

tag: survival (months)


title: Hela_DNMDP_tRNA_Rep1

description: tRNA


title: genomic DNA from saliva sample 85

description:
K-SICM saliva sample
I-043

source_name: saliva sample 85

tag: culturemedium

value: K-SICM

tag: Sex

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem


title: RNA CRS T015

source_name: CRS015 matched set, sepsis sample, tumor tissue

value: sepsis sample

tag: tissue

value: 35-39 years

value: Distant

value: Poorly differentiated; Grade III

value: No/Unknown


title: Hela_DNMDP_RPF_Rep2

description: ribosome-protected mRNA fragments (RPF)

data_processing:
raw fastq to trimmed and collapsed fa per RibotoolKit documentation (trimmed using trimgalore, collapsed using fq2collapsedFa.pl)
Single Case RiboToolKit: default parameters except 'Offsets to infer P-sites' for which we used 27,28,29,30,31,32 12,12,12,12,12,12
Genome_build: hg38
Supplementary_files_format_and_content: csv files, codon level coverage data for each transcript

extract_protocol:
HeLa cells were treated with cycloheximide and washed with cold PBS. Cell lysate was incubated with RNase I (ThermoFisher) at room temperature. Monosomes were purified using the Microspin™ S-400 HR (Cytiva). RNA was extracted from isolated monosomes using the RNA Clean & Concentrator-25 kit (Zymo Research). Ribosomal RNA was depleted by RiboMinus™ Eukaryote System v2 (ThermoFisher).
Ribosome-protected fragments (27-32 nt) were purified in 15% TBE-urea gels (ThermoFisher). The RNA fragments were end-repaired with T4 polynucleotide kinase (NEB), converted to Ribo-seq libraries using the TruSeq small RNA Library Prep Kit (Illumina) and sequenced on a NextSeq 500 Illumina (50 bp, single-end read).
Ribo-seq


title: RNA CRS T014N

source_name: CRS014 matched set, non-sepsis sample, tumor tissue

value: Female

value: 70-74 years


title: genomic DNA from saliva sample 86

description:
G3 saliva sample
I-036

source_name: saliva sample 86

tag: allergicproblems

tag: batch


title: Group 4 Weakly Adherent

value: Primary tumor

tag: mouse strain

value: Nod/Skid

tag: cell type

value: MDAMB231 GFP+ Luc+

tag: adhesion profile

value: Weakly adherent


title: Hela_DMSO_tRNA_Rep1

description: tRNA

tag: treatment

value: treated with DMSO for 18 hours


title: genomic DNA from saliva sample 84

description:
G3 saliva sample
I-014

source_name: saliva sample 84


title: Group 5 Strongly Adherent

value: Strongly adherent


title: Hela_DNMDP_RPF_Rep1

description: ribosome-protected mRNA fragments (RPF)

value: treated with DNMDP for 18 hours


title: Group 4 Unsorted

value: Unsorted


title: RNA CRS T014

source_name: CRS014 matched set, sepsis sample, tumor tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: tumor tissue

tag: age group

value: 40-44 years

tag: ethnicity

value: Japanese

tag: tumor stage

value: Moderately differentiated; Grade II

value: Yes


title: Group 4 Strongly Adherent


title: Hela_DMSO_RPF_Rep2

description: ribosome-protected mRNA fragments (RPF)


title: genomic DNA from saliva sample 83

description:
G3 saliva sample
I-045

source_name: saliva sample 83

tag: culturemedium

value: Male


title: RNA CRS T012

source_name: CRS012 matched set, sepsis sample, tumor tissue

value: sepsis sample

tag: Sex

value: 65-69 years

value: Localized

tag: tumor grade

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

tag: survival (months)


title: genomic DNA from saliva sample 82

description:
G3 saliva sample
I-067

source_name: saliva sample 82

value: Female

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems


title: WTFVB

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

institute: Stony Brook University

data_processing:
Single Cell sequencing data were pre-processed by cellranger 6.0.1 from 10X Genomics using default settings.
Downstreaming analysis was performed by Seurat 3.0
Assembly: mm10, GRCh38
Supplementary files format and content: gzipped file format containing "filtered_feature_bc_matrix" folder contents from cellranger outputs

source_name: mammary gland

extract_protocol:
The tumors were digested both mechanically and enzymatically (Collagenase/Hyaluronidase, and DNaseI) and single cell suspensions of viable cells were prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.
Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.

tag: strain

value: FVB

tag: tissue of origin for tumor

value: Mammary gland

tag: genetic alteration

value: WT


title: RNA CRS T011N

source_name: CRS011 matched set, non-sepsis sample, tumor tissue

tag: patient diagnosis

tag: sepsis status

value: non-sepsis sample

tag: tissue

value: 85+ years

value: Regional

value: No/Unknown


title: RNA CRS T013

source_name: CRS013 matched set, sepsis sample, tumor tissue

value: colorectal cancer

value: tumor tissue

tag: age group

value: 75-79 years

tag: ethnicity

tag: tumor stage

value: Distant


title: Hela_DNMDP_mRNA_Rep1

data_processing:
Ran the STAR aligner on the terra platform
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited read counts (by gene) files

extract_protocol:
Total RNA was extracted from cell lysates using the RNA Clean & Concentrator-25 kit (Zymo Research). Ribosomal RNA was depleted by RiboMinus™ Eukaryote System v2 (ThermoFisher). Purified total mRNA was heat-fragmented at 94°C for 25 minutes.
The RNA fragments were end-repaired with T4 polynucleotide kinase (NEB), converted to RNA-seq libraries using the TruSeq small RNA Library Prep Kit (Illumina) and sequenced on a NextSeq 500 Illumina (50 bp, single-end read).

tag: treatment

value: treated with DNMDP for 18 hours


title: CP_279F

source_name: pancreas

value: Congenic

value: Pancreas

value: Ptf1⍺-CreERTM; LSL- KRASG12D


title: Hela_DMSO_mRNA_Rep2

value: treated with DMSO for 18 hours


title: genomic DNA from saliva sample 81

description:
K-SICM saliva sample
I-103

source_name: saliva sample 81

tag: culturemedium

value: K-SICM

tag: Sex

value: Male

tag: batch


title: 57R4

value: FVB

value: Mammary gland

value: MMTV-PyMT


title: Hela_DMSO_RPF_Rep1

description: ribosome-protected mRNA fragments (RPF)


title: genomic DNA from saliva sample 80

description:
G3 saliva sample
I-009

source_name: saliva sample 80

value: Female

tag: samplecollectionage


title: genomic DNA from saliva sample 77

description:
G3 saliva sample
I-127

source_name: saliva sample 77

tag: autismrelateddisorder


title: Hela_DNMDP_mRNA_Rep2

source_name: Hela cell line


title: genomic DNA from saliva sample 79

description:
G3 saliva sample
I-109

source_name: saliva sample 79

tag: urologicalproblem


title: 55R4


title: RNA CRS T013N

source_name: CRS013 matched set, non-sepsis sample, tumor tissue

value: non-sepsis sample

value: Japanese

value: Regional

tag: tumor grade

value: Moderately differentiated; Grade II

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

tag: survival (months)


title: Hela_DMSO_mRNA_Rep1


title: BU3 EBOV 7 dpi replicate 2

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
Fastq files were align to the GRCh38 with Ebola Virus reference genome using STAR v.2.6 and default parameters
Ensembl v67 gene annotations were used for gene counts, gene counts were obtained using STAR v2.6
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: GRCh38 with Ebola Virus genome
Supplementary_files_format_and_content: Matrix of counts per million reads per sample

source_name: BU3 iPSCs

growth_protocol: iPSC-derived hepatocytes were generated in 2D in tissue culture

extract_protocol: After infection, cells were harvested in tissue culture plates using Trizol. Cells were incubated for 10 minutes in Trizol in accordance with Boston University's National Emerging Infectious Diseases Laboratory's inactivation protocols. Total RNA was isolated following manufacturer's instructions for Trizol Reagent.

tag: cell type

value: 2D iPSC-derived hepatocytes

tag: time point

value: 7 dpi

tag: agent

value: Ebola virus (EBOV)

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

value: D19 SFD

tag: isolation method

value: TriZol


title: RNA CRS T010

source_name: CRS010 matched set, sepsis sample, tumor tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: sepsis sample

tag: tissue

value: tumor tissue

tag: age group

value: 75-79 years

tag: ethnicity

tag: tumor stage

value: Localized

value: Unknown

value: Yes


title: genomic DNA from saliva sample 75

description:
K-SICM saliva sample
I-095

source_name: saliva sample 75

tag: culturemedium

value: K-SICM

tag: Sex

value: Female

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: RNA CRS T009N

source_name: CRS009 matched set, non-sepsis sample, tumor tissue

value: non-sepsis sample

value: Male

value: 70-74 years

value: Japanese

value: Regional

tag: tumor grade

tag: chemotherapy (y/n)

value: No/Unknown

tag: radiation treatment (y/n)

tag: survival (months)


title: genomic DNA from saliva sample 74

description:
K-SICM saliva sample
I-037

source_name: saliva sample 74


title: R1

tag: strain

value: FVB

tag: tissue of origin for tumor

value: Mammary gland

tag: genetic alteration


title: genomic DNA from saliva sample 78

description:
G3 saliva sample
I-047

source_name: saliva sample 78


title: L3


title: RNA CRS T011

source_name: CRS011 matched set, sepsis sample, tumor tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

tag: tissue

tag: age group

value: 85+ years

value: Moderately differentiated; Grade II


title: C3L4

source_name: mammary gland


title: genomic DNA from saliva sample 76

description:
G3 saliva sample
I-035

source_name: saliva sample 76

tag: culturemedium

tag: Sex


title: RNA CRS T009

source_name: CRS009 matched set, sepsis sample, tumor tissue

value: sepsis sample

value: tumor tissue

tag: ethnicity

tag: tumor stage


title: RNA CRS T010N

source_name: CRS010 matched set, non-sepsis sample, tumor tissue

value: 75-79 years

value: Localized


title: RNA CRS T012N

source_name: CRS012 matched set, non-sepsis sample, tumor tissue

value: 65-69 years

value: Distant

value: Yes


title: C3R4


title: BU3 EBOV 7 dpi replicate 1

tag: cell type

value: 2D iPSC-derived hepatocytes

tag: time point

value: 7 dpi

tag: agent

value: Ebola virus (EBOV)

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

value: D19 SFD

tag: isolation method

value: TriZol


title: genomic DNA from saliva sample 73

description:
K-SICM saliva sample
I-020

source_name: saliva sample 73

value: K-SICM

value: Male

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: BU3 EBOV 3 dpi replicate 1

value: 3 dpi


title: RNA CRS T007

source_name: CRS007 matched set, sepsis sample, tumor tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

tag: tissue

value: Female

value: 70-74 years

value: Japanese

tag: tumor grade

value: Moderately differentiated; Grade II

tag: chemotherapy (y/n)

value: No/Unknown

tag: radiation treatment (y/n)

tag: survival (months)


title: BU3 Mock 7 dpi replicate 2

tag: cell type

tag: time point

value: mock


title: HDM-3

city: Philadelphia

first: Deepak

last: Deshpande

state: PA

address: 1020 Locust Street

department: Center for Translational Medicine

institute: Thomas Jefferson University

data_processing:
Base-calling was done using Illumina's HiSeq Control Software. bcl2sastq 2.17 was used for obtaining fastq dataset.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result of this step.
Additional data analysis was carried out using Strand NGS 4.0 software
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include all genes expressed and fold change in all the replicate samples

source_name: Lung

extract_protocol:
Lungs were removed, placed in RNAlater solution, cut into small pieces and flash frozen on Liquid nitrogen. Lung tissue was homogenized in Trizol, and total RNA was isolated using a Direct-zol RNA extraction kit. RNA samples were sequenced at GeneWiz Next Generation Sequencing facility using Illumina HiSeq platform.
Libraries were prepared according to Illumina's instructions in 4 steps. These include 1) mRNA enrichment, mRNA fragmentation, and random priming, 2) first and second strand cDNA synthesis, 3) end repair, 5' phosphorylation, and dA tailing, and 4) adapter ligation, PCR enrichment and sequencing on the Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: Animals were treated with HDM intranasally once every day, 5 days/week for 3 weeks. A group of animals were treated with vehicle or 10 mg/kg SF-3-030 intranasally 30 min prior to HDM challenge.

tag: strain

value: BALB/c

value: Lung

tag: age/sex

value: 12 weeks/Female

tag: treatement

value: DMSO+HDM


title: HDM-2


title: BU3 EBOV 3 dpi replicate 2

value: 2D iPSC-derived hepatocytes

tag: agent

value: Ebola virus (EBOV)

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

tag: isolation method


title: SF-3-030+HDM-3


title: SF-3-030+HDM-2


title: RNA CRS T006N

source_name: CRS006 matched set, non-sepsis sample, tumor tissue

value: non-sepsis sample

value: tumor tissue

tag: Sex

tag: age group

tag: ethnicity

tag: tumor stage

value: Regional


title: genomic DNA from saliva sample 71

description:
K-SICM saliva sample
I-025

source_name: saliva sample 71

tag: culturemedium

value: K-SICM

value: Male

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: RNA CRS T007N

source_name: CRS007 matched set, non-sepsis sample, tumor tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

tag: tissue

value: Female

value: 70-74 years

tag: tumor grade

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

tag: survival (months)


title: genomic DNA from saliva sample 70

description:
K-SICM saliva sample
I-031

source_name: saliva sample 70

tag: Sex


title: genomic DNA from saliva sample 72

description:
G3 saliva sample
I-013

source_name: saliva sample 72


title: BU3 Mock 3 dpi replicate 2

source_name: BU3 iPSCs

tag: cell type

tag: time point

value: 3 dpi

tag: agent

tag: developmental stage

tag: culture media

value: D19 SFD

tag: isolation method

value: TriZol


title: Hela_DMSO_tRNA_Rep2

description: tRNA

source_name: Hela cell line

tag: treatment

value: treated with DMSO for 18 hours


title: genomic DNA from saliva sample 68

description:
G3 saliva sample
I-012

source_name: saliva sample 68

tag: culturemedium

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems


title: SF-3-030+HDM-1

tag: strain

value: BALB/c

tag: tissue

value: Lung

tag: age/sex

value: 12 weeks/Female

tag: treatement


title: BU3 Mock 7 dpi replicate 1

value: 2D iPSC-derived hepatocytes

value: 7 dpi

value: mock


title: BU3 EBOV 2 dpi replicate 2

value: 2 dpi

value: Ebola virus (EBOV)

value: differentiated hepatocytes


title: BU3 EBOV 2 dpi replicate 1


title: HDM-1

value: DMSO+HDM


title: genomic DNA from saliva sample 69

description:
K-SICM saliva sample
I-078

source_name: saliva sample 69

value: K-SICM

tag: Sex

value: Male

tag: batch


title: RNA CRS T005

source_name: CRS005 matched set, sepsis sample, tumor tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: sepsis sample

value: tumor tissue

tag: age group

value: 45-49 years

tag: ethnicity

value: Hawaiian

tag: tumor stage

value: Distant

tag: tumor grade

value: Poorly differentiated; Grade III

tag: chemotherapy (y/n)

value: No/Unknown

tag: radiation treatment (y/n)

tag: survival (months)


title: PBS-4

value: BALB/c

value: Lung

value: 12 weeks/Female

value: PBS


title: PBS-2


title: RNA CRS T006

source_name: CRS006 matched set, sepsis sample, tumor tissue

value: 70-74 years

value: Japanese

value: Regional

value: Moderately differentiated; Grade II

value: Yes


title: PBS-3


title: PBS-1


title: genomic DNA from saliva sample 65

description:
G3 saliva sample
I-118

source_name: saliva sample 65

tag: culturemedium

value: Female

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem


title: genomic DNA from saliva sample 66

description:
K-SICM saliva sample
I-093

source_name: saliva sample 66

value: K-SICM

tag: allergicproblems


title: RNA CRS T005N

source_name: CRS005 matched set, non-sepsis sample, tumor tissue

value: colorectal cancer

value: non-sepsis sample

tag: tissue

value: tumor tissue

value: Male


title: genomic DNA from saliva sample 61

description:
K-SICM saliva sample
I-023

source_name: saliva sample 61

tag: Sex


title: RNA CRS T003N

source_name: CRS003 matched set, non-sepsis sample, tumor tissue

value: 55-59 years

value: Hawaiian

value: Distant


title: RNA CRS T003

source_name: CRS003 matched set, sepsis sample, tumor tissue

value: sepsis sample

value: Poorly differentiated; Grade III


title: BU3 Mock 2 dpi replicate 2

tag: cell type

value: 2D iPSC-derived hepatocytes

tag: time point

value: 2 dpi

tag: agent

value: mock

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

value: D19 SFD

tag: isolation method

value: TriZol


title: genomic DNA from saliva sample 67

description:
G3 saliva sample
I-071

source_name: saliva sample 67

tag: batch


title: RNA CRS T003_rep

tag: patient diagnosis

tag: sepsis status

value: Female

tag: age group

tag: ethnicity

tag: tumor stage

value: Regional

tag: tumor grade

tag: chemotherapy (y/n)

value: Yes


title: RNA CRS T004N

source_name: CRS004 matched set, non-sepsis sample, tumor tissue

value: colorectal cancer

value: non-sepsis sample

value: Unknown

value: No/Unknown

tag: radiation treatment (y/n)

tag: survival (months)


title: BU3 Mock 2 dpi replicate 1


title: RNA CRS T002N

source_name: CRS002 matched set, non-sepsis sample, tumor tissue

tag: tissue

value: tumor tissue

tag: Sex

value: 70-74 years

value: Hawaiian

value: Localized

value: Moderately differentiated; Grade II


title: RNA CRS T004

source_name: CRS004 matched set, sepsis sample, tumor tissue

value: sepsis sample

value: Male

value: 55-59 years


title: BU3 Mock 3 dpi replicate 1

tag: cell type

value: 2D iPSC-derived hepatocytes

tag: time point

value: 3 dpi

value: mock

value: differentiated hepatocytes

value: D19 SFD


title: genomic DNA from saliva sample 64

description:
G3 saliva sample
I-120

source_name: saliva sample 64

tag: culturemedium

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor B EBOV replicate 2]

source_name: Human hepatocytes

tag: treatment

value: EBOLA

tag: developmental stage

value: primary hepatocytes

tag: culture media

value: PHH ITS media

tag: isolation method

value: TriZol


title: genomic DNA from saliva sample 63

description:
G3 saliva sample
I-128

source_name: saliva sample 63

value: Female

tag: batch


title: genomic DNA from saliva sample 62

description:
G3 saliva sample
I-016

source_name: saliva sample 62


title: BU3 EBOV 1 dpi replicate 1

source_name: BU3 iPSCs

value: 1 dpi

tag: agent

value: Ebola virus (EBOV)


title: genomic DNA from saliva sample 59

description:
K-SICM saliva sample
I-008

source_name: saliva sample 59

value: K-SICM


title: BU3 EBOV 1 dpi replicate 2


title: RNA CRS T008

source_name: CRS008 matched set, sepsis sample, tumor tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: tumor tissue

tag: age group

value: 70-74 years

tag: ethnicity

value: Japanese

tag: tumor stage

value: Regional

tag: tumor grade

value: Moderately differentiated; Grade II

tag: chemotherapy (y/n)

value: Yes

tag: radiation treatment (y/n)

value: No/Unknown


title: genomic DNA from saliva sample 60

description:
G3 saliva sample
I-007

source_name: saliva sample 60

tag: culturemedium

tag: Sex

tag: samplecollectionage

tag: autismrelateddisorder


title: BU3 Mock 1 dpi replicate 2

tag: cell type

value: 2D iPSC-derived hepatocytes

tag: time point

value: mock

tag: developmental stage

value: differentiated hepatocytes

value: D19 SFD


title: genomic DNA from saliva sample 58

description:
K-SICM saliva sample
I-101

source_name: saliva sample 58

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: genomic DNA from saliva sample 57

description:
K-SICM saliva sample
I-059

source_name: saliva sample 57

value: Male


title: RNA CRS T002

source_name: CRS002 matched set, sepsis sample, tumor tissue

tag: patient diagnosis

tag: sepsis status

value: sepsis sample

tag: tissue

value: Female

value: Hawaiian

value: Localized

tag: survival (months)


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor B Mock replicate 2]

tag: treatment

value: Mock

value: primary hepatocytes

tag: culture media

value: PHH ITS media

tag: isolation method

value: TriZol


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor B Mock replicate 1]


title: RNA CRS T001

source_name: CRS001 matched set, sepsis sample, tumor tissue

value: colorectal cancer

value: tumor tissue

tag: age group

value: 80-84 years

tag: ethnicity

tag: tumor stage

tag: tumor grade

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor A EBOV replicate 2]

value: EBOLA

tag: developmental stage


title: BU3 Mock 1 dpi replicate 1

tag: cell type

value: 2D iPSC-derived hepatocytes

tag: time point

value: 1 dpi

tag: agent


title: RNA CRS T001N

source_name: CRS001 matched set, non-sepsis sample, tumor tissue

tag: patient diagnosis

value: non-sepsis sample

tag: Sex

value: Moderately differentiated; Grade II

value: No/Unknown


title: RNA CRS N014

source_name: CRS014 matched set, sepsis sample, normal tissue

tag: sepsis status

value: sepsis sample

tag: tissue

value: normal tissue

value: 40-44 years

value: Japanese

value: Distant

value: Yes


title: RNA CRS N014N

source_name: CRS014 matched set, non-sepsis sample, normal tissue

value: Female

value: 70-74 years

value: Regional

tag: survival (months)


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor A Mock replicate 2]

tag: treatment

value: Mock

value: primary hepatocytes

tag: culture media

value: PHH ITS media

value: TriZol


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor A EBOV replicate 1]

value: EBOLA

tag: isolation method


title: genomic DNA from saliva sample 54

description:
K-SICM saliva sample
I-075

source_name: saliva sample 54

tag: culturemedium

value: K-SICM

value: Male

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: RNA CRS N015

source_name: CRS015 matched set, sepsis sample, normal tissue

value: colorectal cancer

tag: age group

value: 35-39 years

tag: ethnicity

tag: tumor stage

tag: tumor grade

value: Poorly differentiated; Grade III

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

value: No/Unknown


title: RNA CRS N013N

source_name: CRS013 matched set, non-sepsis sample, normal tissue

tag: patient diagnosis

tag: sepsis status

value: non-sepsis sample

tag: tissue

value: normal tissue

tag: Sex

value: 75-79 years

value: Japanese

value: Moderately differentiated; Grade II


title: genomic DNA from saliva sample 55

description:
G3 saliva sample
I-048

source_name: saliva sample 55


title: RNA CRS N013

source_name: CRS013 matched set, sepsis sample, normal tissue

value: sepsis sample

value: Distant

tag: survival (months)


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor B EBOV replicate 1]

source_name: Human hepatocytes

tag: treatment

tag: developmental stage

value: primary hepatocytes

tag: culture media

tag: isolation method


title: genomic DNA from saliva sample 53

description:
K-SICM saliva sample
I-094

source_name: saliva sample 53

tag: culturemedium

value: Female

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems


title: RNA CRS N012N

source_name: CRS012 matched set, non-sepsis sample, normal tissue

tag: age group

value: 65-69 years

tag: ethnicity

tag: tumor stage

tag: tumor grade

value: Yes


title: 2D iPSC-derived hepatocytes [BU3 EBOV replicate 3]

source_name: BU3 iPSCs

value: EBOLA

value: differentiated hepatocytes

value: D19 SFD

value: TriZol


title: 2D cryopreserved human hepatocytes [PHH 1 week Donor A Mock replicate 1]

value: Mock

value: PHH ITS media


title: genomic DNA from saliva sample 49

description:
K-SICM saliva sample
I-011

source_name: saliva sample 49

value: K-SICM

value: Male

tag: batch


title: 2D iPSC-derived hepatocytes [BU3 EBOV replicate 1]


title: RNA CRS N011N

source_name: CRS011 matched set, non-sepsis sample, normal tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: non-sepsis sample

tag: tissue

value: normal tissue

value: 85+ years

value: Regional

tag: chemotherapy (y/n)

value: No/Unknown

tag: radiation treatment (y/n)


title: genomic DNA from saliva sample 50

description:
K-SICM saliva sample
I-112

source_name: saliva sample 50

tag: Sex

value: Female


title: genomic DNA from saliva sample 51

description:
G3 saliva sample
I-076

source_name: saliva sample 51


title: RNA CRS N011

source_name: CRS011 matched set, sepsis sample, normal tissue

value: sepsis sample

value: Japanese

value: Localized

value: Moderately differentiated; Grade II

tag: survival (months)


title: 2D iPSC-derived hepatocytes [BU3 EBOV replicate 2]

tag: treatment

value: EBOLA

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

value: D19 SFD

tag: isolation method


title: RNA CRS N010N

source_name: CRS010 matched set, non-sepsis sample, normal tissue

value: 75-79 years


title: genomic DNA from saliva sample 56

description:
G3 saliva sample
I-065

source_name: saliva sample 56

tag: culturemedium

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems


title: 2D iPSC-derived hepatocytes [BU3 Mock replicate 3]

value: Mock

value: TriZol


title: genomic DNA from saliva sample 48

description:
G3 saliva sample
I-006

source_name: saliva sample 48

value: Male

tag: batch


title: RNA CRS N010

source_name: CRS010 matched set, sepsis sample, normal tissue

tag: patient diagnosis

value: colorectal cancer

tag: age group

tag: ethnicity

tag: tumor stage

tag: tumor grade

value: Unknown

value: Yes


title: genomic DNA from saliva sample 47

description:
G3 saliva sample
I-022

source_name: saliva sample 47

tag: Sex


title: RNA CRS N009N

source_name: CRS009 matched set, non-sepsis sample, normal tissue

tag: sepsis status

value: non-sepsis sample

tag: tissue

value: normal tissue

value: 70-74 years

value: Regional

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

tag: survival (months)


title: genomic DNA from saliva sample 46

description:
K-SICM saliva sample
I-044

source_name: saliva sample 46

tag: culturemedium

value: K-SICM


title: 2D iPSC-derived hepatocytes [BU2 EBOV replicate 3]

source_name: BU2 iPSCs

tag: treatment

tag: developmental stage

tag: culture media

tag: isolation method


title: RNA CRS N009

source_name: CRS009 matched set, sepsis sample, normal tissue

value: sepsis sample

value: Japanese

value: Localized

value: No/Unknown


title: genomic DNA from saliva sample 52

description:
G3 saliva sample
I-072

source_name: saliva sample 52

value: Female

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: genomic DNA from saliva sample 45

description:
K-SICM saliva sample
I-111

source_name: saliva sample 45


title: NP- Marginal Zone B cells [PBS3MZ]

city: Geneva

first: Viola

last: Puddinu

address: CMU-Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description: i.v.injection with PBS

data_processing:
Illumina bcl2fastq2 v. 2.20 0 was used for base calling.
The reads were mapped with the STAR aligner v.2.7.0f to the UCSC mouse mm10 reference.
The table of counts with the number of reads mapping to each gene feature of the UCSC mouse mm10 reference was prepared with HTSeq v0.9p1.
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.14.0 with a  quasi-likelihood (QL) F-test.
Genome_build: mm10

source_name: Splenic B cells

extract_protocol:
Cells were lysated with Tryzol and stored at -80°C, then RNA was extracted with the RNA clean and concentrator -5 kit from Zymo Research
The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina

treatment_protocol: Mice were intravenously injected with 400 µg GNPs in PBS. Immediately after, a mixture of 100 µg ovalbumin (OVA, Inviviogen) and 10 µg R848 in PBS was subcutaneously injected into mouse flank. On day 14 splenocytes were collected and NP+ cells were sorted by FACS according to the following gating strategy: B cells were defined as CD19+/CD3- cells, after exclusion of doublets, B cells subtypes were defined depending on the expression of CD23 and CD21:  CD21+/CD23+ Follicular cells  (FO), CD21+/CD23- marginal zone cells (MZ), CD21- CD23- cells (DN: double negative). GNP-Cy5+ (NP+) cells from each subpopulation were finally collected.

tag: background strain

tag: cell type

value: CD19+ B cells

value: PBS


title: NP- Follicular B cells [PBS3FO]

description: i.v.injection with PBS


title: 2D iPSC-derived hepatocytes [BU2 EBOV replicate 2]

value: EBOLA

value: differentiated hepatocytes

value: D19 SFD

value: TriZol


title: RNA CRS N008N

source_name: CRS008 matched set, non-sepsis sample, normal tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

tag: Sex

tag: age group

tag: ethnicity

tag: tumor stage

tag: tumor grade

value: Moderately differentiated; Grade II

value: Yes


title: NP- CD21-CD23- B cells [PBS3DN]

description: i.v.injection with PBS

tag: treatment


title: genomic DNA from saliva sample 44

description:
G3 saliva sample
I-028

source_name: saliva sample 44

tag: culturemedium

value: Male


title: 2D iPSC-derived hepatocytes [BU2 EBOV replicate 1]

tag: developmental stage

tag: culture media

tag: isolation method


title: RNA CRS N008

source_name: CRS008 matched set, sepsis sample, normal tissue

tag: tissue

value: normal tissue

value: 70-74 years

value: Regional

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

tag: survival (months)


title: genomic DNA from saliva sample 43

description:
K-SICM saliva sample
I-100

source_name: saliva sample 43

value: K-SICM

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: 2D iPSC-derived hepatocytes [BU2 Mock replicate 3]

value: Mock


title: genomic DNA from saliva sample 42

description:
K-SICM saliva sample
I-135

source_name: saliva sample 42

tag: Sex


title: NP- Marginal Zone B cells [PBS2MZ]

description: i.v.injection with PBS

tag: background strain

tag: cell type


title: RNA CRS N007N

source_name: CRS007 matched set, non-sepsis sample, normal tissue

tag: patient diagnosis

tag: sepsis status

value: non-sepsis sample

tag: age group

tag: ethnicity

value: Japanese

tag: tumor stage

tag: tumor grade

value: No/Unknown


title: 2D iPSC-derived hepatocytes [BU2 Mock replicate 2]

tag: treatment

tag: developmental stage

tag: culture media

tag: isolation method


title: genomic DNA from saliva sample 41

description:
G3 saliva sample
I-108

source_name: saliva sample 41

tag: culturemedium

tag: samplecollectionage

tag: autismrelateddisorder


title: 2D iPSC-derived hepatocytes [BU2 Mock replicate 1]


title: 2D iPSC-derived hepatocytes [BU3 Mock replicate 1]

source_name: BU3 iPSCs


title: RNA CRS N006N

source_name: CRS006 matched set, non-sepsis sample, normal tissue

tag: tissue

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

tag: survival (months)


title: 2D iPSC-derived hepatocytes [BU3 Mock replicate 2]


title: NP- CD21-CD23- B cells [PBS2DN]

description: i.v.injection with PBS

tag: background strain

tag: cell type

value: CD19+ B cells

value: PBS


title: RNA CRS N006

source_name: CRS006 matched set, sepsis sample, normal tissue

tag: patient diagnosis

tag: sepsis status

value: sepsis sample

tag: Sex

tag: age group


title: genomic DNA from saliva sample 40

description:
G3 saliva sample
I-058

source_name: saliva sample 40

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: NP- Marginal Zone B cells [PBS1MZ]

description: i.v.injection with PBS

tag: treatment


title: 2D iPSC-derived hepatocytes [BU1 EBOV replicate 3]

source_name: BU1 iPSCs

value: EBOLA

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

value: D19 SFD

tag: isolation method


title: RNA CRS N005N

source_name: CRS005 matched set, non-sepsis sample, normal tissue

value: colorectal cancer

tag: tissue

value: 45-49 years

tag: ethnicity

value: Hawaiian

tag: tumor stage

value: Distant

tag: tumor grade

value: Moderately differentiated; Grade II


title: NP- Follicular B cells [PBS1FO]

description: i.v.injection with PBS

tag: background strain


title: genomic DNA from saliva sample 39

description:
K-SICM saliva sample
I-089

source_name: saliva sample 39

tag: culturemedium

value: Female

tag: samplecollectionage

tag: autismrelateddisorder


title: 2D iPSC-derived hepatocytes [BU1 EBOV replicate 2]

value: TriZol


title: RNA CRS N004N

source_name: CRS004 matched set, non-sepsis sample, normal tissue

tag: patient diagnosis

tag: sepsis status

value: normal tissue

tag: Sex

value: Male

value: 55-59 years

value: Regional

value: Unknown

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

value: Yes

tag: survival (months)


title: NP- Follicular B cells [PBS2FO]

description: i.v.injection with PBS

tag: cell type

value: CD19+ B cells

tag: treatment

value: PBS


title: NP- CD21-CD23- B cells [PBS1DN]

description: i.v.injection with PBS


title: genomic DNA from saliva sample 38

description:
G3 saliva sample
I-057

source_name: saliva sample 38

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: NP+ Marginal Zone B cells [NP4MZ]

description: i.v. injection with 400 µg GNPs+ s.c of OVA antigen (100 µg) and R848 adjuvant (10 µg)

source_name: Splenic B cells

value: GNPs+ OVA and R848


title: 2D iPSC-derived hepatocytes [BU1 EBOV replicate 1]

value: EBOLA

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

value: D19 SFD

tag: isolation method


title: 2D iPSC-derived hepatocytes [BU1 Mock replicate 3]

value: Mock


title: RNA CRS N004

source_name: CRS004 matched set, sepsis sample, normal tissue

value: colorectal cancer

value: sepsis sample

tag: tissue

tag: age group

tag: ethnicity

value: Hawaiian

tag: tumor stage

tag: tumor grade


title: genomic DNA from saliva sample 37

description:
G3 saliva sample
I-096

source_name: saliva sample 37

tag: culturemedium

tag: Sex

value: Female

tag: samplecollectionage

tag: autismrelateddisorder


title: NP+ Follicular B cells [NP4FO]

tag: background strain

tag: cell type


title: genomic DNA from saliva sample 36

description:
G3 saliva sample
I-117

source_name: saliva sample 36

tag: urologicalproblem


title: 2D iPSC-derived hepatocytes [BU1 Mock replicate 2]

tag: treatment

value: TriZol


title: RNA CRS N003

source_name: CRS003 matched set, sepsis sample, normal tissue

tag: patient diagnosis

tag: sepsis status

value: normal tissue

value: Poorly differentiated; Grade III

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)

tag: survival (months)


title: genomic DNA from saliva sample 35

description:
K-SICM saliva sample
I-001

source_name: saliva sample 35

value: K-SICM

value: Male

tag: allergicproblems

tag: batch


title: RNA CRS N002N

source_name: CRS002 matched set, non-sepsis sample, normal tissue

value: non-sepsis sample

tag: tissue

tag: age group

value: 70-74 years

tag: ethnicity

tag: tumor stage

value: Localized

value: Moderately differentiated; Grade II

value: No/Unknown


title: genomic DNA from saliva sample 34

description:
K-SICM saliva sample
I-063

source_name: saliva sample 34

tag: culturemedium

tag: Sex

tag: samplecollectionage


title: NP+ Marginal Zone B cells [NP3MZ]

tag: background strain

tag: cell type

value: CD19+ B cells

value: GNPs+ OVA and R848


title: 2D iPSC-derived hepatocytes [BU1 Mock replicate 1]

tag: treatment

value: Mock

tag: developmental stage

value: differentiated hepatocytes

tag: culture media

value: D19 SFD

tag: isolation method


title: NP+ Marginal Zone B cells [NP2MZ]


title: Immortalized hepatocarcinoma cells [Huh7 EBOV replicate 3]

source_name: Huh7 cells

value: EBOLA

value: immortalized hepatocytes

value: Standard cell culture media


title: Immortalized hepatocarcinoma cells [Huh7 EBOV replicate 2]

value: TriZol


title: RNA CRS N001

source_name: CRS001 matched set, sepsis sample, normal tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: sepsis sample

value: normal tissue

value: Female

value: 80-84 years

value: Hawaiian

tag: tumor grade

tag: chemotherapy (y/n)

tag: radiation treatment (y/n)


title: NP+ Follicular B cells [NP2FO]


title: genomic DNA from saliva sample 32

description:
G3 saliva sample
I-137

source_name: saliva sample 32

value: Male

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: Immortalized hepatocarcinoma cells [Huh7 EBOV replicate 1]


title: genomic DNA from saliva sample 33

description:
K-SICM saliva sample
I-136

source_name: saliva sample 33

tag: culturemedium

value: K-SICM

tag: Sex


title: NP+ CD21-CD23- B cells [NP2DN]

tag: background strain

value: CD19+ B cells


title: INPUT-CON

city: Guangzhou

first: Jialuo

address: 132# Waihuandong Road, Guangzhou University City

department: School of Pharmaceutical Sciences

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2 with the following configurations
Genome_build: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary_files_format_and_content: bw files were generated using MACS2, UCSC and bedTools
Supplementary_files_format_and_content: peak text files

source_name: prostate cancer cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the BGISEQ-500 following the manufacturer's protocols.

treatment_protocol: C4-2B cells treated with YDGY-3 (20 nM)for 24 h

tag: disease

value: prostate cancer

tag: cell line

tag: chip antibody

value: untreated


title: RNA CRS N003N

source_name: CRS003 matched set, non-sepsis sample, normal tissue

value: non-sepsis sample

tag: tissue

tag: age group

value: 55-59 years

tag: ethnicity

tag: tumor stage

value: Distant

value: Moderately differentiated; Grade II

value: Yes

tag: survival (months)


title: genomic DNA from saliva sample 31

description:
K-SICM saliva sample
I-061

source_name: saliva sample 31

tag: samplecollectionage


title: genomic DNA from saliva sample 30

description:
K-SICM saliva sample
I-130

source_name: saliva sample 30


title: NP+ Marginal Zone B cells [NP1MZ]

tag: cell type

tag: treatment

value: GNPs+ OVA and R848


title: INPUT-3-20nM

value: treated with YDGY-3 20nM for 24 hours


title: NP+ CD21-CD23- B cells [NP4DN]


title: genomic DNA from saliva sample 29

description:
G3 saliva sample
I-107

source_name: saliva sample 29

tag: autismrelateddisorder

tag: urologicalproblem


title: Immortalized hepatocarcinoma cells [Huh7 Mock replicate 2]

value: Mock

tag: developmental stage

value: immortalized hepatocytes

tag: culture media

value: Standard cell culture media

tag: isolation method

value: TriZol


title: NP+ Follicular B cells [NP1FO]

source_name: Splenic B cells

tag: background strain


title: RNA CRS N002

source_name: CRS002 matched set, sepsis sample, normal tissue

tag: patient diagnosis

value: colorectal cancer

tag: sepsis status

value: sepsis sample

value: normal tissue

tag: Sex

value: Female

value: 70-74 years

value: Hawaiian

value: Localized

tag: tumor grade

tag: chemotherapy (y/n)

value: No/Unknown

tag: radiation treatment (y/n)


title: H3K27AC-CON

tag: disease

value: prostate cancer

tag: cell line

tag: chip antibody

value: H3K27ac antibody (abcam, #ab4729)

value: untreated


title: H3K27AC-3-20nM


title: C4-2B YDGY-3BR-20nM-24h

description:
3_CON_IPZ_YDGY3BR_genes_fpkm_expression.txt
YDGY3BR

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C4-2B cells treated with YDGY-3 (20 nM), YDGY-3BR (20 nM) or IPZ (20 mM) for 24 h

tag: tissue

value: prostate

tag: cell type


title: C4-2B IPZ-20mM-24h

description:
3_CON_IPZ_YDGY3BR_genes_fpkm_expression.txt
IPZ

tag: treatment


title: genomic DNA from saliva sample 28

description:
G3 saliva sample
I-077

source_name: saliva sample 28

tag: culturemedium

value: Male

tag: samplecollectionage

tag: autismrelateddisorder

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: genomic DNA from saliva sample 26

description:
K-SICM saliva sample
I-051

source_name: saliva sample 26

value: K-SICM


title: intestine, KO HFD3

city: Bethesda

first: Yuhong

last: Luo

state: MD

address: 37 Convent Dr

department: NCI

institute: NATIONAL INSTITUTES OF HEALTH

data_processing:
12 RNA-seq samples were pooled and sequenced on HiSeq using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing. The samples have 104 to 166 million pass filter reads with more than 88% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome (Mouse - mm10) and the annotated transcripts using STAR.
The mapping statistics were calculated using Picard software. Library complexity was measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: intestine

extract_protocol:
Total RNA was isolated from mouse intestines using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, #74136) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep.

treatment_protocol: 7-8 weeks old male Pparafl/fl and PparaΔIE mice were fed a Chow or 60% HFD for 10 days.

tag: strain

value: intestine

tag: genotype

value: Ppara{delta}IE

value: HFD


title: hPSC-pSHF-DAY20

city: Toronto

first: Gordon

last: Keller

state: Ontario

address: 101 College Street

department: McEwen stem cell institute

country: Canada

institute: University of Toronto

data_processing:
Raw data of Illumina's base call files (Cell Ranger to process 10x Genomics data)
Bam files and read count matrix (QC by Cell Ranger)
Updated read count matrix and imputed it
Genome_build: GRCH38
Supplementary_files_format_and_content: Cell Ranger output files

growth_protocol: FHF mesoderm is specified with 16 ng/mL BMP4, 5ng/mL bFGF and 8 ng/mL ActivinA from HES2-WT-hPSCs, and the SHF mesoderm is generated with 3 ng/mL BMP4, 5ng/mL bFGF and 1.5 ng/mL

extract_protocol:
10X Genomics Single Cell 3ʹ Reagent Kits v3 protocols
10X Genomics 3ʹ Gene Expression Library Construction (fragmentation Mix, purified cDNA for Library Construction, and adaptor ligation mix)

treatment_protocol: Distinctively patterned mesoderm populations are treated with 2 uM IWP2 and 10 ng/mL VEGF (day 3 to day 5) for the generation of cardiac progenitors. At the progenitor stage, aSHF cells are treated with 2 uM retinol and 10 ng/mL BMP4, and pSHF cells are treated with 2 uM of retinol for 3 days (day 5 to day 8). The treated progenitors were cultured to day 20 for the differentiation of cardiomyocytes.

value: pSHF cardiomyocyte

tag: source

value: hPSC-derived


title: C4-2B Vehicle-2

description:
3_CON_IPZ_YDGY3BR_genes_fpkm_expression.txt
CON

value: DMSO


title: genomic DNA from saliva sample 25

description:
G3 saliva sample
I-050

data_processing: The raw data were processed in R using the RnBeads package. SWAN normalisation was carried out before greedycut (p-value threshold 0.05) filtering was applied to remove poor quality sites and samples. Further filtering was carried out to remove sites (i) on the sex chromosomes, (ii) near single nucleotide polymorphisms, (iii) with missing values in more than 5% of samples, (iv) sites not in a CpG context. Samples were also excluded if their predicted sex, predicted using the sEsst package, did not match the recorded sex. The values presented are methylation beta values.

source_name: saliva sample 25

extract_protocol: DNA was extracted from saliva samples using the Saliva DNA Collection, Preservation and Isolation Kit (Norgen Biotek, Canada) according to the manufacturer's instructions.

tag: Sex

value: Female


title: Immortalized hepatocarcinoma cells [Huh7 Mock replicate 3]

value: Mock

tag: developmental stage

value: immortalized hepatocytes

tag: culture media

value: Standard cell culture media

tag: isolation method

value: TriZol


title: intestine, KO HFD2


title: S2-CTRL_HRO_2

city: Bonn

first: Lisa

last: Steinheuer

address: Venusberg Campus 1

department: Institute of Experimental Oncology

institute: University Hospital Bonn

data_processing:
To build the reference for Cell Ranger, human genome (hg38) as well as gene annotation (Ensembl 87) were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger (options: ‘-‑attribute=gene_biotype:protein_coding -‑attribute=gene_biotype:lincRNA -‑attribute=gene_biotype:antisense’).
Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference.
The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software (v2.1.0) provided by 10X Genomics with the option ‘--expect-cells’ set to 5000.
All other options were used as per default.
Genome_build: human genome hg38 (GRCh38) (Ensembl V87)
Supplementary_files_format_and_content: Tab-delimited text files include cell-barcode names (barcodes.tsv) as well as gene names (genes.tsv) corresponding to the count data in matrix.mtx. The h5ad-file includes the processed count data after the scanpy workflow descripted in the publication.

source_name: Human retinal organoid cells

growth_protocol: Human retinal organoids (HROs) were differentiated from an established hiPSC line (5A line from Lojewski et al., 2014) and using a protocol modified from previous works (Lowe et al., 2016, Zhu et al., 2013).

extract_protocol:
21.8 µl of the cells suspension (an estimated number of 9,000-11,000 cells) were carefully mixed with reverse transcription reaction mix using the Chromium Single Cell 3’ Library & Gel beads chemistry v2 and loaded into a Chromium Single Cell A Chip (10X Genomics, Pleasanton, CA). During the encapsulation process in the 10X Genomics Chromium system (Zheng et al., 2017), the cells lysed within the droplet and released polyadenylated RNA bound to the barcoded bead that was captured with the cell.
Following the guidelines of the 10X Genomics user manual, the droplets were directly subjected to reverse transcription, the emulsion was broken and cDNA was purified using Dynabeads MyOne Silane (ThermoFisher Scientific). After the amplification of cDNA with 10 cycles, it underwent purification and a quality control check on the Fragment Analyzer. The cDNA was fragmented for five minutes and dA-tailed, followed by an adapter ligation step and an indexing PCR of 10 cycles in order to generate libraries.
After quantification, the libraries were sequenced on an Illumina NextSeq 500 machine using a high-output flowcell in PE mode (R1: 26 cycles; I1: 8 cycles; R2: 57 cycles), thus generating 220 mio. fragments at minimum per sample.

treatment_protocol: One individual whole HRO (N=1 experiment) at day 200 of differentiation was dissociated using the Papain Dissociation System (Worthington Industries). Dissociated cells were resuspended in PBS with 0.04% BSA, passed through a 50um filter (CellTrics, Sysmex) to remove cell clumps and processed for sequencing immediately. Cells were counted in a Neubauer chamber.

value: hiPSC-derived retinal organoid

tag: time point

value: day 200 of differentiation


title: hPSC-FHF-DAY20

value: FHF cardiomyocyte


title: intestine, KO HFD1

tag: tissue


title: genomic DNA from saliva sample 27

description:
K-SICM saliva sample
I-110

source_name: saliva sample 27


title: hPSC-aSHF-DAY20

tag: cell type

value: aSHF cardiomyocyte


title: C4-2B YDGY-3-20nM-24h

description:
2_DMSO_YDGY-3_genes_fpkm_expression.txt
YDGY_3

value: prostate

tag: treatment


title: C4-2B Vehicle-1

description:
2_DMSO_YDGY-3_genes_fpkm_expression.txt
DMSO


title: genomic DNA from saliva sample 23

description:
G3 saliva sample
I-070

source_name: saliva sample 23

tag: culturemedium

value: Male


title: genomic DNA from saliva sample 24

description:
G3 saliva sample
I-019

source_name: saliva sample 24

tag: samplecollectionage


title: intestine, WT HFD3

value: intestine

value: Pparafl/fl


title: intestine, WT HFD2

value: HFD


title: Immortalized hepatocarcinoma cells [Huh7 Mock replicate 1]

source_name: Huh7 cells


title: hPSC-pSHF-DAY6

value: pSHF progenitor


title: genomic DNA from saliva sample 22

description:
G3 saliva sample
I-046

source_name: saliva sample 22

tag: autismrelateddisorder


title: NP+ CD21-CD23- B cells [NP1DN]

tag: background strain

value: CD19+ B cells

value: GNPs+ OVA and R848


title: intestine, WT HFD1


title: DRG from Mtor WT mice after SNI, replicate 5

first: Lunhao

last: Chen

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
The sequencing data was filtered with SOAPnuke (V1.5.2) by removing reads containing sequencing adapter.
The clean reads were mapped to the reference genome using HISAT2 (v 2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expresssion level of gene was calculated by RSEM (v1.2.12)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM and read counts values for each Sample

source_name: Dorsal root ganglion

extract_protocol:
4 lumber DRGs (bilateral L4 and L5 DRGs) were collected from each mouse before or 7 days after SNI. RNAs were isolated using RNeasy micro kit (Cat# 74004, QIAGEN, Germany) according to the manufacturer’s instructions.
RNA sequencing (RNA-seq) libraries were constructed and sequenced by BGISEQ-500 (BGI, China).

value: Dorsal root ganglion

value: Mtorfl/fl

tag: disease state

value: SNI 7d


title: hPSC-FHF-DAY6

value: FHF progenitor

value: hPSC-derived


title: genomic DNA from saliva sample 21

description:
K-SICM saliva sample
I-099

source_name: saliva sample 21

value: K-SICM

value: Female

tag: urologicalproblem

tag: allergicproblems

tag: batch


title: DRG from Mtor WT mice after SNI, replicate 4

tag: strain

tag: genotype


title: intestine, KO chow3

value: Ppara{delta}IE

value: Chow


title: DRG from Mtor WT mice after SNI, replicate 2


title: hPSC-SHF-DAY4

value: SHF late mesoderm

tag: source


title: hPSC-FHF-DAY4

value: FHF late mesoderm


title: intestine, KO chow2

value: intestine


title: genomic DNA from saliva sample 20

description:
G3 saliva sample
I-132

source_name: saliva sample 20

tag: Sex

value: Male


title: intestine, KO chow1


title: hPSC-aSHF-DAY6

value: aSHF progenitor


title: genomic DNA from saliva sample 18

description:
K-SICM saliva sample
I-053

source_name: saliva sample 18


title: genomic DNA from saliva sample 19

description:
K-SICM saliva sample
I-069

source_name: saliva sample 19


title: DRG from Mtor WT untreated mice, replicate 4

value: basal state


title: intestine, WT chow2

value: Pparafl/fl


title: RD.R3

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description:
RPE-1 cells in DMSO replicate 3
bcc34_Log2CPM.txt

data_processing:
RNA-Seq reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38)  using using HISAT2 version 2.1.0
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes log2 cpm values for each sample

source_name: RPE-1 cell line

growth_protocol: RPE-1 and BJ cells were cultured in media (DMEM-F12 or DMEM, respectively) supplemented with 10% FBS and 100U penicillin/streptomycin, in flasks.

extract_protocol:
RNA was extracted using Qiagen RNEasy kit
Library construction was performed using Lexogen 3’ tagSeq kit and RNAseq was carried out at Bart's and the London Genome Centre.

treatment_protocol: Cells were treated with 0.4micromolar aphidicolin or similar volume vehicle (DMSO) as control, for 24hrs, before RNA was extracted.

tag: cell line

value: DMSO


title: genomic DNA from saliva sample 15

address: Maastricht UMC+

institute: Maastricht University Medical Centre

description:
K-SICM saliva sample
I-113

source_name: saliva sample 15


title: intestine, WT chow3


title: intestine, WT chow1


title: genomic DNA from saliva sample 16

description:
G3 saliva sample
I-116

source_name: saliva sample 16


title: DRG from Mtor WT mice after SNI, replicate 1

value: Dorsal root ganglion


title: genomic DNA from saliva sample 17

description:
K-SICM saliva sample
I-073

source_name: saliva sample 17


title: DRG from Mtor WT untreated mice, replicate 3

value: Mtorfl/fl


title: hPSC-SHF-DAY3

value: SHF mesoderm


title: Brain_Week13_NM2913_4

city: Bar Harbor

first: Robert

last: Burgess

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Filtering of reads was perfomed using NGSQCToolkit/2.3 and custom perls scripts
Read alignment was done using bowtie2/2.2.0
Read count estimations were performed using rsem/1.2.12
Genome_build: We used the Mus musculus GRCm38v74 genome for this work
Supplementary_files_format_and_content: Read counts matrix from rsem

source_name: Brain

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Tissues were lysed and homogenized in TRIzol Reagent (ThermoFisher). After the addition of chloroform, the RNA-containing aqueous layer was removed for RNA isolation according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA Total RNA Nano assay (Agilent Technologies).
Libraries were prepared using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  Libraries were checked for quality and concentration using the D5000 ScreenTape assay (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturers’ instructions.
Libraries were pooled and sequenced 70 bp single-end on the HiSeq 4000 (Illumina) using HiSeq 3000/4000 SBS Kit reagents (Illumina), targeting 30 million reads per sample.

value: Brain

tag: age

value: Week 13

value: male


title: RD.R2

description:
RPE-1 cells in DMSO replicate 2
bcc34_Log2CPM.txt


title: Brain_Week13_NM2913_3

tag: tissue

value: female


title: RA.R3

description:
RPE-1 cells in Aphidicolin replicate 3
bcc34_Log2CPM.txt

value: Aphidicolin


title: DRG from Mtor WT mice after SNI, replicate 3

value: SNI 7d


title: DRG from Mtor WT untreated mice, replicate 2


title: DRG from Mtor-cKO mice after SNI, replicate 4


title: hPSC-FHF-DAY3

tag: cell type

value: FHF mesoderm

value: hPSC-derived


title: RA.R2

description:
RPE-1 cells in Aphidicolin replicate 2
bcc34_Log2CPM.txt

tag: treatment


title: DRG from Mtor-cKO mice after SNI, replicate 3


title: Brain_Week13_NM2913_2


title: genomic DNA from saliva sample 12

city: Maastricht

first: Rebekka

last: Koeck

description:
G3 saliva sample
I-034

source_name: saliva sample 12

tag: culturemedium


title: RA.R1

description:
RPE-1 cells in Aphidicolin replicate 1
bcc34_Log2CPM.txt


title: RD.R1

description:
RPE-1 cells in DMSO replicate 1
bcc34_Log2CPM.txt


title: DRG from Mtor WT untreated mice, replicate 1


title: BD.R3

description:
BJ cells in DMSO replicate 3
bcc34_Log2CPM.txt

source_name: BJ cell line

value: BJ


title: Brain_Week6_NM2913_7

value: Week 6


title: DRG from Mtor-cKO mice after SNI, replicate 2


title: Brain_Week13_NM2913_1


title: Brain_Week6_NM2913_8


title: genomic DNA from saliva sample 11

description:
G3 saliva sample
I-038

source_name: saliva sample 11

value: Male

tag: samplecollectionage


title: DRG from Mtor-cKO untreated mice, replicate 4

value: basal state


title: genomic DNA from saliva sample 14

description:
G3 saliva sample
I-032

source_name: saliva sample 14

value: Female

tag: autismrelateddisorder


title: BD.R1

description:
BJ cells in DMSO replicate 1
bcc34_Log2CPM.txt

value: DMSO


title: DRG from Mtor-cKO mice after SNI, replicate 1

value: Dorsal root ganglion


title: DRG from Mtor-cKO untreated mice, replicate 3


title: Brain_Week6_NM2913_6


title: BD.R2

description:
BJ cells in DMSO replicate 2
bcc34_Log2CPM.txt


title: genomic DNA from saliva sample 9

description:
G3 saliva sample
I-079

source_name: saliva sample 9


title: genomic DNA from saliva sample 8

description:
K-SICM saliva sample
I-056

source_name: saliva sample 8

value: K-SICM


title: genomic DNA from saliva sample 13

description:
K-SICM saliva sample
I-085

source_name: saliva sample 13


title: Brain_Week6_NM2913_5


title: genomic DNA from saliva sample 10

description:
K-SICM saliva sample
I-030

source_name: saliva sample 10


title: DRG from Mtor-cKO untreated mice, replicate 2

source_name: Dorsal root ganglion


title: BA.R3

description:
BJ cells in Aphidicolin replicate 3
bcc34_Log2CPM.txt


title: genomic DNA from saliva sample 6

description:
K-SICM saliva sample
I-086

source_name: saliva sample 6


title: DRG from Mtor-cKO untreated mice, replicate 1


title: genomic DNA from saliva sample 7

description:
G3 saliva sample
I-026

source_name: saliva sample 7


title: BA.R2

description:
BJ cells in Aphidicolin replicate 2
bcc34_Log2CPM.txt


title: Brain_Week6_NM2913_4


title: Brain_Week6_NM2913_3


title: BA.R1

description:
BJ cells in Aphidicolin replicate 1
bcc34_Log2CPM.txt


title: Brain_Week6_NM2913_2


title: genomic DNA from saliva sample 5

description:
G3 saliva sample
I-040

source_name: saliva sample 5


title: Brain_Week6_NM2913_1


title: genomic DNA from saliva sample 4

description:
K-SICM saliva sample
I-049

source_name: saliva sample 4


title: Brain_Week11_NMF421_11

value: Nadk2 +/+

value: Week 11


title: Y3S5

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

description: each sample is genomic material from one animal.

data_processing:
The fastq reads were mapped to the mm10 genome using bowtie2 (V. 2.3.5) (Langmead & Salzberg, 2012). Duplicates were removed using MarkDuplicates program of Picard Tools (V. 2.21.4) (http://broadinstitute.github.io/picard). For mapping spike-in fragments to the yeast genome, the ‘–no-overlap–no-dovetail’ options were set and mapped to a repeat-masked version of the yeast genome (R64) to avoid crossmapping of the mouse genome to that of the yeast genome.
Peak calibration was done as described (Skene & Henikoff, 2017). The peaks were then called using the SEACR-package (V. 1.3) in ‘stringent‘-mode (Meers et al, 2019).
Assembly: mm10
Supplementary files format and content: Peak calibration was done as described (Skene & Henikoff, 2017). The peaks were then called using the SEACR-package (V. 1.3) in ‘stringent‘-mode (Meers et al, 2019).

source_name: Liver tissue

extract_protocol:
50mg of 4 young and 4 old mouse liver tissues were used. 5million of nuclei were extracted using the same process described for the ATAC-seq experiment. CUT&RUN  was performed on 1 million nuclei per sample as previously described with modifications (Skene & Henikoff, 2017). Nuclei were prepared using the Nuclei EZ prep kit (Sigma-Aldrich, NUC-101). Subsequently, nuclei were washed twice with Wash Buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine) and bound to activated Concanavalin A beads for 10 min at room temperature. Cell-bead suspension was then resuspended in antibody buffer (20 mM MHEPES, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 2 mM EDTA) and incubated overnight at 4°C with S2-phospho (ab5095), S5-phospho (ab 5408) and PolII-CTD (ab26721) antibodies from Abcam, in a concentration 1:250. Cell-bead suspension was then washed twice with Digitonin Buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin) and incubated with 2.5 µl EpiCypher CUTANA pAG-MNase, for 10 min. After washing samples twice with Digitonin buffer, 1 µl 100 mM CaCl2 was added to samples which were incubated for 2 h at 4°C, rotating. To stop the reaction, STOP buffer (340 mM Nacl, 20 mm EDTA, 4 mM EGTA, 0.02%Digitonin, 50 µg/ml RNase A, 50 µg/ml Glycogen, sonicated yeast DNA as spike-in) was added in each tube. Samples were incubated at 37°C for 10 min at 500 rpm, and after centrifugation, liquid was collected, DNA was purified using Zymo DNA clean concentrator kit.
Libraries were prepared as described in Tessarz et al, 2014

value: liver

value: 3 months

tag: antibody


title: Ifnar1-/- rep2

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

data_processing:
After sequencing, quality control was performed using FastQC (v0.11.9), and reads were trimmed using Trim Galore! (v0.6.7) Using default parameters except --stringency 3. Trimmed sequences were then aligned to GRCm38 using STAR (v2.7.8a) (Dobin et al., 2012) under default parameters except --sjdbOverhang 100. Quantification was perfprmed with featureCounts (Subread v2.0.3) (Liao et al., 2013) using default parameters. Downstream analysis was performed in R (v4.1.0) using edgeR (Robinson et al., 2009) to filter (filterByExpr()) and normalize data (calcNormFactors()) before statistical testing between groups with exactTest(). Full scripts for downstream analysis are available at https://github.com/jackbibby1/scpa_paper upon publication
Assembly: mm10
Supplementary files format and content: Processed data file "counts.txt" contains the raw output from featureCounts
Supplementary files format and content: Processed data file "tmm_cpm_normalised.csv" contains filtered and TMM normalised, counts per million data from edgeR. Data filtering was done though filterByExpr(), normalisation was done using calcNormFactors(), and extraction was done by cpm() in edgeR.

source_name: Spleen

growth_protocol: Cells were cultured in RPMI with 10% FCS, pen-strep, and L-Glutamine

extract_protocol:
Total RNA was extracted using the RNAqueous™ Total RNA Isolation Kit (Thermo Fisher)
We prepared bulk RNA-seq libraries using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina following the manufacturer’s protocol

treatment_protocol: Cells were stimulated with anti-CD3 and anti-CD28 (2ug/ml) for 24 hours

value: Spleen

value: CD4 T cells


title: Wild type rep1

value: Wild type


title: Ifnar1-/- rep3


title: Y4S5


title: Y1S5


title: Brain_Week11_NMF421_10

value: Brain

value: female


title: Wild type rep2


title: genomic DNA from saliva sample 1

description:
K-SICM saliva sample
I-124

source_name: saliva sample 1


title: Brain_Week11_NMF421_8

source_name: Brain

value: Nadk2 -/-

value: male


title: genomic DNA from saliva sample 3

description:
G3 saliva sample
I-104

source_name: saliva sample 3

value: Male


title: genomic DNA from saliva sample 2

description:
G3 saliva sample
I-119

source_name: saliva sample 2


title: Brain_Week11_NMF421_9


title: O3S5

value: 18 months


title: Wild type rep3


title: Kidney cortex biopsy_baboon_female_HS_17174

city: Winston Salem

first: Laura

middle: A

last: Cox

state: NC

address: 1 Medical Center Blvd

department: Internal Medicine

institute: Wake Forest School of Medicine

description:
HS_17174
20210119_Females_Transcripts_HS_GEO.csv

data_processing:
All transcripts were processed together in Partek Flow with an average read length of greater than 90 (minimum=25) and an average Phred score of greater than 30 (minimum=30).
Reads were aligned to the olive baboon genome (papAnu2.0; March 2012) identifying 53,120 transcripts.
Transcripts were excluded where the sum was less than or equal to 14 among all samples and normalized using TMM with a +1 offset to eliminate zeros for downstream analyses.
The full transcript list generated in Partek Flow was imported into Partek Genomics Suite for principal component analysis (PCA) (Partek®, Inc).
Transcripts were filtered for expression values totaling <14 among all samples and filtered for the top 20,000 transcripts based on coefficient of variation prior to diet-specific WGCNA.
The R package WGCNA was run as a Pearson’s correlation with default settings as described by Langfelder and Horvath34.
Genome_build: papAnu2.0
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from LS samples.
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from HS samples.

organism: Papio hamadryas

source_name: Kidney cortex biopsy

growth_protocol: Animals were maintained on a low salt chow diet their whole life leading up to the study.

extract_protocol:
RNA was isolated from kidney biopsy samples using the Direct-zol RNA Miniprep Plus Kit (Zymo Research). Tissue was homogenized in 600 μL of TRI reagent (Zymo Research) using a BeadBeater for 3 x 30 sec with RNA purification according to the Direct-zol RNA Miniprep Plus Kit instructions. RNA was quantified by Qubit RNA BR Assay Kit (Invitrogen) and RIN was determined by with an RNA ScreenTape Kit on the Tapestation 2200 (Agilent).
cDNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Roche). Libraries were quantified by Qubit dsDNA Assay Kit (Invitrogen) and quality was determined by with a DNA ScreenTape Kit on the Tapestation 2200 (Agilent).

value: kidney cortex

tag: animal id

tag: sample name

tag: diet

value: high sodium diet

tag: colony

value: Southwest national primate research center

tag: collection method

value: Ultrasound guided biopsy snap frozen immediately in liquid nitrogen

tag: surgery anestetic

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.

value: High sodium diet challenge

tag: diet length

value: 6 weeks

tag: sodium in diet

value: 210 mmol Na+/500 g food consumed


title: Kidney cortex biopsy_baboon_female_HS_15122

description:
HS_15122
20210119_Females_Transcripts_HS_GEO.csv

tag: Sex


title: Brain_Week11_NMF421_7

tag: genotype

tag: strain

tag: age

value: Week 11


title: O4S5

tag: tissue

value: liver


title: Kidney cortex biopsy_baboon_female_HS_15113

description:
HS_15113
20210119_Females_Transcripts_HS_GEO.csv

tag: treatment


title: Ifnar1-/- rep1

value: Spleen

tag: cell type

value: CD4 T cells


title: Y2S5

value: 3 months


title: O2S5


title: eyeball organization, Ac-rBc-PI-PLC-A2 protein, 24h rep3

city: wenzhou

first: Bianjin

last: Sun

state: zhejiang

address: No. 270 Xueyuan West Road, Lucheng District

institute: School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: eyeball organization from C57/B6 mouse

growth_protocol: Six- to eight-week-old C57BL/6J mice were purchased from the Chinese Academy of Sciences, Shanghai Laboratory Animal Center (SLAC) .The mice were housed in an environment on a 12 h light/12 h dark cycle.Müller glial cells were cultured in DMEM containing 10% heat-inactivated fetal bovine serum (FBS; Ausvin) and penicillin–streptomycin (50 IU/ml and 50 mg/ml, respectively, Beyotime)

extract_protocol:
RNA was harvested using RNAprep pure Cell / Bacteria Kit (Tiangen)
The RNA samples were qualified for library construction. The mRNA SEq library can be constructed in two ways: common library or strand specific library. Common library construction is used for conventional projects, and strand specific library construction is used for distinguishing the directionality of strands.

treatment_protocol: Mice were anesthetized with a mixed solution of xylazine (5 mg/kg body weight) and ketamine (70 mg/kg body weight).Then,1ul of the corresponding solution was injected by intravitreal injection.

value: eyeball organization from C57/B6 mouse

tag: cell line

value: eyeball organization

value: WT

value: Ac-rBc-PI-PLC-A2 protein

tag: time


title: eyeball organization, Ac-rBc-PI-PLC-A2 protein, 24h rep2


title: O1S5

value: 18 months

tag: antibody


title: Brain_Week11_NMF421_5

value: Nadk2 +/+

value: Brain

value: male


title: Brain_Week11_NMF421_6

value: Nadk2 -/-


title: eyeball organization, Ac-rBc-PI-PLC-A2 protein, 24h rep1


title: Brain_Week11_NMF421_4


title: Y4S2


title: eyeball organization, Inac-rBc-PI-PLC-A2 protein, 24h rep2

value: Inac-rBc-PI-PLC-A2 protein


title: Y3S2


title: eyeball organization, Inac-rBc-PI-PLC-A2 protein, 24h rep3


title: Kidney cortex biopsy_baboon_female_HS_14740

description:
HS_14740
20210119_Females_Transcripts_HS_GEO.csv

value: kidney cortex

tag: animal id

tag: sample name

value: high sodium diet

value: female

value: Southwest national primate research center

value: Ultrasound guided biopsy snap frozen immediately in liquid nitrogen

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.

value: High sodium diet challenge

value: 6 weeks


title: Brain_Week11_NMF421_3

value: Week 11


title: Brain_Week11_NMF421_2


title: Kidney cortex biopsy_baboon_female_HS_14012

description:
HS_14012
20210119_Females_Transcripts_HS_GEO.csv

tag: diet

tag: colony

value: 210 mmol Na+/500 g food consumed


title: Kidney cortex biopsy_baboon_female_HS_14690

description:
HS_14690
20210119_Females_Transcripts_HS_GEO.csv

tag: collection method

tag: surgery anestetic


title: Y1S2

value: liver

value: 3 months


title: Y2S2


title: Kidney cortex biopsy_baboon_female_HS_13988

description:
HS_13988
20210119_Females_Transcripts_HS_GEO.csv

tag: diet length

tag: sodium in diet


title: Brain_Week11_NMF421_1

tag: genotype

tag: Sex


title: eyeball organization, Inac-rBc-PI-PLC-A2 protein, 24h rep1

value: eyeball organization from C57/B6 mouse

value: eyeball organization

value: WT


title: O4S2

tag: strain

tag: age

value: 18 months


title: Kidney cortex biopsy_baboon_female_LS_15122

description:
LS_15122
20210119_Females_Transcripts_LS_GEO.csv

tag: tissue

value: low salt control chow

tag: treatment

value: 17.3 mmol Na+/500 g food consumed


title: Brain_Week5_NMF421_9

value: Nadk2 -/-

value: Brain

value: Week 5

value: male