title: HDC1 KO mutant complemented with full length HDC1 gene sequence, control media, replicate 2

description: HDC1c, C, 2


title: HDC1 KO mutant complemented with full length HDC1 gene sequence, control media, replicate 3

status: Public on Mar 27 2024

type: SRA

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

description: HDC1c, C, 3

library_source: transcriptomic

data_processing:
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software
The raw fastq files were pre-processed to trim the 3’ end adapter and to trim the low quality reads using Cutadapt (version 1.5) and Sickle (version 0.940; flags -q 10 -l 54), respectively.
Transcript expression quantification was performed using Kallisto (version 0.43.0) against the TAIR10 transcriptome.
Read counts related to TAIR10 transcripts were collected, rounded, and summarized into gene-specific read counts.
Differential gene expression was analysewd using DESeq2 (version 1.24.0).
Assembly: TAIR10
Supplementary files format and content: Comma-delimited text fille containing raw gene-count for each sample separately

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were sterilised with 50% bleach solution, wash with dH2O water three times and stored at 4C for two days.

extract_protocol:
RNA was extracted using hot phenol method and treated with DNAse I. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA kit following manufacturer's protocols.

treatment_protocol:
Sterilized seeds were then sown on 1/2 MS 1% sucrose plates with or without 100 mM NaCl.
At day 3 after sowing the seeds were harvested and and snap-frozen with liquid N2.

tag: age

value: 3 days old

tag: tissue

value: seedlings

tag: genotype

tag: treatment

value: control


title: HDC1 KO mutant complemented with full length HDC1 gene sequence, 100 mM NaCl, replicate 1

description: HDC1c, S, 1

value: 100 mM NaCl


title: NRCFs, miR-142-3p antagomiR-2

city: Nanjing

first: Kun

last: Zhao

address: 101Longmian Avenue

country: China

institute: Nanjing Medical University

data_processing:
Quality control was conducted using FastQC. Adapters and low-quality reads were filtered out using Cutadapt . The samples were then aligned to the mRatBN7.2 genome with HISAT2. Quantification of genes expression was achieved through HTSeq. Differentially expressed  were determined using edgeR.
Assembly: mRatBN7.2
Supplementary files format and content: tab delimited text file with FPKM expression

organism: Rattus norvegicus

source_name: Heart

growth_protocol: Primary CFs were isolated from 1- to 2-day-old newborn SD rats (Vital River Biological Co., Ltd.). Briefly, the heart was excised and digested through agitations in buffer containing collagenase type II (Worthington Biochemical Corp., NJ, USA) and pancreatin (Sigma, MO, USA). The atria and great vessels were discarded. The ventricles were cut into small pieces and digested with collagenase type II and pancreatin. Cells from digestion were collected, cultured in complete Dulbecco’s modified Eagle’s medium (DMEM; Biochannel Biotechnology Co., Ltd.) for 2-4 hours to allow for the preferential attachment of CFs. Then, the medium containing cardiomyocytes were removed to enrich CFs. The CFs were cultured at 37°C with 5% CO2 and 95% air. CFs that reached 70%–80% confluency were incubated in the serum-free DMEM medium for overnight starvation.

extract_protocol:
paired-end illumina preparation: Illumina Hiseq 2x150bp configuration single index per lane, RNA library preparation with polyA enrich
Total RNA was extracted using TriPure (Roche), cDNA synthesis was made with Ovation RNA-seq System V2 (NuGEN), Library prep was made with TruSeq  Sample Preparation Kit (Illumina), Hiseq PE Cluster Kit (Illumina) and Hiseq SBS Kit (Illumina) was used for clustering and sequencing

treatment_protocol: We treated cardiac fibroblasts with NC or miR-142-3p antagomiR (n=3).Briefly, 50nM miR-142-3p antagomir or NC was transfected into CFs using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) following the manufacturers’ instructions.

value: Heart

tag: cell line

value: NRCFs

tag: cell type

value: cardiac fibroblasts

value: miR-142-3p antagomiR

value: miR-142-3p knockdown


title: HDC1 KO mutant complemented with full length HDC1 gene sequence, control media, replicate 1

description: HDC1c, C, 1


title: HDC1 KO mutant, 100 mM NaCl, replicate 3

description: hdc1-1, S, 3

value: HDC1 knockout


title: H3K9K14Ac, HDC1 KO mutant, 100 mM NaCl

description: hdc1-1 AC salt

library_source: genomic

data_processing:
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software
The raw fastq files were pre-processed to trim the 3’ end adapter and to trim the low quality reads using Cutadapt (version 1.9.2) and Sickle (version 0.940; flags -q 10 -l 54), respectively.
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie version 0.12.7. Only uniquely mapping reads with at most two mismatches in the first 54 bp were retained.
The alignment files were then sorted, and the duplicated reads of the same orientation were removed using Samtools (version 0.1.19). The locations of the mapped ChIP-seq reads were shifted in the 3'end direction by half of the sample-specific mean fragmernt length to represent the centres of sequenced fragments. Reads were then counted in 200 bp long windows and resulting raw counts stored in WIG files.
For each sample the aligned reads positions were shifted in the 3’end direction by half of the sample-specific mean fragment length to represent the centres of sequenced fragments, counted in 200-bp long windows using Sicer (version 1.03)(Zang et al., 2009) and resulting profiles stored in WIG files,
Assembly: TAIR10
Supplementary files format and content: WIG

molecule: genomic DNA

extract_protocol:
ChIP assays were performed on 2g of tissue as described previously with minor modifications (Sani et al., 2013). A Bioruptor sonicator (Diagenode, B01020001) was used to shear the chromatin using the following settings: 20 cycles x 30 sec ON, 30 sec OFF at high power.
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Prep Kit according to the manufacturer’s protocol, size selected with SPRIselect Beads and amplified by PCR.

treatment_protocol: Sterilized seeds were then sown on 1/2 MS 1% sucrose plates with or without 100 mM NaCl. At day 3 after sowing the seeds were harvested and and snap-frozen with liquid N2.

value: HDC1 KO mutant

tag: chip antibody

value: Anti-H3K9K14Ac (Diagenode pAb-005-050 )


title: HDC1 KO mutant expressing RXT3 sequence of HDC1, 100mM NaCl, replicate 1

description: RXT3, S, 1

value: HDC1 KO mutant expressing RXT3-like domain


title: HDC1 KO mutant, 100 mM NaCl, replicate 1

description: hdc1-1, S, 1


title: K19-HIF2dPA_24M_MUT_4

type: RNA

city: Philadelphia

first: Makarand

last: Risbud

address: 1025 Walnut St

country: USA

institute: Thomas Jefferson University

description: Total RNA from 24M MUT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

hyb_protocol: Affymetrix Gene chips, Mouse Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix).

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the experiment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05. Inclusion cutoffs were defined at a 1.7-fold change and p-value < 0.05.

label: biotin

organism: Mus musculus

source_name: 24M MUT

label_protocol: Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: dPA and K19-dPA mice were aged to 3 months, and were injected with tamoxifen for three consecutive days to activate K19-CreERT driver. Tissues were collected at 11 months and 21 months following the initial injection at 3 months. Genotypes were confirmed by PCR.

extract_protocol: NP tissues were micro-dissected from caudal intervertebral discs of 4 dPA and 4 K19-dPA overexpression animals and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

value: Nucleus Pulposus

tag: Sex

value: female


title: HDC1 KO mutant, control media, replicate 2

description: hdc1-1, C, 2


title: HDC1 KO mutant, control media, replicate 1

description: hdc1-1, C, 1


title: WCE_FBY2829_1

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

data_processing:
Reads were mapped using HISAT2 (Kim et al, 2015) with option --no-splice-alignment on a concatenate genome containing the S. pombe (version ASM294v2.26) and S. cerevisiae chromosomes. Normalization factors were computed based on the proportion of reads mapped to the S. cerevisiae genome as previously described (Larochelle et al, 2018) while the average fragment size was estimated using MACS2 predicted function (Zhang et al, 2008). Based on the normalization factors and averaged fragment size, we used deepTools (Ramirez et al, 2016) to generate normalized coverage files (.bigwig) with options bamCoverage --smoothlength 20 --centerReads -e [average_fragment_size] --scaleFactor [size_factor] -bs 1 -of bigwig. If no spike-in was available (as it is the case for the Pcf11-myc and Set2-TAP ChIP data), the option --normalizeUsing RPKM was used instead of --scale factor.
Assembly: ASM294v2.26
Supplementary files format and content: genome coverage files in bigWig format are provided

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: For each condition (IP), 50 mL of cell cultures were grown to an OD600nm of ∼0.5 at 30 °C in YES .

extract_protocol:
After quenching the solution with glycine (final concentration of 360 mM), cells were washed twice with a cold Tris-buffer saline (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl) and frozen in liquid nitrogen. Cell pellets from 50 ml cultures were thawed and resuspended in 500 µL of cold lysis buffer (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100 and 0.1% Na-deoxycholate) that was supplemented with a protease inhibitor cocktail (1X PMSF and 1X PLAAC) and disrupted vigorously with glass beads in a FastPrep-24TM (MP biomedical) for 3 cycles of 30 sec at 6.5 m/s. Then, 150 µL of cold lysis buffer with proteases was added to increase the volume and samples were sonicated for 12 cycles of 10 sec at 20% amplitude with a Branson digital sonifier. Sonicated chromatin was then incubated overnight at 4 °C with 50 µl of magnetic beads IgG Dynabeads (Life Technologies, 11041) in the case of TAP tagged proteins, or Dynabeads M-280 Sheep Anti-Rabbit IgG (Invitrogen, 11203D) beads coupled with 2 ug of rabbit anti-Histone H3 total (ab1791, abcam), H3K36me3 (ab9050, abcam) or H3K9ac (06-942, Millipore Sigma). Beads were then washed twice for 4 minutes at 4oC with 1 mL of cold lysis buffer, twice with 1 mL of cold lysis buffer with 500 mM NaCl, twice with 1 mL of cold wash buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate and 1 mM EDTA), and once with 1 mL of cold Tris-EDTA (TE: 10 mM Tris-HCl [pH 8.0] and 1 mM EDTA [pH8.0]). Bound material was eluted by resuspending the beads in 50 µl elution buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA and 1% SDS) at 65 °C for 15 min at 1200 rpm in an Eppendorf Thermomixer. After a short centrifugation, reverse-crosslinking was performed by incubating eluted chromatin with 120 µl of TE and 1% SDS or 5 µl of WCE in 165 µl of TE with 1% SDS at 65 °C overnight. For ChIP-Seq experiments, reverse-crosslinking was perfomed by incubating eluted chromatin with 20 µl of WCE in 150 µl of TE and 1% SDS. Samples were treated with a proteinase K mix (150 mg proteinase K, 60 mg glycogen in TE) and DNA was extracted twice with phenol-chloroform-isoamyl alcohol (25:24:1, [pH8.0], Invitrogen) and once with chloroform (Bioshop). Following ethanol precipitation, pellets were resuspended in 30 µl of TE plus 10 µg of RNAse A and incubated 1 h i at 37 °C. RNase-treated DNA was then purified with a QIAGEN PCR purification kit. The input DNA was diluted 400 times while the coimmunoprecipitated DNA was diluted 100 times in water. DNA were analyzed on a LightCycler 96 Instrument system (Roche) with the addition of the 2X SYBR Green in the presence of 0.15 μM of gene-specific oligonucleotide
ChIP-sequencing libraries were prepared using the SPARQ DNA Sample Prep Kit Illumina Platform (Quantabio) according to the manufacturer's instructions.

treatment_protocol: Cultures were cross-linked with 1% formaldehyde for 20 min at room temperature with manual shaking every 5 min.

tag: strain

value: WT Pcf11-myc Rpb3-flag

tag: fraction

value: input

tag: spike-in

value: h- Rpb3-3flag::hygMX6 Pcf11-myc ::natMX6

value: S. pombe cells


title: PT-00177543_NT_EA

type: genomic

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

hyb_protocol: Illumina Infinium HD Methylation

scan_protocol: Illumina iScan Control Software

data_processing:
Illumina GenomeStudio V1
EPIC_Proc_Funnorm.tsv (Normalized Beta values from minfi’s preprocessFunnorm)
EPIC_MatrixSignal.tsv (Unmethylated and methylated signal intensities)

label: Cy3, Cy5

organism: Homo sapiens

source_name: Adjacent Tumor

label_protocol: Illumina Infinium HD Methylation

extract_protocol: QIAamp DNA mini Kit

value: prostate

tag: tissue region

value: Adjacent Tumor

tag: race

value: EA


title: PT-00179840_T_EA

source_name: Tumor

value: Tumor


title: PT-00191831_NT_EA


title: PT-00190763_T_EA


title: PT-00177543_T_EA


title: PT-00179840_NT_EA


title: K19-HIF2dPA_24M_MUT_3


title: PT-00191831_T_EA


title: K19-HIF2dPA_24M_WT_4

description: Total RNA from 24M WT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

source_name: 24M WT


title: K19-HIF2dPA_24M_MUT_1


title: HDC1 KO mutant, control media, replicate 3

description: hdc1-1, C, 3

value: 3 days old

value: seedlings

value: control


title: K19-HIF2dPA_24M_WT_1

value: male


title: K19-HIF2dPA_24M_WT_3


title: K19-HIF2dPA_24M_MUT_2


title: K19-HIF2dPA_14M_MUT_2

description: Total RNA from 14M MUT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

source_name: 14M MUT


title: PT-00193110_NT_EA


title: K19-HIF2dPA_14M_MUT_3


title: PT-00193110_T_EA


title: K19-HIF2dPA_24M_WT_2


title: K19-HIF2dPA_14M_WT_4

description: Total RNA from 14M WT NP tissue; sst-rma normalization; DABG p<0.05; p<0.05; FC 1.7

source_name: 14M WT


title: K19-HIF2dPA_14M_MUT_1


title: K19-HIF2dPA_14M_WT_3


title: DKO IgG replicate

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 76 bp paired-end reads or Illumina NextSeq 2000 generating 66 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Rsubread with duplicates removed with Picard tools MarkDuplicates command
BigWig files were generated with BamCoverage from Deeptools with bamCoverage normalizeUsing RPGC, bs 10 and effectiveGenomeSize 2652783500.
Assembly: mm10
Supplementary files format and content: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 10 bp bin. Coverage was normalization by reads per genomic content (RPGC).

source_name: Thymus

extract_protocol:
ChIP-seq was performed as per (Lee et al. 2006) with amendments as follows: 1) sonication was performed using a Covaris S220 focused-ultrasonicator with the following settings to shear DNA to a size of 300-500 bp suitable for high-throughput sequencing: Fill Level 10, Duty Cycle 10, PIP 175, Cycles/Burst 200 for 60 seconds. 2) Immunoprecipitation was performed overnight at 4degC with rotation using ProteinG Dynabeads (50μL per IP) pre-coupled with antibody (5μL per IP) in 0.5% BSA/PBS for >5h. 3) Final immunoprecipitated DNA was purified using Zymo ChIP DNA Clean & Concentrator kit.
Illumina Tru-seq (1/2 reaction) library preparation was performed.

value: Thymus

value: CD4+CD8+ double positive thymocytes

tag: antibody

value: Rabbit IgG pAb (Abcam ab46540)

value: Male


title: K19-HIF2dPA_14M_WT_1

value: Nucleus Pulposus (NP)

value: female


title: K19-HIF2dPA_14M_MUT_4

value: Nucleus Pulposus


title: DKO whole cell extract replicate

value: whole-cell extract


title: PT-00193349_NT_EA


title: PT-00193228_T_EA


title: PT-00193349_T_EA


title: K19-HIF2dPA_14M_WT_2


title: DKO H3K27me3 replicate

value: H3K27me3 (Cell Signaling Cat#9733S Lot#16)


title: DKO H3K4me3 replicate

value: H3K4me3 (EMD Millipore Cat#07-472, Lot#3746)


title: DKO H3K27ac replicate


title: PT-00193649_NT_EA

value: prostate

value: Adjacent Tumor


title: CON IgG replicate


title: PT-00193829_NT_EA

value: EA


title: PT-00193228_NT_EA


title: PT-00193649_T_EA

value: Tumor


title: PT-00193829_T_EA


title: CON whole cell extract replicate


title: CON H3K27me3 replicate


title: PT-00194403_NT_EA


title: CON H3K27ac replicate


title: CON H3K4me3 replicate


title: PT-00194403_T_EA


title: HDC1 KO mutant, 100 mM NaCl, replicate 2

description: hdc1-1, S, 2

value: 3 days old

value: seedlings

value: HDC1 knockout

value: 100 mM NaCl


title: DKO ATAC-seq replicate 2

description: Experiment 2

data_processing:
Libraries were sequenced on an Illumina NextSeq 2000, generating 165 bp paired-end reads.
After nextera adapter sequences were trimmed, reads were mapped to the mm10 genome with Bowtie2. Duplicates were marked with sambamba. Samtools was used to remove reads on ChrM and reads with flag 1804. BAM files of the biological replicates were merged.
BigWig files were generated with BamCoverage from Deeptools with bamCoverage normalizeUsing RPGC, bs 10 and effectiveGenomeSize 2652783500.
Assembly: mm10
Supplementary files format and content: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 10 bp bin. Coverage was normalization by reads per genomic content (RPGC).

extract_protocol:
DNA was extracted following the Omni-ATAC method (Corces et al. 2017).
ATAC-seq libraries were prepared following the Omni-ATAC method (Corces et al. 2017).

value: Thymus

value: CD4+CD8+ double positive thymocytes


title: PT-00194466_T_EA


title: PT-00194466_NT_EA


title: DKO ATAC-seq replicate 1

description: Experiment 1

value: Male


title: CON ATAC-seq replicate 1

description: Experiment 1


title: PT-00194498_T_EA


title: PT-00194498_NT_EA


title: PT-00196174_NT_EA


title: PT-00196174_T_EA


title: CON ATAC-seq replicate 2

description: Experiment 2


title: PT-00197815_NT_EA


title: PT-00197815_T_EA


title: AC, AD, PolBHT, 3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Once the hybridization reactions have been removed from the thermal cycler, proceed immediately to an nCounter Prep Station. This step can process up to 12 samples per run in approximately 2.5 to 3 hours.

scan_protocol: Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: RRC format files containing the raw data were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Fold changes and p-values are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR).

label: NanoString barcodes

source_name: Auditory Cortex

label_protocol: Label a 12-tube PCR hybridization strip. The purified RNA is diluted in nuclease-free water to 20 ng/uL. Recommended total RNA samples are 20 ng to 100 ng for hybridization assay. The prepared samples are used as input into nCounter hybridization reactions containing NanoString Reporter and Capture probes. First, remove Reporter CodeSet and Capture ProbeSet tubes from the freezer and thaw at room temperature. Second, after it has thawed, inspect the tube of Reporter CodeSet to make sure no colored precipitate is present. Third, If you see a colored precipitate, heat the entire tube to 75°C for 10 minutes and cool at room temperature before using .The purified RNA was hybridized at thermal cycler at 65°C for 16 to 24 hours into nCounter 15 µL of hybridization buffer containing NanoString Reporter and Capture probes. Add 8 μL of Master Mix to each well of a strip tube. Add 5 µL of sample to each tube containing Master Mix. Add 2 µL of Capture ProbeSet to each tube. Maximum hybridization time should not exceed 48 hours.

extract_protocol: Whole cochlea and auditory cortex tissue (5 mg) from the mice were prepared for the extraction of total RNA using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, #12183018A) according to the manufacturer’s protocol.

treatment_protocol: Animal protocol and housing, WT (C57BL6/J), PolB +/- , 3xTgAD, and 3xTgAD/PolB +/- transgenic mice. Mice were fed ad libitum and kept on a 12-h light dark cycle.

value: M

value: 4 weeks

value: heterozygous Polbtm1Rsky_Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm on C57BL6/J background

value: Auditory Cortex


title: AC, AD, PolBHT, 2


title: AC, AD, WT, 3

value: Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm on C57BL6/J background


title: AC, AD, PolBHT, 1


title: PT-00211536_T_EA


title: AC, AD, WT, 1


title: PT-00217159_NT_EA


title: PT-00219496_NT_EA


title: PT-00217159_T_EA


title: AC, PolBHT, 3

value: PolBHT

value: heterozygous Polbtm1Rsky_on C57BL6/J background


title: PT-00222678_NT_EA

value: prostate

value: Adjacent Tumor


title: PT-00225395_NT_EA

value: EA


title: PT-00219496_T_EA

value: Tumor


title: PT-00225118_NT_EA


title: AC, PolBHT, 1


title: AC, PolBHT, 2


title: PT-00211536_NT_EA


title: PT-00225395_T_EA


title: AC, WT, 3

value: WT


title: PT-00222678_T_EA


title: C, AD, PolBHT, 1

source_name: Cochlea

value: Cochlea


title: PT-00225118_T_EA


title: C, AD, PolBHT, 3


title: AC, WT, 2


title: AC, WT, 1


title: C, AD, PolBHT, 2


title: PT-00231030_NT_EA


title: PT-00231030_T_EA


title: PT-00231182_NT_EA


title: PT-00231182_T_EA


title: AC, AD, WT, 2


title: C, AD, WT, 2


title: C, AD, WT, 1


title: PT-00231846_NT_EA


title: C, PolBHT, 3


title: C, PolBHT, 2


title: C, PolBHT, 1


title: C, WT, 3


title: PT-00231846_T_EA


title: IPMYC_FBY2830_2

value: S2A Pcf11-myc Rpb3-flag

value: Pcf11-myc IP

value: h- Rpb3-3flag::hygMX6 Pcf11-myc ::natMX6 CTD S2A-kanR

value: S. pombe cells


title: C, AD, WT, 3

value: M


title: PT-00231995_NT_EA


title: PT-00231995_T_EA


title: PT-00235895_NT_EA


title: PT-00235895_T_EA


title: C, WT, 2

value: 4 weeks


title: TILs from cells treated with DX17 LALAPG antibody, ADT

city: Bethesda

first: Ethan

middle: M

last: Shevach

state: MD

address: 10 Center Drive, Building 10, Room 11N315

institute: NIAID/NIH

description: Antibody Derived Tag (ADT)

library_source: other

data_processing:
10x Genomics Cell Ranger count version 7.1.0 was used to create barcode, feature, and matrix files
Raw counts were analyzed in Seurat v4.3.0. Cells were filtered out if they had less than 500 or greater than 6000 (7500 for DX17 LALAPG) features per cell or greater than 38000 (50000 for DX17 LALAPG) UMI counts per cell. Cells with more than 10% mitochondrial gene expression were filtered out. Doublets were identified with scDblFinder v1.14 and removed. NormalizeData, FindVariableFeatures, ScaleData using all features, RunPCA, RunUMAP dims=1:30, FindNeighbors dims=1:30, and FindClusters resolution=0.1 was applied to the Seurat object. Both objects were integrated with SelectIntegrationFeatures, FindIntegrationAnchors, and IntegrateData. Integrated object was run through NormalizeData, FindVariableFeatures, ScaleData, RunPCA, RunUMAP dims=1:30), FindNeighbors dims=1:30), and FindClusters resolution=0.1. Default parameters were used unless otherwise specified. Cell types were identified using SingleR v2.2.0 using the Noversthern reference available through celldex.
Assembly: hg38
Supplementary files format and content: Cell Ranger output files: hIgG1_LALAPG_barcodes.tsv.gz, hIgG1_LALAPG_features.tsv.gz, hIgG1_LALAPG_matrix.mtx.gz
Supplementary files format and content: Cell Ranger output files: DX17_LALAPG_barcodes.tsv.gz, DX17_LALAPG_features.tsv.gz, DX17_LALAPG_matrix.mtx.gz

molecule: protein

source_name: Primary colorectal cancer biopsy

extract_protocol:
We have conducted a study to investigate how blocking HLA/LILR affects the activation of immune cells in the tumor microenvironment. We perfused a fresh primary colon cancer biopsy sample with hIgG1 LALAPG or DX17 LALAPG for 48 hours. We then isolated CD45+ leukocytes from the tumor sample using magnetic cell sorting. Subsequently, we processed the resulting tumor-infiltrating lymphocytes (TILs) for single-cell RNA-seq and Cite-seq analysis. We compared the transcriptomes of NK cells, monocytes, and memory T cells under the two different culture conditions.
Cells were labeled with oligonucleotide-tagged antibodies for cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq) with TotalSeq-B Human Universal Cocktails B, v1.0.
scRNA-seq and CITE-seq

value: Primary colorectal cancer biopsy

value: CD45+ leukocytes

value: ex-vivo perfused tumors treated with hIgG1 DX17

tag: library type

value: ADT


title: PT-00237328_NT_EA


title: TILs from cells treated with hIgG1 LALAPG antibody, GEX

description: ployA mRNA

library_source: transcriptomic single cell

molecule: polyA RNA

value: ex-vivo perfused tumors treated with hIgG1 LALAPG

value: mRNA


title: single_cell RNA seq data of CSF from patient SMA1_9_nusinersen_10 months

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v6.1.0 (10X Genomics), according to the manufacturer’s instructions. Briefly, raw BCL files were de_multiplexed using the CellRanger mkfastq pipeline. Subsequent read alignments and transcript counting was done individually for each sample using the CellRanger count and CellRanger vdj pipelines with standard parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output format
Supplementary files format and content: gene expression matrix h5
Supplementary files format and content: contig annotations

source_name: CSF

extract_protocol:
CSF cells were processed within 2 hours post lumbar puncture to ensure optimal sample quality. For processing, CSF was collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300x g. CSF cell pellets were resuspended in 5 ml of X_Vivo15 media (Lonza) and stored on crushed ice. The samples were then transported with same day shipping on crushed ice to the laboratory. Cell suspensions were then centrifuged again for 5 min at 400 x g and resuspended in 50 μl of X_Vivo15 media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA_seq.
Single cell suspensions were loaded onto the Chromium Controller (10X Genomics) using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kits v3 and v3.1 (10X Genomics). For TCR sequencing, we applied a previously described technique to sequence antigen receptor information from the 3’ scRNA_seq libraries. In short, the method involves self_circulating the cDNA library, enriching the VDJ region and re_linearizing to remove the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. Library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter). Sequencing was carried out on a local Illumina Nextseq 500/2000 and Novaseq6000 with a 28_8_0_91 read setup.

treatment_protocol: Nusinersen was administered to SMA patients by lumbar puncture on days 1, 14, 28, and 63 followed by a repetitive application every 4 months according to the treatment guideline. Treatment was performed between the years 2017 - 2021 in the center in Essen. Before each nusinersen injection, the same amount (5 mL) of CSF was withdrawn to prevent excessive intra_CSF pressure.

value: CSF leukocytes

tag: diagnosis

value: SMA

value: nusinersen

tag: time point

value: 10 months


title: PT-00237328_T_EA

value: prostate

value: Tumor

value: EA


title: single_cell RNA seq data of CSF from patient SMA1_8_nusinersen_10 months


title: C, WT, 1

tag: age

value: WT

value: Cochlea


title: PT-00251650_T_EA

tag: tissue


title: single_cell RNA seq data of CSF from patient SMA1_7_nusinersen_10 months


title: single_cell RNA seq data of CSF from patient SMA1_7_nusinersen_6 months

value: 6 months


title: single_cell RNA seq data of CSF from patient SMA1_6_nusinersen_10 months


title: OM-dECM_GSCs3

city: Bangkok

first: Ajjima

last: Chansaenroj

address: 34 Henri-Dunant Road

department: Anatomy

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn University

data_processing:
The constructed library was validated using an Agilent 2100 Bioanalyzer and quantified by Qubit 2.0 Fluorometer
Sequencing was performed on the illumine HiSeq platform in a 2X150bp paired-end configuration
Base-calling is performed by Illumina RTA software
Demultiplexing is performed by Illumina bcl2fastq 2.17 software based on index information and the number of reads and quality score (Q30) were counted. Data were aligned to reference genome via software HISAT2 (v2.0.1)
Differential expression analysis used the DESeq2 Bioconductor package
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human gingiva

growth_protocol: The cells were cultured in a growth medium composed of Dulbecco’s Modified Eagle Medium containing 10% fetal bovine serum, 2 mM L-glutamine, 100 unit/ml penicillin, 100 μg/ml streptomycin, and 250 ng/ml amphotericin B. The cells were incubated at 37°C in a humidified 5% carbon dioxide atmosphere. The culture medium was changed every 48 h.

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 5 mg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina®

treatment_protocol: ECM was constructed from DPSCs and GSCs that were cultured in a growth medium supplemented with L-ascorbic acid (N-ECM) or osteogenic induction medium (OM-ECM). The reseeded GSCs on N-ECM and OM-ECM were analyzed by RNA sequencing.

value: human gingiva

value: human gingival-derived mesenchymal stem cells

value: osteogenic induction medium (Day21)


title: TILs from cells treated with DX17 LALAPG antibody, GEX

description: ployA mRNA

value: Primary colorectal cancer biopsy

value: CD45+ leukocytes

value: ex-vivo perfused tumors treated with hIgG1 DX17


title: TILs from cells treated with hIgG1 LALAPG antibody, ADT

description: Antibody Derived Tag (ADT)

value: ex-vivo perfused tumors treated with hIgG1 LALAPG

value: ADT


title: PT-00251650_NT_EA

value: Adjacent Tumor


title: OM-dECM_GSCs1


title: N-dECM_GSCs3

value: growth medium supplemented with L-ascorbic acid (Day21)


title: OM-dECM_GSCs2


title: SAMPLE 12_p63sh_3

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were filtered for detection pValue > 0.01 and normalised using robust spline normalisation with lumi in R
With a detection p-value cutoff of 0.01, probes were filtered, and normalized by using the LUMI package in R with the robust spline normalization method. Qlucore Omics Explorer software version 3.1 (Qlucore AB, Lund, Sweden) was used to explore and analyze microarray gene expression data sets and to generate heat maps.

label: Biotin

source_name: Erwin-Turner tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The human choriocarcinoma cell line JEG3 was obtained from ATCC and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

treatment_protocol: For p63 overexpression, JEG3 cells were infected with a pCMV lentiviral vector carrying deltaNp63alpha (empty vector used as control). For p63 knock-down, the pLKO.1 lentiviral vector carrying either a non-targeting scramble sequence or p63-specific short hairpin (shRNA) was infected in JEG3.

tag: type

value: choriocarcinoma cell line

tag: genotype

tag: replicate

value: replicate 3


title: N-dECM_GSCs1

tag: cell type

tag: treatment


title: OM-dECM_DPSCs3

source_name: human dental pulp

value: human dental pulp

value: human dental pulp stem cells


title: N-dECM_GSCs2


title: SAMPLE 11_p63sh_2

tag: cell line

value: replicate 2


title: OM-dECM_DPSCs1


title: single_cell RNA seq data of CSF from patient SMA1_7_nusinersen_2 months

value: CSF leukocytes

value: SMA

value: nusinersen

value: 2 months


title: SAMPLE 9_Scramble_3

value: Scramble


title: SAMPLE 7_Scramble_1

value: replicate 1


title: SAMPLE 5_p63_2


title: SAMPLE 3_Mock_3

value: Mock


title: SAMPLE 4_p63_1


title: OM-dECM_DPSCs2

value: osteogenic induction medium (Day21)


title: SAMPLE 8_Scramble_2


title: SAMPLE 6_p63_3


title: SAMPLE 10_p63sh_1


title: caco2bbe1_control_mock_rep3

city: Toronto

first: Elena

last: Comelli

state: Ontario

address: 1 King's College Circle

department: Nutritional Sciences

country: Canada

institute: University of Toronto

hyb_protocol: 100 ng of total RNA per sample, was first hybridized with capture and reporter probes which then hybridize to the target molecules, using NanoString miRNA assay kit and following the manufacturer’s instructions (NanoString Technologies, Inc., Seattle, WA, U.S.).

scan_protocol: Following the manufacturer’s instructions (NanoString Technologies, Inc., Seattle, WA, U.S.)

data_processing: Data preprocessing and statistical analyses were performed in R version 3.5.1 using the package NanoStringDiff. Raw count data was normalized using the estNormalizationFactors function. Differential expression was assessed using the normalized data and the glm.LRT function, which calculates an FDR using the Benjamini-Hochberg procedure

label: Fluorescent barcode and biotin moiety

source_name: Caco-2BBe1 cells

label_protocol: Not supplied

growth_protocol: Caco-2BBe1 cells were grown in a humidified incubator at 37ºC with 5% CO2 at a density of 2x10^6 cells in a total of 15 ml of DMEM supplemented with 10% FBS, 1% antibiotic-antimycotic solution, and 0.01 mg/ml transferrin in 72 cm^2 flasks. All media reagents were of cell culture grade (Wisent Inc). For experiments, cells between passages 32-35 were seeded into six-well plates at a density of 2x10^5 cells per well and were differentiated for 20 days after reaching confluency (approximately 3 days) before treatments were applied

extract_protocol: Total RNA was extracted from cell pellets using the mirVana miRNA Isolation Kit (Invitrogen), according to the manufacturer's protocol. The concentration and purity of the RNA samples were determined spectrophotometrically using a Nanodrop 2000 (Thermo Fisher Scientific)

treatment_protocol: Not applied

value: Enterocyte

tag: disease origin

value: Colorectal adenocarcinoma

tag: pre-treatment (concentration)

value: DMEM control

tag: pre-treatment exposure time

value: 24 hours

tag: il-1β stimulation

value: mock (0 ng/ml)

tag: il-1β or mock exposure time

value: 3 hours


title: N-dECM_DPSCs2

value: human dental pulp

value: growth medium supplemented with L-ascorbic acid (Day21)


title: caco2bbe1_control_mock_rep2


title: caco2bbe1_control_mock_rep1


title: caco2bbe1_control_IL1B_rep3

value: 1 ng/ml


title: N-dECM_DPSCs1

value: human dental pulp stem cells


title: SNU1196_sphere cultured_rep2

city: Seoul

first: Si Young

last: Song

address: 50-1, Yonsei-ro

department: Department of Internal Medicine

country: South Korea

institute: Yonsei University College of Medicine

hyb_protocol: The labeled cDNA was fragmented and hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 high-density oligonucleotide Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The microarrays were washed using a GeneChip Fluidics Station 450 (Affymetrix) and scanned using a GeneChip Array Scanner 3000 7G (Affymetrix).

data_processing:
Expression data were generated using Affymetrix Expression Console software version 1.1 using MAS5 algorithm normalization. The expression intensity data in the CEL file were normalized using the MAS5 algorithm to reduce noise.
HG-U133_Plus_2.cdf
HuEx-1_0-st-v2.re.dt1.hu18.full.mps

source_name: SNU1196, sphere cultured

label_protocol: cDNA was prepared using 6 μg aliquots of total RNA, amplified using polymerase chain reaction (PCR), and labeled with biotin using an IVT labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Cells were trypsinized and resuspended at a density of 1.0 × 103 cells/well in D/F12 (Invitrogen Gibco) medium supplemented with 10 ng/mL epidermal growth factor (R&D Systems Inc., Minneapolis, MN, USA), 10 ng/mL basic fibroblast growth factor (R&D Systems Inc.), 1X insulin-transferring selenium (Invitrogen), 0.5% bovine serum albumin (Invitrogen), and 0.5% FBS in ultra-low attachment culture plates (Corning Inc., Corning, NY, USA). Adherent cultured cells, as a control, were seeded in culture dishes (Nalgene Nunc Intl, Rochester, NY, USA) with a sphere formation medium. After seven days, cells were collected and dissociated with Accutase (Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol: Total RNA was extracted for RT-PCR using RNAeasy Mini kits (Qiagen).

value: biliary tract cancer, cancer stem cells


title: N-dECM_DPSCs3


title: caco2bbe1_control_IL1B_rep2


title: caco2bbe1_HPPA_10_mock_rep2

value: 3-(4-hydroxyphenyl)-propionic acid (10 µg/ml)


title: caco2bbe1_control_IL1B_rep1


title: caco2bbe1_HPPA_10_mock_rep3


title: HEK 293T cells, RNA-seq, i14G1-12 rep 3

city: Rehovot

first: Benjamin

last: Weiss

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

data_processing:
Successive mapping to rRNAs, tRNAs with bowtie and lncRNAs (hg38) with HISAT2. Final mapping to transcriptome hg38, MANE Ensemble DB v108  with HISAT2.
genome build/assembly: hg38
processed data files format and content: Counts.txt: tab-delimited text files include raw counts values for each sample

source_name: HEK 293T

growth_protocol: Cells were grown in an humidifed incubator supplemented with 5% CO2 at 37°C

extract_protocol:
After treatment cells were crosslinked with 0.15% formaldehyde on ice for 10 min with slow agitation. Crosslinking was stopped with 37.5 mM glycine. Cells were washed with PBS and lysed with 100 mM KCl, 20 mM Tris-HCl pH 8, 1.5 mM MgCl2, 1.5% (v/v) NP-40, 2 mM DTT supplemented with protease inhibitor. After lysis, lysate was clarified. Total RNA from 10% of the lysate was extracted by hot acid phenol extraction.
TruSeq mRNA stranded Illumina

value: HEK 293T

value: WT


title: HEK 293T cells, RNA-seq, i14G1-12 rep 1


title: HEK 293T cells, RNA-seq, DMSO rep 3

treatment_protocol: DMSO 1hr

value: DMSO


title: caco2bbe1_HPPA_5_mock_rep3

value: 3-(4-hydroxyphenyl)-propionic acid (5 µg/ml)


title: caco2bbe1_HPPA_10_mock_rep1


title: caco2bbe1_HPPA_IL1B_10_rep3


title: SAMPLE 1_Mock_1

value: choriocarcinoma cell line

value: Mock

value: replicate 1


title: caco2bbe1_HPPA_5_mock_rep1

value: Enterocyte

value: Colorectal adenocarcinoma


title: SNU1196_sphere cultured_rep1


title: HEK 293T cells, RNA-seq, DMSO rep 2


title: SNU1196_adherent cultured_rep1

source_name: SNU1196, adherent cultured


title: HEK 293T cells, RNA-seq, i14G1-12 rep 2


title: caco2bbe1_HPPA_IL1B_10_rep1

value: 24 hours


title: SNU245_sphere cultured_rep1

source_name: SNU245, sphere cultured


title: HEK 293T cells, TCP seq, i14G1-12 rep 3

data_processing:
Trimming with cutadapt (CTGTAGGCACCATCAAT -m 16) and QC with TRIMMOMATIC (MINLEN:16 TRAILING:15 SLIDINGWINDOW:5:15).
Successive mapping to rRNAs, tRNAs with bowtie and lncRNAs (hg38) with HISAT2. Final mapping to transcriptome hg38, MANE Ensemble DB v108  with HISAT2.
genome build/assembly: hg38
processed data files format and content: Counts.txt: tab-delimited text files include raw counts values for each sample
Library strategy: Ribo-seq

extract_protocol:
After treatment cells were crosslinked with 0.15% formaldehyde on ice for 10 min with slow agitation. Crosslinking was stopped with 37.5 mM glycine. Cells were washed with PBS and lysed with 100 mM KCl, 20 mM Tris-HCl pH 8, 1.5 mM MgCl2, 1.5% (v/v) NP-40, 2 mM DTT supplemented with protease inhibitor. After lysis, lysate was clarified and digested with Rnase 1 (0.0075 U per µg) for 30 min. Samples was centrifuged on a 4-45% sucrose gradient. RNA corresponding to the 40S fractions was extracted by hot acid phenol extraction.
Ribo-seq, Ingolia et al 2012. Reads from 18 to 80 nt were selected.


title: HEK 293T cells, RNA-seq, DMSO rep 1


title: HEK 293T cells, TCP seq, i14G1-12 rep 2


title: caco2bbe1_HPPA_IL1B_10_rep2

value: 3 hours


title: SNU1196_adherent cultured_rep2


title: caco2bbe1_HPPA_IL1B_5_rep2


title: SNU245_sphere cultured_rep2


title: caco2bbe1_DHPAA_5_mock_rep2

value: 3,4-dihydroxyphenylacetic acid (5 µg/ml)

value: mock (0 ng/ml)


title: caco2bbe1_HPPA_5_mock_rep2


title: HEK 293T cells, TCP seq, i14G1-12 rep 1


title: SAMPLE 2_Mock_2

value: replicate 2


title: caco2bbe1_DHPAA_5_mock_rep3


title: SNU245_adherent cultured_rep1

source_name: SNU245, adherent cultured


title: SNU245_adherent cultured_rep2


title: caco2bbe1_HPPA_IL1B_5_rep3

value: 1 ng/ml


title: caco2bbe1_PAC_100_mock_rep3

value: cranberry proanthocyanidin (100 µg/ml)


title: caco2bbe1_DHPAA_5_IL1B_rep2


title: HEK 293T cells, TCP seq, DMSO rep 2


title: caco2bbe1_DHPAA_5_IL1B_rep1


title: HEK 293T cells, TCP seq, DMSO rep 3


title: caco2bbe1_PAC_100_mock_rep1


title: caco2bbe1_PAC_100_mock_rep2


title: caco2bbe1_PAC_50_mock_rep3

value: cranberry proanthocyanidin (50 µg/ml)


title: caco2bbe1_HPPA_IL1B_5_rep1


title: Serum from participant 250

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

institute: University of Oxford

data_processing:
BCL files were demultiplexed using bcl2fastq and fastq files generated.
Adapters were trimmed using Trim Galore discarding reads that were less than 10bp after trimming and any reads longer than 50bp.
For miRNA analysis, the miRDeep2 pipeline was run. Reads were collapsed and aligned to the hg19 genome using the mapper.pl script, after which the miRDeep2.pl script was run to count both mature and hairpin miRNA species.
Reads were aligned to tRFs using MINTmap
For all other sncRNA subtypes, fastq files were aligned to the hg19 genome using the short-read aligner Bowtie using the following options: -q -k 10 -v 0 -S -t --best --strata. Gene counts were generated using featureCounts
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: serum

extract_protocol:
Total RNA was extracted from serum samples using the miRNeasy Kit (Qiagen, UK) following manufacturers guidelines. Extracted RNA was treated with DNAse1 (Sigma, UK)
Small RNA libraries for small RNA-seq were prepared using the NEBNext Small RNA Library Prep Set for Illumina (E7330) as per manufacturers’ instructions and the concentration of the small RNA libraries was determined by Picogreen before multiplexing for sequencing

tag: Sex

value: Female

tag: condition

value: Sarcopenia

value: serum


title: Serum from participant 251


title: PELI2-CKO rep2

city: Jinan City

first: Yan

last: Xu

address: No. 44 Wenhua West Road

institute: Shandong University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Differential expression was performed using DESeq2 (version 1.4.5).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: WT_and_PELI2_CKO_genes.fpkm.anno.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: bone marrow B220+ cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer.
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ platform.

value: bone marrow B220+ cells

value: PELI2 knockout


title: PELI2-CKO rep3


title: Serum from participant 248

value: Control


title: caco2bbe1_PAC_50_mock_rep1


title: caco2bbe1_PAC_100_IL1B_rep2


title: HEK 293T cells, TCP seq, DMSO rep 1

value: HEK 293T

value: WT

value: DMSO


title: WT rep3


title: Barcode dataset of sample 4

city: Sant Joan d’Alacant

first: Lucia

last: Del-Valle-Anton

address: Av. Santiago Ramón y Cajal s/n

country: Spain

institute: Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández

description: 10x Genomics

data_processing:
Fastq files for both transcriptome and barcoded sequences were obtained by bcl2fastq v2.20.0.422 (Illumina). For barcoded lineage preprocessing, TrackerSeq pipeline was used (https://github.com/mayer-lab/Bandler-et-al_lineage).
Raw barcoded sequence reads were trimmed by BBMap v38.68 (BBMap – sourceforge.net/projects/bbmap/) Whitelist of cell barcodes and barcode extraction from sequence reads were obtained by UMI-tools v1.1.2
After that barcode extracted fastq files were processed to generate sparse matrix with cell barcodes in rows and clone ids in columns.
For lineage transcriptome preprocessing, 10x compatible expression matrices were generated by STARsolo in STAR aligner.
After the obtain expression matrices, empty and pseudo drop cells were filtered by DropletUtils using emptyDrops functions with 100000 iterations and min UMI count < 500.
Assembly: MusPutFur1.0/GCF_000215625.1
Supplementary files format and content: Tab and coma-separated values files and matrix files

organism: Mustela putorius furo

source_name: Brain

extract_protocol:
Embryonic tissue was collected in ice-cold Leibowitz medium and papain dissociation was carried out (Wortington, #LK003150). GFP-possitive cells were FACS sorted and after processed on the 10x Genomic Platform. Gel Beads-in-emulsion and cDNA generation carrying cell- and transcript-specific barcode was done using the Chromium Single Cell 3' Reagent Kit v3.1 (PN-1000121) following the manufacturer’s protocol.
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custumed primers with standard Illumina adapters.

value: Brain

value: wildtype

value: FACSorted for GFP


title: caco2bbe1_PAC_50_IL1B_rep3

value: Enterocyte

value: Colorectal adenocarcinoma

value: 24 hours

value: 3 hours


title: caco2bbe1_DHPAA_5_IL1B_rep3

value: 3,4-dihydroxyphenylacetic acid (5 µg/ml)

value: 1 ng/ml


title: Barcode dataset of sample 3

description: 10x Genomics


title: PELI2-CKO rep1


title: caco2bbe1_PAC_100_IL1B_rep1

value: cranberry proanthocyanidin (100 µg/ml)


title: caco2bbe1_PAC_50_IL1B_rep2

value: cranberry proanthocyanidin (50 µg/ml)


title: caco2bbe1_DHPAA_5_mock_rep1

value: mock (0 ng/ml)


title: caco2bbe1_PAC_50_mock_rep2


title: WT rep2

value: bone marrow B220+ cells


title: Serum from participant 247

value: Female

value: Sarcopenia

value: serum


title: Barcode dataset of sample 1

description: 10x Genomics


title: Barcode dataset of sample 2

description: 10x Genomics


title: caco2bbe1_PAC_50_IL1B_rep1


title: Serum from participant 245


title: Transcriptomic dataset of sample 4

description: 10x Genomics


title: WT rep1

value: WT


title: Serum from participant 249


title: Transcriptomic dataset of sample 3

description: 10x Genomics

value: Brain


title: Transcriptomic dataset of sample 2

description: 10x Genomics

value: wildtype


title: Transcriptomic dataset of sample 1

description: 10x Genomics

value: FACSorted for GFP


title: Serum from participant 244

value: Control


title: NWD1_15601_10

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
TrueSeq adapter sequences were removed with Trimmomatic and quality control was assessed with FASTQC
Reads were mapped with STAR (v2.5.3a) to the mouse mm10 reference genome with gencode annotation (release M15, GRCm38.p5)
Read counts were extraced with Featurecounts (subread 1.5.2) and downstream analysis was performed with DESeq2 (1.36.0)
Assembly: mm10
Supplementary files format and content: DESeq2 processed tab delimited file includes variance stabilizing transformation (VST) values of the counts

source_name: small intestine

extract_protocol:
RNA was isolated from cells using TRIzol Reagent (ThermoFisher Scientific) according to the manufacturer’s instructions
single end RNA libraries were prepared according to TruSeq Library Preparation protocol

treatment_protocol: C57BL/6J mice were fed for 3 months with either NWD1 or AIN76A diet. Whole crypts were extracted from the small intestine, and Paneth cells were sorted with FACS based on the SSChiCD24hicKithi gate.

value: small intestine

value: Paneth cells

tag: strain

tag: time

value: 3 months


title: Serum from participant 243


title: Serum from participant 246


title: NWD1_13940_03


title: NWD1_13505_06


title: Serum from participant 241


title: Serum from participant 242


title: Serum from participant 240


title: AIN_15022_03


title: AIN_13396_02


title: Serum from participant 239


title: AIN_13055_05


title: Serum from participant 238


title: DMN_303_C5_H_R3

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

molecule: other

source_name: liver tumor associated with chronic hepatitis C

growth_protocol: Cryopreserved differentiated HepaRGTM cells (Biopredic International, Saint-Grégoire, France) were cultivated according to the manufacturer’s protocol. Differentiated HepaRGTM cells were thawed and seeded into collagen-coated wells at a density of approximately 0.072 x 106 viable cells per well (i.e. 100 μL of the cell suspension per well) in 96-well plates, using HepaRGTM Thawing/Plating/General Purpose Medium 670 (ADD670C, Biopredic International, Saint-Grégoire, France). After 24h, the media were changed to HepaRGTM Maintenance Medium 620 (ADD620C, Biopredic International, Saint-Grégoire, France) for cell maintenance. Cells were incubated for 7 days at 37°C, 5% CO2 and saturating humidity.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRGTM cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70oC followed by a temperature gradient with a ramp rate of 0.5oC/min to 45oC over a 50 min period, followed by a nuclease digestion at 37oC for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37oC, immediately followed with a 15 min enzyme denaturation at 80oC to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37oC for 10 min, 95oC for 2 min; 6 cycles of 95oC for 30 sec, 54oC for 30 sec, 72oC for 120 sec; 16 cycles of 95oC for 30 sec; 72oC for 2 min; 72oC for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: At day 7, cells were exposed in triplicate to 5 concentrations of test chemical and refreshed with test chemical in HepaRGTM Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to  glycidol (97, 291, 873, 1200 and 1402µM), methyl methanesulfonate (27, 81, 243.3, 400 and 500 µM) and nitrosodimethylamine (80, 240, 720, 2160 and 5454 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMN

tag: chemical long_name

value: nitrosodimethylamine

tag: dose

tag: batch nr_heparg

tag: plate

value: Plate 1 index H

tag: well

tag: dose group

value: H

tag: index

value: TAGCGACAA

value: AGCTAGACC

tag: group

tag: solvent control

value: F

tag: reference rna

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: DMN_330_C5_E_R2

tag: tissue

value: liver tumor associated with chronic hepatitis C

tag: cell line

tag: cell type

value: Plate 2 index E

value: E

value: TAAGGTAGC

value: TGCATCTGC

tag: replicate


title: Serum from participant 237

tag: Sex

value: Female

tag: condition

value: Control

value: serum


title: Serum from participant 236

value: Sarcopenia


title: DMN_326_C5_E_R1

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMN

tag: chemical long_name

tag: dose

tag: batch nr_heparg

value: TGCATGACA

value: AAGGTGTTT


title: Serum from participant 235


title: DMN_303_C4_H_R3

value: nitrosodimethylamine

tag: plate

value: Plate 1 index H

tag: well

tag: dose group

value: H

tag: index

value: GCTATCGAT

value: AGCTAGACC


title: PDO37_ZT20_S1

city: Chicago

first: Deepak

last: Sharma

state: Illinois

address: 1653 W Congress Pkwy #12

institute: Rush University Medical Center

data_processing:
Reads from the RNA-Sequencing data were aligned to the Homo Sapiens genome assembly GRCh38 (mm10) using the STAR software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
The raw count data were normalized, followed by log2 transformation. We filtered out genes with mean read counts < 6. All data preprocessing was performed using R software.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files with feature counts per gene

source_name: Patient derived organoids of pancreatic cancer

growth_protocol: Pancreas cancer tissue was collected from untreated patients undergoing tissue biopsy at Rush University Medical Center. Immediately following the tissue acquisition, the samples were processed as previously described. Briefly, after digestion with collagenase-II, dispase-II, and DNase-I, biopsy tissues were washed several times and then plated in 50 µL Matrigel domes on a 24-welled plate supplemented with 500 µL organoid medium.

extract_protocol:
For RNA extraction, cells and organoids were cultured in a 6-well plate followed by dexamethasone treatment. 24 h after the synchronization, cells were collected and lysed with RLT buffer containing 1% 2-mercaptoethanol (Bio-Rad, CA). According to the instructions, RNA was isolated using RNeasy® extraction kit (Qiagen, Germany).
RNA concentration was measured using a NanoDrop 2000c spectrophotometer (Thermo Scientific, MA). cDNA was prepared from the purified RNA using a cDNA Reverse Transcription Kit (Applied Biosystems, United States).

treatment_protocol: Human pancreatic cell line AsPC-1 (ATCC Cat# CRL-1682TM) was cultured in Roswell Park Memorial Institute medium (RPMI-1640 ATCC Cat# 30-2001), PANC-1 (ATCC Cat# CRL-1469TM) and MIA PaCa-2 1 (ATCC Cat# CRL-1420TM) were cultured in Dulbecco's Modified Eagle's Medium (DMEM), Capan-1 (ATCC Cat# HTB-79TM) was cultured in Iscove's Modified Dulbecco's Medium (IMDM) Cat# 30-2005TM. All the cell culture media were supplemented with 10% FBS (except 20% for IMDM), and 1% penicillin-streptomycin, and cells were incubated in a humidified incubator at 37 °C with 5% CO2.

tag: treatment

value: Dexamethasone treatment

tag: time


title: PDO37_ZT16_S1

value: Patient derived organoids of pancreatic cancer


title: DMN_330_C4_E_R2

value: liver tumor associated with chronic hepatitis C

value: Plate 2 index E

value: E

value: TCAGTACAT

value: TGCATCTGC

tag: group

tag: solvent control

value: F

tag: reference rna

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: PDO37_ZT12_S1

tag: tissue

tag: cell line

tag: cell type


title: Serum from participant 234

tag: Sex

value: Female

tag: condition

value: Sarcopenia

value: serum


title: PDO37_ZT8_S1


title: Serum from participant 233


title: PDO37_ZT4_S1


title: PDO37_ZT0_S1


title: DMN_326_C4_E_R1

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMN

tag: chemical long_name

value: nitrosodimethylamine

tag: dose

tag: batch nr_heparg

tag: plate

value: TAAGGTAGC

value: AAGGTGTTT

tag: replicate


title: Serum from participant 232


title: PDO37_ZT24_S1

value: Patient derived organoids of pancreatic cancer

tag: treatment

value: Dexamethasone treatment

tag: time


title: DMN_303_C3_H_R3

value: liver tumor associated with chronic hepatitis C

value: Plate 1 index H

tag: well

tag: dose group

value: H

tag: index

value: ATTGGTTGC

value: AGCTAGACC

tag: group

tag: solvent control

tag: reference rna


title: Serum from participant 231

value: Control

tag: tissue


title: PDO32_ZT20_S1

tag: cell line

tag: cell type


title: DMN_330_C3_E_R2

tag: chemical short_form

value: Plate 2 index E

value: E

value: ATTCGCTCT

value: TGCATCTGC

value: F

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: PDO32_ZT12_S1


title: caco2bbe1_PAC_100_IL1B_rep3

value: Enterocyte

tag: disease origin

value: Colorectal adenocarcinoma

tag: pre-treatment (concentration)

value: cranberry proanthocyanidin (100 µg/ml)

tag: pre-treatment exposure time

value: 24 hours

tag: il-1β stimulation

value: 1 ng/ml

tag: il-1β or mock exposure time

value: 3 hours


title: Serum from participant 230

tag: Sex

value: Female

tag: condition

value: Sarcopenia

value: serum


title: PDO32_ZT8_S1

value: Patient derived organoids of pancreatic cancer

tag: treatment

value: Dexamethasone treatment

tag: time


title: DMN_326_C3_E_R1

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

value: DMN

tag: chemical long_name

value: nitrosodimethylamine

tag: dose

tag: batch nr_heparg

tag: plate

value: Plate 2 index E

tag: well

tag: dose group

tag: index

value: TCAGTACAT

value: AAGGTGTTT

tag: group

tag: replicate

tag: solvent control

tag: reference rna


title: PDO32_ZT4_S1

tag: tissue

tag: cell line

tag: cell type


title: Serum from participant 229

tag: Sex

tag: condition

value: Control


title: DMN_303_C2_H_R3

tag: chemical short_form

value: Plate 1 index H

value: H

value: TGATTAAGC

value: AGCTAGACC

value: F

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: PDO32_ZT16_S1

value: Patient derived organoids of pancreatic cancer

tag: treatment

tag: time


title: PDO26_ZT24_S1

value: Dexamethasone treatment


title: PDO26_ZT20_S1


title: Serum from participant 227

value: Female

value: Sarcopenia

value: serum


title: Serum from participant 228


title: DMN_330_C2_E_R2

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

value: DMN

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: plate

tag: well

tag: dose group

value: E

value: GTTTATACT

value: TGCATCTGC


title: DMN_326_C2_E_R1

tag: tissue

value: nitrosodimethylamine

value: Plate 2 index E

tag: index

value: ATTCGCTCT

value: AAGGTGTTT

tag: group

tag: replicate

tag: solvent control

tag: reference rna


title: PDO26_ZT12_S1

tag: cell line

tag: cell type


title: PDO26_ZT8_S1


title: PDO32_ZT24_S1


title: 4T1_Followers_rep3

city: Atlanta

first: Adam

last: Marcus

state: Georgia

address: 1365 Clifton Rd NE, Building C, Room 4092

institute: Emory University

hyb_protocol: Bisulfite conversion was performed on the DNA, and the DNA was applied to the Infinium Mouse Methylation BeadChip (Illumina, 20041558)

scan_protocol: standard Illumina scanner

data_processing: Data from each sample was first pre-processed by R package “sesame” and differentially methylated positions (DMPs) were detected by function “dmpFinder” implemented in R package “minfi”

label: Cy5 and Cy3

source_name: Follower cells from the 4T1 cell line

label_protocol: Standard Illumina protocol

growth_protocol: 37 C, 5% CO2; grown in DMEM media with 10% FBS, 1% penicillin-streptomycin

extract_protocol: Cells were grown to 70% confluency, trypsinized and then homogenized using QIAshredder (Qiagen #79654). DNA was isolated using the QIAamp DNA Mini Kit (Qiagen #51304).

treatment_protocol: No treatment

tag: subpopulation

value: Followers


title: Serum from participant 226

tag: Sex

tag: condition

value: Control


title: DMN_303_C1_H_R3

tag: chemical short_form

tag: chemical long_name

value: Plate 1 index H

value: H

value: TCAGCTAAT

value: AGCTAGACC

value: F

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: PDO26_ZT4_S1

value: Patient derived organoids of pancreatic cancer

tag: treatment

value: Dexamethasone treatment

tag: time


title: 4T1_Parentals_rep2

source_name: Parental cells from the 4T1 cell line

value: Parentals


title: PDO26_ZT0_S1

tag: tissue


title: 4T1_Singles_rep2

source_name: Single cells from the 4T1 cell line

value: Singles


title: 4T1_Singles-CDH1_rep2

source_name: Single cells with CDH1 overexpressed from the 4T1 cell line


title: 4T1_Singles_rep3


title: 4T1_Followers_rep2


title: Serum from participant 225

value: Female

value: serum


title: 4T1_Singles-CDH1_rep3


title: 4T1_Parentals_rep1


title: PDO15_ZT24


title: DMN_330_C1_E_R2

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

value: DMN

value: nitrosodimethylamine

tag: dose

tag: batch nr_heparg

tag: plate

value: Plate 2 index E

tag: well

tag: dose group

value: E

tag: index

value: GAACTGTAT

value: TGCATCTGC

tag: group


title: PDO15_ZT20

tag: cell line

tag: cell type


title: 4T1_Leaders_rep1

source_name: Leader cells from the 4T1 cell line

tag: subpopulation

value: Leaders


title: PDO15_ZT12


title: Serum from participant 223

tag: Sex

tag: condition

value: Control


title: 4T1_Followers_rep1

value: Followers


title: DMN_326_C1_E_R1

tag: chemical short_form

tag: chemical long_name

value: ACTCATGTA

value: AAGGTGTTT

tag: replicate

tag: solvent control

value: F

tag: reference rna

tag: technical control

tag: chemical type

value: test


title: PDO15_ZT4

tag: tissue

value: Patient derived organoids of pancreatic cancer

tag: treatment

value: Dexamethasone treatment

tag: time


title: Neg_Lysis_H_NA

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: Negative lysis buffer

tag: dose

tag: batch nr_heparg

tag: plate

value: Plate 1 index H

tag: well

tag: dose group

value: R

value: H

tag: index

value: ATTCGAATC

value: AATAGGTGC

value: T

tag: cas-nr


title: PDO10_ZT24

tag: cell line

tag: cell type


title: 4T1_Leaders_rep3

tag: subpopulation

value: Leaders


title: 4T1_Leaders_rep2


title: PDO10_ZT20


title: PDO10_ZT16


title: Serum from participant 224

tag: Sex

value: Female

tag: condition

value: Sarcopenia

value: serum


title: Serum from participant 221

value: Control


title: PDO15_ZT16


title: Serum from participant 220


title: PDO15_ZT8


title: PDO10_ZT8


title: 4T1_Singles-CDH1_rep1


title: MMS_330_C5_E_R2

value: liver progenitor cells

tag: chemical short_form

value: MMS

tag: chemical long_name

value: methylmethanesulfonate

value: Plate 2 index E

value: E

value: TAAGGTAGC

value: GACCTTGCT

tag: group

tag: replicate

tag: solvent control

value: F

tag: reference rna

tag: technical control

value: test


title: Neg_Lysis_E_NA

tag: tissue

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: Negative lysis buffer

tag: dose

tag: batch nr_heparg

tag: plate

value: R

value: GGGTTGTTA

value: AATTCGGAA

tag: chemical type


title: PDO10_ZT4

value: Patient derived organoids of pancreatic cancer

tag: cell line

tag: treatment

value: Dexamethasone treatment

tag: time


title: 4T1_Singles_rep1

tag: subpopulation

value: Singles


title: Serum from participant 219

tag: Sex

value: Female

tag: condition

value: Sarcopenia

value: serum


title: MMS_326_C5_E_R1

tag: cell type

value: liver progenitor cells

tag: chemical short_form

value: MMS

tag: chemical long_name

value: methylmethanesulfonate

value: Plate 2 index E

tag: well

tag: dose group

value: E

tag: index

value: TGCATGACA

value: GATGGTTGT

tag: cas-nr


title: 4T1_Parentals_rep3

value: Parentals


title: PDO6_ZT20

tag: tissue


title: PDO6_ZT12


title: PDO6_ZT16


title: Serum from participant 218

value: Control


title: Serum from participant 217


title: PDO10_ZT0


title: MMS_303_C4_E_R3

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: dose

tag: batch nr_heparg

value: ATTCGCTCT

value: AGCCTACTT

tag: group

tag: replicate

tag: solvent control

value: F

tag: reference rna

tag: technical control

value: test


title: MMS_303_C5_E_R3

tag: cell line

tag: plate

value: TCAGTACAT

tag: chemical type


title: MMS_330_C4_E_R2

tag: cell type

tag: chemical short_form

value: GACCTTGCT


title: Serum from participant 215

tag: Sex

value: Female

tag: condition

value: serum


title: PDO6_ZT4

value: Patient derived organoids of pancreatic cancer

tag: treatment

value: Dexamethasone treatment

tag: time


title: MIAPACA2_20h

source_name: Pancreatic cancer cell line

tag: tissue

value: Pancreatic cancer cell line


title: MIAPACA2_24h


title: Serum from participant 216

value: Sarcopenia


title: PDO6_ZT0


title: MIAPACA2_16h


title: MMS_303_C3_E_R3

value: liver progenitor cells

value: MMS

tag: chemical long_name

value: methylmethanesulfonate

tag: dose

value: Plate 2 index E

tag: well

tag: dose group

value: E

tag: index

value: ACTCATGTA

tag: cas-nr


title: MIAPACA2_8h


title: MMS_330_C3_E_R2

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: batch nr_heparg

value: ATTCGCTCT

tag: group

tag: replicate

tag: solvent control

tag: reference rna

tag: technical control


title: Serum from participant 214

tag: Sex

value: Control


title: MIAPACA2_12h

tag: cell line

tag: cell type


title: Serum from participant 212

tag: condition


title: MMS_326_C3_E_R1

tag: tissue

tag: chemical short_form

tag: plate

value: TCAGTACAT

value: GATGGTTGT

value: F

tag: chemical type

value: test


title: PDO26_ZT16_S1

value: Patient derived organoids of pancreatic cancer

tag: treatment

value: Dexamethasone treatment

tag: time


title: Serum from participant 213

value: Female

value: Sarcopenia

value: serum


title: PANC1_24h

value: Pancreatic cancer cell line


title: PDO6_ZT8


title: Serum from participant 211


title: MMS_303_C2_E_R3

value: liver progenitor cells

value: MMS

tag: chemical long_name

value: methylmethanesulfonate

tag: dose

value: Plate 2 index E

tag: well

tag: dose group

tag: index

value: GTTTATACT

value: AGCCTACTT

tag: cas-nr


title: MMS_330_C2_E_R2

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: batch nr_heparg

value: E

value: ACTCATGTA

value: GACCTTGCT

tag: group

tag: replicate

tag: solvent control

tag: reference rna

tag: technical control


title: MMS_326_C4_E_R1

tag: tissue

tag: cell line

tag: cell type

tag: chemical short_form

value: TAAGGTAGC

value: GATGGTTGT

value: F

value: test


title: MIAPACA2_0h

tag: treatment

value: Dexamethasone treatment

tag: time


title: PANC1_16h

value: Pancreatic cancer cell line


title: PANC1_8h


title: MMS_326_C2_E_R1

value: liver progenitor cells

tag: chemical long_name

tag: dose

tag: plate

value: ATTCGCTCT

tag: chemical type


title: PANC1_4h


title: MIAPACA2_4h


title: PANC1_0h


title: MMS_303_C1_E_R3

value: MMS

value: methylmethanesulfonate

tag: well

tag: dose group

tag: index

value: GAACTGTAT

tag: cas-nr


title: Serum from participant 209

tag: Sex

value: Female

tag: condition

value: Sarcopenia

value: serum


title: CAPAN1_24h


title: CAPAN1_20h


title: PDO32_ZT0_S1

value: Patient derived organoids of pancreatic cancer


title: MMS_330_C1_E_R2

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: batch nr_heparg

value: Plate 2 index E

value: E

tag: group

tag: replicate

tag: solvent control

tag: reference rna

tag: technical control


title: CAPAN1_16h

tag: tissue

tag: cell line

tag: cell type

tag: treatment

tag: time


title: PANC1_20h


title: 22Rv1, RB1 knockout-1

city: Chiba

first: Yasutaka

last: Yamada

state: MA

address: 1-8-1 Inohana, chuo-ku

department: Urology

country: Japan

institute: Graduate School of Medicine, Chiba University

data_processing:
RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA).
The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA).
The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
Assembly: GRCh38
Supplementary files format and content: 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 Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

source_name: tissue

growth_protocol: The medium for this cell lines is RPMI-1640 Medium supplumented with 10% fetal bovine serum.

extract_protocol:
 Total RNA was extracted from each tissue by using Qiagen's ‘RNeasy’ RNA extraction kit (Qiagen).
RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.

value: tissue

tag: genotype

value: RB1 knockout


title: 22Rv1, RB1 knockout-2


title: Human_ref_R_H_NA

tag: chemical short_form

value: Human reference RNA

tag: chemical long_name

tag: dose

tag: plate

value: Plate 1 index H

tag: well

tag: dose group

value: R

value: H

value: TGGAACGCT

value: GCTGCGTAT

value: F

value: T

tag: chemical type

value: reference


title: CAPAN1_12h

value: Pancreatic cancer cell line

value: Dexamethasone treatment


title: CAPAN1_4h


title: MMS_326_C1_E_R1

value: liver tumor associated with chronic hepatitis C

value: liver progenitor cells

value: MMS

value: methylmethanesulfonate

tag: batch nr_heparg

tag: index

value: ACTCATGTA

value: GATGGTTGT

tag: group

tag: replicate

value: test

tag: cas-nr


title: CAPAN1_0h

tag: tissue

tag: cell line


title: ASPC1_24h

tag: cell type

tag: treatment


title: PANC1_12h

tag: time


title: ASPC1_20h


title: 22Rv1, WT-3

value: tissue

tag: genotype

value: Wilde Type


title: Serum from participant 210

tag: Sex

value: Female

tag: condition

value: Control

value: serum


title: 22Rv1, WT-2


title: 22Rv1, RB1 knockout-3

value: RB1 knockout


title: GLY_303_C5_H_R3

value: HepaRGTM

tag: chemical short_form

value: GLY

tag: chemical long_name

value: glycidol

tag: dose

tag: plate

value: Plate 1 index H

value: H

value: TGCTTATTC

value: AGCTAGACC

tag: solvent control

value: F

tag: reference rna

tag: technical control


title: ASPC1_12h

value: Pancreatic cancer cell line

value: Dexamethasone treatment


title: ASPC1_16h


title: ASPC1_8h


title: 22Rv1, WT-1


title: ASPC1_4h


title: GLY_330_C5_E_R2

value: liver tumor associated with chronic hepatitis C

value: liver progenitor cells

tag: batch nr_heparg

value: Plate 2 index E

tag: well

tag: dose group

value: E

tag: index

value: GGGTTGTTA

value: TGCATCTGC

tag: group

tag: replicate

tag: chemical type

value: test


title: ASPC1_0h

tag: tissue

tag: cell line

tag: cell type

tag: treatment

tag: time


title: FLM3_rna

city: Boston

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

data_processing:
fastq files were run through 10X cellranger pipeline
downstream analysis was done by R package Seurat
Assembly: hg19
Supplementary files format and content: h5 format with cell by gene matrix

source_name: liver metastatase from prostate cancer

extract_protocol:
First, the cell suspensions were fixed in 1ml of fixation buffer for 16-24 hours at 4ºC according to the 10X genomics fixation protocol and later resuspended in quenching buffer. Next, following the 10X Genomics Chromium Fixed RNA profiling protocol, the fixed cells were hybridized with individual probes and later on washed and counted on the Countess II Automated Cell Counter. If multiplexing, the samples were pooled based on the limiting sample (the one with lowest number of cells). As a consequence, in the pool we had the same cell counts per sample. After several washes of the pool, we measured the pool stock concentration. Based on the manufacter's recommendations and our cell stock concentration, the targeted cell recovery was set. Afterwards, the GEM generation took place in the Chromium Next GEM Chip Q. In addition, the GEMs were incubated, pre-amplified and cleaned with the SPRIselect beads, as advised by the manufacter before the library construction.
The library construction was made as described in the 10X Chromium Fixed RNA Profiling protocol. For that, after the pre-amplification PCR clean-up, we proceeded with the Sample Index PCR, in which individual indexes from the Dual Index TS Set A were used for each of the samples. The number of cycles in the PCR was determined based on the targeted cell recovery. After the PCR, the samples went through a size selection clean-up with the SPRIselect beads and eluted in the Qiagen Buffer EB. The Agilent TapeStation High Sensitivity was run to check the traces of the libraries and the Qubit fluorometer was used to quantify their concentrations. Lastly, the libraries were sequenced on the Illumina NovaSeq Platform.

value: liver metastatase from prostate cancer


title: Human_ref_R_E_NA

value: HepaRGTM

tag: chemical short_form

value: Human reference RNA

tag: chemical long_name

tag: dose

value: R

value: TCCTCAGCC

value: GATGGTTGT

value: T

value: reference

tag: cas-nr


title: CAPAN1_8h

value: Pancreatic cancer cell line


title: GLY_326_C5_E_R1

value: GLY

value: glycidol

tag: plate

value: GTTTATACT

value: AAGGTGTTT

tag: solvent control

value: F

tag: reference rna

tag: technical control


title: PM154, decitaine treated, rep2

data_processing:
RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA).
The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA).
The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
GRCh38
Assembly: 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 Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

growth_protocol: The medium for this cell lines is prostate specific media using advanced DMEM.

extract_protocol: RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.

treatment_protocol: Total RNA was extracted from each tissue by using Qiagen's ‘RNeasy’ RNA extraction kit (Qiagen).

value: Prostate cancer cell line

tag: genotype

value: DNMT1 knockout


title: FLM3_batch2_rep2

data_processing:
fastq files were run through cellranger-atac pipepline
QC and downstream analysis were done by R packages Seurat and Signac
Assembly: hg19
Supplementary files format and content: tab-separated values representing genomic locations of DNA fragments from single-cell ATAC sequencing experiments

source_name: liver metastasis of NEPC

extract_protocol:
First, nuclei were isolated from cryopreserved whole cell suspensions. For that, the cells were thawed at 37ºC in a water bath and washed with PBS 1X. Next, the nuclei were isolated from the cellsas described in the OMNI-ATAC protocol (Corces et al. Nature Methods 2017). Right after the isolation, the nuclei were filtered in a 40μm filter and counted with the Countess II Automated Cell Counter. Next, we proceeded with the scATAC protocol from 10X Genomics. Based on the manufacter's recommendations and our nuclei stock concentrations, the targeted nuclei recovery was set, followed by transposition and GEM generation in the Chromium Next GEM Chip H. Before the library construction and after GEM incubation, the GEMs were cleaned with the Dynabeads and SPRIselect reagents.
The library construction was made as described in the 10X Chromium Next GEM Single Cell ATAC protocol. For that, after the post GEM incubation clean-ups, we proceeded with the Sample Index PCR, in which individual indexes from the Single Index N Set A were used for each of the samples. The number of cycles in the PCR was determined based on the targeted nuclei recovery. After the PCR, the samples went through a double-sided size selection clean-up with the SPRIselect beads and eluted in the Qiagen Buffer EB. The Agilent TapeStation High Sensitivity was run to check the traces of the libraries and the Qubit fluorometer was used to quantify their concentrations. Lastly, the libraries were sequenced on the Illumina NovaSeq Platform.

value: liver metastasis of NEPC


title: FLM3_batch1_rep2


title: GLY_330_C4_E_R2

value: liver tumor associated with chronic hepatitis C

value: liver progenitor cells

tag: batch nr_heparg

value: Plate 2 index E

tag: well

tag: dose group

value: E

tag: index

value: AAGACTCTT

value: TGCATCTGC

tag: group

value: test


title: FLM3_batch2_rep1

tag: tissue


title: GLY_326_C4_E_R1

tag: cell line

value: HepaRGTM

tag: cell type

value: GAACTGTAT

tag: replicate

tag: chemical type


title: PM154, Control, rep3

value: Wilde Type


title: PM154, Control, rep2


title: Serum from participant 222

tag: Sex

value: Female

tag: condition

value: Control

value: serum


title: Non-transduced T-cell (replicate 3)

city: HOUSTON

first: Xiaotong

state: Texas

address: 2121 W. Holcombe Blvd

department: CIID

institute: Texas A&M University

data_processing:
Raw FASTQ files were mapped to the human reference genome (hg38) using STAR (version 2.7.2b) RNASeq alignment tool. Biobambam (version 0.0.191) was used to mark duplicates and index raw files before alignment.
HTSeq (version 0.11.0) was utilized to extract raw read counts from STAR-aligned RNAseq files.
Assembly: hg38
Supplementary files format and content: CSV file include raw counts of human genes for each sample

source_name: PBMC

growth_protocol: Human peripheral blood mononuclear cells purchased from STEMCELL was stimulated by OKT-3 and CD28 mAb-coated plates. The cells were washed and replated in complete RPMI 1640 medium with 100 U/ml IL-2 48 hours later. The cells were then maintained in incubators at 37°C with 5% CO2 for expansion.

extract_protocol:
RNA was isolated using the RNeasy Plus mini kit (Qiagen).
Quality control measures were implemented for each sample before library construction to ensure data reliability. Potential RNA degradation and contamination were assessed through agarose gel electrophoresis. Poly-A selection was employed to remove rRNA from the samples. Following the QC procedures, mRNA was enriched from each sample using oligo(dT) beads. Initially, the mRNA underwent random fragmentation by adding a fragmentation buffer. Subsequently, cDNA synthesis was performed using the fragmented mRNA template and random hexamers as primers.Next, the double-stranded cDNA library was completed through a series of steps, including terminal repair, A-ligation, sequencing adaptor ligation, size selection, and PCR enrichment.

value: PBMC

value: Primary

tag: treatment

value: Non-transduced T-cell


title: GLY_303_C3_E_R3

tag: chemical short_form

value: GLY

tag: chemical long_name

value: glycidol

tag: dose

tag: plate

value: GACTTCATT

value: AGCCTACTT

tag: solvent control

value: F

tag: cas-nr


title: Non-transduced T-cell (replicate 2)


title: Metabolic refueling modified HER2 CAR expressed in T-cell (replicate 3)


title: PM154, Control, rep1

value: Prostate cancer cell line

tag: genotype


title: PM154, decitaine treated, rep3

value: DNMT1 knockout


title: GLY_330_C3_E_R2

value: liver tumor associated with chronic hepatitis C

value: liver progenitor cells

tag: batch nr_heparg

value: Plate 2 index E

tag: well

tag: dose group

value: E

tag: index

value: TCCTCAGCC

value: TGCATCTGC

tag: reference rna

tag: technical control

value: test


title: Non-transduced T-cell (replicate 1)

tag: cell line

value: PBMC

tag: cell type


title: Metabolic refueling modified HER2 CAR expressed in T-cell (replicate 2)

value: Primary


title: Brain, 30 Months, Rep12

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

institute: Christian-Albrechts-University Kiel

description:
30M.N12
Brain_30M_N12
brain_RNA_gene_counts.tsv.gz

data_processing:
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (1.12) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a 3’-end quality trimming for a phred-score >=30.
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim also from the 5’-end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using HTSeq count (0.6.1) with reverse stranded information in union mode.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Tabular delimited matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

growth_protocol: All the mice were kept solely for aging in a controlled environment and  a controlled health status.

extract_protocol:
RNA was extracted from tissue samples of liver, colon and left brain hemisphere with the phenol-chloroform extraction method using for each tissue 1ml Qiazol Lysis Reagent (Qiagen, Hilden, Germany).
RNA was reverse transcripted into Illumina shotgun sequencing libraries at Competence Centre for Genomic Analysis (CCGA, Kiel Germany) with TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions and sequenced for 2x75 cycles (2x100 for colon) in paired end mode with ~13 samples per lane on a HiSeq4000 machine. Demultiplexing was done with zero mismatches allowed in the barcodes.

tag: tissue

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

value: 30 Months

tag: library batch

value: Run 1


title: GLY_326_C3_E_R1

value: HepaRGTM

tag: chemical short_form

value: GLY

tag: chemical long_name

value: glycidol

tag: dose

tag: plate

value: AAGGTGTTT

tag: group

tag: replicate

tag: chemical type


title: FLM5

value: liver metastasis of NEPC


title: GLY_303_C4_E_R3

value: liver tumor associated with chronic hepatitis C

value: liver progenitor cells

tag: batch nr_heparg

tag: well

tag: dose group

tag: index

value: TAGCTCTTC

value: AGCCTACTT

tag: solvent control

value: F

tag: cas-nr


title: Metabolic refueling modified HER2 CAR expressed in T-cell (replicate 1)

tag: cell line

tag: cell type

tag: treatment


title: FLM3_batch1_rep1

tag: tissue


title: PM154, decitaine treated, rep1

value: Prostate cancer cell line

tag: genotype

value: DNMT1 knockout


title: Brain, 30 Months, Rep11

description:
30M.N11
Brain_30M_N11
brain_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

tag: library batch


title: HER2 CAR Expressed in T-cell (replicate 1)

value: PBMC

value: Primary

value: HER2 CAR Expressed in T-cell


title: Metabolic refueling modified GPC3 CAR expressed in T-cell (replicate 2)


title: HER2 CAR Expressed in T-cell (replicate 2)


title: Brain, 30 Months, Rep9

description:
30M.N9
Brain_30M_N9
brain_RNA_gene_counts.tsv.gz

value: Brain

value: Male

value: 30 Months


title: Brain, 30 Months, Rep10

description:
30M.N10
Brain_30M_N10
brain_RNA_gene_counts.tsv.gz

value: Run 2


title: Metabolic refueling modified GPC3 CAR expressed in T-cell (replicate 3)


title: Metabolic refueling modified GPC3 CAR expressed in T-cell (replicate 1)


title: GLY_326_C2_E_R1

value: HepaRGTM

tag: chemical short_form

value: GLY

tag: chemical long_name

value: glycidol

tag: dose

tag: plate

value: Plate 2 index E

value: E

value: GATGGTTGT

tag: group

tag: replicate

tag: reference rna

tag: technical control

value: test


title: GPC3 CAR Expressed in T-cell (replicate 2)

tag: cell line

value: GPC3 CAR Expressed in T-cell


title: GPC3 CAR Expressed in T-cell (replicate 1)

tag: cell type


title: Brain, 30 Months, Rep8

description:
30M.N8
Brain_30M_N8
brain_RNA_gene_counts.tsv.gz

value: Run 1


title: GLY_330_C1_E_R2

value: liver tumor associated with chronic hepatitis C

value: liver progenitor cells

tag: batch nr_heparg

tag: well

tag: dose group

tag: index

value: TGCATGACA

value: GACCTTGCT

tag: solvent control

value: F

tag: chemical type

tag: cas-nr


title: Brain, 30 Months, Rep7

description:
30M.N7
Brain_30M_N7
brain_RNA_gene_counts.tsv.gz

tag: tissue

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

tag: library batch


title: HER2 CAR Expressed in T-cell (replicate 3)

value: PBMC

value: Primary

tag: treatment

value: HER2 CAR Expressed in T-cell


title: Brain, 30 Months, Rep6

description:
30M.N6
Brain_30M_N6
brain_RNA_gene_counts.tsv.gz

value: 30 Months


title: GLY_330_C2_E_R2

value: HepaRGTM

tag: chemical short_form

value: GLY

tag: chemical long_name

value: glycidol

tag: dose

tag: plate

value: Plate 2 index E

value: TAGCTCTTC

tag: group

tag: replicate

tag: reference rna


title: GLY_303_C2_E_R3

tag: cell line

tag: cell type

tag: batch nr_heparg

tag: well

tag: dose group

value: E

tag: index

value: AGCCTACTT

tag: technical control

value: test


title: GLY_326_C1_E_R1

tag: tissue

value: liver tumor associated with chronic hepatitis C

value: liver progenitor cells

value: GACTTCATT

value: GATGGTTGT

tag: solvent control

tag: chemical type

tag: cas-nr


title: Brain, 30 Months, Rep5

description:
30M.N5
Brain_30M_N5
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

tag: library batch

value: Run 1


title: DMSO_330_MED_H_R4

tag: chemical short_form

value: DMSO

tag: chemical long_name

value: dimethylsulfoxide

tag: dose

tag: plate

value: Plate 1 index H

value: MED

value: H

value: AGCCGATTA

value: AGCTAGACC

tag: group

value: DMSO H

tag: replicate

value: T

value: F

value: control


title: GLY_303_C1_E_R3

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRGTM

tag: cell type

value: liver progenitor cells

value: GLY

value: glycidol

tag: batch nr_heparg

value: Plate 2 index E

tag: well

tag: dose group

value: E

value: TAAGGTAGC

value: AGCCTACTT

tag: reference rna

value: test


title: Brain, 30 Months, Rep4

description:
30M.N4
Brain_30M_N4
brain_RNA_gene_counts.tsv.gz

tag: tissue

value: Brain

value: Male

value: 30 Months

value: Run 1