title: M233T

city: Ann Arbor

first: Kelly

last: Bakulski

address: 1415 Washington Heights

institute: University of Michigan

data_processing:
Raw fastq files from total RNA sequencing data were trimmed using trimmomatic
Trimmed reads from total RNA were further mapped to sheep reference genome (Oar_rambouillet_v1.0) using Spliced Transcripts Alignment to a Reference (STAR) aligner (2.6.0c)
The reads that aligned to the exons of the reference genome were then counted using featureCounts (1.6.1)
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: matrix table of normalized gene counts for each sample

source_name: Muscle

extract_protocol:
Total RNA was extracted from the liver and muscle after homogenizing the tissues in Trizol reagent (Life Technologies, Carlsbad, CA) following the manufacturer’s recommendations. Any residual contaminating DNA was removed by binding the RNA in a RNeasy binding column, treating the column with RNAse free DNAse (Qiagen, Germantown, MD) and eluting the RNA in nuclease free water. The quality of purified RNA including the purity and RNA integrity were evaluated using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) at the University of Michigan Advanced Genomics Core.
library preparation was carried out using TruSeq RNA Library Prep Kit (Illumina, San Diego, CA)

tag: sheepid

value: female

value: prenatal T-treatment

value: Muscle


title: S20 stage root rep4

status: Public on Oct 31 2021

type: SRA

city: Shanghai

first: Shutao

last: He

address: 320 Yue Yang Road

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
The raw sequence data were assessed for various quality parameters, and high-quality reads were filtered using NGS QC Toolkit (v2.3) (Patel and Jain, 2012).
The filtered high-quality reads were mapped on the sweet potato genome (http://public-genomes-ngs.molgen.mpg.de/cgi-bin/hgGateway?hgsid=9052&clade=plant&org=Ipomoea+batatas&db=ipoBat4) using TopHat (v2.0.0).
The mapped output was processed via RSEM (v1.3.1) to obtain TPM for all the sweet potato genes in each sample.
Genome_build: sweet potato genome (http://public-genomes-ngs.molgen.mpg.de/cgi-bin/hgGateway?hgsid=9052&clade=plant&org=Ipomoea+batatas&db=ipoBat4)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Ipomoea batatas

source_name: Root

extract_protocol:
For RNA-sequencing analysis, total RNA was isolated from the middle sections of fibrous roots (S4 and S8), pencil roots (S10 and S12) and storage roots (S14, S16 and S20) using the RNeasy Mini Kit (Qiagen) with manufacturer’s instruction. Quality of RNAs were checked by determining the RNA Integrity Number (RIN) using an Agilent 2100 Bioanalyzer and Nanodrop 2000 (Thermo Scientific, Waltham, United States).
All the 28 libraries (7 samples in four biological replicates) were prepared using the Illumina TruSeq RNA Sample Prep Kit with 1μg of total RNA.

tag: tissue

value: Root

tag: developmental stage

value: S20 stage (diameter 25 mm)

tag: genotype

value: wild type


title: M185T

state: MI

department: Department of Epidemiology

country: USA

organism: Ovis aries

tag: Sex

tag: treatment


title: Striatum, 7762

city: Bar Harbor

first: Vivek

last: Philip

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
gbrs with the following parameters -md  2 -rl  100 -ei  999 -pc  0.0 -te  0.0001 -db  TRUE -dh  TRUE
Genome_build: We create custom genomes of the eight founder strains by introducing strain-specific SNPs and short indels (Mouse Genome Project [Keane et al., 2011] release v5 available at ftp://ftp-mouse. sanger.ac.uk/REL-1505-SNPs_Indels/) to the reference genome (Genome Reference Consortium Mouse Build 38 available at http://ftp.ensembl.org/pub/release-84/ fasta/mus_musculus/dna/) using g2gtools (http://churchill-lab.github.io/ g2gtools)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Striatum

extract_protocol:
To control for circadian effects, the timing of testing and euthanasia were consistently performed between 8-12AM. Surgical instruments cleaned with RNAase away (ThermoFischer Scientific) were used. Whole intact brains were removed, hemisected and incubated in RNAlater (ThermoFischer Scientific) for 8-14 minutes. Under a dissection scope the striatum, hippocampus and prefrontal cortex were removed and soaked for 24 hours at room temperature and then stored at -80 degrees. The striatum was homogenized and total RNA was isolated by a TRIzol Plus kit (Life Technologies) according to the manufacturer’s method including an on-the-column DNase digestion. The quality of the isolated RNA was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA) and RNA 6000 Nano LabChip assay.  Ribo-depleted RNA was prepared using the RNA RiboErase Stranded cDNA library (Kappa Biosystems). The samples were pair end sequenced on a HiSeq producing paired 100 bp reads at a depth of 50 M read pairs per sample. The External RNA Controls Consortium (ERCC, Ambion) was added to samples to allow for normalization across samples but not used.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: F

tag: generation

value: drug naïve straitum


title: Striatum, 7761


title: HK-2_60µM LPC(18:0)_24H_rep1

type: RNA

city: Nagaizumi-cho

first: Kentaro

last: Yoshioka

state: Shizuoka

address: 465-6, Shimotogari

country: Japan

institute: Kyowa Kirin Co. Ltd.

hyb_protocol: cDNA products were mixed with transcription master mix in the presence of T7 RNA polymerase and Cy3 labelled-CTP and incubated at 40°C for 2 h. Labelled cRNAs were purified and eluted in nuclease-free water. For each hybridization step, Cy3-labelled cRNA was fragmented, and hybridized at 65°C for 17 h to an Agilent SurePrint G3 Human GE v3 8x60K Microarray

scan_protocol: The microarrays were scanned using an Agilent SureScan Microarray Scanner System (G4900DA; Agilent Technologies). Intensity values of each scanned feature were quantified using Agilent feature extraction software version 12.1.1.1, which performs background subtractions.

data_processing: Normalization was performed using Agilent GeneSpring software version 14.9.1 (per chip: normalization to 75th percentile shift). Any array-probe signals that saturated the fluorescence or did not show a significant difference from the background were excluded from the analysis.

organism: Homo sapiens

label_protocol: Total RNA was amplified and labelled with Cyanine 3 (Cy3) using an Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies), as per the manufacturer's instructions. Briefly, total RNA was reverse-transcribed into double-strand cDNA using a poly dT-T7 promoter primer.

extract_protocol: Total mRNA was isolated using an RNeasy kit (74106; Qiagen, Hilden, Germany).

treatment_protocol: For LPC treatment on HK-2 cells, the cells were pre-incubated in the assay medium, which contained DMEM/F12 with 0.1% fatty acid-free bovine serum albumin (BSA; 017-15141; Wako, Osaka, Japan), overnight at 37 °C in an atmosphere containing 5% CO2. LPC (16:0) or (18:0) (855675C or 855775C; Avanti Polar Lipids, Alabaster, AL, USA) were pre-conjugated to fatty acid-free BSA at 37°C for 5 min. The LPC species or control BSA solutions were added to the cells after 100× dilution in assay medium containing 0.1% dimethyl-sulfoxide (D0798; Tokyo Chemical Industry Co., Ltd., Tokyo, Japan), followed by incubation at 37°C in an atmosphere containing 5% CO2 for the indicated times

tag: cell line


title: M063T


title: HK-2_60µM LPC(18:0)_24H_rep3


title: S20 stage root rep2


title: Striatum, 7760


title: M255T


title: Striatum, 7763


title: M048T


title: HK-2_30µM LPC(18:0)_24H_rep2


title: Liver Control4

city: Tokyo

first: Sayaka

last: Katagiri

institute: Tokyo Medical and Dental University

description: Gene expression after multiple  injection and oral administration of saline in the liver

hyb_protocol: cRNAs were analyzed by hybridization onto an Agilent SurePrint G3 Unrestricted Gene Expression 8 × 60 K Microarray (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Fluorescence signals from the hybridized microarrays were detected using the Agilent Microarray Scanner System (Agilent Technologies) according to the manufacturer’s instructions.

data_processing: Raw microarray data were extracted using Feature Extraction Software (ver. 11.0.1.1; Agilent Technologies).

source_name: liver

label_protocol: The Agilent Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, California, USA) was used to generate cRNA with a sample input of 200 ng total RNA for single-color microarray

growth_protocol: C57BL/6J mice, gestational day 18 pregnant

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, California, USA) with NucleoSpin RNA (TaKaRa Bio, Shiga, Japan). cDNA was synthesized using a PrimeScript RT Master Mix (TaKaRa Bio) according to the manufacturer’s instructions.

treatment_protocol: A total of 10^8 colony-forming units (CFU) of sonicated P. gingivalis suspended in 100 μL of saline was  intraveously and orally administered three times per week to the experimented group. Identically, saline was administered to the control group.

tag: cell type

value: Hepatocytes

tag: age

value: Gestational day 18 pregnant

value: saline


title: Liver P.g.4

description: Gene expression after multiple  injection and oral administration of P.gingivalis in the liver

value: P. gingivalis


title: HK-2_con_24H_rep2


title: Liver Control3


title: S20 stage root rep3


title: M201C

value: control


title: Striatum, 7759


title: S20 stage root rep1


title: Liver P.g.2


title: S16 stage root rep3

value: S16 stage (diameter 15 mm)


title: Striatum, 7758


title: S16 stage root rep4


title: Liver P.g.3


title: HK-2_30µM LPC(18:0)_24H_rep1


title: HK-2_con_24H_rep3


title: HK-2_con_24H_rep1


title: Liver P.g.1


title: S16 stage root rep2


title: Striatum, 7757


title: Striatum, 7756


title: Liver Control2


title: Liver Control1


title: S16 stage root rep1


title: Striatum, 7755


title: M131C


title: S14 stage root rep4

value: S14 stage (diameter 10 mm)


title: M098C


title: Striatum, 7754


title: S14 stage root rep3


title: L255T

source_name: Liver

value: Liver


title: M179C


title: BAT P.g.4

description: Gene expression after multiple  injection and oral administration of saline in brown adipose tissue

source_name: brown adipose tissue

value: adipocytes

tag: time point


title: S14 stage root rep2


title: M132C

value: female


title: BAT P.g.3


title: L185T

value: prenatal T-treatment


title: BAT Control4


title: L233T


title: Striatum, 7752


title: S14 stage root rep1


title: Striatum, 7751


title: S12 stage root rep4

value: S12 stage (diameter 5 mm)


title: Striatum, 7750


title: BAT Control3


title: BAT Control2


title: L048T


title: S12 stage root rep3

value: Root


title: Striatum, 7749


title: Striatum, 7753


title: S12 stage root rep2


title: L201C


title: Striatum, 7748


title: healthy control, b6

city: shaoxing

first: guanguan

last: qiu

state: zhejiang

address: Yanan Road123

institute: shaoxing second hospital

hyb_protocol: The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent),and add  the images (.tif) to be extracted to the FE Project,then set FE Project Properties.

source_name: Plasma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Plasma EVs were harvested and preserved with Trizol.RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Plasma from sepsis patients and healthy controls were diluted 1:2 with cold PBS and followed by centrifugation at 2000 g for 30 minutes to remove cellular debris. The supernatant was then diluted 1:5 with PBS and centrifuged at 14,000 g for 30 minutes at 4℃ to remove large membrane vesicles. followed by centrifugation for 2 h at 120,000 g at 4°C in a swinging bucket rotor (Optima XPN- 80, SW 32 Ti rotor, Beckman Coulter). The sediment was washed by PBS again at 120,000 g at 4°C for 2 h.

tag: condition

value: plasma

tag: sample type

value: extracellular vesicles


title: L179C


title: Striatum, 7747

value: F


title: S12 stage root rep1

value: wild type


title: healthy control, b2


title: L063T


title: S10 stage root rep4

value: S10 stage (diameter 3.5 mm)


title: Striatum, 7746

value: drug naïve straitum


title: L131C


title: BAT P.g.1

value: Gestational day 18 pregnant


title: S10 stage root rep3


title: sepsis patient, a6

value: sepsis


title: L098C

value: control


title: sepsis patient, a7


title: Striatum, 7744

value: M


title: BAT P.g.2

value: P. gingivalis


title: BAT Control1

value: saline


title: KO_1

first: Yajuan

last: Zhang

address: 320 Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: FPKM

source_name: HCT116 cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine calf serum (HyClone, Logan, UT, USA)

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.  1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x150 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PHGDH-/-

value: colorectal cancer cell


title: Striatum, 7745


title: KO_2


title: Uninfected_501_600_WH

city: Wuerzburg

first: Martin

last: Fraunholz

address: Theodor-Boveri-Weg

department: Chair of Microbiology

country: Germany

institute: University of Wuerzburg

library_source: genomic

data_processing:
22 nt reads were obtained by Illumina GAIIx
Reads were mapped against the Open Biosystems (Dharmacon; GE Lifesciences) pGIPZ shRNA library (releases 6.1–6.12) using Bowtie and enumerated
Batch effect among different libraries was evident by the RLE plot and carefully removed by RUV methods. Further normalization and differential expression analysis were conducted with edgeR (TMM).

molecule: genomic DNA

source_name: HeLa_sublibrary_501_600 (replicate 2)

growth_protocol: One day before infection 3x10e6 HeLa-shRNA cells (sublibrary IDs  201-300, 301-400, and 401-500) were seeded in seven 15 cm dishes. Six dishes were infected with S. aureus 6850 mRFP at a multiplicity of infection of 30. 20 µg/ml lysostaphin was added 1 hour post-infection (h p.i.) in order to remove extracellular bacteria. 4.5 h p.i. dead cells were removed by two PBS washing steps and adherent viable cells were collected for fluorescence activated cell sorting (FACS). Viable cells were selected via forward and sideward scatter on an FACSAriaIII FACS sorter (BD). The GFP-expressing HeLa-shRNA cells were sorted for S. aureus infection by their mRFP positivity. Infected (mRFP positive) and uninfected (mRFP-negative) population were collected separately. One 15 cm dish of uninfected cells served as input control.

extract_protocol:
Genomic DNA of the sorted uninfected and infected cells and input cells was isolated with the Multisource Genomic DNA Miniprep Kit (Axygen Biosciences). The shRNA cassettes were amplified via PCR and separation from the genomic DNA was obtained via agarose gel electrophoresis. Samples were diluted to a final concentration of 2 ng/μl.
Sequencing libraries were prepared for sequencing using standard Illumina protocols so that the read1 primer reads the first nucleotide of the siRNA.

treatment_protocol: One culture dish served as uninfected control, 6 15 cm culture dishes were infected with S. aureus.

value: epithelial cells

value: Uninfected

value: HeLa


title: S10 stage root rep1

value: Root


title: S10 stage root rep2


title: WT_2


title: Striatum, 7743


title: Uninfected_301_400_WH

source_name: HeLa_sublibrary_301_400 (replicate 2)


title: S8 stage root rep4

value: S8 stage (diameter 2 mm)


title: WT_1


title: Striatum, 7742


title: sepsis patient, a1

value: plasma

value: extracellular vesicles


title: Striatum, 7741


title: Uninfected_1_150_WH

source_name: HeLa_sublibrary_1_150 (replicate 2)


title: S8 stage root rep3

value: wild type


title: Striatum, 7740

value: drug naïve straitum


title: S8 stage root rep2


title: TO Patient1 Control rep3

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

data_processing:
Illumina bcl2fastq2 v2.20 software was used for basecalling.
The adapters were trimmed with fastp 0.21.1 (Chen et al., 2018).
Reads were mapped with STAR 2.7.7a (Dobin et al., 2013).
Count matrix was generated with featureCount tool from ssubread-2.0.1 aligner (Liao et al., 2013, 2014)
Differential expression analysis was conducted using DESeq2 v1.28.1 (Love et al., 2014).
Genome_build: GENCODE release 37 GRCh38.primary assembly
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colorectal tumor organoids

growth_protocol: Cell suspension was mixed with Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning, USA). Then 50 μl drops of the resulting suspension in the extracellular matrix were transferred into the wells of a 24-well culture plate (TPP, Switzerland) and placed into cell culture incubator (37 °C, 5% CO2) for 20 minutes for solidification of the gel. Then, 750 μl of complete cell culture medium (van de Wetering et al., 2015) was added to each well, and the plate was incubated in cell culture incubator. Cell culture medium was replaced every 48 hours. Cells were inspected visually by an inverted Primo Vert microscope (Carl Zeiss, Germany). Organoids were subcultured every two weeks with the help of TrypLE Express (Thermo Fisher Scientific, USA).

extract_protocol:
Cells were lysed with the QIAzol Lysis Reagent (Qiagen, Germany). RNA isolation was performed using miRNeasy Micro Kit (Qiagen, Germany) according to the manufacturer's protocol. Nanodrop ND-1000 (Thermo Fisher Scientific, USA) was used to assess quantity and purity of the extracted RNA. Total RNA samples were also QC-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Libraries for mRNA sequencing were prepared from total RNA samples using Illumina Stranded mRNA Library Prep Kit (Illumina, USA).

treatment_protocol: Tumor organoids were treated with 2uM of 9-ING-41 for 24 hours.

value: No

tag: kras

value: Mutated (G12D)

tag: type

value: Colorectal tumor organoids


title: TO Patient1 Control rep2


title: S8 stage root rep1


title: Striatum, 7739

value: M


title: Uninfected_401_500_WH

source_name: HeLa_sublibrary_401_500 (replicate 2)


title: Uninfected_401_500

source_name: HeLa_sublibrary_401_500 (replicate 1)


title: S4 stage root rep4

value: S4 stage (diameter 1.5 mm)


title: Striatum, 7737


title: TO Patient1 9-ING-41 rep3


title: Uninfected_501_600

source_name: HeLa_sublibrary_501_600 (replicate 1)


title: S4 stage root rep3


title: S4 stage root rep2


title: Striatum, 7736


title: Uninfected_201_300_WH

source_name: HeLa_sublibrary_201_300 (replicate 2)


title: Striatum, 7738


title: Uninfected_1_150

source_name: HeLa_sublibrary_1_150 (replicate 1)


title: Striatum, 7735


title: SMZL3: splenic marginal zone lymphoma sample 3 scRNA-seq

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

description: dataset of digitally extracted human TCD8 and gd T lymphocytes

data_processing:
bcl2 files conversion to FASTQ format using cellranger-mkfastq™ algorithm (10x Genomics)
align to the GRCh38 reference transcriptome using cellranger-count
Preprocessing, normalization of UMI, and QC for discarding cell doublets and dying cells were performed using the R package Seurat 3
Integrated and normalized scRNAseq datasets were then scored for several multigene signatures. The signature scores of each single cell were computed with Single-Cell Signature Explorer (Pont et al., 2019), to apply the Score and Gate procedure for isolation of the gd T and T CD8 lymphocytes as described (Cerapio et al, 2021).
The integrated (cell x gene) matrices of the isolated gd T and T CD8 single cells are provided.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: splenic marginal zone lymphoma

growth_protocol: Cells were thawed before sequencing without growth protocol.

extract_protocol:
For the experiment, 10 000 cells of each sample were loaded in Chromium device for emulsion-based production of single cell mRNA libraries with the 10XGenomics platform chemistry 3’V3. Reverse transcription was performed on the C1000 Touch Thermal Cycler, and cDNA were amplified for 12 cycles. cDNA quality control and dosage were performed on Fragment Analyzer, and then by PCR.
Chromium Controller Single-Cell Instrument and Chromium Single Cell 3 Library & Gel Bead Kit (V3) were used to prepare individually barcoded single-cell RNA-Seq libraries. Double sided size selection of PCR products was performed with SPRIselect Reagent Kit (Beckman Coulter, France). The sequencing-ready library was cleaned up with SPRIselect beads and the sequencing was performed on a NextSeq 550 instrument (Illumina).

treatment_protocol: Dead Cell Removal Kit was used to improve cell viability

value: spleen

value: 66 yrs

value: Female

tag: stage of the disease

value: diagnosis

value: splenic marginal zone lymphoma


title: S4 stage root rep1

source_name: Root


title: TO Patient1 9-ING-41 rep1


title: Uninfected_201_300

source_name: HeLa_sublibrary_201_300 (replicate 1)

value: epithelial cells

value: Uninfected

value: HeLa


title: TO Patient1 Control rep1


title: Uninfected_301_400

source_name: HeLa_sublibrary_301_400 (replicate 1)


title: SMZL2: splenic marginal zone lymphoma sample 2 scRNA-seq

value: 75 yrs

value: Male


title: Input_501_600_WH

value: Input control


title: Input_401_500_WH


title: Striatum, 7731

source_name: Striatum

value: drug naïve straitum


title: Input_201_300_WH


title: LCY002_Gal_rep3

city: Shenzhen

first: Li

last: Cheng

address: Xueyuan Boulevard

department: Institute of Synthetic Biology

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
The sequencing data was filtered with SOAPnuke (v1.4.0) 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 (v2.1.0)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set
expression level of gene was calculated by RSEM (v1.2.8)
Genome_build: Saccharomyces_cerevisiae_S288C R64
Supplementary_files_format_and_content: results files include FPKM values for each Sample

organism: Saccharomyces cerevisiae

growth_protocol: The yeast strains (BY4741, LCY001 and LCY002) were cultured in SC-His media, overnight. Then dilute into three different cultures – containing either glucose, galactose or ethanol/glycerol as the carbon source – at OD600 of 0.1/ml. Grow until OD600 reached about 1.0. Every sample had three repeats from individual colonies. Cells (30 OD) were collected by centrifugation at 4°C at 3000 rpm for 10 min, washed with iced PBS buffer and frozen in liquid nitrogen, then stored at -80°C.

extract_protocol:
Yeast RNA was extracted using the TRIzol® method following the manufacturer’s protocol. Bulk cells or filamentous fungus are grounded to a powder using liquid nitrogen, and the powder was transferred into the 2 mL tube contains 1.5 mL Trizol reagent. The mix was shaked for 3 min, and kept for 5 min at room temperature, then was Centrifuged at 10,000×g for 5 min at 4 °C. The supernatant was added 200 μL of chloroform/isoamyl alcohol (24:1) with 1 mL lysis reagents. After centrifuged at 10,000×g for 10 min at 4 °C, the supernatant was transferred into another new tube with equal volume of isopropanol and put in the refrigerator at -20 °C for 1 h. After centrifuged at 13,600×g for 20 min at 4 °C, the supernatant was precipitated by 1 mL of 75% ethanol and let dry for 3-5 min. The RNA pellet was dissolved with 30-100 μL of DEPC water or RNase-free water. The concentration of the extracted RNA samples was determined using a Nanodrop system (NanoDrop, Madison, USA), and the integrity of the RNA was examined by the RNA integrity number (RIN) using an Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA).
Oligo(dT)-attached magnetic beads were used to purified 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 BGIseq500 platform (BGI-Shenzhen, China).

tag: stain

value: his3{delta}1  leu2{delta}0  met15{delta}0  ura3{delta}0 CEN-HIS3-gene array [GLK1-HXK1-HXK2-GAL80-GAL4-GAL3-GAL1-GAL10-GAL7-GAL2-PGM1-PGM2-PGI1-PFK1-FBA1-PFK2-TPI1-TDH1-TDH2-TDH3-PGK1-GPM1-ENO1-ENO2-PYK2-CDC19-ERG1-ERG2-ERG3-ERG4-ERG5-ERG6-ERG7-ERG9-ERG11-ERG20-ERG24-ERG25-ERG26-ERG27]


title: LCY002_Gal_rep2


title: Input_301_400_WH


title: TO Patient1 9-ING-41 rep2

value: Mutated (G12D)


title: SMZL1: splenic marginal zone lymphoma sample 1 scRNA-seq

tag: tissue

value: 59 yrs


title: LCY002_Gal_rep1


title: Input_401_500


title: LCY002_Glc_rep3


title: Striatum, 7728

value: M


title: IAV-infected 25mM IA rep 3

city: Hannover

first: Frank

last: Pessler

address: Feodor-Lynen-Str. 7-9

department: Experimental Infection Research

institute: Center for Experimental and Clinical Infection Research GmbH

description:
25mM IA IAV
Human cell line without genetic modifications
Gene expression data from dTHP-1 cells IAV-infected 25mM IA treated for 12 hours

hyb_protocol: Hybridization was done for 16 hrs at conditions recommended by the manufacturer. Clariom™ S  chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000. Image analysis was done by Affymetrix® GeneChip® Command Console® Software (AGCC) and  Affymetrix® Expression Console™ Software

data_processing: Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, pathways, and network interactions.

label: biotin

molecule: polyA RNA

label_protocol: affymetrix protocol

growth_protocol: THP1 were cultured in RPMI for media supplemented with 10% FCS  and glutamax. THP1 cell were stimulated with PMA for differentation for 48 hours.

extract_protocol:
mRNA was extracted and purified from dTHP-1 cells using MN NucleoSpin RNA kit.
Complementary RNA (cRNA) amplification and coversion to biotinylated double-stranded cDNA (ds-cDNA) was done by Clariom™ S Pico Assay, human Affymetrix protocol from10 ng total RNA (GeneChip® Pico UserGuide 703308 Rev. 4 Affymetrix).

treatment_protocol: dTHP-1 cells  were cultured in 6 well plated with IA, DI or without any treatment for 24 hours. Followed by 24 hour pre-treatment, cell were either infected or not with Influena A virus and kept in respective treatments for 12 hours.

tag: infection

value: IAV-infected

value: 25mM IA

value: differentiated THP-1 cells


title: Input_1_150_WH


title: Striatum, 7730


title: Input_501_600


title: Striatum, 7734


title: Uninfected 25mM IA rep 1

description:
25mM IA C
Human cell line without genetic modifications
Gene expression data from dTHP-1 cells uninfected 25mM IA treated for 12 hours

source_name: dTHP-1 cells uninfected 25mM IA treated

value: uninfected


title: IAV-infected 25mM IA rep 2

source_name: dTHP-1 cells IAV-infected 25mM IA treated


title: Input_301_400


title: Input_201_300


title: LCY002_Glc_rep1

tag: genotype


title: Striatum, 7732

tag: Sex


title: Striatum, 7733


title: LCY002_Glc_rep2


title: Striatum, 7727


title: IAV-infected 25mM IA rep 1

tag: treatment


title: Striatum, 7729

tag: strain


title: Striatum, 7726

tag: generation


title: Uninfected 25mM IA rep 2

tag: cell line


title: Uninfected 25mM IA rep 3


title: Input_1_150

tag: cell type


title: Striatum, 7725

value: F


title: IAV-infected 1mM DI rep 3

description:
1mM DI IAV
Human cell line without genetic modifications
Gene expression data from dTHP-1 cells IAV-infected 1mM DI treated for 12 hours

value: 1mM DI treated


title: LCY002_GE_rep2


title: Striatum, 7724


title: IAV-infected 1mM DI rep 2

source_name: dTHP-1 cells IAV-infected 1mM DI treated


title: IAV-infected 1mM DI rep 1


title: Striatum, 7723


title: Infected_401_500_WH

value: epithelial cells

value: Infected


title: LCY002_GE_rep1


title: Infected_301_400_WH

value: HeLa


title: Infected_201_300_WH


title: LCY001_Gal_rep3

value: his3{delta}1  leu2{delta}0  met15{delta}0  ura3{delta}0 CEN-HIS3


title: Uninfected 1mM DI rep 3

description:
1mM DI C
Human cell line without genetic modifications
Gene expression data from dTHP-1 cells uninfected 1mM DI treated for 12 hours

source_name: dTHP-1 cells uninfected 1mM DI treated


title: LCY001_Gal_rep2


title: Infected_1_150_WH


title: LCY002_GE_rep3


title: Striatum, 7721


title: Striatum, 7722


title: Infected_501_600_WH

source_name: HeLa_sublibrary_501_600 (replicate 2)


title: Striatum, 7720


title: LCY001_Gal_rep1


title: Uninfected 1mM DI rep 1


title: IAV-infected untreated rep 3

description:
Untreated IAV
Human cell line without genetic modifications
Gene expression data from dTHP-1 cells IAV-infected untreated for 12 hours

source_name: dTHP-1 cells IAV-infected untreated

value: untreated


title: LCY001_Glc_rep3


title: Infected_501_600


title: Striatum, 7719


title: Uninfected 1mM DI rep 2


title: IAV-infected untreated rep 2


title: LCY001_Glc_rep2


title: IAV-infected untreated rep 1


title: Infected_401_500


title: Striatum, 7718


title: LCY001_Glc_rep1


title: Uninfected untreated rep 3

description:
Untreated C
Human cell line without genetic modifications
Gene expression data from dTHP-1 cells uninfected untreated for 12 hours

source_name: dTHP-1 cells uninfected untreated


title: Infected_301_400


title: Infected_201_300


title: Striatum, 7717


title: LCY001_GE_rep3


title: Striatum, 7716


title: Infected_1_150


title: LCY001_GE_rep2


title: Striatum, 7715


title: Uninfected untreated rep 1


title: BY4741_Gal_rep3

value: his3{delta}1  leu2{delta}0  met15{delta}0  ura3{delta}0


title: IAV infected untreated rep3

description:
IAV Untreated
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 IAV-infected untreated for 24 hours

source_name: Human alveolar epithelial cell line A549 IAV-infected untreated for 24 hours

growth_protocol: A549 cells were cultured in DMEM media supplemented with 10% FCS  and glutamax.

extract_protocol:
mRNA was extracted and purified from A549 cells using MN NucleoSpin RNA kit.
Complementary RNA (cRNA) amplification and coversion to biotinylated double-stranded cDNA (ds-cDNA) was done by Clariom™ S Pico Assay, human Affymetrix protocol from10 ng total RNA (GeneChip® Pico UserGuide 703308 Rev. 4 Affymetrix).

treatment_protocol: A549 cells  were cultured in 6 well plated with IA, DI or without any treatment for 24 hours. Followed by 24 hour pre-treatment, cell were either infected or not with Influena A virus and kept in respective treatments for 24 hours.

value: IAV-infected untreated for 24 hours

value: Cell Line from human lung (carcinoma)


title: LCY001_GE_rep1


title: Striatum, 7712

value: drug naïve straitum


title: BY4741_Gal_rep2


title: BY4741_Gal_rep1


title: Striatum, 7714


title: Striatum, 7713


title: MOCK

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

data_processing:
The Cell Ranger software pipeline (version 5.0) provided by 10X Genomics was used to demultiplex celluar barcodes, map reads to the genome
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Lung

extract_protocol:
From single-cell suspensions of mock and IAV-infected lungs at 7 and 14 days after infection, CD8 T cells were FACS sorted by positive staining with anti-mouse CD8-APC and CD3-FITC using BD Aria II flow cytometer sorter. The purity of CD8+ T cells was confirmed by flow cytometry.2x106 cells were resuspended in media containing 10% DMSO and 20% FBS and allowed to slow freeze in Mr Frosty
RNA libraries were prepared with the Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: Lung

tag: age

value: wild type

value: mock


title: D7

value: IAV infection, day 7


title: Striatum, 7711


title: D14

value: IAV infection, day 14


title: BY4741_Glc_rep3


title: Striatum, 7710


title: Uninfected untreated rep 2

value: uninfected

value: differentiated THP-1 cells


title: IAV infected untreated rep2

value: IAV-infected


title: BY4741_Glc_rep2


title: healthy control, b1

source_name: Plasma

value: control

value: plasma

value: extracellular vesicles


title: IAV infected untreated rep1


title: IAV infected DI 0.25mM rep3

description:
IAV 0.25mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 IAV-infected and 0.25mM DI treated for 24 hours , with 24 hours pre-treatment with 0.25mM DI

source_name: Human alveolar epithelial cell line A549 IAV-infected and 0.25mM DI treated for 24 hours , with 24 hours pre-treatment with 0.25mM DI

value: 0.25mM DI treated for 24 hours, with 24 hours pre-treatment with 0.25mM DI


title: CV34: 21d replicate A

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
The raw reads were subjected to quality control using FastQC
The reads were aligned to the latest version of UCSC mouse genome (mm10) using TopHat version 2.0.9 for 64bit Linux x86 (Kim et al. 2013) with default parameters that have been optimized for mammalian genomes.
Raw read counts for all the samples and genes were loaded into R version 3.0.1 for 64bit Linux x86 and computed the regularized log transform of the count data transforming it to log2 scale by fitting a model with term for each sample and a prior distribution on the coefficients which is estimated from the data.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated file of raw read counts readcounts_gene.tsv, Tab-separated file of RPKM normalized read counts readcounts_gene_rpkm.tsv

growth_protocol: αMEM+10% iFBS

extract_protocol:
RNA was extracted from cell culture samples with Nucleospin RNA Plus kit (Macherey-Nagel) after homogenization in RNA lysis buffer using Ultra-Turrax T25 homogenizer (Janke&Kunkel, Germany) and eluted to 2x30µl aqua.
RNA-seq was performed on the Illumina2000 platform as 51 bp paired-end reads

treatment_protocol: Cells collected after 0d were treated with differentiation medium consisting of αMEM + 10% + 100 U/ml penicillin-streptomycin + iFBS + 50 µg/ml ascorbic acid + 10 mM β-glycerophosphate

value: Osteoblast

tag: day of experiment

value: Differentiation treatment


title: Striatum, 7709

value: F


title: CV33: 14d replicate B


title: IAV infected DI 0.25mM rep2

value: Cell Line from human lung (carcinoma)


title: BY4741_Glc_rep1

value: his3{delta}1  leu2{delta}0  met15{delta}0  ura3{delta}0


title: IAV infected DI 0.25mM rep1


title: CV32: 14d replicate A


title: IAV infected DI 0.5mM rep3

description:
IAV 0.5mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 IAV-infected and 0.5mM DI treated for 24 hours , with 24 hours pre-treatment with 0.5mM DI

source_name: Human alveolar epithelial cell line A549 IAV-infected and 0.5mM DI treated for 24 hours , with 24 hours pre-treatment with 0.5mM DI

value: 0.5mM DI treated for 24 hours, with 24 hours pre-treatment with 0.5mM DI


title: Striatum, 7708

value: drug naïve straitum


title: IAV infected DI 0.5mM rep2


title: BY4741_GE_rep3


title: Striatum, 7707


title: Striatum, 7706


title: CV35: 21d replicate B


title: CV31: 24h replicate B


title: BY4741_GE_rep2


title: IAV infected DI 0.5mM rep1


title: IAV infected IA 20mM rep2

description:
IAV 20mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 IAV-infected and 20mM IA treated for 24 hours , with 24 hours pre-treatment with 20mM IA

source_name: Human alveolar epithelial cell line A549 IAV-infected and 20mM IA treated for 24 hours , with 24 hours pre-treatment with 20mM IA

value: 20mM IA treated for 24 hours, with 24 hours pre-treatment with 20mM IA


title: Striatum, 7704

value: M


title: CV29: Confluent replicate B

value: confluent

value: Growth medium


title: CV30: 24h replicate A


title: BY4741_GE_rep1


title: Striatum, 7705


title: Striatum, 7700


title: Striatum, 7701


title: CV28: Confluent replicate A


title: M34

type: genomic

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

hyb_protocol: The hybridization solution was prepared and added to the samples obtaining a total volume of 20 µl, which was poured onto the CGH microarray chip, where the hybridization process was carried out and incubated at 42ºC for 72 hours.

scan_protocol: Immediately after this process, the samples were scanned with the NimbleGen MS 200 Microarray scanner from Roche.

data_processing: The results were analyzed using the DEVA V1.2 program (Roche) and the UCSC Genome Bioinformatics program was used to obtain the affected genes with duplications and deletions.

source_name: M34 aCGH LLA-B

label_protocol: Once the genomic DNA was obtained, the marking with fluorochromes was carried out, 7μg of the samples to be analyzed were placed. Cy5 was added to the reference samples and Cy3 to the samples from patients with ALL. The samples were passed to a 98 degree thermal cycler for 10 minutes and subsequently rapidly cooled. A solution containing dNTP, water and Klenow fragment was added and incubated for 2 hrs at 37ºC. Later, Stop solution was added to stop the reaction and it was centrifuged. The buttons obtained were washed with 80% frozen ethanol and centrifuged again, removing the supernatant. Samples were dried in a DNA vacuum concentrator. Once the button was obtained, it was resuspended in 35μl of water and quantified to obtain 31μg, both of the samples and the references, and both were combined in a 1.5ml tube.

extract_protocol: 5x10E were used from bone marrow of individuals with acute lymphoblastic leukemia, using the DNA Quick-gDNA ™ MiniPrep kit (catalog D3006Zymo research). Following the manufacturer's instructions, the product was diluted in 60 µl of DNA Elution Buffer and the product was stored ≤ 20ºC until CGH was performed.

tag: disease state

value: acute lymphoblastic leukemia

tag: gender

value: male

value: Bone Marrow

source_name: common reference

value: common reference DNA


title: CV26: Subconfluent replicate A

value: subconfluent


title: CV27: Subconfluent replicate B


title: M28

source_name: M28 aCGH LLA-B


title: IAV infected IA 20mM rep1

value: IAV-infected


title: M35

source_name: M35 aCGH LLA-B


title: M29

source_name: M29 aCGH LLA-B

value: female


title: IAV infected IA 40mM rep2

description:
IAV 40mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 IAV-infected and 40mM IA treated for 24 hours , with 24 hours pre-treatment with 40mM IA

source_name: Human alveolar epithelial cell line A549 IAV-infected and 40mM IA treated for 24 hours , with 24 hours pre-treatment with 40mM IA

value: 40mM IA treated for 24 hours, with 24 hours pre-treatment with 40mM IA


title: a2

city: Boston

first: Tao

state: MA

address: 450 Brookline Avenue

department: Medical oncology

institute: Dana-Farber Cancer Institute

description: Treatment group

data_processing:
Illumina software was used for basecalling.
HISAT2 software was used for alignment.
Subread software (featureCounts) was used for filtering.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: CD8+ T cells

extract_protocol:
Splenic CD8+ T cells were isolated by immunomagnetic separation beads (Miltenyi Biotec, Bergisch Gladbach, Germany), and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8+ T cells

value: anti-CD3 and anti-CD28 plus IFNA (2000 U/ml) for 48 hours

value: Spleen


title: M32

source_name: M32 aCGH LLA-T

value: Bone marrow


title: IAV infected IA 40mM rep1

value: Cell Line from human lung (carcinoma)


title: Striatum, 7699

source_name: Striatum

value: drug naïve straitum


title: IAV infected IA 40mM rep3


title: Uninfected untreated rep2

description:
C Untreated
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 uninfected untreated for 48 hours

source_name: Human alveolar epithelial cell line A549 uninfected untreated for 48 hours

value: uninfected

value: untreated for 48 hours


title: M19

source_name: M19 aCGH LLA-B


title: IAV infected IA 20mM rep3

value: 20mM IA treated for 24 hours, with 24 hours pre-treatment with 20mM IA


title: Uninfected untreated rep3


title: Striatum, 7698

value: M


title: a1

description: Treatment group


title: Striatum, 7695


title: U2 VPA scRNA-seq

city: Hengyang

first: Qingtuan

last: Meng

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

data_processing:
Raw RNA-seq data were processed (including alignment, quantification) using Cell Ranger (v6.0.0) pipeline (10X Genomics)
“min.cells=3, min.features = 200” filtering criteria was used to preliminary filter the data
Cells with less than 500 detected genes, or more than 7437 detected genes (mean+3SD) were further filtered out.
Cells with more than 10% reads aligned to mitochondrial genes were then excluded
Doublets were removed that detected by either DoubletFinder (v2.0.3) or Scrublet (v0.2.2) algorithm.
Clustree (v0.4.3) was used to cluster cells based on the Louvain algorithm with multilevel refinement algorithm
The Wilcoxon test was used to identify cell type-specific DEGs (adjust P value < 0.05) between the VPA-exposed and control groups.
Genome_build: hg38

source_name: U2F organoid

growth_protocol: Human forebrain organoids were cultured in media reported in published protocols

extract_protocol:
Using the 10X Genomics standard pipeline
Sequencing libraries were prepared for RNA-seq using standard Illumina protocols

treatment_protocol: VPA (final concentration is 1 mM) was added to the organoid culture media. 72 hours later, organoids were dissociated into single cells using Accutase.

value: forebrain organoid

value: 1 mM VPA for 72h


title: C2

description: Control group

value: anti-CD3 and anti-CD28 for 48 hours


title: M12

source_name: M12 aCGH LLA-T

value: acute lymphoblastic leukemia

value: male

value: Bone Marrow

value: common reference DNA


title: Uninfected DI 0.25mM rep2

description:
C 0.25mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 uninfected treated with 0.25mM DI for 48 hours

source_name: Human alveolar epithelial cell line A549 uninfected treated with 0.25mM DI for 48 hours

value: treated with 0.25mM DI for 48 hours


title: U2 NC scRNA-seq

value: untreated


title: Striatum, 7693


title: Uninfected DI 0.25mM rep3


title: M15

source_name: M15 aCGH LLA-B

value: female


title: C1

description: Control group

value: CD8+ T cells

value: Spleen


title: Striatum, 7697

value: drug naïve straitum


title: M13

source_name: M13 aCGH LLA-T


title: Striatum, 7696


title: JURKAT

source_name: JURKAT aCGH ALL-T

value: JURKAT Cell line


title: Uninfected DI 0.25mM rep1

value: uninfected

value: Cell Line from human lung (carcinoma)


title: Striatum, 7690

value: M


title: U1 VPA scRNA-seq

source_name: U1M organoid

value: forebrain organoid


title: Uninfected DI 0.5mM rep2

description:
C 0.5mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 uninfected treated with 0.5mM DI for 48 hours

source_name: Human alveolar epithelial cell line A549 uninfected treated with 0.5mM DI for 48 hours

value: treated with 0.5mM DI for 48 hours


title: M5

source_name: M5 aCGH LLA-B

source_name: common reference


title: CEM

source_name: CEM aCGH ALL-T

value: CEM Cell line


title: 201852C05

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v25) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Salmon (v0.13.1) using GRCh38 GENCODE transcripts (v25)
Genome_build: hg38
Supplementary_files_format_and_content: comma separated text file with raw counts
Supplementary_files_format_and_content: comma separated text file with TPM counts

source_name: oral mucosa

extract_protocol:
miRNeasy micro kit (Qiagen, Cat No. 217084)
KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, USA) from 100ng total RNA

tag: organ

value: oral cavity

tag: subject

tag: time point

value: Female

tag: race

value: Asian


title: Uninfected DI 0.5mM rep3


title: Striatum, 7692

extract_protocol:
To control for circadian effects, the timing of testing and euthanasia were consistently performed between 8-12AM. Surgical instruments cleaned with RNAase away (ThermoFischer Scientific) were used. Whole intact brains were removed, hemisected and incubated in RNAlater (ThermoFischer Scientific) for 8-14 minutes. Under a dissection scope the striatum, hippocampus and prefrontal cortex were removed and soaked for 24 hours at room temperature and then stored at -80 degrees. The striatum was homogenized and total RNA was isolated by a TRIzol Plus kit (Life Technologies) according to the manufacturer’s method including an on-the-column DNase digestion. The quality of the isolated RNA was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA) and RNA 6000 Nano LabChip assay.  Ribo-depleted RNA was prepared using the RNA RiboErase Stranded cDNA library (Kappa Biosystems). The samples were pair end sequenced on a HiSeq producing paired 100 bp reads at a depth of 50 M read pairs per sample. The External RNA Controls Consortium (ERCC, Ambion) was added to samples to allow for normalization across samples but not used.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue


title: U1 NC scRNA-seq


title: Striatum, 7687


title: 201852C06


title: ILM S7

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (Gencode, release 35, https://www.gencodegenes.org/human/releases.html) with RNA STAR (Galaxy Version 2.7.5b, default parameters) using the Gencode annotation file (Gencode, Release 35).
Three BAM files for each sample (one for each lane) were combined in one BAM file per sample using Merge BAM files (Galaxy Version 1.2.0).
Reads mapped to the human reference genome were counted via featureCounts (Galaxy Version 1.6.4, default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (version 1.4.1103, R Version 4.0.3).
Genesymbols and genetypes were determined based on Ensembl (Release 101, download: 28.10.2020). Genes with 0 reads in all samples were removed from further analysis. Principal component analysis (PCA) was applied to check for potential batch effects. Normalized reads and differential gene expression were calculated using the R package DESeq2 (version 1.30.1) with default parameters (Benjamini-Hochberg adjusted p-values.
Genome_build: hg38
Supplementary_files_format_and_content: normalized reads

source_name: Macular hole

extract_protocol:
Tissue samples were stored in RNAlater (Qiagen) at 2-8° until sequencing was performed. RNA extraction, library preparation and RNA sequencing were conducted at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Germany; www.kfb-regensburg.de) as previously described (Boeck et al., 2020). In brief, total RNA was extracted from RNV and ILM tissue samples and stabilized in RNAprotect Cell Reagent according to the RNeasy Plus Micro Kit protocol (Qiagen). After pelleting, the RNAprotect buffer was removed, replaced by RLT Plus buffer and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was eliminated using gDNA Eliminator spin columns. Next, ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, total RNA was eluted in 12 μl of nuclease-free water.
RNA sequencing analysis was performed for 24 samples. The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories) was used to generate first-strand cDNA from 750 pg total-RNA. Double-stranded cDNA was amplified by LD PCR (12 cycles) and purified via magnetic bead clean-up. Library preparation was carried out, as described in the Illumina Nextera XT Sample Preparation Guide (Illumina). 150 pg of input cDNA was tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems). Equimolar amounts of each library were pooled, and the pools then used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in bcl files, which were converted into fastq files with the bcl2fastq v2.18 software.

value: Macular hole


title: Striatum, 7694

first: Vivek

institute: The Jackson Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
gbrs with the following parameters -md  2 -rl  100 -ei  999 -pc  0.0 -te  0.0001 -db  TRUE -dh  TRUE
Genome_build: We create custom genomes of the eight founder strains by introducing strain-specific SNPs and short indels (Mouse Genome Project [Keane et al., 2011] release v5 available at ftp://ftp-mouse. sanger.ac.uk/REL-1505-SNPs_Indels/) to the reference genome (Genome Reference Consortium Mouse Build 38 available at http://ftp.ensembl.org/pub/release-84/ fasta/mus_musculus/dna/) using g2gtools (http://churchill-lab.github.io/ g2gtools)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample


title: Striatum, 7689


title: 201852C04


title: Uninfected IA 20mM rep3

description:
C 20mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 uninfected treated with 20mM IA for 48 hours

source_name: Human alveolar epithelial cell line A549 uninfected treated with 20mM IA for 48 hours

tag: infection

value: treated with 20mM IA for 48 hours


title: Striatum, 7651

source_name: Striatum


title: 201852C03


title: ILM S2


title: ILM S6


title: Striatum, 7688


title: 201838C06


title: ILM S5


title: ILM S4


title: Striatum, 7650


title: Uninfected IA 20mM rep1


title: Uninfected untreated rep1

source_name: Human alveolar epithelial cell line A549 uninfected untreated for 48 hours

value: untreated for 48 hours


title: Uninfected DI 0.5mM rep1


title: 201852C02


title: Uninfected IA 40mM rep2

description:
C 40mM
Human cell line without genetic modifications
Gene expression data from human alveolar epithelial cell line A549 uninfected treated with 40mM IA for 48 hours

source_name: Human alveolar epithelial cell line A549 uninfected treated with 40mM IA for 48 hours

value: treated with 40mM IA for 48 hours


title: 201852C01


title: Striatum, 7649


title: Striatum, 7686


title: 201838C03


title: Uninfected IA 40mM rep3


title: Gliosis S9

source_name: Macular pucker

value: Macular pucker


title: 201838C04


title: ILM S1


title: Striatum, 7647


title: Gliosis S8


title: ILM S3


title: 201838C05


title: Uninfected IA 20mM rep2


title: Gliosis S7


title: 201838C01


title: PBMCs infected with IAV and IA treated rep4

source_name: Human PBMCs infected with IAV and treated with IA for 12 hours

label_protocol: Afymetrix protocol

extract_protocol:
Primary human monocytes were isolated from buffy coats from healthy blood donors by density gradient centrifugation.
mRNA was extracted and purified from PBMCs using MN NucleoSpin RNA kit.
Complementary RNA (cRNA) amplification and coversion to biotinylated double-stranded cDNA (ds-cDNA) was done by Clariom™ S Pico Assay, human Affymetrix protocol from10 ng total RNA (GeneChip® Pico UserGuide 703308 Rev. 4 Affymetrix).

treatment_protocol: PBMCs were cultured in 6 well plated with/without Influena A virus. Infected cells were either treated with DI, IA or 4OI for 12 hours.

value: Peripheral Blood Mononuclear Cells (primary cells)

value: infected with Influenza A virus and treated with itaconic acid (IA) for 12 hours


title: Uninfected IA 40mM rep1


title: PBMCs infected with IAV and 4OI treated rep4

source_name: Human PBMCs infected with IAV and treated with 4OI for 12 hours

value: infected with Influenza A virus and treated with 4 Octyl Itaconate (4OI) for 12 hours


title: Striatum, 7648

value: drug naïve straitum


title: 201838C02


title: Uninfected PBMCS rep4

source_name: Uninfected Untreated PBMCs cultured for 12 hours

value: uninfected and untreated, cultured for 12 hours


title: Gliosis S4


title: Gliosis S5


title: PBMCs infected with IAV and DI treated rep4

source_name: Human PBMCs infected with IAV and treated with DI for 12 hours

value: infected with Influenza A virus and treated with dimethyl itaconate (DI) for 12 hours


title: Gliosis S3


title: Striatum, 7646

value: M


title: Gliosis S6


title: 201836C06

value: Caucasian


title: Gliosis S10


title: 201836C02


title: Striatum, 7641


title: PBMCs infected with IAV and IA treated rep3


title: 201836C04


title: Striatum, 7644


title: 201836C05


title: Striatum, 7639


title: PBMCs infected with IAV rep4

description: IAV

source_name: Human PBMCs infected with IAV for 12 hours

value: infected with Influenza A virus for 12 hours


title: 201870C06

value: oral cavity


title: Striatum, 7645


title: 201836C03

value: Female


title: Gliosis S2


title: Striatum, 7643


title: Uninfected PBMCS rep3


title: PDR S6

source_name: RNV

value: RNV


title: 201870C05

value: Asian


title: PBMCs infected with IAV and DI treated rep3


title: PBMCs infected with IAV and 4OI treated rep3


title: Striatum, 7637


title: Uninfected PBMCS rep2


title: Striatum, 7640


title: Gliosis S1


title: 201836C01


title: Striatum, 7636


title: 201870C03


title: PBMCs infected with IAV rep3

description: IAV


title: PDR S7


title: PBMCs infected with IAV and IA treated rep2


title: Striatum, 7638


title: Striatum, 7634


title: PBMCs infected with IAV and 4OI treated rep2


title: PDR S2


title: PBMCs infected with IAV and DI treated rep2


title: 201870C01


title: PDR S4


title: PDR S5


title: PDR S1


title: 201870C04


title: Striatum, 7635


title: PDR S3


title: 201870C02


title: AS-1 OE Set A

city: Singapore

first: Azhar

middle: B

last: Ali

address: 14 Medical Drive MD6 #11-01

department: CSI Singapore

country: Singapore

institute: National University of Singapore

description: RNA-seq

data_processing:
For RNA-seq data quality control, FASTp was used to filter reads containing adapter or low quality.
Reads were mapped to reference genome using STAR and quantified using HTSeq.
Differential expression of genes between 2 samples was done using DESeq2.
GO enrichment analysis, KEGG pathway enrichment analysis, reactome pathway enrichment analysis, DO enrichment analysis were done using cluster profiler.
Genome_build: hg19
Supplementary_files_format_and_content: txt file recoding FPKM values

source_name: NCI-H1703 lung cancer cell line

growth_protocol: Vector and long noncoding RNA EGFR-AS1 overexpressed NCI-H1703 cells were cultured with RPMI supplemented with 10% fetal bovine serum. The cells were passage every 3 to 4 days.

extract_protocol:
RNA was extracted using GeneJet RNA purification kit.
RNA-seq library were prepared by sequencing provider, Novogene IT.  250-300bp insert stranded-specific cDNA library (Eukaryotic mRNA) was used for sequencing.

treatment_protocol: 100µg/ml Hygromycin selection antibody

value: Lung cancer cell line

tag: passage


title: pCDNA Set B

description: RNA-seq


title: PBMCs infected with IAV rep2

description: IAV


title: Striatum, 7633

city: Bar Harbor

last: Philip

address: 600 Main Street

tag: Sex


title: 201867C06


title: AS-1 OE Set B

description: RNA-seq


title: 201867C02


title: Striatum, 7632


title: Striatum, 7631


title: PBMCs infected with IAV and DI treated rep1

tag: treatment


title: ChIP-seq TBI Input, 1-day rep 1

city: Davis

first: Alex

middle: S.

last: Nord

state: CA

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

data_processing:
The differential gene expression between the TBI and sham control samples was done by individually aligning the FASTQ reads from the RNA-seq experiment to the rat genome (rn5) using STAR version 2.4.2a, after quality control evaluation using FASTQC version 0.11.8  and counting reads with featureCounts version 1.5.0 , with UCSC gene annotations. Thesamples were then analyzed using a custom R script running the limma-voom model
FASTQ files from ChIP and input control samples were quality-checked and trimmed for adapter sequences using FASTQC and Trim Galore! Version 0.5.0, respectively. The filtered reads were aligned to the rn5 genome (UCSC gene annotation) with bwa version 0.7.16a, with duplicate reads removed with Samtools version 1.8. We generated read coverage genome wide estimates and peak calls for sham and TBI samples using the pileup outputs from MACS2 version 2.1.2. Using custom R scripts, coverages (pileups) from H3K4me3 in TBI samples and respective sham controls were intersected, and filtered those annotated to gene promoters
Genome_build: rn5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Peak Files in text format

organism: Rattus norvegicus

source_name: Envigo, Livermore, CA, USA

extract_protocol:
Rats were placed in a chamber with continuous flow of 4% isoflurane. They were then removed from the chamber and rapidly decapitated. The brain was exposed and rolled out of the skull and placed on filter paper atop a glass dish sitting on ice. The cortex was hemisected rostral-to-caudal, then and rolled back (medial to lateral) exposing the underlying hippocampus. A curved, plastic spatula was used to roll the hippocampus out of the cortex and onto the filter paper. The same spatula was used to completely separate the hippocampus from the cortex and place it into a sterile microcentrifuge tube.
(1) Total RNA was isolated from the samples using Ambion RNAqueous (Thermo Scientific cat # AM1912) and assayed using an Agilent BioAnalyzer instrument. We used TruSeq Stranded mRNA kits (Illumina P/N 20020594) to prepare the stranded mRNA libraries, that were sequenced on the Illumina HiSeq platform using a single-end 50-bp strategy. (2) Frozen hippocampus tissue samples were individually crosslinked with a 1% formaldehyde buffer solution for 10 min, then washed and isolated. The resuspended crosslinked pellets were treated with protease inhibitor and sheared by sonication. Samples were then washed off of unbound DNA and free proteins, and incubated with Histone H3K4me3 antibody (mAb, Active Motif cat # 61979) and magnetic beads (Dynabeads) for 2 hr at 4 ºC. After reaction, beads were magnetically separated, washed and de-crosslinked. The resulting DNA was then purified, size selected, and libraries were. prepared using Ovation Ultralow System V2 preparation kit (NuGEN P/N 0344). Input control libraries were prepared from DNA before antibody pulldown. The libraries were quantified and pooled prior to submission for sequencing.

treatment_protocol: Adult male Sprague-Dawley rats (300-375g; Envigo, Livermore, CA, USA) were randomly assigned to sham control (n = 6) and LFP injury (n = 8) groups. Sham animals received identical surgical procedures as TBI, including duration of anesthesia, except the fluid percussion injury was not administered.  Anesthesia was induced using 4% isoflurane (in air).  Animals were then intubated, shaved, transferred to a stereotaxic frame, and mechanically ventilated to maintain a surgical plane of anesthesia. A midline scalp incision was made, and the skin was retracted to expose the dorsal cranial surface.  A circular 4.8 mm diameter parasagittal craniectomy was made over the right hemisphere midway between bregma and lambda and 3 mm lateral to midline using a trephine.  Two stainless steel screws (0-80”) were secured in the skull, anterior and posterior to the craniectomy.  A custom designed plastic tube injury hub was placed in the craniectomy and cemented to the skull. The fluid percussion device was calibrated to produce a moderate injury with persistent spatial learning deficits for at least two weeks post-injury. Immediately following injury, animals were observed for the return of the toe pinch withdrawal, and then were returned to 2.5% isoflurane. Finally, the injury hub was removed, and the wound was sutured closed, and the animal was placed in a heated cage and observed until they became sterile.

tag: breed

value: Sprague-Dawley

value: hippocampus

tag: protocol

value: TBI


title: 201867C04


title: 201867C05


title: PBMCs infected with IAV and IA treated rep1

value: Peripheral Blood Mononuclear Cells (primary cells)


title: PBMCs infected with IAV and 4OI treated rep1


title: PBMCs infected with IAV rep1

description: IAV


title: Striatum, 7630

tag: strain

tag: generation


title: Striatum, 7627


title: 201867C03

tag: age


title: Uninfected PBMCS rep1


title: 201867C01


title: Striatum, 7628


title: ChIP-seq TBI ChIP, 1-day rep 2

tag: chip antibody


title: pCDNA Set A

description: RNA-seq


title: Striatum, 7629


title: 180-mv4-Intervention

first: Neerja

last: Karnani

address: 30 Medical drive

institute: Singapore Institute for Clinical Sciences, A*STAR

data_processing:
FastQC was used to perform quality check (QC) on the sequencing reads. All samples passed the mean per base sequence quality scores ≥30. Average length of sequenced reads was 51nt, inclusive of the adaptors.
Trimmomatic 0.38 was used to remove the adapter sequences, and sequence reads < 10nt were excluded from the subsequent analysis.
For miRNA expression analysis, mapper.pl and quantifier.pl modules of the miRDeep2 tool and the latest miRBase release 22 were used.
For tRF analysis, the sperm sncRNA sequencing reads were mapped to the extracted tRNA sequence (including 100 bases upstream and 200 bases downstream) by using the BLASTn tool. The blast output file was parsed to get information on the mapped position of small RNA on the tRNA genes and segregate the sequences into specific subtypes: 5’ tiRs, 5’ (a,b,c), 3’ (a,b,c) and 1-tRFS
For piRNA expression analysis, Genboree platform was used to quantify and profile the human piRNAs from the piRNABank.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file comprising of raw counts for miRNA(Sheet 1) , tRF(Sheet 2) and piRNA (Sheet 3) for all 34 samples
Supplementary_files_format_and_content: Excel file comprising of filtered (CPM >=1 in atleast 8 samples) and TMM normalised counts for miRNA(Sheet 1) , tRF(Sheet 2) and piRNA (Sheet 3) for all 34 samples

source_name: sperm

extract_protocol:
Total RNA including sncRNA was extracted from frozen sperm pellets using the RNeasy Micro Kit (Qiagen, UK) with a modified protocol adapted from Goodrich, et al., 2012 which was optimised for recovery of sperm RNA. Briefly, sperm pellets were thawed, mixed with Qiazol (Qiagen, UK) and manually disrupted. Chloroform was added, samples incubated (room temperature for 5 minutes) and centrifuged (12000 x g) for 20 minutes. The upper aqueous layer was removed and mixed with ethanol. Samples were added to micro RNeasy spin columns (Qiagen, UK) and centrifuged for 15 seconds (8000 x g). Spin columns were washed using supplied buffers and ethanol. Samples were transferred to RNAse free collection tubes and total RNA eluted. RNA concentrations were quantified using Qubit total and microRNA assays (Thermo Fisher, UK), RNA was snap frozen on dry ice and stored at -80 degrees.
Sperm RNA samples were selected from both control and dietary intervention groups based on the quantity of RNA post extraction (n=17). 10µl of RNA was used to perform small RNA-seq (~15 million reads) using the smallRNA workflow (Oxford Genomics, OGC). NEBNext Small RNA Library Prep Set for Illumina (E7330) was used as per manufacturers’ instructions. Briefly, 3’ SR adapter ligation was carried out followed by RT primer hybridisation to the mRNA. Denatured 5’ SR adapter was then ligated, and first strand cDNA reverse transcription was performed. After second strand synthesis with indexed (TruSeq-based single indexed i7) and P5 primers, dsDNA was then cleaned-up using Ampure XP beads, and the libraries were size selected by Pippin (125-160bp). The concentration of the small RNA libraries was determined by Picogreen before multiplexing for sequencing. The final size distribution of the pooled library was determined using Agilent Tapestation, and quantified by Qubit (Thermofisher, UK), before sequencing on the HiSeq2500 (Illumina, UK) (2X runs) as 50bp single reads. Data were aligned to the reference genome and FASTQ files generated.

tag: sample id

tag: visit

tag: index no.

tag: category

value: control / intervention:Intervention


title: ChIP-seq Sham Input, 1-day rep 2

value: Sham

tag: time point


title: 190-mv1-Control

value: control / intervention:Control


title: Striatum, 7625

value: drug naïve straitum


title: 180-mv1-Intervention


title: 190-mv4-Control


title: ChIP-seq TBI ChIP, 1-day rep 1


title: 201837C06

tag: organ

tag: subject

tag: gender

tag: race


title: ChIP-seq TBI Input, 1-day rep 2

tag: tissue


title: Striatum, 7626

tag: Sex


title: 201837C03


title: 201837C04


title: 201837C01


title: 201837C02


title: ChIP-seq Sham Input, 1-day rep 1

tag: breed


title: ChIP-seq Sham ChIP, 1-day rep 2

tag: protocol


title: ChIP-seq Sham ChIP, 1-day rep 1


title: 153-mv4-Control


title: Striatum, 7622

tag: strain


title: 153-mv1-Control


title: 063-mv4-Control


title: RNA-seq TBI, 14-day rep 3

description:
TBI_GENE_MATRIX.txt
TBI.14.rep3


title: 201837C05


title: Striatum, 7621

tag: generation


title: 201856C06

tag: age

value: Male

value: Hispanic


title: RNA-seq TBI, 14-day rep 2

description:
TBI_GENE_MATRIX.txt
TBI.14.rep2


title: 063-mv1-Control


title: 062-mv1-Control


title: 201856C05


title: Striatum, 7624

value: M


title: Striatum, 7623


title: 201856C04


title: RNA-seq TBI, 14-day rep 1

description:
TBI_GENE_MATRIX.txt
TBI.14.rep1


title: 061-mv4-Control


title: 201856C03


title: Striatum, 7620


title: Striatum, 7618


title: Striatum, 7617


title: RNA-seq TBI, 14-day rep 4

description:
TBI_GENE_MATRIX.txt
TBI.14.rep4


title: Striatum, 7642


title: 201856C02


title: RNA-seq TBI, 1-day rep 4

description:
TBI_GENE_MATRIX.txt
TBI.1.rep4


title: 062-mv4-Control


title: 201845C06

value: Caucasian


title: Striatum, 7615

value: F


title: 201856C01

value: oral cavity


title: Striatum, 7616


title: RNA-seq TBI, 1-day rep 2

description:
TBI_GENE_MATRIX.txt
TBI.1.rep2


title: RNA-seq TBI, 1-day rep 3

description:
TBI_GENE_MATRIX.txt
TBI.1.rep3


title: Striatum, 7619


title: Striatum, 7614


title: 058-mv4-Intervention


title: 060-mv1-Intervention


title: Striatum, 7613


title: RNA-seq TBI, 1-day rep 1

description:
TBI_GENE_MATRIX.txt
TBI.1.rep1


title: RNA-seq Sham, 14-day rep 4

description:
TBI_GENE_MATRIX.txt
Sham.14.rep4


title: 201845C04

value: Female


title: 058-mv1-Intervention


title: RNA-seq Sham, 14-day rep 3

description:
TBI_GENE_MATRIX.txt
Sham.14.rep3


title: 201845C03


title: 056-mv4-Intervention


title: Striatum, 7612


title: 061-mv1-Control


title: RNA-seq Sham, 14-day rep 2

description:
TBI_GENE_MATRIX.txt
Sham.14.rep2


title: 060-mv4-Intervention


title: RNA-seq Sham, 14-day rep 1

description:
TBI_GENE_MATRIX.txt
Sham.14.rep1


title: 056-mv1-Intervention


title: 201845C02


title: 048-mv4-Intervention


title: 201845C05


title: 201845C01


title: 201801C06


title: 048-mv1-Intervention


title: 201801C05


title: Striatum, 7609


title: Striatum, 7608


title: Striatum, 7606


title: RNA-seq Sham, 1-day rep2

description:
TBI_GENE_MATRIX.txt
Sham.1.rep2


title: 043-mv4-Control


title: Striatum, 7610


title: Striatum, 7607


title: 043-mv1-Control


title: 201801C04


title: Striatum, 7605


title: 201801C03


title: Striatum, 7604


title: 038-mv4-Intervention


title: Test_3209_IVP

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
The RNAseq read pairs were mapped to the bovine reference genome (bosTau9) with STAR aligner (v. 2.7), generating the genome index with the gene Bos taurus release 102 annotation.
Read counts were estimated at gene level using HTSeq-count.
Genome_build: bosTau9
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing raw read counts for each sample.

organism: Bos taurus

source_name: Testicle

extract_protocol:
Tissues samples were shipped in dry ice to the BGI TECH SOLUTIONS Company (Hong Kong), which performed the RNA extraction, quality control, library preparation and sequencing. All samples met the requirements for library preparation (adequate concentration and quantity, purity as OD260/280 = 1.8~2.0 and RIN > 7).
RNA sequencing (RNAseq) was run in the RNA samples through non-stranded & polyA-selected mRNA library preparation and PE100 sequencing with 5Gb clean data per sample on DNBSEQ. After library preparation and sequencing, raw data with adapter sequences or low-quality sequences were filtered to remove contamination and obtain valid data. This step was completed by the SOAPnuke software developed by BGI Company.

treatment_protocol: Holstein embryos were produced in vitro or in vivo (by ovarian superstimulation followed by AI) and transferred to synchronized recipients. Pregnancies were monitored until delivery when the birthweights of the calves were recorded. Calves were maintained in similar condition during the postnatal period until euthanasia at around 100 days of age.

tag: embryo origin

value: IVP

tag: age (days)

tag: weight at birth (kg)

tag: weight at sample collection (kg)

value: Testicle

value: Holstein

tag: individual


title: Test_3208_IVP


title: Pit_5932_MOET

source_name: Pituitary

value: MOET

value: Pituitary


title: Striatum, 7603


title: 038-mv1-Intervention

tag: sample id

tag: visit

tag: index no.

tag: category


title: 201801C02

source_name: oral mucosa

tag: organ

tag: subject

tag: time point

tag: gender

tag: race


title: 201801C01


title: 028-mv4-Control


title: RNA-seq Sham, 1-day rep1

description:
TBI_GENE_MATRIX.txt
Sham.1.rep1

tag: breed

value: Sprague-Dawley

tag: tissue

value: hippocampus

tag: protocol


title: Pit_5833_IVP

tag: embryo origin

tag: Sex


title: Pit_5841_IVP

tag: age (days)

tag: weight at birth (kg)


title: Striatum, 7602

tag: strain

tag: generation


title: 028-mv1-Control

tag: sample id

tag: visit


title: Test_3213_MOET

tag: weight at sample collection (kg)

tag: individual


title: 201842C06

tag: organ

tag: subject

tag: age


title: 201842C05

tag: time point

tag: gender

tag: race


title: 022-mv4-Intervention

tag: index no.

tag: category

value: control / intervention:Intervention


title: Pit_3218_MOET

tag: embryo origin

tag: Sex

tag: tissue

tag: breed


title: 022-mv1-Intervention


title: 201842C04


title: 201842C03


title: Pit_3217_MOET

tag: age (days)

tag: weight at birth (kg)


title: Striatum, 7598

tag: strain

tag: generation


title: Striatum, 7597


title: Striatum, 7601


title: 201842C02


title: Pit_3213_MOET

tag: weight at sample collection (kg)

tag: individual


title: Striatum, 7596


title: Pit_3209_IVP


title: 009-mv4-Control

tag: sample id

tag: visit

value: control / intervention:Control


title: 201842C01

tag: organ

tag: subject

tag: time point

tag: age


title: 009-mv1-Control

tag: index no.

tag: category


title: Pit_3208_IVP

tag: embryo origin

tag: Sex


title: 201832C06

tag: gender

tag: race


title: Striatum, 7595

tag: tissue

value: drug naïve straitum


title: Striatum, 7600

tag: strain


title: 008-mv1-Intervention


title: Hypo_5841_IVP

source_name: Hypothalamus

tag: age (days)

tag: weight at birth (kg)

value: Male

value: Hypothalamus

tag: breed


title: Hypo_5932_MOET

tag: weight at sample collection (kg)

tag: individual


title: 005-mv4-Control

tag: sample id

tag: visit


title: 201832C05

tag: organ

tag: subject

tag: time point


title: Striatum, 7594

source_name: Striatum

tag: generation


title: Striatum, 7593


title: 201832C04

tag: age


title: 005-mv1-Control

tag: index no.

tag: category


title: 201832C03

tag: gender

tag: race


title: Hypo_5833_IVP

tag: embryo origin

tag: Sex

tag: tissue


title: Striatum, 7592

tag: strain


title: Hypo_3218_MOET

tag: age (days)

tag: weight at birth (kg)

tag: weight at sample collection (kg)

tag: breed


title: 201832C02

tag: organ


title: Striatum, 7591


title: Hypo_3217_MOET

tag: individual


title: 008-mv4-Intervention

tag: sample id

tag: visit


title: Striatum, 7590

tag: generation


title: 201832C01

tag: subject

tag: time point

tag: age


title: Hypo_3213_MOET


title: Hypo_3208_IVP


title: H3122 CR rep2

city: Zhengzhou

first: Yueqin

last: Wang

address: No.1 Jianshedong Rd

institute: Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University

data_processing:
RNA-Seq was performed on Illumina Novaseq platform with 150bp pair-end sequence strategy
the RNA-Seq reads were mapped to reference transcriptome by HISAT2 software
Supplementary_files_format_and_content: gene_count_H31CR_H3122_tpm_tpm.txt

source_name: H3122 cells

extract_protocol:
Total RNA was extracted from the cells seeded in 10cm2 plates by using TRIZOL (Ambion, 15596018). Enrichment of mRNA from total RNA was performed using Dynabeads® mRNA Purification Kit (Ambion, 61006) according to the manufacturer’s instructions with some modifications. The cDNA Library was constructed by KAPA Stranded mRNA-Seq Kit Illumina platform (KAPA, KK8420-24 Libraries).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: H3122 crizotinib-resistant cells (H3122CR) were established by gradually increasing the concentration of crizotinib from 0.1μM to 10μM. During cell culturing, the medium was changed normally and maintained with the effect of the drug. Higher drug concentration was added if no more cells were died.

tag: cell line

value: H3122 cells

tag: phenotype

value: crizotinib-resistant


title: Hypo_3209_IVP

tag: embryo origin

tag: Sex


title: Striatum, 7588

tag: strain

value: F

tag: tissue


title: H3122 CR rep3


title: H3122 con rep3

value: control


title: H3122 CR rep1


title: Striatum, 7587


title: Striatum, 7586


title: Adr_5841_IVP

source_name: Adrenal

tag: age (days)

tag: weight at birth (kg)

value: Adrenal


title: Adr_5932_MOET

tag: weight at sample collection (kg)

tag: breed


title: Striatum, 7585


title: Adr_5833_IVP

value: IVP

tag: individual


title: H3122 con rep2


title: Striatum, 7589


title: H3122 con rep1


title: 26М biological rep 6

first: Polina

last: Vishnyakova

address: Oparina 4

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: Gene expression data from patient

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7g

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software  version 4.0.2 using Affymetrix default analysis settings and RMA algorithm

source_name: CD16+ monocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Peripheral venous blood samples were collected prior to the caesarian section in EDTA-treated tubes. CD14+ and CD16+ monocytes were isolated using magnetic sorting and immediately lysed in QIAZOL reagent for the following RNA extraction

extract_protocol: Ordinary extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Monocytes did not undergo any treatment

tag: disease


title: Adr_3218_MOET


title: Striatum, 7583


title: 29М biological rep 6

description: Gene expression data from patient

value: late-onset preeclampsia


title: 24М biological rep 5

description: Gene expression data from patient


title: 23М biological rep 4

description: Gene expression data from patient


title: 22М biological rep 3

description: Gene expression data from patient


title: 20М biological rep 5

description: Gene expression data from patient


title: 21М biological rep 2

description: Gene expression data from patient


title: Adr_3213_MOET

value: Holstein


title: Adr_3217_MOET

value: MOET


title: Striatum, 7581


title: Striatum, 7582


title: 19М biological rep 1

description: Gene expression data from patient


title: Striatum, 7584


title: 18M biological rep 4

description: Gene expression data from patient


title: Adr_3209_IVP


title: Adr_3208_IVP


title: Striatum, 7579


title: Striatum, 7580


title: Striatum, 7578


title: Test_5932_MOET

value: Testicle


title: Test_5841_IVP


title: Test_5833_IVP


title: 15M biological rep 2

description: Gene expression data from patient


title: 14M biological rep 1

description: Gene expression data from patient


title: 12M biological rep 6

description: Gene expression data from patient

source_name: CD14+ monocytes


title: F1i

city: Taipei

first: Dhivya

last: Appan

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

department: Graduate Institute of Brain and Mind Sciences

country: Taiwan

institute: National Taiwan University

data_processing:
Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's basecalling program bcl2fastq v2.20.
adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Alignment Tool: HISAT2
Differential expression analysis was performed using cuffdiff (cufflinks v2.2.1) with genome bias detection/correction and Welgene Biotech's in-house pipeline.
Functional enrichment assay in differentially expressed genes of each experiment design was performed using clusterProfiler v3.6.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

source_name: Brain

extract_protocol:
RNA was extracted from left hemispheres of 5 mice per group pooled together using RNeasy Lipid Tissue mini kit from Qiagen (cat. No. 74804) following the manufacturor's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

value: C57BL/6 x CAST/EiJ

value: brain

tag: genotype

value: Wild Type


title: B6


title: Test_3218_MOET


title: F1r

value: CAST/EiJ x C57BL/6


title: CAST

value: CAST/EiJ


title: 17M biological rep 3

city: Moscow

description: Gene expression data from patient


title: P. aeruginosa 10 h, replicate 3, run B

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Genome_build: NC_008463.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

organism: Pseudomonas aeruginosa PA14

source_name: P. aeruginosa cultivated in LB medium

growth_protocol: 50 mL of LB medium was inoculated with an overnight culture to an OD600 of 0.05. The culture was grown for 10 h in a shaker at 37°C and 180 rpm. Two runs were performed on separate days.

extract_protocol:
For isolation and purification the RNeasy Plus kit (Qiagen) in combination with QIAshredder columns (Qiagen) was used according to the manufacturer’s manual. Modifications are listed below. Cell lysis was performed with 8 mg/mL lysozyme in Tris-EDTA-buffer (pH 8.0). RLT buffer with mecaptoethanol was added. Samples were frozen at -70°C for 60 min and then processed with QIAshredder columns. The remaining steps were performed according to the manufacturer's manual. After RNA elution, samples were treated with DNase (DNA-free Kit DNase Treatment & Removal, ambion).
RNA was fragmented (150–350 bp) by FastAP buffer (Thermo). End repair was performed with DNase (Thermo) and FastAP. Barcodes were ligated to each sample by T4 RNA ligase 1 (NEB). Samples were purified with the RNA Clean & Concentrator-25 Kit (Zymo). The RiboZero Bacteria Kit (Illumina) was used to remove ribosomal RNA. cDNA libraries were generated using SMARTscribe reverse transcriptase (Clonetech). Enrichment was done by AccuPrime HiFi Taq (Thermo) and all purification steps using RNAClean XP beads (Agencourt). Libraries were sequenced in paired-end mode on an Illumina Novaseq 6000 device (2 x 50 bp).

tag: time (h)

tag: replicate

tag: run

value: B


title: P. aeruginosa 10 h, replicate 2, run B


title: 11M biological rep 5

description: Gene expression data from patient


title: 13M biological rep 7

description: Gene expression data from patient


title: 9M biological rep 5

description: Gene expression data from patient


title: 8M biological rep 4

description: Gene expression data from patient


title: 10M biological rep 6

description: Gene expression data from patient


title: ETC_T24_4

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

data_processing:
tophat2 --b2-very-sensitive
Conversion to bigWig R (3.5.1)
Genome_build: dm6
Supplementary_files_format_and_content: Genome coverage in bigWig format

organism: Drosophila melanogaster

source_name: Drosophila ph505 tumor cell line

growth_protocol: Drosophila ph505 cells were maintained at 25 °C in Shields and Sang M3 Insect medium (US Biological), supplemented with 2% Fetal Bovine Serum (FBS) (PAN Biotech), 2.5% fly extract, 5 µg/ml human insulin (Sigma), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, Life Technologies) and subcultured every 3-7 days at a ratio of 1:(4-8).

extract_protocol:
RNA was extracted using an Arcturus PicoPure RNA Isolation kit (Applied Biosystems).
The library was prepared with SMARTSeq2 NexteraXT.

treatment_protocol: Drosophila ph505 cells a were treated with 5 μM 20-Hydroxyecdysone (Sigma) for 4, 8 or 16 hours.

tag: treatment

value: Ecdysone 24 hours


title: ETC_T24_2

tag: cell line


title: P. aeruginosa 10 h, replicate 3, run A

value: A


title: ETC_T24_3


title: ETC_T24_1


title: 5М biological rep 1

description: Gene expression data from patient


title: P. aeruginosa 9 h, replicate 3, run B


title: 6М biological rep 2

description: Gene expression data from patient


title: 4М biological rep 4

description: Gene expression data from patient


title: ETC_T16_4

value: Ecdysone 16 hours


title: 3М biological rep 3

description: Gene expression data from patient


title: ETC_T16_3


title: ETC_T16_1


title: P. aeruginosa 8 h, replicate 3, run B


title: ETC_T16_2


title: P. aeruginosa 10 h, replicate 1, run B


title: 7M biological rep 3

description: Gene expression data from patient


title: ETC_T8_4

value: Ecdysone 8 hours


title: P. aeruginosa 9 h, replicate 1, run B


title: P. aeruginosa 8 h, replicate 1, run B


title: ETC_T8_2


title: ETC_Ctrl_4

value: Control


title: ETC_Ctrl_3


title: 1М biological rep 1

description: Gene expression data from patient

value: control


title: P. aeruginosa 7 h, replicate 2, run B


title: P. aeruginosa 7 h, replicate 3, run A


title: ETC_Ctrl_2


title: ETC_T8_1


title: ETC_Ctrl_1


title: Test_3217_MOET

value: Male


title: 2М biological rep 2

description: Gene expression data from patient


title: P. aeruginosa 8 h, replicate 3, run A


title: P. aeruginosa 9 h, replicate 3, run A


title: P. aeruginosa 6 h, replicate 3, run B


title: P. aeruginosa 8 h, replicate 2, run B


title: IVT_IP_3

description: in vitro transcribed biotinylated let-A incubated with cell extract and isolated with Streptavidin beads

data_processing:
Alignment for paired end reads was performed using TopHat version 2.0.12 with --b2-very-sensitive --segment-length 18
RPKM were calculated by determining overlaps of aligned reads with Ensembl gene annotation ffor dm6 using R 3.5.1 and GenomicAlignment package.
Genome_build: dm6
Supplementary_files_format_and_content: RPKM of dm6 UCSC Ensembl Gene Annotation

source_name: in vitro transcription of RNA from DNA template

growth_protocol: RNA was transcribed from linearized pGEM plasmids using MEGAscript T7 Transcription (Ambion) and purified using MEGAclear (Ambion). Active cellular extract was prepared as described (Crevel & Cotterill, 1991) with additional 2 mM ATP.

extract_protocol:
The IVT RNA extract mixture was extracted two times with 20 uL of MyONE Streptavidin T1 (Invitrogen) for 15 minutes at 25 °C. Beads were washed twice and eluted using 2 mM avidin (IBA) at 25 °C for 15 minutes. Thereafter the RNA was isolated using TRIzol.
Ribo-Zero Gold rRNA Removal Kit followed by Illumina TruSeq Stranded Library Prep

treatment_protocol: 35 μl (140 ug) of extract active cellular extracts were mixed with 375 ng of IVT RNA (diluted in 15 μl extraction buffer) and incubated at 25 °C for 15 minutes.

value: affinity purified with Streptavidin beads


title: P. aeruginosa 7 h, replicate 3, run B


title: KO1_XRN610

city: Indianapolis

first: Travis

last: Johnson

state: IN

department: Biostatistics

institute: Indiana University School of Medicine

data_processing:
alignmentSTAR 2.7.3a
quantificationRSEM 1.3.0 (gene level)
Genome_build: GRCm38
genome annotationgencode vM25

source_name: Stimulated with aCD3-CD28 for 4 h

growth_protocol: For α-CD3-CD28 stimulation, sorted WT and Gpx4-deficient Treg cells were cultured in Click’s medium (plus β-mercaptoethanol) supplemented with 10% (vol/vol) FBS and 1% (vol/vol) penicillin–streptomycin.

extract_protocol:
RNA of WT and Gpx4-deficient Treg cells was extracted using the RNeasy Micro Kit (Qiagen)
RNA (600 ng/ sample) was used to prepare single indexed strand specific cDNA library using TruSeq stranded mRNA library prep kit (Illumina). The library prep was assessed for quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer.

treatment_protocol: WT and Gpx4-deficient Treg cells were stimulated with plate-bound α-CD3-CD28 (5 μg/ml) for 4 h

tag: age

value: 11 weeks

tag: cell type

value: Treg


title: KO2_XRN611


title: WT3_XRN592

value: WT


title: IVT_IP_2


title: KO3_XRN612


title: P. aeruginosa 6 h, replicate 2, run B


title: IVT_IP_1


title: P. aeruginosa 7 h, replicate 1, run B


title: WT2_XRN591


title: P. aeruginosa 6 h, replicate 3, run A


title: P. aeruginosa 9 h, replicate 2, run B


title: IVT_Ctrl_2

description: in vitro transcribed biotinylated let-A mixed with cell extracts


title: WT1_XRN590


title: TNFalpha 24hr IgG rep2

city: Boulder

first: Edward

middle: Boyi

last: Chuong

state: CO

address: JSC Biotech Building, 3415 Colorado Ave

department: BioFrontiers Institute and Molecular, Cellular & Developmental Biology Department

institute: University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 using options ‘ktrim=r k=31 mink=11 hdist=1 tpe tbo qtrim=r trimq=10’. Trimmed reads were aligned to the hg38 assembly using BWA-MEM v0.7.15, and only uniquely mapping reads with a minimum MAPQ of 10 were retained. Fragments aligning to the mitochondrial genome were removed. For one sample (untreated H3K27ac rep2), the original and resequenced files were merged into one bam file. Peak calling was performed using complete and size subsetted alignment files with MACS2 v2.1.1 in a two-step process where separate sets of peaks were called with (1) single-end options ‘--format BAM --shift=-75 --extsize=150 --pvalue 0.01’ and (2) paired-end option ‘--format BAMPE --pvalue 0.01’, and then peaks were merged for each sample. Bigwig files were prepared from the MACS2 normalized bedgraph files using bedGraphToBigWig v4.
Genome_build: hg38
Supplementary_files_format_and_content: Normalized signal tracks corresponding to read coverage per 1 million fragments in UCSC bigwig format
Supplementary_files_format_and_content: Tab-delimited text files including unfiltered narrowPeaks called by MACS2 in UCSC BED format

source_name: Colorectal cancer cell line

growth_protocol: HCT116 cells were routinely grown at 37C in 5% CO2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in McCoy’s 5A (Gibco #16600082) supplemented 1X penicillin-streptomycin (Gibco #15140122), and 10% fetal bovine serum (Gibco #10437010).

extract_protocol:
CUT&RUN pulldowns were generated using a protocol from Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). All buffers were prepared according to the “High Ca2+/Low Salt” section of the protocol using 0.05% digitonin. 500,000 viable cells were used for each pulldown. The following antibodies were used: rabbit anti-mouse IgG (1:100, Abcam #ab46540) and rabbit anti-H3K27ac (1:100, Abcam #ab4759). pA-MNase (gift from Steve Henikoff) was added to each sample following primary antibody incubation at a final concentration of 700 ng/mL. Chromatin digestion, release, and extraction was carried out according to Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). Pulldown success was determined by Qubit dsDNA High Sensitivity and TapeStation 4200 HSD5000 before proceeding with library preparation.
Libraries were generated using a modified protocol for use with the KAPA HyperPrep Kit. Briefly, the full volume of each pulldown (~30 uL) was diluted to 50 uL in nuclease-free water, and libraries were generated following the manufacturer’s protocol with the following modifications. Freshly diluted 0.200 uM single-index adapters were added to each library at a low concentration (9 nM) to minimize adapter dimer formation. Adapter-ligated libraries underwent a double-sided 0.8X/1.0X cleanup with KAPA Pure Beads. Purified, adapter-ligated libraries were amplified using the following PCR cycling conditions: 45 s at 98°C, 14x(15 s at 98°C, 10 s at 60°C), 60 s at 72°C. Amplified libraries underwent 2 double-sided 1.0X cleanups with KAPA Pure Beads. The final libraries were quantified using Qubit dsDNA High Sensitivity and TapeStation 4200 HSD5000. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core) as 150bp paired-end reads.

treatment_protocol: Cells were either untreated or treated with 1 uM Cobimteinib or 100 ng/mL TNF-alpha for 24h.

tag: antibody

value: Rabbit anti-mouse IgG (Abcam #ab46540)

value: TNFalpha

tag: timepoint


title: TNFalpha 24hr H3K27ac rep2

value: Rabbit polyclonal H3K27ac (Abcam #ab4729)


title: TNFalpha 24hr H3K27ac rep1


title: IVT_Ctrl_1


title: TNFalpha 24hr IgG rep1


title: KO3_XRN608

source_name: Unstimulated

tag: strain