title: HZ_26-1Y_S20

description: Herpes Zoster resolved (1Y)

value: M

value: Herpes Zoster resolved (1Y)


title: A_TFI_21, biol rep1

status: Public on Sep 08 2023

type: SRA

city: Barcelona

first: Lucas

middle: Esteban

last: Wange

address: Dr. Aiguader 88

department: Institut de Biologia Evolutiva

country: Spain

institute: Universitat Pompeu Fabra

description: TCTTATCCTCGA

library_source: transcriptomic

data_processing:
demultiplexing, deML
adapter trimming, cutadapt, version 3.4
mapping and counting, zUMIs, version 2.9.7c
normalisation and differential expression analysis, DESeq2
Assembly: hg38
Supplementary files format and content: raw count matrix as generated by zUMIs

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

growth_protocol: healthy donor derived human adapter CAR-T cells

extract_protocol:
prime-seq bead extraction
prime-seq RNA-sequencing

treatment_protocol: time course

tag: tissue

value: Bone Marrow

tag: cell line

value: A

tag: cell type

tag: genotype

tag: treatment

value: TFI


title: NYU1609-N (RNA-seq)

city: New York

first: Aristotelis

last: Tsirigos

address: 435 E 30th St

country: USA

institute: NYU School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the human genome (build hg38/GRCh38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Assembly: hg38
Supplementary files format and content: CSV files contain raw and normalized counts for all genes and samples

source_name: Lung adjacent normal

extract_protocol:
DNase treatment to remove genomic DNA, cDNA synthesis from the input RNA, single primer isothermal amplification (SPIA) of the resultant cDNAs, enzymatic fragmentation and construction of unique barcoded libraries, PCR library amplification and a final step to remove rRNA transcripts.
1 ng of total RNA was used to prepare libraries using Trio RNA-Seq library prep kit (Tecan Genomics) following the manufacturer's instructions. The Agencourt AMPure XP bead (Beckman Coulter) purified libraries were quantified using qPCR and the size distribution was checked using Agilent TapeStation 2200.

tag: patient

value: Lung adjacent normal

tag: progression type

value: Locoregional

tag: progression

value: Progression

tag: recurrence

value: Recurrence


title: HZ_21_S27

city: Antwerp

first: Pieter

last: Meysman

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: University of Antwerp

description: Herpes Zoster

data_processing:
Sequencing reads from fastq files were checked for quality using FastQC, trimmed for polyA-tails and further read processing using Trimmomatic v0.36. The reads were then aligned against the human reference genome (GRCh38 from Ensembl) using HISAT2 v2.0.4, and the read count table was assembled using HTSeq. Subsequent expression analysis was performed using the DESeq2 v1.32.0 R package.
Assembly: GRCh38 from Ensembl
Supplementary files format and content: Processed read counts in tabular format

molecule: polyA RNA

source_name: Whole blood

extract_protocol:
RNA extraction from whole blood collected in PAXGene tubes was performed via a column-based RNA extraction using the PaxGene blood RNA extraction kit (Cat. No./ID: 762174, Qiagen) following the manufacturer’s instructions. Subsequently, RNA was concentrated using the RNA clean & concentrator-5 kit (R1013, Zymo research). RNA concentration was measured using the Qubit™ RNA BR Assay Kit (Cat n°: Q10211, Thermo Fisher) on a Qubit 4 fluorometer (Invitrogen).
All RNA samples were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD  for Illumina (Lexogen   GmbH) following the standard protocol for long fragments. Resulting cDNA libraries were equimolarly pooled, up to 40 samples for one NextSeq 500/550 sequencing run (high output v2.5 kit, 150 cycles, single read, Illumina)

value: Whole blood

tag: Sex

value: F

tag: disease state

value: Herpes Zoster


title: S_CONT_21, biol rep2

description: GGATTCACCGAA

value: S

value: healthy donor derived human adapter CAR-T cells

value: CONT


title: iEC 12 weeks (3)

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

description: TdTom+ cells sorted from mouse liver 12 weeks post-transplantation

data_processing:
Align to Ensembl reference genome GRCh38.91 using STAR
Count transcriptomic reads using featureCounts
Sum reads across technical replicates (separate lanes)
Filter non or lowly epxressed genes using filterByExpr function from edgeR
calculate normalisation factors using calcNormFactors (edgeR)
Calculate CPM values using the cpm function (edgeR)
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab separated text of CPM values per sample

source_name: hiPSC-endothelial cells

extract_protocol:
Genomic DNA removal and RNA extraction using Qiagen Rneasy Plus Mini Kit (Cat. 74134)
SMARTer® Stranded Total RNA-Seq Pico Input Mammalian kit v2 (Takara Bio, Shiga, Japan). Libraries were sequenced on a HiSeq 2500 System

treatment_protocol: Cells either in pellet form or monolayer culture lysed and processed for RNAseq

tag: fluorescent tag

value: TdTom+

tag: ex vivo or in vitro

value: Ex vivo FACS isolated


title: NYU1603-T (RNA-seq)

source_name: Tumor

value: Tumor

value: No Progression (>5y)


title: iEC 12 weeks (2)


title: iEC 4 weeks, 1

description: single cell RNA seq

data_processing:
Alignment and transcript counting using cellranger (v3.1)
Replicates are counted at the same time for each sample
Genome_build: hg38
Supplementary_files_format_and_content: h5 filtered counts matrixes containing transcript counts and cell barcodes

extract_protocol:
10X Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 used for GEM generation and barcoding
10X Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 used for library construcion. Libraries sequenced using a HiSeq 2500 System.

treatment_protocol: FACS isolation of cells, resuspended in HBSS with bovine serum albumin. Cell viability confirmed prior to proceeding with GEM generation and barcoding.

tag: tissue origin

value: Liver


title: A_CONT_14, biol rep1

description: AACAGCGCCATG

value: Bone Marrow

value: A


title: NYU1603-N (RNA-seq)

value: Lung adjacent normal


title: HZ_21-1Y_S28

description: Herpes Zoster resolved (1Y)

value: Herpes Zoster resolved (1Y)


title: HZ_2-1Y_S4

description: Herpes Zoster resolved (1Y)


title: NYU1597-T (RNA-seq)


title: iEC 12 weeks (1)


title: AM_CONT_14, biol rep3

description: AGTAGTTAGCCG

value: AM


title: NYU1597-N (RNA-seq)


title: iEC 4 weeks (4)

description: TdTom+ cells sorted from mouse liver 4 weeks post-transplantation


title: HZ_22-1Y_S30

description: Herpes Zoster resolved (1Y)

value: M


title: HZ_19_S25

description: Herpes Zoster

value: Whole blood


title: A_TFI_14, biol rep1

description: AAGTGGTTGCGG

value: TFI


title: NYU1595-T (RNA-seq)

value: Second Primary

value: Progression


title: iEC 4 weeks (3)


title: S_TFI_14, biol rep2

description: TACCTAGGTGTA

value: S

value: healthy donor derived human adapter CAR-T cells


title: NYU1595-N (RNA-seq)


title: S_CONT_14, biol rep2

description: CCAAGATCCGTA

value: CONT


title: iEC 4 weeks (2)

value: TdTom+

value: Ex vivo FACS isolated


title: HZ_15_S13

description: Herpes Zoster

value: Herpes Zoster


title: iEC 4 weeks (1)


title: AM_TFI_14, biol rep3

description: CAGCACTTCACA


title: NYU1562-T (RNA-seq)

value: Tumor


title: HZ_15-1Y_S14

description: Herpes Zoster resolved (1Y)


title: NYU1555-T (RNA-seq)


title: iEC 2 weeks (2)

description: TdTom+ cells sorted from mouse liver 2 weeks post-transplantation


title: HZ_19-1Y_S26

description: Herpes Zoster resolved (1Y)

value: F


title: AM_CONT_0, biol rep3

description: GTTGTGCTCCAA

value: Bone Marrow


title: S_CONT_0, biol rep2

description: TCGGCTGTCCAA


title: HZ_1_S1

description: Herpes Zoster


title: NYU1555-N (RNA-seq)

value: Lung adjacent normal


title: HZ_14_S11

description: Herpes Zoster


title: iEC 2 weeks (1)


title: A_CONT_0, biol rep1

description: CTGGACTAACAA

value: A


title: NYU1551-T (RNA-seq)

value: No Progression (>5y)


title: HZ_14-1Y_S12

description: Herpes Zoster resolved (1Y)

value: Herpes Zoster resolved (1Y)


title: NYU1562-N (RNA-seq)


title: NYU1551-N (RNA-seq)


title: iEC 2 weeks (3)


title: iEC 1 week (2)

description: TdTom+ cells sorted from mouse liver 1 week post-transplantation


title: HZ_12_S16

description: Herpes Zoster

value: Whole blood


title: NYU1512-T (RNA-seq)

value: Short Follow Up (<5y)


title: HZ_13-1Y_S10

description: Herpes Zoster resolved (1Y)


title: w1118  BeadexMS1096-Gal4 , ScRNA-seq

city: Stockholm

first: Mubasher

last: Mohammed

state: Stockholm lan

address: Svante Arrhenius Väg 20c, MBW, Stockholms University

department: Department of Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

library_source: transcriptomic single cell

data_processing:
A reference genome Drosophila melanogaster (Dm6 v r6.37) was indexed and raw fastq files were used in mapping to the genome using STAR v 2.7.2
gene expression was measured using featureCounts v 2.0.0
using default settings. expression matrix was filtered to obtain high-quality cells using the following criteria: cells with >5% mitochondrial transcripts (stressed/dead/dying cells), <200 genes (low-quality cells), those expressing more than 4000 features (genes) (potential doublets or triplets) were removed in each replicate and the remaining cells were subjected to subsequent computational analysis
Assembly: Dm6 v r6.37
Supplementary files format and content: tab-seprated values matrix files and metadata csv files

organism: Drosophila melanogaster

source_name: salivary gland

growth_protocol: w1118, BeadexMS1096-Gal4 (Referred here as Bx: 8860/Bl), BeadexMS1096-Gal4; EaterDsRed, w1118, w1118;p35 (5072/Bl), w1118;;UAS-RasV12(4847/Bl), w1118;p35;UAS-RasV12 flies were used in the experiments. Flies were cultured in a 25°C, 12-h dark/light cycle room. Female virgins were collected for 5 days and crossed with respective males on day 7. Progeny larvae were kept as described in (20). Twenty to thirty salivary gland pairs were fixed in 4% PFA for 20 min. Samples for extracellular staining were washed 3 x 10 min with 1x phosphate-buffered saline (PBS). Antibodies against P1 (Plasmatocytes, 1:50), L1 (Lamellocytes, 1:50), C4 (Crystal cells, 1:50) were incubated for 1 h at room temperature in PBS and subsequently, washed 3 x 10 min in PBS. The samples were incubated with secondary antibody Anti-Mouse-546 (1:500, ThermoFisher #A11030), DAPI (1:500, Sigma-Aldrich D9542) for 1 hour at room temperature and washed 3 x 10 min with PBS before mounting in Fluoromount-G (ThermoFisher, 00-4958-02).

extract_protocol:
Ten pairs of salivary glands per genotype were dissected into individual droplets of 200 µl PBS. A fluorescent microscope Leica DMi8 (Leica, Germany) was used to locate the attached hemocytes at the surface of the salivary gland. The hemocytes were collected using micromanipulator TransferMan NK2 (Eppendorf, Germany) with ø 7 µm collection capillary and separated by piezo-vibrator PiezoXpert (Eppendorf, Germany). Single-cell state hemocytes were individually transferred to 2.3 µl of lysis buffer (38) and each sample library was prepared
cDNA libraries of single attached hemocytes were generated using a modified version of the Smart-seq2 protocol,  cDNA synthesis was performed using universal primers, and PCR amplification was carried out over 24 cycles. cDNA products were subsequently purified using CA beads Combinatorial indexing via tagmentation was carried out in 96-well plates using 200 pg (measured in a Qubit fluorometer) of amplified cDNA, for a final volume of 10 mL/well. cDNA fragmentation using Tn5 transposase was carried out for 20 min on ice using the Illumina Nextra XT DNA sample preparation kit. Ligation and amplification of adaptors were carried out over 15 cycles in a final volume of 25 mL/well, Tagmented and barcoded amplicons were then purified using CA beads for size selection. Quality control and fragment size distribution of the cDNA libraries were performed on a Bioanalyzer with the Agilent high-sensitivity DNA chip (catalog no. 5067-4626). Concentrations of each sample of cDNA libraries were measured on a PicoGreen 96-well plate NucleoScan fluorometer using a high-sensitivity double-stranded DNA (dsDNA). To perform library dilutions, the average fragment sizes of all cDNA libraries were measured for a final concentration of 2 nM in each sample. Finally, cDNA libraries were pooled and sequenced using Illumina NextSeq with 75-bp paired-end reads

value: salivary gland

value: w1118, BeadexMS1096-Gal4 (Referred here as Bx:8860/Bl)

value: 4% PFA for 20 min and washed 3 x 10 min with 1x phosphate-buffered saline (PBS)


title: iEC 1 week (1)


title: RasV12 UAS-RasV12(4847/Bl) , ScRNA-seq


title: HZ_12-1Y_S17

description: Herpes Zoster resolved (1Y)


title: SPG, TDP43 overexpression, replicate 3

first: Oliver

middle: H

last: Tam

state: New York

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

data_processing:
Libraries were sequenced on NextSeq to 76 bp read length and converted to FASTQ.
3' Illumina adapters were removed with cutadapt. Reads were aligned to the dm6 genome using STAR, allowing for 4% mismatch and up to 100 alignments per read to ensure capture of young transposon sequences.
Abundance of gene (UCSC curated Refseq) and transposon (UCSC RepeatMasker) sequences was calculated with TEtranscripts.
Assembly: dm6
Supplementary files format and content: A tab-delimited table of raw counts for each gene and transposable element quantified

source_name: Brain

growth_protocol: Flies were reared at 21°C and maintained on standard propionic acid food for all experiments in this study.  All were backcrossed to Canton-S derivative w1118 (isoCJ1), our laboratory wild-type strain, for at least five generations. Female flies were utilized throughout the study.

extract_protocol:
Two day old female flies were anesthetized with CO2 and flash frozen in liquid nitrogen before being stored at -80°C until an appropriate number of flies were collected for each group (>1,000,000 cells for all groups except SPG, for which cell number was >300,000). Fly heads were separated, homogenized, and incubated with an antibody against GFP before being bound to protein A beads, cleaved, and rebound to protein G beads. Twice purified TAPIN-tagged nuclei were then burst and nuclear RNA was collected and stored at -80°C
TAPIN-generated nuclear RNA was treated with DNase and purified by the Arcturus PicoPure system. Purified RNA was amplified to cDNA via Nugen Ovation v2 system and was then fragmented with a Covaris s-series to 200bp. Fragmented cDNA was repaired and underwent second strand synthesis before being ligated to barcoded linkers.

treatment_protocol: Using celltype specific Gal4 lines and the temperature sensitive Gal80 (Gal-80ts) approach, we induced post development over-expression of TDP-43 in each of the 5 individual glial cell types.

value: Brain

value: Subperineurial glia

value: TDP43 overexpression


title: NYU1512-N (RNA-seq)


title: NYU1502-T (RNA-seq)

value: Systemic

value: Progression

value: Recurrence


title: iEC in vitro (3)

description: hiPSC differentiated into endothelial cells, purified based on hCD31 expression

value: TdTom+

value: Plated & expanded - in vitro


title: HZ_11_S14

description: Herpes Zoster

value: F

value: Herpes Zoster


title: SPG, TDP43 overexpression, replicate 2


title: iEC in vitro (2)


title: HZ_11-1Y_S15

description: Herpes Zoster resolved (1Y)


title: SPG, TDP43 overexpression, replicate 1


title: NYU1502-N (RNA-seq)

value: Lung adjacent normal


title: iEC in vitro (1)


title: HZ_13_S9

description: Herpes Zoster


title: iEC 1 week (3)

value: Ex vivo FACS isolated


title: HZ_10_S36

description: Herpes Zoster

value: Whole blood

value: M


title: SPG, control, replicate 3

value: Control


title: NYU1487-T (RNA-seq)

value: Tumor

value: No Progression (>5y)


title: hLSEC plated (3)

description: Non-parenchymal cells from human liver plated in endothelial selective medium and expanded in culture

source_name: human liver sinusoidal endothelial cells


title: NYU1487-N (RNA-seq)


title: SPG, control, replicate 2

value: Brain


title: HZ_10-1Y_S37

description: Herpes Zoster resolved (1Y)

value: Herpes Zoster resolved (1Y)


title: SPG, control, replicate 1

value: Subperineurial glia


title: hLSEC plated (2)


title: HZ_1-1Y_S2

description: Herpes Zoster resolved (1Y)


title: NYU1448-T (RNA-seq)

value: Short Follow Up (<5y)


title: PNG, TDP43 overexpression, replicate 3

value: Perineurial glia

value: TDP43 overexpression


title: ERC_CO271_S8

description: Healthy control

value: Healthy control


title: NYU1448-N (RNA-seq)


title: NYU1445-T (RNA-seq)


title: ERC_CO109_S40

description: Healthy control

value: Unknown


title: hLSEC plated (1)

value: Plated & expanded - in vitro


title: PNG, TDP43 overexpression, replicate 2


title: hLSEC FACS (4)

description: hCD31+ cells sorted from human liver


title: ERC_CO053_S24

description: Healthy control

value: F


title: hLSEC FACS (3)

description: hCD31+ cells sorted from human liver


title: PNG, TDP43 overexpression, replicate 1


title: PNG, control, replicate 3


title: NYU1445-N (RNA-seq)

value: Lung adjacent normal


title: NYU1443-T (RNA-seq)

value: Systemic

value: Progression

value: Recurrence


title: CO_9-1Y_S18

description: Healthy control

value: Whole blood

value: M


title: CO_8-1Y_S7

description: Healthy control


title: hLSEC FACS (1)

description: hCD31+ cells sorted from human liver

value: Ex vivo FACS isolated


title: OLG cells, Sp7KO, Rep2

city: Chicago

first: Benayahu

last: Elbaz

state: Illinois

address: 303 E. Chicago Ave. Ward 7-641. Chicago, IL 60611

department: Neurology

institute: Northwestern University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim-galore/0.6.7 and cutadapt/3.4
Trimmed sequence reads were mapped to mm10 using STAR version 2.7.10a with default parameters. PCR duplicates and low quality mapped reads were removed using Picard and SAMtools respictively.
number of reads (counts) associated with each gene were performed using featureCounts
differentially expressed features from the count tables were determined using the Deseq2 R package.
Assembly: mm10
Supplementary files format and content: BAM file for for each Sample

organism: Mus musculus

source_name: Primary cultured oligodendrocyte

growth_protocol: Primary oligodendrocyte progenitor cells were isolated and maintained in Sato serum-free Dulbecco's modified Eagle medium with the addition of B27 supplement. platelet-derived growth factor-AA (PDGF-AA; 10 ng/ml), neurotrophin-3 (1 ng/ml), forskolin (0.01 mM), and ciliary neurotrophic factor (CNTF; 10 ng/ml) were added.

extract_protocol:
RNA was harvested using Aurum Total RNA Kit (Bio-Rad #732-6820).
RNA libraries were prepared using Illumina TruSeq Total RNA-Seq Library Prep and sequenced by Illumina HiSeq 4000 sequencers using HiSeq Kit.

treatment_protocol: To stimulate differentiation, the platelet-derived growth factor-AA (PDGF-AA) was removed and triiodothyronine (40 ng/ml) was added. Media was changed every other day and differentiated cells were collected after 5 days in differentiation media.

value: Primary cultured oligodendrocyte

value: Sp7fl/fl;Olig2-Cre mice

tag: time

value: Day 5 in differentiation media


title: NYU1443-N (RNA-seq)


title: OLG cells, Sp7KO, Rep1


title: CO_6_S10

description: Healthy control


title: EG, TDP43 overexpression, replicate 3

value: Brain

value: Ensheathing glia


title: CO_6-1Y_S11

description: Healthy control


title: NYU1435-N (RNA-seq)

value: No Progression (>5y)


title: EG, TDP43 overexpression, replicate 2

value: TDP43 overexpression


title: OLG cells, Control, Rep1


title: CO_5-1Y_S16

description: Healthy control

value: Healthy control


title: EG, TDP43 overexpression, replicate 1


title: EG, control, replicate 3

value: Control


title: NYU1433-N (RNA-seq)


title: NYU1433-T (RNA-seq)

value: Tumor


title: CO_4_S8

description: Healthy control

value: F


title: PNG, control, replicate 1

value: Perineurial glia


title: NYU1428-T (RNA-seq)


title: ArimaHiC_D0_3T3L1_siRNA_scrmb_2

city: Farmington

first: Sabriya

last: Syed

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

library_source: genomic

data_processing:
HiSeq4000, paired end read, 50 bases
Fastq files were mapped to the mm10 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019) (https://github.com/mirnylab/cooler.git)
Genome_build: mm10
Supplementary_files_format_and_content: 10kb matrices are provided as .cool files

molecule: genomic DNA

growth_protocol: Mouse 3T3-L1 cells (obtained from ATCC) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, #11965118, Gibco) supplemented with 10% calf serum (#26140079, Gibco) and 1% pen/strep (#15140163, Gibco).

extract_protocol:
Hi-C libraries generated using Hi-C 2.0 protocol (Belaghzal et at.2017) and using the Arima-HiC kit, according to the manufacturers protocols. Flash frozen cross-linked cells were lysed and then digested with DpnII-containing enzyme mix at 37°C. The DNA overhanging ends were then marked with biotin followed by proximal end ligation. DNA was reversed crosslinked and ligation products were purified and then fragmented by sonication to an average size of 200-300 bp and size-selected to fragments of < 350 bp. We then performed end repair and Biotin-enrichment.
For library construction, dA-tailing was performed on Hi-C samples followed by Illumina TruSeq adapter ligation. Samples were amplified by RT-PCR and libraries were purified.

treatment_protocol: Cells were transfected at 60–70% confluence using the Lipofectamine 2000 (Invitrogen) reagent with 24 nM siRNA (scrambled or Prmt5 siRNA oligo3). Cells were incubated with siRNA in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin for 6 hours, after which media was replaced. Cells were harvested two days after reaching confluency.

value: mouse fibroblast-derived preadipocyte line

tag: genotype/variation


title: NYU1435-T (RNA-seq)


title: PNG, control, replicate 2


title: EG, control, replicate 2


title: CO_4-1Y_S9

description: Healthy control


title: HiC_D0_3T3L1_siRNA_Prmt5Oligo3_1


title: CO_3_S39

description: Healthy control


title: OLG cells, Control, Rep2


title: EG, control, replicate 1


title: NYU1417-T (RNA-seq)


title: HiC_D0_3T3L1_siRNA_scrmb_1


title: CO_5_S15

description: Healthy control


title: NYU1417-N (RNA-seq)

value: Lung adjacent normal


title: CG, TDP43 overexpression, replicate 3

value: Cortex glia


title: ArimaHiC_D0_3T3L1_siRNA_Prmt5Oligo3_2


title: CO_2_S22

description: Healthy control

value: Whole blood


title: RNA-seq, LMNA R453W-3

city: Zhunan

first: Chiou Hwa

last: Yuh

address: 35, Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

data_processing:
Raw data qulity contol by fastQC
Trimmomatic, those that meet the following conditions will be deleted: 1) Base quality <3 from either 3’ or 5’ end. 2) Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3) Read length <36.
Post-Trimming quality control
read alignmnet by HISAT2
Supplementary files format and content: Differential expression analysis by DESeq2 (with biological replicates)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: muscle

growth_protocol: We established transgenic fish overexpressing wild-type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility (TZFC), which operates under an automatic 14/10-hour light/dark cycle and maintains the water temperature at 28 °C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.

extract_protocol:
RNA was harvested using NucleoSpin® RNA kit (MACHEREY-NAGEL). 5 ug of total RNA was used for the construction of sequencing libraries.
TruSeq® Stranded mRNA Library Prep

value: muscle

value: LMNA R453W


title: RNA-seq, LMNA R453W-2


title: CG, TDP43 overexpression, replicate 1


title: NYU1416-N (RNA-seq)

value: Short Follow Up (<5y)


title: CG, TDP43 overexpression, replicate 2


title: CO_23-1Y_S39

description: Healthy control

value: M


title: NYU1416-T (RNA-seq)


title: CG, control, replicate 2

value: Brain


title: CO_22-1Y_S38

description: Healthy control


title: RNA-seq, LMNA L35P-3

value: LMNA L35P


title: RNA-seq, LMNA L35P-2


title: NYU1428-N (RNA-seq)

value: No Progression (>5y)


title: NYU1368-T (RNA-seq)

value: Second Primary

value: Progression


title: NYU1368-N (RNA-seq)


title: CG, control, replicate 1

value: Control


title: CO_21-1Y_S17

description: Healthy control

value: Healthy control


title: RNA-seq, LMNA E358K-3

value: LMNA E358K


title: ALG, TDP43 overexpression, replicate 3

value: Astrocyte-like glia

value: TDP43 overexpression


title: NYU1364-N (RNA-seq)

value: Lung adjacent normal


title: CO_3-1Y_S40

description: Healthy control


title: RNA-seq, LMNA A539V-3

value: LMNA A539V


title: CO_20-1Y_S29

description: Healthy control

value: Whole blood


title: ALG, TDP43 overexpression, replicate 2


title: CO_2-1Y_S23

description: Healthy control

value: F


title: NYU1364-Intra-OPB-T (RNA-seq)

value: Tumor


title: RNA-seq, LMNA A539V-2

value: muscle


title: ALG, TDP43 overexpression, replicate 1


title: CO_1_S19

description: Healthy control

value: M


title: NYU1355-T (RNA-seq)


title: ALG, control, replicate 2

value: Brain


title: RNA-seq, LMNA WT-3

value: LMNA WT


title: ALG, control, replicate 1


title: NYU1351-T (RNA-seq)

value: Systemic

value: Recurrence


title: RNA-seq, LMNA WT-2


title: CO_18-1Y_S27

description: Healthy control


title: CO_17-1Y_S36

description: Healthy control


title: NYU1355-N (RNA-seq)

value: Second Primary

value: Progression


title: NYU1351-N (RNA-seq)


title: Pituitary, Young, rep1, scRNAseq

city: Gwangju

first: Yunwon

last: Kang

state: Other

address: 123, Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea

department: Biomedical Science and Engineering

country: South Korea

institute: Gwangju Institute of Science and Technology

description: 10x Genomics

data_processing:
First, the quality and basis statistics of raw sequencing data were checked through FastQC (REF). Then, the raw data were processed through Cell Ranger v6.0.2 (10X Genomics) count pipeline using mouse reference (GRCm39). The Mouse genome and transcriptome information were downloaded from the Ensembl FTP server, and indexes were constructed by processing with Cell Ranger mkref protocol. The Cell Ranger count pipeline produces gene expression matrices containing the UMI counts per gene, per barcode.
Assembly: GRCm39
Supplementary files format and content: gz
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pituitary gland

extract_protocol:
Fresh specimens were immediately stored in the Tissue storage solution (miltenyi biotech, cat no. 130-100-008) at 4°C. Prior to dissociation, tissues were washed with Phosphate buffered saline (PBS) and minced into 1–2 mm pieces. The tissue pieces were then dissociated using the Multi Tissue Dissociation Kit 1 (miltenyi biotech, cat no. 130-110-201) and gentleMACS dissociator (miltenyi biotech), following the manufacturer’s instructions. Following dissociation, cell suspension was sequentially passed through 30-μm strainer to separate cells from cell debris and undigested tissue chunks. The cell suspensions were pelleted by centrifuging at 300g, 4°C, for 5 min and then erythrocytes were removed using red blood cell lysis solution (Miltenyi biotech, cat no. 130-094-183) on 25°C for 5 minutes. Cells were washed 2 times with cold Ca2+ and Mg2+ free 0.04 % BSA/PBS at 300g for 5min at 4°C. Samples were gently resuspended in cold Ca2+ and Mg2+ free 0.04% BSA/PBS, and then counted with a LUNA-FX7™ Automated Fluorescence Cell Counter (logos biosystems) using an acridine orange (AO) and propidium iodide (PI) staining (logos biosystems, cat no. F23001).
According to the 10x Chromium Single Cell 3’ v3.1 protocol (10x Genomics, document no. CG000315) Single Cell RNA-seq libraries were prepared using the 10x Chromium controller and Next Gem Single cell 3’ Reagent v3.1 kits (10x genomics, PN-1000123). Briefly, the cell suspension (target recovery 10,000 cells) was mixed with reverse transcription master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell G Chip (10x genomics, PN-1000120) to generate single-cell Gel Bead-in-emulsion (GEM). Poly-adenylated mRNA from single cells were uniquely barcoded and reverse-transcribed within GEM. After barcoded full-length cDNA was generated from mRNA through GEM-RT incubation, the barcoded cDNA molecules were amplified with PCR.For 3’ Gene Expression Library construction,the enriched cDNA was sequentially subjected to the enzymatic fragmentation, end-repair, A-tailing, adaptor ligation and index PCR. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). The library was sequenced using HiSeq X platform (Illumina), and 150 bp paired-end reads were generated. The sequencing depth of 3’ Gene expression library was about 20,000 read pairs per cell.

tag: strain

value: Pituitary gland

value: Male

tag: age

value: 2 months old


title: Pituitary, Old, rep1, scRNAseq

description: 10x Genomics

tag: tissue

value: 20 months old


title: NYU1334-T (RNA-seq)


title: hLSEC FACS (2)

description: hCD31+ cells sorted from human liver

value: Ex vivo FACS isolated


title: CO_16-1Y_S21

description: Healthy control

value: Healthy control


title: KO11-28-3

city: Qingdao

first: Li

last: Hui

address: 72 Binhai Road, Jimo District, Qingdao, Shandong

country: China

institute: Shandong University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff.
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: Ovary

extract_protocol:
The RNA was amplificated according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

treatment_protocol: Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six  hours later, they were euthanized, and their  oocytes were collected  in PBS-PVA Buffer.  Lysised cells in MCB Buffer , on ice for 30 min, centrifuge lysates, 12,000 x g, 10 min, 4C, supernatant (~800 µg) was loaded on 15-50% sucrose gradient (10ml) , centrifuge, Beckman SW41 rotor, 38000rpm, 3h, 4C,  collected gradient in 28 fractions, 1ml per fraction.RNAs from the polysome(11-28 fractions) or RNP fractions(1-10 fractions) were precipitated with ethanol overnight and purified with RNeasy Plus Micro kit (Qiagen)

value: Ovary

tag: cell type

value: oocyte

value: Lsm14b KO

value: Scarce Sample Polysome Profiling


title: RNA-seq, LMNA WT-1

value: muscle

tag: genotype


title: CO_15-1Y_S33

description: Healthy control

value: Whole blood

value: F


title: AORTITIS_REP19

city: Rochester

first: Yuki

last: Sato

state: MN

address: 200 1st ST SW

department: Rheumatology

institute: Mayo Clinic

data_processing:
The raw reads were preprocessed using the nf-core RNA-seq pipeline (v.3.3), aligned to the human reference genome GRCh38.
For PCA, the counts were normalized by ‘regularized log’ transformation using DESeq2 (v.1.34.0) followed by removing gender effect using limma (v.3.50.3).
To identify the differential gens, the mean-variance trend modelled on logCPM values of each gene along with sample weight adjustment using voomWithQualityWeights
Using the normalized weighted matrix linear model is fitted. The differential genes between Aortitis and Control group were calculated by fitting contrast to the model followed by the empirical Bayes moderation.
Assembly: GRCh38
Supplementary files format and content: Tab-separated matrix file

source_name: aorta

extract_protocol:
FFPE-derived RNA were placed in a QIAcube for the RNA extraction.
TruSeq RNA Exome Capture kit (illumina) was used.

value: aorta

value: AORTITIS


title: CONTROL_REP17

value: CONTROL


title: KO11-28-2

tag: treatment


title: NYU1321-T (RNA-seq)

tag: patient

value: Tumor

value: No Progression (>5y)


title: CO_14-1Y_S26

description: Healthy control

value: M


title: CO_19-1Y_S28

description: Healthy control


title: KO11-28-1


title: NYU1321-N (RNA-seq)

value: Lung adjacent normal

tag: progression type


title: RNA-seq, LMNA A539V-1

value: LMNA A539V


title: CONTROL_REP9


title: KO1-10-3


title: CO_12-1Y_S6

description: Healthy control


title: NYU1319-T (RNA-seq)

value: Second Primary

tag: progression

value: Progression


title: AORTITIS_REP1


title: KO1-10-2

value: Ovary


title: KO1-10-1

value: oocyte


title: NYU1334-N (RNA-seq)

value: Systemic

tag: recurrence

value: Recurrence


title: NYU1319-N (RNA-seq)


title: AORTITIS_REP14


title: WT11-28-3

value: WT

value: Scarce Sample Polysome Profiling


title: NYU1284-T (RNA-seq)

value: Locoregional


title: CO_10-1Y_S34

description: Healthy control

value: Whole blood

tag: Sex

value: F

value: Healthy control


title: CO_1-1Y_S20

description: Healthy control

tag: disease state


title: AORTITIS_REP5

value: aorta

value: AORTITIS


title: WT11-28-2


title: NYU1284-N (RNA-seq)


title: t90-TCDD-H3K27ac-ChIP

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using BWA.
The bamCoverage script was used to generate and normalize bigwig files with the RPKM formula.
The peak calling was performed with the MACS2 (Zhang et al., 2008) against a reference input sample from the same cell line with standard settings and a q value of 0.05.
Association of peaks to genes and associated GO annotation were performed with GREAT.
k-means clustering and heat map and band plot generation were carried out with a Python package fluff.
HOMER (http://homer.salk.edu/homer/motif/) was used for motif scan against corresponding background sequences.
Assembly: hg19 (NCBI version 37)
Supplementary files format and content: peak file

source_name: skin

extract_protocol:
Chromatin for ChIP was prepared as previously described(Kouwenhoven et al., 2010). ChIP assays were performed following a standard protocol (Novakovic et al., 2016) with minor modifications. On average, 0.5M keratinocytes were used in each ChIP. For histone mark H3K27ac, 2x ChIP reactions were pooled to prepare 1x ChIP-seq sample; for AHR, 4x ChIP reactions are pooled to prepare 1 ChIP-seq sample. Antibodies against H3K27ac (Diagenode #C15410174) and AHR (Santa Cruz Biotechnology, #sc-5579) were used in each ChIP assay. Resulted DNA fragments from four independent ChIP assays were purified and subjected to a ChIP-qPCR quality check.
5ng DNA fragments were pooled and proceeded on with library construction using KAPA Hyper Prep Kit according to the standard protocol. The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols.

value: skin

value: primary keratinocytes

value: TCDD 90min

tag: chip antibody

value: H3K27ac (Diagenode #C15410174)


title: AORTITIS_REP2


title: t30-TCDD-H3K27ac-ChIP

value: TCDD 30min


title: NYU1280-T (RNA-seq)

value: Tumor

value: Second Primary

value: Progression


title: CO_13-1Y_S7

description: Healthy control

value: M


title: WT11-28-1

value: Ovary

value: oocyte

value: WT


title: CONTROL_REP20

value: CONTROL


title: WT1-10-3

value: Scarce Sample Polysome Profiling


title: t0-control-H3K27ac-ChIP

value: no treatment


title: WT1-10-2


title: CONTROL_REP10

value: aorta


title: CO_11-1Y_S35

description: Healthy control

value: Whole blood

value: Healthy control


title: NYU1261-T (RNA-seq)

value: No Progression (>5y)


title: CONTROL_REP7


title: NYU1261-N (RNA-seq)

value: Lung adjacent normal


title: AORTITIS_REP4

value: AORTITIS


title: WT1-10-1


title: NYU1222-N (RNA-seq)


title: NYU1222-T (RNA-seq)


title: CONTROL_REP2


title: AORTITIS_REP9


title: t0-AhR-ChIP-input

value: skin

value: primary keratinocytes


title: Den5

city: Shanghai

first: Jin

last: Li

address: 99 Shangda Road

institute: Shanghai University

description: gastrocnemius muscles from mice that have undergone denervation of the right sciatic nerve,which is muscla atrophy model

data_processing:
The raw image data files obtained from high-throughput sequencing are transformed into raw sequenced sequences by Base Calling analysis, which we call Raw Data or Raw Reads, and the results are stored in FASTQ (abbreviated as fq) file format, which contains the sequence information of sequenced sequences (reads) and their corresponding sequencing quality information.
A large amount of sample double-end sequencing data was obtained through the Illumina platform. In view of the impact of data error rate on the results, we used Trimmomatic software to pre-process the raw data for quality and summarize the statistics of the number of reads throughout the quality control process.
The CIRI software uses the BWA software to compare with the reference gene sequences, generate SAM files, and analyze the CIGAR values in the SAM files to scan for PCC signals (paired chiastic clipping signals) from the SAM files. the CIGAR values in the junction reads are characterized as xS/HyM or xMyS/H, where x and y represent the number of bases, M is mapped on, S is soft clipping, and H is hard clipping. for double-ended Reads, the CIRI algorithm considers a pair of reads, one of which can be mapped to circRNA and the other also needs to be mapped to the interval of circRNA. For single-exon loops, or "long exon1-short exon-long exon2" loops, the CIGAR value should be xS/HyMzS/H and (x+y)S/HzM or xM(y+z)S/H. The CIRI software can separate these two cases well. For splicing signals (GT-AG), CIRI also considers other weak splicing information for example (AT-AC), and the algorithm extracts the exon boundary positions from the GTF/GFF files and filters false positives with known boundaries.
Based on the annotation information of protein-coding genes and transcripts released from the database, the transcripts with the largest overlap in position with circRNA were obtained by position information matching, and the sequence of circRNA was predicted based on this transcript information.
The overlap genes are extracted for annotation according to the location of circRNA chromosomes, and IGV is used to graphically demonstrate the distribution of circRNAs on the genome and their positional relationships with related linear RNAs.
FEELnc software counts circRNA types in four directions, namely direction, type, location and subtype, based on the position of circRNA reverse shear sites in relation to known protein-coding transcripts.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: muscle tissue

growth_protocol: All mice maintained in specific pathogen-free (SPF) laboratory animal facility of Shanghai University (Shanghai, China). All procedures with animals followed guidelines on the use and care of laboratory animals for biomedical research published by National Institutes of Health (No. 85-23, revised 1996), and approved by the committee on the Ethics of Animal Experiments of Shanghai University.

extract_protocol:
Total RNA were isolated using mirVanaTM RNA Isolation Kit according to the manufacturer's instructions.
To sequence the circRNA transcriptome, the total RNA of the sample was extracted and the ribosomal RNA was digested with the kit ribo-zero; after that, the linear RNA was removed by RNase R; the enriched circRNA was broken into short fragments by adding interruption reagent, and the interrupted circRNA was used as the template to synthesize one-stranded cDNA with six-base random primers, and then the two-stranded cDNA was prepared. The dUTP was used instead of dTTP in the synthesis of cDNA, and then the different junction was connected, and then one strand containing dUTP was digested by UNG enzyme method, and only the cDNA strand with different junction was retained; the cDNA strand was purified by using the kit; the purified cDNA strand was then end-repaired, A-tail was added and sequencing junction was connected, and then fragment size selection was performed. The purified cDNA strands were then end-repaired, A-tailed and sequenced, followed by fragment size selection, and finally PCR amplification; the constructed libraries were quality-checked by Agilent 2100 Bioanalyzer.

treatment_protocol: The model of denervation-induced muscle atrophy was achieved through cutting a small section of the sciatic nerve by micro clipping and ensuring no docking of the severed nerve. Mice that had not severed the sciatic nerve were used as controls. gastrocnemius muscles samples were harvested 7 days post denervation and snap frozen in liquide nitrogen.

value: muscle tissue

value: Wild type

value: right sciatic nerve denervation


title: Den6


title: t30-TCDD-AhR-ChIP

value: TCDD 30min

value: AHR (Santa Cruz Biotechnology, #sc-5579)


title: NYU1280-N (RNA-seq)

value: Second Primary

value: Progression


title: AORTITIS_REP11


title: CONTROL_REP24

value: CONTROL


title: NYU1213-T (RNA-seq)

value: Tumor


title: siTFAP2A_TCDD_rep1

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using STAR 2.5.0 with default options. Briefly, STAR has the option to generate in-house reference genome from the genome fastq file. In this study, hg19 genome was used to generate the in-house reference genome with the following command: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir directory/ --genomeFastaFiles hg19.fa --sjdbGTFfile Homo_sapiens.GRCh37.75.gtf --sjdbOverhang 100. Then STAR was run and it automatically generated read-counts directly.
Genes with the mean of DESeq2-normalized counts (“baseMean”)> 10 were considered to be expressed. Differential gene expression (adjusted P value <0.05) and principal-component analysis were performed with the R package DESeq2 using read counts per gene.
Functional annotation of genes was performed with DAVID.
For data visualization, wigToBigWig from the UCSC genome browser tools was used to generate bigwig files and uploaded to UCSC genome browser.
Assembly: hg19 (NCBI version 37)
Supplementary files format and content: ReadsPerGene

growth_protocol: Human primary keratinocytes were cultured in Keratinocyte Basal Medium (KBM, Lonza #CC-4131) supplemented with 0.4% (vol/vol) bovine pituitary extract, 0.5 μg/mL hydrocortisone, 5 μg/mL insulin and 10 ng/mL epidermal growth factor (Lonza #CC-4131). Medium was refreshed every other day until near confluency before treatment commencement.

extract_protocol:
Total RNA was isolated using the Favorprep total tissue RNA kit (Favorgen Biotech, Taiwan), according to the manufacturer’s protocol.
5 ng total cDNA as measured by Qubit (Invitrogen) was used for RNA-seq library preparation. Adaptors were ligated to the DNA fragments, followed by a pre-PCR of 4 cycles, size selection (∼300 bp), and subsequently 11 cycles of PCR amplification. Cluster generation and sequencing (50 bp) was performed with the hiSeq Solexa Genome analyzer according to standard Illumina protocols.

treatment_protocol: Dimethylsulfoxide (DMSO) was purchased from Merck (Darmstadt, Germany), 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) was purchased from Accustandard (New Haven, USA), and coal tar (CT) was purchased from Fagron BV (Capelle aan den IJssel, The Netherlands). Cells were treated with either DMSO (0.1% vol/vol), CT (4 µg/mL), or TCDD (10 nM). For siRNA knockdown, human primary keratinocytes were grown to 10-15% confluency before 500 nM of Accell human SMARTpool gene targeting or non-targeting siRNA (Dharmacon, Lafayette, CO, USA) was added for 48 hours. Culture medium was subsequently refreshed and supplemented with siRNA for another 48 hours. Keratinocyte were thereafter allowed to differentiate for 24 hours in the presence of TCDD and were harvested for transcriptional analysis and western blotting as described above.  siRNA SMARTpools include: Accell Human TFAP2A (7020) SMARTpool (#E-006348-00) and Accell Non-targeting Control Pool (#D-001910-10).

value: siTFAP2A, TCDD 24h


title: NYU1213-N (RNA-seq)


title: Den4


title: CONTROL_REP23

value: aorta


title: Den3


title: siCtrl_TCDD_rep2

value: control siRNA, TCDD 24h


title: NYU1210-T (RNA-seq)


title: sham4

description: gastrocnemius muscles from mice that without denervation of the right sciatic nerve, which is control

value: sham surgery


title: t90-TCDD-AhR-ChIP

value: TCDD 90min


title: siCtrl_TCDD_rep1


title: CONTROL_REP16


title: NYU1210-N (RNA-seq)

value: Lung adjacent normal


title: CONTROL_REP11


title: sham3


title: tcdd_2h_rep2

value: skin

value: TCDD 2h


title: sham1

value: muscle tissue


title: siTFAP2A_TCDD_rep2

value: primary keratinocytes


title: AORTITIS_REP22

value: AORTITIS


title: NYU1206-N (RNA-seq)

value: No Progression (>5y)


title: Il7cKO_3

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

country: Japan

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed using Trimmomatic (version 0.33) to remove poor quality reads.
Read data was then aligned to the mouse genome (mm10) with Hisat2 (version 2.1.0)
The aligned reads were used for the transcript quantification by using featureCounts from the subread package (version 1.6.5)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung ILC2s

extract_protocol:
3000 lung ILC2s (CD3−CD4−CD8−CD11b−CD11c−CD19−Gr-1−B220−CD5−FceRⅠ−CD45−Ter119) were sorted by BD LSR Fortessa, and cells were lasated by Buffer RLT (QIAGEN). Then total RNA was harvested using Agencourt AMPure XP (Beckman Coulter) size selection beads. Takara SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Cat#634890) was used with all extracted RNA for cDNA library.  Illumina Nextera XT DNA Library Preparation Kit (Cat#FC-131-1024) and Nextera XT Index Kit (Cat#FC-131-1001) were used with 1 ng of cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung


title: tcdd_2h_rep1


title: NYU1206-T (RNA-seq)


title: AORTITIS_REP24


title: tcdd_24h_rep2

value: TCDD 24h


title: CONTROL_REP18


title: Il7cKO_2


title: NYU1205-N (RNA-seq)

value: Systemic

value: Progression

value: Recurrence


title: NYU1205-T (RNA-seq)

value: Tumor


title: tcdd_24h_rep1


title: Il7cKO_1


title: control_24h_rep2

value: DMSO 24h


title: NYU1196-T (RNA-seq)

value: Short Follow Up (<5y)


title: AORTITIS_REP18

value: aorta


title: Control_3


title: Control_2


title: AORTITIS_REP25


title: NYU1196-N (RNA-seq)


title: control_24h_rep1


title: AORTITIS_REP21


title: Control_1


title: AORTITIS_REP8


title: control_0h_rep2

value: DMSO 0h


title: NYU1141-N (RNA-seq)

value: Lung adjacent normal


title: control_0h_rep1

value: skin


title: Il15cKO_iILC1_rep4

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed using Trimmomatic (version 0.33) to remove poor quality reads.
Read data was then aligned to the mouse genome (mm10) with Hisat2 (version 2.1.0)
The aligned reads were used for the transcript quantification by using featureCounts from the subread package (version 1.6.5)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow immature ILC1s (iILC1s)

extract_protocol:
2000 bone marrow iNK cells (CD3−NK1.1+IL-7Ra−DX5+CD11b−CD27+) or iILC1 (CD3−NK1.1+IL-7Ra+CD49a+) were sorted by BD LSR Fortessa, and cells were lasated by Buffer RLT (QIAGEN). Then total RNA was harvested using Agencourt AMPure XP (Beckman Coulter) size selection beads. Takara SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Cat#634890) was used with all extracted RNA for cDNA library.  Illumina Nextera XT DNA Library Preparation Kit (Cat#FC-131-1024) and Nextera XT Index Kit (Cat#FC-131-1001) were used with 1 ng of cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: immature ILC1


title: Il15cKO_iILC1_rep3


title: NYU1141-T (RNA-seq)

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the human genome (build hg38/GRCh38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Assembly: hg38
Supplementary files format and content: CSV files contain raw and normalized counts for all genes and samples

extract_protocol:
DNase treatment to remove genomic DNA, cDNA synthesis from the input RNA, single primer isothermal amplification (SPIA) of the resultant cDNAs, enzymatic fragmentation and construction of unique barcoded libraries, PCR library amplification and a final step to remove rRNA transcripts.
1 ng of total RNA was used to prepare libraries using Trio RNA-Seq library prep kit (Tecan Genomics) following the manufacturer's instructions. The Agencourt AMPure XP bead (Beckman Coulter) purified libraries were quantified using qPCR and the size distribution was checked using Agilent TapeStation 2200.


title: NYU113-N (RNA-seq)


title: coaltar_2h_rep1

value: primary keratinocytes

value: coaltar 2h


title: AORTITIS_REP6

value: AORTITIS


title: NYU1124-T (RNA-seq)

value: No Progression (>5y)


title: CONTROL_REP12

value: CONTROL


title: NYU113-T (RNA-seq)


title: Il15cKO_iILC1_rep2


title: Il15cKO_iILC1_rep1


title: coaltar_24h_rep2

value: coaltar 24h


title: NYU1124-N (RNA-seq)


title: CONTROL_REP1


title: coaltar_2h_rep2


title: Control_iILC1_rep3


title: NYU1079-T (RNA-seq)


title: Control_iILC1_rep2


title: CONTROL_REP3


title: CONTROL_REP14


title: CONTROL_REP22


title: NYU1079-N (RNA-seq)


title: CTLA-4 and FMT rep 2

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

description: C19_18052022_ERAS220037079.1r_HW2WMDSX3_L1

data_processing:
Sequencing reads were trimmed and filtered to remove adaptor contamination and poor-quality bases using trimmomatic.
The resulting read files were mapped to the GRCm38 genome assembly using Hisat2 with default parameters.
The number of reads mapping to the genomic features annotated in Ensembl with a MAPQ score higher than or equal to 10 was calculated using htseq-count with default parameters.
Assembly: GRCm38
Supplementary files format and content: Text file in comma-separated value format with the raw counts of read pairs uniquely and concordantly mapped to each gene

source_name: colon

extract_protocol:
2cm distal colon segments were taken from mice after confirmation of death, and placed into 1 ml of RNA later. RNA was extracted with Qiazol reagent (Invitrogen). Distilled solutions of RNA were purified using chloroform and isopropanol and eluted with ethanol before being resuspended in RNAse free water. RNA was cleaned up using the Qiagen RNeasy Microkit according to the manufacturer’s guidelines.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structure were ligated. The library fragments were then purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: Faecal content extracted from the caecum of TRUC mice was spun down and reconstituted in sterile PBS with 25% glycerol and then 200µl was orally gavaged into mice at the beginning of the experiment only. Mice treated with immune checkpoint blockade drugs were intraperitoneally administered anti-CTLA-4 (9H10, BioXCell) using doses of 200μg and anti-PD-1 (RMP1-14, BioXCell) at a dose of 250μg once per week for 3 weeks.

value: colon

value: Balb/C

value: CTLA-4 therapy and faecal microbiota transplant


title: CTLA-4 and FMT rep 3

description: C20_18052022_ERAS220037080.1b_HW2WMDSX3_L1


title: CONTROL_REP8


title: CTLA-4 and FMT rep 1

description: C17_18052022_ERAS220037077.1r_HW2WMDSX3_L1


title: AORTITIS_REP10


title: NYU1057-T (RNA-seq)

value: Tumor


title: Control_iILC1_rep1


title: Il15cKO_iNK_rep4

source_name: Bone marrow immature NK (iNK) cells

value: immature NK cell


title: coaltar_24h_rep1


title: PD-1 therapy and FMT rep 3

description: C14_18052022_ERAS220037074.1r_HW2WMDSX3_L1

value: PD-1 therapy and faecal microbiota transplant


title: PD-1 therapy and FMT rep 2

description: C12_18052022_ERAS220037072.1r_HW2WMDSX3_L1


title: Il15cKO_iNK_rep3


title: NYU1037-T (RNA-seq)

value: Short Follow Up (<5y)


title: CONTROL_REP5

value: aorta


title: AORTITIS_REP17


title: Il15cKO_iNK_rep2


title: PD-1 therapy and FMT rep 1

description: C10_18052022_ERAS220037070.1b_HW2WMDSX3_L1


title: NYU1037-N (RNA-seq)

source_name: Lung adjacent normal

value: Lung adjacent normal


title: AORTITIS_REP12


title: Il15cKO_iNK_rep1

value: Bone marrow


title: Combination CTLA-4 and PD-1 therapy and FMT rep 3

description:
C7_18052022_ERAS220037067.1a_HCHT3DSX5_L2
C7_18052022_ERAS220037067.1a_HW2WMDSX3_L1

value: Combination CTLA-4 and PD-1 therapy and faecal microbiota transplant


title: CONTROL_REP15


title: NYU1027-T (RNA-seq)


title: Combination CTLA-4 and PD-1 therapy and FMT rep 2

description: C6_18052022_ERAS220037066.1r_HW2WMDSX3_L1


title: AORTITIS_REP13


title: NYU1027-N (RNA-seq)


title: breast cancer, R2-S4

city: Tomsk

first: Tashireva

last: Liubov

address: 5 Kooperativny Street, Tomsk

department: Cancer Research Institute

country: Russia

institute: Tomsk National Research Medical Center

description:
Sample info for slides with two samples: One sample
FFPE sample

data_processing:
Raw sequencing data were processed using the 10x Genomix Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger`s default setting
Gene expression level of Refseq coding genes were quantified using Space Ranger`s default setting
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: hires_image.png: hi-res image of tissue
Supplementary files format and content: lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifyng spots
Library strategy: Spatial transcriptomics

source_name: Breast cancer

extract_protocol:
FFPE were prepared according to standard operating procedure and 10 µm sections were cut with microtome
Spatial transcriptome sequensing libraries were preparied with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer`s construction

value: Breast cancer

value: anthracyclines, taxanes


title: Combination CTLA-4 and PD-1 therapy and FMT rep 1

description: C5_18052022_ERAS220037065.1b_HW2WMDSX3_L1


title: CONTROL_REP21


title: NYU1019-T (RNA-seq)

source_name: Tumor

value: Systemic

value: Progression

value: Recurrence


title: NYU1057-N (RNA-seq)

value: No Progression (>5y)


title: Control_iNK_rep2


title: untreated rep 3

description:
C4_30032022_ERAS220037030.1b_HCHT3DSX5_L2
C4_30032022_ERAS220037030.1b_HW2WMDSX3_L1

value: colon


title: AORTITIS_REP16

value: AORTITIS


title: NYU1019-N (RNA-seq)


title: untreated rep 2

description: C2_30032022_ERAS220037028.1b_HW2WMDSX3_L1

value: Balb/C


title: AORTITIS_REP7


title: untreated rep 1

description:
C1_30032022_ERAS220037027.1a_HCHT3DSX5_L2
C1_30032022_ERAS220037027.1a_HW2WMDSX3_L1


title: NYU965-N (snRNA-seq)

description: Celsius Therapeutics

data_processing:
Sequencing reads were trimmed of adapter sequences using cutadapt
Barcode processing and gene quantification was performed with STARsolo 2.7.3a55 using the GRCh38 human reference transcriptome (refdata-cellranger-GRCh38-3.0.0 provided by 10x Genomics
Nuclei were filtered to only include those with >500 detectable genes, >1000 UMIs, and <10% of transcripts coming from mitochondrial genes. The UMI counts were normalized by the total number of UMIs per nucleus, multiplied by a scale factor of 10,000, and log-transformed.
Likely doublets/multiplets were identified and removed using the scDblFinder package56.
Assembly: hg38
Supplementary files format and content: h5ad, tsv

extract_protocol:
Snap frozen Stage I lung cancer tumor and matching adjacent lung specimens (within the same lobe, segment, or wedge resection) from 143 patients having R0 resection with lymph node dissection were prospectively collected and archived at -80oC from 2005-2015 under an IRB approved NYULH protocol (i8896)
Nuclei were prepared for 10x Genomics-based single nuclei RNA seq analysis according to a previously published protocol
single-nucleus RNA sequencing

tag: sequencing type

value: Single nuclei

tag: recurrence status

value: NoRecurrence

tag: # _of_cells


title: NYU965-T (snRNA-seq)

description: Celsius Therapeutics

value: Tumor


title: AORTITIS_REP20


title: NYU706-T (snRNA-seq)

description: Celsius Therapeutics


title: Rat Young 6 (3 Months), Liver

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

institute: University of Gothenburg

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Algorithm for mapping sequences: HISAT2 is selected to map the filtered sequenced reads to the reference genome
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Liver tissues were homogenized in Trizol (Invitrogen, Carlsbad, CA, USA) and total RNA was isolated with Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.
RNA concentrations were measured with a NanoPhotometer® (Implen, Westlake Village, CA, USA). Equal amounts of RNA were, reverse-transcribed (High-Capacity cDNA Reverse Transcription Kit, Applied Biosystems, Foster City, CA, USA).

value: Liver


title: NHR66FLAG_1

city: Worcester

first: Mohamad

middle: Ali

last: Nasrallah

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

data_processing:
The raw sequencing data were first clipped for adaptor sequences and then mapped to the C. elegans genome (ce11, UC Santa Cruz) by the Burrows-Wheeler Aligner algorithm (BWA MEM, BWA version 0.7.15). The output SAM files were processed and sorted with the Picard tools. The output mapping files (BAM files) were filtered with SAMtools to remove any read that had a mapping quality less than 10 (SAMtools view –b –q 10 input.bam > output.bam). Peaks were determined using MACS version 2.1 with the no-model parameter. The final set of peaks were called if the difference in intensity values of samples had a significance level of p-value < 0.01.
Assembly: ce11
Supplementary files format and content: excel files includes fold enrichment of promoter regions of wt vs. nhr-66::3xflag

organism: Caenorhabditis elegans

source_name: Whole animal

extract_protocol:
Exposed animals were collected and washed with 4℃ M9 and phosphate-buffered saline to remove bacteria. Cross-linking of protein and DNA was performed in 2% formaldehyde for 30 minutes at room temperature. Cross-linking was quenched with 100 mM glycine, animals were washed in M9, resuspended in lysis buffer (50 mM Hepes–KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate, 0.5% (v/v) N-Lauroylsarcosine, and protease inhibitors) and lysed with a Teflon homogenizer. Lysates were then sonicated using a Bioruptor UCD-200 for 10 cycles (30 s on, 30 s off) to obtain 500-1000 bp DNA fragments. Sonicated lysates (2 mg) were pre-cleared with protein G Dynabeads (Invitrogen) and incubated with 5 μg anti-GFP antibody (Roche) overnight. Immune complexes were collected with protein G Dynabeads, washed, and eluted from beads. Cross-links were reversed at 65℃ overnight and DNA fragments were purified with PCR purification columns (Qiagen).
DNA-ends were repaired, 3'-dA overhang, and ligation of methylated sequencing adaptor. Products were PCR amplified and size selected (100-300bp, including adaptor sequence). Library was qualified for sequencing.

treatment_protocol: Synchronized L1 staged C. elegans wild-type and nhr-66::3xflag animals were grown to L4  at 20°C on E. coli (OP50)

tag: developmental stage

value: RPW 451


title: NHR66FLAG_2

growth_protocol: Synchronized L1 staged C. elegans wild-type and nhr-66::3xflag animals were grown to L4  at 20°C

tag: strain


title: NHR66FLAG_3


title: CPI and FMT treated sample 3


title: N2_3

value: WT


title: Control_iNK_rep3

tag: age

value: Bone marrow

value: immature NK cell


title: CPI and FMT treated sample 2

tag: tissue

value: Combination CTLA-4 and PD-1 therapy and faecal microbiota transplant


title: Rat Young 5 (3 Months), Liver


title: NYU689-T (snRNA-seq)

city: New York

first: Aristotelis

last: Tsirigos

address: 435 E 30th St

institute: NYU School of Medicine

description: Celsius Therapeutics


title: CPI and FMT treated sample 1


title: N2_2


title: NYU608-T (snRNA-seq)

description: Celsius Therapeutics


title: FMT treated sample 3

value: Faecal microbiota transplant


title: Control_iNK_rep1

tag: cell type


title: NYU32-T (snRNA-seq)

description: Celsius Therapeutics


title: FMT treated sample 2

tag: genotype


title: N2_1

tag: treatment


title: Rat Young 2 (3 Months), Liver


title: NYU318-N (snRNA-seq)

description: Celsius Therapeutics

tag: patient

value: Lung adjacent normal


title: Rat Young 1 (3 Months), Liver


title: NYU318-T (snRNA-seq)

description: Celsius Therapeutics

tag: progression type


title: FMT treated sample 1


title: CPI treated sample 3

value: Combination CTLA-4 and PD-1 therapy


title: Rat Aging 6 (19 Months), Liver


title: CPI treated sample 2


title: NYU268-N (snRNA-seq)

description: Celsius Therapeutics


title: Rat Aging 5 (19 Months), Liver


title: NYU1845-N (snRNA-seq)

description: Celsius Therapeutics

value: Recurrence

value: SecondaryPrimary


title: intestinal epithelium HuR knockout, replicate 2

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description:
HuR_KO_2
10X Genomics

data_processing:
Count matrices were generated using cellranger
Seurat objects were created using count matrices and the counts were normalized for library size
Seurat objects of normalized counts for all samples were integrated into one combined object
Assembly: mm10
Supplementary files format and content: Tab-delimited text files of raw counts for each sample generated using cellranger

source_name: small intestinal epithelium

growth_protocol: normal feeding/drinking

extract_protocol:
EDTA/trypsin incubation
Single-cell suspension samples were loaded on the Chromium platform (10X Genomics) for cell barcoding and library preparation was done using the Chromium Single Cell 5’ Reagent kit (10X Genomics) using the manufacturer’s instructions. Briefly, single-cell gel beads in emulsion (GEMs) generated from the Chromium controller were reverse transcribed to produce 10X barcoded cDNA. cDNA was then amplified, and the library generated.
Sequencing was performed on the Illumina NovaSeq6000 platform according to Illumina standard conditions with 10X Genomics recommended read parameters.

value: small intestinal epithelium

value: HuR knockout


title: intestinal epithelium HuR knockout, replicate 1

description:
HuR_KO_1
10X Genomics


title: CPI treated sample 1

value: colon

value: Balb/C


title: littermate, replicate 3

description:
control3
10X Genomics

value: wild-type


title: littermate, replicate 2

description:
control2
10X Genomics


title: Rat Young 3 (3 Months), Liver


title: NYU1845-T (snRNA-seq)

description: Celsius Therapeutics

value: Single nuclei

value: Tumor


title: Rat Young 4 (3 Months), Liver

value: Liver


title: intestinal epithelium HuR knockout, replicate 3

description:
HuR_KO_3
10X Genomics


title: Rat Aging 4 (19 Months), Liver


title: Rat Aging 3 (19 Months), Liver


title: Control sample 3


title: NYU178-T (snRNA-seq)

description: Celsius Therapeutics

value: NoRecurrence


title: littermate, replicate 1

description:
control1
10X Genomics


title: Control sample 2


title: liver, unfasted, rep2

city: Konstanz

first: Rebekka

last: Lambrecht

address: Universitaetsstrasse 10

country: Germany

institute: University of Konstanz

data_processing:
Obtained raw paired-end data was processed using the public server usegalaxy.org
Trimmomatic, STAR, and featureCounts tools were used for generation of gene counts.
Quality control was repeatedly checked using FastQC and MultiQC tools.
Generated count matrix was further analyzed in R environment (R studio).
Gene counts were filtered, normalized, log-transformed and DEGs were calculated with an adjusted p-value <0.05 using the R package DESeq2 (version 1.32.0).
Visualization was performed using the R package “EnhancedVolcano” (version 1.10.0) and pheatmap (version 1.0.12). Gene set enrichment, gene ontology/pathway and cluster net analysis were performed using the R packages clusterProfiler (version 4.0.5) and enrichplot (version 1.12.3).
Assembly: GRCm39/mm39
Supplementary files format and content: tab-separated text files containing raw counts for each sample

source_name: liver

growth_protocol: Mice were housed in groups of 2-6 animals in IVC cages in 12:12 h light/dark cycle.

extract_protocol:
total RNA was isolated using the SV Total RNA Isolation System (Promega)
RNA libraries for RNA-Seq were prepared by NGS platform facility in Bern.

treatment_protocol: Age and sex-matched C57BL/6J wild type mice were fasted overnight with unlimited access to water. Control animals were not fasted (unfasted) and had permanent access to food and water ad libitum.

value: liver

value: male

value: wild type, C57BL/6

value: fasted


title: Rat Aging 2 (19 Months), Liver


title: Control sample 1


title: NYU1636-T (snRNA-seq)

description: Celsius Therapeutics


title: NYU1738-N (snRNA-seq)

description: Celsius Therapeutics

value: Lung adjacent normal


title: liver, unfasted, rep1


title: liver, fasted, rep2


title: Rat Aging 1 (19 Months), Liver


title: ok940_OP50_3

data_processing:
Raw fastq reads were evaluated by FastQC (version 0.11.5), clean reads were aligned to the C. elegans reference genome (WBcel235) and quantified using Kallisto (version 0.45.0). Differentially expressed genes were identified using Sleuth (version 0.30.0).
Assembly: WBcel235
Supplementary files format and content: tsv files include TPM transcript abundance values for each sample

extract_protocol:
RNA was isolated using TriReagent (Molecular Research Center, Inc.) and purified with RNeasy columns (Qiagen)
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Synchronized L1 staged C. elegans wild-type and nhr-66 loss of function animals were grown to L4 on E. coli OP50

tag: exposure


title: NYU1630-N (snRNA-seq)

description: Celsius Therapeutics


title: liver, fasted, rep1


title: ok940_OP50_2

growth_protocol: Synchronized L1 staged C. elegans wild-type and nhr-66 loss of function animals were grown to L4


title: NYU1562-N (snRNA-seq)

description: Celsius Therapeutics


title: neil123_2_un_biol_repB

city: Trondheim

first: Magnar

last: Bjørås

address: Erling Skjalgssonsgate 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Faculty of Medicine and Health Sciences,NTNU

data_processing:
Sequence reads were trimmed with TrimGalore, in single-end mode, clipping 10 bases at the 5’ of each read to remove sequencing bias, and filtering out all low-quality bases from reads (<30 Phred score).
Trimmed sequence reads were mapped to GRCh38/hg38 using HISAT2, with --dta in additional to default parameters.
Aligned sequence reads were sorted by coordinates and indexed using samtools.
Indexed sequence reads were annotated using featureCounts.
Read count normalization was performed with DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: comma-separated values (.csv) file includes normalized counts for each Sample (normalization by median of ratios method).

source_name: HAP1 cells

extract_protocol:
Total RNA was purified with Allprep DNA/RNA/Protein Mini Kit (Cat. No. / ID: 80004), according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HAP1 cells

value: media


title: neil123_2_un_biol_repA


title: prenatal Abx exposed ILC2-rep2, ATAC-Seq

city: Tianjin

first: Jie

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

data_processing:
nf-core atacseq pipline (version 1.2.2)  software used for basecalling.
Adapter trimming was accomplished by Trim Galore (version 0.6.5).
Clean reads sequence alignment was performed using the mouse reference genome (mm10) with BWA (version 0.7.17)  and then filtered with default parameters using SAMtools (version 1.10)  as well as Picard.
MAnorm2 was applied to normalize data from different samples as well as identify the specific peaks.
Signaling pathway-related genes were chosen from the Molecular Signatures Database (MSigDB, version 7.5.1) meanwhile their transcripts were collected from UCSC Table Browser (mm10, NCBI RefSeq).
Assembly: mm10
Supplementary files format and content: Bigwig files for each Sample.

source_name: Lung

extract_protocol:
A total of 50000 lung ILC2s(prenatal antibiotic exposure group and control group) were collected  in 1.5 mL RNase-free tubes  for ATAC-sequencing (n=2).
ATAC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 pregnant mice were randomly supplemented with a broad-spectrum antibiotics cocktail, termed Abx, in their drinking water from gestation day 10 to day 14 to eliminate gut commensal microflora.

value: Lung

value: primary cell

value: Lung group 2 innate lymphoid cell

value: wild type

value: Abx treated pregnant mice


title: control ILC2-rep1, ATAC-Seq

value: Control group


title: prenatal Abx exposed ILC2-rep1, ATAC-Seq


title: neil123_2_bso_biol_repA

value: BSO


title: control ILC2-rep2, ATAC-Seq


title: N2_OP50_3


title: neil123_2_bso_biol_repB


title: NYU1555-N (snRNA-seq)

description: Celsius Therapeutics

value: Single nuclei

value: Recurrence

value: SecondaryPrimary


title: ok940_OP50_1


title: NYU1630-T (snRNA-seq)

description: Celsius Therapeutics

value: Tumor


title: NYU1555-T (snRNA-seq)

description: Celsius Therapeutics


title: N2_OP50_2


title: NYU1562-T (snRNA-seq)

description: Celsius Therapeutics


title: LSK cells from STZ-induced diabetic mice

type: RNA

city: Otsu

first: Miwako

last: Katagi

address: seta tukinowa-cho

institute: Shiga university of medical science

hyb_protocol: 2.0 μg of Cy3-labelled cDNA was filled up to 50 μl containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Lineage(-), Sca1(+), ckit(+) cells (LSK cells) from STZ-induced diabetic mice (n=3)

label_protocol: cDNA was amplified by OvationR Pico WTA System V2（NuGEN Technologies) from 8.3 ng total RNA according to the manufacturer's instructions. Amplified cDNA yield was checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared with Genomic DNA Enzymatic Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: total RNA were extracted by Rneasy Micro Plus kit (Qigen)

value: bone marrow cells

tag: gender

value: female

value: STZ-DM mice


title: N2_OP50_1


title: EWAT_KIKO_4

city: Rome

first: Fabio

last: Zaccaria

address: Via della Ricerca Scientifica 1

country: Italy

institute: University of Rome "Tor Vergata"

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TRIMMOMATIC
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2
Read count extraction and normalization were performed using DeSeq2 (R package)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Adipose Tissue

extract_protocol:
Total RNAs from cells and tissues were extracted using Direct-zolTM RNA MiniPrep (ZYMO RESEARCH) according to the manufacturer’s instructions. Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from 50 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl), which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 75 cycle strategy (Illumina Inc.).

value: Visceral White Adipose Tissue

value: KIKO


title: neil123_1_un_biol_repB

value: HAP1 cells

value: media


title: 35SALKBH10B_GT_3_F_4hr

city: Philadelphia

first: Brian

middle: D

last: Gregory

state: PA

address: 433 South University Avenue

department: Biology

institute: University of Pennsylvania

description: polyA mRNA + GMUCT 5' Adaptor selection

data_processing:
In order to call m6A peaks reads from all samples were aligned to the Col-0 reference genome/annotation file TAIR10 using STAR. All non-unique reads were discarded from downstream analysis. Mapped read coverage was split into + and minus strand fractions and macs2 callpeak was then used to call m6A peaks on each strand, respectively, using parameters --nomodel --extsize 50 genome size was set to ½ the transcriptome using -g 32542107 and with an FDR cutoff of < 0.05. m6A peaks are provided in bedgraph format in supplementary excel file.
Assembly: TAIR10
Supplementary files format and content: m6A peak are presented in narrowPeak format with respect to treatment.

organism: Arabidopsis thaliana

source_name: 14 day old seedling

growth_protocol: for 14 day old and 4wk old plants 16 h light/8 h dark, average lighting of 120 µmol/m2/s, 20°C day/18°C night, 60% hygrometry.

extract_protocol:
Following control or treatement, leaves were immediately placed on liquid N2 and ground using a mortar and pestle. RNA was extracted using Qiazol (Qiagen) according to manufacturers instructions. 2 rounds of PolyA+ selection was performed using the Dynabeads mRNADirect kit (Thermo).
Paired end libraries used TRueSEq RNA sample prep kit, standard illumina protocols

treatment_protocol: For 14day old flg22 treated: One day before treatment, liquid medium (same medium without agar) was added to the plates under sterile conditions, and plates were transferred onto the bench. Seedlings were treated with a final concentration of 1 μM flg22 for 0 min (no treatment), 30 min or 4 h. Seedlings were finally harvested, rapidly dried with paper, ﬂash-frozen in liquid nitrogen, and stored at -80°C. For 4 week old pst treated: Four week-old plant leaves were infiltrated with bacteria at a concentration of 106 cfu/ml using a needleless syringe.

value: 14 day old whole seedling

value: 1uM flg22 peptide 4 hours


title: neil123_1_un_biol_repA


title: NYU1534-N (snRNA-seq)

description: Celsius Therapeutics

value: Lung adjacent normal


title: NYU1534-T (snRNA-seq)

description: Celsius Therapeutics


title: 35SALKBH10B_GT_3_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection

value: untreated


title: neil123_1_bso_biol_repB


title: neil123_1_bso_biol_repA


title: LSK cells from nondiabetic mice

source_name: Lineage(-), Sca1(+), ckit(+) cells (LSK cells) from nondiabetic mice (n=3)

tag: disease state

value: nondiabetic mice


title: 35SALKBH10B_GT_2_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: EWAT_KIKO_1


title: 35SALKBH10B_GT_1_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: EWAT_WT_4

value: WT


title: neil3_2_un_biol_repA


title: 35SALKBH10B_GT_2_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: neil3_2_un_biol_repB


title: NYU1368-N (snRNA-seq)

description: Celsius Therapeutics

value: Single nuclei


title: EWAT_WT_2


title: EWAT_KIKO_3


title: neil3_2_bso_biol_repB

value: BSO


title: MTA_GT_3_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection

value: mta


title: neil3_2_bso_biol_repA


title: 35SALKBH10B_GT_1_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: EWAT_WT_1


title: NYU1364-N (snRNA-seq)

description: Celsius Therapeutics

value: Recurrence

value: SecondaryPrimary


title: NYU1364-T (snRNA-seq)

description: Celsius Therapeutics

value: Tumor


title: MTA_GT_3_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: NYU1351-T (snRNA-seq)

description: Celsius Therapeutics

value: Systemic


title: NYU1368-T (snRNA-seq)

description: Celsius Therapeutics


title: EWAT_KIKO_2

value: Visceral White Adipose Tissue


title: NYU1351-N (snRNA-seq)

description: Celsius Therapeutics


title: MTA_GT_2_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: NYU1435-N (snRNA-seq)

description: Celsius Therapeutics

value: NoRecurrence


title: EWAT_WT_3


title: neil3_1_un_biol_repA

value: HAP1 cells


title: neil3_1_bso_biol_repB


title: MTA_GT_2_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: neil3_1_un_biol_repB

value: media


title: NYU1321-T (snRNA-seq)

description: Celsius Therapeutics


title: NYU1321-N (snRNA-seq)

description: Celsius Therapeutics


title: NYU1057-N (snRNA-seq)

description: Celsius Therapeutics


title: MTA_GT_1_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection

value: 14 day old whole seedling


title: NYU1057-T (snRNA-seq)

description: Celsius Therapeutics


title: neil3_1_bso_biol_repA


title: COL_GT_3_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: neil2_biol_rep11.2_un


title: MTA_GT_1_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: COL_GT_3_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection

value: 1uM flg22 peptide 4 hours


title: neil2_biol_rep12_bso


title: HT1080 wild-type 1 µM tubastatin 3

city: New Orleans

first: Terry

middle: J

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.39 with default settings
Trimmed sequence reads were mapped to GrCh38.83 using bowtie2 v2.4.5 as implemented by RSEM v1.3.3, with default settings
Mapped sequences were annotated and counted using RSEM v1.3.3 with default settings
Read count extraction was performed using tximport v1.26.1
Read count statistical analysis was performed using DESeq2 v1.38.2
Assembly: Human NCBI genome build GrCH38 build 83
Supplementary files format and content: Expected counts from RSEM output for all conditions and ENSEMBL entries, cross-referenced to gene names and UNIPROT entries

source_name: Connective tissue

growth_protocol: HT1080 cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
3x10^6 cells were pelleted, resuspended in MEM with 5% glycerol, and frozen at -80 °C. Cells were shipped on dry ice, and total RNA extracted by Creative Genomics using a commercially available kit. Quality of RNA was verified using RNA Screen Tape (Agilent). RNA was rRNA-depleted using the Ribo-Zero plus kit (Illumina).
Libraries were prepared using the PE150 platform (Illumina) following the manufacturer's instructions.

value: Connective tissue

value: fibrosarcoma

value: 1 microM tubastatin A

tag: time point

value: 2 days


title: Prostate_tumor_RIB0025400

city: Leipzig

first: Michael

last: Rade

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Gene expression of prostate biopsy prior to RP (FFPE)

data_processing:
Processing of primary sequencing data was done using the workflow management software UAP (https://github.com/fraunhofer-izi/uap).
Demultiplexing of Illumina raw files was performed with the Illumina bcl2fastq software v2.19.
Paired-end FASTQ reads were trimmed and filtered using AdaptorRemoval v2.2.1 with additional parameters to trim ambiguous bases (N) at 5’/3’ termini (–trimns), remove low-quality bases (–trimqualities, –minquality 20) and keep reads with a minimum read length of 30bp (–minlength 30).
Trimmed reads were mapped to the human reference genome version GRCh38/hg38 by HISAT2 v2.1.0 by specifying a reverse stranded library.
Gene level quantification was performed using HTSeq v0.11.2 with following parameters: –mode intersection-strict, –stranded reverse and –type exon. To ensure that the putative novel intergenic genes from the ProstaTrend signature (DOI: 10.1016/j.eururo.2020.06.001) are also represented in the FFPE_Bx cohort, we extended the human reference gene annotation GENCODE (release 36 GRCh38.p12) used for HTSeq as follows: we used the annotation of expression quality filtered novel transcripts classified as “u”(unknown intergenic) of the cohort FF_seq_RP as described previously (DOI: 10.1016/j.eururo.2020.06.001). Since these annotations are based on GRCh37/hg19, we updating the annotation using UCSC liftOver tool to GRCh38/hg38 (Chain file: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz. After converting the coordinates all prognostic genes from the ProstaTrend signature (classified as unknown intergenic and FDR <0.05) could be retained.
179 samples passed the quality filter, 3 samples were excluded because time to BCR was not recorded. In total, we analyzed transcriptome data from 176 patients.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Matrix table (HTSeq output) with raw gene counts for each sample as a separate file. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)
Supplementary files format and content: Comma-delimited text file with rawcounts for each gene and sample. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)
Supplementary files format and content: Comma-delimited text file with variance stabilizing transformation (VST) counts for each gene and sample. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)

source_name: FFPE PCa biopsy

extract_protocol:
From up to five FFPE tissue slices of 10 μm we isolated RNA using Deparaffinization Solution (Qiagen) according to the miRNEASY protocol. A pathologist evaluated HE-stained flanking tissue slices and tumor content was assessed, ranging between 5% and 100% (mean= 41%). After subsequent proteinase K digestion and formalin-de-crosslinking, we transferred the samples onto RNeasy MinElute spin columns. We used the miRNeasy FFPE kit on the QIAcube (Qiagen) following the manufacturer’s instruction for the final RNA purification. To eliminate all traces of genomic DNA, we performed DNAse-digestion (TURBO DNA free Kit, Thermo Fisher) twice in each sample. The RNA was concentrated using a standard precipitation protocol if necessary. Finally, we quantified extracted RNA using a Qubit RNA-Kit and the Qubit 2.0 instrument (Thermo Fisher). We analyzed the quality of RNA on a Bioanalyzer 2100 instrument (Agilent Technologies) and calculated the DV200 values (the percentage of fragments >200 nucleotides), ranging between 5% and 63% (mean=37%). Because of the well-known quality issues of old FFPE specimens, we decided to include all samples in further analysis.
For RNA-sequencing of FFPE specimens, we used 200 ng RNA per sample (when available). We prepared RNA libraries using TruSeq-Stranded Total RNA Sample Prep kit (Illumina), including an rRNA depletion step according to manufacturers’ protocol, i.e., Ribo-Zero Gold rRNA Removal Kit. Following Illumina's recommendation, we skipped the fragmentation step for all samples. We analyzed the quality and quantity of each prepared library with the Denovix instrument (Qubit DNA-Kit) and with the Bioanalyzer 2100, calculated the molarity of each library and pooled equal amounts, which were used for subsequent sequencing (12 pM). We sequenced 2 x 126-bp paired-end reads using SBS V4 chemistry with a HiSeq 2500 (Illumina) on four eight-lane flow cells: the first one with 32 and the others with 51 libraries each (185 in total).

value: FFPE PCa biopsy

tag: alternative sample_id

tag: tumor type

value: Primary tumor

tag: biochemical relapse_(bcr)

value: yes

tag: gleason score

tag: pathological t_stage

tag: pathological n_stage

value: pNA

tag: total psa_(ng/ml,_pre-biopsy)

tag: tumor cell_content_(%)


title: HT1080 wild-type 5 µM PCI-34051 2

tag: tissue

tag: cell type

tag: genotype

value: WT

value: 5 microM PCI-34051


title: HT1080 wild-type 5 µM PCI-34051 3

tag: treatment


title: HT1080 wild-type 5 µM PCI-34051 1


title: COL_GT_2_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: neil2_biol_rep11.2_bso

value: BSO


title: neil2_biol_rep11.1_un


title: neil2_biol_rep12_un


title: neil2_biol_rep11.1_bso


title: Cortex, PN35, snRNAseq

city: Cleveland

first: Marissa

last: Scavuzzo

state: OH

address: 2109 Adelbert Rd

department: Genetics

institute: Case Western Reserve University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Filtered datasets in h5 format are from CellBender (https://github.com/broadinstitute/CellBender).
Assembly: mm10
Supplementary files format and content: Tab-separated values files, h5 files, and matrix files
Supplementary files format and content: Supplementary files provided as .rds

source_name: Cortex

growth_protocol: Mouse duodenal tissue was dissected from the junction of the stomach to approximately 3cm distal at the turn of the intestine, flushed with PBS to remove luminal contents, and snap frozen in liquid nitrogen. Snap frozen tissues were stored at -80oC until nuclei isolation.

extract_protocol:
We used CitraPrep to isolate nucle from high degradative tissues. Frozen tissue was placed into a petri dish on ice and cut into 0.2cm cubed pieces or smaller using clean scissors and forceps in 1mL of CitraHB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8, 10mM citric acid, 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine tetrahydrochloride, 0.5mM spermidine trihydrochloride, and cOmplete, EDTA-free protease inhibitor). Chopped tissue (totaling less than 1.5cm cubed) was transferred to the glass dounce homogenizer on ice and 4mL of CitraHB was added. Tissue was incubated on ice for 7 minutes. Tissue was homogenized 20x with loose pestle before adding 320uL of NP-40 and homogenizing 40x with tight pestle. If tissue does not homogenize, an electric homogenizer with short bursts may be used. Nuclei were observed under the microscope for quality control before proceeding. Tissue lysate was filtered through a 40um strainer into a 50mL conical tube. Next, 5mL of 50% iodixanol solution (5 volumes OptiPrep and 1 volume of Diluent composed of 150mM KCl, 30mM MgCl2, 120mM Tricine-KOH pH 7.8 mixed, plus 10mM citric acid, 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine) was added to the filtered tissue lysate to make a 25% iodixanol solution and vortexed to mix. The tissue lysate was slowly underlaid with 30% iodixanol solution (30% OptiPrep in CitraHB with 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine), then slowly underlaid with 40% iodixanol solution (40% OptiPrep in CitraHB with 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine). Without disturbing the layers, the 50mL tube was weighed and balanced before centrifugation at 10,000g for 18 minutes at 4oC with no brake. Nuclei were collected from the interface layer with a 1000mL pipette and placed into a new tube with 10mL nuclei wash buffer (1x PBS, 1% BSA, 0.5U/uL RNasin, and 0.5U/uL SUPERase RNase inhibitor) and vortexed before filtering through a 20um filter. Nuclei were pelleted by centrifugation at 500g for 5 minutes at 4oC. Supernatant was removed and tissue was washed a second time. The pellet was resuspended in 250uL of nuclei wash buffer and nuclei were counted using a hemocytometer.
Library was performed according to the manufacter’s instructions (single cell 3’ GEM v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Cortex

tag: age

tag: Sex

value: female

tag: strain background

value: wildtype


title: COL_GT_1_F_4hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: HT1080 wild-type 1 µM tubastatin 2

tag: cell line


title: Male Duodenum replicate 2, snRNAseq

description: 10x Genomics

source_name: Duodenum

value: Duodenum

value: male


title: COL_GT_1_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection

value: 14 day old whole seedling

value: untreated


title: neil1_biol_rep13.2_un

value: HAP1 cells

value: media


title: COL_GT_2_C_0hr

description: polyA mRNA + GMUCT 5' Adaptor selection


title: HT1080 wild-type 1 µM tubastatin 1

value: Connective tissue

value: fibrosarcoma

value: 1 microM tubastatin A

tag: time point

value: 2 days


title: MTA_m6_3_F_4hr

description: PolyA, m6AIP

value: 1uM flg22 peptide 4 hours

value: mta


title: neil1_biol_rep13.2_bso


title: MTA_m6_3_C_0hr

description: PolyA, m6AIP


title: Female Duodenum replicate 2, snRNAseq

description: 10x Genomics


title: neil1_biol_rep13.1_un


title: MTA_m6_2_F_4hr

description: PolyA, m6AIP


title: HT1080 KDAC8H143A 4


title: MTA_m6_2_C_0hr

description: PolyA, m6AIP


title: neil1_biol_rep12_un


title: Female Duodenum replicate 1, snRNAseq

description: 10x Genomics


title: Tox4 cKO CD8 RNA-seq rep5

city: Shanghai

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Fragment count were obtained using featureCounts v1.6.1.
Assembly: mm10 for mouse.
Supplementary files format and content: Tab-delimited text files include fragment count values of genes for each sample.

source_name: CD8 thymocytes

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR. Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

value: CD8 thymocytes


title: HT1080 KDAC8H143A 1


title: MTA_m6_1_F_4hr

description: PolyA, m6AIP


title: Tox4 cKO CD8 RNA-seq rep4


title: HT1080 KDAC8H143A 2


title: neil1_biol_rep12_bso

value: BSO


title: neil1_biol_rep13.1_bso


title: wt_p1_un

value: wt


title: MTA_m6_1_C_0hr

description: PolyA, m6AIP


title: Tox4 cKO CD8 RNA-seq rep2


title: COL_m6_3_F_4hr

description: PolyA, m6AIP


title: Male Duodenum replicate 1, snRNAseq

description: 10x Genomics


title: HT1080 KDAC6H611A 3


title: wt_p1_bso


title: HT1080 KDAC6H611A 2


title: COL_m6_3_C_0hr

description: PolyA, m6AIP


title: Tox4 WT CD8 RNA-seq rep5


title: HT1080 KDAC8H143A 3


title: HT1080 KDAC6H611A 1


title: Tox4 cKO CD8 RNA-seq rep3


title: wt_1.3_un_biol_repB


title: COL_m6_2_F_4hr

description: PolyA, m6AIP


title: Tox4 WT CD8 RNA-seq rep3


title: COL_m6_2_C_0hr

description: PolyA, m6AIP


title: wt_1.3_un_biol_repA


title: Tox4 WT CD8 RNA-seq rep4


title: HT1080 KDAC6H216A 3


title: HT1080 KDAC6H216A 2


title: Tox4 WT CD8 RNA-seq rep1


title: wt_1.3_bso_biol_repB


title: Tox4 WT CD8 RNA-seq rep2


title: HT1080 KDAC6H611A 4


title: wt_1.3_un


title: 35SALKBH10B_m6_3_F_4hr

description: PolyA, m6AIP


title: Tox4 cKO CD8 RNA-seq rep1


title: COL_m6_1_C_0hr

description: PolyA, m6AIP


title: HT1080 wild-type 4

value: WT


title: HT1080 KDAC6H216A 1


title: wt_1.3_bso