title: KYSE-30_FXR1KO_RNAseq_rep3

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then ATAC-seq reads were mapped to hg19 using BWA, RNA-seq reads using STAR.
MACS2 was used for ATAC-seq peak calling,
bam file were transform into bigwig format using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: KYSE-30 cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). Genomic DNA was isolated with QIAmp DNA Mini kits (Qiagen).
Sequencing libraries for ATAC-seq and RNA-seq were prepared following the manufacturer’s instructions and sequencing was conducted using Illumina Novaseq6000 PE150 platform.

value: esophageal squamous carcinoma cells

tag: genotype/variation


title: A11_0_1

status: Public on Sep 09 2022

type: SRA

city: Kunming

first: Xuemei

last: Li

state: Yunnan

address: wuhuaqu

country: China

institute: majorbio

library_source: transcriptomic

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
Assembly: HiSat2 and StringTie
Supplementary files format and content: xls file includes tpm value for each sample
Supplementary files format and content: Expression analysis table include TPM values for each WT and Atg11 sample
Supplementary files format and content: Total difference statistics between WT and Atg11 mutants

molecule: total RNA

organism: Orbilia oligospora

source_name: Fungal hyphae cells

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: cell type

value: Fungal hyphae cells

tag: genotype

value: deltaAoatg11 mutant strain

tag: treatment

value: no treatment


title: 408, 0 Gy, VMC, Day 7, rep1

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

country: USA

institute: University of California, Los Angeles

description:
9_408_0Gy_Vmc_1
nGEC
Untreated VMC Day 7 replicate 1

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to GRCh38 using STAR spliced read aligner
Count read using HT-seq with GRCh38 as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using egdeR.
Assembly: GRCh38
Supplementary files format and content: Counts

organism: Homo sapiens

source_name: 408, 0 Gy, VMC, Day 7

growth_protocol: Cells were maintained in growth media containing DMEM:F12 with B27 supplement and Pen-strep containing growth factors EGF and FGF, and sorted GEC and GPC were maintained in endothelial media and pericyte media respectively.

extract_protocol:
RNA extraction was performed using Qiagen RNEasy Microkit
cDNA libraries were prepared using TruSeq Stranded RNA (100ng) + Ribozero Gold

treatment_protocol: Cells infected with CDH5-mCherry and DES-mCherry were radiated and FACS sorted using mCherry at 7 days.

value: GBM cells

tag: cell type (sorted)

value: GEC

tag: time

value: Day 7

value: Untreated

tag: cell line


title: KYSE-30_FXR1KO_RNAseq_rep2

city: Guangzhou

first: shuang

last: deng

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

molecule: polyA RNA

growth_protocol: KYSE-30 cells were cultured in DMEM medium (Invitrogen) supplemented with 10% fetal bovine serum

treatment_protocol: Short hairpin RNA (shRNA) targeting METTL3, TET1, FXR1 or scramble control or plasmids was commercially synthesis and transfected using lipofectamine 3000 (Life Technologies). Stable knockdown cells were generated by lentiviral infection and puromycin selection.


title: WT_N_3

value: wild type

value: Nitrogen deficiency induction


title: A_0_3


title: 408, 0 Gy, Day 7, rep2

description:
2_408_0Gy_2
0 Gy
Untreated Day 7 replicate 2


title: A_0_2


title: KYSE-30_FXR1KO_RNAseq_rep1


title: A11_N_1


title: 408, 0 Gy, Day 7, rep1

description:
1_408_0Gy_1
0 Gy
Untreated Day 7 replicate 1


title: KYSE-30_TET1KO_RNAseq_rep3


title: mesF

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

data_processing:
cellranger pipeline using default parameters with forced recovery of 7000 cells for each library
cells filtered for minimum 250 (vs2) or 350 (vs3) detected genes
library names were appended to barcodes from individual libraries
count matrices were concatenated into a single dataset
Assembly: Reads were mapped to the JGI genome assembly (Vs1) using a customized transcriptome (David Fredman 2013), wherein all gene models were extended by 1000bp in the 3’ direction, or until the start of the next gene model in the same orientation.
Supplementary files format and content: alldata.mtx: count matrix after demultiplexing, mapping, and UMI reduction for all libraries
Supplementary files format and content: alldata.genes.csv text file with gene names (NVE models: rows)
Supplementary files format and content: alldata.cells.csv text file with sample names (columns)
Supplementary files format and content: NVEmodels.gtf mapping coordinates for genome mapping

organism: Nematostella vectensis

source_name: Mesentery female tissue dissection

extract_protocol:
Whole embryos, animals, or dissected tissues were treated with TrypLETM Select Enzyme (A1217702, Thermo Fisher Scientific). Enzyme concentration and incubation time were adapted to each stage. Cell viability and counts were assayed with a Cellometer X2 (Nexcelom). Cell suspensions were diluted and loaded into a 10x Genomics single cell platform using vs2 and vs3 reagents.
10X Genomics Chromium v2/v3 chemistry

tag: sample type

value: Mesentery female tissue dissection


title: KYSE-30_TET1KO_RNAseq_rep2


title: 408, GBM, 8Gy, Day7-2

description: Radiation, single dose of 8 Gy, Day 7 replicate 2

growth_protocol: Cells were maintained in growth media containing DMEM:F12 with B27 supplement and Pen-strep containing growth factors EGF and FGF.

treatment_protocol: Cells were first radiated for 7 day time point and then radiated for 2-day time point to collect all samples on the same day.

value: Radiation, single dose of 8 Gy


title: A_0_1


title: phbw

source_name: Pharynx/BW tissue dissection

value: Pharynx/BW tissue dissection


title: KYSE-30_TET1KO_RNAseq_rep1


title: 408, GBM, 8Gy, Day2-3

description: Radiation, single dose of 8 Gy, Day 2 replicate 3

value: Day 2


title: 408, GBM, 8Gy, Day7-3

description: Radiation, single dose of 8 Gy, Day 7 replicate 3


title: KYSE-30_METTL3KO_RNAseq_rep3


title: 408, GBM, 8Gy, Day2-1

description: Radiation, single dose of 8 Gy, Day 2 replicate 1


title: 408, GBM, 8Gy, Day7-1

description: Radiation, single dose of 8 Gy, Day 7 replicate 1


title: planula5d

source_name: Tentacle bud 5 dpf

value: Tentacle bud


title: KYSE-30_NC_RNAseq_rep3

value: NC


title: polyp8d

source_name: Primary polyp 8dpf

value: Primary polyp


title: 408, GBM, 0Gy, Day7-3

description: Untreated, Day 7 replicate3


title: 408, GBM, 0Gy, Day7-2

description: Untreated, Day 7 replicate2


title: polyp16d

source_name: Primary polyp 16dpf


title: KYSE-30_NC_RNAseq_rep2

value: esophageal squamous carcinoma cells


title: KYSE-30_METTL3KO_RNAseq_rep1


title: KYSE-30_FXR1KO_ATAC_rep2

library_source: genomic

molecule: genomic DNA


title: planula4d

source_name: Late planula live 4 dpf

value: Late planula live


title: planula2d

source_name: Early planula 2dpf

value: Early planula


title: 408, GBM, 8Gy, Day2-2

description: Radiation, single dose of 8 Gy, Day 2 replicate 2


title: 408, GBM, 0Gy, Day7-1

description: Untreated, Day 7 replicate1


title: planula4d2c

source_name: Late planula cryo 4 dpf

value: Late planula cryo


title: 408, GBM, 0Gy, Day2-3

description: Untreated, Day 2 replicate3

value: GBM cells


title: KYSE-30_NC_RNAseq_rep1


title: KYSE-30_FXR1KO_ATAC_rep1


title: Gastrula2

source_name: Gastrula 25 hpf

value: Gastrula


title: gastrula18h

source_name: Blastula-gastrula intermediate 18 hpf

value: Blastula-gastrula intermediate


title: KYSE-30_TET1KO_ATAC_rep2


title: 408, GBM, 0Gy, Day2-1

description: Untreated, Day 2 replicate1

value: Untreated


title: gastrula3

source_name: Gastrula 24 hpf


title: KYSE-30_METTL3KO_RNAseq_rep2


title: 408, GBM, 0Gy, Day2-2

description: Untreated, Day 2 replicate2


title: Nematostella vectensis Sub-adult bodywall single cell RNA sequencing run 1

data_processing:
cellranger 2.1.0 pipeline using default parameters with forced recovery of 7000 cells for each library
The sequences for all NVE gene models are publicly available here:
https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
with the exception that the gtf file of transcript coordinates was modified
by extending all gene models 1000bp in the 3' direction or until
Genome_build: intersecting the next gene model in the same orientation, whichever
Supplementary_files_format_and_content: occurred first.
Supplementary_files_format_and_content: Barcodes.tsv = column names (cell index)
Supplementary_files_format_and_content: genes.tsv = row names (genes)

source_name: Sub-adult bodywall

extract_protocol:
5-month old Nematostella vectensispolyps were dissected into 4 separate tissues: tentacles, mesenteries, pharynx, bodywall. Tissue pieces were treated with undiluted TrypLETM Select (Thermo Fisher, A1217701). For 1 hour the tissues were allowed to disintegrate in the enzyme with gentle agitation on a shaker, then dissociation into single-cell suspensions was completed with occasional pipetting over the course of another 1.5 hrs. Cell viability and counts were assayed with a Cellometer X2 (Nexcelom), and suspensions were diluted to 1000 – 1700 cells/uL and loaded into a 10x Genomics single cell platform using Vs.2 reagents.
10X Genomics Chromium v2 chemistry

tag: tissue

value: bodywall


title: KYSE-30_TET1KO_ATAC_rep1


title: planula3d

source_name: Midplanula 3dpf

value: Midplanula 3dpf


title: KYSE-30_METTL3KO_ATAC_rep1


title: Nematostella vectensis Sub-adult pharynx single cell RNA sequencing run 1

source_name: Sub-adult pharynx

value: phaynx


title: KYSE-30_METTL3KO_ATAC_rep2

source_name: KYSE-30 cells


title: Nematostella vectensis Sub-adult tentacle single cell RNA sequencing run 1

source_name: Sub-adult tentacles

value: tentacle


title: Nematostella vectensis Sub-adult mesentery single cell RNA sequencing run 1

source_name: Sub-adult mesentery

value: mesentery


title: KYSE-30_NC_ATAC_rep2


title: KYSE-30_NC_ATAC_rep1


title: KYSE-30 WT FXR1 CUT&Tag rep1

data_processing:
Library strategy: CUT&Tag
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then RIP-seq reads were mapped to hg19 using STAR, CUT&Tag and PARCLIP reads using Bowtie2, WGBS was processed by Bismark.
MACS2 was used for m6A and CUT&Tag peak calling, Piranha was used for CLIP peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file, CpG information file

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). Genomic DNA was isolated with QIAmp DNA Mini kits (Qiagen).
Sequencing libraries for m6A-IP and input were prepared following the manufacturer’s instructions and sequencing was conducted using Illumina HiSeqX Ten PE150 platform. The WGBS library was sequenced on an Illumina HiSeq2500 sequencers and generated paired-end reads (2× 125 bp). CUT&Tag sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions. PAR-CLIP seqiencing was performed in NEBNext small RNA library prep kit (E7330S) and sequenced on Illumina. Hiseq4000.

value: wild type


title: HF female placenta RNA rep 4

city: Sainte-Anne-de-Bellevue

first: Anne-Sophie

last: Pépin

state: QC

address: 21111 Lakeshore road

department: Department of Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Reads were trimmed using Trim Galore (version 0.5.0, parameters: --paired --retain_unpaired --phred33 --length 70 -q 5 --stringency 1 -e 0.1) (Krueger, 2015). Trimmed reads were aligned to the Ensembl Genome Reference Consortium mouse reference 38 (GRCm38) primary assembly using hisat2 (version 2.1.0, parameters: -p 8 --dta) (Kim, Langmead and Salzberg, 2015). Aligned files with SAM format were converted to binary SAM format (BAM) and sorted by genomic position using SAMtools (version 1.9) (Li et al., 2009). Transcripts were assembled and gene abundances calculated using Stringtie (version 2.1.2, parameters: -p 8 -e -B -A) (Pertea et al., 2015).
Assembly: mm10
Supplementary files format and content: gtf files generated by Stringtie

organism: Mus musculus

source_name: Placenta

extract_protocol:
E14.5 placentas were collected at necropsy and snap frozen in liquid nitrogen. RNA extraction was performed using Qiagen’s RNeasy Mini Kit following the manufacturer’s protocol.
Libraries were prepared for illumina sequencing, and samples were sequenced on the illumina NovaSeq 6000 platform with 100 bp paired-end reads.

treatment_protocol: Male mice were fed either a control or a high-fat diet for 8-10 weeks starting at 6 weeks of age

value: Placenta

tag: developmental stage

tag: Sex

value: female

value: paternal high-fat diet


title: KYSE-30 shControl Pol II CUT&Tag rep1

value: Control


title: KYSE-30 WT FXR1 CUT&Tag rep2


title: HFD sperm H3K4me3 rep 3

data_processing:
Sequencing reads were trimmed using Trimmomatic on single-end mode to remove adapters and filter out low-quality reads (version 0.36, parameters: 2:30:15 LEADING:30 TRAILING:30) (Bolger, Lohse and Usadel, 2014). Trimmed reads were aligned to the Mus Musculus mm10 genome assembly using Bowtie2 (version 2.3.4) (Salzberg, 2013). Unmapped reads were removed using SAMtools (version 1.9) (Li et al., 2009), and those with 3 mismatches or more were filtered out using Perlcode. BAM coverage files (BigWig) were generated using deeptools2 bamCoverage function (version 3.2.1, parameters: -of bigwig -bs 25 -p 20 --normalizeUsing RPKM -e 160 --ignoreForNormalization chrX) (Ramírez et al., 2016).
Assembly: mm10
Supplementary files format and content: bigwig coverage files

source_name: Sperm

extract_protocol:
For sperm isolation, spermatozoa were collected from paired caudal epididymides as previously described (Hisano et al., 2013). ChIP-sequencing was performed using a previously described protocol (Hisano et al., 2013, Lismer et al., 2021). Sperm from 2-7 animals were pooled for a total of 12 million spermatozoa used per sample. Samples were thawed on ice and washed with PBS. Dithiothreitol (1M) was used to decondense the chromatin and N-ethylmaleimide  to quench the reaction. Cells were lysed and aliquoted into 6 tubes and 15 units of MNase enzyme were added in each tube for 5 minutes, and the reaction was stopped with EDTA. Samples were centrifuged and the supernatants of aliquots from each sample pooled back together. Pre-clearing of the chromatin was done for 1 hour and immunoprecipitation of the chromatin was performed for 8 hours with 5 µg of antibody targeting histone H3 lysine 4 trimethylation (H3K4me3). Samples were subjected to a 3-step wash, the chromatin eluted and then treated with RNase A followed by Proteinase K. DNA was extracted and purified using the ChIP DNA Clean and Concentrator kit (Zymo Research) using the manufacturer’s protocol.
Libraries were prepared for illumina sequencing, and samples were sequenced on the illumina HiSeq2500 platform with 100 bp single-end reads.

value: Sperm

tag: age

value: 5 months

value: male

value: high-fat diet

tag: chip antibody

value: anti-H3K4me3, Cell Signaling Technology, cat#9751


title: HFD sperm H3K4me3 rep 2


title: CD sperm H3K4me3 rep 3

value: control diet


title: CD sperm H3K4me3 rep 1


title: KYSE-30 METTL3 CUT&Tag rep2


title: KYSE-30 shMETTL3 Pol II CUT&Tag rep2


title: HFD sperm H3K4me3 rep 1


title: 16026X1_Sg Cxcl1 12dpi

city: Salt Lake City

first: Amber

last: Syage

state: Utah

address: 2000 Circle of Hope

department: Pathology

institute: University of Utah

description: 10x Genomics, 5'

library_source: transcriptomic single cell

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 2.2.0 to create I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-1.2.0 reference from 10X Genomics.
Barcodes and UMIs were counted using cellranger count with expected-cells=6,000
mm10
Assembly: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: Brain

extract_protocol: Tissue was extracted from isofluorine euthanized mice after saline cardiac perfusion. Single cell suspensions were generated from tissue samples by grinding with frosted microscope slides. Immune cells were then enriched via a 2-step Percoll cushion (90% and 63%) and cells were collected at the interface of the two Percoll layers. These cells were then FACS sorted for CD45+DAPI- using CD45-APC conjugated Flow antibodies.

value: CD45+ cells

value: Brain

value: rtTA-GFAP Single Tg

value: 6-8 weeks old


title: 16026X2_Dg Cxcl1 12dpi

description: 10x Genomics, 5'

value: pBI-CXCL1-rtTA DoubleTg


title: KYSE-30 WT Pol II CUT&Tag rep2


title: HF male placenta RNA rep 4


title: HF female placenta RNA rep 3


title: KYSE-30 shMETTL3 Pol II CUT&Tag rep1


title: MI+CIH6

city: beijing

first: hui

middle: yun

last: du

state: beijing

address: 2 Anzhen Rd, Chaoyang District, Beijing

department: the Beijing Institute of Heart, Lung, and Blood Vessel Diseases

institute: Beijing Anzhen Hospital, Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
miRmiRNA expression levels were estimated by TPM ( transcript per million million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped read count/Total  reads*1000000
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited csv files include TPM values for each Sample

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Multiplex Small RNA Library Prep Set for Illumina was used with 3 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart


title: CON male placenta RNA rep 4

value: paternal control diet


title: MI+CIH4


title: KYSE-30 WT Pol II CUT&Tag rep1

value: wild type


title: MI+CIH3


title: KYSE-30 shFXR1 TET1 CUT&Tag rep2


title: CON female placenta RNA rep 4

value: Placenta

value: female


title: KYSE-30 METTL3 CUT&Tag rep1


title: CD sperm H3K4me3 rep 2


title: KYSE-30 shControl Pol II CUT&Tag rep2

value: Control


title: MI+CIH7


title: HF male placenta RNA rep 3

value: paternal high-fat diet


title: MI+CIH1


title: KYSE-30 shFXR1 TET1 CUT&Tag rep1


title: MI+CIH5


title: KYSE-30 WT TET1 CUT&Tag rep2


title: CON female placenta RNA rep 3


title: CIH4


title: HF male placenta RNA rep 2


title: KYSE-30 WT TET1 CUT&Tag rep1


title: seed, WT, salt stress, rep2

city: nanjing

first: Jiajun

last: Liu

address: Weigang no.1, Xuanwu District, Nanjing City, Jiangsu Province

institute: Nanjing Agricultural University

data_processing:
The low-quality reads in the raw data were removed by the useful Perl script: (1) Trim Smart-seq2 public primer sequence from the Reads; (2) Remove the contaminated reads for adapters; (3) Remove the low quality reads; (4) Remove the reads whose N base more than 5% for total bases
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa

source_name: seed

extract_protocol:
RNA was harvested using pBIOZOL Plant Total RNA Extraction Reagent (BSC55M1). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA   Library Prep Kit for Illumina® (#E7530L, NEB, USA) following manufacturer's protocols.

treatment_protocol: Before germination, the seeds were disinfected with 70% ethanol for 1 min and shaken with 1% sodium hypochlorite for 30 min. The seeds were washed with sterile water for five times and placed on plates (9 cm diameter) containing three layers of filter paper. Each plate was supplied with 20 mL of water or 300 mM NaCl stress, which were replaced every 24 h. The plates were placed in a chamber under a 15 h light/9 h dark cycle at 28 °C.

value: seed

value: WT

tag: stress

value: salt


title: CIH3


title: seed, WT, salt stress, rep3


title: seed, WT, water control, rep3

value: water control


title: CON male placenta RNA rep 3

value: male


title: HF male placenta RNA rep 1


title: seed, WT, salt stress, rep1


title: CIH2


title: HF female placenta RNA rep 2


title: seed, WT, water control, rep2


title: PC9-H-2

city: Shenzhen

first: huibin

last: song

address: No.1017, Dongmen North Road, Luohu District

institute: Shenzhen People's Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence or hight N ratio reads, then mapped to mm8 whole genome using  STAR  (v2.5.1b) with the method of Maximal Mappable Prefix(MMP).
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: lung

growth_protocol: PC9 cells (3×10 5 cells/well) were cultured in a 6-cm dish in the presence of epigambogic acid A (0, 0.5, 0.75, and 1 μM) at 37℃, 5% CO2.

extract_protocol:
Total RNA was isolated from PC9 cells using Trizol Reagent (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA)
Libraries were generated using the NEBNext UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) for the Illumina system by following the manufacturer’s instructions. Sequencing was conducted using the Illumina NovaSeq 6000 platform.

treatment_protocol: One replicate was 0.5 μmol epigambogic acid A treated for 72 hours;One replicate was 0.75 μmol epigambogic acid A treated for 72 hours;One replicate was 1 μmol epigambogic acid A treated for 72 hours;

value: PC9 cells

value: epithelial-derived PC9 cells

value: lung

tag: disease state

value: adenocarcinoma

value: treated with 1 μmol epigambogic acid A for 72 h


title: PC9-H-3


title: MI4

value: Heart


title: CIH1


title: PC9-H-1


title: MI+CIH2


title: seed, osmft1, salt stress, rep3

value: OsMFT1 knockout


title: CON male placenta RNA rep 2

value: paternal control diet


title: CON female placenta RNA rep 2

value: Placenta


title: PC9-M-3

value: treated with 0.75 μmol epigambogic acid A for 72 h


title: MI3


title: seed, osmft1, salt stress, rep2


title: MI2


title: PC9-L-3

value: treated with 0.5 μmol epigambogic acid A for 72 h


title: HF female placenta RNA rep 1

value: female

value: paternal high-fat diet


title: PC9-M-1


title: sham5


title: seed, osmft1, water control, rep3

value: seed


title: MI1


title: CON male placenta RNA rep 1


title: seed, osmft1, salt stress, rep1

value: salt


title: seed, osmft1, water control, rep2

value: water control


title: PC9-L-2


title: sham4


title: PC9-L-1


title: seed, WT, water control, rep1

value: WT


title: PC9-3

value: PC9 cells

value: untreated


title: HFD-WT3

city: Nanjing

first: Zechuan

last: Zhang

address: Zhongshan Road

institute: Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HISAT2.01 mapping to reference genome
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: liver

extract_protocol:
Hepatocytes RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hepatocyte

value: liver

value: HFD for 26weeks

value: wild type


title: HFD-ARRB1-KO2


title: HFD-ARRB1-KO3


title: sham2

value: Heart


title: sample3_WT-CD45

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Reads were aligned against the mouse genome (mm10) and counted by StarSolo.
Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 21 cells in total that did not express between 300 and 10000 genes or had an mitochondrial content less than 20%. Further, we filtered genes if they were detected in less than 30 cells (<0.3%).
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: mm10
Supplementary files format and content: starsolo outputs

organism: Mus

source_name: Lung

extract_protocol:
LLC1 or KRasLA2 tumor bearing mice CD45 cell isolation. Briefly, lungs were minced into small pieces and treated with Collagenase 5% and DNAase 1% containing buffer for 30 min at 37°C. Afterwards cells were passed through a 100µM cell strainer followed by 40µm nylon mesh. After a 10 min centrifugation step at 500 x g, cells were incubated in 2ml Erylysis buffer for red blood cell removal. After 4 min incubation time, lysis was stopped by adding 23 ml PBS. Cells were resuspended in PBS and FACS sorted for CD45 cells using an AriaIII-sorter and 7-AAD as indicator for dead cells.
After sorting the cell suspensions were counted with MOX Z cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics). Single cell RNAseq library preparation was done using standard protocol.

value: Lung

tag: strain background

value: CD45 positive


title: seed, osmft1, water control, rep1

value: OsMFT1 knockout


title: HFD-ARRB1-KO1


title: CON female placenta RNA rep 1

value: Placenta

value: paternal control diet


title: sham3


title: HFD-WT2


title: PC9-2

value: epithelial-derived PC9 cells

value: lung

value: adenocarcinoma


title: PC9-M-2

value: treated with 0.75 μmol epigambogic acid A for 72 h


title: sample2_LLC1

value: LLC1 tumor bearing


title: sham1


title: PC9-1

value: PC9 cells


title: HFD-WT1


title: U2OS VC - rep 3

status: Public on Sep 08 2022

city: Frankfurt am Main

first: Astrid

middle: Stefanie

last: Kahnt

address: Max-von-Laue-Straße 9

department: Institute of Pharmaceutical Chemistry

institute: Goethe University

description: NextSeq 2000 SE50

data_processing:
Base calling was automatically performed by RTA3 on NextSeq 2000
FASTQ generation was automatically performed by FASTQ generator v 1.0.0 via BaseSpace (Illumina)
Sequenced reads were trimmed (adapter & poly(A)reads) and filtered for low-quality, annotiation against GRCh38 using STAR
Differential expression analysis (WT vs. KO and KO vs. KI) was performed using DESeq2 included in Bluebee (Lexogen) with p ≤ 0.05 and an log2(foldchange) > 1
Differentially expressed genes were merged with the corresponding 5-LO KO single cell clone(s)
Genome_build: hg38
Supplementary_files_format_and_content: Normalized data matrices containing normalized abundance data

growth_protocol: HT-29 were kept in McCoy’s5A medium supplemented with 10% FBS, 1% sodium pyruvate and 1% penicillin/streptomycin.  HCT-116 and U-2OS were cultured in DMEM supplemented with 10% FBS, 1% sodium pyruvate and 1% penicillin/streptomycin concentrate. All three cell lines were cultured at 37°C, 5% CO2 in a humidified atmosphere.

extract_protocol:
Total mRNA was isolated from 5*106 cells per cell line using the RNA Plus Mini Kit (QIAGEN GmbH, Hilden, Deutschland)
The library preparation was performed with the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH, Vienna, Austria) to generate an Illumina compatible library of sequences close to the 3’ end of polyadenylated RNA, according to the manufacturers’ protocols.

value: empty vector control


title: sample1_Kras LA2

value: KRasLA2 tumor bearing


title: U2OS 5-LO KO C4 - rep 2

description: NextSeq 2000 SE50

value: 5-LO KO clone C4


title: U2OS 5-LO KO H5 - rep 3

description: NextSeq 2000 SE50

value: 5-LO KO clone H5


title: U2OS 5-LO KO H5 - rep 1

description: NextSeq 2000 SE50


title: U2OS 5-LO KO H5 - rep 2

description: NextSeq 2000 SE50


title: U2OS VC - rep 2

description: NextSeq 2000 SE50


title: U2OS 5-LO KO C4 - rep 1

description: NextSeq 2000 SE50


title: U2OS 5-LO KO C4 - rep 3

description: NextSeq 2000 SE50


title: U2OS VC - rep 1

description: NextSeq 2000 SE50


title: HT-29 5-LO KO G6 - rep 3

description: NextSeq 2000 SE50

value: 5-LO KO clone G6


title: U2OS WT - rep 1

description: NextSeq 2000 SE50

value: wild type


title: U2OS WT - rep 2

description: NextSeq 2000 SE50


title: HT-29 5-LO KO F4 - rep 2

description: NextSeq 2000 SE50

value: 5-LO KO clone F4


title: U2OS WT - rep 3

description: NextSeq 2000 SE50


title: HT-29 5-LO KO G6 - rep 2

description: NextSeq 2000 SE50


title: HT-29 5-LO KO G6 - rep 1

description: NextSeq 2000 SE50


title: HT-29 5-LO KO A2 - rep 2

description: NextSeq 2000 SE50

value: 5-LO KO clone A2


title: HT-29 5-LO KO F4 - rep 3

description: NextSeq 2000 SE50


title: HT-29 5-LO KO F4 - rep 1

description: NextSeq 2000 SE50


title: HT-29 5-LO KO A2 - rep 1

description: NextSeq 2000 SE50


title: HT-29 VC - rep 3

description: NextSeq 2000 SE50


title: HT-29 VC - rep 2

description: NextSeq 2000 SE50


title: HT-29 VC - rep 1

description: NextSeq 2000 SE50


title: HT-29 WT - rep 3

description: NextSeq 2000 SE50


title: HT-29 WT - rep 2

description: NextSeq 2000 SE50


title: HCT-116 5-LO KO H11 - rep 3

description: NextSeq 2000 SE50

value: 5-LO KO clone H11


title: HT-29 5-LO KO A2 - rep 3

description: NextSeq 2000 SE50


title: HCT-116 5-LO KO H11 - rep 2

description: NextSeq 2000 SE50


title: HCT-116 5-LO KO H11 - rep 1

description: NextSeq 2000 SE50


title: HCT-116 5-LO KO G6 - rep 2

description: NextSeq 2000 SE50


title: HCT-116 5-LO KO G6 - rep 1

description: NextSeq 2000 SE50


title: HCT-116 5-LO KO F5 - rep 3

description: NextSeq 2000 SE50

value: 5-LO KO clone F5


title: HCT-116 5-LO KO F5 - rep 2

description: NextSeq 2000 SE50


title: HCT-116 VC - rep 3

description: NextSeq 2000 SE50


title: HCT-116 WT - rep 3

description: NextSeq 2000 SE50


title: HCT-116 5-LO KO F5 - rep 1

description: NextSeq 2000 SE50


title: HCT-116 VC - rep 2

description: NextSeq 2000 SE50


title: HCT-116 WT - rep 2

description: NextSeq 2000 SE50


title: HCT-116 WT - rep 1

description: NextSeq 2000 SE50


title: HT-29 WT - rep 1

description: NextSeq 2000 SE50


title: Rosette leaves, High light VPZ#4 6 h replicate 2

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

country: Spain

institute: Centre for Research in Agrigenomics

data_processing:
Illumina sequencing reads were generated by Novogene Biotech (Beijing, China).
Reads were treated with Trimmomatic to remove adapter sequences, aligned to the Araport11 genome reference with Tophat 2.1.1 and the counts and differential expression files generated with featureCounts/DESeq2.
Genome_build: Araport11
Supplementary_files_format_and_content: Excel spread sheet including normalised counts provided according to featureCounts.

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: Arabidopsis thaliana Col-0 and two VPZ lines (#2 and #4) seeds were stratified at 4ºC for 2 days, sown in 9x9 cm pots and cultivated under standard intermediate day conditions [12 h light (125 µmol photons·m-2·s-1) at 22ºC and 12 h darkness at 18ºC].

extract_protocol:
Total RNA from plants was isolated using Trizol and purified using the Direct-zol RNA MiniPrep Plus columns (Zymo Research) according to the manufacturer’s instructions.
Generation of mRNA (mRNA-Seq) libraries and sequencing using the paired-end mode were conducted at Novogene Biotech (Beijing, China) with standard Illumina protocols. Libraries were sequenced on an Illumina HiSeq 2500 system.
RNA-Seq for First Read unstranded libraries

treatment_protocol: After 21 days of growth under standard conditions in intermediate day, WT plants and VPZ lines #2 and #4 were exposed to fluctuating light conditions (12h at 23°C and cycles of alternative cycles of  50 µmol photons·m-2·s-1 for 5 min and 500 µmol photons·m-2·s-1  for 1 min  / 12h dark at 18 °C ) or under hight light (diurnal light at 500 µmol photons·m-2·s-1). Sampling was carried out at 0 h, 6 h and 30 h by fast harvesting in liquid nitrogen. Transcriptome profiles for Col0 and VPZ lines in each time point and condition were compared to the corresponding sample before treatments.

tag: ecotype

tag: Stage

value: 22-d-old plants

tag: line

value: high light 6 h

value: rosette leaves


title: Rosette leaves, Fluctuating light VPZ#4 30 h replicate 1

value: fluctuating light 30 h


title: Rosette leaves, Fluctuating light VPZ#4 30 h replicate 2


title: Rosette leaves, High light VPZ#4 30 h replicate 3

value: high light 30 h


title: Rosette leaves, High light VPZ#4 6 h replicate 1


title: Rosette leaves, Fluctuating light VPZ#4 30 h replicate 3


title: Rosette leaves, High light VPZ#4 6 h replicate 3


title: HCT-116 5-LO KO G6 - rep 3

description: NextSeq 2000 SE50

tag: genotype


title: Rosette leaves, Fluctuating light VPZ#4 6 h replicate 1

tag: treatment

value: fluctuating light 6 h


title: Rosette leaves, High light VPZ#4 30 h replicate 1


title: Rosette leaves, Fluctuating light VPZ#4 6 h replicate 2


title: Rosette leaves, High light VPZ#4 30 h replicate 2


title: Rosette leaves, Fluctuating light VPZ#4 6 h replicate 3


title: Rosette leaves, Control VPZ#4 30 h replicate 2

value: control 30 h


title: Rosette leaves, Control VPZ#4 30 h replicate 1


title: Rosette leaves, Control VPZ#4 30 h replicate 3


title: HCT-116 VC - rep 1

description: NextSeq 2000 SE50

value: empty vector control


title: Rosette leaves, Control VPZ#4 6 h replicate 3

value: control 6 h


title: Rosette leaves, Control VPZ#4 6 h replicate 2


title: Rosette leaves, Control VPZ#4 0 h replicate 2

value: control 0 h


title: Rosette leaves, Control VPZ#4 6 h replicate 1


title: Rosette leaves, Control VPZ#4 0 h replicate 1


title: Rosette leaves, Control VPZ#4 0 h replicate 3


title: Rosette leaves, High light VPZ#2 30 h replicate 3


title: Rosette leaves, High light VPZ#2 6 h replicate 2


title: Rosette leaves, High light VPZ#2 6 h replicate 1


title: Rosette leaves, High light VPZ#2 30 h replicate 1


title: Rosette leaves, High light VPZ#2 30 h replicate 2


title: Rosette leaves, High light VPZ#2 6 h replicate 3


title: Rosette leaves, Fluctuating light VPZ#2 30 h replicate 3


title: Rosette leaves, Fluctuating light VPZ#2 30 h replicate 1


title: Rosette leaves, Control VPZ#2 30 h replicate 1


title: Rosette leaves, Fluctuating light VPZ#2 6 h replicate 2


title: Rosette leaves, Control VPZ#2 30 h replicate 3


title: Rosette leaves, Control VPZ#2 6 h replicate 3


title: Rosette leaves, Fluctuating light VPZ#2 6 h replicate 3


title: Rosette leaves, Fluctuating light VPZ#2 30 h replicate 2


title: Rosette leaves, Control VPZ#2 30 h replicate 2


title: Rosette leaves, Control VPZ#2 6 h replicate 1


title: Rosette leaves, Fluctuating light VPZ#2 6 h replicate 1


title: Rosette leaves, High light WT 30 h replicate 1

value: WT


title: Rosette leaves, Control VPZ#2 0 h replicate 2


title: Rosette leaves, Fluctuating light WT 30 h replicate 2


title: Rosette leaves, High light WT 30 h replicate 2


title: Rosette leaves, Control VPZ#2 0 h replicate 3


title: Rosette leaves, High light WT 6 h replicate 1


title: Rosette leaves, Control VPZ#2 0 h replicate 1


title: Rosette leaves, Control VPZ#2 6 h replicate 2


title: Rosette leaves, Fluctuating light WT 6 h replicate 3


title: Rosette leaves, Fluctuating light WT 6 h replicate 1


title: Rosette leaves, Control WT 30 h replicate 3


title: Rosette leaves, High light WT 30 h replicate 3


title: Rosette leaves, Fluctuating light WT 30 h replicate 3


title: Rosette leaves, Control WT 30 h replicate 1


title: Rosette leaves, Fluctuating light WT 30 h replicate 1


title: Rosette leaves, High light WT 6 h replicate 2


title: Rosette leaves, Fluctuating light WT 6 h replicate 2


title: Rosette leaves, Control WT 30 h replicate 2


title: Rosette leaves, Control WT 6 h replicate 3


title: Rosette leaves, Control WT 6 h replicate 1


title: Rosette leaves, Control WT 6 h replicate 2


title: Rosette leaves, Control WT 0 h replicate 2


title: Rosette leaves, Control WT 0 h replicate 1


title: Rosette leaves, High light WT 6 h replicate 3


title: Rosette leaves, Control WT 0 h replicate 3


title: KTPB14_IGO_11254_11_S11

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: Pancreas tumor

growth_protocol: Mice undergo a survival surgery where the pancreas is exposed and 100.000 cells of the different genotypes are injected. Mice are then monitored and when they have overt disease assessed by palpation (~4 weeks after injection), the tumors are collected and a piece is flash frozen for total RNA extraction.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Mice were pre-treated with either IgG or anti-IFNAR1 antibodies (200 ug i.p. 3 times a week) starting one week before injection of cells and kept until the end of the experiment.

value: Pancreas tumor

value: Whole tissue

value: IgG antibody

value: KrasG12D; sgP53; dL


title: KTPB20_IGO_11254_16_S16

value: IFNAR1 antibody


title: KTPB17_IGO_11254_13_S13


title: KTPB18_IGO_11254_14_S14


title: KTPB15_IGO_11254_12_S12


title: KTPB12_IGO_11254_10_S10


title: KTPB06_IGO_11254_6_S6

value: KrasG12D; sgP53; dS


title: KTPB08_IGO_11254_8_S8


title: KTPB05_IGO_11254_5_S5


title: KTPB03_IGO_11254_3_S3


title: KTPB04_IGO_11254_4_S4


title: KTPB01_IGO_11254_1_S1


title: OGT-KO macrophages, 24h

city: shang hai

first: Qian

address: xiangyin road 800

institute: Second military medical university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed using StringTie
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BMDM

growth_protocol: Bone marrow cells were induced by recombinant mouse M-CSF (20 ng/ml, PEPROTECH) in complete RPMI 1640 medium (Gibco) containing 2mM L-glutamine, 10mM glucose, 100 U/ml of penicillin/streptomycin, and 10% FBS for 7 days.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 20ng/mL IL-4 was used for M2 polarization of BMDMs for 24h.

tag: cell type

value: BMDM

value: OGT knockout

value: IL-4 stimulation

value: 24 hour


title: Wild-type macrophages, 24h

tag: time


title: Wild-type macrophages, 0h

value: 0 hour


title: KTPB19_IGO_11254_15_S15


title: i21-CFZ-18-t24-r2

city: Oxford

first: Adam

last: Cribbs

state: Oxfordshire

address: Botnar Research Centre

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Pseudoalignment. Kallisto. Version >=0.43.0. Parameters k-mer k = 31,
Genome_build: hg19
Supplementary_files_format_and_content: genes.tsv.gz- a compressed tsv file. A gene-count matrix with columns for samples and rows for genes. The values represent the gene abundance count for the given sample

source_name: Myeloma cell line

extract_protocol:
Approximately 300,000 cells were harvested for each sample for RNA extraction. Cells were centrifuged for 5 minutes at 1500rpm, the supernatant was removed, and the cell pellets were resuspended in 300ul of Trizol. 6-hour samples were stored at -80C overnight and 24 hour samples were kept on ice, prior to RNA extraction. RNA was extracted using Direct-zol RNA Miniprep kits (Zymo Research, USA), following the manufacturer’s instructions. RNA was quantified using a NanoDropTM 2000 spectrophotometer and standardised to 100ng of RNA in 50ul of nuclease free water.
Library prep was performed using Nebnext Ultra II directional RNA library prep kit for Illumina with Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA), following the manufacturer’s instructions

treatment_protocol: AMO-1 cells and CFZr L363 cells at a confluence of 1x10^6/ml were treated with 1microM of NCP22, NCP26, MAZ1392 (halofuginone) and MAZ1805 (halofuginol), or DMSO-treated controls, for 6 and 24 hours. All conditions were performed in triplicate.

tag: cell line

value: CFZr L363

value: Halofuginol


title: i22-CFZ-18-t24-r3


title: i19-CFZ-13-t24-r3

value: Halofuginone


title: i15-CFZ-22-t24-r2


title: i17-CFZ-13-t24-r1


title: i18-CFZ-13-t24-r2


title: KTPB11_IGO_11254_9_S9


title: i13-CFZ-26-t24-r3


title: KTPB02_IGO_11254_2_S2


title: i12-CFZ-26-t24-r2


title: Patient 10034 dam

city: Cambrdige

first: Yunyu

state: MA

address: 22 Windsor Ave

institute: Novartis Institute for Biomedical Research

description:
norm_counts.txt
raw_counts.txt
10034_dam

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ENSEBML Human Genome 76 reference transcriptome (http://ftp.ensembl.org/pub/grch37/release-76/) using the BOWTIE2 aligner (Langmead 2012).
Gene counts were calculated using HTseq (Anders 2015) and summerized as counts based GRh38 Refseq genes.
Normalization on library size was performed using calcNormFactors.DGEList from edgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.txt, norm_counts.txt

source_name: knee cartilage

extract_protocol:
Total RNA was extracted from knee cartilage of consented subjects and quality-controlled in the experiment. RNA quality was evaluated with Agilent 2100 Bioanalyzer System using Eukaryote Total RNA Pico chips.
The sequencing libraries were prepared following the Pico Input Mammalian protocol of the Clontech SMARTer Stranded Total RNA-Seq Kit v2. When possible, 250 pg of RNA per sample were used as input for the sequencing library preparation. In the case of limited amount of material, the highest possible amount of the sample was used for the sequencing library preparation Libraries were clustered in a high-output flow cell using HiSeq PE (paired-end) Cluster Kit v4 on a cBot (Illumina).
After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using HiSeq SBS kit v4 (Illumina). DNA was sequenced from both ends (paired-end) with a read length of 76 bp.

value: knee cartilage

tag: patient id

value: 69 years

value: female

tag: pathology

value: damaged

value: placebo

tag: treatment time

tag: rna library size

tag: rna library complexity


title: KTPB07_IGO_11254_7_S7

tag: tissue

value: Pancreas tumor

value: Whole tissue


title: Patient 10034 undam

description:
norm_counts.txt
raw_counts.txt
10034_undam

tag: age

tag: Sex

value: undamaged


title: i09-CFZ-DMSO-t24-r2

value: DMSO


title: i08-CFZ-DMSO-t24-r1


title: i14-CFZ-22-t24-r1


title: i11-CFZ-26-t24-r1


title: OGT-KO macrophages, 0h

value: BMDM


title: i16-CFZ-22-t24-r3


title: i07-CFZ-18-t6-r3


title: Patient 10030 dam

description:
norm_counts.txt
raw_counts.txt
10030_dam

value: 66 years


title: i06-CFZ-18-t6-r2


title: Patient 10028 dam

description:
norm_counts.txt
raw_counts.txt
10028_dam

value: 62 years


title: Patient 10030 undam

description:
norm_counts.txt
raw_counts.txt
10030_undam


title: Patient 10029 undam

description:
norm_counts.txt
raw_counts.txt
10029_undam

value: 70 years


title: i20-CFZ-18-t24-r1


title: i04-CFZ-13-t6-r3


title: Patient 10029 dam

description:
norm_counts.txt
raw_counts.txt
10029_dam


title: i03-CFZ-13-t6-r2


title: i47-CFZ-22-t6-r1


title: Patient 10028 undam

description:
norm_counts.txt
raw_counts.txt
10028_undam


title: Patient 10026 dam

description:
norm_counts.txt
raw_counts.txt
10026_dam


title: i48-CFZ-22-t6-r2


title: Patient 10025 undam

description:
norm_counts.txt
raw_counts.txt
10025_undam

value: 60 years


title: i01-CFZ-22-t6-r3

value: CFZr L363


title: Patient 10026 undam

description:
norm_counts.txt
raw_counts.txt
10026_undam


title: i10-CFZ-DMSO-t24-r3


title: Patient 10023 undam

description:
norm_counts.txt
raw_counts.txt
10023_undam

value: 51 years


title: Patient 10025 dam

description:
norm_counts.txt
raw_counts.txt
10025_dam


title: i41-CFZ-DMSO-t6-r1


title: i05-CFZ-18-t6-r1

value: Halofuginol


title: i46-CFZ-26-t6-r3


title: i02-CFZ-13-t6-r1

value: Halofuginone


title: i45-CFZ-26-t6-2


title: i43-CFZ-DMSO-t6-r3


title: Patient 10023 dam

description:
norm_counts.txt
raw_counts.txt
10023_dam

value: knee cartilage


title: Patient 10022 undam

description:
norm_counts.txt
raw_counts.txt
10022_undam

value: 54 years

value: male


title: Patient 10024 undam

description:
norm_counts.txt
raw_counts.txt
10024_undam

value: 65 years


title: Patient 10022 dam

description:
norm_counts.txt
raw_counts.txt
10022_dam

value: damaged

value: placebo


title: i35-WT-18-t24-r2

value: AMO-1 WT


title: i42-CFZ-DMSO-t6-r2

value: DMSO


title: i34-WT-18-t24-r1


title: Patient 10019 dam

description:
norm_counts.txt
raw_counts.txt
10019_dam

value: female


title: Patient 10019 undam

description:
norm_counts.txt
raw_counts.txt
10019_undam

value: undamaged


title: Patient 10021 dam

description:
norm_counts.txt
raw_counts.txt
10021_dam

value: 74 years


title: Patient 10024 dam

description:
norm_counts.txt
raw_counts.txt
10024_dam


title: i32-WT-13-t24-r2


title: Patient 10018 undam

description:
norm_counts.txt
raw_counts.txt
10018_undam


title: i31-WT-13-t24-r1


title: i30-WT-22-t24-r3


title: i44-CFZ-26-t6-r1


title: i29-WT-22-t24-r2


title: Patient 10018 dam

description:
norm_counts.txt
raw_counts.txt
10018_dam


title: Patient 10017 undam

description:
norm_counts.txt
raw_counts.txt
10017_undam


title: i27-WT-26-t24-r3


title: Patient 10017 dam

description:
norm_counts.txt
raw_counts.txt
10017_dam


title: i36-WT-18-t24-r3


title: i26-WT-26-t24-r2


title: i25-WT-26-t24-r1


title: Patient 10011 dam

description:
norm_counts.txt
raw_counts.txt
10011_dam

value: 73 years


title: i28-WT-22-t24-r1


title: Patient 10008 dam

description:
norm_counts.txt
raw_counts.txt
10008_dam

value: 58 years


title: Patient 10011 undam

description:
norm_counts.txt
raw_counts.txt
10011_undam


title: Patient 10001 dam

description:
norm_counts.txt
raw_counts.txt
10001_dam

value: 59 years


title: Patient 10021 undam

description:
norm_counts.txt
raw_counts.txt
10021_undam


title: Patient 10008 undam

description:
norm_counts.txt
raw_counts.txt
10008_undam


title: i23-WT-carf-t24-r2

value: Carfilzomib


title: i24-WT-carf-t24-r3


title: i33-WT-13-t24-r3


title: i21-WT-DMSO-t24-r3


title: Patient 10001 undam

description:
norm_counts.txt
raw_counts.txt
10001_undam


title: i20-WT-DMSO-t24-r2


title: i22-WT-carf-t24-r1


title: normal colon

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq cellranger mkfastq (see characteristics for version)
Single-cell RNAseq data was produced using the 10x genomics platform. Data were processed using cellranger version 6.0.1 with alignment to a modified version of the GENCODE mouse genome (GRCm38), version M23 (Ensembl 98) target provided by 10x genomics. The modification was the addition of the GFP selectable marker. Cellranger filtered data was imported into R version 4.1.0 (R Core Team 2021) and analyzed with Seurat version 4.0.3 (Stuart et al. 2019).
Genome_build: mm10 with GENCODE M23
Supplementary_files_format_and_content: genes.gtf.gz is a gtf file describing mm10 GENCODE version M23 (Ensembl 98) plus GFP selectable marker
Supplementary_files_format_and_content: genome.fa.gz is the mm10 assembly plus the GFP selectable marker
Supplementary_files_format_and_content: tar archive of filtered_feature_bc_matrix

source_name: Rspondin 3-GFP positive cells sorted from colon

growth_protocol: 8-12 week C57Bl6 background

extract_protocol:
10x Genomics Single Cell 3' v3
scRNA-Seq

tag: strain

tag: cellranger mkfastq version

value: untreated

tag: gfp status

value: GFP Positive cells from Rspo3-GFP transgenic mice


title: control small intestine rep 2

source_name: Rspondin 3-GFP positive cells sorted from small intestine

value: unirradiated control mice


title: i18-WT-18-t6-r3

value: Halofuginol


title: radiation-treated small intestine rep 2

value: 12 Gy irradiated mice

value: Rspondin 3-GFP positive cells sorted from small intestine


title: radiation-treated small intestine rep 1


title: normal small intestine rep 2


title: i19-WT-DMSO-t24-r1


title: control small intestine rep 1


title: i16-WT-18-t6-r1


title: i13-WT-13-t6-r1

value: Halofuginone


title: i14-WT-13-t6-r2


title: SG511-02 [QOBWO071A8]

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

data_processing:
Alignment: HISAT2, version  , parameters --no-spliced-alignment --rna-strandness R
Counting: featureCounts, version 1.6.4, parameters -s 2 -t transcript -g locus_tag
Assembly: NZ_CP076660.1
Supplementary files format and content: counts.txt: A tab separated matrix with samples as columns and genes as rows

organism: Staphylococcus aureus

source_name: lab grown bacteria

growth_protocol: S. aureus cultures  were grown in TSB at 37 °C with shaking until an OD600 of 1.0 was reached.

extract_protocol:
RNA was extracted using the Monarch™ Total RNA Miniprep Kit (New England Biolabs) following the manufacturer’s instructions and stored at −80 °C. Quality and quantity of total RNA were determined by agarose gel electrophoresis.
Per replicate, a total amount of 400 ng RNA was subjected to rRNA depletion. For rRNA depletion and cDNA library construction the IlluminaTM Stranded Total RNA Prep Ligation with Ribo Zero Plus Kit was used according to the manufacturer’s instructions. Libraries were sequenced as single-read (101 bp read length) on a NovaSeq 6000 platform (Illumina)

treatment_protocol: 20 mL culture were harvested (5 min, 8,000 x g, RT), the cells were resuspended in 1 mL RNA protect buffer (New England Biolabs, Frankfurt am Main, Germany) and incubated for 5 min at RT. The cells were resuspended in 200 µL TE buffer with 25 µg lysostaphin and cell lysis was achieved by incubation at 37 °C for 30 min.

tag: genotype/phenotype

value: control


title: SG511-03 [QOBWO072AG]


title: i12-WT-22-t6-r3

value: AMO-1 WT


title: i08-WT-26-t6-r2


title: SG511-01 [QOBWO070A0]


title: SG511-CMR-02-03 [QOBWO027AL]

value: Cervimycin resistent 2


title: i15-WT-13-t6-r3


title: normal small intestine rep 1


title: i11-WT-22-t6-r2


title: SG511-02REV-03 [QOBWO030A6]

value: Cervimycin resistent 2, suppressor mutant


title: SG511-02REV-02 [QOBWO029A3]


title: SG511-CMR-02-02 [QOBWO026AD]


title: SG511-CMR-02-01 [QOBWO025A5]


title: i10-WT-22-t6-r1


title: i09-WT-26-t6-r3


title: SG511-02REV-01 [QOBWO028AT]


title: i01-WT-DMSO-t6-r1

value: DMSO


title: i06-WT-carf-t6-r3


title: i07-WT-26-t6-r1


title: i17-WT-18-t6-r2


title: i05-WT-carf-t6-r2


title: DOX_MG132_4sUSeq_R2

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads or CUT&RUN rerads were aligned with Bowtie2 to hg19 and to mm10 or e.coli for the spike-in
human reads were normalized to the number of spike-in reads
For 4sU Seq, only intron spanning reads were considered and read normalized before analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: osteosarcoma cell line

growth_protocol: RNA-Seq

extract_protocol:
treat with DMSO, MG-132, Aphidicolin or hydroxyurea
Mnase digestion for 30 min
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: U2OS Myc TetON in DMEM with 5% FCS

value: U2OS Myc TetON

value: MG132 20 microM, 5H

value: Doxycycline (1 microg/ml), 9H

value: 4sU 2 mM (15min)

tag: chip antibody

tag: label


title: DOX_MG132_4sUSeq_R3

tag: treatment


title: i02-WT-DMSO-t6-r2

tag: time


title: i04-WT-carf-t6-r1

tag: cell line

value: Carfilzomib


title: ETOH_MG132_4sUSeq_R3


title: DOX_DMSO_4sUSeq_R3


title: ETOH_MG132_4sUSeq_R1


title: i03-WT-DMSO-t6-r3


title: DOX_MG132_4sUSeq_R1


title: DOX_DMSO_4sUSeq_R1


title: ETOH_MG132_4sUSeq_R2


title: ETOH_DMSO_4sUSeq_R3


title: CNTO148UCO2001-100168 colon biopsy week 0

type: RNA

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 10.

label: biotin

source_name: colon biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

value: colon

tag: donor id

tag: visit

value: week 0

tag: diagnosis

value: ulcerative colitis

value: golimumab 200mg

tag: mucosal healing at week 6

value: Y

tag: clinical remission at week 6

value: N


title: CNTO148UCO2001-100154 colon biopsy week 0

tag: tissue


title: CNTO148UCO2001-100164 colon biopsy week 0


title: CNTO148UCO2001-100158 colon biopsy week 0


title: CNTO148UCO2001-100163 colon biopsy week 0


title: DOX_DMSO_4sUSeq_R2


title: CNTO148UCO2001-100152 colon biopsy week 0


title: CNTO148UCO2001-100162 colon biopsy week 0


title: Hippocampus_P-group_5

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

hyb_protocol: cRNA 15µg were flagmentated, and hybridized for 16hr at 45 on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized using the statistical software R, and the qFARMS method.

organism: Rattus norvegicus

source_name: Hippocampus_powder diet

label_protocol: Biotin-labeled cRNA was synthesized from 100ng total RNA according to the manufacture's protocol.

growth_protocol: Rats were housed under controlled conditions at a temperature of 20–26°C and humidity of 40–60% under a 12/12-h light-dark cycle, with ad libitum feed and water intake.

extract_protocol: Total RNA was extracted from the hippocampul sample using TRIzol Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol. The extracted total RNA was cleaned up with RNeasy Mini Kit (QIAGEN).

treatment_protocol: Rats were administered powdered or solid feed for 8 days.

tag: gender

value: male

tag: age

value: 4 weeks old

tag: diet

value: powder chow


title: Hippocampus_P-group_4


title: CNTO148UCO2001-100160 colon biopsy week 0


title: Hippocampus_C-group_5

source_name: Hippocampus_chow diet

value: solid chow


title: ETOH_DMSO_4sUSeq_R2


title: CNTO148UCO2001-100167 colon biopsy week 0


title: CNTO148UCO2001-100134 colon biopsy week 0


title: CNTO148UCO2001-100161 colon biopsy week 0


title: CNTO148UCO2001-100150 colon biopsy week 0


title: Colonic stromal cells Rspo3-GFP negative rep 2

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
1784.colon.GFP.m.D20.142009

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Transcripts were quantified using Salmon version 1.1.0 (Patro et al. 2017) and the mm10 mouse assembly with the Ensembl version 98 transcriptome.  Gene level summaries were prepared using tximport version 1.12.1 (Soneson, Love, and Robinson 2015) running under R version 3.6.1 (R Core Team 2021).
Genome_build: mm10 with ensembl version 98 annotation
Supplementary_files_format_and_content: ngoto_200211YilA_IntCt.txt.gz tab is a delimited text file of integer count data
Supplementary_files_format_and_content: ngoto_200211YilA_l2tpm.txt.gz is a tab delimited text file of l2tpm data

source_name: Colonic stromal cells

extract_protocol:
Qiagen RNAeasy Kit
ZapR

tag: cell type

value: Colonic stromal cells

tag: strain

tag: rspo3-gfp transgene expression

value: negative


title: Hippocampus_C-group_2


title: Colonic stromal cells Rspo3-GFP positive rep 3

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
3672.colon.GFP.p.D20.142012

value: positive


title: CNTO148UCO2001-100146 colon biopsy week 0


title: Hippocampus_P-group_3


title: Colonic stromal cells Rspo3-GFP negative rep 3

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
3672.colon.GFP.m.D20.142011


title: ETOH_DMSO_4sUSeq_R1

value: U2OS Myc TetON

tag: chip antibody


title: Hippocampus_P-group_1


title: Hippocampus_C-group_4


title: FOXA1 KO UM-UC-1 cell clone 9 rep2

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

data_processing:
RSEM v1.3.1 (rsem-calculate-expression function w/ STAR aligning), GRCh38
DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated text file of genes x18 samples matrix

source_name: bladder carcinoma cell line

growth_protocol: Wild-type and FOXA1 KO UMUC-1 cells were cultured in Minimal Essential Medium supplemented with 10% fetal bovine serum. To establish UM-UC-1 FOXA1 knockout (KO), UM-UC-1 (2x105) cells were transfected with 2.5 mg of HNF-3alpha CRISPR/Cas9 KO plasmid (Santa Cruz, sc-400743) using lipofectamine3000 (Thermo fisher scientific). Three GFP-positive cells were sorted in a single well of 96-well plate containing 100 ml of medium by Aria II cell sorter (BD Biosciences). Sorted cells were expanded and knockout of FOXA1 in UM-UC-1 cells was confirmed by western blot analysis.

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen, Germantown, MD, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder carcinoma

tag: genotype

value: FOXA1 KO


title: FOXA1 KO UM-UC-1 cell clone 10 rep2


title: Small intestinal stromal cells Rspo3-GFP positive rep 3

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
3672.SI.GFP.p.D20.142006

source_name: Small intestinal stromal cells

value: Small intestinal stromal cells


title: CNTO148UCO2001-100151 colon biopsy week 0

value: colon

tag: treatment


title: CNTO148UCO2001-100139 colon biopsy week 0

value: week 0


title: Small intestinal stromal cells Rspo3-GFP negative rep 3

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
3672.SI.GFP.m.D20.142005


title: Hippocampus_P-group_2


title: Colonic stromal cells Rspo3-GFP positive rep 2

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
1784.colon.GFP.p.D20.142010


title: Hippocampus_C-group_1


title: CNTO148UCO2001-100131 colon biopsy week 0

value: ulcerative colitis


title: CNTO148UCO2001-100132 colon biopsy week 0

value: golimumab 200mg


title: Hippocampus_C-group_3


title: Small intestinal stromal cells Rspo3-GFP positive rep 1

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
SI.1.GFP.p.D20.142002


title: Colonic stromal cells Rspo3-GFP positive rep 1

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
colon.GFP.p.D20.142008


title: FOXA1 KO UM-UC-1 cell clone 9 rep1


title: CNTO148UCO2001-100121 colon biopsy week 0

value: Y


title: Small intestinal stromal cells Rspo3-GFP negative rep 2

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
SI.2.GFP.m.D20.142003


title: FOXA1 KO UM-UC-1 cell clone 10 rep1


title: parental UM-UC-1 cell rep1

value: parental


title: ChIPSEQ_Pooled_Input

description: chromatin

data_processing:
trim_blaore (v0.3.3)used to trim read adapt (0.4.1)
bowtie2 (v2.1.0) aligning to genome
Picard (v2.20)Markduplicates to remove duplicates
macs2 (v2.1.0) peak calling
DiffBind (v3.0.15, bioconductor/R package) used to identify the different peaks between genotypes
Genome_build: GRCh37 was used
Supplementary_files_format_and_content: peaks

extract_protocol:
Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated, and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended, and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 mg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 mg of antibody against H3K27ac (Active Motif, cat# 39133, Lot# 28518012). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on an Illumina NextSeq 500 (75 nt reads, single end).

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.

value: bladder urothelium

tag: disease state

value: bladder cancer

value: mixed (pooled)

value: none (input)


title: Colonic stromal cells Rspo3-GFP negative rep 1

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
colon.GFP.m.D20.142007

value: Colonic stromal cells


title: Small intestinal stromal cells Rspo3-GFP negative rep 1

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
SI.1.GFP.m.D20.142001

value: negative


title: Small intestinal stromal cells Rspo3-GFP positive rep 2

description:
ngoto_200211YilA_IntCt.txt.gz
ngoto_200211YilA_l2tpm.txt.gz
SI.2.GFP.p.D20.142004

value: positive


title: parental UM-UC-1 cell rep2

tag: cell line


title: ChIPSEQ_FOXA1KO_H3K27Ac_rep2

description: chromatin

source_name: UMUC1-FOXA1 KO

value: H3K27Ac Active Motif cat# 39133; lot number 28518014


title: ChIPSEQ_FOXA1KO_H3K27Ac_rep1

description: chromatin

source_name: UMUC-1 FOXA1 KO


title: ChIPSEQ_Ctrl_H3K27Ac_rep2

description: chromatin

value: WT


title: ChIPSEQ_Ctrl_H3K27Ac_rep1

description: chromatin


title: CNTO148UCO2001-100126 colon biopsy week 0

tag: donor id

value: N


title: CNTO148UCO2001-100120 colon biopsy week 0

tag: visit


title: CNTO148UCO2001-100123 colon biopsy week 0

tag: diagnosis


title: CNTO148UCO2001-100116 colon biopsy week 0

tag: mucosal healing at week 6


title: CNTO148UCO2001-100117 colon biopsy week 0

tag: clinical remission at week 6


title: CNTO148UCO2001-100119 colon biopsy week 0

tag: tissue


title: CNTO148UCO2001-100114 colon biopsy week 0


title: CNTO148UCO2001-100111 colon biopsy week 0


title: CNTO148UCO2001-100107 colon biopsy week 0


title: CNTO148UCO2001-100112 colon biopsy week 0


title: CNTO1275CRD3002-20675 rectum biopsy week 0

source_name: rectum biopsy

value: rectum

value: Crohn's disease

value: Ustekinumab 130 mg IV

tag: inflamed area at week 0

value: Colon only

tag: mucosal healing at week 8


title: CNTO148UCO2001-100105 colon biopsy week 0

value: colon

value: week 0

value: ulcerative colitis

value: golimumab 200mg


title: CNTO148UCO2001-100104 colon biopsy week 0


title: CNTO1275CRD3002-20358 rectum biopsy week 0

value: Placebo IV

value: Ileum and colon


title: CNTO1275CRD3002-20237 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (260 mg)


title: CNTO148UCO2001-100103 colon biopsy week 0


title: CNTO1275CRD3002-20404 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)


title: CNTO148UCO2001-100102 colon biopsy week 0

value: Y


title: CNTO1275CRD3002-20194 rectum biopsy week 0


title: CNTO148UCO2001-100100 colon biopsy week 0


title: CNTO1275CRD3002-20170 rectum biopsy week 0


title: CNTO1275CRD3002-20151 rectum biopsy week 0


title: CNTO148UCO2001-100099 colon biopsy week 0


title: CNTO1275CRD3002-21016 rectum biopsy week 0


title: CNTO148UCO2001-100097 colon biopsy week 0


title: genomic DNA from DLB brain tissue 6

type: genomic

city: Royal Oak

first: Stewart

middle: F.

last: Graham

state: MI

address: 3811 W.13 Mile Road

department: Obstetrics and Gynecology

institute: Oakland University William Beaumont School of Medicine

description: Post-mortem brain tissue from DLB patient

hyb_protocol: the DNA samples were bisulfite converted using EZ DNA Methylation-Direct Kit (Zymo Research, Orange, CA) according to manufacturer’s protocol. Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC using standard Illumina protocol

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

data_processing: The Illumina EPIC array raw intensity data was processed and analyzed using the methylation analysis R package Minfi (version 1.36.0).

label: Cy5 and Cy3

source_name: DLB brain tissue 6

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from the lyophilized and milled brain tissue using QIAamp DNA Mini Kit (Qiagen)

tag: gender

value: M

value: DLB

value: Brain


title: genomic DNA from DLB brain tissue 15

source_name: DLB brain tissue 15


title: CNTO148UCO2001-100095 colon biopsy week 0

value: N


title: genomic DNA from DLB brain tissue 8

source_name: DLB brain tissue 8

value: F


title: genomic DNA from DLB brain tissue 14

source_name: DLB brain tissue 14


title: genomic DNA from DLB brain tissue 4

source_name: DLB brain tissue 4


title: genomic DNA from DLB brain tissue 7

source_name: DLB brain tissue 7


title: genomic DNA from DLB brain tissue 12

source_name: DLB brain tissue 12


title: genomic DNA from DLB brain tissue 2

source_name: DLB brain tissue 2


title: CNTO1275CRD3002-21019 rectum biopsy week 0

value: rectum

value: Crohn's disease


title: genomic DNA from normal brain tissue 14

description: Post-mortem brain tissue from non-cognitively impaired controls

source_name: Normal brain tissue 14

value: Normal


title: CNTO1275CRD3002-21010 rectum biopsy week 0


title: genomic DNA from DLB brain tissue 13

source_name: DLB brain tissue 13


title: genomic DNA from DLB brain tissue 11

source_name: DLB brain tissue 11


title: genomic DNA from DLB brain tissue 1

source_name: DLB brain tissue 1


title: genomic DNA from DLB brain tissue 3

source_name: DLB brain tissue 3


title: 99_005_P5.4H

city: Boston

first: Sonu

last: Subudhi

address: 100 Blossom St, Cox 7

department: Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
raw sequencing reads aligned to hg38 (GENCODE v32) using STAR (v2.7.3a)
Gene expression was quantified using RSEM (v1.3.1)
Genes with rowSums ==0 were filtered out
Common genes selected between main and validation cohort

source_name: specific T cells from pre_DAA patient (T cell target: conserved)

extract_protocol:
RNAeasy Micro Kit (Qiagen)
Smart Seq2 protocol

tag: sex (1=male;_2=female)

tag: t cell_type

value: specific T cells

tag: tetramer type_or_celltype

tag: number of_cells

tag: epitope sequence

value: conserved

tag: infection status

tag: cohort (1=main;_2=validation)


title: genomic DNA from normal brain tissue 15

source_name: Normal brain tissue 15

tag: disease state


title: genomic DNA from normal brain tissue 13

source_name: Normal brain tissue 13


title: genomic DNA from normal brain tissue 10

source_name: Normal brain tissue 10


title: 15_129_P9.C63b

source_name: specific T cells from post_DAA patient (T cell target: conserved)


title: CNTO148UCO2001-100091 colon biopsy week 0

source_name: colon biopsy

value: colon

tag: donor id

value: week 0

value: ulcerative colitis

tag: treatment


title: 15_129_P11.C63b


title: CNTO1275CRD3002-20681 rectum biopsy week 0

source_name: rectum biopsy

tag: visit

tag: diagnosis

value: Ileum and colon


title: genomic DNA from DLB brain tissue 5

source_name: DLB brain tissue 5


title: genomic DNA from normal brain tissue 9

source_name: Normal brain tissue 9


title: genomic DNA from DLB brain tissue 10

source_name: DLB brain tissue 10


title: 15_129_P11.198

source_name: specific T cells from post_DAA patient (T cell target: escaped)

value: escaped


title: CNTO1275CRD3002-20929 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (520 mg)


title: genomic DNA from normal brain tissue 16

source_name: Normal brain tissue 16


title: 15_090_P8.4H


title: 15_090_P3.4H


title: 99_005_P5.174D

source_name: specific T cells from pre_DAA patient (T cell target: escaped)


title: CNTO148UCO2001-100092 colon biopsy week 0

value: golimumab 200mg

tag: mucosal healing at week 6

tag: clinical remission at week 6


title: CNTO1275CRD3002-20829 rectum biopsy week 0

tag: tissue

value: Placebo IV

tag: inflamed area at week 0


title: CNTO148UCO2001-100086 colon biopsy week 0


title: CNTO148UCO2001-100085 colon biopsy week 0


title: genomic DNA from normal brain tissue 11

source_name: Normal brain tissue 11

tag: gender

value: M


title: CNTO1275CRD3002-20937 rectum biopsy week 0

value: Colon only

tag: mucosal healing at week 8


title: genomic DNA from normal brain tissue 12

source_name: Normal brain tissue 12

value: Brain


title: CNTO148UCO2001-100084 colon biopsy week 0

value: N


title: CNTO148UCO2001-100082 colon biopsy week 0

value: Y


title: genomic DNA from normal brain tissue 8

source_name: Normal brain tissue 8

value: F


title: 14_103_P4.127D

tag: sex (1=male;_2=female)

tag: t cell_type


title: 14_103_P11.C63b

tag: tetramer type_or_celltype

tag: number of_cells


title: 14_103_P11.127D

tag: epitope sequence

tag: infection status


title: 14_140_P4.140G

source_name: specific T cells from pre_DAA patient (T cell target: partial_escape)

tag: cohort (1=main;_2=validation)


title: 14_103_P4.C63b

source_name: specific T cells from pre_DAA patient (T cell target: conserved)


title: 14_021_P8.C63b


title: CNTO1275CRD3002-20295 rectum biopsy week 0

value: rectum

tag: donor id

value: Crohn's disease

value: Ustekinumab 130 mg IV


title: genomic DNA from normal brain tissue 6

source_name: Normal brain tissue 6

tag: disease state

value: Normal


title: genomic DNA from DLB brain tissue 9

source_name: DLB brain tissue 9

value: DLB


title: CNTO148UCO2001-100079 colon biopsy week 0

value: colon

tag: visit

value: week 0

value: ulcerative colitis

tag: treatment


title: 14_140_P10.C63b

value: specific T cells

value: conserved


title: CNTO148UCO2001-100081 colon biopsy week 0

tag: diagnosis

value: golimumab 200mg

tag: mucosal healing at week 6


title: CNTO148UCO2001-100089 colon biopsy week 0

tag: tissue

tag: clinical remission at week 6


title: 99_005_P12.4H


title: 14_021_P14.C63b


title: CNTO1275CRD3002-20292 rectum biopsy week 0

value: Placebo IV

tag: inflamed area at week 0

value: Ileum and colon


title: 14_021_P14.140G


title: 12_054_P6.127D


title: 12_054_P13.C63b


title: CNTO148UCO2001-100077 colon biopsy week 0


title: 12_054_P13.127D

source_name: specific T cells from post_DAA patient (T cell target: partial_escape)


title: CNTO1275CRD3002-20514 rectum biopsy week 0

tag: mucosal healing at week 8


title: 15_050_P4.140G

tag: sex (1=male;_2=female)


title: 06K_late_resolver_temra

source_name: temra T cells from late_resolver patient (T cell target: NA)

tag: t cell_type

value: temra T cells

value: temra


title: BR-3000_late_resolver_temra

tag: tetramer type_or_celltype


title: genomic DNA from normal brain tissue 3

source_name: Normal brain tissue 3

tag: gender

value: Brain


title: CNTO1275CRD3002-21035 rectum biopsy week 0

source_name: rectum biopsy

value: Colon only

value: N


title: 12-140_late_resolver_temra

tag: number of_cells

tag: epitope sequence


title: 14_140_P4.C63b

tag: infection status

tag: cohort (1=main;_2=validation)


title: genomic DNA from normal brain tissue 7

source_name: Normal brain tissue 7

value: F

tag: disease state


title: genomic DNA from normal brain tissue 4

source_name: Normal brain tissue 4


title: genomic DNA from normal brain tissue 2

source_name: Normal brain tissue 2


title: BR-320_late_resolver_temra


title: genomic DNA from normal brain tissue 5

source_name: Normal brain tissue 5


title: 15_050_P4.C63b

source_name: specific T cells from pre_DAA patient (T cell target: NA)


title: CNTO1275CRD3002-20886 rectum biopsy week 0

value: rectum

tag: donor id

tag: visit

value: Crohn's disease

value: Ustekinumab 6 mg/kg (390 mg)


title: CNTO148UCO2001-100070 colon biopsy week 0

source_name: colon biopsy

value: colon

tag: diagnosis

tag: treatment


title: CNTO1275CRD3002-20783 rectum biopsy week 0

tag: tissue


title: 08-023_late_resolver_temra


title: CNTO148UCO2001-100076 colon biopsy week 0

value: week 0

tag: mucosal healing at week 6

tag: clinical remission at week 6


title: BR-320_late_resolver_naive

source_name: naive T cells from late_resolver patient (T cell target: NA)

value: naive T cells

value: naive


title: CNTO148UCO2001-100080 colon biopsy week 0

value: ulcerative colitis

value: Y


title: BR-3000_late_resolver_naive


title: 12-140_late_resolver_naive


title: 06K_late_resolver_naive


title: 09-038_late_resolver_naive


title: CNTO148UCO2001-100067 colon biopsy week 0

value: golimumab 200mg


title: genomic DNA from normal brain tissue 1

source_name: Normal brain tissue 1

value: Normal


title: 08-023_late_resolver_naive


title: 09-038_late_resolver_temra

value: temra T cells


title: 08-023_late_resolver_em

source_name: em T cells from late_resolver patient (T cell target: NA)

value: em T cells

value: em


title: 12-140_late_resolver_em


title: BR-320_late_resolver_em


title: CNTO1275CRD3002-20653 rectum biopsy week 0

tag: inflamed area at week 0

value: Ileum and colon

tag: mucosal healing at week 8


title: CNTO1275CRD3002-20928 rectum biopsy week 0

value: N


title: CNTO1275CRD3002-20922 rectum biopsy week 0

value: Placebo IV


title: CNTO1275CRD3002-20367 rectum biopsy week 0

value: rectum


title: CNTO148UCO2001-100066 colon biopsy week 0


title: CNTO1275CRD3002-20472 rectum biopsy week 0

value: Crohn's disease


title: CNTO1275CRD3002-20980 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)


title: CNTO1275CRD3002-20547 rectum biopsy week 0


title: CNTO148UCO2001-100058 colon biopsy week 0

value: colon


title: 06K_late_resolver_cm

source_name: cm T cells from late_resolver patient (T cell target: NA)

tag: sex (1=male;_2=female)

tag: t cell_type

value: cm T cells

value: cm


title: 09-038_late_resolver_em

tag: tetramer type_or_celltype


title: CNTO148UCO2001-100065 colon biopsy week 0

value: week 0


title: CNTO148UCO2001-100064 colon biopsy week 0

value: ulcerative colitis


title: BR-3000_late_resolver_cm

tag: number of_cells


title: 14_021_P8.140G

source_name: specific T cells from pre_DAA patient (T cell target: conserved)

value: specific T cells

tag: epitope sequence

value: conserved


title: CNTO148UCO2001-100054 colon biopsy week 0

value: golimumab 200mg


title: CNTO1275CRD3002-20838 rectum biopsy week 0

value: Y


title: BR-320_late_resolver_cm

tag: infection status


title: 06K_late_resolver_em

value: em T cells

tag: cohort (1=main;_2=validation)


title: BR-3000_late_resolver_em

value: em


title: 12-140_late_resolver_cm


title: CNTO148UCO2001-100062 colon biopsy week 0


title: CNTO148UCO2001-100052 colon biopsy week 0


title: CNTO148UCO2001-100078 colon biopsy week 0


title: CNTO148UCO2001-100053 colon biopsy week 0


title: 08-023_late_resolver_cm


title: 09-038_late_resolver_cm


title: 08-023_late_resolver_c63b

source_name: specific T cells from late_resolver patient (T cell target: conserved)


title: 09-038_late_resolver_c63b


title: BR-3000_late_resolver_c63b


title: CNTO1275CRD3002-20959 rectum biopsy week 0

value: Colon only


title: CNTO1275CRD3002-21032 rectum biopsy week 0

value: Ustekinumab 130 mg IV

value: Ileum and colon


title: 08-023_late_resolver_b27-284


title: CNTO1275CRD3002-20791 rectum biopsy week 0

value: rectum

value: Placebo IV

value: N


title: 06K_late_resolver_143d


title: 09-038_late_resolver_140g


title: CNTO1275CRD3002-20148 rectum biopsy week 0

value: Crohn's disease


title: 12-140_late_resolver_140g


title: CNTO148UCO2001-100050 colon biopsy week 0

value: colon


title: BR-320_late_resolver_127d


title: CNTO1275CRD3002-20481 rectum biopsy week 0


title: 15-019_post_DAA_temra

source_name: temra T cells from post_DAA patient (T cell target: NA)

value: temra T cells

value: temra


title: 15-100_post_DAA_temra


title: CNTO1275CRD3002-20290 rectum biopsy week 0


title: CNTO148UCO2001-100047 colon biopsy week 0

value: week 0

value: ulcerative colitis


title: 15-113_post_DAA_temra


title: CNTO1275CRD3002-20971 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (520 mg)


title: CNTO1275CRD3002-20531 rectum biopsy week 0


title: 07-039_post_DAA_temra


title: CNTO148UCO2001-100051 colon biopsy week 0

value: golimumab 200mg


title: CNTO148UCO2001-100045 colon biopsy week 0


title: CNTO148UCO2001-100042 colon biopsy week 0


title: CNTO1275CRD3002-20432 rectum biopsy week 0


title: CNTO148UCO2001-100046 colon biopsy week 0


title: 14-134_post_DAA_temra


title: CNTO1275CRD3002-20051 rectum biopsy week 0


title: 07-039_post_DAA_naive

source_name: naive T cells from post_DAA patient (T cell target: NA)

value: naive T cells

value: naive


title: 15-077_post_DAA_temra


title: CNTO1275CRD3002-20637 rectum biopsy week 0


title: CNTO148UCO2001-100038 colon biopsy week 0


title: CNTO1275CRD3002-20559 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)


title: 15-113_post_DAA_naive


title: CNTO148UCO2001-100036 colon biopsy week 0


title: 15-077_post_DAA_naive


title: 14-134_post_DAA_naive


title: 15-019_post_DAA_naive


title: 15-100_post_DAA_naive


title: 14-134_post_DAA_em

source_name: em T cells from post_DAA patient (T cell target: NA)

value: em T cells

value: em


title: 15-077_post_DAA_em


title: CNTO148UCO2001-100033 colon biopsy week 0

value: Y


title: 07-039_post_DAA_em


title: 15-100_post_DAA_em


title: 15-113_post_DAA_em


title: 15-019_post_DAA_em


title: CNTO1275CRD3002-20969 rectum biopsy week 0

value: rectum

value: Ustekinumab 6 mg/kg (260 mg)

value: Ileum and colon


title: CNTO1275CRD3002-20962 rectum biopsy week 0

value: Crohn's disease


title: 14-134_post_DAA_cm

source_name: cm T cells from post_DAA patient (T cell target: NA)

value: cm T cells

value: cm


title: 15-019_post_DAA_cm


title: CNTO1275CRD3002-20604 rectum biopsy week 0

source_name: rectum biopsy

value: Placebo IV

value: N


title: 15-100_post_DAA_cm


title: CNTO1275CRD3002-21043 rectum biopsy week 0


title: CNTO148UCO2001-100032 colon biopsy week 0

value: colon

value: week 0

value: ulcerative colitis


title: CNTO148UCO2001-100029 colon biopsy week 0

value: golimumab 200mg


title: CNTO148UCO2001-100035 colon biopsy week 0


title: CNTO1275CRD3002-20198 rectum biopsy week 0

value: Ustekinumab 130 mg IV


title: CNTO148UCO2001-100027 colon biopsy week 0


title: 07-039_post_DAA_cm


title: CNTO1275CRD3002-20459 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)

value: Colon only


title: CNTO148UCO2001-100028 colon biopsy week 0


title: CNTO148UCO2001-100021 colon biopsy week 0


title: 15-113_post_DAA_cm


title: 15-077_post_DAA_c63b

source_name: specific T cells from post_DAA patient (T cell target: escaped)

value: specific T cells

value: escaped


title: 15-019_post_DAA_174d


title: CNTO1275CRD3002-20245 rectum biopsy week 0

value: rectum


title: CNTO1275CRD3002-20438 rectum biopsy week 0


title: 15-100_post_DAA_140g


title: CNTO148UCO2001-100020 colon biopsy week 0

value: Y


title: CNTO148UCO2001-100030 colon biopsy week 0


title: 07-039_post_DAA_127d


title: 15-113_post_DAA_c63b

source_name: specific T cells from post_DAA patient (T cell target: conserved)

value: conserved


title: 14-134_post_DAA_127d


title: 15-077_post_DAA_cm


title: CNTO1275CRD3002-20781 rectum biopsy week 0

value: Crohn's disease

value: Ileum and colon


title: 15-019_post_DAA_c63b


title: 07-039_post_DAA_c63b


title: 15-100_post_DAA_c63b


title: CNTO1275CRD3002-21011 rectum biopsy week 0


title: CNTO1275CRD3002-20732 rectum biopsy week 0


title: 15-113_post_DAA_140g


title: 15-077_post_DAA_127d


title: CNTO148UCO2001-100019 colon biopsy week 0


title: 15-100_pre_DAA_temra

source_name: temra T cells from pre_DAA patient (T cell target: NA)

value: temra T cells

value: temra


title: 15-113_pre_DAA_temra


title: 15-019_pre_DAA_temra


title: CNTO1275CRD3002-20087 rectum biopsy week 0

value: N


title: CNTO1275CRD3002-20656 rectum biopsy week 0


title: 07-039_pre_DAA_temra


title: 14-134_post_DAA_c63b


title: CNTO1275CRD3002-20865 rectum biopsy week 0

value: Placebo IV


title: CNTO1275CRD3002-20217 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (260 mg)


title: CNTO148UCO2001-100003 colon biopsy week 0

value: colon

value: week 0

value: ulcerative colitis


title: CNTO148UCO2001-100017 colon biopsy week 0

value: golimumab 200mg


title: CNTO148UCO2001-100002 colon biopsy week 0


title: 14-134_pre_DAA_temra


title: 15-077_pre_DAA_temra


title: CNTO148UCO2001-100012 colon biopsy week 0


title: BU-HY-38

city: Jacksonville

first: Tadafumi

middle: Clark

last: Ikezu

address: 4500 San Pablo Rd

institute: Mayo Clinic

data_processing:
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-Seq analytic pipeline: MAP-RSeq Version 3.0 (Kalari et al., 2014).
Reads were mapped to the mouse reference genome mm10 using STAR v.2.5.2b using default settings (Dobin et al., 2013). The gene counts were generated using FeatureCounts v.1.5.1 (Liao et al., 2014) with the gene definitions files from Ensembl v78. Quality checks after alignment was done using RSeqQC v.3.0.0 (Wang et al., 2012).
Genes were filtered out from further analyses if there were not at least four samples with 10 counts of the gene. Trimmed Mean of M-values (TMM) normalization was performed with calcNormFactors from the edgeR R package (Lun ATL et al, 2016). Using this selection threshold, 20,337 genes were included in the downstream analysis.
Sample BU-HY-19 had outlying gene count percentage (39%) and strand-ness check (0.5009), and was removed from subsequent analyses.
Assembly: mm10
Supplementary files format and content: .tsv file of raw gene counts

source_name: cortex

extract_protocol:
Total RNA was extracted from the cortex using Trizol reagent and cleaned using RNeasy spin columns with DNase treatment to remove contaminating genomic DNA.
RNA libraries were prepared from 200 ng of total RNA using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, employing poly-A mRNA enrichment using oligo-dT magnetic beads. The final adaptor-modified cDNA fragments were enriched by 15 cycles of PCR using Illumina TruSeq PCR primers. The concentration and size distribution of the completed libraries were determined using an Agilent Tape Station, (Agilent, Santa Clara, CA) and Qubit fluorometer (Invitrogen, Carlsbad, CA).
Libraries from all the 40 samples were sequenced on Illumina’s NovaSeq 6000 at 75 million fragment reads/sample following Illumina’s standard protocol on a S2 flow cell.

treatment_protocol: No specific trearment was applied to each group of mice.

tag: cohort

value: non-amyloid

tag: genotype

value: WT

tag: Sex

value: female


title: BU-HY-40

value: amyloid

value: Hom

value: male


title: BU-HY-39


title: 15-113_pre_DAA_naive

source_name: naive T cells from pre_DAA patient (T cell target: NA)

value: naive T cells

value: naive


title: CNTO148UCO2001-100009 colon biopsy week 0

source_name: colon biopsy

tag: donor id

tag: visit

tag: diagnosis


title: CNTO1275CRD3002-20678 rectum biopsy week 0

tag: tissue

value: rectum

value: Crohn's disease

tag: treatment

value: Ileum and colon


title: 07-039_pre_DAA_naive


title: CNTO148UCO2001-100007 colon biopsy week 0

tag: mucosal healing at week 6

value: N

tag: clinical remission at week 6


title: CNTO1275CRD3002-20848 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (520 mg)

tag: inflamed area at week 0

tag: mucosal healing at week 8


title: 14-134_pre_DAA_naive

tag: sex (1=male;_2=female)

tag: t cell_type

tag: tetramer type_or_celltype


title: 15-077_pre_DAA_naive

tag: number of_cells

tag: epitope sequence

tag: infection status


title: CNTO1275CRD3002-20231 rectum biopsy week 0

value: Placebo IV

value: Colon only


title: BU-HY-37

tag: cohort

tag: genotype


title: CNTO1275CRD3002-20329 rectum biopsy week 0

tag: donor id

value: Ustekinumab 6 mg/kg (260 mg)


title: 15-019_pre_DAA_naive

tag: cohort (1=main;_2=validation)


title: BU-HY-36

tag: Sex


title: CNTO148UCO2001-100010 colon biopsy week 0

tag: tissue

value: colon

tag: visit

value: week 0

tag: diagnosis

value: ulcerative colitis

value: golimumab 200mg


title: 14-134_pre_DAA_em

source_name: em T cells from pre_DAA patient (T cell target: NA)

value: em T cells

value: em


title: 15-100_pre_DAA_naive


title: 15-077_pre_DAA_em


title: 07-039_pre_DAA_em


title: BU-HY-34

value: amyloid

value: Hom

value: female


title: 15-019_pre_DAA_em


title: BU-HY-33


title: 15-100_pre_DAA_cm

source_name: cm T cells from pre_DAA patient (T cell target: NA)

value: cm T cells

value: cm


title: 15-113_pre_DAA_em


title: CNTO1275CRD3002-20215 rectum biopsy week 0

value: rectum

value: Crohn's disease

tag: treatment

value: Ustekinumab 6 mg/kg (390 mg)

value: Ileum and colon


title: 15-100_pre_DAA_em


title: 14-134_pre_DAA_cm


title: 07-039_pre_DAA_cm


title: 15-019_pre_DAA_cm


title: BU-HY-32

value: WT


title: BU-HY-31

value: non-amyloid

value: male


title: CNTO1275CRD3002-20082 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (260 mg)

tag: inflamed area at week 0

value: Colon only


title: 15-077_pre_DAA_cm


title: 15-113_pre_DAA_cm


title: CNTO1275CRD3002-20304 rectum biopsy week 0

value: Ustekinumab 130 mg IV

tag: mucosal healing at week 8

value: N


title: 15-077_pre_DAA_c63b

source_name: specific T cells from pre_DAA patient (T cell target: escaped)

tag: sex (1=male;_2=female)

value: specific T cells

value: escaped


title: CNTO1275CRD3002-20104 rectum biopsy week 0


title: CNTO1275CRD3002-20219 rectum biopsy week 0


title: CNTO1275CRD3002-20623 rectum biopsy week 0

value: Y


title: CNTO1275CRD3002-20244 rectum biopsy week 0

value: Placebo IV


title: CNTO1275CRD3002-20798 rectum biopsy week 0


title: 15-100_pre_DAA_140g

tag: t cell_type


title: CNTO1275CRD3002-20182 rectum biopsy week 0


title: BU-HY-28


title: 15-113_pre_DAA_140g

tag: tetramer type_or_celltype


title: 07-039_pre_DAA_127d

tag: number of_cells


title: BU-HY-30

value: amyloid

value: Hom


title: BU-HY-27


title: 14-134_pre_DAA_127d

tag: epitope sequence


title: 15-019_pre_DAA_c63b

value: conserved

tag: infection status


title: BU-HY-26

tag: cohort

value: female


title: CNTO1275CRD3002-20279 rectum biopsy week 0

value: rectum

value: Crohn's disease


title: 14-134_pre_DAA_c63b


title: BU-HY-25

tag: genotype


title: BU-HY-29

value: WT


title: 07-039_pre_DAA_c63b


title: BU-HY-23

value: non-amyloid


title: 15-019_pre_DAA_174d


title: 15-077_pre_DAA_127d


title: 6.Normal

city: Beijing

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
After sequencing, adapters and low-quality bases were trimmed from reads by using the Trimmomatic software (v0.36). Overlapped paired-end reads were merged as single fragments by using the PEAR software (v0.9.11). Non-overlapped paired-end reads and assembled fragments were aligned to the human reference genome (assembly version: GRCh38) independently by using the STAR software (v2.5.2b).
Chimeric reads (backspliced reads) reported by the STAR software were filtered: if both arms of a chimeric read were located in the same transcript; if either one arm of a chimeric read was located in repetitive regions; Afterwards, arms for the left chimeric reads were re-aligned to the human reference genome by the BLASTN software (v2.5.0) with the following parameters: -evalue 0.05 -word_size 7.
Chimeric reads with two arms that could be aligned linearly in the genome by BLASTN were further filtered to remove false-positive backsplicing events which are potentially raised by segmental duplications, pairwise genes with high degree of homology, or possible alignment errors.
The high-quality chimeric reads detected by both STAR and BLASTN were used to define rt-circRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol (Invitrogen) protocol. 4 μg of total RNA was used for the construction of sequencing libraries.
total RNA and proceeded through fragmentation, first-strand synthesis, second-strand synthesis (including end repair and A-tailing) adaptor ligation, purified with magnetic beads, according to VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina protocol. Agilent SureSelect Human All Exon V6 probes, were then used to capture cDNA.

value: liver

tag: cell type

value: liver cells

value: Normal


title: 5.Normal


title: CNTO1275CRD3002-20504 rectum biopsy week 0

tag: donor id

value: Ileum and colon


title: CNTO1275CRD3002-20345 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)


title: CNTO1275CRD3002-20621 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (260 mg)


title: CNTO1275CRD3002-20529 rectum biopsy week 0

value: Colon only

value: N


title: 3.NASH

value: NASH


title: 15-113_pre_DAA_c63b

source_name: specific T cells from pre_DAA patient (T cell target: conserved)

value: specific T cells

tag: cohort (1=main;_2=validation)


title: BU-HY-22

value: amyloid

tag: Sex

value: male


title: BU-HY-21

value: Hom


title: 15-100_pre_DAA_c63b

value: conserved


title: 2.NASH

tag: tissue


title: BU-HY-24

value: female


title: SW1736, Hypoxia #1

city: Baltimore

first: Bonita

middle: H

state: MD

address: 733 N Broadway, MRB 8 829

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

data_processing:
FASTQC run before and after adapter trimming. The reads were aligned to the reference transcriptomes in a sequential manner.   First, all reads were mapped to RNA species with low sequence complexity and/or high number of repeats: rRNA, tRNA, RN7S, snRNA, snoRNA, scaRNA, VT-RNA, Y-RNA as well as mitochondrial chromosome (mtRNA). All reads that did not map to the above RNAs were aligned to premiRNA reference, then to protein coding mRNA transcripts (pc) and long non-coding RNAs (lncRNAs). Please note that some % of reads always overlaps between pc and lncRNAs. The reads which did not map to premiRNA, protein coding (pc) transcripts and lncRNAs were aligned to the remaining transcriptome [other ncRNAs containing mostly pseudogenes and non-protein coding parts of mRNAs]. Finally, all reads which did not map to human transcriptome were aligned to the hg38 genome reference (rest_hg38).
The mapping was performed with bowtie2 default settings for all references except premiRNA. For premiRNA alignment I used sequential mapping with bowtie using settings with: 0 mismatch tolerance, then 1 mismatch tolerance and finally 2 mismatches tolerance.
Assembly: Hg38
Supplementary files format and content: counts

source_name: Thyroid

extract_protocol:
Total RNA was extracted from cells by Ambion mirVana miRNA isolation Kit
Small RNA libraries were constructed using the CATS ligation-independent method for 3'OH only ends following the protocol by Diagenode.

tag: cell line

tag: disease state

value: Anaplastic Thyroid Cancer

tag: stress

value: Hypoxia


title: BU-HY-20

value: non-amyloid


title: SW1736, Hypoxia #2


title: 1.NASH

value: liver

value: liver cells


title: SW1736, Hypoxia #3


title: BU-HY-19


title: SW1736, Normoxia #1

value: Normoxia


title: CNTO1275CRD3002-20805 rectum biopsy week 0

value: rectum

tag: visit

tag: diagnosis

value: Crohn's disease

tag: treatment

value: Placebo IV

tag: inflamed area at week 0

tag: mucosal healing at week 8


title: SW1736, Normoxia #2


title: CNTO1275CRD3002-20176 rectum biopsy week 0

value: Colon only

value: N


title: SW1736, Normoxia #3


title: 4.Normal

value: Normal


title: CNTO1275CRD3002-20541 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (520 mg)

value: Ileum and colon


title: CNTO1275CRD3002-20878 rectum biopsy week 0


title: CNTO1275CRD3002-20757 rectum biopsy week 0


title: BU-HY-17

value: WT


title: BU-HY-18

value: male


title: CNTO1275CRD3002-20187 rectum biopsy week 0

value: Y


title: BU-HY-15

value: female


title: BU-HY-14

value: Hom