title: B1003; azacitidine 2, rep 2

city: HOUSTON

first: Ajay

middle: Kumar

last: Saw

state: TX

address: 7900 Cambdrige St

department: Department of Genomic Medicine

institute: University Of Texas MD Anderson Cancer Center, Houston, Texas, USA.

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC  and aligned to the hg19 reference genome using Bowtie, and  sorted and indexed using samtools
removal of PCR duplicates and the exclusion of mitochondrial reads  using picard tool
Model based analysis of ChIP-seq (MACS) used for  peak calling
Assembly: hg19
Supplementary files format and content: bed peak file

source_name: Patient-derived xenograft

growth_protocol: PDX tumors were implanted into 4-6 week-old female immunodeficient nu/nu mice subcutaneously.

extract_protocol:
Nuclei were isolated from snap-frozen PDX tumor tissues as described previously with few modifications and subjected to transposition using Tagment DNA enzyme (Illumina).
Library preparation and DNA cleanup using SPRISelect beads.

treatment_protocol: PDXs were treated with the vehicle control (phosphor-buffered saline) or 5-azacitidine (0.5mg/kg, intraperitoneal injections, twice a week (Sigma Aldrich)).

value: Patient-derived xenograft


title: B1003; azacitidine 3, rep 1

status: Public on Sep 01 2024

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: treatment


title: B1003; azacitidine 2, rep 1


title: B1003; azacitidine 1, rep 2


title: B1003; azacitidine 1, rep 1


title: B1003; control 3, rep 1

value: control


title: B1003; control 3, rep 2


title: B1003; control 2, rep 2


title: D-Allose_8

type: RNA

city: Itami

first: Akane

last: Kanasaki

state: Hyogo

address: 5-3 Kita-Itami

country: Japan

institute: Matsutani Chemical Industry Co., Ltd.

description: Gene expression data from the hippocampus of aged mice continuously fed a diet with D-alloset.

hyb_protocol: Biotin-labeled cDNA was injected onto the microarray and hybridized with the probes using a GeneChip hybridization apparatus (Hybridazation oven 645).

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner.

data_processing: All microarray datasets were analyzed using Affymetrix default analysis settings and global scaling as a normalization method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse fed a diet with D-allose

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: hippocampus

value: continuously fed a diet with D-alloset.


title: B1003; control 2, rep 1


title: D-Allose_5


title: D-Allose_2


title: D-Allose_4


title: B1003; azacitidine 3, rep 2


title: B1003; control 1, rep 2


title: D-Allose_7


title: D-Allose_3


title: B1003; control 1, rep 1


title: Control_7

description: Gene expression data from the hippocampus of aged mice continuously fed a diet without D-alloset.

source_name: mouse fed a diet without D-allose


title: D-Allose_1


title: B1003; azacitidine 3; Input; ChIP

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC  and aligned to the hg19 reference genome using Bowtie, and  sorted and indexed using samtools
Model based analysis of ChIP-seq (MACS) used for  peak calling
Assembly: hg19
Supplementary files format and content: bed peak file

extract_protocol:
Snap-frozen tumor tissues were harvested, crosslinked for 10 minutes with formaldehyde, and quenched for 5 minutes with 125 mM glycine. After lysis and sonication with Bioruptor (Diagenode), immunoprecipitation with antibodies was performed.
ChIP-seq libraries were prepared using NEB Ultra II DNA library prep kit.

tag: cell type


title: Control_3

value: continuously fed a diet without D-alloset.


title: Control_1


title: Escherichia coli DH5a, TCMV0120 pDM2.1 pBAD33 replicate 2

city: Norwich

first: Thomas

middle: Cameron

last: McLean

state: Norfolk

address: Norwich Research Park

department: Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
Reads were mapped to the DH5a + plasmid genome fasta using Bowtie2 giving the BAM and BAI files
Perbase command line tool (https://github.com/sstadick/perbase) was used on the BAM files in "only-depth" mode to count read coverage per base for each BAM file giving the xyle#.csv files
Custom python script was used to calculate the average read depth from the Perbase output file for each region: DH5a chromosome, plasmid 1, plasmid 2 and plasmid 3 giving the xyle#_regions.csv files. This was then used to create a normalised plasmid copy number per chromosome for each sample
Assembly: GenBank: CP026085.1
Supplementary files format and content: CSV files: comma-seperated value files with read-depth per base of each sample
Supplementary files format and content: CSV files: comma-seperated value files with average read-depth per genomic loci of each sample
Library strategy: Deep-sequencing

organism: Escherichia coli

growth_protocol: E. coli DH5a cells containing relevant expression plasmids were grown to a logarithmic phase from a 1:100 dilution of overnight culture. Induction of KorB WT expression was achieved with 0.2% arabinose. Induction of KorA WT required no additional IPTG. 5 mL of culture was pelleted for deep-sequencing.

extract_protocol:
Cultures for deep-sequencing prepared as for xylE reporter gene assays with 5 mL of culture resuspended in 300 µL Puregene cell lysis solution (Qiagen, UK) before being incubated at 50°C for 10 min. 2 µL RNase A (20 mg/mL) was added and the samples were mixed by inversion 25 times before incubation at 37°C for 60 min. The samples were cooled to room temperature and 100 µL Puregene protein precipitation solution (Qiagen, UK) was added. Samples were briefly vortex, incubated on ice for 10 min and protein precipitate removed via centrifugation. The supernatant was removed to a fresh microcentrifuge tube containing 600 µL isopropanol and mixed via inversion 50 times. DNA was pelleted via centrifugation, supernatant removed and pellet washed with 600 µL 70% ethanol before a final centrifugation. The supernatant was carefully removed and the DNA resuspended in 100 µL distilled water
Illumina sequencing libraries were prepared using the tagmentation-based and PCR-based Illumina DNA Prep kit and custom IDT 10bp unique dual indices (UDI) with a target insert size of 280 bp. Not additional DNA fragmentation or size selection steps were performed.

tag: genotype

value: Control

value: 0.2% arabinose


title: Control_2


title: B1003; azacitidine 3; H3K27me3; ChIP

tag: chip antibody

value: H3K27me3 (Diagenode)


title: Control_5


title: Control_8


title: B1003; azacitidine 3; H3K4me3; ChIP

value: H3K4me3 (Abcam)


title: WT-MEF-CAPE-IR

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: Gene expression data from Wild type murine embryonic fibroblasts (plus CAPE) treated with x-rays

hyb_protocol: Following fragmentation, 5.5ug of cRNA were hybridized on Affymetrix Clariom S Mouse GeneChips. Washing and staining were performed with the  were washed and stained in the Affymetrix GeneChip Fluidics Station 450s.

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

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis Console v4.0 using default analysis settings with the sst-rma-gene-full normalization method

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip WT PLUS protocol from 175ng total RNA

growth_protocol: Murine embryonic fibroblasts were obtained from embryonic day 15 from Wild type, STING knocout, cGAS knockout and IRF3 knockout mice and cultured in complete DMEM supplemented with 10% FBS and 1X Antibiotics.

extract_protocol: Total RNA was extracted from the cells using E.Z.N.A Total RNA Kit (Omega Bio-Tek, # R6834-02) following to the manufacturer's instructions.

treatment_protocol: Wild type, STING knocout, cGAS knockout and IRF3 knockout murine embryonic fibroblasts were irradiated by x-rays at 50 Gy and incubated for 3 days.

value: Fibroblasts

value: Wild type

value: treated with x-rays


title: WT-MEF-CAPE

description: Gene expression data from Wild type murine embryonic fibroblasts (plus CAPE) without x-rays

value: without x-rays


title: Control_6


title: B1003; azacitidine 3; H3K9me3; ChIP

value: H3K9me3 (Diagenode)


title: IRF3KO-MEF-IR

description: Gene expression data from IRF3KO knockout murine embryonic fibroblasts treated with x-rays


title: B1003; azacitidine 2; Input; ChIP


title: IRF3KO-MEF

description: Gene expression data from IRF3KO knockout murine embryonic fibroblasts without x-rays


title: Control_4


title: CKO-MEF-IR

description: Gene expression data from cGAS knockout murine embryonic fibroblasts treated with x-rays

value: cGAS-/-


title: B1003; azacitidine 2; H3K4me3; ChIP


title: B1003; azacitidine 2; H3K27me3; ChIP


title: CKO-MEF

description: Gene expression data from cGAS knockout murine embryonic fibroblasts without x-rays


title: B1003; azacitidine 3; H3K27ac; ChIP

value: H3K27ac (Abcam)


title: B1003; azacitidine 2; H3K27ac; ChIP


title: B1003; azacitidine 2; H3K9me3; ChIP


title: B1003; azacitidine 1; Input; ChIP


title: B1003; azacitidine 1; H3K4me3; ChIP


title: B1003; azacitidine 1; H3K27ac; ChIP


title: B1003; azacitidine 1; H3K9me3; ChIP


title: B1003; control 3; Input; ChIP


title: corpus, culture+EVs, rep5

city: Washington

first: Danielle

last: Sosnicki

state: DC

address: 3001 Connecticut Ave NW

institute: Smithsonian's National Zoo and Conservation Biology Institute

library_source: transcriptomic

data_processing:
Reads were trimmed using Trimmomatic 0.38. Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
trimmed reads were mapped to the felis catus genome using HISAT2 version 2.1.0, Bowtie2 2.3.4.1
StringTie version 2.1.3b was used to assemble known genes and transcripts
Assembly: NCBI Felis catus genome
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Felis catus

source_name: epididymis

extract_protocol:
RNA extraction was performed using an RNAeasy kit (Qiagen)
Libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit

value: epididymis

value: culture+EVs


title: corpus, fresh tissue, rep5

value: fresh


title: SKO-MEF-IR

description: Gene expression data from STING knockout murine embryonic fibroblasts treated with x-rays

value: STING-/-


title: B1003; control 3; H3K4me3; ChIP

value: Patient-derived xenograft

value: control


title: corpus, culture, rep5

value: culture


title: SKO-MEF

description: Gene expression data from STING knockout murine embryonic fibroblasts without x-rays


title: B1003; control 3; H3K9me3; ChIP


title: B1003; control 3; H3K27ac; ChIP


title: corpus, culture, rep4


title: corpus, fresh tissue, rep4


title: WT Lumbar NP Tissue 4

city: Philadelphia

first: Makarand

middle: V

last: Risbud

state: PA

address: 1025 Walnut St., Suite 511 College Building

department: Orthopedic Surgery

institute: Thomas Jefferson University

description: Total RNA from WT NP tissue; sst-rma normalization; DABG p<0.05; FDR<0.05; FC 2.0

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

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

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the expeirment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05. Inclusion cutoffs were defined at a 2.00-fold change and p-value < 0.05.

source_name: WT Lumbar NP Tissue 4

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

growth_protocol: Mice wildtype (WT) or knockout (KO) for Syndecan 4 knockout were aged to 6-month of age at Thomas Jefferson University.

extract_protocol: NP and AF tissues were micro-dissected from lumbar intervertebral discs of 4 WT control and 4 KO mice and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a Pellet Pestle Motor (Sigma Aldrich, Z359971) and RNA was extracted from tissue lysates using RNeasy Micro Kit (Qiagen 74004), according to the manufacturer's instructions.

value: Wildtype

tag: age

value: Nucleus Pulposus


title: corpus, culture+EVs, rep4


title: B1003; azacitidine 1; H3K27me3; ChIP

value: H3K27me3 (Diagenode)


title: WT-MEF-IR

description: Gene expression data from Wild type murine embryonic fibroblasts treated with x-rays

value: Fibroblasts


title: WT-MEF

description: Gene expression data from Wild type murine embryonic fibroblasts without x-rays

value: Wild type


title: KO Lumbar NP Tissue 4

description: Total RNA from KO NP tissue; sst-rma normalization; DABG p<0.05; FDR<0.05; FC 2.0

source_name: KO Lumbar NP Tissue 4

value: SDC4 KO


title: KO Lumbar NP Tissue 2

source_name: KO Lumbar NP Tissue 2


title: KO Lumbar NP Tissue 1

source_name: KO Lumbar NP Tissue 1


title: WT Lumbar NP Tissue 3

source_name: WT Lumbar NP Tissue 3


title: WT Lumbar NP Tissue 1

source_name: WT Lumbar NP Tissue 1


title: corpus, culture+EVs, rep3


title: B1003; control 2; H3K4me3; ChIP

value: H3K4me3 (Abcam)


title: corpus, fresh tissue, rep3


title: B1003; control 2; H3K27ac; ChIP


title: B1003; control 3; H3K27me3; ChIP


title: B1003; control 2; H3K9me3; ChIP

value: H3K9me3 (Diagenode)


title: corpus, culture+EVs, rep2


title: B1003; control 2; Input; ChIP


title: corpus, culture, rep2


title: B1003; control 1; Input; ChIP


title: B1003; control 1; H3K4me3; ChIP


title: corpus, fresh tissue, rep2


title: corpus, culture, rep1


title: B1003; control 1; H3K27ac; ChIP


title: B1003; control 2; H3K27me3; ChIP


title: corpus, fresh tissue, rep1


title: Muscle,Ang II-induced AAA,rep4

city: Guangzhou

first: Ying

last: Wen

address: jinsui road NO.9

country: China

institute: Guangzhou Medical University

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)
1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5) .
The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Aorta

extract_protocol:
RNA was harvested using TRIzol/chloroform/isoamyl alcohol. 1.0 ug of total RNA was used for the construction of sequencing lilbraries.
RNA libraries for RNA-seg were prepared using MGIEaSy mRNA-Seg Library Prep Kit following manufacturer's protocols.

value: Aorta

value: Vascular cells

value: ApoE knock out

tag: Sex

value: male

value: The mini osmotic pump for Ang II-induction

tag: time

value: 28 days


title: B1003; control 1; H3K9me3; ChIP

value: Patient-derived xenograft


title: B1003; azacitidine 3

data_processing:
Trim Galore tool was utilized for adapter removal in cases where adapter contamination was detected
Trimmed sequenced read were mapped Homo sapiens genome (Gencode version 29) transcriptomes using the Salmon tool
Read count and normalization were performed using  tximeta R-package
DESeq2 package has been used for differential expression analysis
Assembly: hg19
Supplementary files format and content: csv text file includes raw counts of each Sample

growth_protocol: Patient-derived xenograft model (B1003) of colorectal cancer harboring BRAFV600E mutation was subcutaneously implanted into nude mice.

extract_protocol:
Snap frozen tumor tissue (~40mg) was used for RNA extraction conducted from Admera Health.
Library was constructed from Admera Health.

treatment_protocol: Mice were randomized and treated with either vehicle control (PBS) or 5-azacitidine.


title: Muscle,Ang II-induced AAA,rep3


title: pollen, flowering stage, Bisulfite-seq rep1

city: Shanghai

first: Hongbo

last: Gao

address: 800 Dongchuan Rd

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim-Galore (parameter- clip_R1:9  clip_R2:9)
Trimmed sequence reads were mapped to NHCC001 reference genome using BSMAPz (parameters-  v: 0.15 w:1 n: 1 L: 100)
Methylation ratio data from the mapped readswas extracted using methratio.py script (parameter- -N: 1, -r, -u)
Methylated cytosines with more than 5 informative sequencing reads were retained using awk command
Assembly: NHCC001
Supplementary files format and content: tab-delimited gff file includes methylated cytosines for each Sample

organism: Brassica rapa

source_name: pollen

extract_protocol:
Cell lysis and bisulfite conversion of DNA were performed using the ZYMO EZ DNA Methylation-Gold kit. Bisulfite-converted DNA was used for the construction of sequencing libraries.
Libraries for bisulfite-seq were prepared according to the protocol  described by Smallwood in 2014.

tag: cultivar

value: Non-heading Chinese cabbage (Brassica rapa. ssp. Chinensis)

value: pollen

value: WT


title: pollen, flowering stage, Bisulfite-seq rep2


title: microspore, mononuclear leaning stage, Bisulfite-seq rep2

source_name: microspore

value: microspore


title: microspore, mononuclear leaning stage, Bisulfite-seq rep1


title: B1003; azacitidine 2


title: WT Lumbar NP Tissue 2

source_name: WT Lumbar NP Tissue 2

value: Wildtype

value: Nucleus Pulposus


title: B1003; azacitidine 1


title: B1003; control 1; H3K27me3; ChIP

value: H3K27me3 (Diagenode)

value: control


title: Muscle,Ang II-induced lesion,rep3


title: Muscle,Ang II-induced AAA,rep1


title: meiocyte, meiotic prophase I, Bisulfite-seq rep1

source_name: meiocyte

value: meiocyte


title: B1003; control 3


title: corpus, culture+EVs, rep1

value: epididymis

value: culture+EVs


title: pollen, flowering stage, RNA-seq rep3

data_processing:
Trim the raw reads using Trim-Galore followed by mapping to the reference genome of NHCC001 using hisat2 , and remove the PCR duplicated fragments using Picard
Read count extraction was performed using HTSeq
Assembly: NHCC001
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Isolated cells were lysed and total RNA was harvested according to the method described by Picelli in 2014
Strand-specific RNA-seq libraries were prepared according to the protocol described by Picelli in 2014


title: Muscle,Ang II-induced lesion,rep2

value: Aorta

value: Vascular cells


title: leaf, stalk leaf, Bisulfite-seq rep1

source_name: leaf

value: leaf


title: pollen, flowering stage, RNA-seq rep2


title: microspore, mononuclear leaning stage, RNA-seq rep3


title: pollen, flowering stage, RNA-seq rep1


title: Muscle,Ang II-induced lesion,rep1

value: ApoE knock out

value: male

value: The mini osmotic pump for Ang II-induction


title: meiocyte, meiotic prophase I, RNA-seq rep3

value: Non-heading Chinese cabbage (Brassica rapa. ssp. Chinensis)


title: microspore, mononuclear leaning stage, RNA-seq rep2


title: B1003; control 1

value: Patient-derived xenograft


title: Muscle,sham control,rep3

value: sham control

value: 28 days


title: Muscle,Ang II-induced AAA,rep2


title: CANVAS3, RFC1, DIV70

city: Ann Arbor

first: Connor

middle: J

last: Maltby

state: MI

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

description: rRNA Depleted Total RNA

data_processing:
Raw FASTA read files were delivered by sFTP transfer and analyzed in Command Line and R-Studio. Read files were quality controlled using FastQC(v0.12.0), pre-processed and trimmed using fastp(v0.23.4), and aligned to GRCh38 (NCBI GCF_000001405.40) genome using STAR(v2.7.11a) two-pass alignment.
Transcript and gene count matrices were produced using featureCounts(Subread v2.0.6)40. Read count matrices were imported into R-Studio (vRtidyverse/4.2.0)) where count normalization and differential gene expression analysis was conducted using DESeq2(v1.40.2).
Assembly: Hg38 - GRCh38 (NCBI GCF_000001405.40)
Supplementary files format and content: .csv file(s) containing normalized gene expression count matrix and DESeq2 differential expression analysis results

growth_protocol: iPSCs were differentiated to Neural Precursor Cells (NPCs) and Glutamatergic Forebrain neurons using a modified dual-SMAD inhibition protocol. Briefly, iPSCs were detached and plated as a monolayer at 100% confluence in TeSRTM-E8TM media containing 10 µM ROCK Inhibitor (Y-27632) for 24 h. On day 2, media was changed to 3N+A Media (241 ml DMEM/F12 with HEPES + L-Glut, 241 ml Neurobasal Medium, 5 ml NEAA, 2.5 ml N2 supplement, 5 ml B27 (- Vitamin A), 2.5 ml Glutamax, 2.5 ml Pen/Strep, 125 µl Insulin, and 3.5 µl BME) supplemented with two SMAD inhibitors: 10 µM SB431542 (Cayman Chemical) and 1 µM dorsomorphin (Cayman Chemical). At day 10-12, neuroepithelial sheets were combed into large clumps, passaged, and maintained on GeltrexTM coated plates in 3N+A media supplemented with 20 ng/ml Fibroblast Growth Factor (FGF), with daily media changes until neuronal rosettes appeared. Rosettes were manually picked and dissociated into single cell NPCs using Accutase and plated on to GeltrexTM coated plates in neural expansion medium (3N+A containing 20 ng/ml FGF and 20 ng/ml epidermal growth factor (EGF)) with media changes every other day and passaged as needed using AccutaseTM. Neuronal differentiation was achieved by plating high-density NPCs and switching to Neuronal Induction Media (490 ml Brainphys, 10 ml SM1, 5 ml N2, 20 ng/ml Brain Derived Neurotrophic Factor (BDNF), 20 ng/ml Glial Derived Neurotrophic Factor (GDNF), 200 nM L-ascorbic acid, and 1 mM bucladesine(dbcAMP)). Neurons were maintained with half medium changes twice per week, with Neuronal Induction Media supplemented with 1 µg/ml laminin once per week. After 3 weeks of neuronal induction, post-mitotic neurons were detached using AccutaseTM and replated at a uniform density on PEI & laminin coated plates before experimentation.

extract_protocol:
For RNA-seq experiments, patient iPSC-derived neurons were plated and aged to ~10 weeks as previously described. Total RNA was extracted using TRIzol and chloroform, followed by isopropanol precipitation. RNA pellets were washed in 75%+ ethanol and resuspended in nuclease free H2O. Contaminating gDNA was removed by DNase I digestion (Fisher Scientific) and cleaned up using an RNA clean & concentrator kit (Zymo). Total RNA was quantified by NanoDrop UV/Vis spectrophotometry, analyzed for integrity by Bioanalyzer, and 1.5-2 µg total RNA was sent to Genewiz (Azenta) for rRNA-depletion library preparation and paired-end (PE) sequencing, where between 20-25m paired-end reads were achieved per sample.
Conducted by Azenta.

treatment_protocol: pLV-eF1-RFC1-eGFP full-length RFC1 expression plasmid was designed and synthesized by VectorBuilder, and pSMART-eF1-RFC1shRNA-tGFP expression plasmids were designed and produced by Horizon Discovery (Table 1). Plasmids were prepped for lentiviral production by bacterial transformation followed by maxi-prep. 80 µg of plasmid DNA was used for lentiviral particle generation at University of Michigan Viral Vector Core. Lentivirus particles were delivered resuspended in DMEM media at 100x concentration (1x108 TU/mL). Lentivirus transduction of patient iPSC-derived neurons occurred on DIV7 post-differentiation: neurons were first treated with 1 µg/mL polybrene for 30 minutes, before being washed with fresh complete Brainphys media and subsequently changed to conditioned media containing lentiviral particles diluted to their working concentration. Neurons were changed to fresh media 24 h after transduction, and fluorescently positive cells appeared ~72 h post-transduction.

tag: cell line

value: Stem Cell Derived Neurons

value: CANVAS

value: RFC1 Full-Length Lentivirus


title: microspore, mononuclear leaning stage, RNA-seq rep1

value: microspore

value: WT


title: Muscle,sham control,rep2


title: meiocyte, meiotic prophase I, RNA-seq rep2

value: meiocyte


title: CANVAS2, RFC1, DIV70

description: rRNA Depleted Total RNA


title: meiocyte, meiotic prophase I, RNA-seq rep1


title: leaf, stalk leaf, Bisulfite-seq rep2


title: meiocyte, meiotic prophase I, Bisulfite-seq rep2


title: leaf, stalk leaf, RNA-seq rep3


title: CANVAS1, RFC1, DIV70

description: rRNA Depleted Total RNA


title: leaf, stalk leaf, RNA-seq rep2


title: KO Lumbar NP Tissue 3

source_name: KO Lumbar NP Tissue 3

value: SDC4 KO

value: Nucleus Pulposus


title: B1003; control 2

value: control


title: CANVAS3, GFP, DIV70

description: rRNA Depleted Total RNA

value: GFP Lentivirus


title: MIA PaCa-2 cells, trametinib treatment  (5 μM)

first: Jiaqi

last: Tan

state: Shanghai

address: Cailun road 1200

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
SOAPnuke v1.5.2
The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5).
The expression level of genes was calculated by RSEM (v1.2.8)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
RNA was isolated from the cell pellet using TRIzol™ Reagent. 1.3 ug of total RNA was used for the construction of sequencing libraries.
The 23S and 16S rRNA were depleted using MicrobExpresskit. Genomic DNA was removed with two digestions usingAmplification grade DNAse 1. The RNA was sheared andreverse transcribed using random primers to obtain cDNA which wasused for library construction. The library quality was determined byusing Bioanalyzer 2100.

value: Pancreatic ductal adenocarcinoma

value: MIA PaCa-4 cells

value: Adenoma

value: Trametinib treatment  (5 μM)


title: CANVAS2, GFP, DIV70

description: rRNA Depleted Total RNA


title: ATAC-seq_SKBR3_FOXA1KD_01

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

country: South Korea

institute: Korea University College of Medicine

data_processing:
The quality of sequenced ATAC-seq data was evaluated with FastQC. All sequencing data were mapped onto the hg38 human genome assembly using Bowtie2.
SAMtools was used to remove duplicate reads, only non-duplicate reads kept in the BAM format were used for the subsequent analysis. Peak calling on nucleosome-free reads was performed by MACS2 using the module ‘‘callpeak’’.
Picard Tools and ggplot2 were used to analyze and plot the distribution of paired-end sequencing fragment sizes. For data normalization and visualization, the BAM files were converted to the bigWig format using the “bamCoverage”.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: MCF7, SKBR3 control and FOXA1 knockdown cells were cultured in DMEM +GlutaMAX-1 containing 10% Fetal bovine serum and pen/strep at 37˚C in 5% CO2. MCF10A cells were cultured in DMEM/F12 containing 5% horse serum, EGF, hydrocortisone, cholera toxin, insulin, and pen/strep at 37˚C in 5% CO2.

extract_protocol:
After a wash step in cold cell wash buffer, outer membranes were disrupted in lysis buffer for 2 min on ice. After a centrifugation step at 1,500g for 10 min, pelleted nuclei were kept for the next step. In a 50-μl final volume, tagmentation was performed for 30 min at 37 °C, using the Nextera DNA library prep kit. After addition of SDS to 0.2% final concentration, DNA was purified on AMPure XP beads using a 2:1 ratio (v/v) of beads:tagmented DNA.
Freshly eluted DNA was barcoded and amplified in 110-μl PCR volume to generate a library with the following PCR program: 65 °C, 5 min; 98 °C, 30 s; 11 cycles of (98 °C, 10 s ramping to 65 °C, 30 s), 4 °C hold. ATAC libraries were then pooled at equimolar concentration and were sequenced multiplexed on the Illumina NextSeq550 with 50-bp paired-ends

value: Human breast cancer

value: FOXA1 knockdown


title: MIA PaCa-2 cells, NBT treatment  (1 μM) and trametinib treatment  (5 μM)

value: MIA PaCa-5 cells


title: ATAC-seq_SKBR3_FOXA1KD_02


title: MIA PaCa-2 cells, NBT treatment  (1 μM)

value: MIA PaCa-3 cells

value: NBT treatment  (1 μM)


title: ATAC-seq_SKBR3_01


title: Control3, RFC1, DIV70

description: rRNA Depleted Total RNA

value: Stem Cell Derived Neurons

value: Control

value: RFC1 Full-Length Lentivirus


title: ATAC-seq_SKBR3_02

value: WT


title: CANVAS1, GFP, DIV70

description: rRNA Depleted Total RNA

value: CANVAS


title: MIA PaCa-2 cells, control

value: MIA PaCa-2 cells


title: SKBR3 cells, FOXA1 knockdown 4

data_processing:
The raw sequencing reads files in Fastq format were assessed for quality with FastQC.
Pseudo-alignment was achieved using Salmon (version 1.9) with hg38 referece genome.
Subsequent analysis were performed using DESeq2 (version 3.16) with output quantification files.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: SKBR3 control and FOXA1 knockdown cells were cultured in DMEM +GlutaMAX-1 containing 10% Fetal bovine serum and pen/strep at 37˚C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. RNA sequencing was performed using Illumina NextSeq550 system, with paired-end 2 x 101 bp read length.
RNA-seq libraries were constructed following Illumina NextSeq 550 standard mRNA protocol.


title: SKBR3 cells, FOXA1 knockdown 2


title: SKBR3 cells, FOXA1 knockdown 1


title: Control2, RFC1, DIV70

description: rRNA Depleted Total RNA

source_name: NLXa

value: NLXa


title: SKBR3 cells, Control 4


title: Muscle,sham control,rep1

value: Aorta

value: Vascular cells

value: ApoE knock out

value: male

value: sham control

value: 28 days


title: IP_GhD53_1

city: Xi`an

first: Chen

middle: Hao

last: Ren

state: Shannxi

address: No. 620, West Chang'an Street, Chang'an District, Xi'an City

department: College of Life Sciences

institute: Shannxi Normal University

description:
IP_D53_1_vs_IN_D53_1_1.promoter_peak.peak_annotation.txt
IP_D53_1_vs_IN_D53_1_2.promoter_peak.peak_annotation.txt

data_processing:
Align the clean reads data to the reference genome using BWA software [3] (version: 0.7.15-r1140)
Count the distribution of aligned reads on various functional elements of genes in the genome, and use the ChIPseeker R package to draw Venn-pie charts and UpSet plots for the distribution of Reads on gene functional elements.
Using the deeptools software (version: 2.5.4) to analyze and compare the distribution of reads within 2kb upstream and downstream of the transcription start site (TSS) in the aligned bam file, and the distribution of reads within 2kb upstream and downstream of the gene body region, and generate reads density plots for both.
Recombine the originally numerous indicators with certain relevance (distribution characteristics of reads) into a new set of mutually independent comprehensive indicators, so as to reduce the complexity of the problem and study the principal component relationships among samples.
After obtaining qualified sample comparison results, the core step of DAP-seq, enrichment interval analysis, will be performed. The whole genome will be scanned to preliminarily determine the intervals with a certain depth for establishing the basic data model. Combining high-quality aligned sequences within these intervals, a Poisson distribution model will be used to perform genome-wide testing and analysis to screen for intervals with significant enrichment with a q-value meeting the requirement, defined as potential peaks.
Assembly: Gossypium_hirsutum_v2.1
Supplementary files format and content: IP_D53_1_vs_IN_D53_1_1.promoter_peak.peak_annotation.txt (q is less than 0.05 and the FoldEnrichment is greater than 2)
Supplementary files format and content: IP_D53_1_vs_IN_D53_1_2.promoter_peak.peak_annotation.txt (p is less than 0.001 and the FoldEnrichment is greater than 1)
Library strategy: DAP-seq

organism: Gossypium hirsutum

source_name: fiber

extract_protocol:
The gene sequence of the transcription factor is inserted into a vector containing an affinity tag to construct a protein expression vector for in vitro protein expression. The expressed transcription factor will carry the affinity tag. Genomic DNA is extracted from the sample to construct a DNA library, and then the in vitro expressed transcription factor with the affinity tag and the DNA library are combined in vitro. Subsequently, all paired DNA-protein complexes are separated out.
Genomic DNA is extracted from the sample to construct a DNA library
DAP-seq (DNA affinity purification sequencing) is a high-throughput method for discovering TF binding sites by using in vitro expressed TFs to probe genomic DNA. The DAP-seq dataset can also provide insights into the biology and binding site architecture of many TFs. It is a high-throughput detection method that uses in vitro expressed TF to interrogate bare gdna fragments in order to establish binding locations (peaks) and sequence motifs.

value: fiber

tag: fraction

value: IP


title: IN_GhD53_1

value: input


title: Control1, RFC1, DIV70

description: rRNA Depleted Total RNA


title: SKBR3 cells, Control 3

value: Human breast cancer


title: SKBR3 cells, Control 2


title: PRP3

city: China

first: hongwei

last: Wei

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

data_processing:
CLC Genomics Workbench y 11.0.1
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CC genomic benchwork
Assembly: imm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: ovary

growth_protocol: Newborn 3 day post-partum mouse ovary were maintained in DMEM/F12 supplemented with 1% antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using ReliaPrep™ RNA Tissue Miniprep System (Promega). 2 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 manufacturers protocols

treatment_protocol: Mouse ovary were treated with DMEM/F12 supplemented with or without 2% PRP for 2 hours

value: ovary

value: In vitro culture treatment with PRP drug addition


title: leaf, stalk leaf, RNA-seq rep1

value: Non-heading Chinese cabbage (Brassica rapa. ssp. Chinensis)

value: leaf


title: SKBR3 cells, Control 1

value: WT


title: PRP2


title: MCF7, input

data_processing:
The raw sequencing reads from FOXA1 and matched input DNA were mapped to the human reference genome using the Burrows-Wheeler Aligner mem program.
After alignment, PCR duplicates were removed with Picard tools and FOXA1 binding regions were identified using MACS tool.
Peaks were annotated using annotatePeaks.pl script from HOMER.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: SKBR3 and MCF7 cells were cultured in DMEM +GlutaMAX-1 containing 10% Fetal bovine serum and pen/strep at 37˚C in 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor for 20min at high output.
DNA was purified with a QIAquick PCR purification kit (Qiagen, Germantown, MD, USA) for sequencing. ChIP-seq library preparation was done using the TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA) and sequenced on the Illumina NextSeq550 sequencing platform.

tag: chip target

value: none (input)


title: MCF7, FOXA1, ChIP


title: Control2, GFP, DIV70

description: rRNA Depleted Total RNA

value: NLXa

value: Stem Cell Derived Neurons

value: Control

value: GFP Lentivirus


title: PRP1


title: SKBR3 cells, FOXA1 knockdown 3

value: FOXA1 knockdown


title: Control1, GFP, DIV70

description: rRNA Depleted Total RNA


title: SK-L029-HEK293T-KAS_ATAC-600k_Kethoxal_pulldown

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
read alignment, KAS-ATAC, ATAC-seq and KAS-seq data Bowtie 1.0.1
bigWig file generation custom code
read alignment, Hi-C Juicer
Assembly: genome builds hg38
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for KAS-ATAC, ATAC-seq and KAS-seq
Library strategy: KAS-ATAC

growth_protocol: GM12878 and HEK293T cells were grown using the standard protocols for each cell lines -- RPMI 1640, 2 mM L-glutamine, 15% fetal bovine serum and 1% penicillin-streptomycin for GM12878 cells, and DMEM + sodium pyruvate, 6 mM L-glutamine, 10% fetal bovine serum and 1% penicillin-streptomycin for HEK293T cells.

extract_protocol:
Cells resuspended in 500 uL of media were supplemented with 5 mM N3-kethoxal (final concentration), then incubated for 10 minutes at 37C with shaking at 500 rpm in a Thermomixer, then pelleted by centrifuging at 500 g for 5 minutes at 4C. The ATAC-seq step was then carried out, by resuspending cells in 50 uL ATAC-RSB-Lysis buffer, incubation on ice for 3 minutes, addition of 1 mL ATAC-RSB-Wash buffer, centrifugation at 500 g for 5 min at 4C, and transposition in a total volume of 50 uL. DNA purification was carried out using the MinElute PCR Purification Kit. Multiple parallel ATAC reactions were carried out, including ~50,000 cells each, then were pooled together for the click reaction and biotin pull down. Click reaction was carried out by combining transposed DNA, 5 uL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma 760749), 20 mM K3BO3 (pH 7.0) and 20 uL 10XPBS in a final volume of 200 uL. Biotinylated DNA was purified using the MinElute PCR Purification Kit. For streptavidin pulldown of biotin-labeled DNA, 10 uL of 10 mg/mL Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) were separated on a magnetic stand, then washed with 300 uL of 1X TWB (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20). The beads were resuspended in 300 uL of 2X Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl), the biotinylated DNA was added (diluted to a final volume of 300 uL if necessary), and the beads were incubated for >15 minutes at room temperature on a rotator. After separation on a magnetic stand, the beads were washed with 300 uL of 1X TWB, and heated at 55C in a Thermomixer with shaking for 2 minutes. After removal of the supernatant on a magnetic stand, the TWB wash and 55C incubation were repeated.
Libraries were prepared on beads using the same settings as for ATAC-seq (72C for 3 minutes, 98C for 30 seconds, 10 cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 30 seconds). Beads were separated on a magnetic stand, and the supernatant was cleaned up using the MinElute PCR Purification Kit.


title: SKBR3, input


title: CANVAS 2, Rep2, DIV70

description: rRNA Depleted Total RNA

value: CANVAS


title: SK-L028-HEK293T-KAS_ATAC-600k_Kethoxal_supernatant

data_processing:
read alignment, KAS-ATAC, ATAC-seq and KAS-seq data Bowtie 1.0.1
bigWig file generation custom code
read alignment, Hi-C Juicer
Assembly: genome builds hg38
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for KAS-ATAC, ATAC-seq and KAS-seq

extract_protocol:
ATAC-seq experiments were carried out following the Omni-ATAC protocol. Briefly, ~50,000 cells were centrifuged at 5,00 g, then resuspended in 500 UL 1x PBS and centrifuged again. Cells were then resuspended in 50 UL ATAC-RSB-Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, 0.01% Digitonin) and incubated on ice for 3 minutes. Subsequently 1 mL ATAC-RSB-Wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.01% Digitonin) were added, the tubes were inverted several times, and nuclei were centrifuged at 500 g for 5 min at 4C. Transposition was carried out by resuspending nuclei in a mix of 25 uL 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 uL Tn5 transposase (custom produced) and 22.5 uL nuclease-free H2O, and incubating at 37C for 30 min in a Thermomixer at 1000 RPM.
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified (72C for 3 minutes, 98C for 30 seconds, 10 cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 30 seconds). Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 as 2x38mers.


title: CT2

value: In vitro culture treatment without drug addition


title: CT3


title: CANVAS 3, Rep1, DIV70

description: rRNA Depleted Total RNA


title: SK-L025-HEK293T-KAS_ATAC-600k_supernatant


title: CANVAS 3, Rep2, DIV70

description: rRNA Depleted Total RNA


title: SK-L024-HEK293T-Biotin_ATAC_600k_pulldown

data_processing:
read alignment, KAS-ATAC, ATAC-seq and KAS-seq data Bowtie 1.0.1
bigWig file generation custom code
read alignment, Hi-C Juicer
Assembly: genome builds hg38
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for KAS-ATAC, ATAC-seq and KAS-seq
Library strategy: biotin-ATAC

extract_protocol:
Biotin-ATAC experiments were carried out following the Omni-ATAC protocol followed by streptavidin pulldown. Briefly, ~50,000 cells were centrifuged at 5,00 g, then resuspended in 500 UL 1x PBS and centrifuged again. Cells were then resuspended in 50 UL ATAC-RSB-Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20, 0.01% Digitonin) and incubated on ice for 3 minutes. Subsequently 1 mL ATAC-RSB-Wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.01% Digitonin) were added, the tubes were inverted several times, and nuclei were centrifuged at 500 g for 5 min at 4C. Transposition was carried out by resuspending nuclei in a mix of 25 uL 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 uL Tn5 transposase carrying biotinylated adapters (custom produced) and 22.5 uL nuclease-free H2O, and incubating at 37C for 30 min in a Thermomixer at 1000 RPM.
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and subjected to streptavidin pulldown, then PCR amplified on beads (72C for 3 minutes, 98C for 30 seconds, 10 cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 30 seconds). Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 as 2x38mers.


title: CANVAS 1, Rep2, DIV70

description: rRNA Depleted Total RNA


title: BKO, PAD, TA5

city: Chicago

first: Pei

last: Zhu

state: IL

address: 420 E. Superior St

department: Biochemistry and Molecular Genetics

institute: northwestern university

data_processing:
Sequence reads were trimmed for adaptor sequences using the Trimmomatic (v0.33) tool
The trimmed reads were mapped to the mm10 Mus musculus reference genome using STAR aligner (v2.5.2).
The number of alignments mapped to each gene was counted using RSEM (v1.3.3), followed by passing to DESeq2 using the tximport package
Differentially expressed genes (DEGs) were identified through the results function in DESeq2 and corrected for multiple testing (an adjusted P-value was generated using the Benjamini-Hochberg correction).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: Tibialis Anterior (TA) muscle

extract_protocol:
Total RNA was extracted using Ambion TRIzolTM Reagent in combination with the Direct-zol RNA MicroPrep kit (Zymo Research).
cDNA libraries were constructed from 1 μg of total RNA using the TruSeq stranded total RNA library preparation kit (Illumina 20020596).

treatment_protocol: Bmal1fx/fx mice were crossed with ACTA-rtTA-TRE-Cre transgenic mice. Bmal1 deletion in the skeletal muscle was triggered by administering concentrated doxycycline water via oral gavage for three consecutive days. A week after the last oral gavage dose, both control (Bmal1fxfx; ACTA-rtTA-TRE-Cre+/+) and Bmal1 skeletal muscle-conditional knockout (Bmal1fxfx; ACTA-rtTA-TRE-Cre-/-, Bmal1muscle) mice were underwent unilateral femoral artery ligation to simulate lower limb ischemia. Tibialis anterior (TA) muscles from the femoral artery ligated limb (PAD) and the contralateral limb (Intact) were collected at day 36 post-surgery.

value: Tibialis Anterior (TA) muscle

value: Bmal1 knockout

value: unilateral femoral artery ligation


title: SK-L013-HEK293T-ATAC_Kethoxal_with_biotin_enriched-1


title: SK-L015-HEK293T-ATAC_Kethoxal_pulldown_supernatant-1


title: SK-L014-HEK293T-ATAC_Kethoxal_with_biotin_enriched-2


title: CT1


title: SK-L020-HEK293T-ATAC-Kethoxal-2


title: BKO, PAD, TA6


title: SK-L027-HEK293T-KAS_ATAC-600k_input


title: Control3, GFP, DIV70

description: rRNA Depleted Total RNA


title: CANVAS 2, Rep1, DIV70

description: rRNA Depleted Total RNA


title: SK-L018-HEK293T-ATAC_Kethoxal_input-2


title: SK-L017-HEK293T-ATAC_Kethoxal_input-1


title: SK-L012-HEK293T-ATAC_Kethoxal-2


title: Control2, shRFC1, DIV70

description: rRNA Depleted Total RNA

value: RFC1 shRNA lentivirus


title: corpus, culture, rep3

data_processing:
Reads were trimmed using Trimmomatic 0.38. Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
trimmed reads were mapped to the felis catus genome using HISAT2 version 2.1.0, Bowtie2 2.3.4.1
StringTie version 2.1.3b was used to assemble known genes and transcripts
Assembly: NCBI Felis catus genome
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: epididymis

extract_protocol:
RNA extraction was performed using an RNAeasy kit (Qiagen)
Libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit

value: epididymis

value: culture


title: SKBR3, FOXA1, ChIP

value: Human breast cancer


title: SK-L016-HEK293T-ATAC_Kethoxal_pulldown_supernatant-2


title: BKO, Intact, TA4

value: untreated


title: SK-L009-GM12868-ATAC_Kethoxal_input-1


title: Control3, shRFC1, DIV70

description: rRNA Depleted Total RNA


title: SK-L008-GM12868-ATAC_Kethoxal_biotin_pulldown-2


title: SK-L011-HEK293T-ATAC_Kethoxal-1


title: SK-L019-HEK293T-ATAC-Kethoxal-1


title: SK-L010-GM12868-ATAC_Kethoxal_input-2


title: SK-L007-GM12868-ATAC_Kethoxal_biotin_pulldown-1


title: BKO, Intact, TA3


title: SK-L006-GM12868-ATAC_Kethoxal-2


title: Control3, DIV70

description: rRNA Depleted Total RNA


title: SK-L005-GM12868-ATAC_Kethoxal-1


title: BKO, PAD, TA2


title: CANVAS 1, Rep1, DIV70

description: rRNA Depleted Total RNA


title: BKO, Intact, TA5


title: BKO, Intact, TA1


title: Control1, DIV70

description: rRNA Depleted Total RNA


title: BKO, Intact, TA2


title: SK-L001-GM12868-ATAC-1


title: SK-L002-GM12868-ATAC-2


title: Control2, DIV70

description: rRNA Depleted Total RNA


title: subject 88-CF medium_only time 6 h

city: Prague 5

first: Ondrej

last: Cinek

address: V Uvalu 84

department: Dept of Medical Microbiology

country: Czech Republic

institute: Charles University

data_processing:
Global differences in gene expression were examined using PCA ordination plots visualising time and ETI exposure. The count matrix was first subjected to a variance-stabilising transformation, which for higher read counts is almost equal to base 2 logarithm of normalized counts, while solving problems with a steep slope at low counts. Sample-to-sample distances were calculated using 2500 genes with the highest variance and evaluated over time and after ETI. Dissimilarity between gene transcription profiles was calculated using Spearman and Pearson correlations, as well as a Euklidean distance of individual gene expression vectors. Trajectory lengths were compared between the wells exposed to ETI and those incubated with medium only, using models similar to those used above.    Negative binomial models implemented in the DESeq2 package were used for gene expression modelling. All models had the organoid donor as a fixed term. The primary analysis was a comparison of organoids with ETI and with culture medium only after 4 hours of incubation in 12 subjects with CF (excluding the healthy technical control). We also assessed the effect at 4 and 6 hours and the interaction of ETI exposure with time; a variant of this model also included a term for being a good responder (6 patients) or a poor responder (6 patients) in the FIS assay. Finally, we tested for spontaneous changes in gene expression under the control treatment (a change of culture medium at time 0, followed by incubation for 2, 4 and 6 hours; Supplementary Figure 1, blue wells). Approximate Posterior Estimation for generalised linear model was used as an effect size shrinkage estimator for visualisation and gene ranking for downstream analyses.
Assembly: Genes were annotated using the Gencode annotation of the human genome (GRCh38), version 38 (Ensembl 104) of March 2021. Only protein-coding nuclear genes were included in the downstream analyses, due to the nature of the library preparation method relying on the presence of poly-A tails.
Supplementary files format and content: DESeq / matrix

source_name: intestinal organoid

growth_protocol: Previously established intestinal organoid cultures selected for the present transcriptomic experiment were retrieved from long-term storage in liquid nitrogen, thawed and the culture expanded according to the standard protocol for organoid culture and FIS assay preparation. To simulate FIS assay plate preparation conditions, grown organoids were mechanically split into 7 aliquots and each aliquot was plated in 4 uL drops of extracellular matrix Matrigel (Corning Inc, Corning, NY, U.S.A.) in a 12-well plate (fourteen drops per culture well), covered with culture medium and incubated at 37 °C for approximately 20 hours. The next day, the ETI exposure experiment was performed.

extract_protocol:
For each RNA extraction, one well of a 12-well plate with fourteen 4 µl drops of Matrigel containing organoids was harvested using 1 ml of cold RNAprotect Tissue Reagent (Qiagen, Hilden, Germany). Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) after homogenisation using a Beadbug homogeniser (Benchmark Scientific, Sayreville, NJ, U.S.A.). The quantity and purity of extracted RNA was verified using a Nanodrop (ThermoFisher, Waltham, MA, U.S.A.), and RNA integrity was evaluated with Agilent RNA 6000 Nano Kit on a Bioanalyser (both Agilent Technologies, Santa Clara, CA, U.S.). All RNA samples had a RNA Integrity Number (RIN) between 8 and 10.
Gene transcription profiles were obtained by 3’-mRNA sequencing. Sequencing libraries were prepared using the Collibri 3’ mRNA Library Prep Kit (ThermoFisher) and sequenced unidirectionally with a read length of 75 bases on a NextSeq 500 instrument using the NextSeq500/550 High Output v2.5 sequencing kit (both Illumina, Foster City, CA, U.S.A.). All libraries were constructed using one batch of the Collibri kit, and sequenced together in a single run.

value: intestinal organoid

value: medium_only, time 6 h


title: WT, PAD, TA5

value: wildtype


title: Control3, shControl, DIV70

description: rRNA Depleted Total RNA

value: Stem Cell Derived Neurons

value: Control shRNA lentivirus


title: L1626-GM12878_KAS

data_processing:
read alignment, KAS-ATAC, ATAC-seq and KAS-seq data Bowtie 1.0.1
bigWig file generation custom code
read alignment, Hi-C Juicer
Assembly: genome builds hg38
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for bigWig files for KAS-ATAC, ATAC-seq and KAS-seq
Library strategy: KAS-seq

extract_protocol:
500-mM N3-kethoxal solution was brought to 37C, then added to 1 mL of culture at a final concentration of 5 uM. Cells were then incubated for 5 minutes at 37c in a ThermoMixer at 1000 RPM. Cells were then pelleted by centrifugation, resuspended in 100 uL 1x PBS buffer, and DNA was immediately isolated using the Monarch Genomic DNA Purification Kit (NEB, Cat # T3010S), with the modification that elution was carried out with 87.5 uL 25 mM K3BO3 solution (pH 7.0). Biotin was clicked onto kethoxal-modified guanines by mixing 87.5 uL DNA, 2.5 uL 20 mM DBCO-PEG4-biotin (Sigma, Cat # 760749; DMSO solution), and 10 uL 10x PBS, and incubating at 37C for 90 minutes. DNA was isolated using AMPure XP beads and eluted in 130 uL 25 mM K3BO3 (pH 7.0), then sheared on a Covaris E220 for 120 seconds down to ~150-200 bp.
Libraries were built on beads using the NEBNext Ultra II DNA Library Prep kit (NEB, Cat # E7645L). Biotin pull down was initiated py pipetting 20 uL Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific, Cat # 65306) into DNA lo-bind tubes. Beads were separated on magnet, resuspended in 200 uL of 1x TWB buffer (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20), then separated on magnet again and  resuspended in 300 uL of 2x BB (Binding Buffer; 10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl). The DNA (130 uL) was added together with 170 uL 0.1x TE buffer, and incubated at RT on rotator for ~15 minutes. Beads were separated on magnet, resuspended in 200 uL of 1x TWB, and incubated at 55C in a Termomixer for 2 minutes with shaking at 1000 rpm. Beads were again separated on magnet and the 200-uL 55C TWB wash step was repeated. Beads were separated on magnet and resuspended in 50 uL 0.1x TE. End repair was carried out by adding 7 uL NEB End Repair Buffer and 3 uL NEB End Repair Enzyme, incubating at 20C for 30 minutes, then at 65C for 30 minutes. End repair was followed by adaptor ligation by adding 2.5 uL NEB Adaptor, 1 uL NEB Ligation Enhancer and 30 uL NEB Ligation Mix, incubating at 20C for 20 minutes, then adding 3 uL USER Enzyme and incubating at 37C for 15 minutes. Beads were separated on magnet, resuspended in 200 uL of 1X TWB, then incubated at 55C in a Thermomixer for 2 minutes with shaking at 1000 rpm. Subsequently beads were separated on magnet and resuspended in 100 uL of 0.1X TE, separated on magnet again, resuspended in 15 uL of 0.1X TE Buffer, and transfered to PCR tubes. Beads were then incubated at 98C for 10 minutes, and libraries were amplified by adding 5 uL of i5 primer, 5 uL of i7 primer and 25 uL of 2X Q5 Hot Start Polymerase Mix, using the following PCR program: 30 seconds at 98C; 15 cycles of 98C for 10 seconds, 65C for 30 seconds, and 72C for 30 seconds; and a final extension at 72C for 5 minutes. Beads were separated on magnet and the final libraries were purified from the supernatant using 50 uL AMPure XP beads, eluting in 0.1X TE buffer.


title: Control1, shRFC1, DIV70

description: rRNA Depleted Total RNA

value: Control


title: subject 88-CF medium_only time 2 h

value: medium_only, time 2 h


title: WT, PAD, TA6


title: WT, PAD, TA4


title: subject 88-CF ETI time 6 h

value: ETI, time 6 h


title: subject 88-CF medium_only time 4 h

value: medium_only, time 4 h


title: Control2, shControl, DIV70

description: rRNA Depleted Total RNA

value: NLXa


title: Control1, shControl, DIV70

description: rRNA Depleted Total RNA


title: BKO, PAD, TA4

value: Tibialis Anterior (TA) muscle

value: Bmal1 knockout


title: CANVAS Isogenic, Rep2, DIV70

description: rRNA Depleted Total RNA

value: CANVAS Isogenic


title: subject 76-CF medium_only time 6 h


title: subject 88-CF ETI time 2 h

value: ETI, time 2 h


title: WT, PAD, TA2

value: unilateral femoral artery ligation


title: subject 76-CF medium_only time 4 h


title: CANVAS Isogenic, Rep1, DIV70

description: rRNA Depleted Total RNA


title: subject 76-CF medium_only time 2 h


title: WT, Intact, TA5


title: subject 76-CF medium_only time 0 h

value: medium_only, time 0 h


title: subject 76-CF ETI time 6 h


title: CANVAS 3, Rep2, DIV70

description: rRNA Depleted Total RNA

value: CANVAS


title: WT, Intact, TA4

value: untreated


title: subject 76-CF ETI time 2 h

value: intestinal organoid


title: subject 88-CF medium_only time 0 h


title: CANVAS 3, Rep1, DIV70

description: rRNA Depleted Total RNA


title: subject 76-CF ETI time 4 h

value: ETI, time 4 h


title: WT, Intact, TA3

value: wildtype


title: subject 88-CF ETI time 4 h


title: CANVAS 2, Rep2, DIV70

description: rRNA Depleted Total RNA

value: Stem Cell Derived Neurons


title: WT, Intact, TA2


title: subject 64-CF medium_only time 6 h

value: medium_only, time 6 h


title: subject 64-CF medium_only time 0 h


title: CANVAS 2, Rep1, DIV70

description: rRNA Depleted Total RNA


title: subject 64-CF medium_only time 4 h


title: subject 64-CF medium_only time 2 h

value: medium_only, time 2 h


title: subject 64-CF ETI time 4 h


title: subject 64-CF ETI time 6 h

value: ETI, time 6 h


title: WT, Intact, TA6


title: CANVAS 1, Rep2, DIV70

description: rRNA Depleted Total RNA


title: subject 64-CF ETI time 2 h


title: subject 59-CF medium_only time 6 h


title: Tumor-bearing_mus_T3, lung, 10 weeks

city: Rizhao

first: Huifang

last: Shi

address: No. 126 Taian Road

institute: The Rizhao People’s Hospital Affiliated to Jining Medical University

data_processing:
Clean data was obtained from raw data by filtering reads with low quality. Bioinformatic analysis was performed using BMKCloud
Assembly: mm9
Supplementary files format and content: the SRPBM of detected circRNAs

source_name: lung

extract_protocol:
Total RNA from freshly frozen lungs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Then the RNA concentration and purity of each sample were assessed using NanoDrop 2000, and their integrity was verified via Agilent2100/LabChip GX Assay, with an OD260/OD280 ratio of 1.8 to 2.0 deemed suitable for further experimentation.RNA-seq library was prepared and sequencing was carried out on an Illumina platform.

value: lung


title: Tumor bearing_mus_T2, lung, 10 weeks


title: subject 59-CF medium_only time 2 h


title: CANVAS 1, Rep1, DIV70

description: rRNA Depleted Total RNA


title: subject 59-CF medium_only time 4 h

value: medium_only, time 4 h


title: subject 59-CF medium_only time 0 h


title: Tumor bearing_mus_T1, lung, 10 weeks


title: Control3, Rep.1, DIV70

description: rRNA Depleted Total RNA

value: Control


title: subject 59-CF ETI time 4 h


title: Wildtype_mus_C2, lung, 10 weeks


title: Wildtype_mus_C3, lung, 10 weeks


title: subject 59-CF ETI time 2 h


title: Control2, Rep.2, DIV70

description: rRNA Depleted Total RNA

value: NLXa


title: Control3, Rep.2, DIV70

description: rRNA Depleted Total RNA


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 24h, biol rep 3

city: London

first: Daniel

last: Goncalves-Carneiro

address: Sir Alexander Fleming Building, Imperial College Rd

institute: Imperial College London

data_processing:
Reads containing adapters or reads of low quality were removed and clean reads were mapped onto Genome assembly GRCm38 (mm10) using STAR aligner. Gene counts were extracted and downstream analysis was performed using DESeq2. Analysis of differential gene expression was also performed by Novogene by normalization of read counts and estimation of model dependent p-value and false discovery rate based on multiple hypothesis by Novogene's standard analysis pipelines.
Assembly: GCA_000001635.2 (GRCm38/mm10)
Supplementary files format and content: File: gene_count_spleen.xls, contains read counts of each gene for each Spleen sample with corresponding gene annotation. Excel file.

source_name: Spleen

extract_protocol:
Extracted spleens were washed in cold PBS and submerged in RNAlater preservation solution. Samples were kept at -80˚C until further processing. Spleens were then thawed and homogenized in a solution of TRIzol reagent and ultrapure water (3:1 ratio). Total RNA was extracted according to manufacturer's guidelines. RNA quality was assessed by nanodrop and independently by Novogene Corporation Inc.
Ribosomal RNA was removed from total RNA samples, followed by cDNA synthesis through reverse transcription. RNA libraries were prepared for RNA sequencing by Novogene following Novogene's standard protocols.

treatment_protocol: Three 9-week old mice were used per group. Poly I:C-treated mice were injected intraperitoneally with a solution of 5% glucose, jetPEI transfection reagents and 10µL of a 10mg/ml poly I:C solution. Mock-treated mice were injected with a solution of 5% glucose and jetPEI transfection reagent.

value: Spleen

value: ZAP-/-

value: Poly I:C-treated


title: Control1, Rep.2, DIV70

description: rRNA Depleted Total RNA


title: subject 58-CF medium_only time 6 h


title: subject 58-CF medium_only time 2 h


title: Wildtype_mus_C1, lung, 10 weeks


title: Control2, Rep.1, DIV70

description: rRNA Depleted Total RNA


title: subject 58-CF medium_only time 4 h


title: subject 58-CF medium_only time 0 h

value: medium_only, time 0 h


title: subject 58-CF ETI time 4 h


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 24h, biol rep 1


title: Control1, Rep.1, DIV70

description: rRNA Depleted Total RNA


title: subject 54-CF medium_only time 6 h


title: subject 58-CF ETI time 2 h

value: ETI, time 2 h


title: subject 58-CF ETI time 6 h


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 24h, biol rep 2


title: DU145_PSF_rep1

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie-1.1.2 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.19.
Signal scores in bed files were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-3)
Assembly: hg19
Supplementary files format and content: Bed files that summarized significant peak regions (P-value < 1.0xE-3)

growth_protocol: 22Rv1 and DU145 cells were cultured in RPMI 1640 containing 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN). 300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction. Size selected adaptor-modified DNA fragments are amplifiedand the resulting PCR products are purified by MinElute column (QIAGEN). The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent).

treatment_protocol: For p53 ChIP-seq analysis, 22Rv1 cells were treated with C-30 for 24 h.

value: prostate cancer cells

value: PSF (Sigma WH0006421M2 )

value: vehicle for 24h


title: subject 59-CF ETI time 6 h

value: intestinal organoid


title: subject 54-CF medium_only time 2 h


title: subject 54-CF medium_only time 4 h


title: subject 54-CF medium_only time 0 h


title: DU145_PSF_rep2


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 24h, biol rep 2

value: WT


title: DU145_input

value: input


title: subject 54-CF ETI time 4 h

value: ETI, time 4 h


title: subject 54-CF ETI time 6 h

value: ETI, time 6 h


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 24h, biol rep 1


title: subject 54-CF ETI time 2 h


title: subject 53-CF medium_only time 6 h

value: medium_only, time 6 h


title: 22Rv1_input


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 12h, biol rep 2


title: 22Rv1_C30_p53_2

value: p53 (Santacruz Do1)

value: C-30 2 microMfor 24h


title: subject 53-CF medium_only time 2 h

value: medium_only, time 2 h


title: subject 53-CF medium_only time 4 h

value: medium_only, time 4 h


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 12h, biol rep 1

value: Spleen

value: ZAP-/-


title: subject 53-CF medium_only time 0 h

value: medium_only, time 0 h


title: 22Rv1_C30_p53_1

value: C-30 0.5 microMfor 24h


title: 22Rv1_PSF_rep2

value: prostate cancer cells


title: subject 53-CF ETI time 2 h

value: ETI, time 2 h


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 12h, biol rep 3

value: Poly I:C-treated


title: subject 52-CF medium_only time 6 h

value: intestinal organoid


title: subject 52-CF medium_only time 2 h


title: subject 52-CF medium_only time 4 h


title: subject 53-CF ETI time 4 h


title: hADSCs-1013,scRNA-seq

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.

institute: Peking University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Adipose tissue

extract_protocol:
Cells were harvested and resuspended at 1 x 106 cells per milliliter in PBS supplemented with 0.04% BSA.
Using Single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension containing 300-600 living cells per microliter was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. On an S1000TM Touch Thermal Cycler (Bio Rad), captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEM. These steps were carried out at 53 °C for 45 minutes, followed by 85 °C for 5 minutes, and held at 4 °C. Single-cell RNA sequencing libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics) and sequenced by IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150).

value: Adipose tissue

value: hADSC


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 24h, biol rep 3

value: WT


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 12h, biol rep 2


title: 22Rv1_PSF_rep1

value: PSF (Sigma WH0006421M2 )

value: vehicle for 24h


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 12h, biol rep 3


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 6h, biol rep 3


title: subject 52-CF ETI time 2 h


title: subject 45-CF medium_only time 6 h

value: medium_only, time 6 h


title: subject 52-CF ETI time 6 h

value: ETI, time 6 h


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 6h, biol rep 2


title: subject 52-CF ETI time 4 h

value: ETI, time 4 h


title: subject 45-CF medium_only time 4 h

value: medium_only, time 4 h


title: hASFs-0721,scRNA-seq

description: 10x Genomics

source_name: Skin

value: Skin

value: dermal fibroblats


title: hCiLB-1013,scRNA-seq

description: 10x Genomics

source_name: induced from hADSC

value: induced from hADSC


title: ZAP-/- C57BL/6 mouse spleen, poly I:C-treated, 6h, biol rep 1

value: Spleen

value: ZAP-/-


title: subject 45-CF medium_only time 0 h

value: medium_only, time 0 h


title: subject 45-CF ETI time 6 h


title: subject 53-CF ETI time 6 h


title: DQ571591_mimics3

first: Chuandong

last: Wang

address: 320 Yueyang Road

institute: SJTU

description:
DQ571591_mimics3
mRNA_raw_counts.txt

data_processing:
Blastn (2.9.0+) software was used to identify piRNAs and obtain the read count number quantitatively
According to the CPM value of each sample, violin and density charts were made to show the distribution of the CPM of each sample
Assembly: Ensembl_v107
Supplementary files format and content: mRNA FPKM values for each sample
Supplementary files format and content: piRNA CPM values for each sample

source_name: cell line

extract_protocol:
RNA was isolated from peripheral blood plasma using an EZ-press Serum/Plasma RNA Purification Kit (EZB Bioscience, #EZB-RN2).
RNA samples were treated with 3'-terminal ligation, reverse transcription primer hybridization, 5'-terminal ligation, cDNA single strand synthesis, library amplification

value: cell line

value: Lung cancer cells

value: Transfected with DQ571591_mimics


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 6h, biol rep 3

value: Poly I:C-treated


title: subject 52-CF medium_only time 0 h

value: intestinal organoid


title: subject 45-CF ETI time 2 h

value: ETI, time 2 h


title: subject 45-CF ETI time 4 h


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 12h, biol rep 1

value: WT


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 6h, biol rep 2


title: DQ571591_mimics1

description:
DQ571591_mimics1
mRNA_raw_counts.txt


title: subject 35-CF medium_only time 6 h

value: medium_only, time 6 h


title: subject 35-CF medium_only time 4 h


title: ZAP+/+ C57BL/6 mouse spleen, poly I:C-treated, 6h, biol rep 1


title: subject 35-CF medium_only time 2 h

value: medium_only, time 2 h


title: mimics_NC3

description:
mimics_NC3
mRNA_raw_counts.txt

value: Transfected with mimics NC


title: hCiLB-0721,scRNA-seq

description: 10x Genomics

source_name: induced from skin fibroblats

value: induced from skin fibroblats


title: subject 35-CF medium_only time 0 h


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 24h, biol rep 3

value: Mock-treated


title: subject 35-CF ETI time 6 h

value: ETI, time 6 h


title: mimics_NC2

description:
mimics_NC2
mRNA_raw_counts.txt


title: subject 35-CF ETI time 4 h

value: ETI, time 4 h


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 24h, biol rep 2

value: Spleen


title: subject 45-CF medium_only time 2 h


title: subject 35-CF ETI time 2 h


title: subject 27-CF medium_only time 6 h


title: mimics_NC1

description:
mimics_NC1
mRNA_raw_counts.txt


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 24h, biol rep 1

value: ZAP-/-


title: subject 27-CF medium_only time 4 h

value: medium_only, time 4 h


title: subject 27-CF medium_only time 0 h

value: medium_only, time 0 h


title: subject 27-CF medium_only time 2 h


title: LysoIP-Seq of HeLa cells 2

city: Oxford

first: Pauline

last: Lascaux

address: The MRC Weatherall Institute of Molecular Medicine

department: Department of Oncology

institute: University of Oxford

description: Sequencing of ssDNA and dsDNA pooled

library_source: other

data_processing:
Raw data Quality Control (Trimmomatic)
Assembly: hg38
Supplementary files format and content: Reads aligned with BWA-MEM, Conversion of BAM files aligned to BigWig files using Galaxy

molecule: other

source_name: HeLa

growth_protocol: HeLa cells (ATCC Cat#CCL-2) were modified by the lentivirus pLJC5-TMEM192-3xHA (RRID:Addgene_102930) produced in HEK293T with the following packaging plasmids pAmphoRand CMV and Δ8.2R.  Clonal selection was conducted with puromycin and stable expression of TMEM192-3xHA was confirmed by western blotting and immunofluorescence staining. Selected clone was grown in Dulbecco’s modified Eagle medium (DMEM) containing 10 % foetal bovine serum (FBS) and 5 % Penicillin/Streptomycin, at 37 °C at 5 % CO2.

extract_protocol:
The DNA fragments sequenced were purified from the lysosomes vesicles of HeLa cells by LysoIP. LysoIP of two biological replicates was performed in HeLa expressing TMEM192-3×HA as described in Abu-Remaileh, M. et al., Science, 2017. Cells were collected by scraping in KPBS (136 mM KCl, 10 mM KH2PO4, adjusted pH 7.25 with KOH) and homogenized with 20 strokes of a 2 ml homogenizer. The homogenate was centrifuged at 1000 x g for 2 min at 4°C. The supernatant containing the cellular organelles including lysosomes was incubated with anti-HA magnetic beads (Thermo Fisher Scientific, Cat# 88837) on a rotator shaker for 15 min at 4 °C. Beads were washed four times in KPBS and eluted in 50 mM Tris pH 7.4, 150 mM NaCl and 0.2 % Triton.
Library construction and sequencing was performed by Genscript. Samples were denatured at 95 °C to convert dsDNA into ssDNA. Adapters were added to both ends of the ssDNA fragments using the T4 polynucleotide kinase and the T4 ligase. Subsequently, a digestion enzyme was used to remove excess adapters, adapter dimers and unligated ssDNA samples. PCR amplification of the library was performed by the KAPA HiFi HotStart (Roche). Library was sequenced on Illumina NovaSeq platform.
PE150 (Paired-End 150) sequencing method

treatment_protocol: Cells were treated for 6 hours with 50 nM Camptothecin (CPT, Sigma-Aldrich, Cat# 208925) and 50 nM Bafilomycin A1 (BAF, LKT Labs, Cat# B0025)

value: HeLa

value: Human epithelial cell adenocarcinoma uterus, cervix

tag: sample type

value: lysosomes vesicles

value: Stable cell lines modified by lentivirus with pLJC5-TMEM192-3xHA (RRID:Addgene_102930)

value: Treatment for 6 hours with 50 nM CPT and 50 nM BAF


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 24h, biol rep 3

value: WT


title: DQ571591_mimics2

description:
DQ571591_mimics2
mRNA_raw_counts.txt

value: cell line

value: Lung cancer cells

value: Transfected with DQ571591_mimics


title: LysoIP-Seq of HeLa cells 1

description: Sequencing of ssDNA and dsDNA pooled


title: subject 27-CF ETI time 6 h

value: intestinal organoid


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 24h, biol rep 2

value: Mock-treated


title: subject 27-CF ETI time 2 h

value: ETI, time 2 h


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 24h, biol rep 1


title: subject 22-CF medium_only time 4 h


title: CD8T_PBS_rep2

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

institute: West China Hospital

data_processing:
Off-Line Basecaller software (OLB V1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome using Hisat2.
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM value.
Genes differential expression analysis was performed by DESeq2 software between two different groups. The genes with the parameter of false discovery rate (FDR) below0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CD8+ T cells

growth_protocol: Cells were cultured at 37°C in a humidified incubator with 5% CO2 in RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA of CD8+ T cells was extracted  and purified using Trizol reagent. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit.
RNA libraries were prepared for sequencing using Illumina Novaseq TM 6000 sequence platform protocols

treatment_protocol: CD8+ T cells in the Norathyriol versus PBS-treated co-culture system with HCC cells

value: CD8+ T cells lymphocytes

tag: agent

value: PBS-treated co-culture system


title: subject 22-CF medium_only time 6 h

value: medium_only, time 6 h


title: CD8T_PBS_rep1


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 12h, biol rep 3

value: Spleen

value: ZAP-/-


title: subject 22-CF medium_only time 2 h

value: medium_only, time 2 h


title: subject 22-CF medium_only time 0 h

value: medium_only, time 0 h


title: CD8T_Norathyriol_rep1

value: Norathyriol-treated co-culture system


title: subject 22-CF ETI time 6 h

value: ETI, time 6 h


title: subject 22-CF ETI time 4 h

value: ETI, time 4 h


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 12h, biol rep 1


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 12h, biol rep 2


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 12h, biol rep 3

value: WT


title: subject 22-CF ETI time 2 h


title: CD8T_Norathyriol_rep2


title: Input DNA replicate 2

city: Glasgow

first: Shaun

middle: David

last: Patterson

address: University Avenue

institute: University of Glasgow

data_processing:
Reads (as Fastq files) trimmed using Trimmomatic (v0.36.5) and aligned to hg19 human genome build using BWA-MEM (v0.7.17.1), for reads >100 bp.
PCR duplicates removed from BAM files using RmDup and reads with Phred<20 removed; done with from samtools (v1.3.1).
BamCompare was used to normalise NFATc2 peaks to input DNA signal and generate bigwig files. Using these, peaks were called using epic2 (v0.0.52), for three biological replicates, pooled, using band width 300 bp and q-value<0.1 cutoff.
Blacklisted genomic regions (n=880) for hg19 build, from ENCODE database, were removed from epic2 peak data.
ChIPseeker package (v1.18.0) used to annotate peaks with Ensembl gene IDs.
Assembly: hg19
Supplementary files format and content: bigwig (excluding input samples)
Supplementary files format and content: bed file (for three pooled replicates, epic2 output)

source_name: THP-1 cells

growth_protocol: THP-1 cell culture: RPMI, 10% foetal bovine serum (FBS), 2 mM glutamine; cultured in a humidified incubator at 37'C with 5% CO2.

extract_protocol:
Per IP, 11x10^6 cells were fixed using 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min. Cells were lysed and the lysates sonicated using an EpiShear Probe Sonicator.
ChIP-seq libraries prepared from DNA using a Diagenode MicroPlex Library Preparation Kit and cleaned up using Beckman Coulter Ampure XP Beads.

value: THP-1 cells

value: Acute myeloid leukaemia


title: T21 CA 2

city: Boulder

first: Meaghan

last: Courvan

state: CO

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

data_processing:
Raw files were mapped separately to both human (hg38) and drosophila (dm6) genomes using the NascentFlow pipeline (https://github.com/Dowell-Lab/Nascent-Flow). Gene body reads from mapped .bam files were counted using featureCounts (Liao et al. Bioinformatics 2014).
Bidirectional reads for the human genome were identified using the BidirectionalFlow pipeline (https://github.com/Dowell-Lab/Bidirectional-Flow). A master "annotation" file of every bidirectional site in every sample was created from this output, and was used to count bidirectional reads in each sample using featureCounts.
Bidirectional reads from BidirectionalFlow and mapped .bam files from NascentFlow were input into Transcription Factor Enrichment Analysis (https://github.com/Dowell-Lab/TFEA) to characterize relative transcription factor activity
Assembly: hg38
Assembly: dm6
Supplementary files format and content: All *.rcc.tdf files were generated as part of NascentFlow pipeline using hg38
Supplementary files format and content: featurecounts_hg38_5ptrunc.txt file is the output of featureCounts for reads mapping to hg38 gene bodies. This was counted using an annotation file in which the 5' end of genes was truncated to eliminate the effects of disproportionately high transcription observed across 5' ends
Supplementary files format and content: featurecounts_hg38_bidir.txt file is the output of featureCounts for bidirectional transcription reads, generated from the output of BidirectionalFlow
Supplementary files format and content: featurecounts_dm6_diff53prime.txt file is the output of featureCounts for reads mapping to dm6 gene bodies.
Library strategy: PRO-seq

source_name: Immortalized cells

growth_protocol: Lymphoblastoid suspension cells were grown in RPMI medium supplemented with 20% fetal bovine serum, pennicilin/strep, and L-glutamine in incubators set to 37C and 5% CO2

extract_protocol:
45 minutes after vehicle treatment, cells were collected, spun down, washed once in PBS,  then nuclei were isolated using a lysis buffer containing 10 mM Tris pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1 uL/10 mL SUPERase-In, and protease/phosphatase inhibitor cocktail. Nuclei were snap-frozen in freezing buffer consisting of 50 mM Tris pH 8.3, 5 mM MgCl2, 40% glycerol. 0.1 mM EDTA, and SUPERase-In until library preparation
10 million human nuclei/replicate were mixed with 100,000 Drosophila melanogaster nuceli per replicate. Nuclear run-ons were performed in the presence of biotinylated CTP and nascent RNA was isolated using strepdavidin beads. Library preparation was performed as described in Fant et al. Mol Cell 2021 (PMID 32229306)

treatment_protocol: Cells were split and plated on T75 flasks, allowed to recover for 24 hours, then media containing either vehicle (final concentration 0.01% DMSO) or Cortistatin A (100 nM) was added to each flask. After 30 minutes, media containing vehicle (final concentration 40 μM Tris pH 7.4) was added to cells.

value: Immortalized cells

value: Lymphoblastoid

value: B cells

value: 100 nM Cortistatin A + 40 uM Tris pH 7.4


title: Input DNA replicate 3


title: T21 CA 1


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 12h, biol rep 2

value: Mock-treated


title: Input DNA replicate 1


title: T21 V 1

value: 0.01% DMSO + 40 uM Tris pH 7.4


title: KKG185

type: genomic

city: Tartu

first: Alena

last: Kushniarevich

address: Riia 23b

department: Institute of Genomics

country: Estonia

institute: UNIVERSITY OF TARTU

description: Genomic DNA extracted from blood was genotyped using InfiniumOmniExpress-24v1.2 (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on an iSCAN System (Illumina).

data_processing:
Image data was analyzed using Genomestudio 2.0.5 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master, according to the manufacturer's protocol. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix and resuspended in hybridization buffer.

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: project

tag: samplewell

tag: population

value: Sart-Kalmak

tag: geographic location

value: Kyrgyzstan


title: subject 27-CF ETI time 4 h

tag: tissue

value: intestinal organoid

tag: treatment


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 12h, biol rep 1

value: Spleen

tag: genotype


title: NFATc2 IP replicate 3

description: Galaxy17-[epic2_on_data_9,_data_5,_and_others__BED].bed

tag: cell type

tag: chip antibody

value: NFAT1 (D43B1) XP Rabbit mAb #5861 (CST)


title: NFATc2 IP replicate 2


title: cKO27 hypothalamus, control, week 6

city: Safed

first: Evan

last: Elliott

address: Henrietta Szold Street, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt
Resulting reads shorter than 30bp were discarded.
Reads were mapped to the M. musculus reference genome GRCm39 using STAR,  supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04).
Expression levels for each gene were quantified using htseq-count,  using the gtf above.
Differentially expressed genes were identified using DESeq2 with the betaPrior, cooksCutoff and independentFiltering parameters set to False.
Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was run using snakemake.
Assembly: M. musculus reference genome GRCm39
Supplementary files format and content: excel file

source_name: Prefrontal cortex

growth_protocol: 8 week old mice

extract_protocol:
RNA havrasted using Qiagen mini kit (cat# 74104), purification of total RNA from animal tissues according to manufaturer's
RNA libraries were made using mRNS isolation (NEB protocol E7490), than NEBNext Ultra II RNA Library prep (E7770L) according manufacturer's protocol

treatment_protocol: wild type and knockout, 6 weekas aftre tamoxifen treatment, oral gavage.

value: Prefrontal cortex

tag: Sex

value: Female

value: 6 weeks after tamoxifen treatment

value: floxed Smc3 and Camk2a-cre/ERT2+ (Cre+)

value: Tamoxifen


title: KKG157


title: KKG160


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 6h, biol rep 3

value: ZAP-/-


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 6h, biol rep 2


title: KKG182


title: cKO24 hypothalamus, control, week 6

tag: time


title: ZAP-/- C57BL/6 mouse spleen, mock-treated, 6h, biol rep 1


title: cKO23 hypothalamus, control, week 6


title: ZAA45

value: Mongol Tsaatan

value: Mongolia


title: T21 V 2

value: Immortalized cells

value: Lymphoblastoid

value: B cells


title: NFATc2 IP replicate 1

value: THP-1 cells

value: Acute myeloid leukaemia


title: SK494, DMSO control

first: Sonia

middle: S

last: Kupfer

department: Human Genetics

institute: University of Chicago

data_processing:
RNA-seq equence alignment and gene expression value estimation was performed using RSEM (v.1.3.1) using the STAR aligner in paired-end mode.
RNA-seq differential expression analysis was performed with the R package DESeq2 (v1.30.1) after first filtering for protein coding biotype and using DESeq's independent filtering.
Assembly: transcriptome reference was generated from the 1000genomes Phase2 Reference Genome Sequence (hs37d5) and transcript annotations from the Gencode comprehensive gene annotation GTF (Release 29)
Supplementary files format and content: RSEM output files of transcript level abundances in tab-delimited plain text format

source_name: colonic organoid

growth_protocol: Organoids were derived using a protocol adapted from Sato et al 2011

extract_protocol:
RNA-seq: mRNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were prepared using Illumina mRNA TruSeq kits as protocolled by Illumina.

treatment_protocol: Organoids were treated with either 3mM ASA or vehicle control (0.1% DMSO) for 24 hours.

value: colonic organoid

value: F

tag: age

tag: ethnicity

value: EA

value: DMSO


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 6h, biol rep 3

value: Spleen

value: WT

value: Mock-treated


title: SK494, ASA treatment

tag: cell line

value: ASA


title: cKO22 hypothalamus, control, week 6

value: Prefrontal cortex

value: Female

value: 6 weeks after tamoxifen treatment

value: floxed Smc3 and Camk2a-cre/ERT2+ (Cre+)

value: Tamoxifen


title: TODG36

value: Tuvan Tozhu

value: Russia


title: SK490, DMSO control

value: M

value: AA


title: KKG150

value: Sart-Kalmak

value: Kyrgyzstan


title: TODG62


title: Wt26 hypothalamus, control, week 6

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)


title: TODG101


title: cKO21 hypothalamus, control, week 6


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 6h, biol rep 1


title: ZAA13

value: Mongol Tsaatan

value: Mongolia


title: LZ_sort-IP_4

city: Rehovot

first: Ziv

last: Shulman

address: 234 Herzl st.

department: Department of Immunology

institute: Weizmann Institute of Science

description: MARS-seq bulk RNAseq

data_processing:
Reads were quality trimmed using cutadapt. Mapped to the genome using STAR.
Htseq count was used to create count matrix
Assembly: mm10
Supplementary files format and content: counts: xlsx file with counts per sample per gene

molecule: polyA RNA

source_name: Lymph node

extract_protocol:
mRNA was isolated using the Dynabeads mRNA direct kit according to the manufacturer’s instructions (Life Technologies).
A bulk adaptation of the massively parallel single-cell RNA sequencing protocol (MARS-seq) was used (Jaitin et al. Science 2014) to generate RNA-seq libraries for transcriptomic analysis.

value: Lymph node

value: B cells


title: LZ_sort-IP_3

description: MARS-seq bulk RNAseq


title: cKO2- hypothalamus, control, week 6


title: SK488, DMSO control

value: colonic organoid

value: EA

value: DMSO


title: Wt25 hypothalamus, control, week 6

value: Prefrontal cortex

value: Female

value: 6 weeks after tamoxifen treatment


title: Wt19 hypothalamus, control, week 6

value: Tamoxifen


title: LZ_sort-IP_2

description: MARS-seq bulk RNAseq


title: SK486, DMSO control

value: F


title: TODG17

value: Tuvan Tozhu

value: Russia


title: Wt18 hypothalamus, control, week 6


title: ZAA19


title: ZAP+/+ C57BL/6 mouse spleen, mock-treated, 6h, biol rep 2

value: Spleen

value: WT

value: Mock-treated


title: LZ_sort_4

description: MARS-seq bulk RNAseq


title: ZAA4

value: Mongol Tsaatan


title: SK486, ASA treatment

value: ASA


title: TODG0


title: SK490, ASA treatment

value: M

value: AA


title: MG42

value: Mongol Torgut

value: Mongolia


title: LZ_sort_1

description: MARS-seq bulk RNAseq

value: Lymph node

value: B cells


title: Wt16 hypothalamus, control, week 6

value: Prefrontal cortex

value: Female

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)


title: SK484, DMSO control

value: colonic organoid

value: DMSO


title: cKO12 hypothalamus, control, week 6

value: Male

value: 6 weeks after tamoxifen treatment

value: floxed Smc3 and Camk2a-cre/ERT2+ (Cre+)

value: Tamoxifen


title: ZAA1

value: Mongol Tsaatan


title: LZ_sort_3

description: MARS-seq bulk RNAseq


title: cKO14 hypothalamus, control, week 6


title: SK484, ASA treatment

value: ASA


title: KSS7

value: Kalmyk Xinjiang

value: China


title: cKO10 hypothalamus, control, week 6


title: DZ_sort-IP_4

description: MARS-seq bulk RNAseq


title: LZ_sort_2

description: MARS-seq bulk RNAseq


title: SK488, ASA treatment

value: M

value: EA


title: MG6

value: Mongol Derbet

value: Mongolia


title: DZ_sort-IP_2

description: MARS-seq bulk RNAseq

value: Lymph node

value: B cells


title: LZ_sort-IP_1

description: MARS-seq bulk RNAseq


title: cKO8 hypothalamus, control, week 6

value: Prefrontal cortex


title: KSS18


title: SK476, ASA treatment

value: colonic organoid

value: F

value: AA


title: SK472, DMSO control

value: DMSO


title: SK474, ASA treatment


title: SK474, DMSO control


title: DZ_sort-IP_3

description: MARS-seq bulk RNAseq


title: Wt5 hypothalamus, control, week 6

value: Male

value: 6 weeks after tamoxifen treatment

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)


title: NEWBV32

value: Kalmyk Buzav

value: Russia


title: cKO9 hypothalamus, control, week 6

value: floxed Smc3 and Camk2a-cre/ERT2+ (Cre+)

value: Tamoxifen


title: SK472, ASA treatment

value: ASA


title: cKO13 hypothalamus, control, week 6


title: SK476, DMSO control


title: DZ_sort_3

description: MARS-seq bulk RNAseq


title: Wt4 hypothalamus, control, week 6


title: MG14

value: Mongol Derbet


title: SK464, DMSO control

value: M

value: EA


title: Wt6 hypothalamus, control, week 6


title: MG32

value: Mongol Torgut

value: Mongolia


title: DZ_sort-IP_1

description: MARS-seq bulk RNAseq

value: Lymph node

value: B cells


title: Wt3 hypothalamus, control, week 6

value: Prefrontal cortex


title: MG40


title: DZ_sort_4

description: MARS-seq bulk RNAseq


title: SK470, DMSO control

value: colonic organoid

value: DMSO


title: KT133

value: Kalmyk Torgut


title: MG7


title: SK470, ASA treatment


title: spleen leukemic T cells, BCAT1 KO 3, rep2

city: Padova

first: Erich

last: Piovan

address: via Gattamelata 64

department: Surgery, Oncology and Gastroenterology

country: Italy

institute: University of Padova

data_processing:
reads were trimmed for adapter sequences using trimgalore
trimmed reads were mapped to the genome using the STAR algorithm with default settings
The number of fragments overlapping genes were counted using featureCountsin Subread software packages
differential analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: spleen

growth_protocol: deltaE-NOTCH1  transduced BM progenitor cells (GFP+Lineage-cKit+Sca1+) from Bcat1 KO and Bcat1 WT  were transplanted into lethally irradiated C57BL/6J hosts .

extract_protocol:
Total RNA was isolated from the cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104)
2 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)

treatment_protocol: deltaE-NOTCH1 leukemia bearing mice were injected i.p. with three doses of ERG245 (30mg/kg) at 8 h intervals or vehicle (PBS)

value: spleen

value: mouse primary tumour spleen leukemic T cells

value: BCAT1 knock-out

value: PBS


title: DZ_sort_2

description: MARS-seq bulk RNAseq


title: HCT-116 cells, Heteronemin+Tetrac-3

city: Taipei City

first: Sukanya

last: Unson

address: No. 250, Wuxing Street, Xinyi District

department: Cancer biology and drug discovery

country: Taiwan

institute: Taipei medical university

hyb_protocol: Followed nCounter PanCancer Progression Panel protocol.

scan_protocol: Raw counts of mRNA were counted using the NanoString nCounter SPRINT Profiler Instrument.

data_processing:
Data were quantified, normalized and analyzed using the NanoString nSolver software analysis vers.4.0.
Gene Expression CodeSet profiling 770 genes; All data was normalized to internal reference controls (740 endogenous genes + 30 housekeeping genes).
Technical and biological normalization of the raw counts of each gene was performed using the NanoString nSolver software analysis vers.4.0.

label: Fluorescent barcode-labeled hybridization probes

source_name: Large intestine; Colon

growth_protocol: HCT-116 cells were seeded in six-well plates overnight at a density of 10^5 cells/well

extract_protocol: Total RNA was isolated using the TRIzol reagent

treatment_protocol: Cells were treated with heteronemin, tetrac, or their combination for 24 h.

value: Large intestine; Colon

value: Epithelial, Carcinoma

value: Heteronemin+Tetrac


title: KT159

value: Russia


title: SK462, ASA treatment

value: F

value: AA

value: ASA


title: Wt1 hypothalamus, control, week 6

value: Male

value: 6 weeks after tamoxifen treatment

value: floxed Smc3 and Camk2a-cre/ERT2- (Cre-)

value: Tamoxifen


title: spleen leukemic T cells, BCAT1 KO 3, rep1


title: SK464, ASA treatment

value: colonic organoid

value: M

value: EA


title: spleen leukemic T cells, BCAT1 KO 3, rep3

value: spleen

value: mouse primary tumour spleen leukemic T cells


title: SK462, DMSO control

value: DMSO


title: MG39

value: Mongol Torgut

value: Mongolia


title: SK456, DMSO control


title: SK448, DMSO control


title: NEWBV33

value: Kalmyk Buzav


title: HCT-116 cells, Tetrac-2

label_protocol: Followed nCounter PanCancer Progression Panel protocol.

value: Large intestine; Colon

value: Epithelial, Carcinoma

value: Tetrac


title: HCT-116 cells, Heteronemin+Tetrac-1

value: Heteronemin+Tetrac


title: spleen leukemic T cells, BCAT1 KO 7, rep1

value: BCAT1 knock-out

value: PBS


title: SK456, ASA treatment

value: ASA


title: spleen leukemic T cells, BCAT1 KO 7, rep2


title: MG3

value: Mongol Derbet


title: SK448, ASA treatment

value: colonic organoid

value: F

value: AA


title: spleen leukemic T cells, BCAT1 KO 7, rep3

value: spleen


title: HCT-116 cells, Tetrac-1


title: HCT-116 cells, Heteronemin+Tetrac-2


title: MG68


title: DZ_sort_1

description: MARS-seq bulk RNAseq

value: Lymph node

value: B cells


title: HCT-116 cells, Tetrac-3


title: MG25

value: Mongol Torgut


title: spleen leukemic T cells, WT6, rep2

value: mouse primary tumour spleen leukemic T cells

value: BCAT1 WT


title: spleen leukemic T cells, WT6, rep1


title: spleen leukemic T cells, WT6, rep3


title: SK444, DMSO control

value: EA

value: DMSO


title: SK446, DMSO control


title: HCT-116 cells, Heteronemin-3

value: Large intestine; Colon

value: Epithelial, Carcinoma

value: Heteronemin


title: HCT-116 cells, Heteronemin-2


title: HCT-116 cells, Heteronemin-1


title: MG5

value: Mongolia


title: SK446, ASA treatment

value: ASA


title: MG31


title: SK444, ASA treatment