title: X35SATWATRECOSROOT3

city: Riverside

first: Mauricio

middle: A

last: Reynoso

address: 4126 Genomics Bldg

department: Botany and Plant Sciences

institute: University of California Riverside

description:
DNA
Tagmented libraries

data_processing:
Genome_build: Genome_build:  RICE: IRGSP-1.0-30 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Rice RNA-seq raw reads were aligned to the IGRSP-1.0-30, with the splice junction aware short read alignment suite Bowtie2/Tophat2, allowing unique alignments with 2 or less mismatches
Rice read count data for RNA-seq was generated for features of exons-by-genes using the summarize Overlaps function of the GenomicRanges package in R.
ATAC-seq raw reads were aligned to the genome using Bowtie2 with default parameters
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<10.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1"
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the proccessed with limma-voom to quantile normalize samples
For accurate visualization, all filtered ATAC-seq bigwig files were scaled with quantile normalization and combined per condition to create a single merged bigwig  file for a condition using a bin size resolution of 1 base pair.
Supplementary_files_format_and_content: Transcripts per per million reads (TPM) values for polyA RNA or TRAP RNA datasets were calculated from count data after quantile normalization
Supplementary_files_format_and_content: Read counts values for ATAC datasets were calculated for regions 2kb upstream of ATG

organism: Oryza sativa Japonica Group

source_name: 27 days-old plant roots

growth_protocol: For plate experiments, seeds were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min, rinsed ten times with sterile distilled water and grown on plates (100 cm2) containing 0.5x Murashige and Skoog medium (MS), 1% (w/v) agar 1% (w/v) sucrose for 7 days (16h day / 8h night; at 28°C/25°C day/night; 110 μEm-2s-1). For greenhouse experiments, seeds were imbibed for 2 d in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote consistent germination. The seeds were then rinsed with distilled water and returned to 28° C in darkness for 24 h. Germinated seeds (21) were transferred to pots (15 cm diameter and 18 cm height), filled with Profile® Greens GradeTM and placed in a greenhouse at the University of California, Riverside California during June and July 2016. Temperature was controlled at 28° C for 16 h per day and at 25° C for 8 h per night. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at solar midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). For the field experiments, seedlings were germinated in Magenta boxes on selective medium after sterilization, transferred to Profile®, and grown for 14 d in the greenhouse before before transplantation into a pre-fertilized paddy at the Agricultural Operations field at the University of California Riverside Agricultural Experiment Station. The paddy was maintained at 8-10 cm depth for 35 d. Planting of genotypes was based on a randomized design with ten plants per biological replicate.

extract_protocol:
Nuclei were purified from frozen and pulverized tissue as previously described for O. sativa (Reynoso et al, 2018). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. For low number cell populations tissue and extraction buffer was scaled up. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB-T, NPB supplemented with 0.1% (v/v) Triton X-100, in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 7 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles first to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 7 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube.
Tn5 tagmented ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al., 2017, Reynoso et al., 2019)
Nuclei were purified from frozen and pulverized tissue as previously described for O. sativa (Reynoso et al., 2018) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Reynoso et al., 2019), with slight modifications. Minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3) using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described  (Mustroph et al., 2009, Reynoso et al., 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least three biological replicates for each condition.

treatment_protocol:
For plate experiments, Oryza sativa cv. Nipponbare seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min, rinsed ten times with sterile distilled water and grown on plates (100 cm2) containing 0.5x Murashige and Skoog medium (MS), 1% (w/v) agar 1% (w/v) sucrose for 7 days (16h day / 8h night; at 28°C/25°C day/night; 110 μEm-2s-1). For greenhouse experiments, seeds were imbibed for 2 d in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote consistent germination. The seeds were then rinsed with distilled water and returned to 28° C in darkness for 24 h. Germinated seeds (21) were transferred to pots (15 cm diameter and 18 cm height), filled with Profile® Greens GradeTM and placed in a greenhouse at the University of California, Riverside California. Temperature was controlled at 28° C for 16 h per day and at 25° C for 8 h per night. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). For the field experiments, seedlings were germinated in Magenta boxes on selective medium after sterilization, transferred to Profile®, and grown for 14 d in the greenhouse before before transplantation into a pre-fertilized paddy at the Agricultural Operations field at the University of California Riverside Agricultural Experiment Station. The paddy was maintained at 8-10 cm depth for 35 d. Planting of genotypes was based on a randomized design with ten plants per biological replicate.
Five independent biological replicates were grown for each treatment. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at solar midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). A fiber optic oxygen meter (Neofox Sport, Ocean Optics, Dunedin, USA), in five replicates was used to determine the percentage of dissolved oxygen in the submergence tanks was measured at the start and end of the experiment. Oxygen content was stable a 18.90 ± 0.03% at the start (0 d) and end of the experiment.

value: 27 days-old plant roots

tag: cultivar

value: Nipponbarre

tag: line

value: p35S:NTF2 (Reynoso et al., 2018)

tag: condition

value: Waterlogged recovery in greenhouse


title: X35SATWATRECOSROOT2

status: Public on May 02 2022

type: SRA

state: CA

country: USA

description:
DNA
Tagmented libraries

library_source: genomic

molecule: genomic DNA

tag: tissue


title: BxPC-3_KD2

city: Tainan City

first: Po-Hsien

last: Huang

address: No.1, University Road

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Cheng Kung University

description: Bisulfite-treated mRNA

data_processing:
Base-calling conducted by Illlumina bcl2fastq2
Sequence reads were first filtered to remove low-quality reads (Q < 20) and adapter contaminations by Galaxy Trim Galore! with read1 parameters “-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC” and read2 parameters “-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT”. A number of libraries were sequence twice to make each sample with approximately 30M expected mapped reads, therefore the reads of two runs were pooled after filtered and trimmed. The filtered reads then mapped to in silico converted human genome GRCh38 using the splice-aware alignment tool meRanGh from meRanTK with parameters “-mmr 0.1”.
5-methylcytosine calling was conducted by meRanCall with parameters “-md 5 –ei 0.1 –cr 0.99 -mcov 10 –gref -mr 0.05 -fdr 0.05”
The Multi-Join tool in Galaxy (usegalazy.org) was utilized to combine multiple 5-methylcytosine sites called from libraries in each cell line, and only sites present in at least 2 control (CT) libraries in each cell line were kept.
By comparing the average methRate of CT and KD samples, the sites with at least 0.05 decreased methR in each cell lines were identified. Finally, the differential mehtylated  sites that are common in at least 2 cell lines were classified into NSUN2-m5C sites.
Assembly: hg38
Supplementary files format and content: NSUN2-dependent 5-methylcytosine sites text file

molecule: total RNA

organism: Homo sapiens

growth_protocol: BxPC-3 cells were maintained in the RPMI medium supplemented with 10% FBS, 100 units/ml penicillin and 100 ug/ml streptomycin. MiaPaCa-2 cells were maintained in the DMEM medium supplemented with 10% FBS, 100 units/ml penicillin and 100 ug/ml streptomycin. PANC1 cells were maintained in the DMEM medium supplemented with 10% FBS, 100 units/ml penicillin and 100 ug/ml streptomycin. All three cells were incubated at 37℃ and maintained with 5% CO2.

extract_protocol:
About 1 X 10^7 cells were lysed with 900µl TRI reagent, and the total RNA was extracted with Direct-zol RNA miniPrep Plus (Zymo, Irvine, CA)  according to manufacturer's instruction. Average 30-40 µg total RNA was proceed to mRNA enrichment, which were done by oligo (dT)25 magnetic beads from Dynabeads mRNA DIRECT purification kit (Thermo Fisher Scientific, Waltham, MA). Then, the enriched mRNA samples were subjected to bisulfite conversion using EZ RNA methylation kit (Zymo, Irvine, CA) according to manufacturer's instruction. With one adjustment that the incubation step was modified into three cycles of 70℃ 10 minutes and 64℃ for 45 minutes followed by Amort et al. method.
About 20ng of bisulfite-treated mRNA was used to generate sequencing library. Libraries were built with NEBNext Ultra Ⅱ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) arrording to manufacturer's instruction. The fragmentation step was omitted due to previous bisulfite treatment had already resulted in fragmentation of RNA sequences to 200-500nt.

treatment_protocol: Cells were infected with lentivirus at the indicated multiplicity of infection (MOI) value of 2 to 3 in the presence of polybrene (BxPC-3: 2µg/ml, PANC1: 4µg/ml, and MiaPaCa-2: 2µg/ml). After 24 hours of incubation, the medium was changed to puromycin supplemented medium (BxPC-3: 1µg/ml, PANC1: 4µg/ml, and MiaPaCa-2: 1µg/ml) to select stable target gene knockdown clones.

tag: cell type

value: pancreatic cancer cell

tag: treatment

value: shNSUN2 Lentivirus


title: Xeno_VTP50469_10d-1 [T1XeVTP1]

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

description: RNA-seq in a human GIST cell line xenograft treated with the indicated drug

library_source: transcriptomic

data_processing:
RNA-seq data were aligned to hg19 using STAR with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Assembly: hg19
Supplementary files format and content: Gene expresion in FPKM are in text format

molecule: polyA RNA

source_name: GIST-T1 cell line xenograft

growth_protocol: Cell lines were grown in Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs Cat# E7645S). Paired-end 150 bp sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: Cells were treated with the indicated drugs for either 24 hours or 5 days. Xenografts were treated with the indicated drugs for either 5 or 10 days.

tag: cell line

value: KIT-dependent GIST cell line GIST-T48

value: Gastrointestinal stromal tumor (GIST)

value: VTP50469 10 day treatment


title: X35SATWATRECOSROOT1

description:
DNA
Tagmented libraries


title: IgAN_sample5

city: Seoul

first: Sehoon

last: Park

address: Daehak-ro 101

country: South Korea

institute: Seoul National University Hospital

data_processing:
Bowtie2 (version 2.1.0.0) for mapping
featureCounts was used to quantify gene expression (uniquely mapped reads)
Genome_build: GRCh73.p13
Supplementary_files_format_and_content: tab-delimited text files include raw read counts

source_name: Kidney tubulointerstitium

extract_protocol:
Biopsy cores from kidney disease patients were obtained from punch biopsies performed between 2010 and 2017 and stored in RNAlater (Qiagen, Hamburg, Germany) at -80°C. We collected samples from 46 patients with IgA nephropathy, 3 with diabetes mellitus nephropathy, 3 with focal segmental glomerulosclerosis, 3 with lupus nephritis, 4 with membranous nephropathy, and 9 with minimal change disease, according to sample availability. Patients with profound kidney dysfunction and those with an estimated glomerular filtration rate (eGFR) < 30 mL/min/1.73 m2 were not considered for this study. To establish the control group, normal cortical tissues were collected from the non-cancer-affected cortex of 22 renal carcinoma patients who exhibited no evidence of CKD (eGFR < 60 mL/min/1.73 m2 or detected dipstick albuminuria). These nephrectomy control group samples were also stored in RNAlater immediately after surgical excision via the same protocol used for the biopsy core tissues. The frozen cortical tissues from the nephrectomy controls were initially cut into the size of a biopsy core, and all collected kidney tissues were manually microdissected under a stereomicroscope (Olympus, Japan) to remove glomeruli. After thorough removal of glomeruli, total RNA was extracted from the remaining tubulointerstitial tissues using an RNeasy Micro Kit (Qiagen, Hamburg, Germany).
A TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) was used to construct cDNA libraries. Paired-end RNA-seq was performed on the HiSeq 2500 platform (Illumina, CA, USA), and 100-base-pair sequences were obtained as in FASTQ format.

value: Kidney tubulointerstitium

tag: diagnosis

value: IgAN

tag: estimated gfr (ckd-epi)

tag: technical outlier

value: No


title: X35SATWATOSROOT3

description:
DNA
Tagmented libraries

source_name: 26 days-old plant roots

value: 26 days-old plant roots

value: Waterlogged in greenhouse


title: Xeno_VTP50469_5d-3 [XeVTP5d3]

value: KIT-dependent GIST cell line GIST-T54

value: VTP50469 5 day treatment


title: Xeno_Imatinib5d-4 [XeIM5d4]

value: KIT-dependent GIST cell line GIST-T47

value: Imatinib 5 day treatment


title: BxPC-3_KD1

description: Bisulfite-treated mRNA


title: Xeno_Imatinib5d-3 [XeIM5d3]

value: KIT-dependent GIST cell line GIST-T46


title: X35SATWATOSROOT2

description:
DNA
Tagmented libraries

value: Nipponbarre

value: p35S:NTF2 (Reynoso et al., 2018)


title: Xeno_Imatinib5d-2 [XeIM5d2]

value: KIT-dependent GIST cell line GIST-T45


title: X35SATWATOSROOT1

description:
DNA
Tagmented libraries


title: MiaPaCa-2_CT1

description: Bisulfite-treated mRNA

value: pancreatic cancer cell

value: no treatment


title: Xeno_Imatinib5d-1 [XeIM5d1]

value: KIT-dependent GIST cell line GIST-T44

value: Gastrointestinal stromal tumor (GIST)


title: BxPC-3_CT2

description: Bisulfite-treated mRNA

value: control Lentivirus


title: BxPC-3_CT1

description: Bisulfite-treated mRNA


title: X35SATSUBRECOSROOT3

description:
DNA
Tagmented libraries

value: 27 days-old plant roots

value: Submergence recovery in greenhouse


title: HCT116 - Nipbl KD replicate 2

city: Philadelphia

first: Jing

last: Luan

address: 3615 Civic Center Blvd, ARC 315

institute: University of Pennsylvania

description: Nipbl; replicate #2

data_processing:
Seqtk (https://github.com/lh3/seqtk/blob/master/README.md) was run to trim the 6-base UMI.
Reads were mapped to human (hg38) genomes
Only primary alignments with mapq score at least 20 and without INDEL were reported and saved in bam files.
Duplicated reads with the same UMI and aligned to the same genomic loci were removed.
Bigwig files were generated and normalized using the sample size factor calculated by DEseq2.
Genome_build: hg38

source_name: Colorectal carcinoma

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Nuclei were isolated for PRO-seq, followed by run-on reactions, nascent RNA isolation, and cDNA library preparaion as described in the paper: Mahat, D.B., Kwak, H., Booth, G.T., Jonkers, I.H., Danko, C.G., Patel, R.K., Waters, C.T., Munson, K., Core, L.J., Lis, J.T., 2016a. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc 11, 1455–1476. doi:10.1038/nprot.2016.086
PRO-Seq

tag: genotype

value: Nipbl KD


title: X35SATSUBRECOSROOT2

description:
DNA
Tagmented libraries


title: X35SATSUBRECOSROOT1

description:
DNA
Tagmented libraries


title: Xeno_Imatinib10d-4 [XeIM10d2]

value: KIT-dependent GIST cell line GIST-T43

value: Imatinib 10 day treatment


title: HCT116 - Nipbl KD replicate 1

description: Nipbl; replicate #1


title: X35SATSUBOSROOT3

description:
DNA
Tagmented libraries

value: 26 days-old plant roots

value: Submergence in greenhouse


title: HCT116 - CTCF KD replicate 2

description: CTCF KD; replicate #2

value: CTCF KD


title: Xeno_Imatinib10d-2 [T1XeIM4]

value: KIT-dependent GIST cell line GIST-T41


title: Xeno_Imatinib10d-1 [T1XeIM1]

value: KIT-dependent GIST cell line GIST-T40


title: X35SATSUBOSROOT2

description:
DNA
Tagmented libraries

value: Nipponbarre

value: p35S:NTF2 (Reynoso et al., 2018)


title: BxPC-3_CT3

description: Bisulfite-treated mRNA

value: pancreatic cancer cell


title: Xeno_Control-3 [T1XeCon3]

value: KIT-dependent GIST cell line GIST-T38

value: Vehicle control treatment


title: HCT116 - Control replicate 1

description: No treatment; replicate #1

value: control


title: HCT116 - Control replicate 2

description: No treatment; replicate #2


title: HCT116 - CTCF KD replicate 1

description: CTCF KD; replicate #1


title: X35SATSUBOSROOT1

description:
DNA
Tagmented libraries


title: X35SATFIELDOSROOT2

description:
DNA
Tagmented libraries

source_name: 49 days-old plant roots

value: 49 days-old plant roots

value: Field grown


title: X35SATFIELDOSROOT3

description:
DNA
Tagmented libraries


title: GIST-T1_input

data_processing:
All Chip-Seq and CUT&Tag data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Genome_build: hg19

source_name: KIT-dependent GIST cell line GIST-T1

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 or paired-end 37 bp sequencing on an Illumina NextSeq 550 were prepared with a ThruPLEX DNA-seq Kit (Takara).

value: Gastrointestinal stromal tumor (GIST)

tag: antibody

tag: technique

value: ChIP-seq

tag: target


title: Xeno_Control-4 [T1XeCon4]

value: KIT-dependent GIST cell line GIST-T39


title: Xeno_Control-2 [T1XeCon2]

value: KIT-dependent GIST cell line GIST-T37


title: X35SATFIELDOSROOT1

description:
DNA
Tagmented libraries


title: Xeno_Control-1 [T1XeCon1]

value: KIT-dependent GIST cell line GIST-T36


title: GIST-T1_H3K9ac

value: H3K9ac, Active Motif Cat# 39137

value: Endogenous H3K9ac


title: Xeno_Imatinib10d-3 [XeIM10d1]

value: KIT-dependent GIST cell line GIST-T42

value: Imatinib 10 day treatment


title: X35SATDRORECOSROOT3

description:
DNA
Tagmented libraries

value: 27 days-old plant roots

value: Nipponbarre

value: Water deficit recovery in greenhouse


title: EPZ5676-4

description: RNA-seq in a human GIST cell line treated with the indicated drug

value: KIT-dependent GIST cell line GIST-T35

value: EPZ5676 treatment


title: EPZ5676-2

value: KIT-dependent GIST cell line GIST-T33


title: X35SATDRORECOSROOT1

description:
DNA
Tagmented libraries

value: p35S:NTF2 (Reynoso et al., 2018)


title: X35SATDRORECOSROOT2

description:
DNA
Tagmented libraries


title: EPZ5676-3

value: KIT-dependent GIST cell line GIST-T34


title: overexpression-3

city: Ann Arbor

first: Lyle

middle: A.

last: Simmons

state: MI

address: 1105 N. University Ave.

department: Molecular, Cellular, & Developmental Biology

institute: University of Michigan

data_processing:
Library strategy: DNA-seq
Reads aligned using BWA
Reads with mapping quality < 20 were removed using Samtools
Duplicates were removed & sorted by read-name using SortSam and MarkDuplicates
BAM files converted to BED files
1 kb windows made of PY79 genome using BEDtools
Counts in each window were quantified (annotateBed from BEDtools)
Normalized read counts by total number of reads and log2-transformed
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/CP006881
Supplementary_files_format_and_content: .txt files containing read counts in 1 kB windows for each sample

organism: Bacillus subtilis

source_name: whole cells

growth_protocol: OD=0.05 of WT cells were grown at 30C with shaking. Once the culture reached OD=0.2, treatment was administered. Cells were collected once the densities reached OD=0.65-0.9.

extract_protocol: Genomic DNA extraction was performed.

treatment_protocol: Water (vehicle control) for KJW1 and KJW117 or 0.1% xylose (KJW119)

tag: strain

tag: replicate

value: delta_ccrZ, amyE::Pxyl-ccrZ-cat


title: YAP1 ChIPseq

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

description:
HUVEC_YAP_ChIPseq
YAP1 immunoprecipitated DNA

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
Reads were aligned to the human genome (hg38) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig

source_name: Primary HUVECs from pooled donors at 48h

growth_protocol: Pooled human umbilical vein endothelial cells (HUVECs) were purchased from Lonza (#CC-2519) and cultured in endothelial basal medium (EBM, Lonza) supplemented with hydrocortisone (1 µg/mL), bovine brain extract (12 µg/mL), gentamicin (50 µg/mL), amphotericin B (50 ng/mL), human recombinant epidermal growth factor (10 ng/mL), and 10% fetal bovine serum (FBS, Life Technologies).

extract_protocol:
HUVECs were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 μg of antibody against YAP1 (abcam) or TAZ (Sigma). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: HUVECs were cultured for 48 hours before endogenous chromatin immunoprecipitation was performed.

value: HUVEC

value: Wild type

tag: chip antibody

value: YAP1 (abcam #ab52771)


title: TAZ ChIPseq

description:
HUVEC_TAZ_ChIPseq
TAZ immunoprecipitated DNA

value: TAZ (Sigma #HPA007415)


title: overexpression-1


title: RNAseq YAP S94A/S127A overexpression at 48h (replicate 3)

description:
YAP-dOE_3
YAP_TAZ_processedRNAseqData.xlsx

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
RNA-seq reads were mapped to the human reference genome with Star software. Reads counts were estimated for human Ensembl genes annotation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: YAP_TAZ_processedRNAseqData.xlsx

extract_protocol:
RNA was isolated from HUVECs using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a LabChip Gx Touch 24 (Perkin Elmer). 4 μg of total RNA was used as input for TruSeq Stranded mRNA Library preparation following the low sample protocol (Illumina).
Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 32M reads per library with 1x75bp single end setup.

value: YAP S94A/S127A overexpression

tag: time


title: X35SATDROOSROOT3

description:
DNA
Tagmented libraries

value: 26 days-old plant roots

tag: cultivar

tag: line

value: Water deficit in greenhouse


title: HUVEC pooled input

description:
HUVEC_pooled_input
Input DNA


title: VTP50469_WM1119-4

value: KIT-dependent GIST cell line GIST-T31

value: Gastrointestinal stromal tumor (GIST)

value: Combination VTP50469 and WM1119 treatment


title: RNAseq YAP S94A/S127A overexpression at 48h (replicate 1)

description:
YAP-dOE_1
YAP_TAZ_processedRNAseqData.xlsx


title: deletion-2


title: VTP50469_WM1119-3

value: KIT-dependent GIST cell line GIST-T30


title: X35SATCONOSROOT3

description:
DNA
Tagmented libraries

tag: tissue

value: Nipponbarre

tag: condition

value: Control in greenhouse I


title: RNAseq YAP S94A/S127A overexpression at 48h (replicate 2)

description:
YAP-dOE_2
YAP_TAZ_processedRNAseqData.xlsx

tag: cell type

tag: treatment


title: X35SATDROOSROOT2

description:
DNA
Tagmented libraries


title: deletion-3


title: RNAseq YAP S127A overexpression at 48h (replicate 3)

description:
YAP_3
YAP_TAZ_processedRNAseqData.xlsx

value: YAP S127A overexpression


title: WT-3

value: WT


title: deletion-1


title: WM1119-3

tag: cell line

value: KIT-dependent GIST cell line GIST-T26

value: WM1119 treatment


title: X35SATCONOSROOT1

description:
DNA
Tagmented libraries

value: p35S:NTF2 (Reynoso et al., 2018)


title: X35SATDROOSROOT1

description:
DNA
Tagmented libraries


title: VTP50469_WM1119-2

value: KIT-dependent GIST cell line GIST-T29


title: WT-1


title: RNAseq TAZ S51A/S89A overexpression at 48h (replicate 3)

description:
TAZ-dOE_3
YAP_TAZ_processedRNAseqData.xlsx

value: HUVEC

value: TAZ S51A/S89A overexpression


title: EPZ5676-1

value: KIT-dependent GIST cell line GIST-T32

value: EPZ5676 treatment


title: WM1119-1

value: KIT-dependent GIST cell line GIST-T24


title: VTP50469_WM1119-1

value: KIT-dependent GIST cell line GIST-T28


title: overexpression-2

value: delta_ccrZ, amyE::Pxyl-ccrZ-cat


title: WM1119-2

value: KIT-dependent GIST cell line GIST-T25

value: Gastrointestinal stromal tumor (GIST)


title: QHBATDROOSROOT3

description:
DNA
Tagmented libraries

value: 26 days-old plant roots

value: Nipponbarre

value: Water deficit in greenhouse


title: RNAseq YAP S127A overexpression at 48h (replicate 2)

description:
YAP_2
YAP_TAZ_processedRNAseqData.xlsx

value: YAP S127A overexpression


title: RNAseq TAZ S51A/S89A overexpression at 48h (replicate 2)

description:
TAZ-dOE_2
YAP_TAZ_processedRNAseqData.xlsx


title: RNAseq TAZ S89A overexpression at 48h (replicate 3)

description:
TAZ_3
YAP_TAZ_processedRNAseqData.xlsx

value: TAZ S89A overexpression


title: X35SATCON2OSROOT1

description:
DNA
Tagmented libraries

value: Control in greenhouse II


title: X35SATCON2OSROOT2

description:
DNA
Tagmented libraries

value: p35S:NTF2 (Reynoso et al., 2018)


title: X35SATCONOSROOT2

description:
DNA
Tagmented libraries

value: Control in greenhouse I


title: WT-2

value: WT


title: RNAseq TAZ S51A/S89A overexpression at 48h (replicate 1)

description:
TAZ-dOE_1
YAP_TAZ_processedRNAseqData.xlsx

value: HUVEC

value: TAZ S51A/S89A overexpression


title: RNAseq YAP S127A overexpression at 48h (replicate 1)

description:
YAP_1
YAP_TAZ_processedRNAseqData.xlsx


title: WM1119-4

value: KIT-dependent GIST cell line GIST-T27

value: WM1119 treatment


title: RNAseq TAZ S89A overexpression at 48h (replicate 2)

description:
TAZ_2
YAP_TAZ_processedRNAseqData.xlsx


title: VTP50469-4

value: KIT-dependent GIST cell line GIST-T23

value: VTP50469 treatment


title: QHBATDROOSROOT2

description:
DNA
Tagmented libraries


title: VTP50469-2

value: KIT-dependent GIST cell line GIST-T21


title: RNAseq TAZ S89A overexpression at 48h (replicate 1)

description:
TAZ_1
YAP_TAZ_processedRNAseqData.xlsx


title: VTP50469-3

value: KIT-dependent GIST cell line GIST-T22

value: Gastrointestinal stromal tumor (GIST)


title: VTP50469-1

value: KIT-dependent GIST cell line GIST-T20


title: RNAseq Control at 48h (replicate 2)

description:
CTRL_2
YAP_TAZ_processedRNAseqData.xlsx

value: Control


title: QHBATDROOSROOT1

description:
DNA
Tagmented libraries

value: 26 days-old plant roots

value: Nipponbarre

value: Water deficit in greenhouse


title: DMSO-4

value: KIT-dependent GIST cell line GIST-T19

value: DMSO control


title: QHBATCONOSROOT3

description:
DNA
Tagmented libraries

value: Control in greenhouse I


title: QHBATCONOSROOT1

description:
DNA
Tagmented libraries


title: CMZATWATRECOSROOT2

description:
DNA
Tagmented libraries

value: 27 days-old plant roots

value: Waterlogged recovery in greenhouse


title: DMSO-2

value: KIT-dependent GIST cell line GIST-T17


title: LT9

city: liege

first: Kristel

last: Van Steen

state: BELGIUM

address: BAT B34, GIGA-R Medical Genomics-BIO3

country: Belgium

institute: GIGA-R, Medical Genomics, University of Liege

data_processing:
After quality control and adaptor trimming with Trimmomatic , sequence data were mapped to the Genome Reference Consortium GRCh38 assembly using STAR v2.5.2.
Read counts for known genes were generated using the function HTSeq-count v0.6.1p
Normalised read counts were used  for identification of differential expressed genes (DEGs) across two groups of survivors (Short-term and long-term).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file Gene Ids  followed by raw read count

extract_protocol:
RNA was extracted using an All Prep DNA/RNA/miRNA Universal kit (Qiagen, Belgium) according to the manufacturer’s protocol
Paired-end RNA libraries were prepared using Truseq  RNA Access kit from Illumina
RNA-Seq of probe-captured coding transcripts

tag: subject status

value: long-term (LT) PDAC survivor

value: Pancreas

tag: tissue type

value: Tumor


title: CMZATWATRECOSROOT3

description:
DNA
Tagmented libraries


title: DMSO-3

value: KIT-dependent GIST cell line GIST-T18


title: LT6


title: LT8


title: RNAseq Control at 48h (replicate 3)

description:
CTRL_3
YAP_TAZ_processedRNAseqData.xlsx

value: HUVEC


title: sgMEN1-1

description: RNA-seq in a human GIST cell line treated with VTP50469, WM1119 or control.

value: KIT-dependent GIST cell line GIST-T13

value: Gastrointestinal stromal tumor (GIST)

value: sgMEN1 expression


title: LT5


title: CMZATWATOSROOT3

description:
DNA
Tagmented libraries

value: 26 days-old plant roots

value: Waterlogged in greenhouse


title: sgMEN1-3

value: KIT-dependent GIST cell line GIST-T15


title: CMZATWATOSROOT1

description:
DNA
Tagmented libraries

value: Nipponbarre


title: sgKMT2A-3

value: KIT-dependent GIST cell line GIST-T12

value: sgKMT2A expression


title: X35SATCON2OSROOT3

description:
DNA
Tagmented libraries

value: p35S:NTF2 (Reynoso et al., 2018)

value: Control in greenhouse II


title: QHBATCONOSROOT2

description:
DNA
Tagmented libraries

value: Control in greenhouse I


title: CMZATWATRECOSROOT1

description:
DNA
Tagmented libraries

value: 27 days-old plant roots

value: Waterlogged recovery in greenhouse


title: LT7

value: long-term (LT) PDAC survivor

value: Pancreas

value: Tumor


title: sgMEN1-2

value: KIT-dependent GIST cell line GIST-T14


title: LT3


title: LT4


title: CMZATFIELDOSROOT3

description:
DNA
Tagmented libraries

value: 49 days-old plant roots

value: Field grown


title: CMZATWATOSROOT2

description:
DNA
Tagmented libraries

value: 26 days-old plant roots


title: sgKMT2A-1

value: KIT-dependent GIST cell line GIST-T10

value: Gastrointestinal stromal tumor (GIST)


title: CMZATFIELDOSROOT2

description:
DNA
Tagmented libraries

value: Nipponbarre


title: RNAseq Control at 48h (replicate 1)

description:
CTRL_1
YAP_TAZ_processedRNAseqData.xlsx

value: HUVEC

value: Control


title: LT2


title: CMZATFIELDOSROOT1

description:
DNA
Tagmented libraries


title: sgLuc-3

value: KIT-dependent GIST cell line GIST-T9

value: sgLuc expression


title: sgLuc-1

value: KIT-dependent GIST cell line GIST-T7


title: LT1


title: CMZATDRORECOSROOT2

description:
DNA
Tagmented libraries

value: 27 days-old plant roots

value: Water deficit recovery in greenhouse


title: CMZATDRORECOSROOT1

description:
DNA
Tagmented libraries


title: sgKAT6A-3

value: KIT-dependent GIST cell line GIST-T6

value: sgKAT6A expression


title: DMSO-1

value: KIT-dependent GIST cell line GIST-T16

value: DMSO control


title: sgKMT2A-2

value: KIT-dependent GIST cell line GIST-T11

value: sgKMT2A expression


title: ST9

value: short-term (ST) PDAC survivor

value: Pancreas

value: Tumor


title: ST10


title: sgLuc-2

value: KIT-dependent GIST cell line GIST-T8

value: Gastrointestinal stromal tumor (GIST)


title: ST7


title: ST8


title: CMZATDROOSROOT2

description:
DNA
Tagmented libraries

value: 26 days-old plant roots

value: Nipponbarre

value: Water deficit in greenhouse


title: CMZATCONOSROOT2

description:
DNA
Tagmented libraries

value: Control in greenhouse I


title: ST4


title: sgKAT6A-1

value: KIT-dependent GIST cell line GIST-T4


title: CMZATDRORECOSROOT3

description:
DNA
Tagmented libraries

value: 27 days-old plant roots

value: Water deficit recovery in greenhouse


title: sgBRPF1-3

value: KIT-dependent GIST cell line GIST-T3

value: sgBRPF1 expression


title: sgBRPF1-1

description: RNA-seq in a human GIST cell line treated with the indicated sgRNA

value: KIT-dependent GIST cell line GIST-T1


title: CMZATDROOSROOT3

description:
DNA
Tagmented libraries


title: ST6


title: CMZATDROOSROOT1

description:
DNA
Tagmented libraries


title: ST3


title: CMZATCONOSROOT1

description:
DNA
Tagmented libraries


title: sgKAT6A-2

value: KIT-dependent GIST cell line GIST-T5

value: sgKAT6A expression


title: ST2

value: short-term (ST) PDAC survivor


title: CMZATCONOSROOT3

description:
DNA
Tagmented libraries


title: ST5

value: Pancreas


title: ST1

value: Tumor


title: ChIP-Seq TCF1 KO DN3 cells - NIPBL Rep2

first: Wenliang

last: Wang

state: PENNSYLVANIA

address: 421 Curie Boulevard

data_processing:
ChIP-seq libraries were pair-end sequenced by Illumina NextSeq 550. bowtie2 was used for alignment of ChIP-seq data. Reads aligned to the mitochondrial genome or chrY as well as reads mapping to multiple genomic loci were discarded from downstream analyses.
Callpeak function of macs2 was used to call the peaks of each experiment.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated by bedtools genomecov and wigToBigWig normalizing tracks to tags-per-million

organism: Mus musculus

source_name: Scid.adh cell line

extract_protocol:
Cells were chemically cross-linked by 1% formaldehyde. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the NEBNext Ultra II Library Prep Kit for Illuina (Part# E7645S). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+37 bp) was performed on a NextSeq 550 following the manufacturer's protocol.

value: NIPBL (Bethyl A301-779A)

value: TCF1 KO

value: Scid.adh cell line


title: ChIP-Seq TCF1 KO DN3 cells - NIPBL Rep1


title: sgBRPF1-2

value: KIT-dependent GIST cell line GIST-T2

value: Gastrointestinal stromal tumor (GIST)


title: ChIP-Seq Wild type DN3 cells - NIPBL Rep1

value: empty vector


title: Unvaccinated_unstimulated_VC58

city: Cologne

first: Richard

middle: James

last: Acton

state: North Rhine-Westphalia

address: CECAD Cluster of Excellence at the University of Cologne, Joseph-Stelzmann-Straße 26

department: Bioinformatics Core

country: Germany

institute: CECAD

description: Unvaccinated unstimulated

data_processing:
nf-core RNA-seq pipeline v3.0 https://nf-co.re/rnaseq/3.0, https://doi.org/10.5281/zenodo.1400710
nextflow pull nf-core/rnaseq -r 3.0
nextflow run nf-core/rnaseq --input design_merged.csv --fasta ftp://ftp.ensembl.org/pub/release-103/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --gff ftp://ftp.ensembl.org/pub/release-103/gff3/homo_sapiens/Homo_sapiens.GRCh38.103.gff3.gz --gtf_count_type exon --gtf_group_features gene_id --gtf_extra_attributes Name --skip_biotype_qc -profile singularity -r 3.0
Pairwise differential gene expression between conditions was computed with DESeq2, log fold change values have been subject to shrinkage with the 'ashr' method.
Assembly: GRCh38 from Ensembl version 103

growth_protocol: PBMCs from individuals 1-3 weeks after second mRNA SARS-CoV-2 vaccination were isolated by density gradient centrifugation and selected for CD14 positive cells by magnetic seperation. CD14+ cells were grown for 5 days in in RPMI 1640 Medium containing 10% fetal bovine serum and 50 ng/ml M-CSF for macrophage differentiation at 37°C and 5% CO2. PBMCs from unvaccinated individuals were used as control.

extract_protocol:
Total RNA of 3 x 2.5x10^5 macrophages were isolated using the mirVana RNA isolation Kit (ThermoFisher)
RNA-Seq library prep was performed with 100 ng total RNA input and the NEBNext Ultra RNA library prep protocol according to standard procedures. Libraries were validated and quantified (Tape Station 4200).
All libraries were quantified by using the KAPA Library Quantification Kit and the 7900HT Sequence Detection System. Sequencing was done with NovaSeq6000 sequencers with a PE100bp read length aiming at 50 M reads/sample. Demultiplexing and FastQ file generation was performed using Illumina’s bcl2fastq2 software (v2.20.0).

treatment_protocol: Medium of differentiated macrophages was exchanged. After medium exchange, lipopolysaccharide (LPS) (5 µg/ml) or SARS-CoV-2 spike protein (S-protein) (0.1 ug/ml) were added for additional 4 h. Unstimulated cells were used as control. All experimentes were performed in technical triplicates.

value: macrophages

tag: vaccinated

value: no

tag: Sex

value: female

tag: stimulation

value: unstimulated

tag: internal patient id

tag: internal sample id

tag: long description

value: Macrophages of unvaccinated individual #4; Macrophages left unstimulated.


title: Unvaccinated_unstimulated_VC59

description: Unvaccinated unstimulated

value: male

value: Macrophages of unvaccinated individual #5; Macrophages left unstimulated.


title: ChIP-Seq Wild type DN3 cells - H3K27Ac Rep1

tag: chip antibody

value: H3K27Ac (Abcam ab4729)


title: Vaccinated_unstimulated_VC53

description: Vaccinated unstimulated

value: yes (Biontech)

value: Macrophages of vaccinated individual #3; Macrophages left unstimulated.


title: ChIP-Seq Wild type DN3 cells - NIPBL Rep2


title: Unvaccinated_unstimulated_VC61

description: Unvaccinated unstimulated

value: Macrophages of unvaccinated individual #6; Macrophages left unstimulated.


title: Vaccinated_unstimulated_VC55

description: Vaccinated unstimulated

value: Macrophages of vaccinated individual #4; Macrophages left unstimulated.


title: Vaccinated_unstimulated_VC57

description: Vaccinated unstimulated

value: Macrophages of vaccinated individual #6; Macrophages left unstimulated.


title: RNA-Seq DN3 TCF-1 KO Rep2

data_processing:
RNA-seq libraries were pair-end sequenced by Illumina NextSeq 550. RNA-seq samples were aligned by STAR_2.5.0a_alpha with parameters ‘--readFilesCommand zcat --outFilterMultimapNmax 1--outSAMtype SAM--alignEndsTypeLocal--outReadsUnmapped Fastx--outFilterMismatchNmax 1--alignMatesGapMax 400000--sjdbGTFfile’, with the GTF file being either the mus musculus GRCm38.91 gtf file for C57BL/6 strain or the mus musculus GRCm38.91 gtf shifted to NOD coordinates for the NOD strain.
HTSeq v0.6.1 facilitated counting RNA-seq reads on Gencode vM11 gene models with parameters ‘-s yes-t exon-m intersection-nonempty’.
Genome_build: mm10

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (QIAGEN). RNA integrity numbers were determined using a TapeStation 2200 (Agilent), and all samples used for RNA-seq library preparation had RIN numbers greater than 9.
Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara). Indexed libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired end sequencing (38 bp+37 bp) was performed on a NextSeq 550 following the manufacturer's protocol.

treatment_protocol: Cells were washed once with 1x PBS before resuspending pellet in 350 μL Buffer RLT Plus (QIAGEN) with 1% 2-Mercaptoethanol (Sigma), vortexed briefly, and stored at −80°C.

tag: genotype

value: Scid.adh cell line

value: TCF1 KO


title: Unvaccinated_unstimulated_VC50

description: Unvaccinated unstimulated

value: Macrophages of unvaccinated individual #1; Macrophages left unstimulated.


title: Vaccinated_unstimulated_VC56

description: Vaccinated unstimulated

value: Macrophages of vaccinated individual #5; Macrophages left unstimulated.


title: Unvaccinated_unstimulated_VC51

description: Unvaccinated unstimulated

value: macrophages

value: Macrophages of unvaccinated individual #2; Macrophages left unstimulated.


title: ChIP-Seq TCF1 KO DN3 cells - H3K27Ac Rep1


title: ChIP-Seq Wild type DN3 cells - H3K27Ac Rep2

value: empty vector


title: Vaccinated_unstimulated_VC44

description: Vaccinated unstimulated

value: yes (Moderna)

value: female

value: unstimulated

value: Macrophages of vaccinated individual #2; Macrophages left unstimulated.


title: ChIP-Seq TCF1 KO DN3 cells - H3K27Ac Rep2

value: H3K27Ac (Abcam ab4729)


title: 20150311

type: RNA

city: Kyoto

first: Toshiyuki

last: Minami

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine,

hyb_protocol: Following fragmentation, 2.3 μg of cDNA was hybridized for 16 hr at 45°C on a Human Gene 2.0 ST Array (Thermo Fisher Scientific) according to the manufacturer’s instructions. GeneChips were washed and stained using a GeneChip Fluidics Station 450 according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System (Thermo Fisher Scientific).

data_processing: CEL files were processed using Transcriptome Analysis Console Software (Thermo Fisher Scientific) and subjected to normalization using the Robust Multiarray Analysis (RMA) method.

label: biotin

source_name: uterus

label_protocol: Fragmented and labeled cDNA was prepared by using the GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific) from 80 ng total RNA according to the manufacturer’s instructions.

growth_protocol: OE and EE samples were obtained from endometriosis patients and NE samples were obtained from two reproductive-age females who underwent surgery for uterine leiomyoma and mature cystic teratoma.

extract_protocol: Total RNA was extracted from excised NE, EE and OE tissues by using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: NE, EE and OE tissues were washed, and then minced.

tag: disease state

value: ovarian endometrioma

value: cystic tissue


title: RNA-Seq DN3 wild type Rep1

value: wild type


title: 20141219-02

value: endometrium with endometriosis

value: uterus


title: 20150127-02


title: 20150616

value: normal endometrium


title: RNA-Seq TCF1 induced 3T3 Rep2

value: Tcf7 induced

value: TCF1 induced


title: RNA-Seq DN3 TCF-1 KO Rep1

value: Scid.adh cell line

value: TCF1 KO


title: V272M+PAT

city: Shanghai

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

country: China

institute: Shanghai Jiaotong University

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg38 using STAR
Read counts were calculated by using htseq count
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes FPKM value of each sample

source_name: Pleura/pleural effusion, lymphocyte, Myeloid

growth_protocol: U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 37℃ under 5% CO2.

extract_protocol:
Total RNA was isolated using total RNA Purification Kit (B518651, Sangon Biotech). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U937 cells with p53-V272M and p53-R273H were treated with or without 10 μM PAT for 24 hr. No treatment on U937 cells expressing wild-type p53 or vehicle.

tag: cell lines

tag: p53 status

tag: pat treatment

value: yes


title: 20141217

tag: tissue


title: Control 3-weeks old rep5

city: London

first: Kerri

last: Kinghorn

state: London

address: Gower Street

department: Genetics, Evolution and Environment

country: United Kingdom

institute: University College London (UCL)

data_processing:
Reads mapping to the Drosophila genome (downloaded from FlyBase.org, version dmel_r6.31_FB2019_06).
Reads sorting by gene name.
Gene counts was performed with featureCounts (v.2.0.0) (https://doi.org/10.1093/bioinformatics/btt656) [default parameters]  using the transcriptome (downloaded from FlyBase.org, version dmel_r6.31_FB2019_06/gtf).
Differential gene experssion using DESeq2 (https://doi.org/10.1186/s13059-014-0550-8).
Genome_build: dmel_r6.31_FB2019_06
Supplementary_files_format_and_content: raw counts

organism: Drosophila melanogaster

source_name: Heads

growth_protocol: SYA food

extract_protocol:
Flies were flash frozen in liquid nitrogen, and decapitated on dry ice. RNA was harvested using Trizol reagent. Samples were polyA enriched using the Kapa mRNA HyperPrep kit. Illumina NextSeq v2.5, 150 cycles was used with 120ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aged the Gba1b-/- flies and their W1118 controls to 1 week and 3 weeks on standard SYA food.

value: fly heads

tag: age

value: 3 weeks


title: R273H

value: no


title: Unvaccinated_unstimulated_VC52

description: Unvaccinated unstimulated

tag: cell type

value: macrophages

value: female

value: unstimulated

value: Macrophages of unvaccinated individual #3; Macrophages left unstimulated.


title: Vaccinated_unstimulated_VC43

description: Vaccinated unstimulated

value: yes (Moderna)

value: Macrophages of vaccinated individual #1; Macrophages left unstimulated.


title: ORC2BP8, biological rep2

city: Charlottesville

first: Anindya

last: Dutta

state: Virginia

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Gene expression data from ORC2 mutant cell line

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol  (wtplus_reagentkit_assay_manual, 2013, Affymetrix).

scan_protocol: Standard scanner settings. Affymetrix scanner 3000 with 7G upgrade, Fluidics Stations 450

data_processing: The data were analyzed with Affymetrix Expression Console  using Affymetrix default analysis settings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol  (wtplus_reagentkit_assay_manual, 2013, Affymetrix).

growth_protocol: Cells were grown in a 37ºC incubator at 5% CO2.

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

treatment_protocol: No treatment.

tag: cell line


title: RNA-Seq TCF1 induced 3T3 Rep1

tag: treatment


title: V272M


title: ORC1B14, biological rep2

description: Gene expression data from ORC1 mutant cell line


title: RNA-Seq DN3 wild type Rep2

value: wild type

value: empty vector


title: Control 3-weeks old rep4


title: R273H+PAT


title: ORC2B2, biological rep2


title: ORC2B2, biological rep1


title: RNA-Seq Normal 3T3 Rep1

value: untreated


title: Vector


title: Wild-type

value: p53-wild -type


title: ORC1BP32, biological rep2


title: RNA-Seq Normal 3T3 Rep2


title: WT, biological rep2

description: Gene expression data from WT cells

source_name: WT


title: Control 3-weeks old rep3


title: cnt58-2

city: Medford

first: David

last: Angeles-Albores

address: 61 Locust St

institute: Northwestern University

description: Wild-type C. elegans, 58hrs old, no ascr#10 exposure, replicate 2

data_processing:
Data quantification was performed using a nextflow pipeline, nf-core/rnaseq v3.1. The relevant config file is provided. The pipeline can be found at https://github.com/nf-core/rnaseq
salmon
Genome_build: cel235; gtf version 104

organism: Caenorhabditis elegans

source_name: Whole organism, synchronized via L1 starvation

growth_protocol: Synchronized populations of L1s were obtained by hypochlorite treatment as above and pipetted onto control or ascr#10 plates that had been seeded with 20μL drops of OP50 the previous day. Care was taken to keep the density between 30 and 50 L1s per plate. Sixteen plates (eight control and eight ascr#10 plates) were prepared in this manner for the “50 hour” sample and twelve plates (six control and six ascr#10 plates) were prepared for the “58 hour” sample. Worms were allowed to develop on these plates at 20oC until the allotted times. Just prior to harvesting the worms, each plate was closely examined for developmentally delayed or abnormal worms and males which were removed.

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Mini Kit (Cat. No. 74104) and on-column DNase digestion done with Qiagen RNase-Free DNase (Cat. No. 79254) according to the manufacturer’s protocols. Three independent samples were prepared and analyzed for each condition each time the experiment was performed. 1μg of total RNA was used in library preparation with NEBNext® UltraTM II Directional RNA Library Prep with Sample Purification Beads Kit for Illumina (NEB#E7765).
NEBNext® UltraTM II Directional RNA Library Prep with Sample Purification Beads Kit for Illumina (NEB#E7765)

treatment_protocol: Concentrated ascr#10 was stored in ethanol at -20oC. This stock was diluted with water and a total of 100μL (for 60mm plates) or 50μL (for 35mm plates) of ascaroside solution (containing 2.2 or 1.1 femtograms per plate, respectively) was applied to the plate and spread evenly with a sterile bent glass rod. Plates were incubated at 20oC overnight to allow the ascaroside to be absorbed. Control plates were prepared in the same manner using water as the control. The following day the plates were seeded with 20μL of a 1:10 dilution of OP50 overnight culture and allowed to grow at 20oC before use.

tag: strain

tag: age at collection

value: 58hrs post-L1 synchronization

tag: exposure

value: water

value: Whole organism


title: cnt58-3

description: Wild-type C. elegans, 58hrs old, no ascr#10 exposure, replicate 3


title: WT, biological rep1

description: Gene expression data from WT cells


title: ChIP-Seq Wild type DN3 cells - TCF1 Rep1

value: TCF1 (CST 2206S)

value: Scid.adh cell line


title: ChIP-Seq Wild type DN3 cells - TCF1 Rep2


title: ORC1BP32, biological rep1


title: ORC2BP8, biological rep1


title: Control 3-weeks old rep1

value: fly heads

value: 3 weeks


title: ORC1B14, biological rep1


title: ChIP-Seq Wild type DN3 cells - Smc1 Rep2

value: Smc1 (Bethyl A300-055A)


title: 20150318

value: normal endometrium

value: uterus


title: ChIP-Seq TCF1 KO DN3 cells - Smc1 Rep2

value: TCF1 KO


title: cnt50-3

description: Wild-type C. elegans, 50hrs old, no ascr#10 exposure, replicate 3


title: GBA 3-weeks old rep5


title: GBA 3-weeks old rep4


title: cnt50-2

description: Wild-type C. elegans, 50hrs old, no ascr#10 exposure, replicate 2


title: Control 3-weeks old rep2


title: 21_LUNG

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

description: Normalization and summarizzation performed with RMA algorith

hyb_protocol: Arrays were prepared according to Affymetrix GeneChip™ Hybridization, Wash, and Stain Kit

scan_protocol: Scanner 3000 7G

data_processing: Expression console software and Transcriptome console software 3.0 from Affymetrix

source_name: LUNG

label_protocol: Arrays were prepared according to Affymetrix specifications with GeneChip™ WT Pico Reagent Kit

growth_protocol: cells were cultured in minimum supplemented medium (DMEM+10% FBS + 1% PEN/STREP)

extract_protocol: Total RNA from the cells was extracted with the Trizol protocol followed by Qiagen RNeasy Mini Kit

treatment_protocol: Subculturing of plasmid or shRNA expressing cell lines is done in DMEM + 10% FBS + 4-6 µM puromycin

tag: sample type

value: benign murine lung tissue


title: ChIP-Seq Wild type DN3 cells - Smc1 Rep1


title: cnt50-1

description: Wild-type C. elegans, 50hrs old, no ascr#10 exposure, replicate 1


title: 49_BMDM

source_name: BMDM

value: bone-marrow macrophages from naive wildtype mice


title: GBA 3-weeks old rep3


title: cnt58-1

description: Wild-type C. elegans, 58hrs old, no ascr#10 exposure, replicate 1


title: ChIP-Seq TCF1 KO DN3 cells - Smc1 Rep1


title: 64_BMMC

source_name: BMMC

value: bone-marrow mast cells from naive wildtype mice


title: GBA 3-weeks old rep1


title: 56_TEC

description: Normalization and summarizzation performed with RMA algorithm

source_name: TEC

value: benign murine tissue


title: ChIP-Seq TCF1 KO DN3 cells - CTCF Rep1

value: CTCF (Millipore 07-729)


title: Control 1-week old rep5

value: 1 week


title: 34_CULA

source_name: CULA

value: urethane induced lung adenocarcinoma cell line from C57BL/6


title: ChIP-Seq TCF1 KO DN3 cells - CTCF Rep2


title: ChIP-Seq Wild type DN3 cells - CTCF Rep2

value: empty vector


title: ascr58-2

description: Wild-type C. elegans, 58hrs old, exposed to ascr#10, replicate 2

value: 58hrs post-L1 synchronization

value: Whole organism


title: 20_FULA1

value: urethane induced lung adenocarcinoma cell line from FVB mice


title: ascr58-3

description: Wild-type C. elegans, 58hrs old, exposed to ascr#10, replicate 3


title: ChIP-Seq Wild type DN3 cells - CTCF Rep1

value: Scid.adh cell line


title: 55_PANO2pC

value: pancreatic cancer cell line; lentiviral transduction of pControl


title: 15_PAN02pKRAS

value: pancreatic cancer cell line; lentiviral transduction of pKrasG12C


title: GBA 3-weeks old rep2

value: fly heads

value: 3 weeks


title: Control 1-week old rep3


title: Control 1-week old rep4


title: ascr50-3

description: Wild-type C. elegans, 50hrs old, exposed to ascr#10, replicate 3


title: ChIP-Seq TCF1 induced NIH-3T3 cells - Smc1

value: Smc1 (Bethyl A300-055A)

value: TCF1 induced


title: 14_PAN02wt

value: pancreatic cancer cell lines


title: ChIP-Seq TCF1 induced NIH-3T3 cells - TCF1

value: TCF1 (CST 2206S)


title: ascr50-1

description: Wild-type C. elegans, 50hrs old, exposed to ascr#10, replicate 1


title: Control 1-week old rep2


title: ascr58-1

description: Wild-type C. elegans, 58hrs old, exposed to ascr#10, replicate 1


title: ChIP-Seq TCF1 induced NIH-3T3 cells - CTCF Rep2


title: GBA 1-week old rep5


title: ascr50-2

description: Wild-type C. elegans, 50hrs old, exposed to ascr#10, replicate 2


title: ChIP-Seq Normal NIH-3T3 cells - Smc1

value: untreated


title: 52_B16F10pC

value: naturally derived skin tumor and development of immortal cell line; lentiviral transduction of pControl


title: Control 1-week old rep1

value: 1 week


title: ChIP-Seq Normal NIH-3T3 cells - CTCF Rep2

value: CTCF (Millipore 07-729)


title: 53_B16F10pKRAS

value: naturally derived skin tumor and development of immortal cell line; lentiviral transduction of pKRASG12C


title: N2-58h-cnt_3

description: Wild-type C. elegans, 58hrs old, no ascr#10 exposure, replicate 3, batch 2

value: 58hrs post-L1 synchronization

value: water


title: N2-58h-cnt_1

description: Wild-type C. elegans, 58hrs old, no ascr#10 exposure, replicate 1, batch 2

value: Whole organism


title: ChIP-Seq Normal NIH-3T3 cells - CTCF Rep1


title: GBA 1-week old rep3


title: 12_B16F10wt

value: naturally derived skin tumor and development of immortal cell line


title: GBA 1-week old rep4


title: 16_MC38

value: colon carcinoma cell line


title: GBA 1-week old rep2


title: ChIP-Seq TCF1 induced NIH-3T3 cells - CTCF Rep1


title: 09_AE17shKras

value: development by intraperitoneal asbestos injection and lentiviral transduction of shKras


title: N2-58h-ascr_3

description: Wild-type C. elegans, 58hrs old, exposed to ascr#10, replicate 3, batch 2


title: N2-58h-ascr_1

description: Wild-type C. elegans, 58hrs old, exposed to ascr#10, replicate 1, batch 2


title: HiChIP TCF1_3T3

data_processing:
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The validPairs from HiC-Pro were converted to .hic and .cool files
VlidPairs and Smc1 ChIPseq peaks were fed to hichipper (version 0.7.8b0) to call Smc1 loops.
Genome_build: mm10

source_name: NIH 3T3

extract_protocol:
HiChIP was performed as described (Mumbach et al., 2016) using antibody against Smc1 (Bethyl A300-055A). Briefly, 10 × 106 cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific, cat# 28908) for 10 min and subsequently quenched with 0.125 M glycine (Invitrogen, cat# 15527-013). Chromatin was digested using MboI restriction enzyme (NEB, cat# R0147), followed by biotin incorporation with Biotin-14-dATP (Invitrogen, cat# 19524-016) during repair, ligation, and sonication. Sheared chromatin was 4-fold diluted with ChIP dilution buffer (16.7mM Tris pH 7.5, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100), pre-cleared, and then incubated with Smc1 antibody at 4°C overnight. Chromatin-antibody complexes were captured by Protein-A magnetic beads (Pierce, cat# 88846) and subsequently washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and eluted. DNA was purified with MinElute PCR Purification Kit (QIAGEN, cat# 28004) and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851). 50-150ng was used for capture with Dynabeads MyOne Streptavidin C-1 (Invitrogen, cat# 65001) and an appropriate amount of Tn5 enzyme (Illumina, cat# FC-121-1030) was added to captured DNA to generate the sequencing library.
Libraries were validated for quality and size distribution using a TapeStation 2200 (Agilent). Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.
HiChIP

value: TCF-1 induced


title: N2-58h-cnt_2

description: Wild-type C. elegans, 58hrs old, no ascr#10 exposure, replicate 2, batch 2


title: HiChIP Norm_3T3

value: control


title: N2-58h-ascr_2

description: Wild-type C. elegans, 58hrs old, exposed to ascr#10, replicate 2, batch 2


title: GBA 1-week old rep1

value: fly heads


title: 02_LLCshKras

source_name: LLCshKras

value: naturally derived lung tumor and development of immortal cell line; lentiviral transduction of shKras


title: 01_LLC

source_name: LLC

value: naturally derived lung tumor and development of immortal cell line


title: NSCLC_cells_miR17-5p_2_Repl

status: Public on May 01 2022

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

hyb_protocol: Samples were hybridized at 65 °C for 21 hours.

scan_protocol: Samples were purified and then loaded onto the nCounter Cartridge by using the nCounter Prep Station, and RNA was quantified by using the Digital nCounter Nanostring.

data_processing:
RCC files deriving from counting process were first evaluated by using nSolver 4.0 Analysis Software (Nanostring) performing a quality control through the fields of view (FOVs) count, binding density parameter, positive control linearity and limit of detection QC and the eventual presence of any warning flags.
Data were then analyzed by using the Advanced Analysis. 4.0 plug-in of nSolver system. Target genes which achieved ≥ 1.5 and ≤ -1.5-fold change and p-value <0.05 were considered for analysis.

label: Biotin

source_name: NSCLC cells, miR17-5p, 2nd Replicate

label_protocol: Briefly, 150 ng of total RNA, were bound with a Reporter CodeSet and a Capture ProbeSet.

growth_protocol: NSCLC cells were cultured in RPMI culture medium and 10% foetal bovine serum under the standard conditions with 5% CO2 atmosphere with 37°C.

extract_protocol: Total RNA, including the miRNAs, was extracted using miRNeasy (Qiagen)

treatment_protocol: 5x10^4 A549 cells were seeded in 24 well plates and transfected with 50 nM miRCURY miR (hsa-miR-130a-3p: YM00472237-ADA, hsa-miR-17-5p: YM00471966-ADA and Negative Control 4: YM00479903-ADA miRCURY miR, Qiagen) with lipofectamine 2000 (Invitrogen/ThermoFisher Scientific), according to manufacturer’s instructions. After 72 hours, the cells were harvested for the RNA extraction.

value: NSCLC cell line (A549; ICLC HTL03001; Cell bank  IRCCS Ospedale Policlinico San Martino)


title: CS2248_tetOiec5_rep2_MNase

city: New York

first: Songtao

last: Jia

state: New York

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University

data_processing:
Sequencing reads were de-multiplexed and aligned to the S. pombe reference genome, obtained from Pombase (Lock et al. 2019) with Bowtie using default parameters (Langmead et al. 2009). Genome-wide coverage was calculated with deepTools2 (Ramirez et al. 2016) and normalized to counts per million (CPM).
MNase-seq reads of each sample were mapped to the genome assembly of Schizosaccharomyces pombe using HISAT2 (v2.1.0). Potential PCR duplicates were removed using the function "MarkDuplicates" of Picard (v2.22.0, REMOVE_DUPLICATES=true). The fragment size distribution was measured by the function "CollectInsertSizeMetrics" of Picard (v2.22.0). Only mono-nucleosome sized fragments (<200 bp) were used for the downstream analysis.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Genome-wide coverage calculated by deepTools2, normalized to CPM, in bigWig format

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in YEA until mid-log phase

extract_protocol:
ChIP-seq: Log-phase yeast cells were crosslinked with 1% formaldehyde for 20 minutes with shaking at room temperature, followed by 5 minutes quenching with 125mM glycine. Cells were harvested, washed with PBS (phosphate-buffered saline), and resuspended in 100 ul ChIP lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1% Triton X-100, 0.1% Deoxycholate, 1mM PMSF). 200 ul ice-cold glass beads were added and the mixtures were vigorously disrupted in a bead-beater with four 30 s rounds. The lysates were collected, to which 400 ul NP buffer was added (10 mM Tris, pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl 2 , 1 mM CaCl 2 ). MNase was added to the reaction and the reactions were incubated at 37°C for 20 minutes. MNase amount was titrated empirically so that the chromatin was digested to yield mainly mono- and di-nucleosomes. The reaction was stopped by adding 12 µl 0.5 M EDTA and the tubes were placed on ice. 100 µl 5X ChIP lysis buffer was added to the reaction, mixed by short vortexing, and the tubes were incubated on ice for 30 minutes. The reactions were then cleared by centrifugation at 16,000 x g for 10 minutes. 20 µl of the cleared supernatant was reserved as input and the rest used for immunoprecipitation.The cleared cell lysates were incubated with H3K9me2 antibody overnight at 4°C. The beads were then washed with ChIP lysis buffer twice, ChIP lysis buffer containing 0.5 M NaCl, Wash buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA), and TE (50 mM Tris pH 8.0, 1 mM EDTA). The bound chromatin fragments were eluted with TES (50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS) and the crosslinking was reversed by incubating at 65°C overnight. The protein DNA mixture was then subjected to proteinase K treatment and phenol:chloroform extraction before the DNA was precipitated by ethanol.   MNase-seq:MNase-seq sample preparation was the same as the ChIP-seq except that MNase was titrated to yield mainly mononucleosomes (~80% mono-nucleosomes) and the immunoprecipitation step was omitted.
ChIP-seq: 5-10 ng of ChIP and input DNA were used for library construction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB). Mnase-seq:100 ng of extracted DNA was used for library construction as above.

tag: genotype/variation

tag: media

value: YEA


title: NSCLC_cells_miR17-5p_3_Repl

source_name: NSCLC cells, miR17-5p, 3rd Replicate


title: NSCLC_cells_miR17-5p_1_Repl

source_name: NSCLC cells, miR17-5p, 1st Replicate


title: NSCLC_cells_miR17-5p_4_Repl

source_name: NSCLC cells, miR17-5p, 4th Replicate


title: SK209_dcr1_rep1_MNase


title: NSCLC_cells_miR130a-3p_4_Repl

source_name: NSCLC cells, miR130a-3p, 4th Replicate


title: SK209_dcr1_rep2_MNase


title: CS2243_tetOwt_rep2_MNase

value: WT


title: CS2248_tetOiec5_rep1_MNase


title: NSCLC_cells_miR130a-3p_1_Repl

source_name: NSCLC cells miR130a-3p, 1st Replicate


title: CS2441_dcr1iec5_rep2_MNase

source_name: CS2441_dcr1Δ iec5Δ

value: dcr1{delta} iec5{delta}


title: NSCLC_cells_Neg_CTRL_3_Repl

source_name: NSCLC cells, Neg CTRL, 3rd Replicate


title: CS2243_tetOwt_rep1_MNase


title: Tat-Beclin1-repeat

city: cleveland

first: Yong

last: Lu

address: 9500 euclid avenue, NB40

institute: Cleveland Clinic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2
We used featureCounts to collect the raw gene count information with the following configurations -t exon -g gene_name.
Assembly: mm10
Supplementary files format and content: tab-delimited file with gene names in column one and counts in the second column.

source_name: SKOV3: ovarian cancer cell line

growth_protocol: SKOV3 cells (1×106) were seeded into 6-well plates for 24 hrs. Cells were cultured in DMEM Medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (Thermo Scientific), and 100 U/ml penicillin-streptomycin and 2 mM L-glutamine (Invitrogen).

extract_protocol:
Total RNA was extracted from the SKOV3 cells for RNA-Seq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBS, MV, CAR-T or CAR-TMV cells were cocultured with SKOV3 cells (1×106) in 6-well plates for 24 hrs. Tat-Beclin1 was resuspended (10 μM) and coincubated with SKOV3 cells for 1.5 hrs.

value: epithelial

value: Ovary; Ascites

value: coculture with Tat-Beclin1 cells for 1.5 hours


title: CS2441_dcr1iec5_rep1_MNase


title: NSCLC_cells_Neg_CTRL_1_Repl

source_name: NSCLC cells, Neg CTRL, 1st Replicate


title: RNA_Longread_BxPC3_SV

city: Beijing

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

description: SMRT, 12 lanes of data produced from a single library, each lane of data is represented by an independent SRR ID.

data_processing:
Clean reads were mapped to the Homo Sapiens genome (hg19) using Bowtie2 (v2.3.4). An optimized and flexible pipeline filtered out unmapped, multi-mapped, or invalid paired-end reads by Hi-C Pro. Only uniquely valid paired-end reads were retained for analyses. The interaction matrices at various resolutions (i.e., with the genome partitioned into bins of different sizes were constructed using HiC-Pro software (v2.7.1) with default settings. Hi-C interaction matrices were constructed with bin sizes of 1mb,100kb,40kb,20kb,10kb,5kb at the genome-wide level following the methods of HiC-Pro software (v2.7.1) with default settings. Briefly, we utilized an improved computational efficiency ICE (Iterative Correction) method to remove potential Hi-C interaction bias. The genome-wide Hi-C resolutions were calculated based on the interaction maps according to previously published definitions.
We used NGMLR (https://github.com/philres/ngmlr) to do the Alignment with default parameters.  We used sniffles to find out structure variation by using default parameters and identify cancer-specific structure variation by BEDTools
Reads were aligned against the hg19 reference genome using HISAT2 with default parameters (v2.1.0), and the expression level of each gene was normalized by the method developed by Traver Hart which is based on the fragments per kilobase per million mapped fragments (FPKM) values
Genome_build: hg19
Supplementary_files_format_and_content: .hic
Supplementary_files_format_and_content: .vcf
Supplementary_files_format_and_content: fpkm.txt

source_name: pancreatic cancer cells

growth_protocol: HPDE6-C7, PANC1 and BxPC3 were obtained from American Type Culture Collection (ATCC). All cell lines were cultured under recommended conditions (Furukawa, T. et al, Liu, N. et al).

extract_protocol: We used 40ml 2% formaldehyde solution to crosslink the tissue for 15mins at room temperature in vacuum. Then, we added 4.324ml 2.5M Gly to quench the cross-linking reaction. Remove the supernatant and tissues were in the precipitate. We kept the tissue in liquid nitrogen.  Tissues can be resuspended by 25ml extraction buffer (10 mM Tris-HCl at pH 8, 10 mM MgCl2,0.4 M sucrose, 0.1 mM phenylmethylsulfonyl fluoride [PMSF], 5 mM b-mercaptoethanol, and 13 protease inhibitor; Roche). Next filtered by miracloth (Calbiochem).  We then did the centrifugation at 4000rpm at 4℃ for 20mins. After that, resuspended the pellet by 1ml extraction II buffer (10 mM Tris-HCl pH8, 1% Triton X-100, 0.1mM PMSF, 0.25 M sucrose, 10mM MgCl2, 5mMb mercaptoethanol, 13 protease inhibitor). Later, the solution was centrifuged for 10 mins at 14000 rpm in 4℃. Resuspended the pellet by 300μl extraction buffer III (10mM Tris-HCl pH8, 1.7M sucrose, 2mM MgCl2, 1μL protease inhibitor, 0.1mM PMSF, 5mM b-mercaptoethanol, 0.15% Triton X-100). Afterwards, load another 300μl clean extraction buffer III and centrifuged at 14000rpm for 10mins. Removed the supernatant and then washed the pallet by 500ul ice-cold 1x CutSmart buffer, centrifuged at 2500g for 5mins each time. The remaining pallets were the nuclei. Hereafter, we used the restriction enzyme buffer to wash the pallet twice and moved to a safe-lock tube.  The next step has solubilized the chromatin with dilute SDS and incubated at 65℃ by 10mins. Then quenched SDS by Triton X-100 Overnight. Next, the nuclei were digested by 4 cutter restriction enzyme (400 units MboI) at 37℃ on a rocking platform. The next step was marked the DNA ends by biotin-14-dCTP and then did the blunt-end ligation between cross-linked fragments. Thus, the ligation enzyme could ligate the proximal chromatin DNA. We incubated the nuclear complexes with proteinase K at 65℃ and then the nuclear complexes were reversed cross-linked.  DNA was then purified by phenol-chloroform extraction. We used T4 DNA polymerase to remove the Biotin-C from non-ligated fragments. Next, we used sonication to shear the fragments to 200-600 base pairs and repair the fragments by the mixture of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. Biotin-labeled DNA fragments were then enriched by streptavidin C1 magnetic beads. The Hi-C library from the beads was sequenced on the Illumina HiSeq X Ten platform with 150 bp paired-end reads.


title: NSCLC_cells_miR130a-3p_2_Repl

source_name: NSCLC cells miR130a-3p, 2nd Replicate


title: NSCLC_cells_Neg_CTRL_4_Repl

source_name: NSCLC cells, Neg CTRL, 4th Replicate


title: 08_AE17

description: Normalization and summarizzation performed with RMA algorith

value: development by intraperitoneal asbestos injection


title: CAR-TMV-repeat

value: coculture with CAR-TMV cells for 24 hours


title: RNA_Longread_PANC1_SV

description: SMRT

source_name: human pancreatic carcinoma cells


title: RNA_Longread_HPDE6C7_SV

description: SMRT

source_name: human pancreatic duct epithelial cells


title: CAR-T-repeat

value: coculture with CAR-T cells for 24 hours


title: NSCLC_cells_Neg_CTRL_2_Repl

source_name: NSCLC cells, Neg CTRL, 2nd Replicate


title: MV

value: coculture with MV for 24 hours


title: sequencing of untreated naïve primary human melanocytes (carrying a q61 NRAS mutation) cells

city: San Francisco

first: Valentin

last: Feichtenschlager

address: 2340 Sutter Street

department: Dermatology

institute: UCSF

description: Sample 5

data_processing:
Evaluate sequence quality
trim reads
map reads to genome
generate hit counts for genes/exons
compare hit counts
Genome_build: hg19, GRCh38
Supplementary_files_format_and_content: xlsx files with identifiers and gene expression values

source_name: skin

growth_protocol: cells were cultivated in cell culture media at 37 celsius and 5% C02

extract_protocol:
Total RNA was isolated using the RNeasy® mini-Kit (QIAGEN N.V.) following the manufacturer’s protocol. Followed by ribosomal RNA depletion, RNA Fragmentation and Random Priming, First and second strand cDNA synthesis, end repair, 5'phosphorylation and dA-Tailing, Adaptor Ligation, PCR Enrichment
Samples 1-5: Sequence reads were aligned to the human genome (hg19) using TopHat (Version 2.0.11). Samples 6-11: Sequence reads were aligned to the GRCh38 reference genome.

treatment_protocol: 6-11 were treated with Antisense Oligonucleotides (50nmol) and Lipofectamine 3000 (2ul/ml)

value: melanocyte

tag: knockdown


title: sequencing of untreated naïve D04 cells

description: Sample 1

value: melanoma

value: no vector


title: MV-repeat


title: CAR-TMV


title: PBS

value: coculture with PBS for 24 hours


title: PBMCs, L37

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to hg19 Refseq annotation using Bowtie 2 version 2.2.2 as part of Tophat 2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene count matrix

source_name: PBMCs

extract_protocol:
PBMCs were isolated from fresh whole blood using Ficoll (Ficoll-Paque Plus, GE Healthcre) and total RNA was extracted from 10e7 PBMCs using TRIzol reagent (Life Technologies). Messenger RNA was isolated with Oligotex mRNA mini kit (Qiagen)
Scriptseq RNA-seq library preparation kit (Epicentre) was used to generate the RNA-seq libraries according to the manufacturer's protocol.

value: PBMCs

tag: individual (subject_id)

value: Lyme seronegative


title: PBMCs, L36

tag: disease state


title: PBMCs, L33-1

value: early Lyme seropositive


title: PBMCs, L35


title: Tat-Beclin1


title: CAR-T


title: NSCLC_cells_miR130a-3p_3_Repl

source_name: NSCLC cells, miR130a-3p, 3rd Replicate

value: NSCLC cell line (A549; ICLC HTL03001; Cell bank  IRCCS Ospedale Policlinico San Martino)


title: sequencing of untreated naïve primary human melanocytes (carrying an empty vector) cells

description: Sample 4

value: empty pENTR/D-topo vector


title: sequencing of untreated naïve primary human melanocytes cells

description: Sample 3


title: PBMCs, L30

value: late Lyme seropositive


title: PBS-repeat

value: epithelial


title: PBMCs, B6

value: bacteremia


title: PBMCs, L34


title: PBMCs, L40

value: Lyme


title: PBMCs, B4


title: PBMCs, L38


title: sequencing of untreated naïve mm415 cells

description: Sample 2


title: PBMCs, B3


title: PBMCs, L23-2


title: PBMCs, L39


title: PBMCs, L29-1


title: PBMCs, B5


title: PBMCs, L31


title: PBMCs, L32


title: PBMCs, I6

value: influenza


title: PBMCs, B2


title: PBMCs, I1


title: PBMCs, I5


title: PBMCs, I4


title: PBMCs, I3


title: PBMCs, C17

value: uninfected


title: PBMCs, C18


title: PBMCs, C15


title: PBMCs, C13-2


title: PBMCs, I2


title: PBMCs, C16


title: PBMCs, B1


title: S10-026075T2(1)_T

city: Montreal

first: Pierre

last: Thibault

state: Quebec

address: 2950 Chem. de Polytechnique

country: Canada

institute: Institute of Research in Immunology and Cancer (IRIC)

description:
title in publication:
S4 tumor

data_processing:
Sequences were trimmed using Trimmomatic version 0.35 and aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 33, based on Ensembl 99) using STAR version 2.7.1a
Gene expressions were obtained both as read count directly from STAR as well as computed using RSEM to obtain normalized gene and transcript-level expression, in transcript-per-million (TPM) values, for these stranded RNA libraries.
Genome_build: GRCh38 (encode version 33, based on Ensembl 99)
Supplementary_files_format_and_content: tab-separated value files containing TPM values for each sample

source_name: colon

growth_protocol: All cell lines were grown in their respective ATCC-recommended media and maintained at 37°C with 5% CO2

extract_protocol:
TriZol + RNeasy Mini kit (Qiagen) (samples 1-5) or AllPrep DNA/RNA/miRNA Universal kit (Qiagen) (samples 6-17)
KAPA mRNAseq Hyperprep kit (Roche)

value: ascending colon

value: adenocarcinoma

tag: tumor stage

value: IIA


title: S6-026240T2(1)_T

description:
title in publication:
S5 tumor

value: sigmoid


title: S9-026075T1(1)_N

description:
title in publication:
S4 NAT

value: colon


title: S4-026241T2(1) _T

description:
title in publication:
S2 tumor


title: PBMCs, C14


title: S8-026214T2(1)_T

description:
title in publication:
S3 tumor


title: Gata3+/- biological replicate 1

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

institute: University of Toronto

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 microarrays for 16 hours in the Affy640 hybridization oven at a speed of 60 rpm.

scan_protocol: GeneChip arrays were scanned using a GeneChip Scanner 3000.

data_processing: Initial probe set intensities were quantified using the GeneChip Operating Software (GCOS).

source_name: ESC-derived T-cell progenitor

label_protocol: cRNA was purified and biotin-labeled using Affymetrix GeneChip Sample Cleanup Module.

growth_protocol: Gata3+/- and Gata3-/- ESCs were maintained in vitro in ES media. ESCs were cultured on OP9/OP9-DL1 cells for differentiation towards the hematopoietic and T-cell lineages.

extract_protocol: T-cell progenitors were FACS sorted, RNA isolated using Qiagen RNAeasy, cDNA generated using Affymetrix cDNA synthesis kit, and cRNA generated using Affymetrix IVT labeling kit.

treatment_protocol: During growth protocol, cells were treated with and maintained in the presence of IL-7 and Flt3L.

tag: genotype

value: ESC-derived T-cell progenitor


title: Gata3-/- biological replicate 3


title: S1-026250T1(2)_N

description:
title in publication:
S1 NAT


title: S7-026214T1(3)_N

description:
title in publication:
S3 NAT


title: S5-026240T1(9) _N

description:
title in publication:
S5 NAT


title: hCMEC2_ATAC

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
For ATAC-seq results: Reads were mapped to the GRCh38 version of the human genome using Bowtie2 with default paired-end settings (Langmead and Salzberg, 2012). Mitochondrial reads, reads with a MAPQ < 10, and reads which did not align to the reference genome were removed using Samtools (version 1.13) (Danecek et al., 2021). Duplicated reads were then removed with Picard MarkDuplicates (Institute, 2019). Peak calling was carried out with MACS2 (callpeak  --nomodel –broad) (v2.2.7.1)(Zhang et al., 2008). Diffbind (version 3.2) (Ross-Innes et al., 2012; Stark R, 2011) was used to import peaksets (min.overlap= 0.66) into RStudio Server (version 1.4.1717, https://www.rstudio.com) using R (version 4.1 (Team, 4.1). dba.blacklist function was used to filter out peaks that overlap with the ENCODE blacklist. Consensus peaks were converted to mm10 using the liftOver tool available from the UCSC Genome Browser. A region was considered conserved if a minimum 0.95 ratio of bases remap. Selected regions were also examined using the ECR Browser (Ovcharenko et al., 2004) where the regions were analyzed using rVista 2.0 (Loots and Ovcharenko, 2004) in order to identify conserved transcription factor motifs. The TRANSFAC professional V10.2 vertebrate library was used with default parameters.
For RNA-seq results: Reads were first mapped to the human genome (GRCh38) using Salmon (version 1.5.1) (Patro et al., 2017). Transcript level quantification was then imported using txtimport (version 1.20.0) (Soneson et al., 2015) and analyzed using DESeq2 (Love et al., 2014). Genes were kept and considered actively expressed if they had more than 10 raw counts and >2 log2 fold change normalized expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig, bam and peak files for ATAC data. RNA-seq results contain sf abundance quantification file: Plain-text, tab-separated file with a single header line (which names all of the columns) that contains Name, Length, EffectiveLength, TPM and NumReads.

source_name: Brain microvascular cells

growth_protocol: Immortalized hCMEC/D3 (Millipore, SCC066) cells were grown to confluence using endothelial cell medium (ScienCell, #1001) on plates coated with Collagen Type I Rat Tail (Sigma-Aldrich, #C7661). Passages 4-6 were used for experiments.

extract_protocol:
RNA was extracted using Trizol reagent.
ATAC libraries were processed as previously described (Corces et al., 2017). The quality of purified DNA libraries was assessed using the Agilent High Sensitivity DNA kit (Agilent Technologies). Paired end, 2 x 75 bp sequencing was performed on an Illumina Nextseq 500 instrument. RNA from all samples was thawed and following confirmation of integrity and concentration using a Bioanalyzer, 100 ng was used for low-input library preparation using the NEBNext Ultra II RNA Library Prep kit for Illumina. The libraries were then quantified and sequenced using an Illumina NovaSeq 6000 at a depth of 20 million reads per sample.


title: ATCC cell line RKO

description:
title in publication:
RKO

value: carcinoma


title: ATCC cell line SW620

description:
title in publication:
SW620

value: Dukes' type C, colorectal adenocarcinoma


title: ATCC cell line HIEC-6

description:
title in publication:
HIEC-6

source_name: small intestine

value: small intestine


title: Gata3+/- biological replicate 3


title: ATCC cell line HCT116

description:
title in publication:
HCT116

value: colorectal carcinoma


title: S12-026019T2(1)_T

description:
title in publication:
S6 tumor


title: NCIH211_C11orf53_sg3

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing reads were first trimmed and filtered with Trimmomatic (0.39-Java-11) with minimal read length 50 using default settings for ChIP-Seq. For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using Hisat2 2.1.0 with default  setting.
For ChIP-Seq, Reads that passed the quality control were then mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting and 2 mismatches are allowed
For ChIP-Seq, Bam files are then  sorted with Samtools 1.11 with default settings. PCR duplicates were removed with Picard  2.21.6 with default settings and indexed with Samtools. Peaks were called with Macs2 2.2.7.1 with  input as negative control with default settings and a 5% FDR as cutoff.
Bedtools 2.30.0 was used to intersect as well as merge peaks from different experiments to generate high-confidence peaks or all C11orf53-OCT11 occupying sites (54, 55). Homer v4.11 makeTagDirectory and makeUCSCfile were used to generate bigwigs files for visualizing ChIP-Seq tracks on UCSC genome browser. The annotatePeaks was used to annotate peak features for C11orf53-OCT11 occupying peaks as well as  calculating tag counts on C11orf53/OCT11 intensity on all C11orf53-OCT11 binding sites with +/- 250  bp around peak center. MEME SUIT 5.4.1 MEME was used to discover motifs enriched on defined peak  regions.
For scRNA-seq, the Cell Ranger  pipeline (v5.0.0, 10X Genomics) was used to align FASTQ reads to the mouse reference genome (gexmm10-  2020-A, 10X Genomics) and produce digital gene-cell counts matrices. The resulting genebarcode  matrices were fed into Scanpy 1.8.1 for secondary analysis.
For RNA-seq, differentially expressed genes were analyzed using counts from HTSeq-count 0.13.5. Genes  with TPM >= 2 in at least one condition were then fed into DESeq2 with masking structural RNAs and  non-coding RNA for calculating fold change. TPM was quantified with Salmon 1.0.0 with  default settings.
Genome_build: hg38
Supplementary_files_format_and_content: TPM or htseq-count matrix for RNA-Seq, h5ad and h5 files for scRNA-seq. Trimmed fastq file, bigwig, bam/bai and peak files for ChIP-Seq.

source_name: small cell lung cancer tuft variant

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin.streptomycin except NCIH1048, which was cultured in DMEM:F12 supplemented with 0.005 mg/mL insulin, 0.01 mg/mL transferrin, 30 nM sodium  selenite, 10 nM hydrocortisone, 10 nM β-estradiol, 4.5 mM L-glutamine and 5% FBS.

extract_protocol:
Total RNA was extracted using TRIzol following the standard protocol; cells were fixed with 1% formaldehyde for 10 minutes and quenched with glycine following standard protocol (see method in paper) for ChIP-Seq.
polyA RNA was selected and fragmented with NEBNext Poly (A) mRNA Magnetic isolation  module (NEB #E7350) and the library was prepared with NEBNext Ultra II RNA Library Prep kit for  Illumina (NEB #E7770) with 2 ug RNA according to the manufacturer's protocol. For single cell RNA-seq, cell suspensions were stained for viability with Sytox blue (ThermoFisher S34857) and sorted on a Sony  SH800S (Sony Biotechnology Inc, San Jose, CA) using a 100 μm chip (Catalog #LE-C3110) in “Ultra  Purity” mode. Sorted cells were washed and resuspended in PBS containing 0.04% BSA. An aliquot  was stained with ViaStain AOPI (Nexcelom #CS2-0106-5mL) and counted using a Countess FL II  automated cell. Up to 12,000 cells were loaded per lane on 10X Chromium microfluidic chips. Single  cell capture, barcoding, and library preparation were performed using the 10X Chromium chemistry,  using the NextGEM Single-Cell 3’ Library Kit v3.1 (1000121; 10X Genomics). ChIP-seq library was prepared using the NEBNext Ultra II DNA Library Prep Kit  for Illumina (E7645) following manufacturer's protocol with AMPure XP beads (Beckman, A63881)  with no size selection.

treatment_protocol: see above


title: NCIH211_C11orf53_sg2


title: Gata3-/- biological replicate 2


title: NCIH211_C11orf53_sg1


title: NCIH211_OCT11_sg3


title: Gata3+/- biological replicate 2


title: S11-026019T1(3)_N

description:
title in publication:
S6 NAT


title: NCIH211_OCT11_sg2


title: NCIH211_COLCA2_sg3


title: NCIH211_sgNEG2


title: NCIH211_sgNEG1


title: NCIH104_sgNEG1


title: NCIH526_OCT11_sg3


title: NCIH104_COLCA2_sg2


title: NCIH104_sgNEG2


title: NCIH104_COLCA2_sg1


title: NCIH526_C11orf53_sg3


title: NCIH526_C11orf53_sg2


title: NCIH104_OCT11_sg2


title: CORL311_OCT11_sg2


title: NCIH526_sgNEG2

value: sgNEG


title: NCIH526_sgNEG1


title: CORL311_OCT11_sg3


title: Gata3-/- biological replicate 1


title: NCIH104_OCT11_sg3


title: CORL311_sgNEG2


title: CORL311_C11orf53_sg3


title: CORL311_sgNEG1


title: NCIH526_POU2F3_PF_Ab1

tag: chip antibody

value: in house raised OCT11 Antibody

value: endogeneous


title: NCIH526_POU2F3_Rb_2


title: NCIH526_OCT11_sg2


title: NCIH526_Input


title: NCIH211_POU2F3_Rb_2


title: NCIH211_OCA-T_Ab2

value: in house raised C11orf53 Antibody


title: NCIH211_POU2F3_Input


title: NCIH526_OCA-T_Ab1


title: NCIH211_p300

value: p300 antiboby active motif AB_2716754


title: NCIH526_H3K27Ac

value: H3K27Ac, abcam Ab4729


title: S2-026250T2(1)_T

description:
title in publication:
S1 tumor

tag: tissue

value: cecum

value: IIC


title: NCIH211_POU2F3_Ab1


title: NCIH211_H3K27Ac


title: NCIH211_MED1

value: MED1, bethyl A300-793A


title: NCIH211_Input


title: NCIH211_Cherry_EV_HA

value: Pierce HA magentic baeds (88837)

value: lentivirally over-expressed HA Cherry


title: NCIH211_Cherry_FL_HA

value: lentivirally over-expressed HA C11orf53


title: NCIH211_Cherry_FL_input


title: NCIH211_OCA-T_Ab1


title: NCIH526_OCA-T_Ab2


title: CORL311_C11orf53_sg2


title: NCIH1048_Input


title: NCIH211_BRD4

value: BRD4 antibody (Bethyl, A700-004)


title: NCIH1048_CST

value: Anti-HA (CST mAb #3724)

value: lentivirally over-expressed HA COLCA2


title: NCIH1048_K27Ac


title: NCIH211_POU2F3_ChIP

value: POU2F3, santa cruz, sc330


title: NCIH1048_12CA5


title: CORL311_POU2F3-Rb2


title: CORL311_POU2F3-P_F-1


title: CORL311_OCAT-P_F-1


title: CORL311_OCAT-P_F-2


title: NCIH211_Cherry_ev_input


title: CORL311_K27Ac