title: mouse kidney_rhabdomyolysis_24h_3

value: kidney

value: WT

value: rhabdomyolysis


title: RNA-seq_No injection ctrl TrimAway rep1_H08

status: Public on Sep 18 2024

type: SRA

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

library_source: transcriptomic

data_processing:
Raw FastQ files were trimmed using Trim Galore (v0.6.5, Cutadapt v2.3) and mapped to the mouse GRCm38 genome assembly using HISAT2 (v2.1.0) (D. Kim et al., 2015), with the options –dta –no-softclip –no-mixed –no-discordant.
Assembly: GRCm38_v95
Supplementary files format and content: Tab delimited text file of read counts over genes

molecule: polyA RNA

organism: Mus musculus

source_name: 2 cell stage embryos

extract_protocol:
polyA RNA-seq following the scNMT-seq protocol https://www.protocols.io/view/scnmt-seq-kxygxmwwwl8j/v2
Nextera XT, using dual indexing

tag: tissue

value: 2 cell stage embryos

tag: genotype

value: No injection ctrl


title: Distal, Group 2, scRNAseq

city: Ithaca

first: Coulter

last: Ralston

state: NY

address: 237 Tower Rd

department: Biomedical Engineering

country: USA

institute: Cornell University

description:
mD2
10X Genomics (Single Cell 3' v2)

library_source: transcriptomic single cell

data_processing:
The raw sequencing reads were aligned to the mm39 reference genome and quantified using the cellranger (v6.1.2, 10x Genomics) count function. The outputs are barcode, feature, and matrix files for further analysis involving gene counts
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Uterine Tube (Oviduct)

extract_protocol:
Each uterine tube was placed in sterile PBS containing 100 IU ml-1 of penicillin and 100 µg ml-1 streptomycin (Corning, 30-002-Cl), and separated in distal and proximal regions. Tissues from the same region were combined in a 40 µl drop of the same PBS solution, cut open lengthwise, and minced into 1.5-2.5 mm pieces with 25G needles. Minced tissues were transferred with help of a sterile wide bore 200 µl pipette tip into a 1.8 ml cryo vial containing 1.2 ml A-mTE-D1 (300 IU ml-1 collagenase IV mixed with 100 IU ml-1 hyaluronidase; Stem Cell Technologies, 07912, in DMEM Ham’s F12, Hyclone, SH30023.FS). Tissues were incubated with loose cap for 1 h at 37°C in a 5% CO2 incubator. During the incubation tubes were taken out 4 times and tissues suspended with a wide bore 200 µl pipette tip. At the end of incubation, the tissue-cell suspension from each tube was transferred into 1 ml TrypLE (Invitrogen, 12604013) pre-warmed to 37°C, suspended 70 times with a 1000 µl pipette tip, 5 ml A-SM [DMEM Ham’s F12 containing 2% fetal bovine serum (FBS)] were added to the mix, and TE cells were pelleted by centrifugation 300x g for 10 minutes at 25°C. Pellets were then suspended with 1 ml pre-warmed to 37°C A-mTE-D2 (7 mg ml-1 Dispase II, Worthington NPRO2, and 10 µg ml-1 Deoxyribonuclease I, Stem Cell Technologies, 07900), and mixed 70 times with a 1000 µl pipette tip. 5 ml A-mTE-D2 was added and samples were passed through a 40 µm cell strainer, and pelleted by centrifugation at 300x g for 7 minutes at +4°C. Pellets were suspended in 100 µl microbeads per 107 total cells or fewer, and dead cells were removed with the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) according to the manufacturer’s protocol. Pelleted live cell fractions were collected in 1.5 ml low binding centrifuge tubes, kept on ice, and suspended in ice cold 50 µl A-Ri-Buffer (5% FBS, 1% GlutaMAX-I, Invitrogen, 35050-079, 9 µM Y-27632, Millipore, 688000, and 100 IU ml-1 penicillin 100 μg ml-1 streptomycin in DMEM Ham’s F12). Cell aliquots were stained with trypan blue for live and dead cell calculation. Live cell preparations with a target cell recovery of 5,000-6,000 were loaded on Chromium controller (10X Genomics, Single Cell 3' v2 chemistry) to perform single cell partitioning and barcoding using the microfluidic platform device. After preparation of barcoded, next-generation sequencing cDNA libraries samples were sequenced on Illumina NextSeq500 System.
The libraries were prepared with the chromium Single Cell 3' reagent kit (10X Genomics, Single Cell 3' v2 chemistry) following the maunfacturer's instructions. Live cell preparations were loaded with a target cell recovery of 5,000-6,000.

value: Uterine Tube (Oviduct)

tag: tissue section

value: distal section

tag: strain


title: VEH-SK-UT-1 13 RNA

city: San Antonio

first: Azad

last: Khosh

state: TX

address: 7703 Floyd Curl Dr

institute: UTHSCSA

data_processing:
The quality of reads controlled using FastQC, version 0.73 then reads were processed  using Trimmomatic, and parameters were chosen to trim the reads  according to FastQC results. The reads were mapped to the human reference genome,  version hg38 using Hisat2, version 2.2.1. Next, raw reads were mapped to the  human reference transcriptome using featurecounts, version 2.0.3 and annotation  file of Gencode, version V41. Gene counts pre-processed and normalized using  the DESeq2 package in R, version 1.36.0. quality of samples examined using  comparative boxplot and PCA and outlier samples excluded from the analysis.  Differentially expressed genes identify using DESeq2.
Assembly: HG38
Supplementary files format and content: csv format

molecule: total RNA

organism: Homo sapiens

source_name: uterine leiomyosarcoma cell line

extract_protocol:
We performed whole transcriptome analysis to determine the mechanism  underlying the inhibitory effect of BET protein inhibition on the uLMS. The SK-UT-1 cells  were treated with BET protein inhibitors JQ1 and I-BET 762 at a concentration of 5 µM  for 48 h. RNA was isolated using Trizol. RNA quality and quantity were assessed using  the Agilent bio-analyzer.
Strand-specific RNA-Seq libraries were prepared using a  TruSeq total RNA-Seq library protocol (Illumina provided). Library quality and quantity  were assessed using the Agilent bio-analyzer, and libraries were sequenced using an  Illumina NovaSEQ6000 (illumine provided reagents and protocols).

value: uterine leiomyosarcoma cell line

tag: cell line

tag: cell type

value: human uterine leiomyosarcoma

tag: treatment

value: VEH


title: Aorta_24mo_3

city: Osaka-shi

first: Masaki

last: Takasugi

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

country: Japan

institute: Osaka Metropolitan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC.
Trimmed sequence reads were mapped to GRCm39 using STAR.
Read count extraction was performed using RSEM.
Count data were normalized using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Aorta

extract_protocol:
Mice were euthanized and tissues were collected and immediately frozen pulverized in liquid nitrogen. Pulverized tissues were homogenized in RNAiso Plus (Takara) reagent using pestle and then RNA was isolated following the manufacturer's instructions.
The sequencing libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina) following the manufacturer's instructions.

value: Aorta

value: Wild-type


title: RNA-seq_No injection ctrl TrimAway rep3_H04


title: RNA-seq_No injection ctrl TrimAway rep3_G04


title: RNA-seq_No injection ctrl TrimAway rep3_D04


title: Aorta_24mo_1


title: RNA-seq_No injection ctrl TrimAway rep1_F08


title: RNA-seq_No injection ctrl TrimAway rep1_F09


title: RNA-seq_No injection ctrl TrimAway rep1_G08


title: Aorta_24mo_2


title: SPF_NCD, replicate2, scRNA-seq

city: Yokohama

first: Takaharu

last: Sasaki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Thurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

description: 10x Genomics

data_processing:
FASTQ raw files were processed by Cell Ranger v3.0.2 software and aligned to the mouse reference genome mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peyer's patches

extract_protocol:
Peyer's patches dissected from mice were minced with scissors and then stirred in a 20-mL conical flask containing 10 mL of RPMI medium supplemented with 2% (v/v) FCS, 1 mg/mL Collagenase (WAKO), and 50 μg/mL DNase, using a stir bar at 37°C and 500 rpm for 15 minutes. The suspension was then passed through an 18 G needle 10 times and stirred at 37°C and 500 rpm for an additional 15 minutes. Samples were filtered through a 100-μm Cell Strainer, centrifuged at 4°C and 500 g for 5 minutes, and CD19-negative PI-negative cells were sorted by FACS for subsequent scRNA-seq analysis.
Library was prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacter's instructions.

value: Peyer's patches

value: 10-12 weeks old

value: wild-type (SPF)

value: NCD


title: VEH-SK-UT-1 16 RNA


title: RNA-seq_No injection ctrl TrimAway rep3_E04


title: IL4_IL13_72h_rep3

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
The  quality assessment of all RNA-Seq datasets was conducted using FastQC v0.11.7
Trimming of reads, including removal of low-quality ends and adapters, was performed using cutadapt v4.4_dev with Python 3.8.10 with default parameters.
the trimmed and adapter-clipped raw reads underwent a second round of quality checks using FastQC v0.11.7
The RNA sequencing reads were aligned to the human reference genome assembly GRCh38 using the HISAT2 algorithm and its corresponding genome indexes.
Transcript abundance was determined using the featurecounts function from the Rsubread v1.34.4 R package with  Rstudio version 1.1.453, using Ensembl annotation version 105
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: THP-1 cells (ATCC TIB-202, USA) were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% FBS (Gibco, USA) (culture media). Cells were cultured in 75 cm2 flasks at a density < 1 × 106 cells/ml. Cells were differentiated in 12 well plates, with 500,000 cells/ well (127,000 cells/cm2), in the culture media supplemented with 50 nM of phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich, USA) for 48h

extract_protocol:
Cells were lysed on the plate and the RNeasy mini kit (Qiagen, Germany) was used as per the vendor’s instructions.
Novogene NGS RNA  Library Prep Set (PT042)

treatment_protocol: After PMA differentiation, cells are exposed to two different cytokines cocktails and fresh media for 24h, 48h, and 72h. In particular, to simulate a PI environment the cells are exposed to LPS (Merck) 10 pg/ml and IFNγ (Sigma-Aldrich, USA) 20 ng/ml; to induce an AI phenotype instead, the cells are exposed to IL-13 (Sigma-Aldrich, USA) 20 ng/ml and IL-4 20 (Sigma-Aldrich, USA) ng/ml.

tag: time

tag: replicate

tag: other treatment

value: before the exposure 30.9 ng/ml PMA for 48h

value: monocyte


title: Aorta_15mo_4


title: VEH-SK-UT-1 14 RNA


title: RNA-seq_No injection ctrl TrimAway rep1_E09


title: Aorta_15mo_3


title: IL4_IL13_72h_rep2


title: RNA-seq_No injection ctrl TrimAway rep1_D08


title: RNA-seq_No injection ctrl TrimAway rep1_D09


title: Aorta_15mo_2


title: RNA-seq_No injection ctrl TrimAway rep1_C09


title: LPS_INFgamma_72h_rep3

value: LPS-INFgamma


title: RNA-seq_No injection ctrl TrimAway rep1_A09


title: RNA-seq_No injection ctrl TrimAway rep1_B09


title: Aorta_15mo_1


title: LPS_INFgamma_72h_rep2


title: RNA-seq_IgG TrimAway rep3_F03

value: IgG


title: RNA-seq_IgG TrimAway rep3_G03

value: 2 cell stage embryos


title: Aorta_6mo_3


title: RNA-seq_IgG TrimAway rep3_E03


title: Aorta_6mo_2


title: RNA-seq_IgG TrimAway rep3_C03


title: RNA-seq_IgG TrimAway rep3_B04


title: RNA-seq_No injection ctrl TrimAway rep1_E08

value: No injection ctrl


title: IL4_IL13_72h_rep1


title: no_treatment_72h_rep2

value: C


title: no_treatment_72h_rep1


title: Aorta_6mo_1


title: RNA-seq_IgG TrimAway rep3_A04


title: Aorta_6mo_4


title: RNA-seq_IgG TrimAway rep3_B03


title: KO_GC111891_ATAC

city: Leuven

first: Jore

last: Van Wauwe

address: Herstraat 49 bus911

country: Belgium

institute: KU Leuven

description:
10X multiome GENOMICS
ko_GC111891.h5,ko_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
Cell Ranger Arc v1.0.1 10X Genomics
CellBender v0.1.0 to remove ambient RNA.
Assembly: mm10
Supplementary files format and content: RNA and ATAC counts in .h5 format per sample, ATAC fragment file in tsv format and index tbi file.

molecule: genomic DNA

source_name: Cardiac left ventricle

extract_protocol:
Seven-day-old pups were decapitated and hearts were immediately removed and placed in PBS, all done on ice. The atria, part of the base and the entire right ventricle were removed, and the remaining left ventricle was cut into small pieces and snap-frozen in liquid N2. Four samples per genotype were pooled to obtain approximately 80 mg of heart tissue per sample, into gentleMACS M tubes containing Lysis Buffer (5 mM CaCl2, 3 mM MgAc, 2 mM EDTA, 0.5 mM EGTA, and 10 mM Tris-HCl pH 8 in H2O, supplemented prior to use with 1 mM DTT, 1 µg/mL Actinomycin D, 0.05% Protease Inhibitor Cocktail, and 0.04 U/µL RNA inhibitors-RNAse OUT). Isolation protocol is adapted from Amoni et.al., DOI: 10.1161/CIRCEP.122.011677. The first step of the isolation protocol was a mechanical dissociation using the gentleMACS dissociator. After mechanical dissociation, tissue was exposed to lysis buffer supplemented with NP-40 (0.1%) and digitonin (0.01%) for lysis of the cell membrane. After a 15-minute incubation on ice, the homogenate was passed through a 30 µm filter and spun down. The pellet was dissolved in sucrose buffer (1 M sucrose, 3 mM MgAc, 10 mM Tris-HCl pH 8 in H2O, supplemented with 1 mM DTT, 1µg/mL Actinomycin D, 0.05% Protease Inhibitor Cocktail and 0.04 U/µL RNA inhibitors-RNase OUT). To isolate the nuclei from the cell debris, the nuclei-containing sucrose solution was pipetted gently on top of fresh sucrose buffer. After centrifugation, nuclei were pelleted followed by multiple rounds of resuspension in washing buffer (750 µg/mL UltraPureTM BSA, 0.04 U/µL RNA inhibitors-RNAse OUT in PBS) prior to sorting. Nuclei were sorted on an ARIA3 FACS sorter based on 7-AAD staining. Sorted nuclei were counted on a LUNA cell counter, spun down and resuspended in washing buffer to the desired concentration according to the 10X Genomics recommendations.
According to 10X Genomics. After FACsorting, samples were submitted to the KU Leuven Genomics Core and processed using the 10X Genomics Next GEM Single cell multiome Assay for Transposase-Accessible Chromatin (ATAC) + Gene Expression Reagents kit to generate the Gel beads in Emulsion (GEMs) containing single nuclei. Next, joint single nuclei RNA and single nuclei ATAC libraries were generated according to the 10X Genomics protocol. Finally, libraries were sequenced at a depth of 30K on an Illumina Novaseq 6000 by the KU Leuven Genomics Core.

value: Cardiac left ventricle

tag: age

value: 7 day old

value: Prdm16 KO


title: RNA-seq_IgG TrimAway rep3_A03


title: RNA-seq_IgG TrimAway rep3_H03


title: WT_GC111890_ATAC

description:
10X multiome GENOMICS
wt_GC111890.h5, wt_atac_fragments.tsv.gz

value: WT


title: LPS_INFgamma_72h_rep1


title: RNA-seq_IgG TrimAway rep2_E01


title: RNA-seq_IgG TrimAway rep2_C01


title: RNA-seq_IgG TrimAway rep3_D03


title: IL4_IL13_48h_rep3


title: KO_GC111891_RNA

description:
10X multiome GENOMICS
ko_GC111891.h5

molecule: nuclear RNA


title: RNA-seq_IgG TrimAway rep2_D01


title: no_treatment_72h_rep3


title: IL4_IL13_48h_rep1


title: KO_453

city: Turku

first: Michael

last: Gabriel

address: Kiinamyllynkatu 10

institute: University of Turku

data_processing:
Illumina Casava1.8 software used for basecalling.
Aligment performed using HISAT2 (2.0.5)
Transcript abundance was quantified using FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced).
Sequencing depth was at least 20 million reads per sample and reads were mapped to mouse genome (Mus_musculus_Ensemble_94) using HISAT2 (2.0.5).
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Assembly: Mus musculus Ensemble 94
Supplementary files format and content: Comma-separated value file includes normalized count for every gene and every sample
Supplementary files format and content: Comma-separated value file includes normalized RPKM values for each sample

source_name: Liver

extract_protocol:
Liver tissue samples collected from the left lateral liver lobe of 8 week old mice. Approximately 50 mg of tissue was snap frozen in liquid N2. Total RNA was extracted from frozen tissues using TRIsure™ (Bioline, London, UK) and DNase treated using DNase I kit (Sigma-Aldrich, Saint Louis, MO, USA). RNA-sequencing of total RNA was performed using Illumina Novaseq sequencer (Illumina, San Diego, CA, USA) at Novogene (Cambridge, UK).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene

value: Liver

value: 2 months old

tag: Sex

value: male


title: RNA-seq_IgG TrimAway rep2_B01


title: RNA-seq_IgG TrimAway rep1_H09


title: WT_GC111890_RNA

description:
10X multiome GENOMICS
wt_GC111890.h5


title: RNA-seq_IgG TrimAway rep2_A01


title: RNA-seq_IgG TrimAway rep1_G10


title: LPS_INFgamma_48h_rep2


title: IL4_IL13_48h_rep2


title: LPS_INFgamma_48h_rep3


title: RNA-seq_IgG TrimAway rep1_F10


title: KO_434


title: LPS_INFgamma_48h_rep1


title: RNA-seq_IgG TrimAway rep1_C10


title: KO_435


title: RNA-seq_IgG TrimAway rep1_G09


title: RNA-seq_IgG TrimAway rep1_D10


title: RNA-seq_IgG TrimAway rep1_E10


title: no_treatment_48h_rep2


title: RNA-seq_IgG TrimAway rep2_F01


title: RNA-seq_IgG TrimAway rep1_A11


title: no_treatment_48h_rep3


title: no_treatment_48h_rep1


title: KO_425


title: RNA-seq_a-Smarca5 TrimAway rep3_H05


title: KO_404


title: RNA-seq_a-Smarca5 TrimAway rep3_D05


title: RNA-seq_a-Smarca5 TrimAway rep3_E05


title: KO_402


title: IL4_IL13_24h_rep1


title: KO_391


title: RNA-seq_a-Smarca5 TrimAway rep3_F05


title: RNA-seq_a-Smarca5 TrimAway rep3_A05


title: RNA-seq_IgG TrimAway rep1_B10


title: LPS_INFgamma_24h_rep3


title: KO_416


title: RNA-seq_IgG TrimAway rep1_A10


title: KO_372


title: RNA-seq_a-Smarca5 TrimAway rep2_G02


title: RNA-seq_IgG TrimAway rep1_H10


title: RNA-seq_a-Smarca5 TrimAway rep2_F02


title: KO_414


title: WT_441


title: RNA-seq_a-Smarca5 TrimAway rep2_E02


title: LPS_INFgamma_24h_rep1


title: IL4_IL13_24h_rep2


title: RNA-seq_a-Smarca5 TrimAway rep3_G05


title: RNA-seq_a-Smarca5 TrimAway rep3_B05


title: RNA-seq_a-Smarca5 TrimAway rep3_C05


title: WT_429


title: RNA-seq_a-Smarca5 TrimAway rep2_A02


title: WT_415


title: RNA-seq_a-Smarca5 TrimAway rep1_H06


title: RNA-seq_a-Smarca5 TrimAway rep1_G07


title: LPS_INFgamma_24h_rep2


title: IL4_IL13_24h_rep3


title: RNA-seq_a-Smarca5 TrimAway rep1_F07


title: 501Mel, sh8, dox-induced, Rep2

city: Dortmund

first: Kim

middle: Denise

last: Fischer

address: Otto-Hahn-Straße 15

country: Germany

institute: Max Planck Institute for molecular Physiology

data_processing:
The raw fastq files were processed using the zarp pipeline and the adapters are trimmed using Cutadapt
The reads were mapped to the human genome(hg38, Genome Reference Consortium GRCh38) using STAR
Assembly: hg38, Genome Reference Consortium GRCh38
Supplementary files format and content: Tap seperated values files includes normalized counts for each sample

extract_protocol:
RNA was extracted using TRIzol™ Reagent.
Prior to library preparation, rRNA was removed using QIAseq FastSelect-rRNA HMR Kit according to the manufacturer’s guidelines. Libraries were prepared using QIAseq Stranded RNA Lib Kit UDI according to the corresponding handbook.


title: RNA-seq_a-Smarca5 TrimAway rep2_D02


title: WT_427


title: RNA-seq_a-Smarca5 TrimAway rep2_C02


title: RNA-seq_a-Smarca5 TrimAway rep2_B02


title: no_treatment_24h_rep3


title: no_treatment_24h_rep2


title: 501Mel, sh8, dox-induced, Rep1


title: JQ1 -SK-UT-1 18 RNA

value: uterine leiomyosarcoma cell line

value: human uterine leiomyosarcoma


title: MCF-7_Nutlin-3a_3

city: Jena

first: Martin

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

library_source: genomic

data_processing:
Informed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports, we used Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10.
Potential sequencing errors were detected and corrected using Rcorrector v1.0.4.
The reads were aligned to hg38 using segemehl (split-read option disabled). Mappings were filtered for uniqueness and properly aligned mate pairs with Samtools
Peaks were calles using MACS2 v2.2.7.1
Assembly: hg38
Supplementary files format and content: MACS2 narrowPeaks

source_name: breast

growth_protocol: MCF-7 cells (ATCC, Manassas, Virginia, USA) were grown in high glucose Dulbecco's modified Eagle's media (DMEM) with pyruvate (Thermo Fisher Scientific, Darmstadt, Germany). Culture media were supplemented with 10 % fetal bovine serum (FBS; Thermo Fisher Scientific), penicillin/streptomycin (Thermo Fisher Scientific), and non-essential amino acids (Thermo Fisher Scientific).

extract_protocol:
The Omni-ATAC protocol (Corces et al., 2017, Nat. Methods) was followed. Briefly, dead cells were removed using Annexin V magnetic beads (Miltenyi Biotec) and the remaining cells were treated with 200 U/ml DNase. Subsequently, 50,000 cells were pelleted at 500 g at 4°C and resuspended in lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 0.01% digitonin).
After 3 min, the lysis buffer was washed out with 1 ml resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1 % Tween-20), cells were pelleted (500 g, 4°C, 10 min) and resuspended in 50 µl transposition mixture (25 µl 2xTD buffer (Illumina), 2.5 µl TD enzyme (Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). After incubation (37°C, 1000 rpm, 30 min), DNA was purified and Illumina adapters were added.
The libraries were pooled and sequenced on a HiSeq 2500 using a 100 cycle (50 bp paired-end) rapid run

treatment_protocol: Cells were treated with DMSO solvent control (0.15 %; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 µM; Sigma Aldrich) for 24 h

value: breast

value: epithelial cells

value: wild-type

value: Nutlin-3a 10 uM 24 h


title: RNA-seq_a-Smarca5 TrimAway rep1_E07


title: Aorta_24mo_4

value: Aorta

value: Wild-type


title: Distal, Group 1, scRNAseq

description:
mD1
10X Genomics (Single Cell 3' v2)

value: Uterine Tube (Oviduct)

value: distal section


title: RNA-seq_a-Smarca5 TrimAway rep1_H07

value: 2 cell stage embryos


title: MCF-7_Nutlin-3a_2


title: 501Mel, sh4, dox-induced, Rep1


title: RNA-seq_No injection ctrl TrimAway rep3_F04

value: No injection ctrl


title: no_treatment_24h_rep1

value: C

value: before the exposure 30.9 ng/ml PMA for 48h

value: monocyte


title: WT_409

value: Liver

value: 2 months old


title: RNA-seq_a-Smarca5 TrimAway rep1_G06


title: WT_408

value: male


title: MCF-7_Nutlin-3a_4


title: RNA-seq_a-Smarca5 TrimAway rep1_F06


title: WT_389


title: MCF-7_DMSO_4

value: DMSO 24 h


title: 501Mel, shlacZ, dox-induced, Rep2


title: WT_407


title: 501Mel, sh4, dox-induced, Rep2


title: WT_406


title: RNA-seq_a-Smarca5 TrimAway rep1_E06


title: MCF-7_DMSO_2

value: breast


title: Lung, chronic_infected_D1

city: Milan

first: Federico

last: Di Marco

state: Outside U.S./Canada

address: Via Olgettina 60

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: 10x Genomics

data_processing:
The Fastq files underwent processing using the Spaceranger software from 10x (version 1.3.1) while adhering to default parameters. Reference dataset was modified accordingly for the detection of custom probes as stated in the 10x technical note (10x Genomics. Custom Probe Design for Visium Spatial Gene Expression and Chromium Single Cell Gene Expression Flex, CG000621, Rev A 2023). Following processing, the resultant filtered count matrices were imported and subjected to in-depth analysis through employment of the R package Seurat (version 4.1.0).
Assembly: mm10
Supplementary files format and content: counts.tsv.gz: gene expression matrix
Supplementary files format and content: *json: alignment file
Supplementary files format and content: *tif: tissue image
Library strategy: Visium Spatial Gene Expression

source_name: Lung

extract_protocol:
Probe Hybridization (User guide CG000407) we introduce our customized probes according with 10x Technical note. We refined the Visium protocol to reinforce the Probe Hybridization and we exploited the Diluted Permeabilization Enzyme B at 100X in Buffer EB. Similar approach was also used for the control uninfected lung.
Formalin Fixed Paraffin-embedded tissues (FFPEs) were sectioned at 5 µm in thickness and attached to a Visium Spatial Gene expression slide. The tissue sections underwent hematoxylin and eosin staining using the Visium Spatial Gene Expression protocol designed for FFPE tissue - Deparaffinization, H&E Staining, Imaging & Decrosslinking demonstrated protocol. Imaging was performed using a scanning tile microscope (Aperio AT2, Leica). Then slides underwent tissue removal and library preparation following Visium Spatial Gene Expression for FFPE libraries demonstrated protocol.

value: Lung

tag: group

tag: agent

value: Mycobacterium abscessus (ATCC 19977 strain)


title: 501Mel, sh8, IFNγ-treated, dox-induced, Rep1


title: mC2_2

city: Shanghai

first: Christopher

last: Heeschen

address: 227 Chongqin South Rd.

department: Center for Single-Cell Omics

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Skewer software to trime adaptor and low-quality fragments
FastQC for quality control
STAR for genome mapping
StringTie for transcript assembling
gffcompare for classification of assembled transcripts
Assembly: STAR/StringTie
Supplementary files format and content: .xls file containing accession ID, gene symbol, and FPKM of all samples

source_name: Pancreatic cancer cell

growth_protocol: Cells were cultured in DMEM/F12 medium supplemented with 5% fetal bovine serum and 1% penicillin and streptomycin in humidified atmosphere at 37C

extract_protocol:
RNA was extracted using TRIZol, 1 ug total RNA was used to construct library, 28S:18S>1.5, OD260/280: 1.8-2.2, Qubit to determine RNA concentration (>500 ng/ul)
Enrich mRNA with Oligo (dT) magnetic beads, fragmentated to 200 bp, use random primers to synthesize 1st strand cDNA, replace dTTP with dUTP in 2nd strand cDNA synthesis, purify double strand cDNA with AMPure XP beads, blunt with End Repair Mix, add poly (A) tail and ligation; digest double strand cDNA with USER enzyme to produce one strand cDNA, amplify at ~15 cycles with PCR to obtain final cDNA library.

value: Pancreatic cancer cell

value: No treatment


title: 501Mel, sh8, IFNγ-treated, uninduced, Rep2


title: RNA-seq_a-Smarca5 TrimAway rep1_B07


title: RNA-seq_a-Smarca5 TrimAway rep1_D06


title: RNA-seq_a-Smarca5 TrimAway rep1_B06


title: 501Mel, shlacZ, dox-induced, Rep3


title: Lung, control_A1

description: 10x Genomics

value: control

value: sham


title: RNA-seq_a-Smarca5 TrimAway rep1_D07


title: MCF-7_DMSO_3

value: epithelial cells

value: wild-type


title: 501Mel, sh4, IFNγ-treated, dox-induced, Rep2


title: MCF-7_Nutlin-3a_1

value: Nutlin-3a 10 uM 24 h


title: 501Mel, shlacZ, dox-induced, Rep1


title: WT_390


title: RNA-seq_a-Smarca5 TrimAway rep1_C06

value: 2 cell stage embryos


title: RNA-seq_a-Smarca5 TrimAway rep1_B08


title: mC2_1


title: 501Mel, sh4, IFNγ-treated, dox-induced, Rep1


title: 501Mel, sh8, IFNγ-treated, uninduced, Rep1


title: 2K-WT_1

value: WT (shControl)


title: RNA-seq_a-Smarca5 TrimAway rep1_C07


title: RNA-seq_a-Smarca5 TrimAway rep1_A07


title: 501Mel, sh8, IFNγ-treated, dox-induced, Rep2


title: RNA-seq_a-Smarca5 TrimAway rep1_A06


title: MCF-7_Nutlin-3a_4_QuantSeq

data_processing:
Informed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports, we used Trimmomatic 66 v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10 67.
Potential sequencing errors were detected and corrected using Rcorrector v1.0.4 68.
The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v102, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option disabled. Mappings were filtered for uniqueness and properly aligned reads by Samtools v1.12.
Pre-processed data was split into strand-specific subsets using Samtools. PEAKachu v0.2.0 was used over all replicates including both conditions to call cell and strand-specific peaks. When the distance between peaks was within 50 bp, Bedtools v2.30.0 was used to merge the peaks.
Assembly: hg38
Supplementary files format and content: PEAKachu peak files

growth_protocol: MCF-7 and U2OS cells were grown in high glucose DMEM with pyruvate. RPE-1 hTERT cells were cultured in DMEM:F12 media. Culture media were supplemented with 10% FBS and penicillin/streptomycin. In addition, DMEM was supplemented with non-essential amino acids for culturing MCF-7 cells.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. Total RNA was quantified and quality checked using a 2100 Bioanalyzer in combination with RNA 6000 assay or a 4200 Tapestation instrument in combination with RNA ScreenTape
QuantSeq libraries were prepared from 500 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit REV (Lexogen, Vienna, Austria) following the manufacturer's instructions. Quantification and quality check of libraries was done using a 2100 Bioanalyzer instrument and DNA 7500 kit or a 4200 Tapestation instrument and a DNA 1000 kit (Agilent Technologies).
Libraries were pooled and sequenced on a HiSeq 2500 using 50 cycle high-output reagents or a NextSeq 500 using 75 cycle high-output v2.5 reagents

treatment_protocol: Cells were treated with Nutlin-3a 10 µM or DMSO control for 24 h


title: mC1_2


title: MCF-7_DMSO_1


title: RNA-seq_a-Smarca5 TrimAway rep1_A08


title: 2K-WT_2


title: RNA-seq_no embryo_F05

value: no embryo


title: MCF-7_DMSO_4_QuantSeq


title: mC1_1


title: 501Mel, sh4, IFNγ-treated, uninduced, Rep1


title: MCF-7_Nutlin-3a_1_QuantSeq


title: RNA-seq_no embryo_H03


title: 501Mel, sh4, IFNγ-treated, uninduced, Rep2


title: 501Mel, shlacZ, IFNγ-treated, dox-induced, Rep1


title: MCF-7_Nutlin-3a_2_QuantSeq


title: MCF-7_Nutlin-3a_4_CAGE-seq

description: m7-cap-filtered 5'RNA

data_processing:
Informed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports, we used Trimmomatic 66 v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10 67.
Potential sequencing errors were detected and corrected using Rcorrector v1.0.4 68. In addition, Cutadapt was used with adapter parameter ‘XG’ to clip the first position of CAGE-seq reads if that was a guanin base to correct for CAGE-seq’s 5’-end guanin addition bias.
The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v102, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option disabled. Mappings were filtered for uniqueness and properly aligned reads by Samtools v1.12.
Pre-processed data was split into strand-specific subsets using Samtools. PEAKachu v0.2.0 was used over all replicates including both conditions to call cell and strand-specific peaks. When the distance between peaks was within 50 bp, Bedtools v2.30.0 was used to merge the peaks.
Assembly: hg38
Supplementary files format and content: PEAKachu peak files

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. Total RNA was quantified and quality checked using a 2100 Bioanalyzer in combination with RNA 6000 assay or a 4200 Tapestation instrument in combination with RNA ScreenTape
CAGE-seq libraries were prepared from 5000 ng of total RNA using the CAGE Preparation Kit (Kabushiki Kaisha DNAFORM, Yokohama, Japan) following the manufacturer's instructions. Quantification and quality check of libraries was done using a 2100 Bioanalyzer instrument and DNA 7500 kit or a 4200 Tapestation instrument and a DNA 1000 kit (Agilent Technologies).
Libraries were pooled and sequenced on a NextSeq 500 v2 300 cycles runs. System run in 151 cycle/paired-end mode.


title: MLO-Y4 cell, differentiated, control, sample 3

city: Houston

first: Robert

middle: L

last: Satcher

address: 1515 Holcombe

department: Orthopaedic Oncology

institute: MD Anderson Cancer Center

data_processing:
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using salmon package.
The transcript abundances for each sample was estimated with StringTie, and the TPM value for gene and transcript level were calculated with R package .
Assembly: mm10
Supplementary files format and content: quantification file, plain-text, tab-separated file with a single header line (which names all of the columns).

growth_protocol: MLO-Y4 osteocytes were cultured on rat tail collagen-type I-coated plates (0.15 mg/mL) to maintain an osteocyte-like phenotype. Recombinant human BIGH3 protein with/without HCQ, or with/without anti-BIGH3 antibodies at the indicated doses. For differentia

extract_protocol:
RNA was harvested and 1~2 ug was used for library preparation. Library quality was deemed suitable for sequencing.
Library preparation followed KAPA Standard RNA-Seq Library Prep Kit (Illumina)

treatment_protocol: Recombinant human BIGH3 protein with/without HCQ, or with/without anti-BIGH3 antibodies at the indicated doses. For differentiation, cells were cultured in α-MEM supplemented with 10% fetal bovine serum, 50 µg/mL ascorbic acid, and 4 mM β- β-glycerophosphate.

value: osteocyte

value: WT

value: differentiated, control


title: MLO-Y4 cell, differentiated, BIGH3 treated, sample 3

value: differentiated, BIGH3


title: MCF-7_DMSO_2_QuantSeq

value: breast

value: DMSO 24 h


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_A05

value: Smarca5 +/- (mat KO)


title: MCF-7_DMSO_3_QuantSeq


title: RNA-seq_no embryo_G03


title: 501Mel, shlacZ, IFNγ-treated, dox-induced, Rep2


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_C05


title: MCF-7_DMSO_1_QuantSeq


title: MCF-7_Nutlin-3a_3_CAGE-seq

description: m7-cap-filtered 5'RNA


title: 501Mel, shlacZ, IFNγ-treated, uninduced, Rep2


title: MLO-Y4 cell, differentiated, control, sample 1


title: PN0129B_P_48h_5FU_blue

city: Belfast

first: Deborah

middle: Y.

last: Moss

address: 97 Lisburn Road

department: Patrick G. Johnston Centre for Cancer Research

institute: Queen's University Belfast

data_processing:
RNA-seq reads were aligned to the human genome (hg37) using STAR aligner and the number of reads mapping to genes annotated in Gencode build 37 (v22) were calculated using HTseq.
Assembly: The indexes used for these libraries were from the KAPA Unique Dual-Indexed Adapter kit.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Colon adenocarcinoma

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1 mM sodium pyruvate and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using the KAPA RNA HyperPrep kit with RiboErase and processed as per manufacturer's protocols
NGS library construction from 25 ng–1 μg of total RNA and depletes both cytoplasmic (5S, 5.8S, 18S and 28S) and mitochondrial (12S and16S) ribosomal RNA species

treatment_protocol: HCT116 cells were either treated with vehicle control or 2 µM 5FU for 24 or 48 hrs.

value: Colon adenocarcinoma

value: colorectal cancer cell line

value: KRAS G13D

value: 2µM 5FU, 48hr


title: MLO-Y4 cell, control, sample 2

value: control


title: MCF-7_DMSO_4_CAGE-seq

description: m7-cap-filtered 5'RNA

value: epithelial cells

value: wild-type


title: MLO-Y4 cell, differentiated, BIGH3 treated, sample 1


title: MLO-Y4 cell, differentiated, control, sample 2


title: PN0129B_P_48h_5FU_red


title: MCF-7_Nutlin-3a_1_CAGE-seq

description: m7-cap-filtered 5'RNA

value: Nutlin-3a 10 uM 24 h


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_D05

value: 2 cell stage embryos


title: MLO-Y4 cell, control, sample 3


title: 501Mel, shlacZ, IFNγ-treated, uninduced, Rep1


title: PN0129B_P_48h_5FU_black


title: MCF-7_Nutlin-3a_2_CAGE-seq

description: m7-cap-filtered 5'RNA


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_B05


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_A03


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_F03


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_E05


title: PN0129B_P_24h_5FU_blue

value: 2µM 5FU, 24hr


title: PN0129B_P_24h_5FU_black


title: MLO-Y4 cell, BIGH3 treated, sample 2

value: osteocyte


title: MLO-Y4 cell, BIGH3 treated, sample 1

value: WT


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_C03


title: MCF-7_DMSO_1_CAGE-seq

description: m7-cap-filtered 5'RNA


title: MCF-7_DMSO_3_CAGE-seq

description: m7-cap-filtered 5'RNA


title: PN0129B_P_24h_5FU_red


title: MLO-Y4 cell, differentiated, BIGH3 treated, sample 2


title: MCF-7_DMSO_2_CAGE-seq

description: m7-cap-filtered 5'RNA


title: MLO-Y4 cell, BIGH3 treated, sample 3


title: MLO-Y4 cell, control, sample 1


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_D03


title: PN0129B_P_0h_Ctrl_black

value: Vehicle control


title: PN0129B_P_0h_Ctrl_blue


title: PN0129B_P_0h_Ctrl_red


title: Lung, control

description: 10x Genomics

data_processing:
The Fastq files underwent processing using the Spaceranger software from 10x (version 1.3.1) while adhering to default parameters. Reference dataset was modified accordingly for the detection of custom probes as stated in the 10x technical note (10x Genomics. Custom Probe Design for Visium Spatial Gene Expression and Chromium Single Cell Gene Expression Flex, CG000621, Rev A 2023). Following processing, the resultant filtered count matrices were imported and subjected to in-depth analysis through employment of the R package Seurat (version 4.1.0).
Supplementary files format and content: counts.tsv.gz: gene expression matrix
Supplementary files format and content: *json: alignment file
Supplementary files format and content: *tif: tissue image
Library strategy: Visium Spatial Gene Expression

value: Lung

tag: infection

value: sham control


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_E03

data_processing:
Raw FastQ files were trimmed using Trim Galore (v0.6.5, Cutadapt v2.3) and mapped to the mouse GRCm38 genome assembly using HISAT2 (v2.1.0) (D. Kim et al., 2015), with the options –dta –no-softclip –no-mixed –no-discordant.
Assembly: GRCm38_v95
Supplementary files format and content: Tab delimited text file of read counts over genes


title: ATACseq_TPA_Gastric premalignant organoids, Trp53-/-;sgPten;sgArid1a_rep2

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

data_processing:
The Illumina NovaSeq 6000 platform was utilized to sequence the library. To remove adapters from the 150 bp paired-end raw data, NGmerge was employed with the option "NGmerge -a -v -n 20". Bowtie2 software was used to construct an index for the mouse genome (mm10), followed by alignments using the option "--very-sensitive -X2000 -x mm10". Duplicates were removed using Picard's MarkDuplicates tool. Mitochondrial genome contamination was eliminated using SAMtools and awk commands, resulting in bam files. Normalized bw files were generated using deepTools with the option "bamCoverage -bs=1 --normalizeUsing BPM" for subsequent visualization in the Integrated Genome Viewer (IGV).The HMMRATAC standard workflow was utilized for peak calling in ATAC-seq. The genomic distribution of accessibility sites was determined using ChIPseeker with the option "annotatePeak", and the TSS region "tssRegion" was set as (-3000, 3000). The "gappedPeak" files were transformed into GrangesList forms, and the peaks were converted into consensus counts. Data normalization and differential comparison were performed using DESeq2. Regions of differential accessibility were identified for downstream analyses using a p-value cutoff of 0.05 (Wald test).
Assembly: mm10
Supplementary files format and content: bigWig, gappedPeak

source_name: Gastric premalignant organoids

growth_protocol: Mouse organoid cultures were established and maintained as described previously. Specifically, normal mice stomach was mechanically minced into pieces of 5-mm3 cubes and incubated in DPBS with 2.5 mM EDTA on ice. After incubation, the released gastric gland fractions were resuspended with Matrigel (Corning, Cat# 356237) and seeded in 48-wells plate. Tumor tissues were harvested and washed with ice-cold DPBS, and then minced into pieces. Incubating the minced tumor tissue in digestion medium containing 0.5 mg/ml collagenase IV (GIBCO, Cat# 17104-019) and 1.0 mg/ml collagenase I (GIBCO, Cat# 17100-017) in DMEM/F12 medium at 37°C until it dissociates into single cells or cell clusters. Tumor cells were collected by centrifugation and resuspended with Matrigel. Organoid culture medium was DMEM/F12 (GIBCO, Cat# C11330500BT) supplemented with 2 mM GlutaMAX (GIBCO, Cat# 35050-061), 1% Penicillin and Streptomycin (GIBCO, Cat# 15140-122), 1× B27 (GIBCO, Cat# A3582801), 1× N2 (GIBCO, Cat# 17502048),10 mM Y-27632, 200ng/ml FGF10 (Peprotech, Cat# 100-26-1000), 500nM A-8301 (Peprotech, Cat# 9094360), 50ng/ml mouse recombinant EGF (Peprotech, Cat# AF-100-15-1000), 100 ng/ml mouse recombinant noggin (Peprotech, Cat# 120-10C-250), 10mM Nicotinamide (Sigma, Cat# N0636), 1 mM N-acetylcysteine (Sigma, Cat# A9165), 10% Wnt3a condition medium, 10% R-spondin1 condition medium). Organoid medium was refreshed every 2-3 days.

extract_protocol: Organoids (5X104 cells/each group) were harvested to construct ATAC-Seq libraries using a Chromatin Profile Kit (Novoprotein, Cat. N248-01A). 1ml ice-cold PBS suspended organoids, then centrifuged at 500g at 5min. The supernatant was removed and 50ul lysis buffer gently resuspended organoids. Tubes were placed on ice for 5 min and added into 950ul wash buffer, then gently blow for 5 times, which was centrifuged at 500g for 5min at 4°C. The sediment was added into 40ul fragmented mixture and transferred to PCR tubes for 30min at 37°C. Then 10ul stop buffer used to end the reaction for 5min at 55°C. The DNA extracted beads was used for purifying fragments. Transposed DNA fragments were amplified using the PCR system from this kit. PCR conditions: 72 °C for 3 min, 98 °C for 30 s, followed by 9-18 cycles of 98 °C for 15 s, 60°C for 15 s and 72 °C for 10 s, 72 °C for 2min. Amplified libraries were purified with the DNA Clean Beads.

value: Gastric premalignant organoids


title: ATACseq_TPA_Gastric premalignant organoids, Trp53-/-;sgPten;sgArid1a_rep1


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_B03

extract_protocol:
polyA RNA-seq following the scNMT-seq protocol https://www.protocols.io/view/scnmt-seq-kxygxmwwwl8j/v2
Nextera XT, using dual indexing

value: Smarca5 +/- (mat KO)


title: Lung, chronic_infected

description: 10x Genomics

value: Mycobacterium abscessus


title: small RNA FiveFUEV_3

city: Nashville

first: Hua-Chang

last: Chen

state: TN

address: 2525 West End Avenue, Suite 1100

department: Department of Biostatistics

institute: Vanderbilt University Medical Center

description:
FiveFUEV_3
sEVl, 5-FU treatment, rep3

data_processing:
Demultiplexing and bioinformatic analyses was performed using the TIGER pipeline (58).  Briefly, Cutadapt (v1.16) was used to trim 3′ adaptors and then trim 4 nt from both 5' and 3' end (the random-mer sequence introduced by NEXTFlex samll RNA library preparation kit) and all reads with < 16 nucleotides (nts) were removed (59).  Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.11.9)(www.bioinformatics.babraham.ac.uk/projects/fastqc).  The adaptor-trimmed reads were mapped to the hg19 genome, with additional rRNA and tRNA reference sequences, by Bowtie1 (v1.1.2) allowing only one mismatch (60).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: sEV

growth_protocol: DLD-1 cells were validated as heterozygous KRAS mutant (G13D) cells by PCR amplification of genomic DNA and DNA sequencing.  Cells were seeded at 6.5x 106 in T175 flasks and cultured in DMEM medium with 10% fetal bovine serum, 2 mM L-glutamine, 1x MEM non-essential amino acids, 100 U/mL of penicillin, and 100 U/mL of streptomycin.  When the cells reached 70% confluence, they were washed three times with phosphate-buffered saline (PBS) and cultured in a serum-free medium with or without 10 mM 5-FU for 48 hrs.

extract_protocol:
Cells were collected by scraping, washed in PBS, and resuspended in PBS prior to isolation of total RNA using the Quick-RNA Miniprep kit (Zymo Research).  Total RNA from pelleted sEVs in PBS was isolated using the same kit.
RNA libraries were generated using the NEXTFlex Small RNA Library Preparation Kits v3 (Perkin) with the following modifications: (1) 3′- and 5′-adaptors were diluted 1:8, (2) 3′-adaptor ligations were performed overnight in multiple steps –25°C for 2 h, 20°C for 4 h and 16°C overnight, (3) following cDNA synthesis and before barcoding PCR, step F protocol was followed, and (4) PCR amplification was 20 cycles.  Following PCR amplification, individual libraries were size-selected (136–200 bp product) using Pippin Prep (Sage Sciences).  Size-selected libraries were quantified using Qubit Fluorometer.  Libraries were checked for quality and sequenced using Illumina short-read technology.  Libraries were pooled (equimolar multiplexed libraries) and sequenced (PE150) using the NovaSeq6000 (Illumina) platform at the VANTAGE Core (Vanderbilt University).

treatment_protocol: 5-FU treatment involved exposure of cells to 10uM 5-Fu for 48 hours

value: sEV

value: colorectal adenocarcinoma cell lines

value: 10 uM 5-FU for 48 hrs


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_F04


title: small RNA FiveFUEV_2

description:
FiveFUEV_2
sEVl, 5-FU treatment, rep2

value: KRAS G13D


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_C04


title: ATACseq_TP_Gastric premalignant organoids, Trp53-/-;sgPten_rep2


title: ATACseq_TP_Gastric premalignant organoids, Trp53-/-;sgPten_rep1


title: ums53_T24B8-5p_PA14_3

city: Worcester

first: Read

last: Pukkila-Worley

state: MA

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

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

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Synchronized C. elegans wild-type (N2) and rotr-1(ums53) loss-of-function mutants were grown on Escherichia coli (OP50) from the L1 to L4 stage.

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

treatment_protocol: Synchronized C. elegans wild-type (N2) and rotr-1(ums53) loss-of-function mutants at the L4 stage were transferred to either Escherichia coli (OP50) or Pseudomonas aeruginosa (PA14) for 4 hours at 25°C.

value: Whole animal

tag: developmental stage


title: 457 [mRNA]

type: RNA

first: Hao

last: Lin

state: Shanghai

address: No. 389, Xincun Road

department: Department of Cardiology

institute: Tongji Hospital, School of Medicine, Tongji University,

description: Gene expression after overexpression of hsa_circ_0122319 and hsa_circ_0002457 in HUVEC

hyb_protocol: The labeled RNA was purified and hybridized with the chip, and the original image was scanned with the Agilent Scanner G2505C (Agilent Technologies) after elution.

scan_protocol: The original image was scanned with the Agilent Scanner G2505C (Agilent Technologies) after elution.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 13.1, Agilent Technologies) was employed to finish the basic analysis with the raw data.

label_protocol: Total RNA is dephosphorylated, denatured, and then further labeled with Cyanine-3-CTP (Cy3).

growth_protocol: HUVEC cultured in Dulbecco’s Modified Eagle Medium (DMEM, low glucose, Hyclone) supplemented with 5% FBS (Gibco), 3% penicillin/streptomycin (Gibco)

extract_protocol: Extraction of total RNA using the TRIZOL reagent (Invitrogen, CA, United States). And the total RNA was reverse transcribed using PrimeScript™ RT Master Mix (RR036A, Takara, Dalian, China).

value: HUVEC

value: overexpression of hsa_circ_0002457


title: small RNA FiveFUEV_1

description:
FiveFUEV_1
sEVl, 5-FU treatment, rep1


title: ums53_T24B8-5p_PA14_2


title: small RNA SFEV_3

description:
SFEV_3
sEV, serum-free medium control, rep3

value: serum-free medium


title: 319 [mRNA]

value: overexpression of hsa_circ_0122319


title: 457-1 [mRNA]


title: CUTTag_antiARID1A_Gastric premalignant organoids, Trp53-/-;sgPten_rep2

description:
CUTTag_ARID1A_in_TP.bs1.bw
CUTTag_ARID1A_in_TP_peaks.narrowPeak

data_processing:
The Illumina NovaSeq 6000 platform was employed to perform genomic sequencing. Following quality control by the fastp standard workflow, the Bowtie2 software was utilized to construct an index for the mouse genome (mm10) and align paired-end clean data of 150 bp length using the options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700". The SAMtools program was utilized to convert sam files to sorted bam files. Picard's MarkDuplicates tool was used to remove duplicates with the option "REMOVE_DUPLICATES=true". Normalized bw files were generated using deepTools with the option "bamCoverage -bs=1 --normalizeUsing BPM" for further visualization in the Integrated Genome Viewer (IGV). Peak calling was performed using the MACS2 software with the option "macs2 callpeak --broad -q 1e-5 -f BAMPE -g mm --keep-dup all". ChIPseeker was employed to identify the genomic distribution of the peaks, with the TSS region "tssRegion" set as (-3000, 3000) for annotation. The "narrowPeak" files were transformed into GrangesList forms, and the peaks were converted into consensus counts. Data normalization and differential comparison were performed using DESeq2. Regions of differential modification were identified for downstream analyses using a p-value cutoff of 0.05 (Wald test).
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol: Organoids (3-10X104 cells/each group) were harvested in 1.5ml tubes for CUT&Tag assay using NOovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein, Cat. N259-YH01-01A). 10ul ConA beads were added into tube and incubated with cells for 10min at 25°C. The supernatant was removed and added primary antibody buffer with proper primary antibody for 2h at 25°C or overnight at 4°C. The supernatant was removed and added secondary antibody buffer for 1h at 25°C. Beads were washed for 2 times. The chromatin was combined with ChiTag TM2.0 Transposome, then fragmented using Tagmentation Buffer for 1h at 37°C. ChIP DNA was purified using DNA Clean Beads and amplified using the PCR system from this kit. PCR conditions: 72 °C for 3 min, 98 °C for 30 s, followed by 10-25 cycles of 98 °C for 15 s, 60°C for 15 s and 72 °C for 10 s, 72 °C for 2min. Amplified libraries were purified with the DNA Clean Beads.. The purified ChIP DNA was used for library preparation.

tag: chip antibody

value: antiARID1A, Cell signaling technology,Cat#12354


title: NC [mRNA]

source_name: NC

value: NC


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_H04

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

institute: The Babraham Institute

tag: tissue

value: 2 cell stage embryos


title: ums53_T24B8-5p_PA14_1

tag: genotype


title: small RNA SFEV_2

description:
SFEV_2
sEV, serum-free medium control, rep2


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_D04


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_A04


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_G04


title: CUTTag_antiARID1A_Gastric premalignant organoids, Trp53-/-;sgPten_rep1


title: ums53_T24B8-5p_OP50_3


title: small RNA SFEV_1

description:
SFEV_1
sEV, serum-free medium control, rep1


title: ums53_T24B8-5p_OP50_2


title: CUTTag_antiBRD9_Gastricpremalignant organoids, Trp53-/-;sgPten;sgArid1a_rep3

value: antiBRD9, Thermo Fisher Scientific,Cat#A303-781A


title: small RNA FiveFU_3

description:
FiveFU_3
cell, 5-FU treatment, rep3

source_name: cell

value: cell


title: 319-1 [mRNA]


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_E04


title: ums53_T24B8-5p_OP50_1


title: RNA-seq_SMARCA5  +/- 2 cell stage embryos (matKO females)_rep2_B04


title: small RNA FiveFU_1

description:
FiveFU_1
cell, 5-FU treatment, rep1


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_H05

value: Smarca5 +/+


title: CUTTag_antiBRD9_Gastricpremalignant organoids, Trp53-/-;sgPten;sgArid1a_rep1

value: Gastric premalignant organoids


title: CUTTag_antiBRD9_Gastricpremalignant organoids, Trp53-/-;sgPten_rep2


title: T24B8-5p_PA14_2


title: small RNA SF_3

description:
SF_3
cell, serum-free medium control, rep3


title: CUTTag_antiBRD9_Gastricpremalignant organoids, Trp53-/-;sgPten_rep3


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_A01


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_G05


title: T24B8-5p_OP50_3


title: small RNA SF_1

description:
SF_1
cell, serum-free medium control, rep1


title: CUTTag_antiBRD9_Gastricpremalignant organoids, Trp53-/-;sgPten_rep1


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_F01


title: T24B8-5p_PA14_1


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_C01


title: T24B8-5p_OP50_2


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a, treated with 10μM dBRD9_rep2

description:
RNAseq_dBRD9_treat_Counts.csv
RNAseq_dBRD9_treat_Normalized_data.csv

data_processing:
Transcriptome sequencing was conducted using the Illumina NovaSeq 6000 platform with 150 bp paired-end sequencing. After removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference mouse genome (mm10) using STAR _2.6.0. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v.1.22.2).
Assembly: mm10
Supplementary files format and content: csv files include counts and DESeq2 normalized data

source_name: Gastric tumor organoids

extract_protocol:
Total RNA extraction using TRIzol reagent (Thermo Fisher Scientific, Cat# 15596026) and complementary DNA (cDNA) synthetization using HiScript-III RT SuperMix kit (Vazyme, Cat# R323-01).
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

treatment_protocol: TP and TPA mouse tumor organoids were dissociated in TrypLETM and seeded into 96-well plates (2000 cells per well). After 24h culturing, organoids were treated with 10μM dBRD9.

value: Gastric tumor organoids

value: treated with 10μM dBRD9


title: small RNA FiveFU_2

description:
FiveFU_2
cell, 5-FU treatment, rep2

value: colorectal adenocarcinoma cell lines


title: CUTTag_antiBRD9_Gastricpremalignant organoids, Trp53-/-;sgPten;sgArid1a_rep2


title: small RNA SF_2

description:
SF_2
cell, serum-free medium control, rep2


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a, treated with 10μM dBRD9_rep1


title: FiveFU_3

description: 5-FU treatment, rep3

data_processing:
After sequencing, samples (libraries) were demultiplexed and analyzed.  Briefly, reads were trimmed to remove adapter sequences using Cutadapt v2.10)(59) and aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.8a)(61).  Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping.  Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.11.9).  FeatureCounts (v2.0.2)(62) was used to count the number of mapped reads to each gene.  Heatmap3 (63) was used for cluster analysis and visualization.  Significant differential expressed genes with absolute fold change > 2 or < 0.5, and adjusted p value (padj) < 0.05 were determined using DESeq2 (v1.30.1)(64).  Genome Ontology and KEGG pathway over-representation analyses were performed on differentially expressed genes using the WebGestaltR package (NULL)(65).  Gene set enrichment analysis (GSEA) was performed using GSEA package (v4.3.2)(66) on database v2022.1.Hs.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: colon cancer

extract_protocol:
Cells were collected by scraping, washed in PBS, and resuspended in PBS prior to isolation of total RNA using the Quick-RNA Miniprep kit (Zymo Research).  Total RNA from pelleted sEVs in PBS was isolated using the same kit.
Bulk RNA sequencing libraries were prepared using Universal RNAseq kits (Tecan), as per manufacturer’s instructions.  Libraries were cleaned (Zymo), checked for quality using the Agilent bioanalyzer, quantified (Qubit), and pooled based on equimolar concentrations of libraries.  Pooled libraries were sequenced using Illumina short-read technology based on PE150 on the NovaSeq6000 (Illumina).

value: colon cancer

value: 10 uM 5-FU for 48 hrs


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_H01

source_name: 2 cell stage embryos


title: zebrafish embryo, 5dpf, sas10 mutant, rep 2

city: Hangzhou

first: Shuyi

last: Zhao

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

data_processing:
Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat.
Trimmed sequences were deduplicated, zebrafish 5'ETS sequence searched, and mapped to zebrafish pre-rRNA reference sequence to analyze the 3' end of each read.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file including each read's relative postion in pre-rRNA, corresponding sequence, modification status and modification size.

organism: Danio rerio

source_name: embryo

extract_protocol:
Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent (Aidlab, RN0102), with three independent biological repeats each, and was treated with DNase I (New England Biolabs, M0303S) to remove genomic DNA contamination.
Total RNA for each sample was ligated with 3'RACE_adapter, followed by 3'RACE_adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish 5'ETS sequence and reverse primers (Illumina RPIs).

value: embryo

value: sas10 mutant


title: FiveFU_2

description: 5-FU treatment, rep2

value: KRAS G13D


title: FiveFU_1

description: 5-FU treatment, rep1


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_D01


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a, treated with DMSO_rep3

value: treated with DMSO


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a, treated with DMSO_rep2


title: zebrafish embryo, 5dpf, sas10 mutant, rep 1


title: SF_3

description: serum-free medium control, rep3

value: serum-free medium


title: zebrafish embryo, 5dpf, wild type, rep 2

value: wild type


title: SF_2

description: serum-free medium control, rep2


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_E01


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_G01


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a, treated with 10μM dBRD9_rep3


title: SF_1

description: serum-free medium control, rep1


title: zebrafish embryo, 5dpf, wild type, rep 1


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_B01


title: T24B8-5p_OP50_1

value: Whole animal


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a_rep3

description:
RNAseq_Tumor_Organoids_Counts.csv
RNAseq_Tumor_Organoids_Normalized_data.csv


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a_rep2


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_A02

value: 2 cell stage embryos


title: NK2

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

data_processing:
RNA-Seq reads were aligned using STAR (STAR_2.6.1c) to a concatenated reference comprised of the Homo sapiens (GRCh38.p12 assembly) and Mus musculus (GRCm38.p6 assembly) genomes.
The resulting alignments were separated into species-specific bam files, converted back to fastq files and processed through individual human and mouse pipelines
Assembly: GRCh38.p12 assembly and GRCm38.p6 assembly

growth_protocol: All animal studies were performed in accordance with protocols approved by the New York Medical College Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA was extracted from tumors using RNeasy mini kit (Qiagen) after homogenization of tumors by Tumor Dissociation Kit (Miltenyi Biotec) combined with the gentleMACS Dissociator.
Library was constructed using RNA as input using Illumina TruSeq Stranded Total RNA library preparation kit

treatment_protocol: NK cells were injected at dose of 1x107 cells/animal via i.v. injection

value: Natural killer cell


title: NK1

value: cell


title: zebrafish embryo, 5dpf, sas10 mutant, replicate 2

data_processing:
Sequence reads were trimmed for adaptor sequence and low-quality sequence by fastp (version 0.20.0)
Trimmed sequence reads were mapped to GRCz11 using HISAT2 (version 2.2.1)
Transcripts per million (TPM) for each gene was obtained through featureCounts (version 2.0.1) and was adopted to quantify the expression level.
TPM-based quantification of different regions across the pre-rRNA transcript, including 5’ETS, ITS1, 18S, ITS2, 5.8S, and 28S, was achieved by Salmon (version 0.12)
DESeq2 R package (version 1.40.2) was used to get differentially expressed genes (DEGs).
Assembly: GRCz11
Supplementary files format and content: tab-dilimited text file containing raw counts for each sample
Supplementary files format and content: csv file containing information of differentially expressed genes for each sample, including log2FoldChange, padj etc.
Supplementary files format and content: csv file containing quantification of different regions across the pre-rRNA transcript for each sample

extract_protocol:
RNA was extracted using TRIpure Reagent (Aidlab)  following manufacturer's instructions, and 3 μg RNA was used for library construction.
RNA libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for lllumina (Vazyme) following manufacturer's instructions.


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a_rep1


title: zebrafish embryo, 5dpf, sas10 mutant, replicate 1


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_C02

value: Smarca5 +/+


title: PDAC, GSDMC-NTF, ChIP

data_processing:
SKEWER (0.2.2) was used to remove low-quality and adaptor sequences, then exclude shorter sequences (<50bp): -Q 30, -k 5, -l 50.
FASTQC was used for quality control
BOWTIE2 (2.2.3) was used for unique mapping to genome, and remove duplicated reads (default parameters)
MACS2 (2.2.7.1) was used for peak calling (-q 0.01)
bigWig files were created using DEEPTOOLS (3.5.0)
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: RMPI1640, 10% fetal bovine serum, 1x penicillin/streptomycin, cells were culture in 37C with 5% CO2.

extract_protocol:
SimpleChIP® Plus Enzymatic Chromatin IP Kit (CST, #9005) was used for sample preparation as manufacturer's protocol strictly followed
VAHTS Universal DNA Library Prep Kit for Illumina V3 was used for library construction

value: Primary culture


title: zebrafish embryo, 5dpf, wild type, replicate 3


title: Gastric tumor premalignant organoids, Trp53-/-;sgPten_rep2

value: Gastric tumor organoids


title: Gastric tumor organoids, Trp53-/-;sgPten;sgArid1a, treated with DMSO_rep1


title: MCF-7_Nutlin-3a_3_QuantSeq

data_processing:
Informed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports, we used Trimmomatic 66 v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10 67.
Potential sequencing errors were detected and corrected using Rcorrector v1.0.4 68.
The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v102, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option disabled. Mappings were filtered for uniqueness and properly aligned reads by Samtools v1.12.
Pre-processed data was split into strand-specific subsets using Samtools. PEAKachu v0.2.0 was used over all replicates including both conditions to call cell and strand-specific peaks. When the distance between peaks was within 50 bp, Bedtools v2.30.0 was used to merge the peaks.
Assembly: hg38
Supplementary files format and content: PEAKachu peak files

value: breast

value: epithelial cells

value: wild-type

value: Nutlin-3a 10 uM 24 h


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_H02


title: Gastric tumor premalignant organoids, Trp53-/-;sgPten_rep1


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_D02


title: Gastric premalignant organoids, Trp53-/-;sgPten;sgArid1a_rep2

description:
RNAseq_Premalignant_Organoids_Counts.csv
RNAseq_Premalignant_Organoids_Normalized_data.csv

value: Gastric premalignant organoids


title: zebrafish embryo, 5dpf, wild type, replicate 2

value: embryo


title: zebrafish embryo, 5dpf, sas10 mutant, replicate 3

value: sas10 mutant


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_E02


title: Gastric premalignant organoids, Trp53-/-;sgPten_rep2


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_G02


title: PDAC, Input


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_F02


title: JDM1 NT_5.30.22_D18 [S87]

city: Durham

first: Gregory

middle: A.

last: Taylor

state: NC

address: 182 GRECC VA Med Ctr, 508 Fulton St

department: Department of Medicine, Division of Geriatrics, and Center for theStudy of Aging and Human Development

institute: Duke University Medical Center

data_processing:
Sequenced data was processed using the fastp toolkit to trim low-quality bases and sequencing adapters from the 3’ end of reads, then mapped STAR RNA-seq alignment tool.
Assembly: GRCh38
Supplementary files format and content: counts.csv

source_name: Myobundle

growth_protocol: Primary myoblasts were isolated and washed with phosphate buffered saline (PBS) and antibiotic-antimycotic (ThermoFisher), minced, and then enzymatically digested with pre-warmed 0.05% trypsin for 30 minutes. Muscle tissue was collected by centrifugation and pre-plated at 37C for 2 hours prior to transfer to Matrigel (BD Biosciences) coated flask for attachment. Cells were expanded in human skeletal muscle growth media (hGM) containing low glucose DMEM (1 g/L; LG, Gibco Life Technologies), with 10% fetal bovine serum (Sigma-Aldrich) and supplements from Lonza (epidermal growth factor, gentamicin without insulin, dexamethasone, fetuin). Myogenic cells were cryopreserved in 90% growth media and 10% DMSO at 1-2 million cells per aliquot at passage 4. At time of culture, myoblasts were thawed and plated on Matrigel-coated flasks and grown for up to 1 week in hGM until they reached 80% confluency.

extract_protocol:
RNA extraction from flash frozen myobundles was performed using an RNeasy Mini Kit (Qiagen). Samples were stored at -80C until assayed.
RNA libraries were built using stranded mRNA kit (Roche: 07962207001) and libraries were sequenced as 50 pair-ended base pairs with a NovaSeq 6000 S-Prime

treatment_protocol:
Myobundle fabrication: each myobundle consisted of myoblasts (7.5 x 105 cells) mixed with fibrinogen (10 µL of 20 mg/mL in DMEM), Matrigel (10 µL on ice), thrombin (2 µL of 50 U/mL in 0.1% BSA in PBS), and hGM (5 µL).  This solution polymerized into myobundles within custom-made polydimethylsiloxane (PDMS) molds (cast from Teflon masters and pretreated with pluronic) between beams of a porous nylon (Cerex Advanced Fabrics) frame. Myobundles were cultured in hGM containing 1.5 mg/mL 6-aminocaproic acid (ACA) on a rocker (0.33 Hz) at 37C. The hGM was changed daily for 4 days prior to removing myobundles attached to the frames from the molds and switching to differentiation media (DM), which consisted of LG-DMEM with 1% N2 supplement (Gibco), 0.1% gentamycin (1x), 0.1% amphotericin B (1x), and 2 mg/mL ACA. Myobundles were differentiated on a rocker at 37C with DM exchanged every other day for 7 days.
After differentiation, myobundles were treated with one or a combination of the following reagents added to DM exchanged every other day:  IFN (Sigma-Aldrich, 10 µg/mL in 0.1% BSA in PBS), IFN (PeproTech, 10 µg/mL in 0.1% BSA in PBS), tofacitinib (suspended in H2O), and/or baricitinib (suspended in DMSO 0.01%). To test the effect of IFN I, healthy donor-derived myobundles were treated with IFN or IFN diluted to 0 (control condition), 5, 10, or 20 ng/mL for 7 days then flash frozen in liquid nitrogen on day 18. To test the effect of JAK inhibitors, healthy donor-derived myobundles were treated with IFN 0 (control) or 20 ng/mL for 10 days (day 11 through 21) with concurrent treatment of tofacitinib 1 µM or baricitinib 500 nM on day 15 through 21. Control myobundles were treated with DMSO 0.01% on day 15 through 21. On day 21, these myobundles were flash frozen. Finally, JDM donor-derived myobundles were treated every other day with 0 (control condition) or tofacitinib 1 µM on days 11 through 18 prior to being flash frozen.

value: Myobundle

tag: batch


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep2_B02


title: SH-Sdc1

first: Yun

last: Liu

address: No. 2200, Xietu Road, Xuhui District, Shanghai, China

institute: Shanghai Cancer Institute

description: 10x Genomics

data_processing:
Libraries were sequenced on an Illumina Novaseq 6000 System, using a Novaseq 6000 S2 Reagent Kit (100 cycles; 20012862, Illumina).
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to human reference genome (refdata-cellranger-mm10-3.0.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Assembly: mm10_Ensembl100
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes.

source_name: Tumor

growth_protocol: Wild-type mice were immunized subcutaneously with irradiated B16-GM-CSF cells at the left flank. 12 days later, shsdc1 or shRFP B16 tumor cells were injected into the right flank. 16 days later, tumors in each group were pooled together, and were dissected, mechanically minced and incubated in DMEM mixing with 5% FBS, collagenase Ⅰ (50 μg ml-1, Sigma-Aldrich), collagenase Ⅳ (50 μg ml-1, Sigma-Aldrich), hyaluronidase (25 μg ml-1, Sigma-Aldrich) and DNase Ⅰ (10 μg ml-1, Roche) for 15 min at 37℃.

extract_protocol:
Digested tissues were filtered through 70-μm filters, and red blood cells were lysed with RBC lysis buffer (Biolegend) for 5 min. The cells were stained with a Viability Dye and CD45 antibody. Lived CD45+ population were isolated by Fluorescence-activated cell sorting (FACS) according to expression of CD45 and analyzed using scRNAseq.
RNA libraries were generated by 10x Genomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols.

value: Tumor

value: CD45+ immune cells

value: Sdc1 knock out (KO)


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_D09

value: 2 cell stage embryos

value: Smarca5 +/- (mat KO)


title: JDM1 NT_5.30.22_D18 [S85]


title: JDM1 NT_5.30.22_D18 [S86]


title: PDAC, GSDMC-CTF, ChIP


title: Gastric premalignant organoids, Trp53-/-;sgPten_rep1


title: SH-RFP

description: 10x Genomics

value: wild type (WT)


title: Skin_30mo_4

city: Osaka-shi

first: Masaki

last: Takasugi

address: 1-4-3 Asahimachi, Abeno-ku

institute: Osaka Metropolitan University

description: Skin.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC.
Trimmed sequence reads were mapped to GRCm39 using STAR.
Read count extraction was performed using RSEM.
Count data were normalized using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Skin

extract_protocol:
Mice were euthanized and tissues were collected and immediately frozen pulverized in liquid nitrogen. Pulverized tissues were homogenized in RNAiso Plus (Takara) reagent using pestle and then RNA was isolated following the manufacturer's instructions.
The sequencing libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina) following the manufacturer's instructions.

value: male

tag: strain

value: Skin

value: Wild-type


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_E09


title: PDAC, IgG_2, ChIP

tag: cell line

value: Primary culture


title: JDM1 tofa 1uM_5.30.22_D18 [S83]


title: Skin_30mo_3

description: Skin.txt


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_G09


title: zebrafish embryo, 5dpf, wild type, replicate 1

value: wild type


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_H09


title: Gastric premalignant organoids, Trp53-/-;sgPten;sgArid1a_rep1

tag: cell type


title: JDM1 tofa 1uM_5.30.22_D18 [S82]

tag: treatment


title: Skin_30mo_2

description: Skin.txt


title: JDM1 tofa 1uM_5.30.22_D18 [S81]


title: T119 DMSO 0.01_8.8.22_D21 [S79]

value: control-dmso


title: T119 DMSO 0.01_8.8.22_D21 [S80]


title: Skin_24mo_2

description: Skin.txt


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_B09


title: JDM1 NT_5.30.22_D18 [S84]


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_F09


title: T119 IFNb 20+bari 500 nM_8.8.22_D21 [S78]


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_D08


title: Skin_24mo_3

description: Skin.txt


title: T119 IFNb 20+bari 500 nM_8.8.22_D21 [S77]


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_C08


title: Skin_24mo_1

description: Skin.txt


title: T119 IFNb 20+tofa 1uM_8.8.22_D21 [S75]


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_B08


title: Skin_15mo_4

description: Skin.txt


title: Skin_30mo_1

description: Skin.txt


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_F08


title: T119 IFNb 20+tofa 1uM_8.8.22_D21 [S76]


title: Skin_15mo_3

description: Skin.txt


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_A09


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_A08


title: T119 IFNb 20_8.8.22_D21 [S73]


title: Skin_15mo_2

description: Skin.txt


title: T119 IFNb 20_8.8.22_D21 [S74]


title: T119 NT_8.8.22_D21 [S72]

value: control


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_D07

value: Smarca5 +/+


title: Skin_15mo_1

description: Skin.txt


title: Skin_6mo_4

description: Skin.txt


title: T119 NT_8.8.22_D21 [S71]


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_C07


title: Skin_6mo_3

description: Skin.txt


title: T117 DMSO 0.01_7.26.22_D21 [S70]


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_E07


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_E08


title: Skin_6mo_2

description: Skin.txt


title: T117 DMSO 0.01_7.26.22_D21 [S69]


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_G07


title: Skin_6mo_1

description: Skin.txt


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_H07


title: T117 IFNb 20+Bari 500nM_7.26.22_D21 [S68]


title: T117 IFNb 20+Bari 500nM_7.26.22_D21 [S67]


title: Muscle_30mo_4

description: Muscle.txt

source_name: Muscle

value: Muscle


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_B07


title: Skin_24mo_4

description: Skin.txt


title: Muscle_30mo_3

description: Muscle.txt


title: T117 IFNb 20+Tofa 1uM_7.26.22_D21 [S66]


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_A07


title: T117 IFNb 20_7.26.22_D21 [S64]


title: Muscle_30mo_2

description: Muscle.txt


title: Trim-Away 2 cell stage _rep3 no injection ctrl_H04

data_processing:
Data was aligned to GRCm38 and processed using Bismark (version v0.23.1) in single-end mode.
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.

extract_protocol:
DNA extracted and processed as described in the scNMT-sq protocol
bisulphite libraries were generated as described in scNMT-seq protocol; At the sample collection stage,  the individual embryos were incubated with GpC methyltransferase

value: No injection ctrl


title: RNA-seq_SMARCA5 +/+ 2 cell stage embryos (matKO females)_rep1_F07

data_processing:
Raw FastQ files were trimmed using Trim Galore (v0.6.5, Cutadapt v2.3) and mapped to the mouse GRCm38 genome assembly using HISAT2 (v2.1.0) (D. Kim et al., 2015), with the options –dta –no-softclip –no-mixed –no-discordant.
Assembly: GRCm38_v95
Supplementary files format and content: Tab delimited text file of read counts over genes


title: Muscle_24mo_4

description: Muscle.txt


title: T117 IFNb 20_7.26.22_D21 [S63]

value: Myobundle


title: Muscle_30mo_1

description: Muscle.txt


title: Trim-Away 2 cell stage _rep3 no injection ctrl_F04


title: Muscle_24mo_3

description: Muscle.txt


title: Muscle_24mo_2

description: Muscle.txt


title: T117 NT_7.26.22_D21 [S62]


title: T116 DMSO 0.01_5.30.22_D21 [S60]


title: T117 NT_7.26.22_D21 [S61]


title: Muscle_24mo_1

description: Muscle.txt


title: Trim-Away 2 cell stage _rep3 no injection ctrl_D04


title: Trim-Away 2 cell stage _rep3 no injection ctrl_G04


title: T116 IFNb 20+Bari 500nm_5.30.22_D21 [S58]


title: Trim-Away 2 cell stage _rep3 IgG_D03

value: IgG


title: Trim-Away 2 cell stage _rep3 IgG_B03


title: T116 DMSO 0.01_5.30.22_D21 [S59]


title: Muscle_15mo_3

description: Muscle.txt


title: T117 IFNb 20+Tofa 1uM_7.26.22_D21 [S65]


title: Muscle_15mo_2

description: Muscle.txt


title: T116 IFNb 20+Bari 500nm_5.30.22_D21 [S57]


title: Trim-Away 2 cell stage _rep3 no injection ctrl_E04


title: T116 IFNb 20+Tofa 1um_5.30.22_D21 [S56]


title: Trim-Away 2 cell stage _rep3 IgG_B04


title: Trim-Away 2 cell stage _rep3 IgG_A03


title: Muscle_6mo_4

description: Muscle.txt


title: Muscle_15mo_1

description: Muscle.txt


title: T116 IFNb 20+Tofa 1um_5.30.22_D21 [S55]


title: Muscle_6mo_3

description: Muscle.txt


title: T116 IFNb 20_5.30.22_D21 [S54]


title: Trim-Away 2 cell stage _rep3 IgG_F03


title: Muscle_15mo_4

description: Muscle.txt


title: T116 IFNb 20_5.30.22_D21 [S53]


title: Muscle_6mo_2

description: Muscle.txt


title: Trim-Away 2 cell stage _rep3 IgG_G03


title: Muscle_6mo_1

description: Muscle.txt


title: T116 NT_5.30.22_D21 [S52]


title: Lung_30mo_4

description: Lung.txt

value: Lung


title: Lung_30mo_3

description: Lung.txt


title: Lung_30mo_2

description: Lung.txt


title: T119 IFNb 20_1.21.22_D18 [S50]


title: Trim-Away 2 cell stage _rep3 a-Smarca5_D05


title: T119 IFNb 20_1.21.22_D18 [S49]


title: Trim-Away 2 cell stage _rep3 IgG_E03


title: Lung_30mo_1

description: Lung.txt


title: T119 IFNb 10_1.21.22_D18 [S48]


title: Lung_24mo_4

description: Lung.txt


title: T119 IFNb 10_1.21.22_D18 [S47]


title: Trim-Away 2 cell stage _rep3 IgG_A04


title: Trim-Away 2 cell stage _rep3 a-Smarca5_A05


title: T24B8-5p_PA14_3

value: Whole animal


title: Trim-Away 2 cell stage _rep3 a-Smarca5_F05

value: 2 cell stage embryos


title: Lung_24mo_3

description: Lung.txt


title: Trim-Away 2 cell stage _rep3 IgG_C03


title: T119 NT_1.21.22_D18 [S44]


title: Trim-Away 2 cell stage _rep3 a-Smarca5_G05


title: Lung_24mo_2

description: Lung.txt


title: Trim-Away 2 cell stage _rep3 a-Smarca5_E05


title: T116 NT_5.30.22_D21 [S51]


title: Trim-Away 2 cell stage _rep3 a-Smarca5_H05


title: T119 IFNb 5_1.21.22_D18 [S46]


title: T119 IFNb 5_1.21.22_D18 [S45]


title: Trim-Away 2 cell stage _rep3 a-Smarca5_C05


title: Lung_24mo_1

description: Lung.txt


title: Trim-Away 2 cell stage _rep3 a-Smarca5_B05


title: T119 IFNa 20_3.4.22_D18 [S41]


title: T119 IFNa 20_3.4.22_D18 [S42]


title: Trim-Away 2 cell stage _rep2 no embryo_G01

value: no embryo


title: Lung_15mo_4

description: Lung.txt


title: T119 IFNa 10_3.4.22_D18 [S40]


title: Lung_6mo_4

description: Lung.txt


title: Lung_15mo_3

description: Lung.txt


title: Lung_15mo_2

description: Lung.txt


title: T119 IFNa 10_3.4.22_D18 [S39]


title: Lung_15mo_1

description: Lung.txt


title: SNCA Tri organoid 11

city: Jacksonville

first: Yunjung

last: Jin

email: Jin.Yunjung@mayo.edu, tcikezu@gmail.com

address: 4500 San Pablo Rd

institute: Mayo Clinic

description: 10x Genomics v3

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using cellranger v6.1.1
Assembly: GRCh38-2020-A
Supplementary files format and content: compressed tab-separated and matrix values

source_name: Human induced pluripotent stem cells (hIPSCs)

extract_protocol:
Protocol of Neural Tissue Dissociation Kits (Miltenyi Biotec) according to manufacturer’s instructions
Chromium platform (10x Genomics)

tag: subclone id

value: SNCA trip

value: Male

tag: flow cell

value: C

tag: lane

tag: collection date


title: Trim-Away 2 cell stage _rep2 no embryo_F01


title: Trim-Away 2 cell stage _rep2 IgG_C01


title: Trim-Away 2 cell stage _rep2 IgG_D01


title: PDAC, IgG_1, ChIP


title: RNA-seq_SMARCA5 +/- 2 cell stage embryos (matKO females)_rep1_C09

value: Smarca5 +/- (mat KO)


title: T119 NT_3.4.22_D18 [S37]


title: Lung_6mo_2

description: Lung.txt

source_name: Lung

tag: Sex

value: male

tag: age

value: Wild-type


title: Lung_6mo_3

description: Lung.txt


title: SNCA Tri organoid 10

description: 10x Genomics v3

value: Human induced pluripotent stem cells (hIPSCs)


title: T119 IFNa 5_3.4.22_D18 [S38]


title: Trim-Away 2 cell stage _rep2 a-Smarca5_E02


title: T119 NT_1.21.22_D18 [S43]

value: control


title: T117 IFNa 20_9.3.21_D18 [S36]


title: Lung_6mo_1

description: Lung.txt


title: Liver_30mo_4

description: Liver.txt

source_name: Liver

value: Liver


title: SNCA Tri organoid 8

description: 10x Genomics v3


title: Trim-Away 2 cell stage _rep2 IgG_A01


title: SNCA Tri organoid 12

description: 10x Genomics v3


title: SNCA Tri organoid 7

description: 10x Genomics v3


title: Liver_30mo_3

description: Liver.txt


title: T117 IFNa 10_9.3.21_D18 [S34]


title: Trim-Away 2 cell stage _rep2 IgG_B01


title: Liver_30mo_1

description: Liver.txt


title: Trim-Away 2 cell stage _rep2 a-Smarca5_G02


title: T117 IFNa 10_9.3.21_D18 [S33]


title: Trim-Away 2 cell stage _rep2 a-Smarca5_B02


title: Ctrl organoids 12

description: 10x Genomics v3

value: Ctrl


title: Liver_30mo_2

description: Liver.txt


title: T117 IFNa 5_9.3.21_D18 [S32]


title: T117 IFNa 5_9.3.21_D18 [S31]


title: Trim-Away 2 cell stage _rep2 a-Smarca5_C02


title: Trim-Away 2 cell stage _rep2 a-Smarca5_A02


title: Liver_24mo_4

description: Liver.txt


title: Ctrl organoids 10

description: 10x Genomics v3

value: B


title: SNCA Tri organoid 6

description: 10x Genomics v3


title: T117 IFNa 20_9.3.21_D18 [S35]

value: Myobundle


title: SNCA Tri organoid 9

description: 10x Genomics v3


title: SNCA Tri organoid 5

description: 10x Genomics v3


title: Liver_24mo_3

description: Liver.txt


title: Trim-Away 2 cell stage _rep2 a-Smarca5_F02


title: Liver_24mo_2

description: Liver.txt


title: T117 NT_9.3.21_D18 [S30]


title: Liver_24mo_1

description: Liver.txt


title: SNCA Tri organoid 4

description: 10x Genomics v3


title: Trim-Away 2 cell stage _rep2 a-Smarca5_D02


title: T117 IFNb 20_5.22.21_D18 [S28]


title: T117 IFNb 20_5.22.21_D18 [S27]


title: Ctrl organoids 11

description: 10x Genomics v3


title: Trim-Away 2 cell stage _rep1 no injection ctrl_H03

value: No injection ctrl


title: Ctrl organoids 8

description: 10x Genomics v3

value: Female


title: T117 NT_9.3.21_D18 [S29]


title: Liver_15mo_3

description: Liver.txt


title: Trim-Away 2 cell stage _rep1 no injection ctrl_B04


title: Liver_15mo_4

description: Liver.txt


title: Trim-Away 2 cell stage _rep1 no injection ctrl_D03


title: Ctrl organoids 7

description: 10x Genomics v3


title: Trim-Away 2 cell stage _rep1 no injection ctrl_F04


title: Liver_15mo_1

description: Liver.txt


title: Trim-Away 2 cell stage _rep1 no injection ctrl_A04


title: SNCA Tri organoid 3

description: 10x Genomics v3


title: T117 IFNb 10_5.22.21_D18 [S25]


title: Liver_6mo_4

description: Liver.txt


title: T117 IFNb 5_5.22.21_D18 [S23]


title: T117 IFNb 5_5.22.21_D18 [S24]


title: Ctrl organoids 9

description: 10x Genomics v3


title: Liver_6mo_3

description: Liver.txt


title: SNCA Tri organoid 1

description: 10x Genomics v3

value: A


title: Trim-Away 2 cell stage _rep1 no injection ctrl_F03

value: 2 cell stage embryos


title: Liver_15mo_2

description: Liver.txt


title: Liver_6mo_2

description: Liver.txt


title: Trim-Away 2 cell stage _rep1 no injection ctrl_G03


title: Ctrl organoids 6

description: 10x Genomics v3


title: Liver_6mo_1

description: Liver.txt


title: T116 IFNb 20_8.6.21_D18 [S20]


title: Ctrl organoids 5

description: 10x Genomics v3


title: Trim-Away 2 cell stage _rep1 no injection ctrl_E04


title: Ctrl organoids 4

description: 10x Genomics v3


title: Ctrl organoids 3

description: 10x Genomics v3


title: Kidney_30mo_4

description: Kidney.txt

source_name: Kidney

value: Kidney


title: Trim-Away 2 cell stage _rep1 no injection ctrl_C04


title: T117 NT_5.22.21_D18 [S21]


title: Trim-Away 2 cell stage _rep1 no injection ctrl_D04


title: Kidney_30mo_3

description: Kidney.txt


title: T116 IFNb 10_8.6.21_D18 [S18]


title: Kidney_30mo_2

description: Kidney.txt


title: Ctrl organoids 1

description: 10x Genomics v3


title: Trim-Away 2 cell stage _rep1 no injection ctrl_E03


title: Kidney_30mo_1

description: Kidney.txt


title: Trim-Away 2 cell stage _rep1 IgG_C05

value: IgG


title: T116 IFNb 5_8.6.21_D18 [S16]


title: Trim-Away 2 cell stage _rep1 no embryo

value: no embryo


title: SNCA Tri organoid 2

description: 10x Genomics v3

value: SNCA trip

value: Male


title: Ctrl organoids 2

description: 10x Genomics v3


title: LBD brain (SNCA Tri)

description: 10x Genomics v3

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using cellranger v7.0.1
Assembly: GRCh38-2020-A
Supplementary files format and content: compressed tab-separated and matrix values

source_name: Postmortem brain

extract_protocol:
Nuclei were isolated from the frozen superior temporal cortices as described previously with some modifications (Jakel, S. et al., Nature, 2019). Briefly, the frozen tissue samples were briefly exposed to 2 mL of Nuclei EZ Lysis Buffer (Sigma), supplemented with EDTA-free protease inhibitors (Sigma) and recombinant RNase inhibitors (Takara Bio USA) at 4°C. The tissue was then homogenized using a glass Dounce tissue grinder through 10-15 strokes with pestle A, followed by 10 strokes with pestle B. Then, an additional 2 mL of lysis buffer containing protease and RNase inhibitors was added to the homogenized tissue, followed by 5-minute incubation. Subsequently, the nuclei suspension was filtered using a 40-μm cell strainer and pelleted by centrifugation at 300 x g for 5 minutes. The nuclei pellets were resuspended in 900 μL of debris removal solution (Miltenyi Biotech) containing 0.4 U μL−1 RNase inhibitors and 3.1 mL of calcium and magnesium-free Dulbecco's phosphate-buffered saline (DPBS). Next, 4 mL of DPBS was carefully overlayed onto the nuclei resuspension was performed, followed by another centrifugation at 3,000 x g for 5 minutes. Post-centrifugation, the supernatant was discarded, and the nuclei were resuspended in the solution consisting of 1% BSA in DPBS, supplemented with 0.4 U μL−1 RNase inhibitors. Throughout the process, the nuclei were kept on ice or at 4°C. Lastly, the density of the nuclei suspension was calculated using a C-chip-disposable hemocytometer (INCYTO) with trypan blue staining (Bio-Rad).
Chromium platform (10x Genomics)

value: Postmortem brain

tag: npid

tag: type

value: LBD

tag: pathdx

value: M

tag: apoe

tag: rin

tag: seqsat


title: LBD brain 3

description: 10x Genomics v3

tag: tissue

tag: batch


title: T116 IFNb 20_8.6.21_D18 [S19]

tag: genotype


title: T116 IFNb 10_8.6.21_D18 [S17]


title: T116 IFNb 5_8.6.21_D18 [S15]


title: Kidney_24mo_4

description: Kidney.txt

value: male

tag: strain

value: Wild-type


title: Trim-Away 2 cell stage _rep1 IgG_H06


title: Trim-Away 2 cell stage _rep1 IgG_H04


title: T116 NT_8.6.21_D18 [S14]

tag: treatment

value: control


title: Trim-Away 2 cell stage _rep1 IgG_D05


title: T116 NT_8.6.21_D18 [S13]


title: Kidney_24mo_3

description: Kidney.txt


title: Trim-Away 2 cell stage _rep1 IgG_F05


title: Kidney_24mo_2

description: Kidney.txt


title: Ctrl brain 3

description: 10x Genomics v3

value: DLBD


title: Kidney_24mo_1

description: Kidney.txt


title: LBD brain (SNCA Dup)

description: 10x Genomics v3

value: TLBD


title: T117 IFNb 10_5.22.21_D18 [S26]

value: Myobundle


title: Trim-Away 2 cell stage _rep1 IgG_A05


title: Kidney_15mo_4

description: Kidney.txt


title: T116 IFNa 20_6.25.21_D18 [S11]


title: Trim-Away 2 cell stage _rep1 IgG_G05


title: Kidney_15mo_3

description: Kidney.txt


title: T116 IFNa 10_6.25.21_D18 [S10]


title: Trim-Away 2 cell stage _rep1 IgG_G04


title: LBD brain 1

description: 10x Genomics v3

value: Ctrl

value: Normal


title: Ctrl brain 2

description: 10x Genomics v3


title: LBD brain 2

description: 10x Genomics v3


title: Ctrl brain 1

description: 10x Genomics v3


title: T116 IFNa 5_6.25.21_D18 [S8]


title: T116 IFNa 10_6.25.21_D18 [S9]


title: Trim-Away 2 cell stage _rep1 IgG_H05

value: 2 cell stage embryos


title: Kidney_6mo_4

description: Kidney.txt

value: Kidney


title: Trim-Away 2 cell stage _rep1 IgG_E05

value: IgG


title: ΔLmna_2

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Pre-processed ATAC-Seq reads were mapped against reference genome (mm10) with a pipeline that used bowtie as aligner, Piccard to mark duplicate alignments, and samtools to eliminate duplicates.
Bigwig files for visualizing were created with Deeptools and Wiggletools. Tracks were represented in IGV browser.
Assembly: Mouse sequenced genome mm10 (GRCm38)
Supplementary files format and content: BW files of mapped fragments
Supplementary files format and content: Detected peak file in txt tab-delimited file

source_name: BMDC

extract_protocol:
50,000 BMDCs (WT or KO) were isolated and cryopreserved in 10% DMSO + 90% SF (n = 3 for each condition). After rapidly unfrozen, cells were counted, lysed (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% TritonX-100 for 5 min at 4ºC and centrifuged at 800 x g.
Supernatant was discarded and nuclei were resuspended in transposase reaction buffer with transposase5 (1 µl Tn5 / 10.000 cells) and incubated for 30 min at 37 ºC. Later, SDS at a final concentration of 0.1% was added to stop the reaction (30 min, 40°C) and DNA was isolated with KAPA Pure beads (SPRI beads). Briefly, lysates were incubated with SPRI beads (2x), placed on the magnet, washed twice with 70% ethanol, and air-dried. DNA was eluted with elution buffer (EB) and its concentration measured with Qubit kit (Invitrogen). For DNA library generation, qPCR with i5 and i7 primers (NEXTERA barcoding) was performed (98ºC 2´, 98ºC 20¨, 63ºC 30¨, 72 ºC 1´, 4ºC ∞; 14 cycles). Then, a size cut off was conducted. First, amplified DNA was incubated with 0.5x concentration of SPRI beads. Then, beads were discarded and supernatant was incubated with 1.8x concentration of SPRI beads. Beads were washed twice with 70% ethanol, eluted with EB, and measured with Qubit. Finally, Agilent HS Bionalyzer was performed to assess peak sizes and percentages.

treatment_protocol: Treated with LPS for 24h

tag: cell type

value: BMDC

value: Lmna-/-

value: LPS


title: ΔLmna_1


title: Kidney_15mo_1

description: Kidney.txt


title: T116 IFNa 5_6.25.21_D18 [S7]


title: Kidney_6mo_3

description: Kidney.txt


title: WT_2

value: WT


title: T116 IFNa 20_6.25.21_D18 [S12]


title: Trim-Away 2 cell stage _rep1 a-Smarca5_B03


title: T116 NT 6.25.21_D18 [S5]


title: T117 NT_5.22.21_D18 [S22]


title: WT_1


title: T116 NT 6.25.21_D18 [S6]


title: Kidney_15mo_2

description: Kidney.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_C01


title: Kidney_6mo_1

description: Kidney.txt


title: Sen-IR Tg treat, ATF4-Δ transfected, rep 3, expt 2

city: Baltimore

first: Emmanouil

last: Maragkakis

state: MD

address: 251 Bayview Blvd, 10B133 Baltimore

department: Laboratory of Genetics and Genomics (LGG)

institute: National Institute on aging

description:
ITg_d_3
20240718_all_genome_counts.txt

data_processing:
FAST5 files were basecalled into FASTQ files and demulitplexxed (pcb111-24) using Guppy and then aligned to the human transcriptome using minimap.
Assembly: hg38
Supplementary files format and content: processed data exists as a merged table of read counts for each gene where the columns are samples and the rows are genes. Counts are obtained as a sum of all transcriptomic counts for a particular gene.

growth_protocol: Cells were grown in 10% FBS DMEM high glucose media supplemented with non-essential amino acids

extract_protocol:
RNA was extracted from cells using Trizol and then subjected to  DNase treatment.
RNA was used in the Nanopore PCR-cDNA library kit (PCB
Long-read sequencing

treatment_protocol: Cells were treated with acute proteotoxic stress (thapsigargin, tg) and then allowed to recover after its removal. Senescence was explored using etoposide induction (Etop) or ionizing radiaiton induction (IR) and compared to healthy cycling cells (Cyc). The effects of stress were examined 24h post-stress unless otherwise indicated. The stress-induced changes in senescent cells were also rescued through addition of in vitro transcribed ATF4 lacking regulatory uORFS (ATF4-Δ)  transfected post-stress during the recovery period.

tag: cell line

value: fibroblast


title: Sen-IR Tg treat, ATF4-Δ transfected, rep 2, expt 2

description:
ITg_d_2
20240718_all_genome_counts.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_A03


title: OLFM4-MV, rep3

first: Fuping

last: Wen

address: Yanchang Middle Road

institute: Shanghai Tenth People's Hospital

data_processing:
After quantified, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
Supplementary files format and content: tab-delimited text files include TPM values for each sample

growth_protocol: HGC-27 cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using Trizol following the standard protocol
Libraries were prepared according to Illumina's instructions

treatment_protocol: Cultured cells were treated with control MV or OLFM4 over expression MV for 24h

value: Gastric cancer cells

value: Wild type


title: Heart_30mo_4

description: Heart.txt

source_name: Heart

value: male

value: Heart

value: Wild-type


title: Trim-Away 2 cell stage _rep1 a-Smarca5_E02


title: OLFM4-MV, rep1


title: OLFM4-MV, rep2


title: Trim-Away 2 cell stage _rep1 IgG_B05


title: Heart_30mo_3

description: Heart.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_D01


title: Heart_30mo_2

description: Heart.txt


title: Sen-IR Tg treat, ATF4-Δ transfected, rep 1, expt 2

description:
ITg_d_1
20240718_all_genome_counts.txt