title: WT, risdiplam, 1 day post risdiplam, rep3

description:
WTR3
RISH3.markdup.bam
WT_Adult_risdiplam.txt


title: H1836, ASCL1, ChIP, rep2

status: Public on Apr 13 2025

type: SRA

city: NEW YORK

first: Kenta

last: Kawasaki

state: NEW YORK

address: 417 East 68th Street

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Raw sequencing reads were trimmed with Trim Galore (v0.4.4). Reads were aligned to human assembly hg38 using bowtie2 v2.3.4 with the default settings
Enriched binding regions were called against the input using MACS2 with p value less than 0.001. The bigwig format for each sample was created using the BEDTools suite (https://bedtools.readthedocs.io) with the normalization factor 10 million
Assembly: Human GRCh38
Supplementary files format and content: bigwiz file is uploaded as processed data
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: H1836 was cultured with DMEM/F12 HITES media, SHP-77 with RPMI+10% fetal bovine serum (FBS).

extract_protocol:
ChIP-seq on cell lines (H1836, SHP-77)  were performed using 1x107 cells. Samples were crosslinked at room temperature for 10 min by swirling with 1% formaldehyde (Sigma Aldrich) followed by addition of 125 mM glycine to quench the reaction. After washing the cells with PBS, cells were resuspended with ChIP lysis buffer supplemented with protease inhibitors (Roche cOmplete mini EDTA-free protease inhibitor tablets, Cat #: 11836170001) and phosphatase inhibitors (Thermo Scientific, Halt Phosphatase Inhibitor Cocktail, Cat #: 78427, 1:1000). Cell lysates in 1 mL ChIP lysis buffer were sonicated to shear chromatin to 200-500 bp. Supernatants were incubated with the antibodies (IgG: Cell Signaling Technology, Cat #: 2729S and ASCL1: Cell Signaling Technology, Cat #: 43666S) at 4ºC overnight on a rotator. Dynabeads™ Protein G were blocked with 2.5 mg/mL UltraPure™ BSA (Thermo Scientific, Cat #: AM2616) at 4ºC overnight. The beads were washed three times with ChIP buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100) and incubated with the chromatin-antibody samples. These samples were washed with high salt ChIP buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% of Triton X-100, 0.1% of SDS) followed by washings with Tris-EDTA (TE) buffer. Chromatin complexes were eluted in TE with 1% ultrapure SDS (ThermoFisher Scientific) at 65ºC for 15 min, and reverse-crosslinked with RNAse A (ThermoFisher Scientific, Cat #: EN0531), followed by incubation with Proteinase K solution (ThermoFisher Scientific, Cat #: EO0491). DNA was purified using QIAquick PCR Purification Kit (Qiagen).
Sequencing libraries were sent to the MSK Integrated Genomics Operation core facility for sequencing on a NovaSeq 6000.

tag: tissue

tag: cell line

value: Small cell lung cancer

tag: chip antibody


title: H1836, ASCL1, ChIP, rep1


title: SNU-BXDM-2

city: Fuzhou

first: xiuli

last: Zhang

address: No. 1 Qiuyang Road, Minhou Street, Fuzhou City, Fujian Province

country: China

institute: Fujian University of Chinese Medicine

description:
Library name: Sample 17
SNU cells treated with 1 mg/mL of BXD

library_source: transcriptomic

data_processing:
Utilize the bcl2fastq software to perform Base Calling on the original image files from Illumina high-throughput sequencing and convert them into original sequencing reads.
Use the FastQC software to analyze the base quality from 5' to 3' of the sequencing reads and assess the content of A, T, C, and G bases in the sequencing data, evaluating the base type ratio at each position from an overall level.
Utilize the fastp software to filter the raw data, removing reads that do not meet the analysis criteria, in order to obtain clean reads that can be used for subsequent alignment, statistics, and further analysis.
After quality control of the raw sequencing data, clean data is obtained. The clean data is then assessed to review the effectiveness of the quality control, and ultimately, the clean data is used for analysis.
Read count extraction and normalization were performed using RseQC software
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: SNU-1 cells

extract_protocol:
RNA was harvested using TRIzol® Reagent (invitrogen.). 1 µgof total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nebnext ultra-RNA library preparation kit following manufacturer's protocols.

value: SNU-1 cells

value: human gastric adenocarcinoma cell line

tag: cell type

value: epithelial cells

tag: genotype

value: SNU-BXDM

tag: treatment

value: BXD ( 1 mg/mL)


title: AAV-injection, risdiplam,11 days post risdiplam,  rep1

city: Beijing

first: Zhan

last: Chen

address: 38 Xueyuan Rd, Haidian District, Beijing, China

institute: Peking University Health Science Center

description:
OFFR1
H16Aligned.sortedByCoord.out.bam
OFF_counts_CLEAN.txt

data_processing:
FastQC (v0.11.9)
trim_galore (v0.6.7)
STAR (v2.7.9a)
featureCounts (v2.0.1)
Assembly: mm10; hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

organism: Mus musculus

source_name: heart apex

extract_protocol:
Total RNA was purified using TransZol Up Plus RNA Kit (ER501-01-V2, TransGene) with genome DNA removed.
Libraries were constructed by the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (12301, Yeasen).

value: heart apex

value: 10 mg/kg risdiplam

tag: time

value: P20, 11 days post risdiplam


title: SNU-BXDM-1

description:
Library name: Sample 16
SNU cells treated with 1 mg/mL of BXD


title: AAV-injection, risdiplam,11 days post risdiplam,  rep2

description:
OFFR2
H17Aligned.sortedByCoord.out.bam
OFF_counts_CLEAN.txt


title: WT, risdiplam, 1 day post risdiplam, rep2

description:
WTR2
RISH2.markdup.bam
WT_Adult_risdiplam.txt

value: 8 weeks, 1 day post risdiplam


title: SNU-BXDL-3

description:
Library name: Sample 15
SNU cells treated with 0.5 mg/mL of BXD

value: SNU-BXDL

value: BXD ( 0.5 mg/mL)


title: FOXA2-PDXLx1231, ATAC,rep2

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and running version 1.15 of cutadapt and version 0.11.5 of FastQC. Version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) was employed to align reads to mouse assembly mm10 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 (https://github.com/taoliu/MACS) with a p-value setting of 0.001, filtered for blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz), and a peak atlas was created using +/- 250 bp around peak summits. The BEDTools suite (http://bedtools.readthedocs.io) was used to create normalized bigwig files. Version 1.6.1 of featureCounts (http://subread.sourceforge.net) was used to build a raw counts matrix and DESeq2 was employed to calculate differential enrichment for all pairwise contrasts.
Peak-gene associations were created by assigning all intragenic peaks to that gene, while intergenic peaks were assigned using linear genomic distance to transcription start sites (TSS). Pathway enrichment was calculated by assigning each gene a unique score based on the associated peak with the greatest magnitude change and running GSEA in pre-ranked mode. Motif signatures were obtained using Homer v4.5 (http://homer.ucsd.edu) on differentially enriched peak regions.
Assembly: Human GRCh38
Supplementary files format and content: bigwiz file is uploaded as processed data
Supplementary files format and content: bigWig

source_name: PDX

extract_protocol:
For ATAC-seq, 50,000 PDX derived cells per condition and patient derived FFPE samples (2x10um slides) were analyzed by the MSK Epigenetics Research Innovation Lab by ATAC-seq as previously described using the Tagment DNA TDE1 Enzyme (Illumina, Cat #:20034198) following the manufacturer’s instructions. Briefly, upon isolation, nuclei were centrifuged for 10min at 800g at 4°C, followed by the addition of 50 μL transposition reaction mix (25 μL TD buffer, 2.5 μL Tn5 transposase and 22.5 μL ddH2O) using Tagment DNA TDE1 enzyme. Samples were then incubated at 37°C for 35min. DNA was isolated using a ZYMO Kit (D4014).
ATAC-seq libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB, Cat #:M0541) using a uniquely barcoded primer per sample, and a universal primer.

value: PDX


title: SNU-BXDM-3

description:
Library name: Sample 18
SNU cells treated with 1 mg/mL of BXD


title: WT, risdiplam, 1 day post risdiplam, rep1

description:
WTR1
RISH1.markdup.bam
WT_Adult_risdiplam.txt


title: SNU-BXDL-2

description:
Library name: Sample 14
SNU cells treated with 0.5 mg/mL of BXD


title: AAV-injection, solvent, 11 days post solvent, rep3

description:
OFFS3
H15Aligned.sortedByCoord.out.bam
OFF_counts_CLEAN.txt

value: solvent

value: P10, 11 days post solvent


title: AAV-injection, solvent, 11 days post solvent, rep2

description:
OFFS2
H14Aligned.sortedByCoord.out.bam
OFF_counts_CLEAN.txt


title: FOXA2-PDXLx1231, ATAC,rep1


title: FOXA2+PDXLx891, ATAC,rep2


title: C3

city: Hangzhou

first: Wumin

last: Yu

address: 548 Binwen Road, Binjiang District, Hangzhou City, Zhejiang Province

department: School of basic medicine

institute: Zhejiang Chinese Medicine University

data_processing:
The Fastp software (https://github.com/OpenGene/fastp) was utilized to eliminate reads containing adapter contamination, low-quality bases, and undetermined bases using default parameters.  Subsequently, the sequence quality was confirmed using Fastp.  The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.  Following this, all transcriptomes from the samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).  Once the final transcriptome was generated, StringTie was employed to estimate the expression levels of all transcripts.  Expression levels for mRNAs were determined using StringTie by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length (kB)]).  Differentially expressed mRNAs were identified based on fold changes > 1 or < 0.5, and parametric F-test comparing nested linear models (P value < 0.05) was conducted using the R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mm10
Supplementary files format and content: Presented in tabular form, the content mainly describes their differential genes

source_name: Hippocampal

growth_protocol: HT22 cells were cultured in DMEM complete medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.  HT22 cells were cultured at 37°C in a constant temperature incubator with a 5% CO2 atmosphere.

extract_protocol:
The RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).  Subsequently, the RNA integrity was evaluated with the Bioanalyzer 2100 (Agilent, CA, USA).  Poly (A) RNA was isolated using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) and then fragmented into smaller pieces using the Magnesium RNA Fragmentation Module (NEB, cat. e6150, USA).  The cleaved RNA fragments were reverse-transcribed to generate cDNA utilizing SuperScript™ II Reverse Transcriptase (Invitrogen, cat.  1896649, USA), followed by the synthesis of U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat. m0209, USA), RNase H (NEB, cat. m0297, USA), and dUTP Solution (Thermo Fisher, cat. R0133, USA).  An A-base was added to the blunt ends of each strand to facilitate ligation to the indexed adapters.  Each adapter possessed a T-base overhang for adapter ligation to the A-tailed fragmented DNA.  Single- or dual-index adapters were ligated to the fragments, and size selection was carried out using AMPureXP beads.  Following treatment with the heat-labile UDG enzyme (NEB, cat. m0280, USA) of the U-labeled second-stranded DNAs, the ligated products were amplified via PCR.  The average insert size for the final cDNA library was 300±50 bp.  Finally, 2×150bp paired-end sequencing (PE150) was performed on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China)
RNA lilbraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit

treatment_protocol: The cells were exposed to IL-17

value: Hippocampal

value: HT22 cells

value: WT

value: No special treatment


title: C2


title: SNU-BXDL-1

description:
Library name: Sample 13
SNU cells treated with 0.5 mg/mL of BXD

value: SNU-1 cells

value: human gastric adenocarcinoma cell line


title: AAV-injection, solvent, 11 days post solvent, rep1

description:
OFFS1
H13Aligned.sortedByCoord.out.bam
OFF_counts_CLEAN.txt


title: SLE-1 w and w/o IL-4_4 hrs [BCR]

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell ranger(v3.1.0) count pipeline was used to analyze sequencing data with feature barcode reference
The hash coding for the data is as follows: hash1 (control), hash2 (IL4), hash3 (IL4_IL2), hash4 (IL4_IL2_antiFNAR), and hash5 (IL4_IL2_IFN).
Cell ranger(v3.1.0) vdj pipeline was used to analyze V(D)J seq data
Seurat (v.4.1.3), implemented using the R package was applied to exclude low-quality cells, identify clusters and differently expression genes.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files contain feature counts for each sample.
Supplementary files format and content: The annotation file for each sample, "filtered_contig_annotations.csv," is an output from the Cell Ranger VDJ pipeline.
Supplementary files format and content: cell ranger feature reference file: IL4tr_human_feature_ref.csv

source_name: peripheral blood mononuclear cells

extract_protocol:
Single cells were captured into Gel Bead-in-EMulsions using a 10x chromium controller.
Single-cell 5’ biased transcriptome libraries were prepared using a 5’ Library & Gel Bead Kit (PN-1000014) according to the 10x Genomics manual
Single-cell mRNA was reverse transcribed into cDNA, which was then captured by a gel bead carrying barcoding DNA oligos that include a cell barcode and unique molecular identifier (UMI) attached to the VDJ region of the cDNA. The cDNA was subsequently amplified, fragmented, and constructed into a 5’ biased library for RNA sequencing.

treatment_protocol: B cells were stimulated in RPMI with 10% FBS supplemented with or without 20 ng/ml IL-4 for 1 h. Cells were then stimulated with 2 μg/ml CL264, a TLR7 ligand, 2 μg/ml goat F(ab′)2 anti-human Ig, 20 ng/ml IL-21, 20 ng/ml IFNɣ, and 20 ng/ml BAFF.  Cells were harvested at 4 and 18 hrs, followed by hash-tag antibody labeling and scRNA-seq analysis.

value: peripheral blood mononuclear cells

value: B cells

value: mixed samples(control,IL4tr,IL4_IL2tr,IL4_IL2_antiFNAR, and IL4_IL2_IFN)


title: FOXA2+PDXLx891, ATAC,rep1

value: Small cell lung cancer


title: AAV-injection, risdiplam, 30 day post risdiplam, rep1

data_processing:
FastQC (v0.11.9)
trim_galore (v0.6.7)
STAR (v2.7.9a)
featureCounts (v2.0.1)
Assembly: mm10; hg38

value: heart apex

value: 10 mg/kg risdiplam

value: P40, 30 day post risdiplam


title: C1


title: SNU-BXD0-2

description:
Library name: Sample 11
SNU cells treated with ddH2O

value: epithelial cells


title: AAV-injection, risdiplam,1 day post risdiplam,  rep3

description:
ONR3
H18Aligned.sortedByCoord.out.bam
ON_counts_CLEAN.txt

value: P10, 1 day post risdiplam


title: M3

value: exposed to IL-17


title: AAV-injection, risdiplam,1 day post risdiplam,  rep2

description:
ONR2
H17Aligned.sortedByCoord.out.bam
ON_counts_CLEAN.txt


title: FOXA2+PDXLx328, ATAC,rep1

value: PDX


title: M2

value: Hippocampal


title: AAV-injection, risdiplam,1 day post risdiplam,  rep1

description:
ONR1
H9Aligned.sortedByCoord.out.bam
ON_counts_CLEAN.txt


title: M1

value: HT22 cells


title: SNU-BXD0-1

description:
Library name: Sample 10
SNU cells treated with ddH2O


title: AGS-BXDM-2

description:
Library name: Sample 8
AGS cells treated with 1 mg/mL of BXD

source_name: AGS cells

value: AGS cells

value: AGS-BXDM

value: BXD ( 1 mg/mL)


title: AAV-injection, solvent, 1 day post solvent, rep2

description:
ONS2
H5Aligned.sortedByCoord.out.bam
ON_counts_CLEAN.txt

value: solvent

value: P10, 1 day post solvent


title: AGS-BXDM-1

description:
Library name: Sample 7
AGS cells treated with 1 mg/mL of BXD

value: human gastric adenocarcinoma cell line


title: AAV-injection, solvent, 1 day post solvent, rep1

description:
ONS1
H4Aligned.sortedByCoord.out.bam
ON_counts_CLEAN.txt


title: AAV-injection, solvent, 1 day post solvent, rep3

description:
ONS3
H16Aligned.sortedByCoord.out.bam
ON_counts_CLEAN.txt


title: CS4, chronic stress, scRNA-seq

city: Shijiazhuang

first: yaping

last: li

state: China

address: 河北医科大学

institute: 河北医科大学

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Left ventricle

extract_protocol:
Single-cell sample preparation was performed according to the10xGenomics® Cell Preparation Guide, which describes the best practices and general protocols for washing, counting and concentrating cells from both abundant and limited cell suspensions (greater than or less than 100000 total cells, respectively) in preparation for use in 10x Genomics Single Cell Protocols.
library was performed according to the manufacturer’s instructions (Single Cell 3’v3 protocol, 10X Genomics).

value: Left ventricle

value: chronic stress


title: FOXA2+PDXLx101, ATAC,rep2

value: Small cell lung cancer


title: Met-associated primary tumor, FFPE-ATAC,rep1

source_name: primary lung

value: primary lung


title: Never-met primary tumor, FFPE-ATAC,rep2


title: AGS-BXDL-3

description:
Library name: Sample 6
AGS cells treated with 0.5 mg/mL of BXD

value: AGS-BXDL

value: BXD ( 0.5 mg/mL)


title: CS2, chronic stress, scRNA-seq


title: CS3, chronic stress, scRNA-seq


title: SNU-BXD0-3

description:
Library name: Sample 12
SNU cells treated with ddH2O

value: SNU-1 cells

value: epithelial cells


title: AGS-BXDL-2

description:
Library name: Sample 5
AGS cells treated with 0.5 mg/mL of BXD


title: CS1, chronic stress, scRNA-seq


title: FOXA2+PDXLx328, ATAC,rep2

value: PDX


title: TG3F

type: RNA

city: Calgary

first: Jonathan

last: Epp

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

description: 247-gene panel applied to FFPE tissue

hyb_protocol: Followed Xenium In Situ Gene Expression protocol from the manufacturer (CG000582)

scan_protocol: Followed Xenium Analyzer User Guide (CCG000584)

data_processing:
Raw sequencing data were processed in R using Seurat v5.1.0 packages
Processed data: column 1 gene id; column 2 cell id; column 3 total UMI count per cell and gene combination; RDS

label: Xenium Mouse Brain Gene Expression panel

source_name: 5xFAD mouse brain tissue, 5um sections

label_protocol: Followed Xenium In Situ for FFPE - Tissue Preparation Guide from the manufacturer (CG000578)

extract_protocol: Mice were perfused with 0.1M phosphate buffered saline followed by 4% formaldehyde. Tissue was post-fixed for 24 hours, embedded in paraffim, and sectioned at 5μm

value: brain

tag: model

tag: Sex

value: F


title: Never-met primary tumor, FFPE-ATAC,rep1


title: AGS-BXDL-1

description:
Library name: Sample 4
AGS cells treated with 0.5 mg/mL of BXD

value: AGS cells


title: CON4, control, scRNA-seq

value: control


title: TG2F

description: 247-gene panel applied to FFPE tissue


title: FOXA2+PDXLx101, ATAC,rep1


title: GPM6B was overexpressed in PC9 cells and RNA was extracted for sequencing 2

city: Anhui

first: Xueyi

last: Feng

address: TangHe street

department: College of Life Science

institute: Anhui Medical University

data_processing:
Cutadapt/Tophat2/bowtie
Assembly: hg38

source_name: Lung

growth_protocol: PC-9 cells were cultured in DMEM medium (Vivocell) with 10% FBS. They were all cultured at 37 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using RNA isolater Total RNA Extraction Reagent(Vazyme) . 2ug of total RNA  was used for construction of sequencing libraries.
RNA library for RNA-seq was prepared follwing manufacturer's protocols.

treatment_protocol: PC9 cells are transfected with GPM6B over-expression or control virus.

value: Lung

value: Human non-small cell lung cancer cells

value: GPM6B over-expression


title: AGS-BXDM-3

description:
Library name: Sample 9
AGS cells treated with 1 mg/mL of BXD

value: human gastric adenocarcinoma cell line

value: AGS-BXDM

value: BXD ( 1 mg/mL)


title: CON3, control, scRNA-seq

value: Left ventricle


title: Met-associated primary tumor, FFPE-ATAC,rep2

value: primary lung

value: Small cell lung cancer


title: RNA was extracted from PC9 cells unloaded for sequencing 2

value: WT


title: AGS-BXD0-2

description:
Library name: Sample 2
AGS cells treated with ddH2O


title: CON2, control, scRNA-seq


title: WT2F

description: 247-gene panel applied to FFPE tissue

source_name: wildtype mouse brain tissue, 5um sections


title: RNA was extracted from PC9 cells unloaded for sequencing 1


title: AGS-BXD0-1

description:
Library name: Sample 1
AGS cells treated with ddH2O


title: TG4F

description: 247-gene panel applied to FFPE tissue


title: GPM6B was overexpressed in PC9 cells and RNA was extracted for sequencing 1


title: WT1F

description: 247-gene panel applied to FFPE tissue


title: CON1, control, scRNA-seq


title: Kras

status: Public on Apr 12 2025

city: Cincinnati

first: Zheng

state: OH

address: 8760 Sturbridge Dr

department: Division of Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: sample 3
10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Intestinal epithelium

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Intestinal epithelium

value: villin-CreER; KrasLSL-G12D +


title: MIA PaCa-2 cells, NSD2i, day5, NicE-seq, biol rep 1

city: Stanford

first: Or

last: Gozani

state: CA

address: 327 Campus Drive

department: Biology

institute: Stanford University

data_processing:
Raw reads trimmed with CutAdapt
Trimmed reads mapped with Bowtie2
Low quality aligned reads filtered with Samtools
Quality reads shifted with AlignmentSieve
Assembly: hg38
Supplementary files format and content: none
Library strategy: NicE-seq

source_name: MIA PaCa-2

growth_protocol: MIA PaCa-2 cells were maintained in DMEM supplmented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Accessible chromatin was profiled by One-Pot Universal NicE-seq with minor modification. In brief, cells (-/+ treatment; DMSO or NSD2i) were crosslinked with 4% formaldehyde for 10 min at room temperature (RT), quenched in 125mM glycine for 5 min, washed, resuspended in cryopreservation buffer [growth media supplemented with 10% DMSO], slow-frozen (-1C / min) and stored at -80C. After thaw, nuclei were extracted and 200k used for accessible chromatin labeling and protection (limited Nt.CviPII digestion and repair in presence of biotinylated- and 5-methyl- dCTPs). Unprotected genomic DNA was then fragmented with excess Nt.CviPII (37C for 2 h), followed by enzyme inactivation (65oC for 10 min). To capture biotin-labeled DNA, 30 µl of magnetic streptavidin beads (NEB S1420S) were added to each reaction, and incubated (4C for 2 h) in 2 M NaCl.
Libraries were prepared and amplified (seven PCR cycles) with the NEBNext Ultra II DNA Library Prep Kit (NEB #E7645S)

treatment_protocol: MIA PaCa-2 cells were either treated with DMSO(vehicle) or NSD2i 100nM

value: MIA PaCa-2

value: Pancreas epithelial Carcinoma


title: MIA PaCa-2 cells, NSD2i, day5, NicE-seq, biol rep 2


title: MIA PaCa-2 cells, DMSO, day5, NicE-seq, biol rep 2


title: MIA PaCa-2 cells, DMSO, day5, NicE-seq, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day1, NicE-seq, biol rep 2


title: CDC42 KO

description:
Library name: sample 2
10x genomics

value: villin-CreER; CDC42flox/flox


title: WT

description:
Library name: sample 1
10x genomics

value: villin-CreER; CDC42flox/+


title: Surrogate siRNA 10 mg/kg group 8

city: SHANGHAI

first: XIAN

last: JIN

state: SHANGHAI

address: Cailun Road 720, 2-404

institute: ENNOVABIO

data_processing:
FastQC was utilized to evaluate the quality of the original sequencing data, ensuring the integrity of subsequent analyses. Trimmomatic was then applied to eliminate adaptors, low-quality reads, and short sequences. The paired-end transcriptome reads were aligned to the mouse reference genome (GRCm38) using the STAR spliced read aligner, and count matrices were created from the aligned reads with the Rsubread package in R, which features the function featureCounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

extract_protocol:
Total RNA was isolated from the snap frozen liver samples using the TRizol kit, and the RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed using the VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina, following the manufacturer’s protocol.

value: liver

value: siR6.1 10 mg/kg


title: AGS-BXD0-3

description:
Library name: Sample 3
AGS cells treated with ddH2O

value: AGS cells

value: epithelial cells


title: MIA PaCa-2 cells, DMSO, day1, NicE-seq, biol rep 2


title: MIA PaCa-2 cells, DMSO, day1, NicE-seq, biol rep 1


title: Surrogate siRNA 10 mg/kg group 6


title: WT3F

description: 247-gene panel applied to FFPE tissue

value: brain

value: F


title: Surrogate siRNA 10 mg/kg group 7


title: Surrogate siRNA 10 mg/kg group 5


title: MIA PaCa-2 cells, NSD2i, day9, IgG, biol rep 1

data_processing:
Raw reads trimmed with CutAdapt
Trimmed reads mapped with Bowtie2
Low quality aligned reads filtered with Samtools and SamClip
BigWig files generated with deepTools 'bamCoverage'
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed with lightly fiXed MiaPaCa2 cells (-/+ treatment; DMSO or NSD2i) by an automated protocol (autoCUT&RUN). All steps were performed on Tecan Freedom EVO robotics platforms with gentle rocking for incubation steps and magnetic capture for media exchange / washing steps. In brief, for each reaction 500K cells [at 5 million cells/mL; in 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1X EDTA/EGTA-free Complete Protease Inhibitor (Roche #11873580001)] were dispensed to individual wells of a 96-well plate, immobilized to Concanavalin-A beads (EpiCypher #21-1401), and incubated overnight (4C) with desired antibody. pAG-MNase (EpiCypher #15-1016) was added and activated (2 hours at 4C), and CUT&RUN enriched DNA purified by Serapure beads after mixing at 2:1 (Bead:DNA). Recovered DNA was quantified by PicoGreen (ThermoFisher Scientific #P11495) and reactions normalized to 5ng DNA
Library was prepared with CUT&RUN Library Prep kit (EpiCypher #14-1001) as per supplier’s instructions.

tag: cut&run antibody

value: IgG(EpiCypher 13-0041)


title: Surrogate siRNA 10 mg/kg group 4


title: MIA PaCa-2 cells, NSD2i, day9, IgG, biol rep 2


title: MIA PaCa-2 cells, NSD2i, day5, IgG, biol rep 2


title: Surrogate siRNA 10 mg/kg group 3


title: MIA PaCa-2 cells, NSD2i, day5, IgG, biol rep 1


title: Surrogate siRNA 10 mg/kg group 2


title: Surrogate siRNA 10 mg/kg group 1


title: CDC42 KO/Kras

description:
Library name: sample 4
10x genomics

value: villin-CreER; CDC42flox/flox; KrasLSL-G12D +


title: MIA PaCa-2 cells, NSD2i, day1, IgG, biol rep 2


title: MIA PaCa-2 cells, NSD2i, day1, IgG, biol rep 1


title: Surrogate siRNA 1 mg/kg group 8

value: siR6.1 1 mg/kg


title: Surrogate siRNA 1 mg/kg group 7


title: MIA PaCa-2 cells, NSD2i, day1, NicE-seq, biol rep 1


title: Surrogate siRNA 1 mg/kg group 6


title: Surrogate siRNA 1 mg/kg group 5


title: MIA PaCa-2 cells, DMSO, day5, IgG, biol rep 2


title: Surrogate siRNA 1 mg/kg group 3


title: MIA Paca-2 cells, DMSO, day1, IgG, biol rep 2


title: Surrogate siRNA 1 mg/kg group 2


title: MIA PaCa-2 cells, DMSO, day1, IgG, biol rep 1


title: Surrogate siRNA 1 mg/kg group 4


title: MIA PaCa-2 cells, DMSO, day5, IgG, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day9, NSD2, biol rep 1

value: NSD2(EpiCypher 13-0002)


title: Surrogate siRNA 1 mg/kg group 1


title: Negative control siRNA group 7

value: NC-siR 10 mg/kg


title: MIA PaCa-2 cells, NSD2i, day9, NSD2, biol rep 2


title: Negative control siRNA group 8


title: MIA PaCa-2 cells, NSD2i, day5, NSD2, biol rep 2


title: MIA PaCa-2 cells, NSD2i, day5, NSD2, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day1, NSD2, biol rep 2


title: Negative control siRNA group 5


title: Negative control siRNA group 6


title: Negative control siRNA group 4


title: MIA PaCa-2 cells, DMSO, day9, NSD2, biol rep 2


title: Negative control siRNA group 3


title: MIA PaCa-2 cells, NSD2i, day1, NSD2, biol rep 1


title: MIA PaCa-2 cells, DMSO, day9, IgG, biol rep 2


title: MIA PaCa-2 cells, DMSO, day9, NSD2, biol rep 1


title: Negative control siRNA group 2


title: MIA PaCa-2 cells, DMSO, day5, NSD2, biol rep 2


title: MIA PaCa-2 cells, DMSO, day9, IgG, biol rep 1


title: MIA PaCa-2 cells, DMSO, day5, NSD2, biol rep 1


title: MIA PaCa-2 cells, DMSO, day1, NSD2, biol rep 2


title: Negative control siRNA group 1


title: GFT505_30 mg/kg group 8

value: GFT505_30 mg/kg


title: GFT505_30 mg/kg group 5


title: GFT505_30 mg/kg group 7


title: MIA PaCa-2 cells, NSD2i, day9, H3K9me3, biol rep 2

value: H3K9me3(Thermofisher 720093)


title: MIA PaCa-2 cells, DMSO, day1, NSD2, biol rep 1

value: MIA PaCa-2


title: GFT505_30 mg/kg group 4


title: GFT505_30 mg/kg group 2


title: MIA PaCa-2 cells, NSD2i, day5, H3K9me3, biol rep 2

value: Pancreas epithelial Carcinoma


title: MIA PaCa-2 cells, NSD2i, day5, H3K9me3, biol rep 1


title: GFT505_30 mg/kg group 3


title: MIA PaCa-2 cells, NSD2i, day1, H3K9me3, biol rep 2


title: MIA PaCa-2 cells, DMSO, day9, H3K9me3, biol rep 2


title: Model group 8

value: saline


title: Model group 6


title: Model group 5


title: MIA PaCa-2 cells, DMSO, day5, H3K9me3, biol rep 2


title: MIA PaCa-2 cells, DMSO, day5, H3K9me3, biol rep 1


title: GFT505_30 mg/kg group 1


title: Model group 4


title: Model group 7


title: GFT505_30 mg/kg group 6


title: Model group 2


title: MIA PaCa-2 cells, DMSO, day1, H3K9me3, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day9, H3K36me3, biol rep 2

value: H3K36me3(EpiCypher 13-0058)


title: MIA PaCa-2 cells, NSD2i, day9, H3K9me3, biol rep 1


title: Sham group 5

value: liver


title: MIA PaCa-2 cells, NSD2i, day5, H3K36me3, biol rep 2


title: Model group 1


title: MIA PaCa-2 cells, NSD2i, day9, H3K36me3, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day5, H3K36me3, biol rep 1


title: Sham group 4


title: Sham group 3


title: MIA PaCa-2 cells, NSD2i, day1, H3K9me3, biol rep 1


title: MIA PaCa-2 cells, DMSO, day9, H3K9me3, biol rep 1


title: Sham group 2


title: MIA PaCa-2 cells, NSD2i, day1, H3K36me3, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day1, H3K36me3, biol rep 2


title: MIA PaCa-2 cells, DMSO, day9, H3K36me3, biol rep 2


title: Sham group 1


title: OT-I T cell WT

city: Aurora

first: Ross

middle: M

last: Kedl

state: CO

address: 12800 E. 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: 10x Genomics

data_processing:
scRNAseq reads were aligned to mm10 and collapsed into unique molecular identifier (UMI) counts using the 10X Genomic Cloud Cell Ranger Count software (version 7.1.0) o generate the the output files: matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz
Assembly: mm10
Supplementary files format and content: CellRanger output files: matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz

source_name: spleen

extract_protocol:
A physiologically relevant number (500) of congenically marked (CD45.1) OT1 T cells were adoptively transferred into a naïve B6 recipient (CD45.2). Recipient mice were infected intravenously (i.v.) with LM.Ova.ActA as described previously. On day 5, T cells were isolated and pooled from 4 mice prior to cell sorting of CD45.1+ CD8+ CD19- cells. Naïve cells were isolated using Biolegend CD8 isolation kit. Naïve and d5 cells for each genotype were pooled at a 1:1 ratio and roughly 10,000 cells were loaded onto Single Cell A chips (10X Genomics) and partitioned into Gel Bead In-Emulsions in a Chromium Controller (10X Genomics).
Single-cell RNA libraries were prepared according to the 10X Genomics Chromium Single Cell 5’ Reagent Kits v3.1 User Guide and sequenced on a NovaSeq 6000 (Illumina)  by the CU Anchutz Genomics Core.

value: spleen

value: T cell

value: OT-I

value: LM.Ova.ActA infection


title: MIA PaCa-2 cells, DMSO, day5, H3K36me3, biol rep 2


title: MIA PaCa-2 cells, DMSO, day1, H3K9me3, biol rep 2


title: Model group 3


title: GT1-7 cells, control, 24hours, rep3

city: Shanghai

first: Yating

last: Lin

address: Minhang District

institute: Children’s Hospital of Fudan University

data_processing:
Following library qualification, sequencing was conducted using the Illumina NovaSeq 6000 (Illumina, USA). The image data measured by the high-throughput sequencer are convert sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and and thus a better mapping result than other non-splice mapping.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

source_name: GT1-7 cells

growth_protocol: The GT1-7 cells were grown in Dulbecco’s modified Eagle’s medium with high glucose, supplemented with 10% fetal bovine serum  and 1 penicillin/streptomycin at 37°C and 5%CO2.

extract_protocol:
Total RNA was extracted separately from both the Alisol B intervention group and the control group cells using TRIzol reagent (TaKaRa). 800ng of total RNA was used for the construction of sequencing libraries.
The RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system was used to assess the total amounts and integrity of RNA. Eligible RNA samples were used to construct cDNA libraries.

treatment_protocol: When the GT1-7 cells reached 70-80% confluence, they were starved in serum-free medium for 12 hours. Afterward, they were incubated for 24 hours with or without 0.125μM Alisol B

value: GT1-7 cells

value: control


title: MIA PaCa-2 cells, DMSO, day9, H3K36me3, biol rep 1


title: MIA PaCa-2 cells, DMSO, day5, H3K36me3, biol rep 1


title: GT1-7 cells, control, 24hours, rep1


title: MIA PaCa-2 cells, DMSO, day1, H3K36me3, biol rep 2


title: OT-I T cell Opa1 KO

description: 10x Genomics

value: OT-I Opa1 fl/fl dlck Cre+


title: GT1-7 cells, Alisol B intervention, 24hours, rep3

value: Alisol B intervention


title: GT1-7 cells, Alisol B intervention, 24hours, rep2


title: MIA PaCa-2 cells, DMSO, day1, H3K36me3, biol rep 1


title: GT1-7 cells, Alisol B intervention, 24hours, rep1


title: MIA PaCa-2 cells, NSD2i, day9, H3K36me2, biol rep 2


title: mlMGec_5

city: Wuhan, Hubei

first: Minghao

last: Dong

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital

data_processing:
Illumina Casava 1.7 software used for basecalling.
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4[3] with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: Ensembl_release104
Supplementary files format and content: tab-delimited text files include Count values for each Sample
Supplementary files format and content: Matrix table with Count values for every gene and every sample

source_name: ECs in primary culture

growth_protocol: Primary microglia were isolated from neonatal wild-type and LDLR-/- mice at P1-P2 as reported before. In brief, mixed glial cells were raised in DMEM/F12 medium complemented with 10% fetal bovine serum (FBS) for the initial three days. And then, the medium was substituted with high glucose DMEM medium containing 10% FBS for the next 6 days. Microglia were separated by shuddering at 200 rpm at 37°C for 1 hour. After microglia were removed, 0.25% trypsin was applied separate Oligodendrocyte precursor cells (OPCs) from the firmly attached astrocyte layer. The cell suspension was collected and centrifuged at 100g for 10 min. For the microglia-induced differentiation of oligodendrocytes, OPCs were cultured with OPC basal media without any growth factors, but co-cultured with treated

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: A 0.4-μm pore size Transwell (Corning) coculture system was established to explore whether the activity of oligodendrocytes or endothelial cells could be affected by different groups of microglia (Naïve-MG, Myelin-MG, and Myelin-LDL-MG). Microglia were planted with 5×105cells/well in the upper chamberof a 12-well plate, which was then treated as described previously. After respective exposure, the inserts were gently washed 3 times and then placed on another 12-well plate with the OPCs/mBMECs already seeded on the bottom of the cells. and submerged in the medium for 24 h. The OPCs/mBMECs media: microglia culture media = 1:1.

value: ECs

tag: strain

value: cocultured with MG (Myelin+LDL)


title: MIA PaCa-2 cells, NSD2i, day9, H3K36me2, biol rep 1


title: mlMGec_3


title: mlMGec_4


title: mlMGec_2


title: mlMGec_1


title: mMGec_5

value: cocultured with MG (Myelin)


title: mMGec_4


title: MIA PaCa-2 cells, NSD2i, day5, H3K36me2, biol rep 2


title: MIA PaCa-2 cells, NSD2i, day5, H3K36me2, biol rep 1


title: mMGec_3


title: Arabidopsis, hira-1, 12DAG, Group1, Rep2

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

description:
Library name: 12DAG_hira-1_Group1_R2
Treatment

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).
The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Quantification was performed with Rsubread package (version 2.12.0) and normalized using TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: TAIR 10
Supplementary files format and content: Tab-delimited text includes raw counts for each sample.
Supplementary files format and content: Txt files include TPM values for each sample.

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
total RNA was extracted by using RNA extraction  columns (Axygen, UE-MN-MS-RNA-250) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.

value: 12DAG seedling


title: GT1-7 cells, control, 24hours, rep2


title: Arabidopsis, Columbia-0, 12DAG, Group1, Rep3

description:
Library name: 12DAG_Columbia-0_Group1_R3
Control


title: MIA PaCa-2 cells, NSD2i, day1, H3K36me2, biol rep 1

value: MIA PaCa-2


title: naiveMGec_2

value: cocultured with naïve MG


title: MIA PaCa-2 cells, DMSO, day9, H3K36me2, biol rep 2

value: Pancreas epithelial Carcinoma


title: Arabidopsis, Columbia-0, 12DAG, Group1, Rep1

description:
Library name: 12DAG_Columbia-0_Group1_R1
Control


title: mMGec_2


title: naiveMGec_4


title: naiveMGec_5


title: Arabidopsis, hira-1, 12DAG, Group1, Rep1

description:
Library name: 12DAG_hira-1_Group1_R1
Treatment


title: MIA PaCa-2 cells, DMSO, day5, H3K36me2, biol rep 2


title: mMGec_1


title: Arabidopsis, Columbia-0, 12DAG, Group1, Rep2

description:
Library name: 12DAG_Columbia-0_Group1_R2
Control


title: mlMGopc_4

source_name: OPCs in primary culture

value: OPCs


title: naiveMGec_1


title: naiveMGec_3


title: mlMGopc_5


title: MIA PaCa-2 cells, NSD2i, day1, H3K36me2, biol rep 2


title: WGBS-GDE1-3FLAG-gde1-1ov-rep3

city: Los Angeles

first: Steven

middle: E.

last: Jacobsen

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45. BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T).
Assembly: tair10
Supplementary files format and content: bigWig, narrowpeak

source_name: unfertilized ovules (Ov)

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under long-day condition (16h light and 8h dark).

extract_protocol:
For ChIP-seq experiments, 1~2 g of unopen flower buds  from the T2 lines were collected. For sRNA-seq and WGBS, ovule or anther tissues (stage 9 or earlier) from 5- to 6-week-old plants were harvested.
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. Whole genome bisulfite sequencing libraries were prepared using the Nugen Ultralow Methyl Kit. RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina).  Libraries were sequenced on NovaSeq 6000 (Illumina).

value: unfertilized ovules (Ov)


title: WGBS-GDE1-3FLAG-gde1-1ov-rep2


title: mlMGopc_2


title: mlMGopc_1


title: MIA PaCa-2 cells, DMSO, day5, H3K36me2, biol rep 1


title: mMGopc_5


title: mlMGopc_3


title: Arabidopsis, hira-1, 12DAG, Group1, Rep3

description:
Library name: 12DAG_hira-1_Group1_R3
Treatment


title: MIA PaCa-2 cells, DMSO, day1, H3K36me2, biol rep 2


title: WGBS-GDE1-3FLAG-gde1-1ov-rep1


title: mMGopc_4


title: MIA PaCa-2 cells, DMSO, day9, H3K36me2, biol rep 1


title: MIA PaCa-2 cells, DMSO, day1, H3K36me2, biol rep 1


title: mMGopc_1


title: mMGopc_2


title: MIA PaCa-2 cells, NSD2i, day9, H3K36me1, biol rep 2

value: H3K36me1(Abclonal A2364)


title: WGBS-gde1-1ov-rep3


title: WGBS-gde1-1ov-rep2


title: mMGopc_3


title: WGBS-gde1-1ov-rep1


title: naiveMGopc_4


title: Sample 44C

city: London

first: Paul

last: Sharpe

address: Guy's Hospital

department: Centre for Craniofacial and Regenerative Biology

country: United Kingdom

institute: King's College London

data_processing:
Galaxy version 1.0.2
Raw fastq files were mapped to GRCh38 (hg38) human genome reference using HISAT2 (Galaxy Version 2.1.0)
Aligned read counts of each gene were generated by featureCounts (Galaxy Version 2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Human primary mesenchymal cells

growth_protocol: Primaryl cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Quick-RNA MicroPrep Kit (Zymo Research, Irvine, CA)
RNA libraries for RNA-seq were prepared using SMARTseq V4/Nugen Protocol following manufacturer's protocols.

value: Human primary mesenchymal cells

value: gingiva mesenchymal cells


title: MIA PaCa-2 cells, NSD2i, day5, H3K36me1, biol rep 2


title: Sample 44F


title: MIA PaCa-2 cells, NSD2i, day5, H3K36me1, biol rep 1


title: WGBS-colov-rep1

value: WT


title: naiveMGopc_3


title: Sample 41C


title: WGBS-colov-rep3


title: WGBS-colov-rep2


title: MIA PaCa-2 cells, NSD2i, day9, H3K36me1, biol rep 1


title: Sample 41F


title: WGBS-clsy3clsy4ov-rep3


title: naiveMGopc_1


title: Sample 40C


title: MIA PaCa-2 cells, NSD2i, day1, H3K36me1, biol rep 2


title: Sample 40F


title: WGBS-clsy3clsy4ov-rep2


title: naiveMGopc_2


title: naiveMGopc_5


title: Myelin_LDL_7

source_name: Microglia in primary culture

value: Microglia

value: Myelin+LDL


title: Sample 39C


title: Sample 39F


title: MIA PaCa-2 cells, DMSO, day9, H3K36me1, biol rep 1


title: WGBS-clsy3clsy4ov-rep1


title: Myelin_LDL_6


title: Myelin_LDL_5


title: MIA PaCa-2 cells, DMSO, day5, H3K36me1, biol rep 2


title: CW9019,DMSO,16h,Rep2

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

description: Library name: sample 12

data_processing:
Low quality and adapter sequences were trimmed using Trim_galore
Trimmed sequences were mapped to hg38 using STAR with 2-pass approach
Reads were assigned to features using featureCounts
Normalization, differential analysis and statistical reports were done using DESeq2 and SARTools
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw and normalized counts for each sample generated by DESeq2
Supplementary files format and content: tab-delimited text file include log2FoldChange, p-values adjusted and other the statistics generated by DESeq2 for each sample

growth_protocol: A673 cells were grown in DMEM + 10% FBS + PSQ + 1% Sodium Pyruvate. TTC466, 402-91, 1765-92, SUCCS1 and DTC1 cells were grown in RPMI-1640 + 10% FBS + PSQ. DL221 cells were grown in DMEM + 10% FBS + PSQ. JN-DSRCT and BER cells were grown in DMEM/F12 + 10% FBS + PSQ.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen). 300ng of total RNA was used for library prep.
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were seeded at 30% confluency and left to adhere overnight. After 24 hours, cells were dosed with DMSO or Seclidemstat equating calculated IC90 for that cell line. Cells were harvested for RNA extraction after 48 hours.

value: Rhabdomyosarcoma

value: wildtype

value: DMSO

tag: replicate


title: sRNA-seq-triple-2an-rep3

source_name: anther (stage 9 or earlier)

value: anther (stage 9 or earlier)

value: rem12 val rem46 triple


title: sRNA-seq-triple-2an-rep1


title: CW9019,DMSO,16h,Rep1

description: Library name: sample 11


title: MIA PaCa-2 cells, NSD2i, day1, H3K36me1, biol rep 1


title: Myelin_LDL_3


title: MIA PaCa-2 cells, DMSO, day1, H3K36me1, biol rep 2


title: Myelin_LDL_4


title: sRNA-seq-triple-1an-rep3


title: CW9019,SP2509,48h,Rep1

description: Library name: sample 9


title: MIA PaCa-2 cells, DMSO, day5, H3K36me1, biol rep 1


title: sRNA-seq-triple-2an-rep2


title: MIA PaCa-2 cells, NSD2i, day9, H3K4me1, biol rep 2

value: H3K4me1(EpiCypher 13-0057)


title: Myelin_LDL_1


title: RH30,DMSO,16h,Rep2

description: Library name: sample 8


title: sRNA-seq-triple-1an-rep1


title: MIA PaCa-2 cells, DMSO, day9, H3K36me1, biol rep 2

value: MIA PaCa-2


title: CW9019,SP2509,48h,Rep2

description: Library name: sample 10


title: Myelin_7

value: Myelin


title: MIA PaCa-2 cells, NSD2i, day9, H3K4me1, biol rep 1

value: Pancreas epithelial Carcinoma


title: RH30,DMSO,16h,Rep1

description: Library name: sample 7


title: MIA PaCa-2 cells, NSD2i, day5, H3K4me1, biol rep 2


title: sRNA-seq-gde1-1an-rep2


title: RH30,SP2509,48h,Rep2

description: Library name: sample 6


title: sRNA-seq-triple-1an-rep2


title: RH30,SP2509,48h,Rep1

description: Library name: sample 5


title: MIA PaCa-2 cells, NSD2i, day5, H3K4me1, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day1, H3K4me1, biol rep 1


title: MIA PaCa-2 cells, NSD2i, day1, H3K4me1, biol rep 2


title: Myelin_6


title: Myelin_4


title: RH4,DMSO,16h,Rep1

description: Library name: sample 3


title: Myelin_LDL_2


title: RH4,DMSO,16h,Rep2

description: Library name: sample 4


title: Myelin_2


title: sRNA-seq-colan-rep2


title: RH4,SP2509,48h,Rep2

description: Library name: sample 2


title: sRNA-seq-colan-rep1


title: Myelin_5


title: Myelin_3


title: MIA PaCa-2 cells, DMSO, day1, H3K36me1, biol rep 1


title: Myelin_1


title: MIA PaCa-2 cells, DMSO, day9, H3K4me1, biol rep 1


title: sRNA-seq-gde1-1an-rep3


title: MIA PaCa-2 cells, DMSO, day5, H3K4me1, biol rep 2


title: sRNA-seq-clsy3clsy4-rep3


title: RH4,SP2509,48h,Rep1

description: Library name: sample 1


title: Control_6

value: untreated


title: MIA PaCa-2 cells, DMSO, day9, H3K4me1, biol rep 2


title: sRNA-seq-gde1-1an-rep1


title: sRNA-seq-clsy3clsy4-rep2


title: sRNA-seq-colan-rep3


title: Control_5


title: Healthy control 3

first: Zihui

last: Zhao

address: Dongan Road No.130

institute: Shanghai Institute of Infectious Disease and Biosecurity, Fudan University

description:
Library name: hc_mc257
Quantified single-cell transcriptomics matrix

data_processing:
We used MobiVision (https://www.mobidrop.com/bioinformatics-analysis-software/mobivision-news/software-download) version 3.1 for barcode processing and transcript counting. The reference was constructed based on GRCh38.p14, downloaded from GENCODE (https://www.gencodegenes.org/human/). Transcript counting was performed using the “quantify” module within MobiVision, and the reference index was generated using the “mkindex” tool.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: blood

extract_protocol:
Peripheral blood (10 mL) was drawn from the 6 enrolled patients using purple EDTA tubes, and the samples were transported on dry ice as quickly as possible. In addition, peripheral blood (10 mL) was collected from 3 healthy male volunteers aged 25 years in the morning while fasting, resulting in a total of 9 peripheral blood samples.Peripheral blood mononuclear cells (PBMCs) were isolated.
We employed the MobiNova®-100 Single Cell System (MobiDrop (Zhejiang) Co., Ltd.) for single-cell sequencing library preparation. The quality-controlled single-cell suspension was loaded onto a system-specific microfluidic chip along with beads pre-coated with universal cell barcodes and unique molecular identifiers (UMIs). The microfluidic system within the chip precisely controlled the fluid flow at the oil–water interface, and through droplet generation technology, individual cells were co-encapsulated with a single barcode bead in a water-in-oil droplet. Inside the droplets, cells were rapidly lysed by lysis buffer, releasing intracellular mRNA. Because the beads were functionalized with oligonucleotides carrying poly(dT) primers, these primers specifically bound to mRNA molecules with poly-A tails.

value: blood

value: peripheral blood mononuclear cell

tag: disease

value: Not applicable


title: Healthy control 2

description:
Library name: hc_mc256
Quantified single-cell transcriptomics matrix


title: MIA PaCa-2 cells, DMSO, day5, H3K4me1, biol rep 1


title: sRNA-seq-clsy3clsy4-rep1


title: MIA PaCa-2 cells, DMSO, day1, H3K4me1, biol rep 2


title: Healthy control 1

description:
Library name: hc_mc255
Quantified single-cell transcriptomics matrix


title: sRNA-seq-triple-3gde1-1ov-rep5

value: unfertilized ovules (Ov)

value: rem12 val rem46 triple gde1-1


title: sRNA-seq-triple-3gde1-1ov-rep6


title: Control_4

value: Microglia


title: MIA PaCa-2 cells, DMSO, day1, H3K4me1, biol rep 1


title: Control_2


title: Control_3


title: HIV-only infected patient2

description:
Library name: hiv_mc246
Quantified single-cell transcriptomics matrix

value: HIV-only infection

value: No


title: HIV-only infected patient3

description:
Library name: hiv_mc247
Quantified single-cell transcriptomics matrix


title: Control_1


title: MIA PaCa-2 cells, NSD2i, day9, H3K27AC, biol rep 2

value: H3K27Ac(EpiCypher 13-0045)


title: sRNA-seq-triple-2ov-rep6


title: HIV-only infected patient1

description:
Library name: hiv_mc245
Quantified single-cell transcriptomics matrix


title: MIA PaCa-2 cells, NSD2i, day9, H3K27AC, biol rep 1


title: H1373 cells, NSD2i, biol rep 3

description: Library name: H1373_NSD2i_Rep3

data_processing:
Raw reads trimmed with CutAdapt
Trimmed reads mapped with STAR aligner
Feature counts extracted with featureCounts
TPM quantification with salmon
Assembly: hg38
Supplementary files format and content: MIA PaCa2 cells' gene counts
Supplementary files format and content: A549, KP2, NCI-H1373 and PSN1 cells' gene counts

growth_protocol: MIA PaCa-2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and antibiotics in humidified atmosphere with 5% CO2 at 37C; KP2, NCI-H1373, cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen)
Library was prepared by BGI following stanford Strand-Specific Transcriptome Library Contraction Protocol(DNBSEQ)

treatment_protocol: MIA PaCa-2, KP2, and NCI-H1373 cells were either treated with DMSO (vehicle) or NSD2i 100nM.

value: Lung adenocarcinoma cell line

value: NSD2i 100nM


title: HIV-MTB co-infected patient3

description:
Library name: ht_mc261
Quantified single-cell transcriptomics matrix

value: HIV/MTB co-infection


title: sRNA-seq-triple-2ov-rep5

value: rem12 val rem46 triple


title: MIA PaCa-2 cells, NSD2i, day5, H3K27AC, biol rep 2

value: MIA PaCa-2


title: MIA PaCa-2 cells, NSD2i, day5, H3K27AC, biol rep 1


title: H1373 cells, NSD2i, biol rep 2

description: Library name: H1373_NSD2i_Rep2


title: HIV-MTB co-infected patient2

description:
Library name: ht_mc243
Quantified single-cell transcriptomics matrix


title: H1373 cells, NSD2i, biol rep 1

description: Library name: H1373_NSD2i_Rep1


title: sRNA-seq-triple-2ov-rep4


title: MIA PaCa-2 cells, NSD2i, day1, H3K27AC, biol rep 2


title: sRNA-seq-triple-2clsy3clsy4ov-rep6

value: rem12 val rem46 triple clsy3 clsy4


title: HIV-MTB co-infected patient1

description:
Library name: ht_mc241
Quantified single-cell transcriptomics matrix


title: H1373 cells, DMSO, biol rep 3

description: Library name: H1373_Control_Rep3

value: DMSO


title: sRNA-seq-triple-3gde1-1ov-rep4


title: sRNA-seq-triple-2clsy3clsy4ov-rep5


title: H1373 cells, DMSO, biol rep 2

description: Library name: H1373_Control_Rep2


title: MIA PaCa-2 cells, NSD2i, day1, H3K27AC, biol rep 1

value: Pancreas epithelial Carcinoma


title: TATU7

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

data_processing:
Reads underwent quality check with FastQC (v0.11.9); Kallisto (v0.46.1) was used to map reads to the human reference genome (HomoSapien GRCh38) and to generate transcript counts.
Assembly: HomoSapien GRCh38
Supplementary files format and content: 3col.tsv- Long format of aligned raw gene counts
Supplementary files format and content: GeneCounts_ RAW DATA.xlsx- Wide format of aligned raw gene counts

source_name: vastus lateralis muscle

extract_protocol:
RNA was extracted using AllPrep RNA/RNA/miRNA universal kit (Qiagen) according to manufacturer instructions
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol

treatment_protocol: Ten healthy females aged 18-35 years undertook a randomised cross-over study of nine nights’ sleep restriction (SR; 5-h time in bed) and normal sleep (NS; ≥7 h time in bed) with a minimum 6-week washout. Participants completed four REx sessions per trial  (day 3, 5, 7 and 9). Muscle biopsies were collected pre- and post-REx on days 3 and 9.

value: vastus lateralis muscle

value: Skeletal Muscle

value: Female

tag: age of_donor

value: CON

tag: day of_collection


title: sRNA-seq-triple-2clsy3clsy4ov-rep4

value: unfertilized ovules (Ov)


title: sRNA-seq-triple-1ov-rep6


title: MIA PaCa-2 cells, DMSO, day9, H3K27AC, biol rep 1


title: TATU3

value: SLEEP


title: MIA PaCa-2 cells, DMSO, day5, H3K27AC, biol rep 2


title: KP2 cells, NSD2i, biol rep 3

description: Library name: KP2_NSD2i_Rep3

value: Pancreatic adenocarcinoma cell line


title: TATU1


title: KP2 cells, NSD2i, biol rep 2

description: Library name: KP2_NSD2i_Rep2


title: SASY7


title: MIA PaCa-2 cells, DMSO, day5, H3K27AC, biol rep 1


title: KP2 cells, NSD2i, biol rep 1

description: Library name: KP2_NSD2i_Rep1


title: sRNA-seq-triple-1ov-rep4


title: MIA PaCa-2 cells, DMSO, day1, H3K27AC, biol rep 2


title: SASY1


title: sRNA-seq-clsy3clsy4ov-rep6


title: KP2 cells, DMSO, biol rep 3

description: Library name: KP2_Control_Rep3


title: KP2 cells, DMSO, biol rep 2

description: Library name: KP2_Control_Rep2


title: TATU5


title: sRNA-seq-clsy3clsy4ov-rep5


title: MIA PaCa-2 cells, DMSO, day9, H3K27AC, biol rep 2


title: NACR5


title: KP2 cells, DMSO, biol rep 1

description: Library name: KP2_Control_Rep1


title: MIA PaCa-2 cells, NSD2i, day9, H3K27me3, biol rep 1

value: H3K27me3(EpiCypher 13-0055)


title: MIA PaCa-2 cells, DMSO, day1, H3K27AC, biol rep 1

value: H3K27Ac(EpiCypher 13-0045)


title: sRNA-seq-clsy3clsy4ov-rep4


title: NACR3


title: H1373 cells, DMSO, biol rep 1

description: Library name: H1373_Control_Rep1

value: Lung adenocarcinoma cell line


title: sRNA-seq-gde1-1ov-rep6


title: sRNA-seq-triple-1ov-rep5


title: MIA PaCa-2 cells, NSD2i, day5, H3K27me3, biol rep 2


title: primary  chondrocytes, mimic transfection-2,12h

city: Nanjing

last: Liu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University

description: Library name: mimic_2

data_processing:
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Homo sapiens from GRCh38.87 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Assembly: GRCh38.87
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: primary osteoarthritic chondrocytes

growth_protocol: The chondrocytes were cultured in DMEM/F12 containing 10% FBS and 1% P/S.

extract_protocol:
Total RNAs were extracted from primary osteoarthritic chondrocytes using TRIzol Reagent.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® .

treatment_protocol: primary human chondrocytes were transfected with either miR-23b-3p mimics at 100 nM or NC using Lipofectamine 2000.

value: primary osteoarthritic chondrocytes

value: chondrocytes

value: miR-23b-3p mimic transfected


title: KISZ7


title: MIA PaCa-2 cells, NSD2i, day5, H3K27me3, biol rep 1

value: MIA PaCa-2


title: sRNA-seq-gde1-1ov-rep4


title: primary  chondrocytes, mimic transfection-1, 12h

description: Library name: mimic_1


title: sRNA-seq-colov_rep6

value: WT


title: primary chondrocytes nc transfection-3, 12h

description: Library name: nc_3

value: nc transfected


title: MIA PaCa-2 cells, NSD2i, day9, H3K27me3, biol rep 2

value: Pancreas epithelial Carcinoma


title: NACR7

value: vastus lateralis muscle


title: MIA PaCa-2 cells, NSD2i, day1, H3K27me3, biol rep 1


title: KISZ3

value: Skeletal Muscle


title: sRNA-seq-colov_rep5


title: primary chondrocytes, nc transfection-2, 12h

description: Library name: nc_2


title: KISZ1

value: Female


title: sRNA-seq-colov_rep4


title: MIA PaCa-2 cells, DMSO, day9, H3K27me3, biol rep 1


title: sRNA-seq-GDE1-3FLAG-gde1-1ov_rep3


title: NACR1


title: MIA PaCa-2 cells, DMSO, day9, H3K27me3, biol rep 2


title: primary  chondrocytes, nc transfection-1,12h

description: Library name: nc_1


title: primary chondrocytes, mimic transfection-3, 12h

description: Library name: mimic_3


title: JEHA5

value: CON


title: MIA PaCa-2 cells, DMSO, day5, H3K27me3, biol rep 2


title: sRNA-seq-GDE1-3FLAG-gde1-1ov_rep2

value: unfertilized ovules (Ov)


title: only osteocyte-enriched subchondral bone; high stress area;2

description: Library name: treat_2

source_name: osteocyte-enriched subchondral bone

extract_protocol:
Total RNAs were extracted from osteocyte-enriched human tissues (LS/HS tissues)  using TRIzol Reagent.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina®.

value: osteocyte-enriched subchondral bone

value: high stress area


title: MIA PaCa-2 cells, DMSO, day5, H3K27me3, biol rep 1

value: H3K27me3(EpiCypher 13-0055)


title: MIA PaCa-2 cells, NSD2i, day1, H3K27me3, biol rep 2


title: JEHA3

value: SLEEP


title: sRNA-seq-GDE1-3FLAG-gde1-1ov_rep1


title: only osteocyte-enriched subchondral bone; high stress area;1

description: Library name: treat_1


title: KISZ5


title: only osteocyte-enriched subchondral bone; high stress area;3

description: Library name: treat_3


title: MIA PaCa-2 cells, DMSO, day1, H3K27me3, biol rep 2


title: JEHA1


title: sRNA-seq-clsy3clsy4ov_rep3


title: only osteocyte-enriched subchondral bone; low stress area;3

description: Library name: ctr_3

value: low stress area


title: MIA PaCa-2 cells, DMSO, day1, H3K27me3, biol rep 1


title: HABA7


title: sRNA-seq-clsy3clsy4ov_rep2


title: only osteocyte-enriched subchondral bone; low stress area;2

description: Library name: ctr_2


title: JEHA7


title: MIA PaCa-2 cells, NSD2i, day9, H3K4me3, biol rep 2

value: H3K4me3(EpiCypher 13-0042)


title: HABA5


title: sRNA-seq-clsy3clsy4ov_rep1


title: MIA PaCa-2 cells, NSD2i, day5, H3K4me3, biol rep 2


title: MIA PaCa-2 cells, NSD2i, day9, H3K4me3, biol rep 1


title: sRNA-seq-gde1-1ov_rep2


title: HABA1


title: sRNA-seq-gde1-1ov_rep3


title: MIA PaCa-2  cells, NSD2i, day9 biol rep 3

data_processing:
Raw reads trimmed with CutAdapt
Trimmed reads mapped with STAR aligner
Feature counts extracted with featureCounts
TPM quantification with salmon
Assembly: hg38
Supplementary files format and content: gene counts

value: NSD2i 100nM


title: MIA PaCa-2 cells, NSD2i, day5, H3K4me3, biol rep 1


title: HABA3


title: GEKN5


title: MIA PaCa-2  cells, NSD2i, day9 biol rep 2


title: sRNA-seq-colov_rep3


title: sRNA-seq-gde1-1ov_rep1


title: MIA PaCa-2 cells, NSD2i, day1, H3K4me3, biol rep 2


title: MIA PaCa-2 cells, NSD2i, day1, H3K4me3, biol rep 1


title: GEKN7


title: MIA PaCa-2  cells, NSD2i, day9 biol rep 1


title: GEKN3


title: MIA PaCa-2 cells, DMSO, day9, H3K4me3, biol rep 2


title: sRNA-seq-colov_rep2


title: MIA PaCa-2 cells, DMSO, day9  biol rep 4

value: DMSO


title: GEKN1


title: sRNA-seq-colov_rep1


title: MIA PaCa-2 cells, DMSO, day9, H3K4me3, biol rep 1

value: MIA PaCa-2


title: only osteocyte-enriched subchondral bone; low stress area;1

description: Library name: ctr_1


title: GEDA7


title: ChIP-seq-VDD-3FLAG-rep2-clsy34

source_name: floral tissue

value: floral tissue

value: chip antibody:Anti-FLAG M2 (Sigma, F1804)


title: MIA PaCa-2 cells, DMSO, day9  biol rep 2

value: Pancreas epithelial Carcinoma


title: sRNA-seq-gde1-1ov-rep5


title: GEDA5

value: vastus lateralis muscle


title: MIA PaCa-2 cells, DMSO, day9  biol rep 1


title: MIA PaCa-2 cells, DMSO, day5, H3K4me3, biol rep 2


title: ChIP-seq-VDD-3FLAG-rep1-clsy34


title: MIA PaCa-2  cells, NSD2i, day9 biol rep 4


title: ChIP-seq-VDD-3FLAG-rep2

value: WT


title: MIA PaCa-2 cells, DMSO, day5, H3K4me3, biol rep 1


title: MIA PaCa-2 cells, DMSO, day1, H3K4me3, biol rep 2


title: MIA PaCa-2 cells, NSD2i, day5 biol rep 4


title: GEDA3

value: Skeletal Muscle

value: Female


title: GEDA1


title: MIA PaCa-2 cells, NSD2i, day5 biol rep 3


title: MIA PaCa-2 cells, DMSO, day1, H3K4me3, biol rep 1


title: ELLI7

value: CON


title: ChIP-seq-VDD-3FLAG-rep1


title: MIA PaCa-2 cells, DMSO, day9  biol rep 3


title: ChIP-seq-NPVDDZFcol-rep2


title: MIA PaCa-2 cells, NSD2i, day5 biol rep 1


title: ChIP-seq-GDE1_3FLAG-rep1


title: ELLI5


title: ELLI3


title: ChIP-seq-GDE1_3FLAG-rep2


title: MIA PaCa-2 cells, DMSO, day5 biol rep 3


title: MIA PaCa-2 cells, DMSO, day5 biol rep 4


title: ANLI7


title: PPD5 silent Ese1 neuron 8

city: Baton Rouge

first: Yanlin

last: He

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

description:
Library name: YH-Sample28
indexed and pooled samples, 75bp forward read

data_processing:
reads trimmed with cutadapt v.4.6; params: -a AAAAAAAAAAAAAAAAAAAA -m 20 -O 20 -n 1
reads trimmed with cutadapt v.4.6; params: -a AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 20 -O 3 -q 10
reads trimmed with cutadapt v.4.6; params: -a AAAAAAAAAAAAAAAAAA -m 20 -O 3
reads trimmed with cutadapt v.4.6; params: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 20 -O 20
reads aligned with STAR v.2.7.11a; params: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
features counted with htseq v.2.0.4
genes annotated with biomaRt v.2.58.0, R v4.3.2
differential expression analysis with DESeq2 v.1.42.0; R v4.3.2
Assembly: GRCm39, release 111
Supplementary files format and content: comma-delimited tsv; raw counts

source_name: brain

growth_protocol: 11-14 week old female mice

extract_protocol:
Single Esr1 neuron was collected after whole cell patch-clamp recording
Quant-Seq  3' mRNA-Seq Library Prep Kit

treatment_protocol: Recorded Esr1 neuron was treated with 100 nM PPT

value: brain

value: Esr1 positive neurons

tag: regroup

tag: batch


title: ChIP-seq-NPVDDZFcol-rep1

tag: tissue


title: PPD5 silent Ese1 neuron 6

description:
Library name: YH-Sample26
indexed and pooled samples, 75bp forward read


title: PPD5 silent Ese1 neuron 9

description:
Library name: YH-Sample29
indexed and pooled samples, 75bp forward read


title: ELLI1


title: ChIP-seq-Col_3FLAG-rep2

tag: cell line


title: PPD5 silent Ese1 neuron 7

description:
Library name: YH-Sample27
indexed and pooled samples, 75bp forward read


title: MIA PaCa-2 cells, DMSO, day5 biol rep 2

source_name: MIA PaCa-2


title: MIA PaCa-2 cells, NSD2i, day5 biol rep 2


title: ANLI5


title: MIA PaCa-2 cells, DMSO, day5 biol rep 1


title: PPD5 silent Ese1 neuron 5

description:
Library name: YH-Sample25
indexed and pooled samples, 75bp forward read


title: ChIP-seq-VDD-9myc-rep2

value: chip antibody:Anti-myc (cell signaling, 2278S)


title: PPD5 silent Ese1 neuron 10

description:
Library name: YH-Sample30
indexed and pooled samples, 75bp forward read


title: MIA PaCa-2 cells, NSD2i, day1 biol rep 4


title: PPD5 silent Ese1 neuron 4

description:
Library name: YH-Sample24
indexed and pooled samples, 75bp forward read


title: ANLI3

value: SLEEP


title: MIA PaCa-2 cells, NSD2i, day1 biol rep 3


title: ChIP-seq-VDD-9myc-gde1-rep2


title: PPD5 silent Ese1 neuron 2

description:
Library name: YH-Sample22
indexed and pooled samples, 75bp forward read


title: FaDu_smoke_radiation_3

city: Townsville

first: Lionel

last: Hebbard

state: QLD

address: 1 James Cook Dr, Douglas QLD 4811

institute: James Cook University

data_processing:
The RNA-seq data passed the quality control conducted using FastQC and MulitQC
Sequencing reads were mapped to the human reference genome GRCh38.p13 (NCBI) using RSEM/1.3.1 with bowtie2
Alignment passed quality control using MultiQC
.genes.results files imported to r using Bioconductor/tximport/1.18.0 and normalisation performed using Bioconductor/DESeq2/1.30.0
Assembly: GRCh38.p13
Supplementary files format and content: DESeq2_normalised_genes.csv: Comma separated file containing gene names in the first column followed by a column of DESeq2-normalised counts for each sample
Supplementary files format and content: RSEM/Bowtie2 output of transcript quantification. A tab separated file with the following columns: gene_id; transcript_id(s); length; effective_length; expected_count; TPM; FPKM

source_name: Pharynx

extract_protocol:
RNA was isolated from treated cells with an Isolate II RNA Mini Kit (Bioline) and RNA integrity checked with an Agilent TapeStation. All RIN scorces exceeded 9.8.
TruSeq mRNA Library Prep with polyA selection and unique dual indexing, sequencing on the Illumina NovaSeq 6000, 100bp Paired-End, 20M read pairs.

value: Pharynx

value: FaDu

value: Squamous Cell Carcinoma Cell

value: Wild-Type

value: Smoke and Radiation


title: MIA PaCa-2 cells, NSD2i, day1 biol rep 2

value: MIA PaCa-2

value: NSD2i 100nM


title: ChIP-seq-VDD-9myc-gde1-rep1

value: floral tissue


title: FaDu_smoke_radiation_1


title: ANLI1

value: vastus lateralis muscle


title: ChIP-seq-VDD-9myc-rep1

value: WT


title: ChIP-seq-VAL-9myc-rep2


title: MIA PaCa-2 cells, NSD2i, day1 biol rep 1

value: Pancreas epithelial Carcinoma


title: FaDu_radiation_3

value: Radiation


title: PPD5 silent Ese1 neuron 1

description:
Library name: YH-Sample21
indexed and pooled samples, 75bp forward read


title: ChIP-seq-VAL-9myc-rep1


title: PPD5 spontaneous firing Esr1 neuron 10

description:
Library name: YH-Sample20
indexed and pooled samples, 75bp forward read


title: PPD5 spontaneous firing Esr1 neuron 9

description:
Library name: YH-Sample19
indexed and pooled samples, 75bp forward read


title: MIA PaCa-2 cells, DMSO, day1 biol rep 4

value: DMSO


title: ChIP-seq-Col_3FLAG-rep1

value: chip antibody:Anti-FLAG M2 (Sigma, F1804)


title: FaDu_radiation_2


title: PPD5 spontaneous firing Esr1 neuron 8

description:
Library name: YH-Sample18
indexed and pooled samples, 75bp forward read

value: brain

value: Esr1 positive neurons


title: MIA PaCa-2 cells, DMSO, day1 biol rep 2


title: ChIP-seq-REM22-9myc-rep1

value: chip antibody:Anti-myc (cell signaling, 2278S)


title: FaDu_radiation_1

value: Pharynx


title: MIA PaCa-2 cells, DMSO, day1 biol rep 1


title: PPD5 silent Ese1 neuron 3

description:
Library name: YH-Sample23
indexed and pooled samples, 75bp forward read


title: PPD5 spontaneous firing Esr1 neuron 7

description:
Library name: YH-Sample17
indexed and pooled samples, 75bp forward read


title: FaDu_smoke_radiation_2

value: FaDu


title: FaDu_smoke_3

value: Squamous Cell Carcinoma Cell

value: Smoke


title: Ctrl2

city: Taipei

first: Chien-Wei

last: Lee

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

data_processing:
RNA was extracted by TRIzol method. NanoDrop (Thermo Fisher Scientific) and the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) were used to determine RNA content and quality. Samples with an OD260/OD230 > 1.8, OD260/OD280 ratios around 2.0 were subjected to small RNA sequencing on the DNBSEQ platform (BGI Genomics, Shenzhen, China), with an average yield of 31.55 M reads per sample. The results were analyzed by BGI. Briefly, fastQC software was used to conduct the quality control of the raw data. After impurities in raw data were filtered out, we used Bowtie2 to align the clean reads to the reference genome (GCF_000001405.39_GRCh38.p13). Total Mapping percentage around 86.9-91.6% in samples, with an average 89.54%. A total of 361 miRNAs were detected. To identify the differentially expressed (DE) miRNAs, we applied the criteria of an FDR value of 0.001 and a fold-value change of ≥ 2. For the target prediction, we used QIAGEN Ingenuity Pathway Analysis (QIAGEN, Hilden, Germany) with database
Assembly: Bowtie2, GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: EVs from naïve human adipose tissue-derived MSCs

growth_protocol: hADSCs were selected as the cell source of EVs in this study. hADSCs were cultured in 10-cm dishes at a cell density of 1x106 cells/cm2 with serum culture medium (α-MEM, 10% FBS, 10 ng/mL bFGF and 1% PSG) for 3 days.

extract_protocol: hADSC and BG-primed hADSC CM were concentrated using Vivaspin 20 centrifugal concentrator at 2,000 g at 4 °C. Then, the concentrated supernatant solution (around 200 μL left in the concentrator) was collected and added with Exo-Prep solution in a ratio of 1:1. The mixed solution was incubated on ice for 1 hour, then the solution was centrifuged for 20 minutes at 10,000 g at 4 °C to obtain EV pellets.

treatment_protocol: Then, hADSC culture medium was changed by serum-free medium (α-MEM, 10 ng/mL bFGF and 1% PSG) with or without BG stimulation for 48 hours, followed by collection, and then centrifuged at 3,000 g for 10 minutes at 4 °C to remove cellular debris.

tag: evs from

value: naïve human adipose tissue-derived MSCs

value: untreated


title: FaDu_smoke_2

tag: cell type

value: Wild-Type


title: ChIP-seq-REM19-9myc-rep2

value: floral tissue

tag: genotype


title: ChIP-seq-REM19-9myc-rep1


title: PPD5 spontaneous firing Esr1 neuron 6

description:
Library name: YH-Sample16
indexed and pooled samples, 75bp forward read


title: MIA PaCa-2 cells, DMSO, day1 biol rep 3

value: MIA PaCa-2

tag: treatment


title: FaDu_smoke_1


title: ChIP-seq-REM13-9myc-rep2

value: WT


title: PPD5 spontaneous firing Esr1 neuron 4

description:
Library name: YH-Sample14
indexed and pooled samples, 75bp forward read


title: PPD5 spontaneous firing Esr1 neuron 5

description:
Library name: YH-Sample15
indexed and pooled samples, 75bp forward read


title: BG1

source_name: EVs from bioglass-primed human adipose tissue-derived MSCs

value: bioglass treatment


title: ChIP-seq-REM13-9myc-rep1


title: PPD5 spontaneous firing Esr1 neuron 3

description:
Library name: YH-Sample13
indexed and pooled samples, 75bp forward read


title: FaDu_control_3


title: FaDu_control_2


title: PBS 24 hours

city: Zurich

first: Maries

last: van den Broek

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description: control

data_processing:
read alignment, cell barcode demultiplexing, deduplication of reads, generation of expression matrices and quality report were done using the Rhapsody Sequence Analysis Pipeline v2.0 (https://www.bdbiosciences.com/en-us/products/software/rhapsody-sequence-analysis-pipeline)
Assembly: mm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: liver

extract_protocol:
Livers were harvested in RPMI supplemented with 10% FCS and digested with collagenase IV (1 mg/ml, Thermo Fisher Scientific) and DNase I (50 µg/ml, Roche) for 45 minutes at 37°C on a rotating device. Cells were washed with PBS containing 2 mM EDTA and filtered through a 70-µm strainer (Biologix). Red blood cells were lysed using a red blood cell lysis buffer (17 mM Tris pH 7.2, 144 mM NH4Cl) for 2 minutes and cells were washed with PBS. Lymphocyte enrichment was performed using a density gradient centrifugation step (Percoll, Sigma-Aldrich).
Library amplification was carried out following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (Doc ID: 23-24119 (02))

value: liver

value: female

tag: age

value: 12 weeks old

value: NKT cells

value: PBS


title: ChIP-seq-REM8-9myc_rep2

value: chip antibody:Anti-myc (cell signaling, 2278S)


title: FaDu_control_1

value: Pharynx


title: ChIP-seq-REM22-9myc-rep2


title: PPD5 spontaneous firing Esr1 neuron 2

description:
Library name: YH-Sample12
indexed and pooled samples, 75bp forward read

value: brain

value: Esr1 positive neurons


title: PPD5 spontaneous firing Esr1 neuron 1

description:
Library name: YH-Sample11
indexed and pooled samples, 75bp forward read


title: APTKA 24 hours

description: metastasis

value: APTKA


title: virgin D phase spontaneous firing Esr1 neuron 10

description:
Library name: YH-Sample10
indexed and pooled samples, 75bp forward read


title: ChIP-seq-PolIV-9myc-gde1_rep2


title: N_HFD.LNAME [7411]

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry road

department: Cardiovascular Medicine

description: RNA-sequencing analysis

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --unpaired, --trim1
Trimmed reads were then aligned with STAR (2.6) to Gencode hg38 reference genome with parameters: $STAR_RUN --genomeDir $GENOME_DIR --readFilesCommand zcat --readFilesIn $INPUT_DIR/fastq/${VAR}.txt.gz --sjdbGTFfile $GENOME_DIR/gencode.v28.annotation.gtf --sjdbOverhang 99 --quantMode GeneCounts --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${RESULTS_DIR}/Alignment/${VAR}_
DESeq2 (1.22.1) within R (3.2.1) was then run to get to final differential expression results comparing failing (HF) to non-failing (NF) hearts.
Assembly: c57bl_6NJ_107.gtf
Supplementary files format and content: .xlsx file containing differentially expressed genes based on HFD-LNAME versus Normal Chow

source_name: Heart - Left Ventricle

extract_protocol:
Left ventricle samples were removed, flash frozen on dry ice, and RNA was harvested using RNEasy® Fibrous tissue reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12-wk-old mice subjected to either HFD-LNAME diet or normal chow for 9 weeks.

value: Heart - Left Ventricle

value: HFD-LNAME


title: sRNA_gde1ov3_for_mutantGDE1

description: Library name: GSM124

data_processing:
Adaptor sequence (TGGAATTCTCGG) of small RNA-seq reads were trimmed with trim_galore, and trimmed reads were mapped to the reference genome TAIR10 using Bowtie2 with only one unique hit and zero mismatches. sRNA reads that mapped to chloroplast, mitochondrial DNA, tRNA, rRNA, small nucleolar RNAs (snoRNAs), and small nuclear RNAs (snRNAs) were removed using bedtools (v2.26.0). The deeptools version 3.1.3 was used to generate Bigwig tracks. The bamCoverage of deeptools version 3.1.3 was used to normalize the data with RPKM57.
Assembly: tair10
Supplementary files format and content: bigwig

extract_protocol:
Pistils and anther (stage 9 or younger) of each genotype were collected and ground into fine powder with liquid nitrogen. Total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo) according to the manufacturer’s instructions. Two micrograms of total RNA were mixed with equal volume of the 2x RNA loading dye, denatured at 65◦C for 10 min and immediately chilled on ice. Denatured total RNA was separated on 15% TBE urea gel (Invitrogen) and small RNAs from 15-30 nts were excised. The excised gel pieces were mashed by pestles. Small RNA was eluted with 400 uL nuclease-free water at 70◦C for 10 mins and then precipitated with ethanol.
Small RNA libraries were made using NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) according to the manufacturer’s instructions

value: unfertilized ovules (Ov)

tag: ecotype


title: N_HFD.LNAME [7410]

description: RNA-sequencing analysis


title: Ctrl1

value: naïve human adipose tissue-derived MSCs

value: untreated


title: ChIP-seq-PolIV-9myc-gde1_rep1

value: floral tissue


title: BG2

value: bioglass-primed human adipose tissue-derived MSCs

value: bioglass treatment


title: virgin D phase spontaneous firing Esr1 neuron 9

description:
Library name: YH-Sample09
indexed and pooled samples, 75bp forward read


title: N_HFD.LNAME [7370]

description: RNA-sequencing analysis


title: sRNA_gde1ov2_for_mutantGDE1

description: Library name: GSM123


title: ChIP-seq-PolIV-9myc_rep2

value: WT


title: virgin D phase spontaneous firing Esr1 neuron 8

description:
Library name: YH-Sample08
indexed and pooled samples, 75bp forward read


title: sRNA_gde1ov1_for_mutantGDE1

description: Library name: GSM122


title: N_HFD.LNAME [7336]

description: RNA-sequencing analysis


title: ChIP-seq-PolIV-9myc_rep1


title: virgin D phase spontaneous firing Esr1 neuron 7

description:
Library name: YH-Sample07
indexed and pooled samples, 75bp forward read


title: N_CON [7445]

description: RNA-sequencing analysis

value: Normal Chow


title: ChIP-seq-CLSY4-9myc-gde1-rep2


title: virgin D phase spontaneous firing Esr1 neuron 6

description:
Library name: YH-Sample06
indexed and pooled samples, 75bp forward read


title: sRNA_GDE1E251AY252AY255A_in_gde1ov2

description: Library name: GSM120


title: sRNA_GDE1E251AY252AY255A_in_gde1ov3

description: Library name: GSM121


title: N_CON [7426]

description: RNA-sequencing analysis


title: ChIP-seq-CLSY4-9myc-gde1-rep1


title: ChIP-seq-REM8-9myc_rep1


title: sRNA_GDE1E251AY252AY255A_in_gde1ov1

description: Library name: GSM119


title: N_CON [7424]

description: RNA-sequencing analysis


title: virgin D phase spontaneous firing Esr1 neuron 5

description:
Library name: YH-Sample05
indexed and pooled samples, 75bp forward read


title: ChIP-seq-CLSY3-9myc-gde1-rep2


title: virgin D phase spontaneous firing Esr1 neuron 4

description:
Library name: YH-Sample04
indexed and pooled samples, 75bp forward read


title: sRNA_WTGDE1_in_gde1ov3

description: Library name: GSM118


title: N_CON [7331]

description: RNA-sequencing analysis


title: ChIP-seq-CLSY3-9myc-gde1-rep1


title: virgin D phase spontaneous firing Esr1 neuron 3

description:
Library name: YH-Sample03
indexed and pooled samples, 75bp forward read


title: virgin D phase spontaneous firing Esr1 neuron 2

description:
Library name: YH-Sample02
indexed and pooled samples, 75bp forward read


title: virgin D phase spontaneous firing Esr1 neuron 1

description:
Library name: YH-Sample01
indexed and pooled samples, 75bp forward read


title: ChIP-seq-CLSY4-9myc-rep2


title: sRNA_suvh456ov3

description: Library name: GSM115


title: Arabidopsis, hira-1_H3.3_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_hira-1_H3.3_3xFlag_Rep2,ChIP

data_processing:
ChIP-seq reads were trimmed using the fastp tool (version 0.23.4)  with a quality score threshold of 20 for the final base.Reads shorter than 35 bp after trimming were discarded.
The clean reads were aligned to the TAIR 10 genome(https://www.arabidopsis.org/) using Bowtie2 with default parameters.
To create ChIP-Seq coverage plots,the locations of the mapped ChIP-Seq reads were extended to the ChIP length form Cross-Correlation analysis, RPGC (reads per genome coverage) normalized and reformatted in the BigWig file format.
Peaks were identified utilizing the 'callpeak' function of MACS2 (version 3.0.1).
Assembly: TAIR 10
Supplementary files format and content: BigWig files were generated by using the Deeptools  (version 3.5.2).The BigWig files for making plot were  assessed by merging results from 'bigwigcompare' of two independent biological replicates, employing the 'mean' operation.

source_name: 12DAG seedling

growth_protocol: Plants were grown on GM in a growth chamber under long-day conditions supplemented with 1% sucrose under long-day photoperiod and ~21°C. Seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
Tissue was fixed with 1% formaldehyde for 12mins and stopped by adding glycine to a final concentration of 0.125M and incubating for 6 extra mins.After nuclear lysis,chromatin was sonicated using using Bioruptor® Pico with the following conditions: 14 cycles,10 sec ON/30 sec OFF at 4°C.
ChIP-Seq libraries were prepared using Ovation® Ultralow System V2 Library Preparation Kit (PART NO. 0344, 0344NB).

value: 12DAG seedling

tag: chip antibody

value: Flag antibody (Sigma, F3165)


title: sRNA_suvh456ov2

description: Library name: GSM114

source_name: unfertilized ovules (Ov)


title: Arabidopsis, H3.1_H3.3_3xFlag, 12DAG, INPUT

description: Library name: 12DAG_H3.1_H3.3_3xFlag,INPUT


title: ChIP-seq-CLSY3-9myc-rep2

value: chip antibody:Anti-myc (cell signaling, 2278S)


title: sRNA_WTGDE1_in_gde1ov1

description: Library name: GSM116


title: Arabidopsis, hira-1_H3.3_3xFlag, 12DAG, Rep1

description: Library name: 12DAG_hira-1_H3.3_3xFlag_Rep1,ChIP


title: ChIP-seq-CLSY4-9myc-rep1


title: sRNA_suvh456ov1

description: Library name: GSM113


title: ChIP-seq-CLSY3-9myc-rep1


title: EP mouse prostate organoids, sgERG, Luminal sort, Rep C

city: Philadelphia

first: Weiran

last: Feng

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description:
Library name: sgERG-Lum-Rep C
E-C-L

data_processing:
Raw reads were aligned to mm10 genome using STAR
Raw counts in each known gene from the Ensembl database were enumerated using htseq-count from the HTSeq package
Assembly: mm10
Supplementary files format and content: raw count for all samples in csv format

source_name: prostate

extract_protocol:
RNA was preserved and extracted by Trizol
RNA libraries for RNA-seq were prepared at Integrated Genomics Operation core at MSKCC using SMARTerAmpSeq following manufacturer’s protocols

value: prostate

value: EP

value: organoids

value: ERG+PTEN-

value: sgERG; luminal sort


title: ChIP-seq-Col-9myc-rep2


title: EP mouse prostate organoids, sgERG, Basal sort, Rep C

description:
Library name: sgERG-Bas-Rep C
E-C-B

value: sgERG; basal sort


title: Arabidopsis, fas2-4_H3.3_3xFlag, 12DAG, Rep1

description: Library name: 12DAG_fas2-4_H3.3_3xFlag_Rep1,ChIP


title: EP mouse prostate organoids, sgERG, Basal sort, Rep B

description:
Library name: sgERG-Bas-Rep B
E-B-B


title: Arabidopsis, Columbia-0_H3.3_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_Columbia-0_H3.3_3xFlag_Rep2,ChIP


title: sRNA_clsy12ov3

description: Library name: GSM112

value: unfertilized ovules (Ov)


title: sRNA_clsy12ov2

description: Library name: GSM111


title: sRNA_WTGDE1_in_gde1ov2

description: Library name: GSM117


title: Evs from osteocyte-enriched subchondral bone; high stress area;3

description: Library name: YING_3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
For the samples with biological replicates:Differential expression analysis of two conditions/groups was performed using the DESeq R package (3.0.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P value of 0.05 was set as the threshold for significantly differential expression by default.
Assembly: homo_sapiens_Ensembl_97
Supplementary files format and content: tab-delimited file includes raw counts for each sample

extract_protocol:
The purification of total exosome-derived RNA was carried out by the exoRNeasy Maxi Kit (Qiagen).
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: osteocyte-enriched subchondral bone

value: high stress area


title: Arabidopsis, Columbia-0_H3.3_3xFlag, 12DAG, Rep1

description: Library name: 12DAG_Columbia-0_H3.3_3xFlag_Rep1,ChIP


title: EP mouse prostate organoids, sgERG, Basal sort, Rep A

description:
Library name: sgERG-Bas-Rep A
E-A-B


title: sRNA_clsy12ov1

description: Library name: GSM110


title: Arabidopsis, hira-1_H3.1_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_hira-1_H3.1_3xFlag_Rep2,ChIP


title: Evs from osteocyte-enriched subchondral bone; high stress area;2

description: Library name: YING_2


title: EP mouse prostate organoids, sgERG, Luminal sort, Rep A

description:
Library name: sgERG-Lum-Rep A
E-A-L


title: Arabidopsis, fas2-4_H3.3_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_fas2-4_H3.3_3xFlag_Rep2,ChIP


title: EP mouse prostate organoids, sgNT, Basal sort, Rep C

description:
Library name: sgNT-Bas-Rep C
N-C-B

value: sgNT; basal sort


title: EP mouse prostate organoids, sgNT, Luminal sort, Rep C

description:
Library name: sgNT-Lum-Rep C
N-C-L

value: sgNT; luminal sort


title: sRNA_colov2_for_suvh456_c12

description: Library name: GSM108


title: EVs  from osteocyte-enriched subchondral bone; low stress area;3

description: Library name: FEI_3

value: low stress area


title: Evs from osteocyte-enriched subchondral bone; high stress area;1

description: Library name: YING_1


title: Arabidopsis, fas2-4_H3.1_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_fas2-4_H3.1_3xFlag_Rep2,ChIP


title: sRNA_colov1_for_suvh456_c12

description: Library name: GSM107

value: WT


title: sRNA-seq-rem8ov3

description: Library name: GSM106


title: Arabidopsis, fas2-4_H3.1_3xFlag, 12DAG, Rep1

description: Library name: 12DAG_fas2-4_H3.1_3xFlag_Rep1,ChIP


title: Arabidopsis, Columbia-0_H3.1_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_Columbia-0_H3.1_3xFlag_Rep2,ChIP


title: ChIP-seq-Col-9myc-rep1

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45. BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T).
Assembly: tair10
Supplementary files format and content: bigWig, narrowpeak

extract_protocol:
For ChIP-seq experiments, 1~2 g of unopen flower buds  from the T2 lines were collected. For sRNA-seq and WGBS, ovule or anther tissues (stage 9 or earlier) from 5- to 6-week-old plants were harvested.
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. Whole genome bisulfite sequencing libraries were prepared using the Nugen Ultralow Methyl Kit. RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina).  Libraries were sequenced on NovaSeq 6000 (Illumina).

value: floral tissue


title: EP mouse prostate organoids, sgERG, Luminal sort, Rep B

description:
Library name: sgERG-Lum-Rep B
E-B-L


title: EP mouse prostate organoids, sgNT, Luminal sort, Rep B

description:
Library name: sgNT-Lum-Rep B
N-B-L


title: Arabidopsis, fas2-4, 12DAG, Group2, Rep3

description:
Library name: 12DAG_fas2-4_Group2_R3
Treatment

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).
The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Quantification was performed with Rsubread package (version 2.12.0) and normalized using TPM (Transcripts Per Kilobase of exon model per Million mapped reads).
Assembly: TAIR 10
Supplementary files format and content: Tab-delimited text includes raw counts for each sample.
Supplementary files format and content: Txt files include TPM values for each sample.

extract_protocol:
total RNA was extracted by using RNA extraction  columns (Axygen, UE-MN-MS-RNA-250) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.

value: 12DAG seedling


title: sRNA-seq-rem8ov2

description: Library name: GSM105


title: Arabidopsis, Columbia-0_H3.1_3xFlag, 12DAG, Rep1

description: Library name: 12DAG_Columbia-0_H3.1_3xFlag_Rep1,ChIP

value: Flag antibody (Sigma, F3165)


title: EP mouse prostate organoids, sgNT, Basal sort, Rep B

description:
Library name: sgNT-Bas-Rep B
N-B-B


title: sRNA-seq-rem8ov1

description: Library name: GSM104


title: EP mouse prostate organoids, sgNT, Basal sort, Rep A

description:
Library name: sgNT-Bas-Rep A
N-A-B


title: EVs  from osteocyte-enriched subchondral bone; low stress area;1

description: Library name: FEI_1


title: Arabidopsis, fas2-4_FAS2_3xFlag, 12DAG, INPUT

description: Library name: 12DAG_fas2-4_FAS2_3xFlag,INPUT


title: Arabidopsis, fas2-4, 12DAG, Group2, Rep2

description:
Library name: 12DAG_fas2-4_Group2_R2
Treatment


title: sRNA-seq-colov3_for_rem8ov

description: Library name: GSM103


title: EP mouse prostate organoids, sgNT, Luminal sort, Rep A

description:
Library name: sgNT-Lum-Rep A
N-A-L


title: sRNA_colov3_for_suvh456_c12

description: Library name: GSM109


title: Arabidopsis, hira-1_H3.1_3xFlag, 12DAG, Rep1

description: Library name: 12DAG_hira-1_H3.1_3xFlag_Rep1,ChIP


title: Arabidopsis, hira-1,fas2-4_FAS2_3xFlag, 12DAG, Rep2

description: Library name: 12DAG_hira-1,fas2-4_FAS2_3xFlag_Rep2,ChIP