title: Scr_1

value: Mecp2-Luciferase Fibroblast


title: Donor B DP 7

status: Public on Nov 12 2025

type: SRA

city: Muenster

first: Markus

last: Fehrholz

address: Mendelstr. 17

country: Germany

institute: Monasterium Laboratory GmbH

library_source: transcriptomic

data_processing:
Sequencing was performed on a NovaSeq 6000 using 2x100 bp read length with an output of appr. 50 M clusters (10 Gb) per sample.
Demultiplexing: Illumina bcl2fastq v2.20; adapter trimming: Skewer v0.2.2; Pico v2 SMART adapter trimming: Cutadapt v1.12.
Quality trimming of the reads was not performed. The quality of the FASTQ files was analyzed with FastQC v0.11.9.
Trimmed raw reads were aligned to a GRCh38.105 reference using STAR (version 2.7.10a). Only samples with a mapping rate > 50% and a phred score > 30 were included in the analysis.
Normalized counts were created using DESeq2 v1.28.1 in R v4.0.2.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: hair follicle

extract_protocol:
Total RNA was isolated from hair follicle tissue collected via laser capture microdissection using the PicoPure™ RNA-Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol.
Library preparation was performed using the SMART-Seq® stranded total RNA kit (Takara Bio, USA) according to the manufacturer's protocol with a maximal input of 7 µL.

tag: tissue

value: hair follicle

tag: compartment

value: DP

tag: Sex

value: male

tag: treatment

value: untreated


title: Donor B gHM 7

value: gHM


title: CAMA1_WT_Abema_n3

city: Montréal

first: Robin

last: Minati

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: Library name: CAMA1_WT_Abema_n3

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 33 (based on Ensembl 99)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

tag: cell line

tag: cell type

value: HR+ BC cell line

tag: genotype

value: WT

value: 50nM Abemaciclib for 96h

tag: strand

value: forward


title: Mecp2 Pool 1

city: New York

first: Richard

last: Pan

address: 1150 St Nicholas Ave

country: USA

institute: Columbia University

data_processing:
low quality reads were filtered using fastQC
reads comparing Pcsk9 vs Scr samples were mapped to either mm39 using Hisat2 v2.0.5, reads comparing Mecp2 Pool to Scr samples were mapped to mm10 using STAR 2.5.0a
normalized read count data was obtained using featureCounts v1.5.0-p3
Assembly: mm39, mm10
Supplementary files format and content: tab-delimited text file contains normalized counts data for Pcsk9 vs Scr samples
Supplementary files format and content: tab-delimited text file contains normalized counts data for Mecp2 Pool vs Scr samples

organism: Mus musculus

source_name: Mecp2-Luciferase Fibroblast

growth_protocol: Mecp2-Luciferase fibroblasts were cultured in DMEM supplemented with 10% CCS and antibiotics in 37C with 5% CO2

extract_protocol:
RNA was extracted using Zymo Direct-zol RNA miniprep kit
mRNA was purified from total RNA using poly-T beads and fragmented, then reverse transcribed into cDNA. Adapters were then ligated and PCR amplified with specified indices before sequencing

value: Fibroblast

value: Mecp2 Pool sgRNAs


title: DNV_VEH_6

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Library name: DNV_VEH_6

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (TrimGalore), then mapped to mRatBN7.2.112 whole genome using STAR 2.7.3a with default parameters. Count matrices were generated using featureCounts v2.0.3 (-B -C -t exon -p --countReadPairs -s 2) and DESeq2 1.44 used to calculate normalized counts and perform differential expression analysis.
Assembly: mRatBN7.2.112
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text files includes DESeq2 normalized counts for all samples
Supplementary files format and content: tab-delimited text files includes differential gene expression analysis output from DESeq2

organism: Rattus norvegicus

source_name: Skeletal muscle (diaphragm)

extract_protocol:
Total RNA was extracted from the diaphragm using TRIzol (Life Technologies, Carlsbad, CA). RNA integrity was analyzed using Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).
Approximately ~1 ug of sample total RNA was used for cDNA library preparation performed according to the Illumina mRNA stranded poly-A tail enrichment Kit manufacturer’s instructions (Illumina, San Diego, CA). RNA sequencing was carried out using the Illumina NextSeq 2000 (NextSeq 2x100pb, 8.4-13.9 million paired-end reads depth).

tag: strain

value: Wistar

value: Skeletal muscle (diaphragm)

value: Unilateral diaphragm denervation 12 h + vehicle


title: DNV_VEH_8

description: Library name: DNV_VEH_8


title: CAMA1_WT_Abema_n2

description: Library name: CAMA1_WT_Abema_n2


title: Scr 2

source_name: Liver

value: Liver

value: LSL-dC-D

value: Scr sgRNA


title: Scr 3


title: Donor B DC 7

value: hair follicle

value: DC


title: CAMA1_WT_Abema_n1

description: Library name: CAMA1_WT_Abema_n1


title: DNV_VEH_4

description: Library name: DNV_VEH_4

value: male


title: DNV_VEH_3

description: Library name: DNV_VEH_3


title: CAMA1_WT_DMSO_n4

description: Library name: CAMA1_WT_DMSO_n4

value: DMSO for 96h


title: Scr 1


title: CAMA1_WT_DMSO_n3

description: Library name: CAMA1_WT_DMSO_n3


title: Donor J bORS 2

value: bORS

value: female

value: untreated


title: siEln2

city: New Haven

first: Junichi

last: Saito

state: CT

address: 300 George Street, 7th Floor

department: Internal Medicine

institute: Yale University

description: Sample 5

data_processing:
BOWTIE2 was used to align trimmed reads to the reference genome (hg19). Annotation was done using Ensembl release 75. Differential analysis was performed with DESeq2
Assembly: hg19
Supplementary files format and content: tab-determined text file includes raw counts for each Sample

source_name: Aorta

growth_protocol: Human aortic smooth muscle cells were maintained in M199 medium supplemented with 10% fetal bovine serum, epidermal growth factor (3 µg/ml), and fibroblast growth factor (2 µg/ml) (PeproTech).

extract_protocol:
RNA was harvested using RNA lysis buffer (Qiagen, 7400)
RNA libraries for RNA-seq were prepared using mRNA-seq library Prep Kit (Roche Kapa mRNA Hyper Prep Cat# KR1352) following manufacturer's protocols.

treatment_protocol: Human aortic smooth muscle cells were transfected with Lipofectamine 2000 (Life Technologies) containing Scr RNA or siRNA targeting elastin (Horizon Discovery Biosciences Limited, 50 nM) for 6 hours. Cells were then washed in M199 medium and cultured for 72 hours prior to collection for bulk RNA-seq.

value: Aorta

value: Primary cells

value: SMCs

value: Silencing of ELN

value: siRNA targetting ELN


title: siEln3

description: Sample 6


title: Pcsk9 1

value: Pcsk9 sgRNAs


title: HSC, DCV, rep2

city: Cleveland

first: Xianfang

last: Wu

state: Ohio

address: 9500 Euclid Avenue/NE20, Office NE2-308, Office NE2-308

department: Infection Biology

institute: Cleveland Clinic

description:
Library name: Sample 4
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were processed with Cell Ranger v6.0.1 on Cleveland Clinic’s HPC. Reads were aligned to the mm10 genome using STAR, and UMI counts were extracted to generate expression matrices.
Expression matrices were imported into Seurat v4.3.0 in R. Quality control, normalization, PCA, UMAP, clustering, and DE analysis were performed. Four samples (DMSO-1/2, DCV-1/2) were integrated into one final object.
The final Seurat object was uploaded to BioTuring for visualization and interpretation.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38)
Supplementary files format and content: integrated Seurat object (.rds) files; single cell expression data of the samples

growth_protocol: hiPSC-derived hepatocytes, hepatic stellate cells, and macrophages were differentiated separately and assembled into a coculture. Cocultures were maintained in a basal maintenance medium (BMM) that is consisted of glucose-free DMEM supplemented with 4% knockout serum replacement (KOSR), 2% B-27, 3U/ml heparin, 200μg/ml Transferrin, 30ng/ml EGF, 5μM retinol, and 0.5μM dexamethasone. Cocultures were placed on an orbital shaker platform at a speed of 30 rpm/min, with fresh medium replenished every two days.

extract_protocol:
Cocultures were gently washed with Versene and incubated in Versene at 37°C for 20–25 minutes to loosen cell contacts. After washing with pre-warmed DMEM/F12, cells were incubated with a pre-warmed collagenase mix (2.0 mg/mL collagenase, 1.0 mg/mL dispase, 100 U/mL DNase I, and 0.2% DMSO in HBM) at 37°C for 35–40 minutes, with gentle pipetting to aid dissociation. The cell suspension was then collected in Versene and centrifuged at 400 × g for 5 minutes. Cells were resuspended in Versene and incubated again at 37°C for 45 minutes, resulting in mostly single cells. To separate hepatocytes from HSCs, the single-cell suspension was blocked with 1% BSA on ice for 1 hour, stained with mouse anti-ASGR1 antibody, and incubated with anti-mouse IgG magnetic microbeads. Magnetic separation was performed at 4°C. Hepatocytes were collected from the magnet-bound fraction, while HSCs were collected from the flow-through after a second round of hepatocyte depletion.
Library preparation was performed according to the manufacturer’s instructions (Single Cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded, along with partitioning oil and gel beads, into the chip to generate gel bead-in-emulsions (GEMs). The poly-A RNA from lysed cells within each GEM was reverse transcribed into cDNA, incorporating an Illumina Read 1 primer sequence, a Unique Molecular Identifier (UMI), and a 10x barcode. The pooled, barcoded cDNA was then purified using Silane DynaBeads, amplified by PCR, and size-selected using SPRIselect reagent to enrich for fragments ranging from 300 to 700 base pairs for subsequent library construction.
The returned Fastq files of DMSO and DCV samples (DMSO-1, DMSO-2, DCV-1, and DCV-2) were analyzed with Cell Ranger and converted to Seurat objects by running the corresponding scRNA-seq codes that have been published in github and provided by the Cleveland Clinic Center for Immunotherapy and Precision Immuno-Oncology (CITI) on the Cleveland Clinic’s internal High Performance Computing (HPC) platform. The final integrated Seurat object generated from the four Fastq files was uploaded to BioTuring for analysis.

treatment_protocol: Cocultures were infected with HCVcc for 6 days before being treated with either DMSO or DCV (daclatasvir, 10nM) for additional 12 days before cocultured hepatoyctes were depleted. The remaining HSCs were subject to single cell RNA sequencing analysis.

value: hiPSC-Hepatic stellate cells

value: stellate cells

value: Daclatasvir


title: Sham_2

description: Library name: Sham_2

value: Wistar

value: Skeletal muscle (diaphragm)

value: WT

value: Sham-operated


title: Pcsk9 3

value: Liver

value: LSL-dC-D


title: Donor B HM2 6

value: hair follicle

value: male


title: CAMA1_WT_DMSO_n2

description: Library name: CAMA1_WT_DMSO_n2

value: HR+ BC cell line

value: DMSO for 96h

value: forward


title: Pcsk9 2


title: Sham_5

description: Library name: Sham_5


title: HSC. DCV, rep1

description:
Library name: Sample 3
10x Genomics


title: Scr3

description: Sample 3

value: Aorta

value: Primary cells

value: SMCs

value: Control

value: Scramble RNA


title: siEln1

description: Sample 4

value: Silencing of ELN

value: siRNA targetting ELN


title: Scr2

description: Sample 2


title: Eln(-/-) SMCs, e15.5_5

description: Sample 10

data_processing:
Adapters were trimmed with Cutadapt112, alignment was done using mm10 as reference with STAR - 2.7.3a , annotation done using Ensembl release 100, differential analysis done with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-determined text file includes raw counts for each sample.

growth_protocol: Isolated smooth muscle cells were subjected to RNA extraction

extract_protocol:
RNA was harvested using RNA lysis buffer (Qiagen, 7400)
RNA libraries for RNA-seq were prepared using mRNA-seq library Prep Kit (NEB Low Input E6420L) following manufacturer's protocols.

treatment_protocol: No treatment was performed.

value: Smooth muscle cells

value: Non


title: Hey shZKSCAN3_RNA-seq_2

city: Wuhan

first: suli

last: LV

address: Wuhan, Hubei, China

country: China

institute: Huazhong University of Science and Technology

description:
ZKSCAN3-KD_featureCounts_raw reads.txt
ZKSCAN3-KD_featureCounts_raw reads.txt

data_processing:
Raw reads were first filtered with Trim-Galore
Reads were aligned by STAR to human hg38 assembly with the Gencode V39 genome annotation.
Alignments with MAPQ > 10 were kept
Bam files were then further filtered with 'RmDup' to remove PCR duplicate
Gene-level counts were generated with featureCounts and further analyzed for gene differential expression with DeSeq2 with default parameters
Assembly: hg38
Supplementary files format and content: gene_level Counts by "featureCounts" in a text file
Supplementary files format and content: Differentially regulated genes in a text file
Supplementary files format and content: Genomic coverage file generated by bamCoverage tool in bigwig format
Supplementary files format and content: narrow peak generated by MACS2 in .bed format

source_name: Hey

growth_protocol: Hey cells were cultured in Dulbecco’s modified Eagle’s medium (Gibco #12800-082) supplemented with 10% fetal bovine serum (FBS)(PAN, Germany. #ST30-3302). Cells were maintained in 37 °C incubator with 5% CO2.

extract_protocol:
Cells were then collected into Trizol reagent (Invitrogen #15596026) in RNAase-free microcentrifuge tubes for subsequent RNA extraction. Total RNA was extracted as recommended by the manufacturer.
Sample processing and sequencing were performed by BGI.inc (Shenzhen China). Briefly, messenger RNA was purified with magnetic beads conjugated with Oligo-dT and then fragmented with fragmentation buffer. Then first-strand cDNA was synthesized with random primer. After second-strand cDNA synthesis, A-tailing and RNA index adapters were added. The cDNA fragments were amplified by PCR and products were purified by Ampure XP Beads. The product was analyzed on the Agilent Technologies 2100 bioanalyzer for quality control. The PCR product was heat-denatured and circularized by the splint oligo sequence to get the final library. The final library was amplified with Phi29 DNA Polymerase to make DNA nanoball (DNB) which had more than 300 copies of one molecular. Pair-end 150 bases reads were generated on MGISEQ-2000RS platform (BGI, Shenzhen, China).

treatment_protocol: Hey cells were transduced with lentivirus carrying ZKSCAN3-shRNA and Control sequence respectively. 24 hours after lentivirus infection, cells were divided into 6cm dishes. Puromycin (InvivoGen #ANT-PR-1) was added at a final concentration of 1 μg/ml 12 hours later. Cells were selected with puromycin for 3 days and then collected for RNA extraction.

value: Hey

value: Ovarian cell Carcinoma


title: Eln(-/-) SMCs, e15.5_4

description: Sample 9


title: Hey_Input_1

description: HA-ZKSCAN3 narrow peak.bed.txt

library_source: genomic

data_processing:
Raw reads were first filtered with Trim-Galore
Reads were aligned by Bowtie2 to human hg38 assembly
Alignments with MAPQ > 10 were kept
Bam file were then further filtered with 'RmDup' to remove PCR duplicate
Genomic coverage was generated with bamCoverage. Peak calling was done with MACS2.
Assembly: hg38
Supplementary files format and content: gene_level Counts by "featureCounts" in a text file
Supplementary files format and content: Differentially regulated genes in a text file
Supplementary files format and content: Genomic coverage file generated by bamCoverage tool in bigwig format
Supplementary files format and content: narrow peak generated by MACS2 in .bed format

molecule: genomic DNA

extract_protocol:
Cells were then resuspended in buffer A (10mM HEPES PH7.9, 1.5mM MgCl2, 10mM KCl, 0.5% NP40, 0.5mM DTT) and incubated on ice for 10 minutes. Afterward, cells were resuspended in ChIP Lysis buffer (50mM Tris-Cl PH8.0, 5mM EDTA, 0.2% SDS) and sonicated with BioRuptor (Diagenode). Cell lysate was then cleared by centrifugation at 15000 g for 10 minutes at 4_C. Supernatant was taken and mixed 1:1 with ChIP dilution buffer (300mM NaCl, 2% Triton X-100) and then HA-tag antibody (Cell Signaling Technology #3724). Immunocomplex was then pulled-down with ChIP-Grade Magnetic Protein-G beads (CST 9006). Immunoprecipitate was washed extensively and immunocomplex was eluted by ChIP elution buffer (0.1M NaHCO3 and 1%SDS) with shaking at 65_C for 15 minutes. De-crosslinking was then done at 65_C overnight. DNA was purified for Next generation sequencing.
A-tailing and index adapters were added. The DNA fragments were purified by Ampure XP Beads and then amplified by PCR. PCR product was purified with Ampure XP Beads again and then analyzed on the Agilent Technologies 2100 bioanalyzer for quality control. Pair-end 150 bases reads were generated on MGISEQ-2000RS(BGI, Shenzhen, China).

treatment_protocol: Hey were transduced with lentivirus carrying HA-ZKSCAN3 and then selected with Blasticidin.

value: HA-ZKSCAN3 expressing


title: Scr1

description: Sample 1


title: Sham_7

description: Library name: Sham_7

value: Wistar

value: Skeletal muscle (diaphragm)

value: WT

value: Sham-operated


title: HSC, DMSO, rep1

description:
Library name: Sample 1
10x Genomics

value: Liver

value: hiPSC-Hepatic stellate cells

value: stellate cells

value: DMSO


title: Hey shZKSCAN3_RNA-seq_1


title: Eln(-/-) SMCs, e15.5_3

description: Sample 8

value: Aorta

value: Primary cells


title: HSC, DMSO, rep2

description:
Library name: Sample 2
10x Genomics


title: Sham_4

description: Library name: Sham_4

value: male


title: granulosa cells with negative control transfected in vitro,rep 3

city: nanjing

first: Yongjin

last: Bao

state: jinagsu

address: weigang No.1

institute: nanjing agricultural university

data_processing:
The eukaryotic mRNA was enriched with magnetic beads with Oligo (dT), and the mRNA was randomly interrupted by adding Fragmentation Buffer.
Using the mRNA as a template, the first cDNA strand was synthesized with random hexamers, then buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second cDNA strand.
After that, the cDNA was purified with AMPure XP beads. The purified double-stranded cDNA was then subjected to end repair, A-tailed and connected to sequencing adapters, using the AMPure XP beads for selection of fragment size.
Finally, PCR enrichment was conducted to obtain a cDNA library. After the library is constructed, quantitative Real-Time PCR (qRT-PCR) method was used to accurately quantify the effective concentration of the library (library effective concentration > 2 nM) to ensure the quality of the library.
After the library check was qualified, the library would be pooled according to the target data volume and sequenced on the Illumina platform.
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: mRNA expression

organism: Ovis aries

source_name: granulosa cells

extract_protocol:
TRIZOL was used to extract total RNA and the concentration and purity of RNA were detected by the Nanodrop 2000 spectrophotometer.
The eukaryotic mRNA was enriched with magnetic beads with Oligo (dT), and the mRNA was randomly interrupted by adding Fragmentation Buffer. Using the mRNA as a template, the first cDNA strand was synthesized with random hexamers, then buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second cDNA strand. After that, the cDNA was purified with AMPure XP beads. The purified double-stranded cDNA was then subjected to end repair, A-tailed and connected to sequencing adapters, using the AMPure XP beads for selection of fragment size. Finally, PCR enrichment was conducted to obtain a cDNA library. After the library is constructed, quantitative Real-Time PCR (qRT-PCR) method was used to accurately quantify the effective concentration of the library (library effective concentration > 2 nM) to ensure the quality of the library.

value: primary granulosa cells

tag: sirna

value: control


title: Eln(-/-) SMCs, e15.5_2

description: Sample 7

value: Smooth muscle cells

value: Non


title: scRNA-seq of ccRCC arising in the setting of VHL disease

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V3.0
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat
Assembly: GRCh38 for human data
Supplementary files format and content: The barcodes, genes, expression matrix files for scRNA-seq.

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v3 user guide to perform single cell suspension which were prepared before. Briefly, the single-cell samples were passed through a 40μm cells strainer and counted using a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the oils onto the 10x Genomics single-cell-A chip and run this machine. After droplet generation, samples were transferred onto a PCR tube and reverse transcription was performed using T100 Thermal Cycler (BIO-RAD). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics followed by a Silane DynaBead clean-up as outlined in the user guide. Purified cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to determine cDNA concentration.
10X Genomics Single Cell 3' v3 Reagent Kit

value: Total clear cell renal cell carcinoma Homogenate


title: Hey shControl_RNA-seq_2

value: Hey

value: Ovarian cell Carcinoma


title: MDA_DMSO_3

description: Library name: MDA_DMSO_3

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 37 (based on Ensembl 103)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

value: TNBC cell line

value: DMSO for 96h

tag: batch

value: forward


title: CAMA1_WT_DMSO_n1

description: Library name: CAMA1_WT_DMSO_n1

value: HR+ BC cell line

value: WT


title: granulosa cells with negative control transfected in vitro,rep 2


title: Eln(+/+) SMCs, e15.5_5

description: Sample 5


title: Hey_HA-ZKSCAN3_ChIP_1

description: HA-ZKSCAN3 narrow peak.bed.txt

value: HA-ZKSCAN3 expressing


title: MDA_DMSO_2

description: Library name: MDA_DMSO_2


title: Eln(-/-) SMCs, e15.5_1

description: Sample 6


title: Hey shControl_RNA-seq_1


title: Eln(+/+) SMCs, e15.5_4

description: Sample 4


title: granulosa cells with negative control transfected in vitro,rep 1


title: MDA_DMSO_1

description: Library name: MDA_DMSO_1


title: Nsun7ko_testis

city: Shanghai

first: Jing

last: Li

address: Haike Road 230

department: School of Life Science and Technology

institute: ShanghaiTech University

description:
Library name: Sample 2
scRNA-seq of Nsun7 knockout testis

data_processing:
PISA was used to calculate the gene expression of cells and create a gene × cell matrix for each library.
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv, features.tsv and matrix.mtx of scRNA-seq

source_name: testis

growth_protocol: adult WT and Nsun7 KO mice

extract_protocol:
testis samples were minced, and enzymatically digested using the MACS Tumor Dissociation Kit (Miltenyi) for 30 min with agitation. The dissociated cells were subsequently passed throughcell-strainer and centrifuged. The pelleted cells were then suspended in cell lysis buffer (Tiangen), and washed with 0.04% BSA in DPBS. Finally, the cell concentration was adjusted to 1,000 cells/μL(viability>80%) in all samples.
Single-cell RNA-seq libraries were prepared with DNBelab C Series High-throughput Single-Cell RNA Library according to the manufacturer’s instructions. Libraries were purified and quantified using the Qubit ssDNA kit (Thermo) and Qsep100 (Bioptic), and subsequently sequenced on DNBelab C4 /DNBelab TaiM4 Series Single-Cell Library Prep Set (MGI).

value: testis

value: Nsun7 knockout


title: granulosa cells with INHBA siRNA transfected  in vitro,rep 3

value: INHBA siRNA


title: MDA_Abema_3

description: Library name: MDA_Abema_3

value: 300nM Abemaciclib for 96h


title: Eln(+/+) SMCs, e15.5_3

description: Sample 3

value: Aorta

value: Primary cells


title: WT_testis

description:
Library name: Sample 1
scRNA-seq of WT testis


title: granulosa cells with INHBA siRNA transfected  in vitro,rep 2

value: primary granulosa cells


title: HCT116 cell line, long-read, Nanopore

city: St. Louis

first: Christopher

last: Maher

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

description:
circRNA-RCA RNA
Oxford Nanopore long-read
HCT116_Nanopore
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz

data_processing:
STAR v2.7.3a for short-read RNA-Seq alignment
CIRCexplorer2 v2.3.8 for short-read circRNA detection
LoRDEC v0.9 for long-read correction
isoCirc v1.0.6 and CIRI-long v1.0.3 for long-read circRNA detection
featureCounts v1.6.0 for short-read linear gene quantification
Assembly: Gene annotations were combined from Gencode v23, RefSeq downloaded from the UCSC Genome Browser, and the Broad long noncoding RNA (lncRNA) catalog (see supplementary file hg38_annotation.gtf.gz in Accession GSE221240)
Supplementary files format and content: For short-read cell lines, tab-delimited text files include 1) Raw counts for each sample for circRNAs; 2) TPM values for each sample for circRNAs.
Supplementary files format and content: For long-read, tab-delimited text files include 1) Raw counts for each sample for circRNAs detected by isoCirc; 2) Raw counts for each sample for circRNAs detected by CIRI-long.

growth_protocol: For cell lines, HCT116 and HT29 cells were grown in McCoy’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. SW480 and SW620 cells were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Sigma, St. Louis, MO) and 1% penicillin/streptomycin. LoVo cells were grown in DMEM/F12 (Invitrogen) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin.

extract_protocol:
For cell line short-read samples, total RNA inputs of 1μg were used to generate libraries using the Illumina (San Diego, CA) TruSeq Stranded Total RNA with Ribo-Zero Fold.  For long-read samples, the RNA of the cells lines HCT116, HT29, and LoVo was isolated using the Macherey-Nagel NucleoSpin RNA, Mini kit (MACHEREY-NAGEL, Düren, Germany). The RNA of patient trio samples was isolated using the Invitrogen TRIzol protocol (ThermoFisher Scientific, Waltham, MA) with DNase treatment (ZYMO RESEARCH, Irvine, CA).
For cell line short-read samples, 200ng aliquots of each library were pooled and used as input for cDNA-Capture. The IDT xGen Exome Research Panel v2 including 415,115 exon probes was used for exome capture. For long-read samples, the published protocol in Xin et al. (https://www.nature.com/articles/s41467-020-20459-8) was used for circRNA enrichment and rolling circle amplification for long-read sequencing with the following exceptions. We used the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (#E7400X, New England BioLabs, Ipswich, MA) to remove the rRNA. Per the manufacturer’s protocol, multiple reactions were set up to accommodate a 25µg total RNA input. The rRNA depleted RNA was concentrated using RNAClean XP beads (2.0X) (#A63987, Beckman Coulter, Brea, CA) and eluting in 17μL of nuclease-free water. The RNase R treated sample was the purified using RNAClean XP beads (1.8X) and eluted in 10µL of nuclease-free water. The reverse transcription reaction was incubated for 5 minutes at 25°C, 1 hour at 42°C, and 10 minutes at 65°C. Precipitated circDNA was used as input for a 250μL rolling circle amplification reaction, per the TempliPhi 100 Amplification Kit protocol (#25-6400-10, GE Healthcare, Chicago, IL). The amplified sample was then purified using AMPure XP beads (1.8X) and eluted in 42µL of nuclease-free water. The purified sample was digested to remove branched structures by adding 5μL of 10X NEBuffer2 and 2.5µL of T7 Endonuclease I (#M0302L, New England BioLabs, Ipswich, MA) and incubating for 1 hour at 37°C. The digested sample was then size selected using two round of AMPure XP beads (0.5X). The sample was eluted with 36μL of 10mm Tris (pH 8.0).  For samples sequenced using the Nanopore platform, a 2µg input of cDNA was used with Oxford Nanopore’s Ligation Sequencing Kit (#SQK-LSK110, Oxford, United Kindom) to prepare a sequence ready library. The library was run on one flow cell on the GridION instrument. For samples sequenced using the PacBio platform, a 500ng input of cDNA was used to generate the long read sequencing library following the Iso-seq protocol (Pacific Biosciences, Menlo Park, CA). The library was run on a single SMRT cell on the Sequel II.
cDNA-Cap RNA-Seq for cell line short-read samples; Oxford Nanopore long-read RNA-seq for two HCT116 cell line samples; PacBio long-read RNA-seq for other cell line and patient samples.

value: Humancolon cancercell line


title: Eln(+/+) SMCs, e15.5_2

description: Sample 2

value: Smooth muscle cells

value: Non


title: MDA_Abema_2

description: Library name: MDA_Abema_2


title: granulosa cells with INHBA siRNA transfected  in vitro,rep 1


title: Eln(+/+) SMCs, e15.5_1

description: Sample 1


title: HCT116 cell line, long-read, Nanopore pilot

description:
circRNA-RCA RNA
Oxford Nanopore long-read
HCT116_Nanopore_Pilot
WUSTL_cell_lines_and_patients_long_read_isoCirc_circRNA_count.csv.gz
WUSTL_cell_lines_and_patients_long_read_CIRI_long_circRNA_count.csv.gz


title: MDA_Abema_1

description: Library name: MDA_Abema_1


title: P3-hTSCs-EP300-1

status: Public on Nov 11 2025

city: Tianjin

first: Chunxiao

last: Chen

state: Tianjin

address: Xuefu Road

department: College of Life Science

institute: Nankai University

description: Library name: CUT_Tag sample11

data_processing:
For MeRIP-seq, raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.  Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1).  Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”.  Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1).  Differentially methylated peaks were identified by exomePeak2 (v1.10.0).  Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”.  Gene Ontology analysis was performed using DAVID (v2024q2).  For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates.  For CUT&Tag, raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of EP300 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CUT&Tag

source_name: cell

extract_protocol:
For MeRIP-seq, total RNA was extracted with TRIzol reagent. CUT&Tag was performed according to the manufacturer’s protocol (Vazyme, TD904). Nuclei were isolated, lysed, and incubated with Tn5 transposase according to the manufacturer’s protocol (Vazyme, TD501). Transposed DNA was isolated using a DNA Clean & Concentrator kit (Zymo).
For MeRIP-seq,the SMARTer Stranded Total RNA-Seq Kit-version 2 (Pico Input Mammalian, Takara/Clontech, 634413) was used to construct libraries for both the input and IP samples. For CUT&Tag, Library preparation and amplification was followed by manufacturer’s protocol (Vazyme, TD904).

value: cell

value: trophoblast stem cell

value: KO

value: w/o DOX


title: P0-hTSCs-EP300-1

description: Library name: CUT_Tag sample9

value: DOX


title: P3-hTSCs-EP300-2

description: Library name: CUT_Tag sample12


title: P0-hTSCs-EP300-2

description: Library name: CUT_Tag sample10

value: WT


title: Day 6-STB-IP-rep2

description: Library name: MeRIP-seq sample7

data_processing:
For MeRIP-seq, raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.  Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1).  Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”.  Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1).  Differentially methylated peaks were identified by exomePeak2 (v1.10.0).  Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”.  Gene Ontology analysis was performed using DAVID (v2024q2).  For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates.  For CUT&Tag, raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of EP300 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

value: Cytotrophoblast derived

value: syncytiotrophoblast

value: STB differentiation day 6


title: Day 6-STB-IP-rep1

description: Library name: MeRIP-seq sample5


title: Day 6-STB-input-rep1

description: Library name: MeRIP-seq sample6


title: CT-hTSCs-input-rep2

description: Library name: MeRIP-seq sample4

value: control


title: Day 6-STB-input-rep2

description: Library name: MeRIP-seq sample8


title: CT-hTSCs-IP-rep2

description: Library name: MeRIP-seq sample3


title: CT-hTSCs-input-rep1

description: Library name: MeRIP-seq sample2


title: bulk RNA-seq of patient-derived GBM20, replicate GBM20A

city: London

first: Victoria

last: Tsang

state: Select a State

address: Charterhouse Square Campus

department: Translational Medicine and Therapeutics

country: United Kingdom

institute: Queen Mary University of London

description:
Library name: GBM20A
cell line derived from recurrent tumor of a 50-year-old male patient treated with radiotherapy, temozolomide, and IMA950

data_processing:
1. Raw sequencing reads were pre-processed using fastp to generate clean, high-quality data (quality filtering at Phred score ≥20).
2. High-quality reads were aligned to the human reference genome UCSC Homo sapiens version hg38 using STAR (Spliced Transcripts Alignment to a Reference).
3. Gene-level quantification was performed using RSEM to generate counts for each transcript.
4. Genes with fewer than 10 average reads across samples were filtered out.
5. Differential gene expression between GBM20 and GBM1 was calculated using DESeq2 in R/Bioconductor.
6. Further RNA-seq analysis was performed in R Studio, including volcano plots (ggplot2), Gene Ontology enrichment, and Gene Set Enrichment Analysis (clusterProfiler, fgsea) to identify significantly enriched biological processes and pathways.
Assembly: UCSC Homo sapiens version hg38
Supplementary files format and content: GBM1A/B/GBM20A/B.genes.counts.tsv: Raw gene-level read counts per sample
Supplementary files format and content: sample_wise_gene_read_counts_normalized.tsv: Normalized counts per sample
Supplementary files format and content: GBM20_VS_GBM1.foldchange.tsv: Differential expression fold-change table

growth_protocol: Cells were cultured 5 μg/mL poly-L-ornithine (PLO) (Sigma) and 2 μg/mL laminin (Thermofisher) coated plates in Neurobasal medium (Invitrogen) supplemented with 0.5X B27 (Invitrogen), 0.5X N2 (Invitrogen), 40 ng/mL epidermal growth factor (EGF) (R&D Systems), and 40 ng/mL basic-fibroblast growth factor (b-FGF) (Invitrogen).

extract_protocol:
The GBM1 and GBM20 cell lines were rinsed once with PBS, detached with TrypLE, snap-frozen in pellets of 10^6 cells, and submitted to Eurofins Genomics, Germany, under Project ID NG-29040.
RNA libraries were prepared by Eurofins Genomics using standard Illumina-compatible RNA-seq library construction protocols.

value: GBM tumor cells


title: bulk RNA-seq of patient-derived GBM1, replicate GBM1B

description:
Library name: GBM1B
cell line derived from the primary tumor of a 58-year-old female patient


title: bulk RNA-seq of patient-derived GBM1, replicate GBM1A

description:
Library name: GBM1A
cell line derived from the primary tumor of a 58-year-old female patient


title: PBMC, pH3, rep2

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

description: Library name: S9b

data_processing:
The count files in RDS format were acquired from fastq files using zUMIs.
Assembly: GRCh38 (mouse), GRCh38 (human), B73-NAM 5.0 (maize)
Supplementary files format and content: RDS for raw counts; h5ad for the filted barcodes and combined datasets.

molecule: nuclear RNA

source_name: blood

extract_protocol:
The cells were fixed directly with 10x volumes of methanol at -20°C. The murine tissues were lyzed by pestle in a pH3 citrate buffer or a lysis buffer contaning a RNase inhibitor. The maize roots and shoots were dissociated with dounce homogenizer (20 strokes) in spermidine- or divalent cation-containing buffers supplemented with the RNase inhibitor. The released nuclei from these tissues were filtered through 800-mesh-size nylon membrane, purified using iodixanol density-gradient centrifugation (30%), and fixed in a organic solvent as with the cells.
The barcoded cells/nuclei containing cDNA were lyzed. The cDNA were tailed with a PCR handle using TdT. Following second-strand systhesis and preamplification with KAPA HiFi, the cDNA were purified with carboxylic paramagnetic beads in a PEG/NaCl solution. The eluted DNA were tagmenmented with Tn5 and amplified with KAPA HiFi using primers containg P5 and P7 ends and multiplex indices. The amplified products were subjected to size selection, targeting libraries with peaks in the 450bp region.

value: blood

value: whole organ

value: mixed

value: one-pot lysis


title: PBMC, pH3, rep1

description: Library name: S9a


title: PBMC, pH3, rep3

description: Library name: S9c


title: HEK293T, additional parameters

description: Library name: S8

source_name: cell line

value: cell line

value: human embryonic kidney cells

value: different temperatures, randomer lengths and enzymes during RT


title: HEK293T, methanol or extra glyoxal fixation, rep4

description: Library name: S2d

value: fixation with metanol or methanol plus glyoxal


title: HEK293T, methanol or extra glyoxal fixation, rep3

description: Library name: S2c


title: HEK293T, methanol or extra glyoxal fixation, rep1

description: Library name: S2a


title: HUES8-TSC STM2 P12

description: Library name: RNA-seq_sample4

data_processing:
For RNA-seq, raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was employed to count mapped reads for genomic features.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For RNA-seq, total RNA was extracted with TRIzol reagent.
For RNA-seq, Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: trophoblast stem cell


title: HUES8-TSC STM1 P12

description: Library name: RNA-seq_sample3


title: HUES8-TSC Control2 P10

description: Library name: RNA-seq_sample2

value: DMSO


title: HEK293T, methanol or extra glyoxal fixation, rep2

description: Library name: S2b


title: OCI-AML2 cell line IKZF1-ko  rep 3

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

description: Library name: S37

data_processing:
Paired reads were trimmed using Trimmomatic with the adapter filters provided with the package
Trimmed fastq files were aligned to the GRCh38 reference genome using STAR with bam formatted output and a GeneCount table
Read counts from the '2nd strand' column of the GeneCount table were summarized into a matrix
Assembly: GRCh38
Supplementary files format and content: Comma-seperated file containing gene-level read counts per sample

growth_protocol: OCI-AML2 cells were grown in RPMI 1640 (Life Technologies Inc.) supplemented with 20% FBS (Cytiva), 2% L-glutamine (Life Technologies Inc.) and 1% penicillin/streptomycin (Life Technologies Inc.).  Cell lines were tested regularly for mycoplasma using the Mycoplasma PCR Detection Kit (Applied Biological Materials Inc, Cat. No. G238) and authenticated by the DNA sequencing core at OHSU.

extract_protocol:
RNA was isolated from OCI-AML2 parental and CRISPR derived knockout cells in triplicate using the RNeasy Mini Kit (Qiagen Inc.).
Libraries were prepared using the Illumina Stranded mRNA prep kit and sequenced on a NovaSeq 6000


title: HUES8-TSC Control1 P10

description: Library name: RNA-seq_sample1


title: OCI-AML2 cell line IKZF1-ko  rep 2

description: Library name: S36


title: OCI-AML2 cell line IKZF1-ko  rep 1

description: Library name: S35


title: bulk RNA-seq of patient-derived GBM20, replicate GBM20B

description:
Library name: GBM20B
cell line derived from recurrent tumor of a 50-year-old male patient treated with radiotherapy, temozolomide, and IMA950


title: CT-hTSCs-IP-rep1

description: Library name: MeRIP-seq sample1

value: cell


title: OCI-AML2 cell line NT control  rep 1

description: Library name: S29

value: NT control


title: OCI-AML2 cell line palbociclib treated rep 2

description: Library name: LIB240222JT_Palbo2_A5

data_processing:
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Counting of trimmed reads matching CRISPR sgRNA library using custom Python script
Assembly: Custom reference created from CRISPR library
Supplementary files format and content: Read counts per sgRNA for each sample
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted
Libraries amplified via PCR and sequenced on a NovaSeq 6000

treatment_protocol: Cas9-expressing OCI-AML2 cells were generated using lentiCas9-Blast (Addgene #52962) as described above and single cell sorted to create a clonal Cas9 line with high functionality. Cas9 functionality was tested by transducing Cas9 containing cells with pKLV2-U6gRNA5(Empty)-PGKmCherry2AGFP-W (Addgene #362132) or pKLV2-U6gRNA5(gGFP)-PGKmCherry2AGFP-W (Addgene #362132) vectors. After 5 days cells were analyzed for GFP and mCherry positivity by FACS. Clonal OCI-AML2 Cas9 C6 cells were used for genome wide knockout with sgRNA library (Addgene #67989).  After 5-7 days of puromycin selection, transduced cells were treated with DMSO, 1uM palbociclib, 200nM venetoclax, or a combination of 1uM palbociclib and 200nM venetoclax. Cells were collected at days 0 and 21 for library preparation.

value: palbociclib


title: OCI-AML2 cell line NT control  rep 2

description: Library name: S30


title: OCI-AML2 cell line NT control  rep 3

description: Library name: S31


title: OCI-AML2 cell line DMSO treated rep 2

description: Library name: LIB240222JT_DMSO2_A3


title: OCI-AML2 cell line palbociclib treated rep 1

description: Library name: LIB240222JT_Palbo1_A4


title: OCI-AML2 cell line venetoclax treated rep 1

description: Library name: LIB240222JT_Ven1_A6

value: venetoclax


title: GCRC2015 Palbo rep2

city: Montreal

first: April

last: Rose

address: 3755 chem. de la côte ste Catherine

department: Lady Davis Institute

institute: McGill University

description:
Library name: GCRC2015P_2
column name in GCRC2015_DESEq_Counts.csv GCRC2015P_2

data_processing:
RNA counts were normalized using the DESeq2 (version 1.42.0) algorithm in R (version 4.3.2).
Assembly: The genome dataset was aligned with the human genome GCRh38 and annotated with ANNOVAR.
Supplementary files format and content: csv files include DESeq counts for each sample

source_name: patient derived xenograft

growth_protocol: All cell lines were kept in culture with either DMEM supplemented with 5% FBS and 1% PS (MDA-MB-231) or with RPMI supplemented with 10% FBS and 1% PS (HMV-II, FM95, 22RV1).

extract_protocol:
Flash-frozen tumor tissue samples were pulverized in liquid nitrogen using a mortar and pestle. Tumor tissue DNA and RNA was extracted with the Zymo Research Quick-DNA Microprep Kit (cat. no. D3020) and the Qiagen RNeasy Kit (cat. no. 74134), respectively, according to the manufacturer’s instructions. RNA quantification and quality assessment was performed using the NanoDrop Spectrophotometer ND-1000 (software version 3.8.1).
Quantified libraries were pooled and sequenced on Illumina platforms and paired-end reads were generated. Hisat2 v2.0.5 were used to build the reference genome and align the paired-end reads. Gene expression was obtained with featureCounts v1.5.0-p3.

treatment_protocol: Parental and resistant cells were plated and the following day, treated for 24hrs with DMSO or the corresponding dose of Bini+Enco that the resistant cells are grown in.

value: human melanoma tumour cells

value: Palbo


title: OCI-AML2 cell line venetoclax and palbociclib combination treated rep 2

description: Library name: LIB240222JT_Combo2_A9

value: venetoclax and palbociclib combination


title: GCRC2015 Bini+Enco rep2

description:
Library name: GCRC2015BE_2
column name in GCRC2015_DESEq_Counts.csv GCRC2015BE_2

value: Bini+Enco


title: GCRC2015 Palbo rep1

description:
Library name: GCRC2015P_1
column name in GCRC2015_DESEq_Counts.csv GCRC2015P_1


title: OCI-AML2 cell line venetoclax treated rep 2

description: Library name: LIB240222JT_Ven2_A7


title: OCI-AML2 cell line venetoclax and palbociclib combination treated rep 1

description: Library name: LIB240222JT_Combo1_A8


title: GCRC2015 Bini+Enco rep1

description:
Library name: GCRC2015BE_1
column name in GCRC2015_DESEq_Counts.csv GCRC2015BE_1


title: OCI-AML2 cell line untreated treated rep 1

description: Library name: LIB240222JT_Day0_A1

value: untreated


title: OCI-AML2 cell line DMSO treated rep 1

description: Library name: LIB240222JT_DMSO1_A2


title: GCRC2015 Vehicle rep2

description:
Library name: GCRC2015Veh2
column name in GCRC2015_DESEq_Counts.csv GCRC2015Veh2

value: Vehicle


title: DU145 cells, Normoxia, plate 4

city: Derio

first: Arkaitz

last: Carracedo

address: Bizkaia Science and Technology Park, building 801A

country: Spain

institute: CIC bioGUNE

description:
Library name: Nx_Ve_E4
2x150 paired-end sequence reads

data_processing:
RNA-seq  reads were aligned usig Vast-tools v2.5.1 to identify alternative splicing events.
Aligned reads from single and paired datasets were merged with Vast-tools v2.5.1.
Differentially spliced events were identified using Matt v.1.3.0 with a minimum abs(deltaPSI) > 10% and a Wilcoxon p-value < 0.01 after excluding events with PSIRANGE_ALL = NA and LENGTH= 0.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes PSI values for each sample

growth_protocol: DNEM, 15% fetal bovine serum, 2 mM glutamine, 1 x penicillin/streptomycin. Cells were cultured at 37C at 5% Coxigen.

extract_protocol:
RNA was extracted using NucleoSpin RNA isolation kit from Macherey-Nagel.
RNA libraries were prepared using Illumina Stranded mRNA Library Prep Kit following manufacture's protocol.

treatment_protocol: Mice in a mixed background were housed under controlled environmental conditions, such as time-controlled lighting on standard 12:12 light: dark cycles, controlled temperature at 22 ± 2ºC and 30-50% relative humidity. Mice were fed regular chow diet ad libitum and fasted for 6 h prior to tissue harvest (9 am-3 pm) to prevent metabolic alterations due to immediate food intake.

value: Metastatic prostate cancer

value: Control


title: DU145 cells, Normoxia, plate 3

description:
Library name: Nx_Ve_E3
2x150 paired-end sequence reads


title: DU145 cells, Normoxia, plate 2

description:
Library name: Nx_Ve_E2
2x150 paired-end sequence reads


title: GCRCMel1 Bini+Enco+Palbo rep1

description:
Library name: GCRCMelBEP_1
column name in GCRCMel_Counts_DESEQ.csv GCRCMelBEP_1

value: Bini+Enco+Palbo


title: GCRCMel1 Bini+Enco+Palbo rep2

description:
Library name: GCRCMelBEP_3
column name in GCRCMel_Counts_DESEQ.csv GCRCMelBEP_3


title: DU145 cells, Normoxia, plate 1

description:
Library name: Nx_Ve_E1
2x150 paired-end sequence reads


title: DU145 cells, Pladenolide for 24 hours, plate 4

description:
Library name: Nx_Pl_E4
2x150 paired-end sequence reads

value: Pladenolide (10 μM) for 24 hours


title: GCRCMel1 Palbo rep2

description:
Library name: GCRCMelP_2
column name in GCRCMel_Counts_DESEQ.csv GCRCMelP_2


title: DU145 cells, Pladenolide for 24 hours, plate 3

description:
Library name: Nx_Pl_E3
2x150 paired-end sequence reads


title: GCRCMel1 Palbo rep1

description:
Library name: GCRCMelP_1
column name in GCRCMel_Counts_DESEQ.csv GCRCMelP_1


title: GCRCMel1 Bini+Enco rep2

description:
Library name: GCRCMelBE_2
column name in GCRCMel_Counts_DESEQ.csv GCRCMelBE_2


title: DU145 cells, Pladenolide for 24 hours, plate 2

description:
Library name: Nx_Pl_E2
2x150 paired-end sequence reads


title: GCRCMel1 Bini+Enco rep1

description:
Library name: GCRCMelBE_1
column name in GCRCMel_Counts_DESEQ.csv GCRCMelBE_1


title: GCRCMel1 Vehicle rep2

description:
Library name: GCRCMelVeh_3
column name in GCRCMel_Counts_DESEQ.csv GCRCMelVeh_3


title: DU145 cells, Hypoxia for 24 hours, plate 3

description:
Library name: Hx_Ve_E3
2x150 paired-end sequence reads

value: Hypoxia (1% oxigen) for 24 hours


title: DU145 cells, Hypoxia for 24 hours, plate 4

description:
Library name: Hx_Ve_E4
2x150 paired-end sequence reads


title: DU145 cells, Hypoxia for 24 hours, plate 2

description:
Library name: Hx_Ve_E2
2x150 paired-end sequence reads


title: BVR-O-17 Bini+Enco+Palbo rep2

description:
Library name: BVRO17BEP_2
column name in BVR17_DESeqCounts.csv BVRO17BEP_2

value: human colorectal tumour cells


title: DU145 cells, Hypoxia for 24 hours, plate 1

description:
Library name: Hx_Ve_E1
2x150 paired-end sequence reads


title: BVR-O-17 Bini+Enco+Palbo rep1

description:
Library name: BVRO17BEP_1
column name in BVR17_DESeqCounts.csv BVRO17BEP_1


title: BVR-O-17 Palbo rep2

description:
Library name: BVRO17P_2
column name in BVR17_DESeqCounts.csv BVRO17P_2


title: DU145 cells, Hypoxia + Pladenolide for 24 hours, plate 3

description:
Library name: Hx_Pl_E3
2x150 paired-end sequence reads

value: Hypoxia (1% oxigen)  and pladenolide (10 μM) for 24 hours


title: BVR-O-17 Bini+Enco rep2

description:
Library name: BVRO17BE_2
column name in BVR17_DESeqCounts.csv BVRO17BE_2


title: GCRC2015 Vehicle rep1

description:
Library name: GCRC2015Veh1
column name in GCRC2015_DESEq_Counts.csv GCRC2015Veh1


title: DU145 cells, Hypoxia + Pladenolide for 24 hours, plate 1

description:
Library name: Hx_Pl_E1
2x150 paired-end sequence reads


title: BVR-O-17 Vehicle rep2

description:
Library name: BVRO17Veh_2
column name in BVR17_DESeqCounts.csv BVRO17Veh_2


title: BVR-O-17 Vehicle rep1

description:
Library name: BVRO17Veh_1
column name in BVR17_DESeqCounts.csv BVRO17Veh_1


title: DU145 sh4AMD1 cells, Doxycycline + Spermine 48 hours, plate 3

description:
Library name: DOX_Spermine_29
2x150 paired-end sequence reads

value: Doxycycline (100 ng/mL) and spemine (10 μM) for 48 hours


title: DU145 sh4AMD1 cells, Doxycycline + Spermine 48 hours, plate 2

description:
Library name: DOX_Spermine_19
2x150 paired-end sequence reads


title: BVR-O-15 Bini+Enco+TNO155 rep2

description:
Library name: B8_BVR_O_15BET2
column name in BVR-O-15-DESEQ.csv BVR_O_15BET2


title: BVR-O-15 Bini+Enco+TNO155 rep1

description:
Library name: B7_BVR_O_15BET1
column name in BVR-O-15-DESEQ.csv BVR_O_15BET1


title: DU145 cells, Pladenolide for 24 hours, plate 1

description:
Library name: Nx_Pl_E1
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, Doxycycline + Spermidine 48 hours, plate 4

description:
Library name: DOX_Spermidine_37
2x150 paired-end sequence reads

value: Doxycycline (100 ng/mL) and spemidine (10 μM) for 48 hours


title: BVR-O-15 Bini+Enco rep2

description:
Library name: B4_BVR_O_15BE2
column name in BVR-O-15-DESEQ.csv BVR_O_15BE2


title: GCRCMel1 Vehicle rep1

description:
Library name: GCRCMel_Veh2
column name in GCRCMel_Counts_DESEQ.csv GCRCMel_Veh2


title: BVR-O-15 Bini+Enco rep1

description:
Library name: B3_BVR_O_15BE1
column name in BVR-O-15-DESEQ.csv BVR_O_15BE1


title: DU145 cells, Hypoxia + Pladenolide for 24 hours, plate 4

description:
Library name: Hx_Pl_E4
2x150 paired-end sequence reads


title: BVR-O-15 TNO155 rep1

description:
Library name: B5_BVR_O_15TNO1
column name in BVR-O-15-DESEQ.csv BVR_O_15TNO1


title: DU145 sh4AMD1 cells, Doxycycline + Spermidine 48 hours, plate 1

description:
Library name: DOX_Spermidine_7
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, Doxycycline + Putrescine 48 hours, plate 4

description:
Library name: DOX_Putrescine_35
2x150 paired-end sequence reads

value: Doxycycline (100 ng/mL) and putrescine (10 μM) for 48 hours


title: BVR-O-17 Palbo rep1

description:
Library name: BVRO17P_1
column name in BVR17_DESeqCounts.csv BVRO17P_1


title: DU145 cells, Hypoxia + Pladenolide for 24 hours, plate 2

description:
Library name: Hx_Pl_E2
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, Doxycycline + Spermidine 48 hours, plate 3

description:
Library name: DOX_Spermidine_27
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, Doxycycline + Putrescine 48 hours, plate 3

description:
Library name: DOX_Putrescine_25
2x150 paired-end sequence reads


title: BVR-O-15 Vehicle rep1

description:
Library name: B1_BVR_O_15Veh1
column name in BVR-O-15-DESEQ.csv BVR_O_15Veh1


title: BVR-O-15 Vehicle rep2

description:
Library name: B2_BVR_O_15Veh2
column name in BVR-O-15-DESEQ.csv BVR_O_15Veh2


title: BVR-O-13 Bini+Enco+TNO155 rep2

description:
Library name: BVR_O_13BET2
column name in BVR_O_13_DESeqCounts.csv BVR_O_13BET2


title: DU145 sh4AMD1 cells, Doxycycline + Putrescine 48 hours, plate 1

description:
Library name: DOX_Putrescine_5
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, Doxycycline + Spermine 48 hours, plate 4

description:
Library name: DOX_Spermine_39
2x150 paired-end sequence reads


title: BVR-O-17 Bini+Enco rep1

description:
Library name: BVRO17BE_1
column name in BVR17_DESeqCounts.csv BVRO17BE_1


title: BVR-O-13 Bini+Enco+TNO155 rep1

description:
Library name: BVR_O_13BET1
column name in BVR_O_13_DESeqCounts.csv BVR_O_13BET1


title: DU145 sh4AMD1 cells, Doxycycline + Spermine 48 hours, plate 1

description:
Library name: DOX_Spermine_9
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, Doxycycline 48 hours, plate 4

description:
Library name: DOX_33
2x150 paired-end sequence reads

value: Doxycycline (100 ng/mL) for 48 hours


title: BVR-O-13 Bini+Enco rep2

description:
Library name: BVR_O_13BE_2
column name in BVR_O_13_DESeqCounts.csv BVR_O_13BE_2


title: DU145 sh4AMD1 cells, Doxycycline 48 hours, plate 2

description:
Library name: DOX_13
2x150 paired-end sequence reads


title: BVR-O-13 Bini+Enco rep1

description:
Library name: BVR_O_13BE_1
column name in BVR_O_13_DESeqCounts.csv BVR_O_13BE_1


title: BVR-O-13 TNO155 rep2

description:
Library name: BVR_O_13T_2
column name in BVR_O_13_DESeqCounts.csv BVR_O_13T_2


title: BVR-O-13 TNO155 rep1

description:
Library name: BVR_O_13T_1
column name in BVR_O_13_DESeqCounts.csv BVR_O_13T_1


title: DU145 sh4AMD1 cells, Doxycycline 48 hours, plate 1

description:
Library name: DOX_3
2x150 paired-end sequence reads


title: BVR-O-15 TNO155 rep2

description:
Library name: B6_BVR_O_15TNO2
column name in BVR-O-15-DESEQ.csv BVR_O_15TNO2


title: DU145 sh4AMD1 cells, Doxycycline + Spermidine 48 hours, plate 2

description:
Library name: DOX_Spermidine_17
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, noDoxycycline, plate 3

description:
Library name: noDOX_21
2x150 paired-end sequence reads


title: BVR-O-13 Vehicle rep2

description:
Library name: BVR_O_13Veh2
column name in BVR_O_13_DESeqCounts.csv BVR_O_13Veh2


title: DU145 sh4AMD1 cells, noDoxycycline, plate 4

description:
Library name: noDOX_31
2x150 paired-end sequence reads


title: BVR-O-12 Bini+Enco rep2

description:
Library name: BVR_O_12BE_2
column name in BVR_O_12_DESeqCounts.csv BVR_O_12BE_2


title: DU145 sh4AMD1 cells, Doxycycline + Putrescine 48 hours, plate 2

description:
Library name: DOX_Putrescine_15
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, noDoxycycline, plate 1

description:
Library name: noDOX_1
2x150 paired-end sequence reads


title: BVR-O-12 Bini+Enco+TNO155 rep1

description:
Library name: BVR_O_12BET1
column name in BVR_O_12_DESeqCounts.csv BVR_O_12BET1


title: BVR-O-13 Vehicle rep1

description:
Library name: BVR_O_13Veh1
column name in BVR_O_13_DESeqCounts.csv BVR_O_13Veh1


title: DU145 sh4AMD1 cells, noDoxycycline, plate 2

description:
Library name: noDOX_11
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, DOX + CX4945 48 hours, plate 3

description:
Library name: DOX_CK2i_36
2x150 paired-end sequence reads

value: Doxycycline (100 ng/mL) and CX4945 (10 μM) for 48 hours


title: BVR-O-12 Bini+Enco rep1

description:
Library name: BVR_O_12BE_1
column name in BVR_O_12_DESeqCounts.csv BVR_O_12BE_1


title: DU145 sh4AMD1 cells, noDOX, CX4945 48 hours,, plate 2

description:
Library name: noDOX_CK2i_21
2x150 paired-end sequence reads

value: CX4945 (10 μM)for 48 hours


title: BVR-O-12 TNO155 rep2

description:
Library name: BVR_O_12T_2
column name in BVR_O_12_DESeqCounts.csv BVR_O_12T_2


title: DU145 sh4AMD1 cells, DOX 48 hours, plate 2

description:
Library name: DOX_18
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, noDOX, CX4945 48 hours,, plate 1

description:
Library name: noDOX_CK2i_9
2x150 paired-end sequence reads


title: BVR-O-10 Bini+Enco rep1

description:
Library name: BVR_O_10BE_1
column name in BVR_O_10_DESeqCounts.csv BVR_O_10BE_1

value: human cholangiocarcinoma cells


title: DU145 sh4AMD1 cells, DOX 48 hours, plate 1

description:
Library name: DOX_6
2x150 paired-end sequence reads


title: BVR-O-10 Vehicle rep2

description:
Library name: BVR_O_10Veh2
column name in BVR_O_10_DESeqCounts.csv BVR_O_10Veh1


title: DU145 sh4AMD1 cells, DOX 48 hours, plate 3

description:
Library name: DOX_30
2x150 paired-end sequence reads


title: BVR-O-10 Vehicle rep1

description:
Library name: BVR_O_10Veh1
column name in BVR_O_10_DESeqCounts.csv BVR_O_10Veh1


title: DU145 sh4AMD1 cells, Doxycycline 48 hours, plate 3

description:
Library name: DOX_23
2x150 paired-end sequence reads


title: BVR-O-12 TNO155 rep1

description:
Library name: BVR_O_12T_1
column name in BVR_O_12_DESeqCounts.csv BVR_O_12T_1


title: DU145 sh4AMD1 cells, DOX + CX4945 48 hours, plate 2

description:
Library name: DOX_CK2i_24
2x150 paired-end sequence reads


title: BVR-O-12 Vehicle rep2

description:
Library name: BVR_O_12Veh2
column name in BVR_O_12_DESeqCounts.csv BVR_O_12Veh2


title: BVR-O-12 Bini+Enco+TNO155 rep2

description:
Library name: BVR_O_12BET2
column name in BVR_O_12_DESeqCounts.csv BVR_O_12BET2


title: DU145 sh4AMD1 cells, noDOX, CX4945 48 hours,, plate 3

description:
Library name: noDOX_CK2i_33
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, noDOX, plate 3

description:
Library name: noDOX_27
2x150 paired-end sequence reads


title: DU145 sh4AMD1 cells, DOX + CX4945 48 hours, plate 1

description:
Library name: DOX_CK2i_12
2x150 paired-end sequence reads


title: BVR-O-04 Bini+Enco+Palbo rep2

description:
Library name: BVR_O_04BEP2
column name in BVR-O-04_DESeqCounts.csv BVR_O_04BEP2


title: DU145 sh4AMD1 cells, noDOX, plate 2

description:
Library name: noDOX_15
2x150 paired-end sequence reads


title: BVR-O-04 Palbo rep2

description:
Library name: BVR_O_04P_2
column name in BVR-O-04_DESeqCounts.csv BVR_O_04P_2

value: Palbo


title: BVR-O-04 Bini+Enco+Palbo rep1

description:
Library name: BVR_O_04BEP1
column name in BVR-O-04_DESeqCounts.csv BVR_O_04BEP1


title: keloid3, K3, scRNA-seq

city: wuhan

first: jia

last: chen

address: 215 Zhongshan Dadao, Qiaokou District, Wuhan City, Hubei Province

department: Department of Dermatology

institute: Traditional Chinese and Western Medicine Hospital of Wuhan

description:
Library name: sample6
10x Genomics

data_processing:
Quality control
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.7.5a
aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Assembly: GRCh38
Supplementary files format and content: expression matrix file using RNA raw count

source_name: Skin

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×10^5 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

value: Skin


title: DU145 sh4AMD1 cells, noDOX, plate 1

description:
Library name: noDOX_3
2x150 paired-end sequence reads


title: keloid2, K2, scRNA-seq

description:
Library name: sample5
10x Genomics


title: BVR-O-04 Palbo rep1

description:
Library name: BVR_O_04P_1
column name in BVR-O-04_DESeqCounts.csv BVR_O_04P_1


title: BVR-O-12 Vehicle rep1

description:
Library name: BVR_O_12Veh1
column name in BVR_O_12_DESeqCounts.csv BVR_O_12Veh1

value: Vehicle


title: keloid1, K1, scRNA-seq

description:
Library name: sample4
10x Genomics


title: BVR-O-10 Bini+Enco rep2

description:
Library name: BVR_O_10BE_2
column name in BVR_O_10_DESeqCounts.csv BVR_O_10BE_2

value: Bini+Enco


title: BVR-O-04 Bini+Enco rep2

description:
Library name: BVR_O_04BE_2
column name in BVR-O-04_DESeqCounts.csv BVR_O_04BE_2


title: BVR-O-04 Bini+Enco rep1

description:
Library name: BVR_O_04BE_1
column name in BVR-O-04_DESeqCounts.csv BVR_O_04BE_1


title: normal skin2, N1-Z, scRNA-seq

description:
Library name: sample2
10x Genomics


title: BVR-O-04 Vehicle rep2

description:
Library name: BVR_O_04Veh2
column name in BVR-O-04_DESeqCounts.csv BVR_O_04Veh2


title: BVR-O-04 Vehicle rep1

description:
Library name: BVR_O_04Veh1
column name in BVR-O-04_DESeqCounts.csv BVR_O_04Veh1


title: normal skin1, N1-B, scRNA-seq

description:
Library name: sample1
10x Genomics


title: MCF7 expressing CDK6-D224Y-1

city: taipei

first: Jiun-I

last: Lai

state: State...

address: no 155, linong street

institute: National Yang-Ming Chiao-Tung University

description: MCF7 expressing CDK6-D224Y-1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to H.  sapiens, GRCh38 using HISAT2 software (v 2.1.0) (parameters- default)
Read count extraction  were performed using FeatureCounts (v 2.0.0 )
Normalization were performed using DEGseq (v 1.40.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: MCF-7 were treated DMEM/F12 medium, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Total RNA Isolate Kit (NovelGene). 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer's protocols.

treatment_protocol: cells overexpressing vector, CDK6, CDK6-D224Y

value: breast


title: 22RV1 Resistant 24h Bini+Enco rep2

description:
Library name: r22r_D5_N3
column name in 22RV1_DESeq_counts.csv r22r_D5_N3

value: prostate cancer cells

value: Bini+Enco 24h


title: MCF7 expressing CDK6-1

description: MCF7 expressing CDK6-1


title: MCF7 vector-1

description: MCF7 vector-1

value: vector


title: 22RV1 Resistant 24h DMSO rep2

description:
Library name: r22D4DMSO_N2
column name in 22RV1_DESeq_counts.csv r22D4DMSO_N2

value: DMSO 24h


title: B_37_D

city: Boston

first: Margaret

last: Stefater-Richards

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
"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 thus a better mapping result than other non-splice mapping tools." "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 thus a better mapping result than other non-splice mapping tools." "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 thus a better mapping result than other non-splice mapping tools." "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 thus a better mapping result than other non-splice mapping tools." 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 thus a better mapping result than other non-splice mapping tools.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: homo Sapiens(GRCh38/hg38)
Supplementary files format and content: Tab-delimited txt file contains fpkm values for each sample

source_name: intestine

extract_protocol:
RNA was extracted from frozen tissue samples by homogenization in trizol followed by chloroform separation and extraction in an RNAeasy mini column (Qiagen Inc., Germantown, MD) prior to cleaning using the RNase-Free DNaseSet (Qiagen Inc., Germantown, MD).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification(Figure A). For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification(Figure B). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: RYGB surgery

value: intestine

value: pre-RYGB


title: B_35_D


title: 22RV1 Parental 24h Bini+Enco rep1

description:
Library name: p22p_D5_N1
column name in 22RV1_DESeq_counts.csv p22p_D5_N1


title: 22RV1 Resistant 24h Bini+Enco rep1

description:
Library name: r22D4_D5_N1
column name in 22RV1_DESeq_counts.csv r22D4_D5_N2


title: 22RV1 Parental 24h DMSO rep2

description:
Library name: p22pDMSO_N2
column name in 22RV1_DESeq_counts.csv p22pDMSO_N2


title: 22RV1 Parental 24h Bini+Enco rep2

description:
Library name: p22p_D5_N2
column name in 22RV1_DESeq_counts.csv p22p_D5_N2


title: B_36_D


title: B_34_D


title: 22RV1 Parental 24h DMSO rep1

description:
Library name: p22pDMSO_N1
column name in 22RV1_DESeq_counts.csv p22pDMSO_N1


title: B_33_D


title: B_31_C


title: B_32_D


title: FM95 Resistant 24h Bini+Enco rep2

description:
Library name: FMrD4D5_N2
column name in FM95_DESeq_counts.csv FMrD4D5_N2

value: melanoma cells


title: normal skin3, N4, scRNA-seq

description:
Library name: sample3
10x Genomics


title: FM95 Resistant 24h Bini+Enco rep1

description:
Library name: FMrD4D5_N1
column name in FM95_DESeq_counts.csv FMrD4D5_N1


title: B_30_C


title: FM95 Resistant 24h DMSO rep1

description:
Library name: FMrD4DMS_N1
column name in FM95_DESeq_counts.csv FMrD4DMS_N1


title: FM95 Resistant 24h DMSO rep2

description:
Library name: FMrD4DMS_N2
column name in FM95_DESeq_counts.csv FMrD4DMS_N2


title: B_28_D


title: B_29_C


title: FM95 Parental 24h Bini+Enco rep2

description:
Library name: FM95pD5_N2
column name in FM95_DESeq_counts.csv FM95pD5_N2


title: B_27_C


title: FM95 Parental 24h Bini+Enco rep1

description:
Library name: FM95pD5_N1
column name in FM95_DESeq_counts.csv FM95pD5_N1


title: B_23_D


title: B_25_D


title: 22RV1 Resistant 24h DMSO rep1

description:
Library name: r22D4DMSO_N1
column name in 22RV1_DESeq_counts.csv r22D4DMSO_N1


title: FM95 Parental 24h DMSO rep2

description:
Library name: FM95pDMS_N2
column name in FM95_DESeq_counts.csv FM95pDMS_N2


title: HMV-II Resistant 24h DMSO rep2

description:
Library name: HMVrDMSO_2
column name in HMV-II_DESeq_counts.csv HMVrDMSO_2

value: HMV-II


title: HMV-II Resistant 24h Bini+Enco rep1

description:
Library name: HMVrBE_1
column name in HMV-II_DESeq_counts.csv HMVrBE_1


title: HMV-II Resistant 24h Bini+Enco rep2

description:
Library name: HMVrBE_2
column name in HMV-II_DESeq_counts.csv HMVrBE_1


title: B_21_D


title: B_19_D


title: B_16_C


title: B_20_D


title: HMV-II Parental 24h Bini+Enco rep2

description:
Library name: HMVpBE_2
column name in HMV-II_DESeq_counts.csv HMVpBE_2


title: HMV-II Parental 24h Bini+Enco rep1

description:
Library name: HMVpBE_1
column name in HMV-II_DESeq_counts.csv HMVpBE_1


title: HMV-II Resistant 24h DMSO rep1

description:
Library name: HMVrDMSO_1
column name in HMV-II_DESeq_counts.csv HMVrDMSO_1


title: HMV-II Parental 24h DMSO rep2

description:
Library name: HMVpDMSO_2
column name in HMV-II_DESeq_counts.csv HMVpDMSO_2


title: B_15_C


title: B_13_C


title: MDA-MB-231 Resistant 24h Bini+Enco rep2

description:
Library name: MDAresD5BE_2
column name in 231RNAseq_DESeqNormalized.csv MDAresD5BE_2_count

value: breast cancer cells


title: B_11_D


title: HMV-II Parental 24h DMSO rep1

description:
Library name: HMVpDMSO_1
column name in HMV-II_DESeq_counts.csv HMVpDMSO_1


title: B_09_C


title: B_04_C


title: B_08_D


title: B_10_D


title: FM95 Parental 24h DMSO rep1

description:
Library name: FM95pDMS_N1
column name in FM95_DESeq_counts.csv FM95pDMS_N1


title: MDA-MB-231 Resistant 24h Bini+Enco rep1

description:
Library name: MDAresD5BE_1
column name in 231RNAseq_DESeqNormalized.csv MDAresD5BE_1_count


title: MDA-MB-231 Resistant 24h DMSO rep1

description:
Library name: MDAresDMSO_1
column name in 231RNAseq_DESeqNormalized.csv MDAresDMSO_1_count


title: B_02_C


title: MDA-MB-231 Resistant 24h DMSO rep2

description:
Library name: MDAresDMSO_2
column name in 231RNAseq_DESeqNormalized.csv MDAresDMSO_2_count


title: B_01_C


title: MDA-MB-231 Parental 24h Bini+Enco rep1

description:
Library name: MDAparD5BE_1
column name in 231RNAseq_DESeqNormalized.csv MDAparD5BE_1_count


title: B_18_C


title: MDA-MB-231 Parental 24h Bini+Enco rep2

description:
Library name: MDAparD5BE_2
column name in 231RNAseq_DESeqNormalized.csv MDAparD5BE_2_count


title: P_37_D

value: post-RYGB


title: MDA-MB-231 Parental 24h DMSO rep2

description:
Library name: MDAparDMSO_2
column name in 231RNAseq_DESeqNormalized.csv MDAparDMSO_2_count


title: MDA-MB-231 Parental 24h DMSO rep1

description:
Library name: MDAparDMSO_1
column name in 231RNAseq_DESeqNormalized.csv MDAparDMSO_1_count


title: P_34_D


title: I19

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

description: Library name: I19

data_processing:
Reads were mapped to the GRCh38 reference genome (GENCODE release 44) using STAR aligner (v2.7.9a), and gene-level counts were quantified with HTSeq-count (v2.0.2).
Assembly: GRCh38 reference genome (GENCODE release 44)
Supplementary files format and content: tab-delimited text file includes raw counts from HTSeq-count for each sample

growth_protocol: GSC1478 were cultured in GSC medium, which includes DMEM/F12 medium (Thermo Fisher Scientific, 11320-033), 2% B27 supplement (Thermo Fisher Scientific, 17504-044), 1 × antibiotic-antimycotic (Thermo Fisher Scientific, 15240062), 5 mg/mL heparin (Sigma-Aldrich, 9041-08-1), 20 ng/mL EGF (Peprotech, 100-15R), and 20 ng/mL bFGF (Peprotech, 100-18B). Cells were cultured in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sepuencing libraries.
RNA library for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module, Ultra II RNA Library Prep Kit, and Multiplex Oligos (NEB, Cat #E7490, E7775, E6609) according to the manufacturer’s instruction.

value: patient-derived glioma stem-like cells

value: Overexpress dCasRx-RBM25 and gRNA I19


title: I16_rep1

description: Library name: I16_rep1

value: Overexpress dCasRx-RBM25 and gRNA I16


title: P_36_D


title: P_33_D


title: NC_rep2

description: Library name: NC_rep2

value: Overexpress dCasRx-RBM25 and control gRNA


title: NC_rep1

description: Library name: NC_rep1


title: P_31_C


title: I16_rep2

description: Library name: I16_rep2


title: B_03_C


title: P_29_C


title: P_28_D


title: Pacemaker cells, mCherry overexpression, GFP

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description:
Library name: Control
10XGenomics

data_processing:
The demultiplexing, mapping, barcoded processing, gene counting, deduplication and aggregation were made using RNA STARSolo software 2.7.11a
Assembly: Human hg19
Supplementary files format and content: Tab seperated values files and matrix files

source_name: Human iPSCs

extract_protocol:
Cells were dissociated using 1x TrypLE Select (Thermo Fisher Scientific #12563011). The cells were then resuspended in PBS supplemented with 1% BSA.
Single-cell RNA sequencing libraries were prepared according to the manufacturer’s instructions using the 10x Genomics Chromium Single Cell 3' v2 Reagent Kit. Briefly, single-cell suspensions were loaded onto the Chromium Controller to encapsulate individual cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs), where cell lysis and barcoded reverse transcription occurred. Each GEM contained a unique 10x barcode, a unique molecular identifier (UMI), and poly(dT) primers to capture mRNA molecules. Following reverse transcription, cDNA was amplified using PCR and size-selected for optimal library construction. Sequencing libraries were prepared by enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, and sample index PCR. Libraries were quantified using TapeStation (Agilent) and pooled for sequencing.

treatment_protocol: AAV transduction

value: Human iPSCs

value: WT

value: Pacemaker Differentiation


title: Pacemaker cells, PITX2c overexpression, GFP

description:
Library name: Overexpression
10XGenomics

value: PITX2c Overexpression


title: P_35_D


title: MOLM-13, RUNX1, biol rep 2 (CUT&Run)

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

description: Library name: MOLM-13 RUNX1 CUT_Run biological replicate 2

data_processing:
Datasets were validated with FastQC before and after removing Illumina universal adapters with Cutadapt.
Paired-end reads were mapped to UCSC hg38 using bowtie2 with parameters: --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700. Spike-in reads were mapped to E. coli K-12 genome with parameters: --end-to-end --very-sensitive --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700
Aligned files were then filtered for mapped reads with MAPQ>30, sorted, and indexed with SAMtools, with duplicate reads marked and removed by Picard MarkDuplicates.
Continuous-valued data tracks (bedGraph and bigWig) were generated using genomecov in bedtools v2.30.0 (-bg option) and calibrated using total number of spike-in reads.
Peak identification was done for PTBP1 and RUNX1 samples using MACS3 with a q-value threshold of 10-7
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak (for PTBP1 and RUNX1 only)
Library strategy: CUT&Run

extract_protocol:
DNA was extracted using the phenol–chloroform extraction method and precipitated using chilled 75% ethanol.
DNA pellets were dissolved in 30 µl of 0.1 × TE (1 mM Tris pH 8, 0.1 mM EDTA) supplemented with a 1:400 dilution of 10 mg/ml RNase A (Thermo Scientific cat. no. EN0531) and incubated in a 37 °C water bath for 15 min. Libraries were amplified by addition of 2 µl each of barcoded 10 mM i5 and i7 primer solutions and NEBNext HiFi 2 × PCR Master mix (NEB cat. no. M0541) with 13 rounds of amplification as described previously. Sequencing libraries were purified using a 1.3× ratio of HighPrep PCR Cleanup beads (MagBio genomics cat. no. AC-60500) as per manufacturer’s instructions and eluted in 0.1 × TE. Library quality and concentrations were determined using the D1000 TapeStation system (Agilent).

value: acute myeloid leukemia

tag: cut&tag antibody

value: RUNX1 (Abcam)


title: P_32_D


title: P_27_C


title: MOLM-13, H3K27me3, biol rep 2 (CUT&Run)

description: Library name: MOLM-13 H3K27me3 CUT_Run biological replicate 2

value: H3K27me3 (CST)


title: P_30_C

value: intestine


title: dCasRx_RBM25_only

description: Library name: dCasRx_RBM25_only

value: Overexpress dCasRx-RBM25


title: MOLM-13, IgG, biol rep 2 (CUT&Run)

description: Library name: MOLM-13 IgG CUT_Run biological replicate 2

value: IgG (CST, Danvers, MA)


title: MOLM-13, H3K27me3, biol rep 1 (CUT&Run)

description: Library name: MOLM-13 H3K27me3 CUT_Run biological replicate 1


title: P_20_D


title: MOLM-13, RUNX1, biol rep 1 (CUT&Run)

description: Library name: MOLM-13 RUNX1 CUT_Run biological replicate 1


title: MOLM-13, PTBP1, biol rep 1 (CUT&Run)

description: Library name: MOLM-13 PTBP1 CUT_Run biological replicate 1

value: PTBP1 (Thermo)


title: P_21_D


title: P_23_D


title: P_19_D


title: MOLM-13, IgG, biol rep 1 (CUT&Run)

description: Library name: MOLM-13 IgG CUT_Run biological replicate 1


title: MOLM-13, PTBP1, biol rep 2 (CUT&Run)

description: Library name: MOLM-13 PTBP1 CUT_Run biological replicate 2


title: P_15_C


title: P_18_C


title: MOLM-13, RUNX1, biol rep 2 (CUT&Tag)

description: Library name: MOLM-13 RUNX1 CUT_Tag biological replicate 2

data_processing:
Datasets were validated with FastQC before and after removing Illumina universal adapters with Cutadapt.
Paired-end reads were mapped to UCSC hg38 using bowtie2 with parameters: --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700. Spike-in reads were mapped to E. coli K-12 genome with parameters: --end-to-end --very-sensitive --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700
Aligned files were then filtered for mapped reads with MAPQ>30, sorted, and indexed with SAMtools, with duplicate reads marked and removed by Picard MarkDuplicates.
Continuous-valued data tracks (bedGraph and bigWig) were generated using genomecov in bedtools v2.30.0 (-bg option) and calibrated using total number of spike-in reads.
Peak identification was done for PTBP1 and RUNX1 samples using MACS3 with a q-value threshold of 10-7
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak (for PTBP1 and RUNX1 only)
Library strategy: CUT&Tag


title: P_13_C


title: MOLM-13, RUNX1, biol rep 1 (CUT&Tag)

description: Library name: MOLM-13 RUNX1 CUT_Tag biological replicate 1


title: P_11_D


title: P_16_C


title: MOLM-13, IgG (CUT&Tag)

description: Library name: MOLM-13 IgG CUT_Tag


title: P_09_C


title: P_04_C


title: P_10_D


title: P_03_C


title: MOLM-13, PTBP1, biol rep 1 (CUT&Tag)

description: Library name: MOLM-13 PTBP1 CUT_Tag biological replicate 1


title: OPC, Cortex, repeat-3

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

description: GABA Con3

data_processing:
Clean reads after filtering were aligned to the reference genome with HISAT.
Bowtie2 were used to align the clean reads to the reference genes.
Differential expression analysis was performed using DESeq2.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: xlsx file includes normalized read count.

source_name: Cortex

growth_protocol: For Cultured OPC, OPC were isolated and cultured in OPC proliferation medium for 2 days, followed by 200 uM GABA or 200 uM Glutamate treatment for 24 h, then subjected to RNA sample collection by Trizol.

extract_protocol:
For acute-isolated OPC, Mice were anesthetized and transcardially perfused with ice-cold HBSS. The brains were isolated with the meninges removed, followed by dissection of the cortex and hippocampus, which were then minced and digested by 1% papain. OPCs were isolated from the resulting cell suspension via immunopanning and directly lysed on the panning plate by Trizol.
Poly-A selected method was used to prepare the RNA-seq library. Sequencing was performed on the DNBSEQ platform with SE50 sequencing length

value: Cortex

value: Cultured OPC

value: wild type


title: P_25_D

value: post-RYGB


title: OPC, Cortex, repeat-2

description: GABA Con2


title: P_08_D


title: OPC, Cortex, GABA, repeat-3

value: GABA treatment


title: OPC, Cortex, GABA, repeat-2


title: OPC, Cortex, GABA, repeat-1


title: P_02_C


title: P_01_C


title: OPC, Cortex, Glutamate, repeat3

value: Glutamate treatment


title: OPC, Cortex, Glutamate, repeat2


title: ATAC_TSCM_D3_P2_2

data_processing:
For RNA-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was employed to count mapped reads for genomic features. For MeRIP-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”. Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1). Differentially methylated peaks were identified by exomePeak2 (v1.10.0). Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”. Gene Ontology analysis was performed using DAVID (v2024q2). For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates. For CUT&Tag, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of H3K27me3 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization. For ATAC-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. MACS2 (v2.2.7.1) was used to call accessible peaks. Csaw was utilized to identify differentially accessible peaks using the TMM (trimmed mean of M-values) method, following a previously established pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For RNA-seq and MeRIP-seq, total RNA was extracted with TRIzol reagent. CUT&Tag was performed according to the manufacturer’s protocol (Vazyme, TD904). For ATAC-seq, 50,000 cells were collected and washed twice in pre-cold PBS without DNase. Nuclei were isolated, lysed, and incubated with Tn5 transposase according to the manufacturer’s protocol (Vazyme, TD501). Transposed DNA was isolated using a DNA Clean & Concentrator kit (Zymo).
For RNA-seq, Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). For MeRIP-seq, The NEBNext® Ultra™ II RNA Library Prep Kit (NEB, E7770) was used to construct libraries for both the input and IP samples. For CUT&Tag, Library preparation and amplification was followed by manufacturer’s protocol (Vazyme, TD904). For ATAC-seq, Libraries were prepared by amplifying DNA for 12 cycles using the TruePrep DNA Library Prep Kit (Vazyme). After amplification, libraries were purified using VAHTS DNA Clean Beads (Vazyme).

value: embryonic stem cells

value: METTL3 inducible knockout


title: OPC, Cortex, Glutamate, repeat1


title: MOLM-13, PTBP1, biol rep 2 (CUT&Tag)

description: Library name: MOLM-13 PTBP1 CUT_Tag biological replicate 2


title: ATAC_TSCM_D3_P2_1


title: ATAC_TSCM_D3_P0_2

value: DOX


title: OPC, Cortex, repeat3

description: GLU Con3


title: OPC, Cortex, repeat2

description: GLU Con2


title: ATAC_TSCM_D3_P0_1


title: OPC, Cortex, repeat1

description: GLU Con1


title: HUDEP-2_ASO23_ATAC

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: Library name: sample2

data_processing:
Adaptor sequence were trimmed from raw reads with Trim_Galore (v0.6.6) with the –nextera parameter.
The processed reads were mapped to human genome with Bowtie (v1.1.2) with parameter -k 1 and -m 1.
Duplicates were removed using MarkDuplicates with parameter --REMOVE_DUPLICATES true
To create the coverage track, bam file was converted to bed file with BEDTools (v2.25.0). The resulting BED files were converted to WIG format, followed by conversion to BigWig format using the wigToBigWig command from the UCSC Kent Utilities.
Assembly: hg38
Supplementary files format and content: bigWig format

extract_protocol:
ATAC-seq was performed using Zymo-Seq ATAC Library Kit (Zymo D5458) following manufacturer’s instructions.
Amplified DNA was collected with column and validated with Aligent Analyzer 4200.

value: cell line

value: human erythroid progenitor cells

value: E+58 ASO treated


title: TSC_min_DOX_P3_1_input

data_processing:
For RNA-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was employed to count mapped reads for genomic features. For MeRIP-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”. Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1). Differentially methylated peaks were identified by exomePeak2 (v1.10.0). Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”. Gene Ontology analysis was performed using DAVID (v2024q2). For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates. For CUT&Tag, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of H3K27me3 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization. For ATAC-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. MACS2 (v2.2.7.1) was used to call accessible peaks. Csaw was utilized to identify differentially accessible peaks using the TMM (trimmed mean of M-values) method, following a previously established pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: MeRIP-seq

value: trophoblast stem cell

value: KO

value: wo DOX P3


title: TSC_min_DOX_P3_2_input