title: U2OS-PTBP1 knockout cells, untreated, cytoplasmic fraction, replicate 2

description:
Library name: U2OS-PTBP1-KO_UNT_CYT_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

data_processing:
Basecalling and demultiplexing was performed using BCL Convert
Transcript abundance was estimated using Kallisto (0.46.1) with parameters --bootstrap-samples 30 --single-overhang --rf-stranded. The ensembl GRCh38 cdna transcriptome build was used, appended with ERCC control transcript sequences.
Gene-level counts were generated in R using the tximport package. Counts were normalized to ERCC spike-ins using DESeq2, implemented with the function "estimateSizeFactors" with the option "controlGenes" set to the identities of the 92 ERCC transcripts. Counts were filtered for protein coding genes.
Assembly: GRCh38
Supplementary files format and content: CSV file of ERCC spike-in normalized counts for each sample

extract_protocol:
At assay endpoint cells were trypsinized, counted using a hemacytometer, pelleted, washed with PBS, and moved immediately to cellular fractionation. Cells were lysed in a hypotonic lysis buffer and left to swell on ice for 10 minutes. 1/3 of the lysate was removed and saved as the whole cell lysate (WCL) fraction. The samples were then spun for 30 seconds at 12000xg at 4 degrees. Supernatant was saved as the cytoplasmic (CYT) fraction. nuclei were washed 1x in wash buffer, the lysed in nuclei lysis buffer. Lysates were all normalized for differences in surfactant concentrations using a 10x nuclear lysis buffer. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134) according to manufacturer protocol. To facilitate absolute RNA quantification, polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were diluted 1:10 in nuclease-free water, and added to each sample at 1 µL/1,000,000 cells (or equivalently, 1,000,000 cells worth of nuclei or cytoplasm). ERCC spike-ins were added immediately following lysis of cells in RLT-plus buffer, and prior to all subsequent total RNA extraction steps using the RNeasy Plus kit. mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490).
RNAseq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit using the NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7765 and E7600).

treatment_protocol: Cells were seeded onto 15 cm plates (3 million cells per plate) and left to adhere overnight. Cells were then drugged with 1 µM triptolide the next day.

value: PTBP1 knockout

value: DMSO

value: 8 hours


title: U2OS-PTBP1 knockout cells, untreated, nuclear fraction, replicate 2

status: Public on Dec 13 2024

type: SRA

city: Worcester

first: Michael

last: Lee

state: MA

address: 368 Plantation Street

country: USA

institute: UMASS Chan Medical School

description:
Library name: U2OS-PTBP1-KO_UNT_NUC_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells were maintained in high glucose DMEM supplemented with 10% fetal bovine serum, penicillin/streptomycin, and glutamine in a humidified incubator with 5% CO2 at 37C

tag: cell line

tag: cell type

value: osteosarcoma

tag: genotype

tag: treatment

tag: time


title: U2OS-PTBP1 knockout cells, untreated, nuclear fraction, replicate 1

description:
Library name: U2OS-PTBP1-KO_UNT_NUC_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-PTBP1 knockout cells, untreated, cytoplasmic fraction, replicate 1

description:
Library name: U2OS-PTBP1-KO_UNT_CYT_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: mDCs from MS patient 26

city: Badalona

first: eva

last: martinez caceres

address: Cami des escoles s/n

country: Spain

institute: Institut Germans Trias i Pujol

data_processing:
kallisto alignment
Assembly: NCBI build 36
Supplementary files format and content: tsv

molecule: total RNA

source_name: Blood

extract_protocol:
Monocytes were isolated from MS patients and Healthy donors using CD14 positive enrichment by negative selection followed by CD14 positive selection
poly A enrichment

tag: sample group

tag: tissue

value: Blood

tag: cohort

value: MS

value: dendritic cell

tag: gender

value: Male


title: U2OS-PTBP1 knockout cells, treated, nuclear fraction, replicate 2

description:
Library name: U2OS-PTBP1-KO_TRT_NUC_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 1 µM triptolide


title: 207854510094_R12C02

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human primary cell DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).

value: Spleen

tag: modification

tag: age

tag: Sex

value: M


title: mDCs from MS patient 25


title: tolDCs from MS patient 24

value: Female


title: U2OS-PTBP1 knockout cells, treated, nuclear fraction, replicate 1

description:
Library name: U2OS-PTBP1-KO_TRT_NUC_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R12C01

value: Testis


title: U2OS-PTBP1 knockout cells, treated, cytoplasmic fraction, replicate 2

description:
Library name: U2OS-PTBP1-KO_TRT_CYT_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-PTBP1 knockout cells, treated, cytoplasmic fraction, replicate 1

description:
Library name: U2OS-PTBP1-KO_TRT_CYT_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R11C03

value: Placenta

value: F


title: mDCs from MS patient 34


title: tolDCs from MS patient 22


title: U2OS cells, untreated, nuclear fraction, replicate 2

description:
Library name: U2OS_UNT_NUC_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: WT


title: U2OS cells, untreated, whole cell lysate, replicate 2

description:
Library name: U2OS_UNT_WCL_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: mDCs from MS patient 22


title: 207854510094_R11C02

value: Ovary


title: 207854510094_R11C01

value: Heart


title: U2OS cells, untreated, nuclear fraction, replicate 1

description:
Library name: U2OS_UNT_NUC_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: DMSO


title: 207854510094_R10C03

value: Eye


title: U2OS cells, untreated, cytoplasmic fraction, replicate 2

description:
Library name: U2OS_UNT_CYT_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: osteosarcoma

value: 8 hours


title: U2OS cells, treated, whole cell lysate, replicate 2

description:
Library name: U2OS_TRT_WCL_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS cells, untreated, cytoplasmic fraction, replicate 1

description:
Library name: U2OS_UNT_CYT_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: tolDCs from MS patient 26

value: Blood

value: MS


title: mDCs from MS patient 21

value: dendritic cell


title: tolDCs from MS patient 21


title: 207854510094_R10C02


title: U2OS cells, treated, nuclear fraction, replicate 2

description:
Library name: U2OS_TRT_NUC_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 1 µM triptolide


title: U2OS cells, treated, whole cell lysate, replicate 1

description:
Library name: U2OS_TRT_WCL_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R10C01


title: U2OS cells, treated, nuclear fraction, replicate 1

description:
Library name: U2OS_TRT_NUC_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: tolDCs from MS patient 15

value: Male


title: U2OS cells, treated, cytoplasmic fraction, replicate 1

description:
Library name: U2OS_TRT_CYT_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS cells, untreated, whole cell lysate, replicate 1

description:
Library name: U2OS_UNT_WCL_Rep_1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: tolDCs from MS patient 20


title: U2OS cells, treated, cytoplasmic fraction, replicate 2

description:
Library name: U2OS_TRT_CYT_Rep_2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R09C03


title: 207854510094_R09C02

value: Bladder


title: 207854510094_R09C01


title: U2OS-NUP93 knockout cells, untreated, replicate 1

description:
Library name: NUP93_Unt_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

data_processing:
Basecalling and demultiplexing was performed using BCL Convert v4.3.6
Transcript abundance was estimated using Kallisto (0.46.1) with parameters --bootstrap-samples 30 --single-overhang --rf-stranded. The ensembl GRCh38 cdna transcriptome build was used, appended with ERCC control transcript sequences.
Gene-level counts were generated in R using the tximport package. Counts were normalized to ERCC spike-ins using DESeq2, implemented with the function "estimateSizeFactors" with the option "controlGenes" set to the identities of the 92 ERCC transcripts. Counts were filtered for protein coding genes.
Assembly: GRCh38
Supplementary files format and content: CSV file of ERCC spike-in normalized counts for each sample

extract_protocol:
At assay endpoint cells were trypsinized, counted using a hemacytometer, pelleted, washed with PBS, and moved immediately to RNA extraction. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134) according to manufacturer protocol. To facilitate absolute RNA quantification, polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were diluted 1:100 in nuclease-free water, and added to each sample at 1 µL/100,000 cells. ERCC spike-ins were added immediately following lysis of cells in RLT-plus buffer, and prior to all subsequent total RNA extraction steps using the RNeasy Plus kit. mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490).
RNAseq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit using the NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7765 and E7600).

treatment_protocol: Cells were seeded onto six-well plates (300,000 cells per well) and left to adhere overnight. Cells were then drugged with 1 µM triptolide the next day.

value: NUP93 knockout


title: tolDCs from healthy donor 13

value: HD

value: Female


title: U2OS-NUP93 knockout cells, treated, replicate 2

description:
Library name: NUP93_Trt_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-NUP93 knockout cells, treated, replicate 1

description:
Library name: NUP93_Trt_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-Nontargeting cells, untreated, replicate 2

description:
Library name: NONT_Unt_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: WT (Nontargeting)


title: U2OS-NUP93 knockout cells, untreated, replicate 2

description:
Library name: NUP93_Unt_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R08C03

value: Colon

value: M


title: tolDCs from healthy donor 2


title: U2OS-Nontargeting cells, untreated, replicate 1

description:
Library name: NONT_Unt_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-Nontargeting cells, treated, replicate 2

description:
Library name: NONT_Trt_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: mDCs from healthy donor 2


title: U2OS-Nontargeting cells, treated, replicate 1

description:
Library name: NONT_Trt_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R08C01

value: Testis


title: Monocytes from MS patient 43

value: monocyte


title: U2OS-EXOSC5 knockout cells, treated, replicate 2

description:
Library name: EXOSC5_Trt_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: EXOSC5 knockout


title: U2OS-EXOSC5 knockout cells, untreated, replicate 2

description:
Library name: EXOSC5_Unt_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: osteosarcoma

value: DMSO


title: 207854510094_R07C03

value: Placenta

value: F


title: U2OS-EXOSC5 knockout cells, untreated, replicate 1

description:
Library name: EXOSC5_Unt_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 8 hours


title: Monocytes from healthy donor 42

value: Blood


title: U2OS-EXOSC5 knockout cells, treated, replicate 1

description:
Library name: EXOSC5_Trt_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 1 µM triptolide


title: U2OS cells, Day 1, replicate 2

description:
Library name: WT_1d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

treatment_protocol: Cells were seeded onto six-well plates (300,000 cells per well) and left to adhere overnight. Cells were then drugged with 1 µM triptolide the next day (D0). To evaluate the transcriptome of WT cells after 1 day of triptolide, cells were cotreated with 50 µM Z-VAD to inhibit loss of material from cell death

value: Wild-type

value: 1 day


title: U2OS cells, Day 1, replicate 1

description:
Library name: WT_1d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: Monocytes from MS patient 41

value: MS


title: mDCs from MS patient 15

value: dendritic cell

value: Male


title: Monocytes from MS patient 40

value: Female


title: U2OS cells, Day 0, replicate 2

description:
Library name: WT_0d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 0 days


title: 207854510094_R07C02

value: Bladder

value: M


title: U2OS-BAX-BAK1 -/- cells, Day 8, replicate 1

description:
Library name: DKO_8d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: BAX Knockout, BAK1 knockout

value: 8 days


title: 207854510094_R06C03

value: Colon


title: Monocytes from healthy donor 38

value: HD

value: monocyte


title: 207854510094_R08C02

value: Stomach


title: U2OS-BAX-BAK1 -/- cells, Day 6, replicate 2

description:
Library name: DKO_6d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: osteosarcoma

value: 6 days


title: U2OS-BAX-BAK1 -/- cells, Day 6, replicate 1

description:
Library name: DKO_6d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 1 µM triptolide


title: 207854510094_R06C02

value: Trachea


title: 207854510094_R06C01

value: Testis


title: U2OS-BAX-BAK1 -/- cells, Day 4, replicate 2

description:
Library name: DKO_4d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 4 days


title: U2OS-BAX-BAK1 -/- cells, Day 4, replicate 1

description:
Library name: DKO_4d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: Monocytes from MS patient 36

value: Blood

value: MS


title: U2OS-BAX-BAK1 -/- cells, Day 2, replicate 1

description:
Library name: DKO_2d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 2 days


title: U2OS-BAX-BAK1 -/- cells, Day 2, replicate 2

description:
Library name: DKO_2d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R05C03

value: Thyroid

value: F


title: U2OS-BAX-BAK1 -/- cells, Day 10, replicate 2

description:
Library name: DKO_10d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: BAX Knockout, BAK1 knockout

value: 10 days


title: Monocytes from healthy donor 35

value: Female


title: U2OS-BAX-BAK1 -/- cells, Day 10, replicate 1

description:
Library name: DKO_10d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS cells, Day 0, replicate 1

description:
Library name: WT_0d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: Wild-type

value: 0 days


title: 207854510094_R05C02

value: Bladder

value: M


title: Monocytes from MS patient 34

value: monocyte

value: Male


title: U2OS-BAX-BAK1 -/- cells, Day 0, replicate 2

description:
Library name: DKO_0d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: osteosarcoma

value: 1 µM triptolide


title: 207854510094_R07C01


title: U2OS-BAX-BAK1 -/- cells, Day 0, replicate 1

description:
Library name: DKO_0d_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R05C01


title: 207854510094_R04C02

value: Trachea


title: 207854510094_R04C03

value: Liver


title: p21Low_Plate3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Sequenced samples were quality and adapter trimmed using cutadapt v4.1 (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -n 1 -m 31 --nextseq-trim 20 --max-n 0)
Trimmed reads were quantified using salmon v1.9.0 against the Ensembl GRCh38.107 cDNA and ncRNA annotations (-l A --softclip --softclipOverhangs --allowDovetail --seqBias --gcBias)
Analysis of differential expression was performed within R using the DESeq2 package (v1.34.0), opimising p values using IHW (1.22.0), and applying fold change skrinkage using ashr (2.2-54)
Quality assessments were performed, including PCA and hierarchical clustering, prior to analysis of differential expression using the Wald test with a specified FDR (alpha<0.05) and fold change requirement (absolute log2FC>1.5) using a design considering batch.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files containing raw outputs from Salmon

source_name: NCI-H1944 mRuby-PCNA p21-mVenus

growth_protocol: Cells were grown in RPMI-1640 medium (Gibco) supplemented with 10% FBS and 1% Penicillin/Streptomycin (Sigma). Cells were passaged every 3-4 days, 1:6.

extract_protocol:
Total cell RNA was extracted using the Qiagen Rneasy extraction kit according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepard using NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module following manufacturer's protocols.

treatment_protocol: Untreated NCI-H1944 mRuby-PCNA p21-mVenus cells were trypsinised, washed in PBS, resuspended in sterile PBS/1%BSA and filtered into 5ml round bottomed polystyrene test tubes with cell strainer snap caps. Cells were FACS sorted to isolate p21High, mRuby-PCNA low (quiescent) and p21Low, mRuby-PCNA high (proliferating) populations. Cells were then centrifuged, washed in PBS and RNA extracted.

value: NCI-H1944 mRuby-PCNA p21-mVenus

tag: group

tag: replicate


title: p21Low_Plate4


title: Monocytes from healthy donor 39

value: Blood

value: HD


title: p21Low_Plate1


title: p21Low_Plate2


title: p21High_Plate4


title: p21High_Plate3


title: Monocytes from healthy donor 32


title: Monocytes from healthy donor 33


title: U2OS-BAX-BAK1 -/- cells, Day 8, replicate 2

description:
Library name: DKO_8d_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 8 days


title: 207854510094_R03C03

value: Thyroid


title: Monocytes from healthy donor 31


title: p21High_Plate2


title: 207854510094_R04C01

value: Spinal Cord

value: F


title: p21High_Plate1


title: Monocytes from healthy donor 29

value: Female


title: Rb2-2

city: Changchun

first: Qingxia

last: Huang

state: Jilin

address: Boshuo Road No.1035

department: Notheast Asia Research nstitute of Traditional Chinese Medicine

country: China

institute: 长春中医药大学

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: mm10

organism: Rattus norvegicus

growth_protocol: The H9c2 cells were cultured in gibco DMEM basal medium containing 10%FBS and 1% penicilliomycin mixture, and passed once every 2-3 days.

extract_protocol:
Tiangen DP411 kit was used  complete nucleic acid extraction.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: H9C2 cells were pretreated with ginsenoside Rb2 for 48h, and then treated with glucose-oxygen deprivation in a three-gas incubator for 4-6 h, and reoxygenated with glucose-reoxygenation for 12 h.

value: Embryonic cardiomyocyte

value: WT

value: ginsenoside Rb2


title: 207854510094_R03C02

value: Bladder


title: Rb2-3


title: Monocytes from healthy donor 28

value: monocyte


title: Rb2-1


title: Ctrl-3

value: NC


title: 207854510094_R03C01

source_name: Human cell line DNA


title: Ctrl-2


title: 207854510094_R02C03

value: M


title: Ctrl-1


title: Monocytes from healthy donor 27


title: 207854510094_R02C02

value: Trachea


title: Kit_positive_1

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

description:
Bulk RNA-seq
counts_table.csv

data_processing:
Bulk sequencing reads were aligned to the GRCm39 reference genome and transcriptome (version 105) using the STAR aligner (version 2.7.8a) and counted using featureCounts (version 2.0.0) (bulk)
Single cell reads are mapped to the mouse transcriptome and counted using cellranger (version 6.1.2) (single-cell)
Assembly: Ensembl GRCm39/105 mm10 (bulk) and cellranger reference buil 2020-A mm10 (single-cell)
Supplementary files format and content: Raw bulk counts in CSV format (bulk) and filtered feature barcode matrices in h5 format (single-cell)

organism: Mus musculus

extract_protocol:
RNA extraction from sorted P14 T cells was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen)
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA).

value: spleen

tag: collect


title: 207854510094_R02C01

value: Heart


title: SC_Batch_2_Arm_d8

description: Single cell RNA-seq

source_name: P14 T cells, day 8 LCMV Armstrong

extract_protocol:
Sorted P14 T cells were hashtagged following the manufacturer's protocol (Biolegend)
Sample preparation followed by 10x Genomics scRNA-seq v3 chemistry protocol. Samples were processed as described on the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).


title: Monocytes from MS patient 26

value: Blood

value: MS

value: Male


title: Monocytes from healthy donor 37

value: HD


title: Kit_positive_2

description:
Bulk RNA-seq
counts_table.csv


title: SC_Batch_1_Arm_d8_lane_A

description: Single cell RNA-seq


title: Monocytes from MS patient 25


title: 207854510094_R01C03

value: Thyroid


title: CD62L_positive_1

description:
Bulk RNA-seq
counts_table.csv


title: 207854510094_R01C02

value: F


title: Monocytes from MS patient 23

value: Female


title: CD62L_positive_2

description:
Bulk RNA-seq
counts_table.csv


title: 207854510094_R01C01


title: SC_Batch_2_Arm_d21

description: Single cell RNA-seq

source_name: P14 T cells, day 21 LCMV Armstrong


title: SC_Batch_1_Clone13_d21_lane_B

description: Single cell RNA-seq

source_name: P14 T cells, day 21 LCMV clone13


title: Monocytes from MS patient 20


title: SC_Batch_1_Clone13_d21_lane_A

description: Single cell RNA-seq


title: Monocytes from healthy donor 30


title: Double_negative_1

description:
Bulk RNA-seq
counts_table.csv


title: SC_Batch_1_Arm_d21_lane_B

description: Single cell RNA-seq


title: Double_negative_2

description:
Bulk RNA-seq
counts_table.csv


title: Prkd3-/-_MEF_clone15_immortalized

city: St. John's

last: Leitges

state: NL

address: 300 Prince Philip Drive

department: Division of BioMedical Sciences, Faculty of Medicine

country: Canada

institute: Memorial University of Newfoundland

description: Library name: immortalizedMEF_Prkd3-/-_clone15

data_processing:
The quality of the FASTQ files were analyzed using FASTQC (version 0.12.0)
Pair-end reads obtained from RNA-seq data were mapped to the mouse reference genome (mm10) using STAR (version 2.7.10a) software with default parameters
Samtools (version 1.18) was used to convert the sequence alignment map (SAM) files were subsequently into the Binary Alignment Map (BAM) format.
Gene counts were assigned based on reads uniquely mapped to annotated genes in the Ensembl Mus_musculus.GRCm38.102.gtf using featureCounts function of Subread (version 2.0.6)
Assembly: mm10/GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Mouse Embryonic Fibroblast

growth_protocol: MEFs were cultured in DMEM – high glucose (Sigma-Aldrich) supplemented with 10% FCS, 1X non-essential amino acids (Cytiva), 1% Pen Strep (Gibco) and β-mercaptoethanol (Gibco).

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, ID: 80204)
Poly A-enriched RNA library preparation and sequencing was outsourced to Centre d’expertise et de services Génome Québec (Montreal, Canada)

treatment_protocol: Modified NIH 3T3 spontaneous immortalization protocol. Primary MEFs were passaged serially until they reached senescence. Once MEFs became senescent, culture media was shifted to MEF culture medium with 20% FCS. Prolonged cell culture gave rise to spontaneously immortalized cells (colonies), which then established immortalized MEF cell lines

value: Mouse Embryonic Fibroblast

value: immortalized Mouse Embryonic Fibroblast

value: immortalized


title: Prkd3-/-_MEF_clone14_immortalized

description: Library name: immortalizedMEF_Prkd3-/-_clone14


title: siUSP9X-5

city: Tianjin

first: Yi

last: Lei

address: Qixiangtai street NO.22

institute: Tianjin Medical University General Hospital

data_processing:
To identify DEGs, the expression level of each transcript was calculated acordng to the TPMmethod, RSEM was used to quantify gene abundance. We use DESeq2 and functional-enrichment analysis including Wiki pathway at P-value <0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file included raw counts for each sample

source_name: brain

extract_protocol:
Cells were harvested for RNA extraction using TRIzol reagent (SIGMA, #101254514). RNA concentration was determined by spectrophotometry using a Nanodrop ND-1000 (Thermo Fisher Scientific, USA).
RNA libraries for RNA-seq were prepared following Illumina Stranded mRNA Prep, Ligation using iug of totel RNA

value: brain

value: cell line

value: endothelial cell


title: Monocytes from MS patient 21

value: monocyte


title: SC_Batch_1_Arm_d21_lane_A

description: Single cell RNA-seq


title: siUSP9X-4


title: GFP_KRD_MORC2_cNF71_rep3

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Reads were aligned using STAR v2.7.1.a with options --outFilterMultimapNmax 100 --winAnchorMultimapNmax 200 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript counts were quantified using TEtranscripts v2.2.3
Assembly: hg38, gencode v35, and repeatmasker along with Nano and Firefly Lucifease CDS (spike-in mRNA) was included.
Supplementary files format and content: Transcript counts are stored in tab-delimited files with one row per transcript, quantification done using TEtranscripts. Both spike in normalized (normalized using DEseq2) and raw counts are included.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin/streptomycin

extract_protocol:
Cells washed once in PBS, then resuspended in TRIzol reagent (Life Technologies) and extracted according to manufacturer's instruction.
NEBNext Ultra II RNA Library Prep Kit was used with ribosomal RNA depletion for library preparation.

treatment_protocol: GFP transgene expression was induced with 1 ug/mL doxycycline for 2 days and cells were harvested on plate with Trizol.

value: HeLa

value: MORC2 knockout

tag: gfp transgene_overexpression


title: siUSP9X-3


title: Prkd3-/-_MEF_clone13a_immortalized

description: Library name: immortalizedMEF_Prkd3-/-_clone13a


title: Monocytes from MS patient 18


title: Monocytes from MS patient 16


title: Monocytes from MS patient 15


title: Prkd3-/-_MEF_clone15_primary

description: Library name: primaryMEF_Prkd3-/-_clone15

value: primary Mouse Embryonic Fibroblast

value: primary


title: GFP_KRD_MORC2_cNF71_rep1


title: Monocytes from MS patient 22

value: Blood

value: MS


title: siUSP9X-2


title: SC_Batch_2_Clone13_d21

description: Single cell RNA-seq

value: spleen


title: Prkd3-/-_MEF_clone13_immortalized

description: Library name: immortalizedMEF_Prkd3-/-_clone13


title: Monocytes from MS patient 19


title: GFP_WT_MORC2_cNF70_rep3


title: Monocytes from healthy donor 14

value: HD

value: Male


title: GFP_KRD_MORC2_cNF71_rep2


title: siUSP9X-1


title: siCtrl-5

value: siCtrl


title: GFP_WT_MORC2_cNF70_rep1


title: TCR_Library

city: Boston

first: Cody

last: Nelson

address: 221 Longwood Ave

institute: Brigham and Women's Hospital

library_source: transcriptomic single cell

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

source_name: CD4 T cells

extract_protocol:
Live CD4+CD19-CXCR5+GITR- cells were sorted based on VFP and TdTomato expression into Tfh0 (VFP-TdTomato-), Tfh21 single positive (VFP+TdTomato-), Tfh 21/13 double positive (VFP+TdTomato+) and Tfh13 single positive (VFP-TdTomato+). Cells were stained with TotalSeq-C Hashtags (Biolegened) and pooled in a single sample before loading.
Cells were resuspended in 0.4% BSA in PBS at a concentration of 2,000 cells per μl, then loaded onto a single lane (Chromium chip K, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′kit V2, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. 5’ mRNA library was sequenced to an average of 50,000 reads per cell, V(D)J library and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, all using Illumina Novaseq.

value: CD4 T cells

value: Mouse CD4 T  cell

value: 6-8 weeks


title: Monocytes from healthy donor 12


title: GFP_WT_MORC2_cNF70_rep2


title: Monocytes from healthy donor 13

value: Female


title: Monocytes from healthy donor 17


title: siCtrl-3

value: brain

value: cell line


title: siCtrl-2

value: endothelial cell


title: Prkd3-/-_MEF_clone14_primary

description: Library name: primaryMEF_Prkd3-/-_clone14

value: Mouse Embryonic Fibroblast


title: GEX_HTO_Library


title: Monocytes from MS patient 9

value: monocyte


title: Kdm5c fl/O female ESC + mKdm5d Tg clone 1

city: Ann Arbor

first: Sundeep

last: Kalantry

state: MI

address: 3710 Med Sci II 1241 Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Raw sequencing fastq data was adaptor-trimmed using the trimmomatic software (v0.36) with the settings ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:5:true SLIDINGWINDOW:5:30.  Trimmed data was aligned to the mouse mm9 (MGSCv37) genome assembly using STAR (v2.5.2a) with the options --outFilterMismatchNmax 10 and --outFilterMultimapNmax 1.  SAM files were converted to BAM files, sorted by coordinate, and indexed using the samtools software (v0.1.19).  Reads were aligned to exons defined by RefSeq and counted by the Python package HTseq by running the command HTSeq.scripts.count (Python v3.8).
bam files were converted to wiggle files using bamToWig.py
Assembly: mm9
Supplementary files format and content: Bigwig files include genome coverage after normalizing with a specified wigsum of 100000000. Tab-delimited counts files include the raw read counts aligned to exons using HTSeq.

source_name: Kdm5c fl/O + mKdm5d Tg Clone 10

growth_protocol: Mouse ESC lines were derived and cultured as described in PMCID: PMC7311189.

extract_protocol:
Total RNA was isolated from cell pellets by TRIzol (Invitrogen, #15596-018) extraction following the manufacturer’s protocol.  poly-A RNA purification from 1 µg total RNA was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490L) following the manufacturer’s instructions.
Libraries were prepared using purified mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7765L) following the manufacturer’s instructions.

value: Kdm5c fl/O + mKdm5d Tg Clone 10

value: embryonic stem cells

value: Kdm5c fl/O + mKdm5d Tg


title: siCtrl-1


title: Kdm5c fl/O female ESC + mKdm5d Tg clone 3

source_name: Kdm5c fl/O + mKdm5d Tg Clone 6

value: Kdm5c fl/O + mKdm5d Tg Clone 6


title: Kdm5c fl/O female ESC + mKdm5d Tg clone 2

source_name: Kdm5c fl/O + mKdm5d Tg Clone 2

value: Kdm5c fl/O + mKdm5d Tg Clone 2


title: GFP_cNF69_rep3

value: HeLa

value: MORC2 knockout

value: GFP


title: GFP_cNF69_rep1


title: 4sU labeling, 1µM ETO, rep3

city: Bethesda

first: Jun

last: Lyu

state: Maryland

address: 37 Convent Drive

department: Laboratory of Biochemistry and Molecular Biology

institute: National cancer institute

description: Library name: SLAMseq_ETO_J.rep3

data_processing:
Raw sequencing data of scRNA-seq was subjected to fastq calling, reads alignment, and quantification using cellranger7.1.0  with default parameters and standard pipeline.
Raw sequencing data of SLAM-seq were first trimmed using cutadpt (v1.15) and then analyzed using SLAM-DUNK (v0.4.3) to map, filter and quantify reads containing T-to-C mutation.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separate values files and matrix files

source_name: Jurkat T Clone E6-1

extract_protocol:
For single cell RNA sequencing, single cell suspension was prepared for 10X Genomics sample loading. For RNA-seq, RNA was extracted using RNeasy Mini Kit (Qiagen).
For NOTE-seq, Libraries were constructed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E) with serval additional steps detaied in the Method section. For regular 10xgenomics, libraries were constructed using  Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E). For SLAM-seq, 2 µg RNA were combined with 10 mM iodoacetamide (Sigma-Aldrich, St. Louis, MO, USA), 50 mM sodium phosphate buffer (pH 8.0) and 50% DMSO, followed by 15 min of incubation at 50°C. The reaction was stopped by adding 20 mM DTT, followed by RNA purification using 1.8X RNA beads (Aline Bioscience) and RNA elution with 11 µl nuclease-free water. Then, 500 ng RNA was subject to library construction using Quant-seq 3′ mRNA-Seq Library Prep Kit (Lexogen)

value: Jurkat T Clone E6-1

value: T lymphocytes


title: Kdm5c ∆/Y;Kdm5d∆ male ESC biol.rep3

source_name: Kdm5c delta/Y;Kdm5d delta number 8

value: Kdm5c delta/Y;Kdm5d delta number 8

value: Kdm5c delta/Y;Kdm5d delta


title: Monocytes from healthy donor 8

value: Blood

value: HD

value: Male


title: Monocytes from MS patient 6

value: MS

value: Female


title: Prkd3-/-_MEF_clone13_primary

description: Library name: primaryMEF_Prkd3-/-_clone13

value: Mouse Embryonic Fibroblast

value: primary Mouse Embryonic Fibroblast

value: primary


title: HS Groin Perilesion 2

city: New York

first: Catherine

last: Lu

state: NY

address: 540 1st Avenue

department: Plastic Surgery

institute: NYU School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: hg19
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

source_name: HS Groin Perilesion

extract_protocol:
Surgical biopsied tissue was digested into cell suspensions and isolated using anti-human hashtag antibodies.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)
scRNA-seq and V(D)J seq

value: Hidradenitis suppurativa (HS) skin

tag: tissue type

value: perilesional (non-inflammed)

value: mixed skin cells

tag: sample type

value: patient sample single cell suspension


title: siCtrl-4

value: brain

tag: cell line

value: cell line

tag: cell type

value: endothelial cell

value: siCtrl


title: HS Groin Perilesion 1


title: 4sU labeling, 1µM ETO, rep2

description: Library name: SLAMseq_ETO_J.rep2

value: Jurkat T Clone E6-1

value: T lymphocytes


title: Kdm5c ∆/Y;Kdm5d∆ male ESC biol.rep2

source_name: Kdm5c delta/Y;Kdm5d delta number 6

value: Kdm5c delta/Y;Kdm5d delta number 6

value: embryonic stem cells

tag: genotype

value: Kdm5c delta/Y;Kdm5d delta


title: Monocytes from healthy donor 2

source_name: Blood

value: Blood

value: HD

value: monocyte

value: Female


title: Monocytes from MS patient 10

value: MS


title: Kdm5c ∆/Y;Kdm5d∆ male ESC biol.rep1

source_name: Kdm5c delta/Y;Kdm5d delta number 1

value: Kdm5c delta/Y;Kdm5d delta number 1


title: Monocytes from healthy donor 1

value: Male


title: 4sU labeling, 1µM ETO, rep1

description: Library name: SLAMseq_ETO_J.rep1


title: HS Groin Lesion 1

source_name: HS Groin Lesion

value: Hidradenitis suppurativa (HS) skin

value: lesional (inflammed)

value: mixed skin cells

value: patient sample single cell suspension


title: 4sU labeling, 50nM CPT, rep3

description: Library name: SLAMseq_CPT_J.rep3


title: GFP_cNF69_rep2

value: HeLa

value: MORC2 knockout

value: GFP


title: HS Axilla Lesion 2

source_name: HS Axilla Lesion


title: Kdm5d ∆ male ESC biol.rep2

source_name: Kdm5d delta number 4

value: Kdm5d delta number 4

value: Kdm5d delta


title: Kdm5d ∆ male ESC biol.rep3

source_name: Kdm5d delta number 9

value: Kdm5d delta number 9

value: embryonic stem cells


title: HS Axilla Perilesion 1

source_name: HS Axilla Perilesion

value: perilesional (non-inflammed)


title: 4sU labeling, 50nM CPT, rep2

description: Library name: SLAMseq_CPT_J.rep2

value: Jurkat T Clone E6-1

value: T lymphocytes


title: 4sU labeling, 50nM CPT, rep1

description: Library name: SLAMseq_CPT_J.rep1


title: HS Groin Lesion 2


title: DN.mTEClo.DonorD

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Samples were individually encapsulated using 10X single cell 3' RNA-seq kit

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as transcript-by-cell count matrices using Cell Ranger (v7.0, 10x Genomics).
Cells with high mitochondrial content, low or high gene number, or lineage markers of contaminants were filtered out in Seurat
Assembly: hg38
Supplementary files format and content: tsv files for barcodes and features, and mtx file for counts

extract_protocol:
Tissue was minced with scissors and lymphocyte-rich supernatant was removed, then thymic fragments were digested with collagenase and dispase. EpCAM+ cells were magnetically enriched (Donors A, B, and E) or CD45+ cells were magnetically depleted (Donors C and D). Cells were stained with fluorescent antibodies and flow sorted into DMEM/25 mM HEPES/10% FCS. Single cells were encapsulated following 10x Genomics protocols.
10x Genomics library prep, 3' v3.1 chemistry

value: 3 months

tag: organ

value: Thymus

tag: treatment

tag: hashid


title: Kdm5d ∆ male ESC biol.rep1

source_name: Kdm5d delta number 2

value: Kdm5d delta number 2


title: HS Axilla Lesion 1

tag: tissue

value: Hidradenitis suppurativa (HS) skin


title: 4sU labeling, control, rep2

description: Library name: SLAMseq_control_J.rep2


title: Kdm5c ∆/Y male ESC biol.rep2

source_name: Kdm5c delta/Y number 10

value: Kdm5c delta/Y number 10

value: Kdm5c delta/Y


title: Normal Groin

source_name: Normal Groin

value: healthy/normal skin

value: mixed skin cells

value: patient sample single cell suspension


title: Normal Axilla

source_name: Normal Axilla


title: DN.mTEClo.DonorB

value: 2 days

value: Male


title: 4sU labeling, control, rep1

description: Library name: SLAMseq_control_J.rep1


title: DN.mTEClo.DonorC

value: 4 days

value: Female


title: Monocytes from MS patient 4

tag: sample group

value: Blood

tag: cohort

value: MS

value: monocyte

tag: gender


title: Kdm5c fl/Y male ESC biol.rep3

source_name: Kdm5c fl/Y number 8

value: Kdm5c fl/Y number 8

value: embryonic stem cells

value: Kdm5c fl/Y


title: DN.mTEClo.DonorA

value: Trisomy 21

tag: age

value: 4 months

tag: Sex

value: Thymus


title: BG7_WT_3

city: Jinan

first: Anjing

last: Chen

address: 107 Wenhua Xi Road

institute: Shandong University

data_processing:
following Spliced Transcripts Alignment to a Reference(STAR)
Assembly: GRCh38.primary_assembly.genome.fa.gz and gencode.v41.annotation.gtf.gz
Supplementary files format and content: tsv, count

source_name: glioblastoma

extract_protocol:
RNA was harvested using TRIzol
RNA libraries for RNA-seg were prepared using RNA Nano 6000 Assay Kit following manufacturer's protocols

value: glioblastoma

value: glioblastoma stem cell

tag: overexpression

value: HNRNPK (wildtype)

value: IDH wildtype, TP53 wildtype


title: deltaNp63beta,HCT116,TP53-/-,500ng/mL doxycycline,rep_2

city: Albany

first: Morgan

middle: A

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

description:
Library name: deltaNp63_beta_Dox_2
TPM values from kallisto

data_processing:
For RNAseq, Paired end RNA-seq reads were quantified using kallisto v0.46.2 in quant mode with 100 bootstraps against the Human transcriptome (ENSEMBL Homo sapiens v104 release) was downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz Resulting kallisto-derived TPM counts were imported into the R statistical computing enrvironment using tximport, followed by differential gene expression analysis via DEseq2
Paired end RNA-seq reads were quantified using kallisto v0.46.2 in quant mode with 100 bootstraps against the Human transcriptome (ENSEMBL Homo sapiens v104 release) was downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz Resulting kallisto-derived TPM counts were imported into the R statistical computing enrvironment using tximport, followed by differential gene expression analysis via DEseq2
Assembly: ENSEMBL homo sapies v104 transcriptome release
Supplementary files format and content: tab-separated value files containing standardized ENSMBL gene name, gene length, estimated tag counts, and transcripts per million (TPM) values; output from Kallisto that was imported into DEseq2 via tximport.

source_name: colon

growth_protocol: HCT116 TP53-/- cells were grown in McCoy's 5A medium supplemented with 10% fetal bovine serum.

extract_protocol:
For RNAseq, Total RNA was extracted using Zymo Quick RNA miniprep. PolyA+ mRNA was extracted using oligo-d(T) beads before library construction.
RNAseq libraries were constructed from polyA+ RNA by Azenta/GeneWiz.

treatment_protocol: 500ng/mL doxycycline (induced) or water (uninduced) for 24hrs.

value: colon

value: 500ng/mL doxycycline

tag: batch


title: BG7_WT_2


title: deltaNp63beta,HCT116,TP53-/-,500ng/mL doxycycline,rep_3

description:
Library name: deltaNp63_beta_Dox_3
TPM values from kallisto


title: DN.mTEClo.DonorE

value: 3 months


title: Kdm5c ∆/Y male ESC biol.rep1

source_name: Kdm5c delta/Y number 2

value: Kdm5c delta/Y number 2

value: Kdm5c delta/Y


title: M5_3

city: china

first: lianmin

last: li

state: changchun

address: No. 2888 Xincheng Street

institute: Jilin Agriculture University

description: Library name: M5_3

data_processing:
Qubit2.0 Fluorometer
Assembly: reference sequence
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: xls files include FPKM values for each Sample

extract_protocol:
total RNA was extracted following the manufacturer's instructions (TransZol Up Plus RNA Kit, Trans Gen Biotech).
The RNA sample was accurately tested for RNA integrity by the Agilent 2100 bioanalyzer, and the qualified RNA samples were used to build a library using the Illumina TruSeq RNA Library Prep Kit v2. Simply put, the obtained mRNA is fragmented and used as a template to synthesize cDNA. PCR amplification after purification and screening of cDNA. A library was constructed using the purified PCR products.

value: Macrophages

value: infected with M5 Brucella


title: M5_2

description: Library name: M5_2


title: Kdm5c fl/Y male ESC biol.rep2

source_name: Kdm5c fl/Y number 7

value: Kdm5c fl/Y number 7


title: M5_1

description: Library name: M5_1


title: LT_3

description: Library name: LT_3

value: infected with WT Brucella


title: BG7_WT_1


title: deltaNp63beta,HCT116,TP53-/-,500ng/mL doxycycline,rep_1

description:
Library name: deltaNp63_beta_Dox_1
TPM values from kallisto


title: 4sU labeling, control, rep3

description: Library name: SLAMseq_control_J.rep3

source_name: Jurkat T Clone E6-1

value: Jurkat T Clone E6-1

value: T lymphocytes


title: BG7_K422R_3

value: HNRNPK (422 site mutate from lysine to argnine)


title: deltaNp63beta,HCT116,TP53-/-,water,rep_3

description:
Library name: deltaNp63_beta_noDox_3
TPM values from kallisto

value: water


title: Kdm5c ∆/Y male ESC biol.rep3

source_name: Kdm5c delta/Y number 13

value: Kdm5c delta/Y number 13

value: embryonic stem cells


title: Kdm5c ∆/∆ female ESC biol.rep3

source_name: Kdm5c delta/delta number 12

value: Kdm5c delta/delta number 12

value: Kdm5c delta/delta


title: LT_2

description: Library name: LT_2


title: BG7_K422R_2

value: glioblastoma

value: glioblastoma stem cell

value: IDH wildtype, TP53 wildtype


title: deltaNp63beta,HCT116,TP53-/-,water,rep_2

description:
Library name: deltaNp63_beta_noDox_2
TPM values from kallisto

value: colon


title: Kdm5c ∆/∆ female ESC biol.rep2

source_name: Kdm5c delta/delta number 11

value: Kdm5c delta/delta number 11


title: LT_1

description: Library name: LT_1

value: Macrophages


title: deltaNp63beta,HCT116,TP53-/-,water,rep_1

description:
Library name: deltaNp63_beta_noDox_1
TPM values from kallisto


title: Endpoint_LNCaP_bioRep3

city: Vancouver

first: Nathan

last: Lack

state: BC

address: 2660 Oak S

institute: Vancouver Prostate Centre

description:
Library name: Endpoint_LNCaP_bioRep3
Endpoint- biological replicate 3

library_source: genomic

data_processing:
MAGeCK algorithm39 (version 0.5.9.2) was used through all steps of the analysis such as sgRNA quantification and identification of significantly depleted genes. For each sample, R1 fastq files were processed by MAGeCK's count function to provide sgRNA level counts shown below. Biological replicates were presented as individual input files during sgRNA counting. All samples were combined and median normalized by `–norm-method “median”` argument of MAGeCK’s count. Identification of essential genes was calculated by MAGeCK’s test function. For each comparison, replicates were pooled as “-t Arep1,Arep2,Arep3” and “-c Brep1,Brep2,Brep3” for conditionA and conditionB respectively. In addition, negative control sgRNA were supplied with “--control-sgrna” function. Median normalized combined tables were used for visualization. R (version 2021.09.0) and ggplot2 package (version 3.3.5) were used for boxplot and density plots. For area under the curve (AUC) analysis, publicly available python code “AUC Calculation (https://github.com/mhegde)’ downloaded from the source 80. AUC calculation was run following the instructions on GitHub (https://github.com/mhegde/auc-calculation). All calculated AUC data were plotted using R (version 2022.07.2).
Supplementary files format and content: data.count_normalized_publication.txt: files contain normalized counts from every sample from that batch.
Supplementary files format and content: RepMerged-gene_summary.txt: files contain analysis related to merged samples.
Library strategy: CRISPR Screen

source_name: Prostate

growth_protocol: LNCaP, RWPE-1 and HEK293T cell lines were purchased from ATCC. LNCaP-abl (Abl) cell line was a kind gift from Dr.Helmut Klocker and MR49F cell line was a kind gift from Dr. Amina Zoubeidi and Dr. Martin Gleave from Vancouver Prostate Center. ENZA-R cell line was generated by chronically treating LNCaP cells with increasing doses of enzalutamide in Koc University. LNCaP cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) and 1 % penicillin/streptomycin (Gibco, USA). LNCaP-abl cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 5% charcoal-stripped fetal bovine serum (Gibco, USA) and 1 % penicillin/streptomycin (Gibco, USA). MR49F and ENZA-R cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA), 1 % penicillin/streptomycin (Gibco, USA) and 10 μM enzalutamide. RWPE-1 cells were cultured in Keratinocyte SFM media (Gibco, USA) supplemented with 0.05 mg mL-1 bovine pituitary extract and 5 ng mL-1 human recombinant epidermal growth factor (Gibco, USA). HEK293T cells were cultured in DMEM (Gibco, USA), supplemented with 10% FBS and 1% penicillin/streptomycin. All cell lines were maintained in a humidified incubator at 37°C with 5% CO2. Cells were regularly tested for mycoplasma.

extract_protocol:
From the collected cells, genomic DNA was isolated by PureLink Genomic DNA mini kit (Invitrogen, K1820) according to the manufacturer’s instructions.
Integrated sgRNA sequences were amplified by PCR reaction. For this, 4 μg genomic DNA was amplified for 25 cycles by using Kapa HiFi HotStart ReadyMix (Roche, KK2602) mixed with 10 μM external forward and reverse primers. To introduce sequencing adapters, external PCR products were pooled and amplified for 15 cycles using internal primers. PCR product was gel-isolated. After quality check, PCR products were sequenced by Genewiz, USA. Each screen was repeated three times.

value: Prostate

value: LNCaP

value: Prostate carcinoma


title: Kdm5c ∆/∆ female ESC biol.rep1

source_name: Kdm5c delta/delta number 6

value: Kdm5c delta/delta number 6


title: Baseline_LNCaP_bioRep3

description:
Library name: Baseline_LNCaP_bioRep3
Baseline - biological replicate 3


title: BG7_Flag_2

value: Flag


title: deltaNp63alpha,HCT116,TP53-/-,500ng/mL doxycycline,rep_2

description:
Library name: deltaNp63_alpha_Dox_2
TPM values from kallisto

value: 500ng/mL doxycycline


title: Kdm5c fl/O female ESC biol.rep3

source_name: Kdm5c fl/O number 4

value: Kdm5c fl/O number 4

value: Kdm5c fl/O


title: Kdm5c fl/Y male ESC biol.rep1

source_name: Kdm5c fl/Y number 4

value: Kdm5c fl/Y number 4

value: embryonic stem cells

value: Kdm5c fl/Y


title: Endpoint_LNCaP_bioRep2

description:
Library name: Endpoint_LNCaP_bioRep2
Endpoint- biological replicate 2


title: BG5_WT_3

value: glioblastoma

value: HNRNPK (wildtype)


title: Kdm5c fl/O female ESC biol.rep1

source_name: Kdm5c fl/O number 1

value: Kdm5c fl/O number 1


title: Baseline_LNCaP_bioRep2

description:
Library name: Baseline_LNCaP_bioRep2
Baseline - biological replicate 2


title: deltaNp63alpha,HCT116,TP53-/-,500ng/mL doxycycline,rep_3

description:
Library name: deltaNp63_alpha_Dox_3
TPM values from kallisto

value: colon


title: deltaNp63alpha,HCT116,TP53-/-,500ng/mL doxycycline,rep_1

description:
Library name: deltaNp63_alpha_Dox_1
TPM values from kallisto


title: Kdm5c fl/∆ female ESC biol.rep3

source_name: Kdm5c fl/delta number 10

value: Kdm5c fl/delta number 10

value: Kdm5c fl/delta


title: BG5_WT_2

value: glioblastoma stem cell

value: IDH wildtype, TP53 wildtype


title: Baseline_LNCaP_bioRep1

description:
Library name: Baseline_LNCaP_bioRep1
Baseline - biological replicate 1

value: Prostate

value: LNCaP

value: Prostate carcinoma


title: Kdm5c fl/∆ female ESC biol.rep2

source_name: Kdm5c fl/delta number 7

value: Kdm5c fl/delta number 7


title: Endpoint_LNCaP_bioRep1

description:
Library name: Endpoint_LNCaP_bioRep1
Endpoint- biological replicate 1


title: deltaNp63alpha,HCT116,TP53-/-,water,rep_1

description:
Library name: deltaNp63_alpha_noDox_1
TPM values from kallisto

value: water


title: Kdm5c fl/O female ESC biol.rep2

source_name: Kdm5c fl/O number 2

value: Kdm5c fl/O number 2

value: Kdm5c fl/O


title: BG5_WT_1


title: deltaNp63alpha,HCT116,TP53-/-,water,rep_2

description:
Library name: deltaNp63_alpha_noDox_2
TPM values from kallisto


title: Kdm5c fl/∆ female ESC biol.rep1

source_name: Kdm5c fl/delta number 6

value: Kdm5c fl/delta number 6

value: embryonic stem cells


title: deltaNp63alpha,HCT116,TP53-/-,water,rep_3

description:
Library name: deltaNp63_alpha_noDox_3
TPM values from kallisto


title: BG7_Flag_3

source_name: glioblastoma

value: glioblastoma

value: Flag


title: Baseline_MR49F_bioRep3

description:
Library name: Baseline_MR49F_bioRep3
Baseline - biological replicate 3

value: Enzalutamide


title: KO-8

source_name: brain

value: brain

value: Tissue

value: endothelial cell


title: BG7_Flag_1

value: glioblastoma stem cell


title: KO-3


title: Kdm5c fl/fl female ESC biol.rep2

source_name: Kdm5c fl/fl number 20

value: Kdm5c fl/fl number 20

value: Kdm5c fl/fl


title: Kdm5c fl/fl female ESC biol.rep3

source_name: Kdm5c fl/fl number 4

value: Kdm5c fl/fl number 4


title: Endpoint_MR49F_bioRep2

description:
Library name: Endpoint_MR49F_bioRep2
Endpoint- biological replicate 2

value: Prostate

value: Prostate carcinoma


title: Baseline_MR49F_bioRep2

description:
Library name: Baseline_MR49F_bioRep2
Baseline - biological replicate 2


title: BG5_K422R_1

value: HNRNPK (422 site mutate from lysine to argnine)

value: IDH wildtype, TP53 wildtype


title: Endpoint_MR49F_bioRep1

description:
Library name: Endpoint_MR49F_bioRep1
Endpoint- biological replicate 1


title: BG5_Flag_3


title: Kdm5c fl/fl female ESC biol.rep1

source_name: Kdm5c fl/fl number 18

value: Kdm5c fl/fl number 18


title: P20 Testis, Dis3WT

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: 10x  Genomics

data_processing:
Raw base call (BCL) files were demultiplexed with bcl2fastq; Cell Ranger (version 3.1) from 10x genomics was used to align reads, generate feature-barcode matrices for both Control and KO samples
cellranger mkfastq was used to generate FASTQ files
cellranger count performs alignment, filtering, barcode counting, and UMI counting
Assembly: mm10
Supplementary files format and content: hd5 file, data matrix from cell ranger export

source_name: P20 Testis

growth_protocol: All animal procedures were approved by the Ethics Committee for Animal Research of School of Life Sciences, Shandong University, China. All experiments with mice were performed in accordance with guidelines of the care and use of laboratory animals.. Testes isolated from P20 aged control and knockout mice.

extract_protocol:
Single testicular cells were isolated from P20 control and knockout mice. Testes were digested into single cell suspensions with 0.25% trypsin/EDTA.
scRNA-seq libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics) according to the manufacturer’s instructions. Briefly, single cells were mixed with a suspension containing barcoded beads and UMI (unique molecular identifier) elements that allow specific tagging of messenger RNA. After partitioning thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and barcoding, full-length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Libraries were constructed by fragmentation, end repair, A-tailing, adaptor ligation and index PCR. After ensuring adequate quality of the cDNA libraries, the samples were sequenced on a NovaSeq platform.

value: P20 Testis

value: WT


title: P20 Testis, Dis3cKO

description: 10x  Genomics

value: KO


title: WT-7

value: siCtrl


title: Wild type, in cell DMS experiment, Amplicon 4, untreated, replicate 2

city: Chapel Hill

first: Justin

last: Waldern

state: NC

address: 250 Bell Tower Dr

institute: The University of North Carolina at Chapel Hill

description:
Library name: WT_A4_DMSic_untreated_rep2
MaP_profiles.tar.gz

data_processing:
Shapemapper2 v2.1.5
ShapeJumper  v1.0
JuMP filtering: SHAPE-JuMP frequencies were calculated with using the data from normalizeDeletionRates.py in the ShapeJumper package, with low count (<20) JuMP events omitted. Low count JuMP events were omitted because they can be artificially high in this system due to both a low JuMP count and a low read depth (i.e., 1 event in 1 read is a 100% frequency), where the low read depth occurs on JuMPs deep into the read from the poor processivity of the reverse transcriptase. Differences are taken as the AMT-treated minus the untreated values.
Assembly: GRCh38/hg38
Supplementary files format and content: MaP_profiles.tar.gz contains files of the format _profile.txt from ShapeMapper v2.1.5. Each row in these tables describes per-nucleotide mutation rates and normalized reactivity profiles
Supplementary files format and content: JuMP_data.tar.gz contain csv files of processed -JuMP data. These files contain position information for each deletion recorded (nucleotide_position_i, and nucleotide_position_j), as well as information on the counts and read-depth normalized frequencies of deletions in AMT-treated and untreated conditions

source_name: HeLa

growth_protocol: For in-cell probing (library names include "DMSic") HeLa cells (ATCC number CCL 2) were cultured in high glucose DMEM (Gibco) supplemented with10% fetal bovine serum (Sigma) and 0.5 % pen/strep (Gibco). Cells were maintained at 37° C and 5% CO2. Plasmid constructs were transfected into cells, and cells were later DMS probed

extract_protocol:
For in-cell probing, RNA was isolated with Trizol reagent. For in vitro probing, RNA was generated by in vitro transcription with NEB HiScribe T7 High Yield RNA Synthesis kit
For MaP RT, superscript II was used to generate cDNA. For JuMP, C8 enzyme was used to perform RT. In-cell and SHAPE-JuMP libraries were constructed with two rounds of PCR to add Illumina adaptor sequences and barcodes. In vitro MaP libraries were prepared using the NEBNext Ultra II FS DNA Library Prep kit for Illumina

value: HeLa

value: wild type

value: untreated


title: BG5_Flag_2

value: glioblastoma

value: Flag


title: BG5_K422R_3

value: glioblastoma stem cell


title: BG5_Flag_1


title: P3_WT_3

value: HNRNPK (wildtype)

value: IDH wildtype, TP53(R175Y)


title: Endpoint_MR49F_bioRep3

description:
Library name: Endpoint_MR49F_bioRep3
Endpoint- biological replicate 3

value: Prostate

value: Enzalutamide


title: KO-5

value: brain

value: Tissue

value: endothelial cell


title: Baseline_RWPE1_bioRep3

description:
Library name: Baseline_RWPE1_bioRep3
Baseline - biological replicate 3

value: benign prostate epithelial cells


title: Wild type, in cell DMS experiment, Amplicon 4, untreated, replicate 1

description:
Library name: WT_A4_DMSic_untreated_rep1
MaP_profiles.tar.gz


title: BG5_K422R_2

value: HNRNPK (422 site mutate from lysine to argnine)

value: IDH wildtype, TP53 wildtype


title: WT-2

value: siCtrl


title: BG7_K422R_1


title: P3_WT_2


title: KO-1


title: Endpoint_RWPE1_bioRep3

description:
Library name: Endpoint_RWPE1_bioRep3
Endpoint- biological replicate 3


title: WT-4


title: Endpoint_RWPE1_bioRep2

description:
Library name: Endpoint_RWPE1_bioRep2
Endpoint- biological replicate 2


title: Wild type, in cell DMS experiment, Amplicon 4, DMS-treated, replicate 2

description:
Library name: WT_A4_DMSic_DMS_rep2
MaP_profiles.tar.gz

value: HeLa

value: DMS


title: P3_WT_1


title: Baseline_MR49F_bioRep1

description:
Library name: Baseline_MR49F_bioRep1
Baseline - biological replicate 1

value: Prostate carcinoma


title: NEUROD1 ASCL1: HES1 promoter driving ASCL1, NEUROD1, and GFP

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

description:
Library name: SC223_NEUROD1_ASCL1_GFP
Chromium Next GEM single Cell 3’ Reagent kits v3.1

data_processing:
Fastqs were aligned to transcriptome GRCh38-2020 using cellranger-8.0.0 and analyzed using Seurat to identify cell classes and examine gene expression information.
Assembly: GRCh38-2020
Supplementary files format and content: Processed files are compressed (.tar.gz) cellranger filtered_feature_bc_matrix out folders, which contain the corresponding barcodes, features, and matrix files for each sample.

source_name: Human fetal retinosphere

growth_protocol: Human retinal tissues were provided from the Birth Defect Research Laboratory at the University of Washington following the approved protocol Retinospheres (UW5R24HD000836). Retinospheres were cultured as previously debrided (Wohlschlegel, 2023; Sridhar, 2020). Briefly, retinospheres are maintained in low binding attachment plate in Retinal Differentiation Medium (RDM 5%; supplemented with 5% fetal bovine serum (FBS), DMEM/DMEM/F12, 2% B27, 1% Pen-Strep) at 37ºC incubator with 5% CO2.

extract_protocol:
Retinospheres were dissociated into single cells as previously described (Wohlschlegel, 2023). Following dissociation cells were passed through a 35 µm strainer. Fluorescent Activated Cell Sorting (FACS) was performed to isolate the GFP+ cells using a BD FACSAria III cell sorter (BD Bioscience).
Following FACS purification, GFP+ cells were centrifuged at 300g at 4ºC for 5 mins. For each sample, cells were resuspended in RDM5% to reach a concentration of 1000 cells per µl. Libraries construction were done using the Chromium Next GEM single Cell 3’ Reagent kits v3.1 (Dual Index) following the manufacturer’s instructions. Libraries were next sequenced using Illumina NextSeq.

treatment_protocol: Retinospheres of desired ages were collected and dissected in half. Each retinospheres was then placed in an individual well of a normal attachment 96 well plate. For each condition, individual retinosphere received the same master mix containing RDM5%, Neuraminidase (MilliporeSigma), Polybrene, DMSO, EdU and the virus. The following day, retinospheres were transferred to an individual well of a low binding attachment plate without removing the medium. The next day the medium was replaced with fresh RDM5% and EdU. Viral vectors were sources from VectorBuilder.

value: Human fetal retinosphere

value: Muller glia

value: Lentiviral infection with HES1_ASCL1_NEUROD1_GFP construct


title: P3_K422R_3

value: glioblastoma

value: glioblastoma stem cell


title: Wild type, in cell DMS experiment, Amplicon 4, DMS-treated, replicate 1

description:
Library name: WT_A4_DMSic_DMS_rep1
MaP_profiles.tar.gz

value: wild type


title: Endpoint_RWPE1_bioRep1

description:
Library name: Endpoint_RWPE1_bioRep1
Endpoint- biological replicate 1

source_name: Prostate

value: Prostate


title: ASCL1: HES1 promoter driving ASCL1 and GFP

description:
Library name: SC222_ASCL1_GFP
Chromium Next GEM single Cell 3’ Reagent kits v3.1

value: Lentiviral infection with HES1_ASCL1_GFP construct


title: WT-6

value: brain

value: Tissue


title: P3_K422R_2

value: IDH wildtype, TP53(R175Y)


title: Baseline_RWPE1_bioRep1

description:
Library name: Baseline_RWPE1_bioRep1
Baseline - biological replicate 1

value: benign prostate epithelial cells


title: Control: HES1 promoter driving GFP

description:
Library name: SC221_CTL_GFP
Chromium Next GEM single Cell 3’ Reagent kits v3.1

value: Lentiviral infection with HES1_GFP construct


title: Wild type, in cell DMS experiment, Amplicon 3, untreated, replicate 2

description:
Library name: WT_A3_DMSic_untreated_rep2
MaP_profiles.tar.gz

value: untreated


title: HCT116 TP53-/-, H3K27ac ChIP, negControl, rep 2

description: Library name: H3K27ac_ChIP_negControl_2

data_processing:
ChIPseq reads were aligned to the hg38 human reference genome using HiSat2 and files were output as sorted, bam files using SAMTOOLS. P63 peaks were called using MACS2 using a merged negative control (deltaNp63 ChIP-seq in negative control/vector only control cell line) as the genomic background. H3K27ac peaks were called using MACS2 using no background/no control. q-value cutoff of 0.01 and the homo sapiens (-hs) genome size.
Assembly: Human reference genome hg38
Supplementary files format and content: Tab-separated bed file with MACS-derived peaks

source_name: colon

extract_protocol:
For ChIP-seq, nuclei were isolated using the Diagenode iDeal ChIP-seq kit for Transcription Factors (Diagenode #C01010170) and sheared using  the Diagenode Bioruptor Plus for 50 cycles (30s on/off).
DNA sequencing libraries were prepared using the NEBNext Ultra II DNA Library prep kit using standard protocols.

treatment_protocol: 500ng/mL doxycycline (induced) or water (uninduced) for 24hrs. For ChIP-seq, cells were fixed with 1% methanol-free formaldehyde for 10minutes followed by quenching with 250mM glycine.

value: colon

value: 500ng/mL doxycycline


title: Wild type, in cell DMS experiment, Amplicon 3, untreated, replicate 1

description:
Library name: WT_A3_DMSic_untreated_rep1
MaP_profiles.tar.gz

value: HeLa


title: P3_K422R_1

value: HNRNPK (422 site mutate from lysine to argnine)


title: HCT116 TP53-/-, H3K27ac ChIP, negControl, rep 1

description: Library name: H3K27ac_ChIP_negControl_1


title: Wild type, in cell DMS experiment, Amplicon 3, DMS-treated, replicate 2

description:
Library name: WT_A3_DMSic_DMS_rep2
MaP_profiles.tar.gz

value: DMS


title: Endpoint_LNAbl_bioRep3

description:
Library name: Endpoint_LNAbl_bioRep3
Endpoint- biological replicate 3

value: LNCaP-abl

value: Prostate carcinoma

value: Castration condition


title: Baseline_LNAbl_bioRep3

description:
Library name: Baseline_LNAbl_bioRep3
Baseline - biological replicate 3


title: P3_Flag_3

value: glioblastoma

value: glioblastoma stem cell

value: Flag


title: HCT116 TP53-/-, H3K27ac ChIP, deltaNp63beta, rep 2

description: Library name: H3K27ac_ChIP_deltaNp63beta_2


title: Wild type, in cell DMS experiment, Amplicon 3, DMS-treated, replicate 1

description:
Library name: WT_A3_DMSic_DMS_rep1
MaP_profiles.tar.gz

value: wild type


title: P3_Flag_2


title: Baseline_RWPE1_bioRep2

description:
Library name: Baseline_RWPE1_bioRep2
Baseline - biological replicate 2

value: Prostate


title: Wild type, in cell DMS experiment, Amplicon 2, untreated, replicate 2

description:
Library name: WT_A2_DMSic_untreated_rep2
MaP_profiles.tar.gz


title: Endpoint_LNAbl_bioRep2

description:
Library name: Endpoint_LNAbl_bioRep2
Endpoint- biological replicate 2


title: Baseline_LNAbl_bioRep2

description:
Library name: Baseline_LNAbl_bioRep2
Baseline - biological replicate 2


title: Wild type, in cell DMS experiment, Amplicon 2, untreated, replicate 1

description:
Library name: WT_A2_DMSic_untreated_rep1
MaP_profiles.tar.gz


title: HCT116 TP53-/-, H3K27ac ChIP, deltaNp63alpha, rep 2

description: Library name: H3K27ac_ChIP_deltaNp63alpha_2


title: P3_Flag_1

value: IDH wildtype, TP53(R175Y)


title: Wild type, in cell DMS experiment, Amplicon 2, DMS-treated, replicate 2

description:
Library name: WT_A2_DMSic_DMS_rep2
MaP_profiles.tar.gz


title: Endpoint_LNAbl_bioRep1

description:
Library name: Endpoint_LNAbl_bioRep1
Endpoint- biological replicate 1


title: Donor34

city: Beijing

first: Jingtao

last: Guo

address: Beichen West Road

institute: Chinese Academy of Sciences

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Testicle

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to collagenase IV and trypsin digestion for ~5 min at 37 C, respectively. The reaction was terminated by addition of FBS. Then, cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v3.1 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 2 X 150 cycle paired-end run via a Illumina Novaseq 6000 instrument. Each sample was sequenced in one separate sequencing lane.

value: Testicle

tag: age (years)


title: HCT116 TP53-/-, H3K27ac ChIP, deltaNp63alpha, rep 1

description: Library name: H3K27ac_ChIP_deltaNp63alpha_1


title: Baseline_LNAbl_bioRep1

description:
Library name: Baseline_LNAbl_bioRep1
Baseline - biological replicate 1


title: Wild type, in cell DMS experiment, Amplicon 1, untreated, replicate 2

description:
Library name: WT_A1_DMSic_untreated_rep2
MaP_profiles.tar.gz


title: Wild type, in cell DMS experiment, Amplicon 2, DMS-treated, replicate 1

description:
Library name: WT_A2_DMSic_DMS_rep1
MaP_profiles.tar.gz


title: Donor35


title: U2OS-Cas9 cells, Untreated, replicate B

city: Worcester

first: Michael

last: Lee

address: 368 Plantation Street

institute: UMASS Chan Medical School

description:
Library name: UNT_B_S4_L007_R1_001
Live cells collected after 32 hours of DMSO

data_processing:
The FASTX-Toolkit (0.0.14) was used to trim reads to get just CRISPR guide sequences (parameters: -f 23 -l 42)
Trimmed reads were mapped to the TKOv3 library with Bowtie (1.3.0) allowing for 2 mismatches (parameters: -v 2 -m 1)
Assembly: TKOv3
Supplementary files format and content: CSV file of raw guide counts for each sample
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega).
Sequencing libraries were generated using 2 sequential PCR reactions: the first to amplify sgRNAs from genomic DNA, and the second to add multiplexing barcodes.

treatment_protocol: Cas9-expressing U2OS cells were infected with the Toronto KnockOut Library v3 (TKOv3) sgRNA library at an MOI of 0.3, in duplicate, maintaining a coverage of > 650x for each replicate. Puromycin selected cells were then expanded for 2 additional days, then seeded onto 15 cm plates. The following day, T0 samples were harvested, and the remaining cells were given 1 µM triptolide or DMSO for 32 hours. At assay endpoint, drug treated samples were further separated into live and dead fractions, and cells were harvested and frozen. All samples were collected at a coverage >= 650x.

value: osteosarcoma

value: DMSO

tag: time

value: 32 hours


title: HCT116 TP53-/-, deltaN ChIP, negControl, rep 2

description: Library name: deltaN_ChIP_negControl_2

value: colon

value: 500ng/mL doxycycline


title: Donor19


title: Donor30


title: HCT116 TP53-/-, deltaN ChIP, deltaNp63beta, rep 2

description: Library name: deltaN_ChIP_deltaNp63beta_2


title: Wild type, in cell DMS experiment, Amplicon 1, untreated, replicate 1

description:
Library name: WT_A1_DMSic_untreated_rep1
MaP_profiles.tar.gz

value: HeLa

value: untreated


title: U2OS-Cas9 cells, Untreated, replicate A

description:
Library name: UNT_A_S3_L007_R1_001
Live cells collected after 32 hours of DMSO


title: Donor14


title: Wild type, in cell DMS experiment, Amplicon 1, DMS-treated, replicate 2

description:
Library name: WT_A1_DMSic_DMS_rep2
MaP_profiles.tar.gz

value: DMS


title: HCT116 TP53-/-, deltaN ChIP, deltaNp63beta, rep 1

description: Library name: deltaN_ChIP_deltaNp63beta_1


title: U2OS-Cas9 cells, T0, replicate B

description:
Library name: T0_B_S2_L007_R1_001
T0 samples collected at time of drugging

value: 0 days


title: HCT116 TP53-/-, deltaN ChIP, negControl, rep 1

description: Library name: deltaN_ChIP_negControl_1


title: HCT116 TP53-/-, H3K27ac ChIP, deltaNp63beta, rep 1

description: Library name: H3K27ac_ChIP_deltaNp63beta_1


title: U2OS-Cas9 cells, T0, replicate A

description:
Library name: T0_A_S1_L007_R1_001
T0 samples collected at time of drugging


title: Donor13


title: HCT116 TP53-/-, deltaN ChIP, deltaNp63alpha, rep 1

description: Library name: deltaN_ChIP_deltaNp63alpha_1


title: Wild type, in cell DMS experiment, Amplicon 1, DMS-treated, replicate 1

description:
Library name: WT_A1_DMSic_DMS_rep1
MaP_profiles.tar.gz


title: U2OS-Cas9 cells, Live fraction, replicate B

description:
Library name: LIVE_B_S6_L007_R1_001
Mechanically isolated live cells

value: 1 µM triptolide, Live cells


title: Donor10


title: U2OS-Cas9 cells, Live fraction, replicate A

description:
Library name: LIVE_A_S5_L007_R1_001
Mechanically isolated live cells


title: Donor9


title: si-YTHDF2-3

city: harbin

first: youlin

last: wang

address: the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China.

institute: The Second Affiliated Hospital of Harbin Medical University,

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30
Matching genomes to obtain expression profile data
Analysis of differences
GO，KEGG enrichment analysis
Assembly: HG38
Supplementary files format and content: The table contains information about the identified differential mrna differential sites

source_name: HaCat

extract_protocol:
Total RNA was extracted using Trizol reagent
the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions

value: HaCat


title: M1001,scRNA-seq

city: Shanghai

first: Xueliang

last: Zhou

state: --- Select One ---

address: Shanghai

institute: Ruijin hospital, Shanghai Jiao Tong university School of medicine

description: 10X Genomics

data_processing:
After data integration, pre-processing, and rigorous quality control, the final cells were collected for subsequent analyses. The detailed procedures of pre-processing and quality control were as follows: (1) Raw data quality control; (2) Data comparison and mapping; (3) Cell Barcode Correction; (4) UMI disaggregation; (5) Count matrix generation; (6) Quality control indicators; (7) Data standardization and normalization; (8) Identification of highly variable genes (HVGs); (9) Filtering condition settings: nCount_RNA > 1000 & nFeature_RNA < 3000 & percent.mt < 10 & nFeature_RNA > 200. The t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm was used for downscaling and cell clustering, and the "SingleR" R package was used for cell annotation. The "CellChat" and "NicheNet" R packages were used for cell communication. The "monocle2" was used for cell trajectory analysis.
Assembly: hg18
Supplementary files format and content: Table-separated values files and matrix files

source_name: colorectal cancer tissue

extract_protocol:
Ensure that the volume of colorectal cancer tissue samples is adequate, fresh tissue samples should be ≥200mg, and use pre-cooled PBS or saline to wash tissue samples to remove blood stains and impurities. Remove fat, connective tissue or necrotic tissue around the sample and cut the tissue into small pieces of about 2mm³. Submerge the processed tissue samples in pre-cooled tissue preservation solution and maintain a 4°C environment. The samples were transported to the laboratory for single-cell sequencing experiments within 48 hours. In the laboratory, the tissue samples were cut up and preserved using tissue preservation solution, followed by single cell suspension preparation.
Library was performed accroding to manufacturer's instructions (Illumina NextSeq 500,10X Genomics).Briefly, high quality cells were isolated from colorectal cancer tissues to ensure cell viability and purity. Individual cells are lysed and total RNA is extracted.RNA is converted to cDNA using reverse transcriptase, often with primers bearing cell-specific barcodes and unique molecular identifiers (UMIs). Amplify the cDNA by PCR or other methods to increase coverage during sequencing. The amplified cDNA is fragmented and sequencing junctions are added to construct libraries that can be used for high-throughput sequencing. Use a bioanalyser to detect the size distribution and concentration of the library. The library was loaded onto the sequencing platform for high-throughput sequencing.

value: colorectal cancer tissue


title: mTEChi.DonorE

data_processing:
Data were preprocessed according to the ImmGen preprocessing protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf). Reads were aligned to the GRCh38 human genome with STAR and gene counts quantified with featureCounts (Subread package) with GENCODE annotation (v34). The standard ImmGen quality control filters were applied to ensure sample exclusion if a sample had <8,000 genes with more than ten reads, high hematopoietic-cell transcript contamination, housekeeping gene median transcript integrity number below 45, or poor replicate correlation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: mTEChi

extract_protocol:
Tissue was minced with scissors and lymphocyte-rich supernatant was removed, then thymic fragments were digested with collagenase and dispase. EpCAM+ cells were magnetically enriched (Donors A, B, and E) or CD45+ cells were magnetically depleted (Donors C and D), and cells were stained with fluorescent antibodies. The cells were double-sorted directly into 5 μl TCL (Qiagen) buffer containing 1% 2-mercaptoenthonol (Sigma). Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

value: mTEChi

value: 3 months

value: Female

value: Thymus


title: U2OS-Cas9 cells, Dead fraction, replicate A

description:
Library name: DEAD_A_S7_L007_R1_001
Mechanically isolated dead cells

value: 1 µM triptolide, Dead cells


title: Donor8

value: Testicle


title: mTEChi.DonorB

value: 2 days

value: Male


title: si-YTHDF2-1


title: NC-3

value: NC


title: Donor6


title: mTEChi.DonorA

value: Trisomy 21

value: 4 months


title: NC-2


title: mTEChi.DonorC

value: 4 days


title: NC-1


title: Donor15


title: WGBS-SNU398WT

first: Mahmoud

middle: Adel

last: Bassal

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

data_processing:
For WGBS analysis, the leading 3 bases and adaptor sequences were trimmed from paired-end reads by TrimGalore. The resulting FASTQ files were analyzed by BISMARK.  PCR duplicates were removed by SAMtools rmdup. Then bismark_methylation_extractor continued the extraction of the DNA methylation status on every cytosine sites.
For 4C-Seq analysis, raw fq files were aligned to a masked hg19 reference. Bam files were converted to read coverage files by bedtools genomecov. Read coverage was normalized according to the sequencing depth. Processed alignment files were analyzed using r3CSeq. Chromosome 9 was selected as the viewpoint, and Csp6I, DpnII were used as the restriction enzyme to digest the genome. Smoothed bam coverage maps were generate using bamCoverage from the deeptools suite and plotted using the Bioconductor package Sushi to get the viewpoint coverage depth maps.  BigInteract files for UCSC and bedpe files were manually generated with the “score” values being calculated as -log( interaction_q-value_from_r3CSeq + 1*10-10 ).
Genome_build: hg19
Supplementary_files_format_and_content: bed, bw files

growth_protocol: SNU-398 (wild type and DAC and CRISPR-DiR treated) cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI) (Life Technologies, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (Invitrogen) and 2 mM L-Glutamine (Invitrogen). Maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
1). WGBS: gDNA was harvested by lysing the cells in 50mM Tris-HCl pH8, 100mM NaCl, 25mM EDTA and 1%SDS buffer with 1mg/mL of proteinase K and incubate at 65C overnight.   2). 4C-Seq: Cell were fixed with 1% formaldehyde and the chromatin fraction were isolated. Chromatin were digested by restriction enzyme Csp6I or DpnII, followed by ligation and second digestion with NlaIII and second ligation. The library was constructed by inverse PCR and nested PCR. And 200 to 600 bp DNA were sequenced.
1). WGBS library were prepared by BGI using standard Illumina WGBS protocol.   2). Libraries were prepared using KAPA HiFi HotStart ReadyMix (KK2602) with primers containing i5 and i7 barcodes. Constructed libraries were PAGE purified and only libraries with 250 to 600bp were used for sequencing. NextSeq 500/550 Mid Output kit V2.5 (150 Cycles) (20024904, Illumina) was used for single end Nextseq sequencing.

treatment_protocol: 1). For WGBS, 2.5uM Decitabine was added to fresh medium everyday for 3 days.   2). For 4C-Seq, cells were stably introduced with CRISPR-DiR non-targeting (DN2) or Targeting (D1+D3).

value: HCC cell line

value: Wild type

tag: culturing days

value: 14 days


title: Donor23


title: WGBS-SNU398DAC

value: Decitabine (2.5uM) treated for 3 days


title: VCaP, SQK-RNA004, untrimmed

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

description: direct RNA long read sequencing,  dorado's adapter trimming disabled

data_processing:
For Nanopore direct RNA sequencing using kits SQK-RNA002 and SQK-RNA004, raw FASTQ files were generated with Dorado v0.5.2 utilizing models "rna002_70bps_hac@v3" and "rna004_130bps_hac@v3.0.1," respectively.
Adapter trimming was disabled, generating untrimmed FASTQ files (–no-trim); otherwise, default FASTQ files were produced.
For Nanopore direct cDNA sequencing using the SQK-DCS109 kit, raw FASTQ files were generated with Dorado v0.5.2 using the "dna_r9.4.1_e8_hac@v3.3" model.
Raw fastq reads were align to reference genome hg38 using minmap2 v2.26 with “-ax splice -uf -k14” options.
Assembly: hg38
Supplementary files format and content: The processing of oriented and trimmed Nanopore direct cDNA reads was performed using Pychopper (https://github.com/epi2me-labs/pychopper, version 2.7.9) and Cutadapt (version 4.2), following the protocol outlined by Grünberger et al. (2022).
Supplementary files format and content: Gene counts were calculated by IsoQuant (v3.1.2)

source_name: VCaP

extract_protocol:
Total RNA was extracted  using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the protocol of the manufacturer. The quality and concentration of RNA were assessed using an Agilent 2100 Bioanalyzer.
Poly(A)+ RNA was then enriched from the total RNA using the Dynabeadstm mRNA Purification Kit (Invitrogen, Cat# 65001), which utilizes oligo (dT) beads for selective mRNA binding.

tag: cell line

value: VCaP

value: epithelial cell

value: WT


title: DP.mTEClo.DonorE

tag: cell type

value: 3 months

value: Female


title: VCaP, SQK-RNA004, default

description: direct RNA long read sequencing, dorado's default parameter

tag: genotype


title: si-YTHDF2-2

value: HaCat


title: Flooding 2

city: Tokyo

first: Nobuhiro

last: Suzuki

state: 東京都

address: 7-1, Kioicho, Chiyoda

country: Japan

institute: Sophia University

data_processing:
FPKM values were calculated from mapped reads by normalizing to total counts and transcript. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0). The list of differentially expressed genes detected by DESeq2 (basemean > 5 and fold-change < 0.25, or basemean > 5 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include CPM (FPKM, peak) values for each sample.

organism: Arabidopsis thaliana

source_name: Shoot

extract_protocol:
Frozen Arabidopsis shoots were ground in liquid nitrogen and total RNA was extracted by using Trizol reagent.
After poly (A) + RNA enrichment by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), double-stranded cDNA libraries (RNA-seq libraries) were prepared using SMARTer stranded RNA-Seq kit v2 (Clontech) ※ according to the manufacturer’s instruction.

value: Shoot

value: Flooding with 8L/s flow


title: Flooding 3


title: Donor22

value: Testicle


title: U2OS-Cas9 cells, Dead fraction, replicate B

state: MA

description:
Library name: DEAD_B_S8_L007_R1_001
Mechanically isolated dead cells

value: osteosarcoma

value: 1 µM triptolide, Dead cells

value: 32 hours


title: Donor17


title: Flooding 1


title: Ophiomastix wendtii specimen 3, tissue sample 2, inner arm core, read pair 1

city: Kannapolis

first: Robert

last: Reid

address: 150 Research Campus Drive, Suite 3333

department: Bioinformatics and Genomics

institute: UNC Charlotte

data_processing:
The quality of the raw sequencing data was assessed with FastQC v0.11.9, focusing on identifying and correcting common issues, such as low-quality bases and leftover adapter sequences.
De novo transcriptome assembly was performed with Trinity v2.14.0.
We quantified transcript and gene abundance across three different sample types: the whole arm segments, the inner arm core, and the stomach (control). The count tables were generated by the RSEM v1.3.3 and Bowtie v2.5.1 in OmicsBox and used as input for a comprehensive differential expression analysis with edgeR v3.18.
Assembly: No reference genome exists for Ophiomastix wendtii. Assembled contigs are available in TSA (https://www.ncbi.nlm.nih.gov/nuccore/GKWM00000000)
Supplementary files format and content: counts_genes.txt

organism: Ophiomastix wendtii

source_name: Stomach

growth_protocol: Adult individuals of O. wendtii were collected at the Keys Marine Laboratory (Lay- ton, FL) and transported in the natural seawater chilled in a box with water ice to the University of North Carolina at Charlotte. Once in the laboratory, the animals were allowed to acclimate gradually to the ambient room temperature overnight. The next day, the brittle stars were transferred to a tank with artificial aerated seawa- ter (“InstantOcean”), whose salinity was adjusted to the natural seawater from the animal habitat (40 ppt). The animals were allowed to acclimate for five days.

extract_protocol:
Tissue samples for RNA isolation (13–95 mg) were homogenized in 500 μL of ice-cold TRI Reagent (Millipore Sigma, cat. no. T9424) using sterile closed-system disposable microtissue homogenizers (Kimble, cat. no. K7496250030). The homogenized samples were briefly vortexed, and an additional 500 μL of the TRI Reagent was added to each sample. The samples were frozen at -80◦C for one week before RNA extraction. Upon retrieval from storage, the samples were thawed on ice, the insoluble material was precipitated by brief centrifugation, and the clear supernatant was transferred into fresh tubes. After a 5-minute incubation at room temperature, 100 μL of 1-bromo-2-chloropropane (BCP) was added to each tube. The samples were then emulsified by vigorous shaking and allowed to sit at room temperature for 10 minutes. The organic and aqueous phases were separated by centrifugation at 16,000×g for 45 min at 4◦C, and the aqueous phase was carefully aspirated and transferred into a fresh tube. The RNA was precipitated by adding 500 μL of isopropanol to each sample, incubating at -20◦C for 1 hour, and centrifugation. The pellet was washed twice with ice-cold 70% ethanol and dissolved in 50 μL of RNase-free water. The quantity of total RNA was determined with a NanoDrop Spectrophotometer.
The RNA-Seq libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina, USA), following Illumina Stranded mRNA Prep Reference Guide (25). The fragmentation was enzyme-based. We conducted quality control on the final libraries to assess RNA concentration with a Qubit dsDNA BR (broad range) assay kit and quality by Tapestation 4200 analysis using the High Sensitivity D1000 Screentape (Agilent, USA). We prepared 16 Illumina paired-end read sequencing libraries to account for both the biological and technical replicates.
Sequencing was performed on an Illumina NextSeq 2000 (Illumina, USA)

treatment_protocol: The animals were anesthetized in 0.1% solution of 1-phenoxy-2-propanol (Millipore Sigma, cat. no. 484423) in seawater until they stopped responding to touch. Tissue samples for both RNA-Seq and microscopic analysis were harvested from three individuals, including one male and two females.

value: Stomach


title: DP.mTEClo.DonorA

city: Boston

value: Trisomy 21

value: 4 months

tag: organ

value: Thymus


title: DP.mTEClo.DonorB

value: 2 days

value: Male


title: Donor16


title: Donor25


title: Ophiomastix wendtii specimen 3, tissue sample 1, stomach, read pair 1


title: Donor24


title: DN.mTEClo.DonorE


title: Submergence 2

tag: treatment

value: Submergence for 30 min


title: Submergence 3


title: Ophiomastix wendtii specimen 2, tissue sample 2, stomach, read pair 1


title: mTEChi.DonorD

value: mTEChi

value: 2 months


title: Donor20


title: DN.mTEClo.DonorB


title: Submergence 1


title: Ophiomastix wendtii specimen 2, tissue sample 1, stomach, read pair 1


title: Donor18


title: Ophiomastix wendtii specimen 1, tissue sample 2, stomach, read pair 1


title: RNAseq, MOLM13, HMX3 KD 2355, rep 3

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
The GRCh38 reference genome was indexed using STAR aligner (version 2.7.9a) with Ensembl gene annotation
Paired-end reads were trimmed and quality was assessed using Trim Galore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore).
The resulting trimmed reads were mapped against the indexed reference genome in two-pass mode with the same parameters as the GDC mRNA Analysis Pipeline version Dr15plus (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#rna-seq-alignment-workflow).
Gene expression levels were determined using FeatureCounts (v2.0.3) with protein coding gene annotation from Ensembl GRCh38 (version 95)
Assembly: GRCh38
Supplementary files format and content: tab-delimited value file include raw counts for each Sample

growth_protocol: Cells were cultured at 37 °C and 5% CO2, and were cultured in RPMI Medium 1640 (1X) (DMEM, Gibco, cat# 21875-034) supplemented with 10% heat inactivated Fetal Calf Serum (FCS) (Biowest, cat# S1810-500). Cells were passed according to the manufacturer’s instructions.

extract_protocol:
RNA was isolated using the Nucleospin RNA plus kit (Macherey-Nagel).
Library generation was performed using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems, Potters Bar, UK), with an RNA fragmentation of approximately 300 bp fragments

value: HMX3 shRNA


title: Control 3

value: Control


title: Ophiomastix wendtii specimen 1, tissue sample 1, stomach, read pair 1


title: Donor12


title: Ophiomastix wendtii specimen 3, tissue sample 6, inner arm core, read pair 1

source_name: Inner arm core

value: Inner arm core


title: Control 2

value: Shoot


title: Control 1


title: RNAseq, MOLM13, HMX3 KD 2355, rep 2


title: Donor7

value: Testicle


title: Ophiomastix wendtii specimen 3, tissue sample 4, inner arm core, read pair 1


title: HR_3, R3A

city: Nantong

first: Baoying

last: Hu

state: JIANGSU

address: No.9 Seyuan road

institute: Nantong University

data_processing:
The sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: The clean reads were mapped to the reference genome using HISAT2
Supplementary files format and content: Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively

growth_protocol: H9C2 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using the Trizol reagent (Life Technologies). 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the BGI mRNA-Seq Library Kit following the manufacture's protocols.

treatment_protocol: The H/R injury cell model group was established by culturing H9C2 cells in 1% oxygen, 5% CO2, and 94% nitrogen in a tri-gas incubator for 12 h and then reoxygenated in 5% CO2 normal oxygen conditions for 6 h.  While H9C2 cells without H/R treatment were the control group.

value: cardiomyocytes

value: Hypoxia/reoxygenation


title: RNAseq, MOLM13, Non-targeting control 1418, rep 3

value: Non-targeting shRNA


title: Ophiomastix wendtii specimen 2, tissue sample 4, inner arm core, read pair 1


title: Ophiomastix wendtii specimen 2, tissue sample 2, inner arm core, read pair 1


title: Donor5


title: RNAseq, MOLM13, Non-targeting control 1418, rep 2


title: Donor11


title: RNAseq, MOLM13, Non-targeting control 1418, rep 1


title: DN.mTEClo.DonorA

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

value: Female


title: HR_1, R1A


title: Donor4


title: HR_2, R2A


title: Donor21


title: Con_3, N3A


title: RNAseq, HMX3 KMT2A-MLLT3 AML, HMX3 KD, rep2

source_name: primary

growth_protocol: Mononuclear cells from KMT2A::MLLT3-positive patients (>90% blasts) were cultured for 3 days on an MSC feeder layer in StemSpan SFEM (Stemcell Technologies, cat# 9655) supplemented with 100 ng/mL rh-TPO (Peprotech, cat# AF-300-18), 150 ng/mL rh-SCF (Immunotools, cat#, 11343327), 10 ng/mL rh-Flt3L (Immunotools, cat#, 11343305), 10 ng/mL rh-IL3 (Immunotools, cat#, 11340035), 10 ng/mL rh-GM-CSF (Immunotools, cat#, 11343125), 1.35 µM UM729 (Stemcell Technologies, cat# 72332), and 750 nM Stem regenin-1 (Bio-connect, cat# c7710-1s)) before transduction

value: primary

value: blasts

value: shRNA HMX3 KD (2)


title: Ophiomastix wendtii specimen 1, tissue sample 4, inner arm core, read pair 1