title: Schwann (G497_SL27)

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. BBDuk was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing Ensembl gene annotation (GRCh38.78).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read counts are provided in a Lee_et_al_read_counts.csv file.

source_name: Schwann cells

growth_protocol: Human MPNST cell lines were maintained in RPMI 1640 medium with 1X Penicillin-Streptomycin and 10% fetal bovine serum (FBS). Glioblastoma cell lines were cultured in DMEM medium with 1X Penicillin-Streptomycin-Glutamine and 10% (FBS). Schwann cells were cultured in the Schwann cell medium. All the cell lines were cultured in a CO2 incubator at 37°C.

extract_protocol:
Total RNA was extracted from the cells (MPNST or Schwann cells) with or without drug or vehicle-treated cells using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. The NanoDrop 2000 spectrophotometer (Thermo Scientific) and 2100 Bioanalyzer (Agilent) were used to assess RNA quantity and quality, with the calculation of RNA integrity number (RIN). Samples were included for RNA-Seq if RIN > 6 and total RNA> 500 ng.
Illumina RNA-Seq was performed according to the manufacturer’s instructions. Briefly, the cDNA libraries were prepared using TruSeq® Stranded mRNA Library Prep kit as per the manufacturer's instructions. The final product was assessed for its size distribution and concentration using the BioAnalyzer High Sensitivity DNA Kit (Agilent).
Pooled libraries were diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions.

treatment_protocol: The overnight cultured cells (~2 x 10^6 per 100 mm dish) were exposed with various concentrations of a drug(s) or vehicle for 24 h.

value: Schwann cells

tag: passages

value: untreated


title: Colchicine (24 nM) and Fludarabine (60  µM)_STS-26T-luc (G434_SL05)

status: Public on Oct 21 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: MPNST cells

tag: cell type

value: Sporadic MPNST cells

tag: treatment


title: Fludarabine (800 nM)_T98G (G454-11-SL17)

source_name: Glioblastoma cells

value: Glioblastoma cells

value: Fludarabine (800 nM)


title: Vehicle_STS-26T-luc (G434_SL02)

value: Vehicle


title: Colchicine (6 nM) and Fludarabine (30  µM)_STS-26T-luc (G434_SL03)


title: Vehicle_STS-26T-luc (G434_SL01)


title: Fludarabine (800 nM)_STS-26T-luc (G454-08-SL14)


title: Vehicle_T98G (G454-10-SL16)


title: Frontal bone, biological replicate 1

city: Pittsburgh

first: Matthew

middle: Brian

last: Rogera

state: Pennsylvania

address: 325 Sutherland Drive

department: Oral and craniofacial sciences

institute: University of Pittsburgh

data_processing:
Reads were mapped using TopHat, and transcripts were assembled using Cufflinks. Differential abundances were calculated using EdgeR with counts fitted to a generalized linear model and tested using a likelihood ratio test (GLMLRT).
Genes with counts per million of less than 1, in two biological replicates were excluded from the analysis. Genes were considered significant with a FDR (false discovery rate) of <0.05.
Assembly: mm38
Supplementary files format and content: genes.count_tracking

organism: Mus musculus

source_name: microdissected frontal bones including metopic suture

growth_protocol: Timed-pregnant CD-1 females were purchased from Charles River Laboratory. We collected embryos via C-section after CO2 euthanasia of the pregnant dam on the appropriate day and we confirmed embryo staging by morphology. All animal husbandry, procedures and protocols were approved by and performed under the oversight of the University of Pittsburgh Institutional Animal Care and Use Committee.

extract_protocol:
The tissues were lysed with the Trizol reagent, followed by further disruption with QiaShredder followed by RNA extraction with Qiagen RNAeasy kit.
Axeq generated and sequenced the libraries as 100 bp paired end reads on an Illumina HiSeq2000 sequencer

treatment_protocol: To perform frontal and parietal bone-derived calvarial osteoblast cultures we dissected the skull cap off, removed the overlying tissue and dissected the bones out along the naso-frontal, coronal and lambdoidal sutures (Fig 1A). The dissection included the interfrontal suture between the frontal bones and the sagittal suture joining the parietal bones. We pooled 3 pairs of frontal bones and 3 pairs of parietal bones to make one biological replicate for RNASeq analysis.

tag: tissue

value: embryonic organ

tag: genotype

value: wildtype

tag: strain


title: Fludarabine (800 nM)_STS-26T-luc (G454-07-SL13)


title: Colchicine (24 nM) and Fludarabine (60  µM)_STS-26T-luc (G434_SL06)


title: Vehicle_STS-26T-luc (G454-05-SL11)


title: Vehicle_STS-26T-luc (G454-06-SL12)


title: Fludarabine (800 nM)_T98G (G454-12-SL18)


title: Vehicle_T98G (G454-09-SL15)


title: Colchicine (6 nM) and Fludarabine (30  µM)_STS-26T-luc (G434_SL04)


title: Vehicle_ST88-14 (G454-02-SL08)

value: NF1 MPNST cells


title: Fludarabine (800 nM)_ST88-14 (G454-03-SL09)


title: Schwann (G497_SL28)


title: A549-TiO2_m6A_IP_rep3

city: xiamen

first: jie

last: zeng

state: fujian

address: No. 4221-120, Xiang An Nan Road

country: China

institute: School of Life Sciences, Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Peak-calling were perform by using ExomePeak
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: ITAG3.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: A549 was cultured in DMEM/F-12 (Hyclone) in an incubator at 37℃ and 5%CO2 for routine culture

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The A549 cells were divided into three groups, except for the control group, the other two groups of cells were treated with 10mg/L BPQD and 100mg/L TiO2 for 24 hours.

tag: cell line

value: treated with 100mg/L TiO2 for 24 hours

tag: antibody


title: A549-TiO2_m6A_IP_rep1


title: A549-TiO2_m6A_IP_rep2


title: A549-BPQDs_m6A_IP_rep3

value: treated with 10mg/L BPQDs for 24 hours


title: A549-BPQDs_m6A_IP_rep2


title: A549-BPQDs_m6A_IP_rep1


title: A549_m6A_IP_rep3


title: HeLa cell, Day 30, replicate1

status: Public on Oct 22 2023

city: Beijing

first: Wenze

last: Huang

address: Tsinghua street

institute: Tsinghua University

description:
HeLa_D30_1
HeLa.count.txt

library_source: genomic

data_processing:
The raw reads in FASTQ files were trimmed using cutadapt to remove flanking sequences.
The clean reads of each sample were subsampled to 8 million reads using vsearch.
The clean reads were mapped to the reference library we designed using Bowtie2.
The MAGeCK tool was used to obtain read count tables for all samples from the SAM files of mapping results.
Assembly: The design pair crRNA library
Supplementary files format and content: Tap-separated values files
Library strategy: CRISPR screens

molecule: genomic DNA

source_name: HeLa

growth_protocol: All cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS (Dox-free, BI) and 1 × antibiotic-antimycotic (Gibco), and were grown at 37 °C in a 5% CO2 cell culture incubator.

extract_protocol:
The genomic DNA was isolated from 4 × 106 cells using the Genomic DNA Kit (TianGen Biotech) for each replicated sample, and a total of 32 μg of the recovered products, representing at least 200 × coverage of the initial library size, were used as amplification templates in 16 independent PCR tubes (50 μl system each).
The genomic barcode regions encoding paired crRNAs introduced by lentivirus infection were PCR amplified using Q5 High Fidelity Polymerase (NEB) with 22 cycles using two primers targeting the upstream U6 promoter and the downstream CMV promoter. In a second round of PCR, adaptors for sequencing purposes with different barcodes were added for different samples (replicates and time points). Finally, the PCR products of all samples were pooled and purified with DNA Clean & Concentrator-5 kit (Zymo Research).

value: HeLa

tag: time point

value: Day 30


title: A549_m6A_IP_rep1


title: A549_m6A_IP_rep2


title: A549-TiO2_input_rep2

value: none, input


title: A549-BPQDs_input_rep3


title: A549-TiO2_input_rep1


title: A549-BPQDs_input_rep1


title: A549_input_rep1


title: Fludarabine (800 nM)_ST88-14 (G454-04-SL10)


title: Vehicle_ST88-14 (G454-01-SL07)


title: A549-TiO2_input_rep3


title: A549_input_rep3


title: A549-BPQDs_input_rep2


title: A549_input_rep2


title: 200796210101_J_Shef3 Ery I

type: RNA

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background corrected and normalized using with Lumi in R

label_protocol: Biotin labelling of cRNA was performed with Illumina total prep-96 RNA amplification kit following the manufacturers instructions

extract_protocol: RNA was extracted using Isolate II RNA Min kit in accordance with the prescribed protocol provided by the kit

tag: channel count

value: H EMBRYONIC STEM CELL LINE

tag: differentiation stage

value: DIFF Ery PIII


title: 9284936005_F_RH1 M/E8 I

value: IPS WT FIBROBLAST-DERIVED cell line

value: Meso/Ery MD8


title: 200796220106_A_BSG KO C5 II

source_name: BASIGIN KO C5B2

value: IPS KO CRL-DERIVED cell line

value: UNDIFFERENTIATED


title: 200796210101_E_SF2 Ery I


title: 200796220106_E_ATP2B4 KO I

source_name: ATP2B4 KO


title: 200796220106_C_BSG KO C5 III

source_name: BASIGIN KO C5B3


title: 200796210101_L_Shef3 Ery II


title: 200796210101_G_SF2 Ery II


title: 9284936005_H_RH1 M/E8 II


title: 9284936005_L_RH1 M/E8 C II

value: Meso/Ery MD8 C


title: 200796210101_F_Shef3 M/E12 II

value: Meso/Ery MD13


title: 200796210101_I_Shef3 I


title: FosTRAP2;Ai14, the nucleus reuniens of the thalamus, snRNA-Seq, with sleep deprivation [MW2]

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description:
10x Genomics V3.1
snRNA-Seq

library_source: transcriptomic single cell

data_processing:
snRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Assembly: mm10

extract_protocol: snRNA-Seq following 10x V3.1 guideline

value: The nucleus reuniens of the thalamus

tag: age

value: 2 months old

tag: Sex

value: Male

value: with sleep deprivation


title: FosTRAP2;Ai14, the nucleus reuniens of the thalamus, snRNA-Seq, without sleep deprivation [MW10]

description:
10x Genomics V3.1
snRNA-Seq

value: without sleep deprivation


title: FosTRAP2;Ai14, the nucleus reuniens of the thalamus, snRNA-Seq, with sleep deprivation [MW12]

description:
10x Genomics V3.1
snRNA-Seq


title: FosTRAP2;Ai14, the nucleus reuniens of the thalamus, snRNA-Seq, without sleep deprivation [MW9]

description:
10x Genomics V3.1
snRNA-Seq


title: FosTRAP2;Ai14, the nucleus reuniens of the thalamus, snRNA-Seq, with sleep deprivation [MW11]

description:
10x Genomics V3.1
snRNA-Seq


title: 200796210101_K_Shef3 II


title: 200796220106_I_ATP2B4 KO III


title: 9284936005_D_BLOODII

source_name: BLOOD

value: BLOOD tissue

value: Primary RBC


title: 9284936005_B_BLOODI


title: 200796220106_G_ATP2B4 KO II


title: 200796220106_K_ATP2B4 KO Ery

value: DIFF Ery (PIII)


title: 9284936005_J_RH1 M/E8 C I


title: FosTRAP2;Ai14, the nucleus reuniens of the thalamus, snRNA-Seq, without sleep deprivation [MW1]

description:
10x Genomics V3.1
snRNA-Seq


title: 200796210101_H_Shef3 M/E12 III

value: Meso/Ery MD14


title: 200796210101_D_Shef3 M/E12 I

value: H EMBRYONIC STEM CELL LINE

value: Meso/Ery MD12


title: Spinal cord tissue, SCI 2

city: Guangzhou

first: Xiao

middle: Lin

last: Zeng

state: Guangdong

address: 58 Zhongshan 2nd Road

institute: Sun Yat-sen University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Spinal cord tissue

growth_protocol: The C57/BL6 mice (aged 3-5 weeks, 18-20g) were housed four to a cage with free access to food/water and kept under standardized atmosphere (temperature: 22°C, humidity: 55%, 12/12 h cycle). All mice were specific-pathogen-free grade.

extract_protocol:
Mice were anesthetized at 3 days after surgery with an adequate dose of 1% pentobarbital sodium (40 mg/kg) and T8-T12 segments spinal cord specimens were dissected. Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Mice were anesthetized by intraperitoneal injection of 1% pentobarbital sodium. Then, muscle and fat were cleared from thoracic vertebrae 9 and 10 (T9 and T10) and the spinal cord was exposed via laminectomy(sham group). The spinal cord was crushed for 5 seconds with a vascular clip (SCI gourp, 60 g force, FST, Heidelberg, Germany)

value: Spinal cord tissue

value: Spinal cord injury 3 days


title: Spinal cord tissue, SCI 3


title: Spinal cord tissue, SCI 1


title: Spinal cord tissue, Sham 3

value: untreated


title: Spinal cord tissue, Sham 2


title: 200796210101_C_SF2 II

value: IPS WT FIBROBLAST-DERIVED cell line

value: UNDIFFERENTIATED


title: 200796210101_B_Shef3 III


title: 200796210101_A_SF2 I


title: Spinal cord tissue, Sham 1


title: 200796210099_K_CD3 II

value: IPS WT BLOOD-DERIVED cell line


title: 3T3_EGFP18_48h_DoxPlus_H3K27ac_Rep02 (ChIL-seq)

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Library strategy: ChIL-seq
For ChIL-seq analysis, raw sequencing data were trimmed using Cutadapt (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option:  --2colour 20.
The reads were mapped by the aligning software bowtie2 (B. Langmead et al., 2012) (version 2.3.5.1) to the reference genome (UCSC mm10, Bowtie 2 index), and the uniquely mapped reads were retained.
Mapped data of the same sample were merged by samtools (H. Li, 2009, H. Li, 2011) (version 1.9-170-ge5bac55) with “merge” option.
ChIL-seq signal tracks (bigWig) were generated using  the software deepTools (Ramírez et al., 2016) (version 3.3.0) with the options: bamCoverage --binSize 100 --normalizeUsing CPM --smoothLength 1000.
Genome_build: GRCm38/mm10

source_name: NIH3T3 cell line (Dox inducible H3mm18)

growth_protocol: NIH3T3 cells were grown in DMEM supplemented with 10% calf serum.

extract_protocol: Sequencing was performed in an Illumina NovaSeq 6000 system with 51 cycles using NovaSeq 6000 S1 Reagent Kit for ChIL-seq.

treatment_protocol: Introduction of MyoD into NIH3T3 cells was carried out using the retroviral vector MyoD.

value: NIH3T3 cell line (Dox inducible H3mm18)

value: Differentiated for 48 hours

tag: chil antibody

value: mouse anti-H3K27ac CMA309 [PMID 18227620]


title: 3T3_EGFP18_48h_DoxPlus_H3K27ac_Rep01 (ChIL-seq)


title: 3T3_EGFP18_48h_DoxMinus_H3K27ac_Rep01 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxPlus_H3K27ac_Rep01 (ChIL-seq)

value: Differentiated for 24 hours


title: 3T3_EGFP18_48h_DoxMinus_H3K27ac_Rep02 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxPlus_H3K27ac_Rep02 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxMinus_H3K27ac_Rep02 (ChIL-seq)


title: 200796210099_J_K4 Ery I

value: DIFF Ery PIII


title: 200796210099_I_CD3 I


title: 3T3_EGFP18_0h_DoxPlus_H3K27ac_Rep02 (ChIL-seq)

value: Differentiated for 0 hours


title: 3T3_EGFP18_0h_DoxPlus_H3K27ac_Rep01 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxMinus_H3K27ac_Rep01 (ChIL-seq)


title: 200796210099_G_GB1 Ery I


title: 200796210099_E_GB1 Ery1 I

value: DIFF Ery PI


title: 3T3_EGFP18_0h_DoxMinus_H3K27ac_Rep02 (ChIL-seq)


title: 200796210075_L_GB1 I


title: 200796210099_D_K4 I


title: 200796210099_F_K4 II


title: 200796210099_A_GB1 II


title: 3T3_EGFP18_UI_DoxPlus_H3K27ac_Rep02 (ChIL-seq)

value: Before retroviral infection (UnInfected, UI)


title: 200796210099_B_CD3 III


title: 3T3_EGFP18_0h_DoxMinus_H3K27ac_Rep01 (ChIL-seq)


title: 3T3_EGFP18_UI_DoxPlus_H3K27ac_Rep01 (ChIL-seq)


title: 200796210075_K_CD5 III


title: 200796210099_H_K4 Ery1 I


title: 200796210075_J_CD5 Ery III


title: 200796210099_C_GB1 III


title: 3T3_EGFP18_UI_DoxMinus_H3K27ac_Rep01 (ChIL-seq)


title: 3T3_EGFP18_UI_DoxMinus_H3K27ac_Rep02 (ChIL-seq)


title: 3T3_EGFP18_48h_DoxPlus_H3K4me3_Rep02 (ChIL-seq)

value: mouse anti-H3K4me3 CMA304  [PMID 18227620]


title: 3T3_EGFP18_48h_DoxMinus_H3K4me3_Rep03 (ChIL-seq)


title: HEK293 cells, parental, doxycycline, biol rep 3

city: La Jolla

first: Valeria

last: Burghi

address: 3855 Health Sciences Drive, Room 2345

department: Pharmacology

institute: University of California San Diego

data_processing:
The quantification of transcripts was calculated using Salmon (version 1.7.0), which provides accurate expression estimates.
The differential gene expression analysis including quality control, model fitting, and hypothesis testing was conducted using DESeq2.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium
Supplementary files format and content: SF files containing count values of each sample generated by Salmon (version 1.7.0).

growth_protocol: HEK293 parental and PKA Cα cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (D6429, Sigma) supplemented with 10% fetal bovine serum (FBS) (F2442, Sigma) and 1% penicillin/streptomycin (A5955, Sigma) and maintained in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
After treatment, the cells were washed with PBS, total RNA was isolated with a RNeasy Mini Kit (74104, Qiagen) including an on-column DNase I digestion and quantified using a Nanodrop ND-1000 (Thermo Scientific).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount.

treatment_protocol: HEK293 wild type and PKA Cα cells were seeded in poly-D-lysine coated 6 well-plates and treated with 1 μg/ml doxycycline for 48 hours.

value: embryonic

value: wild type

value: incubation with doxycycline

tag: time

value: 48 hours


title: 200796210075_I_RH1 Ery 1 I


title: 3T3_EGFP18_48h_DoxPlus_H3K4me3_Rep01 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxPlus_H3K4me3_Rep02 (ChIL-seq)


title: 3T3_EGFP18_48h_DoxMinus_H3K4me3_Rep01 (ChIL-seq)


title: 200796210075_H_CD5 Ery II


title: 200796210075_E_RH1 M/E7 II

value: Meso/Ery MD7


title: 200796210075_D_CD5 II


title: 200796210075_B_CD5 I


title: 200796210075_G_RH1 M/E7 III

value: IPS WT FIBROBLAST-DERIVED cell line


title: 200796210075_C_RH1 M/E7 I


title: 3T3_EGFP18_24h_DoxPlus_H3K4me3_Rep01 (ChIL-seq)


title: 200796210075_F_CD5 Ery I


title: 3T3_EGFP18_24h_DoxMinus_H3K4me3_Rep02 (ChIL-seq)


title: 3T3_EGFP18_0h_DoxPlus_H3K4me3_Rep01 (ChIL-seq)


title: 3T3_EGFP18_0h_DoxPlus_H3K4me3_Rep02 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxMinus_H3K4me3_Rep01 (ChIL-seq)


title: 3T3_EGFP18_UI_DoxPlus_H3K4me3_Rep02 (ChIL-seq)


title: 3T3_EGFP18_0h_DoxMinus_H3K4me3_Rep02 (ChIL-seq)


title: 3T3_EGFP18_UI_DoxPlus_H3K4me3_Rep01 (ChIL-seq)


title: 3T3_EGFP18_0h_DoxMinus_H3K4me3_Rep01 (ChIL-seq)


title: 200796210041_K_ATP2B4 Ery 1 II

value: IPS KO CRL-DERIVED cell line


title: 3T3_EGFP18_UI_DoxMinus_H3K4me3_Rep02 (ChIL-seq)


title: 200796210075_A_RH1 Meso III

value: Meso MDII


title: 3T3_EGFP18_UI_DoxMinus_H3K4me3_Rep01 (ChIL-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)


title: 200796210041_F_ATP2B4 Ery II


title: 200796210041_J_RH1 Meso I


title: 200796210041_G_ATP2B4 M/E7 III

value: Meso/Ery MD10


title: 200796210041_L_RH1 Meso II


title: 3T3_EGFP18_48h_DoxPlus_H3p3_Rep02 (ChIL-seq)

value: Differentiated for 48 hours

value: rat anti-H3.3 clone 4H2D7 [PMID 22569126]


title: 3T3_EGFP18_48h_DoxMinus_H3p3_Rep02 (ChIL-seq)


title: 3T3_EGFP18_48h_DoxPlus_H3p3_Rep01 (ChIL-seq)


title: 200796210041_E_ATP2B4 M/E7 II

value: Meso/Ery MD9


title: 200796210041_I_ATP2B4 Ery1 I


title: 3T3_EGFP18_48h_DoxMinus_H3p3_Rep01 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxMinus_H3p3_Rep03 (ChIL-seq)

value: Differentiated for 24 hours


title: 3T3_EGFP18_24h_DoxPlus_H3p3_Rep01 (ChIL-seq)


title: 3T3_EGFP18_24h_DoxPlus_H3p3_Rep02 (ChIL-seq)


title: 200796210041_A_ATP2B4 Meso III


title: 200796210041_C_ATP2B4 M/E7 I

value: Meso/Ery MD8


title: 200796210041_H_ATP2B4 Ery1 III

value: DIFF Ery PI


title: 200796210041_B_ATP2B4 Ery 1 III


title: 3T3_EGFP18_24h_DoxMinus_H3p3_Rep02 (ChIL-seq)


title: 200796210041_D_ATP2B4 Ery I

value: DIFF Ery PIII


title: 3T3_EGFP18_0h_DoxPlus_H3p3_Rep02 (ChIL-seq)

value: Differentiated for 0 hours


title: 200790250047_L_ATP2B4 Meso II


title: 200790250047_K_HEL C+E REP1

source_name: HEL

value: BLOOD CANCER cell line

value: DIFF CISPLATIN+EPO


title: 200790250047_J_ATP2B4 Meso I


title: 200790250047_F_ATP2B4 KO G5 II

source_name: ATP2B4 KO G6

value: UNDIFFERENTIATED


title: 3T3_EGFP18_0h_DoxMinus_H3p3_Rep02 (ChIL-seq)


title: 200790250047_E_HEL CIS REP1

value: DIFF CISPLATIN


title: 200790250047_G_HEL CIS REP2


title: PyMT NEKO tumor 2538

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the mouse reference genome (Gencode GRCm38) using TopHat 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for HTSeq 0.11.0 in order to generate read count data on gene level (parameters: -s no  -m union)
Assembly: GRCm38
Supplementary files format and content: raw read count data generated by htseq-count 0.11.0 for each sample

source_name: TNBC tumors

growth_protocol: PyMT mice, both WT and NEKO were maintained in pathogen-free small animal facility at MDACC

extract_protocol:
RNA was harvested using the TRIzol (Thermo-Fisher Scientific) reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by polyA capture (or rRNA removal) and reverse transcription of cDNA, outsourced commercially to Novogene

treatment_protocol:
No treatments
No treatments

value: FVB/nJ

tag: gender

value: Female

value: TNBC tumors

value: NE knockout

value: No treatment

value: 12-14 weeks age


title: 200790250047_I_HEL CIS REP3


title: PyMT NEKO tumor 2663


title: PyMT NEKO tumor 2605


title: PyMT NEKO tumor 2540


title: 200790250047_D_ATP2B4 KO G5 I

source_name: ATP2B4 KO G5

value: IPS KO CRL-DERIVED cell line


title: PyMT NEKO tumor 1619


title: 3T3_EGFP18_0h_DoxMinus_H3p3_Rep01 (ChIL-seq)

value: NIH3T3 cell line (Dox inducible H3mm18)

value: rat anti-H3.3 clone 4H2D7 [PMID 22569126]


title: PyMT WT tumor 2548

value: WT


title: 3T3_EGFP18_UI_DoxPlus_H3p3_Rep02 (ChIL-seq)

value: Before retroviral infection (UnInfected, UI)


title: 3T3_EGFP18_UI_DoxPlus_H3p3_Rep01 (ChIL-seq)


title: PyMT WT tumor 1662


title: PyMT WT tumor 2036


title: 3T3_EGFP18_0h_DoxPlus_H3p3_Rep01 (ChIL-seq)


title: 200790250047_B_HEL C+E REP2


title: PyMT WT tumor 2515


title: 200781960082_K_HEL EPO REP3

value: DIFF EPO


title: 200781960082_L_BSG KO C5 I

source_name: BASIGIN KO C5B1


title: 200790250047_A_HEL HEM REP1

value: DIFF HEMATIN


title: 3T3_EGFP18_UI_DoxMinus_H3p3_Rep01 (ChIL-seq)


title: PyMT WT tumor 2656


title: Blood_migration_Induced_at_Neonate_TA-LL829-SP-HSC

city: Hangzhou

first: SHOU-WEN

last: WANG

state: Zhejiang Province

address: Shilongshan ST #18, Xihu District

institute: Westlake University

data_processing: DATA are processed with CARLIN pipeline, except CARLIN libraries from Camellia-seq, which were analyzied with a customized script.

extract_protocol:
Each sample has its corresponding CARLIN protocol as shown above. The CARLIN DNA or RNA materials are extracted from either 1) bulk cell populations sorted with FACS or 2) single-cell samples prepared with 10X encapsulation or individually sorted single cells from Camellia-seq
We used bulk RNA or DNA as starting material. RNA were converted to DNA with SuperScrit III. Then we used a nested PCR approach with locus specific primers to perform targeted amplification with Q5 High-Fidelity DNA Polymerase (New England Biosciences, M0491L). We used 1.5X Ampure XP beads (Beckman Coulter, A63881) to purify the PCR product from each step once except the final indexing PCR product (0.8X, twice purification). The final indexing libraries were pooled and quantified (Kappa Biosystems, KK4835) and sequenced on Illumina MiSeq using paired-end 500 cycles v2 kits (Illumina, MS-102-2003) with 5% PhiX sequencing control v3 (Illumina, FC-110-3001).

tag: carlin protocol

tag: carlin locus

value: TA


title: Blood_migration_Induced_at_Neonate_TA-LL829-SP-MyP

tag: cell type


title: Blood_migration_Induced_at_Neonate_TA-LL829-SP-Meg


title: 200781960082_J_RH1 Ery 2 II

value: IPS WT FIBROBLAST-DERIVED cell line

value: DIFF Ery PIII


title: Blood_migration_Induced_at_Neonate_TA-LL829-SP-MPP


title: 200790250047_C_HEL HEM REP2

value: BLOOD CANCER cell line


title: H3mm18KO-Day14-CTX-m1 (BRB-seq)

data_processing:
Library strategy: BRB-seq
For CEL-Seq2 and BRB-seq, extraction of sample barcodes and unique-molecular-identifiers (UMIs) was performed using UMI-tools (T. S. Smith et al., 2017) (version 1.0.1) with the following commands: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout for CEL-Seq2, and umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern= NNNNNNCCCCCCCCC --read2-stdout for BRB-seq.
The reads were trimmed using Cutadapt (M. Martin, 2011)  (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option:  -a GATCGTCGGACT.
The reads were mapped by the aligning software HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0) to the reference genome (GRCm38, pre-built HISAT2 index, genome_snp_tran).
Read counts per gene were obtained using featureCounts (Liao Y et al., 2014) (version 2.0.1). Note that UMIs were not used and mitochondrial chromosome genes are excluded in the analysis.
DESeq2 software (M. I. Love et al., 2014) (1.28.1) was used to calculate normalized counts.
*.csv files include comma-delimited read count matrices and normalized count matrices.
Genome_build: GRCm38/mm10

source_name: Tibialis anterior (TA) muscle of 12-week-old H3mm18-/- mice

extract_protocol:
Total RNA was extracted from cells using Sepasol-RNA I Super G (Nacalai Tesque) and reverse-transcribed with PrimeScript II Reverse Transcriptase (Takara) and either oligo-dT primer or random 6-mer according to the manufacturer’s protocols.
BRB-seq was carried out as described previously (Alpern et al. 2019 Genome Biol) except that cDNA was synthesized with RT primers for CEL-Seq2 instead of those described in the original BRB-seq protocol.. Sequencing was performed using HiSeq PE Rapid Cluster Kit v2 (Illumina) in an Illumina HiSeq 1500 system with 15 cycles for read 1 and 45 cycles for read 2 in BRB-seq for mouse samples.

treatment_protocol: For muscle regeneration experiments, cardiotoxin (CTX) was injected into the tibialis anterior (TA) muscle of 12-week-old mice as described previously (Harada et al. 2017 Nat Commun).

value: H3mm18 KO

value: 14 days after cardiotoxin (CTX) injection to tibialis anterior (TA) muscle

tag: sample barcode

value: ATTAGAAGG


title: Blood_migration_Induced_at_Neonate_TA-LL829-SK-MyP


title: H3mm18KO-Day14-CTX-m2 (BRB-seq)

tag: tissue

value: Tibialis anterior (TA) muscle of 12-week-old H3mm18-/- mice

value: ACCATCAGA


title: Blood_migration_Induced_at_Neonate_TA-LL829-SK-Meg


title: Blood_migration_Induced_at_Neonate_TA-LL829-SK-HSC


title: 3T3_EGFP18_UI_DoxMinus_H3p3_Rep02 (ChIL-seq)

tag: genotype


title: Blood_migration_Induced_at_Neonate_TA-LL829-SK-MPP


title: Blood_migration_Induced_at_Neonate_TA-LL829-RL-MyP


title: H3mm18KO-Day14-CTX-f3 (BRB-seq)

value: ACACCGATA


title: Blood_migration_Induced_at_Neonate_TA-LL829-RL-Meg


title: H3mm18KO-Day14-CTX-f2 (BRB-seq)

value: AGTCAGAGT


title: 200790250047_H_ATP2B4 KO G5 III

source_name: ATP2B4 KO G7

value: IPS KO CRL-DERIVED cell line

value: UNDIFFERENTIATED


title: O EC

city: New York

first: Bi-Sen

last: Ding

state: NY

address: York Avenue

institute: Weill Cornell

hyb_protocol: Fragmented cRNA was hybridized to the gene chips, washed, and stained with streptavidin phycoerythrin.

scan_protocol: The probe arrays were scanned with the Genechip System confocal scanner.

data_processing: Affymetrix Microarray suite 4.0 (GCOS ver 1.4) was used to analyze the data. MAS5 data.

label: Biotin

source_name: Old lung vascular cells, after pneumonectomy

label_protocol: The Superscript choice kit (Invitrogen, Carlsbad, CA) was used to make cDNA with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. The biotin labeled cRNA was made by in vitro transcription (Enzo Diagnostics).

growth_protocol: Vascular cells were isolated from the mouse lung via flow sorting and subjected to RNA extraction and analysis.

extract_protocol: The protocol used to extract RNA was according to Manufacturers specifications QIAGEN Rneasy kit.

treatment_protocol: Young and old mice were anesthetized and ventilated. Left lung lobe was resected, and residual right lung lobes were isolated from the mice for vascular cell isolation.

tag: strain

value: mature lung

value: old


title: Blood_migration_Induced_at_Neonate_TA-LL829-RL-MPP


title: 200781960082_H_RH1 Ery 2 I

tag: cell line


title: H3mm18KO-Day14-CTX-f1 (BRB-seq)

value: ACTGATATG


title: Blood_migration_Induced_at_Neonate_TA-LL829-RL-HSC


title: WT-Day14-CTX-m2 (BRB-seq)

source_name: Tibialis anterior (TA) muscle of 12-week-old mice

value: AGCTGTTGG


title: 200781960082_F_RH1 2 III


title: 200781960082_G_HEL EPO REP1

value: DIFF EPO


title: WT-Day14-CTX-m1 (BRB-seq)

value: Tibialis anterior (TA) muscle of 12-week-old mice

value: ATCGTGTGA


title: Blood_migration_Induced_at_Neonate_TA-LL829-LL-MPP

value: TA


title: Blood_migration_Induced_at_E17_TA-LL839-SP-MyP


title: Blood_migration_Induced_at_Neonate_TA-LL829-LL-HSC


title: Y EC

source_name: Young lung vascular cells, after pneumonectomy

value: young


title: 200781960082_E_HEL-Cas9 REP3

value: BLOOD CANCER cell line

value: CONTROL


title: WT-Day14-CTX-f3 (BRB-seq)

value: 14 days after cardiotoxin (CTX) injection to tibialis anterior (TA) muscle

value: TGCAGGCCG


title: Blood_migration_Induced_at_E17_TA-LL839-SP-HSC


title: Blood_migration_Induced_at_E17_TA-LL839-SP-MPP


title: Blood_migration_Induced_at_E17_TA-LL839-SP-Meg


title: 200781960082_I_HEL EPO REP2


title: WT-Day14-CTX-f2 (BRB-seq)

value: TACGTATAG


title: WT-Day14-CTX-f1 (BRB-seq)

value: TATATTCCA


title: Blood_migration_Induced_at_E17_TA-LL839-SK-MyP


title: Blood_migration_Induced_at_Neonate_TA-LL829-LL-MyP


title: Blood_migration_Induced_at_Neonate_TA-LL829-LL-Meg


title: 200781960082_D_RH1 2 II

value: IPS WT FIBROBLAST-DERIVED cell line


title: Blood_migration_Induced_at_E17_TA-LL839-SK-MPP


title: 200781960082_C_HEL-Cas9 rep2


title: Blood_migration_Induced_at_E17_TA-LL839-SK-Meg


title: 200781960082_B_RH1 2 I

value: UNDIFFERENTIATED


title: Blood_migration_Induced_at_E17_TA-LL839-SK-HSC


title: 200055410086_G_BSG KO C5 M/E8 B II

source_name: BASIGIN KO C5B4

value: IPS KO CRL-DERIVED cell line

value: Meso/Ery MD8 B II


title: 200055410086_I_BSG KO C5 Ery I

source_name: BASIGIN KO C5B5

value: DIFF Ery PIII


title: H3mm18KO-Day5-CTX-m1 (BRB-seq)

value: Tibialis anterior (TA) muscle of 12-week-old H3mm18-/- mice

value: H3mm18 KO

value: 5 days after cardiotoxin (CTX) injection to tibialis anterior (TA) muscle

value: TGGTACACC


title: Blood_migration_Induced_at_E17_TA-LL839-RL-MPP

value: TA


title: Blood_migration_Induced_at_E17_TA-LL839-RL-Meg


title: H3mm18KO-Day5-CTX-f3 (BRB-seq)

value: TCCTGGAAC


title: Blood_migration_Induced_at_E17_TA-LL839-RL-HSC


title: Blood_migration_Induced_at_E17_TA-LL839-RL-MyP


title: Blood_migration_Induced_at_E17_TA-LL839-LL-MPP


title: H3mm18KO-Day5-CTX-f2 (BRB-seq)

value: TATAATCGC


title: Blood_migration_Induced_at_E17_TA-LL839-LL-MyP


title: H3mm18KO-Day5-CTX-f1 (BRB-seq)

value: GTGTTCGAT


title: Blood_migration_Induced_at_E17_TA-LL839-LL-Meg


title: 200055410086_K_BSG KO C5 Ery II

source_name: BASIGIN KO C5B6


title: WT-Day5-CTX-m1 (BRB-seq)

value: Tibialis anterior (TA) muscle of 12-week-old mice

value: GAGACAGTC


title: H3mm18KO-Day5-CTX-m2 (BRB-seq)

value: TGCACACAG


title: Blood_migration_Induced_at_Adult_TA-LL784-SP-Meg


title: 200055410086_E_BSG KO C5 M/E8 B I

source_name: BASIGIN KO C5B3

value: Meso/Ery MD8 B I


title: Blood_migration_Induced_at_Adult_TA-LL784-SP-MyP


title: Blood_migration_Induced_at_E17_TA-LL839-LL-HSC


title: 200055410086_C_BSG KO C5 II

source_name: BASIGIN KO C5B2


title: Blood_migration_Induced_at_Adult_TA-LL784-SP-MPP


title: WT-Day5-CTX-f3 (BRB-seq)

value: GTACACTGC


title: Blood_migration_Induced_at_Adult_TA-LL784-SP-HSC


title: 200055410086_A_BSG KO C5 I

value: UNDIFFERENTIATED


title: WT-Day5-CTX-f2 (BRB-seq)

value: GAAGGTTGC


title: 200055410057_K_RH1 M/E12B II

value: IPS WT FIBROBLAST-DERIVED cell line

value: Meso/Ery MD12B


title: Blood_migration_Induced_at_Adult_TA-LL784-SK-MyP


title: 200055410057_J_RH1 Ery I

value: DIFF Ery PIII


title: Blood_migration_Induced_at_Adult_TA-LL784-SK-MPP


title: 200055410057_L_RH1 Ery II


title: Blood_migration_Induced_at_Adult_TA-LL784-SK-Meg


title: Blood_migration_Induced_at_Adult_TA-LL784-SK-HSC


title: Blood_migration_Induced_at_Adult_TA-LL784-RL-MPP


title: H3mm18KO-f869-SKM (BRB-seq)

value: Tibialis anterior (TA) muscle of 12-week-old H3mm18-/- mice

value: H3mm18 KO

value: Before cardiotoxin (CTX) injection (Day 0)

value: CACAGAGAG


title: Blood_migration_Induced_at_Adult_TA-LL784-RL-Meg

value: TA


title: Blood_migration_Induced_at_Adult_TA-LL784-RL-HSC


title: H3mm18KO-f177-SKM (BRB-seq)

value: CGGCCTCTA


title: Blood_migration_Induced_at_Adult_TA-LL784-LL-MyP


title: Blood_migration_Induced_at_Adult_TA-LL784-LL-Meg


title: WT-f870-SKM (BRB-seq)

value: CTGATGCAT


title: HeLa cells, BETF enriched cytoplasmic RNA, update

first: Haofan

last: Sun

address: Grindtorpsvägen 11 7tr Lgh 1803, Grindtorpsvägen 11, 183 32 Täby

institute: National Center for Protein Sciences, Beijing

data_processing:
To estimate the content of RNA biotypes in libraries, reads were aligned to the hg38 assembly using STAR.
Counting was performed with HTSeq-count using the gene set annotated by GENCODE Release 21 (GRCh38) and using the GTF feature ‘gene’ for counting.
Assembly: hg38
Supplementary files format and content: Tab-separated values files

molecule: cytoplasmic RNA

source_name: Hela

extract_protocol:
RNAs were purified by TRIzol following the manufacturer’s instructions
The RNA samples were prepared with the TruSeq RNA Library Prep Kit v2.

value: Hela

value: Human cervix carcinoma

tag: treatment

value: BETF enrichment


title: Blood_migration_Induced_at_Adult_TA-LL784-RL-MyP


title: WT-Day5-CTX-f1 (BRB-seq)

value: Tibialis anterior (TA) muscle of 12-week-old mice

value: 5 days after cardiotoxin (CTX) injection to tibialis anterior (TA) muscle

value: GCCGCACAG


title: 200055410057_H_RH1 M/E12 II

value: Meso/Ery MD12


title: WT-f179-SKM (BRB-seq)

value: CTCTATGCC


title: HeLa cells, cytoplasmic RNA, update

value: density gradient centrifugation


title: 200055410057_I_RH1 M/E12B I

value: IPS WT FIBROBLAST-DERIVED cell line

value: Meso/Ery MD12B


title: 200055410057_F_RH1 M/E12 I


title: 200055410057_E_RH1 M/E8B I

value: Meso/Ery MD8 B


title: 200055410057_D_RH1 M/E8 II

value: Meso/Ery MD8


title: Blood_migration_Induced_at_Adult_TA-LL784-LL-HSC


title: Blood_migration_Induced_at_Adult_TA-LL784-LL-MPP


title: 200055410057_C_RH1 II

value: UNDIFFERENTIATED


title: WT-m181-SKM (BRB-seq)

value: Before cardiotoxin (CTX) injection (Day 0)

value: CGGCCTGAT


title: 200055410057_B_RH1 M/E8 I


title: 200055410057_G_RH1 M/E8B II

value: Meso/Ery MD8B


title: 200055410057_A_RH1 I


title: p88kd1_treatment

status: Public on Oct 20 2023

city: Malmo

first: Dmytro

last: Kryvokhyzha

address: Jan Waldenströms gata 35

department: Clinical Sciences

country: Sweden

institute: Lund University

data_processing:
QC with fastQC 0.11.9 and multiQC 1.9
mapping and counting with Salmon 1.5.0
Assembly: Rnor_6.0 ensembl 104 transriptome
Supplementary files format and content: tab-delimited file includes raw counts and TPM for each Sample

organism: Rattus norvegicus

extract_protocol:
NucleoSpin RNA (Macherey Nagel, Prod# 740955.250)
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: Control cells were treated with negative control siRNA and the KD samples treated with an siRNA for GPR162

value: pancreatic islet beta-cell

value: siRNA for GPR162


title: p93kd2_treatment


title: p88kd2_treatment


title: p80kd2_treatment


title: p93kd1_treatment


title: p88nc1_control

value: negative control siRNA


title: p80kd1_treatment


title: p3nc1_control


title: p93nc2_control


title: p93nc1_control


title: H3mm18KO-m182-SKM (BRB-seq)

value: Tibialis anterior (TA) muscle of 12-week-old H3mm18-/- mice

value: H3mm18 KO

value: CATGCAACT


title: p2nc1_control


title: p1nc1_control


title: HeLa cells, nuclear RNA, update

molecule: nuclear RNA

value: Hela

value: Human cervix carcinoma


title: Dormant_24hr_rep2

city: Kawasaki

first: Naoto

last: Kawakami

state: Kanagawa

address: 1-1-1 Higashimita, Tama-ku

department: Department of Life Sciences

institute: Meiji University

description: Gene expression in dormant seed after 24hr of imbibition at 26°C

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilnt Arabidopsis 4 Oligo Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) for 1 minute at room temperature and with Gene Expression Wash Buffer 2 (Agilent) for 1 minute at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel was set to Green, and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_QCMT_Oct12. and Grid: 021169_D_F_20170524) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

source_name: Dormant, 24hr, 26°C

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The seeds were stratified at 4°C for 4 days in 0.1% agar solution, and sown on soil (Co-op N-150; Katakura & Co-op Agri, Co., Tokyo,Japan). The seedlings were grown in a growth chamber under continuous illumination at 22°C. The seeds from the plants were harvested at physiological maturity, at about 24 days after flowering, and were stored in a desiccator at room temperature for after-ripening.

extract_protocol: RNA was prepared using the RNAqueous Small scale phenol-free total RNA isolation kit (Ambion :catalog #1912) and Plant isolation aid (Ambion :catalog #9690) following the manufacturer's recommendations. RNA was quantified using a UV-1800 (Shimadzu) and its integrity was monitored with agarose gel electrophoresis.

treatment_protocol: 20 mg of seeds were surface sterilized with 70% ethanol for 5 minutes, rinsed twice with 100% ethanol, then dried in an evaporator for 10 minutes. The seeds were imbibed on two sheets of filter paper in a round Petri dish. The lid was fixed with plastic tape and the seeds were incubated at constant temperature under continuous illumination. After incubation, the seeds were collected with spatula and covered with aluminum foil, then immediately frozen with liquid nitrogen and stored at -80°C until use for RNA preparation.

tag: ecotype

value: dormant seed

value: imbibition

tag: temperature

tag: days after harvest


title: Thermoinhibition_24hr_rep2

description: Gene expression in after-ripened seed after 24hr of imbibition at 34°C

source_name: After-ripened, 24hr, 34°C

value: after-ripened seed


title: Thermoinhibition_24hr_rep3


title: Thermoinhibition_6hr_rep2

description: Gene expression in after-ripened seed after 6hr of imbibition at 34°C

source_name: After-ripened, 6hr, 34°C


title: Dormant_0hr_rep2

description: Gene expression in dormant dry seed

source_name: Dormant, 0hr, 26°C

value: dormant dry seed

value: control


title: Dormant_24hr_rep3


title: After-ripened_24hr_rep3

description: Gene expression in after-ripened seed after 24hr of imbibition at 26°C

source_name: After-ripened, 24hr, 26°C


title: Thermoinhibition_24hr_rep1


title: After-ripened_24hr_rep2


title: After-ripened_24hr_rep1


title: Thermoinhibition_6hr_rep1


title: After-ripened_6hr_rep3

description: Gene expression in after-ripened seed after 6hr of imbibition at 26°C

source_name: After-ripened, 6hr, 26°C


title: Thermoinhibition_6hr_rep3


title: After-ripened_6hr_rep1


title: Dormant_24hr_rep1


title: Dormant_6hr_rep1

description: Gene expression in dormant seed after 6hr of imbibition at 26°C

source_name: Dormant, 6hr, 26°C


title: After-ripened_6hr_rep2


title: Dormant_6hr_rep3


title: After-ripened_0hr_rep3

description: Gene expression in after-ripened dry seed

source_name: After-ripened, 0hr, 26°C

value: after-ripened dry seed


title: Dormant_0hr_rep1

description: Gene expression in dormant dry seed


title: 120d Lohmann layers,  uterus, rep3

city: Chengdu

first: Lingqian

last: Yin

address: 211 Huimin Road, Wenjiang, Chengdu, Sichuan Province

institute: Sichuan Agricultural University

data_processing:
Quality control filtering of Raw Data using fastqc V0.11.6
The Adapter from the Illumina platform's FASTQ sequence was removed using Trimmomatic V0.32
Clean Reads were mapped to reference genomes (Gallus Gallus 5.0) using TopHat2 2.0.8
Identify the single base mismatch and  potential SNP sites using GATK v3.8; Annotate variation (SNP, InDel) and predict the impact of variation using SnpEff v1.9.6
Calculates the sequencing numbers compared to each gene and then calculates FPKM based on the length of each gene and the number of sequenced fragments using Cufflinks v2.0.2
Assembly: Gallus Gallus 5.0
Supplementary files format and content: The list file for all gene fpkm
Supplementary files format and content: The list file for all gene counts

organism: Gallus gallus

source_name: oviduct

extract_protocol:
Total RNA was extracted using RNAsimple Total RNA Kit (DP419,Tiangen), 3ul total RNA was used to construct sequencing libraries
Library was constructed using Smarter mRNA-seq Library Prep Kit

value: oviduct

tag: time point


title: 300d Lohmann layers,  uterus, rep2


title: 300d Lohmann layers, uterus, rep1


title: 120d Lohmann layers,  uterus, rep2


title: 300d Lohmann layers, magnum, rep3


title: 300d Lohmann layers, uterus, rep3


title: After-ripened_0hr_rep1


title: 300d Lohmann layers, magnum, rep2


title: 300d Lohmann layers, magnum, rep1


title: 120d Lohmann layers, uterus, rep1


title: 120d Lohmann layers, magnum, rep3


title: 120d Lohmann layers, magnum, rep2


title: After-ripened_0hr_rep2


title: 120d Lohmann layers, magnum, rep1


title: rhesus_M_HiC

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

data_processing:
HiC data were subject to quality control and alignment with bowtie2 using the HiCUP pipeline.
Bam files were paired and converted to .cool format using cooltools.
TADs were called using HicExplorer, HicFindTADs with parameters --minDepth 100000, --maxDepth 600000, --delta 0.01, --correctForMultipleTesting fdr
Supplementary_files_format_and_content: BED files with TAD boundary regions

organism: Macaca mulatta

source_name: Liver

extract_protocol: Arima HiC

value: Liver

value: Rhesus macaque

tag: protocol

value: Arima


title: rhesus_F_HiC


title: ChIP.07_MRTK.103_antiSMARCB1_CTRL

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description: ChIP-seq in MRT organoids P103, after 4 days lentiviral transduction with the Luciferase gene

data_processing:
ChIP-seq were mapped to a hg38 reference. The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools. The coverage files of ChIP-seq data were generated using “normalize to 1X genome coverage” methods in deepTools. Peak calling was performed using MACS2 (version 2.1.1.20160309) (Liu, 2014) at a q-value cutoff of 0.01. CUT&RUN data were mapped to the hg38 reference genome using BWA-MEM (version 0.7.15-r1140). The mapped reads were filtered using SAMtools, discarding reads with mapping quality score <15, as well as optical PCR duplicates. The coverage files were produced using the deepTools (version 3.0) method “normalize to 1X genome coverage”.
Assembly: hg38
Supplementary files format and content: bigWig files

source_name: MRT organoids P103

growth_protocol: The cell pellets were seeded in growth factor-reduced BME (Trevigen, 3533-010-02) and cultured in kidney organoid medium (AdDF+++ supplemented with 1.5% B27 supplement (Gibco), 10% R-spondin-conditioned medium, EGF (50 ng ml−1, Peprotech), FGF-10 (100 ng ml−1, Peprotech), N-acetylcysteine (1.25 mM, Sigma), Rho-kinase inhibitor Y-27632 (10 µM, Abmole) and A83-01 (5 µM, Tocris Bioscience). Medium was changed every 3–4 days, and organoids were passaged every 1–3 weeks. Depending on organoid morphology, organoids were either passaged using mechanical dissociation (Wilms tumour organoids, MRTK organoids), or TrypLE Express (Invitrogen, 12605036) containing 10 µM Y-27632 (Wilms tumour organoids, RCCs). Following the addition of 5–10 ml AdDF+++ and centrifugation at 250×g, cells were reseeded in BME and topped with kidney organoid medium. All organoid cultures are stored in the biobank of the Princess Máxima Center and made available to the scientific community according to the rules and regulations under which the patients and parents gave informed consent for donating the tissue.

extract_protocol:
ChIP-seq experiments were performed using a published protocol (Liu et al., 2021). For chromatin preparation, the MRT cells were cross-linked by a final concentration of 1% formaldehyde for 10 min. To perform a double-crosslinking reaction, a first cross-linking was performed by adding 2mM disuccinimidyl glutarate (DSG, 20593, Thermo Fisher) for 45 minutes at room temperature and washed once with 1x PBS before second cross-linking reaction. Subsequently, cells were cross-linked with a final concentration of 1% formaldehyde for 10 minutes. The cross-linking reaction was quenched using 2.0 M glycine. The cross-linked cells were then lysed and sonicated to obtain ~300 bp chromatin using Bioruptor Plus sonication device (Diagenode). For ChIP assays, antibodies were first coupled with Protein G beads (ThermoFisher Scientific), and then the sonicated chromatin were incubated overnight at 4oC with the antibody coupled Protein G beads. After over incubation, captured chromatin was washed, eluted and de-crosslinked. The released DNA fragments were purified using MiniElute PCR Purification Kit (Qiagen). The ChIP experiments were performed using the following antibodies: (1) CTCF (07-729, Merck Millipore), (2) RAD21 (ab154769, Abcam), and (3) H3K27ac (ab4729, Abcam).
ChIP-seq libraries were prepared according to the protocol of KAPA HTP Library Preparation Kit (Roche).

treatment_protocol: For SMARCB1 re-expression, MRT organoids were lentivirally transduced with pLKO.1-UbC-luciferase-blast40 or pLKO.1-UbC-hSMARCB1-blast lentiviruses. After 2 days, 10 µg/ml blasticidin was added to the culture medium.

value: MRT organoids P103

value: Malignant rhabdoid tumor cells

value: Luciferase plasmid


title: human_cortex

first: Ryan Mulqueen

last: Mulqueen

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Molecular and Medical Genetics

institute: Oregon Health and Science

description: single-cell ATAC seq via custom chemistry

library_source: genomic single cell

data_processing:
FastQ files were generated from BCL files using bcl2fastq (v 2.19.0, Illumina Inc.) with the following options with-failed-reads, no-lane-splitting, fastq-compression-level=9, create-fastq-for-index-reads
Data were demultiplexed with scitools (https://github.com/adeylab/scitools) fastq-dump-10x function; briefly FastQ reads were assigned to their expected primer index sequence allowing for sequencing error (Hamming distance ≤2) and indexes were concatenated to form a “cellID”. cellIDs are stored in the FastQ header
Demultiplexed reads were aligned with scitools fastq-align function to a concatenated reference genomes GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) and GRCh38 (“hg38”,Genome Reference Consortium Human Reference 38 (GCA_000001405.2) via bwa mem (v0.7.15-r1140) .
Aligned reads then underwent a barcode-specific duplicate removal via scitools
Alignment rates of human (hg38) and mouse (mm10) per cellID were then generated with scitools function barnyard-compare and cellIDs were assigned as human, mouse, or mixed.
CellIDs that were assigned to a single genome and realigned to the respective genome (hg38 or mm10), underwent barcode-based removal of duplicates and then filtered to those with >= 10,000 unique reads, and a percentage unique reads of <= 90%.
Persisting barcodes (cellID) were then filtered and fragments files were generated for Signac input.
See "txci-ATAC-seq, a massive-scale single-cell technique to profile chromatin accessibility" methods for further cell type annotation and differential analysis.
Assembly: GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2); GRCh38 (“hg38”,Genome Reference Consortium Human Reference 38 (GCA_000001405.2)
Supplementary files format and content: *_metadata.tsv: Tab-separated file detailing annotations and metadata per cell (each row being a cell).
Supplementary files format and content: *_SeuratObject.PF.Rds: Signac/Seurat R data object files. Can be read in with R function "readRDS" in Signac v 1.0. Contains multiple assays (ATAC, GeneActivity, Chromvar analysis) per cell used in downstream analysis in manuscript.
Supplementary files format and content: *.counts.sparseMatrix.cols.gz;*.counts.sparseMatrix.rows.gz;*.counts.sparseMatrix.values.gz: Sparse Matrix format files of raw fragment counts from called peaks (generated through cellranger)
Supplementary files format and content: *.merged.fragments.tsv.gz,*.merged.fragments.tsv.gz.tbi; Fragment file (modified bed format) with index file generated through samtools and tabix from aligned bam file.

source_name: middle frontal gyrus

extract_protocol:
Human cortex samples from the middle frontal gyrus were sourced from the Oregon Brain Bank from a 50-year-old female of normal health status. Samples were collected by an OHSU neuropathologist, placed into a labeled cassette, and cryopreserved in an airtight container in a -80 °C freezer. The duration of time between the time of death and brain biopsy sample freezing, or post-mortem interim (PMI), was <24 hours. Mouse brain tissue was collected as discarded tissue from mice used for unrelated studies approved by the OHSU IACUC. Whole mouse brains were dissected from sacrificed C57BL/6J mice and flash-frozen in an isopentane-LN2 double-bath and stored at -80 °C.
At the time of nuclei dissociation, 50 ml of nuclei isolation buffer (NIB-HEPES) was freshly prepared with final concentrations of 10 mM HEPES-KOH (Fisher Scientific, BP310-500 and Sigma Aldrich 1050121000, respectively), pH 7.2, 10 mM NaCl (Fisher Scientific S271-3), 3mM MgCl2 (Fisher Scientific AC223210010), 0.1 % (v/v) IGEPAL CA-630 (Sigma Aldrich I3021), 0.1 % (v/v) Tween-20 (Sigma-Aldrich P-7949) and diluted in PCR-grade Ultrapure distilled water (Thermo Fisher Scientific 10977015). After dilution, two tablets of Pierce™ Protease Inhibitor Mini Tablets, EDTA-free (Thermo Fisher A32955) were dissolved and suspended to prevent protease degradation during nuclei isolation.
An at-bench dissection stage was set up prior to nuclei extraction. A petri dish was placed over dry ice, with fresh sterile razors pre-chilled by dry-ice embedding. 7 ml capacity Dounce homogenizers were filled with 2 ml of NIB-HEPES buffer and held on wet ice. Dounce homogenizer pestles were held in ice-cold 70% (v/v) ethanol (Decon Laboratories Inc 2701) in 15 ml tubes on ice to chill. Immediately prior to use, pestles were rinsed with chilled distilled water. For tissue dissociation, mouse and human brain samples were treated similarly. The still-frozen block of tissue was placed on the clean pre-chilled petri dish and roughly minced with the razors. Razors were then used to transport roughly 1 mg of the minced tissue into the chilled NIB-HEPES buffer within a Dounce homogenizer. Suspended samples were given 5 minutes to equilibrate to the change in salt concentration prior to douncing. Tissues were then homogenized with 5 strokes of a loose (A) pestle, another 5-minute incubation, and 5-10 strokes of a tight (B) pestle. Nuclei were transferred to a 15 ml conical tube and pelleted with a 400 r.c.f centrifugation at 4 °C in a centrifuge for 10 minutes. The supernatant was removed and pellets were resuspended in 5 ml of ATAC-PBS buffer (APB) consisting of 1X PBS (Thermo Fisher 10010) and 0.04mg/ml (f.c.) of bovine serum albumin (BSA, Sigma Aldric A2058). Samples were then filtered through a 35 µm cell strainer (Corning 352235). A 10 μl aliquot of suspended nuclei was diluted in 90 μl APB (1:10 dilution) and manually counted on a hemocytometer with Trypan Blue staining (Thermo Scientific T8154). The stock nuclei suspension was then diluted to a concentration of 2,857 nuclei/μl in APB. Dependent on experimental schema, pools of tagmented nuclei were combined to allow for the assessment of pure samples and to test index collision rates.
Tagmentation plates were prepared by the combination of 1430 μl of TBS with 770 μl nuclei solution. The TBS recipe was described in “Blocking barcode-swapping”, but a different version of Digitonin (Bivision 2082-1) was used here. This solution was mixed briefly on ice. 20 μl of the mixture was placed into the 96-well iTSM plate (see “Sample multiplexing” for details). Tagmentation was performed at 37 °C for 60 minutes on a 300 r.c.f Eppendorf ThermoMixer with a lid heated to 65 °C. Following this incubation, plate temperature was brought down with a 5-minute incubation on ice to stop the reaction. Tagmented nuclei were then pooled into a single 15 ml conical tube. 5 ml of tagmentation wash buffer (TMG) was prepared consisting of a final concentration of 10 mM Tris Acetate pH 7.5 (Sigma 93352 and Sigma A6283, respectively), 5 mM MgAcetate (Sigma M5661), and 10% (v/v) glycerol (Sigma G5516), diluted in PCR grade water. 1 ml of TMG was added on top of the chilled tagmented nuclei. Nuclei were pelleted at 500 r.c.f for 10 minutes at 4 °C. Most of the supernatant was removed with care not to disturb the pellet. Then 500 μl of TMG was added to the pellet and the tube was once again spun at 500 r.c.f. for 5 minutes at 4 °C. 490 μl was removed leading to a low volume of concentrated nuclei. Loading buffer was prepared consisting of 10% (v/v) glycerol, 20 mM NaCl, 10 mM Tris-Cl pH 7.5 (Life technologies AM9855), 0.02 mM EDTA (Fisher Scientific AM9260G), 0.2 mM DTT (VWR 97061-340), and 0.2x (v/v) TB1 (Illumina Inc.). The nuclear pellet was resuspended with an additional 30 μl of loading buffer. An aliquot of 2 μl of sample was diluted 20-50X and quantified with Trypan Blue on a hemocytometer. Depending on the experiment, a 14 μl nuclei solution containing the desired amount of nuclei in the loading buffer was then combined with 1 μl of 75 μM short SBS oligo (Table S8).
The 10X Chromium was then run with the custom nuclei solution as per the manufacturer’s instructions (10x Document CG000209 Rev D) with the following adaptations. In step 2.4e during GEM aspiration and transfer, 100 μl GEM volume was split into two tubes, with one receiving 10 μl and the other 90 μl (henceforth referred to as 10% and 90% samples). In step 2.5.a, GEM incubation cycles were limited to 6. For Pre-PCR wash elution (Step 3.2.j) the 10% sample was eluted in 8.5 μl whereas the 90% sample was eluted in 32.5 μl. For step 3.2.n, the 10% sample had 8 μl transferred to a new strip, while the 90% sample had 32 μl transferred to a new strip. At step 4.1.b, the sample Index PCR mix was split with 11.5 μl and 46 μl being combined with the 10% and 90% samples, respectively. For step 4.1.c, 1 μl and 2 μl of a 10 μM i7 TruSeq primer was used, respectively. For step 4.1.d, 8 and 7 PCR cycles were used, respectively. Libraries were then checked for quality and quantified by Qubit DNA HS assay (Agilent Q32851) and Tapestation D5000 (Agilent 5067-5589) following the manufacturer’s instructions. Libraries were then diluted and sequenced on a NextSeq 500 Mid flow cell or a NovaSeq 6000 S4 flow cell (Illumina Inc.).

value: middle frontal gyrus


title: Dormant_0hr_rep3

description: Gene expression in dormant dry seed


title: Dormant_6hr_rep2


title: hypothalamic_maternal inulin treatment_rep1

type: genomic

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: maternal inulin treatment

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

label: Cy 5

source_name: MeDIP DNA from maternal inulin treatment

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from hypothalamic samples using Dneasy Blood & Tissue Kit.

value: hypothalamic tissue

tag: age

value: 16 week

tag: group

value: maternal inulin treatment

tag: molecule type

value: MeDIP DNA

label: Cy 3

source_name: input DNA from maternal inulin treatment

value: input DNA


title: HUDEP2_RIP_FAM_PFA

city: hangzhou

first: ke

last: yang

state: zhejiang

address: 1369 West Wenyi Road, Hangzhou

institute: Liangzhu Laboratory, Zhejiang University

data_processing:
The RNA-seq data reads were aligned to the grch38_tran index using Hisat2 v2.2.1 to generate a SAM file.
The SAM files were then processed using samtools v1.18 and converted into sorted BAM files.
The BAM files were further converted into bigwig files using deeptools v3.5.1 .
The gene count was calculated from the BAM file using featureCounts v2.0.1
Target genes were identified based on the criterion of FAM46C-RIP/blank-RIP >2 and RIP/input >2.
Assembly: hg38
Supplementary files format and content: BigWig file is a binary format of Wig file, value represents pile-up signal of mapped reads

molecule: polyA RNA

source_name: HUDEP-2 cells

extract_protocol:
The lentiviral vector TRE-FAM46C-strep was introduced into E6E7 cells through transfection, followed by selection with puromycin for a duration of 3 days. After a 24-hour induction with Doxycycline (Dox), a total of 2 million cells were collected for RNA immunoprecipitation (RIP) analysis. For the purpose of formaldehyde crosslinking, the cells were first centrifuged and then resuspended in 500 μl of phosphate-buffered saline (PBS) containing 1.5 μl of 37% formaldehyde, resulting in a final concentration of 0.1%. The cells were then incubated at room temperature for 10 minutes. Subsequently, the crosslinking reaction was quenched by the addition of 37.5 μl of 2M glycine, and the cells were incubated for an additional 10 minutes at room temperature. Following this, the cells were centrifuged at 500g for 5 minutes, and the resulting cell pellet was resuspended in 500 μl of buffer A (10mM HEPES, pH 7.9, 10mM KCl, 0.1mM EDTA, 0.1mM EGTA, 1mM DTT, 1x proteinase inhibitor, RNase inhibitor) on ice for a duration of 15 minutes. To this suspension, 34.4 μl of 10% NP40 was added, and the mixture was vortexed for 1 minute. The samples were then subjected to centrifugation at 6000g, 4℃ for 5 minutes. Next, Strep beads (IBA, 2-4090-002) were washed three times with wash buffer (10 mM Tris/HCl pH 8.0, 150 mM NaCl, 0.5 mM EDTA) and then resuspended in the supernatant of the samples. Additionally, 15 μl of 5M NaCl was added to the suspension, which was subsequently incubated at 4℃ for 2 hours on a roller. After the incubation period, the supernatant was removed from the samples, which were then subjected to four washes in wash buffer (300 mM NaCl) using a magnetic rack. Subsequently, 50 μl of biotin elution buffer (100 mM Tris/HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 50 mM biotin) was added to the samples and incubated for 10 minutes at room temperature. The elution was mixed with 250 μl of proteinase K buffer and 4 μl of 20 mg/ml proteinase K, and incubated overnight at 65℃. RNA extraction was then carried out using TRIZOL. For UV-RIP analysis, cells were subjected to UV crosslinking at 254nm, 4000 (400mJ/cm2) in cold PBS, with the remaining steps being similar to the aforementioned protocol.
RNA was used to construct an RNA Next-Generation Sequencing (NGS) library using the TruePrep RNA Library Prep Kit for Illumina (vazyme, TR503-01) before sequencing.

value: HUDEP-2 cells

value: dox 24h


title: HUDEP2_RIP_WT_PFA

value: WT


title: hypothalamic_maternal obesity_rep3

description: maternal obesity

source_name: MeDIP DNA from maternal high fat diet

value: maternal high fat diet

source_name: input DNA from maternal obestiy


title: ChIP.08_MRTK.103_antiSMARCB1_SMARCB1

description: ChIP-seq in MRT organoids P103, after 4 days lentiviral transduction with the SMARCB1 gene

value: a wild-type full-length SMARCB1 gene plasmid


title: hypothalamic_maternal inulin treatment_rep2

description: maternal inulin treatment


title: hypothalamic_maternal obesity_rep2

description: maternal obesity


title: HUDEP2_RIP_FAM_input


title: HUDEP2_RIP_FAM_UV


title: hypothalamic_maternal obesity_rep1

description: maternal obesity


title: HUDEP2_2B11_WT_24h_rep2

data_processing:
The RNA-seq data reads were aligned to the grch38_tran index using Hisat2 v2.2.1 to generate a SAM file.
The SAM files were then processed using samtools v1.18 and converted into sorted BAM files.
The gene count was calculated from the BAM file using featureCounts v2.0.1
The count files of all samples were imported into R for subsequent analysis. A heatmap was generated using the Heatmap package.
DEGs were calculated using DEseq2 V1.34.0 .
GO analysis was performed using ClusterProfiler V4.1.4 .
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using Trizol. 1ug of total RNA was used for the construction of sequencing libraries.
RNA library for RNA-seq were prepared using RNA Library Prep Kit for Illumina.

value: FAM46C knockout + TRE-FAM46C


title: CR_TBP_HDP2_Day4

data_processing:
bowtie v2.2.9 was used to align fragments to hg19
The SAM files were then processed using samtools v1.18 and converted into sorted BAM files.
Duplications were eliminated using picard v2.27.1 .
The BAM files were further converted into bigwig files using deeptools v3.5.1 .
Assembly: hg19
Supplementary files format and content: BigWig file is a binary format of Wig file, value represents pile-up signal of mapped reads
Library strategy: CUT&RUN

extract_protocol:
Two million HUDEP-2 cells were collected and subjected to a single wash with PBS. Subsequently, the cell pellets were resuspended in 300 μl of NE buffer (comprising 20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM spermidine, 0.1% triton X-100, 20% glycerol, and 1x protease inhibitor) and incubated on ice for a duration of 20 minutes. ConA beads, measuring 30 μl, were washed twice with 250 μl of cold binding buffer (consisting of 20mM HEPES-KOH, pH 7.9, 10mM KCl, 1mM CaCl2, and 1mM MnCl2), and subsequently resuspended in 30 μl of binding buffer. This mixture was then combined with the nuclear solution in NE buffer and incubated at room temperature for 10 minutes. The supernatant was removed, and the cells were resuspended in 250 μl of cold blocking buffer (composed of 20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM spermidine, 0.1% BSA, 2mM EDTA, and 1x protease inhibitor), followed by a 5-minute incubation at room temperature. The cells were then washed with 500 μl of cold wash buffer (comprising 20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM spermidine, 0.1% BSA, and 1x protease inhibitor), and subsequently resuspended in 150 μl of cold wash buffer containing the primary antibody at a dilution of 1:100. This suspension was incubated for 2 hours at temperature. Following the incubation with the primary antibody, the supernatant was removed, and the cells were washed twice with cold wash buffer. The cells were then resuspended in 250 μl of cold wash buffer containing pA-MNase at a dilution of 1:2000 (resulting in a final concentration of 600ng/ml) and incubated at 4℃ for 1 hour with rolling. After the incubation, the supernatant was removed, and the cells were washed twice with cold wash buffer before being resuspended in 150 μl of cold wash buffer. The sample was subsequently cooled on ice for 10 minutes. To the sample, 3 μl of 100mM CaCl2 was added and mixed rapidly, followed by an incubation on ice for 30 minutes. The reactivation process was halted by the addition of 150 μl of 2x stop buffer (consisting of 200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RnaseA, and 40ug/mL glycogen). The samples were then centrifuged for 5 minutes at 16000g, and the supernatant was collected. To this supernatant, 3 μl of 10% SDS and 2.5 μl of 20mg/ml proteinase K were added, followed by an overnight incubation at 50℃. The DNA was subsequently purified using phenol-chloroform extraction and ethanol precipitation.
NEBNext Ultra II DNA library Prep Kit (E7645S) was employed to construct the library as described.

tag: antibody

value: TBP

value: differentiation 4 days


title: CR_H3K4me1_HDP2_BCKO_Day4


title: HUDEP2_2B11_mut_0h_rep1

value: FAM46C knockout + TRE-FAM46C-9092mut

value: dox 0h


title: HUDEP2_2B11_WT_24h_rep1


title: HUDEP2_2B11_mut_0h_rep2


title: HUDEP2_RIP_WT_input


title: HUDEP2_RIP_WT_UV


title: HUDEP2_2B11_mut_24h_rep1


title: HUDEP2_2B11_mut_24h_rep2


title: HUDEP2_2B11_WT_0h_rep1


title: CR_H3K27ac_HDP2_Day4


title: HUDEP2_2B11_WT_0h_rep2


title: HUDEP2_WT_rep2


title: HUDEP2_WT_rep1


title: HUDEP2_2B11_KO_rep3

value: FAM46C knockout


title: HUDEP2_WT_rep3


title: CR_GATA1_HDP2_Day4


title: CR_TAL1_HDP2_Day4


title: HUDEP2_2B11_KO_rep2


title: HUDEP2_shGFP_rep3

value: shGFP control


title: HUDEP2_shGFP_rep2


title: HUDEP2_shGFP_rep1


title: HUDEP2_shFAM46C_3_rep3

value: shFAM46C-3 knockdown


title: HUDEP2_2B11_KO_rep1


title: HUDEP2_shFAM46C_2_rep2

value: shFAM46C-2 knockdown


title: HUDEP2_shFAM46C_2_rep3


title: HUDEP2_shFAM46C_2_rep1


title: HUDEP2_FAM_7aa_adar

data_processing:
The RNA-seq data reads were aligned to the grch38_tran index using Hisat2 v2.2.1 to generate a SAM file.
The SAM files were then processed using samtools v1.18 and converted into sorted BAM files.
Duplications were eliminated using picard v2.27.1 .
Variant calling was performed using bcftools v1.5 and retained mutations from A to G in forward-strand transcripts and T to C in reverse-strand transcripts for ADAR, or from C to T in forward-strand transcripts and G to A in reverse-strand transcripts for APOBEC1.
The significant editing sites were identified by comparing them with GFP-ADAR/APOBEC1 using Fisher's exact test, with a p-value less than 0.05.
The results of different linker lengths were merged, and the target genes were identified using map_snp_to_gene from the snpsettest package v0.1.1 .
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes all A-G/C-T sites, containing chr, position, ref number, alt number; csv file includes target genes

value: dox 48h


title: HUDEP2_GFP_7aa_adar


title: HUDEP2_shFAM46C_3_rep1


title: HUDEP2_FAM_74aa_apo


title: HUDEP2_GFP_7aa_apo


title: HUDEP2_FAM_47aa_adar


title: HUDEP2_FAM_74aa_adar


title: HUDEP2_FAM_7aa_apo


title: HUDEP2_FAM_27aa_apo


title: HUDEP2_shFAM46C_3_rep2


title: Multiplexed_CMO: [468, CSF] + [468, TME (GM)] + [469, CSF] + [469, TME (GM)]

city: Adelaide

first: Cedric

last: Bardy

state: SA

address: North Terrace

country: Australia

institute: South Australian Health and Medical Research Institute (SAHMRI)

data_processing:
Cell Ranger v6.1.1 with default settings was used for demultiplexing pooled samples, read alignment to the GRCh38-2020-A genome and generating gene counts.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files for each sample

source_name: Glioblastoma

growth_protocol: GBM patient-derived cell lines were cultured in glioma medium (GM also termed TME; DMEM/F12 with GlutaMax supplemented with SM1 with vitamin A, N2A and 5 ng/mL EGF and 5 ng/mL bFGF) or CSF until sub-confluent.

extract_protocol:
Single-cell suspensions of sub-confluent GBM cells, cultured in parallel in either GM or CSF were added to weels of an 8-channel microfluidic chip and transferred to a Chromium Controller. Six cell lines (468, 469, 497, BAH1, HW1 and MN1) were labelled with lipid-conjugated Cell Multiplexing Oligonucleotides (10X Genomics) according to manufacturer’s recommendations for cell pooling prior to loading onto a 10X Genomics chip.
Single-cell pooled suspensions were loaded on a GemCode Single Cell Instrument (10X Genomics) to generate single-cell gel beads in emulsion (GEM). scRNA-seq libraries were prepared from GEMs using a 3’ CellPlex Kit Set A (10X Genomics) and a Chromium i7 Multiplex kit (10X Genomics) according to the manufacturer’s instructions.

value: in vitro patient-derived glioblastoma cell line

value: Glioblastoma

value: Pooled samples:[CSF] + [TME (GM)]

tag: tumor type

value: Pooled samples:Primary

tag: library type

value: Multplexing Capture


title: Multiplexed_GEX: [497, CSF] + [497, TME (GM)] + [BAH1, CSF] + [BAH1, TME (GM)]

tag: cell type

value: Pooled samples:Recurrent (497) + Primary (BAH1)

value: Gene Expression


title: Multiplexed_GEX: [468, CSF] + [468, TME (GM)] + [469, CSF] + [469, TME (GM)]

tag: tissue


title: 448, TME (GM)

value: TME (GM)

value: Primary


title: HUDEP2_FAM_27aa_adar

value: HUDEP-2 cells

tag: genotype


title: 448, CSF

value: CSF


title: Multiplexed_CMO: [497, CSF] + [497, TME (GM)] + [BAH1, CSF] + [BAH1, TME (GM)]


title: HUDEP2_FAM_52aa_apo


title: barcode_1_CKDL230002468-1A

city: Philadelphia

first: Ning

last: Li

address: 3800 Spruce St.

department: Biomedical Sciences

institute: UPENN

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains CMO Tag reads
gene_by_cell_count_matrix.txt
cell_annotation.csv
gene_annotation.csv

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to GRCh38 reference genome.
An initial filtering was performed on the raw gene-barcode matrix output by the Cell Ranger cellranger count function, removing barcodes that have less than 1000 transcripts (quantified by unique molecular identifier (UMI)) and 500 expressed genes (“expressed” means that there is at least 1 transcript from the gene in the cell).
Assembly: GRCh38
Supplementary files format and content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, tissue type, cell type, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.

source_name: Mixed

growth_protocol: Organoid from adjacent normal colon and tumor were generated by culturing on top of the MatriGel. The medium  contains advanced Dulbecco’s modified Eagle medium/F12 including supplement N2 (Invitrogen; 17502-048), B27 (Invitrogen; 17504-044), N-acetylcysteine (MilliporeSigma; A9165, 1 mM), mEGF (Invitrogen; PMG8041, 50 ng/ml), mNoggin (Peprotech, 250-38, 100 ng/ml), and R-spondin 1 (PeproTech, 315-32).

extract_protocol:
Using the Chromium controller (10x Genomics) and reagents from the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics), cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) where each cell's trascriptome was indexed with a specific 10x BarCode. cDNA were amplified and purified for library preparation.
cDNA were used for library preparation using the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics) according to manufacturer’s protocol.
Read 1: 28 bp. i7 Index: 8 bp. i5 Index: 0 bp. Read2: 91 bp.

treatment_protocol: Patient derived monocyte were cultured for 7 days and differentiated into macrophage. Organoid from tumor or normal colon were co-cultured with macrophage for 48 hours in organoid medium before downstream analysis.

value: Mixed

value: mixed

value: CMO

tag: antibodies/tags

value: T_8/ATGAGGAATTCCTGC; M+T_8/CATGCCAATAGAGCG; F+M+T_8/CCGTCGTCCAAGCAT; M+CMT_8/AACGTTAATCACTCA; M+F/CGCGATATGGTCGGA; T_24/AAGATGAGGTCTGTG; M+T_24/AAGCTCGTTGGAAGA; F+M+T_24/CGGATTCCACATCAT; M+CMT_24/GTTGATCTATAACAG; M/GCAGGAGGTATCAAT


title: Multiplexed_GEX: [HW1, CSF] + [HW1, TME (GM)] + [MN1, CSF] + [MN1, TME (GM)]


title: Lib_2_CKDL230002468-1A

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
gene_by_cell_count_matrix.txt
cell_annotation.csv
gene_annotation.csv

value: mRNA


title: barcode_2_CKDL230002468-1A

value: O_8/ATGAGGAATTCCTGC; M+O_8/CATGCCAATAGAGCG; F+M+O_8/CCGTCGTCCAAGCAT; M+CMO_8/AACGTTAATCACTCA; F_5/CGCGATATGGTCGGA; O_24/AAGATGAGGTCTGTG; M+O_24/AAGCTCGTTGGAAGA; F+M+O_24/CGGATTCCACATCAT; M+CMO_24/GAATCGTGATTCTTC; F_12/ACATGGTCAACGCTG


title: HeLa cells, BLTF enriched nuclear RNA, update

city: Beijing

source_name: Hela

tag: cell line

value: Hela

value: Human cervix carcinoma

value: BLTF enrichment


title: Lib_1_CKDL230002468-1A


title: WT_neuron_HiC_rep2

data_processing:
Raw Hi-C sequencing was processed using the HiCUP pipeline.
Alignments were converted to a multi-resolution Hi-C matrix using pairtools.
Hi-C data between biological replicates.
Insulation scores were calculated using the hicFindTADs command from HiCExplorer.
hg38
Bedfiles containing genome-wide insulation scores based on the HiC data merged between replicates of wild-type and knock-out neurons.

source_name: iPSC-derived human neurons

extract_protocol:
We used the Arima HiC kit to process the samples. Briefly, frozen cell pellets were lysed and conditioned before chromatin digestion. The digested chromatin was then filled in and biotinylated before ligation. Next, chromatin was protein-digested and reverse crosslinking overnight, followed by purification. The purified DNA was then sonicated using the bioruptor pico (Diagenode) and size selected before library preparation using the NEB DNA Ultra II, following Arima’s protocol.
The Hi-C DNA was bound to streptavidin beads before enzymatic end prep, adaptor ligation, DNA release by heat incubation, and lastly, PCR to barcode and amplify the libraries.

value: iPSC-derived human neurons

value: WTC11 Ngn2 derived

value: wild-type


title: B14804_KO_neuron_HiC_rep2

value: homozygous B14804 KO


title: B14804_KO_neuron_HiC_rep1


title: WT_neuron_HiC_rep1


title: HUDEP2_FAM46C_Capture

data_processing:
Data was processed with capC-MAP, which incorporates the following detail steps
cutadapt v1.18 was used to trim adapter sequence
in silico restriction enzyme digestion (Dpn II) on hg38 genome with capC-MAP
bowtie v1.1.1 was used to align fragments to hg38 in single-end read mode
samtools v1.3.1 was used to sort mapped fragments by read name
genome restriction fragment map,identify “target” and “reporter” fragments, generate pile-ups of interactions for each target, binning parameters (400, 800)
Assembly: hg38
Supplementary files format and content: pile-up bedGraph files
Library strategy: Capture-C

extract_protocol:
10^7 cells were collected, and washed with PBS. We resuspend cells with 9 ml PBS and added 1ml 10% formaldehyde (freshly prepared) for a final concentration of 1%, and incubated 10 min at room temperature on a roller mixer, and added 1.1 ml 2M glycine to quenched the reaction, incubated 10 min at room temperature on a roller mixer and on ice for 5 min. Cells were centrifuged for 10 min, 800g at 4℃, and the cell pellet was resuspended in 500 μl lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.5% NP-40, 1x proteinase inhibitor cocktail) and incubated on ice for 50 min. cells were centrifuged for 10 min, 2500g at 4℃. We then washed nuclear pellet once by 1x NEBuffer, resuspended by 80μl 0.5% SDS, incubated for 10min at 62℃, 900 rpm in thermomixer, and add 4μl proteinase inhibitor，226μl H2O，40μl 10% Triton X-100 to quenched SDS for 15min at 37℃, 900rpm in thermomixer SDS 37℃. For enzyme digestion, we added 40μl 10x NEBuffer, 5μl DpnII (250U) incubating at 37℃, 900 rpm, and added another 5μl DpnII before overnight at 37℃, 900 rpm. After digestion, we deactivated the enzyme at 62℃ for 20 min, cooled the tube and added 96μl 10X ligase buffer，4.8μl BSA（20mg/ml）, 80μl 10% triton x-100，4μl T4 ligase (NEB M202M, 8000 U), 369.6μl H2O, and 5.6 μl proteinase inhibitor, incubated at 16℃, 900rpm for 8h. After ligation, We centrifuged for 10 min at 5000g, and resuspend the pellet with 300 μl proteinase K buffer(50 mM Tris-HCl, pH 7.5, 2.5mM EDTA, 50 mM NaCl, 0.5% SDS) and 3 μl proteinase K(20mg/ml), and incubated at 55℃ overnight. We purified DNA from nuclear via phenol-choloroform extraction and ethanol precipitation, and fragmented DNA to 200 bp via covaries (Duty Factor 10 %, PIP 175 W, 180s, 200 cycles per burst, 4 °C).he DNA library preparation was preformed via KAPA Hyper prep kit (KR0961), and oligonucleotide capture was performed via xGen hybridization capture and wash kit (IDT, 1080584).
The DNA library preparation was preformed via KAPA Hyper prep kit (KR0961)

tag: treatment

value: differentiation 5 days


title: CUT&Tag_H3K4me2_ES2_shLSD1_rep3

first: Lei

last: Tao

address: No.17, Section 3, Renmin Nan Road

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

institute: Sichuan University

data_processing:
The Illumina NovaSeq 6000 was used to sequence the library of  CUT&Tag-seq assay in each sample with the mode of paired-end 150bp.
The bowtie2 (v2.3.4.2, RRID:SCR_016368) was used to align the sequencing data with the hg19 as the reference with parameters of --very-sensitive -X 2000.
The samtools (v0.1.18, RRID:SCR_002105) was used to convert the sam files to bam files.
The statistic values and variation degree of peaks signal and regions were calculated by DESeq2 (v1.26.0).
The ChIPseeker (v1.22.1, RRID:SCR_021322) was used to annotate the peaks signal and regions in each sample.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: ovarian cancer cells

growth_protocol: ES2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) with 10% FBS. All cell lines were maintained in standard conditions at 37 °C and 5% CO2.

extract_protocol: The NovoNGS CUT&Tag 3.0 High-Sensitivity kit (Novoprotein Scientific, N259-YH01) was used to prepare the library of CUT&Tag-seq assay in each sample.

value: ovarian cancer cells

value: WT

tag: chip antibody

value: H3K4me2 Abcam, ab32356


title: CUT&Tag_H3K4me2_ES2_Control_rep3

value: Control


title: CUT&Tag_H3K4me2_ES2_shLSD1_rep2


title: CUT&Tag_H3K9me2_ES2_shLSD1_rep3

value: H3K9me2 Abcam, ab1220


title: CUT&Tag_H3K4me2_ES2_Control_rep2


title: CUT&Tag_H3K4me2_ES2_Control_rep1


title: CUT&Tag_H3K9me2_ES2_shLSD1_rep1


title: CUT&Tag_H3K4me2_ES2_shLSD1_rep1


title: CUT&Tag_H3K9me2_ES2_shLSD1_rep2


title: CUT&Tag_H3K9me2_ES2_Control_rep2


title: CUT&Tag_LSD1_ES2_ZY0511_rep2

value: LSD1 Millipore, 17-10531


title: CUT&Tag_H3K9me2_ES2_Control_rep1


title: CUT&Tag_H3K9me2_ES2_Control_rep3


title: CUT&Tag_LSD1_ES2_ZY0511_rep3


title: CUT&Tag_LSD1_ES2_Control_rep3


title: CUT&Tag_LSD1_ES2_ZY0511_rep1


title: RNA_seq_A2780_ZY0511_rep3

data_processing:
RNA libraries were sequenced on an Illumina NovaSeq 6000 sequencing machine with 150-base pair (bp) paired-end reads.
Transcript abundance was normalized and measured by FPKM.
DESeq2 (v.1.26.0, RRID:SCR_000154) was used to identify differentially expressed genes
Assembly: hg38
Supplementary files format and content: Excel files include RPKM values for each Sample

growth_protocol: A2780 cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (FBS). ES2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) with 10% FBS. All cell lines were maintained in standard conditions at 37 °C and 5% CO2.

extract_protocol:
Total RNA was purified from A2780 and ES2 cells after dimethyl sulfoxide (DMSO) or ZY0511 (1μM) treatment for 24 h and stored in TRIzol (Invitrogen, USA)
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kit (NEB, E7770) according to the manufacturer’s protocol.

treatment_protocol: A2780 and ES2 cells were treated with 1 µM LSD1 inhibitor ZY0511 or DMSO for 24 hours.


title: RNA_seq_A2780_ZY0511_rep1


title: RNA_seq_A2780_Control_rep3


title: RNA_seq_A2780_Control_rep2


title: RNA_seq_ES2_ZY0511_rep1


title: RNA_seq_ES2_Control_rep3


title: CUT&Tag_LSD1_ES2_Control_rep2


title: RNA_seq_ES2_ZY0511_rep2


title: RNA_seq_ES2_ZY0511_rep3


title: ATAC_seq_ES2_shLSD1_rep2

data_processing:
The Illumina NovaSeq 6000 was used to sequence the library of ATAC-seq assay in each sample with the mode of paired-end 150bp.
The bowtie2 (v2.3.4.2, RRID:SCR_016368) was used to align the sequencing data with the hg19 as the reference with parameters of --very-sensitive -X 2000 and the duplicated reads were filter by the GATK pipeline (v4.1.3.0, RRID:SCR_001876).
The samtools (v0.1.18, RRID:SCR_002105) was used to convert the sam files to bam files, and to remove the reads mapped on the mitochondrial genome. The bamCoverage (v3.5.0) was used to generate the bw files in each sample with BPM normalization.
The HMMRATAC (v1.2.5) was used to detect the open region and peak signals and only the enriched scores are higher than 10 would be reminded.
The deeptools (v3.5.0, RRID:SCR_016366) was used to visualize the global signal of peaks on TSS regions. The function implemented in soGGi (v1.18.0) was used to identify and generate the common open regions detected in all samples. The Rsubread (v2.0.1, RRID:SCR_016945) was used to quantify the counts of each peak signal in each sample.The ChIPseeker (v1.22.1, RRID:SCR_021322) was used to annotate the peaks signal and regions in each sample.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol: The ATAC assay was performed using a Chromatin Profile Kit for Illumina (Novoprotein Scientific, N248).


title: ATAC_seq_ES2_Control_rep2


title: ATAC_seq_ES2_shLSD1_rep3


title: ATAC_seq_ES2_Control_rep1


title: RNA_seq_ES2_Control_rep1


title: ATAC_seq_ES2_ZY0511_rep2


title: CUT&Tag_LSD1_ES2_Control_rep1


title: RNA.09_MRTK.78_CTRL_rep1

description:
RNA-seq in MRT organoids P78, after 4 days lentiviral transduction with the Luciferase gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt

data_processing:
Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Homo Sapiens GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Assembly: hg38
Supplementary files format and content: bigWig files, read counts

source_name: MRT organoids P78

extract_protocol:
RNA was isolated following a standard TRIzol RNA isolation protocol (Ambion). The cells were lysed using 1 ml of TRIzol reagent, and 200 µl chloroform was added to the lysates. The mixture was vortexed and centrifuged at 12,000 g at 4°C for 15 min. Upper phase was homogenized with 0.5 ml of 100% isopropanol, incubated at room temperature for 10 min, and centrifuged at 4°C for 10 min. The resulted RNA pellet was washed with 75% ice-cold ethanol, dried at room temperature for 10 min, and resuspended in RNase-free water. The isolated RNA was treated with DNase using RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using a TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: For SMARCB1 re-expression, MRT organoids were lentivirally transduced with pLKO.1-UbC-luciferase-blast40 or pLKO.1-UbC-hSMARCB1-blast lentiviruses. After 2 days, 10 µg/ml blasticidin was added to the culture medium; For BRD9 inhibition experiments, MRT organoids were mechanically dissociated and plated at a density of 10.000 cells/ul in 10ul BME droplets. After 24h, 10µM I-BRD9 inhibitor (MedChemExpress, HY-18975) was added to the organoids.

value: MRT organoids P78

value: Malignant rhabdoid tumor cells

value: Luciferase plasmid


title: ATAC_seq_ES2_shLSD1_rep1


title: ATAC_seq_ES2_ZY0511_rep1


title: RNA.08_MRTK.60_SMARCB1_rep2

description:
RNA-seq in MRT organoids P60, after 4 days lentiviral transduction with the SMARCB1 gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt

source_name: MRT organoids P60

value: MRT organoids P60

value: a wild-type full-length SMARCB1 gene plasmid


title: RNA_seq_ES2_Control_rep2


title: ATAC_seq_ES2_Control_rep3


title: RNA.10_MRTK.78_CTRL_rep2


title: RNA.07_MRTK.60_SMARCB1_rep1


title: RNA.05_MRTK.60_CTRL_rep1

description:
RNA-seq in MRT organoids P60, after 4 days lentiviral transduction with the Luciferase gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt


title: RNA.04_MRTK.103_SMARCB1_rep2

description:
RNA-seq in MRT organoids P103, after 4 days lentiviral transduction with the SMARCB1 gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt

value: MRT organoids P103


title: RNA_seq_A2780_ZY0511_rep2


title: RNA.12_MRTK.78_SMARCB1_rep2

description:
RNA-seq in MRT organoids P78, after 4 days lentiviral transduction with the SMARCB1 gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt


title: Multiplexed_CMO: [HW1, CSF] + [HW1, TME (GM)] + [MN1, CSF] + [MN1, TME (GM)]

value: in vitro patient-derived glioblastoma cell line

value: Glioblastoma

value: Pooled samples:[CSF] + [TME (GM)]

value: Pooled samples:Primary

value: Multplexing Capture


title: ATAC_seq_ES2_ZY0511_rep3

value: ovarian cancer cells


title: CCLP1 cells

city: Shanghai

first: Yuanyuan

last: Shi

address: changhailu 168

institute: the First Affiliated Hospital of Naval Medical University

data_processing:
For RNA-seq analysis, 2×150 bp paired-end sequencing (PE150) was performed on an Illumina Novaseq 6000 (LC-Bio).
The Fastp software (https://github.com/OpenGene/fastp) was used to remove reads containing adaptor contamination, low-quality bases, and undetermined bases with default parameters.
HISAT2 (https://ccb.jhu.edu/software/hisat2) was used to map the reads to the reference genome of Homo sapiens GRCh38.
StringTie was used to perform expression levels by calculating FPKM (fragments per kilobase of exon model per million mapped fragments).
Assembly: genes enriched in the proteasome and lysosome pathway
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested following the standard protocol. 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: cancer cell line

value: Untreated cells


title: RNA.06_MRTK.60_CTRL_rep2


title: HEK293T cells, HuB/C/D triple overexpressing cells, biological replicate 3

first: Hachung

last: Chung

state: New York

address: 701 W 168th St, HHSC Rm 1506

department: Microbiology & Immunology

institute: Columbia University

data_processing:
Quality check was done by using FastQC v0.11.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.20.1 (--qualified_quality_phred 20 -f 5 -t 5)
Deduplicated reads were removed using fastuniq v1.1
Trimmed and deduplicated reads were mapped to hg38 using STAR v2.7.3a (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
Read counts were performed using featureCounts v1.6.4 (-p  -t exon -g gene_name -s 2) with GENCODE v38 primary assembly annotation file
bigWig files were generated by bedtools v2.30.0 (-bga -split -trackline) with uniquely mapped reads
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample
Supplementary files format and content: bigWig

source_name: kidney

extract_protocol:
RNA was harvested using Direct-zol RNA Mini prep kit (Zymo research). The ERCC spike-in RNA mixture (Invitrogen) was added and rRNA was depleted by RiboMinus™ Eukaryote Kit (Invitrogen)
RNA sequencing libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB) following manufacturer's protocols.

value: kidney

value: Human embryonic kidney

value: HuB/C/D overexpression

value: Lipofectamine 2000


title: HiC.01_MRTK.103_CTRL

description: Hi-C in MRT organoids P103, after 4 days lentiviral transduction with the Luciferase gene

data_processing:
Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
Assembly: hg38
Supplementary files format and content: hic files

extract_protocol:
Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Liu et al., 2021). For each template, 10 million cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI, and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down.
Hi-C libraries were prepared using a standard end-repair and A-tailing method.

value: Malignant rhabdoid tumor cells


title: SK cells


title: HuCCT1 cells


title: HEK293T cells, empty vector transfected, biological replicate 1

value: WT


title: RNA.01_MRTK.103_CTRL_rep1

description:
RNA-seq in MRT organoids P103, after 4 days lentiviral transduction with the Luciferase gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt

value: Luciferase plasmid


title: RNA.03_MRTK.103_SMARCB1_rep1

value: a wild-type full-length SMARCB1 gene plasmid


title: HEK293T cells, empty vector transfected, biological replicate 2