title: UPCI-SCC-152 shNSD2

city: Milano

first: Susanna

last: Chiocca

address: Via Adamello 16

institute: European Institute of Oncology, IEO

description: Library name: Sample14

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package between shNSD2 and scr conditions
Assembly: hg38
Supplementary files format and content: DEGs_HPVminus_dup.txt = tab-delimited text file containing differential gene expression analysis form DESeq2 of the HPV- HNSCC cell lines (UM-SCC-4; UM-SCC-6; UM-SCC-18; UM-SCC-19)
Supplementary files format and content: DEGs_HPVplus_dup.txt = tab-delimited text file containing differential gene expression analysis form DESeq2 of the HPV+ HNSCC cell lines (UD-SCC-2; UM-SCC-104; UPCI-SCC-152)
Supplementary files format and content: df_count_minus.txt = tab-delimited text file of RNA-seq raw counts of HPV- HNSCC cell lines
Supplementary files format and content: df_count_plus.txt = tab-delimited text file of RNA-seq raw counts of HPV+ HNSCC cell lines

growth_protocol: HNSCC cell lines were growth in DMEM supllemented with 10% North America (NA) Fetal Bovine Serum (FBS),1% Non-essential aminoacids (NEAA) and antibiotics in humidified athmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from each samples with the Quick-RNA MiniPrep kit (Zymo Research ##D4020). RNA quality and integrity were assessed with an Agilent 2100 bioanalyzer using an RNA 6000 Nano Kit (Agilent Technologies)
mRNA-Seq library was prepared from 500 ng of total RNA with the TruSeq Stranded Total RNA (Illumina)

treatment_protocol: Cells were infected with plko.1 plasmid containing the shNSD2 or scrambled sequence. After the infection, cells were cultured under puromycin selection for three days. Once expanded, cells were plated in 100 mm plates and harvested after 72 hrs.

value: squamous cell carcinoma

value: NSD2 knock-down


title: MORC2_TRIM28_double_CRISPRi_MOI4_Rep3

status: Public on Feb 11 2026

type: SRA

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: MORC2_TRIM28_double_CRISPRi_MOI4_Rep3

library_source: transcriptomic

data_processing:
RNAseq Unique mapping (L1 loci mapping): STAR aligner (version 2.7.8a; --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.03).
RNAseq Genes were quantified using featureCounts (Subread version 1.6.3), forcing matching strandness of the reads to the features being quantified (-s 2).
RNAseq BAM files were indexed using samtools (version 1.16.1) and converted to bigwig files using deeptools bamCoverage (version 2.5.4) (--normalizeUsingRPKM)
Assembly: GRCh38
Supplementary files format and content: Bigwigs for genome browser visualization
Supplementary files format and content: Bulk RNAseq read count matrix for genes

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Total RNA for bulkRNAseq was isolated using the RNeasy Mini Kit (Quiagen) with on column DNAse treatment following the manufacturer’s instructions. RNA sequencing was performed using 3 biological replicates.
Libraries for RNA sequencing were generated using Illumina TruSeq Stranded mRNA library prep kit (with poly-A selection).

tag: cell line

tag: lentivirus

tag: type

value: human neuroepithelial-like stem cells

tag: target gene


title: MORC2_CRISPRi_Rep3

description: Library name: MORC2_CRISPRi_Rep3


title: UD-SCC-2 scr

country: Italy

description: Library name: Sample9

molecule: total RNA

tag: cell type

tag: genotype

value: wt


title: UPCI-SCC-152 scr

description: Library name: Sample13


title: UM-SCC-19 shNSD2

description: Library name: Sample8


title: UM-SCC-19 scr

description: Library name: Sample7


title: UM-SCC-18 shNSD2

description: Library name: Sample6


title: UM-SCC-18 scr

description: Library name: Sample5


title: UM-SCC-104 shNSD2

description: Library name: Sample12


title: UD-SCC-2 shNSD2

description: Library name: Sample10


title: Donor R29800, FACS sorted CD8+ CD28+/CD57+ EM T cells, H3K27me3(Cut and Run)

city: Kyoto

first: Hiroyuki

last: Matsui

state: Kyoto

address: 54 Shogoin-Kawahara-cho

department: Hematology

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Library name: B4800

library_source: genomic

data_processing:
Quality control and trimming of original FASTQ files were performed using Rfastp package with default parameters.
QC and trimmed FASTQ files were aligned using subjunc function of Rsubread package with the hg38 human reference genome.
Generated BAM files were sorted and indexed using Rsamtools.
Sorted and indexed BAM files were converted to Bigwig file by using coverage to create RLElist objects and then export.bw function in the rtracklayer to export them as bigwig files.
Assembly: hg38
Supplementary files format and content: Genome-wide normalized signal tracks from Cut&Run experiments. Each bigWig file represents the processed read density (signal intensity) for a given sample, generated after alignment to the human reference genome (hg38) and normalization by sequencing depth.
Supplementary files format and content: bigwig files for each sample
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Peripheral blood

extract_protocol:
Of the FACS sorted CD8 T cells, 100,000 from each sorted population was collected for each respective immunoprecipitation pull down assay and an input sample. Some modifications were made to the manufacturer's protocol for the CUT & RUN Assay Kit (Cell Signaling Technologies, #86652). Briefly, live cells were washed (+spermine, +PIC) and mixed with activated Concanavalin A beads. After incubation, for IP samples: antibody binding buffer (+spermidine +PIC +digitonin) was added to clean cell:bead suspensions. Each reaction was incubated overnight with the respective antibody; anti-H3K4me3 (CST-C42D8), anti-H3K27me3 (CST-C36B11). Cells were washed and lysed with Digitonin Buffer (+spermidine, +PIC, +digitonin) and resuspended in the presence of pAG-MNase. Excess pAG-MNase was washed, and Calcium Chloride was added to activate the enzyme. The reaction was stopped with Stop Buffer (+digitonin, +RNase A, +spike-in DNA), and spun to collect the supernatant containing the fragmented DNA. Fragmented DNA was purified using Spin Columns (CST#14209) per manufacturer’s protocol.
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

tag: tissue

value: Peripheral blood

value: CD8+ CD28+/CD57+ EM T cell

tag: cut&run antibody


title: UM-SCC-6 scr

description: Library name: Sample3


title: UM-SCC-6 shNSD2

description: Library name: Sample4


title: Donor R29796, FACS sorted CD8+ CD28+/CD57+ EM T cells, H3K27me3(Cut and Run)

description: Library name: B4796


title: OS018

city: Beijing

first: Jichuan

last: Wang

state: Beijing

address: No. 11 Xizhimen South St.

country: China

institute: Peking University People's Hospital

description:
Library name: OSBR018
Osteosarcoma tumor sample.

data_processing:
Raw sequencing data were quality-filtered and trimmed.Reads were mapped to the human reference genome (hg38) using STAR (v2.7).Gene-level expression was quantified using featureCounts.Expression data were normalized as FPKM.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing gene-level expression quantified as FPKM.

source_name: primary osteosarcoma

extract_protocol:
Fresh-frozen tumor specimens from 70 patients were processed under sterile con-ditions, immediately cryopreserved in liquid nitrogen, and maintained at -80 °C until analysis. Total RNA isolation was performed using TRIzol reagent (Invitrogen, CA, USA) in accordance with the manufacturer's guidelines. RNA purity and concentration were determined using a NanoDrop 2000 spectropho-tometer (Thermo Fisher Scientific, USA), and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Samples with RNA integrity number (RIN)>=7 were subjected to library construction. Sequencing libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, China) according to the manufacturer's instructions, and sequenced on an Illumina NovaSeq 6000 platform generating 150-bp paired-end reads.

value: primary osteosarcoma


title: Donor R29797, FACS sorted CD8+ CD57+ EMRA T cells, H3K27me3(Cut and Run)

description: Library name: B3797

value: CD8+ CD57+ EMRA T cell


title: Donor R29797, FACS sorted CD8+ CXCR3- CM T cells, H3K27me3(Cut and Run)

description: Library name: B2797

value: CD8+ CXCR3- CM T cell


title: UM-SCC-4 shNSD2

description: Library name: Sample2


title: Donor R29796, FACS sorted CD8+ CXCR3+ CM T cells, H3K27me3(Cut and Run)

description: Library name: B1796

value: CD8+ CXCR3+ CM T cell


title: Donor R29797, FACS sorted CD8+ CXCR3+ CM T cells, H3K27me3(Cut and Run)

description: Library name: B1797


title: UM-SCC-4 scr

description: Library name: Sample1


title: Donor R29797, FACS sorted CD8+ CD57+ EMRA T cells, H3K4me3(Cut and Run)

description: Library name: A3797

value: H3K4me3 (CST-C42D8)


title: Donor R29797, FACS sorted CD8+ CD28+/CD57+ EM T cells, H3K27me3(Cut and Run)

description: Library name: B4797


title: Donor R29800, FACS sorted CD8+ CD57+ EMRA T cells, H3K27me3(Cut and Run)

description: Library name: B3800


title: Donor R29796, FACS sorted CD8+ CD57+ EMRA T cells, H3K27me3(Cut and Run)

description: Library name: B3796


title: Donor R29797, FACS sorted CD8+ CD28+/CD57+ EM T cells, H3K4me3(Cut and Run)

description: Library name: A4797


title: Donor R29797, FACS sorted CD8+ CXCR3- CM T cells, H3K4me3(Cut and Run)

description: Library name: A2797


title: Donor R29800, FACS sorted CD8+ CXCR3- CM T cells, H3K27me3(Cut and Run)

description: Library name: B2800


title: Donor R29800, FACS sorted CD8+ CXCR3+ CM T cells, H3K27me3(Cut and Run)

description: Library name: B1800


title: Donor R29800, FACS sorted CD8+ CD57+ EMRA T cells, H3K4me3(Cut and Run)

description: Library name: A3800


title: Donor R29796, FACS sorted CD8+ CXCR3+ CM T cells, H3K4me3(Cut and Run)

description: Library name: A1796


title: NCI-H460 cells, siControl

city: Pittsburgh

first: Simone

last: Brixius-Anderko

state: PA

address: 335 Sutherland Dr

department: Pharmaceutical Sciences

country: USA

institute: University of Pittsburgh

description:
Library name: NCI_H460_siControl
column names match with gene_count_all_samples.txt: A1WT

data_processing:
Raw reads of fastq format were firstly processed through fastp software. Clean reads were obtained by removing reads containing adapter, reads containing ploy-N, and low quality reads from raw data.
Clean reads were mapped to the reference genome using HISAT2 (2.2.1)
featureCounts (2.0.6) was used to quantify gene-level read counts. FPKM of each gene was calculated based on gene length and mapped read counts.
Read counts were adjusted using the edgeR R package (4.0.16) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Lung; Pleural effusion

growth_protocol: NCI-H460 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
RNA was harvested using trizol (invitrogen) and was cleaned by RNA clean & concentrator kit (Zymo). 500 ng of total RNA was used for the construction of sequencing libraries
RNA was purified using poly-T-oligo-attached megnetic beads, followed by dUTP based strand specific cDNA synthesis and directional library prepartion involving fragmentation, adapter ligation, and USER enzyme digestion. The final library was quatified by Qubit and qPCR and assessed for fragment size using a bioanalyzer.

treatment_protocol: siRNA targeting CYP4F11 was transfected using lipofectamine RNAiMAX transfection reagent for 24h following manufactourer's protocols.

value: Lung; Pleural effusion

value: large cell lung carcinoma cells

value: WT

tag: treatment

value: transfected without CYP4F11 targeting siRNA as a control

tag: batch


title: MOLM13, RIP, METTL3

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

description:
Library name: METTL3-RIP-seq
METTL3-RIP-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq, DRIP-seq, DRIPc-seq, RIP-seq, 4C-seq, ChIRP-seq, sgAPEX-seq, ChIP-seq, and HiC-seq from MOLM13 AML cells were aligned to the hg19  genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks and visualization files were created using deepTools version 3.0
Peak annotation was performed with HOMER(version 4.10)
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for RNA-seq Samples, and bigwig and bed peaks for DRIPseq, DRIPc-seq, RIP-seq, ChIRP-seq, sgAPEX-seq, ATAC-seq, MeRIP-seq, ChIP-seq, 4C-seq and HiC-seq.

source_name: leukemia cells

growth_protocol: Human MOLM13 leukemia cells were culture at RMPI1640 medium with 10% FBS media.

extract_protocol:
Total RNA was purified from cells using the TRIzol reagent (TIANGEN, cat# DP424), followed by standard chloroform phase separation and alcohol precipitation. cDNA was synthesized from 1 μg total RNA, and reverse transcription was performed using the HiScript II Q RT SuperMix kit (Vazyme, cat#R222-01) according to the manufacturer’s instructions. The ATAC-seq assay was performed as described previously. Brieﬂy, 5x104 cells were washed twice with PBS and lysed in lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1 % NP-40. The lysate was washed in PBS and treated with Tn5 transposase at 37°C for 30 minutes. DNA was puriﬁed using the DNA purification Kit (TIANGEN, Cat# DP214). DNA library was then generated by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, cat# TD711-01).
RNA sequencing libraries were prepared from 1 μg of total RNA using the VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, cat# NR605-01/02) following the manufacturer instructions.  ChIP-DNA and ChIRP-DNA libraries were prepared using the Illumina’s VAHTS Universal Pro DNA Library Prep Kit according to the manufacturer’s instructions (Vazyme, cat# ND608-01/02).  The ATAC-seq DNA was puriﬁed using the DNA purification Kit (TIANGEN, Cat# DP214). ATAC chromatin DNA library was then generated by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, cat# TD711-01). Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications.

treatment_protocol: Immediately extract RNA from MOLM13 AML cells without any treatment

value: leukemia cells

value: MOLM13 cells

value: acute myeloid leukemia

value: no treatment

tag: antibody

value: METTL3 (Abclonal, Cat#A26858)


title: Donor R29796, FACS sorted CD8+ CXCR3- CM T cells, H3K27me3(Cut and Run)

description: Library name: B2796


title: Donor R29800, FACS sorted CD8+ CD28+/CD57+ EM T cells, H3K4me3(Cut and Run)

description: Library name: A4800


title: Donor R29796, FACS sorted CD8+ CD57+ EMRA T cells, H3K4me3(Cut and Run)

description: Library name: A3796


title: Donor R29800, FACS sorted CD8+ CXCR3- CM T cells, H3K4me3(Cut and Run)

description: Library name: A2800


title: Donor R29796, FACS sorted CD8+ CXCR3- CM T cells, H3K4me3(Cut and Run)

description: Library name: A2796


title: Donor R29797, FACS sorted CD8+ CXCR3+ CM T cells, H3K4me3(Cut and Run)

description: Library name: A1797


title: NCI-H460 cells, siCYP4F11

description:
Library name: NCI_H460_siCYP4F11
column names match with gene_count_all_samples.txt: A2KO_4F11

value: CYP4F11 knockdown

value: transfected with CYP4F11 targeting siRNA for gene knockdown


title: Donor R29800, FACS sorted CD8+ CXCR3+ CM T cells, H3K4me3(Cut and Run)

description: Library name: A1800

value: Peripheral blood


title: MOLM13, APEX, sgRX-2

description:
Library name: sgAPEX-2-seq
sgAPEX-2-seq


title: MOLM13, ChIRP, MALAT1

description:
Library name: MALAT1-ChIRP-seq
MALAT1-ChIRP-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq, DRIP-seq, DRIPc-seq, RIP-seq, 4C-seq, ChIRP-seq, sgAPEX-seq, ChIP-seq, and HiC-seq from MOLM13 AML cells were aligned to the hg19  genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks and visualization files were created using deepTools version 3.0
Peak annotation was performed with HOMER(version 4.10)
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for RNA-seq Samples, and bigwig and bed peaks for DRIPseq, DRIPc-seq, RIP-seq, ChIRP-seq, sgAPEX-seq, ATAC-seq, MeRIP-seq, ChIP-seq, 4C-seq and HiC-seq.
Library strategy: ChIRP-seq


title: MOLM13, APEX, sgRX-1

description:
Library name: sgAPEX-1-seq
sgAPEX-1-seq


title: UM-SCC-104 scr

description: Library name: Sample11

value: squamous cell carcinoma

value: wt


title: MOLM13, HiC, shMETTL3

description:
Library name: shMETTL3-HiC-seq
shMETTL3-HiC-seq


title: METTL3, CHIP, RNase

description:
Library name: METTL3-ChIP-seq_RNase
METTL3-ChIP-seq_Rnase


title: CONTROL_82, type: CONTROL, diagnosis: control, progression: control

city: Brno

first: Robin

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

description:
Library name: CONTROL_82_control_control
column name in miRNA_counts.tsv=CONTROL_82_control_control

data_processing:
The raw sequencing data were converted to the fastq format using bcl2fastq (version 2.20.0). Raw reads were quality checked with the FATSQC package (version 0.11.8). Adapter sequences were identified by Kraken package (15-065) and trimmed using Cutadapt (version 1.18) while tolerating a 10% error rate. Collapsing was performed utilizing unique molecular identifiers (UMIs) with FASTX-Toolkit (version 0.0.14). Subsequently, UMIs were trimmed with cutadapt as well and reads shorter than 15bp were discarded. Reads originating from snoRNAs, snRNAs, rRNAs, tRNAs, piRNAs, and YRNAs (downloaded from Ensembl and RefSeq databases) were identified using Bowtie (version 1.2.2) and removed from the data. Remaining reads were mapped against the miRBase v. 22 and quantified using miraligner tool v 3.2. MiRNAs were filtered if they did not have at least 10 counts in at least 10% of samples. For differential expression analysis data were normalized using DESeq2 package v 1.30.1.
Assembly: GRCh38 / miRBase v22
Supplementary files format and content: Tab-delimited text file containg raw miRNA counts

source_name: blood plasma

extract_protocol:
The peripheral blood samples were collected in EDTA tubes and centrifuged at 4 °C/10 min/2000 g. Blood plasma was stored at -80 °C. RNA was extracted using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturer’s instructions and stored at -80 °C.
cDNA libraries were prepared using the QIAseq miRNA UDI Library Kit (QIAGEN). The quantity and quality of the libraries was checked by Qubit 4.0 Fluorometer (Invitrogen) and Tape Station 2200 System (Agilent). Sequencing analysis was performed using the NovaSeq 6000 S2 v1.5 Kit - 100 cycles using the NovaSeq 6000 instrument (both Illumina).

value: blood plasma

tag: group

value: CONTROL

tag: diagnosis

value: control

tag: progression

tag: Sex

value: Female

tag: menarche status

value: postmenarche

tag: age


title: 7 genes KD in K562 (CRISPR)

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

description:
Library name: K562_CROPseq_CRISPR
CRISPR sgRNA
CRISPR library: read1 file contains cell barcode and UMI; read 2 file contains sgRNA sequence

library_source: other

data_processing:
Gene expression and sgRNA libraries were processed using the 10X Cell Ranger version 7.0.1 following default settings.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv, features.tsv, matrix.mtx
Supplementary files format and content: Including both mRNA matrix and gRNA matrix.

molecule: other

source_name: Blood

extract_protocol:
After pooled gRNA lentivirus transduction, cells were collected in PBS + 5% FBS and FACS sorting for mCherry (dCas9-KARB) and TagBFP (sgRNA) double-positive population. Sorted cells were cultured with fresh medium maintaining at a density of 100k cells/ml. Seven days after pooled sgRNA transduction (day 7), cells were sorted again for viability and double positive. The harvested cells were sent for sequencing immediately.
Single cells were collected for the construction of 5’ single-cell gene expression (GEX) libraries and CRISPR guide RNA (gRNA) capture libraries using the Chromium X platform (10x Genomics, PN-1000287, PN-1000451, PN-1000263, PN-1000215). The libraries were prepared with a target recovery of approximately 10,000 cells. Both GEX and CRISPR libraries were sequenced on an Illumina NovaSeq 6000 system using a 100-cycle kit.

value: Blood

tag: cell line

value: human leukemia cell

value: WT

value: No

tag: library type

value: sgRNA


title: CONTROL_83, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_83_control_control
column name in miRNA_counts.tsv=CONTROL_83_control_control

value: Male

value: male


title: 7 genes KD in K562 (GEX)

description:
Library name: K562_CROPseq_GEX
PolyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read 2 file contains transcript

library_source: transcriptomic single cell

value: mRNA


title: CONTROL_88, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_88_control_control
column name in miRNA_counts.tsv=CONTROL_88_control_control

value: premenarche


title: CONTROL_77, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_77_control_control
column name in miRNA_counts.tsv=CONTROL_77_control_control


title: CONTROL_86, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_86_control_control
column name in miRNA_counts.tsv=CONTROL_86_control_control


title: CONTROL_8, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_8_control_control
column name in miRNA_counts.tsv=CONTROL_8_control_control


title: CONTROL_87, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_87_control_control
column name in miRNA_counts.tsv=CONTROL_87_control_control


title: CONTROL_9, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_9_control_control
column name in miRNA_counts.tsv=CONTROL_9_control_control


title: CONTROL_78, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_78_control_control
column name in miRNA_counts.tsv=CONTROL_78_control_control


title: CONTROL_76, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_76_control_control
column name in miRNA_counts.tsv=CONTROL_76_control_control


title: CONTROL_72, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_72_control_control
column name in miRNA_counts.tsv=CONTROL_72_control_control


title: CONTROL_84, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_84_control_control
column name in miRNA_counts.tsv=CONTROL_84_control_control


title: CONTROL_85, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_85_control_control
column name in miRNA_counts.tsv=CONTROL_85_control_control


title: CONTROL_89, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_89_control_control
column name in miRNA_counts.tsv=CONTROL_89_control_control


title: CONTROL_80, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_80_control_control
column name in miRNA_counts.tsv=CONTROL_80_control_control


title: CONTROL_79, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_79_control_control
column name in miRNA_counts.tsv=CONTROL_79_control_control


title: CONTROL_75, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_75_control_control
column name in miRNA_counts.tsv=CONTROL_75_control_control


title: CONTROL_74, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_74_control_control
column name in miRNA_counts.tsv=CONTROL_74_control_control


title: CONTROL_73, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_73_control_control
column name in miRNA_counts.tsv=CONTROL_73_control_control


title: CONTROL_70, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_70_control_control
column name in miRNA_counts.tsv=CONTROL_70_control_control


title: CONTROL_7, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_7_control_control
column name in miRNA_counts.tsv=CONTROL_7_control_control


title: CONTROL_71, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_71_control_control
column name in miRNA_counts.tsv=CONTROL_71_control_control


title: CONTROL_67, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_67_control_control
column name in miRNA_counts.tsv=CONTROL_67_control_control


title: CONTROL_68, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_68_control_control
column name in miRNA_counts.tsv=CONTROL_68_control_control


title: CONTROL_60, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_60_control_control
column name in miRNA_counts.tsv=CONTROL_60_control_control


title: CONTROL_61, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_61_control_control
column name in miRNA_counts.tsv=CONTROL_61_control_control


title: CONTROL_6, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_6_control_control
column name in miRNA_counts.tsv=CONTROL_6_control_control


title: CONTROL_65, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_65_control_control
column name in miRNA_counts.tsv=CONTROL_65_control_control


title: CONTROL_66, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_66_control_control
column name in miRNA_counts.tsv=CONTROL_66_control_control


title: CONTROL_69, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_69_control_control
column name in miRNA_counts.tsv=CONTROL_69_control_control


title: CONTROL_64, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_64_control_control
column name in miRNA_counts.tsv=CONTROL_64_control_control


title: CONTROL_63, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_63_control_control
column name in miRNA_counts.tsv=CONTROL_63_control_control


title: CONTROL_59, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_59_control_control
column name in miRNA_counts.tsv=CONTROL_59_control_control


title: CONTROL_57, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_57_control_control
column name in miRNA_counts.tsv=CONTROL_57_control_control


title: CONTROL_55, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_55_control_control
column name in miRNA_counts.tsv=CONTROL_55_control_control


title: CONTROL_62, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_62_control_control
column name in miRNA_counts.tsv=CONTROL_62_control_control


title: CONTROL_58, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_58_control_control
column name in miRNA_counts.tsv=CONTROL_58_control_control


title: CONTROL_54, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_54_control_control
column name in miRNA_counts.tsv=CONTROL_54_control_control


title: CONTROL_50, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_50_control_control
column name in miRNA_counts.tsv=CONTROL_50_control_control


title: CONTROL_53, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_53_control_control
column name in miRNA_counts.tsv=CONTROL_53_control_control


title: CONTROL_56, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_56_control_control
column name in miRNA_counts.tsv=CONTROL_56_control_control


title: CONTROL_48, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_48_control_control
column name in miRNA_counts.tsv=CONTROL_48_control_control


title: CONTROL_49, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_49_control_control
column name in miRNA_counts.tsv=CONTROL_49_control_control


title: CONTROL_51, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_51_control_control
column name in miRNA_counts.tsv=CONTROL_51_control_control


title: CONTROL_44, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_44_control_control
column name in miRNA_counts.tsv=CONTROL_44_control_control


title: CONTROL_5, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_5_control_control
column name in miRNA_counts.tsv=CONTROL_5_control_control


title: CONTROL_45, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_45_control_control
column name in miRNA_counts.tsv=CONTROL_45_control_control


title: CONTROL_46, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_46_control_control
column name in miRNA_counts.tsv=CONTROL_46_control_control


title: CONTROL_52, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_52_control_control
column name in miRNA_counts.tsv=CONTROL_52_control_control


title: CONTROL_40, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_40_control_control
column name in miRNA_counts.tsv=CONTROL_40_control_control


title: CONTROL_4, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_4_control_control
column name in miRNA_counts.tsv=CONTROL_4_control_control


title: CONTROL_43, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_43_control_control
column name in miRNA_counts.tsv=CONTROL_43_control_control


title: CONTROL_42, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_42_control_control
column name in miRNA_counts.tsv=CONTROL_42_control_control


title: CONTROL_47, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_47_control_control
column name in miRNA_counts.tsv=CONTROL_47_control_control


title: CONTROL_39, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_39_control_control
column name in miRNA_counts.tsv=CONTROL_39_control_control


title: CONTROL_41, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_41_control_control
column name in miRNA_counts.tsv=CONTROL_41_control_control


title: CONTROL_38, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_38_control_control
column name in miRNA_counts.tsv=CONTROL_38_control_control


title: CONTROL_36, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_36_control_control
column name in miRNA_counts.tsv=CONTROL_36_control_control


title: CONTROL_34, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_34_control_control
column name in miRNA_counts.tsv=CONTROL_34_control_control


title: CONTROL_35, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_35_control_control
column name in miRNA_counts.tsv=CONTROL_35_control_control


title: CONTROL_32, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_32_control_control
column name in miRNA_counts.tsv=CONTROL_32_control_control


title: CONTROL_31, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_31_control_control
column name in miRNA_counts.tsv=CONTROL_31_control_control


title: CONTROL_30, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_30_control_control
column name in miRNA_counts.tsv=CONTROL_30_control_control


title: CONTROL_3, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_3_control_control
column name in miRNA_counts.tsv=CONTROL_3_control_control


title: CONTROL_28, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_28_control_control
column name in miRNA_counts.tsv=CONTROL_28_control_control


title: CONTROL_24, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_24_control_control
column name in miRNA_counts.tsv=CONTROL_24_control_control


title: CONTROL_29, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_29_control_control
column name in miRNA_counts.tsv=CONTROL_29_control_control


title: CONTROL_27, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_27_control_control
column name in miRNA_counts.tsv=CONTROL_27_control_control


title: CONTROL_37, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_37_control_control
column name in miRNA_counts.tsv=CONTROL_37_control_control


title: CONTROL_33, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_33_control_control
column name in miRNA_counts.tsv=CONTROL_33_control_control


title: CONTROL_21, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_21_control_control
column name in miRNA_counts.tsv=CONTROL_21_control_control


title: CONTROL_23, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_23_control_control
column name in miRNA_counts.tsv=CONTROL_23_control_control


title: CONTROL_26, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_26_control_control
column name in miRNA_counts.tsv=CONTROL_26_control_control


title: CONTROL_2, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_2_control_control
column name in miRNA_counts.tsv=CONTROL_2_control_control


title: CONTROL_19, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_19_control_control
column name in miRNA_counts.tsv=CONTROL_19_control_control


title: CONTROL_22, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_22_control_control
column name in miRNA_counts.tsv=CONTROL_22_control_control


title: CONTROL_20, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_20_control_control
column name in miRNA_counts.tsv=CONTROL_20_control_control


title: CONTROL_13, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_13_control_control
column name in miRNA_counts.tsv=CONTROL_13_control_control


title: CONTROL_15, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_15_control_control
column name in miRNA_counts.tsv=CONTROL_15_control_control


title: CONTROL_17, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_17_control_control
column name in miRNA_counts.tsv=CONTROL_17_control_control


title: CONTROL_16, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_16_control_control
column name in miRNA_counts.tsv=CONTROL_16_control_control


title: CONTROL_14, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_14_control_control
column name in miRNA_counts.tsv=CONTROL_14_control_control


title: CONTROL_11, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_11_control_control
column name in miRNA_counts.tsv=CONTROL_11_control_control


title: CONTROL_12, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_12_control_control
column name in miRNA_counts.tsv=CONTROL_12_control_control


title: CONTROL_18, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_18_control_control
column name in miRNA_counts.tsv=CONTROL_18_control_control


title: CASE_99, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_99_med_juvenile
column name in miRNA_counts.tsv=CASE_99_med_juvenile

value: CASE

value: juvenile

value: med


title: CONTROL_25, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_25_control_control
column name in miRNA_counts.tsv=CONTROL_25_control_control

value: blood plasma


title: CONTROL_1, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_1_control_control
column name in miRNA_counts.tsv=CONTROL_1_control_control

value: CONTROL


title: CASE_98, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_98_med_juvenile
column name in miRNA_counts.tsv=CASE_98_med_juvenile


title: CASE_96, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_96_high_adolescent
column name in miRNA_counts.tsv=CASE_96_high_adolescent

value: adolescent

value: high


title: CASE_97, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_97_high_adolescent
column name in miRNA_counts.tsv=CASE_97_high_adolescent

value: Female


title: CASE_95, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_95_low_adolescent
column name in miRNA_counts.tsv=CASE_95_low_adolescent

value: low

value: postmenarche


title: CASE_94, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_94_high_adolescent
column name in miRNA_counts.tsv=CASE_94_high_adolescent


title: CASE_91, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_91_low_juvenile
column name in miRNA_counts.tsv=CASE_91_low_juvenile


title: CASE_92, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_92_high_juvenile
column name in miRNA_counts.tsv=CASE_92_high_juvenile


title: CASE_88, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_88_high_juvenile
column name in miRNA_counts.tsv=CASE_88_high_juvenile


title: CASE_93, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_93_high_juvenile
column name in miRNA_counts.tsv=CASE_93_high_juvenile


title: CASE_9, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_9_med_adolescent
column name in miRNA_counts.tsv=CASE_9_med_adolescent


title: CASE_89, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_89_high_juvenile
column name in miRNA_counts.tsv=CASE_89_high_juvenile


title: CASE_90, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_90_low_adolescent
column name in miRNA_counts.tsv=CASE_90_low_adolescent


title: CASE_85, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_85_low_juvenile
column name in miRNA_counts.tsv=CASE_85_low_juvenile


title: CASE_87, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_87_low_juvenile
column name in miRNA_counts.tsv=CASE_87_low_juvenile


title: CASE_86, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_86_low_adolescent
column name in miRNA_counts.tsv=CASE_86_low_adolescent


title: CASE_83, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_83_low_adolescent
column name in miRNA_counts.tsv=CASE_83_low_adolescent


title: CASE_82, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_82_low_adolescent
column name in miRNA_counts.tsv=CASE_82_low_adolescent


title: CASE_84, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_84_high_juvenile
column name in miRNA_counts.tsv=CASE_84_high_juvenile


title: CASE_81, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_81_low_juvenile
column name in miRNA_counts.tsv=CASE_81_low_juvenile


title: CASE_79, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_79_med_juvenile
column name in miRNA_counts.tsv=CASE_79_med_juvenile


title: CASE_8, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_8_low_juvenile
column name in miRNA_counts.tsv=CASE_8_low_juvenile


title: CASE_80, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_80_high_juvenile
column name in miRNA_counts.tsv=CASE_80_high_juvenile


title: CONTROL_81, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_81_control_control
column name in miRNA_counts.tsv=CONTROL_81_control_control

value: control


title: CASE_77, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_77_high_adolescent
column name in miRNA_counts.tsv=CASE_77_high_adolescent


title: CASE_74, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_74_low_adolescent
column name in miRNA_counts.tsv=CASE_74_low_adolescent


title: CASE_75, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_75_med_juvenile
column name in miRNA_counts.tsv=CASE_75_med_juvenile


title: CASE_72, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_72_high_adolescent
column name in miRNA_counts.tsv=CASE_72_high_adolescent


title: CASE_71, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_71_high_adolescent
column name in miRNA_counts.tsv=CASE_71_high_adolescent


title: CASE_69, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_69_low_adolescent
column name in miRNA_counts.tsv=CASE_69_low_adolescent


title: CASE_70, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_70_low_juvenile
column name in miRNA_counts.tsv=CASE_70_low_juvenile


title: CONTROL_10, type: CONTROL, diagnosis: control, progression: control

description:
Library name: CONTROL_10_control_control
column name in miRNA_counts.tsv=CONTROL_10_control_control


title: CASE_7, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_7_high_adolescent
column name in miRNA_counts.tsv=CASE_7_high_adolescent


title: CASE_73, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_73_med_juvenile
column name in miRNA_counts.tsv=CASE_73_med_juvenile


title: CASE_67, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_67_high_adolescent
column name in miRNA_counts.tsv=CASE_67_high_adolescent


title: CASE_66, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_66_med_adolescent
column name in miRNA_counts.tsv=CASE_66_med_adolescent


title: CASE_68, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_68_med_adolescent
column name in miRNA_counts.tsv=CASE_68_med_adolescent


title: CASE_65, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_65_med_adolescent
column name in miRNA_counts.tsv=CASE_65_med_adolescent


title: CASE_78, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_78_med_adolescent
column name in miRNA_counts.tsv=CASE_78_med_adolescent


title: CASE_63, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_63_low_juvenile
column name in miRNA_counts.tsv=CASE_63_low_juvenile


title: CASE_62, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_62_low_adolescent
column name in miRNA_counts.tsv=CASE_62_low_adolescent


title: CASE_76, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_76_med_juvenile
column name in miRNA_counts.tsv=CASE_76_med_juvenile


title: CASE_64, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_64_high_adolescent
column name in miRNA_counts.tsv=CASE_64_high_adolescent


title: CASE_60, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_60_med_juvenile
column name in miRNA_counts.tsv=CASE_60_med_juvenile


title: CASE_6, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_6_low_juvenile
column name in miRNA_counts.tsv=CASE_6_low_juvenile


title: CASE_58, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_58_high_adolescent
column name in miRNA_counts.tsv=CASE_58_high_adolescent


title: CASE_57, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_57_med_adolescent
column name in miRNA_counts.tsv=CASE_57_med_adolescent


title: CASE_55, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_55_low_juvenile
column name in miRNA_counts.tsv=CASE_55_low_juvenile


title: CASE_56, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_56_high_adolescent
column name in miRNA_counts.tsv=CASE_56_high_adolescent


title: CASE_61, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_61_med_adolescent
column name in miRNA_counts.tsv=CASE_61_med_adolescent


title: CASE_54, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_54_high_adolescent
column name in miRNA_counts.tsv=CASE_54_high_adolescent


title: CASE_52, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_52_med_juvenile
column name in miRNA_counts.tsv=CASE_52_med_juvenile


title: CASE_53, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_53_high_juvenile
column name in miRNA_counts.tsv=CASE_53_high_juvenile


title: CASE_5, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_5_med_adolescent
column name in miRNA_counts.tsv=CASE_5_med_adolescent


title: CASE_50, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_50_high_juvenile
column name in miRNA_counts.tsv=CASE_50_high_juvenile


title: CASE_59, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_59_low_juvenile
column name in miRNA_counts.tsv=CASE_59_low_juvenile


title: CASE_48, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_48_high_adolescent
column name in miRNA_counts.tsv=CASE_48_high_adolescent


title: CASE_45, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_45_high_adolescent
column name in miRNA_counts.tsv=CASE_45_high_adolescent


title: CASE_44, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_44_low_adolescent
column name in miRNA_counts.tsv=CASE_44_low_adolescent


title: CASE_46, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_46_low_juvenile
column name in miRNA_counts.tsv=CASE_46_low_juvenile


title: CASE_42, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_42_med_adolescent
column name in miRNA_counts.tsv=CASE_42_med_adolescent


title: CASE_47, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_47_low_adolescent
column name in miRNA_counts.tsv=CASE_47_low_adolescent


title: CASE_43, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_43_low_adolescent
column name in miRNA_counts.tsv=CASE_43_low_adolescent


title: CASE_40, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_40_high_juvenile
column name in miRNA_counts.tsv=CASE_40_high_juvenile


title: CASE_39, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_39_high_juvenile
column name in miRNA_counts.tsv=CASE_39_high_juvenile


title: CASE_49, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_49_high_adolescent
column name in miRNA_counts.tsv=CASE_49_high_adolescent


title: CASE_38, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_38_med_adolescent
column name in miRNA_counts.tsv=CASE_38_med_adolescent


title: CASE_4, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_4_med_adolescent
column name in miRNA_counts.tsv=CASE_4_med_adolescent


title: CASE_51, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_51_med_adolescent
column name in miRNA_counts.tsv=CASE_51_med_adolescent


title: CASE_36, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_36_high_adolescent
column name in miRNA_counts.tsv=CASE_36_high_adolescent


title: CASE_37, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_37_med_adolescent
column name in miRNA_counts.tsv=CASE_37_med_adolescent


title: CASE_33, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_33_med_juvenile
column name in miRNA_counts.tsv=CASE_33_med_juvenile


title: CASE_31, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_31_low_juvenile
column name in miRNA_counts.tsv=CASE_31_low_juvenile


title: CASE_30, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_30_med_adolescent
column name in miRNA_counts.tsv=CASE_30_med_adolescent


title: CASE_41, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_41_med_juvenile
column name in miRNA_counts.tsv=CASE_41_med_juvenile


title: CASE_35, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_35_low_adolescent
column name in miRNA_counts.tsv=CASE_35_low_adolescent


title: CASE_3, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_3_low_adolescent
column name in miRNA_counts.tsv=CASE_3_low_adolescent


title: CASE_23, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_23_high_juvenile
column name in miRNA_counts.tsv=CASE_23_high_juvenile


title: CASE_20, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_20_low_juvenile
column name in miRNA_counts.tsv=CASE_20_low_juvenile


title: CASE_19, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_19_med_juvenile
column name in miRNA_counts.tsv=CASE_19_med_juvenile


title: CASE_17, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_17_med_juvenile
column name in miRNA_counts.tsv=CASE_17_med_juvenile


title: CASE_28, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_28_high_adolescent
column name in miRNA_counts.tsv=CASE_28_high_adolescent


title: CASE_29, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_29_low_juvenile
column name in miRNA_counts.tsv=CASE_29_low_juvenile


title: CASE_16, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_16_low_juvenile
column name in miRNA_counts.tsv=CASE_16_low_juvenile


title: CASE_26, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_26_low_adolescent
column name in miRNA_counts.tsv=CASE_26_low_adolescent


title: CASE_27, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_27_high_adolescent
column name in miRNA_counts.tsv=CASE_27_high_adolescent


title: CASE_22, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_22_med_adolescent
column name in miRNA_counts.tsv=CASE_22_med_adolescent


title: CASE_34, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_34_high_juvenile
column name in miRNA_counts.tsv=CASE_34_high_juvenile


title: CASE_18, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_18_med_adolescent
column name in miRNA_counts.tsv=CASE_18_med_adolescent


title: CASE_32, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_32_high_juvenile
column name in miRNA_counts.tsv=CASE_32_high_juvenile


title: CASE_2, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_2_high_adolescent
column name in miRNA_counts.tsv=CASE_2_high_adolescent


title: CASE_112, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_112_med_adolescent
column name in miRNA_counts.tsv=CASE_112_med_adolescent


title: CASE_113, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_113_high_adolescent
column name in miRNA_counts.tsv=CASE_113_high_adolescent


title: CASE_21, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_21_high_adolescent
column name in miRNA_counts.tsv=CASE_21_high_adolescent


title: CASE_24, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_24_low_adolescent
column name in miRNA_counts.tsv=CASE_24_low_adolescent


title: CASE_111, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_111_med_adolescent
column name in miRNA_counts.tsv=CASE_111_med_adolescent


title: CASE_15, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_15_high_juvenile
column name in miRNA_counts.tsv=CASE_15_high_juvenile


title: CASE_14, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_14_low_adolescent
column name in miRNA_counts.tsv=CASE_14_low_adolescent


title: CASE_13, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_13_high_adolescent
column name in miRNA_counts.tsv=CASE_13_high_adolescent


title: CASE_114, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_114_med_adolescent
column name in miRNA_counts.tsv=CASE_114_med_adolescent


title: CASE_25, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_25_med_adolescent
column name in miRNA_counts.tsv=CASE_25_med_adolescent


title: CASE_12, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_12_high_juvenile
column name in miRNA_counts.tsv=CASE_12_high_juvenile


title: CASE_11, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_11_med_adolescent
column name in miRNA_counts.tsv=CASE_11_med_adolescent


title: CASE_104, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_104_low_juvenile
column name in miRNA_counts.tsv=CASE_104_low_juvenile


title: CASE_108, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_108_high_juvenile
column name in miRNA_counts.tsv=CASE_108_high_juvenile


title: KOLF cells, WT, Day 0, biol rep 4

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

description: Library name: Stem_WT4

data_processing:
Raw sequencing reads were processed using the ENCODE/DCC pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline)
Reads were aligned to GRCh38 and quantified using kallisto.
Kallisto quantificiation files were read into edgeR/limma using the tximport package in R to generate counts matrices
Assembly: GRCh38
Supplementary files format and content: RawCountsMatrix.tsv contains the Kallisto-quantified counts for all genes for all samples.

source_name: KOLF cell, Day 0

growth_protocol: KOLF2-C1 (KOLF2) cells were grown in 6-well plates coated with Matrigel® hESC-Qualified Matrix, LDEV-free (Corning®) maintained in TeSR-E8 media (STEMCELL Technologies), and media changed daily. Cells were split with Gentle Cell Dissociation Reagent (STEMCELL Technologies) (16). Cell cryopreservation was in KnockOut™ Serum Replacement medium (Gibco™) supplemented with 10% DMSO. All cultures were maintained at 37°C humidified 5% CO2 incubator, unless otherwise stated, and were routinely tested for mycoplasma. Both variant and control KOLF2 iPSCs, were differentiated using the STEMdiff Ventricular or Atrial Cardiomyocyte Differentiation Kits (STEMCELL, Australia) and subsequently maintained in the corresponding Maintenance Kit.

extract_protocol:
RNA was extracted from cells using the RNeasy Minikit (Qiagen).
RNA libraries were prepared with the SureSelect Strand-Specific XT HS2 Poly-A kit and sequenced at Genomics WA (Perth, Australia) on an Illumina NovaSeq 6000 platform (paired-end, 100bp. ~30 million reads per sample).

value: KOLF cell, Day 0

value: induced pluripotent stem cell

value: WT


title: CASE_105, type: CASE, diagnosis: juvenile, progression: low

description:
Library name: CASE_105_low_juvenile
column name in miRNA_counts.tsv=CASE_105_low_juvenile


title: CASE_106, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_106_high_juvenile
column name in miRNA_counts.tsv=CASE_106_high_juvenile

value: Male

value: male


title: CASE_109, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_109_high_adolescent
column name in miRNA_counts.tsv=CASE_109_high_adolescent

value: premenarche


title: CASE_103, type: CASE, diagnosis: juvenile, progression: med

description:
Library name: CASE_103_med_juvenile
column name in miRNA_counts.tsv=CASE_103_med_juvenile

value: CASE


title: CASE_101, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_101_high_adolescent
column name in miRNA_counts.tsv=CASE_101_high_adolescent


title: CASE_110, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_110_low_adolescent
column name in miRNA_counts.tsv=CASE_110_low_adolescent


title: CASE_102, type: CASE, diagnosis: adolescent, progression: med

description:
Library name: CASE_102_med_adolescent
column name in miRNA_counts.tsv=CASE_102_med_adolescent


title: CASE_107, type: CASE, diagnosis: adolescent, progression: high

description:
Library name: CASE_107_high_adolescent
column name in miRNA_counts.tsv=CASE_107_high_adolescent


title: KOLF cells, HDR, Day 0, biol rep 4

description: Library name: Stem_HDR4

value: HDR


title: KOLF cells, WT, Day 0, biol rep 2

description: Library name: Stem_WT2


title: CASE_100, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_100_high_juvenile
column name in miRNA_counts.tsv=CASE_100_high_juvenile

value: juvenile


title: KOLF cells, HDR, Day 0, biol rep 2

description: Library name: Stem_HDR2


title: KOLF cells, WT, Day 0, biol rep 1

description: Library name: Stem_WT1


title: CASE_10, type: CASE, diagnosis: juvenile, progression: high

description:
Library name: CASE_10_high_juvenile
column name in miRNA_counts.tsv=CASE_10_high_juvenile

value: blood plasma


title: KOLF cells, HDR, Day 0, biol rep 1

description: Library name: Stem_HDR1


title: CASE_1, type: CASE, diagnosis: adolescent, progression: low

description:
Library name: CASE_1_low_adolescent
column name in miRNA_counts.tsv=CASE_1_low_adolescent


title: KOLF cells, WT, Day 0, biol rep 3

description: Library name: Stem_WT3


title: KOLF cells, WT, Day 18, biol rep 4

description: Library name: Cardio_WT4

source_name: KOLF cell, Day 18

value: KOLF cell, Day 18

value: Cardiomyocyte


title: KOLF cells, WT, Day 18, biol rep 3

description: Library name: Cardio_WT3


title: KOLF cells, HDR, Day 18, biol rep 3

description: Library name: Cardio_HDR3


title: KOLF cells, WT, Day 18, biol rep 2

description: Library name: Cardio_WT2


title: KOLF cells, HDR, Day 18, biol rep 4

description: Library name: Cardio_HDR4


title: KOLF cells, HDR, Day 18, biol rep 2

description: Library name: Cardio_HDR2


title: KOLF cells, WT, Day 18, biol rep 1

description: Library name: Cardio_WT1


title: Perturb seq in Naive cells, gene expression library, replicate2

city: Jerusalem

first: Gal

last: Keshet

state: Yerushalayim

address: Institute of Life Sciences, Givat Ram

department: Genetics

country: Israel

institute: The Hebrew Univerisy

description:
Library name: naive_sample2
Seurat_after_mixscape_naive.RData

data_processing:
Sequencing reads from the mRNA and CRISPR libraries were mapped to the hg38 reference genome using Cell Ranger software (version 6.1.2). For gene annotation, the GTF creation procedure as in the 10X genomics website was performed (https://www.10xgenomics.com/support/software/cell-ranger/downloads/cr-ref-build-steps). Because 1 gene included in the perturb-seq library was not present in the GTF generated using this approach (ZNF286B), this gene was manually added to the GTF.  For each cell, the gRNA identity was assigned with the Cell Ranger software’s CRISPR Guide Capture pipeline (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-feature-bc). Only cells which were assigned with 1 gRNA were kept for further analysis. Count matrices were loaded into the Seurat R package (version 5.1.0).65 To retain good quality cells, cells bearing < 2000 genes detected or >10% mitochondrial gene content were removed from downstream analysis. For identification of cells with an effective perturbation, the Mixscape pipeline was implemented23 following the guidelines in Seurat website (https://satijalab.org/seurat/articles/mixscape_vignette), with slight modifications. Briefly, the perturbation signature of each cell was calculated using the CalcPerturbSig function with default parameters. Cells bearing effective perturbations were then identified using the RunMixscape function, setting min.de.genes = 1 and logfc.threshold = 0 for increased sensitivity.
Assembly: hg38
Supplementary files format and content: Rdata file, representing Seurat objects for the Primed and Naïve datasets

extract_protocol:
Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) kit (10x Chromium) was used for Single Cell 3' Gene Expression and CRISPR Screening analysis. It was done by partitioning ten thousand cells per reaction into Gel Beads-in-emulsion (GEMs)
The cells (16.5K cells were used in order to get recovery target of 10K cells), were then subjected to the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10× Genomics, CA, USA) and DNA libraries protocol for generating Single Cell 3' Gene Expression and CRISPR Screening dual index libraries from single cells were prepared according to manufacture recommendations (10x Chromium). In brief, and for Single-cell RNA-seq (scRNA-seq) Gene Expression Library preparation, the pellet was cleaned up after cDNA PCR product was selected with 0.6X SPRIselect reagent (Beckman Coulter), washed twice with 80% ethanol and then eluted in 40 ul Elution buffer (EB). While for the and CRISPR Screening, 75 of the supernatants from the previous step was transferred to a new tube and 30 ul of SPRIselect reagent (Beckman Coulter) 1.2X was added and then washed twice with 80% ethanol and finally eluted in 40 ul EB. Both libraries were prepared for sequencing following manufacturer company instructions (10x Chromium, CG000316, Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268 ). Sequencing was done using Illumina Novaseq6000 platform with following sequencing conditions: 28 bp (Read1) and 90 bp (Read2). For the primed perurb-seq, 2 samples were sequenced in 2 batches. For the naïve experiment, 2 samples were sequenced in the same batch.

value: mRNA

value: Human pluripotent stem cells


title: KOLF cells, HDR, Day 18, biol rep 1

description: Library name: Cardio_HDR1


title: Perturb seq in Primed cells, gRNA library, replicate1

description:
Library name: guide_sample1
Seurat_after_mixscape.RData

value: gRNA


title: Perturb seq in Primed cells, gRNA library, replicate2

description:
Library name: guide_sample2
Seurat_after_mixscape.RData


title: Perturb seq in Naive cells, gene expression library, replicate1

description:
Library name: naive_sample1
Seurat_after_mixscape_naive.RData


title: Perturb seq in Naive cells, gRNA library, replicate1

description:
Library name: naïve_guide_sample1
Seurat_after_mixscape_naive.RData


title: Colorectal tumor, Patient 10

city: Huddinge

first: Anne

last: Marchalot

address: Alfred Nobel Allé 8, Center for Infectious Medicine

institute: Karolinska Institutet

description: Library name: P10_CRC

data_processing:
CellRanger version 7.0.1 (algnment)
Seurat version 4.1 (quality control, data normalization, data scaling, dimension reduction (both linear and non-linear), clustering)
Harmony (batch correction)
Assembly: GRCh38
Supplementary files format and content: rds files include R Seurat Object of all patients and all tissues cells, filtered and batch corrected

source_name: Colorectal tumor

extract_protocol:
Colon samples were dissected to remove fat and muscle layers. PM were dissected to isolate the tumor from the surrounding unaffected tissue, i.e. peritoneum/omentum. All samples were thinly cut into 1-2mm pieces before subsequent enzymatic digestion into 5 ml of Iscove modified Dulbecco media (IMDM) (supplemented with antibiotics), collagenase II (0.25 mg/ml; Sigma), and deoxyribonuclease (0.25 mg/ml; Roche). Magnetic stirring was performed at 37°C and 450 rpm for 30min. Enzymatic digestion was stopped by adding IMDM media supplemented with 10% FBS and the samples were passed through a 40uM cell strainer before being counted.
10X 5' Gene expression v2 protocol, user guide CG000331 Rev E and F

value: Colorectal tumor

value: ILC and NK cells

tag: patient

value: Patient 10


title: Colorectal tumor, Patient 9

description: Library name: P9_CRC

value: Patient 9


title: PC metastasis, Patient 9

description: Library name: P9_PC

source_name: PC metastasis

value: PC metastasis


title: Perturb seq in Primed cells, gene expression library, replicate1

description:
Library name: ES_sample1
Seurat_after_mixscape.RData


title: PC metastasis, Patient 8

description: Library name: P8_PC

value: Patient 8


title: Colon, Patient 11

description: Library name: P11_Colon

source_name: Colon

value: Colon

value: Patient 11


title: Colorectal tumor, Patient 11

description: Library name: P11_CRC


title: Colon, Patient 10

description: Library name: P10_Colon


title: PC metastasis, Patient 7

description: Library name: P7_PC

value: Patient 7


title: Perturb seq in Naive cells, gRNA library, replicate2

description:
Library name: naïve_guide_sample2
Seurat_after_mixscape_naive.RData


title: Perturb seq in Primed cells, gene expression library, replicate2

description:
Library name: ES_sample2
Seurat_after_mixscape.RData


title: Colon, Patient 9

description: Library name: P9_Colon


title: Colorectal tumor, Patient 7

description: Library name: P7_CRC


title: PC metastasis, Patient 6

description: Library name: P6_PC

value: Patient 6


title: Colon, Patient 7

description: Library name: P7_Colon


title: Colon, Patient 4

description: Library name: P4_Colon

value: Patient 4


title: Colon, Patient 3

description: Library name: P3_Colon

value: Patient 3


title: Colorectal tumor, Patient 4

description: Library name: P4_CRC


title: Colorectal tumor, Patient 3

description: Library name: P3_CRC


title: PC metastasis, Patient 5

description: Library name: P5_PC

value: Patient 5


title: PC metastasis, Patient 2

description: Library name: P2_PC

value: Patient 2


title: PC metastasis, Patient 1

description: Library name: P1_PC

value: Patient 1


title: AML194 500 nM mivebresib, 2 16 hrs

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description:
Library name: KBr_AML194-500nM-MIV-3
KBr_AML194-500nM-MIV-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

growth_protocol: AML cells  AML191, and AML194 cells were cultured in 20% FBS containing RPMI media and supplemented with 10 ng/mL of GMCSF.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

treatment_protocol: AML cells were treated with mivebresib (500 nM) for 16 hours at 37°C and harvested into RNA lysis buffer. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: lymphocyte

tag: disease state

value: Acute myeloid leukemia

value: 500 nM mivebresib


title: AML194 500 nM mivebresib, 1 16 hrs

description:
Library name: KBr_AML194-500nM-MIV-2
KBr_AML194-500nM-MIV-2

tag: cell type


title: AML194 Control 2 16 hrs

description:
Library name: KBr_AML194-0-3
KBr_AML194-0-3

value: Control


title: AML191 500 nM mivebresib, 1 16 hrs

description:
Library name: KBr_AML191-500MIV-2
KBr_AML191-500MIV-2


title: AML194 Control 1 16 hrs

description:
Library name: KBr_AML194-0-2
KBr_AML194-0-2


title: FACS sorted CD8+ Naive T cells from R10357

description:
Library name: T5357
column name in Norm Gene Counts.txt: Naïve_357

data_processing:
Quality control and trimming of original FASTQ files were performed using Rfastp package with default parameters.
QC and trimmed FASTQ files were aligned using subjunc function of Rsubread package with the hg38 human reference genome.
Generated BAM files were sorted and indexed using Rsamtools.
Transcript counts per gene were generated using the summarizeOverlaps function of GenomicAlignments package.
Normalization and log transformation of gene counts were performed using the rlog function of DESeq2 package.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes normalized gene counts for each sample
Supplementary files format and content: Norm Gene Counts.txt

extract_protocol:
Total RNA was extracted from FACS-sorted CD8 T cells using Quick RNA Microprep kit (Zymo Research) following manufacturer's protocol.
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.

value: Peripheral blood

value: CD8+ Naive T cell


title: AML191 Control 1 16 hrs

description:
Library name: KBr_AML191-0-1
KBr_AML191-0-1


title: FACS sorted CD8+ Naive T cells from R10143

description:
Library name: T5143
column name in Norm Gene Counts.txt: Naïve_143


title: FACS sorted CD8+ Naive T cells from R00154

description:
Library name: T5154
column name in Norm Gene Counts.txt: Naïve_154


title: AML191 Control 2 16 hrs

description:
Library name: KBr_AML191-0-3
KBr_AML191-0-3


title: FACS sorted CD8+ Naive T cells from R10358

description:
Library name: T5358
column name in Norm Gene Counts.txt: Naïve_358


title: FACS sorted CD8+ Naive T cells from R10146

description:
Library name: T5146
column name in Norm Gene Counts.txt: Naïve_144


title: FACS sorted CD8+ CD28+/CD57+ EM T cells from R10358

description:
Library name: T4358
column name in Norm Gene Counts.txt: CD28posCD57pos_EM_358

value: CD8+ CD28+/CD57+ EM T cell


title: FACS sorted CD8+ CD28+/CD57+ EM T cells from R10357

description:
Library name: T4357
column name in Norm Gene Counts.txt: CD28posCD57pos_EM_357


title: FACS sorted CD8+ CD28+/CD57+ EM T cells from R10356

description:
Library name: T4356
column name in Norm Gene Counts.txt: CD28posCD57pos_EM_356


title: FACS sorted CD8+ CD28+/CD57+ EM T cells from R00154

description:
Library name: T4154
column name in Norm Gene Counts.txt: CD28posCD57pos_EM_154


title: FACS sorted CD8+ CD57+ EMRA T cells from R10358

description:
Library name: T3358
column name in Norm Gene Counts.txt: CD57pos_EMRA_358

value: CD8+ CD57+ EMRA T cell


title: FACS sorted CD8+ Naive T cells from R10356

description:
Library name: T5356
column name in Norm Gene Counts.txt: Naïve_356


title: FACS sorted CD8+ CD57+ EMRA T cells from R10357

description:
Library name: T3357
column name in Norm Gene Counts.txt: CD57pos_EMRA_357


title: FACS sorted CD8+ CD28+/CD57+ EM T cells from R10146

description:
Library name: T4146
column name in Norm Gene Counts.txt: CD28posCD57pos_EM_146


title: FACS sorted CD8+ CD57+ EMRA T cells from R10356

description:
Library name: T3356
column name in Norm Gene Counts.txt: CD57pos_EMRA_356


title: FACS sorted CD8+ CD57+ EMRA T cells from R00154

description:
Library name: T3154
column name in Norm Gene Counts.txt: CD57pos_EMRA_154


title: FACS sorted CD8+ CD57+ EMRA T cells from R10146

description:
Library name: T3146
column name in Norm Gene Counts.txt: CD57pos_EMRA_146


title: FACS sorted CD8+ CD57+ EMRA T cells from R10143

description:
Library name: T3143
column name in Norm Gene Counts.txt: CD57pos_EMRA_143


title: FACS sorted CD8+ CXCR3- CM T cells from R10356

description:
Library name: T2356
column name in Norm Gene Counts.txt: CXCR3neg_CM_356

value: CD8+ CXCR3- CM T cell


title: FACS sorted CD8+ CXCR3- CM T cells from R10357

description:
Library name: T2357
column name in Norm Gene Counts.txt: CXCR3neg_CM_357


title: FACS sorted CD8+ CXCR3- CM T cells from R10358

description:
Library name: T2358
column name in Norm Gene Counts.txt: CXCR3neg_CM_358


title: FACS sorted CD8+ CXCR3- CM T cells from R00154

description:
Library name: T2154
column name in Norm Gene Counts.txt: CXCR3neg_CM_154


title: FACS sorted CD8+ CXCR3- CM T cells from R10146

description:
Library name: T2146
column name in Norm Gene Counts.txt: CXCR3neg_CM_146


title: FACS sorted CD8+ CXCR3- CM T cells from R10143

description:
Library name: T2143
column name in Norm Gene Counts.txt: CXCR3neg_CM_143


title: FACS sorted CD8+ CXCR3+ CM T cells from R10146

description:
Library name: T1146
column name in Norm Gene Counts.txt: CXCR3pos_CM_146

value: CD8+ CXCR3+ CM T cell


title: FACS sorted CD8+ CXCR3+ CM T cells from R10356

description:
Library name: T1356
column name in Norm Gene Counts.txt: CXCR3pos_CM_356


title: FACS sorted CD8+ CXCR3+ CM T cells from R10357

description:
Library name: T1357
column name in Norm Gene Counts.txt: CXCR3pos_CM_357


title: FACS sorted CD8+ CXCR3+ CM T cells from R00154

description:
Library name: T1154
column name in Norm Gene Counts.txt: CXCR3pos_CM_154


title: FACS sorted CD8+ CD28+/CD57+ EM T cells from R10143

description:
Library name: T4143
column name in Norm Gene Counts.txt: CD28posCD57pos_EM_143


title: FACS sorted CD8+ CXCR3+ CM T cells from R10358

description:
Library name: T1358
column name in Norm Gene Counts.txt: CXCR3pos_CM_358


title: KYSE410R_IR_2

city: 上海市

first: meilian

last: yao

state: 上海

address: 上海市黄埔区重庆南路

department: 医学院

institute: 上海交通大学

description:
Library name: sample11
irradiation, 4Gy

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by Agilent5300 and quantified using the ND-2000 (NanoDrop Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Esophageal Squamous cells

tag: genotype

value: WT

value: Irradiation


title: KYSE410R_IR_3

description:
Library name: sample12
irradiation, 4Gy


title: FACS sorted CD8+ CXCR3+ CM T cells from R10143

description:
Library name: T1143
column name in Norm Gene Counts.txt: CXCR3pos_CM_143

tag: tissue


title: KYSE410R_1

description:
Library name: sample7
no irradiation

value: control


title: KYSE410R_3

description:
Library name: sample9
no irradiation


title: KYSE410_IR_3

description:
Library name: sample6
irradiation, 4Gy


title: KYSE410R_IR_1

description:
Library name: sample10
irradiation, 4Gy


title: KOLF cells, HDR, Day 0, biol rep 3

description: Library name: Stem_HDR3

value: KOLF cell, Day 0

value: induced pluripotent stem cell

value: HDR


title: KYSE410_IR_1

description:
Library name: sample4
irradiation, 4Gy


title: AML191 500 nM mivebresib, 2 16 hrs

description:
Library name: KBr_AML191-500MIV-3
KBr_AML191-500MIV-3

value: lymphocyte


title: KYSE410_2

description:
Library name: sample2
no irradiation


title: KYSE410_3

description:
Library name: sample3
no irradiation


title: KYSE410R_2

description:
Library name: sample8
no irradiation


title: SETDB1_CRISPRi_guide2_Rep2

description: Library name: Seq179_168_hNES_Sai2_bulkRNA_CRISPRi_SETDB1g2_LV3806_Rep2

data_processing:
Paired-end reads (2x150) were aligned to the hg38 genome using STAR v2.6.0c. Both unique (--outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.03) and multimapping (--outFilterMultimapNmax 100 --winAnchorMultimapNmax 200) steps were performed
SAM files were converted to BAM and further sorted and indexed using SAMtools v1.9.
Coverage tracks were made with bamCoverage v2.4.3 normalizing with a reads per kilobase million factor (RPKM)
Read count over genes and transposable elements was performed using FeatureCounts v1.6.3 taking into consideration the strandedness of the genomic element
Assembly: GRCh38
Supplementary files format and content: BigWig file format normalized according to RPKM for each sample

growth_protocol: An embryo-derived human neural epithelial-like stem cell line with the characteristics of human neural progenitor cells (hNPC), Sai2, was used (Tailor et al 2013). The hNPCs were cultured according to standard protocol (Falk et al 2012). Briefly, the cells were kept in DMEM/F12 (Thermo Fisher Scientific) supplemented with Glutamine (2mM, Sigma), Penicillin/Streptomycin (1x, Gibco), N2 (1x, Thermo Fisher Scientific), B27 (0.05x, Thermo Fisher Scientific), EGF and FGF2 (both 10ng/ml, Thermo Fisher Scientific). 10 mM Y27632 Rock inhibitor (Miltenyi) was also used. Cells were grown on Nunc multidishes or T25 flasks pre-coated with Poly L-Ornithine (15μg/ml, Sigma) and Laminin (2μg/ml, Sigma). Cells were passaged 1:3 every 2-3 days using TrypLE Express enzyme (GIBCO) and Trypsin Inhibitor (GIBCO).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Quiagen) with on column DNAse treatment following the manufacturers protocol.
RNA-seq

treatment_protocol: To transcriptionally silence SETDB1 we designed single guide RNA (sgRNA) sequences targeting the transcription start site using the GPP Portal (Broad institute). As a control we used an sgRNA targeting LacZ, a bacterial sequence not present in the human genome. sgRNAs were cloned into lentiviral backbone plasmids (pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP) containing a catalytically inactive Cas9 (deadCas9) fused to a KRAB transcriptional repressor domain (Johansson et al 2022). Lentiviruses were produced as described before (Zuffery et al. 1997). Cells were after transduction expanded for 10 days prior to FACS isolation (FACSAria, BD sciences) of GFP+ cells with reanalysis showing >95% purity. Cells were pelleted at 400g for 10 min before being snap frozen on dry ice and stored at -80°C until RNA isolation.

value: human neuroepithelial-like stem cells

value: SETDB1 knockdown

value: CRISPR interference


title: SETDB1_CRISPRi_guide1_Rep2

description: Library name: Seq179_168_hNES_Sai2_bulkRNA_CRISPRi_SETDB1g1_LV3808_Rep2


title: SETDB1_CRISPRi_guide1_Rep1

description: Library name: Seq179_168_hNES_Sai2_bulkRNA_CRISPRi_SETDB1g1_LV3808_Rep1


title: KYSE410_1

description:
Library name: sample1
no irradiation


title: SETDB1_CRISPRi_Control_Rep3

description: Library name: Seq178_168_hNES_Sai2_bulkRNA_CRISPRi_LACZ_LV3599_Rep3

value: Control


title: SETDB1_CRISPRi_guide2_Rep1

description: Library name: Seq179_168_hNES_Sai2_bulkRNA_CRISPRi_SETDB1g2_LV3806_Rep1


title: SETDB1_CRISPRi_Control_Rep2

description: Library name: Seq178_168_hNES_Sai2_bulkRNA_CRISPRi_LACZ_LV3599_Rep2


title: KYSE410_IR_2

description:
Library name: sample5
irradiation, 4Gy


title: hiPSC-derived retinal organoids DD225, 14x HTO [HTO]

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

description:
Library name: HTO
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software (v7.1.0)
Singlets were filtered in order to keep only cells with nFeature_RNA between 500 and 7000, nCount_ RNA < 30000, and percent.mt <12. The normalization method used was “LogNormalize”, with scale.factor = 30000
Assembly: GRCh38
Supplementary files format and content: Processed data file contains genes and HTO information per sample

source_name: Retinal organoid

growth_protocol: ISO-CTRL and USH2A 13KO hiPSCs were differentiated into retinal organoids using a previosuly reported differentiation protocol (McDonald et al., 2024)

extract_protocol:
Retinal organoids were dissociated following an adapted protocol from the Papain Dissociation kit. 24 hours prior to the procedure, the excess of RPE was carefully cut away from every retinal organoid, which was subsequently mechanically divided into very small pieces with the help of tweezers. Each retinal organoid was incubated at 37 °C for 90 minutes on an orbital shaker set to 90 rpm in the presence of 500 µl of freshly prepared dissociation solution (20 units/ml papain and 0.005% DNase). Then, they were gently triturated for 5-6 times using a 1 mL pipettor, making sure to avoid the formation of bubbles. The 48-wells plate was placed back in the incubator for 10 minutes, after which the organoids were further triturated until obtaining a single cell suspension. This was added to a tube containing 1 mL of albumin ovomucoid protease inhibitor solution with DNase. Each well is further washed with an extra 1 mL of solution. Tubes were centrifuged at 300x g for 5min. After removing the supernatant, cells were resuspended in PBS with 2% BSA/0.01% TWEEN 20 and filtered through a 40 µm cell strainer to remove cell aggregates. A viable cell count was performed. 1 million cells per sample were resuspended in 100 µl staining buffer (2% BSA/0.01 % TWEEN 20, PBS) in low bind tubes, with 10 µl Fc Blocking reagent (FcX) for 10 minutes on ice. Then, 0.5µg of unique Cell Hashing antibodies were added to each tube and incubated for 20 minutes on ice. After three washing steps with 1mL staining buffer, stained cells were centrifuged at 4 ˚°C for 5 minutes at 350g. Concentration and cell viability were assessed for each sample (Bio-Rad, TC20). After counting, all samples were merged and resuspended at the desired concentration for single cell sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics)

value: Retinal organoid

value: ISO-CTRL, 13KO E11, 13KO G8, 13KO B7


title: PBMC_TAIII_2

city: Hefei

first: Mingqi

last: Hou

institute: USTC

description:
Library name: Sample5
TA1.0-2

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: peripheral blood

extract_protocol:
Bulk-seq: RNA was extracted by trizol method (Invitrogen, USA), RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries. sc-RNA-seq: The cell suspension was loaded into Chromium microfluidic chips with 3’ v2 chemistry and barcoded with a 10× Chromium Controller. RNA from the barcoded cells was subsequently reverse-transcribed and constructed sequencing libraries.
Bulk-seq:Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. sc-RNA-seq:Sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions.

value: peripheral blood

value: PBMC

value: TAIII


title: SETDB1_CRISPRi_Control_Rep1

description: Library name: Seq178_168_hNES_Sai2_bulkRNA_CRISPRi_LACZ_LV3599_Rep1


title: SETDB1_CRISPRi_Control_Rep4

description: Library name: Seq178_168_hNES_Sai2_bulkRNA_CRISPRi_LACZ_LV3599_Rep4


title: PBMC_DMSO_1

description:
Library name: Sample1
DMSO-1

value: NECA


title: PBMC_DMSO_3

description:
Library name: Sample3
DMSO-3

value: WT


title: PBMC_TAIII_1

description:
Library name: Sample4
TA1.0-1


title: Human_meningioma_scRNAseq_BWH8_2300008

city: Boston

first: Wenya Linda

last: Bi

state: MA

address: 60 Fenwood Rd

department: Neurosurgery

institute: Mass General Brigham

description: Library name: Sample 8

data_processing:
scRNA-seq reads were processed with Cell Ranger 6.0.1 for 7 meningiomas and 1 arachnoid (Samples 2-9) and Cell Ranger 3.1.0 for 1 meningioma (Sample 1).
Assembly: GRCh38-3.0.0 human reference genome.
Supplementary files format and content: Tab-separated value files and matrix files including matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz.

source_name: Human meningioma

extract_protocol:
Cell Ranger version 3.1.0.
Cells were isolated by FACS and resuspended in 0.4% BSA in PBS at a concentration of 1,000 cells per μl. 10K cells were loaded onto a single lane (Chromium chip, 10X Genomics) for encapsulation in lipid droplets, using the Single-cell 3’ Kit (V3) in 1 meningioma (Sample 1) and the 5' Kits (V2) in 7 meningiomas and 1 arachnoid (Samples 2-9).

value: Human meningioma

value: female

tag: who grade


title: Human_meningioma_scRNAseq_BWH7_2300007

description: Library name: Sample 7

value: male


title: hiPSC-derived retinal organoids DD225, 14x HTO [GEX]

description:
Library name: GEX
10x Genomics


title: Human_arachnoid_scRNAseq_BWH_2300009

description: Library name: Sample 9

source_name: Human arachnoid

value: Human arachnoid

value: not provided


title: Human_meningioma_scRNAseq_BWH6_2300006

description: Library name: Sample 6


title: PBMC_DMSO_2

description:
Library name: Sample2
DMSO-2

tag: treatment


title: PBMC_TAIII_3

description:
Library name: Sample6
TA1.0-3


title: Human_meningioma_scRNAseq_BWH5_2300004

description: Library name: Sample 5


title: Cont_F20Y-4

city: Dindaeng

first: Kanokwan

last: Sriwattanapong

state: กรุงเทพมหานคร

address: 558/392, Lumpini suite dindaeng-ratchaprarop

country: Thailand

institute: Chulalongkorn University, Faculty of Dentistry

description: Library name: Cont_F20Y-4

data_processing:
RNA libraries were map to Homo sapiens (UCSC hg19) reference genome using Illumina RNA-Seq Alignment | Version: 2.0.2.
The alignment data was annotated and gene count of each sample was calculated using DESeq2 Global Analysis 3.18.20.11.
Assembly: Homo sapiens (UCSC hg19)
Supplementary files format and content: tab-delimited text file containing raw gene count of each sample

source_name: Gingival fibroblast cells

extract_protocol:
Total RNA was extracted using Rneasy plus mini kit (QIAGEN)
RNA lbraries for RNA-seq were prepared using TruSeq stranded mRNA library prep kit.

value: Gingival fibroblast cells


title: Human_meningioma_scRNAseq_BWH4_2300003

description: Library name: Sample 4


title: Human_meningioma_scRNAseq_BWH2_2300001

description: Library name: Sample 2


title: Cont_F20Y-3

state: กรุงเทพมหานคร

description: Library name: Cont_F20Y-3


title: Cont_F20Y-1

state: กรุงเทพมหานคร

description: Library name: Cont_F20Y-1


title: FAM20A-F20Y-1.2

state: กรุงเทพมหานคร

description: Library name: FAM20A-F20Y-1.2

value: FAM20A variants


title: FAM20A-F20Y-1.1

state: กรุงเทพมหานคร

description: Library name: FAM20A-F20Y-1.1


title: Human_meningioma_scRNAseq_BWH1_BRI_709

description: Library name: Sample 1


title: MOLM13, shMETTL3, shMET-1

description:
Library name: shMETTL3-1-RNA-seq
shMETTL3-1-RNA-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq, DRIP-seq, DRIPc-seq, RIP-seq, 4C-seq, ChIP-seq, and HiC-seq from MOLM13 AML cells were aligned to the hg19  genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks and visualization files were created using deepTools version 3.0
Peak annotation was performed with HOMER(version 4.10)
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for RNA-seq Samples, and bigwig and bed peaks for DRIPseq, DRIPc-seq, RIP-seq, ATAC-seq, MeRIP-seq, ChIP-seq, 4C-seq and HiC-seq.

extract_protocol:
Total RNA was purified from cells using the TRIzol reagent (TIANGEN, cat# DP424), followed by standard chloroform phase separation and alcohol precipitation. cDNA was synthesized from 1 μg total RNA, and reverse transcription was performed using the HiScript II Q RT SuperMix kit (Vazyme, cat#R222-01) according to the manufacturer’s instructions. The ATAC-seq assay was performed as described previously. Brieﬂy, 5x104 cells were washed twice with PBS and lysed in lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1 % NP-40. The lysate was washed in PBS and treated with Tn5 transposase at 37°C for 30 minutes. DNA was puriﬁed using the DNA purification Kit (TIANGEN, Cat# DP214). DNA library was then generated by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, cat# TD711-01).
RNA sequencing libraries were prepared from 1 μg of total RNA using the VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, cat# NR605-01/02) following the manufacturer instructions.  ChIP-DNA libraries were prepared using the Illumina’s VAHTS Universal Pro DNA Library Prep Kit according to the manufacturer’s instructions (Vazyme, cat# ND608-01/02).  The ATAC-seq DNA was puriﬁed using the DNA purification Kit (TIANGEN, Cat# DP214). ATAC chromatin DNA library was then generated by Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, cat# TD711-01). Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications.

value: leukemia cells

value: MOLM13 cells

value: acute myeloid leukemia

tag: chip antibody

value: no treatment


title: Human_meningioma_scRNAseq_BWH3_2300002

description: Library name: Sample 3


title: MOLM13, shMETTL3, shMET-2

description:
Library name: shMETTL3-2-RNA-seq
shMETTL3-2-RNA-seq


title: Cont_F20Y-2

state: กรุงเทพมหานคร

description: Library name: Cont_F20Y-2

value: Control


title: MOLM13, shYTHDC1, shYTH-2

description:
Library name: shYTHDC1-2-RNA-seq
shYTHDC1-2-RNA-seq


title: MOLM13, Control, Ctrl-2

description:
Library name: Ctrl-2-RNA-seq
Ctrl-2-RNA-seq


title: MOLM13, shYTHDC1, shYTH-1

description:
Library name: shYTHDC1-1-RNA-seq
shYTHDC1-1-RNA-seq


title: MOLM13, DRIPc, Control

description:
Library name: DRIPc-seq
DRIPc-seq

value: S9.6 Antibody (Kerafast, Cat#ENH001)


title: MOLM13, RIP, CTCF

description:
Library name: CTCF-RIP-seq
CTCF-RIP-seq

value: CTCF (CST, Cat# 2899)


title: MOLM13, RIP, m6A

description:
Library name: m6A-RIP-seq
m6A-RIP-seq

value: m6A (Proteintech, Cat# 68055)


title: MOLM13, 4C, RNase

description:
Library name: RNase-4C-seq
RNase-4C-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq, DRIP-seq, DRIPc-seq, RIP-seq, 4C-seq, ChIP-seq, and HiC-seq from MOLM13 AML cells were aligned to the hg19  genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks and visualization files were created using deepTools version 3.0
Peak annotation was performed with HOMER(version 4.10)
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values for RNA-seq Samples, and bigwig and bed peaks for DRIPseq, DRIPc-seq, RIP-seq, ATAC-seq, MeRIP-seq, ChIP-seq, 4C-seq and HiC-seq.
Library strategy: 4C-seq


title: MOLM13, Control, Ctrl-1

description:
Library name: Ctrl-1-RNA-seq
Ctrl-1-RNA-seq


title: MOLM13, 4C, shYTHDC1

description:
Library name: shYTHDC1-4C-seq
shYTHDC1-4C-seq


title: MOLM13, 4C, Control

description:
Library name: Ctrl-4C-seq
Ctrl-4C-seq


title: MOLM13, RIP, YTHDC1

description:
Library name: YTHDC1-RIP-seq
YTHDC1-RIP-seq

value: YTHDC1 (Abclonal, Cat#ab122340)


title: MOLM13, HiC, RNase

description:
Library name: RNase-HiC-seq
RNase-HiC-seq

value: WT


title: MOLM13, HiC, shYTHDC1

description:
Library name: shYTHDC1-HiC-seq
shYTHDC1-HiC-seq


title: MOLM13, ATAC, Control

description:
Library name: Ctrl-ATAC-seq
Ctrl-ATAC-seq


title: MOLM13, ATAC, shYTHDC1

description:
Library name: shYTHDC1-ATAC-seq
shYTHDC1-ATAC-seq


title: MOLM13, DRIP, shYTHDC1

description:
Library name: shYTHDC1-DRIP-seq
shYTHDC1-DRIP-seq


title: MOLM13, DRIP, Control

description:
Library name: Ctrl-DRIP-seq
Ctrl-DRIP-seq


title: MOLM13, DRIP, RNase

description:
Library name: RNase-DRIP-seq
RNase-DRIP-seq


title: H3K27ac, CHIP, shYTHDC1

description:
Library name: shYTHDC1-H3K27ac-ChIP-seq
shYTHDC1-H3K27ac-ChIP-seq

value: H3K27ac (Abclonal, Cat#A7253)


title: MOLM13, ATAC, RNase

description:
Library name: RNase-ATAC-seq
RNase-ATAC-seq


title: H3K27ac, CHIP, Control

description:
Library name: Ctrl-H3K27ac-ChIP-seq
Ctrl-H3K27ac-ChIP-seq


title: MOLM13, HiC, Control

description:
Library name: Ctrl-HiC-seq
Ctrl-HiC-seq