title: BMDM, W3

description: Library name: sample6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each smple

source_name: ID8 and BMDM in vitro co-culture

value: BMDM


title: BMDM, W2

status: Public on Jul 24 2025

type: SRA

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

country: China

institute: Zhejiang Chinese Medical University

description: Library name: sample5

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was extracted using TRIzol and the quality and quantity of total RNA were evaluated using an Agilent 2100 Bioanalyzer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

tag: cell type

tag: treatment

value: PBS


title: BMDM, W1

description: Library name: sample4


title: BMDM, C3

description: Library name: sample3

value: 40μM cisplatin


title: Day 194 SFTPCtdT/WT iAT2s

status: Public on Jul 25 2025

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

country: USA

institute: Center for Regenerative Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: H5 files

organism: Homo sapiens

growth_protocol: To generate iAT2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 16, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 17 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI+Y medium, consisting of complete serum-free differentiation medium (cSFDM) base supplemented with 3 µM CHIR99021, 10 ng/ml rhKGF (CK), 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 3’,5’-cyclic monophosphate sodium salt (Sigma), 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI), and 10 μM Y-27632 (Tocris). SFTPCtdTomato+ cells were sorted on days 45, 87, and 182 of differentiation. iAT2s were single-cell passaged in self-renewing 3D alveolosphere cultures approximately every 10-14 days through day 194. On day 194, all live cells, irrespective of SFTPCtdTomato expression, were sorted and encapsulated for scRNA-seq using the 10X Chromium System.

extract_protocol:
Cells were resuspended in buffer at a concentration of 1000 cells/ul and captured using a 10X chromium instrument (10X Chromium, Pleasanton, CA), following standard Chromium 10x guidelines.
Libraries were prepared using a Chromium Single-Cell 30 Library Kit (10X Genomics) and loaded on a NextSeq500 (Illumina) with a custom sequencing setting to obtain a sequencing depth of ~40k reads/cell

tag: cell line

value: Induced pluripotent stem cell-derived alveolar epithelial type 2 cells (iAT2s)

tag: genotype

value: SFTPC tdTomato/WT

value: CK+DCI+Y


title: BMDM, C1

description: Library name: sample1


title: BMDM, C2

description: Library name: sample2


title: CTRL2_d200_1

city: Tuebingen

first: Kevin

last: Achberger

address: Oesterbergstrasse 3

country: Germany

institute: University Tübingen

description: Library name: 24022a001

data_processing:
The sequencing aimed to achieve a depth of approximately >20 million clusters per sample. Read quality of RNA-seq data in fastq files was assessed using ngs-bits (2023_11-253-gc83b16dc), to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification. Reads were aligned using STAR v2.7.10b (Dobin et al.,2013) to the GRCh38 and alignment quality was analyzed using ngs-bits and visually inspected in the Integrative Genome Viewer (v2.15.4). Normalized read counts for all genes were obtained using Subread (v2.0.4).
Assembly: GRCh38
Supplementary files format and content: tsv files for raw, tpm, cpm, fpkm

source_name: Retinal organoids

growth_protocol: ROs were differentiated from hiPSCs based on a previously described protocol by Zhong et al., 2014 with additional modifications  (Achberger et al., 2019)

extract_protocol:
RNA was extracted using the Qiagen MicroRNeasy Kit. The concentration of RNA was measured using the Qubit Fluorometric Quantitation and RNA Broad-Range Assay (Thermo Fisher Scientific, USA). RNA Integrity Number RIN was determined using the Fragment Analyzer 5300 and the Fragment Analyzer RNA kit (Agilent Technologies, USA) and presented a good integrity (RIN>7).
For library preparation, the mRNA fraction was enriched using polyA capture from 100ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). Subsequently, libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext UDI UMI (NEB, USA) following the manufacturer’s instructions. To minimize technical batch effects, library preparations were performed using the liquid handler Biomek i7 (Beckman). The library molarity was determined by measuring the library size (approximately 400 bp) using the Fragment Analyzer 5300 and the Fragment Analyzer DNA HS NGS fragment kit (Agilent Technologies, USA) and the library concentration (>2 ng/µl) using Qubit Fluorometric Quantitation and dsDNA High sensitivity assay (Thermo Fisher Scientific, USA). The libraries were denaturated according to the manufacturer’s instructions, diluted to 150 pM and sequenced as paired-end 100bp reads on an Illumina NovaSeqX (Illumina, USA).

treatment_protocol: On day 0 of treatment, one RO was placed in each well of non-adherent 96-well plates in 80 µl BRDM with 10% FBS and 100 µM taurine (depending on the age of the ROs, the medium was additionally supplemented with RA, as mentioned above). AAVs were thawed in ice and added via a 50% medium change to obtain a genome copy number of 1.67x10^11 gc/well. On day 1, 20 µl of medium were added per well in order to have a final volume of 100 µl/well. The medium was changed twice per week by a 70% replacement. On day 7 the medium volume was increased to 150 µl/well and on day 35 the ROs were transferred to a 48-well plate with 300 µl culture medium. From day 49, the ROs were cultured in 500 µl/well. A. For the scRNA-seq analysis, the organoids were cultured for 70 days after treatment.

tag: tissue

value: Retinal organoids

value: hIPSC-derived Retinal Organoids

value: CTRL

tag: batch


title: LLC cells, control, rep3

city: Beijing

first: Lijian

last: Wu

state: Beijing

address: 30 Shuangqing Rd, Haidian District, Beijing

department: School of Medicine

institute: 清华大学

description:
Library name: Sample 6
Column name in count_DESeq2_normalized.csv: control-3

data_processing:
STAR v2.6.1d, Salmon v0.14.1, tximport v1.22.0, DESeq2 v1.34.0
RNA-seq reads were aligned to mm10 genome vM25 using STAR v2.6.1d.
Read alignments were quantified by Salmon v0.14.1 in its alignment-based mode.
Gene-level counts from quantification files were prepared for normalization and differential expression analysis with tximport v1.22.0.
Normalization and differential expression analysis were performed by DESeq2 v1.34.0 with default parameters.
Assembly: mm10
Supplementary files format and content: comma-delimited csv files include DESeq2 normalized values for each Sample

source_name: Lewis lung carcinoma (LLC)

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

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

treatment_protocol: Control and Calr KO LLC cells were seeded in 6-well plates and grown for 48 hours.

value: Lewis lung carcinoma (LLC)

value: murine lung cancer cell

value: WT

value: Cell culture, Untreated

value: batch 1


title: LLC cells, control, rep2

description:
Library name: Sample 5
Column name in count_DESeq2_normalized.csv: control-2


title: Sequencing data for 5hmC from CSD mouse cerebellum tissue by DDD-seq

city: Wuhan

first: Shan

last: Zhang

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

library_source: genomic

data_processing:
Sequencing reads were processed following previously reported methods. Briefly, data quality was assessed using FastQC software. Low-quality bases and adapter sequences were removed from the raw reads with Trimmomatic. The trimmed reads were then mapped to the reference genome (hg19) using Bismark. PCR duplicates and overlapping read pairs were eliminated and clipped utilizing Bismark and BamUtil.
Assembly: hg19
Supplementary files format and content: Average methylation fraction of 10kb regions in different groups.
Library strategy: DDD-seq

molecule: genomic DNA

source_name: mouse cerebellum tissue

extract_protocol:
Genomic DNA of mouse cerebellum tissues was extracted using Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA) according to the manufacturer's recommended procedure.
The DNA mixture was glycosylated and subsequently deaminated by SsdAcat. The deaminated DNA was amplificated by PCR with 5 cycles using pre-P5 primer, pre-P7 primer and Q5U Hot Start High-Fidelity DNA polymerase (New England Biolabs). After purification using 0.8× KAPA Pure beads, DNA products were then amplificated by PCR with 10 cycles using P5-index primer, P7-index primer and Q5 Hot Start High-Fidelity DNA polymerase (New England Biolabs). The PCR products were purified with 0.8× KAPA Pure beads and examined using 1.5% agarose gel electrophoresis. Library quality was assessed on the Agilent Bioanalyzer 2100 system. The library was then sequenced on an Illumina NovaSeq 6000 platform (Novogene Co., Ltd, Nanjing, China).

value: mouse cerebellum tissue

value: chronic sleep deprivation


title: Sequencing data for 5hmC from mouse cerebellum tissue by ACE-seq

data_processing:
Sequencing reads were processed following previously reported methods. Briefly, data quality was assessed using FastQC software. Low-quality bases and adapter sequences were removed from the raw reads with Trimmomatic. The trimmed reads were then mapped to the reference genome (hg19) using Bismark. PCR duplicates and overlapping read pairs were eliminated and clipped utilizing Bismark and BamUtil.
Assembly: hg19
Supplementary files format and content: Average methylation fraction of 10kb regions in different groups.
Library strategy: ACE-seq

value: normal/control


title: 4T1 splenic MDSC, Pooled input

city: Columbus

first: William

middle: E

last: Carson III

state: Ohio

address: 420 W 12th Street, 620 Tzagournis Research Facility

institute: The Ohio State University

description:
Library name: MDSC, POOLED INPUT
Files are made available for public use.

data_processing:
Sequences (50 bp, paired end) were aligned to the mouse genome (mm10) and to the Drosophila genome (dm6) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
DeepTools was used to convert filtered BAM files into bigWig format, employing a normalization method with a per-sample scaling factor calculated using the ratio of spike-in reads to mouse genome reads.
Peaks were identified using the MACS2 algorithm with a cutoff of FDR < 0.1 using an input. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Spleen

growth_protocol: RPMI 1640 media, 10% FBS, 1% antibiotic/antimycotic, 10 ng/mL IL-6 and GM-CSF

extract_protocol:
Cells were fixed for 15min by adding 1/10 volume of 37% formaldehyde (Sigma-Aldrich #F-8775) and quenched with 1/20 volume 2.5M glycine. Cells were washed with 0.5% Igepal/PBS and 1nM PMSF and snap-frozen before delivery to Active Motif.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs using the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation using automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification, the resulting DNA libraries were quantified and sequenced on Illumina NovaSeq 6000.

treatment_protocol: DMSO vehicle control or PLX51107 125 nM for 24 hours

value: Spleen

value: Primary cells

value: Myeloid cells

tag: chip antibody


title: 4T1 splenic MDSC, DMSO vehicle control 24 hour (BRD4 ChIP)

description:
Library name: MDSC DMSO, BRD4 ChIP
Files are made available for public use.

value: BRD4 (ActiveMotif, #AB_2813829)

value: DMSO control


title: 4T1 splenic MDSC, PLX51107 125nM 24 hour (BRD4 ChIP)

description:
Library name: MDSC PLX51107, BRD4 ChIP
Files are made available for public use.


title: LLC cells, Calr KO, rep1

description:
Library name: Sample 1
Column name in count_DESeq2_normalized.csv: Calr-1

value: Calr KO


title: LLC cells, control, rep1

description:
Library name: Sample 4
Column name in count_DESeq2_normalized.csv: control-1


title: LLC cells, Calr KO, rep3

description:
Library name: Sample 3
Column name in count_DESeq2_normalized.csv: Calr-3


title: LLC cells, Calr KO, rep2

description:
Library name: Sample 2
Column name in count_DESeq2_normalized.csv: Calr-2


title: Sequencing data for 5hmC from nomal mouse cerebellum tissue by DDD-seq


title: mINTS11_KO_HPC_R1

city: Miami

first: Pradeep

middle: Reddy

last: Cingaram

state: FL

address: 1501 N.W. 10th Avenue

department: Human genetics

institute: University of Miami

data_processing:
Raw fastq PRO-seq data were processed as described previosly (Beckedorff, Blumenthal et al. 2020). Briefly PRO-seq reads were trimmed by Cutadapt 1.14 (Martin, 2011) and Trimmomatic v0.32 (Bolger etal., 2014), and aligned to the human genome (hg19) genome or the drosophila genome (dm3) by bowtie 1.1.2 (Langmead etal., 2009). PRO-seq signalwas normalized by the number of reads mapped to spike-in dm3 genome, and then converted to bigwig data, which were used for downstream analyses.Quantification of nascent transcription per region was generated with an in-house script based on pyBigWig [Devon Ryan, B. G. F. R., doi:10.5281/zenodo.45238 (2016)] used to extract the normalized reads (CPM) per position from the bigwig files with a bin size of 1 bp upon merging the signal across two replicates.
Assembly: hg19 and mm10
Supplementary files format and content: The processed data files are in bigWig format : PRO-seq and rPRO-seq: bigwigs were normalized by Count Per Million produced from DeepTools2. PRO-seq and rPRO-seq: bigwigs were with Bedtools v2.26 with genomecov.

source_name: bone marrow cells

growth_protocol: HeLa  cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations.

extract_protocol:
To investigate hematopoietic progenitor cells (HPC), we employed an inducible whole-body knockout model. This involved crossing our animal model with Rosa26-CreERT2 (Cre recombinase-estrogen receptor T2) mice obtained from Jackson Laboratory (Stock No: 008463). Both control and Ints11 floxed mice received intraperitoneal injections of tamoxifen (75mg/Kg per day) for five consecutive days to induce the deletion of Ints11. To isolate HPC cells, we utilized the Direct Lineage Cell Depletion Kit and cKit (CD117) MicroBeads from Miltenyi Biotec, following the manufacturer's instructions. In brief, BM cells were initially stained with a cocktail of lineage marker antibodies directly coupled to MicroBeads and then passed through a column. Subsequently, the cells were further purified using cKit MicroBeads to enrich hematopoietic stem and progenitor cell populations.
For rPRO-seq experiments were conducted following established protocols (see detailed protocol in supplementary file 1). Initially, a mixture of HeLa nuclei and Drosophila S2 cell nuclei as spike-ins was prepared. Nuclear run-on assays were executed by incubating nuclei at 30°C for 3 minutes with 25 μM Biotin-11-ATP/UTP/CTP/GTP (PerkinElmer). Subsequently, total RNA was extracted using Direct-zol RNA Miniprep and fragmented with 0.2 M NaOH for 10 minutes on ice, followed by purification of biotinylated nascent RNAs using streptavidin beads M-280 (Invitrogen). The 3’ RNA adaptor ligation process employs pre-adenylated single-stranded DNAs (P-3’ App-DNA), and T4 RNA ligase 2, truncated KQ, is utilized, incubated at 25°C for 1 hour. Additionally, on-bead 5’ RNA end repair involved using RppH (NEB) to remove the 5' cap and repair the triphosphate, followed by PNK-mediated repair of the 5' hydroxyl. The hybridization of DBO involves incorporating the dimer blocking oligonucleotide (DBO) into the RNA within the DBO mix. This is followed by a thermocycler program and subsequent combination with the 5’ adaptor ligation mixes in the RNA DBO mix, with a 1-hour incubation at 25°C. After adapter ligation, SuperScript III reverse transcription was employed. PCR amplification generated 140–350 bp libraries, which were size-selected using AMpure XP beads and sequenced using single-read runs on a NovaSeq 6000.

value: bone marrow cells

tag: fraction

value: rPROseq RNA


title: mINTS11_WT_HPC_R2


title: mINTS11_KO_HPC_R2


title: EV extracted from Abx treated mouse plasma sample6_3

city: Los Angeles

first: Brian

middle: George

last: Dias

state: CA

address: 4650 Sunset Blvd

department: Division of Endocrinology

institute: Children's Hospital Los Angeles

description: Library name: Sample6_3_Abx

data_processing:
library prep with QIAseq UPXome RNA seq library kit (QIAGEN)
Illumina MiSeq Sequencing
STAR aligner
KrakenUnique
Assembly: Genome Research Consortium mouse genome version 39 (GRCm39); krakendb-2023-08-08-MICROBIAL
Supplementary files format and content: tab-separated text file, metagenome species count

source_name: Plasma

extract_protocol:
Norgen Plasma/Serum RNA Purification Kit
QIAseq UPXome RNA seq library kit (QIAGEN)

treatment_protocol: ProteinaseK, RNAse, and DNAse

value: Plasma

value: Extracellular vesicles

value: Abx


title: EV extracted from Control mice (no ABX) sample7_2

description: Library name: Sample7_3_Cont

value: Cont


title: EV extracted from Control mice (no ABX) sample7_3

description: Library name: Sample8_1_Cont


title: mINTS11_WT_HPC_R1


title: EV extracted from Abx treated mouse plasma sample2

description: Library name: Sample2_Abx


title: EV extracted from Control mice (no ABX) sample7_1

description: Library name: Sample7_1_Cont


title: EV extracted from Control mice (no ABX) sample4

description: Library name: Sample4_Cont


title: EV extracted from Abx treated mouse plasma sample6_1

description: Library name: Sample6_1_Abx


title: EV extracted from Control mice (no ABX) sample3

description: Library name: Sample3_Cont


title: EV extracted from Control mice (no ABX) sample1

description: Library name: Sample1_Cont


title: EV extracted from Abx treated mouse plasma sample6_2

description: Library name: Sample6_2_Abx


title: EV extracted from Abx treated mouse plasma sample3

description: Library name: Sample3_Abx


title: AGM-MW16 week 16

city: Guildford

first: Falko

last: Steinbach

address: Daphne Jackson Road

department: School of Veterinary Medicine

country: United Kingdom

institute: University of Surrey

description: Library name: Sample 13

data_processing:
sequencing reads QA
adapters removal
Reads base correction and filtering
Reads mapping and counting
Sample outliers removal
Normalization
Differential expression calculation
Assembly: GCF_024166365.1
Supplementary files format and content: A tab-separated values (TSV) file containing normalized gene counts, with genes in rows and samples in columns.

organism: Elephas maximus

source_name: blood

extract_protocol:
TRIzol followed by RNeasy MinElute Cleanup Kit
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was utilised in conjunction with the NEBNext rRNA Depletion Kit

treatment_protocol: 300 µl of lithium heparinised blood was transferred to 2-ml tubes containing rEE2 or rMCP antigens, prediluted in 50 µl PBS; final concentration of 10 µg ml-1

value: blood

value: Antigen


title: AGM-MW19 week 19

description: Library name: Sample 14


title: PBS-SW20 week 20

description: Library name: Sample 4

value: PBS


title: PBS-SW16 week 16

description: Library name: Sample 3


title: AGM-SW16 week 16

description: Library name: Sample 10


title: PBS-MW16 week 16

description: Library name: Sample 7


title: AGM-MW2 week 2

description: Library name: Sample 12


title: PBS-MW19 week 19

description: Library name: Sample 8


title: AGM-SW20 week 20

description: Library name: Sample 11


title: PBS-SW2 week 2

description: Library name: Sample 2


title: PBS-SW1 week 1

description: Library name: Sample 1


title: EV RNAi_3

city: kunming

first: meng

last: zhou

state: yunnan

address: tuanjiexiang

institute: Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China;

description: Library name: sample 6

data_processing:
Raw reads were trimmed with trim_galore, mapped to hg38 using HISAT 2.2.1, and counted in genes by featureCounts. Normalized to CPM, differential expression was analyzed with DESeq2 (≥10 reads in at least one condition; adjusted P<0.01, |log2FC|≥1)
Data Quality Control (Obtaining Clean Data) The Raw Data (in FASTQ format) from the sequencer was filtered: Reads containing adapters were removed. Low-quality Reads were removed (those with an N proportion >10% or with bases having a quality value Q≤10 accounting for more than 50% of the entire Read). High-quality Clean Data was obtained, and indicators such as base quality (Q30 ≥89.14%) and GC content were statistically analyzed.
Alignment with Reference Genome Reference genome version: Caenorhabditis_elegans.GCF_000002985.6.genome.fa. Clean Reads were aligned to the reference genome using HISAT2 software to obtain positioning information. The alignment results were assembled using StringTie software to reconstruct the transcriptome.
Assembly: Caenorhabditis_elegans.GCF_000002985.6.genome.fa
Supplementary files format and content: xlsx files include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: Whole Organism

growth_protocol: C. elegans N2 were maintained on nematode growth media (NGM) and fed with E.coli OP50

extract_protocol:
The C. elegans N2 were subjected to hda-5RNAi and empty vector RNAi until reach to adult. Then the worms were collected and washed by M9 buffer for three times following re-suspended in PBS, and frozen immediately in liquid nitrogen for RNA sequencing. RNA sequencing was carried out by Biomarker Technologies (BMK) GmbH (Beijing, China). Total RNA of worms were extracted by using RNeasy Plus Mini Kit (Qiagen) and assessed for quality by NanoDrop, Qubit 2.0 and Agilent 2100.
Qualified RNA were processed for library construction. The procedures are described as follow: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within certain size range. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

treatment_protocol: C. elegans N2 L1 larvae were fed with RNAi strains which targe hda-5 or carry empty vector until reach to adulthood.

value: Whole Organism

value: Bristol N2


title: PBS-MW2 week 2

description: Library name: Sample 6


title: mouse kidney, Enalapril, rep2

first: Haochen

last: Wang

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

data_processing:
FastQC (version 0.11.5) software was first used for data quality control. Raw paired-end sequencing reads were trimmed by Trim Galore (version 0.6.10) software to remove adapter sequences and low quality reads. The high quality RNA-seq reads were mapped to the hg38/mm10 genome by using HISAT2 (version 2.2.1) software. SAMtools (version 1.17) software was then used to convert the generated sam files to bam files. To qualify gene expression, the number of reads mapped to each gene was counted using featureCounts (version 2.0.1) software.
Assembly: hg38/mm10
Supplementary files format and content: CSV files include raw counts of each sample

source_name: mouse kidney tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the instructions.
The extracted total RNA was then sent to Novogene for subsequent cDNA library construction.

value: mouse kidney tissue

value: WT

value: Enaparil treatment


title: EV RNAi_1

description: Library name: sample 4


title: EV RNAi_2

description: Library name: sample 5


title: hda-5 RNAi_2

description: Library name: sample 2


title: hda-5 RNAi_3

description: Library name: sample 3


title: hda-5 RNAi_1

description: Library name: sample 1


title: PBS-MW1 week1

description: Library name: Sample 5


title: AGM-SW2 week 2

description: Library name: Sample 9


title: TBB893

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: rejection archetype cluster (nr, tcmr/mixed, nkrl, lowsft)

value: NR


title: TBB894

value: NKRL


title: TBB896

value: lowSFT


title: TBB878


title: TBB890


title: TBB887


title: TBB884


title: TBB895

value: TCMR/Mixed


title: TBB891


title: TBB888


title: TBB882


title: TBB883


title: TBB879


title: TBB876


title: TBB870


title: TBB873


title: TBB892


title: TBB874


title: TBB885


title: TBB875


title: TBB877


title: TBB889


title: Aged + Control + ICH, replicate 3, scRNA-seq

city: Chengdu

first: Xiao-Yi

last: Xiong

address: 37 Shierqiao Road, 610075, Chengdu, China

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
We performed alignment to this amended reference using BSCMatrix (http://www.bmkmanu.com/portfolio/tools) to obtained expression matrices, which employs the STAR sequence aligner
Assembly: GRCm38_release95
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: brain

extract_protocol:
The perihematomal brain tissues from aged ICH mice were dissociated enzymatically to obtain a single-cell suspension with the self-prepared hydrolysate or the hydrolysate kit (MACS Mouse Tumor Dissociation kit DS_130-096-730). Next, Hank’s Balanced Salt Solution with calcium and magnesium (Gibco, Germany) was added to stop the enzymatic reaction. A 70 and 40 μm strainer was used to filter the resulting cell suspension, followed by centrifuging at 300 × g, 4 °C for 10 min. Then, myelin was removed by centrifugation on a 22% Percoll gradient. Briefly, cells were suspended in 25 mL Percoll solution [18.9 mL gradient buffer containing 5.65 mM NaH2PO4H2O, 20 mM Na2HPO42 (H2O), 135 mM NaCl, 5 mM KCl, 10 mM glucose, 7.4 pH; 5.5 mL Percoll (GE Healthcare, Germany); 0.6 mL 1.5 M NaCl)], overlayered with 5 mL PBS and centrifuged for 20 min at 950 × g and 4 °C, without acceleration and brakes.
We prepared single cell suspensions from cultured cell lines and single cells were suspended in PBS containing 0.04% BSA. The cell suspension was loaded onto the BMKMANU C1000 Chip and ran the Droplet Generation Equipment to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation.captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer's protocol. The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100.

value: brain

value: neural cells and myeloid cells

tag: strain

tag: age

value: 18 months old

value: Control + ICH


title: TBB886


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title: Patient ID: MSH009 – Post-PPI responsive esophageal biopsy (CKA)

city: Ann Arbor

first: Simon

last: Hogan

state: Michigan

address: 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan

description:
Library name: CKA
Column name in Chehade_JCII_feature_counts.txt: CKA

data_processing:
The FASTQC program and Trimmomatic tools were used to examine the quality of raw reads and filtering poor quality reads, respectively.
Genome indexing was performed using Bowtie2 and the reads were aligned to the human reference genome (GRCh38) using HiSAT2 program with the default options for paired-ends
Read counts were generated using the feature-counts function from the SourceForge Subread package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Esophageal biopsy tissue

extract_protocol:
Total RNA was extracted from tissues obtained from esophageal biopsies using Rneasy Plus Universal Mini Kit from Qiagen
0.5 micrograms of Total RNA was used to synthesize cDNA libraries using Illumina's TruSeq Stranded mRNA Sample prep kit using Ribo-Zero Plus for rRNA depletion.

value: Esophageal biopsy tissue

value: Post PPI-treatment


title: Patient ID: MSH008 – Post-PPI responsive esophageal biopsy (CHX)

description:
Library name: CHX
Column name in Chehade_JCII_feature_counts.txt: CHX


title: Patient ID: MSH010 – Post-PPI responsive esophageal biopsy (CHH)

description:
Library name: CHH
Column name in Chehade_JCII_feature_counts.txt: CHH


title: Patient ID: MSH004 – Post-PPI responsive esophageal biopsy (CGE)

description:
Library name: CGE
Column name in Chehade_JCII_feature_counts.txt: CGE


title: TBB426


title: TBB408


title: TBB416


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title: TBB399


title: TBB410


title: TBB415


title: TBB413


title: TBB421


title: TBB418


title: TBB423


title: Patient ID: MSH005 – Post-PPI responsive esophageal biopsy (BQZ)

description:
Library name: BQZ
Column name in Chehade_JCII_feature_counts.txt: BQZ


title: TBB411


title: TBB400


title: TBB424


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title: TBB414


title: TBB403


title: TBB404


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title: TBB402


title: TBB412


title: TBB401


title: Patient ID: MSH008 –Pre-PPI responsive esophageal biopsy (CDS)

description:
Library name: CDS
Column name in Chehade_JCII_feature_counts.txt: CDS

value: Pre-PPI treatment


title: Patient ID: MSH009 – Pre-PPI responsive esophageal biopsy (CFV)

description:
Library name: CFV
Column name in Chehade_JCII_feature_counts.txt: CFV


title: Patient ID: MSH010 –Pre-PPI responsive esophageal biopsy (CCQ)

description:
Library name: CCQ
Column name in Chehade_JCII_feature_counts.txt: CCQ


title: Patient ID: MSH004 – Pre-PPI responsive esophageal biopsy (CCI)

description:
Library name: CCI
Column name in Chehade_JCII_feature_counts.txt: CCI


title: Patient ID: MSH005 – Pre-PPI responsive esophageal biopsy (BNT)

description:
Library name: BNT
Column name in Chehade_JCII_feature_counts.txt: BNT


title: Patient ID: MSH022 – Post-PPI  unresponsive patient esophageal biopsy (BNW)

description:
Library name: BNW
Column name in Chehade_JCII_feature_counts.txt: BNW


title: Patient ID: MSH020 – Post-PPI unresponsive patient esophageal biopsy (BGX)

description:
Library name: BGX
Column name in Chehade_JCII_feature_counts.txt: BGX


title: Patient ID: MSH027 – Post-PPI unresponsive patient esophageal biopsy (BEQ)

description:
Library name: BEQ
Column name in Chehade_JCII_feature_counts.txt: BEQ


title: TBB397


title: Patient ID: MSH028 – Pre-PPI unresponsive patient esophageal biopsy (BFH)

description:
Library name: BFH
Column name in Chehade_JCII_feature_counts.txt: BFH


title: Patient ID: MSH022 – Pre-PPI unresponsive patient esophageal biopsy (BJW)

description:
Library name: BJW
Column name in Chehade_JCII_feature_counts.txt: BJW


title: Patient ID: MSH029 – Pre-PPI unresponsive patient esophageal biopsy (BKK)

description:
Library name: BKK
Column name in Chehade_JCII_feature_counts.txt: BKK


title: Patient ID: MSH029 – Post-PPI  unresponsive patient esophageal biopsy (BPY)

description:
Library name: BPY
Column name in Chehade_JCII_feature_counts.txt: BPY


title: TBB398


title: Patient ID: MSH028 – Post-PPI  unresponsive patient esophageal biopsy (BMS)

description:
Library name: BMS
Column name in Chehade_JCII_feature_counts.txt: BMS


title: Patient ID: MSH027 – Pre-PPI unresponsive patient esophageal biopsy (BBZ)

description:
Library name: BBZ
Column name in Chehade_JCII_feature_counts.txt: BBZ


title: TBB407


title: TBB394


title: TBB388


title: Healthy control esophageal biopsy (CBM)

description:
Library name: CBM
Column name in Chehade_JCII_feature_counts.txt: CBM

value: no treatment


title: TBB387


title: TBB396


title: TBB395


title: Patient ID: MSH020 – Pre-PPI unresponsive patient esophageal biopsy (BEL)

description:
Library name: BEL
Column name in Chehade_JCII_feature_counts.txt: BEL


title: TBB389


title: TBB392


title: TBB384


title: TBB385


title: TBB386


title: TBB393


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title: TBB382


title: cord blood CD34+ cell with empty vector control assayed with IgG antibody

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

description: Library name: SJNORM098172_C1-CD34_MPC_day42-IGG-AB14

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim Galore (v0.4.4, RRID:SCR_011847) from cutadapt (RRID:SCR_011841) and FASTQC analysis. A default quality score cutoff of Q20 is used. Quality reads were mapped to the GRCh38/hg38 human genome assembly assayed with bwa (v0.7.12-r1039, RRID:SCR_010910) and converted to a bam file by samtools (v1.2, RRID:SCR_002105).
Duplicate reads were marked with biobambam2 (v2.0.87, RRID:SCR_003308). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name assayed with biobambam2 (v2.0.87, RRID:SCR_003308). bedtools101 (v2.17.0, RRID:SCR_006646) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4, RRID:SCR_005780) and visualized assayed with Integrative Genomics Viewer (IGV, v2.17.4, RRID:SCR_011793).
Peak calling was performed assayed with Macs2 (v2.1.1, RRID:SCR_013291) targeting narrow peaks and SICER (v1.1, RRID:SCR_010843) targeting broad peaks with following command lines. macs2 callpeak -t ${treatmentBed} -c ${controlBed} -f BEDPE -g hg38 --keep-dup all -n ["output file"] -q [0.05] sicer -t ${treatmentBed} -c ${controlBed} -s hg38 -rt 1 -w 200 -f 200 -egf 0.8-6 -g 600 -fdr 0.00001 Peaks called by macs2 or SICER were filtered according to peak scores (>50, corresponding FDR<1.0e-5)  Enrichment of transcription factor binding motifs was assessed by the findMotifsGenome command from HOMER (v4.10, RRID:SCR_010881) with default settings, using merged BED files of SICER and macs2 peaks with statistical significance (peak score > 50 corresponding to FDR < 1.0e-5) as inputs. Top enriched motifs from Known Motif Enrichment for each HA-tagged NUP98-FOs are exported for figures.
PBS (probability of being signal, v02072024) was performed by default settings
Assembly: GRCh38/hg38 human genome assembly
Supplementary files format and content: BAM files, bed files, NarrowPeak files, bigwig files
Library strategy: CUT&Run

source_name: cord blood CD34+ cell

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12-16 cycles depending on input DNA amount

value: cord blood CD34+ cell

value: IgG (Epicypher Cat# 13-0042, RRID:AB_2923178)


title: cord blood CD34+ cell with empty vector control  assayed with H3K27ac antibody

description: Library name: SJNORM098172_C1-CD34_MPC_day42-H3K4me3-AB12

value: H3K27ac (Cell Signaling, 8173S, clone:D5E4, RRID:AB_10949503)


title: TBB376


title: TBB375


title: TBB377


title: SJAML001441_R3 (10X 5'GEX)

description:
Library name: SJAML001441_R3
10X 5' GEX library preparation

data_processing:
The feature-barcode count data matrix for each sample was generated from raw sequence FASTQ files using Cell Ranger (v3.0, RRID:SCR_017344) and the GRCh38/hg38 human genome assembly
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files for individual samples containing single cell data (barcodes, genes, matrix)

source_name: primary acute myeloid leukemia cell

extract_protocol:
Frozen patient samples were thawed followed by dead cell removal using EasySep Dead Cell Removal Kit (StemCell Technologies, 17899) and resuspended in DPBS (Dulbecco's Phosphate Buffered Saline ,Gibco,14190144)+0.04%BSA (Bovine Serum Albumin, Sigma-Aldrich, A7030-50G). Cultured cbCD34 cells are directly suspended in DPBS+0.04% BSA. Cells were prepared and quantified following the 10x Genomics cell thawing protocol for single cell assays (CG000447, rev B).
Cells were isolated for single-cell barcoding and 3’ (NUP98::NSD1 diagnosis and relapse pair) and 5’ (NUP98::KDM5A and NUP98::RAP1GDS1, CD34 models) GEX library preparation using the 10x Genomics Chromium Controller Genetic Analyzer (RRID:SCR_019326) and Next-GEM Single Cell V(D)J Reagent Kit (PN-1000128, PN-1000167) following the manufacturer’s protocol. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 (RRID:SCR_016387) using SP Reagent kit v1.5 (Illumina, 20028401).

value: primary acute myeloid leukemia cell

tag: time


title: cord blood CD34+ cell with empty vector control assayed with NUP98 antibody

description: Library name: SJNORM098172_C1-CD34_MPC_day42-NUP98-AB2

value: NUP98 (Abcam Cat# ab50610, clone:2H10, RRID:AB_881769)


title: SJAML061252_R3 (10X 3'GEX)

description:
Library name: 3227502_SJAML061252_R3_10x_3GEX
10X 3' GEX library preparation


title: SJAML001441_D2 (10X 5'GEX)

description:
Library name: SJAML001441_D2
10X 5' GEX library preparation


title: SJAML015363_D7 (10X 3'GEX)

description:
Library name: 3227503_SJAML015363_D7_10x_3GEX
10X 3' GEX library preparation


title: SJAML016582_D4 (10X 3'GEX)

description:
Library name: 3227501_SJAML016582_D4_10x_3GEX
10X 3' GEX library preparation


title: cord blood CD34 + NUP98::KDM5A+Cas9+gRNA_RB1_2 (10X 3'GEX)

description:
Library name: 3198498_SJNORM095805_C1-CD34_NK5_re_3_SM27_RB1_g3_day35
10X 3' GEX library preparation


title: cord blood CD34 + NUP98::KDM5A+Cas9+gRNA_WT1_1 (10X 3'GEX)

description:
Library name: 3198499_SJNORM095806_C1-CD34_NK5_re_3_CAGE74_WT1_g2_day35
10X 3' GEX library preparation


title: cord blood CD34 + NUP98::KDM5A+Cas9+gRNA_RB1_1 (10X 3'GEX)

description:
Library name: 3198497_SJNORM095804_C1-CD34_NK5_re_3_SM27_RB1_g2_day35
10X 3' GEX library preparation


title: TBB370


title: TBB371


title: TBB372

value: NR


title: TBB374

value: NKRL


title: cord blood CD34 + NUP98::KDM5A+Cas9_gRNA_AAVS_control (10X 3'GEX)

description:
Library name: 3198496_SJNORM095803_C1-CD34_NK5_re_3_RB20_PPP1R12C_g2_day35
10X 3' GEX library preparation


title: TBB367


title: TBB366


title: TBB373


title: TBB368


title: TBB369


title: SJTALL005_D2 (10X 3'GEX)

description:
Library name: 2668862_SJTALL005005_D2_10x_3GEX
10X 3' GEX library preparation

source_name: primary acute lymphoblastic leukemia cell


title: SJAML031254_D5 (10X 3'GEX)

description:
Library name: 2668861_SJAML031254_D5_10x_3GEX
10X 3' GEX library preparation


title: SJAML061263_R3 (10X 3'GEX)

description:
Library name: 2668859_SJAML061263_R3_10x_3GEX
10X 3' GEX library preparation


title: SJALL040121_D2 (10X 3'GEX)

description:
Library name: 2668860_SJALL040121_D2_10x_3GEX
10X 3' GEX library preparation

value: primary acute lymphoblastic leukemia cell


title: SJAML001441_R7 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27me3 antibody

description: Library name: SJAML001441_R7_CnR-H3K27me3-AB5

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim Galore (v0.4.4, RRID:SCR_011847) from cutadapt (RRID:SCR_011841) and FASTQC analysis. A default quality score cutoff of Q20 is used. Quality reads were mapped to the GRCh38/hg38 human genome assembly using bwa (v0.7.12-r1039, RRID:SCR_010910) and converted to a bam file by samtools (v1.2, RRID:SCR_002105).
Duplicate reads were marked with biobambam2 (v2.0.87, RRID:SCR_003308). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87, RRID:SCR_003308). bedtools101 (v2.17.0, RRID:SCR_006646) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4, RRID:SCR_005780) and visualized using Integrative Genomics Viewer (IGV, v2.17.4, RRID:SCR_011793).
Peak calling was performed using Macs2 (v2.1.1, RRID:SCR_013291) targeting narrow peaks and SICER (v1.1, RRID:SCR_010843) targeting broad peaks with following command lines. macs2 callpeak -t ${treatmentBed} -c ${controlBed} -f BEDPE -g hg38 --keep-dup all -n ["output file"] -q [0.05] sicer -t ${treatmentBed} -c ${controlBed} -s hg38 -rt 1 -w 200 -f 200 -egf 0.8-6 -g 600 -fdr 0.00001 Peaks called by macs2 or SICER were filtered according to peak scores (>50, corresponding FDR<1.0e-5)
PBS (probability of being signal, v02072024) was performed by default settings
Assembly: GRCh38/hg38 human genome assembly
Supplementary files format and content: BAM files, bed files, NarrowPeak files, bigwig files
Library strategy: CUT&RUN

tag: expression vector

value: H3K27me3 (Cell Signaling, 9733, clone:C36B11, RRID:AB_2616029)


title: TBB380


title: SJAML061263_R4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27me3 antibody

description: Library name: SJAML061263_R4_CnR-H3K27me3-AB4


title: SJAML061263_R4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27ac antibody

description: Library name: SJAML061263_R4_CnR-H3K27Ac-AB5


title: TBB364


title: SJAML061263_R4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K4me3 antibody

description: Library name: SJAML061263_R4_CnR-H3K4me3-AB12

value: H3K4me3 (Epicypher, 13-0041, Mixed Monoclonal, RRID:AB_3076423)


title: SJAML061263_R4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with NUP98 antibody

description: Library name: SJAML061263_R4_CnR-NUP98-AB2


title: TBB362


title: TBB361

value: TCMR/Mixed


title: TBB365


title: SJAML061263_R4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with IgG antibody

description: Library name: SJAML061263_R4_CnR-IGG-AB14


title: SJAML015347_D3 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27me3 antibody

description: Library name: SJAML015347_D3_CnR-H3K27me3-AB4


title: TBB363


title: TBB360


title: SJAML015347_D3 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27ac antibody

description: Library name: SJAML015347_D3_CnR-H3K27Ac-AB5


title: TBB359


title: TBB356


title: SJAML015347_D3 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K4me3 antibody

description: Library name: SJAML015347_D3_CnR-H3K4me3-AB12


title: SJAML015347_D3 (primary acute myeloid leukemia with NUP98::NSD1) assayed with NUP98 antibody

description: Library name: SJAML015347_D3_CnR-NUP98-AB2


title: TBB358


title: SJAML015347_D3 (primary acute myeloid leukemia with NUP98::NSD1) assayed with IgG antibody

description: Library name: SJAML015347_D3_CnR-IGG-AB14


title: SJAML031570_D2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27me3 antibody

description: Library name: SJAML031570_D2_CnR-H3K27me3-AB4


title: SJAML031570_D2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K4me3 antibody

description: Library name: SJAML031570_D2_CnR-H3K4me3-AB12


title: SJAML031570_D2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27ac antibody

description: Library name: SJAML031570_D2_CnR-H3K27Ac-AB5


title: SJAML031570_D2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with NUP98 antibody

description: Library name: SJAML031570_D2_CnR-NUP98-AB2


title: SJAML031570_D2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with IgG antibody

description: Library name: SJAML031570_D2_CnR-IGG-AB14


title: Healthy control esophageal biopsy (BOP)

description:
Library name: BOP
Column name in Chehade_JCII_feature_counts.txt: BOP


title: Healthy control esophageal biopsy (BIK)

description:
Library name: BIK
Column name in Chehade_JCII_feature_counts.txt: BIK


title: Healthy control esophageal biopsy (ATP)

description:
Library name: ATP
Column name in Chehade_JCII_feature_counts.txt: ATP


title: Healthy control esophageal biopsy (CDA)

description:
Library name: CDA
Column name in Chehade_JCII_feature_counts.txt: CDA


title: SJAML016570_R2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27me3 antibody

description: Library name: SJAML016570_R2_CnR-H3K27me3-AB4


title: cord blood CD34+ cell with empty vector control  assayed with H3K4me3 antibody

description: Library name: SJNORM098172_C1-CD34_MPC_day42-H3K27Ac-AB5


title: SJAML016570_R2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27ac antibody

description: Library name: SJAML016570_R2_CnR-H3K27Ac-AB5


title: SJAML016570_R2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K4me3 antibody

description: Library name: SJAML016570_R2_CnR-H3K4me3-AB12


title: SJAML016570_R2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with NUP98 antibody

description: Library name: SJAML016570_R2_CnR-NUP98-AB2


title: SJAML016570_R2 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with IgG antibody

description: Library name: SJAML016570_R2_CnR-IGG-AB14


title: SJALL040121_D3 (primary acute lymphoblastic leukemia with NUP98::KDM5A) assayed with H3K27ac antibody

description: Library name: SJALL040121_D3_CnR-H3K27Ac-AB5


title: SJALL040121_D3 (primary acute lymphoblastic leukemia with NUP98::KDM5A) assayed with H3K4me3 antibody

description: Library name: SJALL040121_D3_CnR-H3K4me3-AB12


title: SJALL040121_D3 (primary acute lymphoblastic leukemia with NUP98::KDM5A) assayed with H3K27me3 antibody

description: Library name: SJALL040121_D3_CnR-H3K27me3-AB4


title: SJALL040121_D3 (primary acute lymphoblastic leukemia with NUP98::KDM5A) assayed with IgG antibody

description: Library name: SJALL040121_D3_CnR-IGG-AB14


title: SJAML001441_R7 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27ac antibody

description: Library name: SJAML001441_R7_CnR-H3K27Ac-AB5


title: SJAML001441_R7 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K4me3 antibody

description: Library name: SJAML001441_R7_CnR-H3K4me3-AB12


title: SJAML031736_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27me3 antibody

description: Library name: SJAML031736_D4_CnR-H3K27me3-AB4


title: SJAML001441_R7 (primary acute myeloid leukemia with NUP98::NSD1) assayed with IgG antibody

description: Library name: SJAML001441_R7_CnR-IGG-AB14


title: SJAML031736_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27ac antibody

description: Library name: SJAML031736_D4_CnR-H3K27Ac-AB5


title: SJAML031736_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K4me3 antibody

description: Library name: SJAML031736_D4_CnR-H3K4me3-AB12


title: TBB379


title: TBB353


title: TBB381


title: TBB343


title: SJAML031736_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with NUP98 antibody

description: Library name: SJAML031736_D4_CnR-NUP98-AB2


title: TBB330


title: TBB378


title: TBB338


title: TBB350


title: TBB349


title: TBB333


title: TBB347


title: TBB337


title: TBB352


title: TBB339


title: TBB336


title: TBB345


title: TBB355


title: TBB335


title: TBB354


title: TBB340


title: TBB357


title: TBB346


title: TBB342


title: TBB351


title: TBB332


title: TBB344


title: SJAML031736_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with IgG antibody

description: Library name: SJAML031736_D4_CnR-IGG-AB14


title: TBB331


title: SJAML031254_D6 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with H3K27me3 antibody

description: Library name: SJAML031254_D6_CnR-H3K27me3-AB4


title: SJAML031254_D6 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with H3K27ac antibody

description: Library name: SJAML031254_D6_CnR-H3K27Ac-AB5


title: TBB341


title: TBB348


title: TBB334


title: SJAML031254_D6 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with IgG antibody

description: Library name: SJAML031254_D6_CnR-IGG-AB14


title: SJAML031254_D6 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with NUP98 antibody

description: Library name: SJAML031254_D6_CnR-NUP98-AB2


title: SJAML031434_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27me3 antibody

description: Library name: SJAML031434_D4_CnR_H3K27me3_AB4


title: SJAML031434_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with IgG antibody

description: Library name: SJAML031434_D4_CnR_IGG_AB14


title: SJAML031434_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K4me3 antibody

description: Library name: SJAML031434_D4_CnR_H3K4me3_AB12


title: TBB327


title: TBB328


title: SJAML016570_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K4me3 antibody

description: Library name: SJAML016570_D4_CnR_H3K4me3_AB12


title: SJAML031254_D6 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with H3K4me3 antibody

description: Library name: SJAML031254_D6_CnR-H3K4me3-AB12


title: TBB329


title: SJAML016570_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with IgG antibody

description: Library name: SJAML016570_D4_CnR_IGG_AB14


title: SJAML016570_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27me3 antibody

description: Library name: SJAML016570_D4_CnR_H3K27me3_AB4


title: SJAML031434_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27ac antibody

description: Library name: SJAML031434_D4_CnR_H3K27Ac_AB5


title: TBB324


title: SJAML016570_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with H3K27ac antibody

description: Library name: SJAML016570_D4_CnR_H3K27Ac_AB5


title: TBB325


title: TBB326


title: SJAML031434_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with NUP98 antibody

description: Library name: SJAML031434_D4_CnR_NUP98_AB2


title: SJAML001409_R2 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with H3K27me3 antibody

description: Library name: SJAML001409_R2_CnR-H3K27me3-AB4


title: TBB320


title: TBB321


title: TBB323


title: TBB317

value: lowSFT


title: SJAML016570_D4 (primary acute myeloid leukemia with NUP98::KDM5A) assayed with NUP98 antibody

description: Library name: SJAML016570_D4_CnR_NUP98_AB2


title: TBB313


title: TBB318


title: TBB316


title: TBB315


title: TBB314


title: TBB322


title: TBB319


title: SJAML001409_R2 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with H3K4me3 antibody

description: Library name: SJAML001409_R2_CnR-H3K4me3-AB12


title: SJAML001409_R2 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with H3K27ac antibody

description: Library name: SJAML001409_R2_CnR-H3K27Ac-AB5


title: SJAML001409_R2 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with IgG antibody

description: Library name: SJAML001409_R2_CnR-IGG-AB14


title: SJAML001409_R2 (primary acute myeloid leukemia with NUP98::RAP1GDS1) assayed with NUP98 antibody

description: Library name: SJAML001409_R2_CnR-NUP98-AB1


title: SJAML032187_D4 (primary acute myeloid leukemia with RUNX1::RUNX1T1) assayed with H3K4me3 antibody

description: Library name: SJAML032187_D4_CnR_H3K4me3_AB12


title: SJAML032187_D4 (primary acute myeloid leukemia with RUNX1::RUNX1T1) assayed with NUP98 antibody

description: Library name: SJAML032187_D4_CnR_NUP98_AB2


title: TBB311


title: CHRF-288-11 (megakaryocytic acute myeloid leukemia cell line) assayed with NUP98 antibody

description: Library name: SJAML080046_C1_CHRF_R001_CnR_NUP98_AB2


title: SJAML032187_D4 (primary acute myeloid leukemia with RUNX1::RUNX1T1) assayed with IgG antibody

description: Library name: SJAML032187_D4_CnR_IGG_AB14


title: TBB310


title: TBB312


title: TBB307


title: SJAML001441_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27ac antibody

description: Library name: SJAML001441_D4_CnR_H3K27Ac_AB5


title: TBB309


title: TBB305


title: TBB306


title: SJAML001441_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with IgG antibody

description: Library name: SJAML001441_D4_CnR_IGG_AB14


title: TBB303


title: TBB308


title: TBB302


title: SJAML010730_D5 (primary acute myeloid leukemia with UBTF tandem duplication) assayed with NUP98 antibody

description: Library name: SJAML010730_D5_CnR_NUP98_AB2


title: SJAML010730_D5 (primary acute myeloid leukemia with UBTF tandem duplication) assayed with IgG antibody

description: Library name: SJAML010730_D5_CnR_IGG_AB14


title: SJAML010730_D5 (primary acute myeloid leukemia with UBTF tandem duplication) assayed with menin antibody

description: Library name: SJAML010730_D5_CnR_MEN1_AB1

value: menin (Bethyl Cat# A300-105A, polyclonal, RRID:AB_2143306)


title: SJAML032187_D4 (primary acute myeloid leukemia with RUNX1::RUNX1T1) assayed with menin antibody

description: Library name: SJAML032187_D4_CnR_MEN1_AB1


title: SJAML010730_D5 (primary acute myeloid leukemia with UBTF tandem duplication) assayed with H3K4me3 antibody

description: Library name: SJAML010730_D5_CnR_H3K4me3_AB12


title: TBB301


title: TBB300


title: cord blood CD34+ cell with NUP98::KDM5A assayed with NUP98 antibody (Abcam Cat# ab50610)

description: Library name: SJNORM077742_C1-CD34_ntag-NUP-KDM-NUP98-AB2

value: lentiviral overexpression of NUP98::KDM5A


title: TBB304


title: SJAML001441_D4 (primary acute myeloid leukemia with NUP98::NSD1) assayed with H3K27me3 antibody

description: Library name: SJAML001441_D4_CnR_H3K27me3_AB4


title: cord blood CD34+ cell with NUP98::KDM5A assayed with HA antibody

description: Library name: SJNORM077742_C1-CD34_ntag-NUP-KDM-HA-AB3

value: HA (Cell Signaling, 3724, clone:C29F4, RRID:AB_1549585)


title: TBB298


title: TBB297


title: cord blood CD34+ cell with NUP98::KDM5A assayed with H3K4me3 antibody (positive control for SJNORM077742_C1)

description: Library name: SJNORM077742_C1-CD34_ntag-NUP-KDM-H3K4me3-AB12


title: TBB295


title: TBB294


title: TBB296


title: cord blood CD34+ cell with NUP98::KDM5A assayed with IgG antibody

description: Library name: SJNORM077742_C1-CD34_ntag-NUP-KDM-IGG-AB14


title: TBB299


title: CHRF-288-11 (megakaryocytic acute myeloid leukemia cell line) assayed with menin antibody

description: Library name: SJAML077322_C1-CHRF-288-11-MEN1-AB1


title: CHRF-288-11 (megakaryocytic acute myeloid leukemia cell line) assayed with H3K4me3 antibody

description: Library name: SJAML077322_C1-CHRF-288-11-H3K4me3-AB12


title: CHRF-288-11 (megakaryocytic acute myeloid leukemia cell line) assayed with IgG antibody

description: Library name: SJAML077322_C1-CHRF-288-11-IGG-AB14


title: CHRF-288-11 (megakaryocytic acute myeloid leukemia cell line) assayed with H3K27ac antibody

description: Library name: SJAML077322_C1-CHRF-288-11-H3K27Ac-AB5


title: cord blood CD34+ cell with NUP98::HOXA9 assayed with H3K4me3 antibody

description: Library name: SJNORM077219_C1-CD34_ntag-NUP98-HOXA9-H3K4me3-AB12

value: lentiviral overexpression of NUP98::HOXA9


title: cord blood CD34+ cell with NUP98::HOXA9 assayed with menin antibody

description: Library name: SJNORM077219_C1-CD34_ntag-NUP98-HOXA9-MEN1-AB1


title: cord blood CD34+ cell with NUP98::HOXA9 assayed with H3K27ac antibody

description: Library name: SJNORM077219_C1-CD34_ntag-NUP98-HOXA9-H3K27Ac-AB5


title: cord blood CD34+ cell with NUP98::HOXA9 assayed with IgG antibody

description: Library name: SJNORM077219_C1-CD34_ntag-NUP98-HOXA9-IGG-AB14


title: cord blood CD34+ cell with NUP98::HOXA9 assayed with HA antibody

description: Library name: SJNORM077219_C1-CD34_ntag-NUP98-HOXA9-HA-AB3


title: cord blood CD34+ cell with NUP98::HOXA9 assayed with KMT2A antibody

description: Library name: SJNORM077219_C1-CD34_ntag-NUP98-HOXA9-KMT2A-AB1

value: KMT2A (Epicypher, 13-2004, unknown clone, RRID:AB_3076423)


title: cord blood CD34+ cell with NUP98::NSD1 assayed with KMT2A antibody

description: Library name: SJNORM077218_C1-CD34_ntag-NUP98-NSD1-KMT2A-AB1

value: lentiviral overexpression of NUP98::NSD1

value: cord blood CD34+ cell


title: TBB285


title: TBB292


title: TBB288


title: TBB287


title: TBB293


title: TBB291


title: TBB283


title: cord blood CD34+ cell with NUP98::NSD1 assayed with menin antibody

description: Library name: SJNORM077218_C1-CD34_ntag-NUP98-NSD1-MEN1-AB1


title: TBB286


title: TBB289


title: TBB282


title: TBB290


title: TBB284


title: cord blood CD34+ cell with NUP98::NSD1 assayed with H3K27ac antibody

description: Library name: SJNORM077218_C1-CD34_ntag-NUP98-NSD1-H3K27Ac-AB5

value: H3K27ac (Cell Signaling, 8173S, clone:D5E4, RRID:AB_10949503)


title: cord blood CD34+ cell with NUP98::NSD1 assayed with H3K4me3 antibody

description: Library name: SJNORM077218_C1-CD34_ntag-NUP98-NSD1-H3K4me3-AB12


title: cord blood CD34+ cell with NUP98::NSD1 assayed with HA antibody

description: Library name: SJNORM077218_C1-CD34_ntag-NUP98-NSD1-HA-AB3


title: TBB280


title: TBB279


title: cord blood CD34+ cell with NUP98::NSD1 assayed with IgG antibody

description: Library name: SJNORM077218_C1-CD34_ntag-NUP98-NSD1-IGG-AB14

value: IgG (Epicypher Cat# 13-0042, RRID:AB_2923178)


title: cord blood CD34+ cell with NUP98::KDM5A assayed with H3K27ac antibody

description: Library name: SJNORM077217_C1-CD34_ntag-NUP98-KDM5A_2-H3K27Ac-AB5


title: TBB277


title: TBB276


title: TBB274


title: TBB273


title: TBB275


title: cord blood CD34+ cell with NUP98::KDM5A assayed with H3K4me3 antibody

description: Library name: SJNORM077217_C1-CD34_ntag-NUP98-KDM5A_2-H3K4me3-AB12


title: cord blood CD34+ cell with NUP98::KDM5A assayed with IgG antibody (replicate 2)

description: Library name: SJNORM077217_C1-CD34_ntag-NUP98-KDM5A_2-IGG-AB14


title: cord blood CD34+ cell with NUP98::KDM5A assayed with HA antibody (replicate 2)

description: Library name: SJNORM076811_C1-CD34_ntag-NUP98-KDM5A-HA-AB3


title: cord blood CD34+ cell with NUP98::HOXA9 rep3 at day 42

description:
Library name: SJNORM067618_C8
TruSeq Stranded Total RNA Kit, with Ribozero Gold

data_processing:
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using StrongARM pipeline that utilize STAR (v.2.7.9a).
Gene expression count matrix was generated using RSEM (v1.3.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for RSEM count data

extract_protocol:
RNA was harvested using Quikc-RNA Miniprep Kit (Zymo Research R1055). RNA was then NanoDrop2000 (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Kit, with Ribozero Gold (Illumina, 20020598), Ovation RNA sequencing system v2 (Tecan, 7102-32), or Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, 20040529) as indicated for each sample. Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).
Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).


title: cord blood CD34+ cell with NUP98::KDM5A assayed with IgG antibody (replicate 1)

description: Library name: SJNORM076811_C1-CD34_ntag-NUP98-KDM5A-IGG-AB14


title: cord blood CD34+ cell with NUP98::KDM5A assayed with KMT2A antibody

description: Library name: SJNORM077217_C1-CD34_ntag-NUP98-KDM5A_2-KMT2A-AB1


title: cord blood CD34+ cell with NUP98::KDM5A assayed with HA antibody (replicate 1)

description: Library name: SJNORM077217_C1-CD34_ntag-NUP98-KDM5A_2-HA-AB3


title: TBB271


title: TBB278


title: TBB270


title: cord blood CD34+ cell with empty vector control rep3 at day 42

description:
Library name: SJNORM067618_C5
TruSeq Stranded Total RNA Kit, with Ribozero Gold

value: empty vector control


title: cord blood CD34+ cell with NUP98::KDM5A rep3 at day 42

description:
Library name: SJNORM067618_C7
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::NSD1 rep3 at day 42

description:
Library name: SJNORM067618_C6
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::HOXA9 rep3 at day 14

description:
Library name: SJNORM067618_C4
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB267


title: TBB269


title: cord blood CD34+ cell with NUP98::KDM5A rep3 at day 14

description:
Library name: SJNORM067618_C3
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB263


title: TBB272

value: NR


title: cord blood CD34+ cell with NUP98::NSD1 rep3 at day 14

description:
Library name: SJNORM067618_C2
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB265

value: NKRL


title: TBB264


title: cord blood CD34+ cell with empty vector control rep2 at day 14

description:
Library name: SJNORM067618_C1
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB266


title: TBB268


title: cord blood CD34+ cell with NUP98::KDM5A rep2 at day 42

description:
Library name: SJNORM067617_C7
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::HOXA9 rep2 at day 14

description:
Library name: SJNORM067617_C4
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with empty vector control rep3 at day 14

description:
Library name: SJNORM067617_C5
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::NSD1 rep2 at day 42

description:
Library name: SJNORM067617_C6
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::KDM5A rep2 at day 14

description:
Library name: SJNORM067617_C3
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB261


title: TBB260


title: cord blood CD34+ cell with empty vector control rep1 at day 42

description:
Library name: SJNORM067617_C1
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB281


title: TBB262


title: TBB256


title: cord blood CD34+ cell with NUP98::HOXA9 rep1 at day 42

description:
Library name: SJNORM067616_C8
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB258


title: TBB259


title: TBB257


title: cord blood CD34+ cell with NUP98::KDM5A rep1 at day 42

description:
Library name: SJNORM067616_C7
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::NSD1 rep1 at day 42

description:
Library name: SJNORM067616_C6
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with empty vector control rep2 at day 42

description:
Library name: SJNORM067616_C5
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB255


title: TBB252


title: TBB251


title: cord blood CD34+ cell with NUP98::KDM5A rep1 at day 14

description:
Library name: SJNORM067616_C3
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::HOXA9 rep1 at day 14

description:
Library name: SJNORM067616_C4
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::NSD1 rep2 at day 14

description:
Library name: SJNORM067617_C2
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB254


title: cord blood CD34+ cell with NUP98::NSD1 rep1 at day 14

description:
Library name: SJNORM067616_C2
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::KDM5A assayed with NUP98 antibody (Cell Signaling. 2288 for comparison)

description: Library name: SJNORM077742_C1-CD34_ntag-NUP-KDM-NUP98-AB1

value: NUP98 (Cell Signaling. 2288, clone:L205, RRID:AB_561204)


title: TBB249


title: TBB248


title: TBB250


title: cord blood CD34+ cell with empty vector control rep1 at day 14

description:
Library name: SJNORM067616_C1
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: TBB246


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) + Revumenib (1 uM)-treatment (7 days) batch 2 rep3

description:
Library name: 3236621_SJNORM095931_C1-CD34_NK5_Cas9_RB1_1_lot3_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (RB1-gRNA1) + Revumenib (1 uM)-treatment (7 days)


title: TBB243


title: cord blood CD34+ cell with NUP98::KDM5A + Revumenib (1 uM)-treatment (7 days)

description:
Library name: 3236620_SJNORM095930_C1-CD34_NK5_Cas9_non_edited_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: DMSO-treatment (7 days)


title: cord blood CD34+ cell with NUP98::HOXA9 rep2 at day 42

description:
Library name: SJNORM067617_C8
TruSeq Stranded Total RNA Kit, with Ribozero Gold


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) + Revumenib (1 uM)-treatment (7 days) batch 2 rep2

description:
Library name: 3236618_SJNORM095928_C1-CD34_NK5_Cas9_RB1_1_lot2_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) + Revumenib (1 uM)-treatment (7 days) batch 2 rep2

description:
Library name: 3236617_SJNORM095927_C1-CD34_NK5_Cas9_NT_lot2_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (AAVS) + Revumenib (1 uM)-treatment (7 days)


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) + Revumenib (1 uM)-treatment (7 days) batch 2 rep3

description:
Library name: 3236622_SJNORM095932_C1-CD34_NK5_Cas9_WT1_1_lot3_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (WT1-gRNA1) + Revumenib (1 uM)-treatment (7 days)


title: TBB245


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) + Revumenib (1 uM)-treatment (7 days) batch 2 rep1

description:
Library name: 3236615_SJNORM095925_C1-CD34_NK5_Cas9_RB1_1_relot1_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) + Revumenib (1 uM)-treatment (7 days) batch 2 rep1

description:
Library name: 3236616_SJNORM095926_C1-CD34_NK5_Cas9_WT1_1_relot1_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) + Revumenib (1 uM)-treatment (7 days) batch 2 rep1

description:
Library name: 3236614_SJNORM095924_C1-CD34_NK5_Cas9_NT_relot1_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) + DMSO-treatment (7 days) batch 2 rep3

description:
Library name: 3236613_SJNORM095923_C1-CD34_NK5_Cas9_WT1_1_lot3_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (WT1-gRNA1) + DMSO-treatment (7 days)


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) + Revumenib (1 uM)-treatment (7 days) batch 2 rep2

description:
Library name: 3236619_SJNORM095929_C1-CD34_NK5_Cas9_WT1_1_lot2_Rev
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) + DMSO-treatment (7 days) batch 2 rep3

description:
Library name: 3236612_SJNORM095922_C1-CD34_NK5_Cas9_RB1_1_lot3_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (RB1-gRNA1) + DMSO-treatment (7 days)


title: cord blood CD34+ cell with NUP98::KDM5A + DMSO-treatment (7 days)

description:
Library name: 3236611_SJNORM095921_C1-CD34_NK5_Cas9_non_edited_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: TBB244


title: TBB247


title: TBB236


title: TBB242

value: lowSFT


title: TBB241


title: TBB239


title: TBB240


title: TBB235


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) + DMSO-treatment (7 days) batch 2 rep2

description:
Library name: 3236610_SJNORM095920_C1-CD34_NK5_Cas9_WT1_1_lot2_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: TBB237


title: TBB234


title: TBB231


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) + DMSO-treatment (7 days) batch 2 rep2

description:
Library name: 3236608_SJNORM095918_C1-CD34_NK5_Cas9_NT_lot2_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (AAVS) + DMSO-treatment (7 days)


title: TBB238


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) + DMSO-treatment (7 days) batch 2 rep1

description:
Library name: 3236606_SJNORM095916_C1-CD34_NK5_Cas9_RB1_1_relot1_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) + DMSO-treatment (7 days) batch 2 rep2

description:
Library name: 3236609_SJNORM095919_C1-CD34_NK5_Cas9_RB1_1_lot2_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA2) batch 2 rep3 at day 39

description:
Library name: 3200477_SJNORM095855_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot3_WT1_2
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (WT1-gRNA2)


title: TBB229

value: TCMR/Mixed


title: cord blood CD34+ cell with NUP98::KDM5A assayed with menin antibody

description: Library name: SJNORM077217_C1-CD34_ntag-NUP98-KDM5A_2-MEN1-AB1

value: lentiviral overexpression of NUP98::KDM5A

value: cord blood CD34+ cell

value: menin (Bethyl Cat# A300-105A, polyclonal, RRID:AB_2143306)


title: TBB228


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA2) batch 2 rep2 at day 39

description:
Library name: 3200476_SJNORM095854_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot2_WT1_2
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: TBB230


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA2) batch 2 rep1 at day 39

description:
Library name: 3200475_SJNORM095853_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot1_WT1_2
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) batch 2 rep3 at day 39

description:
Library name: 3200474_SJNORM095852_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot3_WT1_1
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (WT1-gRNA1)


title: TBB226


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) + DMSO-treatment (7 days) batch 2 rep1

description:
Library name: 3236607_SJNORM095917_C1-CD34_NK5_Cas9_WT1_1_relot1_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) batch 2 rep2 at day 39

description:
Library name: 3200473_SJNORM095851_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot2_WT1_1
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: TBB233


title: TBB227


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) + DMSO-treatment (7 days) batch 2 rep1

description:
Library name: 3236605_SJNORM095915_C1-CD34_NK5_Cas9_NT_relot1_DMSO
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: TBB232

value: NR


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA2) batch 2 rep1 at day 39

description:
Library name: 3200469_SJNORM095847_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot1_RB1_2
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (RB1-gRNA2)


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA2) batch 2 rep2 at day 39

description:
Library name: 3200470_SJNORM095848_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot2_RB1_2
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: TBB222


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA2) batch 2 rep3 at day 39

description:
Library name: 3200471_SJNORM095849_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot3_RB1_2
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: TBB223

value: NKRL


title: TBB225


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) batch 2 rep3 at day 39

description:
Library name: 3200468_SJNORM095846_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot3_RB1_1
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (RB1-gRNA1)


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) batch 2 rep1 at day 39

description:
Library name: 3200472_SJNORM095850_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot1_WT1_1
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) batch 2 rep2 at day 39

description:
Library name: 3200467_SJNORM095845_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot2_RB1_1
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) batch 2 rep1 at day 39

description:
Library name: 3200466_SJNORM095844_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot1_RB1_1
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) batch 2 rep3 at day 39

description:
Library name: 3200465_SJNORM095843_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot3_cont
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: constitutive expression of NUP98::KDM5A and Cas9 + lentiviral transduction of gRNA (AAVS)


title: TBB253


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) batch 2 rep2 at day 39

description:
Library name: 3200464_SJNORM095842_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot2_cont
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) batch 2 rep1 at day 39

description:
Library name: 3200463_SJNORM095841_C1-CD34_NUP98_KDM5A_Cas9_day39_re_lot1_cont
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA2) batch 1 rep3 at day 34

description:
Library name: 3081396_SJNORM085502_C1-CD34_NUP98_KDM5A_Cas9_day34_lot3_RB1_2
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) batch 1 rep3 at day 34

description:
Library name: 3081398_SJNORM085504_C1-CD34_NUP98_KDM5A_Cas9_day34_lot3_WT1_2
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) batch 1 rep3 at day 34

description:
Library name: 3081394_SJNORM085500_C1-CD34_NUP98_KDM5A_Cas9_day34_lot3_cont
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) batch 1 rep2 at day 34

description:
Library name: 3081393_SJNORM085499_C1-CD34_NUP98_KDM5A_Cas9_day34_lot2_WT1_2
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) batch 1 rep3 at day 34

description:
Library name: 3081395_SJNORM085501_C1-CD34_NUP98_KDM5A_Cas9_day34_lot3_RB1_1
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) batch 1 rep2 at day 34

description:
Library name: 3081390_SJNORM085496_C1-CD34_NUP98_KDM5A_Cas9_day34_lot2_RB1_1
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA2) batch 1 rep2 at day 34

description:
Library name: 3081391_SJNORM085497_C1-CD34_NUP98_KDM5A_Cas9_day34_lot2_RB1_2
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) batch 1 rep2 at day 34

description:
Library name: 3081389_SJNORM085495_C1-CD34_NUP98_KDM5A_Cas9_day34_lot2_cont
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (WT1-gRNA1) batch 1 rep1 at day 34

description:
Library name: 3081388_SJNORM085494_C1-CD34_NUP98_KDM5A_Cas9_day34_lot1_WT1_2
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA2) batch 1 rep1 at day 34

description:
Library name: 3081386_SJNORM085492_C1-CD34_NUP98_KDM5A_Cas9_day34_lot1_RB1_2
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (RB1-gRNA1) batch 1 rep1 at day 34

description:
Library name: 3081385_SJNORM085491_C1-CD34_NUP98_KDM5A_Cas9_day34_lot1_RB1_1
Ovation RNA sequencing system v2


title: cord blood CD34+ cell with NUP98::KDM5A and Cas9 + gRNA (AAVS) batch 1 rep1 at day 34

description:
Library name: 3081384_SJNORM085490_C1-CD34_NUP98_KDM5A_Cas9_day34_lot1_cont
Ovation RNA sequencing system v2


title: ATRT MYC-4 patient tissue viably frozen [snRNA-Seq]

city: Bern

first: Irene

last: Paassen

address: Murtenstrasse 28

department: Biomedical Research

country: Switzerland

institute: Universität Bern

description: Library name: ATRT-MYC-4

data_processing:
Initial processing: cell-ranger arc (version 2.0.0), seurat (version 4.1.1) and signac (version 1.7.0)
Reads were mapped to GRCh38 and cell genotypes were annotated by sourorcell (Heaton et al., 2020)
ATAC peaks were merged using signac (version 1.7.0)
Good quality samples were filtered (RNA counts < 30000 & > 800,  % of mitochondrial genes < 20%)
Assembly: GRCh38
Supplementary files format and content: unnormalized count matrix and metadata table

molecule: nuclear RNA

source_name: Brain

growth_protocol: Viably frozen tissue (10% DMSO, 90% FBS)

extract_protocol:
Tissue was minced into small pieces and further homogenized using a douncer. After cell lysis,each organoid sample was filtered once using a 70 uM filter as well as a 40 uM filter. Intact single nuclei were sorted and two independent samples were mixed based on different gender (male with female). Between 10.000 and 40.000 nuclei were loaded on the ChipJ Chromatin Controller (10X Genomics).
Libraries were prepared followed naufacturere instruction (10X Genomics, protocol: CG000338 Rev D)

value: Brain


title: CHRF-288-11 cell line

description:
Library name: 1153653_SJAMLM7049905_C1-CHFR-288-11
TruSeq Stranded Total RNA Kit, with Ribozero Gold

value: megakaryocytic acute myeloid leukemia cell line


title: ATRT SHH-9 patient tissue viably frozen [snRNA-Seq]

description: Library name: ATRT-SHH-9


title: ATRT SHH-8 patient tissue viably frozen [snRNA-Seq]

description: Library name: ATRT-SHH-8


title: ATRT SHH-7 patient tissue viably frozen [snRNA-Seq]

description: Library name: ATRT-SHH-7


title: TBB219


title: ATRT SHH-6 patient tissue viably frozen [snRNA-Seq]

description: Library name: ATRT-SHH-6


title: TBB216


title: ATRT TYR-6 patient tissue viably frozen [snRNA-Seq]

description: Library name: ATRT-TYR-6


title: TBB206


title: TBB213


title: TBB215


title: TBB205


title: TBB220


title: ATRT TYR-5 patient tissue viably frozen [snRNA-Seq]

description: Library name: ATRT-TYR-5


title: TBB196


title: TBB202


title: TBB210


title: TBB199


title: ATRT-MYC-2 fresh frozen tumor tissue

description: Library name: ATRT-MYC-2

data_processing:
Initial processing: cell-ranger (version 7.0.0), R (version 4.2.0), Seurat (version 4.9.9.9045)
Reads were mapped to GRCh38
RNA counts were merged using Seruat (version 4.9.9.9045)
Good quality samples were filtered (UMI >= 1000, genes >= 500, % mitochondrial RNA <= 5%)
Assembly: GRCh38
Supplementary files format and content: unnormalized count matrix and metadata table

growth_protocol: Fresh frozen tumor tissue

extract_protocol:
Single nucleus RNA-seq was performed following established protocols [PMID: 26551203, PMID: 32888429, PMID: 28696319, PMID: 27317342, PMID: 31015438]. Each sample was thawed, sectioned into smaller pieces (1-2mm3), and minced thoroughly in ice-cold “CHAPS, with salts and Tris” (CS) digestion buffer for five minutes. The homogenized tissues were then filtered twice through 40 µm cell strainers and washed three times with “salt-Tris” (ST) detergent buffer. Subsequently, the samples were centrifuged for 5 mins at 500g at 4 °C and the nuclei pellets were resuspended in PBS + 0.05% BSA and counted using the Luna Automated cell counter (Logos Biosystems). If visible agglomerates and/or cell debris were present, samples underwent an additional filtration step using Flowmi 40 µm cell strainers.
Approximately 20.000 nuclei per sample were loaded into the Chromium single-cell 3’chip (10X Genomics), where each cell and its respective transcriptome were individually partitioned and barcoded. The steps for cDNA amplification and gene expression library preparation were carried out using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics), following the manufacturer’s instructions. The concentration and quality of cDNA and libraries were assessed using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific) and TapeStation (Agilent). Equimolar pooled libraries (multiplexes) were sequenced on a NovaSeq 6000 (Illumina) sequencer, according to the manufacturer’s instructions.


title: ATRT-MYC-3 fresh frozen tumor tissue

description: Library name: ATRT-MYC-3


title: TBB209


title: TBB212


title: ATRT-MYC-1 fresh frozen tumor tissue

description: Library name: ATRT-MYC-1


title: ATRT-SHH-5 fresh frozen tumor tissue

description: Library name: ATRT-SHH-5


title: ATRT-SHH-3 fresh frozen tumor tissue

description: Library name: ATRT-SHH-3


title: ATRT-SHH-2 fresh frozen tumor tissue

description: Library name: ATRT-SHH-2


title: ATRT-SHH-4 fresh frozen tumor tissue

description: Library name: ATRT-SHH-4


title: TBB192


title: TBB193


title: TBB203


title: TBB195


title: ATRT-SHH-1 fresh frozen tumor tissue

description: Library name: ATRT-SHH-1


title: TBB218


title: TBB221


title: ATRT-TYR-4 fresh frozen tumor tissue

description: Library name: ATRT-TYR-4


title: TBB217


title: TBB200


title: TBB211


title: ATRT-TYR-3 fresh frozen tumor tissue

description: Library name: ATRT-TYR-3


title: TBB198


title: ATRT-TYR-2 fresh frozen tumor tissue

description: Library name: ATRT-TYR-2


title: TBB186


title: TBB183


title: TBB185


title: TBB189


title: TBB182


title: ATRT-TYR-1 fresh frozen tumor tissue

description: Library name: ATRT-TYR-1


description: Library name: scATAC-seq part of multiome data AT-SHH15

library_source: genomic single cell

data_processing:
Initial processing: cell-ranger arc (version 2.0.0), seurat (version 4.1.1) and signac (version 1.7.0)
Reads were mapped to GRCh38 and cell genotypes were annotated by sourorcell (Heaton et al., 2020)
ATAC peaks were merged using signac (version 1.7.0)
Good quality samples were filtered (ATAC counts < 50000 & > 800, RNA counts < 30000 & > 800, nucleosome signal < 1.5, TSS enrichment > 1, % of blacklist regions < 3%, % of mitochondrial genes < 20%)
Assembly: GRCh38
Supplementary files format and content: count matrix and metadata table

growth_protocol: ATRT tumoroids cultured in tumor stem medium

extract_protocol:
Organoids were mechanically dissociated into single cell and further homogenized using a douncer. After cell lysis,each organoid sample was filtered once using a 70 uM filter as well as a 40 uM filter. Intact single nuclei were sorted and two independent samples were mixed based on different gender (male with female). Between 10.000 and 40.000 nuclei were loaded on the ChipJ Chromatin Controller (10X Genomics).
Libraries were prepared followed naufacturere instruction (10X Genomics, protocol: CG000338 Rev D)

value: AT-SHH15 tumoroid


title: TBB224


title: TBB201


title: TBB190


title: TBB207


title: TBB208


title: TBB204


description: Library name: scATAC-seq part of multiome data AT-SHH05

value: AT-SHH05 tumoroid


title: TBB214


title: TBB197


title: TBB187


title: TBB191


title: TBB188


description: Library name: scATAC-seq part of multiome data AT-SHH04

value: AT-SHH04 tumoroid


title: TBB181


title: TBB194


title: 25xGFA1 rep2, Copper treated, 60 min

city: Davis

first: Ben

last: Montpetit

address: One Shields Avenue

institute: University of California, Davis

description:
Library name: Sample 37
Column name in raw_counts.csv and row name in Samples.csv: 3662_60min

data_processing:
Sequences were trimmed of their UMIs,truseq adapters, and low quality sequences using Umi Tools v1.1.2 and bbduk (bbmap v38.79; k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Quality control checks were performed using Fastqc v0.11.9, before and after trimming steps
Assembly: The yeast genome was assembled using the STAR aligner v2.7.10a (--sjdbOverhang  99) and GCF_000146045.2_R64_genomics.fna hosted on the NCBI database
Trimmed sequences were aligned to the genome assembly using the STAR aligner v2.7.10a and output as Bam files(--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000)
Readcounts were extracted using samtools v1.10 and htseq v2.0.2
Supplementary files format and content: CSV file includes raw read count expression matrix for each sample (column) and gene (row); Sample.csv contains metadata required for downstream analysis

organism: Saccharomyces cerevisiae

source_name: Haploid, MAT A

growth_protocol: 5 mL of YPD media was inoculated from fresh grown plates and grown for ~8 hrs. Cultures were diluted to OD600 of 0.002 in 100 mL of YPD and grown overnight to reach OD600 of ~1.0. Cells were harvested, washed with copper-free minimal media (Formedium, CYN0901), and resuspended into 200 mL copper-free media such that OD600 = 0.25. Cells were grown for ~2 hrs, baseline samples were collected, and then cultures were induced with 500 mM CuSO4. Samples were collected 5, 10, 15, 20, 25, 30, 45, and 60 min post-CuSO4.

extract_protocol:
RNA was harvested using the Quick-RNA Fungal/Bacterial Miniprep kit (Zymo Research) excluding the kit's DNase I treatment process. RNA was treated with Turbo™ DNase for 30 min at 37°C and cleaned by RNA Clean & Concentrator-5 (Zymo Research).
Lexogen Quantseq 3' mRNA library seq kit

treatment_protocol: All samples were treated with 500 uM Copper Sulfate. 0 min samples are controls before treatment time course.

tag: strain background

value: Haploid, MAT A

value: GFA1 25x Gene array

value: Copper Treatment

value: 60 min


title: TBB184


description: Library name: scRNA-seq part of multiome data AT-SHH05


title: TBB179


title: 25xGFA1 rep2, Copper treated, 5 min

description:
Library name: Sample 36
Column name in raw_counts.csv and row name in Samples.csv: 3662_5min

value: 5 min