title: RNA Cebpa-/p30 Tet2-/- s8

data_processing:
Salmon 0.12.0 was used to quantify expression of transcripts from RNA-seq experiments using mm10/GRCm38_94 Ensembl transcriptome (salmon quant -l U --seqBias --numBootstraps 30)
Assembly: GRCm38.p6 (Ensembl release 94)
Supplementary files format and content: Tab-delimited text file including estimated number of reads mapping to each transcript and relative abundance of transcript in TPM.

extract_protocol:
RNA was isolated from 5*10^5 sorted cells using RNeasy Mini Kit (#74104 Qiagen) according to the manufacturer’s instructions and quality was assessed by RNA 6000 Pico Kit (#5067-1513 Agilent) on a Bioanalyzer 2100 (Agilent).
200 ng RNA was used to generate sequencing libraries using TruSeq RNA Library Prep Kit v2 (#RS-122-2001 Illumina), the libraries were quantified using QubitTM dsDNA BR Assay Kit (#32853 Thermo Fisher Scientific) and size distribution assessed by DNA 1000 Kit (#5067-1504 Agilent) on a Bioanalyzer. Multiplexed libraries were sequenced on a NextSeq 500 (Illumina) using NextSeq 500 High Output v2 Kit (75 cycles; #FC-404-2005 Illumina).

value: KO


title: 1745-MC-18

status: Public on Aug 28 2023

type: SRA

city: Toledo

first: Jennifer

last: Nguyen

state: OH

address: 3000 Arlington Ave

department: Neuroscience

country: USA

institute: University of Toledo

library_source: transcriptomic

data_processing:
MultiQC
Trimmomatic - 0.36
hisat2
samtools
Assembly: GRCm38
Supplementary files format and content: raw counts as csv

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
RNA extraction was performed on homogenized half brain tissue aliquots using the (QIAGEN, Germantown, MD) RNeasy Plus Micro Kit.
The Total RNA Library was prepared using the (Illumina, San Diego, CA)  Illumina NovaSeq (S4) 300 cycle flow cell and reagent kit.

tag: tissue

value: brain

tag: agent

value: deltamethrin


title: RNA Cebpa-/p30 Tet2-/- s7

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

source_name: AML blasts

tag: strain

tag: genotype

tag: cell type

value: AML blasts from bone marrow


title: 1745-MC-17

value: control


title: BatchB_A2B5+ population from human fetal brain 1 [fP_A_Plus_1]

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

data_processing:
Raw FASTQ files were aligned to GRCh38 using Ensembl 95 gene annotations with STAR 2.5.4b in 2-pass mode across all samples
Reads were quantified with RSEM 1.3.1
Genome_build: GRCh38
Supplementary_files_format_and_content: gene count matrix - output from RSEM

organism: Homo sapiens

extract_protocol:
Human brain samples were obtained under approved Institutional Review Board protocols from consenting patients at Strong Memorial Hospital at the University of Rochester.  Brain tissue was obtained from normal GW 18-24 cortical and/or VZ/SVZ dissections or adult white matter/cortex epileptic resections (18,19, and 27 years old for mRNA, 8, 20, 43, and 54 years old for miRNA).  Fetal GPC acquisition, dissociation and immunomagnetic sorting of A2B5+/PSA-NCAM- cells were as described (Windrem et al., 2004). GPCs were isolated from dissociated tissue using a dual immunomagnetic sorting strategy: depleting mouse anti-PSA-NCAM+ (Millipore, DSHB) cells, using microbead tagged rat anti-mouse IgM (Miltenyi Biotech), then selecting A2B5+ (clone 105; ATCC, Manassas, VA) cells from the PSA-NCAM- pool, as described (Windrem et al., 2004; Windrem et al., 2008). After sorting, cells were maintained for 1-14 days in DMEM-F12/N1 with 10 ng/ml bFGF and 20 ng/ml PDGF-AA. Alternatively  CD140a/PDGFRA-defined GPCs were isolated and sorted using MACS as described (Sim et al., 2011b), yielding an enriched population of CD140+ glial progenitor cells.
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent). For batch B, libraries were constructed with the SMART-Seq Ultra Low kit (Clontech) followed by the NexteraXT library preparation kit (Illumina). For batch C, libraries were constructed with the TruSeq RNA Library Prep Kit v2 (Illumina).

value: human fetal brain

tag: batch

value: BatchB

tag: cell type/population

value: A2B5+ population


title: RNA Cebpa-/p30 Tet2-/- s5


title: BatchC_CD140+ population from human fetal brain E [July2014_hfCD140-2p]

value: BatchC

value: CD140+ population


title: 1745-MC-16


title: 1745-MC-12


title: 1745-MC-11


title: BatchB_CD140+ population from human fetal brain 3 [fCd140_3]


title: BatchB_CD140+ population from human fetal brain 2 [fCd140_2]


title: RNA Cebpa-/p30 Tet2+/+ s24

value: WT


title: 1745-MC-15


title: 1745-MC-14


title: 1745-MC-13


title: BatchB_CD140+ population from human fetal brain 1 [fCd140_1]


title: 1745-MC-10


title: 1745-MC-9


title: KO effector CD4+ T cells 3

city: Vienna

first: Nicole

last: Boucheron

address: Lazarettgasse 19

country: Austria

institute: Institute of Immunology

data_processing:
Following the raw data acquisition (HiSeq Control Software) and base calling (Real-Time Analysis Software, RTA, v2.7.7) that was performed on-instrument, the subsequent raw data processing involved programs based on Picard tools (https://broadinstitute.github.io/picard/) to generate sample-specific, unaligned BAM files
Sequence reads were subsequently mapped onto the mouse reference genome assembly build mm10 (a flavor of GRCm38) using Spliced Transcripts Alignment to a Reference (STAR) aligner (Dobin et al, 2013) which was run with options recommended by the ENCODE project
Aligned reads that overlapped Ensembl transcript features were counted with the Bioconductor (v3.12) GenomicAlignments (v1.26.0) package.
Differential expression was tested using the Bioconductor DESeq2 package (v1.30.0) (Love et al, 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text file including Raw counts for each sample
Supplementary files format and content: tab-delimited text file including FPKM values for each sample

source_name: Spleen/peripheral lymph nodes

extract_protocol:
RNA was extracted using the RNAeasy mini plus kit (Qiagen).
RNA-Seq libraries were generated  using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina). Library concentrations were determined with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA)

value: Spleen/peripheral lymph nodes

value: effector CD4+ T cells


title: 1745-MC-7


title: KO effector CD4+ T cells 2


title: Blood, patient 5

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

country: China

institute: Fujian Maternity and Child Health Hospital

description:
FJSFY-P5
All_Differentially_Expressed_miRNA.xlsx

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Differential expression analysis of miRNAs between groups was performed using edgeR with settings of 1.5-fold difference, p-value < 0.05 and within-group CPM mean of 1 to screen for differentially expressed miRNAs.
Assembly: hg38
Supplementary files format and content: Microsoft excel file includes the counts per million (CPM) reads of miRNAs in all samples.

source_name: blood

extract_protocol:
Total RNA from the peripheral blood samples was isolated using a PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s protocol.RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: blood

tag: Sex

value: male

tag: disease state

value: β-thalassemia


title: 1745-MC-6


title: Blood, patient 4

description:
FJSFY-P4
All_Differentially_Expressed_miRNA.xlsx

value: female


title: 1745-MC-5


title: 1745-MC-4


title: Blood, patient 3

description:
FJSFY-P3
All_Differentially_Expressed_miRNA.xlsx


title: KO effector CD4+ T cells 1

value: KO


title: 1745-MC-3

value: brain


title: KO naïve CD4+ T cells 3

value: naive CD4+ T cells


title: 1745-MC-1

value: deltamethrin


title: RNA Cebpa-/p30 Tet2+/+ s23

value: AML blasts from bone marrow


title: Blood, patient 2

description:
FJSFY-P2
All_Differentially_Expressed_miRNA.xlsx


title: 1745-MC-2


title: Blood, normal control 5

description:
FJSFY-C5
All_Differentially_Expressed_miRNA.xlsx

value: healthy


title: WT effector CD4+ T cells 3


title: RNA Cebpa-/p30 Tet2+/+ s19

value: WT\n


title: KO naïve CD4+ T cells 1


title: 1745-MC-8

value: control


title: Ctrl_2, biol rep 2

city: Chongqing

first: Huiping

last: Yang

address: 74 Linjiang Road

department: Cardiology

institute: Chongqing Medical University

data_processing:
Oligo dT enriched mRNA
Fragmented mRNA
Reverse synthetic cDNA
Connect adaptor
Computer sequencing on Illumina platform
Assembly: mm10
Supplementary files format and content: excel file includes raw conuts for each sample
Supplementary files format and content: excel file includes TPM values for each sample

source_name: Heart tissue

extract_protocol:
total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. The total amount of RNA required for a single library construction is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is ≥1.8, and OD260/230 is ≥1.0.
Illumina TruseqTM RNA sample prep Kit was used to construct the library

value: Heart tissue

tag: cell line

value: H9C2 cells

value: Smooth muscle cells

tag: treatment

value: normal diet


title: DCM_3, biol rep 3

value: DCM

value: HFD


title: DCM_2, biol rep2


title: Ctrl_3, biol rep 3


title: Ctrl_1, biol rep 1


title: DCM_1, biol rep 1


title: WT effector CD4+ T cells 2

value: Spleen/peripheral lymph nodes

value: effector CD4+ T cells

value: WT


title: WT effector CD4+ T cells 1


title: Blood, normal control 3

description:
FJSFY-C3
All_Differentially_Expressed_miRNA.xlsx

value: blood

value: male


title: Blood, normal control 4

description:
FJSFY-C4
All_Differentially_Expressed_miRNA.xlsx

value: female


title: Blood, normal control 2

description:
FJSFY-C2
All_Differentially_Expressed_miRNA.xlsx


title: KO naïve CD4+ T cells 2

value: naive CD4+ T cells

value: KO


title: Blood, patient 1

description:
FJSFY-P1
All_Differentially_Expressed_miRNA.xlsx

value: β-thalassemia


title: WT naïve CD4+ T cells 3


title: Blood, normal control 1

description:
FJSFY-C1
All_Differentially_Expressed_miRNA.xlsx

value: healthy


title: WT naïve CD4+ T cells 2


title: ATAC-seq in 4-OH tamoxifen treated (12hrs) PIPER-15 cells replicate 1

city: Oxford

first: Alastair

last: Smith

state: England

address: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Adapters were removed using trim_galore (Cutadapt v0.6.10)
Reads were aligned to the reference genome using Bowtie2 (v2.5.1) adjusting the max insert parameter (--X) to 2000 to enable the mapping of large inserts that are typical of ATAC-seq
PCR duplicates were removed using picard MarkDuplicates v3.0.0.
Problematic genomic regions present in the ENCODE Blacklist (https://doi.org/10.1038/s41598-019-45839-z) were removed from the aligned file.
BigWigs were generated using the deepTools (v3.5.1) bamCoverage command, with the flags –extendReads –normalizeUsing RPKM and the deep learning based peak caller LanceOtron v1.0.8 (with a peak score cut-off value of 0.5) was used to call peaks.
Assembly: mm9
Supplementary files format and content: BigWig

molecule: genomic DNA

growth_protocol: PIPER-15 cells were grown at a density of 0.5-2x106/ml in RPMI supplemented with 10% foetal calf serum, 2 mM L-glutamine, 50 μg/ml streptomycin, 50 U/ml penicillin and 50 μM β-mercaptoethanol at 37oC with 5% CO2

extract_protocol:
Samples were processed according to the Omni-ATAC-seq protocol (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396)
Illumina NovaSeq 6000 sequencing 150bp paired-end reads

value: A-MuLV immortalised pro-B

value: 2 μM 4-hydroxytamoxifen for 12hrs


title: ATAC-seq in DMSO-treated PIPER-15 cells replicate 2

value: DMSO for 12hrs


title: ATAC-seq in 4-OH tamoxifen treated (12hrs) PIPER-15 cells replicate 2


title: RH4, sgNFYC, SIX1, rep2

city: Cold Spring Harbor

first: Christopher

middle: R

last: Vakoc

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
4C mapping was done as described in https://github.com/deWitLab/4C_mapping. PeakC was used to call significant 4C peaks https://github.com/deWitLab/peakC. Wiggletools mean was used to average signal across the two replicates.
Assembly: hg19
Supplementary files format and content: Genome browser tracks for individual replicates and averaged aross the two replicates (wig).
Library strategy: 4-C seq

growth_protocol: Cells were cultured in RPMI + 10% FBS + PS at 37C at 5% CO2.

extract_protocol:
Cells were trypsinized and counted on Invitrogen Countess Automated Cell Counter. 1x107 cells were used per viewpoint and processed in batches. Cells were fixed in 2% formaldehyde fixation buffer at RT for 10 minutes and quenched with 0.125 M glycine on ice. Cells were then washed in PBS and lysed in 1 ml lysis buffer (50mM TRIS, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% Triton X-100 + protease inhibitors) for 10 min on ice. Batch-processed cells were then split into individual conditions for downstream processing.
First digestion was performed with DpnII and the second digestion with Csp6I. Four separate PCR reactions for each viewpoint were carried out using 150-200 ng 4C template input material.The following primers were used (R = reading primer, NR = non-reading primer): ERRFI1_R TACACGACGCTCTTCCGATCTGCCTGATAGTTAGACACTGATC; ERRFI1_NR ACTGGAGTTCAGACGTGTGCTCTTCCGATCAGGACCTTTCCTCCATATTC; JUN_R TACACGACGCTCTTCCGATCTCAAGCGTGTAGGCGATC; JUN_NR ACTGGAGTTCAGACGTGTGCTCTTCCGATCAAACTTAAGTCCCCTTAGGC; PEG3_R TACACGACGCTCTTCCGATCTGGTAGCATTAGATGTGACGATC; PEG3_NR ACTGGAGTTCAGACGTGTGCTCTTCCGATCGGCTGTCTGCCCTAATGC; SIX1_R TACACGACGCTCTTCCGATCTGGGTTGTTGAGACCAGATC; SIX1_NR ACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTTCCAATAAGAAGTGACCA. Reactions were pooled and purified using Ampure XP beads, eluting in 35 µl milliQ water. Ten µl purified PCR1 product was used as input for a second PCR to obtain full Illumina adapter sequences using the universal forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcoded reverse primer (CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCT) with a 6 nucleotide barcode (XXXXXX). PCR reactions were then purified using a Roche high pure PCR purification kit. Pooled 4C reactions were purified once more with Ampure XP beads and sequenced on the Illumina NextSeq 2000 platform using the single end SE75 bp mode of sequencing.

treatment_protocol: RH4 cells stably expressing Cas9 were lentivirally transduced with sgRNAs targeting NFYC or ROSA26 control locus. Infected cells were drug selected and analyzed at day 7 post lentiviral transduction.

value: rhabdomyosarcoma

value: sgNFYC


title: Mouse; Replicate 2_oxLDL+LPS

city: Toronto

first: Myron

middle: I

last: Cybulsky

state: Ontario

address: 101 College Street

department: Toronto General Hospital Research Institute

country: Canada

institute: University Health Network

data_processing:
The adaptor sequences were removed using Trimmomatic (v0.32; recommended parameters). The reads were aligned to the mouse genome reference assembly mm10 (GRCm38) using STAR (v2.5.1b; default parameters).  To count exonic reads we used featureCounts (http://subread.sourceforge.net/, v1.5.0) and annotated them for mouse genes using GENCODE vM4.
Assembly: mm10 (GRCm38)
Supplementary files format and content: count matrix, csv file

source_name: Peritoneal cavity

growth_protocol: Peritoneal macrophages were harvested by lavage 4 days after intraperitoneal injection with 1ml of aged 4% thioglycolate.  Cells were cultured in DMEM + 10% FBS.  Adherent macrophages were used after 18h in culture

extract_protocol:
Total RNA was extracted from 2 × 106 PMφs using RNeasy mini kit (Qiagen, #74104). To eliminate genomic DNA, 20 U of Roche RNase-free DNase I (Roche, Cat#4716728001) was added in the eluant (100 µl), followed by 20 min of incubation at 37°C.  Total RNA was quantified by NanoDrop Spectrophotometer ND-1000 and 750 ng was used to enrich mRNA using NEBNext poly(A) mRNA magnetic isolation module (New England Biolabs Cat#E7490).
Library construction used NEBNext Ultra II directional RNA library prep kit (New England Biolabs Cat#E7760) and NEBNext multiple oligos for Illumina (New England Biolabs # E7335, E7500, E7710, E7730). Libraries were PCR-amplified for 10 cycles, quantified by MiSeq Nano V2, and sequenced on an Illumina NovaSeq S1 flow cell with 150 bp paired-end run to obtain about 30 million reads per sample

treatment_protocol: Peritoneal macrophages were cultured for 24hours with 100µg/mL human medium oxidized LDL, followed by treatment with 10ng/mL ultrapure LPS where indicated.

value: Peritoneal cavity

value: Peritoneal macrophages

value: LPS; OxLDL


title: RH4, sgNFYC, SIX1, rep1


title: Mouse; Replicate 2_oxLDL

value: No LPS; OxLDL


title: Mouse; Replicate 3_oxLDL+LPS

value: WT


title: Mouse; Replicate 3_Control

value: No LPS; No OxLDL


title: Mouse; Replicate 3_oxLDL


title: Tet2mut, RNA, sample4

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

institute: University of Veterinary Medicine, Vienna

description:
HiSeq4A
4_19
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx

data_processing:
RNA-Seq: fastQC, preprocessing with PRINSEQ-lite, alignment against mouse reference genome mm10 with BWA, differential gene expression with DESEQ2
ATAC-Seq: fastQC, preprocessing with PRINSEQ-lite, alignment against mouse reference genome mm10 with BWA, further processing with SAMtools, peakcalling with MACS2
Assembly: mm10
Supplementary files format and content: ATAC: coverage as bigWig files and peaks as bed files
Supplementary files format and content: RNA-seq: tables of normalized expression and differential expression results

source_name: murine Cebpap30/p30

growth_protocol: Cells were maintained in RPMI supplemented 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 µg of total RNA was used for construction of sequencing libraries. gDNA for ATAC-Seq was harvested from 50.000 cells with Nextera DNA Library Preparation Kit (Illumina).
RNA libraries were constructed using QUANTseq 3' mRNA-Seq Library Prep Kit (Lexogen). ATAC libraries were generated at the Biomedical Sequencing Facility of CeMM, using custom Nextera Library Adaptors.

value: murine Cebpap30/p30


title: Mouse; Replicate 3_LPS

value: LPS; No OxLDL


title: Mouse; Replicate 2_LPS


title: Mouse; Replicate 1_oxLDL+LPS


title: Tet2mut, RNA, sample5

description:
HiSeq4A
4_20
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: RH4, sgNFYC, PEG3, rep1


title: Mouse; Replicate 1_oxLDL


title: Mouse; Replicate 1_LPS


title: Tet2mut, RNA, sample3

description:
HiSeq4A
4_15
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: ATAC-seq in DMSO-treated PIPER-15 cells replicate 1


title: RH4, sgNFYC, JUN, rep2


title: Mouse; Replicate 1_Control


title: Tet2mut, RNA, sample2

description:
HiSeq4A
4_9
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: RH4, sgNFYC, JUN, rep1


title: Tet2mut, RNA, sample1

description:
HiSeq4A
4_8
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: Mouse; Replicate 2_Control


title: WT naïve CD4+ T cells 1

value: Spleen/peripheral lymph nodes

value: naive CD4+ T cells


title: RAG D10 Gene Expression

city: Irvine

first: Aaron

last: Longworth

state: California

address: Sprague Hall, 839 Health Sciences Rd

department: Physiology & Biophysics

institute: University of California, Irvine

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned utilizing 10x Genomics Cell Ranger Count 3.0.2 to a dual indexed GRCh38 and mm10 reference genome
Assembly: Dual indexed GRCh38 and mm10
Supplementary files format and content: tab-separated value (*.tsv) files

source_name: Brain

growth_protocol: EO771 cells were cultured in RPMI 1640, 5% FBS, 10U/ml penicillin, 0.1mg/mL streptomycin, 10mmol/L HEPES at 37 °C, 5% CO2, 95% relative humidity. Cells were passaged for one-two weeks prior to intracranial injections

extract_protocol:
Whole dissected brains were chopped into 8 pieces of equal size and placed into C tube (Miltenyi Biotec, Cat#130-093-237) 1mg/mL Collagenase D (Millipore Sigma Cat#11213857001)  Brain tissue was digested using gentleMACS Octo Dissociator with heaters operating the 37°C Adult adult brain dissociation protocol for 30 minutes. After digestion, the cell suspension was strained over a sterile 70μm strainer (Fisher Scientific, Cat#22363548) and washed with 5mL FACS buffer containing ice cold DMEM/F12, 50mM HEPES, and 2% BSA. After removal of myelin by density centrifugation, the cell pellet was washed and remaining red blood cells were lysed with red blood cell lysis buffer. Cells were then re-suspended in FACS buffer and blocked with anti-CD16/32 for 15 minutes on ice. Next, cells were stained with fluorescent antibodies on ice for 15 minutes shielded from light. C57BL/6 and RAG1-KO cells from individual mice were labeled using a CellPlex multiplexed oligo labeling kit in accordance with the manufacturer’s protocol (10x Genomics Cat# 1000261). The labeled cells were washed with 500μL of FACS buffer and resuspended in 500μL of FACS buffer, strained through 40μm strainer prior to sorting on BD FACSAria Fusion sorter.
Cells were resuspended to achieve approximately 1,000 cells/µL. Final cell suspensions were counted on the Countess II automated cell counter to determine actual concentration for droplet generation. Cells were loaded onto the 10x Genomics Chromium Single Cell Gene Expression 3’ v2 Chemistry kits for GEMs generation. Following the Chromium Single Cell 3′ Reagents Kits version 2 user guide (CG00052 Rev B), cells were loaded to achieve approximately 10,000 cells for capture. Libraries were sequenced on the or NovaSeq 6000 platform to achieve an average of read depth of 50,000 mean reads per cell.

treatment_protocol: 100,000 EO771 cells harboring enhanced GFP and firefly luciferase transgenes were injected intracranially in 10 μL PBS to a depth of 3mm into the right coronal suture of five-week-old mice.

value: Brain

value: CD45 hi-int

tag: age

value: 5 weeks

value: 100,000 EO771 cells intracranial


title: RAG D10 Multiplexing

library_source: other

molecule: other


title: RH4, sgNFYC, PEG3, rep2


title: RAG D4 Multiplexing


title: Tet2wt, RNA, sample7

description:
HiSeq4A
LL_wt13
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: RAG D4 Gene Expression


title: Tet2wt, RNA, sample5

description:
HiSeq4A
LL_wt9
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: Tet2wt, RNA, sample4

description:
HiSeq4A
LL_wt8
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: BL6 D4 Multiplexing


title: BL6 D10 Multiplexing


title: C3,CLP88

city: Changsha

first: Desheng

last: Qi

state: Hunan

address: Xiangya Road 87

department: Department of Emergency

institute: Xiangya Hospital, Central South University

data_processing:
1) Sequencing data quality assessment: mainly through the statistics of sequencing error rate, data volume, comparison rate, etc., to evaluate whether the sequencing of the database has reached the standard. If it meets the standard, follow-up analysis will be carried out; otherwise, the database needs to be rebuilt or additional test.
2) Information mining and analysis: The RNA-seq standard analysis process includes quality control, comparison, splicing, screening, quantification, difference significance analysis, functional enrichment and other steps.
3)Standard analysis:RNA-seq standard analysis process mainly includes quality control, comparison, splicing, screening, quantification, difference significance analysis, functional enrichment and other steps.
4)Standard analysis:The central of RNA-seq analysis is the significance of differences in gene expression, using statistics methods to compare the differences in gene expression between two or more conditions (e.g., treatment versus control), identify the differentially related genes.
5)Standard analysis:Further analyze the biological significance of these differentially expressed genes.
Assembly: mm10
Supplementary files format and content: RPKM values for each Sample
Supplementary files format and content: Read count  values for each Sample

source_name: heart

growth_protocol: The experimental object of mice were fed normally in  SPF environment.

extract_protocol:
RNA is extracted from cardiac tissues, followed by strict quality control of RNA samples. Quality control standards mainly include the following three aspects:(1) Agarose gel electrophoresis: analysis of RNA integrity and DNA contamination;(2) Nanodrop: initial quantification, detection of RNA concentration and purity (OD260/280 and OD260/230);(3) Agilent 2100 bioanalyzer: accurately detect RNA integrity.
A strand-specific library was constructed by removing ribosomal RNA. First, ribosomal RNA was removed from total RNA, followed by the use of the RNase R enzyme. The RNA was broken into short fragments of 250 to 300 bp. The first strand of cDNA was synthesized using the fragmented RNA as a template and random oligonucleotides as primers. The RNA strands were subsequently degraded by RNase H. And in the DNA polymerase I system, the second strand of cDNA was synthesized from dNTPs (dUTP, dATP, dGTP, and dCTP). The purified double-stranded cDNA was end-repaired, A-tailed and ligated to A sequencing adaptor.And after screening with AMPure XP beads, about 350 to 400 bp cDNA was selected. The second strand of U-containing cDNA was degraded by USER enzymes, followed by final PCR amplification and library acquisition.

treatment_protocol: Sham operation or cecal ligation and puncture procedure

value: heart

tag: group

value: CLP  normal LVEF


title: WT

first: Wei

last: Fan

address: Youyi Road, No1

department: Urology

institute: The First affiliated hospital of Chongqing Medical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. The library preparations were sequenced on Illumina Novaseq platform at Tianjin Novogene Bioinformatic Technology Co., Ltd. (Beijing, China) and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using fastp[2] (version 0.20.0). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data.
Mapping  Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA[3] (v0.7.12) and clean reads were aligned to the reference genome using BWA mem  -k 32 -T 30 -t 4 -M. These reads were then filtered for high quality (MAPQ ≥ 13), we also removed reads that were not properly paired and with PCR duplicates. Only uniquely mapped(MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
Peak calling  All peak calling was performed with MACS2 [4] (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.  Motif analysis  Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences were performed using findMotifsGenome.pl program in HOMER[5]( v4.9.1) software with ‘-len 8,10,12,14 -gc -size given -homer2 -dumpFasta’.  Peak annotation  The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker[6] (Yu et al., 2015) was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak-related genes[7]. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of peak related genes in KEGG pathways[8].  Different peak analysis  Peaks of different groups were merged using ‘bedtools[9] merge’.We caltulated the mean RPM of each group in the merge peak. Only peaks with fold change of RPM more than 2 were considered as differential peaks. Genes associated with different peaks were identified using ChIPseeker.
Assembly: mm8
Supplementary files format and content: bigWig
Library strategy: CUT& Tag

source_name: spleen

growth_protocol: Naïve CD4+ T cells were sorted by magnetic sorting using a naive CD4+ T Cell Isolation Kit from the spleen and lymph nodes (LNs) of C57BL/6J mice (Stem Cell). 24-well plate was precoated with anti-mouse CD3 (2μg/ml, Biogems) and anti-mouse CD28 (2μg/ml, Biogems) the day before Naïve CD4+ T cells being seeded at 0.5 × 10^6/well. Then, the differentiation of Th17 cell was stimulated by adding 20 ng/ml IL-1β (Peprotech), 20 ng/ml IL-23(Biolegend), 25 ng/ml IL-6 (Peprotech), and 3 ng/ml TGF-β (Peprotech).

extract_protocol:
The cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation.
DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system.( Hyperactive Universal CUT&Tag Assay Kit for Illumina, vazyme).

treatment_protocol: sh-Ikzf1 was used to knockdown the endogenous Ikzf1 of both sample and then Sample WT was overexpressed with WT Ikzf1 and Sample K164R was over expressed with K164R Ikzf1.

value: spleen

value: primary cell

value: CD4 T cells

value: Th17 induction

tag: chip antibody

value: Cell Signaling Technology (CST),  #14859


title: BL6 D4 Gene Expression


title: K164R

value: K164R mutation and Th17 induction


title: BL6 D10 Gene Expression


title: Tet2wt, RNA, sample6

description:
HiSeq4A
LL_wt10
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: C3,CLP95

value: WT


title: C3,CLP90


title: Tet2wt, RNA, sample3

description:
HiSeq4A
LL_wt6
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx

value: murine Cebpap30/p30


title: C3,CLP84


title: Tet2wt, RNA, sample2

description:
HiSeq4A
LL_wt3
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: RH4, sgRosa, PEG3, rep2

value: rhabdomyosarcoma

value: sgRosa


title: RH4, sgRosa, PEG3, rep1


title: C2,CLP83

value: CLP low LVEF


title: RH4, sgRosa, JUN, rep2


title: RH4, sgNFYC, ERRFI1, rep2

description: RH4_sgNFYC_ERRFI1_rep1_rep2_averaged.wig

value: sgNFYC


title: C2,CLP93


title: RH4, sgRosa, SIX1, rep1


title: RH4, sgNFYC, ERRFI1, rep1


title: Tet2wt, RNA, sample1

description:
HiSeq4A
LL_wt2
normalized_expr_quantseq.txt
DESeq_quantseq.xlsx


title: C2,CLP81


title: RH4, sgRosa, JUN, rep1


title: RH4, sgRosa, SIX1, rep2


title: Tet2wt, ATAC, sample4

description: HiSeq


title: C1,CLP97

value: CLP high LVEF


title: C1,CLP92


title: RH4, sgRosa, ERRFI1, rep2

description: RH4_sgRosa_ERRFI1_rep1_rep2_averaged.wig


title: C1,CLP85


title: C1,CLP86


title: Tet2wt, ATAC, sample3

description: HiSeq


title: RH4, sgRosa, ERRFI1, rep1


title: S,Sham80

value: sham


title: S,Sham77


title: S,Sham76


title: S,Sham79


title: Tet2mut, ATAC, sample4

description: HiSeq


title: RH4_sgNFYC_scRNAseq

description: 10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Reads were aligned to the human reference genome version gex-GRCh38-2020-A available from the 10X Genomics website. Matrices from each separate sample were aggregated using the Cell Ranger aggr (v6.0.0) pipeline using the “normalize=mapped” parameter to adjust cross-sample read depth by downsampling.
Gene expression was normalized after masking highly expressed genes using the function scanpy.pp.normalize_total() with the flag exclude_highly_expressed=True, followed by log-transformation. Principal component analysis was restricted to the top 4,000 most highly expressed genes, excluding mitochondrial and ribosomal genes.  The top 50 principal components were used to compute the KNN graph and perform UMAP dimensionality reduction and graph-based clustering via the Leiden modularity optimization algorithm using a default resolution of 0.5
Cells with fewer than 10,000 UMIs or greater than 10% mitochondrial gene content were discarded. This stringent cutoff served to filter droplets containing significant UMI counts but lacking abundant nuclear noncoding RNAs MALAT1 and NEAT1, suggesting they were non-nucleated cell fragments generated during the cell harvesting step.  During our analysis, we also noted a small cluster of cells present in all conditions that was marked by the expression of the dosage compensation noncoding RNA XIST, whereas the majority of cells in the matrix lacked its expression.  The RH4 RMS cell line (female) has not previously been reported to express XIST, and we reasoned that these few cells might represent either a spontaneous mutation, minor contamination, or other artifact.
For pseudotime analysis, Palantir (Setty et al. 2019) was called via the scanpy.external API.  Briefly, gene expression data was first denoised by conducting principal component analysis on the top 4,000 highly variable genes. Scanpy.external.palantir() was used to compute a nearest-neighbor graph (k=30 neighbors) and diffusion maps based on the top 50 principal components. To determine the starting cell for pseudotime calculation, we arbitrarily chose the cell from the “Resting-undifferentiated” cluster with the most extreme UMAP X-coordinate, farthest from the various differentiated cell clusters in the 2D projection.  This was fed into the Palantir “early_cell” parameter, which is used to determine an optimal nearby root cell for pseudotime calculation.  For visualization, cells were embedded in a 2D plane using t-SNE computed from the first 5 Palantir diffusion components.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files in a gzip-compressed tarball archive. Comma-separated metadata file containing sample barcodes included in analysis, cell type labels, computed scores, etc. Scanpy (AnnData) object in .h5ad format containing the full normalized and raw expression matrices, dimensionality reductions, etc.

source_name: rhabdomyosarcoma cell line

extract_protocol:
Cultured cells were harvested by trypsinization, stained with AO/PI (acridine orange / propidium iodide, Nexcelom ViaStain), and checked for viability > 80% using a Countess FL II Automated Cell Counter.
Libraries were constructed according to the manufacturer’s instructions (Single Cell 3’ Gene Expression NextGEM v3.1 protocol, 10x Genomics). Single-cell suspensions were diluted to a concentration targeting a yield of ~5,000 cells per sample before adding to the reaction master mix.

treatment_protocol: RH4 PAX3-FOXO1+ Cas9+ cell line was lentivirally transduced with sgRNAs targeting NFYC, PAX3-FOXO1 or ROSA26 control. Infected cells were drug selected and harvested at day 7 post transduction to assess gene expression changes induced by the gene knockouts.

value: rhabdomyosarcoma cell line


title: RH4_sgPAX3-FOXO1_scRNAseq

description: 10x Genomics


title: PBS2hr rep 2

city: El Paso

first: Enrique

middle: Ivan

last: Ramos

state: Texas

address: 5001 El Paso Dr.

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

data_processing:
Reads were aligned to Mus  musculus GRCm38 transcriptome using the Hisat2 aligner
Read counts were generated using feature counts with Ensembl version 101 mus musculus GRCm38 as reference with "-t exon, -g gene_id or -g exon_id, and -a annotation.gtf" as options.
Differential gene expression was determined using the DeSeq2 package in R
Assembly: Mus musculus GRCm38 transcriptome
Supplementary files format and content: tab delimited txt file with raw read counts for each sample

source_name: C57BL/6 mice

growth_protocol: Bone marrow derived macrophages (BMDMs) were isolated from C57BL/6 mice as described previously. Briefly, mice were euthanized, and its femur and tibia were surgically removed. The outer connective tissues were cleaned using scalpel and scissors and a small portion of bone was cut off on both ends. A hole was made through the end of 0.5ml microfuge tubes using 18G needle, then the 0.5mL tubes with femur and tibia were placed in 1.5mL microfuge tubes and centrifuged at maximum speed for 15 secs. The pelleted cells were incubated with ammonium chloride-potassium (ACK) lysis buffer (Invitrogen) at room temperature for 5 min to lyse the red blood cells. This was neutralized by the addition DMEM medium (Corning, USA) with 10% fetal bovine serum (FBS; HyClone, Logan, UT). Then the cells were collected via centrifugation and plated in 100 mm tissue culture dish with BMDM medium (DMEM, 10% fetal bovine serum,10 ng/ml of M-CSF, 1x Penicillin-Streptomycin) and incubated at 37°C in 5% CO2 for 5-7 days, with replacement of medium for every 2-3 days.

extract_protocol:
BMDMs (1 x10^6 cells/well) in each well of a 6-well culture plate were infected with MSC or MSM at an MOI of 1:5 or uninfected (control cells) and incubated for 2 h at 37°C in a CO2 incubator. After the incubation, the cells were washed with 1xPBS to remove the extracellular bacteria. Then the cells were lifted using cell scraper and collected via centrifugation at 200xg for 10 minutes. Total RNA was isolated from the infected BMDMs using EZ-10 DNAaway RNA Mini-Preps Kit (Bio Basic, Canada). TapeStation (Agilent Technologies 4200) was used to analyze RNA integrity of the preparation, and RNA quantification was done using Nanodrop (Thermo Scientific, USA). 4 ug of total RNA with >9 RIN (RNA Integrity Number) was used for RNA-Seq library preparation.
The quality assessment of RNA samples was carried out by Nanodrop, agarose gel electrophoresis, and Tape station. After the QC procedures, mRNA was enriched using oligo (dT) beads. First, the mRNA was fragmented randomly by adding a fragmentation buffer. Then the cDNA is synthesized by using an mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H, and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of steps, including terminal repair, A ligation, and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. Quality control of the library consists of three steps: Quibit 2.0, Agilent 2100, and Q-PCR. Finally, qualified libraries are fed into Illumina sequencers (NovaSeq 6000) after pooling according to their effective concentration and expected data volume. RNA-sequencing was done at Novogene Corporation Inc. (Sacramento, CA, USA).
Strand-Specific (dUTP-based) paired end libraries

treatment_protocol: MSC and MSM strains were grown in 7H9 medium with appropriate antibiotics to OD600= 1.0. The cells were pelleted, PBS washed, and the clumps were dispersed using a syringe with 23G needle. The colony forming units (CFUs) of the suspensions were determined and stored at -80°C until further analysis. Freshly isolated BMDMs were seeded on 24 well or 6 well tissue culture plate (Corning, USA) in BMDM medium and incubated overnight at 37°C with 5% CO2. Next day the cells were washed with 1x PBS to remove the antibiotics and the cells were infected MSC or MSM at MOI (Multiplicity of infections) 1:5.

value: Bone marrow derived macrophages (BMDMs)


title: Tet2mut, ATAC, sample3

description: HiSeq


title: MSM2hr rep 1


title: MSM2hr rep 2


title: PBS2hr rep 1


title: MSC2hr rep 1


title: Tet2mut, ATAC, sample2

description: HiSeq


title: RH30, seBE, d8, sgCCAAT2a, abNFYB

description: RH30_seBE_d8_sgCtrl2_vs_sgCCAAT2a_differential_p0.001_F2.5.bed

data_processing:
Quality control was performed using FastQC. Adapters were trimmed using Trimmomatic.
Reads were mapped to the reference genome (hg38) using bowtie2.
Peaks were called using MACS2 algorithm at a threshold of p < 0.0000001. NF-Y consensus peak set was derived from NF-YB and NF-YC peak sets using bedtools intersect.
For assessment of differential NF-Y binding following base editing, data was trimmed and aligned as above. Peaks were called using Homer findPeaks. Differentially bound sites were identified using Homer getDifferentialPeaks (pval <=0.001; fold change >2.5 in sgCtrl1). For visualization, bam files were CPM-normalized using bamCoverage.
Assembly: hg38
Supplementary files format and content: peaks (bed); NF-Y consensus peaks (bed); differential peaks between sgCtrl1 and all other sgRNAs (bed); genome browser tracks (CPM normalized for base edited samples) (bw)
Library strategy: CUT&RUN

extract_protocol:
Cells were processed according to Epicypher CUT&RUN protocol (https://www.epicypher.com/content/documents/protocols/cutana-cut&run-protocol.pdf).
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocol (https://www.neb.com/-/media/nebus/files/manuals/manuale7103-e7645.pdf?rev=de09eaf8fcdf45e0ac8a66bf6fee75fb&hash=4617FF2DC70A34462B8C24A16123353B).

treatment_protocol: RH4 cells were untreated. RH30 cell (engineered to express inducible cytosine base editing system) were transduced with sgRNAs. At day 2 post-transduction, cells with sgRNAs cells were drug selected with blasticidin. Two days after the start of drug selection, rapamycin was added to cell cultures to induce base editing. Cells were harvested 8 days post rapamycin addition and CUT&RUN was performed. Base editing at the CCAAT locus was confirmed through Sanger sequencing and trace deconvolution with EditR.

tag: antibody

value: NFYB


title: RH30, seBE, d8, sgCCAAT2b, abNFYB

description: RH30_seBE_d8_sgCtrl2_vs_sgCCAAT2b_differential_p0.001_F2.5.bed


title: Tet2mut, ATAC, sample1

description: HiSeq


title: Immortalized DKO MEF rep2

city: pittsburgh

first: Edward

middle: V.

last: Prochownik

state: PA

address: 4401 Penn Avenue

department: Section of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh

data_processing:
CLC Genomics Workbench v 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Mus musculus (GRCm39.104) using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm39
Supplementary files format and content: tab-delimited text files include CPM(TMM-adjusted) values for each Sample

source_name: embryonic

growth_protocol: Standard MEF cultures were generated from ~E14-E16 embryos with the cells from at least six embryos being pooled, All MEFs were maintained in Dulbecco’s modified minimum essential medium (D-MEM) containing 10% fetal bovine serum, glutamine and penicillin/streptomycin. Quantification of target gene excision was then performed as

extract_protocol:
RNAs were isolated using RNeasy kits, according to the directions of the supplier (Qiagen, Inc. Germantown, MD). RIN values were determined with an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA) and all samples had RIN values >9.6.
Sequencing libraries were generated from triplicate sets of RNAs from control WT MEFs and each KO group using a NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs, Beverly, MA).Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms.

treatment_protocol: To excise the Myc and/or Mlx loci, MEFs were re-established from frozen stocks and allowed to attain log-phase growth before being exposed to 500 nM 4-hydroxytamoxifen (4OHT) or the 70% ethanol vehicle alone, which were changed daily. For MEF immortalization, A lentiviral vector encoding SV40 T-antigen and blasticidin resistance (GenTarget, Inc., San Diego, CA) was used to transduce each of the above three MEF cell lines in 12 well plates.  Following a 72 hr exposure to the viral stock (MOI=1), the cells were expanded over the next week at which point Blasticidin (Thermo Fisher, inc. Pittsburgh, PA) was added at a concentration of 1 μg/ml for five days and then 2 μg/ml for an additional 10 days. Under these conditions, non-transduced cells were completely killed by the antibiotic.

value: embryonic

value: Immortalized DKO MEF

value: murine embryonic fibroblasts

value: DKO


title: Immortalized DKO MEF rep3


title: RH4_sgROSA_scRNAseq

description: 10x Genomics

value: sgROSA


title: RH30, seBE, d8, sgCtrl2, abNFYB


title: Tet2wt, ATAC, sample1

description: HiSeq


title: Immortalized DKO MEF rep1


title: Tet2wt, ATAC, sample2

description: HiSeq


title: CD4+ Tnaive SCD1KO_Rep4

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

data_processing:
raw sequence reads was checked using FastQC version 0.11.8, and nucleotide calls with a quality score of 28 or higher were considered high quality. Adapters were removed using cutadapt v.2.4. Reads were aligned to the mouse genome reference, using STAR (2.5.0e) and a maximum of five mismatches were allowed.
Gene counts were retrieved using htseq-count using the “union” option. After removing absent features (zero counts in all samples), the raw counts were imported to R/Bioconductor package DESeq2 v.3.9 to identify differentially expressed genes among samples. The default DESeq2 options were used,

source_name: Splenocytes

extract_protocol: RNA was extracted with QIAzol reagent, followed by RNA extraction with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: 11 weeks

tag: gender

value: Female

value: CD4+ naive T cells

tag: replicate


title: RH30, seBE, d8, sgCtrl1, abNFYB

description: RH30_seBE_d8_sgCtrl2_vs_sgCtrl1_differential_p0.001_F2.5.bed


title: RH30, seBE, d8, sgCtrl1, abIgG

value: IgG


title: Immortalized MycKO MEF rep1

tag: tissue

value: Immortalized MycKO MEF

value: MycKO


title: Immortalized MycKO MEF rep2


title: CD4+ Tnaive SCD1KO_Rep2


title: MSC2hr rep 2


title: Immortalized MlxKO MEF rep2

value: Immortalized MlxKO MEF

value: MlxKO


title: CD4+ Tnaive SCD1KO_Rep1


title: Immortalized MlxKO MEF rep1


title: CD4+ Tnaive WT_Rep4

value: WT


title: RH4, uninfected, abNFYB

description: RH4_uninfected_NFYB_NFYC_consensus_peaks_hg38.bed

value: rhabdomyosarcoma cell line


title: RH4, uninfected, abIgG


title: CD4+ Tnaive WT_Rep3


title: Immortalized WT MEF rep3

value: Immortalized WT MEF


title: Immortalized WT MEF rep2


title: Immortalized WT MEF rep1


title: Primary DKO MEF rep3

value: Primary DKO MEF


title: Primary DKO MEF rep2

value: embryonic


title: Immortalized MycKO MEF rep3


title: Primary DKO MEF rep1


title: test library, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen

data_processing:
Quality of the sequencing data was assessed using FastQC. Demultiplexing was performed in the command line, using the -grep function.
The reads were mapped to the reference sgRNA library and counted using MAGeCK count function.
For myo-differentiation screens, comparison between samples and calculation of the beta scores for each gene was done using MAGeCK-MLE (using the mageck test and mageck mle commands).
For the test library and both negative selection and myo-differentiation exon scans, MAGeCK-derived sgRNA counts were normalized across timepoints and fold changes (for negative selection: day 3 vs. day 8; for MYH screens: MYH high vs. MYH low) were calculated.
Assembly: N/A
Supplementary files format and content: raw counts mapping to individual sgRNAs (txt); gene essentiality scores from MAGeCK MLE (txt)
Library strategy: CRISPR screens

extract_protocol:
Genomic DNA was extracted using phenol-chlorophorm.
Libraries were constructed through a two-step PCR; first, sgRNA cassette was amplified with the following primers: fwd - TCTTGTGGAAAGGACGAAACACCG; rev - TCTACTATTCTTTCCCCTGCACTGT (cycling conditions: 10 min at 95oC; 25 cycles of 30 seconds at 95oC, 45 seconds at 60oC, 30 seconds at 72oC; 7 min at 72oC). The 242 bp fragments were gel purified using the QIAquick Gel Extraction Kit (Qiagen, 28706X4) and used as a template for the second PCR to incorporate sequencing adapters and barcode the samples. The following primers were used for the second PCR:forward:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNHNNNNATCACGGTGGAAAGGACGAAACACC; reverse:CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTGTTTCCAGCATAGCTCTTAAAC; cycling conditions as above but for 8 cycles total. The libraries (~190 bp) were gel purified and their quality was assessed on Agilent 2100 Bioanalyzer using the Agilent DNA 1000 Assay (Agilent, 5067-1504). Libraries were quantified using Qubit dsDNA BR Assay (Thermo Fisher Scientific, Q32850) and KAPA Library Quantification Kit (KK4824), diluted, pooled at equimolar concentrations and sequenced on the Illumina NextSeq500 platform using the single end SE75 bp mode of sequencing.

treatment_protocol: Myo-differentiation screen: Infected cells were drug selected, harvested at day 7 post-infection, fixed, permeabilized and stained with anti-MYH antibodies. Stained cells were separated by FACS into myosin heavy chain (myo-differentiation marker; MYH) high and low pools, genomic DNA was extracted, sgRNA cassette was amplified and sequenced. Negative selection exon scan: Infected cells were harvested at day 3 post-infection to capture the initial sgRNA representation, then drug selected and harvested again at day 18 post-infection to allow for gene knockouts that lead to loss of cell fitness to drop out from population. Genomic DNA was extracted from each pool of cells, sgRNA cassette was amplified and sequenced.

value: rhabdomyosarcoma

value: sgRNA library (test_library)


title: CD4+ Tnaive WT_Rep2


title: CD4+ Tnaive SCD1KO_Rep3


title: Immortalized MlxKO MEF rep3

value: murine embryonic fibroblasts


title: Primary MycKO MEF rep1

value: Primary MycKO MEF


title: test library, myodifferentiation screen, MYH high


title: exon scan, negative selection screen, day 18

description:
gDNA (sgRNA cassette)
negative selection screen

value: sgRNA library (exon_scan)


title: RH4, uninfected, abNFYC

value: NFYC


title: exon scan, negative selection screen, day 3


title: Primary MlxKO MEF rep3

value: Primary MlxKO MEF


title: Primary MlxKO MEF rep1


title: Primary WT MEF rep3

value: Primary WT MEF


title: exon scan, myodifferentiation screen, MYH low


title: Primary WT MEF rep2


title: Sample 7, Asymptomatic

first: Lbachir

last: BenMohamed

address: 843 Health Sciences Road, Hewitt Hall, 2nd Floor

institute: University of California Irvine

data_processing:
Trimmed sequencing reads were mapped to hg38 and feature count data was generated using htSeq.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes RPKM values for each sample.

source_name: PBMC

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1.5ug of total RNA was used for building sequencing libraries.
RNA libraries for RNA-Seq were prepared using TruSeq Ribo-Zero Total RNA Library preparation Kit following manufacturer's protocols.

value: PBMC

value: Asymptomatic


title: Sample 8, Asymptomatic


title: Primary WT MEF rep1


title: Sample 6, Asymptomatic


title: exon scan, myodifferentiation screen, MYH high


title: Sample 5, Asymptomatic


title: Lyz2-Cre/Myd88 fl/fl 16 Gy 4

city: Portland

first: Michael

middle: J

last: Gough

state: Oregon

address: 4805 NE Glisan St

department: EACRI

institute: Providence Portland Medical Center

description: single cell RNA

data_processing:
Libraries were sequenced using an Illumina NovaSeq 6000 using a NovaSeq 6000 S2 reagent kit (v1.0). Data were processed using the Cell Ranger pipeline (v5.0.0) and subsequently analyzed with the Loupe Browser from 10X Genomics (v5.0).
BCL to fastq conversion using cellranger mkfastq with cellranger v5.0.0 and dependency bcl2fastq2 v2.20.0
cellranger count with default settings run on each sample individually to generate single cell features counts
cellranger aggr with default settings (--normalize=mapped) to aggregate all samples into a single .cloupe file for exploration in Loupe Cell Browser
Genome_build: mm10

source_name: CD45+ cells isolated from subcutaneous PK5L1940 pancreatic tumors

growth_protocol: 0.2 x 10^6 PK5L1940 cells were implanted subcutaneously in syngeneic mice

extract_protocol: 3 days post-RT (16 Gy), single cell suspensions from PK5L1940 tumors were generated. Tumors were manually minced using scissors, followed by a 45 minute enzymatic digestion in HBSS supplemented with 250 U/mL collagenase IV (Worthington) and 30 U/mL DNaseI (Roche), 5 mM CaCl2, and 5% FBS at 37o C with constant agitation. Immune cells from single cell suspensions were positively selected using anti-mouse CD45 MicroBeads (Miltenyi Biotec). Cells were then incubated in PBS containing Live/Dead Aqua, before a secondary incubation with anti-CD45. Live CD45+ cells were sorted using a BD FACSAria. Cells were processed according to the manufacturers protocol for the Chromium Single Cell 3’ Reagent kit (v3.0) from 10X Genomics.

treatment_protocol: 14 days-post implantation, mice were given 16 Gy RT using the Small Animal Radiation Research Platform (Xstrahl)

value: Lyz2-Cre/Myd88 fl/fl

value: 16 Gy


title: Myd88 fl/fl 16 Gy 4

description: single cell RNA

value: Myd88 fl/fl


title: CF3, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
CF3_MLE.txt

value: sgRNA library (CF3)


title: Primary MycKO MEF rep2

value: MycKO


title: Myd88 fl/fl 16 Gy 3

description: single cell RNA


title: Sample 4, Symptomatic

value: Symptomatic


title: Primary MycKO MEF rep3

value: embryonic


title: CF3, myodifferentiation screen, MYH high

value: rhabdomyosarcoma


title: Primary MlxKO MEF rep2

value: MlxKO


title: Sample 3, Symptomatic


title: Myd88 fl/fl Untreated 4

description: single cell RNA

value: Untreated


title: Lyz2-Cre/Myd88 fl/fl 16 Gy 2

description: single cell RNA


title: Myd88 fl/fl Untreated 3

description: single cell RNA


title: Sample 2, Symptomatic


title: Lyz2-Cre/Myd88 fl/fl 16 Gy 3

description: single cell RNA


title: CF2, myodifferentiation screen, MYH high

description:
gDNA (sgRNA cassette)
myo-differentiation screen
CF2_MLE.txt

value: sgRNA library (CF2)


title: Lyz2-Cre/Myd88 fl/fl Untreated 4

description: single cell RNA


title: CF2, myodifferentiation screen, MYH low


title: Lyz2-Cre/Myd88 fl/fl Untreated 3

description: single cell RNA


title: Lyz2-Cre/Myd88 fl/fl Untreated 2

description: single cell RNA


title: Myd88 fl/fl 16 Gy 2

description: single cell RNA


title: Sample 1, Symptomatic


title: CF1, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
CF1_MLE.txt

value: sgRNA library (CF1)


title: CD4+ Tnaive WT_Rep1

value: 11 weeks

value: Female

value: WT

value: CD4+ naive T cells


title: Myd88 fl/fl Untreated 2

description: single cell RNA


title: Lyz2-Cre/Myd88 fl/fl 16 Gy 1

description: single cell RNA


title: CF1, myodifferentiation screen, MYH high


title: DR2, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
DR2_MLE.txt

value: sgRNA library (DR2)


title: Lyz2-Cre/Myd88 fl/fl Untreated 1

description: single cell RNA

value: Lyz2-Cre/Myd88 fl/fl


title: Myd88 fl/fl Untreated 1

description: single cell RNA


title: Tbx1cko_7dpMI

city: Shanghai

first: Min

last: Zhang

state: Shanghai

address: 1678 Dongfang Road

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
CellRanger toolkit v2.1.0 was used to process the raw sequencing data. Reads were aligned to the mm10 genome build.
Genome_build: mm10
Supplementary_files_format_and_content: h5 files contain cell gene matrices

molecule: polyA RNA

source_name: Tbx1cko_pooled endothelial cells and immune cells

extract_protocol:
The pooled endothelial cells and immune cells were loaded into the 10X Genomics Chromium system for library construction.
Each set of cell suspension was subjected to the GemCode Single Cell Instrument to generate single-cell gel beads in emulsion (GEMs), targeting for 8,000 cell yield. Following the lysis step, cDNA was synthesized and amplified using the Chromium Single Cell 3’ Reagent Kits v2 (10× Genomics, USA), as per the standard protocols provided by the manufacturer

tag: disease model

value: myocardial infarction

tag: developmental stage

value: two-month-old

tag: genotype/variation

value: heart

value: enriched CD31+ endothelial cells and CD45+ leucocytes


title: Ctrl_7dpMI

source_name: control_pooled endothelial cells and immune cells

tag: strain

value: Control

tag: cell type


title: DR1, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
DR1_MLE.txt

tag: genotype

value: sgRNA library (DR1)


title: DR2, myodifferentiation screen, MYH high

value: rhabdomyosarcoma


title: Tbx1cko_5dpMI


title: 20-637-117_het_D23

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

data_processing:
Raw fastq reads were subjected to quality control using FastQC (v0.11.7) and quality profiling, filtering for low quality and short reads, adapter trimming and mismatch correction using fastp (v0.20.1)
RNA reads were aligned to the hg38 build of the reference human genome, with transcript annotations from GENCODE, using the STAR aligner.
Gene expression was quantified using RSEM (RNA-Sequencing by Expectation Maximization)
Assembly: hg38
Supplementary files format and content: FOSB_Raw_Counts_RSEM.txt is a tab-delimited text file containing raw counts for each sample (generated using RSEM)

growth_protocol: The BIONi010-C-13 line (donor biosample SAMEA103988285) with doxycycline (DOX)-inducible neurogenin 2 (NGN2) transgene was obtained and is available from the European Bank for Induced pluripotent Stem Cells (EBiSC, www.ebisc.org). The line is derived from a dermal fibroblast sample donated by an 18 year-old healthy male of African-American descent. The EBiSC Bank acknowledges SAMEA103988285 as the source of human induced pluripotent stem cell line BIONi010-C-13 which was generated with support from EFPIA companies and the European Union (IMI-JU).

extract_protocol:
RNA was isolated from hiPSC-derived iNs at days 0, 2, 6, 13, and 23 using the AllPrep DNA/RNA mini kit (Qiagen). Samples were extracted manually according to the manufacturer’s instructions or on a QIAcube using the AllPrep DNA/RNA mini kit protocol (Qiagen).
For each timepoint, RNA from 4 technical replicates (4 independent wells of cells cultured simultaneously) were used per line. RNA library preparation from total RNA was conducted following the manufacturer’s protocol for the Kapa mRNA HyperPrep Kit (Roche). Briefly, 250 ng of total RNA was enriched for mRNA using magnetic oligo-dT beads. The remaining RNA was then fragmented by magnesium under elevated temperature. After fragmentation, RNA was depleted of rRNA and globin mRNA using the QIAseq FastSelect RNA Removal Kit (Qiagen). The depleted RNA then underwent first strand synthesis using reverse transcriptase and random primers. Combined second strand synthesis and A-tailing incorporated dUTP into the second cDNA strand for stranded RNA sequencing and added dAMP to the 3’ ends for adapter ligation. The cDNA fragments were then ligated to sequencing adaptors (IDT xGEN Dual Index UMI adapters) and was enriched using 16 cycles of PCR. Final libraries were assessed using the Agilent Tapestation and Qubit (ThermoFisher) assay methods then sequenced on an Illumina HiSeq 4000 sequencer using 2 x 75bp read length.

treatment_protocol: CRISPR/Cas9-mediated SNP editing of BIONi010-C-13 was completed by the Genomic Engineering & iPSC Center (GEIC) at Washington University School of Medicine. To generate clones Heterozygous for rs148726219, the parental BIONi010-C-13 line was transfected with HiFi Cas9 v3 (IDT), gRNA with sequence GAGCTGTGGGTGGCTAGGGC, and ~60 bp single-stranded DNA oligos as homology arms flanking the PAM site (left HA: cccgggctctttctacccttaacactctggaaagcctgtgaaatgaaattattccacctcT; right HA: ctagccacccacagctctcctggtgctggtggcatcccccaaaacccactcccttcctac). An episomal vector expressing GFP was used for selection of transfected cells by FACS-based single-cell sorting. Clones were expanded and genotypes confirmed by next generation sequencing (NGS). The wild-type clone was generated in the same CRISPR experiment but was untargeted. To generate homozygous clones, heterozygous clones were re-targeted a second time. Directed differentiation of hiPSCs to excitatory iNs was performed as previously described, with modifications.

value: iPSC

value: het

tag: day


title: 20-637-118_hom_D23

value: hom


title: 20-637-116_hom_D23


title: Ctrl_5dpMI


title: DR1, myodifferentiation screen, MYH high


title: KP2, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
KP2_MLE.txt

value: sgRNA library (KP2)


title: 20-637-119_het_D23


title: 20-637-120_hom_D23


title: 20-637-114_hom_D23


title: 20-637-115_het_D23


title: KP2, myodifferentiation screen, MYH high


title: 33736

type: genomic

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

label: Cy3 and Cy5

organism: Canis lupus familiaris

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: phenotype

value: Invasive Urothelial Carcimona

tag: breed

value: Shelties Mix

value: female


title: 33438

value: Border collie


title: 31596

value: Shetland Sheepdog


title: 20-637-113_het_D23

tag: cell line


title: 33269

value: Shetland S+L36:L184heepdog

tag: age

value: male


title: KP1, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
KP1_MLE.txt

tag: treatment

value: sgRNA library (KP1)


title: 30328


title: Myd88 fl/fl 16 Gy 1

description: single cell RNA

value: Myd88 fl/fl

value: 16 Gy


title: KP1, myodifferentiation screen, MYH high


title: 20-637-112_hom_D23

tag: group


title: 24796


title: 20-637-111_wt_D23

value: wt


title: 27343

value: Collie


title: 24651


title: 20-637-110_hom_D23


title: TF3, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
TF3_MLE.txt

value: rhabdomyosarcoma

value: sgRNA library (TF3)


title: 23513


title: Tbx1cko_4dpMI

value: myocardial infarction

value: two-month-old

value: heart

value: enriched CD31+ endothelial cells and CD45+ leucocytes


title: 20-637-109_wt_D23

value: iPSC


title: TF2, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
TF2_MLE.txt

value: sgRNA library (TF2)


title: Ctrl_4dpMI

value: Control


title: TF2, myodifferentiation screen, MYH high


title: 24275

value: Invasive Urothelial Carcimona

value: Australian Shepherd

value: female


title: TF1, myodifferentiation screen, MYH low

description:
gDNA (sgRNA cassette)
myo-differentiation screen
TF1_MLE.txt

value: sgRNA library (TF1)


title: 21481


title: 20-637-107_wt_D23


title: 20-637-108_hom_D23

value: hom


title: cd31_5dpmi_tbx1cko2

description:
Cko2.cd31
Ko5-cd31

data_processing:
Alignment: We used STAR (version 2.5.2b) to align raw reads to mouse genome (Gencode, GRCm38) and annotated transcripts and genes using Gencode mouse genome gtf file (vM10). Read abundance was quantified by STAR quantification mode '--quantMode GeneCounts'
Gene filtering: Raw read counts were loaded in R statistical environment and created a deseq object using DESeq2 package (R version 3.5.1, DESeq2 version 1.20.0). Read counts for individual samples were compiled by genes, low read count genes (total read count ≤ number of biological samples) were removed from downstream analyses. Mitochondrial genes and ribosomal genes were also removed.
Read normalization: Raw read counts were then normalized using DESeq2 command 'counts(deseq.df, normalized = T)'.
Genome_build: mm10
Supplementary_files_format_and_content: normalized read count

extract_protocol:
Total RNA was isolated from hearts using the TRIzol® LS Reagent (ThermoFisher scientific).
The library for mRNA sequencing was generated using Illumnia TruSeq Preparation Kit (RS-122-2001)

tag: strain background

tag: tissue/cell type

value: CD31+ endothelial cells


title: 20-637-105_wt_D23

value: wt


title: TF1, myodifferentiation screen, MYH high


title: 14482

value: Border collie

tag: gender


title: 20-637-106_hom_D23


title: 7966

value: Collie

value: male


title: RH4_sgNFYC_d4_rep2

description: RH4_d4_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

data_processing:
Sequencing reads were debarcoded and quality was assessed using FastQC. Reads were then mapped onto the reference human genome using HISAT2. Reads within genes were  counted using HTSeq-count. Differential gene expression analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 normalized read counts; tab-delimited or csv.

extract_protocol:
Cells were washed with PBS and lysed directly on plates.  RNA was extracted with TRIzol.
Libraries were prepared using the Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer’s Low Sample (LS) protocol.

treatment_protocol: Cas9-expressing cell lines were lentivirally transduced with sgRNAs and drug selected (drug selection start: day 2; drug selection end: day 4). Knockout cells were harvested at day 7 post-transduction.

value: rhabdomyosarcoma

value: sgNFYC


title: cd31_5dpmi_tbx1cko1

description:
CKo1.cd31
Ko3-cd31

value: myocardial infarction

value: two-month-old


title: RH4_sgNFYC_d4_rep1


title: 7647


title: TF3, myodifferentiation screen, MYH high

value: sgRNA library (TF3)


title: cd31_5dpmi_ctrl3

description:
Ctrl3.cd31
Ctrl3-cd31

value: control


title: 20-637-102_het_D23

value: iPSC

value: het


title: 20-637-104_het_D23


title: cd31_5dpmi_ctrl2

description:
Ctrl2.cd31
Ctrl2-cd31


title: 30323

value: Invasive Urothelial Carcimona

value: Mixed breed


title: RH4_sgPAX3-FOXO1_d4_rep1

description: RH4_d4_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular


title: cd31_5dpmi_ctrl1

description:
Ctrl1.cd31
Ctrl1-cd31


title: 7676

value: Sheltie Mix


title: 20-637-098_het_D23


title: 20-637-100_het_D23


title: 29644


title: RH4_sgRosa_d4_rep2

description:
RH4_d4_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular
RH4_d4_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

value: sgRosa


title: 20-637-096_hom_D13

value: hom


title: 28863

value: female


title: 20-637-095_het_D13


title: H3 control for H3.3 (HTR5-RFP) ChIP-seq in ddm1 biol Rep2

first: Jonathan

last: Cahn

institute: CSHL

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_HTR5_H3_Rep2

data_processing:
Adapter trimming with cutadapt
Genome alignement with Bowtie2-2.4.1
Deduplication with samtools
Bigwig made with Deeptools bamCompare with CPM normalization versus the corresponding control
Assembly: TAIR10
Supplementary files format and content: Bigwig files representating log2 fold change of count per million IP/Input or IP/H3(H4)

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were grown on ½ Murashige and Skoog (MS) medium for 10 days, or transplanted to soil after 7days until pollen maturity.

extract_protocol:
ChIP was performed as previously described (Parent et al., 2021), starting with 1g of seedlings. In brief, after crosslinking in 1% formaldehyde for 10 min, the tissue was ground to a fine powder in liquid nitrogen, chromatin was extracted with 1% SDS Tris-based lysis buffer and sonicated to ~200bp fragments. Chromatin was cleared with protein A magnetic beads and incubated overnight with the antibody listed below. Immune complexes were eluted with low, and then high salt buffers, before reversing crosslinks and purifying DNA fragments with ChIP DNA clean and concentrator kit (Zymo Research). Low input ChIP for MGH3-GFP was performed with ~10e8 pollen grains. Fixation was for 15 min and subsequent grinding with acid-washed glass beads. DNA fragments underwent a preliminary phenol-chloroform and ethanol precipitation step before clean up.
NEBNext Ultra II DNA Library Prep Kit

tag: tissue

value: seedlings

tag: background

value: Col0 + pHTR5:HTR5-RFP

tag: chip antibody

value: anti-H3 (Abcam; ab1791)

value: crosslinking


title: 29386

value: Collie

value: male


title: Dbt-P3F1_sgNFYC_d7_rep1

description: Dbt-P3F1_d7_sgRosa_sgNFYC_normalized_counts.csv

value: rhabdomyosarcoma

value: PAX3-FOXO1+ (engineered)

value: sgNFYC


title: 20-637-094_hom_D6

value: iPSC


title: 26350

value: Herding mix


title: RH4_sgPAX3-FOXO1_d4_rep2


title: 20-637-093_het_D6

value: het


title: H3 control for H3.3 (HTR5-RFP) ChIP-seq in WT biol Rep2

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_HTR5_H3_Rep2

extract_protocol:
ChIP was performed as previously described (Parent et al., 2021), starting with 1g of seedlings for the other proteins. In brief, after crosslinking in 1% formaldehyde for 10 min, the tissue was ground to a fine powder in liquid nitrogen, chromatin was extracted with 1% SDS Tris-based lysis buffer and sonicated to ~200bp fragments. Chromatin was cleared with protein A magnetic beads and incubated overnight with the antibody listed below. Immune complexes were eluted with low, and then high salt buffers, before reversing crosslinks and purifying DNA fragments with ChIP DNA clean and concentrator kit (Zymo Research). Low input ChIP for MGH3-GFP was performed with ~10e8 pollen grains. Fixation was for 15 min and subsequent grinding with acid-washed glass beads. DNA fragments underwent a preliminary phenol-chloroform and ethanol precipitation step before clean up.
NEBNext Ultra II DNA Library Prep Kit

value: wild-type


title: 25967

value: Invasive Urothelial Carcimona

value: Australian Shepherd

value: unknown


title: Dbt-P3F1_sgPAX3-FOXO1_d7_rep1

description: Dbt-P3F1_d7_sgRosa_sgPAX3-FOXO1_normalized_counts.csv


title: 20-637-092_hom_D2

value: hom


title: Dbt-P3F1_sgRosa_d7_rep1

description:
Dbt-P3F1_d7_sgRosa_sgPAX3-FOXO1_normalized_counts.csv
Dbt-P3F1_d7_sgRosa_sgNFYC_normalized_counts.csv

value: sgRosa


title: 20-637-091_het_D2


title: 24319

value: Border collie

value: female


title: H3.3 (HTR5-RFP) ChIP-seq in WT biol Rep1

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
WT_HTR5_IP_Rep1

value: seedlings

value: Col0 + pHTR5:HTR5-RFP

value: RFP-trap (ChromoTek; rtma-10)

value: crosslinking


title: H3 control for H3.3 (HTR5-RFP) ChIP-seq in WT biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_HTR5_H3_Rep1

value: anti-H3 (Abcam; ab1791)


title: RH18_sgNFYC_d7_rep2

description: RH18_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

value: rhabdomyosarcoma

value: sgNFYC


title: RH18_sgNFYC_d7_rep1


title: RH4_sgRosa_d4_rep1


title: 24318


title: H3.3 (HTR5-RFP) ChIP-seq in ddm1 biol Rep2

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
ddm1_HTR5_IP_Rep2


title: 20-637-090_hom_D0

value: iPSC


title: RH18_sgPAX3-FOXO1_d7_rep2

description: RH18_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular


title: 20-637-089_het_D0

value: het


title: H3 control for H3K27me1 ChIP-seq in ddm1 biol Rep2

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_H3K27me1_H3_Rep2


title: H3 control for H3.3 (HTR5-RFP) ChIP-seq in ddm1 biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_HTR5_H3_Rep1


title: 24311

value: male


title: H3.3 (HTR5-RFP) ChIP-seq in ddm1 biol Rep1

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
ddm1_HTR5_IP_Rep1


title: RH18_sgPAX3-FOXO1_d7_rep1


title: 8492

value: Invasive Urothelial Carcimona

value: Collie


title: 20-637-088_hom_D13


title: 11429

value: Unaffected

value: Australian Shepherd


title: H3K27me1 ChIP-seq in ddm1 biol Rep2

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
ddm1_H3K27me1_IP_Rep2

value: anti-H3K27me1 (Active Motif; 61015)


title: H3.3 (HTR5-RFP) ChIP-seq in WT biol Rep2

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
WT_HTR5_IP_Rep2

value: wild-type


title: RH18_sgRosa_d7_rep2

description:
RH18_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular
RH18_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

value: sgRosa


title: 20-637-087_het_D13


title: H3 control for H3K27me1 ChIP-seq in ddm1 biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_H3K27me1_H3_Rep1

value: seedlings


title: RH18_sgRosa_d7_rep1


title: 11454


title: 20-637-086_hom_D6

value: hom


title: H3K27me1 ChIP-seq in ddm1 biol Rep1

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
ddm1_H3K27me1_IP_Rep1


title: CTR_sgNFYC_d7_rep2

description: CTR_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

source_name: CTR

value: CTR


title: 11451

source_name: blood

value: female


title: CTR_sgPAX3-FOXO1_d7_rep2

description: CTR_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular


title: 27570

source_name: saliva

value: Shetland Sheepdog


title: H3K27me1 ChIP-seq in WT biol Rep2

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
WT_H3K27me1_IP_Rep2

value: crosslinking


title: CTR_sgNFYC_d7_rep1

value: rhabdomyosarcoma

value: sgNFYC


title: 20-637-085_het_D6

value: iPSC

value: het


title: 20-637-084_hom_D2


title: 11125

value: Border collie


title: H3 control for H3K27me1 ChIP-seq in WT biol Rep2

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_H3K27me1_H3_Rep2

value: anti-H3 (Abcam; ab1791)


title: 12713

value: Unaffected

value: unknown


title: 20-637-082_hom_D0


title: H3K27me1 ChIP-seq in WT biol Rep1

description:
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
WT_H3K27me1_IP_Rep1

value: anti-H3K27me1 (Active Motif; 61015)


title: H3 control for H3K27me1 ChIP-seq in WT biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_H3K27me1_H3_Rep1

value: wild-type


title: 28482

value: Collie

value: male


title: 20-637-083_het_D2


title: 20-637-081_het_D0


title: CTR_sgRosa_d7_rep2

description:
CTR_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular
CTR_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

value: sgRosa


title: CTR_sgPAX3-FOXO1_d7_rep1

value: CTR


title: PouV rxp (MO), replicate 4, bulk RNAseq

first: Laura

last: Kerosuo-Pahlberg

address: 30 Convent Dr

institute: NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCg6a chicken genome using STAR v2.7.2a in single-pass mode
Gene counts were generated with STAR v2.7.2a built-in counting option --quantMode GeneCounts against a custom GRCg6a genome annotation GTF which included select ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRC6a.98
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

organism: Gallus gallus

source_name: midbrain

extract_protocol: Library preparation was performed by Genewiz/Azenta following the protocol for ultra-low input samples. The libraries were then pooled and sequenced on a HiSeq 2500 sequencer (Illumina) on 150x150 paired end mode.

value: midbrain

value: neural crest

value: WT

value: PouV MO (translation blocking morpholino)


title: PouV rxp (MO), replicate 3, bulk RNAseq


title: 20-637-080_hom_D13

value: hom


title: 28454

value: Australian Shepherd


title: RD_sgNFYC_d7_rep2

description: RD_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

source_name: RD

value: RD

value: rhabdomyosarcoma

value: sgNFYC


title: 20-637-079_het_D13

value: iPSC

value: het


title: 28472

value: Unaffected

value: female


title: PouV rxp (MO), replicate 1, bulk RNAseq


title: PouV control, replicate 3, bulk RNAseq

value: control MO


title: 28465


title: RD_sgPAX3-FOXO1_d7_rep2

description: RD_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular


title: PouV control, replicate 1, bulk RNAseq


title: RD_sgPAX3-FOXO1_d7_rep1


title: 20-637-076_hom_D2


title: RD_sgRosa_d7_rep2

description:
RD_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular
RD_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular


title: Nanog exp (MO), replicate 4, bulk RNAseq

value: Nanog MO (translation blocking morpholino)


title: 11425

value: male


title: 13157


title: 20-637-077_het_D6


title: 20-637-075_het_D2


title: 11428


title: Nanog exp (MO), replicate 3, bulk RNAseq


title: 7314


title: 27573


title: RD_sgRosa_d7_rep1

value: sgRosa


title: Nanog exp (MO), replicate 1, bulk RNAseq

value: midbrain


title: 7303

value: Collie


title: RH30_sgNFYC_d7_rep1

description: RH30_d7_sgRosa_sgNFYC_normalized_counts.csv


title: CTR_sgRosa_d7_rep1

value: CTR


title: 20-637-073_het_D0


title: 20-637-078_hom_D6


title: RD_sgNFYC_d7_rep1


title: Nanog exp (MO), replicate 2, bulk RNAseq

value: neural crest

value: WT


title: 20-637-072_hom_D13

value: hom


title: RH30_sgRosa_d7_rep1

description:
RH30_d7_sgRosa_sgPAX3-FOXO1_normalized_counts.csv
RH30_d7_sgRosa_sgNFYC_normalized_counts.csv


title: 7300


title: Nanog control, replicate 4, bulk RNAseq


title: 20-637-071_het_D13


title: Nanog control, replicate 3, bulk RNAseq


title: 7298


title: RH41_sgNFYC_d7_rep2

description: RH41_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular


title: 20-637-074_hom_D0


title: RH41_sgNFYC_d7_rep1


title: 7296


title: 20-637-070_hom_D6


title: 20-637-069_het_D6


title: Nanog control, replicate 1, bulk RNAseq


title: 28507


title: RH41_sgPAX3-FOXO1_d7_rep2

description: RH41_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular


title: 20-637-068_hom_D2


title: KLF4 exp (MO), replicate 4, bulk RNAseq

value: KLF4 MO (translation blocking morpholino)


title: RH41_sgPAX3-FOXO1_d7_rep1

value: rhabdomyosarcoma


title: RH30_sgPAX3-FOXO1_d7_rep1

description: RH30_d7_sgRosa_sgPAX3-FOXO1_normalized_counts.csv


title: 28463

value: Border collie


title: 20-637-067_het_D2

value: iPSC


title: 20-637-066_hom_D0


title: KLF4 exp (MO), replicate 3, bulk RNAseq


title: RH41_sgRosa_d7_rep1

description:
RH41_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular
RH41_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular


title: KLF4 exp (MO), replicate 2, bulk RNAseq


title: RH41_sgRosa_d7_rep2


title: 374


title: 379


title: RH4_sgNFYC_d7_rep2

description: RH4_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

value: sgNFYC


title: KLF4 exp (MO), replicate 1, bulk RNAseq


title: 27579

value: Unaffected


title: KLF4 control, replicate 3, bulk RNAseq


title: Nanog control, replicate 2, bulk RNAseq


title: RH4_sgNFYC_d7_rep1


title: 28461

value: female


title: 20-637-063_wt_D13

value: wt


title: KLF4 control, replicate 1, bulk RNAseq

value: control MO


title: 28459

value: male


title: RH4_sgPAX3-FOXO1_d7_rep2

description: RH4_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular


title: 20-637-062_hom_D6


title: 27576


title: RH4_sgPAX3-FOXO1_d7_rep1


title: Lung fibroblasts, TKS5 KO TGF-beta, 3

city: Vari

first: Vassilis

last: Aidinis

address: 34 Fleming Street

country: Greece

institute: BSRC 'Alexander Fleming'

data_processing:
Base calling was performed by the Ion Torrent Proton provided software.
Sequenced reads were trimmed for low quality read ends (Phred score: 20) using Trim Galore and aligned to GRCm38 using a first round of HISAT2 alignment and a second round of BOWTIE2 alignment for the reads left unmapped by the first round using --local and --very-sensitive switches.
Reads overlapping the Ensembl genome mm10 3' UTRs +/- 50bp window were counted. The final gene counts table was calculated based on the 3' UTR counts.
Read counts normalization was performed using EDAseq method and analyzed for differential expression with PANDORA as implemented in R Bioconductor metaseqR2 package (Moulos and Hatzis, 2015, PMID: 25452340).
Absolute normal scale fold change value of at least 1.2 and FDR-corrected PANDORA p-value of less than 0.05 defined the list of differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Tab-delimited files contain raw 3'UTR counts for each gene (Ensembl) for RNA data.

source_name: lung fibroblasts

growth_protocol: Primary murine lung fibroblasts were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), streptomycin/penicillin and amphotericin (Gibco), in an environment of 37oC and 5% CO2.

extract_protocol:
RNA was collected using Tri Reagent (TR-118; Invitrogen). 1 μL of total RNA was used for sequencing library preparation.
RNA libraries for Quant-seq were prepared using 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™ Vienna, Austria) following manufacturer's protocols.

treatment_protocol: Myofibroblast differentiation was achieved by incubation of 60-80% confluent cell cultures in serum-free medium containing 10 ng/ml TGF-β1 for 24h.

value: lung fibroblasts

value: TKS5 knockout

value: TGF-beta


title: Lung fibroblasts, TKS5 KO TGF-beta, 2


title: 20215

value: Invasive Urothelial Carcimona

value: Shetland Sheepdog


title: 20-637-061_wt_D6


title: 20-637-060_hom_D2


title: Lung fibroblasts, TKS5 KO TGF-beta, 1


title: RH4_sgRosa_d7_rep1

first: Christopher

last: Vakoc

description:
RH4_d7_sgRosa_rep1_sgRosa_rep2_sgPAX3-FOXO1_rep1_sgPAX3-FOXO1_rep2_norm_counts.tabular
RH4_d7_sgRosa_rep1_sgRosa_rep2_sgNFYC_rep1_sgNFYC_rep2_norm_counts.tabular

value: sgRosa


title: RH4_sgRosa_d7_rep2


title: 20-637-065_het_D0

value: het


title: 20-637-059_wt_D2


title: 20204


title: Lung fibroblasts, WT TGF-beta, 3

value: WT


title: 20-637-058_hom_D0

value: hom


title: 20-637-064_hom_D13


title: 20213


title: RepSeq_U2OS_IDH2_WL_rep3

city: New York

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Repli-seq reads were filtered for quality and 3' trimmed for adapter sequences using Trim_galore + cutadapt.
Reads were aligned to human assembly hg19 using bowtie2 (v2.2.2) with default parameters and duplicates were collapsed using Picard.
The hg19 genome assembly was divided into 50kb windows using bedtools makewindows and coverage was generated from Early and Late bam files using bamToBed followed by bedtools intersect and awk to create bedgraph files.
The Early/Late replication timing ratio was calculated as the log2(ratio) for each 50kb window across the three replicates.
Assembly: hg19
Supplementary files format and content: Bedgraph files for early replication, late replication, and early-to-late replication timing ratios. Bedgraph files are in two forms: 1) a per sample (early and late), and 2) in ratio form (log2 of early/late ratio).
Library strategy: Repli-seq

extract_protocol:
Cells were then lysed and genomic DNA extracted using Zymo Quick-DNA Microprep Kit. DNA was fragmented using a Covaris E220 ultrasonicator and genomic libraries generated using the NEBNext Ultra DNA Library Prep Kit. Fragments were then immunoprecipitated with primary mouse anti-BrdU and secondary rabbit anti-mouse antibodies.
Libraries were amplified with NEBNext Multiplex Oligos for Illumina. Libraries were size-selected with AmpureXP beads and quality control performed with Tapestation (Agilent), Q-bit (ThermoFisher) and KAPA quantification (Roche).

treatment_protocol: Asynchronously growing cells were pulsed with 100 μM BrdU for 2 hours and harvested by trypsinization. Cells were then resuspended in ice-cold PBS and fixed with ice-cold EtOH to a concentration of 75%. Fixed cells were labelled for DNA content with PBS/FBS/Propidium Iodide/RNase A solution and sorted for early and late replicated DNA by PI-content.

value: osteosarcoma

value: IDH2 wild type

tag: replication timing

value: late


title: RepSeq_U2OS_IDH2_WL_rep2


title: 20210


title: Lung fibroblasts, WT TGF-beta, 2


title: Lung fibroblasts, WT TGF-beta, 1


title: 20047

value: Unaffected


title: 20-637-057_wt_D0

value: iPSC


title: RepSeq_U2OS_IDH2_WL_rep1


title: 20-637-056_hom_D13


title: 20208


title: 20-637-055_wt_D13

value: wt


title: RepSeq_U2OS_IDH2_WE_rep3

value: early


title: RepSeq_U2OS_IDH2_WE_rep2


title: 16157

value: male


title: 20-637-053_wt_D6


title: RepSeq_U2OS_IDH2_ML_rep3

value: IDH2 R172K mutant


title: 16155

value: female


title: 20-637-052_hom_D2


title: RepSeq_U2OS_IDH2_ML_rep2


title: 20205


title: 20-637-051_wt_D2


title: RepSeq_U2OS_IDH2_ML_rep1


title: 16147


title: Lung_GMO_NM403_0.25_Day3_rep4

type: RNA

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description: Gene expression in lung of GMO rat exposed to NM403 (0.25 mg/rat) 3 days post exposure

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 8 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned within 3 hours after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing:
Agilent Feature Extraction Software (v 12.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)
Data were normalized by shift to 75.0 percentile and filtered by flags and by expression based on the signal intensity values (to remove very low signal values and those that have reached saturation)

organism: Rattus norvegicus

source_name: Rat, Lung, GMO, NM403, Dose 0.25mg/rat, Day 3, replicate 4

label_protocol: For each of the 35 samples (18 Wild Type rats: 6 control, 6 exposed to Mitsui-7, 6 exposed to NM-403; 17 GMO rats: 6 control, 6 exposed to Mitsui-7, 5 exposed to NM-403), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction. Dye incorporation and cRNA yield and quality were checked by spectrophotometry.

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 6.90, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 12 week old female Sprague Dawley rats were exposed by intratracheal instillation once/week for 4 weeks to Mitsui-7 or NM-403 (0.25 mg/rat).

tag: strain

value: Sprague Dawley

value: accessory lobe of lung

value: 12 weeks-old (at the onset of instillation)

value: GMO [heterozygous for p53]


title: RepSeq_U2OS_IDH2_ME_rep3

tag: cell type


title: 20-637-050_hom_D0

tag: genotype


title: Lung_GMO_NM403_0.25_Day3_rep5

source_name: Rat, Lung, GMO, NM403, Dose 0.25mg/rat, Day 3, replicate 5


title: 24770

value: Invasive Urothelial Carcimona

value: Shetland Sheepdog


title: 20206


title: RepSeq_U2OS_IDH2_WE_rep1


title: 20-637-054_hom_D6

value: hom

tag: day


title: RepSeq_U2OS_IDH2_ME_rep2

value: osteosarcoma


title: Lung_GMO_NM403_0.25_Day3_rep3

source_name: Rat, Lung, GMO, NM403, Dose 0.25mg/rat, Day 3, replicate 3


title: Lung_GMO_NM403_0.25_Day3_rep1

source_name: Rat, Lung, GMO, NM403, Dose 0.25mg/rat, Day 3, replicate 1


title: Lung_GMO_Mitsui_0.25_Day3_rep5

description: Gene expression in lung of GMO rat exposed to Mitsui (0.25 mg/rat) 3 days post exposure

source_name: Rat, Lung, GMO, Mitsui, Dose 0.25mg/rat, Day 3, replicate 5


title: 20-637-048_hom_D13


title: Lung_GMO_Mitsui_0.25_Day3_rep6

source_name: Rat, Lung, GMO, Mitsui, Dose 0.25mg/rat, Day 3, replicate 6


title: Lung_GMO_NM403_0.25_Day3_rep2

source_name: Rat, Lung, GMO, NM403, Dose 0.25mg/rat, Day 3, replicate 2


title: 27210

tag: phenotype


title: 20-637-047_wt_D13


title: 23546

tag: breed


title: RepSeq_RKO_IDH2_WL_rep3

source_name: RKO

tag: cell line

value: RKO

value: colon carcinoma

value: IDH2 wild type


title: Lung_GMO_Mitsui_0.25_Day3_rep4

source_name: Rat, Lung, GMO, Mitsui, Dose 0.25mg/rat, Day 3, replicate 4

tag: age


title: Lung_GMO_Mitsui_0.25_Day3_rep3

source_name: Rat, Lung, GMO, Mitsui, Dose 0.25mg/rat, Day 3, replicate 3


title: 20-637-046_hom_D6

value: iPSC


title: 20-637-049_wt_D0

value: wt


title: 26989


title: 20-637-045_wt_D6


title: RepSeq_RKO_IDH2_WL_rep1

value: late


title: RepSeq_RKO_IDH2_WL_rep2


title: 12322


title: 20-637-044_hom_D2


title: 20-637-043_wt_D2


title: 16146

value: Unaffected

value: male


title: RepSeq_RKO_IDH2_WE_rep2

value: early


title: 16128


title: RepSeq_U2OS_IDH2_ME_rep1

value: IDH2 R172K mutant


title: RepSeq_RKO_IDH2_WE_rep3


title: 20-637-041_wt_D0


title: Lung_GMO_Control_Day3_rep6

description: Gene expression in lung of GMO rat exposed to Vehicule (Pluronic) 3 days post exposure

source_name: Rat, Lung, GMO, Control, Day 3, replicate 6

value: Sprague Dawley

value: accessory lobe of lung

value: female


title: RepSeq_RKO_IDH2_WE_rep1


title: 16125


title: 20-637-042_hom_D0


title: 25179

value: Invasive Urothelial Carcimona


title: Lung_GMO_Mitsui_0.25_Day3_rep1

source_name: Rat, Lung, GMO, Mitsui, Dose 0.25mg/rat, Day 3, replicate 1

value: 12 weeks-old (at the onset of instillation)

value: GMO [heterozygous for p53]


title: Lung_GMO_Mitsui_0.25_Day3_rep2

source_name: Rat, Lung, GMO, Mitsui, Dose 0.25mg/rat, Day 3, replicate 2


title: RepSeq_RKO_IDH2_ML_rep3


title: Lung_GMO_Control_Day3_rep5

source_name: Rat, Lung, GMO, Control, Day 3, replicate 5


title: Lung_GMO_Control_Day3_rep4

source_name: Rat, Lung, GMO, Control, Day 3, replicate 4


title: RepSeq_RKO_IDH2_ML_rep2


title: Lung_GMO_Control_Day3_rep2

source_name: Rat, Lung, GMO, Control, Day 3, replicate 2


title: 16140

source_name: blood

value: Shetland Sheepdog


title: 20-637-039_wt_D13


title: Lung_GMO_Control_Day3_rep1

source_name: Rat, Lung, GMO, Control, Day 3, replicate 1


title: 16122


title: RepSeq_RKO_IDH2_ML_rep1

value: RKO


title: 16142


title: RepSeq_RKO_IDH2_ME_rep3

value: colon carcinoma


title: 20-637-038_hom_D6

value: hom


title: 16059

value: unknown


title: 20-637-040_hom_D13

value: iPSC


title: 20-637-037_wt_D6

value: wt


title: RepSeq_RKO_IDH2_ME_rep2


title: Lung_GMO_Control_Day3_rep3

source_name: Rat, Lung, GMO, Control, Day 3, replicate 3


title: 16132


title: 20-637-036_hom_D2


title: Lung_WT_NM403_0.25_Day3_rep6

description: Gene expression in lung of Wild Type rat exposed to NM403 (0.25 mg/rat) 3 days post exposure

source_name: Rat, Lung, Wild Type, NM403, Dose 0.25mg/rat, Day 3, replicate 6

value: Wild Type


title: RepSeq_RKO_IDH2_ME_rep1


title: 15839


title: 22490

value: Sheltie Mix


title: 24752

value: Unaffected

value: male


title: AML25-U

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: BM AML1/ETO positive LSPCs untreated

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software  and analyzed using ArrayStar software (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization.
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: AML1/ETO positive LSPCs untreated

extract_protocol:
Total RNA was extracted from the treated AML LSPCs, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified AML1/ETO positive LSPCs were harvested and LSPCs treated w/o rhIL-33. Treated LSPCs were then harvested for the RNA extraction.

tag: population

value: AML1/ETO positive LSPCs

value: Bone marrow (BM) derived LSPCs


title: AML24-U

description: BM AML1/ETO positive LSPCs untreated


title: 20-637-033_wt_D0

tag: group


title: 20-637-034_hom_D0


title: Lung_WT_NM403_0.25_Day3_rep4

source_name: Rat, Lung, Wild Type, NM403, Dose 0.25mg/rat, Day 3, replicate 4

value: Sprague Dawley

value: accessory lobe of lung

value: female


title: 20-637-035_wt_D2