title: F24FC + OS (14)

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

data_processing:
Salmon v 0.13.0
salmon quant --validateMappings --libType A --seqBias --gcBias
tximport 1.22 with countsFromAbundance = 'lengthScaledTPM'
Assembly: gencode.v30.pc_transcripts.fa.gz
Supplementary files format and content: TPM

source_name: iPSC RPE

growth_protocol: All human samples were collected under an IRB-approved protocol at NEI (protocol #11-E1- 0245). Cells isolated from donor tissue were reprogrammed using Sendai virus-mediated delivery (CytoTune, LifeTechnologies) of the four Yamanaka factors (c-MYC, KLF4, OCT4, SOX2) following the manufacturer's recommendations. For differentiation, iPSCs were seeded onto vitronectin (ThermoFisher) coated 6-well plates followed by guided protocol.

extract_protocol:
RNA was isolated from RPE monolayer eight weeks post-seeding on transwells, using RNeasy Kit (TAKARA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-8 weeks old fully matured, polarized iRPE monolayers were used for all the experiments. iRPE cells were treated for seven days with Bovine POS (InVision BioResources). iRPE cells were treated for 48 hours with 5% CC-HS (EMD Millipore).

tag: cell line

value: RPE derived from patient iPSC, Fed Outer Segments


title: C46 + OS (12)

status: Public on Nov 16 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: STAP+ OS (13)

value: STAP


title: C35+ OS (11)


title: Plate2_F3_S159

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Raw fastq sequence files generated from Smartseq2 libraries were aligned to the mouse genome (v. mm10) associated with the mouse transcriptome annotations (v. gencode M23) using STAR. Subsequently, genome-mapped BAM files were processed through RSEM (v. 1.3.1) for gene quantification. The matrix of gene counts was then used as input for analysis by the R package Seurat (v. 4.1.0). Next, the dataset was normalized by the LogNormalize method implemented by Seurat. To control unwanted experimental noise sources, we “regressed out” the mitochondrial gene abundance and the library size with the ScaleData function.
Additionally, cells containing more than 10% of sequence reads aligned to mitochondrial genes were excluded before normalization. Single cells were clustered, and gene expression was evaluated with the Seurat workflow. Gene signature scoring was performed by using Seurat’s AddModuleScore. Heatmaps were produced with the ComplexHeatmaps package for R. Differentially expressed gene analyses between clusters or biological groups were performed by the Seurat function FindAllMarkers with the non-parametric Wilcoxon Rank sum test. Genes were considered to downstream analysis when having a log2 fold change greater or smaller than 0.5 and exhibiting an adjusted p-value of at least 0.05. We used the Wilcoxon rank-sum test to compare specific genes between b-hex cells (Fig. 3G), and p values were corrected by the Benjamini Hochberg method.
Genome_build: mm10
Supplementary_files_format_and_content: Rsem gene counts

organism: Mus musculus

source_name: Intraepithelial Lymphocytes

extract_protocol:
IELs were stained as above, washed, filtered, and resuspended in complete RPMI before sorting. Single-cells were index-sorted directly into 96-well plates containing 5ul of TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol using a BD FACS Aria II instrument. After sorting, plates were immediately frozen on dry ice and stored at -80ºC before processing. All sorting data were analyzed using FlowJo software v.10.
Each sorted plate contained all conditions assayed in each replicate and libraries were prepared as previously described (9). RNA was extracted from single cells using RNAClean XP Solid Phase Reversible Immobilization (SPRI) beads (Agentcourt, Beckman Coulter), and hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAA CGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) and then reverse transcribed into cDNA using TSO primer (59-AAG- CAGTGGTATCAACGCAGAGTACATrGrGrG-39) and RT maxima reverse transcription (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (59-AAGCAGTGGTATCAACGCAGAGT- 39) and KAPA HiFi HotStart ReadyMix (Thermo Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina) following manufacturer’s instructions. For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A–D (Illumina). Finally, barcoded libraries were pooled and sequenced using Illumina Nextseq 500 platform.

tag: biological sample

tag: group

value: Pre-IEL


title: Plate2_E4_S148


title: C26+ OS (10)


title: Plate2_D9_S141


title: FMSV217

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover. Quality control of the reads was performed with FastQC v0.11.7.
Reads were aligned to the human GRCh38 reference using Bowtie (v1.2.3) (Langmead et al. 2009)  (command line parameters: -m 1 --best --strata -v 3), sorted using SAMtools (v1.13)
The differential enrichment of H3K4me3 regions in control and treatment was performed using csaw (v1.26.0) package with FC>1.5 and FDR<0.05
For the visualization of ChIP-seq tracks, Bedgraph tracks were generated using GenomeCoverageBed function from SAMtools.
Assembly: hg38
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

molecule: genomic DNA

source_name: blood, H3K4me3, low BPA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using  Qsonica 700 sonicator supplied with cup horn 431C2  with parameters:  60% amplitude for 8 minutes, 20 seconds on, 20 seconds off.
Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645S; NEB). We used 3 ng DNA for library preparation, and 15 cycles were used for library amplification. Sequencing was performed on an Illumina HiSeq4000 sequencer using a single-end 50-base read in multiplexed mode

tag: tissue

value: blood

tag: Sex

value: male

tag: condition

value: low BPA

tag: chip antibody


title: D3C+ OS (9)


title: Plate2_D8_S140


title: BEST4C+ OS (8)

value: RPE derived from patient iPSC


title: Plate2_H7_S187

value: Conventional


title: BEST4C (7)


title: Plate2_D5_S137


title: Plate2_D4_S136


title: C46 (5)


title: Plate2_F4_S160


title: Plate2_C9_S129


title: Plate2_D2_S134


title: STAPFKR (2)


title: F24FC (1)


title: Plate2_C8_S128


title: Plate2_D3_S135


title: Plate2_D1_S133


title: Plate2_C7_S127


title: C26 (3)


title: Plate2_C6_S126


title: Plate2_C4_S124


title: Plate2_C3_S123


title: iNSC31_smartseq2

city: London

first: Silvia

last: Marino

address: Blizard Institute, 4 Newark Street

country: United Kingdom

institute: Queen Mary University of London

description:
smartseq2_samples_tpm.csv
DURA031N44B_NSC

data_processing:
FastQC (v. 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to perform quality control of the raw data, to check the Phred score, the GC content distribution, and the duplication levels, then the TrimGalore tool (v. 0.4.5-1) (DOI 10.5281/zenodo.5127898) was used to remove low quality reads (Phred score < 20) and residual adapters.
Alignment was instead performed using pseudoalignment package Salmon (Version 0.13.1), with the output being transcript expression level, which were then pooled to give gene level expression estimates expressed as transcripts per million (TPM). This unit is normalised for library size and transcript length.
Genome_build: Ensembl Human GRCh38 (release 90)
Supplementary_files_format_and_content: RNA-Seq: TPM count table (csv)

source_name: Dura mater

growth_protocol: See SAMPLES section under heading Growth/Treatment Protocols for sample specific methods

extract_protocol:
RNA and DNA were extracted from cell pellets using the RNA/DNA/Protein Purification Plus kit (NORGEN, #47700), following the manufactured protocol.
Illumina HiSeq4000 platform at 75 PE after PolyA or SmartSeq2 library preparation, see SAMPLES section under heading Characteristics: Library Preparation for details on each samples library preparation method

value: Induced Neural Stem Cell

tag: disease state

value: Healthy

tag: library preparation


title: iNSC50_smartseq2

description:
smartseq2_samples_tpm.csv
DURA50N12NSCP4

treatment_protocol: See SAMPLES section under heading Growth/Treatment Protocols for sample specific methods


title: iNSC44_smartseq2

description:
smartseq2_samples_tpm.csv
DURA44N8NSCP4


title: iNSC52_smartseq2

description:
smartseq2_samples_tpm.csv
DURA052N4NSCP314/7/2017


title: iNSC19_smartseq2

description:
smartseq2_samples_tpm.csv
DURA019N8C_NSC


title: Plate2_C2_S122


title: iNSC52_smartseq1

description:
smartseq2_samples_tpm.csv
DURA52N4NSCP2


title: Plate2_C1_S121


title: D3C (6)


title: iNSC50_smartseq1

description:
smartseq2_samples_tpm.csv
DURA050N12NSCP3


title: Plate2_B9_S117


title: iNSC44_smartseq1

description:
smartseq2_samples_tpm.csv
DURA044N8NSCP2


title: C35 (4)


title: iNSC31_smartseq1

description:
smartseq2_samples_tpm.csv
DURA31N44BNSCP3


title: Plate2_B6_S114


title: iNSC19_smartseq1

description:
smartseq2_samples_tpm.csv
DURA19N8CNSCP7

growth_protocol:
EPSCs were then further differentiated into iNSCs with a Gibco commercially available kit (Gibco Cat. #A1647801). iNSCs were cultured on GelTrex (Gibco Cat. #A1413302) coated tissue culture plates and maintained in Neural Expansion media at 37°C, 5% CO2. iNSCs were passaged once they reached 80-90% confluence.        "
See SAMPLES section under heading Growth/Treatment Protocols for sample specific methods


title: Plate2_B5_S113


title: iOPC52_smartseq2

description:
smartseq2_samples_tpm.csv
Dura52_N4_OPC

value: Induced Oligodendrocyte Progenitor Cell


title: iOPC50_smartseq2

description:
smartseq2_samples_tpm.csv
Dura50_N12_OPC


title: iOPC44_smartseq2

description:
smartseq2_samples_tpm.csv
Dura44_N8_OPC


title: Plate2_B3_S111


title: Plate2_B2_S110


title: iOPC19_smartseq2

description:
smartseq2_samples_tpm.csv
Dura19_N8C_OPC


title: Plate2_B1_S109


title: Plate2_A7_S103


title: Plate2_A9_S105


title: Plate2_A8_S104


title: Plate2_A6_S102


title: iOPC31_smartseq2

description:
smartseq2_samples_tpm.csv
Dura31_N44B_OPC


title: iOPC52_smartseq1

description:
smartseq2_samples_tpm.csv
DURA52N4SORTEDOPCB2


title: iOPC31_smartseq1

description:
smartseq2_samples_tpm.csv
DURA31N44BSORTEDOPCB2


title: iOPC44_smartseq1

description:
smartseq2_samples_tpm.csv
DURA44N8SORTEDOPCB2


title: iOPC50_smartseq1

description:
smartseq2_samples_tpm.csv
DURA50N12SORTEDOPCB2


title: GIC44_rep2

description:
polyA_samples_tpm.csv
GBM044_P8

source_name: Tumour

value: Glioblastoma initiating cell

value: Tumour

value: PolyA


title: Plate2_B8_S116


title: Plate2_A3_S99


title: Plate2_B7_S115


title: iNSC52_rep2

description:
polyA_samples_tpm.csv
DURA52N4NSCP2


title: Plate2_A2_S98


title: iOPC19_smartseq1

description:
smartseq2_samples_tpm.csv
DURA19N8CSORTEDOPCB2

growth_protocol:
On Day 0 of our protocol (Day 8 of the Douvaras-Fossati et al protocol) Neural Expansion media was removed, and iNSCs cultured in N2 media with 100 nM RA and 1 µM Smoothened Agonist (SAG) added freshly each day. Media was then changed daily with fresh RA and SAG until Day 4, at which point cells became over-confluent and were detached and placed in N2B27 Media with freshly added RA and SAG. A series of scratches were made with a cell scraper vertically, horizontally, and diagonally across each well, and the contents of a single well transferred into eight wells of an ultra-low attachment 24-well plate (Corning Cat. #3473), with extra N2B27 media. Aggregates were then cultured in suspension for a further eight days, with media changed every 48 hours. On Day 12 of the protocol N2B27 media was replaced with PDGF media, and aggregates were cultured for a further 10 days, with media replaced every 48 hours. On Day 22 of the protocol aggregates were plated onto Poly-L-Ornithine and laminin coated plates and were cultured adherently until Day 67 of the protocol, with PDGF media changes every 48 hours.
See SAMPLES section under heading Growth/Treatment Protocols for sample specific methods


title: Plate2_A1_S97


title: iNSC50_rep2

description:
polyA_samples_tpm.csv
DURA50N12NSCP4


title: Plate1_H9_S93


title: iNSC44_rep2

description:
polyA_samples_tpm.csv
DURA44N8NSCP4


title: GIC44_rep1

description:
polyA_samples_tpm.csv
GBM044_P4

growth_protocol:
Patient consent and ethical approval was available for the study (08/H0716/16 Amendment 1 17/10/2014). GIC were isolated from bulk tumour following a previously described protocol (Pollard et al 2009; doi:10.1016/j.stem.2009.03.014). Fresh GBM tissue was sliced and triturated with razor blade, dissociated with Accumax (Sigma, A7089) at 37˚C for 10 mins then filtered through a 70μm cell strainer. Dissociated cells were plated on laminin-coated 6-well plate in NeuroCult NS-A Proliferation kit media (STEMCELL, 05751), heparin (2 μg/ml; Gibco 12587-010), mEGF (20ng/ml, Prepro Tech, 315-09) and hFGF (10ng/ml; Prepro tech, AF-100-18B). Established cells were passaged when 70% confluent, frozen in Stem Cell Banker (Ambsio ZENOAQ, 11890) and stored in liquid nitrogen. Cell lines used in this study are primary lines derived from human tumours, they have been characterised by transcriptomic profiling and cultured according to current practice, including contamination assessment. Fibroblasts cultures were established from small strips of dura mater, collected at surgery. Tissue was minced with a scalpel then spun down and resuspended in trypsin for 5 minutes at 37 degrees. To stop the reaction fresh fibroblast media (DMEM, Glutamax, 10% Foetal calf serum, 2% L-Glutamin and 1% penicillin-streptomycin) was added. Samples were centrifuged and resuspended in fresh media, then plated in 6 well plates (Corning #BC010). Media was topped up frequently during the first week then changed every other day.
See SAMPLES section under heading Growth/Treatment Protocols for sample specific methods


title: Plate2_B4_S112


title: iNSC44_rep1

description:
polyA_samples_tpm.csv
DURA044_NSC_N8_P2


title: Plate1_H8_S92


title: Plate1_H7_S91


title: iNSC19_rep2

description:
polyA_samples_tpm.csv
DURA19N8CNSCP7

growth_protocol:
EPSCs were then further differentiated into iNSCs with a Gibco commercially available kit (Gibco Cat. #A1647801). iNSCs were cultured on GelTrex (Gibco Cat. #A1413302) coated tissue culture plates and maintained in Neural Expansion media at 37°C, 5% CO2. iNSCs were passaged once they reached 80-90% confluence.
See SAMPLES section under heading Growth/Treatment Protocols for sample specific methods


title: iAPC50_rep2

description:
polyA_samples_tpm.csv
DURA50N12D20ASTROB2

value: Induced Astrocyte Progenitor


title: iAPC52_rep2

description:
polyA_samples_tpm.csv
DURA52N8D20ASTROB3


title: Plate1_H2_S86


title: 217 IBSP at 4D, biological rep2

type: RNA

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Line 217, IBSP at 4D, biological rep2

hyb_protocol: Affymetrix high-density oligonucleotide HG-U133A Plus 2.0 Human Arrays.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings,  background corrected, and Robust Multi-array Average (RMA)  as normalization method.

label: biotin

source_name: IBSP at 4D, biological rep2

label_protocol: manufacture protocol

growth_protocol: Tumors were cultured as described previously 6 in DMEM/F12 medium supplemented with B27 (GIBCO), 20 ng/ml bFGF (Peprotech), 50 ng/mL EGF, penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen) and 5 ug/ml heparin (Sigma-Aldrich).

extract_protocol: Trizol

treatment_protocol: IBSP at 250nM

tag: line

tag: treatment

value: IBSP

tag: culture method


title: Plate1_G4_S76


title: iAPC31_rep2

description:
polyA_samples_tpm.csv
DURA31N44BD20ASTROB2


title: Plate2_A5_S101


title: Plate1_G1_S73


title: iAPC19_rep2

description:
polyA_samples_tpm.csv
DURA19N8CD20ASTROB3


title: Plate1_F9_S69


title: iNSC31_rep2

description:
polyA_samples_tpm.csv
DURA31N44BNSCP3


title: Plate1_H3_S87


title: Plate1_G9_S81


title: iAPC44_rep2

description:
polyA_samples_tpm.csv
DURA44N8D20ASTROB2


title: Plate1_G2_S74


title: 21_D30

city: Rixensart

first: Margherita

last: Coccia

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

hyb_protocol: NuGEN Ovation WB

scan_protocol: GeneChip(r) Scanner

data_processing: R/Bioconductor; GCRMA

source_name: PBMC

label_protocol: NuGEN Ovation WB

extract_protocol: Standard Qiagen Kit

value: PBMC

tag: gender

value: M

tag: timepoint

tag: subjectid

value: TBDN-POS

tag: centre

value: Taiwan


title: iAPC52_rep1

description:
polyA_samples_tpm.csv
DURA52N8D20ASTROB2


title: iAPC50_rep1

description:
polyA_samples_tpm.csv
DURA50N12D20ASTROB1


title: Plate1_F6_S66


title: Plate1_F5_S65


title: iAPC44_rep1

description:
polyA_samples_tpm.csv
DURA44N8D20ASTROB1


title: iAPC31_rep1

description:
polyA_samples_tpm.csv
DURA31N44BD20ASTROB1


title: Plate1_F3_S63


title: Plate1_F1_S61

value: Pre-IEL


title: iAPC19_rep1

description:
polyA_samples_tpm.csv
DURA19N8CD20ASTROB2

growth_protocol:
Differentiation was initiated on Day -1, by seeding dissociated iNSCs at 1.5x10^4 cells/cm^2 density on GelTrex-coated plates in Neural Expansion media. On Day 0 Neural Expansion media was changed to Astrocyte media (ScienCell: Cat. #1801) supplemented with 2% FBS, Astrocyte Growth Supplement (AGS) and penicillin/streptomycin solution, provided with the media. From Day 2 onwards, media was changed every 48 hours for 20 – 30 days. At 80-90% confluence, the cells were passaged back to the starting seeding density (1.5 x 10^4 cells/cm^2), or at an approximate ratio of 1:6. Cells were detached using Accutase, and always cultured in the same Astrocyte media on GelTrex.
See SAMPLES section under heading Growth/Treatment Protocols for sample specific methods


title: MLLr-MLL3-Mut_AML-PDX_RNA_VTP50469_Rep3

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
Genome_build: mm10/hg38
Supplementary_files_format_and_content: Counts tables contain the raw counts quantified by Salmon and DESeq2.

source_name: MLLr; MLL3-Mut AML PDX

growth_protocol: Serially transplanted in NSG mice.

extract_protocol:
NEBNext Ultra II RNA
Leukemia cells were treated with either vehicle or Menin-MLL inhibitor for 4 days. Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit. NEBNext Ultra II RNA Library Prep Kit was used with 1ug of total RNA for construction of sequencing libraries.

tag: cell line

value: MLL3 Mutant PDX

value: Acute myeloid leukemia

tag: genotype

value: MLL-rearranged; MLL3 mutant


title: Plate1_E8_S56

tag: biological sample

tag: cell type

value: Conventional


title: MLLr-MLL3-mut_AML-PDX_RNA_Vehicle_Rep3

value: Vehicle


title: Plate1_E7_S55

tag: group


title: MLLr-MLL3-Mut_AML-PDX_RNA_VTP50469_Rep2


title: Plate1_D8_S44


title: MLLr-MLL3-mut_AML-PDX_RNA_Vehicle_Rep2


title: MLLr-MLL3-WT_AML-PDX_RNA_Vehicle_Rep1

source_name: MLLr; MLL3-WT AML PDX

value: MLL3 WT PDX

value: MLL-rearranged; MLL3 WT


title: Plate1_D4_S40


title: MLLr-MLL3-Mut_AML-PDX_RNA_VTP50469_Rep1


title: MLLr-MLL3-WT_AML-PDX_RNA_Vehicle_Rep2


title: Plate1_D1_S37


title: Plate1_D9_S45


title: MLLr-MLL3-mut_AML-PDX_RNA_Vehicle_Rep1


title: Plate1_C8_S32


title: Plate1_D7_S43


title: OCI-AML3_RNA_MI-503_Rep1

source_name: OCI-AML3 leukemia cells

growth_protocol: Cells were maintained in Iscove's Modified Dulbecco's Medium (IMDM,Gibco) supplemented with 15% fetal bovine serum (Sigma-Aldrich), Penicillin-Streptomycin, L-Glutamine, IL6, IL3, SCF. Cells were harvested four days after being treated with Menin-MLL inhibitor in this same media composition.

value: DNMT3A;NPM1 mutant


title: OCI-AML3_RNA_MI-503_Rep2


title: Plate1_C6_S30


title: Plate1_E3_S51


title: MLLr-MLL3-WT_AML-PDX_RNA_VTP50469_Rep3


title: Plate1_E9_S57


title: OCI-AML3_RNA_MI-503_Rep3


title: MLLr-MLL3-WT_AML-PDX_RNA_VTP50469_Rep2


title: MLLr-MLL3-WT_AML-PDX_RNA_Vehicle_Rep3


title: Plate1_D6_S42


title: Plate1_C9_S33


title: Plate1_D2_S38


title: MLLr-MLL3-WT_AML-PDX_RNA_VTP50469_Rep1


title: Plate1_D5_S41


title: Plate1_E1_S49


title: OCI-AML3_RNA_DMSO_Rep3

value: DMSO


title: Plate1_C4_S28


title: OCI-AML3_RNA_DMSO_Rep2


title: MOLM13_RNA_MI-503_Rep2

source_name: MOLM13 leukemia cells

value: Endogenous MLL-AF9 rearrangement


title: Plate1_C1_S25


title: OCI-AML3_RNA_DMSO_Rep1


title: Plate1_C5_S29


title: Plate1_C3_S27


title: Plate1_C2_S26


title: MOLM13_RNA_MI-503_Rep3


title: MOLM13_RNA_DMSO_Rep3


title: MOLM13_RNA_MI-503_Rep1


title: MOLM13_RNA_DMSO_Rep1


title: Plate1_B4_S16


title: Plate1_B8_S20


title: Plate1_B3_S15


title: MOLM13_RNA_DMSO_Rep2


title: Plate1_B7_S19


title: STARRseq_LCL-Ve-2

city: Rochester

first: Thanh Thanh

middle: Le

last: Nguyen

state: Minnesota

address: 200 1st St. SW

institute: Mayo Clinic

data_processing:
Raw read quality was checked with FASTQC and adapter was trimmed with Trimmomatic
Trimmed DNA sequencing reads were aligned to hg19 using BWA
Reads were counted with Htseq
Variant calling were done with bcftools mpileup
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every loci and every sample

molecule: polyA RNA

source_name: B lymphoblastoid cell line

growth_protocol: 5% charcoal stripped FBS RPMI 1640

extract_protocol:
RNAeasy mini kit per manufacturer’s instruction (Qiagen)
ThruPLEX® DNA-seq Kit V2

treatment_protocol: Drug treatment for 9hour, as specified above

tag: sample type

value: enriched polyA RNA from human STARR-seq vector


title: STARRseq_LCL-Ve-1


title: Plate1_B2_S14


title: STARRseq_LCL-Cort-2

value: 100nM hydrocortisone + 0.1% DMSO


title: Plate1_A8_S8


title: STARRseq_LCL-Cort-1


title: Plate1_A9_S9


title: STARRseq_LCL-C297-2


title: Plate1_A6_S6


title: Plate1_A7_S7


title: STARRseq_LCL-C297-1


title: Plate1_A5_S5


title: STARRseq_Input4

source_name: Cloned loci in plasmid

value: DNA sequence of cloned regions from human STARR-seq vector


title: Plate1_A3_S3


title: Plate1_A4_S4


title: STARRseq_Input1


title: STARRseq_A549-Ve-2

source_name: A549 lung cancer cell line


title: UTX_ChIP_3T3_DMSO

data_processing:
ChIP-seq reads are aligned using Rsubread’s align method and predicted fragment lengths calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs are created using the rtracklayer R Bioconductor package. Peak calls are made in MACS2 software.
Genome_build: mm10/hg38
Supplementary_files_format_and_content: bigwig files normalized to read depth
Supplementary_files_format_and_content: narrowPeak files generated by MACS2

source_name: NIH-3T3 fibroblasts

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (ATCC) and Penicillin-Streptomycin. Cells were harvested four days after being treated with Menin-MLL inhibitor in this same media composition.

extract_protocol:
Cross-linking ChIP in mouse NIH-3T3 cells was performed with 10-20x107 cells per immunoprecipitation. After drug (or vehicle) treatment, cells were collected, washed once with ice-cold PBS, and flash-frozen. Cells were resuspended in ice-cold PBS and cross-linked using 1% paraformaldehyde (PFA) (Electron Microscopy Sciences) for 5 minutes at room temperature with gentle rotation. Unreacted PFA was quenched with glycine (final concentration 125mM) for 5 minutes at room temperature with gentle rotation. Cells were washed once with ice-cold PBS and pelleted by centrifugation (800g for 5 minutes). To obtain a soluble chromatin extract, cells were resuspended in 1mL of LB1 (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1X complete protease inhibitor cocktail) and incubated at 4°C for 10 minutes while rotating. Samples were centrifuged (1400g for 5 minutes), resuspended in 1mL of LB2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1X complete protease inhibitor cocktail), and incubated at 4°C for 10 minutes while rotating. Finally, samples were centrifuged (1400g for 5 minutes) and resuspended in 1mL of LB3 (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N- Lauroylsarcosine, 1X complete protease inhibitor cocktail). Samples were homogenized by passing 7-8 times through a 28-gauge needle and Triton X-100 was added to a final concentration of 1%. Chromatin extracts were sonicated for 14 minutes using a Covaris E220 focused ultrasonicator. Lysates were centrifuged at maximum speed for 10 minutes at 4°C and 5% of supernatant was saved as input DNA. Beads were prepared by incubating in 0.5% BSA in PBS and antibodies overnight (100μL of Dynabeads Protein A or Protein G (Invitrogen) plus 20μL of antibody).
NEBNext Ultra II DNA

value: Fibroblasts

value: UTX


title: STARRseq_A549-Cort-2


title: UTX_ChIP_3T3_MI-503


title: STARRseq_A549-Ve-1


title: Menin_ChIP_3T3_MI-503

value: Menin


title: STARRseq_A549-Cort-1


title: Plate1_A1_S1


title: STARRseq_A549-C297-2


title: Input_ChIP_3T3_MI-503


title: Menin_ChIP_3T3_DMSO


title: Input_ChIP_3T3_DMSO


title: ChIPseq_CA61_Ve-GR

data_processing:
Raw read quality was checked with FASTQC and adapter was trimmed with Trimmomatic
Trimmed DNA sequencing reads were aligned to hg38 using BWA
PCR duplicates were removed with Picard
Peaks were called with MACS2
Genome_build: hg38
Supplementary_files_format_and_content: peak bed files

extract_protocol: ThruPLEX® DNA-seq Kit V2

tag: antibody

value: GR


title: H4K16ac_ChIP_WT-MA9_DMSO

source_name: WT-MA9 leukemia cells

extract_protocol:
Cross-linking ChIP in mouse leukemia was performed with 10-20x107 cells per immunoprecipitation. After drug (or vehicle) treatment, cells were collected, washed once with ice-cold PBS, and flash-frozen. Cells were resuspended in ice-cold PBS and cross-linked using 1% paraformaldehyde (PFA) (Electron Microscopy Sciences) for 5 minutes at room temperature with gentle rotation. Unreacted PFA was quenched with glycine (final concentration 125mM) for 5 minutes at room temperature with gentle rotation. Cells were washed once with ice-cold PBS and pelleted by centrifugation (800g for 5 minutes). To obtain a soluble chromatin extract, cells were resuspended in 1mL of LB1 (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1X complete protease inhibitor cocktail) and incubated at 4°C for 10 minutes while rotating. Samples were centrifuged (1400g for 5 minutes), resuspended in 1mL of LB2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1X complete protease inhibitor cocktail), and incubated at 4°C for 10 minutes while rotating. Finally, samples were centrifuged (1400g for 5 minutes) and resuspended in 1mL of LB3 (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N- Lauroylsarcosine, 1X complete protease inhibitor cocktail). Samples were homogenized by passing 7-8 times through a 28-gauge needle and Triton X-100 was added to a final concentration of 1%. Chromatin extracts were sonicated for 14 minutes using a Covaris E220 focused ultrasonicator. Lysates were centrifuged at maximum speed for 10 minutes at 4°C and 5% of supernatant was saved as input DNA. Beads were prepared by incubating in 0.5% BSA in PBS and antibodies overnight (100μL of Dynabeads Protein A or Protein G (Invitrogen) plus 20μL of antibody).
NEBNext Ultra II DNA

value: Stably expressing pMSCV-MLL-AF9-GFP

tag: chip antibody


title: H4K16ac_ChIP_WT-MA9_MI-503

value: Acute myeloid leukemia


title: STARRseq_Input2


title: ChIPseq_CA61_Ve-input


title: STARRseq_Input3


title: H3K79me2_ChIP_WT-MA9_MI-503


title: Plate1_A2_S2

value: Pre-IEL


title: H3K79me2_ChIP_WT-MA9_DMSO


title: ChIPseq_CA61_Cort-input


title: ChIPseq_CA61_C297-input


title: UTX ChIP_Nfya-KO_WT-MA9_MI-503

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgNfya


title: ChIPseq_CA61_C297-GR


title: UTX ChIP_Nfya-KO_WT-MA9_DMSO


title: ChIPseq_CA61_2x-input

value: 100nM hydrocortisone + 100nM CORT108297


title: ChIPseq_CA61_Cort-GR


title: STARRseq_A549-C297-1


title: UTX ChIP_Nfya-WT_WT-MA9_MI-503

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgChr8


title: ChIPseq_CA61_2x-GR


title: NF-YA_ChIP_WT-MA9_MI-503

value: NF-YA


title: UTX ChIP_Nfya-WT_WT-MA9_DMSO


title: NF-YA_ChIP_WT-MA9_DMSO


title: CA94_C_CortC297_RNAseq

data_processing:
Raw read quality was checked with FASTQC and adapter was trimmed with Trimmomatic
Trimmed RNA sequencing reads were aligned to hg19 using STAR
Raw counts were generated with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNAeasy mini kit per manufacturer’s instruction (Qiagen)
poly(A) enrichment; Illumina TruSeq RNA Library Prep Kit v2


title: CA94_D_C297_RNAseq


title: CA94_B_Cort_RNAseq

value: Hydrocortisone 100nM + CORT108297 100nM


title: H3K4me1_ChIP_WT-MA9_MI-503


title: CA94_A_Ve_RNAseq

value: Hydrocortisone 100nM + 0.1 % DMSO


title: CA93_D_C297_RNAseq


title: H3K4me3_ChIP_WT-MA9_DMSO


title: CA93_A_Ve_RNAseq


title: CA93_C_CortC297_RNAseq


title: MLL3/4_ChIP_WT-MA9_MI-503


title: H3K4me3_ChIP_WT-MA9_MI-503


title: CA93_B_Cort_RNAseq


title: MLL3/4_ChIP_WT-MA9_DMSO


title: CA89_D_C297_RNAseq


title: MLL1_ChIP_WT-MA9_DMSO


title: UTX_ChIP_WT-MA9_MI-503


title: CA89_B_Cort_RNAseq


title: CA89_A_Ve_RNAseq


title: UTX_ChIP_WT-MA9_DMSO


title: MLL1_ChIP_WT-MA9_MI-503


title: CA89_C_CortC297_RNAseq


title: CA86_D_C297_RNAseq


title: Input_UTX_ChIP_WT-MA9_DMSO


title: Menin_ChIP_WT-MA9_MI-503


title: Menin_ChIP_WT-MA9_DMSO


title: CA86_B_Cort_RNAseq


title: CA84_D_C297_RNAseq


title: CA84_C_CortC297_RNAseq


title: CA86_C_CortC297_RNAseq


title: Input_Menin_ChIP_WT-MA9_DMSO


title: CA84_B_Cort_RNAseq


title: H3K4me1_ChIP_WT-MA9_DMSO


title: Eosinophils, Control Ab, rep4

city: Amsterdam

first: Olga

middle: Sophia

last: Blomberg

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Base-calling was done by the sequencer, Illumina software. Demultiplexing of the reads was performed with Illumina’s bcl2fastq2-v2.20.0.422 software.
The 65 bp single end reads were aligned against the mouse reference genome (GRCm38) using HiSat2 v2.10.
Samtools 1.15.1 was used to convert alignments to bam format and sort on genomic coordinates.
 The RNAseq was unstranded, mRNA and cDNA not oriented according to the poly-A tail; alignments and gene counts processed accordingly.
For the counts per gene, itreecount was used, annotated are ensembl gene IDs from the GTF file with version number GRCm38.100.
Assembly: Ensembl GRCm38
Supplementary files format and content: Txt  file with number of reads per gene/sample. Unique file with all the samples.

source_name: Eosinophils

growth_protocol: Blood of mice with metastatic disease was collected by heart puncture. Red blood cells were lysed (lysis buffer: dH2O, NH4Cl, NaHCCO3, EDTA) and cells were resuspended in PBS containing 0.5% BSA and 2mM EDTA.

extract_protocol:
Eosinophils were flow cytometrically sorted in RLT buffer (Qiagen) +1% b-mercapto-ethanol. Total RNA was isolated following RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, but using 80% ethanol instead of RPE buffer.
Smart-seq2 library preparation was performed as previously described (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014). https://doi.org/10.1038/nprot.2014.006), using 2100 Bioanalyzer System (Agilent) for quality control.

treatment_protocol:
Single cells were stained with fluorescencently conjugated monoclonal antibodies against CD45, CD3, CD4, CD8, CD25, CD11b, Ly6g, F4/80 and live/dead marker to identify their cell surface expression. Eosinophils were identified as live, CD45+, CD3-, CD11b+, Ly6g low, SSC high, F4/80+.
na

value: primary cell sorted from blood

value: Eosinophils

value: FVB/N

value: Control antibody

tag: time

value: Day 21 after start of treatment


title: Eosinophils, Control Ab, rep3


title: Eosinophils, CIS+IT, rep7

value: Cisplatin + aPD1 + aCTLA4


title: Eosinophils, Control Ab, rep1


title: CA79_D_C297_RNAseq


title: CA84_A_Ve_RNAseq


title: CA79_B_Cort_RNAseq


title: Eosinophils, Control Ab, rep2


title: CA79_C_CortC297_RNAseq


title: Eosinophils, CIS+IT, rep6


title: CA79_A_Ve_RNAseq


title: Eosinophils, CIS+IT, rep4


title: CA69_C_CortC297_RNAseq


title: CA86_A_Ve_RNAseq


title: Eosinophils, CIS+IT, rep2


title: Plate2_D7_S139


title: Eosinophils, CIS+IT, rep1


title: CA69_B_Cort_RNAseq


title: RPE Zfp503-KO rep3 [160121_OPTIMUS_C7NWYANXX.8.11716129]

data_processing:
STAR 2.4.2a aligned to GRChm38
HTSeq 0.6.1p1 with  gencode.vM8.primary_assembly.annotation.gtf
Genome_build: GRChm38
Supplementary_files_format_and_content: counts

source_name: RPE Zfp503-KO

extract_protocol:
RPE were dissected out, stored in RNAlater and total RNA were isolated using Rneasy plus mini kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Retinal pigment epithelium

tag: age


title: RPE Zfp503-KO rep3 [160121_OPTIMUS_C7NWYANXX.7.11716129]


title: CA68_D_C297_RNAseq

tag: treatment


title: CA68_A_Ve_RNAseq


title: RPE Zfp503-KO rep2 [160121_OPTIMUS_C7NWYANXX.7.11716126]


title: RPE Zfp503-KO rep1 [160121_OPTIMUS_C7NWYANXX.8.11716127]


title: CA66_D_C297_RNAseq


title: CA68_B_Cort_RNAseq


title: CA69_A_Ve_RNAseq


title: CA66_C_CortC297_RNAseq


title: CA66_B_Cort_RNAseq


title: Eosinophils, CIS+IT, rep5


title: RPE WT rep3 [160121_OPTIMUS_C7NWYANXX.7.11716130]

source_name: RPE WT

value: Wild Type


title: RPE WT rep2 [160121_OPTIMUS_C7NWYANXX.8.11716131]


title: RPE Zfp503-KO rep1 [160121_OPTIMUS_C7NWYANXX.7.11716127]


title: Eosinophils, CIS+IT, rep3


title: CA66_A_Ve_RNAseq


title: CA65_D_C297_RNAseq


title: CA69_D_C297_RNAseq


title: RPE WT rep3 [160121_OPTIMUS_C7NWYANXX.8.11716130]


title: CA68_C_CortC297_RNAseq


title: RPE Zfp503-KO rep2 [160121_OPTIMUS_C7NWYANXX.8.11716126]


title: CA65_B_Cort_RNAseq


title: RPE WT rep1 [160121_OPTIMUS_C7NWYANXX.8.11716128]


title: CA65_C_CortC297_RNAseq


title: CA65_A_Ve_RNAseq


title: CA64_D_C297_RNAseq


title: RPE WT rep1 [160121_OPTIMUS_C7NWYANXX.7.11716128]


title: CA64_C_CortC297_RNAseq


title: CA64_A_Ve_RNAseq


title: p16INK4a+ cells

city: San Francisco

first: Peng

last: Tien

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

description: single cell RNA sequencing of adult murine lung p16INK4a+ stromal cells

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v3.0.3 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v3.0.3 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: adult murine lung p16INK4a+ cells

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 °C and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 °C and washed with FACS buffer. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence and GFP+ cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.
droplet-based single cell RNA-Seq

value: lung

tag: developmental stage

value: adult

value: p16INK4a+ stromal cells


title: CA64_B_Cort_RNAseq


title: CA63_D_C297_RNAseq


title: CA63_B_Cort_RNAseq


title: EV9.inp

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
ChIP-seq data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files.
Assembly: hg19
Supplementary files format and content: ChIP signal in bigwig format.

extract_protocol:
For preparation of ChIP-seq libraries, from 10 ng of ChIP and input DNAs were extracted.
NEBNext Ultra II DNA library Prep Kit for Illumina using the manufacturer’s protocol.

tag: ChIP

value: Input

tag: replicate


title: CA61_D_C297_RNAseq


title: CA61_C_CortC297_RNAseq


title: CA63_C_CortC297_RNAseq


title: A41.inp

value: ADIRF-AS1 KO


title: RPE WT rep2 [160121_OPTIMUS_C7NWYANXX.7.11716131]


title: CA63_A_Ve_RNAseq


title: CA61_B_Cort_RNAseq


title: A41.H3K27ac.2

value: Cell Signaling, H3K27ac, Rabbit mAb #8173


title: HEK293T cells, C1

city: Basel

first: Adrian

last: Bertschi

address: Mattenstrasse 26

department: BSSE

country: Switzerland

institute: ETHZ

data_processing:
trimming Illumina adapters with timmomatic
alignment to hg38 with hisat2
samtools: conversion to BAM, sorting, indexing
counting with featureCounts from subjunc using Ensembl v107 gene annotations
Assembly: hg38
Supplementary files format and content: cnt files are textual tables, count files for reads per gene model for a single sample

source_name: kidney

growth_protocol: Cells were seeded at a density of 250000 cells per well of a 6 well plate and left in high glucose DMEM over night. Following moring medium was exchanged to the corresponding medium for the treatment group and cells were grown for an other 24 hours before RNA was extracted.

extract_protocol:
RNA was isolated using a Quick-RNA MiniPrep Kit (Cat. no. R1055, Zymo Research)
The isolated RNA was prepared for sequencing with a TruSeq stranded mRNA Illumina HT kit v2 and sequenced with a NextSeq 500 using Illumina RTA v 2.11.3 with 76 cycles

treatment_protocol: Control samples were grown in high glucose DMEM  containing P/S and 10% FBS; For samples treated with Acetoin, Acetoin was dissolved directly in the same DMEM to a concentration oc 10mM Acetoin.

value: kidney

value: human embryonic kidney cells

value: Untreated Controls


title: HEK293T cells, T3

value: Acetoin [10mM]


title: HEK293T cells, C2


title: EV9.H3K27ac.3

value: ADIRF-AS1 WT


title: CA61_A_Ve_RNAseq

value: Hydrocortisone 100nM + 0.1 % DMSO


title: HEK293T cells, C3


title: EV9.H3K27ac.2


title: A41.H3K27ac.1


title: HEK293T cells, T1


title: CA60_D_C297_RNAseq


title: EV9.H3K27ac.1


title: CA60_B_Cort_RNAseq

value: Hydrocortisone 100nM + CORT108297 100nM


title: Sample 1 Patient 222 [FLU015046]

city: Pamplona

first: Beñat

last: Ariceta

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

data_processing:
Fastq files generated by bcl2fastq v2.20.0
Fastq files aligned using STAR (v2.6.1)
Gene level quantification using Rsubread and Ensembl transcriptome (GRCh38 v92)
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GRCh38
Supplementary files format and content: FLUGAZA_Counts.txt: File with raw counts after gene level quantification of all the samples included.

source_name: Bone Marrow

extract_protocol:
Co-Isolation protocol was performed to extract at the same time DNA and PolyA RNA from the same sample.
Poly-A RNA was selected with Dynabeads Oligo (dT) (Ambion) and reverse-transcribed with AffinityScript Multiple Temperature Reverse Transcriptase (Agilent) using poly-dT oligos carrying a 7 bp-index. Up to 8 samples with similar overall RNA content were pooled together and subjected to linear amplification by IVT using HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs). Next, aRNA was fragmented into 250-350 bp fragments with RNA Fragmentation Reagents (Ambion) and dephosphorylated with FastAP (Thermo) following manufacturer´s instructions. Partial Illumina adaptor sequences (Jaitin, 2014) were ligated with T4 RNA Ligase 1 (New England Biolabs), followed by a second RT reaction. Full Illumina adaptor sequences were added during final library amplification with KAPA HiFi DNA Polymerase (Kapa Biosystems). RNA-seq libraries quality controls consisted in quantification with Qubit 3.0 Fluorometer (Life Technologies) and size profiles examination with Agilent’s 4200 TapeStation System.

value: Bone Marrow

value: Leukemic blasts

tag: patient id

tag: gender

value: Female

tag: karyotype

value: Abnormal

tag: complex karyotype

value: No

value: WT

value: AZA


title: CA60_A_Ve_RNAseq


title: CA60_C_CortC297_RNAseq


title: CA58_D_C297_RNAseq


title: HEK293T cells, T2

tag: cell line

tag: cell type


title: Sample 2 Patient 220 [FLU008061]

value: Normal

value: ND


title: Sample 1 Patient 221 [FLU010037]

value: Yes

value: Mutated


title: Sample 1 Patient 220 [FLU008060]


title: CA58_C_CortC297_RNAseq


title: CA58_B_Cort_RNAseq


title: Sample 1 Patient 219 [FLU005015]

value: Male

value: FLUGA


title: CA58_A_Ve_RNAseq


title: Sample 2 Patient 217 [FLU011071]


title: Sample 1 Patient 218 [FLU004010]


title: Sample 1 Patient 217 [FLU011070]


title: CA56_D_C297_RNAseq


title: CA56_C_CortC297_RNAseq


title: CA56_B_Cort_RNAseq


title: CA56_A_Ve_RNAseq


title: Sample 1 Patient 215 [FLU006008]


title: Sample 1 Patient 216 [FLU009085]


title: Sample 2 Patient 216 [FLU009086]


title: CA50_B_Cort_RNAseq


title: CA50_C_CortC297_RNAseq


title: CA50_D_C297_RNAseq


title: Sample 1 Patient 213 [FLU011006]


title: CA49_D_C297_RNAseq


title: CA49_C_CortC297_RNAseq


title: CA49_A_Ve_RNAseq


title: Sample 1 Patient 211 [FLU009064]


title: Sample 1 Patient 209 [FLU009057]


title: Sample 1 Patient 210 [FLU009067]


title: CA49_B_Cort_RNAseq


title: Sample 1 Patient 208 [FLU015088]


title: CA45_C_CortC297_RNAseq


title: Sample 1 Patient 207 [FLU014066]


title: CA45_D_C297_RNAseq


title: Sample 1 Patient 214 [FLU011087]


title: Sample 2 Patient 205 [FLU010052]


title: CA45_B_Cort_RNAseq


title: Sample 1 Patient 206 [FLU012074]


title: Sample 1 Patient 205 [FLU010051]


title: Sample 1 Patient 212 [FLU010070]


title: CA41_C_CortC297_RNAseq


title: CA50_A_Ve_RNAseq


title: Sample 1 Patient 203 [FLU013064]


title: CA45_A_Ve_RNAseq


title: CA41_B_Cort_RNAseq


title: CA41_A_Ve_RNAseq


title: CA41_D_C297_RNAseq


title: Sample 1 Patient 202 [FLU012017]

value: Sí


title: Sample 1 Patient 201 [FLU011012]


title: CA40_D_C297_RNAseq


title: Sample 1 Patient 204 [FLU015025]


title: Sample 2 Patient 210 [FLU009068]


title: Sample 1 Patient 200 [FLU016088]


title: Sample 1 Patient 198 [FLU012004]


title: Sample 1 Patient 199 [FLU005009]


title: Sample 1 Patient 197 [FLU011054]


title: CA38_D_C297_RNAseq


title: CA40_A_Ve_RNAseq


title: CA40_C_CortC297_RNAseq


title: CA38_C_CortC297_RNAseq


title: CA38_B_Cort_RNAseq


title: CA38_A_Ve_RNAseq


title: CA36_D_C297_RNAseq


title: Sample 1 Patient 195 [FLU011011]


title: CA36_A_Ve_RNAseq


title: CA36_C_CortC297_RNAseq


title: Sample 1 Patient 191 [FLU017032]


title: Sample 1 Patient 193 [FLU009083]


title: Sample 1 Patient 192 [FLU007052]


title: Sample 1 Patient 188 [FLU015028]


title: CA36_B_Cort_RNAseq


title: CA21_D_C297_RNAseq


title: CA40_B_Cort_RNAseq


title: Sample 1 Patient 190 [FLU016050]


title: Sample 1 Patient 187 [FLU013014]


title: CA21_A_Ve_RNAseq


title: Sample 1 Patient 194 [SMD1068]


title: Sample 1 Patient 185 [FLU012021]


title: CA21_C_CortC297_RNAseq


title: Sample 1 Patient 186 [FLU012060]


title: Sample 2 Patient 183 [FLU006073]


title: Sample 1 Patient 184 [FLU007042]


title: Sample 1 Patient 196 [FLU011027]


title: CA21_B_Cort_RNAseq


title: CA18_D_C297_RNAseq


title: CA18_B_Cort_RNAseq


title: Sample 2 Patient 184 [FLU007043]


title: CA18_C_CortC297_RNAseq


title: Sample 1 Patient 189 [FLU015055]


title: CA18_A_Ve_RNAseq


title: Sample 1 Patient 183 [FLU006071]


title: CA15_D_C297_RNAseq


title: Sample 2 Patient 182 [FLU003012]


title: CA15_C_CortC297_RNAseq


title: CA15_B_Cort_RNAseq


title: Sample 1 Patient 182 [FLU003011]


title: CA14_D_C297_RNAseq


title: Sample 1 Patient 180 [FLU002006]


title: Sample 2 Patient 180 [FLU002007]


title: Sample 1 Patient 179 [FLU016085]


title: CA14_A_Ve_RNAseq


title: CA14_C_CortC297_RNAseq


title: CA15_A_Ve_RNAseq


title: Sample 1 Patient 181 [FLU003007]


title: Sample 1 Patient 178 [FLU001012]


title: Sample 2 Patient 178 [FLU001013]


title: CA12_C_CortC297_RNAseq


title: Sample 2 Patient 177 [FLU014012]


title: CA14_B_Cort_RNAseq


title: Sample 1 Patient 177 [FLU014011]


title: CA12_B_Cort_RNAseq


title: CA12_D_C297_RNAseq


title: CA07_D_C297_RNAseq


title: Sample 1 Patient 176 [FLU011066]


title: Sample 2 Patient 175 [FLU011003]


title: CA07_C_CortC297_RNAseq


title: CA12_A_Ve_RNAseq


title: Sample 1 Patient 175 [FLU011002]


title: Sample 1 Patient 174 [FLU010060]


title: CA01_D_C297_RNAseq


title: Sample 2 Patient 181 [FLU003008]


title: CA01_C_CortC297_RNAseq


title: Sample 1 Patient 172 [FLU009089]


title: CA01_B_Cort_RNAseq


title: CA01_A_Ve_RNAseq


title: Sample 2 Patient 169 [FLU001002]


title: Sample 1 Patient 170 [FLU007089]


title: Sample 3 Patient 169 [FLU001003]


title: In vitro trancribed viral lncRNA

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Raw FAST5 files were basecalled with guppy (v4.2).
Sample quality including sequencing quality and alignment quality is checked with pycoQC (v2.5.0.19).
Basecalled fastq files are mapped using minimap2 (v2.17) with parameters "-k 13 -w x splice -N 32 -un".
Poly(A) tail analysis was done with nanopolish (v0.32).
Modification analysis was done with eligos2 (v2.1.0) pair_diff_mod, using IVT sampel as control.
Assembly: Human (hg38), Human herpesvirus strain Toledo (GU937742.2), nanopore DRS callibration strand (YHR174W)
Supplementary files format and content: tab-delimited text files include read count values for each sample

organism: synthetic construct

source_name: Human cytomegalovirus

growth_protocol: HFF were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin (100 U/ml)-streptomycin (100 µg/ml). Kasumi-3 were maintained in RPMI supplemented with 20% FBS, penicillin-streptoycin, 100 µg/mL gentamicin. Cells were incubated at 37ºC under 5% CO2 atmosphere.

extract_protocol:
Total RNAs were extracted using TRIzol reagent and treated with recombinant DNAse 1 for 1h at 37ºC, followed by purification using NucleoSpin RNA Clean-up kit.
Library preparation for nanopore sequencing was performed using the Oxford Nanopore Technologies’s direct RNA sequencing kit (SQK-RNA002) according to the manufacturer’s instruction. To improve the efficiency, we performed reverse transcription using SuperScript III (Thermo Scientific) after the adapter ligation.

treatment_protocol: HFFs were incubated with virus in serum-free DMEM for 1h, washed twice with PBS, and incubated in complex media. For HCMV latent and reactivation infection, Kasumi-3 cells were incubated in X-VIVO 15 for 48h before infection. Cells were infected with HCMV MOI of 1 by incubation in X-VIVO 15 for 4h with rocking every 30 min, followed by spinfection at 1000xg for 30 min. After overnight incubation with virus, cells were treated with trypsin-EDTA to detach remaining viruses and then cushioned onto Ficoll-Pacque to collect live cells from debris and viruses. Cells over cushion were washed with PBS, incubated in X-VIVO 15. For reactivation assay, cells were treated with 20 mM PMA or DMSO for additional 2 days.

value: Human cytomegalovirus

value: Virus

tag: genotype


title: Sample 2 Patient 166 [FLU009032]


title: CA07_B_Cort_RNAseq

value: Hydrocortisone 100nM + 0.1 % DMSO


title: Sample 3 Patient 166 [FLU009033]

value: Bone Marrow


title: Sample 1 Patient 167 [FLU009043]

value: Leukemic blasts


title: Sample 1 Patient 166 [FLU009031]


title: Sample 1 Patient 165 [FLU007059]

value: Female


title: Sample 1 Patient 173 [FLU010020]


title: CA07_A_Ve_RNAseq


title: CD45+ cells, RNA, Vehicle Rep_3

city: San Diego

first: Richard

last: Virgen-Slane

address: 0777 Science Center Drive, CB4-2131, Pfizer La Jolla

department: Global Computational Safety Science, DSRD

institute: Pfizer

library_source: transcriptomic single cell

data_processing:
scRNAseq data were processed using the Cell Ranger v3.0.2 (10x Genomics) to generate count-level data for further analysis. Each lane of cells was processed independently using the Cell Ranger count. The unique molecular identifier (UMI) counts for each sample were then merged using Seurat v3.0.1, requiring that the 6 number of expressed genes for each cell was > 200. Genes expressed in at least three cells were kept and then normalized and scaled using the default setting in Seurat.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Livers (> 0.5g) were chopped in cold DMEM (Gibco) and digested with the liver dissociation kit, mouse (Miltenyi Biotec) in DMEM according to the manufacturer’s instructions. Samples were dissociated with the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) as per the default manufacturers protocol for murine liver digestion. The single cell suspension was filtered through a 70 µM mesh strainer and washed with cold DMEM, resuspended in RBC lysis buffer (eBioscience) then washed twice in autoMACs buffer with BSA (Miltenyi Biotec). CD45+ cells were isolated with CD45 microbeads (Miltenyi Biotec) according to the manufacturer’s protocol with the autoMACs separator.  The single cell suspension was prepared according to the 10X Genomics single cell sample prep protocol. 6000-8000 cells per sample were loaded onto the 10X Chromium Controller
RNA-seq libraries were prepared using Chromium Single Cell 5’ v2 Reagent Kits (10X Genomics).
libraries were sequenced by UCSD IGM Center on an Illumina NGS HiSeq 4000, with 2x 75 paired-end kits.

value: liver

value: CD45+ cells


title: CD45+ cells, RNA, Vehicle Rep_2


title: CD45+ cells, RNA, IDO1 Rep_3


title: CD45+ cells, RNA, IDO1 Rep_4


title: Sample 1 Patient 164 [FLU006083]

value: No

value: WT


title: CD45+ cells, RNA, IDO1 Rep_2


title: Sample 2 Patient 163 [FLU006040]

value: Abnormal


title: Sample 1 Patient 171 [FLU009021]

value: Normal


title: CD45+ cells, RNA, IDO1 Rep_1


title: Sample 1 Patient 163 [FLU006039]


title: MDA-MB231_Pbs_24 h_rep1

city: Qingdao

first: Peipei

last: Shan

address: Dengzhou Rd 38

country: China

institute: Qingdao University

description: Gene expression after 24 hr in PBS treated MDA-MB231 cells

hyb_protocol: On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression （8x60K） for 17 hours at 65Â°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area (61 x 21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software version12.0.3.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.Then Genespring software (version14.8,Agilent Technologies) was used for quantile standardization and subsequent processing. The standardized data is filtered and at least one set of probes labeled 100% Detected is left for subsequent analysis in each set of samples used for comparison.

source_name: MDA-MB231, 24 hr, PBS, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: MDA-MB231 cells were maintained in DMEM with 10% (v/v) fetal bovine serum. MDA-MB231 cells were maintained at 37 °C under a humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.

treatment_protocol: MDA-MB231 cell were treated with YF349 for 24 hr at 2 μmol/L

tag: Sex

value: female

value: control


title: Sample 1 Patient 169 [FLU001001]

value: Mutated


title: Sample 1 Patient 168 [FLU012044]

value: Male

value: ND

value: FLUGA


title: CD45+ cells, RNA, CTLA4_IDO1 Rep_4


title: CD45+ cells, RNA, Vehicle Rep_4


title: Sample 1 Patient 162 [FLU006013]


title: Sample 2 Patient 162 [FLU006014]


title: CD45+ cells, RNA, Vehicle Rep_1


title: Sample 1 Patient 161 [FLU014076]


title: CD45+ cells, RNA, CTLA4_IDO1 Rep_3


title: CD45+ cells, RNA, CTLA4_IDO1 Rep_2


title: Sample 1 Patient 160 [FLU012028]


title: CD45+ cells, RNA, CTLA4_IDO1 Rep_1


title: CD45+ cells, RNA, CTLA4 Rep_3


title: CD45+ cells, RNA, CTLA4 Rep_2


title: Sample 2 Patient 158 [FLU005019]


title: MDA-MB231_YF349_24 h_rep1

description: Gene expression after 24 hr in YF349 treated MDA-MB231 cells

source_name: MDA-MB231, 24 hr, YF349, replicate 1


title: Sample 1 Patient 158 [FLU005018]


title: CD45+ cells, RNA, CTLA4 Rep_4


title: Sample 1 Patient 157 [FLU017003]


title: Sample 1 Patient 159 [FLU010005]

value: Yes


title: Heart D10 Control, rep1

city: New

first: Sean

last: Houghton

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCm38
Supplementary files format and content: counts.txt

source_name: Heart in vivo D10

growth_protocol: cells were isolated from mouse day 10 post tamoxifen induction

extract_protocol:
Mice were intravital injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels. Sorted endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: mice were treated with tamoxifen to induce gene deletion

value: Wild Type

value: Heart

value: Heart in vivo ECs


title: CD45+ cells, RNA, CTLA4 Rep_1


title: Sample 1 Patient 155 [FLU007026]

value: Bone Marrow

value: Leukemic blasts

value: AZA


title: Heart D10 KO, rep2

value: Erg and Fli1 double knockout


title: Sample 1 Patient 156 [FLU013050]

value: No

value: WT


title: Heart D10 Control, rep2


title: Sample 1 Patient 154 [FLU017036]

value: Normal

value: Sí


title: Sample 1 Patient 153 [FLU014090]

value: Female


title: Lung D10 Control, rep3

source_name: Lung in vivo D10

value: Lung

value: Lung in vivo ECs


title: Sample 1 Patient 152 [FLU013055]

value: Male

value: Abnormal

value: Mutated


title: Lung D10 Control, rep2

value: Wild Type


title: Sample 1 Patient 151 [FLU013037]

value: Yes

value: FLUGA


title: Lung D10 Control, rep1


title: Sample 1 Patient 150 [FLU017007]

value: Bone Marrow

value: ND


title: Sample 2 Patient 152 [FLU013056]

value: Leukemic blasts


title: Lung D10 KO, rep1

value: Erg and Fli1 double knockout


title: Lung D10 KO, rep2


title: Lung D10 KO, rep3


title: ATACseq_competent_larvae_rep2

first: Yan

last: Liang

state: London

address: mile end road

department: SBBS

institute: Queen Mary Univerisity of London

data_processing:
RNA-seq: Sequencing adaptors were removed from raw reads by using trimomatic (version 0.39)
RNA-seq:the reads were mapped to the transcriptome by using Kallisto (0.46.2)
RNA-seq: the gene expression profile was normalized from 13 developmental stages by DESeq2 package (1.30.1) in R (version 3.6).
ATAC-seq: The adaptors of raw reads of each library were removed by using cutadaptor (version 2.5).
ATAC-seq: the reads were mapped to the genome by using NextGenMap (version 0.5.5) as paired-end reads (--paired). Duplications were removed by samtools (view -b -F 0x400 -f 0x2) (version 1.9). The mapped reads (bamfiles) were shifted by using deeptools (alignmentSieve ---ATACshift) (version 3.4.3).
ATAC-seq: MACS2 (version 2.2.7.1) were applied to each shifted bam file to call peaks (-f BAMPE; --min-length 100; --max-gap 75; -q 0.01).
genome build: owenia fusiformis
processed data files format and content: RNA-seq:Owenia_annotation_v250920_filtered_mRNA.fasta is the filtered gene model we used for Kallisto mapping; Ofus_gene_expression_matrix.txt is the output results from DESeq2 normalization; ATAC-seq: all the narrowPeak files are the output from MACS2 analysis.

organism: Owenia fusiformis

source_name: Competent larvae stage

growth_protocol: The Owenia fusiformis embryos, larvae and juvenile were reared in artificial sea water, and the larvae were fed with mix algae.

extract_protocol:
RNA-seq: All the fresh samples were snapped freezed by liquid nitrogen, then extracted using the Monarch total RNA Miniprep Kit; ATAC-seq:50,000 cells (~900 blastula, ~500 gastrula, ~300 elongation, ~150 mature larvae and ~40 competent larvae) were washed in 1 ml cold PBS and resuspended in 100  µl cold ATAC lysis buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL, 0.1% (v/v) Tween-20, 0.01% (v/v) Digitonin) and used the pestle to homogenize the samples, then and incubated on ice for 3 minutes to lyse cells. The lysis reaction was stopped by adding 1 ml of cold ATAC wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Tween-20) and inverting the tube for 3 times to mix. The nuclei were pelleted by centrifugation at 500xg for 10 minutes at 4℃ in a fixed angle centrifuge.
RNA-seq: All the libraries were constructed by Oxford genomic center; ATAC-seq:  The supernatant was removed and the nuclei pellet was resuspended in transposition mix containing 5 µl of 10x TMg buffer (100 mM Tris-HCl pH 8.5, 50 mM MgCl2), 5 µl Dimethyl Formamide, 2.5 µl of 100 nM in-house made Tn5 enzyme, 16.5 µl PBS, 0.5 µl of 1% (v/v) digitonin, 0.5 µl of 10% (v/v) Tween-20, and 20 µl H2O. The transposition reaction was incubated at 37°C for 30 minutes in a thermomixer with 1000 rpm mixing. Transposed DNA was cleaned up using the NEB DNA Cleanup kit following manufacturer’s instructions. All 10 µl eluted DNA was subjected to 5 cycles of PCR amplification, and 5 µl of this pre-amplified library was used for qPCR to determine the PCR cycles, finally all the libraries were amplified in 7~12 cycles using the NEBNext High-Fidelity 2X PCR Master Mix.
RNA-seq and ATAC-seq

treatment_protocol: By adding few mud to stimulate the metaphomorphsis of competent larvae to  juvenile.

value: Competent larvae stage

tag: developmental time points

value: 3 weeks past fertilization

tag: morphology

value: larvae


title: ATACseq_mature_larvae_rep2

source_name: Mature larvae stage

value: Mature larvae stage

value: 27h hpf


title: Sample 1 Patient 148 [FLU017041]

value: Female

value: Normal

value: No

value: WT


title: ATACseq_mature_larvae_rep1


title: Sample 1 Patient 146 [FLU016028]

value: Male

value: Abnormal

value: Mutated

value: AZA


title: ATACseq_elongation_rep1

source_name: Elongation stage

value: Elongation stage

value: 13h hpf

value: embryo


title: ATACseq_elongation_rep2


title: Sample 1 Patient 147 [FLU016041]

value: Bone Marrow

value: Leukemic blasts


title: Dnajb6-2

city: Baltimore

first: Yuji

last: Zhang

address: 660 W. Redwood Street

institute: University of Maryland

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads will be mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: right atrium

extract_protocol:
Total RNA was extracted from the right atrium (RA) tissues of 1-year-old Dnajb6+/- heterozygous mutant hearts and WT sibling controls. Six total samples (3 biological replicates for each genotype) were submitted for RNA sequencing (Azenta Life Science, NJ).
Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

tag: strain

value: Dnajb6+/- heterozygous mutant

value: 1 year

value: heart


title: Heart D10 KO, rep1

value: Erg and Fli1 double knockout

tag: tissue

value: Heart

value: Heart in vivo ECs


title: Dnajb6-3

tag: age


title: ATACseq_gastrula_rep2

source_name: Gastrula stage

value: Gastrula stage

value: 9h hpf


title: Dnajb6-1


title: Sample 1 Patient 145 [FLU014087]

value: Male

value: No

value: WT

tag: treatment

value: FLUGA


title: RNAseq_juvenile_rep1

source_name: Juvenile stage

tag: developmental stage

value: Juvenile stage

value: 3 weeks +1h past fertilization

value: Juvenile


title: RNAseq_competent_larvae_rep2

value: Competent larvae stage

value: 3 weeks past fertilization

value: larvae


title: ATACseq_gastrula_rep1

value: embryo


title: DWT-4

value: wildtype

value: 1 year

value: heart


title: Sample 1 Patient 144 [FLU014053]

value: Bone Marrow

value: Leukemic blasts

value: Female

value: Normal

value: Mutated

value: AZA


title: RNAseq_competent_larvae_rep1


title: DWT-3


title: ATACseq_competent_larvae_rep1


title: Sample 1 Patient 149 [FLU016038]

value: Abnormal

value: Yes

value: WT

value: FLUGA


title: Sample 1 Patient 143 [FLU014023]

value: ND


title: Acinetobacter baumannii NCCP 16007

city: Seongbuk-gu

first: sohyeon

last: yun

address: Anam-ro 145

institute: laboratory of molecular environmental microbiology

data_processing:
RNA sequencing was performed on an Illumina Novaseq 6000 platform.
The reference genome sequence was retrieved from the NCBI database.
Quality-filtered reads were aligned to the reference genome sequence using Bowtie2.
The relative abundance of transcripts is presented as FPKM (Fragments Per Kilobase of transcript per Million).
Assembly: PRJNA800215
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Acinetobacter baumannii

source_name: Mid-exponential phase (OD=0.4-0.5)

growth_protocol: Exponential phase on LB (Luria-Berani) media

extract_protocol:
Total RNA was extracted from the mid-exponentially grown both WT and EAB strains (OD600~0.5) using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
Illumina sequencing library was constructed by the TruSeq Stranded Total RNA with Ribo-Zero Plus (Illumina, San Diego, CA, USA) following the manufacturer's protocol

value: Bacterial cells

value: Mid-exponential phase (OD=0.4-0.5)


title: Evolved Acinetobacter baumannii NCCP 16007 2

source_name: Mid-exponential phase (OD=0.4-0.6)

value: evolved NCCP 16007

value: Mid-exponential phase (OD=0.4-0.6)


title: Evolved Acinetobacter baumannii NCCP 16007 1


title: Sample 1 Patient 142 [FLU016012]

value: No


title: Ctel_st8_ATAC_seq_replicate2

data_processing:
ATAC-seq: The adaptors of raw reads of each library were removed by using cutadaptor (version 2.5).
ATAC-seq: the reads were mapped to the genome by using NextGenMap (version 0.5.5) as paired-end reads (--paired). Duplications were removed by samtools (view -b -F 0x400 -f 0x2) (version 1.9). The mapped reads (bamfiles) were shifted by using deeptools (alignmentSieve ---ATACshift) (version 3.4.3).
ATAC-seq: MACS2 (version 2.2.7.1) were applied to each shifted bam file to call peaks (-f BAMPE; --min-length 100; --max-gap 75; -q 0.01).
Assembly: http://ftp.ensemblgenomes.org/pub/metazoa/release-43/fasta/capitella_teleta/dna/Capitella_teleta.Capitella_teleta_v1.0.dna.toplevel.fa.gz
Supplementary files format and content: bed format; peak dynamics

organism: Capitella teleta

growth_protocol: The Owenia fusiformis embryos, larvae and juvenile were reared in artificial sea water with sifted fine mud, feeding with grind fish flakes.

extract_protocol:
ATAC-seq:50,000 cells (~500 64 cell, ~200 gastrula, ~120 st4tt larvae,  90 stage 5 larvae and  50 stage 8 larvae) were washed in 1 ml cold PBS and resuspended in 100  µl cold ATAC lysis buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL, 0.1% (v/v) Tween-20, 0.01% (v/v) Digitonin) and used the pestle to homogenize the samples, then and incubated on ice for 3 minutes to lyse cells. The lysis reaction was stopped by adding 1 ml of cold ATAC wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Tween-20) and inverting the tube for 3 times to mix. The nuclei were pelleted by centrifugation at 500xg for 10 minutes at 4℃ in a fixed angle centrifuge.
The supernatant was removed and the nuclei pellet was resuspended in transposition mix containing 5 µl of 10x TMg buffer (100 mM Tris-HCl pH 8.5, 50 mM MgCl2), 5 µl Dimethyl Formamide, 2.5 µl of 100 nM in-house made Tn5 enzyme, 16.5 µl PBS, 0.5 µl of 1% (v/v) digitonin, 0.5 µl of 10% (v/v) Tween-20, and 20 µl H2O. The transposition reaction was incubated at 37°C for 30 minutes in a thermomixer with 1000 rpm mixing. Transposed DNA was cleaned up using the NEB DNA Cleanup kit following manufacturer’s instructions. All 10 µl eluted DNA was subjected to 5 cycles of PCR amplification, and 5 µl of this pre-amplified library was used for qPCR to determine the PCR cycles, finally all the libraries were amplified in 7~12 cycles using the NEBNext High-Fidelity 2X PCR Master Mix.

treatment_protocol: The female and male worms were separated by 4 nights and then mixed the worms over 8~9 hours, sifted the worms and collected the brooding tubes, dissected the tubes to release the zygote. The fertilzed zygotes were kept in the antibiotic artificial sea water in dishes, and the  samples were collected by developmental time.

value: larva


title: Ctel_st8_ATAC_seq_replicate1


title: Sample 1 Patient 141 [FLU016009]

value: Bone Marrow

value: Male


title: Murine Spleen ILCs sample 2 ADT

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

description: ADT

data_processing:
Cell Ranger software 4.0.0
Low-quality cells were excluded in an initial quality-control (QC) step, by removing genes expressed in fewer than three cells, cells with less than 200 genes expressed. Additional QC has been performed
Genome_build: mm10
Supplementary_files_format_and_content: csv files (gene/cell matrix and metadata)

source_name: Spleen

extract_protocol:
The cells were sorted from spleen, liver, salivary glands and lamina propria and were enriched by centrifugation on Percoll. Lin (CD3, CD19, Ter-119, F4/80, TCRβ, TCRγδ)-CD45+NKp46+NK1.1+ cells were sorted on a FACSAriaIII
10X Genomics Chronium Next GEM Single Cell 3’ v3.1
Single-cell RNAseq

value: sorted CD45+ Lin- NKp46+ NK1.1+ cells

tag: genetic background

value: Spleen


title: Murine Spleen ILCs sample 1 ADT

description: ADT


title: Ctel_st5_ATAC_seq_replicate1


title: Ctel_st4tt_ATAC_seq_replicate1


title: Sample 1 Patient 140 [FLU015034]

value: Leukemic blasts

value: Mutated


title: Sample 1 Patient 139 [FLU014060]

value: Abnormal

value: AZA


title: Murine Salivary Glands ILCs sample 2 ADT

description: ADT

source_name: Salivary gland

value: Salivary gland


title: Ctel_st4tt_ATAC_seq_replicate2


title: Ctel_gastrula_ATAC_seq_replicate2

value: gastrula

value: embryo


title: Sample 1 Patient 138 [FLU016063]

source_name: Bone Marrow

value: Normal

value: WT


title: Murine Liver ILCs sample 3 ADT

description: ADT

source_name: Liver

value: Liver


title: Murine Salivary Glands ILCs sample 1 ADT

description: ADT


title: Sample 1 Patient 137 [FLU016023]


title: Ctel_st7_RNA_seq_replicate2

data_processing:
RNA-seq: Sequencing adaptors were removed from raw reads by using trimomatic (version 0.39)
RNA-seq:the reads were mapped to the transcriptome by using Kallisto (0.46.2)
RNA-seq: the gene expression profile was normalized from 13 developmental stages by DESeq2 package (1.30.1) in R (version 3.6).
Genome_build: Capitella teleta
Supplementary_files_format_and_content: RNA-seq: Ctel_RNAseq_gene_expression.txt is the output results from DESeq2 normalization

extract_protocol:
All the fresh samples were snapped freezed in liquid nitrogen, then extracted using the Monarch total RNA Miniprep Kit.
All the libraries were constructed by Oxford genomic center

treatment_protocol: The female and male worms were separated by 4 nights and then mixed the worms over 8~9 hours, sifted the worms and collected the brooding tubes, disected the tubes to release the zygote. The fertilzed zygotes were kept in the antibiotic artificial sea water in dishes, and the  samples were collected by developmental time.


title: Ctel_64cell_ATAC_seq_replicate2


title: Ctel_64cell_ATAC_seq_replicate1


title: Murine Liver ILCs sample 2 ADT

description: ADT


title: Ctel_st7_RNA_seq_replicate1


title: Ctel_st5_RNA_seq_replicate2


title: Sample 1 Patient 136 [FLU016005]

value: Sí

value: FLUGA


title: Ctel_st5_RNA_seq_replicate1

value: larva


title: DWT-2

value: wildtype

value: 1 year

value: heart


title: Ctel_st4tt_RNA_seq_replicate2


title: Sample 2 Patient 135 [FLU015086]

value: Bone Marrow

value: Female

value: No


title: Murine Liver ILCs sample 1 ADT

description: ADT

value: sorted CD45+ Lin- NKp46+ NK1.1+ cells


title: Ctel_st5_ATAC_seq_replicate2


title: Ctel_st4tt_RNA_seq_replicate1


title: Ctel_gastrula_RNA_seq_replicate1


title: Ctel_gastrula_RNA_seq_replicate2


title: Ctel_gastrula_ATAC_seq_replicate1


title: Ctel_64cell_RNA_seq_replicate2


title: Sample 2 Patient 133 [FLU015023]

value: Leukemic blasts

value: Mutated


title: Sample 1 Patient 134 [FLU015072]

value: Male

value: Abnormal

value: AZA


title: Murine Spleen ILCs sample 2

value: Spleen


title: Murine Gut ILCs sample 1 ADT

description: ADT

source_name: small intestine lamina propria

value: small intestine lamina propria


title: Ctel_64cell_RNA_seq_replicate1

value: embryo


title: Murine Spleen ILCs sample 1


title: Sample 1 Patient 132 [FLU015003]

value: WT


title: Untreated Root tissue replicate 2

city: Tralee

first: Oscar

last: Goñi

address: South Campus Kerry

country: Ireland

institute: Munster Technological University

data_processing:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structures were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Finally, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and paired-end reads were generated with an average read length of PE150.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality 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 with high quality (i.e. Q30 for PE150 reads ≥ 80%).
Solanum lycopersicum (tomato) genome assembly SL3.0 from Solanaceae Genomics Project was used as reference genome. Reference genome and gene model annotation files were downloaded from EnsemblPlants website
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. Then, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions for each tissue (leaf treated vs leaf control and root treated vs root control using three biological replicates per condition and tissue) was performed using DESeq2 R package.
Assembly: SL3.0
Supplementary files format and content: Excel file include FPKM values for each gene for all Samples

organism: Solanum lycopersicum

source_name: Root tissue

growth_protocol: Germination of tomato seeds, transplant of obtained seedlings, fertilization program, and growth conditions (light, temperature, and humidity) was performed as described by Carmody et al. (2019) (DOI: 10.3389/fpls.2020.00807). Prior to the application of salinity stress on the irrigation water, PSI-475 was applied at a rate of 2.5 mL L-1 , 6.25 mL L-1 and 12.5 mL L-1 by foliar spray to 65-day-old plants (early flowering stage). 10 mL of water was applied as a control. After 1 day, salinity stress was started in half of the plants by watering them with 50 mM NaCl (EC: 5.8 dS/m).  To minimize the influence of any positional effect, the relative position of the pots was changed every other day. Artificial pollination using an electric toothbrush was implemented once plants began to flower and was administered twice a week to promote cross pollination. After 27 days of adding saline water, the PSI-475 treatment was applied again as foliar spray at the same rates described above. Control plants were sprayed with equal volume of distilled water. Saline irrigation was maintained under conditions described above to obtain 127-day-old plants. This harvest point was chosen to analyse different plant tissues at fruit filling stage but avoiding the last growth stages (e.g. late fruit ripening in >140-day-old tomato plants) where senescence mechanisms are activated. Phenotypic evaluation was performed at T0 (65-day-old plants) to confirm a homogenous growth stage for plants in the different groups before any treatment application. Additional phenotypical evaluation and tissue sampling was carried out at the end of plant trials (127-day-old plants) at 2 hours after the end of the light period. After harvesting all fruits (ripen and unripen) for yield assessment, plants were divided into roots, lower stems (starting at soil level and ending at old leaves height), old leaves, upper stem (starting from old leaves and ending at young leaves height), young leaves, and flowers. Root tissue was washed carefully with tap water to remove any growth medium particles. Then, every tissue sample of each 21 plants per treatment and condition was pooled, snap-frozen in liquid nitrogen, ground, and kept in -80°C until further analysis.

extract_protocol:
RNA was extracted and purified from 30 mg of frozen ground young leaf and root tissue of 127-day-old tomato plants untreated and treated with PSI-475 applied at 2.5 mL/L growing under salinity stressed conditions according to the manufacturer’s instructions of the Plant/Fungi Total RNA Purification Kit (Norgen Biotek). R
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Foliar application of PSI-475 biostimulant

value: Root tissue

value: Untreated


title: Sample 1 Patient 131 [FLU014038]

value: Normal

value: FLUGA


title: PSI-475 Treated Root tissue replicate 2

value: PSI-475 treated


title: Untreated Root tissue replicate 3


title: Murine Gut ILCs sample 3 ADT

description: ADT


title: PSI-475 Treated Root tissue replicate 3


title: PSI-475 Treated Root tissue replicate 1


title: Murine Salivary Glands ILCs sample 2

value: Salivary gland


title: Sample 1 Patient 135 [FLU015085]

value: Bone Marrow

value: Female

value: No


title: Murine Gut ILCs sample 2 ADT

description: ADT

value: sorted CD45+ Lin- NKp46+ NK1.1+ cells


title: Untreated Root tissue replicate 1


title: PSI-475 Treated Leaf tissue replicate 3

source_name: Leaf tissue

value: Leaf tissue


title: Murine Salivary Glands ILCs sample 1


title: PSI-475 Treated Leaf tissue replicate 2


title: Sample 1 Patient 130 [FLU014029]

value: Leukemic blasts

value: Male

value: Mutated


title: Murine Liver ILCs sample 3

value: Liver


title: Untreated Leaf tissue replicate 2


title: Untreated Leaf tissue replicate 3


title: Sample 1 Patient 128 [FLU015050]

value: ND

value: AZA


title: Murine Liver ILCs sample 2


title: Sample 1 Patient 133 [FLU015022]

value: WT


title: PSI-475 Treated Leaf tissue replicate 1


title: Untreated Leaf tissue replicate 1

value: Untreated


title: Murine Liver ILCs sample 1


title: Murine Gut ILCs sample 3

value: small intestine lamina propria


title: Sample 1 Patient 126 [FLU017052]

value: Normal


title: LC10-RZs14, Day 7, BAL, Hashtag antibody library

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s024_LC10-RZs14_D7_S16.filtered_feature_bc_matrix.h5

library_source: other

data_processing:
Sequence reads for each sample were demultiplexed and converted to a count matrix using Cellranger v3.1
Downstream analysis was carried out on Seurat v4.1
Assembly: mmul10
Supplementary files format and content: 10x genomics output of gene expression and HTO barcode counts in sparse matrix ".h5" format

molecule: protein

organism: Macaca mulatta

source_name: Bronchoalveolar lavage (BAL)

extract_protocol:
Brochoalveolar lavage (BAL) fluid was collected at baseline (BL) before initiation of treatment or infection of animals, then collected at 2 days post infection (dpi), and, depending on necropsy date, at 4dpi and 7dpi. Lung samples were collected upon necropsy.
Library was prepared using Chromium Single Cell 5ʹ protocol (10x Genomics). Cellular mRNA and hashtag-antibody oligos were reverse-transcribed to generate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). These cDNAs were then each prepared for sequencing according to manufacturer instructions. Sequencing was performed on the Illumina NovaSeq 6000 targeting 50k reads/cell for the gene expression libraries and 5k reads/cell for the hashtag-antibody libraries.

treatment_protocol: One group of RMs received a four-day course of IFNmod  (1mg/day, intramuscularly) beginning 1 day prior to infection (day-1) and ending on day 2 post infection while the control group of animals remained untreated

value: Bronchoalveolar lavage (BAL)

tag: timepoint

value: Day 7 post-infection

tag: infection status

value: Untreated (LC10), IFNant (RZs14)

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD298+/B2M:LC10 - TotalSeq-C0252; RZs14 - TotalSeq-C0254


title: KV31-CD68, Day 7, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s008_KV31-CD68_D7_S8.filtered_feature_bc_matrix.h5

value: IFNant (KV31), Untreated (CD68)

value: Anti CD298+/B2M:CD68 - TotalSeq-C0252; KV31 - TotalSeq-C0254


title: Murine Gut ILCs sample 2

value: sorted CD45+ Lin- NKp46+ NK1.1+ cells


title: LG92-LC10, Day 4, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s020_LG92-LC10_D4_S12.filtered_feature_bc_matrix.h5

value: Day 4 post-infection

value: Untreated (LG92), Untreated (LC10)

value: Anti CD298+/B2M:LG92 - TotalSeq-C0251; LC10 - TotalSeq-C0252


title: Murine Gut ILCs sample 1


title: RNi17-RZs14, Day 4, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s021_RNi17-RZs14_D4_S13.filtered_feature_bc_matrix.h5

value: IFNant (RNi17), IFNant (RZs14)

value: Anti CD298+/B2M:RNi17 - TotalSeq-C0253; RZs14 - TotalSeq-C0254


title: Sample 1 Patient 125 [FLU017018]

value: Bone Marrow

value: Leukemic blasts

tag: patient id

tag: gender

value: Female

tag: karyotype

tag: complex karyotype

value: No

value: WT

value: Mutated

value: AZA


title: RMj8-KV31, Day 4, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s007_RMj8-KV31_D4_S7.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: IFNant (RMj8), IFNant (KV31)

value: HTO

value: Anti CD298+/B2M:RMj8 - TotalSeq-C0253; KV31 - TotalSeq-C0254


title: RCk17-RRj11, Day 4, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s014_RCk17-RRj11_D4_S6.filtered_feature_bc_matrix.h5

value: IFNant (RCk17), IFNant (RRj11)

value: Anti CD298+/B2M:RCk17 - TotalSeq-C0253; RRj11 - TotalSeq-C0254


title: RRc17-RGo9, Day 4, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s013_RRc17-RGo9_D4_S5.filtered_feature_bc_matrix.h5

value: Day 4 post-infection

value: Untreated (RRc17), Untreated (RGo9)

value: Anti CD298+/B2M:RRc17 - TotalSeq-C0251; RGo9 - TotalSeq-C0252


title: Sample 1 Patient 127 [FLU017057]

tag: cell type

value: Abnormal

value: FLUGA


title: Sample 1 Patient 129 [FLU013080]

value: Bone Marrow

value: Leukemic blasts


title: WT-MA9_UtxKO_RNA_MI-503_d4_Rep3

city: New York

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Transcript abundance was computed from FASTQ files using Salmon (v0.8.2) and the GENCODE reference transcript sequences, transcript counts were imported into R with the tximport R Bioconductor package, and differential gene expression was determined with the DESeq2 R Bioconductor package
Genome_build: mm10/hg38
Supplementary_files_format_and_content: Counts tables contain the raw counts quantified by Salmon and DESeq2.

source_name: WT-MA9 leukemia cells

extract_protocol:
NEBNext Ultra II RNA
Leukemia cells were treated with either vehicle or Menin-MLL inhibitor for 4 days. Cells were harvested, washed with PBS, and flash frozen in liquid nitrogen. RNA was isolated using QIAGEN RNeasy kit. NEBNext Ultra II RNA Library Prep Kit was used with 1ug of total RNA for construction of sequencing libraries.

tag: cell line

value: Acute myeloid leukemia

tag: genotype

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgUtx


title: RGo9-RRj11, Day 7, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s015_RGo9-RRj11_D7_S7.filtered_feature_bc_matrix.h5

value: Day 7 post-infection

value: Untreated (RGo9), IFNant (RRj11)

value: Anti CD298+/B2M:RGo9 - TotalSeq-C0252; RRj11 - TotalSeq-C0254


title: Sample 1 Patient 124 [FLU016054]

value: Male

value: Normal

value: No

value: WT

value: Mutated

value: Sí


title: Sample 1 Patient 123 [FLU016030]


title: RMs8-CD68, Day 4, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s006_RMs8-CD68_D4_S6.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: Day 4 post-infection

value: Untreated (RMs8), Untreated (CD68)

value: HTO

value: Anti CD298+/B2M:RMs8 - TotalSeq-C0251; CD68 - TotalSeq-C0252


title: Sample 1 Patient 122 [FLU016034]

value: Bone Marrow

value: Leukemic blasts

value: Abnormal

value: FLUGA


title: RNi17-RZs14, Day 2, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s019_RNi17-RZs14_D2_S11.filtered_feature_bc_matrix.h5

value: Day 2 post-infection

value: IFNant (RNi17), IFNant (RZs14)

value: Anti CD298+/B2M:RNi17 - TotalSeq-C0253; RZs14 - TotalSeq-C0254


title: WT-MA9_UtxKO_RNA_MI-503_d4_Rep2

value: Acute myeloid leukemia

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgUtx


title: LG92-LC10, Day 2, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s018_LG92-LC10_D2_S10.filtered_feature_bc_matrix.h5

value: Untreated (LG92), Untreated (LC10)

value: Anti CD298+/B2M:LG92 - TotalSeq-C0251; LC10 - TotalSeq-C0252


title: Sample 1 Patient 121 [FLU012049]

value: Male

value: Yes

value: Mutated

value: WT

value: Sí


title: WT-MA9_UtxKO_RNA_MI-503_d4_Rep1


title: WT-MA9_UtxKO_RNA_DMSO_d4_Rep3

value: DMSO


title: RRc17-RGo9, Day 2, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s011_RRc17-RGo9_D2_S3.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: Untreated (RRc17), Untreated (RGo9)

value: HTO

value: Anti CD298+/B2M:RRc17 - TotalSeq-C0251; RGo9 - TotalSeq-C0252


title: RCk17-RRj11, Day 2, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s012_RCk17-RRj11_D2_S4.filtered_feature_bc_matrix.h5

value: Day 2 post-infection

value: IFNant (RCk17), IFNant (RRj11)

value: Anti CD298+/B2M:RCk17 - TotalSeq-C0253; RRj11 - TotalSeq-C0254


title: RNi17-RZs14, Baseline, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s017_RNi17-RZs14_BL_S9.filtered_feature_bc_matrix.h5

value: Baseline

value: Uninfected

value: IFNant (RNi17), IFNant (RZs14)

value: Anti CD298+/B2M:RNi17 - TotalSeq-C0253; RZs14 - TotalSeq-C0254


title: LG92-LC10, Baseline, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061-s016_LG92-LC10_BL_S8.filtered_feature_bc_matrix.h5

value: Untreated (LG92), Untreated (LC10)

value: Anti CD298+/B2M:LG92 - TotalSeq-C0251; LC10 - TotalSeq-C0252


title: Sample 1 Patient 120 [FLU011035]

value: Bone Marrow

value: Leukemic blasts

value: Male

value: Normal

value: No

value: Mutated

value: FLUGA


title: RMj8-KV31, Baseline, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s003_RMj8-KV31_BL_S11.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: IFNant (RMj8), IFNant (KV31)

value: HTO

value: Anti CD298+/B2M:RMj8 - TotalSeq-C0253; KV31 - TotalSeq-C0254


title: Sample 1 Patient 119 [FLU017048]

value: Female

value: Abnormal

value: Yes

value: WT


title: WT-MA9_UtxKO_RNA_DMSO_d4_Rep1

value: Acute myeloid leukemia

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgUtx

value: DMSO


title: RRc17-RGo9, Baseline, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s009_RRc17-RGo9_BL_S1.filtered_feature_bc_matrix.h5

value: Baseline

value: Uninfected

value: Untreated (RRc17), Untreated (RGo9)

value: Anti CD298+/B2M:RRc17 - TotalSeq-C0251; RGo9 - TotalSeq-C0252


title: RCk17-RRj11, Baseline, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s010_RCk17-RRj11_BL_S2.filtered_feature_bc_matrix.h5

value: IFNant (RCk17), IFNant (RRj11)

value: Anti CD298+/B2M:RCk17 - TotalSeq-C0253; RRj11 - TotalSeq-C0254


title: CD68, Baseline, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s002_CD68-GR1_BL_S10.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: Untreated

value: Anti CD298+/B2M:CD68 - TotalSeq-C0252


title: RMs8, Baseline, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s001_RMs8-GR1_BL_S9.filtered_feature_bc_matrix.h5

value: HTO

value: Anti CD298+/B2M:RMs8 - TotalSeq-C0251


title: LC10, Day 7, Lung, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s025_LC10_D7_Lung_GEX_S17.filtered_feature_bc_matrix.h5

source_name: Lung

value: Lung

value: Day 7 post-infection

value: RNA


title: Sample 1 Patient 116 [FLU015011]

value: Bone Marrow

value: Leukemic blasts

value: Male

value: Abnormal

value: Yes

value: Mutated

value: WT

value: AZA


title: Sample 1 Patient 117 [FLU015040]

value: Female

value: No

value: FLUGA


title: RAz8, Day 2, Lung, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21206-s022_Lung_Raz8_GEX_S8.filtered_feature_bc_matrix.h5

value: Day 2 post-infection

value: IFNant


title: Sample 1 Patient 118 [FLU017035]

value: Normal

value: Sí


title: RZs14, Day 7, Lung, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s026_RZs14_D7_Lung_GEX_S18.filtered_feature_bc_matrix.h5

value: Lung

value: Day 7 post-infection


title: RCd8, Day 2, Lung, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21206-s021_Lung_Red8_GEX.filtered_feature_bc_matrix.h5

value: Untreated

value: RNA


title: KV30, Day 2, Lung, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21206-s014_Lung_KV30_day2_GEX_S36.filtered_feature_bc_matrix.h5


title: WT-MA9_UtxWT_RNA_MI-503_d4_Rep1

value: Acute myeloid leukemia

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgChr8


title: WT-MA9_UtxWT_RNA_DMSO_d4_Rep3

value: DMSO


title: Sample 1 Patient 115 [FLU014083]

value: Bone Marrow

value: Leukemic blasts

value: Male

value: Abnormal

value: Yes

value: Mutated


title: RMj8-KV31, Day 2, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s005_RMj8-KV31_D2_S13.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: Day 2 post-infection

value: IFNant (RMj8), IFNant (KV31)

value: HTO

value: Anti CD298+/B2M:RMj8 - TotalSeq-C0253; KV31 - TotalSeq-C0254


title: LD22, Day 2, Lung, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21206-s013_Lung_LD22_day2_GEX_S35.filtered_feature_bc_matrix.h5

value: Lung

value: IFNant


title: RMs8-CD68, Day 2, BAL, Hashtag antibody library

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
p21061_s004_RMs8-CD68_D2_S12.filtered_feature_bc_matrix.h5

value: Untreated (RMs8), Untreated (CD68)

value: Anti CD298+/B2M:RMs8 - TotalSeq-C0251; CD68 - TotalSeq-C0252


title: WT-MA9_UtxKO_RNA_DMSO_d4_Rep2

value: Acute myeloid leukemia

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgUtx


title: Sample 1 Patient 114 [FLU014050]

value: Bone Marrow

value: No

value: WT

value: FLUGA


title: WT-MA9_UtxWT_RNA_DMSO_d4_Rep2

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgChr8

value: DMSO


title: RGo9-RRj11, Day 7, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s015_RGo9-RRj11_D7_S7.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: Day 7 post-infection

value: Untreated (RGo9), IFNant (RRj11)

value: RNA


title: LC10-RZs14, Day 7, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s024_LC10-RZs14_D7_S16.filtered_feature_bc_matrix.h5

value: Untreated (LC10), IFNant (RZs14)


title: Sample 1 Patient 113 [FLU013032]

value: Leukemic blasts

value: Male

value: Abnormal

value: Yes

value: ND

value: AZA


title: WT-MA9_UtxWT_RNA_MI-503_d4_Rep3

value: Acute myeloid leukemia


title: RNi17-RZs14, Day 4, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s021_RNi17-RZs14_D4_S13.filtered_feature_bc_matrix.h5

value: Day 4 post-infection

value: IFNant (RNi17), IFNant (RZs14)


title: KV31-CD68, Day 7, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061_s008_KV31-CD68_D7_S8.filtered_feature_bc_matrix.h5

value: IFNant (KV31), Untreated (CD68)


title: LG92-LC10, Day 4, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s020_LG92-LC10_D4_S12.filtered_feature_bc_matrix.h5

value: Untreated (LG92), Untreated (LC10)


title: WT-MA9_UtxWT_RNA_DMSO_d4_Rep1

value: Stably expressing pMSCV-MLL-AF9-GFP, lenti-Cas9-Blast, pUSEPB-sgChr8

value: DMSO


title: RCk17-RRj11, Day 4, BAL, Gene expression library

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
p21061-s014_RCk17-RRj11_D4_S6.filtered_feature_bc_matrix.h5

value: Bronchoalveolar lavage (BAL)

value: IFNant (RCk17), IFNant (RRj11)