title: 3T3-L1 cells, shUbe2e2, adipogenic induction 12h, Rep3

city: Pittsburgh

first: Yang

last: Zhang

state: PA

address: 100 Technology Dr.

department: Medicine

institute: University of Pittsburgh

description:
UE2DMI3
shUbe2e2_DMI 12h_3

data_processing:
Transcript counts were generated using Kallisto and converted into gene counts using TxImport pipeline.
Assembly: GRCm38/mm10
Supplementary files format and content: Gene counts Matrix in Comma-separated Values format

growth_protocol: 3T3-L1 were are maintained in DMEM GlutaMAX with 10% FBS

extract_protocol:
Qiagen RNeasy micro kit following the manufacturer protocol
mRNAs were enriched using oligo(dT) beads, and rRNA was removed using the Ribo-Zero kit. Library construction and quality control were performed by Novogene (Novogene, CA, USA) following the Illumina protocol.

treatment_protocol: To induce adipogenesis in 3T3-L1 cells, we replaced their normal culture medium with an adipogenic induction medium containing 1 μM dexamethasone, 10 μg/ml insulin, and 0.5 mM isobutylmethylxanthine. We incubated the cells in this medium for 12 hours, then harvested them for RNA extraction.

value: Preadipocyte cell/fibroblast

value: Ube2e2 knockdown

value: Adipogenic induction medium


title: 3T3-L1 cells, shUbe2e2, adipogenic induction 12h, Rep2

status: Public on Jan 09 2025

type: SRA

country: USA

description:
UE2DMI2
shUbe2e2_DMI 12h_2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: IBBM36

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description:
bm_ab_normalized_counts.csv
IBBM36

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina)
Filtering of low quality reads and removal of adapters with cutadapt v1.7.1
Alignment and quantification with RSEM v1.7.1
Normalization with Limma’s voom v3.46
Assembly: mm10
Supplementary files format and content: normalized TPMs from each tissue

source_name: Bone Marrow

extract_protocol:
Whole RNA was obtained subsequently using mechanical disruption (Polytron PT 6100; Kinematica) and chloroform extraction and cleaned up using silica-based spin columns (Qiagen) according to manufacturer instructions. RNA quality was checked using capillary electrophoresis (Agilent).
Samples were submitted for whole RNA next generation sequencing in the Genomics Unit of CNIC. 200 ng of total RNA was used to generate barcoded RNA sequencing libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Libraries were sequenced with HiSeq2500 (Illumina) to generate 50-nucleotide single reads, with minimum of eight million reads per sample. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina). Reads were further processed using the CASAVA package (Illumina) to demultiplex reads according to adapter indexes and to produce FastQ files. Read quality was determined with the application FastQC. For data analysis, sequencing adaptor contaminations were removed from reads using Cutadapt v1.7.1, and the resulting reads were mapped on the transcriptome (GRCm38 Ensembl gene-build 84) and quantified using RSEM v1.2.20 and Kallisto v0.43.1.

treatment_protocol: Mice were treated with 3 µg/g mouse bodyweight of either anti-Ly6G (neutrophil depleted) or control IgG (nondepleted) antibodies for two consecutive days, in normal light-controlled mouse facility or 12 h inverted light cabinets. In the morning of the third day, mice were bled from the cheek just before the lung harvest to obtain blood samples for confirmation of neutrophil depletion using a standard hemocytometer (ABX Pentra 80; Horiba), as well as flow cytometry. Blood, bone marrow, lung, samples were collected every four hours (ZT1-5-9-13-17-21) from 3 mice per group. In the Mrp8CRE; iDTR model, mice were injected intraperitoneally with 10 μg/kg of diphtheria toxin (DT; Calbiochem) for two consecutive days, and tissues were collected on the third day. Ear skins were harvested after perfusion of mice with saline at ZT1-3-4-5-7-9-10-12-13-15-16-18-19-21-22-24 from one mouse per group and snap-frozen in 1 ml of TRIzol each

tag: tissue

value: Bone Marrow

tag: mouse

value: depleted

tag: time

value: ZT 21

tag: neutropenia model

value: Antibody depletion

value: anti Ly6G (1A8)

value: WT

tag: strain


title: 17_Rotenone_LC10_36h_Eppi-23_Index-A6

city: Leipzig

first: Paul

last: Michaelis

address: Permoserstr. 15

country: Germany

institute: Helmholtz-Centre for Environmental Research (UFZ)

data_processing:
alignment to GRCz11 with HISAT2 (v.2.1.0)
filter reads by quality > 30 (Samtools view v.1.15.1)
generate counts with featureCounts (v.2.0.3)
QC with MultiQC (v.1.11)
Assembly: GRCz11
Supplementary files format and content: counts.tsv: unnormalized counts
Supplementary files format and content: sample_info.tsv: additional metadata for samples

organism: Danio rerio

source_name: whole body

growth_protocol: Wild-type adult zebrafish (D. rerio, strain OBI/WIK, generation F3) were kept at 26°C in 20 L aquaria with 1-2 fish/L, fed twice a day and on a 14h:10h light dark cycle.

extract_protocol:
Trizol, homogenization by a FastPrep 50 (MP Biomedicals), followed by Total RNA Extraction Kit MagMAX, RIN>7
NEBnext Ultra II stranded RNA library preparation kit for Illumina (NEB, Beverly, MA, USA)

treatment_protocol: Exposure to Sorafenib or Rotenone at 2 or 24 hpf, 20 embryos per replicate, incubation at 26°C with 12:12 light:dark photoperiod

value: whole body

value: treatment

tag: substance

value: Rotenone

tag: concentration

tag: unit

value: nM

tag: exposure start_hpf

tag: time hpf


title: DS_176_2, EPOR 2

city: San Francisco

first: Prathamesh

last: Chati

state: CA

address: 1975 4th Street

institute: University of California, San Francisco

description:
Library name: DS_176_2
Column name in both processed files: DS_176_2

data_processing:
Quality control performed by Novogene.
FASTQ files were aligned to the GRCh38 reference genome extended with the synEPOR target sequence and quantified using Salmon (v1.9.0) with default parameters.
Outputted NumReads and TPM for each sample were aggregated into two separate files and were used for downstream analyses.
Assembly: GRCh38 extended with synEPOR sequences.
Supplementary files format and content: CSV files contain sample names along the columns and gene names (symbols) along rows.

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: Human CD34+ HSPCs were cultured in StemSpan SFEMII or Good Manufacturing Practice Stem Cell Growth Medium supplemented with the following cytokines: stem cell factor (100 ng/mL), thrombopoietin (100 ng/mL), Fms-like tyrosine kinase 3 ligand (100 ng/mL), interleukin-6 (100 ng/mL), as well as streptomycin (20 mg/mL) and penicillin (20 U/mL). Additionally, 35 nM of UM171 was added. Cells were maintained in a humidified incubator at 37°C, 5% CO2, and 5% O2.

extract_protocol:
RNA Extraction: Total RNA was extracted from cell pellets (approximately 1×10⁶ cells per sample) using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol. RNA quality and quantity were assessed prior to sequencing library preparation.
Library Construction: RNA sequencing libraries were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's instructions. Approximately 1.3 μg of total RNA was used for library preparation. The libraries were validated for quality and quantified prior to sequencing.

treatment_protocol: Adipogenic differentiation: Following genome editing, human CD34+ HSPCs were cultured in a three-phase differentiation system. During Phase 1 (Day 0–7), cells were cultured at 1×10⁵ cells/mL in SFEMII medium supplemented with stem cell factor (10 ng/mL), interleukin-3 (1 ng/mL), and transferrin (200 μg/mL). During Phase 2 (Day 7–10), interleukin-3 was removed, and transferrin concentration was maintained. During Phase 3 (Day 11–14), transferrin concentration was increased to 1 mg/mL. Differentiation conditions included either the addition of recombinant EPO (3 U/mL) or the absence of EPO with the addition of 1 nM BB dimerizer.

value: Peripheral blood

value: RBC

value: EPOR (synEPOR)

value: Erythroid differentiation

value: Day 14


title: DS_176_1, EPOR 1

description:
Library name: DS_176_1
Column name in both processed files: DS_176_1


title: IBBM35

description:
bm_ab_normalized_counts.csv
IBBM35


title: DS_175_4, HBA1 (EPOR) 4

description:
Library name: DS_175_4
Column name in both processed files: DS_175_4

value: HBA1 (synEPOR)


title: 3T3-L1 cells, shUbe2e2, adipogenic induction 12h, Rep1

description:
UE2DMI1
shUbe2e2_DMI 12h_1

value: Preadipocyte cell/fibroblast

value: Ube2e2 knockdown

value: Adipogenic induction medium


title: 16_Rotenone_LC10_36h_Eppi-21_Index-H5


title: 3T3-L1 cells, shUbe2e2, Control, Rep3

description:
UE2KD3
shUbe2e2_3

value: Normal medium


title: DS_175_3, HBA1 (EPOR) 3

description:
Library name: DS_175_3
Column name in both processed files: DS_175_3


title: IBBM33

description:
bm_ab_normalized_counts.csv
IBBM33

value: Bone Marrow

value: ZT 21

value: Antibody depletion

value: IgG


title: IBBM32

description:
bm_ab_normalized_counts.csv
IBBM32

value: WT


title: DS_175_1, HBA1 (EPOR) 1

description:
Library name: DS_175_1
Column name in both processed files: DS_175_1


title: 44_Sorafenib_LC10_96h_Eppi-69_Index-E9

value: whole body

value: treatment

value: Sorafenib

value: uM


title: DS_175_2, HBA1 (EPOR) 2

description:
Library name: DS_175_2
Column name in both processed files: DS_175_2

value: Peripheral blood

value: RBC


title: 43_Sorafenib_LC10_96h_Eppi-66_Index-D9


title: DS_d14_3, WT HSC Differentiated 3

description:
Library name: DS_d14_3
Column name in both processed files: DS_d14_3

value: Erythroid differentiation

value: Day 14


title: 3T3-L1 cells, shUbe2e2, Control, Rep1

description:
UE2KD1
shUbe2e2_1

value: Preadipocyte cell/fibroblast


title: 3T3-L1 cells, shUbe2e1, adipogenic induction 12h, Rep3

description:
UE1DMI3
shUbe2e1_DMI 12h_3

value: Ube2e1 knockdown


title: 31_Sorafenib_LC10_48h_Eppi-45_Index-G7


title: IBBM30

description:
bm_ab_normalized_counts.csv
IBBM30

value: depleted

value: ZT 17

value: anti Ly6G (1A8)


title: 30_Sorafenib_LC10_48h_Eppi-43_Index-F7


title: DS_d14_1, WT HSC Differentiated 1

description:
Library name: DS_d14_1
Column name in both processed files: DS_d14_1


title: IBBM29

description:
bm_ab_normalized_counts.csv
IBBM29

value: Bone Marrow


title: 3T3-L1 cells, shUbe2e1, adipogenic induction 12h, Rep2

description:
UE1DMI2
shUbe2e1_DMI 12h_2

value: Adipogenic induction medium


title: IBBM28

description:
bm_ab_normalized_counts.csv
IBBM28

value: Antibody depletion


title: 15_Sorafenib_LC10_36h_Eppi-20_Index-G5

value: WT


title: 29_Sorafenib_LC10_48h_Eppi-41_Index-E7

value: whole body


title: 3T3-L1 cells, shUbe2e1, adipogenic induction 12h, Rep1

description:
UE1DMI1
shUbe2e1_DMI 12h_1


title: 3T3-L1 cells, shUbe2e1, Control, Rep3

description:
UE1KD3
shUbe2e1_3

value: Normal medium


title: 45_Sorafenib_LC10_96h_Eppi-70_Index-F9

value: treatment

value: Sorafenib


title: DS_d0_3, WT HSC Undifferentiated 3

description:
Library name: DS_d0_3
Column name in both processed files: DS_d0_3

value: Peripheral blood

value: HSPC

value: Day 0


title: IBBM34

description:
bm_ab_normalized_counts.csv
IBBM34

value: ZT 21


title: DS_d0_2, WT HSC Undifferentiated 2

description:
Library name: DS_d0_2
Column name in both processed files: DS_d0_2


title: 3T3-L1 cells, shUbe2e1, Control, Rep2

description:
UE1KD2
shUbe2e1_2

value: Preadipocyte cell/fibroblast


title: IBBM27

description:
bm_ab_normalized_counts.csv
IBBM27

value: IgG


title: 14_Sorafenib_LC10_36h_Eppi-18_Index-F5

value: uM


title: 3T3-L1 cells, shUbe2e2, Control, Rep2

description:
UE2KD2
shUbe2e2_2

value: Ube2e2 knockdown


title: DS_d0_1, WT HSC Undifferentiated 1

description:
Library name: DS_d0_1
Column name in both processed files: DS_d0_1


title: IBBM26

description:
bm_ab_normalized_counts.csv
IBBM26

value: ZT 17


title: 13_Sorafenib_LC10_36h_Eppi-16_Index-E5


title: IBBM31

description:
bm_ab_normalized_counts.csv
IBBM31

value: Bone Marrow


title: 3T3-L1 cells, shUbe2e1, Control, Rep1

description:
UE1KD1
shUbe2e1_1

value: Ube2e1 knockdown


title: 3T3-L1 cells, Scramble, adipogenic induction 12h, Rep3

description:
ScrDMI3
Scramble_DMI 12h_3

value: shRNA control

value: Adipogenic induction medium


title: IBBM25

description:
bm_ab_normalized_counts.csv
IBBM25

value: WT

value: Antibody depletion


title: Inner ear organoid d40 SOX2-ntdT+ Matrigel

city: Indianapolis

first: Matthew

last: Arkenberg

state: IN

address: 980 W Walnut St

department: Otolaryngology - Head and Neck Surgery

institute: Indiana University School of Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw data was processed using the Cell Ranger pipeline. Cell ranger mkfastq was used to generate fastq files from demultiplex raw base sequence calls.
Fastq files were aligned to human reference genome GRCh38 with RNAseq aligner STAR. Following, aligned reads were traced back to individual cells and gene expression was quantified based on the unique molecular indices( UMIs).
The filtered gene-barcode matrices were used for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Inner ear organoids

growth_protocol: Inner ear organoids were cultured following our established protocol with modifications. On day -2 (D-2) hESCs were dissociated and seeded at 3,500 cells/well in low-adhesion 96-well U-bottom plates along with 100 µL of E8 flex media with 1x Normocin and 20 µM of Y27632 followed by addition of 100 µL of E8 flex media with 1x Normocin. After 48 hrs aggregates in E8fn  were sequentially treated with Essential 6 medium supplemented with as follows: FGF-2 (4 ng/mL), SB-431542 (10 µM), BMP-4 (0.5 ng/mL), and 2% growth factor-reduced Matrigel on d0; FGF-2 (50 ng/mL) and LDN193189 (200 nM) on d3; FGF-2 (40 ng/mL), LDN193189 (200 nM) and CHIR99021 (3 µM) on d7. On d11, the aggregates were embedded in  GelNB-CH hydrogels with 1 mM LAP and  0.1 wt% PEG4SH. Aggregates along with ~5 µL of the culture media were placed individually on a well-plate. Remaining media was aspirated and quickly replaced with ~5 µL of gel precursor solution. After gently mixing the aggregate and the precursor solution, aggregate-laden gels were polymerized for 2 min under UV-light exposure. Encapsulated aggregates were maintained in organoid maturation medium (OMM; 50:50 mixture of Advanced DMEM:F12 and Neurobasal Medium, 0.5×N2 Supplement, 0.5×B27 without Vitamin A, 1×GlutaMAX, 0.1 mM β-mercaptoethanol, and 1× Normocin) with WNT pathway activator CHIR99021 (3 µM) notably without the addition of Matrigel described in our previous protocol. On d15, aggregates were treated with OMM, CHIR, and oDex (0.02%) for 24 hrs. after which the media was replaced with fresh OMM with CHIR. Further CHIR treatment was conducted until d18 in which aggregates were maintained in OMM alone. Starting on d22, media was replaced twice weekly up to d40.

extract_protocol:
Aggregates were collected in a 2 mL tube, centrifuged (200 x g for 3 min), and treated with Accutase at 37 C for 90 min. Aggregates were periodically, gently pipetted with p1000 tips to mechanically dissociate. After confirming dissociation, aggregates were sequentially filtered through a 100 µm and 40 µm cell strainer. Aggregates were then transferred into a 2 mL tube, centrifuged (100 x g for 5 min), and resuspended with fluorescence-activated cell sorting (FACS) buffer containing 2% fetal bovine serum in DPBS. SOX2ntdTomato-positive cells were collected via FACS.
Library preparation was conducted using the 10X Genomics Chromium X platform with the 10X 3’ scRNA-seq standard assay v3.1. The resultant cDNA library was sequenced with an Illumina NovaSeq X Plus system. Illumina’s CellRanger v4.0.0 program was used to generate mapped, filtered gene-barcode matrices.

value: Inner ear organoids

value: WA25 human ESCs

tag: developmental stage

value: Matrigel


title: DS_d14_2, WT HSC Differentiated 2

description:
Library name: DS_d14_2
Column name in both processed files: DS_d14_2

value: Peripheral blood

value: RBC

value: Erythroid differentiation

value: Day 14


title: 56_Sorafenib_EC50_96h_Eppi-85_Index-A11

value: whole body

value: treatment

value: Sorafenib


title: 55_Sorafenib_EC50_96h_Eppi-84_Index-H10

value: uM


title: IBBM24

description:
bm_ab_normalized_counts.csv
IBBM24

value: Bone Marrow

value: depleted

value: ZT 13

value: anti Ly6G (1A8)


title: 3T3-L1 cells, Scramble, adipogenic induction 12h, Rep2

description:
ScrDMI2
Scramble_DMI 12h_2

value: Preadipocyte cell/fibroblast

value: shRNA control

value: Adipogenic induction medium


title: IBBM23

description:
bm_ab_normalized_counts.csv
IBBM23

value: Antibody depletion

value: WT


title: 3T3-L1 cells, Scramble, adipogenic induction 12h, Rep1

description:
ScrDMI1
Scramble_DMI 12h_1


title: 54_Sorafenib_EC50_96h_Eppi-83_Index-G10


title: IBBM22

description:
bm_ab_normalized_counts.csv
IBBM22


title: 39_Sorafenib_EC50_48h_Eppi-60_Index-H8


title: 3T3-L1 cells, Scramble, Control, Rep3

description:
Scr3
Scramble_3

value: Normal medium


title: IBBM21

description:
bm_ab_normalized_counts.csv
IBBM21

value: IgG


title: 38_Sorafenib_EC50_48h_Eppi-59_Index-G8


title: ART PWH Donor #1

city: Washington

first: Natalia

last: Soriano-Sarabia

state: DC

address: 2300 I St. NW

department: Microbiology Immunology and tropical Medicine

institute: George Washington University

library_source: genomic

data_processing:
Resulting material was quantified using iSeq (Illumina) and sequenced with PE42 on the NovaSeq6000 (Illumina). Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality ³1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the 570 genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS v2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Vd1 T cell

extract_protocol:
Human Vd1 T cells were FACS-purified ex vivo from PBMCs isolated from three ART-suppressed people living with HIV and three HIV-seronegative donors using a Sony SH800 cell sorter.
The cells were processed according to the Fixed Cell ATAC-Seq Kit instruction (Active Motif cat# 53151) except for 30 min of cell fixation incubation time with cell fixation buffer.

value: Peripheral Blood


title: HIV- Donor #3


title: 3T3-L1 cells, Scramble, Control, Rep2

description:
Scr2
Scramble_2


title: IBBM20

description:
bm_ab_normalized_counts.csv
IBBM20


title: 3T3-L1 cells, Scramble, Control, Rep1

description:
Scr1
Scramble_1


title: 37_Sorafenib_EC50_48h_Eppi-56_Index-F8


title: HIV-Donor #2


title: Exp26_wt_Soma

city: Cambridge

first: Yasuhiro

last: Itoh

state: MA

address: 7 Divinity Ave

institute: Harvard University

data_processing:
Adapter sequences were clipped, and unpaired reads were trimmed with Trimmomatic version 0.39
Reads were aligned to the GRCm39 mouse genome with STAR (version 2.7.1a)
Reads mapping to exons were quantified with featureCounts (version 1.5.0)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cortex

extract_protocol:
RNA was harvested using RNeasy Plus Micro Kit (Qiagen). 1.8–3.1 ng of total RNA was used for the construction of sequencing libraries of soma samples. 0.19–3.1 ng of total RNA was used for the construction of sequencing libraries of GC samples.
Purified RNA samples were converted to cDNA using the SMART-seq v4 Ultra Low Input RNA Kit (Takara Bio), and cDNA libraries were generated with the Nextera XT DNA Library Preparation Kit (Takara Bio) by the Harvard University Bauer Core Facility.

value: cortex

value: subcerebral projection neurons

value: postnatal day 1


title: 25_Sorafenib_EC50_36h_Eppi-34_Index-A7

value: whole body

value: treatment

value: Sorafenib


title: HIV- Donor #1


title: IBBM19

description:
bm_ab_normalized_counts.csv
IBBM19

value: Bone Marrow


title: Exp26_KO_Soma

value: Bcl11b KO


title: Inner ear organoid d40 SOX2-ntdT+ GelNB-CH

description: 10X Genomics

value: Inner ear organoids

value: WA25 human ESCs

value: GelNB-CH


title: MAIT cells VDJ donor 4 + IL23

city: Paris

first: Sebastien

last: Mella

address: 28 rue du Dr Roux

department: Immunology

country: France

institute: Institut Pasteur

description:
10X Genomics
polyA RNA
VDJ-T: read1 file contains cell barcode and UMI, read2 file contains TCR reads

data_processing:
cellreanger multi (v6.0.1) to generate antibody derived tag (ADT) sequencing librarry, 5' gene expression library and VDJ library
Assembly: 10X human reference refdata-gex-GRCh38-2020-A
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Supplementary files format and content: cellranger multi output mRNA count matrix, ADT count matrix and VDJ information
Library strategy: CITE-seq

molecule: polyA RNA

source_name: PBMC

growth_protocol: Freshly isolated PBMC were cultured in RPMI supplemented with 10% FBS, 1% penicillin/streptomycin and 20UI/mL.

extract_protocol:
MAIT cells were sorted as CD3+MR1/5-OP-RU+ and loaded onto a chromium 5’ chip following the Single Cell 5’ Kit and run on the 10X Chromium.
Gene expression (GEX), V(D)J and antibody-derived tag (ADT) libraries were generated according to the manufacturer’s recommendations using the User Guide CG000330 Rev D, Chromium Next GEM Single Cell 5' Reagent Kits v2 (10X Genomics).

treatment_protocol: MR1/5-OP-RU tetramers (NIH) were added the first day of culture at 40pM, and cells were cultured for 6 days. IL-23 or IL-12 (Miltenyi Biotec) were added at the concentration of 20 ng/mL and renewed after 3 days.

value: PBMC

value: MAIT cells

tag: library type

value: VDJ


title: ART PWH Donor #3


title: 23_Sorafenib_EC50_36h_Eppi-32_Index-G6

value: WT

value: uM


title: 22_Sorafenib_EC50_36h_Eppi-31_Index-F6


title: Exp25_wt_Soma


title: MAIT cells GEX donor 4 + IL23

description:
10X Genomics
polyA RNA
GEX (5' mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript

value: GEX


title: Exp25_KO_Soma

value: cortex


title: IBBM16

description:
bm_ab_normalized_counts.csv
IBBM16

value: depleted

value: ZT 9

value: Antibody depletion

value: anti Ly6G (1A8)


title: ART PWH Donor #2

value: Peripheral Blood


title: MAIT cells ADT donor 4 + IL23

description:
10X Genomics
Antobody-derived oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI, read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein

value: ADT

tag: adt

value: see TS_TotalSeq_01_features.csv


title: Exp22_wt_Soma

value: subcerebral projection neurons

value: postnatal day 1


title: IBBM15

description:
bm_ab_normalized_counts.csv
IBBM15

value: Bone Marrow

value: IgG


title: MAIT cells VDJ donor 4 + IL12

value: PBMC

value: MAIT cells


title: 51_DMSO_Kontrolle1_96h_Eppi-76_Index-D10

value: whole body

value: WT

value: control

value: DMSO


title: IBBM13

description:
bm_ab_normalized_counts.csv
IBBM13


title: MAIT cells GEX donor 4 + IL12

value: GEX


title: Exp15_KO_Soma

value: cortex

value: Bcl11b KO


title: IBBM14

description:
bm_ab_normalized_counts.csv
IBBM14

value: ZT 9

value: Antibody depletion


title: IBBM18

description:
bm_ab_normalized_counts.csv
IBBM18

value: depleted

value: anti Ly6G (1A8)


title: Exp14_wt_Soma

value: subcerebral projection neurons


title: MAIT cells ADT donor 4 + IL12

value: ADT

value: see TS_TotalSeq_01_features.csv


title: MAIT cells VDJ donor 4

value: Tet

value: VDJ


title: IBBM12

description:
bm_ab_normalized_counts.csv
IBBM12

value: Bone Marrow

value: ZT 5


title: 35_DMSO_Kontrolle9_48h_Eppi-54_Index-D8

value: whole body

value: WT


title: IBBM11

description:
bm_ab_normalized_counts.csv
IBBM11


title: Exp14_KO_Soma

value: postnatal day 1


title: MAIT cells GEX donor 4

value: PBMC

value: MAIT cells

value: GEX


title: 34_DMSO_Kontrolle6_48h_Eppi-51_Index-C8

value: control

value: DMSO


title: Exp12_wt_Soma

value: cortex


title: IBBM10

description:
bm_ab_normalized_counts.csv
IBBM10

value: depleted

value: Antibody depletion

value: anti Ly6G (1A8)


title: 21_DMSO_Kontrolle5_36h_Eppi-30_Index-E6


title: 53_DMSO_Kontrolle3_96h_Eppi-78_Index-F10


title: Exp11_wt_GC

source_name: brainstem and spinal cord

value: brainstem and spinal cord

value: subcerebral projection neurons


title: IBBM09

description:
bm_ab_normalized_counts.csv
IBBM09

value: IgG


title: 52_DMSO_Kontrolle2_96h_Eppi-77_Index-E10


title: MAIT cells ADT donor 4

value: Tet

value: ADT

value: see TS_TotalSeq_01_features.csv


title: MAIT cells VDJ donor 3 + IL23

value: VDJ


title: 20_DMSO_Kontrolle4_36h_Eppi-29_Index-D6

value: whole body

value: WT


title: IBBM08

description:
bm_ab_normalized_counts.csv
IBBM08

value: Bone Marrow

value: ZT 5


title: Exp22_KO_Soma

value: Bcl11b KO

value: postnatal day 1


title: 19_DMSO_Kontrolle3_36h_Eppi-28_Index-C6

value: control

value: DMSO


title: MAIT cells GEX donor 3 + IL23

value: PBMC

value: MAIT cells

value: GEX


title: IBBM07

description:
bm_ab_normalized_counts.csv
IBBM07

value: Antibody depletion


title: Exp11_KO_GC

value: brainstem and spinal cord

value: subcerebral projection neurons


title: IBBM17

description:
bm_ab_normalized_counts.csv
IBBM17

value: depleted

value: ZT 9

value: anti Ly6G (1A8)


title: Exp10_wt_GC


title: 36_DMSO_Kontrolle10_48h_Eppi-55_Index-E8

value: whole body


title: 8_Rotenone_LC10_96h_Eppi-10_Index-H4

value: WT

value: treatment

value: Rotenone

value: nM


title: MAIT cells ADT donor 3 + IL23

value: ADT

value: see TS_TotalSeq_01_features.csv


title: MAIT cells VDJ donor 3 + IL12

value: VDJ


title: Exp10_KO_GC

value: Bcl11b KO

value: postnatal day 1


title: IBBM06

description:
bm_ab_normalized_counts.csv
IBBM06

value: Bone Marrow

value: ZT 1


title: 7_Rotenone_LC10_96h_Eppi-9_Index-G4


title: IBBM05

description:
bm_ab_normalized_counts.csv
IBBM05

value: Antibody depletion


title: Exp9_wt_GC

value: brainstem and spinal cord

value: subcerebral projection neurons


title: IBBM04

description:
bm_ab_normalized_counts.csv
IBBM04

value: depleted


title: MAIT cells GEX donor 3 + IL12

value: PBMC

value: MAIT cells

value: GEX


title: 6_Rotenone_LC10_96h_Eppi-8_Index-F4

value: whole body

value: WT

value: treatment


title: 5_Rotenone_LC10_96h_Eppi-6_Index-E4

value: Rotenone

value: nM


title: MAIT cells ADT donor 3 + IL12

value: ADT

value: see TS_TotalSeq_01_features.csv


title: Exp9_KO_GC

value: Bcl11b KO

value: postnatal day 1


title: Exp8_wt_GC


title: MAIT cells VDJ donor 3

value: Tet

value: VDJ


title: 3_Sorafenib_LC10_96h_Eppi-3_Index-C4

value: Sorafenib

value: uM


title: Exp8_KO_GC

value: brainstem and spinal cord

value: subcerebral projection neurons


title: IBBM01

description:
bm_ab_normalized_counts.csv
IBBM01

value: Bone Marrow

value: ZT 1

value: Antibody depletion

value: IgG


title: IBBM03

description:
bm_ab_normalized_counts.csv
IBBM03

value: WT


title: Exp7_wt_GC


title: 2_Sorafenib_LC10_96h_Eppi-2_Index-B4

value: whole body

value: treatment


title: MAIT cells ADT donor 3

value: PBMC

value: MAIT cells

value: ADT


title: IBBM02

description:
bm_ab_normalized_counts.csv
IBBM02


title: Exp7_KO_GC

value: Bcl11b KO

value: postnatal day 1


title: MAIT cells VDJ donor 2 + IL23

value: VDJ


title: 1_Sorafenib_LC10_96h_Eppi-1_Index-A4

value: Sorafenib


title: CCHMC2017-30 Patient BM

city: Cincinnati

first: Mark

last: Wunderlich

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were aligned to the genome by using the standard Illumina sequence analysis pipeline by the Statistical Genomics and Systems Biology Core at the University of Cincinnati.
alignment by TopHat
Assembly: hg19
Supplementary files format and content: tab-delimited text file of raw counts for each gene in each sample

source_name: bone marrow

extract_protocol:
The RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with the total RNA extraction protocol. In brief, cell lysates stored at -80C in Lysis/Binding Buffer were sent to the University of Cincinnati Genomics, Epigenomics and Sequencing Core for total RNA extraction according to the protocol and eluted with 60 µl Elution Buffer. The RNA concentration was measured by Nanodrop (Thermo Scientific, Wilmington, DE) and its integrity was determined by Bioanalyzer RNA 6000 Pico Kit (Agilent, Santa Clara, CA).
NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for poly(A) RNA purification with 50 uL total RNA as input. SMARTer Apollo NGS library prep system (Takara, Mountain View, CA) was used for automated poly(A) RNA isolation. The library for RNA-seq was prepared by using NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA). During the second cDNA synthesis dUTP was incorporated to maintain strand specificity. In short, the isolated poly(A) RNA or rRNA/globin depleted RNA was fragmented (~200 bp), reverse transcribed to the 1st strand cDNA, followed by 2nd strand cDNA synthesis labelled with dUTP. The cDNA was then end repaired and dA-tailed and ligated to the adapter. The dUTP-labelled 2nd strand cDNA was enzymatically removed to maintain strand specificity. After indexing via PCR (13 cycles) enrichment, the amplified libraries together with the negative control were cleaned up for QC analysis. To check the quality and yield of the purified library, one µL library was analyzed by Bioanalyzer (Agilent, Santa Clara, CA) using DNA high sensitivity chip. To accurately quantify the library concentration for the clustering, the library concentration was qPCR measured by NEBNext Library Quant Kit (New England BioLabs) using QuantStudio 5 Real-Time PCR Systems (Thermo Fisher, Waltham, MA).
read length: 51

value: bone marrow

tag: cell line

value: Acute Myeloid Leukemia

value: Patient


title: 9_DMSO_Kontrolle1_96h_Eppi-11_Index-A5

value: control

value: DMSO


title: MAIT cells GEX donor 2 + IL23

tag: cell type

value: GEX


title: 12_DMSO_Kontrolle4_96h_Eppi-14_Index-D5

tag: genotype


title: splenocytes, dnPI3K, rep1

city: Melbourne

first: Graham

middle: William

last: Magor

state: Victoria

address: 99 Commercial Rd

country: Australia

institute: ACBD

data_processing:
Reads aligned to mm9 with BWA (v0.7.12)
BWA command: bwa bwasw -b 7
Unmapped reads were extracted with samtools (v1.3.1) and recovered by in silico NlaIII digest with the R package ‘DECIPHER’
Recovered reads were re-mapped with BWA as above and all aligned reads were merged
Deeptools bamCoverage (v3.1.3) was used to produce a bigwig file with 50 bp bins
Assembly: mm9
Supplementary files format and content: bigwig showing signal coverage aligned to mm9
Library strategy: TLA (targetted locus amplifiication)

source_name: spleen

extract_protocol:
TLA as described in Vree et al., (https://doi.org/10.1038/nbt.2959)
Illumina Tagment DNA Enzyme and Buffer Small Kit (cat# 15027865)

value: spleen

value: splenocytes


title: CCHMC2017-98 Patient BM

value: KRAS G12A - subclonal, NRAS Q61H - subclonal, MLL-MLLT4 (AF6) fusion, PTPN11 E76K - subclonal , S502L - subclonal

tag: treatment


title: MAIT cells ADT donor 2 + IL23

tag: tissue

value: see TS_TotalSeq_01_features.csv


title: I_8h_4_M

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

description: processed file contains DESE2 LRT statistics and abundance measurements (DESEq2 normalized counts) for each sample. Cluster membership of significant genes is also provided in the cluster column

data_processing:
Sequence reads were mapped to the mm10 mouse genome build using STAR v. 2.7.6a
Counts for each transcript were collected using featureCounts from Subread package (v. 2.0.1),  with options -Q 10 -p -B -C -s 2 -g gene_id -t exon and Gencode vM25 annotation.
Differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Excel ile includes DESeq2 normalized counts for each sample and DESe2 LRT test statistics (comparisons across time). PNG file contains sequence logo for the 3’end of Moderna’s mRNA-172 poly(A) tail

source_name: Tissue (mostly muscles) isolated from the mRNA-1273 injection sites

growth_protocol: Mice were bred in the animal house of the Faculty of Biology, University of Warsaw, and maintained under conventional conditions24,25,30 in open polypropylene cages filled with wood chip bedding enriched with nest material and paper tubes. Mice were fed at libutum with a standard laboratory diet (Labofeed B, Morawski). Humidity in the rooms was kept at 55 ± 10%, the temperature at 22 °C ± 2 °C, at  least 15 air changes per hour, and the light regime set at 12 h/12 h (lights on from 6:00 to 18:00). Health monitoring was performed regularly at the IDEXX laboratory.

extract_protocol:
RNA from frozen injection sites (muscles) were isolated by homogenization in TRI-reagent (Sigma, T9424) using Omni Tissue Homogenizer (TH) equipped with 7 x 15 mm Saw Tooth (Fine) Generator Probe, homogenous mixtures were heated to 60 °C and further processed according to the manufacturer’s instructions.
Libraries were prepared using a KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, #08098140702), according to the manufacturer. KAPA UDI Indexes (KAPA Biosystems, #08098140702) were used. Library quality was assessed using chip electrophoresis performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: Mice were immunized by intramuscular (Vastus lateralis region) injection either with 25μl of 0.9% NaCl (controls) or 25μl of Moderna’s mRNA-1273 at 40 ng/ul concentration

value: wild type

value: 8h post immunization with 25ul (40ng/ul) of mRNA-1273


title: I_8h_6_M

value: Tissue (mostly muscles) isolated from the mRNA-1273 injection sites


title: 4_Sorafenib_LC10_96h_Eppi-4_Index-D4

value: whole body

value: WT

value: treatment

value: uM


title: MAIT cells VDJ donor 2 + IL12

value: PBMC

value: MAIT cells

value: VDJ


title: 11_DMSO_Kontrolle3_96h_Eppi-13_Index-C5

value: control


title: CCHMC2017-103 Patient BM

value: bone marrow

value: Acute Myeloid Leukemia

value: FLT3 D835E - subclonal , D835V - subclonal , D835Y - subclonal, KIT D816V, ASXL1 G645fs*58, CBL deletion exon 9, CHEK2 T367fs*15, PTPN11 D61V

value: Patient


title: I_8h_2_M


title: 10_DMSO_Kontrolle2_96h_Eppi-12_Index-B5

value: DMSO


title: I_2h_6_M

value: 2h post immunization with 25ul (40ng/ul) of mRNA-1273


title: MAIT cells GEX donor 2 + IL12

value: GEX


title: MAIT cells ADT donor 2 + IL12

value: ADT

value: see TS_TotalSeq_01_features.csv


title: rlp44_3_3

city: Uppsala

first: Ai

state: Uppsala

address: Biocenter, Almas allé 5

department: Plant Biology

country: Sweden

institute: SLU

description: whole seedling

data_processing:
adapter and low-quality sequences were removed using the fastp software
The cleaned reads were mapped to the Arabidopsis reference TAIR10 using hisat2
The number of reads was counted using htseq
Differentially expressed genes were identified using the DESeq2
Assembly: TAIR10
Supplementary files format and content: Matrix table with raw gene counts for each gene and each sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were surface sterilized with 70% ethanol for 20 minutes, then 95% ethanol for 5 minutes. Sterilized seeds were sown on 1/2MS with 1.2% (w/v) plant agar. After 2 days of stratification at 4 °C, seeds were moved to the growth chamber (8 hours of light/16 hours of dark, ~110 μmol m-2 s−1, 20°C). All seeds were grown vertically.

extract_protocol:
Total RNA was extracted using the ROTI®Prep RNA MINI (Roth) kit.
RNA libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® and NEBNext Multiplex Oligos for Illumina ® for paired end sequencing. The final PCR was for 13 cycles.

treatment_protocol: 7 day-old-seedlings were collected and placed in liquid nitrogen immediately

value: Intact

tag: genetic background

value: 7 day old


title: I_2h_4_M

value: Tissue (mostly muscles) isolated from the mRNA-1273 injection sites

value: wild type


title: MAIT cells VDJ donor 2

value: PBMC

value: Tet


title: MAIT cells GEX donor 3

value: MAIT cells


title: CCHMC2014-59 Patient BM


title: CCHMC2017-14 Patient BM

value: FLT3 D835A (sub) / D835E (sub) / D835Y (sub) / I836del (sub) / V491L (sub), V579A (sub), KRAS G13D, MLL-MVB12B fusion, MLL-MLLT10 (AF10) fusion


title: rlp44_3_1

description: whole seedling


title: I_2h_2_M


title: CCHMC2017-42 Patient BM

value: bone marrow

value: MLL-MLLT3 (AF9) fusion, PC R583H - subclonal, WT1 R462Q - subclonal

value: PDX


title: MAIT cells GEX donor 2


title: CCHMC2013-7 NRGS BM

value: Acute Myeloid Leukemia

value: MLL-MLLT1 fusion, APC-CBX3 rearrangement


title: evg1_1_3

description: whole seedling


title: I_24h_4_M

value: 24h post immunization with 25ul (40ng/ul) of mRNA-1273


title: MAIT cells ADT donor 2


title: CCHMC2017-114 NSGS BM

value: NRAS G13D - subclonal, MLL-MLLT10 (AF10) fusion, PTPN11 E69K


title: I_24h_2_M


title: human MSC, Rep2

data_processing:
Trimmomatic was applied to trim low-quality reads and adapter sequences and remaining reads aligned to human reference genome hg38 by Burrows-Wheeler Aligner and further filtered by SAMtools.
The aligned reads were further filtered by SAMtools and marked Duplicates were marked with Picard tools and peak calling performed by MACS to identify chromatin accessible regions.
Peaks were annotated by R package ChIPseeker to identify their closest genes.
Assembly: hg38
Supplementary files format and content: narrowPeak

growth_protocol: hTERT immortalized adipose-derived human MSCs (hMSCs, ATCC, SCRC-4000) were cultured in MSC basal medium (ATCC PCS-500-030) supplemented with the MSC growth kit (ATCC PCS-500-040) according to the manufacturer's instructions.

extract_protocol:
ATAC-seq samples were prepared following the Omni-ATAC protocol.
Llibray construction was accomplished following the Omni-ATA protocol as described (Corces  et.al, Nat Methods, 2017) by PCR with Nextera index sequences. Library quality control and sequencing were performed by Novogene (Novogene, CA, USA) on a NovaSeq 6000 sequencer.

treatment_protocol: hMSCs  were cultured to confluence without additional treatment.

value: hTERT immortalized adipose derived Mesenchymal stem cells


title: CCHMC2016-97 NSG BM


title: control and neutrophil-depleted mixed sample [FB]

data_processing:
Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).
Fastq files were processed with cellranger to produce the count matrixes
Assembly: mm10
Supplementary files format and content: count matrix for both samples

source_name: Skin

extract_protocol:
Single cell suspension from primary mouse skin was obtained by an hour long digestion with enzymes (Liberase and DNAseII)
Control and neutrophil-depleted samples were barcoded using hashtag antibodies from Biolegend (the Feature Barcoding technology) and the library was constructed according to Illumina's standard protocols.

treatment_protocol: Neutrophils were depleted at steady state for 2 consecutive days with an anti-Ly6G monoclonal antibody (clone: 1A8)

value: Skin

tag: age

value: 8 week old

value: control or neutrophil depleted


title: evg1_1_1

description: whole seedling

value: Intact

value: 7 day old


title: CCHMC2016-97 NRGS BM


title: control and neutrophil-depleted mixed sample [scRNA]


title: rlp44_3_2

description: whole seedling


title: JH331_RUX2_D56

city: Philadelphia

first: Kai

last: Tan

address: 3501 Civic Center Boulevard

department: Pediatrics

institute: Children's Hospital of Philadelphia

description: Bulk ATAC-seq

data_processing:
Reads were aligned to the human genome (hg38) using Bowtie2 with options “--very-sensitive -X 1000 --dovetail”, and duplicates were removed using Picard.
BAM files were converted to BED files, followed by peak calling performed using MACS2 with parameters “--extsize 200 --shift -100 --keep-dup all --call-summits --bdg.”
Assembly: hg38
Supplementary files format and content: Narrow peaks from MACS2

source_name: leukemia

extract_protocol:
Transposition was performed using Illumina Tagment DNA TDE1 kit.
Library preparation was performed using PCR amplification and purified using agarose gel purification.
ATAC-sequencing was performed using Nextera primers and protocol on an Illumina NovaSeq sequencer.

value: leukemia

value: Ph-Like ALL

value: Rux 56 Days


title: CCHMC2016-9 NSG BM

value: EGFR H773Q, FLT3 D835H, FLT3-ITD (G583_S584ins19), MLL-MLLT4 (AF6) fusion, MYST3 HOOK3-MYST3 fusion


title: CCHMC2016-109 Patient BM

value: bone marrow

value: IDH2 R140Q, MLL-MLLT3 (AF9) fusion, TP53 A276S, WT1 E207* / P124fs*34

value: Patient


title: Col0_2

description: whole seedling


title: Pooled CD45.2+ Cells, Nov 07, Lane002

city: SAINT LOUIS

first: Irenaeus

last: Chan

state: Missouri

address: 660 S. Euclid Ave

department: Oncology

institute: Washington University in Saint Louis

description:
Library name: PZ-2803_Pool2_2
10X Genomics Chromium

data_processing:
FASTQ reads were processed using Cell Ranger v7.0.0 'count' workflow to generate gene expression and antibody capture data metrics. Additionally, the Cell Ranger 'multi' pipeline was executed to demultiplex hashed sequencing samples.
The resulting filtered sparse count matrices were loaded into R version 4.0.0 as Seurat version 4.0.6 objects. Multiplets were identified using scDblFinder version 1.10.0 and removed. Further filtering retained: 1) RNA features detected in more than three cells and 2) cells with more than 200 and fewer than 2,500 detected features. The miQC version 1.10.0 was used to identify and filter out low-quality cells based on mitochondrial gene detection and UMI distributions, using a posterior cutoff of 0.95 and flexmix spline models.
Seurat version 4.4.0 was used for data normalization and scaling, focusing on 4,000 highly variable genes. Twenty-five principal components were used for unsupervised clustering and dimensionality reduction. The open-tSNE was generated based on a previously established pipeline.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

extract_protocol:
Bone marrow cells from mice receiving treatments were washed twice with cold PBS before labeling with unique TotalSeqA-compatible HashTags. Subsequently, samples were incubated with mouse Fc receptor-blocking agent and labeled with DAPI for live cell sorting by flow cytometry using an Aria cytometer. After sorting, equal numbers of cells were pooled and submitted for sequencing.
A 10X Genomics Chromium machine was used for 3000-5000 single-cell capture. Cells were washed and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs), where all generated cDNA share a common 10x Genomics Barcode but uses a pool of ~750,000 barcodes to index each cell's transcriptome. The silane magnetic beads and Solid Phase Reversible Immobilization beads were used to clean up the GEM reaction mixture and the barcoded cDNA was then amplified in a PCR step. Libraries were prepared using the Chromium Single Cell 3' Reagent Kits (v3.1): Single Cell 3' Library & Gel Bead Kit v3.1, Single Cell 3' Chip G Kit v3.1 and Single Index Kit T Set A. The P7 and R2 primers were added during the GEM incubation and the P5 and R1 during library contruction via end repair, A-tailing, adapter ligation and PCR.

treatment_protocol: Half of the mice received intraperitoneal injection of trilaciclib (100 mg/kg), and the other half received vehicle (50 mM citrate buffer) solution (3 times per week). 30 min, a single intraperitoneal injection of carboplatin (30 mg/kg) or 0.9% NaCl vehicle control was given every 2 days.

value: Bone Marrow


title: CCHMC2016-9 NRGS BM

value: Acute Myeloid Leukemia

value: PDX


title: Pooled CD45.2+ Cells, Nov 07, Lane001

description:
Library name: PZ-2803_Pool2_1
10X Genomics Chromium


title: JH331_RUX2_D28

description: Bulk ATAC-seq

value: Rux 28 Days


title: Pooled CD45.1+ Cells, Nov 07, Lane002

description:
Library name: PZ-2803_Pool1_2
10X Genomics Chromium


title: JH331_RUX1_D7

description: Bulk ATAC-seq

value: Rux 7 Days


title: CCHMC2016-7 NRGS BM

value: MLL-MLLT3 (AF9) fusion


title: CCHMC2016-7 NSG BM


title: Pooled CD45.1+ Cells, Nov 07, Lane001

description:
Library name: PZ-2803_Pool1_1
10X Genomics Chromium


title: evg1_1_2

description: whole seedling


title: CCHMC2016-35 NSG BM

value: CBFA2T3/GLIS2, KDM5C splice site 1747-1G>T


title: human MSC, Rep1

value: hTERT immortalized adipose derived Mesenchymal stem cells


title: CCHMC2016-35 NRGS BM


title: CCHMC2016-1 NRG BM

value: NF1 Q1775*, PTPN11 A461G - subclonal, CDKN2A/B loss, ETV6 loss, PICALM-MLLT10 fusion, PHF6 R274Q, TP53 K164E - subclonal, Y126*


title: JH331_RUX1_D3

description: Bulk ATAC-seq


title: JH331_RUX1_D28

description: Bulk ATAC-seq


title: Pooled CD45.2+ Cells, Nov 06, Lane001

description:
Library name: PZ-2797_Pool2_1
10X Genomics Chromium


title: Col0_3

description: whole seedling

value: Intact

value: 7 day old


title: JH331_RUX2_D3

description: Bulk ATAC-seq

value: leukemia

value: Ph-Like ALL

value: Rux 3 Days


title: Pooled CD45.2+ Cells, Nov 06, Lane002

description:
Library name: PZ-2797_Pool2_2
10X Genomics Chromium


title: Col0_1

description: whole seedling


title: CCHMC2016-1 NRGS BM

value: bone marrow


title: CCHMC2015-37 NSGS BM

value: NUP98 NUP98-TAF3 fusion


title: Pooled CD45.1+ Cells, Nov 06, Lane002

description:
Library name: PZ-2797_Pool1_2
10X Genomics Chromium


title: JH331_Ctrl2_D3

description: Bulk ATAC-seq

value: Control


title: JH331_Ctrl2_D7

description: Bulk ATAC-seq


title: JH331_Ctrl1_D7

description: Bulk ATAC-seq


title: Pooled CD45.1+ Cells, Nov 06, Lane001

description:
Library name: PZ-2797_Pool1_1
10X Genomics Chromium

value: Bone Marrow


title: CCHMC2013-28 NSGS BM

value: Acute Myeloid Leukemia

value: FLT3-ITD V581_T582insTGSSDNEYFYVDFREYEYALSGFBXW7Y519* NPM1 W288fs*10+


title: JH331_Ctrl1_D3

description: Bulk ATAC-seq


title: JH331_RUX1_D56

description: Bulk ATAC-seq

value: Rux 56 Days


title: ALL4988_RUX2_D7

description: Bulk ATAC-seq

value: Rux 7 Days


title: CCHMC2013-11 NRGS BM

value: NRAS Q61H,  NPM1 truncation, 3' UTR

value: PDX


title: CCHMC2017-30 NSG BM


title: ALL4988_RUX2_D56

description: Bulk ATAC-seq


title: CCHMC2017-30 NSGS BM


title: ALL4988_RUX2_D28

description: Bulk ATAC-seq

value: Rux 28 Days


title: CCHMC2014-15 NSGS BM

value: IKZF1 splice site 711_715+18del23, GATA1 V32fs*7


title: CCHMC2017-94 NSGS BM

value: CDKN2A/B loss of p16INK4a and p14ARF exon 1 and loss of CDKN2B


title: CCHMC2014-59 NSG BM


title: ALL4988_RUX1_D7

description: Bulk ATAC-seq


title: ALL4988_RUX1_D56

description: Bulk ATAC-seq


title: CCHMC2017-10 NRG BM

value: inv11, No sequencing available


title: ALL4988_RUX1_D3

description: Bulk ATAC-seq

value: leukemia


title: CCHMC2017-103 NRGS BM

value: FLT3 D835E - subclonal , D835V - subclonal , D835Y - subclonal, KIT D816V, ASXL1 G645fs*58, CBL deletion exon 9, CHEK2 T367fs*15, PTPN11 D61V


title: ALL4988_RUX1_D28

description: Bulk ATAC-seq

value: Ph-Like ALL


title: SU4312_C3_48_24

type: RNA

hyb_protocol: Agilent Gene Expression Hybridisation Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

scan_protocol: Scanned with the Agilent High-Resolution Microarray Scanner according to the Agilent protocol

data_processing: Cyclic loess normalization between all arrays. Software for data normalization: R v4.3.0

source_name: whole embryo

label_protocol: Low Input Quick Amp WT Labeling Kit according to the Agilent One-Color Microarray-Based Exon Analysis Protocol

extract_protocol: Trizol, homogenization by a FastPrep 50 (MP Biomedicals), followed by Total RNA Extraction Kit MagMAX, RIN>7

treatment_protocol: Exposure to SU4312 at 2 or 24 hpf, 20 embryos per replicate, incubation at 26°C with 12:12 light:dark photoperiod


title: SU4312_C3_12_24


title: SU4312_C3_72_24


title: CCHMC2017-25 NRG BM

value: bone marrow

value: MLL-MLLT3 (AF9) fusion, WT1 E207* / P124fs*34


title: SU4312_C2_72_24


title: SU4312_C3_3_24


title: SU4312_C2_24_24


title: ALL4988_Ctrl2_D3

description: Bulk ATAC-seq

value: Control


title: SU4312_C3_6_24


title: CCHMC2017-14 NRGS BM

value: KRAS G13D, MLL-MVB12B fusion, MLL-MLLT10 (AF10) fusion


title: ALL4988_Ctrl1_D3

description: Bulk ATAC-seq


title: SU4312_C2_48_24


title: ALL4988_RUX2_D3

description: Bulk ATAC-seq

value: Rux 3 Days


title: SU4312_C3_24_24


title: CCHMC2014-31 NSGS BM

value: Acute Myeloid Leukemia

value: NRAS G13D, PTEN loss, MED14-HOXA9 fusion, SRC splice site 704-1G>A


title: CCHMC2014-59 NSGS BM


title: ALL4364_RUX2_D7

description: Bulk ATAC-seq

value: Rux 7 Days


title: CCHMC2017-10 NSGS BM


title: ALL4364_RUX2_D3

description: Bulk ATAC-seq


title: ALL4364_RUX2_D56

description: Bulk ATAC-seq

value: Rux 56 Days


title: CCHMC2017-25 NSGS BM

value: PDX


title: SU4312_C2_3_24


title: CCHMC2017-42 NSGS BM

value: MLL-MLLT3 (AF9) fusion, PC R583H - subclonal, WT1 R462Q - subclonal


title: ALL4364_RUX2_D28

description: Bulk ATAC-seq

value: Rux 28 Days


title: CCHMC2017-114 Patient BM

value: NRAS G13D - subclonal, MLL-MLLT10 (AF10) fusion, PTPN11 E69K

value: Patient


title: SU4312_C2_6_24


title: ALL4364_RUX1_D7

description: Bulk ATAC-seq

value: leukemia


title: SU4312_C0_72_24


title: SU4312_C2_12_24


title: SU4312_C0_48_24


title: ALL4364_RUX1_D56

description: Bulk ATAC-seq


title: CCHMC2016-7 Patient BM

value: MLL-MLLT3 (AF9) fusion


title: ALL4364_RUX1_D28

description: Bulk ATAC-seq

value: Ph-Like ALL


title: ALL4364_RUX1_D3

description: Bulk ATAC-seq


title: SU4312_C0_48_24.1


title: SU4312_C0_24_24


title: CCHMC2016-35 Patient BM

value: bone marrow

value: CBFA2T3/GLIS2, KDM5C splice site 1747-1G>T


title: CCHMC2016-1 Patient BM

value: NF1 Q1775*, PTPN11 A461G - subclonal, CDKN2A/B loss, ETV6 loss, PICALM-MLLT10 fusion, PHF6 R274Q, TP53 K164E - subclonal, Y126*


title: ALL4364_Ctrl2_D3

description: Bulk ATAC-seq

value: Control


title: CCHMC2017-38 NSG BM

value: MLL-MLLT3 (AF9) fusion, NRAS G13D


title: ALL2128_D7_Rep2

description: Bulk ATAC-seq


title: ALL4364_Ctrl1_D3

description: Bulk ATAC-seq


title: CCHMC2017-63 NSGS BM

value: Acute Myeloid Leukemia


title: ALL2128_D7_Rep1

description: Bulk ATAC-seq


title: ALL2128_D56_Rep2

description: Bulk ATAC-seq


title: SU4312_C0_12_24.1


title: CCHMC2013-7 Patient BM

value: MLL-MLLT1 fusion, APC-CBX3 rearrangement


title: CCHMC2016-99 NRGS BM


title: SU4312_C0_24_24.1


title: CCHMC2017-38 NSGS BM


title: SU4312_C0_12_24


title: SU4312_C0_6_24.1


title: ALL2128_D28_Rep2

description: Bulk ATAC-seq


title: ALL2128_D56_Rep1

description: Bulk ATAC-seq


title: ALL2128_D28_Rep1

description: Bulk ATAC-seq


title: CCHMC2017-78 NSGS BM

value: KRAS G12A - subclonal, NRAS Q61H - subclonal, MLL-MLLT4 (AF6) fusion, PTPN11 E76K - subclonal , S502L - subclonal


title: ALL2128_D0_Rep2

description: Bulk ATAC-seq


title: P87

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: Library name: Sample37

data_processing:
The 16S rRNA gene sequencing datasets were processed using the DADA2 package (version 1.16.0).
Files were imported into R using the phyloseq package (Version 1.44.0).
The data was processed using the decontam package (Version 1.20.0), using the isContaminant function with a 0.5 threshold and the environmental control used as a negative control.
Assembly: Other
Supplementary files format and content: comma-separated text file with OTU matrix

source_name: Stool

growth_protocol: Fecal samples from a single healthy or BrM-bearing mouse were collected in sterile tubes directly from the rectum of mice and stored at -80°C.

extract_protocol:
DNA was extracted using the QIAamp PowerFecal Pro DNA kit (Qiagen, cat. no. 51804) following the manufacturer’s protocol in a clean environment using autoclaved tools.
16S rRNA sequencing was performed by an external company (CosmosID) starting from 5 ng of genomic DNA. Libraries were constructed by amplification via PCR with 341F and 805R primers covering the V3-V4 region. Sequencing was performed using the Illumina Miseq platform 2x250bp.

treatment_protocol: Antibiotic treatment: mice were treated via the drinking water with a broad-spectrum cocktail (4-ABX) including Ampicillin (1g/L; Sigma-Merk, cat. no. A9393), Neomycin trisulfate (1g/L; Sigma-Merk, cat. no. N1876), Metronidazole (1g/L, Sigma-Merk, cat. no. M1547), and Vancomycin (0.5 g/L; Goldbio, cat. no. V-200) in sucrose (2%; Axonlab, cat. no. A2211) or the selective cocktail (2-ABX) including Bacitracin (1g/L; Sigma-Merk cat. no. 11702), and Neomycin trisulfate (1g/L) in sucrose (2%), or the CTRL group of sucrose alone (2%).

value: Stool

tag: time

tag: disease state

value: Healthy


title: P86

description: Library name: Sample36


title: P85

description: Library name: Sample35


title: SU4312_C0_3_24.1

tag: substance


title: SU4312_C0_3_24


title: ALL2128_D0_Rep1

description: Bulk ATAC-seq


title: P84

description: Library name: Sample34


title: SU4312_C2_96_0

tag: concentration


title: SU4312_C2_72_0

tag: unit


title: SU4312_C2_48_0


title: SU4312_C2_36_0


title: P83

description: Library name: Sample33


title: SU4312_C2_30_0


title: SU4312_C0_6_24


title: P81

description: Library name: Sample32


title: NH011_Ven_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds

data_processing:
CellRanger-ATAC v1.1.0 (10X Genomics)
scATAC-seq data for each sample was first demultiplexed using the mkfastq function of Cell Ranger-ATAC v1.1.0 (10x Genomics). The fastq files were then processed using the scATAC-pro package with the default settings. Specifically, the cell barcode was written to the name of each read in the fastq files using the demplx_fastq module and then the reads were aligned to the human genome (hg38) using the mapping module with BWA as the sequence aligner. Peaks were then called using the call_peak module using the “MACS2” option. With the called peaks, we then constructed the raw peak by barcode count matrix. Using the call¬_cell module, cells were called if the barcodes had between 2,000 and 60,000 total fragments, fraction of reads in peaks (FRiP) greater than 50%, mitochondrial content less than 10%, and TSS enrichment score greater than 1.
Assembly: hg38
Supplementary files format and content: CellRanger count matricies
Supplementary files format and content: Seurat object after processing, filtering, and analysis

source_name: Leukemia

extract_protocol:
Live human ALL cells were flow-sorted for human CD19+, mouse CD45-, DAPI- population.
Single-cell RNA-seq  was performed using the 10x Genomics Chromium platform using the Next GEM Single Cell ATAC Reagent Kit v2.
10x Genomics v2 was used for library construction and sequencing was performed on an Illumina Novaseq

value: Leukemia

value: Ven


title: CCHMC2013-28 Patient BM

value: FLT3-ITD V581_T582insTGSSDNEYFYVDFREYEYALSGFBXW7Y519* NPM1 W288fs*10+


title: SU4312_C2_27_0


title: NH011_Rux_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds

value: Rux


title: P80

description: Library name: Sample31


title: ER-HoxA9+Combo day 3 rep 2

first: Andres

last: Blanco

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

data_processing:
Adapters were trimmed with Cutadapt with reads < 20 nts being filtered out.
Reads were mapped against mm10 with Bowtie 2.
Duplicate reads were filtered out with samtools rmdup.
Bam files were converted to bed files with bedtools bamtobed.
Peaks were called with MACS2 at FDR < 0.05 as a significance cutoff.
Assembly: mm10
Supplementary files format and content: Coordinates for peaks in bed file format

growth_protocol: ER-HoxA9 cells were grown in RPMI-1640 medium supplemented with 10% of fetal bovine serum (FBS), 100 ng/ml stem cell factor (SCF) (Stemcell Technologies, 78064), 4mM glutamine, 1% penicillin/streptomycin, and 0.5mM beta-estradiol (Sigma Aldrich, E4389).

extract_protocol:
Cells were treated with DNAse I (Life Tech, Cat. #EN0521) to remove genomic DNA contamination. Live cell samples were then quantified and assessed for viability and after cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, Cat. #20034197) for 30 min at 37°C and purified with Minelute PCR Purification Kit (Qiagen, Cat. #28004) to produce tagmented DNA samples.
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, Cat. #FC-131-2001) and amplified via PCR prior to an SPRI Bead cleanup to yield purified DNA libraries.


title: SU4312_C2_12_0


title: NH011_Ven_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: SU4312_C2_6_0


title: ER-HoxA9+Combo day 1 rep 2


title: NH011_Das_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds

value: Das


title: P79

description: Library name: Sample30


title: P78

description: Library name: Sample29


title: ER-HoxA9+LY2090314 day 3 rep 2


title: NH011_Control_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: NH011_Control_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P77

description: Library name: Sample28


title: P75

description: Library name: Sample27

value: CTRL


title: ER-HoxA9+LY2090314 day 1 rep 2


title: P74

description: Library name: Sample26


title: NH011_Combo_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds

value: Ph-Like ALL

value: Combo


title: NH011_Combo_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: ER-HoxA9+GSK-LSD1 day 1 rep 2


title: JH331_Ven_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: SU4312_C2_3_0


title: SU4312_C1_96_0


title: SU4312_C1_48_0


title: SU4312_C1_72_0


title: ER-HoxA9+DMSO day 3 rep 2


title: ER-HoxA9+DMSO day 1 rep 2


title: P70

description: Library name: Sample23


title: JH331_Ven_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: JH331_Rux_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: JH331_Rux_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: SU4312_C1_30_0


title: ER-HoxA9+Combo day 1 rep 1


title: SU4312_C1_27_0


title: P69

description: Library name: Sample22


title: SU4312_C1_36_0


title: ER-HoxA9+LY2090314 day 3 rep 1


title: ER-HoxA9+GSK-LSD1 day 3 rep 2


title: P65

description: Library name: Sample21


title: JH331_Control_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: JH331_Control_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P73

description: Library name: Sample25


title: P71

description: Library name: Sample24


title: SU4312_C1_24_0


title: SU4312_C1_6_0


title: P64

description: Library name: Sample20


title: SU4312_C1_12_0


title: SU4312_C1_3_0


title: ER-HoxA9+Combo day 3 rep 1


title: P63

description: Library name: Sample19


title: ER-HoxA9+LY2090314 day 1 rep 1


title: ER-HoxA9+GSK-LSD1 day 3 rep 1


title: P62

description: Library name: Sample18


title: ER-HoxA9+GSK-LSD1 day 1 rep 1


title: SU4312_C2_24_0


title: P61

description: Library name: Sample17


title: ALL4364_Ven_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: ER-HoxA9+DMSO day 3 rep 1


title: SU4312_C0_96_0.1


title: ALL4364_Ven_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P59

description: Library name: Sample16


title: ER-HoxA9+DMSO day 1 rep 1


title: ALL4364_Rux_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P58

description: Library name: Sample15


title: VSMC, bio rep3 prelaminA, IgG, ChIP

city: London

first: Catherine

last: Shanahan

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

data_processing:
The raw sequences were processed and aligned to the hg19 assembly.
Peak detection was performed using the Dfilter software (http://collaborations.gis.astar.edu.sg/~cmb6/kumarv1/dfilter/)
The peaks were then annotated using the Peak Annotation Visualisation (PAVIS) software (https://manticore.niehs.nih.gov/pavis2/) ±5 kb from the TSS using the Hg19 human genome assembly.
Assembly: hg19 assembly
Supplementary files format and content: bigWig

source_name: Aorta

growth_protocol: VSMCs were maintained in M199 media supplied with 20% fetal bovine serum (FBS) and 1% penicillin/streptomycin/L-glutamate (PSG) in a humidified incubator with 5% CO2.

extract_protocol:
Cells were crosslinked with 1.1% formaldehyde at room temperature for 10 minutes then quenched by glycine buffer. After washing with 1X PBS, fixed cells were lysed followed by sonication for 6 minutes (20 sec on / 30 sec off) in a Branson 150 sonicator and centrifuged at 14000 x g for 5 minutes
Library preparation was performed using the NEBNext Ultra II DNA Library Preparation Kit (NEB)

treatment_protocol: Prelamin A accumulation was introduced by adenoviral infection in early-passage VSMCs for 72 hours. To induce mineralization, VSMCs were treated with osteogenic media composed of M199 media with 5% FBS and 1% PSG, with additional calcium and phosphate buffer which is supplied by 180 mM CaCl2 and 100 mM NaH2PO4,  to reach a final concentration of 2.7 mmol/L and 2 mmol/L, respectively.

value: Aorta

value: Aortic vascular smooth muscle cell

tag: chip antibody

value: Normal Rabbit IgG CST#2729

value: Introducing Prelamin A accumulation by adenoviral infection


title: JH331_Combo_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P56

description: Library name: Sample14


title: ALL4364_Rux_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P55

description: Library name: Sample13


title: VSMC, bio rep3 prelaminA, H3K9me3, ChIP


title: JH331_Combo_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: VSMC, bio rep3 prelaminA, H3K27me3, ChIP


title: ALL4364_Control_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds

value: Control


title: SU4312_C0_48_0.1


title: SU4312_C0_48_0


title: ALL4364_Control_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: SU4312_C0_96_0


title: P53

description: Library name: Sample12


title: ALL4364_Combo_D3

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P52

description: Library name: Sample11


title: VSMC, bio rep3 WT IgG, ChIP

value: Control plasmid with EGFP by adenoviral infection


title: VSMC, bio rep3 prelamin A, Input, ChIP


title: ALL4364_Combo_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P51

description: Library name: Sample10


title: SU4312_C0_72_24.1


title: VSMC, bio rep3 WT H3K27me3, ChIP


title: SU4312_C0_30_0


title: ALL2128_Ven_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: VSMC, bio rep3 WT H3K9me3, ChIP


title: VSMC, bio rep3 WT Input, ChIP


title: SU4312_C0_72_0


title: ALL2128_Rux_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: P49

description: Library name: Sample9


title: P48

description: Library name: Sample8


title: ALL2128_Control_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: SU4312_C0_27_0.1


title: P39

description: Library name: Sample6

value: Endpoint

value: BrM


title: ALL2128_Combo_D28

description:
scATAC-seq
scATAC_Seurat_GEO.rds


title: SU4312_C0_30_0.1


title: SU4312_C0_27_0


title: VSMC, bio rep2 prelaminA, IgG, ChIP


title: SU4312_C0_24_0.1


title: NH011_HTO_Day3

description:
HTO
NH011_Day3_Multiplexed_barcodes.tsv.gz
NH011_Day3_Multiplexed_features.tsv.gz
NH011_Day3_Multiplexed_matrix.mtx.gz
NH011_Day3_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds

data_processing:
CellRanger v3.1.0 or v6.1.2 (10X Genomics)
Analysis in Seurat v4-5: Cells were first filtered for quality, removing cells with fewer than 300 unique genes detected, cells with greater than 20% mitochondrial reads, and cells with less than 10% ribosomal reads. The remaining high-quality cells were used to generate a count matrix of gene expression levels per cell.
HTODemux was used to demultiplex samples combined via antibody hashing
Assembly: hg38
Supplementary files format and content: CellRanger count matricies
Supplementary files format and content: Seurat object after processing, filtering, and analysis

molecule: other

extract_protocol:
Live human ALL cells were flow-sorted for human CD19+, mouse CD45-, DAPI- population. Samples from the same PDX and timepoint were multiplexed using hashtag oligos (HTO).
Single-cell RNA-seq  was performed using the 10x Genomics Chromium platform using the Next GEM Single Cell 3’ Reagent kit v3.1 with feature barcoding.
10x Genomics v3.1 was used for library construction and sequencing was performed on an Illumina Novaseq

value: Control, Venetoclax, Dasatinib, Das/Ven Combo


title: SU4312_C0_36_0.1


title: P38

description: Library name: Sample5

value: Stool


title: VSMC, bio rep2 prelaminA, H3K27me3, ChIP


title: NH011_HTO_Day28

description:
HTO
NH011_Day28_Multiplexed_barcodes.tsv.gz
NH011_Day28_Multiplexed_features.tsv.gz
NH011_Day28_Multiplexed_matrix.mtx.gz
NH011_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds

value: Leukemia


title: SU4312_C0_72_0.1


title: VSMC, bio rep2 prelaminA, H3K9me3, ChIP


title: SU4312_C0_24_0


title: P34

description: Library name: Sample4


title: SU4312_C0_12_0.1


title: P47

description: Library name: Sample7

value: Healthy


title: SU4312_C0_12_0


title: VSMC, bio rep2 prelamin A, Input, ChIP


title: NH011_GEX_Day28

description:
Pooled scRNA-seq
NH011_Day28_Multiplexed_barcodes.tsv.gz
NH011_Day28_Multiplexed_features.tsv.gz
NH011_Day28_Multiplexed_matrix.mtx.gz
NH011_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds


title: P20

description: Library name: Sample3


title: VSMC, bio rep2 WT IgG, ChIP


title: SU4312_C0_6_0.1


title: P19

description: Library name: Sample2


title: JH331_HTO_Day3

description:
HTO
JH331_Day3_Multiplexed_barcodes.tsv.gz
JH331_Day3_Multiplexed_features.tsv.gz
JH331_Day3_Multiplexed_matrix.mtx.gz
JH331_Day3_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds

value: Control, Venetoclax, Ruxolitinib, Rux/Ven Combo


title: P16

description: Library name: Sample1


title: VSMC, bio rep2 WT H3K27me3, ChIP


title: JH331_HTO_Day28

description:
HTO
JH331_Day28_Multiplexed_barcodes.tsv.gz
JH331_Day28_Multiplexed_features.tsv.gz
JH331_Day28_Multiplexed_matrix.mtx.gz
JH331_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds


title: Strain B6-F_resc, CEHC1 rescued, rep 3

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

data_processing:
Alignment to Chlamydomonas reinhardtii reference genome assembly and annotations (v6.1, available at https://phytozome-next.jgi.doe.gov/) with RNA STAR  (v2.7.10b) with the following options: --alignIntronMax 3000 –outMultimapperOrder Random –outSAMmultNmax 1
Normalized counts for all nucleus-encoded transcripts were calculated in terms of fragments per kb of transcript per million mapped reads (FPKMs) with cuffdiff (v2.0.2) with the following options: --multi-read-correct –max-bundle-frags 1000000000 –library-type fr-firststrand.
Assembly: Chlamydomonas reinhardtii reference genome assembly, v6.1, available at https://phytozome-next.jgi.doe.gov/
Supplementary files format and content: CEHC1_study.replicates_FPKMs.tsv is a tab-delimited text file of normalized expression estimates as fragments per kb of transcript per million mapped reads (FPKMs) for all nuclear genes for each experimental replicate (three per strain) .
Supplementary files format and content: CEHC1_study.mean_FPKMs.tsv is a tab-delimited text file of normalized expression estimates as fragments per kb of transcript per million mapped reads (FPKMs) for all nuclear genes averaged from three replicates per strain.

organism: Chlamydomonas reinhardtii

source_name: algal cell

growth_protocol: Triplicate cultures of each strain were grown aerobically in TAP media under a 14 hr light: 10 hr dark regime.  Aeration was obtained by using culture volumes of 200 ml in 2800 ml Fernbach flasks rotated laterally at 95 rpm.  Cell aliquots were collected at six hours into the light period; cell density was ~5 x 106 cells/ml.

extract_protocol:
Culture aliquots containing 3 x 10^7 cells were centrifuged to pellet the cells and lysis buffer was added to the cell pellet.  Processing of each cell sample was completed within 1.5 min.  RNA was isolated using the LiCl precipitation method (Wilkerson et al., 1994).
RNA quality was assessed using the Agilent Bioloanalyzer; RIN value exceeded 8 for each sample.  RNA libraries were prepared for sequencing using standard Illumina protocolsRNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq HiSeq 2500, High Output Mode, Paired End Read, 125 bp

treatment_protocol: All samples were grown and treated similarly

tag: strain

value: algal cell

value: CEHC1 rescued


title: VSMC, bio rep2 WT H3K9me3, ChIP


title: SU4312_C0_6_0


title: SU4312_C0_3_0


title: JH331_GEX_Day3

description:
Pooled scRNA-seq
JH331_Day3_Multiplexed_barcodes.tsv.gz
JH331_Day3_Multiplexed_features.tsv.gz
JH331_Day3_Multiplexed_matrix.mtx.gz
JH331_Day3_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds

value: Ph-Like ALL


title: NH011_GEX_Day3

description:
Pooled scRNA-seq
NH011_Day3_Multiplexed_barcodes.tsv.gz
NH011_Day3_Multiplexed_features.tsv.gz
NH011_Day3_Multiplexed_matrix.mtx.gz
NH011_Day3_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds


title: Strain B6-F_resc, CEHC1 rescued, rep 2


title: Strain B6-F_resc, CEHC1 rescued, rep 1


title: VSMC, bio rep1 prelaminA, IgG, ChIP


title: JH331_GEX_Day28

description:
Pooled scRNA-seq
JH331_Day28_Multiplexed_barcodes.tsv.gz
JH331_Day28_Multiplexed_features.tsv.gz
JH331_Day28_Multiplexed_matrix.mtx.gz
JH331_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds


title: Strain B6-F, cehc1-1 mutant, rep 3

value: cehc1-1 mutant


title: ChIPseq-Input-L3_brain-mutCG11504_rep1

city: Moscow

first: Maksim

last: Erokhin

state: Moscow

address: Vavilov

country: Russia

institute: IGB

description: Library name: ChIPseq-Input-L3_brain-mutCG11504_rep1.gz

data_processing:
BCL Convert v4.2.4 (Illumina)
ChIP-seq reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: The 2 biological replicates for each protein or Input were merged using Merge BAM Files tool (Galaxy Version 1.2.0) and filtered with a minimum MAPQ quality score = 10. BigWig files were generated using bamCoverage (Galaxy Version 3.5.4) with scores representing number of reads normalized by the size of the library. The final bigwig files (representing the protein binding profiles) were obtained using the bigwigCompare tool (Galaxy Version 3.5.4) as a subtract of the Input ChIP signal (all inputs were preliminary smoothed over a 1 kb window).

organism: Drosophila melanogaster

source_name: Brains were dissected from wandering larvae 4-6 hours before puparium formation

growth_protocol: The Drosophila melanogaster wild type and Vostok null mutant stocks were used. All flies were raised at 25°C on standard agar medium.

extract_protocol:
ChIP protocol: crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina NEBNext protocols

treatment_protocol: All flies were maintained at 25°C on the standard yeast medium. For the dissection, wandering larvae were collected approximately 4-6 hours before the puparium formation. Dissected brains for ChIP-Seq were collected in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice for no more than 1 hour. After the dissection, the tissues were warmed up to room temperature and fixed by adding formaldehyde up to 1% for 10 min. Fixation was stopped by adding 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

value: CG11504 null allele, described in a current study

tag: chip antibodies


title: VSMC, bio rep1 prelaminA, H3K27me3, ChIP

value: Aorta

value: Aortic vascular smooth muscle cell


title: ALL4364_HTO_Day3

description:
HTO
ALL4364_Day3_Multiplexed_barcodes.tsv.gz
ALL4364_Day3_Multiplexed_features.tsv.gz
ALL4364_Day3_Multiplexed_matrix.mtx.gz
ALL4364_Day3_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds


title: ChIPseq-Input-L3_brain-mutCG11504_rep2

description: Library name: ChIPseq-Input-L3_brain-mutCG11504_rep2.gz

value: Brains were dissected from wandering larvae 4-6 hours before puparium formation


title: ChIPseq-Input-L3_brain-wt_rep1

description: Library name: ChIPseq-Input-L3_brain-wt_rep1.gz


title: SU4312_C0_3_0.1

first: Paul

address: Permoserstr. 15

institute: Helmholtz-Centre for Environmental Research (UFZ)


title: ChIPseq-Input-L3_brain-wt_rep2

description: Library name: ChIPseq-Input-L3_brain-wt_rep2.gz


title: Strain B6-F, cehc1-1 mutant, rep 2


title: VSMC, bio rep1 prelaminA, H3K9me3, ChIP

value: Introducing Prelamin A accumulation by adenoviral infection


title: ALL4364_GEX_Day3

description:
Pooled scRNA-seq
ALL4364_Day3_Multiplexed_barcodes.tsv.gz
ALL4364_Day3_Multiplexed_features.tsv.gz
ALL4364_Day3_Multiplexed_matrix.mtx.gz
ALL4364_Day3_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds


title: Strain B6, CEHC1 WT, rep 3

value: CEHC1 WT


title: Strain B6-F, cehc1-1 mutant, rep 1


title: ChIPseq-GAF-L3_brain-mutCG11504_rep1

description:
Library name: ChIPseq-GAF-L3_brain-mutCG11504_rep1.gz
ChIPseq-GAF-L3_brain-mutCG11504_rep1+rep2.bigwig

value: anti-GAF (full-lenght) antibodies, (Erokhin et al. Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14930-5. doi:10.1073/pnas.1515276112. )


title: ALL4364_GEX_Day28

description:
Pooled scRNA-seq
ALL4364_Day28_Multiplexed_barcodes.tsv.gz
ALL4364_Day28_Multiplexed_features.tsv.gz
ALL4364_Day28_Multiplexed_matrix.mtx.gz
ALL4364_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds


title: VSMC, bio rep1 WT H3K27me3, ChIP

value: Control plasmid with EGFP by adenoviral infection


title: Strain B6, CEHC1 WT, rep 2


description:
Library name: ChIPseq-CG11504-L3_brain-mutCG11504_rep2.gz
ChIPseq-CG11504-L3_brain-mutCG11504_rep1+rep2.bigwig

value: anti-CG11504 (full-lenght) antibodies, described in a current study


title: VSMC, bio rep2 WT Input, ChIP


description:
Library name: ChIPseq-CG11504-L3_brain-mutCG11504_rep1.gz
ChIPseq-CG11504-L3_brain-mutCG11504_rep1+rep2.bigwig


title: NPC cells,cKO,E15.5,biol rep 3

city: Shanghai

first: Ziyi

last: Zhao

address: 320 Yueyang Road

country: China

institute: Shanghai jiaotong university school of medicine

data_processing:
The sequenced reads were mapped to the mouse genome GRCm39 using hisat2 (version 2.2.1.0), and raw counts were generated and quantified using htseq-count (version 0.9.1). DESeq2 (version 1.20.0) and DESeq (version 1.18.0) were used for differential gene expression analysis. Differentially expressed genes (DEGs) were selected using a fold change threshold of ≥ 2 and an FDR (q-Value) threshold of ≤ 0.05.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: embryonic kidney

growth_protocol: freshly isolated embryonic kidneys

extract_protocol:
E15.5 embryonic kidneys were dissected and cut into small pieces, trypsinized for 30 min at 37℃, and trypsinization was terminated by adding DMEM/F12 supplemented with 10% FBS. After centrifugation, cells were resuspended in DMEM/F12 supplemented with 2% FBS and filtered 2 times through 70µm cell-strainer cap (Biosharp, BS-70-XBS). The single cell suspension was transferred into a polypropylene tube (Falcon, 352063) and kept on ice until FACS. The GFP+ cells were isolated into DMEM/F12 supplemented with 10% FBS using Sony MA900 Cell Sorter. The RNeasy Micro Kit (catalog no. 74004, Qiagen, Hilden, Germany) was used to isolate RNA.
Library construction and RNA sequencing were made by OE Biotech (Shanghai, China).

treatment_protocol: no treatment

value: embryonic kidney

value: nephron progenitor cells

value: E15.5 NPCs

value: Six2Cre-GFP+,Ash2l F/F

value: no treatment


title: ChIPseq-GAF-L3_brain-wt_rep2

description:
Library name: ChIPseq-GAF-L3_brain-wt_rep2.gz
ChIPseq-GAF-L3_brain-wt_rep1+rep2.bigwig


title: VSMC, bio rep1 WT H3K9me3, ChIP


title: ALL2128_HTO_Day28

description:
HTO
ALL2128_Day28_Multiplexed_barcodes.tsv.gz
ALL2128_Day28_Multiplexed_features.tsv.gz
ALL2128_Day28_Multiplexed_matrix.mtx.gz
ALL2128_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds

value: Leukemia

value: Control, Venetoclax, Ruxolitinib, Rux/Ven Combo


title: ChIPseq-GAF-L3_brain-wt_rep1

description:
Library name: ChIPseq-GAF-L3_brain-wt_rep1.gz
ChIPseq-GAF-L3_brain-wt_rep1+rep2.bigwig


title: VSMC, bio rep1 WT Input, ChIP


title: D52Q_SAE_OMI_96

city: St Louis

first: Rita

last: Meganck

address: 660 S Euclid Ave

institute: Washington University in St Louis

description: 10x Genomics

data_processing:
cellranger v6.1.2
SoupX
scDblFinder
Seurat v4
Minimal gene count>400, Percent mitochondrial genes<20%
Assembly: GRCh38, GENCODE v39
Supplementary files format and content: R data serialization (RDS) file, containing gene x cell (barcode) data matrices, dimension reduction embeddings, and cell meta-data.

source_name: Airway epithelium

growth_protocol: LAE/SAE cells were seeded onto the Transwell cell culture inserts. After confluency on the Transwell, the apical medium was removed and the cells were cultured on ALI condition with UNC-ALI medium at least for 4 weeks.

extract_protocol:
The cell dissociation procedure followed the manufacturer’s protocols for the 10x Genomics Chromium system with modifications. A 5 mM EDTA in Accutase solution (Sigma) was administered to both apical and basolateral HBE surfaces and cultures incubated for 20 min at 37 ˚C. The cells detached from the Transwell membrane were centrifuged (300g x 2 min at 4 C) and washed twice with 10% fetal bovine serum (FBS, Sigma) in Dulbecco's Modified Eagle Medium (DMEM, Sigma). The cells were then resuspended in DMEM with 10% FBS with gentle pipetting using wide-bore pipette tips and passed through a 40 µm cell strainer (Fisher Science #22363547) to remove clumps. Cell counting and viability were determined using an automated cell counter (Countess 3FL, Thermo).
Single-cell suspensions targeting approximately 10,000 cells were loaded onto a 10x Genomics Chromium Next GEM Chip G (10x Genomics) device following the manufacturer’s instructions. After GEM generation, the library preparation was performed following the instructions for the 10x Chromium Next GEM Single Cell 3’ GEM Library kit v3.1 (10x Genomics).

treatment_protocol: Infection with SARS-CoV-2 (MOI: 0.05) for 48 or 96 hours

value: Airway epithelium

value: Small airway epithelial

value: Primary air-liquid interface culture

tag: donor

value: Omicron, 96 hours post infection


title: S. aureus treated with DMSO, biological replicate 3

city: Guangzhou

first: Xiancai

last: Li

state: None Selected

address: 723 Xingke Road, Tianhe District, Guangzhou, CN 510650

department: South China Botanical Garden

institute: Chinese Academy of Sciences

description: Library name: Sample 6

data_processing:
Cutadapt was used to remove the sequence of 3 'end band connectors. Reads with average mass scores lower than Q20 were removed. All subsequent analyses are of high quality based on clean data.
Assembly: Bowtie2 was used to establish the reference genome index. Bowtie2 index (http://bowtiebio.sourceforge.net/index.shtml) was used to match the filtered Reads to the reference genome (GCF_002025145.1_ASM202514v1_genomic.fna).
Supplementary files format and content: FASTQ files (.gz), per base quality (.png),per base sequence content (.png), per sequence quality (.png), Genome map (.bam), read distribution (.png and .pdf), geneBodyCoverage curves (.png and .pdf)

organism: Staphylococcus aureus

source_name: culture

growth_protocol: S. aureus ATCC 6538 were grown overnight in BHI medium and diluted 1:100 into fresh medium. The diluted culture was incubated at 37 ℃ and 200 rpm to OD600 = 0.5.

extract_protocol:
RNA was harvested using Total RNA Extractor kit (Trizol).
RNA libraries for RNA-seq were prepared using Zymo-Seq RiboFree Total RNA Library Kit following manufacturer's protocols.

treatment_protocol: S. aureus ATCC 6538 were treated with 0 or 4 μg/mL of longistry A for 4 h and collected for total RNA isolation.

value: culture


title: ChIPseq-CG11504-L3_brain-wt_rep2

description:
Library name: ChIPseq-CG11504-L3_brain-wt_rep2.gz
ChIPseq-CG11504-L3_brain-wt_rep1+rep2.bigwig

value: Brains were dissected from wandering larvae 4-6 hours before puparium formation


title: Strain B6, CEHC1 WT, rep 1

value: algal cell

value: CEHC1 WT


title: D13Q_SAE_OMI_96

description: 10x Genomics


title: ChIPseq-GAF-L3_brain-mutCG11504_rep2

description:
Library name: ChIPseq-GAF-L3_brain-mutCG11504_rep2.gz
ChIPseq-GAF-L3_brain-mutCG11504_rep1+rep2.bigwig

value: CG11504 null allele, described in a current study

value: anti-GAF (full-lenght) antibodies, (Erokhin et al. Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14930-5. doi:10.1073/pnas.1515276112. )


title: NPC cells,cKO,E15.5,biol rep 1

value: embryonic kidney


title: ALL4364_HTO_Day28

description:
HTO
ALL4364_Day28_Multiplexed_barcodes.tsv.gz
ALL4364_Day28_Multiplexed_features.tsv.gz
ALL4364_Day28_Multiplexed_matrix.mtx.gz
ALL4364_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds

value: Ph-Like ALL


title: NPC cells,cKO,E15.5,biol rep 2

value: nephron progenitor cells

value: E15.5 NPCs


title: ChIPseq-CG11504-L3_brain-wt_rep1

description:
Library name: ChIPseq-CG11504-L3_brain-wt_rep1.gz
ChIPseq-CG11504-L3_brain-wt_rep1+rep2.bigwig

value: anti-CG11504 (full-lenght) antibodies, described in a current study


title: VSMC, bio rep1 WT IgG, ChIP

value: Aorta

value: Aortic vascular smooth muscle cell

value: Normal Rabbit IgG CST#2729

value: Control plasmid with EGFP by adenoviral infection


title: S. aureus treated with DMSO, biological replicate 2

description: Library name: Sample 5


title: D02R_SAE_D614G

description: 10x Genomics

value: Airway epithelium

value: Small airway epithelial

value: Primary air-liquid interface culture

value: D614G, 96 hours post infection


title: S. aureus treated with DMSO, biological replicate 1

description: Library name: Sample 4

value: culture


title: VSMC, bio rep1 prelamin A, Input, ChIP

value: Introducing Prelamin A accumulation by adenoviral infection


title: NPC cells,Control,E15.5,biol rep 3

value: Six2Cre-GFP+,Ash2l F/+

value: no treatment


title: Expanded CMP, biol rep 3

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of Tokyo

description:
Library name: GLPR_030_14
Column name in "TMRC_009_2group_N3_totalcount_quantilenormalized.csv" : PVA - TMRC_009_06 (GE) - Expression values

data_processing:
RNAseq data analysis by CLC Genomics Workbench (v10.1.1)
FASTQ : 8 FASTQ files are concatenated by cat command in Linux into 2 files (Read 1 and Read 2)
Import to CLC GW : Imported to CLC GW as paired-end reads
Mapping and quantification : Reads mapped to reference with gene and transcript annotation. Mouse, mm10, 49,585 genes, 103,982 transcript isoforms.
Assembly: mm10
Supplementary files format and content: csv files include total count for each sample.

source_name: Hematopoietic cells

growth_protocol: Fresh CMPs were directly collected from BM, exCMPs were collected from HSCs cultured for 7days.

extract_protocol:
For RNAseq analysis, 10000 cells of exCMPs or fCMPs were sorted into 1.5 mL tubes and lysed in 600 ul Trizol LS reagent (Thermo Fisher Scientific). Subsequently, RNA purification was carried out by Tsukuba i-Laboratory, LLC. Libraries were generated using the SMARTer cDNA synthesis kit (Takara).
Library preparation and next-generation sequencing were carried out by Tsukuba i-Laboratory, LLC. Libraries were generated using the SMARTer cDNA synthesis kit (Takara) and the high-output kit v2 (Illumina), followed by sequencing on a NextSeq 500 sequencer (Illumina) at 2x 36 paired end reads.

treatment_protocol: Murine HSCs were cultured in Ham’s F12 medium (Wako), enriched with 10 mM HEPES (Thermo Fisher Scientific), recombinant cytokines murine TPO (100 ng/mL, Peprotech), and SCF (10 ng/mL, Peprotech), polyvinyl alcohol (PVA, 84% hydrolyzed, Sigma), as well as insulin-transferrin-selenium (ITS, Thermo Fisher Scientific, 1:100 dilution) and 1% Penicillin-Streptomycin-L-Glutamine (PSG, Wako).

value: Hematopoietic cells

value: CMP

value: Expanded CMP

value: WT

value: Ex vivo expansion

tag: batch


title: S. aureus treated with longistry A, biological replicate 3

description: Library name: Sample 3


title: ALL2128_GEX_Day28

description:
Pooled scRNA-seq
ALL2128_Day28_Multiplexed_barcodes.tsv.gz
ALL2128_Day28_Multiplexed_features.tsv.gz
ALL2128_Day28_Multiplexed_matrix.mtx.gz
ALL2128_Day28_Multiplexing_feature_refs.csv
scRNA_Seurat_GEO.rds

value: Leukemia

value: Ph-Like ALL

value: Control, Venetoclax, Ruxolitinib, Rux/Ven Combo


title: NPC cells,Control,E15.5,biol rep 2

value: embryonic kidney

tag: cell line

value: nephron progenitor cells

value: E15.5 NPCs


title: Expanded CMP, biol rep 2

description:
Library name: GLPR_030_13
Column name in "TMRC_009_2group_N3_totalcount_quantilenormalized.csv" : PVA - TMRC_009_05 (GE) - Expression values

tag: cell type


title: NPC cells,Control,E15.5,biol rep 1

tag: genotype


title: D83K_D3_Mock

description: 10x Genomics

value: Airway epithelium

value: Large airway epithelial

value: Primary air-liquid interface culture

tag: treatment

value: Mock infection


title: S. aureus treated with longistry A, biological replicate 2

description: Library name: Sample 2

tag: tissue

value: culture


title: Expanded CMP, biol rep 1

description:
Library name: GLPR_030_12
Column name in "TMRC_009_2group_N3_totalcount_quantilenormalized.csv" : PVA - TMRC_009_04 (GE) - Expression values


title: Fresh CMP, biol rep 3

description:
Library name: GLPR_030_11
Column name in "TMRC_009_2group_N3_totalcount_quantilenormalized.csv" : BM - TMRC_009_03 (GE) - Expression values

value: Fresh CMP

value: Fresh BM


title: NPC cells,cKO,E15.5,K4me3_biol rep 1

data_processing:
Library sequencing and data analysis were performed by Annoroad Gene Tech (Beijing, China). In brief, raw reads were filtered and mapped to mouse genome GRCm38 using bowtie2 (version 2.2.9). Peaks were called using MACS2 (version 2.1.1) and bedtools (version 2-2.20.1) was used for annotation.
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
E15.5 embryonic kidneys were dissected and cut into small pieces, trypsinized for 30 min at 37℃, and trypsinization was terminated by adding DMEM/F12 supplemented with 10% FBS. After centrifugation, cells were resuspended in DMEM/F12 supplemented with 2% FBS and filtered 2 times through 70µm cell-strainer cap (Biosharp, BS-70-XBS). The single cell suspension was transferred into a polypropylene tube (Falcon, 352063) and kept on ice until FACS. The GFP+ cells were isolated into DMEM/F12 supplemented with 10% FBS using Sony MA900 Cell Sorter.
CUT&Tag-seq, For library preparation, the NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit was purchased from Novoprotein, and libraries were generated according to the manufacturer’s instructions. In brief, 1.0×104 cells were bound to ConA-coated beads and incubated with primary antibody against H3K4me3 (diluted 1:50 in primary antibody buffer) for 2 hours at room temperature. The beads were washed several times in wash buffer, incubated at room temperature for 1 hour using goat anti-rabbit IgG secondary antibody (diluted 1:50 in antibody buffer; catalog no. 31210, Invitrogen), again washed several times in wash buffer, then incubated with ChiTagTM pAG-Tn5 transposon (diluted 1:50 in ChiTag buffer) for 1 hour at room temperature. Tagmentation buffer containing MgCl2 was added, and the mixture was incubated at 37 ℃ for 1 hour. Tagmentation was stopped by adding sodium dodecyl sulfate and heating the mixture at 55 °C for 10 minutes. DNA fragments were purified using Tagment DNA Extraction Beads and PCR-amplified in reactions containing 33 μl extracted DNA, 2.5 μl primer i5 and 2.5 μl primer i7 and 10 μl 5×AmpliMix buffer. Amplifications were conducted using 20 cycles. PCR products were purified using NovoNGS® DNA Cleaning Beads.

value: Six2Cre-GFP+,Ash2l F/F

value: no treatment


title: D52Q_LAE_OMI_48

description: 10x Genomics

value: Omicron, 48 hours post infection


title: NPC cells,cKO,E15.5,K4me3_biol rep 2


title: S. aureus treated with longistry A, biological replicate 1

description: Library name: Sample 1


title: NPC cells,Control,E15.5,K4me3_biol rep 2

value: Six2Cre-GFP+,Ash2l F/+


title: mRNA-1273_3_RACE

description: 3’RACE-seq of Moderna’s mRNA-1273 sample. SeqLogo showing the 3’ terminus of mRNA-1273 poly(A) tail is provided

data_processing:
Sequence reads were mapped to the mm10 mouse genome build using STAR v. 2.7.6a
Counts for each transcript were collected using featureCounts from Subread package (v. 2.0.1),  with options -Q 10 -p -B -C -s 2 -g gene_id -t exon and Gencode vM25 annotation.
Differential expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Excel ile includes DESeq2 normalized counts for each sample and DESe2 LRT test statistics (comparisons across time). PNG file contains sequence logo for the 3’end of Moderna’s mRNA-172 poly(A) tail

organism: synthetic construct

source_name: synthetic sample

extract_protocol:
RNA from frozen injection sites (muscles) were isolated by homogenization in TRI-reagent (Sigma, T9424) using Omni Tissue Homogenizer (TH) equipped with 7 x 15 mm Saw Tooth (Fine) Generator Probe, homogenous mixtures were heated to 60 °C and further processed according to the manufacturer’s instructions.
Libraries were prepared using a KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, #08098140702), according to the manufacturer. KAPA UDI Indexes (KAPA Biosystems, #08098140702) were used. Library quality was assessed using chip electrophoresis performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

value: synthetic sample


title: D52Q_SAE_DEL_48

description: 10x Genomics

value: Small airway epithelial

value: Delta, 48 hours post infection


title: Fresh CMP, biol rep 2

description:
Library name: GLPR_030_10
Column name in "TMRC_009_2group_N3_totalcount_quantilenormalized.csv" : BM - TMRC_009_02 (GE) - Expression values

value: Hematopoietic cells

value: CMP

value: WT


title: PapOVA d1 MHCIIhi CD11c+ B220- cells, GX + ADT

city: Newark

first: Yosuke

last: Kumamoto

state: NJ

address: 205 South Orange Ave

department: Center for Immunity and Inflammation

institute: Rutgers New Jersey Medical School

description:
polyA RNA + protein
GX (3' mRNA) library + ADT: R1 contains cell barcode and UMI. R2 contains transcript and antibody-derived tag reads.

data_processing:
Cell Ranger (v3.0.1) and Loupe browser were used for data analysis
Further data processing, analysis and visualisation performed using Partek Flow (Partek Inc)
Assembly: mm10
Supplementary files format and content: Output Files: Naive_GX_processed_data.txt, PapOVA_d1_GX_processed_data.txt
Supplementary files format and content: Output Files: Naive_ADT_processed_data.txt, PapOVA_d1_ADT_processed_data.txt
Library strategy: CITE-seq

source_name: Skin draining lymph node

extract_protocol:
MHCIIhi CD11c+ B220- cells were sorted from popliteal lymph nodes of immunized and naïve mice and used to generate Gel Beads-in-Emulsion (GEMs) using the Chromium Single-Cell 3’ Reagent v3 kit (1000092, 10X Genomics) according to the manufacturer’s protocol.
Cell suspensions with a >90% viability was mixed with RT reagents and loaded onto Chromium Chip B, PN-1000074 along with Gel beads and Partitioning oil in the recommended order and then the chip was processed through 10X Chromium Controller for the generation of GEMs, followed by RT, Cleanup, and cDNA amplification. After the cDNA amplification, size selection was used to separate the cDNA molecules for 3’ Gexp (Gene Expression) library and ADT library construction

value: Skin draining lymph node

value: MHCIIhi CD11c+ B220-

value: immunized

tag: library type

value: mRNA + ADT

tag: adt

value: TotalSeq-A0566 anti-mouse CD301b (MGL2), TotalSeq-A0106 anti-mouse CD11c, TotalSeq-A0014 anti-mouse/human CD11b, TotalSeq-A0212 anti-mouse CD24, TotalSeq-A0002 anti-mouse CD8a, TotalSeq-A0422 anti-mouse CD172a (SIRPa), TotalSeq-A0568 anti-mouse/rat XCR1, TotalSeq-A0117 anti-mouse I-A/I-E, TotalSeq-A0202 anti-mouse CD64 (FcɣRI), TotalSeq-A0013 anti-mouse Ly-6c, TotalSeq-A0201 anti-mouse CD103, TotalSeq-A0449 anti-mouse CD326 (Ep-CAM)


title: NPC cells,Control,E15.5,K4me3_biol rep 1

value: embryonic kidney

value: nephron progenitor cells

value: E15.5 NPCs


title: D49Q_LAE_D614G

description: 10x Genomics

value: Airway epithelium

value: Large airway epithelial

value: Primary air-liquid interface culture

value: D614G, 96 hours post infection


title: D13Q_SAE_DEL_48

description: 10x Genomics

value: Small airway epithelial


title: 12_female PDMCAO aged #2

city: Houston,

first: Gab Seok

last: Kim

state: TX

address: 6431 Fannin St.

department: Department of Neurology

institute: The University of Texas Health Science Center at Houston

description: 10X Genomics

data_processing:
processed by Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Brain

growth_protocol: male and female in young and aged mice

extract_protocol:
brains slice, Miltenyi Adult Brain Dissociation Kitt
10X Genomics

treatment_protocol: sham surgeried or PDCMAO (14 PSD)

value: Brain

value: aged

value: female

value: PDMCAO


title: 12_EGF_IFNgamma_treated_cells_R3

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: single-end, two lanes

data_processing:
The amplified libraries were validated by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled, and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 20 million reads/sample.
Sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter. The quality of raw reads was assessed with FastQC version 0.11.8.
Assembly: Reads were mapped to the GRCh38 human genome assembly
Supplementary files format and content: Tab delimited text file containing EnsemblID,Entrez,GeneSymbol and sample ID's in columns and for each gene with raw counts in rows

source_name: HaCaT

growth_protocol: HaCaT cells (Addex Biological) were grown in DMEM with 1 g/L -glucose and L-glutamine (Thermo Fisher Scientific) with 10% fetal bovine serum (FBS) at 5% CO2 without antibiotics. HaCaT cells were validated by short tandem repeat analysis at the Emory Integrated Genomics Core

extract_protocol:
RNeasy Mini kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA).
Clontech Smart-Seq V4 Ultra Low Input RNA kit (Takara Bio, Shiga, Japan) in combination with the Illumina NexteraXT kit (Illumina, San Diego, CA, USA), as per manufacturer’s instructions, with 10 ng of total RNA as input.

treatment_protocol: Human IFN-γ (Peprotech, NJ) and EGF (Promega, WI) were resuspended in DMEM (200 mg/mL and 2000 ng/ml respectively) and stored at -80°C.  For the treatment of cells, IFN-γ (1 ng/ml), EGF (1000 ng/ml), both, or neither was added to cells and cellular lysates were prepared 24 hours later (Qiagen, CA).

value: HaCaT

value: Keratinocyte

value: EGF plus IFNG


title: Fresh CMP, biol rep 1

description:
Library name: GLPR_030_09
Column name in "TMRC_009_2group_N3_totalcount_quantilenormalized.csv" : BM - TMRC_009_01 (GE) - Expression values

value: Hematopoietic cells

value: CMP

value: Fresh CMP

value: WT

value: Fresh BM