title: inf-MD18

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: RNA-seq profiling of gastric tissue from Myd88-/- KO mice infected with H. felis

data_processing:
For RNA-seq data analysis, the reads were aligned to the combined mouse and H. felis genomes (GRCm38/mm10 and NC_014810.2, respectively) using STAR with default parameters. Only reads that aligned uniquely to a single location acrossin the genomes with a mapping quality score greater than 10 (MAPQ > 10) were used for downstream analysis. Gene expression levels were determined by counting the number of reads overlapping exons for all genes using HOMER’s analyzeRepeats.pl tool and the transcriptome annotation from GENCODE (version M25). Gene expression values were normalized using DESeq2’s rlog function. Gene expression values for genes on the H. felis genome were determined using HOMER’s analyzeRepeats.pl function based on gene annotations associated with NCBI accession number NC_014810.2, and reported as fragments per kilobase per million uniquely mapped fragments (FPKM), normalized to the total number of reads aligning to both the mouse and pathogen genomes.
Assembly: GRCm38/mm10, NC_014810.2
Supplementary files format and content: mouse.rlog.txt: Tab delimited text file of DESeq2 rlog normalized (i.e. log2) gene expression values for all mouse GENCODE genes across all samples.
Supplementary files format and content: hfelis.fpkm.txt: Tab delimited text file of FPKM normalized (to both host and pathogen read counts) gene expression values for all H. felis genes across all samples.

source_name: gastric tissue

growth_protocol: Six- to ten- week-old wild type (WT), MyD88 deficient (Myd88-/-), TRIF deficient (TrifLps2), double knockout (Myd88-/- and TrifLps2, DKO) mice in the C57BL/6 background were used in this study. WT mice were purchased from The Jackson Laboratory (Bar Harbor, ME). Myd88-/- mice were from our breeding colony originally provided by Dr. Akira (Osaka University, Japan) and backcrossed 10 times onto a C57BL/6 background, bred, and maintained at our facility. The DKO mice were bred in our facility by crossing Myd88-/- and TrifLps2. All mice were housed together before and throughout the H. felis infection study for each genotype. The animal procedures were approved by the Institutional Animal Care and Use Committee at the University of California, San Diego, and conducted following accepted veterinary standards. Helicobacter felis, strain CS1 (ATCC 49179) was obtained from the American Type Culture collection (Manassas, VA). The bacteria were cultured on solid Columbia agar (Becton Dickinson, MD) supplemented with 5% laked blood under microaerophilic conditions (5% O2, 10% CO2, 85% N2) at 37 °C and passaged every 2–3 days, following established protocols (7, 16-18). Prior to mouse infections, H. felis was cultured in liquid brain heart infusion broth (BHI, Becton Dickinson) supplemented with 10% fetal calf serum and incubated at 37 °C under microaerophilic conditions for 48 h. Spiral bacteria were enumerated using a Petroff-Hausser chamber before infections.

extract_protocol:
RNA was extracted from gastric tissue obtained from  H. felis-infected and uninfected WT, Myd88-/-, TrifLps, and DKO mice. Gastric tissue samples were homogenized in 1 ml of TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. RNA was extracted using the Direct-zol RNA mini kit (Zymo Research, Irvine CA) as per the manufacturer’s instructions and stored at -70°C until further use. The quality of the extracted RNA was assessed using a Nanodrop system (Thermo Fisher, Waltham MA) by measuring absorbance levels at 260 and 280 nm.
Samples were processed into RNA-seq libraries using the Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero (Human/Mouse/Rat), which involved ribosomal RNA depletion, fragmentation, cDNA synthesis, and cDNA library preparation.

treatment_protocol: This study used a well-characterized cancer mouse model, infecting C57BL/6 mice with H. felis (strain CS1), a close relative of the human gastric pathogen H. pylori. Mice were inoculated with 109 organisms in 300 μL of BHI by oral gavage repeated three times at 2-day intervals, as previously described. Control mice received BHI only. At 1 month, 3 months, and 6 months post-infection, mice were euthanized, and their stomachs removed under aseptic conditions. The stomach tissue was cut longitudinally, and sections were processed for RNA extraction and histopathology. All H. felis-infected mice were confirmed to be colonized by assessing the expression of the flagella filament B (flab) gene using real-time PCR as described in our previous studies.

value: gastric tissue

value: Myd88 KO

value: Infected with H. felis strain CS1 (ATCC 49179)


title: inf-MD11

status: Public on Apr 17 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: CD45+ CD11c+ cells, No Treatment, replicate 2

city: CHICAGO

first: Jason

last: Bugno

state: IL

institute: University of Chicago

data_processing:
Raw data quality control was done using FastQC, trimming was performed using Trimmomatic. Sequenced reads were aligned to the mouse reference genome (mm10) using RNA STAR and quantified by featureCounts. Count data was further analyzed for differential expression using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of DESeq2 output

source_name: Tumor

growth_protocol: B16-OVA tumors were established in mice for 10 days

extract_protocol:
Tumors were collected on day 17. Single cells from tumors were harvested by digestion using 1 mg/mL collagenase IV and 200 μg/mL DNaseI for 45 minutes. Blocking was performed with anti-Fc receptor. Live CD45+ CD11c+ cells were flow sorted from tumors and mixed with Trizol for RNA extraction.
RNA library for sequencing was constructed using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio)

treatment_protocol: At day 10 20 Gy was given. Mice receiving fusion protein received 20 mcg on day 10 and 10 mcg on day 14

value: Tumor

tag: cell type

value: WT

value: No Treatment


title: male_RE2_PRE

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description:
RE2_PRE
BN_Pre

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR
Reads aligning to gene exons (Homo_sapiens.GRCh38.102.gtf) were counted using featureCounts program from Subread package, summarized at gene level.
Differentially expressed genes were identified with a false discovery rate (Benjamini- Hochberg method) adjusted p-value <0.05 using the DESeq2 R package. Genes with total raw counts less then 10 across all samples were excluded from analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized read counts for protein coding genes for all samples
Supplementary files format and content: tab-delimited text files includes differetial gene expression analysis output from DESeq2

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
RNA was isolated using TRI Reagent (Sigma-Aldrich, St Louis, MO, USA). Tissue was homogenized using beads and the Fisher Bead Mill (Fisher, Hanover Park, IL, USA). RNA was further processed on columns using the Direct-zol Kit (Zymo Research, Irvine, CA, USA). Concentration and purity were determined using a BioTek Take3 micro-volume microplate with a BioTek PowerWave XS microplate reader (BioTek Instruments Inc., Winooski, VT).
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq Stranded mRNA

tag: muscle

value: RE

tag: timepoint

value: PRE

tag: timepoint order

tag: sample id

tag: subject

value: BN

tag: subject number

tag: subject id

tag: Sex

value: male

tag: age years

tag: height m

tag: weight kg

tag: bmi


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time4

city: Los Angeles

first: Marcelo

last: Francia

state: CA

address: 1771 Beloit Avenue, Unit 204

department: Neuroscience

institute: University of California, Los Angeles

library_source: genomic

data_processing:
Fastqc software was used to assess the quality of the raw files. Low quality reads were trimmed using TrimGalore and Cutadapt.
Alignment of the raw reads data to human gene Ensembl version GRCh38 was performed using bowtie2 with a 2kb insert size and allowing up to 4 alignments. Reads within black-listed regions alongside PCR duplicates were removed with samtools.
MACS2 software was used to identify open chromatin regions, with parameters -g hs -q 0.01 –nomodel –shift -100 –extsize 200 –keep-dup all -B. PCR.
To compare the ATAC-seq signal across timepoints and subjects, we created a consensus bed file using the bedtools function merge function, combining all the overlapping peak regions across timepoints and subjects into a single bed file.
Featurecounts software was then used to assign read counts to those regions
Assembly: GrCh38
Supplementary files format and content: narrowPeak file

molecule: genomic DNA

source_name: Skin

growth_protocol: Fibroblast cell lines were thawed out and grown to confluence in T75 culture flasks in standard culture media (DMEM containing 10% fetal bovine serum (FBS) and 1x Penicillin-Streptomycin)

extract_protocol:
For the collection of cells for the ATAC protocol, cells were dissociated using 500uL of prewarmed TrypLE (ThermoFisher 12604013) and left for 5 min at 37°C. TrypLE was inactivated using 500uL of DMEM. Cells were then counted using the Logos Biosystems LUNA-FL automated cell counter, and 50x10^4 cells were used as input for tagmentation.
ATAC seq libraries were generated following the previously described protocol (Buenrostro et al. 2015) and sequenced with 75-base double end reads, and sequenced at a targeted depth of 61M reads per sample.

treatment_protocol: 5 days after being plated the cells were treated  with 100 nM Dexamethasone for 30 min. Cells were then washed with PBS and switched to collection media (DMEM containing 5% FBS and 1x Penicillin-Streptomycin)

value: Skin

value: Fibroblast cells

value: Dexamethasone

tag: time

value: Time 4


title: inf-LP34

description: RNA-seq profiling of gastric tissue from Trif LPS2 KO mice infected with H. felis

tag: tissue

value: Trif KO


title: CD45+ CD11c+ cells, No Treatment, replicate 1

tag: genotype


title: inf-LP33

tag: treatment


title: male_RE1_24h

description:
RE1_24h
BI_24h

value: BI


title: CD45+ CD11c+ cells, Fusion protein, replicate 2

tag: cell type

value: Fusion Protein


title: male_RE1_8h

description:
RE1_8h
BI_8h

tag: muscle


title: Mock_TRIM_WT_3

city: Chapel Hill

first: Alexandra

last: Schaefer

state: NC

address: 3109 MHRC

institute: University of North Carolina at Chapel Hill

data_processing:
FastQ file quality was assessed using FastQC and MultiQC.
FastQ reads were mapped and quantified using Kallisto (0.46.0) to the reference build GRCm39
Counts per million (CPM) was calculated and normalized using EdgeR, keeping only rows with at least 5 cells indicating a count-per-million (CPM) of at least 1.
Expression data was filtered and normalized using Limma's VOOM.
Differentially expressed genes (DEGs) were identified by linear modeling and Bayesian statistics using the Limma package.
Assembly: GRCm39
Supplementary files format and content: *.tar.gz files contain one of each file listed below per sample which is indicated by the "*" pattern.
Supplementary files format and content: abundance.tsv files contain abundance quantifications per sample.
Supplementary files format and content: run_info.json files contain Kallisto run information per sample.
Supplementary files format and content: abundance.h5 files are hd5f binary files containing run info, abundance estimates, bootstrap estimates, and transcript length information per sample.

source_name: liver

extract_protocol:
Total RNA was extracted from liver samples using Trizol according to manufacturer's direction.
The RNA sequencing library was generated from 1000 ng total RNA using the KAPA Stranded RNA-Seq kit with RiboErase according to manufacturer’s directions (Roche Sequencing and Life Science). The pooled libraries were sequenced on 3 lanes Illumina NovaSeq 6000 using NovaSeq 6000 S4 XP Reagent Kit 100 Nu, paired end, with an average of 30,000,000 reads per RNA sample.

value: liver

value: mock treated


title: inf-LP32

value: gastric tissue

value: Infected with H. felis strain CS1 (ATCC 49179)


title: male_RE1_3h

description:
RE1_3h
BI_3h

tag: timepoint


title: inf-DK27

description: RNA-seq profiling of gastric tissue from Double KO (for Trif and Myd88) mice infected with H. felis

value: Myd88/Trif DKO


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time44

value: Time 44


title: ATAC Individual 2 skin fibroblast cells, Dexamethasone, Time0

value: Time 0


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time40

value: Time 40


title: male_RE1_30m

description:
RE1_30m
BI_30m

value: RE

tag: timepoint order


title: Mock_TRIM_WT_1


title: Mock_TRIM_WT_2


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time48

value: Time 48


title: inf-DK26


title: inf-DK25


title: Mock_TRIM_KO_3


title: male_RE1_PRE

description:
RE1_PRE
BI_PRE

value: PRE

tag: sample id

value: male


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time36

value: Skin

value: Fibroblast cells

value: Dexamethasone

value: Time 36


title: female_CTRL5_24h

description:
CTRL5_24h
BY_24h

value: CTRL

tag: subject

value: BY

value: female


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: Mock_TRIM_KO_2

value: liver

value: mock treated


title: female_CTRL5_8h

description:
CTRL5_8h
BY_8h

tag: subject number


title: inf-BL9

description: RNA-seq profiling of gastric tissue from wild-type (C57BL/6) mice infected with H. felis

value: gastric tissue

value: Infected with H. felis strain CS1 (ATCC 49179)


title: inf-BL8


title: Mock_TRIM_KO_1


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time24

value: Time 24


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time28

value: Time 28


title: Mock_CC074_D6_3


title: female_CTRL5_3h

description:
CTRL5_3h
BY_3h

tag: subject id


title: ctrl-MD33

description: RNA-seq profiling of gastric tissue from uninfected Myd88-/- KO mice

value: Myd88 KO

value: Uninfected (control)


title: Mock_CC074_D6_2


title: female_CTRL5_30m

description:
CTRL5_30m
BY_30m

tag: Sex


title: inf-BL4


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time20

value: Time 20


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time16

value: Skin

value: Time 16


title: Mock_CC074_D3_4


title: female_CTRL5_PRE

description:
CTRL5_PRE
BY_Pre

value: PRE

tag: age years


title: male_CTRL4_24h

description:
CTRL4_24h
BX_24h

value: BX

value: male

tag: height m


title: ctrl-LP24

description: RNA-seq profiling of gastric tissue from uninfected Trif LPS2 KO mice

value: Trif KO


title: Mock_CC074_D3_3


title: ctrl-LP23


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time12

value: Fibroblast cells

value: Dexamethasone

value: Time 12


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time4

value: Time 4


title: Mock_CC074_D3_2

value: liver

value: mock treated


title: male_CTRL4_3h

description:
CTRL4_3h
BX_3h

value: CTRL

tag: weight kg


title: Mock_CC074_D3_1


title: ctrl-DK21

description: RNA-seq profiling of gastric tissue from uninfected double KO (for Trif and Myd88) mice

value: gastric tissue

value: Myd88/Trif DKO


title: male_CTRL4_30m

description:
CTRL4_30m
BX_30m

tag: bmi


title: male_CTRL4_PRE

description:
CTRL4_PRE
BX_Pre


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time0

tag: time

value: Time 0


title: female_CTRL3_24h

description:
CTRL3_24h
BU_24h

tag: tissue

value: BU

value: female


city: Stanford

first: Ravindra

last: Majeti

address: 875 Blake Wilbur Dr Clinic F

institute: Stanford University

description:
Patient SU926 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

data_processing:
ATAC-sea data was processed based on workflows similar to Corces et al. Science 201826. First, read trimming and quality control was performed using trim_galore using default parameters. Reads were aligned to the GRCh38 reference genome using bowtie2 and the --very-sensitive option. Aligned reads were converted to bam format and sorted using SAMtools, and deduplicated using Picard MarkDuplicates. Reads were subsequently indexed and mitochondrial reads were removed using SAMTools. TagAlign bed files from technical replicate libraries were generated using bedtools, shifted to find ATAC-seq cut sites, and pooled. Peaks were called using MACS2 using p-value cut-off of 0.01 and peaks falling within black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were removed. A consensus peak set was generated using methods from Corces et al. Science 201828. Briefly, called peaks were merged by merging all peak bed files and using an iterative removal process to resolve overlapping peaks. This approach resulted in a consensus set of 115,551 500bp fixed-width peaks covering accessible regions represented in at least 2 or more samples. Count matrices were generated using the consensus peak set, and the number of Tn5 cut sites in each peak were calculated using the CountOverlaps function from the GenomicRanges package in R.
Assembly: Processed data files aligned to hg38 reference genome.
Supplementary files format and content: R data file containing peak counts or gene accessibility scores for each sample.

source_name: AML

extract_protocol:
Sorted AML blasts were prepared for ATAC-seq as previously described54. 5,000-50,000 cells were washed in cold FACS buffer and spun at 4°C for 5 minutes at 500 rcf in a fix-angled centrifuge. Cell pellets were then resuspended in 50 uL of ATAC-seq resuspension buffer (RSB: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) with 0.1% NP40, 0.01% digitonin, and 0.1% Tween-20 and incubated on ice for three minutes. After lysis, 1 mL of ATAC-seq RSB with 0.1% Tween-20 was added and tubes were inverted six times to mix. Isolated nuclei were then spun at 4°C for 10 minutes at 500 rcf in a fix-angled centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (25uL 2xTD buffer, 2.5 uL Tn5 transposase (100 nM final), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, and 5 uL nuclease-free water).
Transposition reactions were incubated at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up using Qiagen MinElute Reaction Cleanup kits and processed as previously described. All libraries were amplified with a target concentration of 20 μl at 4 nM, which is equivalent to 80 femtomoles of product.
All libraries were sequenced on an Illumina NextSeq with 75 bp paired end reads.

value: AML

tag: individual

value: Patient SU926

value: Diagnosis

value: LSC


title: ctrl-BL23

description: RNA-seq profiling of gastric tissue from uninfected wild-type (C57BL/6) mice

tag: genotype

tag: treatment

value: Uninfected (control)


title: Mock_CC011_D6_2


title: Mock_CC074_D6_1


description:
Patient SU926 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: cell type


title: female_CTRL3_8h

description:
CTRL3_8h
BU_8h

tag: muscle

tag: timepoint


title: ctrl-BL22


title: ctrl-MD32

value: Myd88 KO


title: Mock_CC011_D6_1


description:
Patient SU926 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: ATAC Individual 1 skin fibroblast cells, Dexamethasone, Time8

value: Skin

value: Fibroblast cells

value: Dexamethasone

value: Time 8


title: female_CTRL3_3h

description:
CTRL3_3h
BU_3h

value: CTRL

tag: timepoint order

tag: sample id


title: Mock_CC011_D3_4

value: liver

value: mock treated


title: 81_Heart_Male_WT_short_RNA_E5

city: Uppsala

first: Amir

last: Fallahshahroudi

address: Gropgränd 4

department: IMBIM

institute: Uppsala University

description: Short RNA-Seq

library_source: other

data_processing:
Raw reads from each library were aligned to the reference genome using STAR aligner v. 2.7.2b
The alignment process involved generating STAR indices, aligning reads to the reference genome in an annotation-aware manner, and quantifying the number of reads mapped to each gene using the --quantMode GeneCounts option in STAR
The resulting gene count matrices, along with a metadata file containing sample information and the GTF file, were used to create a RangedSummarizedExperiment object
This object was imported into DESeq2 v. 1.24.0 (ref. 47) for downstream analysis.
Raw short RNA-sequencing data were preprocessed using a custom Bash script. Adapter sequences were trimmed and reads were size-selected using Cutadapt version 4.4. The parameters set a maximum error rate of 0.25, targeted the adapter sequence “AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC” with a minimum overlap of 6 nucleotides, and allowed no indels, while selecting for read lengths between 19 and 26 nucleotides. After trimming and size selection, the reads were aligned to the chicken reference genome using STAR following the ENCODE miRNA-seq pipeline49 (www.encodeproject.org/microrna/microrna-seq-encode4/) (May 2017). This alignment process included mapping to the microRNA subset of the chicken GTF gene annotation and quantifying the number of aligned reads in STAR
Assembly: bGalGal1.mat.broiler.GRCg7b; GCA_016699485.1
Supplementary files format and content: DeSeq2 Object containing complete metadata and raw read counts for each gene.
Supplementary files format and content: DeSeq2 Object containing complete metadata and raw read counts for each microRNA..

molecule: other

organism: Gallus gallus

source_name: heart

extract_protocol:
A total of 72 samples from E2, E3, and E5 embryos were used for the generation of RNA sequencing libraries. We extracted total RNA from whole embryos or dissected tissues using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following the manufacturer's protocols. The RNA quality was assessed using the Fragment Analyzer system (Agilent), and all RNA quality numbers (RQNs) were equal to 10, indicating a lack of degradation.
The RNA-seq libraries were prepared from 400 ng of RNA per sample using the NEBNext Ultra II RNA Library Prep Kit for Illumina sequencing was performed on an Illumina NextSeq 2000 system, using NextSeq 2000 P3 Reagents (100 Cycles), with samples multiplexed in two sets of 36. Additionally, we generated small RNA libraries using RNA derived from the same E5 male samples (i.e., those that were also used for the generation of RNA sequencing libraries). This included the generation of small RNA libraries for RNA derived from ZZ (2 replicates), ZKOZ (3 replicates), and ZKOZKO (3 replicates) for each tissue type (head, body, heart), respectively.
The RNA-seq libraries were prepared from 400 ng of RNA per sample using the NEBNext Ultra II RNA Library Prep Kit for Illumina sequencing was performed on an Illumina NextSeq 2000 system, using NextSeq 2000 P3 Reagents (100 Cycles), with samples multiplexed in two sets of 36. short RNA Seq libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina and were sequenced on an Illumina NextSeq 550 system using NextSeq 500/550 High Output Kit v2.5 (75 Cycles), with samples multiplexed in two sets of 12.

value: heart

tag: developmental stage

tag: hh stage

tag: breed

value: Hy-Line

value: WT

value: Male


description:
Patient SU926 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU926


title: 81_Head_Male_WT_short_RNA_E5

description: Short RNA-Seq

source_name: head

value: head

tag: Sex


title: female_CTRL3_30m

description:
CTRL3_30m
BU_30m

tag: subject

value: BU

tag: subject number

tag: subject id

value: female

tag: age years

tag: height m


title: ctrl-DK20

tag: tissue

value: gastric tissue

value: Myd88/Trif DKO

value: Uninfected (control)


title: 81_Body_Male_WT_short_RNA_E5

description: Short RNA-Seq

source_name: body

value: body

tag: genotype


title: Mock_CC011_D3_3

tag: treatment


title: female_CTRL3_PRE

description:
CTRL3_PRE
BU_Pre

value: PRE

tag: weight kg

tag: bmi


description:
Patient SU926 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: individual

tag: timepoint

value: Relapse

tag: cell type

value: LSC


title: Mock_CC011_D6_3

value: liver

value: mock treated


title: Mock_CC011_D3_2


description:
Patient SU926 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: male_CTRL2_24h

description:
CTRL2_24h
BM_24h

tag: muscle

value: CTRL

tag: timepoint order

tag: sample id

value: BM

value: male


title: male_CTRL2_8h

description:
CTRL2_8h
BM_8h

tag: Sex


title: EV_TRIM_WT_D6_5

value: EV infection


description:
Patient SU926 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU926

value: Bulk


title: Mock_CC011_D3_1


description:
Patient SU926 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: 76_Head_Male_WT_short_RNA_E5

description: Short RNA-Seq

value: head

tag: developmental stage

tag: hh stage

tag: breed

value: Hy-Line

value: WT

value: Male


title: EV_TRIM_WT_D6_4


description:
Patient SU926 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Blast


title: male_CTRL2_3h

description:
CTRL2_3h
BM_3h

tag: subject

tag: subject number

tag: subject id

tag: age years


description:
Patient SU926 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: tissue


title: male_CTRL2_PRE

description:
CTRL2_PRE
BM_Pre

value: PRE

tag: height m

tag: weight kg


title: male_CTRL2_30m

description:
CTRL2_30m
BM_30m

tag: bmi


title: EV_TRIM_WT_D6_2

tag: genotype

tag: treatment


title: male_CTRL1_24h

description:
CTRL1_24h
BK_24h

tag: muscle

tag: timepoint

value: BK


description:
Patient SU926 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: individual

value: Diagnosis

tag: cell type


title: 56_Body_Male_KO_short_RNA_E5

description: Short RNA-Seq

value: body

tag: developmental stage

value: G2 Outcross

value: KO

tag: Sex


title: 38_Heart_Male_KO_short_RNA_E5

description: Short RNA-Seq

value: heart

tag: hh stage

tag: breed


title: 76_Heart_Male_WT_short_RNA_E5

description: Short RNA-Seq


title: male_CTRL1_8h

description:
CTRL1_8h
BK_8h

value: CTRL

tag: timepoint order

tag: sample id

tag: subject

tag: subject number

value: male


description:
Patient SU892 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: tissue

value: AML

value: Patient SU892

value: LSC


title: EV_TRIM_WT_D3_5

value: liver

value: EV infection


title: male_CTRL1_3h

description:
CTRL1_3h
BK_3h

tag: subject id

tag: age years

tag: height m

tag: weight kg


title: 38_Head_Male_KO_short_RNA_E5

description: Short RNA-Seq

value: head

tag: genotype


title: EV_TRIM_WT_D6_1

tag: treatment


description:
Patient SU892 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: individual

tag: timepoint


title: 76_Body_Male_WT_short_RNA_E5

description: Short RNA-Seq

tag: developmental stage

value: Hy-Line

value: WT

value: Male


title: 38_Body_Male_KO_short_RNA_E5

description: Short RNA-Seq

tag: Sex


title: male_CTRL1_30m

description:
CTRL1_30m
BK_30m

tag: muscle

value: BK

tag: bmi


title: male_CTRL1_PRE

description:
CTRL1_PRE
BK_Pre

value: PRE

tag: timepoint order


title: EV_TRIM_WT_D3_3


title: EV_TRIM_WT_D3_4


description:
Patient SU892 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis

tag: cell type

value: Bulk


title: 56_Heart_Male_KO_short_RNA_E5

description: Short RNA-Seq

tag: hh stage

tag: breed

value: G2 Outcross

value: KO


title: 33_Heart_Male_HZ_short_RNA_E5

description: Short RNA-Seq

tag: tissue

value: heart

value: HZ


title: 56_Head_Male_KO_short_RNA_E5

description: Short RNA-Seq


description:
Patient SU892 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: 33_Head_Male_HZ_short_RNA_E5

description: Short RNA-Seq


title: EV_TRIM_WT_D3_1


description:
Patient SU892 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU892

value: Relapse


title: 33_Body_Male_HZ_short_RNA_E5

description: Short RNA-Seq

value: body


description:
Patient SU926 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU926

value: Blast


title: EV_TRIM_KO_D6_5

value: liver

value: EV infection


title: Healthy Control 12, ADT

city: Gainesville

first: Rhonda

last: Bacher

address: 2004 Mowry Rd.

institute: University of Florida

description:
ADT (antibody derived tag) reads
PC057_adt

library_source: transcriptomic single cell

data_processing:
Raw data bcl files were first demultiplexed using Cellranger v7.0.1 command mkfastq.
FASTQ lanes 1-4 were combined into R1 and R2 files. FastQC was used to perform quality control on the reads.
Reads were aligned to GRCh38 reference transcriptome using alevin-fry v0.7.0.
Gene expression and protein counts matrices were loaded into R v4.2.1 using the fishpond package v2.7.4.
Downstream analysis was performed using Seurat v5 and custom scripts.
Assembly: GRCh38
Supplementary files format and content: Alevin output containing the UMI counts for cells in each sample.

source_name: whole blood

extract_protocol:
Cells were loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions. QC of cDNA and final libraries was performed. Sequencing was performed on Illumina NovaSeq 6000.
Libraries were prepared according to manufacturer(10x Genomics-Single Cell) instructions for feature barcoding.

value: Healthy Control

tag: cci

value: whole blood

value: circulating immune cells


title: Healthy Control 11, ADT

description:
ADT (antibody derived tag) reads
PC034_adt


description:
Patient SU892 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: LSC


title: 32_Heart_Male_KO_short_RNA_E5

description: Short RNA-Seq

value: Male


title: Healthy Control 10, ADT

description:
ADT (antibody derived tag) reads
PC032_adt


title: EV_TRIM_KO_D6_4


description:
Patient SU892 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: 32_Head_Male_KO_short_RNA_E5

description: Short RNA-Seq

value: head

value: G2 Outcross

value: KO


title: EV_TRIM_KO_D6_3


description:
Patient SU892 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: Healthy Control 9, ADT

description:
ADT (antibody derived tag) reads
PC012_adt


title: Healthy Control 8, ADT

description:
ADT (antibody derived tag) reads
PC011_adt


title: EV_TRIM_WT_D3_2


description:
Patient SU892 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU892


title: EV_TRIM_KO_D6_2


title: Healthy Control 7, ADT

description:
ADT (antibody derived tag) reads
PC009_adt


title: 25_Heart_Male_HZ_short_RNA_E5

description: Short RNA-Seq

value: heart

value: HZ


title: EV_TRIM_KO_D6_1


description:
Patient SU892 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


title: 25_Head_Male_HZ_short_RNA_E5

description: Short RNA-Seq


title: Sepsis 14, Day 4, ADT

description:
ADT (antibody derived tag) reads
P0668_adt

value: Day 4

value: Septic


title: EV_TRIM_WT_D6_3

value: liver

value: EV infection


title: 25_Body_Male_HZ_short_RNA_E5

description: Short RNA-Seq

value: body


description:
Patient SU892 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis

value: Blast


title: EV_TRIM_KO_D3_4


title: 23_Heart_Male_HZ_short_RNA_E5

description: Short RNA-Seq

value: Male


title: 32_Body_Male_KO_short_RNA_E5

description: Short RNA-Seq


title: Sepsis 13, Day 4, ADT

description:
ADT (antibody derived tag) reads
P0667_adt

value: whole blood

value: circulating immune cells


title: Sepsis 12, RAP, Day 14, ADT

description:
ADT (antibody derived tag) reads
P0665-T5_adt

value: Day 14

value: RAP


description:
Patient SU807 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU807


title: EV_TRIM_KO_D3_2


title: 23_Head_Male_HZ_short_RNA_E5

description: Short RNA-Seq

value: head

value: G2 Outcross


title: EV_TRIM_KO_D3_3


title: 23_Body_Male_HZ_short_RNA_E5

description: Short RNA-Seq

value: HZ


description:
Patient SU807 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


description:
Patient SU807 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


title: EV_TRIM_KO_D3_1


title: Sepsis 10, Day 4, ADT

description:
ADT (antibody derived tag) reads
P0664_adt

value: Day 4

value: Septic


description:
Patient SU807 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: EV_CC074_D6_2

value: liver

value: EV infection


title: Sepsis 9, RAP, Day 14, ADT

description:
ADT (antibody derived tag) reads
P0663_adt


title: AML blasts, 20180925-L1-SRA

city: Tampa

first: Rays HY

last: Jiang

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

description: 10x Genomics

data_processing:
The Cell Ranger Single-Cell software Suite (10x Genomics) was used for data processing, sample demultiplexing and gene expression quantification. t-Distributed stochastic neighbor embedding (t-SNE) and k-means clustering were used to reduce the data to a two-dimensional space and identify cell populations. Once the mean expression profiles of all cells were calculated, each cell was assigned to a subpopulation by the highest Spearman’s correlation.
Assembly: GRCh38
Supplementary files format and content: Tab separated value files and matrix file

source_name: Bone Marrow

extract_protocol:
Blast cells from AML patient donors with over 60% blast expansion in marrow biopsies were isolated according to standard tissue-banking protocols, washed and resuspended at 10^6 cells/ml.
Cells were processed using the 10x Genomics Chromium controller and loaded according to standard protocol of the Chromium single cell 3’ library and v3 gel bead kit to capture 2,000 cells/Chromium Chip B. Single-cell capture, cell lysis, reverse transcription, and library preparation were performed per manufacturer instructions. Sequencing was performed on Illumina NextSeq 550 targeting150,000 reads/cell.

value: AML patient donors

value: Bone Marrow

value: Blast Cells


title: CS2_Distal

city: Seattle

first: Benjamin

middle: Henry

last: Gern

state: WA

address: 307 Westlake Ave N

department: Center for Global Infectious Diseases Research

institute: Seattle Children's Research Institute

description: Distal

data_processing:
Raw probe counts from 2 sequencing runs were combined at the fastq levels and then converted to .DCC files via Nanostring’s geomxngspipeline function. The DCC files were uploaded to the DSP instrument and automatically associated with individual scans.  Sequencing and Probe QC was performed using default parameters (Analysis suite version 2.5.1.145). 4 of 32 original samples were removed for low sequencing saturation. Because we intended to pseudobulk ROIs within the same animal and thus required normalization strategies not available on the DSP analysis suite, we exported two datasets: (1) raw, post-qc probe counts and (2) q3 normalized counts (the recommended normalization approach by Nanostring).
To create a pseudobulked data set, we first aggregated all raw, QC-counts originally exported from the DSP, which created 2 sets of data per animal: aggregated counts from granuloma-associated ROIs and counts from distal, uninvolved regions. Due to the removal of samples for low sequencing saturation (see above) 14/16 potential pseudobulk samples remained. Because CLR-transformed values are more appropriately assessed by Aitchison-distance PCoA (which is the Euclidean distance between CLR-transformed samples), PCoA was used for dimensionality reduction.
To perform GSEA, we first calculated log2fc (using the CLR-transformed values) by directly comparing counts between necrotic and non-necrotic granulomas. We then used these log2fc values to rank genes. Ranked gene lists were supplied to a gsea function in R and results for significant enrichment and associated P values were obtained using the C5 Ontology gene sets from MSigDB.
Assembly: mm10
Supplementary files format and content: necrotic_v_non_necrotic_granuloma_clr_counts_and_log2fc.csv: gene expression count data
Supplementary files format and content: 2024_02_27_qc_read_counts_geomx_gern_gerner.csv: log2 fold change gene expression in necrotic vs non-necrotic lesions
Supplementary files format and content: necrotic_v_non_necrotic_granuloma_GSEA.csv: Gene set enrichment analysis of necrotic vs non-necrotic lesions
Library strategy: Spatial Transcriptomics

source_name: Lung

growth_protocol: C3HeB/FeJ mice were infected with Mtb

extract_protocol:
The fixed frozen sample slides were baked for 2 hours at 60°C to ensure lung tissue adhered to slides. Following baking, we performed target retrieval for 20 minutes following all recommended settings (MAN-10115-04). RNA targets were exposed using recommended concentration and duration of proteinase K (1ug/ml for 15 min). In situ probe hybridization took place overnight (18 hours) using standard hybridization solution with no custom spike-in (v1.0) Mouse NGS Whole Transcriptome Atlas RNA - lot # MWTA12002). The next day, off target probes were removed using stringent washes as recommended. Finally, morphology markers (SYTO13, B220 – PE, CD3 – CF594, and CD11b eF660) were added. Following antibody staining, slides and collection plate were loaded into GeoMx DSP instrument as recommended (MAN-10152-01). Slides were identified and records created for each.  Scan parameters were set for each channel: FITC/525 was utilized for SYTO13 nuclear staining, with exposure time of 50ms. Cy3/568nm was used for Alexa 532 to detect B220. Texas Red/615nm was used for Alexa 594 to detect CD3. Cy5/666nm was used for Cy5 to detect CD11b. All non-nuclear exposures were set for 200ms. Configuration files were obtained from the nanostring website. Syto 13 was used for focus. Slides were then scanned. Multiple ROIs were obtained per lesion, including necrotic core (when applicable), inner lesion, outer lesion border, and full thickness (encompassing inner and outer areas), as assessed by nuclear density and autofluorescence pattern. More fine-grained region determination was not possible due to poor performance of antibody staining. ROIs were then collected.
Following collection, GeoMx samples were removed from the machine and allowed to air dry overnight. The following day samples were placed in an open top thermal cycler at 65C for 10 minutes. Next, 10ul of nuclease free water were added to all samples well and pipetted up and down 5 times. PCR was run according to standard GeoMx protocols available in their quick start guide (MAN-10133-03). Pooling and cleanup were also run according to GeoMx protocols, with no deviations. The pooled library was assessed via Bioanalyzer and demonstrated a clean trace. Samples were loaded on the Illumina NextSeq platform at 1.6pM and sequenced twice using the recommended paired end 2 x 27 read acquisition.  Sequenced library included 5% PhiX. Fastq files were assessed by QC metrics prior to further analysis.

treatment_protocol: Lungs were removed and placed in BD Cytofix diluted 1:3 with PBS for 24hr at 4°C. Lungs were then washed two times in PBS and incubated in 30% sucrose for 24 hours at 4°C. Lungs were then embedded in OCT and freezing in a dry ice slurry with 100% ethanol. A CM1950 cryostat (Leica) was used to generate 10μm sections. During the sectioning process, lesions were classified as necrotic or non-necrotic by visual inspection (presence of caseum) and brightfield microscopy (assessing alveolar integrity and presence of necrotic debris).

value: Lung

value: Necrotic


description:
Patient SU758 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU758

value: Blast


title: EV_CC074_D6_1


title: Sepsis 8, RAP, Day 14, ADT

description:
ADT (antibody derived tag) reads
P0661_adt

value: Day 14

value: RAP

value: whole blood

value: circulating immune cells


title: EV_CC074_D3_5


description:
Patient SU758 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: CS2_Lesion3

description: Lesion


title: Sepsis 7, CCI, Day 14, ADT

description:
ADT (antibody derived tag) reads
P0660_adt

value: CCI


title: EV_CC074_D3_4


title: CS2_Lesion2

description: Lesion


title: Sepsis 11, Day 4, ADT

description:
ADT (antibody derived tag) reads
P0665_adt

value: Day 4


description:
Patient SU758 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: CS2_Lesion0

description: Lesion


description:
Patient SU758 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: EV_CC074_D3_2

value: liver


title: Healthy Control 12, GEX

description:
GEX (5' mRNA) library
PC057_gex

value: Healthy Control


title: CS2_Lesion1

description: Lesion


description:
Patient SU708 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU708

value: LSC


description:
Patient SU708 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: CS7_Distal

description: Distal

value: Non-necrotic


title: EV_CC011_D6_5

value: EV infection


title: Healthy Control 11, GEX

description:
GEX (5' mRNA) library
PC034_gex


description:
Patient SU708 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


title: EV_CC074_D3_1


description:
Patient SU708 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: EV_CC011_D6_4


title: CS7_Lesion1

description: Lesion

value: Lung


title: Healthy Control 10, GEX

description:
GEX (5' mRNA) library
PC032_gex


title: EV_CC011_D6_3


title: Healthy Control 9, GEX

description:
GEX (5' mRNA) library
PC012_gex


title: CS7_Lesion2

description: Lesion


title: Sepsis 6, RAP, Day 14, ADT

description:
ADT (antibody derived tag) reads
P0658_adt


title: EV_CC074_D3_3


description:
Patient SU708 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: CS11_Distal

description: Distal


title: Healthy Control 8, GEX

description:
GEX (5' mRNA) library
PC011_gex


description:
Patient SU708 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: CS11_Lesion2

description: Lesion


title: Healthy Control 6, ADT

description:
ADT (antibody derived tag) reads
PC003_adt


title: Healthy Control 7, GEX

description:
GEX (5' mRNA) library
PC009_gex


description:
Patient SU708 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: EV_CC011_D6_1


title: CS7_Lesion3

description: Lesion


description:
Patient SU892 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU892

value: Blast


title: CS11_Lesion1

description: Lesion


title: Sepsis 5, CCI, Day 14, ADT

description:
ADT (antibody derived tag) reads
P0657_adt

value: Day 14

value: whole blood


description:
Patient SU708 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: Sepsis 14, Day 4, GEX

description:
GEX (5' mRNA) library
P0668_gex

value: Septic

value: circulating immune cells


title: CS11_Lesion0

description: Lesion


title: EV_CC011_D3_4


description:
Patient SU708 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: CS6.2_Distal

description: Distal


title: EV_CC011_D3_3


description:
Patient SU708 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: EV_CC011_D3_2

value: liver


title: CS6.2_Lesion3

description: Lesion


title: EV_CC011_D6_2


title: Sepsis 13, Day 4, GEX

description:
GEX (5' mRNA) library
P0667_gex

value: Day 4


title: Sepsis 11, Day 4, GEX

description:
GEX (5' mRNA) library
P0665_gex


title: EV_CC011_D3_1


title: CS6.2_Lesion2

description: Lesion


title: Sepsis 10, Day 4, GEX

description:
GEX (5' mRNA) library
P0664_gex


title: Healthy Control 6, GEX

description:
GEX (5' mRNA) library
PC003_gex

value: Healthy Control


description:
Patient SU708 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU708


title: C3 (GFP-high, TdT-high)

city: St. Louis

first: David

last: Ornitz

state: MO

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St. Louis

data_processing:
Demultiplexing, barcode processing, and gene counting were performed using CellRanger software (v7.0.0) including intronic reads
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: lung

extract_protocol:
Lungs were minced with a razor blade with 50 µl of dispase (5,000 Caseinolytic Units, Discovery Labware, Inc. 354235) and then transferred to PBS containing 833 units /ml dispase, 0.01 mg/ml DNase I (Roche; 10104159001) and 2 mg/ml collagenase/dispase (Roche, 10269638) at 37°C for 40 min with gentle agitation. Digestion enzymes were then inactivated with FACS buffer (10% FBS, 1 mM EDTA in PBS), samples were sequentially filtered through a 70 µM cell strainer (Thermo Fisher Scientific; 22363548), and then a 40 µM cell strainer (Thermo Fisher Scientific; 22363547), and then centrifuged at 800 x g for 4 min. Red blood cells were lysed with ACK lysis buffer (Gibco; A10492-01) and cells were resuspended in FACS buffer. SYTOX blue (1 µl, Thermo Fisher Scientific, S34857) was added to each tube for live/dead sorting. Cells were sorted using a SY3200 “Synergy” cell sorter (Sony Biotechnology) or a Beckman Coulter MoFlo cell sorter (Beckman Coulter Life Sciences) with a 100 µm nozzle directly into FACS buffer or culture media (1.5 ml) on ice. Four cell populations were collected: TDTomato+, GFP-; TDTomato+, GFPHigh; TDTomato-, GFPHigh; and TDTomato-, GFPLow. Single channel controls (Fgf18CreERT2; ROSATDTomato; PdgfrαEGFP mice) were used to set compensation at the time of sorting and fluorescence minus one control (ROSATDTomato , lacking Fgf18CreERT2) was used as a negative control.  Plotted percentage of the four populations of cells was calculated relative to the total number of sorted cells.
Libraries were constructed according to manufacturer's protocol (10X Genomics, 3'v3.1). Cells were loaded in master mix with partitioning oil and beads to a chip and GEMs formed using a 10X Chromium device. Reverse transcription was performed to create barcoded cDNA from poly-A RNAs in each GEM. Pooled cDNA was cleaned with Silane Dynabeads, amplified, and size-selected using SPRIselect. Illumina R2 primer sequence was added along with paired-end constructs with P5/P7 sequences and a sample index for sequencing.

value: lung

value: lung mesenchyme


description:
Patient SU703 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU703

value: Relapse


title: C2 (GFP-high, TdT-neg)


title: CS6.2_Lesion1

description: Lesion

value: Lung

value: Non-necrotic


title: CS23_Distal

description: Distal


title: Sepsis 9, RAP, Day 14, GEX

description:
GEX (5' mRNA) library
P0663_gex

value: RAP


description:
Patient SU703 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Blast


title: CS23_Lesion3

description: Lesion


title: C1 (GFP-low, TdT-neg)


title: Sepsis 8, RAP, Day 14, GEX

description:
GEX (5' mRNA) library
P0661_gex

value: Day 14

value: whole blood


title: EV_CC011_D3_5

value: EV infection


description:
Patient SU703 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: Sepsis 7, CCI, Day 14, GEX

description:
GEX (5' mRNA) library
P0660_gex

value: CCI

value: circulating immune cells


title: Sepsis 12, RAP, Day 14, GEX

description:
GEX (5' mRNA) library
P0665-T5_gex


title: Lung, uninfected pam3CSK4  50ug i.ph one week prior to infection 4

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to transcriptome GRCh38 version using STAR
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was isolated using the RNeasy Serum/Plasma Advanced Kit (50) (cat# 217204) according to the manufacturers’ recommendation (QIAGEN).
The library preparation was done using the QIAseq RNA Library Kit (QIAGEN). A total of 5ul total RNA was converted into RNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR, the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

tag: infection

value: uninfected

value: male

tag: time


description:
Patient Su674 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient Su674


title: CS23_Lesion2

description: Lesion


description:
Patient SU674 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU674


title: CS23_Lesion1

description: Lesion


title: Lung, uninfected pam3CSK4  50ug i.ph one week prior to infection 3

value: lung


title: Sepsis 5, CCI, Day 14, GEX

description:
GEX (5' mRNA) library
P0657_gex


title: Sepsis 6, RAP, Day 14, GEX

description:
GEX (5' mRNA) library
P0658_gex


title: CS6_Distal

description: Distal

value: Necrotic


description:
Patient SU674 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


description:
Patient Su703 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient Su703

value: Relapse


title: Lung, uninfected pam3CSK4  50ug i.ph one week prior to infection 1


title: CS6_Lesion2

description: Lesion

value: Lung


title: BT-40, 5d 5n dabrafenib + 72h withdrawal, rep2

city: Heidelberg

first: Romain

last: Sigaud

address: Im Neuenheimer Feld

country: Germany

institute: Hopp Children’s Cancer Center Heidelberg (KiTZ)

data_processing:
FASTq files were submitted to the OTP RNAseq pipeline (PMID: 28803971) for read-trimming, alignment to the hg19/GRCh37 human genome and calculation of raw read counts, TPM and FPKM values.
Assembly: hg19/GRCh37 human genome
Supplementary files format and content: Raw read counts, TPM and FPKM values are provided in one tsv file for each sample.

growth_protocol: cells were cultured in minimum media (RPMI + 2% FCS)

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (cat. no. 74104, Qiagen) with on-column Dnase digestion according to the manufacturer’s instructions. 500ng RNA was used for library preparation
RNA libraries were generated using the Illumina TruSeq mRNA stranded Kit

treatment_protocol: cells were treated for 5 days with either DMSO (solvent control) or 5nM dabrafenib followed by treatment withdrawal

tag: cell line

value: patient-derived tumor cells


title: BT-40, 5d 5n dabrafenib + 72h withdrawal, rep3


title: CS6_Lesion1

description: Lesion

tag: genotype


description:
Patient SU674 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Blast


description:
Patient SU654 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU654

value: LSC


title: BT-40, 5d 5n dabrafenib + 72h withdrawal, rep1


title: Lung, uninfected CpG 10ug i.ph one week prior to infection 3

tag: treatment


title: Lung, uninfected CpG 10ug i.ph one week prior to infection 4


title: CS6_Lesion3

description: Lesion


title: BT-40, 5d 5n dabrafenib + 24h withdrawal, rep3


description:
Patient SU654 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

tag: individual


title: BT-40, 5d 5n dabrafenib + 24h withdrawal, rep2


description:
Patient SU654 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: timepoint


title: BT-40, 5d 5n dabrafenib + 24h withdrawal, rep1


title: CS21_Distal

description: Distal

value: Non-necrotic


title: CS21_Lesion3

description: Lesion


title: Lung, uninfected pam3CSK4  50ug i.ph one week prior to infection 2


description:
Patient SU654 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: Lung, uninfected CpG 10ug i.ph one week prior to infection 1

value: uninfected


title: BT-40, 5d 5n dabrafenib + 6h withdrawal, rep3


title: Lung, uninfected PBS ctrl 2

value: PBS ctrl

value: male


title: CS21_Lesion2

description: Lesion


title: CS6_Lesion0

description: Lesion


description:
Patient SU654 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: CS21_Lesion1

description: Lesion


title: BT-40, 5d 5n dabrafenib + 6h withdrawal, rep2


description:
Patient SU654 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: BT-40, 5d 5n dabrafenib + 6h withdrawal, rep1


title: Lung, SCV2 + pam3CSK4  50ug i.ph one week prior to infection 4


title: CS9_Distal

description: Distal


title: CS9_Lesion3

description: Lesion


description:
Patient SU654 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Lung, uninfected CpG 10ug i.ph one week prior to infection 2


title: BT-40, 5d 5n dabrafenib + 2h withdrawal, rep3


title: Lung, SCV2 + pam3CSK4  50ug i.ph one week prior to infection 3


title: CS9_Lesion2

description: Lesion


title: BT-40, 5d 5n dabrafenib + 2h withdrawal, rep2


title: Lung, uninfected PBS ctrl 3


title: Lung, SCV2 + pam3CSK4  50ug i.ph one week prior to infection 1


title: BT-40, 5d 5n dabrafenib + 0.5h withdrawal, rep3


title: CS9_Lesion1

description: Lesion


description:
Patient SU654 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


description:
Patient SU654 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: BT-40, 5d 5n dabrafenib + 2h withdrawal, rep1


description:
Patient SU654 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: CS9_Lesion0

description: Lesion


description:
Patient SU654 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Lung, SCV2  +  CpG 10ug i.ph one week prior to infection 4


title: BT-40, 5d 5n dabrafenib + 0.5h withdrawal, rep2


title: Capture HiC-seq at E18.5 in the female urogenital sinus.

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

data_processing:
*library strategy: Capture HiC-seq
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Sequenced DNA fragments were processed with HiCUP version 0.9.2 on mm39 with --re1 ^GATC, bowtie2 version 2.4.5 and samtools version 1.16.1.
The output BAM was converted to pre-juicer medium format with hic2juicer from HiCUP. The pairs with both mates on chr2:72233000–76832000 were selected, sorted and loaded into a 10kb bins matrix with cooler version 0.8.11.The final matrix was balanced with the option --cis-only.
The TADs were computed with HiCExplorer hicFindTADs version 3.7.2 with --correctForMultipleTesting fdr --minDepth 240000 --maxDepth 480000 --step 480000 --minBoundaryDistance 200000.
Assembly: mm39
Supplementary files format and content: *.cool: balanced matrix on the capture region
Supplementary files format and content: validPairs.txt.csort.txt.gz: valid pairs in juicer medium format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> where str = strand (0 for forward, anything else for reverse) see https://github.com/aidenlab/juicer/wiki/Pre#medium-format)
Supplementary files format and content: domains.bed: bed file with TADs

source_name: urogenital sinus

extract_protocol:
E18.5 male UGS were collected and collagenase-treated samples were cross-linked with 1% formaldehyde (Thermo Fisher 28908) for 10 min at RT and stored at −80° until further processing.
Libraries were constructed as previously described in (10.1371/journal.pbio.3000004).

value: urogenital sinus

value: female

tag: Stage

value: wild type

tag: strain


title: Lung, SCV2  +  CpG 10ug i.ph one week prior to infection 2

value: lung

tag: Sex


description:
Patient SU624 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU624


title: Lung, SCV2  +  CpG 10ug i.ph one week prior to infection 3


title: BT-40, 5d 5n dabrafenib + 0.5h withdrawal, rep1


title: Lung, SCV2 + PBS ctrl 4


title: Lung, uninfected PBS ctrl 1


title: ATAC-seq in mouse E18.5 male urogenital sinus replicate 2

data_processing:
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw ATAC-seq paired-end reads were processed with CutAdapt version 4.1 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Nextera adapters and bad quality bases.
Filtered reads were mapped on mm39 for mouse samples and danRer11 where alternative contigs were removed for fish samples with bowtie2 version 2.4.5 with the following parameters: --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -X 1000. Only pairs mapping concordantly outside of mitochondria were kept (Samtools v1.16.1)
PCR duplicates were removed by Picard version 3.0.0 (http://broadinstitute.github.io/picard/index.html). BAM files were converted to BED with bedtools version 2.30.0. Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with --nomodel --keep-dup all --shift -100 --extsize 200 --call-summits -B. Coverages were normalized to million mapped reads.
Assembly: mm39
Assembly: danRer11
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads

extract_protocol:
Mouse and fish tissues were isolated and placed into 1x PBS containing 10% FCS on ice. Collagenase (Sigma-Aldrich C9697) was added to 50ug/ml and incubated at 37º for 20 minutes with shaking at 900rpm.
Cells were washed 3x in 1x PBS. The number of cells was counted and viability confirmed to be greater than 90%. An input of 50000 cells was then processed according to previous description.


description:
Patient SU624 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


title: BT-40, 5d 5n dabrafenib, rep3


title: ATAC-seq in mouse E18.5 female urogenital sinus replicate 2


title: Lung, SCV2  +  CpG 10ug i.ph one week prior to infection 1


title: Lung, SCV2 + PBS ctrl 3


description:
Patient Su624 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient Su624

value: Diagnosis


description:
Patient SU654 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: ATAC-seq in mouse E18.5 female urogenital sinus replicate 1


title: BT-40, 5d 5n dabrafenib, rep2

value: patient-derived tumor cells


title: Lung, SCV2 + pam3CSK4  50ug i.ph one week prior to infection 2


title: EV_TRIM_KO_D3_5

value: liver

value: EV infection


title: Capture HiC-seq at E18.5 in the male urogenital sinus.


title: Lung, SCV2 + PBS ctrl 2


title: ATAC-seq in mouse E18.5 male urogenital sinus replicate 1


title: ten_dpi

city: Philadelphia

first: Ryan

last: Pardy

state: PA

address: 380 South University Ave

department: Pathobiology

institute: University of Pennsylvania

description:
infected_in_vivo_D10_WT
10x Chromium Single Cell 3’ Library v3.1 chemistry, NextSeq 500/550 High Output Kit v2.5 (75 cycles).

data_processing:
Cell Ranger v7.0.0 was used to process sequencing reads and build a reference genome for C. parvum Iowa II (VEuPathDB, release 46). Processed reads from each sample were aligned to this reference genome or to the Mus musculus genome (GRCm38) to generate filtered feature-barcode matrices, which are the features (tsv), barcodes (tsv), and matrix (mtx) files listed in this submission.
Seurat 3.1.4 was used for filtering, normalization, clustering, UMAP visualization, and marker identification between IEC clusters.
Monocle3 was used to produce pseudotime trajectories.
Single-sample gene set enrichment analysis was performed using escape.
Assembly: GRCm38 of the Mus musculus reference genome from the Genome Reference Consortium.
Assembly: Version 46 of the Cryptosporidium parvum Iowa II reference from VEuPathDB.
Supplementary files format and content: The filtered_feature_bc_matrix (Cell Ranger 3.1.0 output) consists of features (tsv), barcodes (tsv), and matrix (mtx) files. The features (tsv) files are the same for all samples, and differ only whether they are for the mouse or C. parvum genome. The RDS files contain the Seurat objects for IEC clusters from each dataset (WT or IFNg_KO), with corresponding csv files containing the metadata information.

source_name: Murine epithelium from the ileum of the small intestine

extract_protocol:
Following isolation and dead cell removal, cells from mice were washed in 1X PBS (calcium and magnesium free) supplemented with 0.04% w/v BSA, centrifuged, and resuspended in 1X PBS (calcium and magnesium free) supplemented with 0.04% w/v BSA. Cells were then loaded onto a chromium chip for encapsulation via the 10x Genomics platform.
10x Chromium Single Cell 3’ Library v3.1 chemistry was used and manufacturer’s instructions were followed for cDNA amplification and library construction. For C57BL/6 samples, the NextSeq 500/550 High Output Kit v2.5 (75 cycles) was used to obtain paired-end reads from an Illumina NextSeq 500 sequencer. For IFNg KO samples, the NextSeq 2000 P3 Kit (100 cycles) was used to obtain paired-end reads from an Illumina NextSeq 2000.

treatment_protocol: C57BL/6 and IFN-gamma KO mice were infected with mouse-adapted C. parvum that has been engineered to express mCherry and nanoluciferase (see Gullicksrud et al. 2021). Two mice per group were infected with 50,000 oocysts and mice were sacrificed on days 4 and 10 (C57BL/6 mice) or 12 hours post-administration of PBS or IFNg (5dpi; IFNg KO mice). Epithelial cells were obtained from the small intestine and pooled within each group.

value: wild-type

value: Infected with 5x10e4 maCp oocysts, 10 dpi

tag: cell preparation

value: single cell


title: BT-40, 5d 5n dabrafenib, rep1


title: BT-40, 5d DMSO, rep3


title: Lung, SCV2 + PBS ctrl 1


title: BT-40, 5d DMSO, rep2


description:
Patient SU562 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU562

value: LSC


description:
Patient SU562 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: four_dpi

description:
infected_in_vivo_D4_WT
10x Chromium Single Cell 3’ Library v3.1 chemistry, NextSeq 500/550 High Output Kit v2.5 (75 cycles).

value: Infected with 5x10e4 maCp oocysts, 4 dpi

value: Murine epithelium from the ileum of the small intestine


title: BT-40, 5d DMSO, rep1


title: nlgf_1mo_m

city: Farmington

first: Riqiang

last: Yan

address: 263 Farmington Ave

institute: Uconn Health

description: 10x genomics

data_processing:
Raw sequencing from the NovaSeq6000 was aligned and annotated using the CellRanger v3.1.0 pipeline. During fastq.gz generation, reads with more than 1 mismatch in the 8bp i7 index were excluded. During alignment using STAR (Dobin et al., 2013), only reads with MAPQ scores greater than 255 aligned to annotated transcripts were retained. Reads containing bases with Q30 scores below 3 were also excluded. After alignment, cell barcodes were filtered up to 1 mismatch against a whitelist of 737,500 barcodes provided by 10X Genomics. Barcodes associated with cells were distinguished from ambient mRNA using an adaptively computed UMI threshold. The raw counts matrix was filtered using cutoff values of mitochondrial transcripts below 25% and between 500 and 7,500 unique features.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
Four P30 retinas, one WT male, one WT female, one NLGF male, and one NLGF female WT were extracted according to the published procedure (Fadl et al., 2020). Briefly, the retinas were dissected in fresh and cold 1X HBSS and individually transferred to a 5 ml polypropylene round-bottom tube containing 1 ml of digestion solution. The individual retinas were then incubated at 8 °C for 40 min followed by a second incubation at 28 °C for 10 min. After the incubation steps, the retina should have remained morphologically intact. Mechanical trituration of the retina was performed in 700 µl of prewarmed (10 min at 28 °C) inactivation solution. Trituration was stopped when the retina was visibly dissociated, and 700 µl of ice-cold washing solution was layered under the cell suspension. Cell suspensions were centrifuged using a swing-bucket rotor at 200 ×g for 5 min at 4 °C. After the supernatant was removed, the cells were resuspended in 500 µl of DPBS containing 0.04% BSA and passed through a 40 μm cell strainer.
Single cell suspensions from retinal dissociation were counted and loaded onto a droplet based 10x Chromium controller to perform single cell partitioning and barcoding.

value: retina

tag: developmental stage

value: nlgf


description:
Patient SU562 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: cell type


title: nlgf_1mo_f

description: 10x genomics


description:
Patient SU624 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU624

value: Blast


title: SH005-HTO

city: New York

first: Falak

last: Sher

state: New York

address: 630 W 168th street

institute: Columbia University

description: Hashtag derived oligonucleotide

data_processing:
The "count" command of CellRanger v6.0.0 was used with "GRCh38-2020-A" transcriptome and feature reference of HTOs to generate filtered UMI count matrix (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: iPSC derived- microglia (iMG)

growth_protocol: iPSCs were first differentiated into hematopoietic progenitor cells STEMdiff from Stem Cell Tech. iMG differentiation was achieved in a mix of human astrocyte conditioned media and an enriched media containing IMDM, defined FBS, IL-3, GM-CSF, and M-CSF

extract_protocol:
iMG were incubated with TruStain FcX blocking reagent (BioLegend, Cat. No. 422301). Hash tagging antibodies were added, and cells were incubated for additional 30 minutes at 4C and washed.  Library preparation was conducted using 10x Chromium Next GEM Single Cell 3' Reagent Kits v3.1 with Feature Barcode technology.
Library was constructed following manufacturer's portocol. Briefly, reverse transcription reagents, barcoded gel beads, and partitioning oil were mixed to generate GEM. After the reverse transcription, GEMs were broken, and Feature Barcode cDNA amplification occurred. Amplified cDNA was separated by SPRI size selection into mRNA and HTO fractions. Sequencing libraries were generated and analyzed using TapeStation D5000 and Qubit HS DNA quantification kit. Sequencing was performed on a NovaSeq 6000 with S4 flow cell (Illumina, San Diego, CA) using paired-end, dual-index sequencing as: 28 cycles for read 1, 10 cycles for i7 index, 10 cycles for i5 index, and 90 cycles for read 2.

value: iPSC derived- microglia (iMG)

value: Microglia

tag: library type

value: HTO

value: WT and SORL1 KO mixed sample

tag: hto

value: TotalSeq™-B0257 anti-human Hashtag 7, TotalSeq™-B0258 anti-human Hashtag 8


title: SH005-GEX

description: polyA RNA

value: mRNA


title: Uninfected

description:
uninfected_in_vivo_WT
10x Chromium Single Cell 3’ Library v3.1 chemistry, NextSeq 500/550 High Output Kit v2.5 (75 cycles).

value: wild-type

value: Uninfected

tag: tissue


description:
Patient SU562 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Relapse

value: Bulk


title: wt_1mo_m

description: 10x genomics

value: wildtype


description:
Patient SU562 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU562


title: wt_1mo_f

description: 10x genomics

value: retina


title: Old High Fat Diet Batch2 rep6

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

data_processing:
Raw reads quality were checked using FastQC v0.11.8
Reads were aligned to mm10 using STAR v2.7.3a with GDC 2-step pass pipeline.
Raw read counts per gene were generated using HTSeq v0.11.2
Batch correction was done using sva(Surrogate Variable Analysis) ComBat v3.40.0.
Batch corrected FPKMs were then generated using R package countToFPKM 1.0
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample after batch correction

source_name: Isolated hepatocytes

extract_protocol:
Isolated hepatocytes were purified and snap frozen in LN2. RNA was derived using trizol chloroform RNA extraction methadology
PolyA capture

treatment_protocol: Mice were rested for at least 2 weeks prior to initiation of diet for 9-weeks. Diets were provided ad libitum and changes weekly. High fat diet 58y1 was purchased from TestDiet consisting of 60% nergy from fat. Normal diet was purchased from Teklad global 18% protein. Mice were maintained on diets for 9-weeks then euthanized using CO2 upon which 2-step liver perfusion was conducted to isolate hepatocytes.

value: Isolated hepatocytes

value: male

tag: age (months)

value: High fat diet


title: Old High Fat Diet Batch2 rep5


description:
Patient SU562 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Blast


title: D067-PSS-439

city: Sejong

first: Sinwoo

last: Park

address: Sejongro

country: South Korea

institute: Korea Universiy

data_processing:
Low qaulity of reads in the raw reads were trimmed using the Trimmomatic (v0.39)
Trimmed reads were align using HISAT2 (v2.2.1)
FeatureCounts (v2.0.3) was used for the quantification of aligned reads.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: blood

extract_protocol:
For Illumina NovaSeq 6000, total RNA was extracted using TruSeq Stranded Total RNA LT Sample Prep Kit (Globin). For MGISEQ-2000RS, total RNA was isolated from tissue using TRI-reagent based method. Total RNA (500 ng) was processed for  preparing whole transcriptome sequencing library.
For Illumina NovaSeq 6000, libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E, For MGISEQ-2000RS,  Enrichment of whole transcriptome RNA by depleting  ribosomal RNA (rRNA) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

value: blood

value: M

tag: disease

value: COPD


title: Old High Fat Diet Batch2 rep4


title: Old High Fat Diet Batch1 rep3


title: mouse spleen myeloid cells

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

description: 10× Genomics

data_processing:
Raw data of single-cell RNA-seq were processed with Cell Ranger (v7.2.0) based on the Ensembl Mus musculus reference genome (GRCm39, v110).
Assembly: Ensembl GRCm39, v110
Supplementary files format and content: Tab-separated values file and matrix file

source_name: spleen

growth_protocol: Spleen was harvested from neonatal C57BL/6J mouse (7 days).

extract_protocol:
Single-cell suspensions from spleen were prepared and treated with ACK lysis buffer. CD3-CD19-CD11b+ cells were sorted with a MoFlo Astrios EQ Cell Sorter.
Sequencing library was prepared using Chromium Single Cell 3’ Reagent Kits (10× Genomics) according to the manufacturer’s instructions.

treatment_protocol: Untreated

value: spleen

value: Myeloid cells

value: WT

value: untreated


description:
Patient SU562 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML


title: D066-KMS-048


description:
Patient SU562 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis

value: LSC


title: CDK12 KO sgNT-2

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

description:
CDK12KO
SI_36578
SI_36571-78.cts.csv

data_processing:
Transcripts were quantified by kallisto with mouse reference genome (mm10) and then summarized to obtain gene level counts and TPM.
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts of each sample

source_name: prostate organoid

extract_protocol:
RNA was extracted from cell pellets  using Qiagen RNA extraction kit. RNA quality was determined using a Bioanalyzer RNA Nano Chip
Poly-A selection was performed with Sera-Mag Oligo(dT)-Coated Magnetic Particles (38152103010150; GE Healthcare Life Sciences), and libraries were generated using a KAPA RNA HyperPrep kit (KK8541; Roche Sequencing Solutions).

value: prostate organoid

value: Epithelial

value: Cdk12 mutant


title: Old High Fat Diet Batch1 rep2

value: Isolated hepatocytes


description:
Patient SU562 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

data_processing:
ATAC-sea data was processed based on workflows similar to Corces et al. Science 201826. First, read trimming and quality control was performed using trim_galore using default parameters. Reads were aligned to the GRCh38 reference genome using bowtie2 and the --very-sensitive option. Aligned reads were converted to bam format and sorted using SAMtools, and deduplicated using Picard MarkDuplicates. Reads were subsequently indexed and mitochondrial reads were removed using SAMTools. TagAlign bed files from technical replicate libraries were generated using bedtools, shifted to find ATAC-seq cut sites, and pooled. Peaks were called using MACS2 using p-value cut-off of 0.01 and peaks falling within black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were removed. A consensus peak set was generated using methods from Corces et al. Science 201828. Briefly, called peaks were merged by merging all peak bed files and using an iterative removal process to resolve overlapping peaks. This approach resulted in a consensus set of 115,551 500bp fixed-width peaks covering accessible regions represented in at least 2 or more samples. Count matrices were generated using the consensus peak set, and the number of Tn5 cut sites in each peak were calculated using the CountOverlaps function from the GenomicRanges package in R.
Assembly: Processed data files aligned to hg38 reference genome.
Supplementary files format and content: R data file containing peak counts or gene accessibility scores for each sample.

extract_protocol:
Sorted AML blasts were prepared for ATAC-seq as previously described54. 5,000-50,000 cells were washed in cold FACS buffer and spun at 4°C for 5 minutes at 500 rcf in a fix-angled centrifuge. Cell pellets were then resuspended in 50 uL of ATAC-seq resuspension buffer (RSB: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) with 0.1% NP40, 0.01% digitonin, and 0.1% Tween-20 and incubated on ice for three minutes. After lysis, 1 mL of ATAC-seq RSB with 0.1% Tween-20 was added and tubes were inverted six times to mix. Isolated nuclei were then spun at 4°C for 10 minutes at 500 rcf in a fix-angled centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (25uL 2xTD buffer, 2.5 uL Tn5 transposase (100 nM final), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, and 5 uL nuclease-free water).
Transposition reactions were incubated at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up using Qiagen MinElute Reaction Cleanup kits and processed as previously described. All libraries were amplified with a target concentration of 20 μl at 4 nM, which is equivalent to 80 femtomoles of product.
All libraries were sequenced on an Illumina NextSeq with 75 bp paired end reads.

value: Patient SU562

value: Bulk


title: D064-NYH-104


description:
Patient SU562 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Old High Fat Diet Batch1 rep1

value: male

value: High fat diet


title: CDK12 KO sgNT-1

description:
CDK12KO
SI_36577
SI_36571-78.cts.csv


title: D063-HTJ-003

value: blood

value: M


description:
Patient SU562 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Blast


title: Old Normal Diet Batch2 rep6

value: Normal Diet


title: D062-YMS-218

value: COPD


title: CDK12 KO sgP53-2

description:
CDK12KO_sgP53
SI_36576
SI_36571-78.cts.csv

value: Cdk12/p53 mutant


title: CDK12 KO sgP53-1

description:
CDK12KO_sgP53
SI_36575
SI_36571-78.cts.csv


title: WT sgP53-2

description:
WT_sgP53
SI_36574
SI_36571-78.cts.csv

value: p53 mutant


title: D061-KHC-762


title: WT sgP53-1

description:
WT_sgP53
SI_36573
SI_36571-78.cts.csv


description:
Patient SU547 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU547

value: Relapse


title: D059-KYS-877


title: D065-KYS-572


description:
Patient SU547 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Old Normal Diet Batch2 rep3


description:
Patient SU547 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


title: D057-PCS-356


title: D058-JJH-903


title: Old Normal Diet Batch1 rep2


title: WT sgNT-2

description:
WT_sgNT
SI_36572
SI_36571-78.cts.csv

value: prostate organoid

value: Epithelial

value: Cdk12 wildtype


description:
Patient SU484 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU484


title: D055-NYG-900


description:
Patient SU547 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: mProstate_+/+; Cre_mTmG_52wk_DVL_repeat

data_processing:
Per-sample FASTQ files were generated from the raw base call files using CellRanger mkfastq. The raw gene count matrices were generated from the FASTQ files using the CellRanger count command and the 10x supplied mm10 reference
Assembly: mm10
Supplementary files format and content: filtered gene by cell count matrix in h5 file

source_name: mouse prostate

extract_protocol:
For tissue scRNA sequencing, mouse prostate was obtained from 52 wk-old animals and cut into small pieces and then digested with 5mg/mL Collagenase II at 37 ℃ for 30 minutes and trypsinzied for 10 min. The tissues were then filtered with 70 µm cell strainers, and then the cells were washed once with PBS
For organoid scRNA sequencing, matrigel was dissociated with disapse and mouse prostate organoids were digested with trypsin at 37 ℃ for 10 minutes. The dissociated cells then passed through 70µm strainer, washed with PBS, and submitted for sequencing
Chromium Next GEM Single Cell 3' HT Kit v3.1 (Dual Index), a product from 10x Genomics, was used following the instructions from the manufacturer.

value: mouse prostate

value: WT


title: D056-LMJ-196

value: blood

value: F


title: Old Normal Diet Batch1 rep1

value: Isolated hepatocytes

value: male


title: Young High Fat Diet Batch2 rep6

value: High fat diet


title: mProstate_KO_52wk_DVL_repeat

value: Cdk12 KO


title: Old Normal Diet Batch2 rep5

value: Normal Diet


title: D054-JYD-781

value: M

value: COPD


title: Young High Fat Diet Batch2 rep5


description:
Patient SU484 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

source_name: AML

value: AML

value: Relapse

value: Blast


description:
Patient SU562 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU562

value: Diagnosis


title: Old Normal Diet Batch2 rep4


title: mProstate_+/+; Cre_mTmG_52wk_DVL


title: Young High Fat Diet Batch2 rep4


title: D053-KMS-169


title: mProstate_KO_52wk_DVL


description:
Patient SU484 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU484


title: mProstate_CDK12KO_BC_Organoid

source_name: mouse prostate organoid

value: mouse prostate organoid

value: Epithelial


title: mProstate_WT_BC_Organoid

value: WT


title: D051-MBG-678

value: blood


description:
Patient SU450 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU450


title: D050-RHS-741


title: WT sgNT-1

description:
WT_sgNT
SI_36571
SI_36571-78.cts.csv

value: prostate organoid

value: Cdk12 wildtype


description:
Patient SU450 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Young High Fat Diet Batch1 rep1

value: Isolated hepatocytes

value: male

value: High fat diet


description:
Patient SU450 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: D049-PSI-068

value: M

value: COPD


title: Lineage traced early postnatal a-SMA+ lung cells

city: Los Angeles

first: Rachana

last: Radhamani Chandran

department: Pediatrics

institute: University of California, Los Angeles - Los Angeles, CA

data_processing:
scRNA-seq data was processed with Cell Ranger v3.1.0. 62.7% of reads were confidently aligned to a modified version of the mouse transcriptome mm10 that includes the sequence for Chandran et al., Supp Methods, p. 3 the gene ZsGreen1. The top cell barcodes selected by Cell Ranger were then utilized for downstream analysis.
All analyses were performed in R (version 3.6.1) using the package Seurat (version 3.1.0). UMI counts were scaled to 10,000 UMIs per cell, then natural log transformed with a pseudo-count of one (log((TPM/100) + 1)). Feature selection, principal component analysis, neighbor embedding and Louvain modularity clustering were recursively performed on the data for the purpose of identifying clusters of discretely identifiable cell populations. Clusters were then annotated as either a multiplet population or known cell type by expert curation of transcriptional marker genes and concordance with the literature. Multiplets were identified as cell populations whose transcriptomic profile resembled a combination of two or more cell populations found in the data. Additionally, cells with less than 900 transcripts or greater than 10% mitochondrial transcripts were removed.
Assembly: mm10
Supplementary files format and content: tsv and matrix

source_name: Adult mouse lung tissue

extract_protocol:
Five Acta2-CreERT2, ROSA26R(Zs/+)mice were injected with 4-OH-TM (200 µg per day) at P6.5, P8.5 and P10.5. At P60.5, lungs were collected, minced and incubated at 37°C for 40 min in the enzyme mixture from Miltenyi Biotec Lung Dissociation Kit. During this incubation, tissue was subjected twice to gentle lung dissociation protocol in a gentleMACS dissociator (Miltenyi Biotec). After inhibiting enzymatic activity with 10% FBS, single cell suspensions from each mouse were pooled together and passed through a 100 µm cell strainer and centrifuged at 700 × gfor 10 min at 4°C. The pellet was washed in 1X PBS with 1% FBS, DAPI (nuclear stain) added to the cell suspension, and Zs+DAPI- cells were isolated by FACS. Trypan blue was used to aid in cell counting. The cells were pooled together in 0.04% bovine serum albumin in PBS and proceeded to library preparation and DropSeq.
Single cell suspension in RT Master Mix (75 μl) was loaded on the Single Cell A Chip     and partitioned with a pool of ~750,000 barcoded gel beads to form nanoliter-scale Gel Beads-    In-Emulsions (GEMs). Each gel bead has primers containing: (i) an Illumina R1 sequence (read    1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI),    and (iv) a poly-dT primer sequence. Upon dissolution of the Gel Beads in a GEM, the primers        were released and mixed and incubated with cell lysate and RT Master Mix, producing barcoded,    full-length cDNA from poly-adenylated mRNA.

treatment_protocol: Enzymatic and Mechanical Digestion

value: Adult mouse lung tissue

value: myofibroblasts/mesenchymal cells

value: tamoxifen


city: Stanford

first: Ravindra

last: Majeti

institute: Stanford University

description:
Patient SU450 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Diagnosis

value: Blast


title: Young Normal Diet Batch2 rep5

value: Normal diet


description:
Patient SU442 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU442

value: Relapse


title: Young High Fat Diet Batch1 rep3


title: Young Normal Diet Batch2 rep6


description:
Patient SU484 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU484


title: Young Normal Diet Batch2 rep4


title: D047-KBS-595

value: blood


title: Young Normal Diet Batch1 rep3


description:
Patient SU442 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


description:
Patient SU442 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: D040-KGB-713

value: F


title: D052-CGH-937


title: D041-JGH-845


title: Young Normal Diet Batch1 rep2

value: Isolated hepatocytes


title: Young High Fat Diet Batch1 rep2

value: male


title: D039-SHS-405


title: D037-KYH-041


title: Young Normal Diet Batch1 rep1


description:
Patient SU383 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Patient SU383


description:
Patient SU442 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: D036-KST-305

value: M


title: SCNd-s, S570

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: University of Zurich

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

data_processing:
Base calling was done using Illumina RTA2
Illumina bc12fastq v2.20 was used for demultiplexing and fastq file generation
Reads were aligned using STAR aligner to GRCm38.p4  to get gene counts (Data-sce-count.txt)
Cells that passed quality control were normalized (Data-sce-normed.txt, Lab-Sara-sce-log.txt)
Differential gene expression was analyzed using DESeq2.
Assembly: GRCm38.p4
Supplementary files format and content: Data-sce-count.txt; raw counts
Supplementary files format and content: Data-sce-normed.txt; normalized counts
Supplementary files format and content: Data-sce-log.txt; log of normalized counts

source_name: interneurons of the suprachiasmatic nucleus

extract_protocol:
single cell extraction via patch pipette
Nextera XT DNA Library Preparation kit

tag: time of_day

value: day

tag: electrophysiology

value: silent

tag: cfos expression

value: cFOS-


title: D032-KYG-874

value: COPD


title: D034-KMC-171


address: 875 Blake Wilbur Dr Clinic F

description:
Patient SU372 Relapse timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU372


title: SCNd+a, S567

value: interneurons of the suprachiasmatic nucleus

value: active

value: cFOS+


title: SCNn-a, S564

value: night


title: SCNn-a, S568


description:
Patient SU383 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis

value: Blast


description:
Patient SU383 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


description:
Patient SU372 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


title: SCNn+s, S562


title: D048-KJS-064

value: blood


title: SCNn+s, S565


title: Hepa1-6 cells: siERRa+siHCFC1 (96h, 200nM) rep3

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

data_processing:
Hisat2 (version 2.0.5) was employed to align the paired-end clean reads to the mouse reference genome mm10.
FeatureCounts (v1.5.0-p3) was used to count the number of reads per gene during the mapping process.
The Fragments per Kilobase of Transcript Sequence per Million Base Pairs Sequenced (FPKM) for each gene were computed based on the gene's length and the read counts mapped to it. Differential expression analysis between two groups (n=3 per group) was carried out using the DESeq2 R package (version 1.20.0) and genes with an adjusted p-value < 0.05 and log2|fold change| ≥ 0.5 were considered significantly altered.
Assembly: mm10
Supplementary files format and content: Excel sheet includes TPM values for all samples (Scholtes_TPM_annotated.xlsx)
Supplementary files format and content: Excel sheets includes dataset comparisons: DESeq2 differential expression analysis with adjusted p-values and fold changes shown (Scholtes_Dataset comparisons.xlsx)

growth_protocol: Hepa 1-6 cells, originally sourced from the ATCC (RRID: CVCL_0327), were maintained in DMEM (319-005-CL, Wisent) supplemented with 10% (v/v) fetal bovine serum (FBS, 12483020, Thermo Fisher Scientific) and 100 units/ml penicillin-streptomycin (450-201-EL, Wisent). Cultured cells were maintained at 37°C with 5% CO2,

extract_protocol:
Total RNA was extracted from frozen Hepa 1-6 cell pellets using the RNeasy Mini kit (74106, QIAGEN) following the manufacturer’s instructions with an on-column DNase digestion step (79254, Qiagen).
The RNA underwent quantification and quality assessment before library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) in accordance with the manufacturer's recommendations at Novogene Bioinformatics Technology Co., Ltd.

treatment_protocol: Hepa 1-6 cells were trypsinized, and 400,000 cells were reseeded in 6 cm plates. Cells were then transfected with 100 nM of either a control pool of scrambled siRNAs (D-001810-01-50, Dharmacon) or siRNAs targeting mouse ERRα (L-040772-00-0050, Dharmacon) or HCFC1 (L-051186-01-0050, Dharmacon). To elaborate, 4 μl of siRNAs were mixed with 37.5 μl of Hiperfect transfection reagent (301707, Qiagen) and enough Optimem Opti-MEM reduced serum medium (31985070, Thermo Fisher) to reach a final volume of 1 ml. This mixture was allowed to incubate at room temperature for 10 min then added to the cells, and media was added to have a final volume of 4 ml, bringing the final siRNA concentration to 100 nM. The siRNA transfection was repeated after 48 h, directly on the attached cells, and the cells were left for another 48h (200 nM siRNA total).

tag: cell line

value: Hepatocyte

tag: genotype

value: WT

tag: treatment

value: siERRa+siHCFC1 (96h, 200nM)


title: D030-LCG-497

value: M


title: SCNn-s, S563

value: silent


title: D029-YDM-743


description:
Patient SU383 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

tag: individual

value: Patient SU383

tag: timepoint


title: SCNn+a, S561


description:
Patient SU372 Diagnosis timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


description:
Patient SU372 Diagnosis timepoint Blast replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: D035-KJW-586

tag: Sex

value: COPD


title: D031-YSB-159


title: SCNn+a, S560


title: D028-PJS-611


title: Hepa1-6 cells: siERRa+siHCFC1 (96h, 200nM) rep2


description:
Patient SU360 Diagnosis timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU360

value: LSC


description:
Patient SU360 Diagnosis timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: SCNn-s, S559

value: interneurons of the suprachiasmatic nucleus

value: cFOS-


title: Hepa1-6 cells: siHCFC1 (96h, 200nM) rep3

value: siHCFC1 (96h, 200nM)


title: Hepa1-6 cells: siHCFC1 (96h, 200nM) rep2


title: D017-JYB-893


title: D018-HSH-578


title: D015-YJY-599

value: F


title: SCNn+s, S557

value: night

value: cFOS+


title: Hepa1-6 cells: siHCFC1 (96h, 200nM) rep1

value: Hepatocyte


description:
Patient SU360 Relapse timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Relapse


description:
Patient SU360 Diagnosis timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis


description:
Patient SU360 Relapse timepoint Bulk replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: Hepa1-6 cells: siERRa (96h, 200nM) rep3

value: WT

value: siERRa (96h, 200nM)


title: Hepa1-6 cells: siERRa (96h, 200nM) rep1


description:
Patient SU360 Relapse timepoint LSC replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds


title: SCNn+s, S558

value: silent


title: D014-KTS-413

value: blood

value: M

value: COPD


title: SCNn+s, S556


title: D013-LJW-868


title: SCNd-a, S553

value: day

value: active


title: SCNn-s, S555

value: interneurons of the suprachiasmatic nucleus


description:
Patient SU360 Relapse timepoint Blast replicate 2 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: AML

value: Patient SU360

value: Blast


title: D011-KJI-926

value: F


title: Hepa1-6 cells: siERRa (96h, 200nM) rep2


description:
Patient SU360 Relapse timepoint Bulk replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Bulk


title: SCNd+a, S551

value: cFOS+


title: Hepa1-6 cells: siERRa+siHCFC1 (96h, 200nM) rep1

value: Hepatocyte

value: siERRa+siHCFC1 (96h, 200nM)


title: Hepa1-6 cells: siC (96h, 200nM) rep1

value: WT


description:
Patient SU360 Diagnosis timepoint LSC replicate 1 ATACseq Sample
bulk_count_matrix_raw.rds
bulk_gene_scores.rds

value: Diagnosis

value: LSC


title: SCNd+s, S549

description:
Data-sce-count.txt
Data-sce-normed.txt
Data-sce-log.txt

value: silent


title: SCNn+s, S552

value: night


title: D009-KYK-670

value: blood

value: M

value: COPD


title: D007-LSB-061