title: rNLS8 4

city: Rochester

first: Shuwen

last: Zhang

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: GEX_S8_ALS-M2
10x Genomics

data_processing:
Single-cell sequence preprocessing was performed using the standard 10x Genomics Cell Ranger Single Cell Software Suite. Raw reads were aligned to the hg38 reference genome, and UMI (unique molecular identifier) counting was performed using Cell Ranger v7.1.0 with default parameters. Seurat v5 was used for all subsequent analyses
Assembly: GRCm38
Supplementary files format and content: seurat rds file (raw data from Cell Ranger output)

source_name: brain

extract_protocol:
Mice were transcardially perfused with cold PBS and cortical regions were quickly dissected and enzymatically digestssss(Miltenyi Biotec, 130-092-628) in the gentleMACS Octo Dissociator with heaters (Miltenyi Biotec) using program 37C_NTDK_1. The myelin was then removed by magnetic bead separation using Myelin Removal Beads II (Miltenyi Biotec, 130-096-733) followed by the red blood cell lysis (Miltenyi Biotec ,130-094-183). Cell suspension was then followed by dead cell removal (Miltenyi Biotec 130-090-101;). The final cell pellet was suspended in Ca/Mg-free PBS with 0.5% BSA, and immediately submitted to the Genome Analysis Core for Single Cell partitioning.
The cells were counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter). The barcoded Gel Beads were thawed from -80 °C and the cDNA master mix was prepared according to the manufacture’s instruction for Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).  Based on the desired number of cells to be captured for each sample, a volume of live cells was mixed with the cDNA master mix.  A per sample concentration of 500,000 cells per milliliter or better is required for the standard targeted cell recovery of up to 10,000 cells. The stock concentration requirements would not change for higher cell recovery numbers. The cell suspension and master mix, thawed Gel Beads and partitioning oil were added to a Chromium Next GEM G chip. The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were partitioned into uniquely labeled GEMs (Gel Beads-In-Emulsion). The GEMs were collected from the chip and taken to the bench for reverse transcription, GEM dissolution, and cDNA clean-up. The resulting cDNA contains a pool of uniquely barcoded molecules. A portion of the cleaned and measured pooled cDNA continues to library construction, where standard Illumina sequencing primers and a unique sample index (Dual Index Kit TT-Set A; 10x Genomics) were added to each cDNA pool, creating gene expression libraries.  All cDNA pools and resulting libraries are measured using Qubit High Sensitivity assays (Thermo Fisher Scientific) and Agilent Bioanalyzer High Sensitivity chips (Agilent).

tag: tissue

value: brain

value: 11 weeks old

value: Male


title: rNLS8 3

status: Public on Sep 22 2025

type: SRA

country: USA

description:
Library name: GEX_S4_ALS-M1
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

treatment_protocol: Dox withdrawal

tag: age

tag: Sex

tag: genotype


title: Multiome, heart, LPS and vehicle,ATAC

city: St. Louis

first: Douglas

last: Mann

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: Heart_LPSandvehicle_ATAC

library_source: genomic single cell

data_processing:
Raw fastq files were aligned using CellRanger ARC to generate fragment files and aligned count matrices
Assembly: mm10
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz

molecule: genomic DNA

source_name: Heart

extract_protocol:
Nuclei were extracted from hearts using the Chromium Nuclei Isolation kit (10x Genomics). For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234, Single Index Kit N Set A, 96 rxns PN-1000212 (ATAC), Dual Index Kit TT Set A, 96 rxns PN-1000215 (3v3.1 GEX), were used.
Multiome 3v3.1 GEX and ATAC libraries were prepared as recommended by 10x Genomics (ChromiumNextGEM Multiome_ATAC_GEX_User_Guide_RevD). The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.

treatment_protocol: Female 10-wk old wild-type (C57BL/6J) mice were injected intraperitoneally with LPS (2.5 mg/kg), b-glucan (1 mg/mouse), 1 ug recombinant interferon-b1/10 ug recombinant interferon-y, or diluent. Mice were then euthanized 7 days later (n=3/group) with hearts collected and used for nuclei isolation and Multiome sequencing (10x Genomics).

value: Heart

tag: cell type

value: Various

value: Wild-type

tag: treatment

value: LPS and vehicle


title: rNLS8 2

description:
Library name: GEX_S7_ALS-F2
10x Genomics

value: Female


title: smRNAseq_Flower_b6_WT_rep2

city: La Jolla

first: Julie

middle: A

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

institute: Salk Institute for Biological Studies

library_source: other

data_processing:
For each sample, fastq files were trimmed using cutadapt (v1.18) with the -a AGATCGGAAGAGC option to remove the adapter sequence and the -m 15 option to discard reads shorter than 15 nt. Clean reads were then mapped to the TAIR10 reference genome using ShortStack (v3.8.5) allowing one mismatch (--mismatches 1). The --mmap f option was also included to assign multiple-mapped reads to a specific locus using the fractional-seeded algorithm. The resulting bam files were then filtered to keep perfectly mapped reads or reads with a single mismatch at the 3’ end using bamtools (v2.5.1) together with an in-house script (JSON_findPerfectMatches_and_TerminalMisMatches_v3) to meet the characteristics of Pol-IV transcription. To facilitate downstream analyses, the filtered bam files were used to generate Tag Directories using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 1 -keepAll. To quantify the expression of smRNAs with specific sizes, the tag directories were split by size (20nt-25nt) using a custom perl script (splitTagDirectoryByLength.dev2.pl) and all subsequent analyses utilized the Tag Directories corresponding to 24nt siRNAs.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

molecule: other

organism: Arabidopsis thaliana

source_name: stage 12 and younger flower buds

growth_protocol: For transgenic lines that required drug selection, seeds were sterilized in sterilization buffer (70% ethanol, 0.05% SDS) for 10 minutes, followed by plating on half strength Linsmaier and Skoog medium (1/2 LS; Caisson Labs, Cat# LSP03) supplemented with 0.6% agar (Phyto Agar, Cat# P1003). The plates were placed in a 4˚C cold room for 4 days before growing in a growth chamber with 16h-light and 8h-dark cycles for 7 days. The seedlings were transplanted and grown under Salk greenhouse conditions. For HEM EMS lines, T-DNA insertion lines, and their corresponding control lines, seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. Approximately five weeks after planting, stage 12 and younger flower buds were collected and frozen in liquid nitrogen.

extract_protocol:
Total RNA extraction and smRNA enrichment was performed following a previously reported protocol. Briefly, 10 μg of total RNA extracted from flower buds (stage 12 and younger) were used for each smRNA library prep.
The smRNA-seq libraries were constructed using the NEBNext Small RNA Library Prep Kit (NEB, Cat# E7330L). The smRNA libraries were further purified using an 8% acrylamide gel and size selected (130-160 bp) relative to the O'RangeRuler 10 bp DNA Ladder (Thermo Scientific, Cat# SM1313). The size selected smRNA libraries were pooled for sequencing with single-end 50 bp kit (SE50) on Illumina Nextseq 2000 or Novaseq X plus platforms.

value: stage 12 and younger flower buds

tag: cultivar

value: Columbia

value: WT

tag: batch

value: experiment batch6


title: Blood neutrophil, 0h, Healthy control, IL-1beta treated, replicate2

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

description:
Library name: IL1B_2
Donor_2

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome (hg38) using Tophat (v2.04)
Counts were generated using featureCounts in R (v3.6.3) profiving the hg38 GTF file (iGenomes)
Assembly: hg38
Supplementary files format and content: Raw gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Neutrophil

growth_protocol: Neutrophils were isolated from whole blood by centrifugation through density-gradient reagent (Polymorphprep). Erythrocytes were removed by hypotonic lysis with ammonium chloride buffer.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen RNAeasy cleanup including on-column DNase digest
50bp Single-end reads

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

value: Neutrophil

value: Healthy

value: 1h IL-1beta (10ng/mL)


title: smRNAseq_Flower_b6_WT_rep1


title: HBCx33 treated with Capecitabine, relapse tumor, biological rep 1

type: RNA

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description: Gene expression data from PDX treated with Capecitabine, relapse tumor

hyb_protocol: 15 µg of fragmented, biotin-labeled cRNA were hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array for 16 hours at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: After hybridization, arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned with the Affymetrix GeneChip Scanner 3000 following the manufacturer’s standard protocols.

data_processing:
Raw Affymetrix CEL files were processed using the GCRMA (GC Robust Multi-array Average) algorithm implemented in the Bioconductor R package `gcrma`. The method performs background correction, quantile normalization, and summarization at the probe set level using the Affymetrix Human Genome U133 Plus 2.0 annotation. The resulting log2-transformed expression values were then exponentiated (2^value) and rounded to the nearest integer to obtain approximate transcript abundance values.
Integer values obtained by applying round(2^x) to log2-transformed GCRMA-normalized signal intensities, resulting in pseudo-counts approximating transcript abundance.

label: biotin

label_protocol: 500 ng of total RNA were used for cDNA synthesis and biotin labeling using the Affymetrix 3’ IVT Express Kit, according to the manufacturer's protocol.

growth_protocol: For PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used a xenograft model generated from two primary triple-negative breast cancer  (HBCx10 and HBCx33) established previously at Institut Curie with informed consent from the patient.

extract_protocol: Total RNA was extracted from tumor samples using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyzer and samples with RIN > 7 were selected for downstream processing.

treatment_protocol: Mice were treated with various methods (Table S2): capecitabine (Xeloda; Roche Laboratories) at a dose of 540 mg/kg, orally 5 d/week, for 25 to 51 days (i.e. pCR); adriamycine (Accord) at 2 mg/kg, intraperitoneal (i.p.)  1×/21 days; cyclophosphamide (Baxter) at 100 mg/kg, i.p. 1×/21 days; cisplatin (Mylan) at 6 mg/kg, i.p. 1×/21 days; or carboplatine (Accord) at 90 mg/kg, i.p. 1x/21 days. Relative tumor volumes (mm3) were measured as described previously. Before downstream analysis, cell suspensions were prepared as previously described (7).

value: Breast

tag: disease

value: TNBC

tag: model

value: patient-derived xenograft (PDX)


title: Blood neutrophil, 0h, Healthy control, IL-8 treated, replicate2

description:
Library name: IL8_2
Donor_2


title: Blood neutrophil, 0h, Healthy control, IFNgamma treated, replicate4

description:
Library name: IFNG_4
Donor_5

value: 1h IFNgamma (10ng/mL)


title: Multiome, heart, LPS and vehicle, GEX

description: Library name: Heart_LPSandvehicle_RNA


title: HBCx33 treated with Capecitabine, residual tumor, biological rep 1

description: Gene expression data from PDX treated with Capecitabine, residual tumor


title: smRNAseq_Flower_b6_3-396


title: Control 3

description:
Library name: GEX_S2_ALS-MC1
10x Genomics

value: brain

value: 11 weeks old

value: Male

value: Control


title: smRNAseq_Flower_b5_WT_rep3

value: experiment batch5


title: rNLS8 1

description:
Library name: GEX_S3_ALS-F1
10x Genomics

value: Female


title: Control 2

description:
Library name: GEX_S5_ALS-FC2
10x Genomics


title: Blood neutrophil, 0h, Healthy control, IFNgamma treated, replicate3

description:
Library name: IFNG_3
Donor_4


title: Blood neutrophil, 0h, Healthy control, IFNgamma treated, replicate2

description:
Library name: IFNG_2
Donor_2


title: smRNAseq_Flower_b5_WT_rep2

value: stage 12 and younger flower buds


title: Control 4

description:
Library name: GEX_S6_ALS-MC2
10x Genomics


title: Blood neutrophil, 0h, Healthy control, IFNgamma treated, replicate1

description:
Library name: IFNG_1
Donor_1


title: Control 1

description:
Library name: GEX_S1_ALS-FC1
10x Genomics


title: nasal-organoids, HNO919line, differentiated, day23, 34C-37Ctreated, rep2

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Raw count and Differentially expressed gene list

growth_protocol: Propagation media +EGF: 10% Noggin, 10%RSPO1, 100ng/ml FGF10, 25ng/ml FGF7, 500nM A83-01, 500nM p38 inhibitor, 5uM Y-27632, 1x B27 supplement,1.25mM N-acetylecystein, 5mM nicotinamide,1x Pen/Strep, 1x hepes, 1x glutamax, DMEMF12, 25ng/ml EGF. Differentiation media: Diff supplement, diff basal media, 0.48ug/ml hydrocortison, 0.01mg/ml heparin solution, 5uM Y-inhibitor

extract_protocol:
Total cellular RNAs were extracted from nasal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer’s protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina’s Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity.
Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 150 bp) was performed on an Illumina HiSeq 4000 for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample.

treatment_protocol: Nasal organoids were seeded on transwells with growth media+ EGF for 4 days. Group 1 of plated organoids were incubated at 34ºC , group 2 in 37ºC and group 3 in 37ºC for 21 days then moved to 34ºC for 2 days. RNA was extracted from undifferentiated (UND) organoids  at day 4, and from diffirentiated organoids after 21 or 23 days.

tag: cell line

tag: differentiation status

value: differentiated

value: mix 34C and 37C

tag: time

value: day 23


title: nasal-organoids, HNO919line, undifferentiated, day4, control, rep1

value: undifferentiated

value: control

value: day 4


title: Blood neutrophil, 0h, Healthy control, IFNalpha treated, replicate2

description:
Library name: IFNA_2
Donor_5

value: Neutrophil

value: Healthy

value: 1h IFNalpha (10ng/mL)


title: smRNAseq_Flower_b5_WT_rep1

value: Columbia

value: WT


title: HBCx33 treated with Capecitabine, residual tumor, biological rep 2

source_name: PDX treated with Capecitabine, residual tumor

value: Breast

value: TNBC

value: patient-derived xenograft (PDX)


title: nasal-organoids, HNO919line, differentiated, day23, 34C-37Ctreated, rep1


title: uterus, Zmiz1-cKO-E24h-9

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description:
Library name: Zmiz1-cKO-E24h-9
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-E24-9_20240403_122501.L022

data_processing:
FASTQ files were imported into Partek Flow (Illumina), aligned to mm10 using Bowtie 2, then quantified to Refseq genes.
counts were normalized
RNA was isolated in 2 different batches, and batch numbers 1 and 2 were assigned to samples from either isolation
Normalized reads were batch corrected
Assembly: mm10
Supplementary files format and content: tab delimited text file containing normalized batch corrected counts exported  from Partek Flow analysis into a single file.

source_name: uterus

growth_protocol: PgrCre mice were intercrossed with Zmiz1-flox (Zmiz1-f/f) mice to produce mice with uterine Zmiz1 deletion (Zmiz1-cKO or Zmiz1-d/d). Ovariectomized mice were held for 10-14 days to allow endogenous hormones to clear.

extract_protocol:
Trizol (Thermo Fisher) was used to isolate RNA from  uterine tissue according to the manufacturer’s protocol. Following chloroform extraction, RNA was prepared from the aqueous layer using the Direct-zol RNA Miniprep Kit (Zymo Research).
Libraries were made using the Illumina Tru Seq Stranded mRNA kit. Several libraries were re-sequenced to obtain additional reads. Reads from both technical replicates were combined for analysis

treatment_protocol: Mice were intra-peritoneally injected with 100 µl of saline vehicle (V; Sigma) or saline containing 2.5 µg/ml of estradiol (E). 22 hours later EdU (100 µl of a 2 mg/ml solution in PBS; Thermo Fisher) was administered by intra-peritoneal injection and uterine tissue was collected 2 hours later and frozen.

value: uterus


title: uterus, Zmiz1-cKO-E24h-8

description:
Library name: Zmiz1-cKO-E24h-8
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-E24-8_20240403_122501.L021


title: nasal-organoids, HNO919line, differentiated, day21, 37Ctreated, rep2

value: day 21


title: Blood neutrophil, 0h, Healthy control, IL-1beta treated, replicate1

description:
Library name: IL1B_1
Donor_1

value: 1h IL-1beta (10ng/mL)


title: Blood neutrophil, 0h, Healthy control, IFNalpha treated, replicate1

description:
Library name: IFNA_1
Donor_7


title: smRNAseq_Flower_b5_pRIM22_RIM22-3xFLAG_line2

value: stage 12 and younger flower buds

value: experiment batch5


title: uterus, Zmiz1-cKO-E24h-7

description:
Library name: Zmiz1-cKO-E24h-7
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-E24-7_20240403_122501.L020


title: nasal-organoids, HNO919line, undifferentiated, day4, control, rep2


title: nasal-organoids, HNO919line, differentiated, day21, 37Ctreated, rep1

value: differentiated


title: smRNAseq_Flower_b5_pRIM22_RIM22-3xFLAG_line1


title: Blood neutrophil, 0h, Healthy control, GM-CSF treated, replicate4

description:
Library name: GMCSF_4
Donor_5

value: 1h GM-CSF (5ng/mL)


title: nasal-organoids, HNO919line, differentiated, day21, 34Ctreated, rep2


title: smRNAseq_Flower_b5_4-336


title: uterus, Zmiz1-cKO-E24h-5a

description:
Library name: Zmiz1-cKO-E24h-5a
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-E24-5a_20240403_122501.L019


title: Blood neutrophil, 0h, Healthy control, GM-CSF treated, replicate3

description:
Library name: GMCSF_3
Donor_4


title: Blood neutrophil, 0h, Healthy control, GM-CSF treated, replicate2

description:
Library name: GMCSF_2
Donor_3


title: smRNAseq_Flower_b4_WT_rep3

value: experiment batch4


title: nasal-organoids, HNO919line, differentiated, day21, 34Ctreated, rep1


title: uterus, Zmiz1-cKO-E24h-5

description:
Library name: Zmiz1-cKO-E24h-5
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-E24-5_20240403_122501.L018


title: uterus, Zmiz1-cKO-E24h-3

description:
Library name: Zmiz1-cKO-E24h-3
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-E24-3_20240403_122501.L017


title: Blood neutrophil, 0h, Healthy control, GM-CSF treated, replicate1

description:
Library name: GMCSF_1
Donor_6


title: nasal-organoids, HNO918line, undifferentiated, day4, control, rep2

value: undifferentiated

value: control

value: day 4


title: smRNAseq_Flower_b4_WT_rep2


title: uterus, Zmiz1-cKO-V-8

description:
Library name: Zmiz1-cKO-V-8
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-V8_20240403_122501.L016

value: V


title: smRNAseq_Flower_b5_pRIM22_RIM22-3xFLAG_line3

value: Columbia


title: Blood neutrophil, 0h, Healthy control, G-CSF treated, replicate3

description:
Library name: GCSF_3
Donor_4

value: Neutrophil

value: Healthy

value: 1h G-CSF (10ng/mL)


title: Blood neutrophil, 0h, Healthy control, G-CSF treated, replicate2

description:
Library name: GCSF_2
Donor_2


title: uterus, Zmiz1-cKO-V-7

description:
Library name: Zmiz1-cKO-V-7
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-V7_20240403_122501.L015


title: nasal-organoids, HNO918line, differentiated, day23, 34C-37Ctreated, rep2

value: mix 34C and 37C

value: day 23


title: smRNAseq_Flower_b4_rim-cr_rep2

value: rim-cr


title: uterus, Zmiz1-cKO-V-6

description:
Library name: Zmiz1-cKO-V-6
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-V6_20240403_122501.L014

value: uterus


title: Blood neutrophil, 0h, Healthy control, G-CSF treated, replicate1

description:
Library name: GCSF_1
Donor_1


title: nasal-organoids, HNO918line, differentiated, day23, 34C-37Ctreated, rep1


title: smRNAseq_Flower_b4_rim-cr_rep1

value: stage 12 and younger flower buds


title: uterus, Zmiz1-cKO-V-5

description:
Library name: Zmiz1-cKO-V-5
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-V5_20240403_122501.L013


title: nasal-organoids, HNO918line, differentiated, day21, 37Ctreated, rep2

value: day 21


title: Blood neutrophil, 0h, Healthy control, untreated, replicate6

description:
Library name: UT_6
Donor_6

value: 1h untreated


title: smRNAseq_Flower_b4_rim22-2


title: Blood neutrophil, 0h, Healthy control, untreated, replicate5

description:
Library name: UT_5
Donor_5


title: uterus, Zmiz1-cKO-V-4

description:
Library name: Zmiz1-cKO-V-4
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-V4_20240403_122501.L012


title: nasal-organoids, HNO918line, differentiated, day21, 37Ctreated, rep1

value: differentiated


title: smRNAseq_Flower_b4_rim16,22_rep2

value: experiment batch4


title: smRNAseq_Flower_b4_rim16,22_rep1


title: nasal-organoids, HNO918line, differentiated, day21, 34Ctreated, rep2


title: uterus, Zmiz1-f/f-E24h-10

description:
Library name: Zmiz1-f/f-E24h-10
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-E24-10_20240403_122501.L010


title: uterus, Zmiz1-cKO-V-2

description:
Library name: Zmiz1-cKO-V-2
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-cKO-V2_20240403_122501.L011


title: Blood neutrophil, 0h, Healthy control, untreated, replicate4

description:
Library name: UT_4
Donor_4


title: nasal-organoids, HNO918line, undifferentiated, day4, control, rep1

value: undifferentiated


title: smRNAseq_Flower_b4_WT_rep1

value: WT


title: smRNAseq_Flower_b4_rim16,22,rim-cr_rep2


title: Blood neutrophil, 0h, Healthy control, untreated, replicate3

description:
Library name: UT_3
Donor_3


title: Blood neutrophil, 0h, Healthy control, untreated, replicate2

description:
Library name: UT_2
Donor_2


title: uterus, Zmiz1-f/f-E24h-9

description:
Library name: Zmiz1-f/f-E24h-9
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-E24-9_20240403_122501.L009


title: Blood neutrophil, 0h, Healthy control, untreated, replicate1

description:
Library name: UT_1
Donor_1


title: smRNAseq_Flower_b4_rim16,22,rim-cr_rep1


title: nasal-organoids, HNO918line, differentiated, day21, 34Ctreated, rep1


title: uterus, Zmiz1-f/f-E24h-8

description:
Library name: Zmiz1-f/f-E24h-8
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-E24-8_20240403_122501.L008


title: nasal-organoids, HNO204line, undifferentiated, day4, control, rep2

value: control

value: day 4


title: nasal-organoids, HNO204line, undifferentiated, day4, control, rep1


title: uterus, Zmiz1-f/f-E24h-7

description:
Library name: Zmiz1-f/f-E24h-7
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-E24-7_20240403_122501.L007


title: smRNAseq_Flower_b4_pol-iv

value: Columbia

value: pol-iv


title: nasal-organoids, HNO204line, differentiated, day23, 34C-37Ctreated, rep2


title: Jak2V617F LT-HSC, vehicle, rep6

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

description: Library name: VFV63_S3

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCM38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Assembly: GRCM38
Supplementary files format and content: RSEM expected read counts

source_name: Bone marrow

growth_protocol: Chimeric Jak2fl-V617F/+, Tg(E2A-cre) recipients were generated by lethally irradiating Ptprcaa/b C57BL/6J mice with 11Gray of whole-body ionising radiation, given as two doses of 5.5Gray delivered 3 hours apart. Within 24hrs post irradiation, mice were transplanted with 2,000,000 whole BM cells isolated from a Jak2fl-V617F/+, Tg(E2A-cre) and a congenic Jak2+/+ donor (Prprca/a) and combined at a 1:1 ratio, in 200ul L-15 media (Gibco) via tail vein injection. Mice were maintained on Baytril 50 (100mg/L, Elanco) drinking water for 2 weeks post-transplant. Engraftment was confirmed via peripheral blood analysis after 4 weeks post-transplant, prior to commencement of treatment. For the isolation of HSPC populations, red blood cells in the BM cell suspension were lysed with BD Pharmlyse (BD Bioscience). The remaining cell suspensions were depleted of mature haematopoietic cells using a cocktail of biotin conjugated antibodies, consisting of anti-mouse TER-119 (BioLegend 116204), Gr-1 (BioLegend 108404), CD11b (BioLegend 101204), B220 (BioLegend 103204), CD3 (BioLegend 100304) and CD5 (BioLegend 100604), and BD IMag Streptavidin Particles Plus (BD Biosciences 557812). HSPC populations were identified using APC-Cy7 conjugated streptavidin (BioLegend 405208), PE-Cy7 conjugated anti mouse Sca1 (BioLegend 108114). APC conjugated anti mouse c-Kit (BioLegend 105812). LT-HSC populations were further discriminated using BV605 conjugated anti mouse CD150 (BioLegend 115927) and Pacific Blue conjugated anti mouse CD48 (BioLegend 103418). Congenic cell populations were discriminated using Alexa Fluor 700 conjugated anti mouse CD45.1 (BioLegend 110723) and BD Horizon V500 conjugated anti mouse CD45.2 (BD Biosciences 562129).  Cell sorting was performed using the BD FACSAria using FACS Diva Software (version 8.0.1).

extract_protocol:
LT-HSCs were isolated on a BD FACSAria and sorted directly in 50ul of Extraction Buffer from the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). RNA was then isolated according to the kit manufacturer’s instructions. Samples were quantitated using a Qubit RNA HS Assay Kit (Molecular Probes), with integrity confirmed using the RNA 6000 PICO Kit (Agilent Technologies) and Agilent 2100 Bioanalyser (Agilent Technologies).
Oligo d(T) captured mRNA (100 μg) was processed for Next Generation Sequencing (NGS) using the NEB Next Ultra II RNA Library Prep Kit for Illumina (NewEngland Biolabs). Quality was assessed using the High Sensitivity DNA Kit (Agilent) on the Agilent 2100 Bioanalyser with quantification using the Qubit DNA HS Assay Kit (Molecular Probes). Final libraries were sequenced using a high output single-end 75 bp flow cell (version 2) on the Illumina Nextseq 550 platform using NextSeq System Suite (version 2.1.2).

treatment_protocol: Mice were treated weekly with 600ng pegylated interferon alpha (pegIFNa, PharmaEssentia) in 200ul of 0.1% bovine serum albumin (BSA)/phosphate buffered saline (PBS) via subcutaneous injection. Recipients were treated with either vehicle (PBS/0.1%BSA) or pegIFNa weekly for a total of 5 doses over 4 weeks. LT-HSCs were isolated from the bone marrow of recipient mice at 48 hours post administration of the final dose of pegIFNa.

value: Bone marrow

value: long-term haematopoietic stem cells

value: C57Bl/6N Jak2V617F/+ Tg(E2A-cre)

value: vehicle


title: uterus, Zmiz1-f/f-E24h-6

description:
Library name: Zmiz1-f/f-E24h-6
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-E24-6_20240403_122501.L006


title: Jak2V617F LT-HSC, vehicle, rep5

description: Library name: VFV61_S2


title: smRNAseq_Flower_b4_clsy4


title: uterus, Zmiz1-f/f-V-9

description:
Library name: Zmiz1-f/f-V-9
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-V9_20240403_122501.L005

value: V


title: nasal-organoids, HNO204line, differentiated, day23, 34C-37Ctreated, rep1

value: mix 34C and 37C

value: day 23


title: Jak2V617F LT-HSC, vehicle, rep4

description: Library name: VFV44_S1


title: smRNAseq_Flower_b4_clsy3,4

value: stage 12 and younger flower buds


title: nasal-organoids, HNO204line, differentiated, day21, 37Ctreated, rep2

value: day 21


title: Jak2V617F LT-HSC, vehicle, rep3

description: Library name: VFV43_S3


title: uterus, Zmiz1-f/f-V-8

description:
Library name: Zmiz1-f/f-V-8
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-V8_20240403_122501.L004

value: uterus


title: smRNAseq_Flower_b4_clsy3

value: experiment batch4


title: uterus, Zmiz1-f/f-V-7

description:
Library name: Zmiz1-f/f-V-7
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-V7_20240403_122501.L003


title: nasal-organoids, HNO204line, differentiated, day21, 37Ctreated, rep1

value: differentiated


title: Jak2V617F LT-HSC, vehicle, rep2

description: Library name: VFV42_S2


title: smRNAseq_Flower_b4_clsy1,2


title: nasal-organoids, HNO204line, differentiated, day21, 34Ctreated, rep2


title: Jak2V617F LT-HSC, vehicle, rep1

description: Library name: VFV41_S1


title: uterus, Zmiz1-f/f-V-6

description:
Library name: Zmiz1-f/f-V-6
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-V6_20240403_122501.L002


title: nasal-organoids, HNO204line, differentiated, day21, 34Ctreated, rep1


title: smRNAseq_Flower_b4_rim16


title: smRNAseq_Flower_b3_WT_rep3

value: WT

value: experiment batch3


title: Jak2V617F LT-HSC, pegIFNa, rep6

description: Library name: VFP53_S9

value: pegIFNa


title: uterus, Zmiz1-f/f-V-5

description:
Library name: Zmiz1-f/f-V-5
column name in Partek_PrCrexZmiz1-flox_E24_uterus_additional_reads_General_linear_model_Batch_effect_adjusted_counts: NOVA0611.Zmiz1-ff-V5_20240403_122501.L001


title: smRNAseq_Flower_b3_WT_rep2

value: Columbia


title: Mouse embryos, 20h p53 inhibition, rep2

city: Pokfulam

first: Yunying

last: Huang

state: Hong Kong

address: Rm503, JCBIR, 5 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: Ms embryos_20h p53 inhibition_rep2

data_processing:
Raw data of RNA-seq was processed using the current best practice pipeline implemented in nfcore.
Sequence reads were mapped to mm10 mouse reference genome or hg38 human reference genome.
RSEM was applied to estimate gene expression levels with default settings.
Assembly: mm10; hg38 human genome
Supplementary files format and content: comma-separated values file or tab-delimited file including raw counts for each sample

source_name: Embryo

extract_protocol:
Total RNA was harvetsed using Trizol reagents 1.0µg of total RNA was used for the construction of sequencing libraries.
RNA libraris for RNA-seq were prepared using magnetic beads for mRNA enrichment followed by cDNA synthesis, adapter ligation and PCR amplification.

value: Embryo

value: p53 inhibition


title: Veh-Mor-S16

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

description: Library name: Veh-Mor-S16

data_processing:
All raw fastq files were aligned to the Ensembl mRatBn7.2 (Rn7) genome using CellRanger v9.0.1 with the associated Ensembl gene transfer format (gtf) file (version 105) modified to add annotation for the Xist gene. CellRanger filtered outputs were analyzed with Seurat v5.2.1 in R v4.4.0.
To filter out background contamination, cell-free ambient RNA was removed using SoupX v.1.6.2. Next, we continued quality filtering in R with Seurat v.5.2.1 by removing nuclei containing <200 genes and >5% of reads mapping to the mitochondrial genome (50,449 nuclei post-processing). The counts data for each individual were then normalized, scaled by a factor of 10,000, and log-transformed. Heterotypic doublets were identified and removed using scDblFinder with the default expected doublet rate of 1% per 1,000 cells. Cell sex was predicted using a logistic regression model, which was trained and validated using previously published rat VTA snRNA-seq data (CITE Twa et al BioRxiv). A classification threshold for cell sex predicted probabilities from 0.25-0.75 was used to exclude cells with low confidence predictions from analysis.
For each sample, we used Seurat to determine the 2,000 genes with highest cell-to-cell variability. We then integrated the individual datasets in Harmony, using the PCA cell embeddings with 50 principal components (PCs). Downstream analysis was performed on the integrated dataset.
Expression for each gene in the integrated dataset was scaled to a mean of 0 and variance of 1 across cells. We first performed dimensionality reduction via PCA retaining 20 PCs, followed by UMAP with the 20 previously identified PCs as input. Cells were then clustered under a graph-based approach by first identifying K-nearest neighbors in PCA space, and then clustering under a Louvain algorithm with a resolution of 0.4. After removing additional low-quality cells, we repeated the dimensionality reduction and clustering steps. We annotated the resulting clusters as specific cell types based on known marker genes from previous work and the Allen Institute's Whole Mouse Brain taxonomy via the MapMyCells web interface.
Differential expression analyses were conducted within each cell type cluster using pseudobulking expression of each GEM well split by predicted sex using DESeq2 likelihood-ratio test. To test the effect of CFA on the transcriptome, CFA(+) (CFA(+)/Mor(-) and CFA(+)/Mor(+)) pseudobulked sample transcriptomes were compared to CFA negative (CFA(-)/Mor(+) and CFA(-)/Mor(-)). For DESeq2 the formula for the full model was ~ CFA, and the reduced model was ~ 1. When testing with adjustment for sex, the full model was ~ CFA + Sex, and the reduced model was ~ Sex. Tests for the effect of morphine with and without adjustment for sex were carried out likewise. To test the interaction effect of treatment the formula for the full model was ~ CFA + Morphine + CFA:Morphine , and ~ CFA + Morphine for the reduced model. Similarly, when testing with adjustment for sex, the full model was ~Sex + CFA + Morphine + CFA:Morphine, and the reduced model was ~Sex + CFA + Morphine. DESeq2 was run using `fittype = local` but otherwise default parameters. This parameter was chosen as the mean absolute residual of the local model was smaller than the default parametric model in all cell types, indicating a better dispersion model fit. For all cell types the sample size was N = 6 (Mor(+)) or N = 8(Mor(-)) per treatment-sex for both analyses unless noted otherwise below. We excluded from analysis the following cell type groups because they did not have at least two CFA(-)/Mor(-) pseudobulk samples from independent GEM wells: Ependymal and Glut.3. For each cell type, genes with <5 total counts were excluded from testing.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

organism: Rattus norvegicus

source_name: ventral tegmental area

growth_protocol: Male and female 8-12 week old adult Sprague-Dawley rats (~200-300g) were purchased from Charles River Laboratories (Wilmington, MA) and pair-housed in an AAALAC-approved animal care facility during the experiment. Rats were maintained on a 12 h light/dark cycle with ad libitum access to food and water and were briefly handled for 3 days prior to beginning baseline Von Frey measurements (1-2min/day) to acclimate them to the experimenters. All experimental procedures were approved by the University of Alabama at Birmingham Institutional Animal Care and Use Committee and were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
One hour after systemic injections of saline or morphine (10mg/kg) rats were euthanized by live decapitation and whole brains were briefly flash frozen in 2-methyl butane. Chilled brains were then blocked into 1-mm-thick coronal sections on a combination of dry and wet ice. Sections containing the VTA (ranging from -4.92-6.46 anterior-posterior (AP) to Bregma) were transferred to glass microscope slides on dry ice, and the VTA was microdissected away from neighboring brain regions (n = 3-4/sex/treatment group). Dissected VTA tissue was then transferred to ice-cold centrifuge tubes, and stored at -80°C until the day of 10X GEM capture. Frozen microdissected VTA tissue was prepared as previously described (Phillips et al., 2022). Briefly, tissue was thawed on wet ice and chopped with a scalpel prior to being transferred to 5 ml of ice cold lysis buffer (10 mM tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal in nuclease-free water (Sigma-Aldrich, 18896-50ML). After 15 min the lysis was quenched with 5 ml of complete Hibernate A media (Thermo Fisher Scientific, A1247501) supplemented with B27, GlutaMAX (Life Technologies, 35050-061), and NxGen RNase Inhibitor (0.2 U/m; Lucigen, 30281-2). Tissue was then triturated by fire-polished Pasteur pipette (three pipettes of decreasing diameter) and filtered with a 40µm pre-wet cell strainer. Samples were pelleted and then washed in nuclei wash and resuspension buffer (phosphate-buffered saline (PBS), 1% bovine serum albumin (BSA), and NxGen RNase Inhibitor). The resulting pellet was resuspended in 800 ml of wash buffer and 7-aminoactinomycin D (7-AAD; Thermo Fisher Scientific, 00-6993-50) was added prior to fluorescence-activated cell sorting (FACS) on a FACSAria instrument (70 µm nozzle, BD Biosciences). Immediately after FACS, nuclei were washed a final time at 250 rcf in 10 ml of supplemented Hibernate A containing 1% BSA and RNase Inhibitor for 5 min at 4C. Nuclei were brought to a concentration of 1,000 nuclei/µL. A total of 8,000 nuclei pooled from two rats (4,000 male nuclei/4,000 female nuclei from the same treatment group) and were loaded into individual wells of the Chromium NextGem Single Cell Chip (10x Genomics, catalog no. 10000121).
Libraries were constructed according to manufacturer’s instructions for Chromium Next GEM single cell 3’ library and gel bead kit (10x Genomics, v3.1 single index, catalog no. 10000121, version 3 chemistry)

treatment_protocol: To assess neuropathic pain response, Complete Freund’s Adjuvant (CFA; Sigma Aldrich, St. Louis, MO) or saline vehicle (100 µl) was injected into the plantar surface of one hind paw of male and female rats (n = 3-4/sex/treatment group). Mechanical sensitivity was then evaluated 48 hours and 7 days after the injection using the Von Frey assay. Morphine (10mg/kg) or saline was administered I.P. 7 days after CFA treatment, creating a 2x2 experimental design.

value: ventral tegmental area

value: 2-3 months

value: pooled male and female

tag: animal no.

value: 1 Male, 1 Female

tag: strain

value: Sprague-Dawley

value: Vehicle, Morphine


title: smRNAseq_Flower_b3_WT_rep1

value: stage 12 and younger flower buds


title: Jak2V617F LT-HSC, pegIFNa, rep4

description: Library name: VFP50_S9

value: Bone marrow

value: long-term haematopoietic stem cells

value: C57Bl/6N Jak2V617F/+ Tg(E2A-cre)


title: Mouse embryos, 20h p53 inhibition, rep1

description: Ms embryos_20h p53 inhibition_rep1


title: smRNAseq_Flower_b3_salk_107926


title: CFA-Sal-S15

description: Library name: CFA-Sal-S15

value: CFA, Saline


title: Mouse embryos, 20h DMSO, rep2

description: Ms embryos_20h DMSO_rep2

value: DMSO


title: Jak2V617F LT-HSC, pegIFNa, rep3

description: Library name: VFP40_S7


title: Veh-Sal-S14

description: Library name: Veh-Sal-S14

value: Vehicle, Saline


title: smRNAseq_Flower_b3_rim16

value: experiment batch3


title: Jak2V617F LT-HSC, pegIFNa, rep2

description: Library name: VFP30_S8

value: pegIFNa


title: Mouse embryos, 20h DMSO, rep1

description: Ms embryos_20h DMSO_rep1

value: Embryo


title: CFA-Mor-S13

description: Library name: CFA-Mor-S13

value: CFA, Morphine


title: smRNAseq_Flower_b3_cs828917

value: Columbia


title: smRNAseq_Flower_b3_clsy3,4


title: CFA-Sal-S12

description: Library name: CFA-Sal-S12

value: ventral tegmental area

value: 2-3 months


title: in vitro cells, Tgfb + FGF treated, day 6

city: Boston

first: April

middle: M

last: Craft

state: MA

address: 320 Longwood Ave

department: Orthopedic Surgery

institute: Harvard Medical School

description: 1 Week TGFB + bFGF

data_processing:
the Cell Ranger pipeline v3 was used to process the fastq files and generate the count matrix. scVelo was used to generate spliced and unspliced count matrix from the 10x output.
the cellranger reference transcriptome was modified to include the sequences for EGFP, tdRFP, and LacZ
Assembly: mm10
Supplementary files format and content: count matrix  for each sample in the loom format

source_name: in vitro derived mesoderm

growth_protocol: in vitro derived mesoderm was maintained in high density cell culture. Media was comprised of high glucose DMEM with ITS, ascorbic acid, proline, and dexamethasone. Cells were additionally cultured with antibiotics and kept in a 5% CO2 incubator

extract_protocol:
Both microdissected limb paddes and high density cell cultures were dissociated using collagenase supplemented with DNAse. We confirmed that the viability of the cells post dissociation was greater than 80%. Cells were counted and loaded onto the 10X chip following the 10x v3.1 protocol
RNA libraries were prepared using the 10x Chromium v2 3' kit following the manufacturer's protocols

treatment_protocol: Cells were treated on day 2 with a combination of TGFB, IWP2, PD, and FGF2. TGFB was maintained for the duration of culture while IWP2, PD, and FGF2 were removed after Day 6. in vivo cells were obtained through microdissections of the limb paddles. Limb paddles were this dispered to single cells and sequenced

value: in vitro derived mesoderm

value: Gdf5-RFP / PRG4-GFP

value: TGFB + FGF

value: Day 6


title: smRNAseq_Flower_b3_clsy1,2

value: stage 12 and younger flower buds


title: Veh-Sal-S11

description: Library name: Veh-Sal-S11

value: pooled male and female

value: 1 Male, 1 Female

value: Sprague-Dawley


title: Veh-Sal-S8

description: Library name: Veh-Sal-S8


title: in vivo mouse limb bud, forelimb, E14, rep 2

description: Mouse E14 autopod

source_name: mouse limb bud

value: mouse limb bud

value: WT


title: WT LT-HSC, vehicle, rep5

description: Library name: WTV61_S5

value: Bone marrow

value: long-term haematopoietic stem cells

value: C57Bl/6N Ptprca

value: vehicle


title: Jak2V617F LT-HSC, pegIFNa, rep5

description: Library name: VFP52_S7

value: C57Bl/6N Jak2V617F/+ Tg(E2A-cre)

value: pegIFNa


title: smRNAseq_Flower_b2_WT_rep3

value: Columbia

value: experiment batch2


title: CFA-Mor-S7

description: Library name: CFA-Mor-S7

value: ventral tegmental area

value: 2-3 months

value: CFA, Morphine


title: in vitro cells, Tgfb treated, day 6

description: 1 Week TGFB

value: in vitro derived mesoderm

value: Gdf5-RFP / PRG4-GFP

value: TGFB

value: Day 6


title: WT LT-HSC, vehicle, rep4

description: Library name: WTV44_S4


title: in vitro cells, Tgfb + PD treated, day 6

description: 1 Week TGFB + PD

value: PD + TGFB


title: in vivo mouse limb bud, forelimb, E14, rep1

description: Mouse E14 Hindlimb

value: mouse limb bud

value: WT


title: Veh-Mor-S6

description: Library name: Veh-Mor-S6

value: pooled male and female

value: 1 Male, 1 Female

value: Sprague-Dawley

value: Vehicle, Morphine


title: smRNAseq_Flower_b2_WT_rep1

value: stage 12 and younger flower buds


title: WT LT-HSC, vehicle, rep3

description: Library name: WTV43_S6

value: Bone marrow

value: long-term haematopoietic stem cells

value: C57Bl/6N Ptprca

value: vehicle


title: CFA-Sal-S5

description: Library name: CFA-Sal-S5

value: ventral tegmental area

value: 2-3 months

value: CFA, Saline


title: Jak2V617F LT-HSC, pegIFNa, rep1

description: Library name: VFP10_S8

value: C57Bl/6N Jak2V617F/+ Tg(E2A-cre)

value: pegIFNa


title: smRNAseq_Flower_b2_rim22-3

value: Columbia

value: experiment batch2


title: WT LT-HSC, vehicle, rep1

description: Library name: WTV41_S4


title: WT LT-HSC, vehicle, rep2

description: Library name: WTV42_S5


title: in vitro cells, Tgfb treated, day 12

description: 2 Week TGFB

value: in vitro derived mesoderm

value: Gdf5-RFP / PRG4-GFP

value: TGFB

value: Day 12


title: smRNAseq_Flower_b2_rim22-2


title: CFA-Mor-S4

description: Library name: CFA-Mor-S4

value: pooled male and female

value: 1 Male, 1 Female

value: Sprague-Dawley

value: CFA, Morphine


title: Veh-Mor-S3

description: Library name: Veh-Mor-S3

value: Vehicle, Morphine


title: WT LT-HSC, vehicle, rep6

description: Library name: WTV63_S6

value: Bone marrow

value: long-term haematopoietic stem cells

value: C57Bl/6N Ptprca

value: vehicle


title: in vitro cells, Tgfb + PD treated, day 12

description: 2 Week TGFB + PD

value: PD + TGFB


title: WT LT-HSC, pegIFNa, rep6

description: Library name: WTP53_S12

value: pegIFNa


title: in vitro cells, Tgfb + IWP treated, day 12

description: 2 Week TGFB + IWP2

value: IWP2 + TGFB


title: WT_2

city: shanghai

first: jingminjie

state: CN

address: shanghai

country: China

institute: Ruijin Hospital

data_processing:
Bowtie2 (v2.3.4) was applied to align the clean reads to the UCSC mm10 genome reference.
Expression level of gene was calculated by RSEM (v1.3.1). Differential expressed gene (DEG) analysis was performed by DESeq2 R package. DEGs were defined as P-value < 0.05 and absolute log2 (fold change) ≥ 0.3.
Assembly: mm10

source_name: Pancreas

extract_protocol:
Total RNA was extracted from freshly isolated islets and livers of Zzef1_KOand WT mice using RNeasy Micro kit (Qiagen), and sample qualities were assessed using an Agilent Bioanalyzer 2100 (Agilent technologies). 2 mg of total RNA samples of each group were then used.
Sequencing libraries were constructed using the BGISEQ-500 platform (BGI, China). Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS). We included at least 3 independent biological replications.

value: Pancreas

value: islets

value: WT

value: normal chow diet


title: LTL331 Subcutaneous Human PDX in Mouse

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

library_source: genomic

data_processing:
Reads trimmed with trim_galore EM-Seq protocol from Bismark manual
Reads aligned with bismark to concatref genome of hg19, puc19, lambda phage, and mm10
Aligned reads deduplicated with bismark
Human reads extracted using CONCATREF methodology (to remove mouse reads and spike in controls)
Methylation bedGraphs generated with bismark_methylation_extractor
Methylation bedGraphs converted to bigWig with Kent tools bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: methylation bigWigs
Library strategy: EM-seq

source_name: Prostate adenocarcinoma from patient-derived xenograft in mouse

growth_protocol: Xenografts grown in the renal capsule or subcutaneously in the flank of mice

extract_protocol:
Dneasy
EM-seq, NEB

treatment_protocol: Castration surgery

tag: timepoint

value: Subcutaneous


title: CFA-Sal-S2

description: Library name: CFA-Sal-S2

value: ventral tegmental area

value: 2-3 months

value: pooled male and female

value: CFA, Saline


title: smRNAseq_Flower_b2_pCLSY3_CLSY3-3xFLAG_clsy3

value: stage 12 and younger flower buds

value: Columbia

value: experiment batch2


title: WT LT-HSC, pegIFNa, rep5

description: Library name: WTP52_S10

value: Bone marrow

value: long-term haematopoietic stem cells

value: C57Bl/6N Ptprca


title: WT_3


title: smRNAseq_Flower_b2_WT_rep2


title: in vivo mouse limb bud, forelimb, E12

description: Mouse E12 Forelimb

value: mouse limb bud


title: smRNAseq_Flower_b2_clsy3,4


title: smRNAseq_Flower_b2_clsy4


title: Veh-Sal-S1

description: Library name: Veh-Sal-S1

value: 1 Male, 1 Female

value: Sprague-Dawley

value: Vehicle, Saline


title: LTL331R Subcutaneous Human PDX in Mouse

value: Prostate adenocarcinoma from patient-derived xenograft in mouse


title: Zzef1_KO_4

value: Pancreas

value: islets

value: Zzef1 knockout

value: normal chow diet


title: WT LT-HSC, pegIFNa, rep3

description: Library name: WTP40_S10

value: pegIFNa


title: LTL331 8 Weeks Post-Castration Renal Capsule Human PDX in Mouse

value: 8 Weeks Post-Castration


title: smRNAseq_Flower_b2_clsy3

value: stage 12 and younger flower buds


title: WT LT-HSC, pegIFNa, rep2

description: Library name: WTP30_S11


title: smRNAseq_Flower_b1_WT_rep2

value: Columbia

value: WT

value: experiment batch1


title: smRNAseq_Flower_b2_clsy1,2

value: experiment batch2


title: LTL331 2 Weeks Post-Castration Renal Capsule Human PDX in Mouse

value: 2 Weeks Post-Castration


title: smRNAseq_Flower_b2_pol-iv

value: pol-iv


title: Zzef1_KO_2


title: Lung, Single dose BLEO-IPF Vehicle, Rep 14

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: Library name: 21613

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38_96/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Lung

extract_protocol:
The inferior lobe samples were homogenised in lysis buffer and RNA was purified using NucleoSpin® RNA binding strips (MACHEREY-NAGEL).
RNA sequence libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, USA) and sequenced on the NextSeq 500 (Illumina) with NextSeq 500/550 High Output Kit V2 (75 CYS, Illumina, San Diego, USA).

value: Lung

value: Single dose BLEO-IPF Vehicle


title: Lung, Single dose BLEO-IPF Vehicle, Rep 13

description: Library name: 21612


title: WT LT-HSC, pegIFNa, rep4

description: Library name: WTP50_S12

value: Bone marrow

value: long-term haematopoietic stem cells

value: C57Bl/6N Ptprca


title: LTL331 Pre-Castration Renal Capsule Human PDX in Mouse

value: Prostate adenocarcinoma from patient-derived xenograft in mouse

value: Pre-Castration


title: smRNAseq_Flower_b1_WT_rep1


title: Lung, Single dose BLEO-IPF Vehicle, Rep 12

description: Library name: 21611


title: Zzef1_KO_1

value: Pancreas

value: islets

value: Zzef1 knockout

value: normal chow diet


title: smRNAseq_Flower_b1_rim22-3

value: stage 12 and younger flower buds

value: Columbia


title: Myc_ChIP_rep2_gcn5∆/esa1 [Pol II_113061]

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

description: MATa his3Δ leu2Δ met15Δ ura3Δ gcn5Δ::kanMX4 esa1L254P STH1-myc13::HIS3

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive --no-mixed --no-unal, to map sequences up to 1 kb with maximum accuracy.
The PCR duplicates were removed by Samtool Rmdup tool
The .Bam files were used to generate the profiles using BamR (https://github.com/rchereji/bamR)
Assembly: SacCer3
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

source_name: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 esa1L254P STH1-myc13::HIS3

growth_protocol: Cells were grown to OD600 0.8 before being formaldehyde crosslinked and harvested

extract_protocol: Libraries were constructed using NEBNext Ultra II kit and Biooscientific NEXTFLEX ChIP-Seq adapters. Protocol was slightly modified from NEBNext manufacturer instuctions.

treatment_protocol: Sonicated extracts were used to ChIP for either. Myc, Rpb3, H3, and TBP antibodies. ChIPs samples were reverse-crosslinked, extracted with chloroform:IAA, then precipitated with ethanol.

tag: characterstics

value: treatment:Formadehyde Crosslinked and sonicated

tag: replicate

value: Biological replicate 2


title: LTL331 22 Weeks Post-Castration Renal Capsule Human PDX in Mouse

value: 22 Weeks Post-Castration


title: smRNAseq_Flower_b1_rim22-2

tag: tissue

value: experiment batch1


title: WT_1

value: WT


title: WT LT-HSC, pegIFNa, rep1

description: Library name: WTP10_S11

value: pegIFNa


title: LTL331 16 Weeks Post-Castration Renal Capsule Human PDX in Mouse

value: 16 Weeks Post-Castration


title: Lung, Single dose BLEO-IPF Vehicle, Rep 10

description: Library name: 21609

value: Lung

value: Single dose BLEO-IPF Vehicle


title: Lung, Single dose BLEO-IPF Vehicle, Rep 11

description: Library name: 21610


title: LTL331 20 Weeks Post-Castration Renal Capsule Human PDX in Mouse

value: Prostate adenocarcinoma from patient-derived xenograft in mouse

value: 20 Weeks Post-Castration


title: smRNAseq_Flower_b1_pol-iv

value: pol-iv


title: Myc_ChIP_rep1_gcn5∆/esa1 [Pol II_113060]

value: Biological replicate 1

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 esa1L254P STH1-myc13::HIS3


title: Lung, Single dose BLEO-IPF Vehicle, Rep 9

description: Library name: 21608


title: BGC823 cells, ALKBH1

city: Beijing

first: Xiaohong

last: Wang

address: Haidian district

institute: Peking university cancer hospital

data_processing:
The quality control of raw data were completed by removing low-quality reads, adaptor sequences, empty reads, reads with N sequences over 10% and rRNA reads.
aligned to the GRCh38 genome assembly using Hisat2（version:2.0.4）
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
The expression levels of the transcripts were expressed as FPKM (fragments per kilobase of transcript per million mapped reads) values of mRNA and lncRNA using the Stringtie v1.3.0
Differentially expressed mRNAs and lncRNAs were calculated by edgeR
Assembly: GRCh38
Supplementary files format and content: Excel files include FPKM values for each Sample

growth_protocol: Cells were cultured in Dulbecco’ s modified Eagle’ s medium (Gibco BRL, supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stably transfected with negative control and ALKBH1 plasmid  respectively.

value: cancer cells

value: DUSP5P1 ectopic expression

value: 10% FBS DMEM

value: 2 weeks


title: BGC823 cells, ctrl


title: smRNAseq_Flower_b1_clsy4

value: stage 12 and younger flower buds

value: Columbia


title: Lung, Single dose BLEO-IPF Vehicle, Rep 8

description: Library name: 21607


title: smRNAseq_Flower_b1_clsy3,4

value: experiment batch1


title: Myc_ChIP_rep1_HS-WT [PolII_L23]

description: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 STH1-myc13::HIS3

source_name: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1-myc13::HIS3

value: treatment:Heat-shock 37 degree, Formadehyde Crosslinked and sonicated


title: BGC823 cells, Input

data_processing:
6mA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
6mA-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Assembly: GRCh38

extract_protocol:
Genomic DNA was extracted from the cell lines, treated with RNase A, and sonicated to produce fragments. Fragmented DNA was incubated with an anti-6mA polyclonal antibody (Synaptic Systems) in immunoprecipitation buffer. The mixture was immunoprecipitated by incubation with protein A/G magnetic beads (Thermo Scientific) at 4°C overnight. After washing, the bound DNA was eluted from the beads at 65°C, treated with proteinase K, and purified using the QIAquick PCR Purification Kit (QIAGEN). Input was used as the control. Libraries for input and immunoprecipitated DNA were prepared and sequenced.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: Myc_ChIP_rep2_HS-WT [PolII_L24]

value: Biological replicate 2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1-myc13::HIS3


title: Myc_ChIP_rep2_esa1ts [Pol II_113057]

description: MATa his3Δ leu2Δ met15Δ ura3Δ esa1L254P STH1-myc13::HIS3

source_name: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} esa1L254P STH1-myc13::HIS3

value: treatment:Formadehyde Crosslinked and sonicated


title: Myc_ChIP_rep1_esa1ts [Pol II_113056]

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} esa1L254P STH1-myc13::HIS3


title: BGC823 cells, 6mA


title: Lung, Single dose BLEO-IPF Vehicle, Rep 7

description: Library name: 21606

value: Lung

value: Single dose BLEO-IPF Vehicle


title: Zzef1_KO_3

value: Pancreas

value: islets

value: Zzef1 knockout

value: normal chow diet


title: Lung, Single dose BLEO-IPF Vehicle, Rep 6

description: Library name: 21605


title: Lung, Single dose BLEO-IPF Vehicle, Rep 5

description: Library name: 21604


title: MGC803 cells, 6mA

value: cancer cells

value: 10% FBS DMEM


title: MethylCseq_Flower_rim22-2

data_processing:
Reads were mapped to the TAIR10 reference genome using the bs_seeker2-align.py function of BS-Seeker2 (v2.1.8) allowing 2 mismatches (-m 2). Redundant reads were removed using the remove_clonal.py function of picard tools (http://broadinstitute. github.io/picard/). The bs_seeker2-call_methylation.py function of BS-Seeker2 was used to call methylation at single cytosine resolution with read coverage greater than 4 (-r 4). To facilitate DNA methylation analyses and visualization, Tag Directory and BigWig data formats were generated as follows: (1) The CGmap output files from the BS-Seeker2 pipeline were converted to wig files using a previously published perl script (BSseeker2_2_wiggleV2_CG_CHG_CHH_allmC.pl), (2) the wig files were converted into BigWig files using wigToBigWig (v2.9) following default options, and (3) Tag Directories were made from the wig files using a previously published perl script (parseWig_noChr.v2.pl) and the makeTagDirectory function of HOMER (v4.10).
To identify differentially methylated regions (DMRs), the genome was split into 100 bp non-overlapping bins and the average levels of DNA methylation in the CG, CHG, and CHH contexts were compared between each mutant and three different wild-type controls. Thresholds used to declare significant DMRs are as follows: (1) The 100-bp bin should contain at least 4 cytosines in the specified context with read coverage greater than 4, (2) the methylation difference between mutant and wild-type control must be greater than 0.4, 0.2, or 0.1 for CG, CHG, and CHH contexts, respectively, and adjusted p-value must be less than 0.01, and (3) the DMR should pass the first two criteria when compared to three replicates of the wildtype control.
Assembly: TAIR10
Supplementary files format and content: wiggle (.wig) file, header with Chromosome, and two columns: position, % methylation

growth_protocol: For wild-type plants (Col-0 ecotype), T-DNA insertion lines, and rim22-3 EMS lines, seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. Approximately five weeks after planting, stage 12 and younger flower buds were collected and frozen in liquid nitrogen.

extract_protocol:
Genomic DNA was extracted from flower buds (stage 12 and younger) using the DNeasy Plant Mini Kit (QIAGEN, Cat# 69014). 2 μg of genomic DNA was fragmented using a Covaris S2 sonicator. The sonicated DNA was size-selected using SpeedBeads (Thermo Scientific #65152105050250) to collect fragments 150-300 bp in length.
The DNA ends were repaired using the End-It DNA repair kit (epicenter # ER81050) and purified using SpeedBeads. The end-repaired fragments were adenylated using the polymerase activity of the Klenow Fragment (N-terminal truncation of DNA Polymerase I, NEB # M0212L), purified using SpeedBeads, and indexed using Trueseq Adapters (BIOO Scientific # 511911) and T4 DNA ligase (NEB # M0202). After purification using SpeedBeads, the fragments were subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, MECOV-50). Bisulfite-converted DNA was amplified by PCR using the KAPA HiFi HotStart DNA polymerase (KAPA BIOSYSTEMS # KK2801). The following program was used for the PCR amplification: 95˚C for 2 min; 98˚C for 30 s; 4 cycles of (98˚C for 15 s, 60˚C for 30 s, 72˚C for 4 min); and 72˚C for 10 minutes. The PCR product was purified using SpeedBeads and pooled for sequencing using the pair-end 50 bp kit (PE50) on the Illumina Nextseq 2000 platform.

value: stage 12 and younger flower buds


title: Myc_ChIP_rep2_sth1∆BrD [Pol II_123613]

description: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 STH1∆BrD(1270-1359)-myc13::HIS3

source_name: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1{delta}BrD(1270-1359)-myc13::HIS3


title: MGC803 cells, Input

value: 2 weeks


title: Lung, Single dose BLEO-IPF Vehicle, Rep 3

description: Library name: 21602


title: Myc_ChIP_rep2_gcn5∆ [Pol II_123587]

description: MATa his3Δ leu2Δ met15Δ ura3Δ gcn5Δ::kanMX4 STH1-myc13::HIS3

source_name: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 STH1-myc13::HIS3


title: MKN74 cells, 6mA


title: MKN74 cells, Input


title: MethylCseq_Flower_rim22-3

source_name: stage 12 and younger flower buds

value: Columbia


title: MethylCseq_Flower_clsy1,2


title: Lung, Single dose BLEO-IPF Vehicle, Rep 2

description: Library name: 21601


title: Myc_ChIP_rep1_sth1∆BrD [Pol II_123612]

value: Biological replicate 1

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1{delta}BrD(1270-1359)-myc13::HIS3


title: Myc_ChIP_rep1_gcn5∆ [Pol II_123586]

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 STH1-myc13::HIS3


title: smRNAseq_Flower_b1_clsy1,2

value: experiment batch1


title: smRNAseq_Flower_b1_clsy3


title: GES1 cells, Input

value: WT


title: MethylCseq_Flower_clsy3,4


title: GES1 cells, 6mA


title: Myc_ChIP_rep2_WT [PolII_113063]

value: treatment:Formadehyde Crosslinked and sonicated

value: Biological replicate 2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1-myc13::HIS3


title: Lung, Single dose BLEO-IPF Vehicle, Rep 4

description: Library name: 21603

value: Lung

value: Single dose BLEO-IPF Vehicle


title: Lung, Single dose BLEO-IPF Vehicle, Rep 1

description: Library name: 21600


title: Myc_ChIP_rep1_WT [PolII_113062]


title: MethylCseq_Flower_clsy3


title: Lung, CTRL Vehicle, Rep 19

description: Library name: 21598

value: CTRL Vehicle


title: MethylCseq_Flower_WT_rep3


title: Lung, CTRL Vehicle, Rep 20

description: Library name: 21599


title: MethylCseq_Flower_WT_rep2


title: AGS cells, Input

source_name: AGS

value: AGS


title: H3_ChIP_rep2_gcn5∆/esa1 [H3_cn-16]

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 esa1L254P STH1-myc13::HIS3


title: H3_ChIP_rep1_gcn5∆/esa1 [H3_cn-15]


title: Lung, CTRL Vehicle, Rep 18

description: Library name: 21597


title: Lung, CTRL Vehicle, Rep 17

description: Library name: 21596


title: MethylCseq_Flower_WT_rep1


title: H3_ChIP_rep2_HS-WT [H3_L6]

value: treatment:Heat-shock 37 degree, Formadehyde Crosslinked and sonicated


title: AGS cells, 6mA

value: cancer cells

value: 10% FBS DMEM


title: Blood, multiple samples, run 2

city: Worcester

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

description:
Library name: Blood2
Multiple samples processed in 96-well format

data_processing:
Sample barcodes were extracted using whitelists of known barcodes and distance 1 correction (umi_tools extract, UMI-tools version 1.1.2). [Data processing details at https://github.com/ElkinsLab/DOBloodRNASeq]
Adapter and polyA were trimmed from R1 reads (cutadapt version 2.9).
Reads were aligned against an 8-way transcriptome of Collaborative Cross parents (bowtie version 1.0.0)
Aligned reads were pre-processed to allow de-duplication by gene rather than transcript, and globin reads were removed (dedup_preprocess_v2.pl, see https://github.com/ElkinsLab/DOBloodRNASeq).
Duplicate reads were removed (umi_tools dedup, UMI-tools version 1.1.2).
Reads were split by sample barcode into individual BAM files and converted to fastq (split_and_convert_bam-2.sh, see https://github.com/ElkinsLab/DOBloodRNASeq).
Each sample fastq file was re-aligned with bowtie using using GBRS parameters (-n2 -a --best --strata), and allele-specific gene expression was quantitated using GBRS quantitate (GBRS version 0.1.5, https://gbrs.readthedocs.io/en/latest/readme.html).
Assembly: mm10
Supplementary files format and content: csv files include de-duplicated read counts for each mouse

source_name: blood

extract_protocol:
For each DO mouse, ~100 µl of blood was collected via tail nick 14 days before and 14 days after vaccination. RNA was extracted using the Mouse Ribopure Blood RNA kit (Ambion), treated with DNase to remove contaminating DNA, and purified using QiaQuick Spin kits (Qiagen).
Libraries were prepared by Qiagen in 96-well format using the QIAseq UPX 3’ Transcriptome kit. During reverse transcription, each sample is tagged with a unique ID, and each RNA molecule is tagged with a unique molecular index (UMI).

treatment_protocol: Diversity Outbred (DO) mice were vaccinated intradermally with 105 CFU of BCG. Eight weeks after vaccination, animals were challenged by aerosol with M. tuberculosis Erdman, with ∼50 CFU delivered to the lungs.

value: blood

value: Diversity Outbred (DO)


title: H3_ChIP_rep1_HS-WT [H3_L5]

value: Biological replicate 1


title: Kidney 5x and 10x replicate 6

city: Godollo

first: Tibor

last: Nagy

address: Páter Károly street 1.

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

hyb_protocol: 200 ng of total RNA labeled and hybridized using Low Input Quick Amp Labeling and Hybridization Protocol (Version 6.0).

scan_protocol: Scanned on an Agilent G4900DA SureScan Microarray Scanner System with Scan Control Software (Version 9.1).

data_processing:
Images were quantified using Agilent Feature Extraction Software (Version 12.1.1.1).
GeneSpring Software (Version 14.9.1) was used to create the gene-level database.

extract_protocol: Total RNA extracted using Qiagen Rneasy kit manufacturer's instructions.

value: kidney

value: NOAEL 5x

value: kideney

value: NOAEL 10x


title: H3_ChIP_rep2_esa1ts [H3_L4]

city: Rochester

value: treatment:Formadehyde Crosslinked and sonicated

value: Biological replicate 2

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} esa1L254P STH1-myc13::HIS3


title: Lung, CTRL Vehicle, Rep 14

description: Library name: 21593

value: Lung


title: H3_ChIP_rep1_esa1ts [H3_L3]


title: Kidney 5x and 10x replicate 7

label_protocol: 200 ng of total RNA labeled and hybridized using Low Input Quick Amp Labeling and Hybridization Protocol (Version 6.0).


title: Kidney 5x and 10x replicate 8


title: H3_ChIP_rep2_gcn5∆ [H3_L2]

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 STH1-myc13::HIS3


title: Lung, CTRL Vehicle, Rep 13

description: Library name: 21592

value: CTRL Vehicle


title: Kidney 5x and 10x replicate 4


title: Blood, multiple samples, run 3

description:
Library name: Blood3
Multiple samples processed in 96-well format


title: Kidney 5x and 10x replicate 5


title: RAB1468 - Terf1FLOX rep4

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Center (CNIO)

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's RTA (Real Time Analysis) integrated primary analysis software. Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Fastq files were pre-processed to remove read adaptors, aligned to the mouse genome GRCm39, and read counts were obtained with featureCounts
Assembly: GRCm39
Supplementary files format and content: Normalized counts were obtained using DESeq2

source_name: liver

extract_protocol:
Mice were euthanized at 15 weeks old and liver were extracted.
Total RNA samples (500ng; RQS/RIN average 7.1, range 5.9-8.6) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina instrument.

treatment_protocol: Tamoxifen (TMX) (Sigma Aldrich, T-5648-1G) was intraperitoneally (i.p.) injected to fifeteen-week-old  female Trf1+/+  Cre+/t and Trf1lox/lox  Cre+/t mice for three times a week for 5 weeks until the sacrifice.

value: liver

tag: Sex

value: female

value: Trf1 flox/flox


title: Kidney 5x and 10x replicate 3


title: RAB1490 - Terf1FLOX rep2

tag: genotype


title: Lung, CTRL Vehicle, Rep 12

description: Library name: 21591


title: H3_ChIP_rep1_gcn5∆ [H3_L1]


title: H3_ChIP_rep2_sth1∆BrD [H3_cn-4]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1{delta}BrD(1270-1359)-myc13::HIS3


title: Lung, CTRL Vehicle, Rep 16

description: Library name: 21595


title: Lung, CTRL Vehicle, Rep 11

description: Library name: 21590


title: RAB1491 - Terf1FLOX rep1


title: Kidney 5x and 10x replicate 1


title: Lung, CTRL Vehicle, Rep 15

description: Library name: 21594


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 10

description: Library name: 23795

value: Repetitive BLEO-IPF Vehicle


title: H3_ChIP_rep1_sth1∆BrD [H3_cn-3]


title: Blood, multiple samples, run 1

description:
Library name: Blood1
Multiple samples processed in 96-well format

value: blood

value: Diversity Outbred (DO)


title: RAB1503 - CONTROL rep5


title: Kidney Control and 1x replicate 8

value: kidney

value: control

value: NOAEL 1x


title: Lung, Repetitive BLEO-IPF Baseline, Rep 9

description: Library name: 23794

value: Repetitive BLEO-IPF Baseline


title: Kidney Control and 1x replicate 7

value: kideney


title: Lung, CTRL Vehicle, Rep 10

description: Library name: 23793


title: RAB1480 - CONTROL rep4


title: RAB1450 - Terf1FLOX rep5


title: H3_ChIP_rep1_WT [H3_cn-1]

value: treatment:Formadehyde Crosslinked and sonicated

value: Biological replicate 1

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1-myc13::HIS3


title: RAB1481 - CONTROL rep3


title: Sth1_ChIP_rep1_H3∆1-28 [NTT_L16]

description: MATa his3Δ200 leu2Δ0 lys2Δ0 trp1Δ63 ura3Δ0 met15Δ0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[H3∆1-28]-URA3 STH1-myc13::TRP1

source_name: MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[H3{delta}1-28]-URA3 STH1-myc13::TRP1

value: Biological replicate 2


title: Kidney Control and 1x replicate 6


title: RAB1458 - Terf1FLOX rep3


title: Sth1_ChIP_rep1_H3∆1-28 [NTT_L15]

value: MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[H3{delta}1-28]-URA3 STH1-myc13::TRP1


title: Kidney Control and 1x replicate 5


title: Lung, Repetitive BLEO-IPF Baseline, Rep 8

description: Library name: 23791

value: Lung


title: RAB1483 - CONTROL rep2

value: liver

value: female


title: Sth1_ChIP_rep1_H4∆1-16 [NTT_L14]

description: MATa his3Δ200 leu2Δ0 lys2Δ0 trp1Δ63 ura3Δ0 met15Δ0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[H4∆1-16]-URA3 STH1-myc13::TRP1

source_name: MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[H4{delta}1-16]-URA3 STH1-myc13::TRP1


title: RAB1430 - CONTROL rep1


title: Kidney 5x and 10x replicate 2

value: NOAEL 5x

value: NOAEL 10x


title: Lung, CTRL Vehicle, Rep 9

description: Library name: 23790

value: CTRL Vehicle


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 8

description: Library name: 23789

value: Repetitive BLEO-IPF Vehicle


title: HFD Zzef1+/+-MipCre+, replicate 2, scRNAseq

description:
Library name: HFD_MIP-Cre_rep2
10x Genomics

data_processing:
We utilized CellRanger (version 7.2.0) for read alignment  and generation of the gene-count matrix. To remove ambient RNA contamination, CellBender (version 0.3.0) was employed. Potential doublets were identified and removed using DoubletFinder (v2.0.3) with a doublet rate of 7.5%.
For cell quality filtering, we retained cells expressing more than 800 genes and fewer than 8000 genes, with mitochondrial gene content below 10%, and ribosomal gene content between 1% and 15%. Raw UMI counts were normalized using the SCTransform function, regressing out mitochondrial and ribosomal gene percentages (vars.to.regress=c("percent.mt", "percent.ribosome")).
The top 2,500 features were selected using the SelectIntegrationFeatures function. These features were then used for PrepSCTIntegration and RunPCA. We applied FindIntegrationAnchors using the top 30 principal components (PCs) to identify integration anchors and integrated libraries using IntegrateData. Dimensionality reduction was performed with PCA, and the top 30 PCs were used for UMAP visualization.
Assembly: mm10
Supplementary files format and content: h5 files of  filtered gene expression matrix

extract_protocol:
Purified mouse islets were treated with trypsin-EDTA (0.05%) at 37 ℃ for 4 min. and gently pipetted. The cell suspension was stained with 0.4% trypan blue to assess cell viability under microscopic observation. Cells with greater than 85% viability were qualified for library construction process. Three mice islet samples (βZKO-Mip and Mip-Cre mice, βZKO-Rip and RIP-Cre mice) were used for one biological capture, and all observations and insights in the single cell analyses derived from two biological replicate per genotype. All sequencing date were captured with two independent experiments.
The single-cell suspension of islets was loaded into the 10X Genomics Chromium Controller (10x 3' Genomics, USA) for encapsulation, barcoding, and cDNA synthesis, following the manufacturer’s protocol

value: Pancreas

tag: cell type

value: islets

value: male

tag: age

value: MIP-Cre


title: Kidney Control and 1x replicate 3

value: kidney

tag: treatment

value: control

value: kideney

value: NOAEL 1x


title: HFD Zzef1+/+-MipCre+, replicate 1, scRNAseq

description:
Library name: HFD_MIP-Cre_rep1
10x Genomics


title: Kidney Control and 1x replicate 4


title: TBP_ChIP-Rep4_gcn5∆/esa1 [TBP_L46]

value: treatment:Heat-shock 37 degree, Formadehyde Crosslinked and sonicated

value: Biological replicate 2

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 esa1L254P STH1-myc13::HIS3


title: Lung, Repetitive BLEO-IPF Baseline, Rep 7

description: Library name: 23788

value: Lung

value: Repetitive BLEO-IPF Baseline


title: H3_ChIP_rep2_WT [H3_cn-2]

value: treatment:Formadehyde Crosslinked and sonicated

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1-myc13::HIS3


title: HFD Zzef1f/f-MipCre+, replicate 2, scRNAseq

description:
Library name: HFD_bZKO_Mip_rep2
10x Genomics

value: beta Zzef1KO-Mip


title: TBP_ChIP-Rep3_gcn5∆/esa1 [TBP_L45]

value: Biological replicate 1


title: HFD Zzef1f/f-MipCre+, replicate 1, scRNAseq

description:
Library name: HFD_bZKO_Mip_rep1
10x Genomics

value: Pancreas


title: Lung, CTRL Vehicle, Rep 8

description: Library name: 23787

value: CTRL Vehicle


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 9

description: Library name: 23792

value: Repetitive BLEO-IPF Vehicle


title: Kidney Control and 1x replicate 1


title: TBP_ChIP-Rep2_WT [TBP_L-22]


title: Liver 5x and 10x replicate 8

value: liver

value: NOAEL 5x

value: NOAEL 10x


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 7

description: Library name: 23786


title: HFD Zzef1+/+-RipCre+, replicate 2, scRNAseq

description:
Library name: HFD_RIP-Cre_rep2
10x Genomics

value: islets

value: male

value: RIP-Cre


title: Liver 5x and 10x replicate 7


title: Lung, Repetitive BLEO-IPF Baseline, Rep 6

description: Library name: 23785


title: Myc_ChIP_rep2_gcn5∆/esa1 [Sth1_L48]

value: Biological replicate 2


title: Liver 5x and 10x replicate 6


title: HFD Zzef1+/+-RipCre+, replicate 1, scRNAseq

description:
Library name: HFD_RIP-Cre_rep1
10x Genomics


title: HFD Zzef1f/f-RipCre+, replicate 2, scRNAseq

description:
Library name: HFD_bZKO_Rip_rep2
10x Genomics

value: beta Zzef1KO-Rip


title: Sth1_ChIP_rep1_H4∆1-16 [NTT_L13]

value: MATa his3{delta}200 leu2{delta}0 lys2{delta}0 trp1{delta}63 ura3{delta}0 met15{delta}0 can1::MFA1pr-HIS3 hht1-hhf1::NatMX4 hht2-hhf2::[H4{delta}1-16]-URA3 STH1-myc13::TRP1


title: Myc_ChIP_rep1_gcn5∆/esa1 [Sth1_L47]

description: MATa his3Δ leu2Δ met15Δ ura3Δ gcn5Δ::kanMX4 esa1L254P STH1-myc13::HIS3

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 esa1L254P STH1-myc13::HIS3


title: Liver 5x and 10x replicate 5


title: Kidney Control and 1x replicate 2

value: kidney

value: control

value: kideney

value: NOAEL 1x


title: HFD Zzef1f/f-RipCre+, replicate 1, scRNAseq

description:
Library name: HFD_bZKO_Rip_rep1
10x Genomics

value: Pancreas


title: Myc_ChIP_rep2_HS-WT [Sth1_L41]

description: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 STH1-myc13::HIS3

value: treatment:Heat-shock 37 degree, Formadehyde Crosslinked and sonicated

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1-myc13::HIS3


title: Liver 5x and 10x replicate 4

value: liver


title: control  DMSO rep3

description:
Library name: MC3_D
Column name in aw_counts_All.tsv: MC3_D

data_processing:
STAR (v2.7.2a) was applied to align the clean reads to the UCSC mm10 genome reference.
Expression level of gene was calculated by SALMON (v.10.1). Differential expressed gene (DEG) analysis was performed by DESeq2 R package. DEGs were defined as P-value < 0.05 and absolute log2 (fold change) ≥ 0.3.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted from freshly isolated islets and livers of Zzef1_KO and WT mice using RNeasy Micro kit (Qiagen), and sample qualities were assessed using an Agilent Bioanalyzer 2100 (Agilent technologies). 2 mg of total RNA samples of each group were then used.
Sequencing libraries were constructed using the DNBSEQ-T7 platform (BGI, China). Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS). We included at least 3 independent biological replications.

value: DMSO


title: Lung, CTRL Vehicle, Rep 6

description: Library name: 23781

value: Lung

value: CTRL Vehicle


title: Myc_ChIP_rep1_HS-WT [Sth1_L39]

value: Biological replicate 1


title: control  DMSO rep2

description:
Library name: MC2_D
Column name in aw_counts_All.tsv: MC2_D

value: islets


title: Liver 5x and 10x replicate 3

value: NOAEL 5x

value: NOAEL 10x


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 5

description: Library name: 23780

value: Repetitive BLEO-IPF Vehicle


title: TBP_ChIP-Rep1_WT [TBP_L-21]

value: treatment:Formadehyde Crosslinked and sonicated


title: Liver 5x and 10x replicate 2


title: Lung, CTRL Vehicle, Rep 7

description: Library name: 23784


title: Lung, Repetitive BLEO-IPF Baseline, Rep 4

description: Library name: 23779

value: Repetitive BLEO-IPF Baseline


title: Myc_ChIP_rep2_gcn5∆ [Sth1_L4]

description: MATa his3Δ leu2Δ met15Δ ura3Δ gcn5Δ::kanMX4 STH1-myc13::HIS3

value: Biological replicate 2

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} gcn5{delta}::kanMX4 STH1-myc13::HIS3


title: Liver Control and 1x replicate 8

value: control

value: NOAEL 1x


title: control Azoramide rep3

description:
Library name: MC3_A
Column name in aw_counts_All.tsv: MC3_A

value: Pancreas

value: Azoramide


title: Myc_ChIP_rep1_esa1ts [Sth1_cn35]

description: MATa his3Δ leu2Δ met15Δ ura3Δ esa1L254P STH1-myc13::HIS3

value: MATa his3{delta} leu2{delta} met15{delta} ura3{delta} esa1L254P STH1-myc13::HIS3


title: control Azoramide rep2

description:
Library name: MC2_A
Column name in aw_counts_All.tsv: MC2_A


title: Myc_ChIP_rep2_esa1ts [Sth1_cn36]


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 6

description: Library name: 23783


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 4

description: Library name: 23777


title: Myc_ChIP_rep1_gcn5∆ [Sth1_L3]


title: Lung, CTRL Vehicle, Rep 5

description: Library name: 23778


title: control Azoramide rep1

description:
Library name: MC1_A
Column name in aw_counts_All.tsv: MC1_A


title: Liver Control and 1x replicate 7

value: liver


title: Lung, Repetitive BLEO-IPF Baseline, Rep 5

description: Library name: 23782

value: Lung


title: Lung, CTRL Vehicle, Rep 4

description: Library name: 23775

value: CTRL Vehicle


title: Myc_ChIP_rep2_sth1∆BrD [Sth1_cn30]

description: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 STH1∆BrD(1270-1359)-myc13::HIS3

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1{delta}BrD(1270-1359)-myc13::HIS3


title: Liver Control and 1x replicate 6


title: Liver Control and 1x replicate 5


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 3

description: Library name: 23774


title: βZKO_Mip DMSO rep1

description:
Library name: MK1_D
Column name in aw_counts_All.tsv: MK1_D

value: islets

value: beta ZKO_Mip

value: DMSO


title: βZKO_Mip  DMSO rep2

description:
Library name: MK2_D
Column name in aw_counts_All.tsv: MK2_D


title: Myc_ChIP_rep1_sth1∆BrD [Sth1_cn29]

value: Biological replicate 1


title: Liver 5x and 10x replicate 1

value: NOAEL 5x

value: NOAEL 10x


title: Myc_ChIP_rep2_WT [Sth1_cn28]

value: treatment:Formadehyde Crosslinked and sonicated

value: Biological replicate 2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 STH1-myc13::HIS3


title: βZKO_Mip Azoramide rep3

description:
Library name: MK3_A
Column name in aw_counts_All.tsv: MK3_A


title: Myc_ChIP_rep1_WT [Sth1_cn27]


title: Lung, Repetitive BLEO-IPF Baseline, Rep 3

description: Library name: 23773

value: Repetitive BLEO-IPF Baseline


title: Lung, CTRL Vehicle, Rep 3

description: Library name: 23772


title: control DMSO rep1

description:
Library name: MC1_D
Column name in aw_counts_All.tsv: MC1_D

value: Pancreas

value: control


title: Liver Control and 1x replicate 3

value: NOAEL 1x


title: βZKO_Mip Azoramide rep2

description:
Library name: MK2_A
Column name in aw_counts_All.tsv: MK2_A

value: Azoramide


title: βZKO_Mip Azoramide rep1

description:
Library name: MK1_A
Column name in aw_counts_All.tsv: MK1_A


title: Liver Control and 1x replicate 2

value: liver


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 2

description: Library name: 23771

value: Lung

value: Repetitive BLEO-IPF Vehicle


title: Lung, Repetitive BLEO-IPF Baseline, Rep 2

description: Library name: 23770


title: Lung, CTRL Vehicle, Rep 2

description: Library name: 23769

value: CTRL Vehicle


title: Zzef1+/+-MipCre+, replicate 2,scRNA-seq

description: 10x Genomics

data_processing:
We utilized CellRanger (version 7.2.0) for read alignment  and generation of the gene-count matrix. To remove ambient RNA contamination, CellBender (version 0.3.0) was employed. Potential doublets were identified and removed using DoubletFinder (v2.0.3) with a doublet rate of 7.5%.
For cell quality filtering, we retained cells expressing more than 800 genes and fewer than 8000 genes, with mitochondrial gene content below 10%, and ribosomal gene content between 1% and 15%. Raw UMI counts were normalized using the SCTransform function, regressing out mitochondrial and ribosomal gene percentages (vars.to.regress=c("percent.mt", "percent.ribosome")).
The top 2500 features were selected using the SelectIntegrationFeatures function. These features were then used for PrepSCTIntegration and RunPCA. We applied FindIntegrationAnchors using the top 30 principal components (PCs) to identify integration anchors and integrated libraries using IntegrateData. Dimensionality reduction was performed with PCA, and the top 30 PCs were used for UMAP visualization.
Assembly: mm10
Supplementary files format and content: h5 files of  filtered gene expression matrix

extract_protocol:
Purified mouse islets were treated with trypsin-EDTA (0.05%) at 37 ℃ for 4 min. and gently pipetted. The cell suspension was stained with 0.4% trypan blue to assess cell viability under microscopic observation. Cells with greater than 85% viability were qualified for library construction process. Three mice islet samples (βZKO-Mip and Mip-Cre mice, βZKO-Rip and Zzef1flox/flox mice) were used for one biological capture, and all observations and insights in the single cell analyses derived from two biological replicate per genotype. All sequencing date were captured with two independent experiments.
The single-cell suspension of islets was loaded into the 10X Genomics Chromium Controller (10x Genomics, USA) for encapsulation, barcoding, and cDNA synthesis, following the manufacturer’s protocol

value: islets

value: MIP-Cre


title: Zzef1+/+-MipCre+, replicate 1,scRNA-seq

description: 10x Genomics


title: CF32_eTRF_Visit4

city: Nuthetal

first: Michail

last: Lazaratos

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke

description:
Library name: CF-32-V4
CF-32-V4

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.11a
Read count extraction via STRINGTIE v2.2.1 and prepDE.py (following Protocol stringtie webpage)
Assembly: GRCh38.110
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Subcutaneous adipose tissue

extract_protocol:
RNA was isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen). 1 µg of total RNA was used for the consruction of sequencing libraries.
done by BGI (Yantian District, Shenzhen, China)

value: Subcutaneous adipose tissue

value: female

value: eTRF


title: Lung, Repetitive BLEO-IPF Vehicle, Rep 1

description: Library name: 23768


title: Zzef1f/f-MipCre+, replicate 2,scRNA-seq

description: 10x Genomics


title: CF32_lTRF_Visit2

description:
Library name: CF-32-V2
CF-32-V2

value: lTRF


title: Lung, Repetitive BLEO-IPF Baseline, Rep 1

description: Library name: 23767


title: CF31_lTRF_Visit4

description:
Library name: CF-31-V4
CF-31-V4


title: Liver Control and 1x replicate 4


title: 4 Avg-irradiated+valproic acid, rep2

city: Buenos Aires

first: Marina

last: Perona

address: Avenida General Paz 1499

department: Radiobiología

country: Argentina

institute: Comisión Nacional de Energía Atómica

description: miRNA expression data from cells incubated with valproic acid for 24 hours and irradiated (2Gy)

hyb_protocol: For each sample, 21.5 µL biotin-labeled sample was loaded prior to hybridization on GeneChipTM miRNA. A Hybridization Cocktail was prepared, injected into the array and  incubated at 48°C and 60 rpm for 16 to 18 hours in the hybridization oven.

scan_protocol: GeneChips were scanned with a GCS 3000 7G scanner (GeneChip Scanner 3000 7G).

data_processing: The analysis was performed using the Transcriptome Analysis Console (TAC) Software (Applied Biosystems, Thermo Fisher Scientific), the R programming language, and different tools of Bioconductor. Data background correction and normalization were done using Robust Multi-array Average (rma). Differential miR expression was evaluated by Limma package (Linear Models for Microarray Data) [17]. The filter criteria was fold change > 2 or < -2 and p value < 0.05.

source_name: Anaplastic thyroid cancer cells (8505c) treated for 24 hours with 1 mM valproic acid (VA) and gamma irradiated at a dose of 2 Gy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (FlashTag™ Biotin HSR RNA Labeling Kit).

growth_protocol: Anaplastic thyroid cancer cells (8505c) were grown in a humidified 5% CO2 atmosphere in RPMI 1640 medium (GibcoTM, USA) supplemented with 10% fetal bovine serum (Natocor, Argentina).

extract_protocol: Total RNA was isolated 4 hours after irradiation using the commercially available GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).

treatment_protocol: Cells were treated with 1 mM VA for 24 hours before irradiation. Irradiation was done with a Cesium 137 (137Cs) of 189 TBq gamma source (IBL- 437C Irradiator; CIS Bio-International, CEBIRSA, Argentina) at a dose rate of 7.7 Gy/min. Cells were divided in the following experimental groups: Control, VA pretreatment (VA), irradiated (IR), and irradiated after VA pretreatment (IR+VA). Controls were sham irradiated.

value: Anaplastic thyroid cancer cells

tag: growth phase

value: exponentially growing cell line

value: valproic acid and gamma irradiated


title: Zzef1f/f-MipCre+, replicate 1,scRNA-seq

description: 10x Genomics

value: Pancreas


title: 4 Avg-irradiated+valproic acid, rep1


title: 3 Avg-irradiated cell, rep3

description: miRNA expression data from irradiated cells (2Gy)

source_name: Anaplastic thyroid cancer cells (8505c) gamma irradiated at a dose of 2 Gy

value: gamma irradiated


title: Zzef1f/f-RipCre-, replicate 2, scRNA-seq

description: 10x Genomics

source_name: Pancreas


title: 3 Avg-irradiated cell, rep2


title: Lung, CTRL Vehicle, Rep 1

description: Library name: 23766


title: Zzef1f/f-RipCre-, replicate 1, scRNA-seq

description: 10x Genomics


title: CF31_eTRF_Visit2

description:
Library name: CF-31-V2
CF-31-V2


title: 4 Avg-irradiated+valproic acid, rep3


title: Zzef1f/f-RipCre+, replicate 2, scRNA-seq

description: 10x Genomics


title: Liver Control and 1x replicate 1

value: control

value: NOAEL 1x


title: CF25_eTRF_Visit2

description:
Library name: CF-25-V2
CF-25-V2


title: TSC1_TSC2_null_Rep4

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

description: 10x Genomics 3' V3

data_processing:
FASTQ files were processed using alevin with GENCODE vM25 transcript annotations to generate cells x genes matrices85. Data were then imported into R v3.6 and Seurat objects were created for each individual sample before being merged
Cells were filtered such that there were at least 1000 UMIs and 500 genes detected, and fewer than 10% of the transcripts were mitochondrially contributed. Data were then scaled and normalized using scTransform and integrated using Seurat
Clusters were identified using Louvain-Jaccard clustering with multilevel refinement (resolution=1.5) performed on the top 100 PCs. Marker genes of each cluster were identified using Presto (https://github.com/immunogenomics/presto), and differential expression analysis was performed using distinct with log2 CPMs in R v4.188. Differential abundance testing comparing cellular proportions for each genotype was performed using the propeller test in the speckle package
Assembly: mm10
Supplementary files format and content: Tab separated values and binary matrix created by Alevin
Supplementary files format and content: Tab separated metadata for each high-quality barcode, including cluster assignment, cluster annotation, tSNE coordinates, UMIs and genes detected per cell, and percent mitochondrial contribution

source_name: Cerebral cortical neurons

extract_protocol:
Single-cell RNA-seq was performed as described previously in Loo et al., 201949 and  Li et al, 201884. Briefly, P0 cerebral cortical neurons from control and TSC1/2 cKO mice were dissociated and stored in 80% methanol at -80°C. Cells were then lysed in TRI-reagent and RNA was extracted using a Direct-zol kit (Zymo Research Cat#R2051) with on-column DNase treatment, following the manufacturer’s instructions.
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the 10xG 3Prime v3 single-cell RNA kit (10X Genomics) according to the manufacturer’s protocol. Libraries were sequenced single-end for a minimum of 76 bp for each index to a depth of approximately 40 million host genome reads on an Illumina NextSeq 500 instrument at the Yale Center for Genomic Analysis.

value: Cerebral cortical neurons


title: TSC1_TSC2_null_Rep3

description: 10x Genomics 3' V3


title: CF25_lTRF_Visit4

description:
Library name: CF-25-V4
CF-25-V4


title: 3 Avg-irradiated cell, rep1


title: 2 Avg-control+valproic acid cell, rep1

description: miRNA expression data from control cells incubated for 24 hours with VA

source_name: Anaplastic thyroid cancer cells (8505c) treated for 24 hours with 1 mM valproic acid (VA)

value: valproic acid


title: CF22_lTRF_Visit4

description:
Library name: CF-22-V4
CF-22-V4


title: TSC1_TSC2_null_Rep2

description: 10x Genomics 3' V3


title: Zzef1f/f-RipCre+, replicate 1, scRNA-seq

description: 10x Genomics


title: 1 Avg-control cell, rep3

description: miRNA expression data from control cells

source_name: Anaplastic thyroid cancer cells (8505c) without treatment


title: CF22_eTRF_Visit2

description:
Library name: CF-22-V2
CF-22-V2


title: TSC1_TSC2_null_Rep1

description: 10x Genomics 3' V3