title: AML21-U

description: BM AML1/ETO positive LSPCs untreated


title: Lung_WT_NM403_0.25_Day3_rep3

status: Public on Aug 28 2023

type: RNA

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

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

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

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

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

molecule: total RNA

organism: Rattus norvegicus

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

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

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

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

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

tag: strain

value: Sprague Dawley

tag: tissue

value: accessory lobe of lung

tag: gender

value: female

tag: age

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

tag: genotype

value: Wild Type


title: Lung_WT_NM403_0.25_Day3_rep2

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


title: 22489

type: genomic

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

country: USA

institute: NHGRI

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

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

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

label: Cy3 and Cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: blood

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

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

tag: phenotype

value: Invasive Urothelial Carcimona

tag: breed

value: Shetland Sheepdog


title: Lung_WT_NM403_0.25_Day3_rep1

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


title: 20-637-032_het_D13

type: SRA

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

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

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

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

tag: cell line

tag: cell type

value: iPSC

tag: group

value: het

tag: day


title: 22484

value: unknown


title: Lung_WT_Mitsui_0.25_Day3_rep6

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

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


title: AML20-U

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description: BM AML1/ETO positive LSPCs untreated

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

source_name: AML1/ETO positive LSPCs untreated

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

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

tag: population

value: AML1/ETO positive LSPCs

value: Bone marrow (BM) derived LSPCs


title: Lung_WT_NM403_0.25_Day3_rep5

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


title: 22506

value: Unaffected


title: 20-637-028_het_D2


title: AML25-T

description: BM AML1/ETO positive LSPCs treated +rhIL-33


title: Lung_WT_Mitsui_0.25_Day3_rep5

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


title: 20-637-026_het_D0


title: 22475

value: male


title: AML24-T

source_name: AML1/ETO positive LSPCs treated +rhIL-33


title: AML21-T


title: Lung_WT_Mitsui_0.25_Day3_rep4

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


title: 20-637-024_het_D13


title: 20-637-022_het_D6


title: AML20-T


title: 22497


title: 22493


title: 20-637-020_het_D2


title: Lung_WT_Mitsui_0.25_Day3_rep3

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


title: Lung_WT_Mitsui_0.25_Day3_rep2

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


title: 21965


title: 20-637-030_het_D6


title: 20-637-018_het_D0


title: Lung_WT_Mitsui_0.25_Day3_rep1

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


title: 22474


title: 21906


title: v8-VeroE6-HF-91_S8

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: genes.tsv.gz

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg38
Supplementary_files_format_and_content: comma-delimited text file of read counts for each sample

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

value: Vero E6

tag: treatment


title: Lung_WT_Control_Day3_rep5

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

source_name: Rat, Lung, Wild Type, Control, Day 3, replicate 5


title: 20-637-016_het_D13


title: Lung_WT_Control_Day3_rep6

source_name: Rat, Lung, Wild Type, Control, Day 3, replicate 6


title: v7-VeroE6-HF-91_S7

description: genes.tsv.gz


title: v6-VeroE6-HF-90_S6

description: genes.tsv.gz


title: 21202


title: 20-637-014_het_D6


title: v5-VeroE6-HF-90_S5

description: genes.tsv.gz


title: 10610


title: Lung_WT_Control_Day3_rep4

source_name: Rat, Lung, Wild Type, Control, Day 3, replicate 4


title: v4-VeroE6-HF-90_S4

description: genes.tsv.gz


title: v9-VeroE6-HF-91_S9

description: genes.tsv.gz


title: 20-637-012_het_D2


title: 15112


title: 20-637-010_het_D0


title: Lung_WT_Control_Day3_rep3

source_name: Rat, Lung, Wild Type, Control, Day 3, replicate 3


title: v3-VeroE6-DMSO_S3

description: genes.tsv.gz

value: DMSO


title: H4 control for H4K16ac ChIP-seq in ddm1 biol Rep2

city: Cold Spring Harbor

first: Jonathan

last: Cahn

state: NY

address: 1 Bungtown Rd

institute: CSHL

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_H4K16ac_H4_Rep2

library_source: genomic

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

organism: Arabidopsis thaliana

source_name: seedlings

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

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

value: seedlings

tag: background

tag: chip antibody

value: anti-H4 (abcam; ab10158)

value: crosslinking


title: H4K16ac ChIP-seq in ddm1 biol Rep2

description:
Compared to its H4 control in processed file (log2 fold change of normalized CPM)
ddm1_H4K16ac_IP_Rep2

value: anti-H4K16ac (EMD millipore; 07-329)


title: 13546


title: v2-VeroE6-DMSO_S2

description: genes.tsv.gz


title: 20-637-006_het_D6


title: 20-637-008_het_D13


title: H4 control for H4K16ac ChIP-seq in ddm1 biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_H4K16ac_H4_Rep1


title: Lung_WT_Control_Day3_rep1

source_name: Rat, Lung, Wild Type, Control, Day 3, replicate 1

value: Sprague Dawley

value: accessory lobe of lung

value: female

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


title: 13016

source_name: blood

value: Invasive Urothelial Carcimona

value: Shetland Sheepdog


title: v1-VeroE6-DMSO_S1

description: genes.tsv.gz


title: v18-VeroE6-SerSA_S18

description: genes.tsv.gz

value: SerSA


title: 20-637-004_het_D2

value: iPSC

value: het


title: 20-637-002_het_D0


title: 12784


title: H4K16ac ChIP-seq in ddm1 biol Rep1

description:
Compared to its H4 control in processed file (log2 fold change of normalized CPM)
ddm1_H4K16ac_IP_Rep1


title: 7751


title: H4 control for H4K16ac ChIP-seq in WT biol Rep2

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_H4K16ac_H4_Rep2

value: wild-type


title: H4K16ac ChIP-seq in WT biol Rep2

description:
Compared to its H4 control in processed file (log2 fold change of normalized CPM)
WT_H4K16ac_IP_Rep2


title: v16-VeroE6-SerSA_S16

description: genes.tsv.gz


title: v17-VeroE6-SerSA_S17

description: genes.tsv.gz


title: Lung_WT_Control_Day3_rep2

source_name: Rat, Lung, Wild Type, Control, Day 3, replicate 2

value: Wild Type


title: 3650

value: Unaffected

value: male


title: v15-VeroE6-ProSA_S15

description: genes.tsv.gz

value: Vero E6

value: ProSA


title: 15045


title: H4 control for H4K16ac ChIP-seq in WT biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_H4K16ac_H4_Rep1

value: seedlings

value: anti-H4 (abcam; ab10158)

value: crosslinking


title: H4K16ac ChIP-seq in WT biol Rep1

description:
Compared to its H4 control in processed file (log2 fold change of normalized CPM)
WT_H4K16ac_IP_Rep1

value: anti-H4K16ac (EMD millipore; 07-329)


title: 20600

value: female


title: 28dpl rep4

city: Detroit

first: Ashley

middle: Catherine

last: Kramer

state: Michigan

address: 540 E. Canfield St

department: Ophthalmology, Visual and Anatomical Sciences

institute: Wayne State University School of Medicine

data_processing:
Reads were aligned to the zebrafish genome (Build dR10) using STAR and tabulated for each gene region using htseq-count.  Differential expression analysis was conducted using edgeR.
Assembly: dR10
Supplementary files format and content: Excel spreadsheet containing raw counts for all genes in each sample on sheet one, all following sheets in the file contain pairwise comparison data for 6 samples in each timepoint compared to the dark-adapted 0hr control dataset.

organism: Danio rerio

source_name: retina

growth_protocol: Adult (6-9 months) albino (alb) zebrafish were used for all experiments. Unless otherwise noted (See treatment protocol), fish were maintained under a daily light cycle of 14 hours light (250 lux):10 hours dark at 28.5º C and fed a combination of flake food and brine shrimp. The Institutional Animal Care and Use Committee at Wayne State University approved all procedures used in this study (Protocol # 19-02-0970)

extract_protocol:
Retinas were surgically removed from euthanized animals and placed in pre-chilled eppendorf tubes. RNA was immediately isolated using the Direct-zol RNA Microprep kit (Zymo Research, Irvine CA, cat#R2062) according to manufacturer protocol and eluted in 15μL of RNAse-free water. RNA integrity and concentration were assesssed on a Nanodrop.
Sequencing libraries were generated from 150-230ng of total RNA using Lexogen's Quantseq 3' mRNA-Seq Library Prep Kit (Lexogen, Inc., Greenland, NH). Libraries were sequenced on a NovaSeq 6000 with a minimum of 5 million reads per sample.

treatment_protocol: The light lesion protocol used for all samples in rows X and below is as follows: Adult zebrafish were dark adapted for 24 hrs in a dark box. 0hr dark-adapted controls were harvested at the conclusion of this adaptation (rows X-X). Following dark adaptation, fish were transfered to a tank setup with 2 x 250W halogen lamps (total ~5,000 lux) directed at the tank for 28 consecutive days. Fish were fed Gemma feed every 3 days and water was exchanged regularly. All labelled timepoints are after onset of the light treatment. The acute light as well as the naive ctl sample information referred to in the publication is available with our previously published manuscript and can be found in the NCBI GEO entry accession no: GSE180518

value: albino

tag: tissue type

value: whole retina

value: 28 days after ~5,000lux "chronic low light" lesion onset


title: 20228

value: Shetland Sheepdog


title: v13-VeroE6-ProSA_S13

description: genes.tsv.gz


title: 28dpl rep3


title: 28dpl rep2


title: 20216


title: 28dpl rep5


title: DDM1 ChIP-seq in ddm1 biol Rep2

description:
Compared to its input in processed file (log2 fold change of normalized CPM)
ddm1_DDM1_IP_Rep2


title: v12-VeroE6-Borrelidin_S12

description: genes.tsv.gz

value: Borrelidin


title: v14-VeroE6-ProSA_S14

description: genes.tsv.gz


title: 28dpl rep1


title: 28dpl rep6


title: v11-VeroE6-Borrelidin_S11

description: genes.tsv.gz


title: v10-VeroE6-Borrelidin_S10

description: genes.tsv.gz


title: DDM1 ChIP-seq in ddm1 biol Rep1

description:
Compared to its input in processed file (log2 fold change of normalized CPM)
ddm1_DDM1_IP_Rep1


title: 14dpl rep6

value: 14 days after ~5,000lux "chronic low light" lesion onset


title: 27144

source_name: saliva

value: Border collie


title: 14dpl rep5


title: 14dpl rep4


title: DS24

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg38
Supplementary_files_format_and_content: comma-delimited text files of read counts for each sample

tag: hf concentration

tag: isrib concentration

tag: agent

value: ISRIB

tag: time point (hrs)


title: 27196

value: Unaffected

tag: age

tag: gender


title: DDM1 ChIP-seq in WT biol Rep2

description:
Compared to its input in processed file (log2 fold change of normalized CPM)
WT_DDM1_IP_Rep2

tag: tissue

tag: genotype

value: wild-type


title: Input for DDM1 ChIP-seq in WT biol Rep2

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_DDM1_Input_Rep2


title: DS23


title: Input for DDM1 ChIP-seq in ddm1 biol Rep2

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_DDM1_Input_Rep2


title: 27104

tag: phenotype

tag: breed

value: Australian Shepherd


title: 14dpl rep3

tag: strain


title: Input for DDM1 ChIP-seq in WT biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
WT_DDM1_Input_Rep1


title: 14dpl rep2


title: 20265

value: male


title: DDM1 ChIP-seq in WT biol Rep1

description:
Compared to its input in processed file (log2 fold change of normalized CPM)
WT_DDM1_IP_Rep1

value: seedlings


title: 27153


title: 27103


title: DS21

value: halofuginone


title: Input for DDM1 ChIP-seq in ddm1 biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_DDM1_Input_Rep1

value: crosslinking


title: 27114

value: Collie


title: DS20


title: 20242

value: female


title: 16126


title: DS19


title: DS18


title: 16074

value: Invasive Urothelial Carcimona


title: DS17


title: 10dpl rep4

value: albino

value: whole retina

value: 10 days after ~5,000lux "chronic low light" lesion onset


title: 10dpl rep3


title: 10dpl rep6


title: 14dpl rep1


title: 24037

value: Shetland Sheepdog


title: 10dpl rep5


title: 10dpl rep2


title: 22234


title: DS15


title: DS22


title: 10dpl rep1


title: DS14


title: 27150


title: 5dpl rep6

value: 5 days after ~5,000lux "chronic low light" lesion onset


title: DS13


title: 23047


title: 26812


title: DS12


title: 5dpl rep4


title: 26810


title: 5dpl rep5


title: 5dpl rep3


title: DS11


title: DS10


title: 27158


title: DS09


title: 5dpl rep2


title: 26636


title: 27157


title: DS16


title: 26355


title: 72hpl rep6

value: 72 hours after ~5,000lux "chronic low light" lesion onset


title: 26915


title: 72hpl rep5


title: DS08

value: ISRIB


title: DS06


title: 5dpl rep1


title: DS07


title: DS05


title: 72hpl rep4


title: 26911


title: 26262


title: 25020

value: Mixed breed


title: DS04


title: DS03


title: DS02


title: 24816


title: 24523

value: Unaffected


title: DS_20


title: 24528


title: 26263


title: DS_19


title: 24460


title: DS_16

value: DMSO


title: 24525


title: DS_15


title: 27134


title: 72hpl rep3


title: 72hpl rep2


title: DS_18


title: 36hpl rep6

value: 36 hours after ~5,000lux "chronic low light" lesion onset


title: 72hpl rep1


title: 36hpl rep2


title: 36hpl rep3


title: 24hpl rep6

value: 24 hours after ~5,000lux "chronic low light" lesion onset


title: 36hpl rep1


title: 36hpl rep5


title: 36hpl rep4


title: DS01


title: DS_13

value: halofuginone


title: 24hpl rep4


title: 27138

value: Border collie


title: 27441


title: DS_12


title: 24572


title: 27331


title: 24hpl rep3


title: DS_11


title: DS_10


title: 24081


title: DS_14


title: DS_9


title: DS_8


title: 24hpl rep1


title: 0hr dark-adapted control rep4

value: housed in dark-box for 24 hours


title: bone metastasized cancer 6 from patient 6

city: Yokohama

first: Shinya

last: Sato

state: Kanagawa

address: 2-3-2, Nakao, Asahi-Ku

country: Japan

institute: Kanagawa Cancer Center Research Institute

data_processing:
We used FastQC （https://www.bioinformatics.babraham.ac.uk/projects/fastqc/） to confirm the read quality.
Alignment to the human genome GRCh37 using STAR-2.5.2a (https://github.com/alexdobin/STAR/releases/tag/2.5.2a)
Expression data was normalized using the VOOM function in the Limma package in R
Checking quality control of BAM for each sample were performed to the Genomon 2 RNA analysis pipeline (https://github.com/Genomon-Project) to check sequencing qualities.
The mapped read count of each sample was calculated using HTseq (https://htseq.readthedocs.io/en/release_0.9.1/).
We carried out normalization of count data, and identification of the differentially expressed genes (DEGs) between two groups from the read count data using “DESeq2” Bioconductor R package (v1.26.0) (http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html).
The threshold value to list DEGs was greater than 2 fold change with p value < 0.05 and p.adjust < 0.05.
Assembly: human genome GRCh37
Supplementary files format and content: count data, log2FC data

source_name: bone metastasized cancer tissue from FFPE specimen

extract_protocol:
RNA was isolated using the RNeasy FFPE Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the SMART-Seq Stranded (Takara Bio, Shiga, Japan), according to the manufacturer’s instructions.

treatment_protocol: Patients undergo surgeries, chemotherapies or radiotherapies.

value: surgery, chemotherapy or radiotherapy

tag: group

value: bone metastasized cancer

tag: individual

value: patient 6


title: 0hr dark-adapted control rep3

value: albino

value: whole retina

tag: treatment


title: 24hpl rep2


title: DS_6


title: 26992

value: Shetland Sheepdog

value: male


title: 0hr dark-adapted control rep5


title: DS_7


title: bone metastasized cancer 5 from patient 5

value: patient 5


title: DS_5


title: bone metastasized cancer 4 from patient 4

value: patient 4


title: 24hpl rep5


title: 24161

value: Invasive Urothelial Carcimona

value: female


title: 24169

value: Unaffected


title: 24140


title: 0hr dark-adapted control rep2


title: 24226


title: 24036


title: 23329


title: DS_4

value: DMSO


title: bone metastasized cancer 3 from patient 3

value: patient 3


title: 0hr dark-adapted control rep1


title: DS_3


title: 23326


title: 0hr dark-adapted control rep6


title: bone metastasized cancer 2 from patient 2

value: patient 2


title: DS_2


title: 22498

value: unknown


title: DS_1


title: S2016-PC1c

city: Ottawa

first: Basit

last: Yousuf

state: ON

address: 2035, Othello Avenue, Ottawa

country: Canada

institute: University of Ottawa

description: CBS2016-05 grown in PCs until early stationary phase

data_processing:
Sequence quality control analysis was performed using FastQC and fastp to assess the quality of the reads.
Transcript quantification was conducted using Salmon and the reads were aligned to the genome using bowtie2.
The 'lfcShrink()' function in DESeq2 was employed for this analysis, which calculates the log2 fold change between the conditions while shrinking the value in cases of high uncertainty in the estimated fold change, often arising from low read counts assigned to the gene.
Assembly: Genome sequences of S. aureus CBS2016-05 and PS/BAC/317/16/W. Accession numbers are CP070991.1 and NZ_CP071104.1, respectively.
Supplementary files format and content: S.aureus_RNAseq_foldchange.xlsx; log2FoldChange = ≥ 1 or ≤ -1, p<0.05
Supplementary files format and content: S.aureus_RNAseq_count_data.xlsx; normalized count data

organism: Staphylococcus aureus

source_name: culture

growth_protocol: S. aureus CBS2016-05 and PS/BAC/317/16/W strains were grown in TSB and PCs at 22-24°C until early stationary phase.

extract_protocol:
The cells of CBS2016-05 and PS/BA/317/16/W from TSB and PCs from early stationary phase were pelleted at 4°C and subjected to RNA extraction using the miRNeasy Mini Kit, following the manufacturer's instructions. To eliminate genomic DNA, the RNA samples from three independent biological replicates were treated with TURBO™ DNase AmbionTM (Thermo Fisher Scientific). Furthermore, the RNA samples from spiked PCs underwent an additional treatment using the MICROBEnrich™ kit (Ambion) to remove eukaryotic RNA.
Input total RNA concentration was measured with the Qubit HS RNA assay (Thermo Q32855). RNA quality was assessed on the Fragment analyzer Standard Sensitivity RNA assay (Agilent DNF-472-0500), with RNA Quality Numbers (RQN) above 8.0.  DNA libraries were prepared using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina 20040525), using 150ng of input total RNA. Quantification of the libraries was performed with the Qubit Double Stranded DNA HS kit (Thermo Q32854) and ran on the AATI Fragment Analyzer with the High Sensitivity NGS assay (Agilent DNF-486-0500) to verify the size distribution of the template library.  The libraries were normalized, pooled, and diluted as required to achieve acceptable cluster density on the NextSeq 500 sequencer (Illumina SY-414-1001). The library pool then underwent 75 Cycle High Output (Illumina 20024906).
RNA-seq was using the NexSeq 500 platform (Illumina).

tag: cell type

value: culture


title: 21966


title: bone metastasized cancer 1 from patient 1

value: surgery, chemotherapy or radiotherapy

value: patient 1


title: S2016-PC1b


title: 20634


title: primary cancer 4 from patient 4

source_name: primary cancer tissue from FFPE specimen

value: primary cancer


title: S2016-TSB1a

description: CBS2016-05 grown in TSB until early stationary phase


title: primary cancer 5 from patient 5


title: S2016-TSB1c


title: MGH3 (HTR10-GFP) ChIP-seq in ddm1 biol Rep1

description:
Compared to its input in processed file (log2 fold change of normalized CPM)
ddm1_MGH3_IP_Rep1

source_name: pollen

value: pollen

tag: background

value: Col0 + pHTR10:HTR10-GFP

tag: chip antibody

value: anti-GFP (Thermofisher scientific; A-11122)

value: crosslinking


title: S2016-TSB1b


title: Input control for MGH3 (HTR10-GFP) ChIP-seq in ddm1 biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM)
ddm1_MGH3_Input_Rep1


title: 20241

value: Shetland Sheepdog

value: male


title: BAC317-PC1c

description: PS/BAC/317/16/W grown in PCs until early stationary phase


title: Input control for MGH3 (HTR10-GFP) ChIP-seq in WT biol Rep1

description:
Used to compared to IP in processed file (log2 fold change of normalized CPM). Processed as single-end (R1) to compare with ddm1 mutant
WT_MGH3_Input_Rep1

value: wild-type


title: 20214


title: 20595

value: Invasive Urothelial Carcimona


title: primary cancer 3 from patient 3


title: 20244

value: Unaffected

value: female


title: primary cancer 2 from patient 2


title: primary cancer 1 from patient 1


title: NdpKO; SmoA1+/- Subdural Meninges Replicate 2

city: Toronto

first: Nenad

middle: T

last: Pokrajac

state: Ontario

address: 60 Leonard Ave

department: Vision Science

institute: University Health Network

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw FASTQ sequencing reads were aligned to the Genome Research Consortium (GRC) mm10-2020-A mouse genome build using Cell Ranger (v6.1.2) for alignment, filtering, barcode counting and unique molecular identified (UMI) counting.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Subdural Meninges

extract_protocol:
Subdural meningeal cells were obtained from SmoA1+/- and NdpKO; SmoA1+/- mixed litters of mice aged P7 to P9 with the same amount of mice from each litter for each genotype. 5 cerebella were pooled for each sample, from a collection of 3 litters per run. Samples were collected in four separate runs, with each SmoA1+/- run litter matched to a NdpKO; SmoA1+/- run. Mice were euthanized by decapitation and brain and skullcap were cut away from the rest of the head. The skullcap, to which the dura mater is adhered, was peeled away from the brain. The brain was placed in a 10 cm2 plate with 1X Ca2+ Mg2+ free HBSS. Fragments of the subdural meninges were peeled off of the cerebellum, ignoring choroid plexus tissue as well as cerebral meningeal tissue. The subdural meningeal fragments were submerged in room temperature 2.5 mg/mL Dispase II solution in Ca2+ Mg2+ HBSS. After dissection, samples were incubated at 37oC for 30 minutes with constant agitation. Post incubation, samples were triturated 25 times using a p1000 pipette, and then returned to the 37oC incubator for 5 additional minutes under constant agitation. Samples were centrifuged at 300xg for 5 minutes and resuspended in 500 µL ion-free HBSS w/ 0.04% BSA. Cell suspensions were then pipetted onto 4 mL of 22% Percoll in a 5 mL Eppendorf tube, and centrifuged at 560xg for 10 minutes, with acceleration and deceleration set to 0 to avoid remixing of the phases. Supernatant was decanted and pellets were resuspended in 100 µL of HBSS w/ 0.04% BSA. The cell suspensions were strained through a 35 µm filter at 100xg for 1 minute. Finally, cells were counted in a haemocytometer and diluted to a concentration of 700-1200 cells/µL.
Samples were provided to the Princess Margaret Genomics Centre. Single cell suspensions were prepared according to Chromium Single Cell 3' Reagent Kit User’s Guide (v3.1 chemistry). Samples were loaded onto a 10X Chromium to generate sequencing libraries and processed according to 10X Genomics methods. Sequences were read using an Illumina HiSeq2500 sequencer and demultiplexed from raw base call files to FASTQ files.

value: Subdural Meninges

value: NdpKO; Neurod2-SmoA1+/-


title: primary cancer 6 from patient 6

value: patient 6


title: S2016-PC1a

value: culture


title: 20207


title: BAC317-PC1a


title: NdpWT; SmoA1+/- Subdural Meninges Replicate 1

description: 10x Genomics

value: NdpWT; Neurod2-SmoA1+/-


title: MGH3 (HTR10-GFP) ChIP-seq in WT biol Rep1

description:
Compared to its input in processed file (log2 fold change of normalized CPM). Processed as single-end (R1) to compare with ddm1 mutant.
WT_MGH3_IP_Rep1


title: 16069


title: BAC317-TSB1c

description: PS/BAC/317/16/W grown in TSB until early stationary phase


title: SupT1/Rev rep2

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

data_processing:
Raw image files were transformed to sequence reads by CASAVA base calling.
Sequenced reads were trimmed for adapater sequences, then mapped to hg19 using STAR.
Differential expression was performed by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: count data and differential expression data

source_name: T-lymphoblast cell line

growth_protocol: SupT1 cells were routinely passaged 2-3 times per week. Twenty-four hours prior to transductions, SupT1 cells were split 1:4.

extract_protocol:
Total RNA was extracted using phenol/chlorform prior to ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SupT1 cells ( 10^6 cells) were transduced with each virus stock using an moi of 2.

tag: cell line

value: T-lymphoblast

value: HIV Rev


title: SupT1/Rev rep3


title: 16127


title: SupT1/EV rep3

value: empty vector


title: SupT1/EV rep2


title: BAC317-TSB1a


title: 13544


title: aCTLA4

first: David

last: Brooks

address: 610, University Ave

institute: Princess Margaret Cancer Centre

data_processing:
Base calling was performed using Illumina RTA (v 3.4.4) and bcl2fastq2 (v 2.20) to generate bcl files. Cell ranger (v 6.0.0) was then used to demultiplex bcl into fastq files and to align reads to the mm10 genome (refdata-gex-mm10-2020-A downloaded from the 10x genomics website).
Quality control and normalization : Data was further analysed using R (v 4.1.1) and the R Seurat (v 4.0.4) package (Hao et al. 2021). Cells meeting the below criteria were considered as good quality cells and were kept for subsequent analyses:
1) Naïve: 500 < genes expressed < 2300 and mitochondrial genes (%) < 10  (7955 cells); 2)Isotype: 500 < genes expressed < 6000 and mitochondrial genes (%) < 12 (1099 cells); 3)aCTLA4: 1000 < genes expressed < 6000 and mitochondrial genes (%) < 7 (4566 cells); 4)Treg depletion: 700 < genes expressed < 7000 and mitochondrial genes (%) < 12 (2186 cells); 5)Treg depletion + aCTLA4: 600 < genes expressed < 6000 and mitochondrial genes (%) < 13 (4343 cells).
Gene expression of all samples were normalized using the LogNormalize method and adjusted to regress out percentage of mitochondrial genes and cell cycle genes. Then data was exported to the SeqGeq application (v 1.8) where data was normalized using the scTransform normalization and clustered using Louvain algorithm method and 0.3 resolution using the Seurat plug-in of SeqGeq.
Assembly: mm10
Supplementary files format and content: raw counts matrix of each sample was saved as a csv file

source_name: SMARTA cells sorted from tumor lymph node

growth_protocol: 1x106 MC38 tumor cells were injected into the mammary fat pad of each mouse. SMARTA cells were sorted from ingunial lymph node at day 8 after implantation. Naïve SMARTA cells were isolated as control

extract_protocol:
Lymph nodes were cut into small fragments and digested as described in the manuscript. CD4 T cells were enriched on autoMACS Pro Separator (Miltenyi Biotec). CD4+CD45.1+ SMARTA cells were FACSorted on a Moflo Astrios (Beckman Coulter) or a BD FACSaria Fusion cell sorter.
After sorting and purity check on flow cytometer, SMARTA cells were then resuspend in 10X Genomics Chromium single cell RNA master mix and loaded onto a 10x chromium chip. cDNA Library was generated using the Chromium Single Cell 3’ Reagents Kits v2 User Guide:CG00052 Rev B, and then sequenced on the Illumina HiSeq 2500 platform to achieve an average of 40,000 reads per cell. Sequencing was performed at the Princess Margaret Genomics Center.

treatment_protocol: Mice were treated with diphtheria toxin or PBS at day 0 and 2 post PyMG tumor injection. Anti-CTLA4 antibody was injected at day 0, 2 and 5 after tumor injection.

value: TCR transgenic CD4 T cells

value: CTLA4 blockade


title: untreat

value: SMARTA cells sorted from tumor lymph node


title: SupT1/Rev rep1


title: 20048

value: Shetland Sheepdog


title: NdpKO; SmoA1+/- Subdural Meninges Replicate 1

description: 10x Genomics


title: NdpWT; SmoA1+/- Subdural Meninges Replicate 2

description: 10x Genomics


title: Treg-depleted

value: Treg depletion


title: Treg-depleted and aCTLA4

value: Treg depletion and CTLA4 blockade


title: BAC317-TSB1b


title: naïve

source_name: SMARTA isolated from spleen

value: SMARTA isolated from spleen


title: SupT1 rep2

value: untreated


title: 20365

value: Unaffected

value: Mixed breed

value: unknown


title: 16124

value: Invasive Urothelial Carcimona

value: female


title: BAC317-PC1b

value: culture


title: SupT1 rep1

value: T-lymphoblast


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

city: Portland

first: Michael

middle: J

last: Gough

state: Oregon

address: 4805 NE Glisan St

department: EACRI

institute: Providence Portland Medical Center

description: Pan-Cancer Immune Profiling

hyb_protocol: Samples were then hybridized with NanoString pan-cancer immune profiling probes for 16 hours and were subsequently loaded into an nCounter FLEX cartridge

scan_protocol: nCounter FLEX Analysis System

data_processing: Raw data were normalized utilizing default settings. Fold changes in gene expression were exported to Ingenuity Pathway Analysis for further analysis

source_name: Whole tumor RNA isolated from subcutaneous Panc02-SIY pancreatic tumors

growth_protocol: 5.0  x 10^6 Panc02-SIY cells were implanted subcutaneously in syngeneic mice

extract_protocol: 7 days post-RT (16 Gy), whole tumor RNA was isolated from snap frozen Panc02-SIY tumors. 10-20 mg of snap frozen tumors were crushed on liquid nitrogen and RNA was extracted using the RNeasy Micro Kit (QIAGEN) according to the manufacturer’s instructions

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

value: Lyz2-Cre/Myd88 fl/fl

value: Panc02-SIY tumor

value: 7 days post-radiation therapy (16 Gy)


title: Myd88 fl/fl 16 Gy 2

description: Pan-Cancer Immune Profiling

value: Myd88 fl/fl


title: XP0962 MNase-assisted H3 ChIP-seq

status: Public on Aug 27 2023

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

description:
MNase-assisted H3 ChIP-seq
Original sequencing data for all samples are available at the European Genome-phenome Archive (http://www.ebi.ac.uk/ega/), hosted by the European Bioinformatics Institute under the accession number EGAS00001002518.

data_processing:
ChIP-seq H3 reads were mapped to the human genome hg19 using Bowtie allowing up to two mismatches and only unique alignments.
DNA fragments with sizes 120-180bp were selected and used for further analysis
BigWig files were calculated with BedTools
Differential nucleosome positioning was defined with NucTools
Genome_build: hg19
Supplementary_files_format_and_content: BED file format
M-CLL_less_Healthy.bed: BED (regions which lost nucleosomes in M-CLL vs healthy)
M-CLL_more_Healthy.bed: BED (regions which gained nucleosomes in M-CLL vs healthy)
U-CLL_less_Healthy.bed: BED (regions which lost nucleosomes in U-CLL vs healthy)
U-CLL_less_M-CLL.bed: BED (regions which lost nucleosomes in U-CLL vs M-CLL
U-CLL_more_Healthy.bed: BED (regions which gained nucleosomes in U-CLL vs healthy)
U-CLL_more_M-CLL.bed: BED (regions which gained nucleosomes in U-CLL vs M-CLL

source_name: B-cells from CLL patient XP

growth_protocol: Cells were cultured on 0.2% v/v gelatine (in PBS) in high glucose DMEM (gibco 31053-028) supplemented with 1 mM sodium pyruvate and 4 mM L-Glutamine (PAA M11-006), 15% v/v FCS (Sigma F7524, lot: 091M3398), 1% v/v Penicillin-Streptomycin (PAN Biotech P06-07100), 100 µM β-mercaptoethanol (Sigma 63689), 1% v/v non-essential amino acids and 0.41% v/v LIF (self-made; supernatant from LIF-producing cells; batch: 7/26/14).

extract_protocol:
Patient derived cells were crosslinked with 1 % methanol-free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS and the cell pellet was frozen in liquid nitrogen. For analysis, the cell pellet was thawn and treated with 4U MNase per 1x106 cells for 15 min. MNase was stopped with 10x covaris buffer and the chromatin was sheared for an additional 15 min with the S2 covaris device and the soluble chromatin was then recovered and subjected to a background-minimizing pre-clearing step with an unspecific IgG antibody. For each ChIP-assay an equivalent of 3x106 cells were used with the following antibody: H3 (Abcam, ab1791). After the IP, chromatin was digested with RNaseA and proteinase K. The purified DNA was cloned into illumina sequencing libraries with the NEBNext Ultra library preparation kit (NEB).
The libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, NEB #E7370) according to the manufacturer’s instructions.

value: B cells

tag: antibody

value: histone H3

tag: diagnosis

value: M-CLL


title: ZV1179 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient ZV


title: 11617

value: Shetland Sheepdog


title: XP0970 MNase-assisted H3 ChIP-seq


title: ZV1188 MNase-assisted H3 ChIP-seq


title: Myd88 fl/fl 16 Gy 1

description: Pan-Cancer Immune Profiling


title: SupT1/EV rep1

value: empty vector


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

description: Pan-Cancer Immune Profiling


title: WW0529 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient WW


title: RC1143 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient RC


title: RC1152 MNase-assisted H3 ChIP-seq


title: TH0456 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient TH


title: WW0538 MNase-assisted H3 ChIP-seq


title: QU1028 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient QU

value: U-CLL


title: PP1102 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient PP


title: PP1093 MNase-assisted H3 ChIP-seq


title: QU1019 MNase-assisted H3 ChIP-seq


title: KL0603 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient KL


title: KL0612 MNase-assisted H3 ChIP-seq


title: GN1125 MNase-assisted H3 ChIP-seq

source_name: B-cells from healthy pool GN

value: healthy


title: IO1212 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient IO


title: EM1161 MNase-assisted H3 ChIP-seq

source_name: B-cells from healthy pool EM


title: GN1134 MNase-assisted H3 ChIP-seq


title: EM1170 MNase-assisted H3 ChIP-seq


title: CX0586 MNase-assisted H3 ChIP-seq

source_name: B-cells from CLL patient CX


title: CX0577 MNase-assisted H3 ChIP-seq


title: BK0916 MNase-assisted H3 ChIP-seq

source_name: B-cells from healthy pool BK


title: Spleen_CK_rep1_RNA

city: chengdu

first: tengda

last: huang

address: gaopeng road

country: China

institute: sichuan university

description: mRNA

data_processing:
For both mRNA and RPF sequencing data sets, high-quality reads were mapped to the mRNA reference sequence (GRCg6a) through the FANSe2 algorithm with the parameters -E5% --indel -S14.
The expression abundance of mRNA and RPFs was normalized by RPKM (reads per kilobase per million reads)
Differentially expressed genes (DEGs) in RNA-seq and Ribo-seq were identified via the edgeR package with |log2-fold change| > 1 and false discovery rate (FDR) < 0.01.
The quotient of RPFs and mRNA expression abundance is translation efficiency (TE). Differential TE genes (DTEGs) were calculated by a t test with |log2-fold change| > 1 and p value < 0.05.
Bioinformatic analysis was performed using Omicsmart, a real-time interactive online platform for data analysis (http://www.omicsmart.com).
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

organism: Gallus gallus

source_name: Spleen

growth_protocol: "White Leghorn" SPF chicken eggs were purchased from Beijing Boehringer Ingelheim Vital Biotechnology Co, Ltd. (Beijing, China). Incubation was performed using a fully automated incubator, after which chicks were transferred to an SPF chicken isolator for rearing. Twenty 7-day-old SPF chickens were randomly divided into two groups of 10 chickens and raised aseptically in an SPF chicken isolator.

extract_protocol:
Total RNA of the spleen in each group was extracted by using TRIzol® RNA extraction reagent (Invitrogen, USA) according to the manufacturer’s instructions. The integrity of RNA was examined by agarose gel electrophoresis, and the concentration of RNA was measured by NanoDrop 2000 spectrophotometers (Thermo Fisher, USA). The mRNA was purified by oligo (dT) magnetic beads and fragmented into short fragments using fragmentation buffer. First-strand cDNA was synthesized with SuperScript II Reverse Transcriptase (Invitrogen) using random primers, and second-strand cDNA was synthesized using the synthesized first strand of cDNA as a template.
The obtained double-stranded cDNA was purified by a VAHTS® mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, China), end repaired, poly(A) added, and then ligated to Illumina sequencing adapters. Sequencing was performed on the Illumina HiSeq-2000 platform for 50 cycles. High-quality reads passed through the Illumina quality filter were retained in fastq.gz format for sequence analysis.

treatment_protocol: Group A was the experimental group (ARV), and each chicken was inoculated with 0.1ml 104 TCID50/0.1ml ARV S1133 virus by foot pad injection. Group B was the control group (CON), which was inoculated with the same amount of PBS via foot pad injection. Samples were collected on day 3 after infection.

value: Spleen

value: White Leghorn

value: wt

value: chicken was inoculated with the same amount of PBS via foot pad injection.Spleen was collected on day 3 after infection.


title: Spleen_ARV_rep2_Ribo

description: total Ribosome protected fiagments

data_processing:
For both mRNA and RPF sequencing data sets, high-quality reads were mapped to the mRNA reference sequence (GRCg6a) through the FANSe2 algorithm with the parameters -E5% --indel -S14.
The expression abundance of mRNA and RPFs was normalized by RPKM (reads per kilobase per million reads)
Differentially expressed genes (DEGs) in RNA-seq and Ribo-seq were identified via the edgeR package with |log2-fold change| > 1 and false discovery rate (FDR) < 0.01.
The quotient of RPFs and mRNA expression abundance is translation efficiency (TE). Differential TE genes (DTEGs) were calculated by a t test with |log2-fold change| > 1 and p value < 0.05.
Bioinformatic analysis was performed using Omicsmart, a real-time interactive online platform for data analysis (http://www.omicsmart.com).
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
Library strategy: Ribo-seq

extract_protocol:
Spleen tissue from each group was added to lysis buffer, ground at low temperature, and then low concentrations of RNase I were added for digestion. The digested samples were pooled and layered on the surface of 15 ml sucrose buffer (30% sucrose in RB buffer). The ribosomes were pelleted by ultracentrifugation at 42500 rpm for 5 h at 4 °C. RPF extraction was then performed using TRIzol, and ribosomal RNA (rRNA) was depleted using the Ribo-off® rRNA Depletion Kit (Vazyme) following the manufacturer’s instructions.
Sequencing libraries of RPFs were constructed following the VAHTS® Small RNA Library Prep Kit for Illumina (Vazyme). The library was resolved by a 6% polyacrylamide gel. The fraction with an insertion size of ~28 nt was excised and purified from the gel. This fraction was sequenced by an Illumina HiSeq-2000 sequencer for 50 cycles. High-quality reads that passed the Illumina quality filters were kept for sequence analysis.

value: chicken was inoculated with 0.1ml 104 TCID50/0.1ml ARV S1133 virus by foot pad injection.Spleen was collected on day 3 after infection.


title: Spleen_ARV_rep2_RNA

description: mRNA


title: Spleen_ARV_rep1_Riibo

description: total Ribosome protected fiagments


title: Spleen_CK_rep2_RNA

description: mRNA


title: Spleen_CK_rep2_Ribo

description: total Ribosome protected fiagments


title: Spleen_ARV_rep1_RNA

description: mRNA


title: IO1203 MNase-assisted H3 ChIP-seq


title: Mpp-E15.5-3

city: Fuzhou City , Fujian Province, China.

first: Yongzhen

last: Lai

state: Fuzhou

address: No. 28, Xinquan Road, Fuzhou City (350001), Fujian Province, China.

institute: Department of Oral and Cranio-maxillofacial Science, Fujian Medical university Union Hospital,

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: palatal processes of the maxilla

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: palatal processes of the maxilla

value: no


title: Mpp-E15.5-2


title: Mpp-E16.5-1


title: Mpp-E14.5-1


title: Mpp-E15.5-1


title: Mpp-E14.5-2


title: Mpp-E14.5-3


title: Mpp-E16.5-2


title: pp-E14.5-1

source_name: palatal processes of the palatine

value: palatal processes of the palatine


title: pp-E16.5-3


title: pp-E15.5-1


title: pp-E14.5-3


title: pp-E15.5-3


title: pp-E14.5-2


title: BK0925 MNase-assisted H3 ChIP-seq


title: pp-E15.5-2


title: pp-E16.5-2


title: Spleen_CK_rep1_Ribo

description: total Ribosome protected fiagments


title: pp-E16.5-1


title: B73 - High-MNase-seq

city: Nanjing City

first: Wenli

last: Zhang

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: Nanjing Agricultural University

data_processing:
For MH-seq, MNase-seq and ChIP-seq data, sequencing reads were trimmed using fastp v0.20.0. Short reads (<50 bp) and reads with quality score (< 20) were removed, all trimmed reads were mapped to Zea mays B73 AGPv4 reference genome using Bowtie2. Aligned reads were sorted using SAMtools v1.5, properly paired reads were extracted using ‘samtools view -f 0x2 -q 20’.
Two biological MH-seq data were merged for MHS peak calling using MACS2 with ‘-f BAMPE -g 2.2e9 –nomodel -q 0.001 --fe-cutoff 5’. The R package ChIPseeker was used for MHS Peak annotation. L/HMNase-seq data were used for global identification of nucleosome positions. Nucleosome positions were identified by DANPOS2 using ‘dpos --paired 1 -p 1e-6 -q 0’. The highest point of each nucleosome was defined as the nucleosome center.
Genome_build: B73 v4
Supplementary_files_format_and_content: bigWig files were generated using deeptools bamCoverage.
Supplementary_files_format_and_content: bed files were generated using DANPOS2.

organism: Zea mays

source_name: B73 seedling

growth_protocol: Seeds of maize (Zea mays “B73”) were soaked in peri dish with wet paper towel and put at 23-25℃ for pregermination. Evenly germinated seeds were transferred to the pots containing soil and continued to grow in a growth chamber at a 16 h/8 h light-dark cycle at 25-28℃ for 10 days. Leaf tissues were collected from 10 individual 10-day-old plants for immediate downstream treatment or stored at -80 ℃ for later use. Sterilized seeds of Arabidopsis seeds (Col-0) were germinated in half-strength MS medium and grown under a 16 h/8 h light/dark cycle at 20-23 ℃ for 2 weeks.

extract_protocol:
MNase-seq: For simultaneous measurement of MHSs and nucleosome positioning in the similar MNase cleavage condition, we specifically recovered approximately 150 bp mononucleosomal DNA fragments from 100 U and 900 U MNase-trimmed native maize nuclei (indicated by the violet box in Fig. 1a) and from 20 U MNase-trimmed fixed Arabidopsis nuclei (indicated by the violet box in Additional file 1: Fig. S4).
MNase-seq: The recovered DNA fragments were used for MNase-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S). The MNase-seq library was quality controlled and sequenced using Illumina NovaSeq platform.

tag: cultivar

value: Leaf

value: 10 days

tag: mnase concentration

value: 900 U MNase


title: B73 - Low-MNase-seq

tag: age

value: 100 U MNase


title: B73 - Low-H3-ChIP-seq

data_processing:
For MH-seq, MNase-seq and ChIP-seq data, sequencing reads were trimmed using fastp v0.20.0. Short reads (<50 bp) and reads with quality score (< 20) were removed, all trimmed reads were mapped to Zea mays B73 AGPv4 reference genome using Bowtie2. Aligned reads were sorted using SAMtools v1.5, properly paired reads were extracted using ‘samtools view -f 0x2 -q 20’.
Two biological MH-seq data were merged for MHS peak calling using MACS2 with ‘-f BAMPE -g 2.2e9 –nomodel -q 0.001 --fe-cutoff 5’. The R package ChIPseeker was used for MHS Peak annotation. L/HMNase-seq data were used for global identification of nucleosome positions. Nucleosome positions were identified by DANPOS2 using ‘dpos --paired 1 -p 1e-6 -q 0’. The highest point of each nucleosome was defined as the nucleosome center.
Genome_build: B73 v4
Supplementary_files_format_and_content: bigWig file was generated using deeptools bamCoverage.
Supplementary_files_format_and_content: bed file was generated using DANPOS2.

growth_protocol: Seeds of maize (Zea mays “B73”) were soaked in peri dish with wet paper towel and put at 23-25℃ for pregermination. Evenly germinated seeds were transferred to the pots containing soil and continued to grow in a growth chamber at a 16 h/8 h light-dark cycle at 25-28℃ for 10 days. Leaf tissues were collected from 10 individual 10-day-old plants for immediate downstream treatment or stored at -80 ℃ for later use.

extract_protocol:
H3-ChIP-seq: Regular histone H3 ChIP-seq was conducted using native nuclei. The ChIP procedures were followed the published protocol. Nuclei with a similar chromatin digestion pattern as 100 U MNase-treated nuclei in Fig. 1a were chosen for incubation with regular histone H3 antibody (ab1791, abcam) (LH3 ChIP).
H3-ChIP-seq: ChIPed DNA was finally recovered for library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S). The LH3 ChIP-seq library was quality controlled and sequenced using Illumina NovaSeq platform.

tag: tissue

value: H3 (ab1791, abcam)


title: Mpp-E16.5-3


title: B73 - MH-seq rep1

description:
B73-leaf-MH-seq-merged.bw
B73_MHS_merged_peaks.narrowPeak

data_processing:
Library strategy: MNase-seq
For MH-seq, MNase-seq and ChIP-seq data, sequencing reads were trimmed using fastp v0.20.0. Short reads (<50 bp) and reads with quality score (< 20) were removed, all trimmed reads were mapped to Zea mays B73 AGPv4 reference genome using Bowtie2. Aligned reads were sorted using SAMtools v1.5, properly paired reads were extracted using ‘samtools view -f 0x2 -q 20’.
Two biological MH-seq data were merged for MHS peak calling using MACS2 with ‘-f BAMPE -g 2.2e9 –nomodel -q 0.001 --fe-cutoff 5’. The R package ChIPseeker was used for MHS Peak annotation. L/HMNase-seq data were used for global identification of nucleosome positions. Nucleosome positions were identified by DANPOS2 using ‘dpos --paired 1 -p 1e-6 -q 0’. The highest point of each nucleosome was defined as the nucleosome center.
Genome_build: B73 v4
Supplementary_files_format_and_content: bigWig files were generated using deeptools bamCoverage.
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2.

extract_protocol:
MH-seq: Two-week-old whole seedlings or small pieces cut from the 10-day-old leaf tissues (2-3 g) were soaked in fixation buffer (20mM HEPES, 1mM EDTA, 100mM NaCl, 1mM PMSF, pH 8.0) containing 1% of final concentration of formaldehyde (Sigma, cat. no. F-8775) under vacuum for 10 min at 23-25℃, then followed by adding 2 M Glycine (Sigma, cat. no. 50046) to a final concentration of 0.125 M under vacuum for additional 5 min for quenching the excessive formaldehyde. The cross-linked leaves were ground to a fine powder in liquid nitrogen. The ground powder was used for nuclei preparation and purification following published procedures. The purified nuclei pellet was resuspended in 1.2 ml of MNase digestion buffer (20 mM Tris-HCl, 4 mM MgCl2, 1mM CaCl2, 60 mM KCl, pH 7.5). The suspended nuclei were equally aliquoted into 5 of 1.5 ml Eppendorf tubes (200 μl each). The aliquoted nuclei were incubated in water bath at 37℃ for 10 min using a series of MNase (M0247, 2,000 gels units/μl, NEB) with a final amount as 0 unit (U), 90 U, 100 U, 700 U and 900 U, respectively, then followed by adding 16 μl 0.5 M EDTA (pH 8.0) to stop enzymatic reaction. Each MNase trimmed nuclei aliquot was added 16 μl 5 M NaCl, 8 μl 20% SDS and 160 μl 1X TE and incubated in 65℃ water bath overnight for reverse cross-linking. After sequential treatment using RNase A at 65℃ for 30 min and proteinase K at 55℃ for 2 h, reversed cross-linked nuclei were sequentially extracted by adding 1 volume of phenol, phenol:chloroform mixture and chloroform, then followed by pellet precipitation using 2 volumes of cold 200 proof ethanol. The air-dry DNA was dissolved using 20 μl EB (10 mM Tris-HCl, pH 8.0). The purified DNA was separated by running 2% of agarose gel in 1xTBE buffer. We chose DNA from 100 U and 900 U MNase-trimmed nuclei, representing the light and heavy MNase digestion condition, respectively, for recovering small-sized DNA fragments ranging from 40-100 bp (indicated by the red box in Fig. 1a).
MH-seq: The recovered small-sized DNA was used for MH-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S). The MH-seq library was quality controlled and sequenced using Illumina NovaSeq platform.


title: B73 - MH-seq rep2


title: C29 Healthy individual

city: Zhengzhou

first: Liping

last: Dai

state: Henan

address: 40 Daxue Road

institute: Zhengzhou University

description: serum miRNA expression in healthy individual

hyb_protocol: Sample array hybridization were performed according to the Agilent miRNA Microarray System with Hyb Kit protocol (Agilent Technology). The labeled cRNA over the procession of inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 10 out of 30 samples have flags in Detected were chosen for further data analysis.

source_name: Serum

label_protocol: Sample labeling was performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp (cy3) under the action of T4 RNA ligase.

extract_protocol: Total RNA was extracted each from 1 ml serum samples using TRIzol® Reagent (Invitrogen life technologies).

value: Serum

tag: gender

value: Female/Female

tag: disease state

value: Healthy individual


title: C30 Healthy individual


title: C28 Healthy individual


title: C27 Healthy individual


title: C24 Healthy individual

value: Male/Male


title: C22 Healthy individual


title: C26 Healthy individual


title: C23 Healthy individual


title: B15 Malignant pulmonary nodule

description: serum miRNA expression in malignant pulmonary nodule

value: Malignant pulmonary nodule


title: B14 Malignant pulmonary nodule


title: B20 Malignant pulmonary nodule


title: C21 Healthy individual


title: B13 Malignant pulmonary nodule


title: B18 Malignant pulmonary nodule


title: B19 Malignant pulmonary nodule


title: B12 Malignant pulmonary nodule


title: B11 Malignant pulmonary nodule


title: A10 Benign pulmonary nodule

description: serum miRNA expression in benign pulmonary nodule

value: Benign pulmonary nodule


title: B17 Malignant pulmonary nodule


title: A8 Benign pulmonary nodule


title: A6 Benign pulmonary nodule


title: A9 Benign pulmonary nodule


title: A4 Benign pulmonary nodule


title: A5 Benign pulmonary nodule


title: C25 Healthy individual


title: A3 Benign pulmonary nodule


title: A2 Benign pulmonary nodule


title: SpibKO_mTEC3_r2

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Data was processed using UTAP transcriptome analysis pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.5.2b (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded using HTSeq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: tab delimited file include raw counts, normalized abundance measurements and DESeq2 analysis

source_name: Thymic epithelial cells

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. TEC populations were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et. Al. 2014)

value: Thymic epithelial cells

tag: genotype

value: Spib KO

value: 5 weeks old

tag: protocol

value: Bulk Mars-Seq (3' end-RNA-seq)


title: B16 Malignant pulmonary nodule


title: SpibWT_mTEC3_r3

value: Spib WT


title: SpibKO_mTEC3_r3


title: SpibKO_mTEC3_r1


title: SpibWT_mTEC3_r1


title: A1 Benign pulmonary nodule


title: SpibWT_mTEC3_r2


title: Insm1_crepos_mTEC3_r2

value: Insm1 cKO

value: 4 weeks old


title: A7 Benign pulmonary nodule


title: Insm1_crepos_mTEC3_r3


title: Insm1_creneg_mTEC3_r3

value: Insm1 WT


title: Insm1_creneg_mTEC3_r2


title: Insm1_crepos_mTEC3_r1


title: IgMKO_mTEC3_r3

description: DESeq2_IgMKO_mTEC3_umi_counts_20221119_060555.xlsx

value: IgM KO


title: Insm1_creneg_mTEC3_r1


title: IgMWT_mTEC3_r1

value: IgM WT


title: IgMKO_mTEC3_r1


title: IgMWT_mTEC3_r2


title: IgMKO_mTEC3_r2


title: Ccr6WT_mTEC3_r2

description: DESeq2_CCR6KO_3_umi_counts_20230313_075749.xlsx

value: Ccr6 WT


title: IgMKO_mTEC3_r4


title: Ccr6WT_mTEC3_r4


title: Ccr6KO_mTEC3_r4

value: Ccr6 KO


title: Ccr6WT_mTEC3_r3


title: Ccr6KO_mTEC3_r3


title: Ccr6KO_mTEC3_r2


title: 3 Heteropost TEC

description:
DESeq2_20220616_mTEC3_umi_counts_20220616_085837.xlsx
DESeq2_CorneoTEC_umi_counts_20220619_115817.xlsx
DESeq2_EndoVSOthers_umi_counts_20220619_115336.xlsx
DESeq2_Hetero-post_TEC_umi_counts_20220619_120042.xlsx
DESeq2_MicrofoldTEC_umi_counts_20220619_115646.xlsx

data_processing:
Data was processed using UTAP  transcriptome analysis pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.5.2b (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded using HTSeq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: tab delimited file include raw counts, normalized abundance measurements and DESeq2 analysis

value: WT

tag: strain


title: 3 MicrofoldTEC


title: 3 CorneoTEC


title: 2 CorneoTEC


title: 2 Heteropost TEC


title: 3 EndoTEC


title: 2 MicrofoldTEC


title: 2 EndoTEC


title: 1 Heteropost TEC


title: 1 MicrofoldTEC


title: 1 CorneoTEC


title: 3 Dump

description:
DESeq2_CilTEC_vs_other_umi_counts_20220619_114702.xlsx
DESeq2_Myo_vs_other_umi_counts_20220619_114752.xlsx


title: 3 MyoTEC


title: 2 Ly6dpos_CorneoTEC


title: 3 CilTEC


title: 3 Ly6dpos_CorneoTEC


title: 2 MyoTEC


title: 2 CilTEC


title: Ccr6KO_mTEC3_r1


title: 1 Dump


title: 1 CilTEC


title: 1 Ly6dpos_CorneoTEC


title: 1 MyoTEC


title: macrophages mono-cultured in 4T1 CM repetition 4 [BM_only_CM_4]

first: Shimrit

last: Mayer

state: Central

address: Herzl St 234

department: Bimolecular sciences

institute: Weizmann Institute

data_processing:
Illumina bcl2fastq software used for base calling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
aligment: STAR v2.4.2a parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis was done for genes having minimum 5 reads in at least one sample
Assembly: mm10
Supplementary files format and content: tab delimited text files include mRNA molecule count values for each sample

source_name: bone marrow drive macrophages

growth_protocol: 8  weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Bone marrow-derived monocytes from BALB/c female mice were differentiated into macrophages by growth in DMEM with 10% FBS, 5% P/S and 20% L929 CM on the petri dish. The medium was replenished on day 3 and the macrophages were reseeded for the experiment on day 7.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: The macrophages were harvested with non-enzymatic cell dissociation solution (Biological Industries,03-071-1B) and washed with PBS without calcium and magnesium. The  fibroblasts  were isolated and expanded for 7 days, after which the fibroblasts were trypsinized and resuspended in an ice-cold MACS buffer (PBS with 0.5% BSA). The samples were pelleted by centrifugation at 350g for 5 min at 4 °C, incubated with anti-EpCAM (Miltenyi, 130-105-958) and anti-CD45 (Miltenyi, 130-052-301) magnetic beads, transferred to LS columns (Miltenyi, 130-042-401) and the fibroblast-enriched, CD45/EpCAM-depleted flow-through was collected. Both cells seeded together 6-well plates precoated with collagen I. The co-cultures with fibroblasts were grown in DMEM with 10% FBS and 5% P/S or with 4T1 cancer CM . Every 3 days 1ml of medium (6well) were replaced with fresh medium.

value: bone marrow

value: BALB/c

value: bone marrow drive macrophages

tag: selection marker

value: Invitro mono-cultured of macrophages in cancer CM


title: macrophages mono-cultured in 4T1 CM repetition 3 [BM_only_CM_3]

tag: treatment


title: macrophages mono-cultured day 0 repetition 3 [BM_only_3]

value: Invitro mono-cultured Day 0


title: macrophages mono-cultured in 4T1 CM repetition 1 [BM_only_CM_1]


title: macrophages mono-cultured in 4T1 CM repetition 2 [BM_only_CM_2]


title: TH0447 MNase-assisted H3 ChIP-seq

tag: cell type

value: B cells

value: histone H3

value: M-CLL


title: macrophages mono-cultured day 0 repetition 1 [BM_only_1]


title: 1 EndoTEC

value: Thymic epithelial cells

value: 5 weeks old

value: Bulk Mars-Seq (3' end-RNA-seq)


title: macrophages mono-cultured day 0 repetition 2 [BM_only_2]


title: macrophages co-cultured with mammary fibroblasts in DMEM repetition 2 [BM_CO_DMEM_2]

value: Invitro co-cultured with fibroblasts in DMEM medium


title: macrophages co-cultured with mammary fibroblasts in DMEM repetition 1 [BM_CO_DMEM_1]


title: macrophages co-cultured with mammary fibroblasts in DMEM repetition 3 [BM_CO_DMEM_3]


title: 2 Dump


title: macrophages co-cultured with mammary fibroblasts  in 4T1 CM repetition 2 [BM_CO_CM_2]

value: Invitro co-cultured with fibroblasts in 4T1-conditioned medium


title: Mammary fibroblasts mono-cultured in DMEM repetition 3 [Mammary_only_3]

source_name: Normal mammary fat pad

extract_protocol:
Normal mammary fat pad and mesometrial fat fibroblasts were isolated and dissociated from the mammary fat pads or fat tissue of two BALB/c females per each biological replicate. Tissue was minced and dissociated using a gentle MACS dissociator, in the presence of an enzymatic digestion solution containing 1 mg/ml collagenase II (Merck Millipore, 234155), 1 mg/ml collagenase IV (Merck Millipore, C4-22) and 70 U/ml DNase (Invitrogen, 18047019) in Dulbecco’s modified Eagle’s medium (DMEM). The samples were filtered through a 70-μm cell strainer into cold PBS and cells were pelleted by centrifugation at 350g for 5 min at 4 °C and resuspended in red blood cell lysis buffer (BioLegend 420301), then washed with PBS and centrifuged at 350g for 5 min at 4 °C. Mammary and fat fibroblasts were seeded on collagen I (Cat. C3867, Sigma-Aldrich, Rehovot, Israel) coated 10cm or 6-well plates, respectively. The cells were expanded for 6 days in DMEM with 5% P/S and 10% of FBS and the media was replaced every 3 days.    Lungs of BALB/c female were excised, dissociated, minced, and incubated with enzymatic digestion solution containing 3 mg/ml collagenase A (Sigma Aldrich, 11088793001) and 70 unit/ml DNase in RPMI 1640 (Biological industries, 01-100-1A) using a gentleMACS dissociator, 30 min at 37oC. The samples were filtered through a 70-μm cell strainer into cold PBS and cells were pelleted by centrifugation at 350g for 5 min at 4 °C and resuspended in red blood cell lysis buffer, then washed with PBS and pelleted at 350g for 5 min at 4 °C. Lung fibroblasts were seeded on 10cm plates coated with collagen I. The cells were expanded for 5 days in DMEM with 5% P/S and 10% FBS and the medium was replaced after 3 days.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: The fibroblasts  were isolated and expanded for 7 days, afterwhich the fibroblasts were trypsinized and resuspended in an ice-cold MACS buffer (PBS with 0.5% BSA). The samples were pelleted by centrifugation at 350g for 5 min at 4 °C, incubated with anti-EpCAM (Miltenyi, 130-105-958) and anti-CD45 (Miltenyi, 130-052-301) magnetic beads, transferred to LS columns (Miltenyi, 130-042-401) and the fibroblast-enriched, CD45/EpCAM-depleted flow-through was collected. The macrophages were harvested with non-enzymatic cell dissociation solution (Biological Industries,03-071-1B) and washed with PBS without calcium and magnesium. The cells seeded together 6-well plates precoated with collagen I. The co-cultures were grown in DMEM with 10% FBS and 5% P/S  or 4T1-conditioned medium. Every 3 days 1ml of medium (6well) were replaced with fresh medium.

value: Normal mammary fat pad

value: Invitro mono-cultured of fibroblasts in DMEM medium


title: macrophages co-cultured with mammary fibroblasts  in 4T1 CM repetition 1 [BM_CO_CM_1]


title: Mammary fibroblasts mono-cultured in DMEM repetition 1 [Mammary_only_1]


title: Mammary fibroblasts co-cultured with macrophages in DMEM repetition 1 [Mammary_CO_DMEM_1]

value: Invitro co-cultured with macrophages in DMEM medium


title: Mammary fibroblasts co-cultured with macrophages in DMEM repetition 3 [Mammary_CO_DMEM_3]


title: Mammary fibroblasts co-cultured with macrophages in DMEM repetition 2 [Mammary_CO_DMEM_2]


title: Mammary fibroblasts co-cultured with macrophages in 4T1 CM repetition 4 [Mammary_CO_CM_4]

value: Invitro co-cultured with macrophages in 4T1-conditioned medium


title: Mammary fibroblasts mono-cultured in 4T1 CM repetition 2 [Mammary_only_CM_2]

value: Invitro mono-cultured of fibroblasts in 4T1-conditioned medium


title: Mammary fibroblasts co-cultured with macrophages in 4T1 CM repetition 3 [Mammary_CO_CM_3]

value: BALB/c


title: Mammary fibroblasts co-cultured with macrophages in 4T1 CM repetition 2 [Mammary_CO_CM_2]


title: Mammary fibroblasts mono-cultured repetition 4

treatment_protocol: The fibroblasts  were isolated and expanded for 7 days, afterwhich the fibroblasts were trypsinized and resuspended in an ice-cold MACS buffer (PBS with 0.5% BSA). The samples were pelleted by centrifugation at 350g for 5 min at 4 °C, incubated with anti-EpCAM (Miltenyi, 130-105-958) and anti-CD45 (Miltenyi, 130-052-301) magnetic beads, transferred to LS columns (Miltenyi, 130-042-401) and the fibroblast-enriched, CD45/EpCAM-depleted flow-through was collected. The macrophages were harvested with non-enzymatic cell dissociation solution (Biological Industries,03-071-1B) and washed with PBS without calcium and magnesium. The cells seeded together 6-well plates precoated with collagen I. The co-cultures were grown in DMEM with 10% FBS and 5% P/S . Every 3 days 1ml of medium (6well) were replaced with fresh medium.

value: Non-immune stromal cells

value: Invitro mono-cultured

tag: mouse age

value: 8 weeks


title: Mammary fibroblasts mono-cultured repetition 5


title: Mammary fibroblasts mono-cultured repetition 2


title: Mammary fibroblasts co-cultured with macrophages in 4T1 CM repetition 1 [Mammary_CO_CM_1]


title: Mammary fibroblasts mono-cultured repetition 3


title: macrophages co-cultured with mammary fibroblasts  in 4T1 CM repetition 4 [BM_CO_CM_4]

value: bone marrow

value: bone marrow drive macrophages


title: Mammary fibroblasts mono-cultured repetition 1


title: Mammary fibroblasts co-cultured with macrophages repetition5

value: Invitro co-cultured with macrophages


title: Mammary fibroblasts co-cultured with macrophages repetition3


title: Mammary fibroblasts co-cultured with macrophages repetition4


title: macrophages co-cultured with mammary fibroblasts  in 4T1 CM repetition 3 [BM_CO_CM_3]


title: Mammary fibroblasts co-cultured with macrophages repetition2


title: Mammary fibroblasts mono-cultured in DMEM repetition 2 [Mammary_only_2]


title: Mammary fibroblasts co-cultured with macrophages repetition1


title: Lung fibroblasts mono-cultured repetition 3


title: Lung fibroblasts mono-cultured repetition 2

source_name: Normal lung

value: Normal lung


title: Lung fibroblasts mono-cultured repetition 1


title: Mammary fibroblasts mono-cultured in 4T1 CM repetition 1 [Mammary_only_CM_1]


title: Lung fibroblasts co-cultured with macrophages repetition3


title: diestrus, rep 2

city: Seoul

first: Hyukjung

last: Kim

address: 120, Neungdong-ro

department: Stem cell and regeneration biotechnology

country: South Korea

institute: Konkuk University

data_processing:
Reads were aligned to the mouse genome (GRCm38) with STAR aligner.
The mapped reads were counted by using featureCounts, a read count summarization function within the Subread package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: uterus

growth_protocol: A vaginal smear assay was performed to determine the estrous cycle in the mice. DPBS was injected into the vagina and the fluid was collected by pipetting several times. The collected fluid was spread onto a slide and dried on a heat block. The slides were stained using a Diff-Quick staining kit (Sysmex). The estrous cycle was determined by analyzing the type and number of cells on slides under a microscope. Once the estrous cycle was identified, mice were sacrificed at each stage and the uterus was excised for further analysis.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeqStranded mRNA Sample Preparation Kit following manufacturer's protocols.

value: uterus

value: ICR

value: 6-8 weeks old

tag: Sex

value: female


title: diestrus, rep 1


title: metestrus, rep 1


title: estrus, rep 1


title: Lung fibroblasts co-cultured with macrophages repetition1


title: Lung fibroblasts co-cultured with macrophages repetition2


title: estrus, rep 2


title: Fat fibroblasts mono-cultured repetition 2

source_name: Normal mesometrial fat

value: Normal mesometrial fat


title: Fat fibroblasts mono-cultured repetition 1


title: proestrus, rep 2


title: Fat fibroblasts co-cultured with macrophages repetition3


title: Fat fibroblasts co-cultured with macrophages repetition2


title: Fat fibroblasts co-cultured with macrophages repetition1


title: NC MGC-803 5-FU treated 24h

city: Shenyang City

first: Zhenning

last: Wang

address: 155 North Nanjing Street

department: Department of Surgical Oncology and General Surgery

institute: The First Affiliated Hospital of China Medical University

hyb_protocol: Labelled cDNA hybridized to Affymetrix GeneChip PrimeView Human Gene Expression Array according to manufacturers instructions and placed in GeneChip Hybridization Oven 620 for 18hr at 45C. Microarrays were washes and stained with Affymettrix Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip® Scanner 7G 3000 laser confocal slide scanner

data_processing: Microarray data data expression was process using Command Console (Affymetrix, Inc) and the raw .CEL files were analyzed using Partek Genomic Suite v7.0 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

label: biotin

source_name: NC MGC-803 gastric cancer cell treated with 5-FU 24h

label_protocol: Total RNA was extracted and used to prepare biotinylated cDNA with Affymetrix WT plus reagent kit

growth_protocol: MGC-803 cells were cultured in RPMI 1640 medium (Invitrogen) with 10% fetal bovine serum (Gibco) and incubated at 37℃ in a humidified incubator (Thermo) with an atmosphere with 5% CO2.

extract_protocol: Total RNA extracted, purified by TRIzol, and RNA intergrity verified on Agilent Bioanalyzer

treatment_protocol: Three gRNA sets were designed and cloned into pSpCas9(BB)-2A-Puro plasmids (Addgene, PX459) to make double nicks on the DNA strand. These were applied to MGC-803 cells and selected for with puromycin (200 μg/ml) for two weeks. At least 20 single-cell derived clones were established and confirmed via PCR. The DDIT4 knockout MGC-803 cell lines (DDIT4−/−) and scrambled control cell lines (DDIT4+/+) were further confirmed via western blot against DDIT4. 10 μM 5-FU was added to their respective wells for 24 hours.

value: Gastric cancer cell


title: HTO library for SpiB replicate1

data_processing:
Processing was done using the Cell Ranger ‘multi’ analysis pipeline (10x Genomics version 7.0), with the reference data file refdata-gex-mm10-2020-A.
Cell hashing oligo sequence for replicate1_KO: ACCCACCAGTAAGAC, for replicate1_HET:GGTCGAGAGCATTCA, for replicate2_KO:AAAGCATTCTTCACG, for replicate2_HET:CTTGCCGCATGTCAT
Assembly: mm10
Supplementary files format and content: Filtered feature-barcode matrix from cellranger

source_name: Thymic hematopoietic cells

extract_protocol:
Thymi from  two 15wk old Spib+/– and two Spib–/– chimeras were surgically removed following perfusion, then trimmed of fat and connective tissues, and placed in PBS on ice. Single cell suspensions were prepared by mechanical dissociation of the thymi through a 40μm strainer using a syringe plunger. Cells were washed with 10 ml MACS buffer. 25 million cells per sample were first stained with 5 μl anti-mouse CD16/CD32 in 50 μl labeling buffer (PBS + 1% BSA) for 10 min at 4 °C, then an antibody mix containing both 5’ hashing antibodies and flow cytometry antibodies in labeling buffer was added to complete to ~100 μl total volume, and cells were incubated for 30 min at 4 °C. Cells were then washed 3 times with 5 ml labeling buffer. 10 minutes before each sample was sorted, it was incubated with a viability dye for 5 min at room temperature, then washed and resuspended in PBS + 2% BSA. CD45.1+CD3– (CD4/CD8DP)–MHCIImid-high cells were sorted into PBS supplemented with 50% FBS and then washed and resuspended in PBS + 0.04% BSA, counted, and volume was adjusted to a concentration of 1,000,000 cells/ml. Each two non-replicate samples were combined evenly into one pool.
The 10x Genomics platform loading and library preparation were done according to the manufacturer’s instructions, as previously described (10x Genomics) and were sequenced with paired-end 100-bp reads on an Illumina NovaSeq6000.
5' single cell RNA-seq

value: Thymic hematopoietic cells


title: macrophages co-cultured with mammary fibroblasts repetition3

extract_protocol:
Bone marrow-derived monocytes from BALB/c female mice were differentiated into macrophages by growth in DMEM with 10% FBS, 5% P/S and 20% L929 CM on the petri dish. The medium was replenished on day 3 and the macrophages were reseeded for the experiment on day 7.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: The macrophages were harvested with non-enzymatic cell dissociation solution (Biological Industries,03-071-1B) and washed with PBS without calcium and magnesium. The  fibroblasts  were isolated and expanded for 7 days, afterwhich the fibroblasts were trypsinized and resuspended in an ice-cold MACS buffer (PBS with 0.5% BSA). The samples were pelleted by centrifugation at 350g for 5 min at 4 °C, incubated with anti-EpCAM (Miltenyi, 130-105-958) and anti-CD45 (Miltenyi, 130-052-301) magnetic beads, transferred to LS columns (Miltenyi, 130-042-401) and the fibroblast-enriched, CD45/EpCAM-depleted flow-through was collected. Both cells seeded together 6-well plates precoated with collagen I. The co-cultures with fibroblasts were grown in DMEM with 10% FBS and 5% P/S . Every 3 days 1ml of medium (6well) were replaced with fresh medium.

value: Invitro co-cultured with mammary fibroblasts


title: macrophages co-cultured with mammary fibroblasts repetition4


title: SpiB replicate1


title: HTO library for SpiB replicate2


title: proestrus, rep 1


title: AireWT_ATAC

description: 10x Genomics

data_processing:
Single cell multiome ATAC + Gene Expression data was processed using the Cell Ranger ARC analysis pipeline (10x Genomics version 2.0.0), with reference data file refdata-cellranger-arc-mm10-2020-A.
Assembly: mm10
Supplementary files format and content: Filtered feature-barcode matrix and fragment files from cellranger

extract_protocol:
Thymi from 4 pooled 5 week old B6.Adig mice were dissociated by enzymatic digestion using Liberase TH  and DNase in RPMI at 37°C until complete digestion. The single cell suspension was then filtered through a 52 µm mesh filter and resolved on a Percoll gradient. The Percoll gradient was centrifuged at 2700rpm at 4°C with no break, for 30 minutes. Stromal cells where collected and washed followed by centrifugation.  Single cell suspensions were further enriched for thymic epithelial cells by staining for EpCAM-APC Cy7 followed by positive selection using anti-APC microbeads and the enriched fraction was stained for cell sorting. 60,000 viable (DAPI negative) CD45-EpCAM+ TECs were sorted into 500 ul PBS supplemented with 0.04% bovine serum albumin and then supplemented with 6,800 CD45-EpCAM+IA-IEloItgb4lo/neg cells. Cells were processed as per manufacturer’s instructions for low cell input nuclei isolation. Briefly, cells were resuspended in 100 μl cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40 substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, RNase inhibitor 1 U/µl) and divided into 2 tubes for 3 min lysis. Nuclei were then washed and resuspended in nuclei buffer to target 7,000 recovered nuclei.
Nuclei transposition and mRNA barcoding were followed by library preparation per the manufacturer’s (10x genomics) instructions which were sequenced with paired-end 100-bp reads on an Illumina NovaSeq6000.
single cell 3' RNA-seq and single cell ATAC-seq

tag: cell line

value: Thymic epithelial cells

value: WT


title: AireWT_GEX

description: 10x Genomics


title: metestrus, rep 2


title: macrophages co-cultured with mammary fibroblasts repetition2

value: BALB/c


title: macrophages co-cultured with lung fibroblasts repetition2

value: Invitro co-cultured with lung fibroblasts


title: SpiB replicate2


title: DRG Ctrl

first: huijing

last: xie

state: Please select an option

address: china

institute: westchina

data_processing:
The libraries were sequenced on an Illumina NovaSeq 150PE.
Reads were trimmed from 3' end until the final base had a quality score > 15, using Trimmomatic v0.33
Reads were aligned to the mm10 genome using bowtie2
Peaks were called using MACS2 with the significance  cut-off p < 0.001
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: DRG

growth_protocol: DRG was dissected from mouse without culture.

extract_protocol:
DRG cells were collected and bounded to concanavalin A-coated magnetic beads. Hyperactive Universal CUT&Tag Assay Kit for Illumina (pG-Tn5) (TD903, Vazyme Biotech) was used for subsequent steps.
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (pG-Tn5) (TD903, Vazyme Biotech) according to the manufacturer’s instructions.

value: DRG

value: Control

tag: antibody

value: H3K18la (PTM-Bio PTM-1406RM)


title: DRG PP2Cm CKO

value: PP2Cm CKO


title: WNK1-KO2

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
Demultiplexed FASTQ files (paired-end,Read 1: 30bp, Read 2:100bp) were generated using the CellRanger mkfastq command. The primary data analyses which included alignment, filtering, barcode counting and UMI quantification, quality control, clustering and statistical analysis were performed using CellRanger count command. Gene positions were annotated using Ensembl build 93 and filtered for biotype. Raw gene expression matrices were imported into R (version 4.0.2) and converted to a Seurat object using the Seurat R package (version 4.0.0). To remove dead cells and doublets, the total number of UMIs and genes and the percentage of UMIs derived from the mitochondrial genome for each cell were counted.  The upper and lower bounds were defined as the mean +/- two standard deviations for both the total UMIs and genes, respectively. Cells which had over 10% UMIs derived from mitochondrial genome were discarded. Finally, cells with total UMIs or genes outside of the upper and lower bounds were removed. For the remaining  cells, gene expression matrices were normalized to the total cellular read count and to mitochondrial read count. Highly variably genes (HVG) were selected from the normalized data using Seurat SCTransform function. The top 3000 HVGs were used as features for dimensionality reduction and clustering. The Seurat RunPCA and JackStraw functions were performed to calculate and to select significant (P-value <0.05) principal components (PCs), respectively.  The RunUMAP function was then applied to plot the selected significant PCs. The FindNeighbors constructed a Shared Nearest Neighbor (SNN) Graph, and FindClusters function with “resolution = 0.1” parameter was carried out to cluster cells into different groups.
Assembly: mm10
Supplementary files format and content: hd5 file, data matrix from cell ranger exprot

source_name: whole testis

extract_protocol:
Approximately 18,000live cells from each sample at a concentration of < 5×105cells/mL were loaded into the Single Cell Chip followed by forming single cell emulsion in Chromium Single Cell Controller (10x Genomics, Chromium Single Cell 3’ Library & Gel Bead Kit). The mRNA reverse transcription, cDNA generation and amplification were carried out according to the protocols provided by the manufacture.
Single cell gene expression library construction were carried using Chromium Single Cell Controller (10x Genomics, Chromium Single Cell 3’ Library & Gel Bead Kit) according to the protocols provided by the manufacture

value: Male

value: 1 testis

value: spermatocytes

value: >5 weeks


title: WNK1-Con2


title: macrophages co-cultured with lung fibroblasts repetition1

value: bone marrow

value: bone marrow drive macrophages

value: 8 weeks


title: macrophages co-cultured with fat fibroblasts repetition3

value: Invitro co-cultured with fat fibroblasts


title: WNK1-KO1


title: DDIT4KO MGC-803 5-FU treated 24h

source_name: DDIT4KO MGC-803 gastric cancer cell treated with 5-FU 24h

value: Gastric cancer cell


title: WNK1-Con1

value: 2 testes from 2 mice


title: macrophages co-cultured with fat fibroblasts repetition2


title: macrophages co-cultured with fat fibroblasts repetition1


title: KO3

city: Philadelphia

first: Yuanyuan

state: PA

address: 3720 Chestnut St, Apt 709

institute: UCLA

data_processing:
Sequence reads were aligned to GRCm38/mm10 by STAR-2.7.1a using two pass mode
Read count extraction and normalization were performed using kallisto (0.46.0)
Differential alternative splicing analysis were performed using rMATS-turbo (v4.1.0)
Assembly: mm10
Supplementary files format and content: tab-delimited tsv files include transcript abundance estimates for each sample
Supplementary files format and content: tab-delimited text file includes the TPM values for each sample

source_name: Prmt9 KO

extract_protocol: RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Preparation Kit following manufacturer's protocols.

value: hippocampus

value: female

value: Prmt9 knockout

tag: developmental stage

value: 2-week old


title: macrophages mono-cultured day 0  repetition4

value: BALB/c

value: Invitro mono-cultured


title: macrophages co-cultured with mammary fibroblasts repetition1

value: Invitro co-cultured with mammary fibroblasts


title: WT3

source_name: WT control

value: WT


title: KO1


title: macrophages mono-cultured day 0  repetition3


title: KO2


title: WT2


title: macrophages co-cultured with lung fibroblasts repetition4

value: Invitro co-cultured with lung fibroblasts


title: macrophages mono-cultured day 0  repetition2


title: Arabidopsis - Low-MNase-seq

source_name: Arabidopsis seedling

tag: cultivar

value: Leaf

value: 2 weeks

value: 20 U MNase


title: WT1


title: macrophages co-cultured with lung fibroblasts repetition3

value: bone marrow

value: bone marrow drive macrophages


title: macrophages mono-cultured day 0  repetition1

value: 8 weeks