title: 45 week Baby abdomen Male skin biopsy sample [GSS2656_69]

description:
GSS2656_69
Gene expression data from infant skin biopsy.

value: 45 week


title: LS-15546_S54_E1-50

status: Public on Oct 06 2021

type: SRA

city: Seattle

first: Hongkui

last: Zeng

state: WA

address: 615 Westlake Ave N

country: USA

institute: Allen Institute for Brain Science

description:
exon_counts.csv.gz
intron_counts.csv.gz
cpm.csv.gz

library_source: transcriptomic

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10
Supplementary_files_format_and_content: cpm.csv.gz
Supplementary_files_format_and_content: exon_counts.csv.gz
Supplementary_files_format_and_content: intron_counts.csv.gz

molecule: polyA RNA

organism: Mus musculus

source_name: retroseq cells mapped to L2/3,L4,L5 IT subclass

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia.

extract_protocol:
We isolated single cells as previously described (Hempel et al., 2007; Sugino et al., 2006; Tasic et al., 2016) with modifications. We mostly employed layer-enriching dissections, with focus on a single layer. Broader dissections (no layer enrichment or multiple layers combined) were employed for lines which label small numbers of cells, in order to facilitate isolation of sufficient number of cells. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

treatment_protocol: For retrogradely-labeled samples, we injected AAV2-retro-EF1a-Cre (Tervo et al., 2016), rabies virus RV-dGdL-Cre (Chatterjee et al., 2018), or CAV-Cre (Hnasko et al., 2006) into brains of Ai14 or RCL-Sun1sfGFP mice, RV-dL-FlpO into Ai65F mice, AAV2-retro-EF1a-dTomato into Cux2-CreERT2;Ai140 mice, Gnb4-IRES2-CreERT2;Ai140 mice or Gnb4-IRES2-CreERT2;Ai148 mice, as previously described (Tasic et al., 2016). RFP+ or GFP+ single cells were isolated from various cortical regions, depending on the injection area.

tag: gender

value: M

tag: age

value: 54 days

tag: region

value: ALM

tag: roi

value: RFP-positive

value: left

value: SSs

value: RV-dGdL-Cre

tag: batch


title: 21 year Adult Buttocks Female skin biopsy sample [GSS2656_64]

type: RNA

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description:
GSS2656_64
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 array plates using the Affymetrix GeneTitan instrument and protocol.

scan_protocol: Affymetrix GeneTitan U219 array plates were scanned using the Affymetrix GeneTitan instrument and protocol.

data_processing: Chip images were converted to numeric data with the probe logarithmic intensity error algorithm as executed in the Affymetrix GeneChip Expression Console.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Purified RNA was converted to biotin-labeled complementary RNA copies with the Affymetrix HT 3’ IVT Plus kit per protocol provided at a Beckman Biomek FXP Laboratory Automation Workstation.

extract_protocol: Total RNA was extracted from biopsies by homogenizing in Trizol Reagent using protocol provided by supplier. Extracted RNA was further purified using Qiagen RNeasy Micro columns and protocol provided by supplier.

value: Female

value: 21 year

tag: tissue

value: Skin

tag: biopsy site

value: Buttocks

tag: subjectid

tag: sampleID


title: COL11_TSA1_S11_ROW17

city: Rochester

first: Jason

last: Myers

state: NY

address: 601 Elmwood Ave.

institute: University of Rochester

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15
Genome Alignment - STAR_2.5.2b, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.5.0p3, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCh38 + gencode25
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: 40 year old female

extract_protocol:
Fluidigm C1 HT scRNAseq protocol, no offline RNA extraction performed
Fluidigm C1 HT scRNAseq library construction protocol

tag: cell line

tag: cell type

value: Invasive Ductal Carcinoma


title: 64 year Adult Buttocks Female skin biopsy sample [GSS2656_65]

description:
GSS2656_65
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 64 year


title: 62 year Adult Buttocks Female skin biopsy sample [GSS2656_66]

description:
GSS2656_66
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 62 year


title: 20 year Adult Buttocks Female skin biopsy sample [GSS2656_59]

description:
GSS2656_59
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 20 year


title: 40.9 week Baby abdomen Male skin biopsy sample [GSS2656_62]

description:
GSS2656_62
Gene expression data from infant skin biopsy.

value: Male

value: 40.9 week

value: abdomen


title: IT355B_WT3

city: Freiburg

first: Connor

last: O'Meara

address: Stuebeweg

country: Germany

institute: MPI

description:
Processed data files generated from multiple samples
processed data file:
log2.NPAS4B.tabular.txt
n.counts.NPAS4B.tabular.txt

data_processing:
Reads were aligned to the reference genome with STAR 2.5.2b-1 (Dobin A. et al. Bioinformatics 2013) and the reference annotation from Ensembl (Zv10.85, http://www.ensembl.org/info/data/ftp/index.html)
Resulting alignments were quantified at the gene level with featureCounts version 1.6.0.1 (Liao Y, Smyth G.K., and Shi W., Bioinformatics 2014) and differential expression performed using DESeq2 version 2.11.40.1 (Love M.I., Huber W. and Anders S. Genome Biol 2014). All tools were used with default parameters unless otherwise stated.
Genome_build: z10.85
Supplementary_files_format_and_content: DESeq2 tables of differential gene expression analysis are provided (log2 fold-change and normalized counts)

organism: Danio rerio

source_name: ENU mutagenesis forward genetic screen

growth_protocol: zebrafish embryos (5 d.p.f)

extract_protocol:
Individual zebrafish embryos (5 d.p.f) from an incross of heterozygous carriers were homogenized in 100 μL of Tri Reagent (Sigma, Cat#93289) and transferred to 2 mL deep 96 well plates containing an additional 400μL of Tri Reagent. The RNA-containing aqueous phase was stored at -80°C until genotyping was completed. DNA was extracted from the interphase and organic phase by phenol-chloroform according to the manufacturer’s instructions. Following genotyping, RNA was extracted from embryos homozygous mutants and sibling homozygous wt. DNA was removed from RNA extraction using TURBO DNA-free kit (Invitrogen, Cat#AM1907). RNA was quantified using Qubit RNA HS Assay Kit (ThermoScientific, Cat#Q32852) and the Qubit 4 Fluoromter (ThermoScientific, Q33226). RNA quality was checked by 18S/28S rRNA ratio using the Fragment Analyzer RNA Kit (ThermoScientific, Cat#DNF-471-0500) and the 5200 Fragment Analyzer System (ThermoScientific, Cat#M5310AA).
cDNA libraries were prepared from 1μg of mRNA following poly-A selection using TruSeq stranded mRNA Library Prep (Illumina, Cat#20020595) according to manufacturer’s instuctions. RNA-Seq was performed using mutant and wt sibling from each zebrafish line (n = 2 – 6). The libraries were sequenced in paired-end 75 bp mode at a depth of 25 million reads on an Illumina HiSeq 2500/3000 instrument.

tag: genotype

value: WT

tag: strain background

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

tag: population

value: whole embryo

tag: surface phenotype

value: normal lymphoid development in thymus


title: LS-15546_S53_E1-50

value: M

value: 54 days

value: ALM

value: RFP-positive

value: left

value: SSs


title: IT355B_WT2


title: COL11_TSA1_S11_ROW16

value: Invasive Ductal Carcinoma


title: COL11_TSA1_S11_ROW15


title: COL11_TSA1_S11_ROW18


title: IT355B_WT4


title: LS-15546_S52_E1-50

value: RV-dGdL-Cre


title: IT355B_WT1


title: IT355B_MUT4

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: COL11_TSA1_S11_ROW14


title: LS-15546_S50_E1-50


title: IT355B_MUT2


title: 36.1 week Baby chest Female skin biopsy sample [GSS2656_61]

description:
GSS2656_61
Gene expression data from infant skin biopsy.

value: Female

value: 36.1 week

value: Skin

value: chest


title: COL11_TSA1_S11_ROW11


title: LS-15546_S49_E1-50


title: 38.7 week Baby abdomen Male skin biopsy sample [GSS2656_72]

description:
GSS2656_72
Gene expression data from infant skin biopsy.

value: Male

value: 38.7 week

value: abdomen


title: IT355B_MUT3

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: 22 year Adult Buttocks Female skin biopsy sample [GSS2656_56]

description:
GSS2656_56
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 22 year

value: Buttocks


title: COL11_TSA1_S11_ROW12


title: Gata3KO macrophage scRNA-seq

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

country: Switzerland

institute: University of Bern

data_processing:
Illumina RTA 1.18.66.3 was used for base calling
Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v3.0.1 (10x Genomics) mkfastq with standard parameters.
Cell Ranger v3.0.1 quant was used to map the demultiplexed reads to the reference genome (mm10, Cell Ranger reference package 3.0.0), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts and estimate the number of cells using standard parameters.
Seurat v3.0.2 was used under R v3.6.1 to filter cells by the number of genes expressed and the percentage of mitochondrial and ribosomal genes. The filtered cells were clustered and visualized based on similarity of gene expression. Marker genes were determined for the individual clusters.
Construction of single cell pseudotime trajectories and identification of genes changing as a function of pseudotime was performed using Monocle3 v0.1.2 under R v3.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with UMI counts per gene per cell after initial filtering in Seurat (min.cells = 5, min.genes = 400)

source_name: Tibialis anterior muscle

growth_protocol: Tibialis anterior muscles were injected with 50 µl of 10µM cardiotoxin from Naja pallida (Latoxan). Muscles were isolated and Zombie aqua-, Ly6G-,CD45+CD11b+ cells were sorted on day 4 post injection.

extract_protocol:
For each sample 8000 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) using Single Cell 3' v3 Gel Beads (10x Genomics) to generate single cell bead emulsions for reverse transcription and cell bar coding according to the manufacturers instructions
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v3 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v3 chemistry.

tag: strain

tag: treatment

value: 4 days post cardiotoxin injection

value: sorted mononuclear cells (Zombie aqua-, Ly6G-, CD45+, CD11b+)


title: 39.5 week Baby abdomen Female skin biopsy sample [GSS2656_55]

description:
GSS2656_55
Gene expression data from infant skin biopsy.

tag: gender

value: 39.5 week


title: LS-15546_S51_E1-50

value: M

tag: age

value: 54 days

value: ALM

value: RFP-positive

value: left

value: SSs

value: RV-dGdL-Cre


title: 64 year Adult Buttocks Female skin biopsy sample [GSS2656_58]

description:
GSS2656_58
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 64 year

value: Skin


title: 23 year Adult Buttocks Female skin biopsy sample [GSS2656_57]

description:
GSS2656_57
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 23 year


title: IP109_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.CMYB.tabular.txt
n.counts.CMYB.tabular.txt

value: WT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: normal lymphoid development in thymus


title: COL11_TSA1_S11_ROW10

value: Invasive Ductal Carcinoma


title: Wt macrophage scRNA-seq

value: 4 days post cardiotoxin injection

value: sorted mononuclear cells (Zombie aqua-, Ly6G-, CD45+, CD11b+)


title: COL11_TSA1_S11_ROW09


title: IT429_MUT4

description:
Processed data files generated from multiple samples
processed data file:
log2.NEK7.tabular.txt
n.counts.NEK7.tabular.txt

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: IP109_WT3


title: COL11_TSA1_S11_ROW13


title: COL11_TSA1_S11_ROW08


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_54]

description:
GSS2656_54
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 24 year

value: Buttocks


title: IT355B_MUT1


title: iGSCs-input

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file

molecule: genomic DNA

source_name: Induction of germline stem cell

growth_protocol: SSCs were cultured on mitotically inactivated STO mouse embryonic fibroblast feeder cells (5 × 104 cells/cm2; ATCC) with culture medium.FGSCs and iGSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Life Technologies), 2 mM L-glutamine (Sigma), 30 mg/mL pyruvate (Amresco) and 50 mM -mercaptoethanol (Biotech).The primary NSCs was seeded onto poly-l-ornithine (Sigma-Aldrich) and laminin (Invitrogen) coated dishes, cultured as monocultures. Neural basal medium with 20ng/ml EGF (PeproTech), 20ng/ml bFGF(PeproTech), 20ng/ml Hepairn (Sigma-Aldrich) and 2% B27 (Invitrogen) was used as NSC proliferation medium. STOs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with high-glucose (Life Technologies), 10% FBS (Life Technologies), 1% non-essential amino acids (Life Technologies), 2mM glutamine (Sigma) and Penicillin (100U/ml, Sigma)/streptomycin (0.1mg/ml, Sigma).

extract_protocol:
genomic DNA (gDNA) was extracted and fragmented with Bioruptor (Connecticut, USA) into fragment sizes of 200–500 bp
Sonicated gDNA was used for end-repair and adaptor ligation. The adaptor-ligated gDNA was denatured and incubated with an antibody (Epigentek, A-1014) conjugated on Protein A+G Magnetic beads (Millipore, 16-663). Immunoprecipitated DNA was amplified by PCR and subjected to Illumina sequencing.

value: Induction of germline stem cell

tag: passages


title: IP109_WT2


title: FGSCs-me

source_name: Female germline stem cell

value: Female germline stem cell


title: COL11_TSA1_S11_ROW06


title: iGSCs-me


title: COL11_TSA1_S11_ROW05


title: COL11_TSA1_S11_ROW07


title: 22 year Adult Buttocks Female skin biopsy sample [GSS2656_50]

description:
GSS2656_50
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 22 year


title: 38.8 week Baby back Male skin biopsy sample [GSS2656_53]

description:
GSS2656_53
Gene expression data from infant skin biopsy.

value: Male

value: 38.8 week

value: Skin

value: back


title: 63 year Adult Buttocks Female skin biopsy sample [GSS2656_52]

description:
GSS2656_52
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 63 year


title: 61 year Adult Buttocks Female skin biopsy sample [GSS2656_51]

description:
GSS2656_51
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 61 year


title: FGSCs-input


title: IP109_WT1

value: WT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: normal lymphoid development in thymus


title: IP109_MUT4

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_49]

description:
GSS2656_49
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 24 year

value: Buttocks


title: SSCs-input

source_name: Spermatogonial stem cell

value: Spermatogonial stem cell


title: COL11_TSA1_S11_ROW25

value: Invasive Ductal Carcinoma


title: IP109_MUT3


title: Female germline stem cell FGSC_Rep1

data_processing:
All RNA-Seq data were trimmed and aligned to the mm9 reference genome using Hisat2 (version 4.8.2)(Pertea et al., 2016) with the default parameters.
Gene expression as FPKM was calculated by Cufflinks (version 2.2.1)(Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Office Excel (xls) file include RPKM values for each Sample

extract_protocol:
Total RNA was extracted from 1–2×106 cells using Trizol Reagent.
The RNA quality was assessed using an Agilent Bioanalyzer 2100. RNA-Seq libraries were prepared using the KAPA Stranded mRNA-Seq kit, following the manufacturer’s instructions.


title: IP109_MUT1


title: SSCs-me


title: COL11_TSA1_S11_ROW04


title: IP109_MUT2


title: Female germline stem cell FGSC_Rep2


title: IP045_WT3

description:
Processed data files generated from multiple samples
processed data file:
log2.JAK3.tabular.txt
n.counts.JAK3.tabular.txt


title: Induction of germline stem cell iGSC_Rep1


title: COL11_TSA1_S11_ROW03


title: 64 year Adult Buttocks Female skin biopsy sample [GSS2656_48]

description:
GSS2656_48
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 64 year


title: IP045_WT4


title: Induction of germline stem cell iGSC_Rep2


title: COL11_TSA1_S11_ROW01


title: Spermatogonial stem cell SSC_Rep2


title: COL10_DMSO2_S32_ROW39


title: Spermatogonial stem cell SSC_Rep1


title: COL10_DMSO2_S32_ROW40


title: COL10_DMSO2_S32_ROW38


title: 21 year Adult Buttocks Female skin biopsy sample [GSS2656_45]

description:
GSS2656_45
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 21 year


title: IP045_MUT4


title: IP045_WT2


title: COL10_DMSO2_S32_ROW37


title: IP045_MUT3


title: COL10_DMSO2_S32_ROW36


title: COL11_TSA1_S11_ROW02


title: 60 year Adult Buttocks Female skin biopsy sample [GSS2656_46]

description:
GSS2656_46
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 60 year

value: Skin


title: IP045_WT1


title: Infected_2

city: Philadelphia

first: Boris

last: Striepen

state: Pennsylvania

address: 380 S University Ave, Room H344

department: Pathobiology

institute: University of Pennsylvania

data_processing:
fastq files were aligned to version 86 of the human reference genome GRCh38 using kallisto
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (>1-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 86 of human reference genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample.

growth_protocol: 6 well culture of HCT-8 were  placed in a 5% CO2 37 °C incubator for 48 hours or 10 hours

extract_protocol:
RNA was isolated using the RNeasy Mini (48hours) Micro (10hours) Kit (Qiagen) and processed as per manufacturer’s instructions.
cDNA synthesis was performed following the clonTechSMART-seq cDNA synthesis protocol (15 cycles). Following DNA cleanup, a Nextera library was prepared.

treatment_protocol: HCT-8 were infected with 1 million C. parvum for all experiments. Total RNA was extracted at 48 hours post infection. For the seond experiment cells were infected for 10 hours followed by flow sorting 10,000 GFP positive cells and 10,000 GFP negative cells from each well

value: wild-type

value: GFP positive/infected

tag: treatment duration

value: 10 hour infection and sort


title: COL10_DMSO2_S32_ROW35


title: Infected_3


title: 23 year Adult Buttocks Female skin biopsy sample [GSS2656_43]

description:
GSS2656_43
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 23 year


title: Bystander_3

value: GFP negative/bystander


title: 20 year Adult Buttocks Female skin biopsy sample [GSS2656_41]

description:
GSS2656_41
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 20 year


title: IP045_MUT1

value: MUT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: Bystander_2


title: COL10_DMSO2_S32_ROW33


title: IP045_MUT2

value: lymphoid development, defect in rag1 expression in thymus


title: IM087_WT3

description:
Processed data files generated from multiple samples
processed data file:
log2.UBE3D.tabular.txt
n.counts.UBE3D.tabular.txt

value: WT

value: normal lymphoid development in thymus


title: Infected_1


title: Bystander_1


title: 61 year Adult Buttocks Female skin biopsy sample [GSS2656_34]

description:
GSS2656_34
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 61 year

value: Buttocks


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_37]

description:
GSS2656_37
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 24 year


title: COL10_DMSO2_S32_ROW34

value: Invasive Ductal Carcinoma


title: 39.7 week Baby back Female skin biopsy sample [GSS2656_39]

description:
GSS2656_39
Gene expression data from infant skin biopsy.

value: 39.7 week

value: Skin

value: back


title: 89.1 week Baby abdomen Male skin biopsy sample [GSS2656_31]

description:
GSS2656_31
Gene expression data from infant skin biopsy.

value: Male

value: 89.1 week

value: abdomen


title: IM087_WT2


title: 23 year Adult Buttocks Female skin biopsy sample [GSS2656_35]

description:
GSS2656_35
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 23 year


title: COL10_DMSO2_S32_ROW32


title: Trans_2

value: wild-type

value: Infected transgenic C. parvum

value: 48 hour infection


title: COL10_DMSO2_S32_ROW30


title: COL11_TSA1_S11_ROW24


title: 36.2 week Baby chest Male skin biopsy sample [GSS2656_40]

description:
GSS2656_40
Gene expression data from infant skin biopsy.

value: 36.2 week

value: chest


title: 36.3 week Baby back Female skin biopsy sample [GSS2656_44]

description:
GSS2656_44
Gene expression data from infant skin biopsy.

value: Female

value: 36.3 week


title: COL10_DMSO2_S32_ROW29


title: IM087_WT4

value: WT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: normal lymphoid development in thymus


title: Trans_3


title: COL10_DMSO2_S32_ROW31

value: Invasive Ductal Carcinoma


title: Trans_1


title: 63 year Adult Buttocks Female skin biopsy sample [GSS2656_24]

description:
GSS2656_24
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 63 year

value: Skin

value: Buttocks


title: 40.2 week Baby chest Female skin biopsy sample [GSS2656_23]

description:
GSS2656_23
Gene expression data from infant skin biopsy.

value: 40.2 week


title: WT_3

value: Infected wild type C. parvum


title: IM087_WT1


title: COL10_DMSO2_S32_ROW28


title: 43.2 week Baby abdomen Male skin biopsy sample [GSS2656_30]

description:
GSS2656_30
Gene expression data from infant skin biopsy.

value: Male

value: 43.2 week

value: abdomen


title: IM087_MUT2

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: IM087_MUT4


title: WT_2

value: wild-type

value: 48 hour infection


title: IM087_MUT1


title: 21 year Adult Buttocks Female skin biopsy sample [GSS2656_22]

description:
GSS2656_22
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 21 year


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_20]

description:
GSS2656_20
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 24 year


title: WT_1


title: 20 year Adult Buttocks Female skin biopsy sample [GSS2656_21]

description:
GSS2656_21
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 20 year


title: 23 year Adult Buttocks Female skin biopsy sample [GSS2656_27]

description:
GSS2656_27
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 23 year


title: COL10_DMSO2_S32_ROW26

value: Invasive Ductal Carcinoma


title: IL015_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.UNC45A.tabular.txt
n.counts.UNC45A.tabular.txt

value: WT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: normal lymphoid development in thymus


title: Control_3

value: Uninfected

value: 48 hour


title: IM087_MUT3


title: IL015_WT3


title: COL10_DMSO2_S32_ROW25


title: Control_2


title: Control_1


title: IL015_WT2


title: COL10_DMSO2_S32_ROW23


title: 42.6 week Baby abdomen Male skin biopsy sample [GSS2656_19]

description:
GSS2656_19
Gene expression data from infant skin biopsy.

value: Male

value: 42.6 week

value: Skin

value: abdomen


title: COL10_DMSO2_S32_ROW24


title: IL015_WT1


title: 61 year Adult Buttocks Female skin biopsy sample [GSS2656_15]

description:
GSS2656_15
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 61 year

value: Buttocks


title: 36.8 week Baby chest Male skin biopsy sample [GSS2656_16]

description:
GSS2656_16
Gene expression data from infant skin biopsy.

value: 36.8 week

value: chest


title: sPE9 [PE29-Pbi-pre_S22]

city: valencia

first: Tamara

last: Garrido

address: Narcís Monturiol Estarriol nº11

country: Spain

institute: Igenomix

data_processing:
The cDNA libraries from total RNA samples (n=40) were prepared by an Illumina TruSeq Stranded mRNA sample prep kit
Indexed and pooled samples were sequenced 150-bp paired-end reads by on the Illumina NextSeq 500/550 platform, according to Illumina library protocol.
Once the sequencing was completed, a quality assessment was done. Check for outliers or any technical issue at raw data (sequence quality, read alignment, quantification,and reproducibility)
Pre-processing analyses were performed over the read counts data (low-count filter and normalization).
The trimmed mean of M-values normalization method was applied to our gene expression values (raw counts) using the Bioconductor package edgeR (version 3.24.3). The same package was used to analyze differentially expressed genes. The glmTreat function was used to find differentially expressed genes between groups. The p-value adjustment method was FDR with a cut-off of 0.05 (FDR<0.05) and the fold-change threshold was 1.2. edgeR analysis was carried out in R version 3.5.1.. The scripts for this analysis can be found at  https://github.com/mclemente-igenomix/garrido_et_al_2021.
Genome_build: hg19_genome_star
Supplementary_files_format_and_content: csv file with raw counts for every gene and every sample
Supplementary_files_format_and_content: Figure1_SourceData1.xlsx: Differentially expressed genes in sPE vs control cases.
Supplementary_files_format_and_content: Figure3_SourceData1.xlsx: List of genes selected as defective decidualization signature in sPE

source_name: sPE_Endometrial biopsy_Train

extract_protocol:
QIAsymphony RNA extraction kit following the manufacturerｴs protocol
Illumina TruSeq Stranded mRNA sample prep kit following the manufacturerｴs protocol

treatment_protocol: Bulk tissue analysis

value: Endometrium

tag: patient

value: sPE (developed sPE in a previous pregnancy)

tag: sample group

value: Train


title: 50.4 week Baby abdomen Male skin biopsy sample [GSS2656_18]

description:
GSS2656_18
Gene expression data from infant skin biopsy.

value: 50.4 week

tag: tissue

tag: biopsy site


title: COL10_DMSO2_S32_ROW21

value: Invasive Ductal Carcinoma


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_14]

description:
GSS2656_14
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Female

value: 24 year

tag: subjectid

tag: sampleID


title: IL015_Mut3

value: MUT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: lymphoid development, defect in rag1 expression in thymus


title: sPE8 [PE28-PbH-pre_S13]


title: IL015_Mut4


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_13]

description:
GSS2656_13
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: Skin


title: IL015_Mut2


title: COL10_DMSO2_S32_ROW20

tag: cell line

tag: cell type


title: sPE7 [PE27-PbG-pre_S12]


title: sPE6 [PE26-PbF-pre_S16]


title: COL10_DMSO2_S32_ROW19


title: COL10_DMSO2_S32_ROW22


title: IL015_Mut1

tag: genotype

tag: strain background


title: COL10_DMSO2_S32_ROW18


title: II032_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.IKZF1.tabular.txt
n.counts.IKZF1.tabular.txt

value: WT

tag: population

tag: surface phenotype

value: normal lymphoid development in thymus


title: 37.5 week Baby back Female skin biopsy sample [GSS2656_11]

description:
GSS2656_11
Gene expression data from infant skin biopsy.

value: 37.5 week

value: back


title: II032_WT3


title: 62 year Adult Buttocks Female skin biopsy sample [GSS2656_08]

description:
GSS2656_08
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 62 year

value: Buttocks


title: 24 year Adult Buttocks Female skin biopsy sample [GSS2656_12]

description:
GSS2656_12
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.


title: 35.9 week Baby scrotum Male skin biopsy sample [GSS2656_09]

description:
GSS2656_09
Gene expression data from infant skin biopsy.

value: Male

value: 35.9 week

value: scrotum


title: sPE3 [PE23-PbC-pre_S11]

value: Endometrium

value: sPE (developed sPE in a previous pregnancy)

value: Train


title: II032_WT2


title: COL10_DMSO2_S32_ROW15

value: Invasive Ductal Carcinoma


title: II032_WT1

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: sPE24 [EP-PE15_S8]

source_name: sPE_Endometrial biopsy_Test

value: Test


title: sPE5 [PE25-PbE-pre_S11]


title: COL10_DMSO2_S32_ROW13


title: sPE23 [EP-PE14_S23]


title: II032_Mut4

value: MUT

value: whole embryo

value: lymphoid development, defect in rag1 expression in thymus


title: sPE22 [EP-PE12_S17]


title: COL10_DMSO2_S32_ROW14


title: II032_Mut3


title: C8

first: Yunchen

last: Luo

address: shanghai hongkou

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA.
Fold change>=2.0, that is, log(FC)>=1.0, p-value<=0.05, and FPKM value>=0.1 in at least one (or a group of) samples as the threshold for differential screening.
Genome_build: MM10

source_name: liver

extract_protocol:
According to the manufacturer's instructions, liver total RNA in db/db mice and control mice was extracted from TRIzol (Invitrogen, CA, USA). Total RNA (1 Î¼g) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer's instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
library construction protocol

value: liver

tag: strain

tag: treatment

value: untreated


title: sPE4 [PE24-PbD-pre_S6]


title: sPE21 [EP-PE11_S14]


title: 20 year Adult Buttocks Female skin biopsy sample [GSS2656_06]

description:
GSS2656_06
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

tag: gender

value: Female

tag: age

value: 20 year

value: Skin


title: COL10_DMSO2_S32_ROW17


title: C7


title: 64 year Adult Buttocks Female skin biopsy sample [GSS2656_02]

description:
GSS2656_02
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.

value: 64 year

value: Buttocks


title: COL10_DMSO2_S32_ROW12


title: II032_Mut2


title: 40.9 week Baby chest Female skin biopsy sample [GSS2656_04]

description:
GSS2656_04
Gene expression data from infant skin biopsy.

value: 40.9 week

value: chest


title: COL10_DMSO2_S32_ROW16


title: sPE20 [EP-PE09_S7]

value: Endometrium

value: sPE (developed sPE in a previous pregnancy)


title: COL10_DMSO2_S32_ROW11

value: Invasive Ductal Carcinoma


title: sPE2 [PE22-PbB-pre_S10]

value: Train


title: II032_Mut1

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: C5


title: COL10_DMSO2_S32_ROW10


title: 64 year Adult Buttocks Female skin biopsy sample [GSS2656_05]

description:
GSS2656_05
Gene expression data from adult none-UV exposure (buttocks) skin biopsy.


title: 66.3 week Baby abdomen Female skin biopsy sample [GSS2656_01]

description:
GSS2656_01
Gene expression data from infant skin biopsy.

value: 66.3 week

value: abdomen


title: db5

value: db/db


title: IG447_WT7

description:
Processed data files generated from multiple samples
processed data file:
log2.PIP5K1BA.tabular.txt
n.counts.PIP5K1BA.tabular.txt

value: WT

value: whole embryo

value: normal lymphoid development in thymus


title: COL10_DMSO2_S32_ROW09


title: C6

value: liver

value: untreated


title: db4


title: sPE18 [EP-PE03_S25]

value: Test


title: IG447_WT6


title: COL10_DMSO2_S32_ROW08


title: db2


title: sPE19 [EP-PE04_S3]


title: db1


title: sPE16 [EP-PE01_S19]


title: IG447_WT5


title: sPE15 [PE35-Pb34-pre_S17]


title: IG447_WT16


title: COL10_DMSO2_S32_ROW07


title: COL10_DMSO2_S32_ROW06


title: COL10_DMSO2_S32_ROW05


title: IG447_WT15


title: sPE14 [PE34-Pb21-pre_S16]


title: COL10_DMSO2_S32_ROW04


title: Cascio

city: Pittsburgh

first: Ronald

middle: J

last: Buckanovich

address: 204 Craft Avenue

department: Department of Medicine

institute: University of Pittsburgh

description: Multiplexed sample of 9 mice

data_processing:
Single-cell cDNA libraries were processed for RNA sequencing using an Illumina NovaSeq 6000 platform.
Raw sequence data were processed via 10x Genomics Cell Ranger 3.1.0. To be specific,  the FASTQ files were generated by running the command cellranger mkfastq. Then with the command cellranger count, the gene expression data was aligned to the mm10 genomo and the antibody hashtag counts for each cell were tabulated.
Explanatory analysis of scRNA-seq data were performed using the Seurat R package. We excluded cells with <400 expressed genes and genes expressed in <3 cells. Then cells were demultiplexed to their original sample-of-origins, and only singlet cells were kept. A basic filtering was performed on the singlets, which removed those with less than 500 expressed genes, or a mitochondrial percentage higher than 35%. The filtered data was then normalized with a scale factor of 1x104, and scaled and centered based on 2000 variable features.
Principal component analysis (PCA) was run for the normalized counts of variable features, excluding genes related to hemoglobin, mitochondria, and ribosomes. The first 40 principal components (PCs) were selected. The data was visualized with t-distributed stochastic neighbor embedding. Seurat “FindClusters” was applied to the first 40 PCs, with the resolution parameter set to 6.5. Cell labels were assigned using marker gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: a h5 files which contains a gene expression matrix, an antibody capture matrix, and cell hashtag counts.
Supplementary_files_format_and_content: a rds file which a Seurat object on normalized abundance measurements

source_name: Ovarian

extract_protocol:
CD45+ cells were isolated from fresh tumors. Samples were labeled with different TotalSeq oligo-conjugated antibodies.
Two thousand cells per sample were loaded into the Chromium instrument (10x Genomics), and the resulting barcoded cDNAs were used to construct libraries

treatment_protocol: Anti-PDL1 was administered for three times, every two days, starting at day 19 after tumor cell injections. IPI-926 was administered every day, for two weeks, starting at day 14 after tumor cell injection

value: CD45+ cells from ovarian tumor


title: Cascio HTO

description: Multiplexed sample of 9 mice


title: IG447_WT8


title: IG447_WT14


title: IG447_WT13


title: IG447_Mut_9

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: sPE17 [EP-PE02_S22]

value: Endometrium


title: COL10_DMSO2_S32_ROW02


title: M5  input

data_processing:
Library strategy: MeRIP-Seq
m6A RNA immunoprecipitation was performed with the GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions.
Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).
The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Fold change>=2.0, that is, log(FC)>=1.0, p-value<=0.0001, and FPKM value>=0.1 in at least one (or a group of) samples as the threshold for differential screening.
Genome_build: MM10
Supplementary_files_format_and_content: MACS_peak

growth_protocol: HFrD containing 10% kcal from fat, 70% kcal from carbohydrate, and 20% kcal from protein were purchased from Research Diets (D08040107, Research Diets, USA). Male C57BL/6J mice aged 10-11 weeks were fed either a normal diet (ND) or HFrD for two weeks.

extract_protocol:
According to the manufacturer's instructions, liver total RNA in HFrD mice and control mice was extracted from TRIzol (Invitrogen, CA, USA). Briefly, m6A RNA immunoprecipitation was performed with the GenSeqâ¢ m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer's instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNextÂ® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina NovaSeq 6000 instrument with 150bp paired-end reads.
MeRIP-m6A-mRNA-seq

tag: diet

value: Mice were fed a HFrD for two weeks.


title: sPE11 [PE31-Pb8-pre_S3]

tag: patient

value: sPE (developed sPE in a previous pregnancy)


title: sPE12 [PE32-Pb10-pre_S15]

tag: sample group


title: sPE13 [PE33-Pb12-pre_S12]

tag: tissue

value: Train


title: M7  input


title: M2  input


title: COL10_DMSO1_S10_ROW40

value: Invasive Ductal Carcinoma


title: COL10_DMSO2_S32_ROW01


title: sPE1 [PE21-PbA-pre_S19]


title: sPE10 [PE30-Pb7-pre_S14]


title: IG447_Mut_4

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: M1  input


title: con-6  input

value: Mice were fed a normal diet for two weeks.


title: IG447_Mut_3


title: COL10_DMSO2_S32_ROW03


title: con-7  input


title: C8 [PE17-Cb23-ctrl_S5]

source_name: Controls_Endometrial biopsy_Train

value: Controls (Non-sPE previous pregnancy)


title: IG447_Mut_2


title: C9 [PE18-Cb43-ctrl_S10]


title: con-1  input


title: COL10_DMSO1_S10_ROW36


title: COL10_DMSO1_S10_ROW37


title: IG447_Mut_12


title: IG447_Mut_1


title: COL10_DMSO1_S10_ROW35


title: C6 [PE14-Cb14-ctrl_S8]


title: con-3  input


title: C5 [PE12-Cb5-ctrl_S6]

source_name: Controls_Endometrial biopsy_Test


title: IG438_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.SPATA5.tabular.txt
n.counts.SPATA5.tabular.txt

value: WT


title: COL10_DMSO1_S10_ROW34


title: M7 [MeRIP-Seq]


title: IG447_Mut_11

value: whole embryo


title: C7 [PE16-Cb21-ctrl_S2]


title: C4 [PE10-Cb3-ctrl_S9]


title: M5 [MeRIP-Seq]


title: COL10_DMSO1_S10_ROW39


title: IG447_Mut_10


title: C3 [PE7-Cbi-ctrl_S21]


title: COL10_DMSO1_S10_ROW33


title: COL10_DMSO1_S10_ROW32


title: M2 [MeRIP-Seq]


title: M1 [MeRIP-Seq]


title: IG438_WT3

value: normal lymphoid development in thymus


title: IG438_WT2


title: con-7 [MeRIP-Seq]

value: liver


title: C25 [EP-C26_S2]


title: COL10_DMSO1_S10_ROW31


title: IG438_WT1


title: COL10_DMSO2_S32_ROW27


title: con-6 [MeRIP-Seq]


title: C22 [EP-C22_S15]


title: IG438_MUT3


title: COL10_DMSO1_S10_ROW28


title: con-3 [MeRIP-Seq]


title: IG438_MUT1


title: COL10_DMSO1_S10_ROW29


title: IG438_MUT4


title: con-1 [MeRIP-Seq]


title: C20 [EP-C18_S9]


title: C21 [EP-C21_S12]


title: M7

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA.
Fold change>=2.0, that is, log(FC)>=1.0, p-value<=0.05, and FPKM value>=0.1 in at least one (or a group of) samples as the threshold for differential screening.
Genome_build: MM10
Supplementary_files_format_and_content: FPKM

extract_protocol:
According to the manufacturer's instructions, liver total RNA in HFrD mice and control mice was extracted from TRIzol (Invitrogen, CA, USA). Total RNA (1 Î¼g) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturerâs instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina NovaSeq 6000 Sequencer according to the manufacturer's instructions.
library construction protocol


title: COL10_DMSO1_S10_ROW27


title: IG438_MUT2


title: C2 [PE6-CbH-ctrl_S18]


title: M5


title: IG335_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.MCM10.tabular.txt
n.counts.MCM10.tabular.txt


title: M2


title: COL10_DMSO1_S10_ROW26


title: COL10_DMSO1_S10_ROW25


title: IG335_WT3


title: COL10_DMSO1_S10_ROW30


title: M1


title: C10 [PE19-Cb46-ctrl_S15]


title: COL10_DMSO1_S10_ROW24


title: COL10_DMSO1_S10_ROW38


title: C18 [EP-C04_S1]


title: COL10_DMSO1_S10_ROW23


title: con-7


title: con-6


title: Lacrimal gland S8

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode release 34) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode annotation file (Gencode 34)
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL release 100 (Human genes, GRCh38.p12, download on 05/25/2020). Reads were normalized using the R package DESeq2 Version 1.22.2 24 with default parameters.
Genome_build: hg38

source_name: Lacrimal gland

extract_protocol:
Total RNA was isolated from ten to fifteen formalin-fixed and paraffin-embedded (FFPE) 4-µm-thick sections of all specimens using the Quick-RNA FFPE Kit (Zymo Research, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, USA). The fragment size of all RNA samples ranged between 120 and 150 bp.
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method. The preparation of MACE libraries was carried out using 1 µg of total RNA, as previously described. The barcoded libraries were sequenced simultaneously on the NextSeq 500 (Illumina, USA) with 1× 75 bp. PCR bias was removed using an unique molecular identifier.

value: Lacrimal gland

tag: disease state

value: healthy


title: IG335_WT1


title: Lacrimal gland S7


title: IG335_MUT4


title: COL10_DMSO1_S10_ROW22


title: C11 [PE20-Cb54-ctrl_S9]


title: COL10_DMSO1_S10_ROW20


title: con-1


title: IG335_MUT2


title: con-3


title: COL10_DMSO1_S10_ROW19


title: IG335_MUT3


title: Lacrimal gland S6


title: Lacrimal gland S5


title: MC38_tumor_HFD

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
cellranger-4.0.0
scanpy-1.7.1
Genome_build: mm10
Supplementary_files_format_and_content: formatted hdf5 file containing mnn integrated matrix

source_name: Mouse xenograft models

growth_protocol: 8-week-old C57BL/6 male mice were fed ad libitum a 10% kcal from fat (low fat) diet or a 45% kcal fat (high fat) diet (Research Diets D12450H and D12451, respectively).

extract_protocol: 10X Single Cell 5' PE; mRNA 5' capture

treatment_protocol: Following 28 weeks of diet treatment mice were injected subcutaneously with 2x105 MC38 cells. Tumors were collected on Day 20 post injection and mechanically and enzymatically digested using miltenyi mouse tumor digestion kit following manufacturer’s instructions. CD45+ cells were separated from tumor suspensions using CD45+ microbeads (miltenyi) and enriched for live cells using a dead cell removal kit (miltenyi). Three samples from each diet treatment group were resuspended in PBS + 0.4% FBS and pooled together in equal number of live cells prior to submitting to single cell sequencing. Cell viability for all samples were >95% via trypan blue prior to submission

tag: Sex

value: male

value: 45% fat

value: tumor


title: IG335_MUT1

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: COL10_DMSO1_S10_ROW18


title: C1 [PE4-CbE-ctrl_S4]

value: Endometrium


title: sample_8_3

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.24.
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6.
Genome_build: Ensembl release 76
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include gene raw counts and normalized CPM (counts per million reads) values for each sample.

source_name: Saline control

extract_protocol:
Brain tissue samples were collected and snap frozen using liquid nitrogen. The extraction of the total RNA from was performed by using kits from Applied Biosystems.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: C57BL mice were purchased at 18 months of age from Jackson Laboratories (Bar Harbor, ME). Mice were acclimated to local conditions for 2 wk and then divided into two weight matched groups (n=15/group). The mice were treated with 90 nmol/kg/d adropin (ABClonal Science, 98.66% purity) suspended in 0.9% sterile saline with 0.1% BSA. The peptide was resuspended daily prior to injection and administered as a single ip. injection (0.1ml volume) at 0900h. Controls received saline diluent only.

value: brain

value: Saline control


title: COL10_DMSO1_S10_ROW17

value: Invasive Ductal Carcinoma


title: HY062_WT3

description:
Processed data files generated from multiple samples
processed data file:
log2.MAT2AA.tabular.txt
n.counts.MAT2AA.tabular.txt

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: Lacrimal gland S2


title: MC38_tumor_LFD

value: 10% fat


title: IG335_WT2

value: WT


title: COL10_DMSO1_S10_ROW16


title: HY062_WT2

value: whole embryo


title: Lacrimal gland S3


title: sample_8_1


title: HY062_WT1

value: normal lymphoid development in thymus


title: Retina central S3

source_name: Retina central

value: Retina central


title: COL10_DMSO1_S10_ROW21


title: Lacrimal gland S4

value: Lacrimal gland


title: HY062_Mut4


title: Retina central S2

value: healthy


title: Retina central S1


title: COL10_DMSO1_S10_ROW15


title: sample_7_1


title: sample_6_2


title: HY062_Mut3


title: COL10_DMSO1_S10_ROW13


title: HY062_Mut2


title: sample_6_1


title: Retina periphery S3

source_name: Retina periphery

value: Retina periphery


title: sample_5_5

source_name: Adropin(34-76) tmt

value: Adropin(34-76) tmt


title: COL10_DMSO1_S10_ROW12

source_name: 40 year old female


title: Lacrimal gland S1


title: Retina periphery S2


title: HY062_WT4

source_name: ENU mutagenesis forward genetic screen


title: COL10_DMSO1_S10_ROW11


title: COL10_DMSO1_S10_ROW10


title: COL10_DMSO1_S10_ROW09


title: sample_7_4


title: HY022_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.IL7R.tabular.txt
n.counts.IL7.tabular.txt


title: HY022_WT2


title: Retina periphery S1


title: HY022_WT3


title: HY062_Mut1


title: sample_4_3


title: COL10_DMSO1_S10_ROW14


title: Healthy conjunctiva replicate 8

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode release 34) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode annotation file (Gencode 32)
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL release 100 (Human genes, GRCh38.p12, download on 05/25/2020). After principal component analysis, differential gene expression with Benjamini-Hochberg adjusted (adj.) p-values was analyzed using the R package DESeq2 Version 1.22.2 24 with default parameters.
Genome_build: hg38

source_name: Healthy conjunctiva

value: conjunctiva


title: sample_4_1


title: HY022_WT1


title: Healthy conjunctiva replicate 6


title: COL10_DMSO1_S10_ROW06


title: Healthy conjunctiva replicate 7


title: COL10_DMSO1_S10_ROW07


title: Healthy conjunctiva replicate 5


title: COL10_DMSO1_S10_ROW08


title: HY022_MUT4

value: MUT


title: sample_5_4


title: HY022_MUT3

value: lymphoid development, defect in rag1 expression in thymus


title: sample_2_4


title: COL10_DMSO1_S10_ROW04


title: sample_2_3


title: COL10_DMSO1_S10_ROW03


title: sample_2_1


title: HY022_MUT1


title: sample_3_3


title: COL10_DMSO1_S10_ROW02


title: sample_1_3


title: Healthy conjunctiva replicate 3


title: Ile VKO GW 3

city: Chuncheon-si

first: Yong-Hyun

last: Han

state: Kangwondo

address: 307-ho, College of Pharmacy, 1, Kangwondaehak-gil

department: College of Pharmacy

country: South Korea

institute: Kangwon National University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Ileum

extract_protocol:
Livers and Ileums were removed, flash frozen on dry ice, and RNA was extrated using Rneasy Mini Kit. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.
KAPA RiboErase

value: Ileum

tag: surgery

value: 75% intestinal resection

value: Abca1 fl/fl X Villin-Cre


title: Healthy conjunctiva replicate 1


title: Ile VKO GW 2


title: COL10_DMSO1_S10_ROW01

tag: cell line

value: Invasive Ductal Carcinoma


title: Healthy conjunctiva replicate 2


title: sample_5_3

value: brain

value: Saline control


title: Healthy conjunctiva replicate 4


title: COL1_DMSO2_S23_ROW39

tag: cell type


title: COL1_DMSO2_S23_ROW40


title: HU319_WT2

description:
Processed data files generated from multiple samples
processed data file:
log2.ATAD5A.tabular.txt
n.counts.ATAD5A.tabular.txt

tag: genotype

value: WT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: HU319_WT1

tag: strain background

value: whole embryo

value: normal lymphoid development in thymus


title: Pterygium S6

source_name: Pterygium

value: Pterygium


title: COL10_DMSO1_S10_ROW05


title: Ile VKO GW 1


title: Pterygium S7


title: Ile VKO 3

value: Vehicle


title: HU319_MUT4

tag: population


title: COL1_DMSO2_S23_ROW38


title: Pterygium S5


title: Ile VKO 2


title: Pterygium S4


title: COL1_DMSO2_S23_ROW37


title: HU319_WT3

tag: surface phenotype


title: Pterygium S8


title: Ile VKO 1

tag: strain


title: HU319_MUT2


title: HU319_MUT1


title: Ile Flox GW 3

value: Abca1 fl/fl

tag: treatment


title: Pterygium S3


title: Ile Flox GW 2


title: Pterygium S2


title: COL1_DMSO2_S23_ROW34


title: Ile Flox GW 1


title: HP327_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.NOL9.tabular.txt
n.counts.NOL9.tabular.txt


title: COL1_DMSO2_S23_ROW33


title: HP327_WT3


title: HU319_MUT3


title: Astrocytes_33879 [F11]

city: Quebec

first: Aurelie

last: de Rus Jacquet

state: QC

address: 2705 Boulevard Laurier

country: Canada

institute: Universite Laval

data_processing:
Sequencing adapters were trimmed from the reads with Cutadapt v2.10 (Martin, 2011) prior to alignment with STAR v2.7.5c (Dobin et al., 2013) to the Homo sapiens GRCh38.p12 genome assembly and annotation from Ensembl (ensembl.org).  Gene counts were generated with the STARsolo algorithm using the following additional parameters: “--soloType CB_UMI_Simple --soloCBwhitelist smartscrb_whitelist.txt --soloCBstart 2 --soloCBlen 8 --soloUMIstart 10 --soloUMIlen 10 -soloBarcodeReadLength 0 --soloCBmatchWLtype 1MM_multi_pseudocounts --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_All --soloUMIfiltering MultiGeneUMI --soloCellFilter None”.  The full set of 384 barcodes designed for this assay was used as the whitelist.  Gene counts for the subset of barcodes used in this experiment were extracted using custom R scripts.  All custom scripts are available by request.
All custom scripts are available by request.
Differential gene expression analysis was performed using EBseq v1.30.0 in R v4.0.3 (Leng et al., 2013).  In the first evaluation, condition 1 was Astrocytes_IM2 (LRRK2 G2019S) and condition 2 was Astrocytes_IM2-GC (wild-type). In the second evaluation, condition 1 was Astrocyes_33879 (LRRK2 G2019S) and condition 2 was Astrocytes_36091 (wild-type).  EBseq calculated a median normalization of the sequencing counts using the median of ratios methods (Anders & Huber, 2010). First, the geometric mean of the sequencing counts was calculated for each gene and across all samples to create a pseudo-reference sample, and the ratio of the sequencing counts to the pseudo-reference counts was calculated for every gene. Then, for each sample, the median value of all the ratios was taken as the normalization factor. Finally, the median normalized sequencing counts were calculated by dividing the sample’s sequencing counts by the sample’s normalization factor.  A false discovery rate of 0.05 and a fold change threshold of 1.4 or 0.7 were used to identify dysregulated genes in LRRK2 G2019S vs WT astrocytes in both evaluations. For Astrocytes_IM2, a k-means clustering algorithm (k=3) was used to group genes into low, moderate, and highly expressed transcripts based on their log10(1+median normalized counts) value, using ComplexHeatmap v2.7.10.9002 in R (Z. Gu et al., 2016). Gene ontology enrichment analysis was done using the Database for Annotation, Visualization, and Integrated Discovery (DAVID v6.8, https://david.ncifcrf.gov/) (Huang da, Sherman, & Lempicki, 2009a, 2009b).  A list of all genes detected in all the samples was exported separately for each EBseq evaluation to use as the background gene set in DAVID.
Genome_build: Homo sapiens Ensembl GRCh38.95
Supplementary_files_format_and_content: single Microsoft Excel file that includes raw count values for all 58768 genes for all 27 samples, a list of 348 differentially expressed genes for IM2/IM2-GC, and a list of 564 differentially expressed genes for Ast_33879/Ast_36091
Supplementary_files_format_and_content: single text file that includes all 384 barcodes for the RNA-seq assay, of which 27 were used in this study

source_name: Astrocytes

growth_protocol: Patient-derived iPSCs with the LRRK2 mutation G2019S and the corresponding isogenic control were provided by Prof. Dr. Thomas Gasser (Universitätsklinikum Tübingen) and Prof. Dr. Hans R. Schöler (Max-Planck Institute). The second line of patient-derived iPSCs with the LRRK2 mutation G2019S and the sex- and age-matched healthy control were provided by Dr. Randall T. Moon (Howard Hughes Medical Institute/University of Washington). The cells were genotyped to confirm the presence of the LRRK2 mutation G2019S using a TaqMan SNP genotyping assay (Thermo Fisher Scientific, Waltham, MA), and karyotyped every 2 months to confirm genomic stability (Cell Line Genetics, Madison, WI). The iPSCs were cultured in mTesR1 or mTesR Plus media (StemCell Technologies, Vancouver, Canada), regularly passaged as aggregates using ReLeSR (StemCell Technologies), and cultured on Geltrex-coated plates (Thermo Fisher Scientific). The step-by-step protocols, media recipes and quality control experiments to prepare iPSC-derived NPCs and astrocytes have been described in exhaustive details in de Rus Jacquet et al., Current Protocols in Cell Biology (2019), https://doi.org/10.1002/cpcb.98.

extract_protocol:
Samples were homogenized in TRIzol and stored at -80 until processing
Total RNA was isolated according to the manufacturer’s instruction, quantified by Nanodrop (Thermo Fisher Scientific) and diluted to 1 ng/µl in nuclease-free water.  A total of 1 ng of RNA was added to 2.5 µl of cell lysis buffer (nuclease-free water with 0.2 % v/v Triton X-100 and 0.1 U/µl RNase inhibitor), and subjected to cDNA synthesis and amplification as described before (Cembrowski et al., 2018). Libraries were prepared using a modified Nextera XT DNA protocol (Illumina, San Diego, CA) where 5 µM P5NEXTPT5 was substituted for the i5 primers in the kit. Libraries were quantified by qPCR (Roche), normalized to 2 nM, then pooled and sequenced on a NextSeq550 flowcell with 25 bases in read 1, 8 bases in the i7 index read, and 50 bases in read 2. The control library phiX (Illumina) was spiked in at a final concentration of 15% to improve color balance in read 1.

treatment_protocol: The cells were not treated.

value: iPSC-derived astrocytes

value: LRRK2 G2019S

tag: platemap well

tag: barcode plate

tag: cdna barcode

value: CTCATGAT


title: Astrocytes_33879 [G11]

value: GCCTAGAT


title: Ile Flox 3

value: Ileum


title: COL1_DMSO2_S23_ROW36

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15
Genome Alignment - STAR_2.5.2b, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.5.0p3, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCh38 + gencode25
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample


title: Ile Flox 2

value: 75% intestinal resection


title: COL1_DMSO2_S23_ROW31


title: HP327_WT2

data_processing:
Reads were aligned to the reference genome with STAR 2.5.2b-1 (Dobin A. et al. Bioinformatics 2013) and the reference annotation from Ensembl (Zv10.85, http://www.ensembl.org/info/data/ftp/index.html)
Resulting alignments were quantified at the gene level with featureCounts version 1.6.0.1 (Liao Y, Smyth G.K., and Shi W., Bioinformatics 2014) and differential expression performed using DESeq2 version 2.11.40.1 (Love M.I., Huber W. and Anders S. Genome Biol 2014). All tools were used with default parameters unless otherwise stated.
Genome_build: z10.85
Supplementary_files_format_and_content: DESeq2 tables of differential gene expression analysis are provided (log2 fold-change and normalized counts)


title: Astrocytes_33879 [E11]

value: CAAACACG


title: COL1_DMSO2_S23_ROW30

value: Invasive Ductal Carcinoma


title: HP327_MUT4

value: MUT

value: lymphoid development, defect in rag1 expression in thymus


title: HP327_WT1

value: WT


title: Astrocytes_33879 [D11]

value: ACTCGGTC


title: Ile Flox 1


title: COL1_DMSO2_S23_ROW35


title: Pterygium S1


title: COL1_DMSO2_S23_ROW29


title: Liv VKO GW 3

source_name: Liver

value: Liver

value: Abca1 fl/fl X Villin-Cre


title: Astrocytes_36091 [C11]

value: Wild-type

value: TAGGGCAA


title: COL1_DMSO2_S23_ROW28


title: HP327_MUT3

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: Astrocytes_36091 [B11]

value: iPSC-derived astrocytes

value: GCCAACCT


title: HP327_MUT2


title: Liv VKO GW 2


title: COL1_DMSO2_S23_ROW32


title: Liv VKO GW 1


title: COL1_DMSO2_S23_ROW27


title: HP327_MUT1


title: Midbrain_astrocytes D03

description:
Midbrain_astrocytes
Midbrain_astrocytes

data_processing:
Smrtscrb2 analysis pipeline: Custom python scripts were used to extract Barcode and UMI sequences from read 1. The correction of barcode error was achieved using starcode v1.1 (Zorita et al., 2015) with the following additional parameters: “-d 1 -q --print_clusters”. Read 2 sequences were renamed using the error-corrected barcode from starcode and UMI sequences from read 1, and were aligned to the Homo sapiens GRCh38.p12 genome assembly and annotation from Ensembl (ensembl.org) using STAR (Dobin et al., 2013) with the following additional parameters: “--alignIntronMax 200000 --outSAMattributes All --outSAMunmapped Within --outSAMtype BAM Unsorted”.  The validity of an alignment was defined by the unique alignment to an exon feature on the correct strand. Gene-level counts were created using valid alignments with at least 50% of the read aligned to an exon feature, using a custom python script to collapse UMIs by gene.  All custom scripts are available by request.
All custom scripts are available by request.
Differential gene expression analysis was performed using EBseq v3.8 in R (Leng et al., 2013), with condition 1 being LRRK2 G2019S and condition 2 being WT. EBseq calculated a median normalization of the sequencing counts using the median of ratios methods (Anders & Huber, 2010). First, the geometric mean of the sequencing counts was calculated for each gene and across all samples to create a pseudo-reference sample, and the ratio of the sequencing counts to the pseudo-reference counts was calculated for every gene. Then, for each sample, the median value of all the ratios was taken as the normalization factor. Finally, the median normalized sequencing counts were calculated by dividing the sample’s sequencing counts by the sample’s normalization factor.  A false discovery rate of 0.05 and a fold change threshold of 1.4 or 0.7 were used to identify dysregulated genes in LRRK2 G2019S vs WT astrocytes. A k-means clustering algorithm (k=3) was used to group genes into low, moderate and highly expressed transcripts based on their log10(1+median normalized counts) value, using ComplexHeatmap v3.11 in R (Z. Gu et al., 2016). Gene ontology enrichment analysis was done using the Database for Annotation, Visualization, and Integrated Discovery (DAVID v6.8, https://david.ncifcrf.gov/) (Huang da, Sherman, & Lempicki, 2009a, 2009b).  A list of all genes detected in all the samples was exported for use as the background gene set in DAVID.
Genome_build: Homo sapiens Ensembl GRCh38.95
Supplementary_files_format_and_content: single Microsoft Excel file that includes raw count values for all 58768 genes for all 20 samples and a list of 752 differentially expressed genes of which 698 were found in the DAVID v6.8 database

growth_protocol: Patient-derived iPSCs with the LRRK2 mutation G2019S and the corresponding isogenic control were provided by Prof. Dr. Thomas Gasser (Universitätsklinikum Tübingen) and Prof. Dr. Hans R. Schöler (Max-Planck Institute). The cells were genotyped to confirm the presence of the LRRK2 mutation G2019S using a TaqMan SNP genotyping assay (Thermo Fisher Scientific, Waltham, MA), and karyotyped every 2 months to confirm genomic stability (Cell Line Genetics, Madison, WI). The iPSCs were cultured in mTesR1 or mTesR Plus media (StemCell Technologies, Vancouver, Canada), regularly passaged as aggregates using ReLeSR (StemCell Technologies), and cultured on Geltrex-coated plates (Thermo Fisher Scientific). The step-by-step protocols, media recipes and quality control experiments to prepare iPSC-derived NPCs and astrocytes have been described in exhaustive details in de Rus Jacquet et al., Current Protocols in Cell Biology (2019), https://doi.org/10.1002/cpcb.98.

value: Human fetal midbrain astrocytes

value: GTCATCTC


title: Liv VKO 2

value: 75% intestinal resection

value: Vehicle


title: HK017_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.ZBTB17.tabular.txt
n.counts.ZBTB17.tabular.txt

value: normal lymphoid development in thymus


title: Liv VKO 3


title: Astrocytes_36091 [A11]

value: CATTGGCG


title: COL1_DMSO2_S23_ROW26

value: Invasive Ductal Carcinoma


title: COL1_DMSO2_S23_ROW25


title: Liv VKO 1


title: HK017_WT3

value: WT


title: Midbrain_astrocytes C03

description:
Midbrain_astrocytes
Midbrain_astrocytes

value: AAAGGCAC


title: COL1_DMSO2_S23_ROW24


title: HK017_WT2


title: HK017_WT1


title: Midbrain_astrocytes B03

description:
Midbrain_astrocytes
Midbrain_astrocytes

value: AGGGAGCA


title: Hippocampal_astrocytes A03

description:
Hippocampal_astrocytes
Hippocampal_astrocytes

value: Human fetal hippocampal astrocytes

value: GGACGATC


title: Liv Flox GW 2

value: Liver

value: Abca1 fl/fl


title: COL1_DMSO2_S23_ROW23


title: COL1_DMSO2_S23_ROW22


title: Hippocampal_astrocytes H02

value: Wild-type

value: TCTATGGG


title: Liv Flox GW 3


title: HK017_MUT3

value: MUT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: lymphoid development, defect in rag1 expression in thymus


title: Liv Flox 3

value: 75% intestinal resection

value: Vehicle


title: COL1_DMSO2_S23_ROW20


title: Hippocampal_astrocytes G02

value: ACATAGCG


title: COL1_DMSO2_S23_ROW21

value: Invasive Ductal Carcinoma


title: HK017_MUT2


title: Cortical_astrocytes F02

description:
Cortical_astrocytes
Cortical_astrocytes

value: Human fetal cortical astrocytes

value: CCAAAAGG


title: Liv Flox 2


title: HK017_MUT1


title: Liv Flox 1


title: COL1_DMSO2_S23_ROW18


title: Cortical_astrocytes E02

description:
Cortical_astrocytes
Cortical_astrocytes

value: GTGTTTCT


title: HJ028_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.UPF1.tabular.txt
n.counts.UPF1.tabular.txt

value: WT

value: normal lymphoid development in thymus


title: COL1_DMSO2_S23_ROW19


title: Neuro-2a GDF11-/- rep3

city: Hangzhou

first: Dixian

last: Wang

state: Zhejiang

address: Yuhangtang Road No.866

department: School of Basic Medical Sciences

institute: Zhejiang University

data_processing:
Sequenced reads were trimmed and filtered by trimmomatic(v 0.38) to get high quality reads.
Clipped reads were aligned to mouse genome (mm10) using tophat (v2.1.1) with the parameters: --library-type  fr-firststrand
Reads whose MAPQ >= 30 were determined as uniquely mapping reads.
Bigwig files were generated from bam files using deeptools (v 3.3.0) bamCoverage, with parameter of "--binSize 1 --normalizeUsing BPM --skipNonCoveredRegions".
DEGs were identified by cuffdiff (v2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: brain

growth_protocol: Neuro-2a cells were cultured on uncoated plastic culture dish in DMEM medium (Hyclone) supplemented with 10% fetal bovine serum(FBS) and 100U/ml penicillin and 0.1mg/ml streptomycin solution).

extract_protocol:
WT and GDF11-/- Neuro-2a cells were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neuroblast

value: untreated


title: COL1_DMSO2_S23_ROW17

extract_protocol:
Fluidigm C1 HT scRNAseq protocol, no offline RNA extraction performed
Fluidigm C1 HT scRNAseq library construction protocol


title: HJ028_WT3

extract_protocol:
Individual zebrafish embryos (5 d.p.f) from an incross of heterozygous carriers were homogenized in 100 μL of Tri Reagent (Sigma, Cat#93289) and transferred to 2 mL deep 96 well plates containing an additional 400μL of Tri Reagent. The RNA-containing aqueous phase was stored at -80°C until genotyping was completed. DNA was extracted from the interphase and organic phase by phenol-chloroform according to the manufacturer’s instructions. Following genotyping, RNA was extracted from embryos homozygous mutants and sibling homozygous wt. DNA was removed from RNA extraction using TURBO DNA-free kit (Invitrogen, Cat#AM1907). RNA was quantified using Qubit RNA HS Assay Kit (ThermoScientific, Cat#Q32852) and the Qubit 4 Fluoromter (ThermoScientific, Q33226). RNA quality was checked by 18S/28S rRNA ratio using the Fragment Analyzer RNA Kit (ThermoScientific, Cat#DNF-471-0500) and the 5200 Fragment Analyzer System (ThermoScientific, Cat#M5310AA).
cDNA libraries were prepared from 1μg of mRNA following poly-A selection using TruSeq stranded mRNA Library Prep (Illumina, Cat#20020595) according to manufacturer’s instuctions. RNA-Seq was performed using mutant and wt sibling from each zebrafish line (n = 2 – 6). The libraries were sequenced in paired-end 75 bp mode at a depth of 25 million reads on an Illumina HiSeq 2500/3000 instrument.


title: HK017_MUT4


title: Liv Flox GW 1

value: Liver

value: Abca1 fl/fl


title: HJ028_WT2


title: Astrocytes_IM2 B02

description:
Astrocytes_IM2
Astrocytes_IM2

value: iPSC-derived astrocytes

value: LRRK2 G2019S

value: CGAAGATG


title: Neuro-2a GDF11-/- rep2


title: Neuro-2a GDF11-/- rep1


title: HY022_MUT2

value: MUT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo

value: lymphoid development, defect in rag1 expression in thymus


title: Astrocytes_IM2 C02

description:
Astrocytes_IM2
Astrocytes_IM2

value: ACGACGCA


title: COL1_DMSO2_S23_ROW16

value: Invasive Ductal Carcinoma


title: COL1_DMSO2_S23_ROW15


title: COL1_DMSO2_S23_ROW14


title: Astrocytes_IM2 A02

description:
Astrocytes_IM2
Astrocytes_IM2

value: AGTACGGT


title: HJ028_Mut4


title: Neuro-2a WT rep3

value: wild type


title: HJ028_WT1

value: WT


title: Astrocytes_IM2-GC H01

description:
Astrocytes_IM2-GC
Astrocytes_IM2-GC

value: Wild-type

value: CGCTTGAC


title: COL1_DMSO2_S23_ROW13


title: Cortical_astrocytes D02

description:
Cortical_astrocytes
Cortical_astrocytes

value: Human fetal cortical astrocytes

value: GTGCCAAC


title: Astrocytes_IM2-GC G01

description:
Astrocytes_IM2-GC
Astrocytes_IM2-GC

value: GACTCACA


title: Neuro-2a WT rep2

value: neuroblast

value: untreated


title: HJ028_Mut3


title: HJ028_Mut2


title: Astrocytes_IM2-GC F01

description:
Astrocytes_IM2-GC
Astrocytes_IM2-GC

value: iPSC-derived astrocytes

value: GTAGTTCG


title: HL-1 cells, HSPA1A_3rd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue <=0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and counts for each Sample

source_name: HL-1 cells

growth_protocol: The mouse HL-1 cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 10e5 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). HSPA1A overexpression plasmid transfection of HL-1 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: OE_RNA against human HSPA1A transfection of HL-1 cells was performed using lipofectAMINE 2000

value: HSPA1A overexpression


title: HJ028_Mut1

value: MUT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: whole embryo


title: NPCs_IM2-GC E01

description:
NPCs_IM2-GC
NPCs_IM2-GC

source_name: Neural progenitor cells

value: iPSCs-derived neural progenitor cells

value: TCAGGTCG


title: COL1_DMSO2_S23_ROW10

value: Invasive Ductal Carcinoma


title: HL-1 cells, HSPA1A_2nd


title: HI020_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.TBCB.tabular.txt
n.counts.TBCB.tabular.txt

value: WT

value: normal lymphoid development in thymus


title: COL1_DMSO2_S23_ROW11


title: HL-1 cells, Ctrl_3rd

value: control plasmid


title: NPCs_IM2-GC D01

description:
NPCs_IM2-GC
NPCs_IM2-GC

value: Wild-type

value: AGACAAGA


title: HI020_WT3


title: COL1_DMSO2_S23_ROW09


title: NPCs_IM2-GC C01

description:
NPCs_IM2-GC
NPCs_IM2-GC

value: GATCTGTT


title: HI020_WT2


title: HL-1 cells, HSPA1A_1st


title: HL-1 cells, Ctrl_2nd


title: iPSCs_IM2-GC A01

description:
iPSCs_IM2-GC
iPSCs_IM2-GC

source_name: iPSCs

value: iPSCs

value: ATTTGTCC


title: COL1_DMSO2_S23_ROW12


title: HL-1 cells, Ctrl_1st


title: Neuro-2a WT rep1

value: neuroblast

value: untreated

value: wild type


title: COL1_DMSO2_S23_ROW06


title: iPSCs_IM2-GC B01

description:
iPSCs_IM2-GC
iPSCs_IM2-GC

value: CCCAATTT


title: COL1_DMSO2_S23_ROW07


title: HI020_MUT4

value: MUT

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen

value: lymphoid development, defect in rag1 expression in thymus


title: HI020_MUT3

value: whole embryo


title: COL1_DMSO2_S23_ROW05

value: Invasive Ductal Carcinoma


title: TLR7KO_4

city: New Haven

first: Maria

last: Tokuyama

state: CT

address: 300 Cedar Street

institute: Yale University School of Medicine

data_processing:
Base-calling: NextSeq500 software
Btrim to trim reads; BWA for alignment to mm10 for ERV analysis and TopHat2 for alignment for cellular gene analysis
Aligned reads for filtered based on previously published method (Treger R. et al., Immunity 2019)
DEseq2 was used to calculate differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: excel spreadsheet of normalized ERV counts and gene counts

source_name: vagina

extract_protocol:
Total RNA using Qiagen RNaesy Kit
polyA library prep using NEBNext Ultra II RNA Library Prep Kit for Illumina

tag: infection

value: HSV-2 186 Syn+


title: KO_B15_Female_Replicate_1

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The raw sequence files were first chekced for quality by FASTQC.
The base quality trimming was performed using fqtrim (v 0.9.4) for phred 30 and minimum read length of 20.
Reference mapping was performed using hisat2 (v 2.0.3).
Counted mapped reads to genes with featureCounts and Ensembl  annotation
edgeR-robust DE analysis with genes filtered at rowSum >1
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text file with raw read counts for each gene

source_name: Fetal brain

growth_protocol: Gestation day 15. The vaginal plug was observed was considered day 0.5 of gestation to detemine gestational age.

extract_protocol:
Freshly collected gestation day 15 placenta and fetal brain from littermate  wildtype and Foxa2 conditional knockout mice were snap frozen in liquid nitrogen. Total RNA was isolated from frozen speciment using a standard TRIzol-based protocol (Catalog 15596026, Thermo Fisher). To eliminate genomic DNA contamination, extracted RNA was treated with DNase I and purified using a RNeasy MinElute Cleanup Kit (Qiagen). The quality and concentration of RNA were determined using a Fragment Analyzer (Advanced Analytical Technologies).
Libraries were prepared by Novogene using an Illumina TruSeq mRNA kit (Illumina Inc.) and sequenced (paired-end 150; 30 million read pairs) using an Illumina NovaSeq 6000.
The strategy was based on lllumina TruSeq mRNA kit.

treatment_protocol: Foxa2 was conditionally deleted in the utterus. Floxed Foxa2 mice were crossed with or LtfiCre  mice to generate conditional knockout animals. Floxed Foxa2f/f mice (stock no. 022620) and LtfiCre mice (stock no. 026030) were obtained from The Jackson Laboratory.  For FOXA2 cKO dams, mice received i.p. injections of recombinant mouse LIF (10 μg in saline; catalog #554008, BioLegend) at 1000 h and 1800 h on GD 3.5

value: Fetal brain

tag: gender

value: Female

value: Foxa2 uterine conditional knockout


title: KO_B15_Female_Replicate_2

tag: tissue


title: TLR7KO_2

value: uninfected


title: COL1_DMSO2_S23_ROW04

first: Jason

last: Myers

address: 601 Elmwood Ave.

institute: University of Rochester


title: KO_B15_Female_Replicate_3


title: HI020_WT1

first: Connor

last: O'Meara

address: Stuebeweg

institute: MPI

value: WT

value: normal lymphoid development in thymus


title: COL1_DMSO2_S23_ROW03


title: TLR7KO_1


title: HI020_MUT1


title: HI020_MUT2


title: COL1_DMSO2_S23_ROW02


title: HG010_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.POLE1.tabular.txt
n.counts.POLE1.tabular.txt


title: Emv2TLR7dKO_4


title: KO_B15_Male_Replicate_1

value: Male


title: Emv2TLR7dKO_3


title: HG010_WT2


title: KO_B15_Male_Replicate_3


title: COL1_DMSO2_S23_ROW01


title: COL1_DMSO1_S1_ROW39


title: Emv2TLR7dKO_2


title: COL1_DMSO1_S1_ROW40


title: HG010_WT3


title: HG010_WT1


title: TLR7KO_3


title: Emv2TLR7dKO_1


title: COL1_DMSO2_S23_ROW08


title: KO_P15_Female_Replicate_1

source_name: Placenta

value: Placenta


title: HU319_WT4


title: KO_P15_Female_Replicate_2


title: COL1_DMSO1_S1_ROW38


title: HG010_Mut4


title: Emv2KO_4


title: HG010_Mut3


title: Emv2KO_3


title: KO_P15_Male_Replicate_1


title: COL1_DMSO1_S1_ROW36


title: KO_B15_Male_Replicate_2


title: COL1_DMSO1_S1_ROW37


title: HG010_Mut2


title: KO_P15_Female_Replicate_3


title: HG010_Mut1


title: KO_P15_Male_Replicate_2


title: Emv2KO_2


title: Emv2KO_1


title: COL1_DMSO1_S1_ROW34


title: HG002_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.PI4KAA.tabular.txt
n.counts.PI4KAA.tabular.txt


title: B6_4

value: wild type B6


title: HG002_WT3


title: WT_B15_Female_Replicate_1

value: Wildtype


title: KO_P15_Male_Replicate_3


title: COL1_DMSO1_S1_ROW33


title: WT_B15_Female_Replicate_3


title: B6_2


title: B6_3


title: WT_B15_Female_Replicate_2


title: COL1_DMSO1_S1_ROW32


title: HG002_WT2


title: COL1_DMSO1_S1_ROW31


title: HG002_WT1


title: WT_B15_Male_Replicate_1


title: COL1_DMSO1_S1_ROW35


title: B6_1


title: HG002_MUT4


title: COL1_DMSO1_S1_ROW30


title: COL1_DMSO1_S1_ROW29


title: EpCAM+ cells isolated from KO mice RNA-seq rep 3

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14)
Trimmed reads were aligned to the ENSEMBL mouse genome version 95 GRCm38 using STAR (2.5.2)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: ascites from ovarian cancer cell xenograft

growth_protocol: EpCAM+ cells were isolated from pooled ascites of WT or TG2-/- tumor-bearing mice (4 mice per group) using EasySep™ Mouse Epithelial Cell Enrichment Kit II (Stem Cell Technologies), snap frozen and stored at -80 degrees.

extract_protocol:
RNA was purified with the RNeasy Qiagen Mini Kit. Genomic DNA was removed using RNase-free DNase Set and RNeasy Mini Elute Spin Columns . Then, mRNA was isolated with Ambion Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.

treatment_protocol: Duplicates per each host genotype containing 2 x 106 cells per sample were resuspended in 350 uL RLT buffer followed by 18-gauge syringe homogenisation before RNA isolation.

value: murine ovarian cancer cell

tag: passage


title: WT_B15_Male_Replicate_3


title: HG002_MUT3

value: MUT


title: EpCAM+ cells isolated from KO mice RNA-seq rep 2


title: HG002_MUT2

value: Ekkwill, Tupfel long fin, wild-typein-Kalkutta, AB, Assam, Tubingen


title: COL1_DMSO1_S1_ROW28


title: EpCAM+ cells isolated from KO mice RNA-seq rep 1


title: COL1_DMSO1_S1_ROW27


title: WT_P15_Female_Replicate_2


title: HG002_MUT1

value: lymphoid development, defect in rag1 expression in thymus


title: EpCAM+ cells isolated from WT mice RNA-seq rep 3


title: COL1_DMSO1_S1_ROW26


title: EpCAM+ cells isolated from WT mice RNA-seq rep 2


title: HA343_WT4

description:
Processed data files generated from multiple samples
processed data file:
log2.TNPO3.tabular.txt
n.counts.TNPO3.tabular.txt

value: whole embryo


title: HA343_WT3


title: EpCAM+ cells isolated from WT mice RNA-seq rep 1


title: COL1_DMSO1_S1_ROW25

value: Invasive Ductal Carcinoma


title: WT_P15_Female_Replicate_1


title: WT_P15_Female_Replicate_3


title: WT_P15_Male_Replicate_1

extract_protocol:
Freshly collected gestation day 15 placenta and fetal brain from littermate  wildtype and Foxa2 conditional knockout mice were snap frozen in liquid nitrogen. Total RNA was isolated from frozen speciment using a standard TRIzol-based protocol (Catalog 15596026, Thermo Fisher). To eliminate genomic DNA contamination, extracted RNA was treated with DNase I and purified using a RNeasy MinElute Cleanup Kit (Qiagen). The quality and concentration of RNA were determined using a Fragment Analyzer (Advanced Analytical Technologies).
Libraries were prepared by Novogene using an Illumina TruSeq mRNA kit (Illumina Inc.).


title: WT_B15_Male_Replicate_2


title: HA343_WT2


title: COL1_DMSO1_S1_ROW23


title: WT_P15_Male_Replicate_2


title: HA343_WT1


title: WT_P15_Male_Replicate_3


title: COL1_DMSO1_S1_ROW24


title: COL1_DMSO1_S1_ROW22


title: HA343_MUT4


title: COL1_DMSO1_S1_ROW21


title: HA343_MUT3


title: OE2_b: Haspin OE2 stem cells rep2

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

data_processing:
Chipster software was used.
Trimming was performed with Trimmomatic
The sequenced reads were aligned using TopHat2 (single end reads, library type: fr-firststrand) on mouse genome GRCm38.87
The aligned reads were counted by HTSeq (union, stranded-reverse)
Differential expression analysis was carried out by DeSeq2 (p value cutoff <0.05 and log2 fold >│1│)
Genome_build: mouse genome GRCm38.87
Supplementary_files_format_and_content: Counts file contains HTSeq output for every sample and Normilized data file contains DeSeq2 output for every pairwise comparison

source_name: E14 stem cells

growth_protocol: E14 stem cells were cultured under standard undifferentiated conditions (serum&LIF).

extract_protocol:
Total RNA was extracted using RNeasy protect mini kit (Qiagen) with on-column DNAse digestion.
Truseq stranded mRNA library kit (Illumina) was used

treatment_protocol: no treatment

value: E14 stem cells

tag: developmental stage

value: Haspin Overexpression


title: OE2_a: Haspin OE2 stem cells rep1


title: OE1_c: Haspin OE1 stem cells rep3


title: COL1_DMSO1_S1_ROW20

city: Rochester


title: HA343_MUT2

city: Freiburg


title: OE1_b: Haspin OE1 stem cells rep2


title: KO2Sti12 BMDM RNA-seq

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

institute: University of Bern

data_processing:
Illumina RTA3 was used for base calling
Paired-end clean reads were mapped to the mouse reference genome (GRCm38/mm10) using HISAT2 (v.2.0.5) software.
HTSeq (v.0.6.1) was used to count the read numbers mapped of each gene, including known and novel genes. Subsequently, RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions with three biological replicates per condition was performed using DESeq2 (v.1.22.2). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with counts per gene per sample with Ensembl identifiers and gene names

source_name: bone marrow

growth_protocol: Macrophage precursors were isolated from bone marrow of wild type or mutant C57BL/6 mice, cultured and diferentiated to macrophages in MCSF-conditioned medium for 5 days.

extract_protocol:
RNA isolation was performed using the RNeasy Mini kit (QIAGEN,Cat No./ID: 74104).
Sequencing libraries were generated from 1ug input material using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions and sequenced on a NovaSeq 6000 platform (paired end 150 bp).

treatment_protocol: Macrophages were treated with the indicated cytokines for 36 h

value: in vitro cultured bone marrow derived macrophages

tag: stimulation


title: COL1_DMSO1_S1_ROW19

source_name: 40 year old female

tag: cell line


title: OE2_c: Haspin OE2 stem cells rep3


title: KO2Sti03 BMDM RNA-seq

tag: cell type


title: KO2_c: Haspin KO2 stem cells rep3

tag: genotype

value: Haspin knock out


title: HA343_MUT1

source_name: ENU mutagenesis forward genetic screen

tag: strain background


title: OE1_a: Haspin OE1 stem cells rep1


title: FOXN1_WT3

description:
Processed data files generated from multiple samples
processed data file:
log2.FOXN1.tabular.txt
n.counts.FOXN1.tabular.txt

tag: population


title: COL1_DMSO1_S1_ROW18


title: COL1_DMSO1_S1_ROW17


title: KO2Sti02 BMDM RNA-seq


title: KO2_b: Haspin KO2 stem cells rep2


title: KO2Sti01 BMDM RNA-seq


title: FOXN1_WT2

tag: surface phenotype


title: COL1_DMSO1_S1_ROW16


title: KO2Sti13 BMDM RNA-seq

tag: strain


title: KO2_a: Haspin KO2 stem cells rep1


title: FOXN1_WT1


title: COL1_DMSO1_S1_ROW15


title: KO1Sti12 BMDM RNA-seq


title: KO1Sti13 BMDM RNA-seq


title: KO1_b: Haspin KO1 stem cells rep2


title: KO1_c: Haspin KO1 stem cells rep3


title: KO2Sti11 BMDM RNA-seq


title: COL1_DMSO1_S1_ROW14


title: KO1Sti11 BMDM RNA-seq


title: FOXN1_WT4


title: COL1_DMSO1_S1_ROW13


title: FOXN1_MUT3


title: FOXN1_MUT2


title: KO1Sti02 BMDM RNA-seq


title: KO1Sti01 BMDM RNA-seq


title: COL1_DMSO1_S1_ROW12


title: COL1_DMSO1_S1_ROW11


title: E14_b: E14 stem cells rep2


title: E14_c: E14 stem cells rep3


title: COL1_DMSO1_S1_ROW10


title: E14_a: E14 stem cells rep1


title: 2012_WT3

description:
Processed data files generated from multiple samples
processed data file:
log2.TOP3A.tabular.txt
n.counts.TOP3A.tabular.txt