title: Raji_Mnase-seq_a-amanitin_18h

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

institute: IGMM

description: Trearted with 2.5 ug/ml of alpha-amanitin for 18 hours

data_processing:
All samples were aligned to human genome (hg19, GRCh37) using Bowtie 2 aligner. Samples were then treated using PASHA pipeline to produce wig files (Fenouil et al. 2016). Uniquely aligned tags were elongated after estimating optimal elongation size in silico for single ended sequencing or between the pairs for paired end sequencing, enabling to use the original fragment length for further processing. Signals were scaled according to the mean signal. The number of tags covering each nucleotide of the genome was computed and averaged in bins of 10 or 50 nucleotides. For MNase-seq datasets, signals were smoothed on 5 bins.
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: Raji B cells

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamin (2 mg/ml) at 37°C and 5% CO2.

extract_protocol:
Fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter. For sequencing of nucleosomal DNA in Raji cells, 35x106 cells were resuspended in 350μl Solution I (150 mM sucrose, 80 mM KCl, 5 mM K2HPO4, 5 mM MgCl2, 0.5 mM CaCl2, 35 mM HEPES pH 7.4) and NP40 was added to a final concentration of 0.2%. Cell membranes were permeabilized for five min at 37°C. MNase was prepared at 50, 25, 12, 6 or 3 units in 0.5L of Solution II (150 mM sucrose, 50 mM Tris pH 8, 50 mM NaCl, 2 mM CaCl2) and incubated with 50 µL of cellular preparation, corresponding to 5.106 cells, for exactly 10 min at 37°C. The reactions were stopped by adding of EDTA to a final concentration of 10 mM. The cells were lysed using 1.45L of SDS Lysis Buffer (1% SDS, 10 mM EDTA pH 8, 50 mM Tris pH 8), with 10 min incubation at 4°C. 200μl aliquots were taken for purification and the remaining extracts were stored at -80°C. An equal volume of TE (200ul) was added to the aliquots, followed by subsequent 2 hour treatments with each 0.2µg/L final concentrations of RNase A and Proteinase K at 37°C and 55°C, respectively. DNA was extracted by two subsequent phenol:chloroform:isoamylalcohol (25:24:1) extractions, further purified using QIAquick PCR purifications colums (Qiagen, Germany). Nucleosomal digestion was verified by running 500ng of DNA on a 1.5% agarose gel as well as on DNA high-sensitivity 2100 Bioanalyzer chips (Agilent, USA). Digestions showing 75% of mononucleomes (running at 150bp) were selected for library preparations.
ChIP-seq
Mnase-seq and ChIP-seq librairies were prepared using Illumina's ChIP Sample Prep Kit according to standard protocol.

treatment_protocol: For the α-amanitin experiments, cells were treated with 2.5 µg/mL at the indicated times. For the Pyridostatin experiments, cells were treated with 10 µM pyridistatin

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji

tag: spike-in reference organisme

tag: spike-in cell line

tag: chip antibody

value: alpha-amanitin for 18 hours

tag: concentration

value: 2.5 ug/ml of alpha-amanitin

tag: duration

value: 18 hours


title: Raji_PolII_a-amanitin_18h

status: Public on Apr 15 2025

type: SRA

country: France

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: strain

tag: cell line

value: Total PolII (N20 - sc899 - Santa Cruz Biotechnology)

tag: treatment


title: Micorwell-seq datasets of patient3_replicate1

city: Hangzhou

first: Lifeng

last: Ma

address: Yuhangtang Road No.388

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-2.5.1. The reads quality under 10 were removed. We took a dark reaction for R1, where R1 measured 24bp and R2 measured 150bp. The cell barcode is at position 1-18 of R1, and the UMI barcode is at position 19-24 of R1.
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

molecule: polyA RNA

source_name: Breast

extract_protocol:
Tissues single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

tag: tissue

value: Breast

value: Inflammation


title: Micorwell-seq datasets of patient4_replicate1

value: Normal


title: FoxP2-R553H-Sox2-EGFP Input Replicate 1

city: Stanford

first: Joanna

last: Wysocka

state: CA

address: 265 Campus Dr.

country: USA

institute: Stanford University

description: Library name: RH_SOX_IN

data_processing:
ChIP-seq reads were trimmed using skewer v0.2.2 and mapped to hg38 assembly using Bowtie2 v2.5.1 using -very-sensitive -X 2000. Reads were deduplicated with samtools v1.13 markdup and only uniquely mapped reads mapped to the main chromosomes were retained. Peaks were called against HEK293 control ChIP using MACS2 v2.2.9.1 with q-value cutoff of 0.01.
Assembly: hg38
Supplementary files format and content: BigWig and narrowPeak (except for inputs)

extract_protocol:
Cells were fixed with 1% formaldehyde in PBS for 10 minutes, and sonicated with diagenode Bioruptor Plus
ChIP-seq libraries were prepared with NEBNext Ultra II DNA library prep kit. The libraries were amplified with 4-8 cycles on the thermocycler and size selection was done with Agencourt AMPure XP beads. The libraries were validated with Agilent D5000 DNA screen tape.

value: Human embryonic kidney

tag: batch


title: FoxP2-R553H-MAFK-EGFP EGFP ChIP Replicate 2

description: Library name: RH_MAF_CHx2

value: Rabbit Anti-GFP (Thermo, cat#A11122)


title: FoxP2-R553H-Sox2-EGFP Input Replicate 2

description: Library name: RH_SOX_INx2


title: FoxP2-R553H-Sox2-EGFP EGFP ChIP Replicate 2

description: Library name: RH_SOX_CHx2


title: Micorwell-seq datasets of patient2_replicate2


title: FoxP2-R553H-Sox2-EGFP EGFP ChIP Replicate 1

description: Library name: RH_SOX_CH


title: Micorwell-seq datasets of patient2_replicate1


title: FoxP2-R553H-MAFK-EGFP Input Replicate 2

description: Library name: RH_MAF_INx2


title: FoxP2-R553H-MAFK-EGFP EGFP ChIP Replicate 1

description: Library name: RH_MAF_CH


title: FoxP2-R553H-EGFP EGFP ChIP Replicate 2

description: Library name: RH_CHx2


title: FoxP2-R553H-MAFK-EGFP Input Replicate 1

description: Library name: RH_MAF_IN


title: Micorwell-seq datasets of patient1_replicate2


title: FoxP2-R553H-EGFP Input Replicate 2

description: Library name: RH_INx2


title: Micorwell-seq datasets of patient1_replicate1


title: FoxP2-EGFP Input Replicate 2

description: Library name: WT_Inx2


title: 23-039 fetus day 1

city: Tucson

first: Sean

middle: W

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

description: Library name: 23039_day_1

data_processing:
Quality check was assesed using FastQC software (version 0.11.9)
Aligment was assessed using STAR software (version 2.7.3a)
Mapped reads were counted using FeatureCounts (version 2.0.3)
Assembly: Sheep genome (Ovis aries Oar_Rambouillet_v2.0) from Ensembl
Supplementary files format and content: rlog.counts_PBMC.csv

molecule: total RNA

organism: Ovis aries

source_name: whole blood

growth_protocol: Columbia-Rambouillet crossbred ewes carrying singleton pregnancies were fed alfalfa pellets and had ad lib access to water.

extract_protocol:
RNA from PBMCs was isolated with Tri-Reagent (Molecular Research Center, Cincinnati, OH).
Libraries were prepared for sequencing adapters using Illumina TruSeq Stranded mRNA Library Prep Kit and sequenced using Illumina's NextSeq500.

treatment_protocol: Pregnant ewes were kept at ambient temperatures (22°C). Fetal and maternal catheters were placed at 119 ± 2 days of gestation. Beginning at 123±2 dGA intravenous LPS (E. coli serotype O55:B5) bolus were administered to the fetus. Four increasing LPS boluses dissolved in saline were given (0.3ug, 1.5ug, 3ug,15ug) on Day 1, Day 3, Day 4, and Day 5, respectively (Figure 1). Peripheral blood mononuclear cells (PBMCs) were collected and isolated on dGA (study day) 123 (1), 126 (4), and 127 (5) prior to the daily LPS bolus.  RNA was isolated from PBMCs for RNA sequencing.

value: whole blood

tag: day of_sample_collection

value: peripheral blood mononuclear cells


title: FoxP2-EGFP EGFP ChIP Replicate 2

description: Library name: WT_CHx2


title: FoxP2-EGFP EGFP ChIP Replicate 1

description: Library name: WT_CH


title: FoxP2-EGFP Input Replicate 1

description: Library name: WT_In


title: 23-034 fetus day 5

description: Library name: 23034_day_5


title: HEK293T Control EGFP ChIP

description: Library name: HEK_CH


title: 23-034 fetus day 1

description: Library name: 23034_day_1


title: CD11C+_Test_rep3

city: Columbus

first: Syed-Rehan

middle: A

last: Hussain

state: Ohio

address: 700 Children's Dr.

department: Abigail Wexner Research Institute

institute: Nationwide Children's Hospital

data_processing:
Data was aligned against the GRCm38.p3 genome using STAR
Features were annotated using Gencode M19
Differenital Expression analysis was performed using DESeq2
Assembly: GRCm38.p3
Supplementary files format and content: Raw counts. .tsv

organism: Mus musculus

source_name: Lung

extract_protocol:
Cells from whole mouse lungs were harvested and FACS performed using standard cell staining techniques with CD11c antibody (Clone N418; catalog no. 12-0114-82, ThermoFisher). RNA isolated using mirVana miRNA and total RNA isolation kit (catalog no. AM1560, Thermo Fisher Scientific).
Following rRNA removal, RNA was used for the construction of sequencing libraries.  Libraries were pooled and sequenced at 2 x 150 bp read lengths on the Illumina HiSeq 4000 platform to generate approximately 60-80 million paired-end reads per sample.

treatment_protocol: C57Bl6 mice were first sensitized (1 mcg, one day) and after 1 week were then challenged for five days with 10 mcg HDM extract. Control group only were given 1 x PBS. Lungs were hravest on day 14 post senitization and cells were stained wth CD11c antibody for FACS.

value: Lung

value: CD11c+ cells

tag: genotype

value: wt

value: HDM


title: 23-039 fetus day 5

description: Library name: 23039_day_5


title: FoxP2-R553H-EGFP EGFP ChIP Replicate 1

description: Library name: RH_CH


title: 23-031 fetus day 1

description: Library name: 23031_day_1


title: CD11C+_Test_rep1


title: 23-031 fetus day 5

description: Library name: 23031_day_5


title: HEK293T Control Input

description: Library name: HEK_IN


title: FoxP2-R553H-EGFP Input Replicate 1

description: Library name: RH_In


title: 23-024 fetus day 5

description: Library name: 23024_day_5


title: CD11C+_Con_rep2

value: PBS


title: CD11C+_Con_rep1


title: whole uterus, Nat10 d/d, replicate 3

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

description: Library name: dd3

data_processing:
Clean reads were mapped to mouse genome (UCSC mm10) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: Female mice were sacrificed on PND21.

value: whole uterus


title: whole uterus, Nat10 d/d, replicate 2

description: Library name: dd2


title: CD11C+_Test_rep2


title: 23-024 fetus day 1

description: Library name: 23024_day_1


title: 92868, BFoxm1, scRNA-seq

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

library_source: transcriptomic single cell

data_processing:
Alignment and QC performed with Cellranger v6.0.1 from 10X Genomics
Normalization, PCA, UMAP, and clustering performed using Seurat software package
Batch effect correction using Harmony software package
Gene set analysis conducted using DAVID
Assembly: Customized build from GRCm38 and transcript annotations from GENCODE. Includes added transgenes
Supplementary files format and content: TSV files and matrix files

source_name: Pancreatic Islet

extract_protocol:
Mouse islets were isolated by collagenase digestion, followed by Ficoll gradient and handpicking
The Single Cell 3’ Reagent Kit v2 or v3 was used for generating scRNA-seq data. All libraries were validated for quality and size distribution using a BioAnalyzer 2100 (Agilent) and quantified using Kapa (Illumina). For samples prepared using ‘The Single Cell 3’ Reagent Kit v2’, the following chemistry was performed on an Illumina HiSeq4000: Read 1: 26 cycles, i7 Index: 8 cycles, i5 index: 0 cycles, and Read 2: 98 cycles. For samples prepared using ‘The Single Cell 3’ Reagent Kit v3’, the following chemistry was performed on an Illumina HiSeq 4000: Read 1: 28 cycles, i7 Index: 8 cycles, i5 index: 0 cycles, and Read 2: 91 cycles.

value: Pancreatic Islet

value: BFoxm1 C57Bl6/J


title: whole uterus, Nat10 d/d, replicate 1

description: Library name: dd1


title: whole uterus, Nat10 f/f, replicate 3

description: Library name: ff3


title: 92867, BFoxm1, scRNA-seq


title: whole uterus, Nat10 f/f, replicate 2

description: Library name: ff2


title: 23-012 fetus day 5

description: Library name: 23012_day_5


title: 92866, WT, scRNA-seq

value: WT C57Bl6/J


title: 23-012 fetus day 1

description: Library name: 23012_day_1


title: Infected_treated_GYY4137-3

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description: Library name: E109

data_processing:
Illumina NovaSeq for sequencing
HISAT2 (v2.2.1) was used for indexing the reference genome (GCF_015252025.1_Vero_WHO_p1.0)
SAMTOOLS (v1.15.1) was used to sort and convert the sam files to bam files
stringtie(v.2.2.1) was used to calculate the raw read counts per gene
Normalisation and differential gene expression analysis was done using edgeR (genes with atleast 10 reads across replicates in any samples, were selected for each comparative analysis)
Assembly: Reference genome used : Chlorosebus sabeus, accession number : GCF_015252025.1
Supplementary files format and content: coma delimited .csv files containing raw reads count, normalized count file and comparison of genes’ expression for sample pairs

organism: Chlorocebus sabaeus

source_name: VeroE6 cells infected with 0.01 MOI SARS-CoV-2 (HK variant) in presence of 5 mM GYY4137 in DMEM medium with 2 % FBS at 48 hours post infection

growth_protocol: VeroE6 cells were passeged thre time before seeding them for infection in a 24 well plate, containing DMEM with 10 % FBS in a humidified CO2 incubator at 37 degree

extract_protocol:
Total RNA was extracted from the cells. mRNA enrichment was performed using NEB mRNA enrichment kit
Fragmentation and random priming of samples was done for 15 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina Novaseq sequencer using 1X50 bp single-end reads and a 1% PhiX spike-in control.

treatment_protocol: VeroE6 cells were pretraeted with 5 mM GYY4137, followed by infection with 0.01 MOI of SARS-CoV-2 for 1 h. After 1 h, viral incolum was removed, cells were washed with 1 x PBS and media was replaced with fresh  media containing drugs. Incuabtion was continued for 48 h

value: VeroE6 cells

value: Infected with SARS-CoV-2 in presence of 5 mM GYY4137


title: 92865, BFoxm1, scRNA-seq


title: 28_blood_control_mother

type: genomic

city: Göttingen

first: Roy

last: Lardenoije

address: Robert-Koch-Str. 40

country: Germany

institute: University Medical Center Göttingen

description: MethylationEPIC BeadChip DNA methylation data obtained from genomic DNA extracted from whole blood of a rhesus macaque infant with a control mother.

hyb_protocol: A total of 500 ng DNA was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo) and hybridized to Infinium MethylationEPIC microarrays (Illumina), according to the instructions of the manufacturers.

scan_protocol: Arrays were scanned using an iScan (Illumina) with standard settings recommended by Illumina.

data_processing:
IDAT files were read into R using readEPIC of the wateRmelon package (version 1.34.0) and the rhesus macaque-conserved probes were subsetted. Potential sample mislabeling was investigated by comparing reported sex of samples with predicted sex, based on X chromosome methylation with predictSex of wateRmelon. No mismatches between reported and predicted sex were identified. Probes targeting the X and Y chromosomes were then removed (10,544). All samples had a bisulfite conversion rate > 90%, as calculated with bscon of wateRmelon. The pfilter function (with perCount = 5, pnthresh = 0.05, perc = 5, pthresh = 5) from wateRmelon was used to further filter probes and samples, leading to the exclusion of 2 samples, 647 probes with a beadcount < 3 in > 5% of samples and 26,983 probes with > 5% of samples having a detection p value > 0.05 . A final sample outlier detection step was performed with outlyx of wateRmelon, but no outliers were detected. Quantile normalization and beta-mixture quantile normalization was then applied sequentially. Any missing values were imputed through k-nearest neighbors imputation (with k = 100), using a modified version of the champ.impute function of the ChAMP package (modified from version 2.16.2). Probes with > 20% missing values (0 probes) and samples with > 10% missing values (0 samples) were excluded. For the statistical analyses, any beta values of exactly 0 or 1 were replaced with the lowest > 0 or highest < 1 value, respectively, before conversion of all beta values to M values with beta2m of lumi (version 2.42.0). A final visual inspection was performed on the processed data, leading to the detection and exclusion of 1 outlying sample based on a hierarchically clustered dendrogram and a multidimensional scaling plot with the first two principal components (using a modified version of champ.QC).
Unprocessed unmethylated and methylated signal intensities of probes succesfully mapped to the rhesus macaque genome (Mmul_10).

label: Cy5 and Cy3

organism: Macaca mulatta

source_name: blood, control mother

label_protocol: Standard Illumina protocol.

growth_protocol: The monkeys lived with their families in large and complex social groups at the Emory University’s Yerkes National Primate Research Center (YNPRC) Field Station in Lawrenceville, GA. Social groups generally consist of 75-150 adult females, 2-3 adult males and younger offspring who have not you reached adulthood. The monkeys were housed in compounds of about 30 by 30 meters, and were able to cross into shared climate-controlled indoor areas. Food was provided twice daily, consisting of seasonal fruits and vegetables, supplemented with LabDiet nutrition (Purina Mills Int., St. Louis, MO). Water was available ad libitum.

extract_protocol: Genomic DNA was extracted from whole blood samples using standard procedures.

treatment_protocol: Whole blood was collected in 5 ml EDTA tubes and frozen at -80ºC until extraction.

tag: Sex

value: M

tag: rank mother

value: low

tag: birth cohort

tag: blood cortisol


title: KrasG12D/+; Trp53R172H/+; Ad-Cre -KPA-2

city: Omaha

first: Imayavaramban

last: Lakshmanan

state: Nebraska

address: Durham Research Center I, Room 7005 Omaha,

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

description:
Library name: KP_Tumor2
Column name in raw counts: KP_Tumor2

data_processing:
Raw sequences were processed for quality control using FastQC
Alignment was done using TopHat v2.0.8
Expression quantification was done in R
Differential expression analysis was run in R using EdgeR
Assembly: mm10 was used as a reference genome
Supplementary files format and content: Supplementary files format and content: raw counts (count_matrix_raw_N_K_KP.txt)

source_name: Tissue

growth_protocol: Normal lung tissue, KA and KPA tumors tissues were used for total RNA isolation

extract_protocol:
RNA isolation was carried out using mirVana miRNA isolation kit and used for the RNAseq experiment.
PolyA library prepreparation

value: Tissue

value: Cancer

value: KrasG12D/+; Trp53R172H/+; Ad-Cre -KPA-2


title: 92863, BFoxm1, scRNA-seq


title: KrasG12D/+; Trp53R172H/+; Ad-Cre -KPA-1

description:
Library name: KP_Tumor1
Column name in raw counts: KP_Tumor1

value: KrasG12D/+; Trp53R172H/+; Ad-Cre -KPA-1


title: 92862, BFoxm1, scRNA-seq


title: 24_blood_control_mother

value: high


title: KrasG12D/+; Trp53R172H/+; Ad-Cre -KPA-3

description:
Library name: KP_Tumor3
Column name in raw counts: KP_Tumor3

value: KrasG12D/+; Trp53R172H/+; Ad-Cre -KPA-3


title: Infected_treated_GYY4137-2

description: Library name: E108


title: whole uterus, Nat10 f/f, replicate 1

description: Library name: ff1


title: Infected-3

description: Library name: E106

source_name: VeroE6 cells infected with 0.01 MOI SARS-CoV-2 (HK variant) in DMEM medium with 2 % FBS at 48 hours post infection

value: Infected with SARS-CoV-2


title: 92864, WT, scRNA-seq


title: KasG12D/+; Ad-Cre-KA-3

description:
Library name: K_Tumor3
Column name in raw counts: K_Tumor3

value: KasG12D/+; Ad-Cre-KA-3


title: 19_blood_maltreated_mother

description: MethylationEPIC BeadChip DNA methylation data obtained from genomic DNA extracted from whole blood of a rhesus macaque infant with a maltreated mother.

source_name: blood, maltreated mother

value: middle


title: Infected-2

description: Library name: E105


title: 92861, WT, scRNA-seq


title: KasG12D/+; Ad-Cre-KA-2

description:
Library name: K_Tumor2
Column name in raw counts: K_Tumor2

value: KasG12D/+; Ad-Cre-KA-2


title: Infected-1

description: Library name: E104


title: Pt29

city: Dunedin

first: Mike

last: Eccles

state: Otago

address: 56 Hanover Street

department: Pathology

country: New Zealand

institute: University of Otago

description:
FFPE melanoma sample
SAMPLE 15

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human 850K MethylationEPIC v1.0 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The RnBeads package was used to load raw microarray data (.idat files) into the statistics program RStudio (Version 1.2.5042) for initial quality control, pre-processing and differential methylation analysis.

source_name: melanoma tissue 15

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from FFPE melanoma samples using the Qiagen QIAamp DNA FFPE Tissue Kit according to standard instructions.

value: melanoma tissue

tag: response to treatment (recist criteria)

value: Non-responder


title: KrasG12D/+; Ad-Cre-KA-1

description:
Library name: K_Tumor1
Column name in raw counts: K_Tumor1

value: KrasG12D/+; Ad-Cre-KA-1


title: Uninfected-3

description: Library name: E103

source_name: VeroE6 cells 48 h post seeding in DMEM medium with 2 % FBS

value: VeroE6 cells


title: 92859, WT, scRNA-seq

value: Pancreatic Islet

value: WT C57Bl6/J


title: Pt31

description:
FFPE melanoma sample
SAMPLE 17

source_name: melanoma tissue 17


title: 92860, BFoxm1, scRNA-seq

value: BFoxm1 C57Bl6/J


title: Uninfected-2

description: Library name: E102


title: Pt5

description:
FFPE melanoma sample
SAMPLE 3

source_name: melanoma tissue 3

value: Responder


title: MG32, Vehicle, Era, Chipseq

data_processing:
QC and adapter trimming of fastq files using fastp
Bowtie2 was used to align fastq files to GRCm39 reference genome
Genrich was used for consensus peak calling
Differential accessibility analysis was performed using DESeq2
ChIPpeakAnno used to annotate differentially accessible peaks
HOMER used to identify binding motifs
Assembly: GRCm39
Supplementary files format and content: bigWig and narrowPeak files

extract_protocol:
bTC6 cells were cultured in 5 mM DMEM supplemented with 10% hormone-depleted fetal bovine serum for one week before treating with vehicle or 100mM 17-b-estradiol in ethanol (final concentration 0.1%) for one hour. Cells were brought up to 10 mL of 1X DPBS and 1% formaldehyde and incubated at room temperature for 8 minutes with rotation. Reaction was brought to 0.125 M glycine for quenching and incubated for 5 minutes at room temperature with rotation. Chromatin was sonicated (Covaris) to recover fragments between 200-800 bps.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were sequenced on the Illumina Hiseq 4000 with 50 bp single-end sequencing with a minimum of 20 million reads per sample.

treatment_protocol: ChIP was performed on five replicates per treatment group. Antibodies included rabbit anti-FOXM1 (Diagenode, Denville, NJ), goat anti-FoxA2 (Santa Cruz, Dallas, TX), rabbit anti-ERa (Santa Cruz), and a rabbit IgG control (Santa Cruz).


title: Normal lung tissue N-3

description:
Library name: Normal3
Column name in raw counts: Normal3

value: Tissue

value: Normal

value: Wild type


title: Uninfected-1

description: Library name: E101


title: Normal lung tissue- N-2

description:
Library name: Normal2
Column name in raw counts: Normal2


title: Pt24

description:
FFPE melanoma sample
SAMPLE 11

source_name: melanoma tissue 11


title: MG31, Vehicle, Era, Chipseq


title: Pt28

description:
FFPE melanoma sample
SAMPLE 14

source_name: melanoma tissue 14


title: Pt27

description:
FFPE melanoma sample
SAMPLE 13

source_name: melanoma tissue 13


title: Infected_treated_GYY4137-1

description: Library name: E107

value: Infected with SARS-CoV-2 in presence of 5 mM GYY4137


title: Normal lung tissue-N-1

description:
Library name: Normal1
Column name in raw counts: Normal1


title: antiPD1TL1A_treatment

city: San Francisco

first: YILE

last: DAI

state: California

address: 590 Minnesota St., Apt. 342

institute: Yale University

description:
Library name: Sample4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.3.0.2 (10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MC38b tumor

extract_protocol:
Cell surface staining of single-cell suspensions from tumors was performed after two times wash with FACS buffer (PBS supplemented with 2% FBS). All samples were first stained with LIVE/DEAD™ Fixable Blue to exclude dead cells and incubated with Fc receptor blocking antibody (Biolegend, #101320). Then, cells were stained with anti-CD45 (30-F11) and anti-CD3 (17A2). Biological replicates for saline control (n=2) and treated group (n=4) were individually processed. Biological replicates were then pooled together at the single cell suspension stage before sorting with equivalent number of cells from each replicate. The following populations were sorted: P1: CD45+CD3+ (TIL cells), P2: CD45+CD3− (non-TIL immune cells), P3: CD45−CD3− (tumor and stromal cells). P1, P2, and P3 for each sample were then mixed back together at a 9:9:2 ratio, respectively.
20,000 cells from each treatment condition were loaded onto the 10x Genomics Chromium System. Library preparation was performed with 10x Genomics reagents according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA). Libraries were then sequenced with an Illumina NovaSeq 6000 at the YCGA.

value: MC38b tumor

value: Tumor cell and immune cell


title: MG30, Vehicle, Era, Chipseq


title: Pt12

description:
FFPE melanoma sample
SAMPLE 7

source_name: melanoma tissue 7


title: Mm_thymus_B6_P28_WT_rep3

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

department: Developmental Immunology

data_processing:
Transcriptomes were analyzed on the Galaxy platform.
Adapters were trimmed with TrimGalore! (version 0.4.3.1).
Reads were aligned to the reference genome with Hisat2  (version 2.1.0).
Counts were generated with featureCounts (version 1.6.1.0).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: thymus

extract_protocol:
Preparations of single TECs were prepared from explanted thymi. Negative enrichment via MACS sorting with anti-CD45 beads (Miltenyi) was performed. Enriched TECs were purified by FACS and sorted directly into TRI reagent (Sigma-Aldrich). RNA was extracted following standard protocols.
Libraries were constructed with the NEBNext Ultra RNA Library Prep kit or the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.

value: thymus

value: Epcam+CD45- TECs

value: WT

tag: age

tag: condition


title: Pt22

description:
FFPE melanoma sample
SAMPLE 10

source_name: melanoma tissue 10

value: melanoma tissue


title: antiPD1_treatment

description:
Library name: Sample3
10x Genomics


title: PBS2_treatment

description:
Library name: Sample2
10x Genomics


title: 27_blood_maltreated_mother

value: F

value: middle


title: Pt20

description:
FFPE melanoma sample
SAMPLE 8

source_name: melanoma tissue 8

value: Non-responder


title: Pt1

description:
FFPE melanoma sample
SAMPLE 1

source_name: melanoma tissue 1


title: Mm_thymus_B6_P28_WT_rep1

institute: Max Planck Institute for Immunobiology and Epigenetics


title: Pt30

description:
FFPE melanoma sample
SAMPLE 16

source_name: melanoma tissue 16


title: PBS1_treatment

description:
Library name: Sample1
10x Genomics


title: Pt25

description:
FFPE melanoma sample
SAMPLE 12

source_name: melanoma tissue 12


title: whole uterus, input control

description: Library name: mouse-uterus-input

data_processing:
After quality control, clean RNA-seq data were aligned to the reference genome (UCSC mm10) with Hisat2 software v2.2.1
Peaks were called uing MACS v3.0.0a7 with the significance cut-off q-value <=0.05
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

value: whole uterus


title: Mm_thymus_B6_P28_WT_rep2


title: Pt21

description:
FFPE melanoma sample
SAMPLE 9

source_name: melanoma tissue 9


title: Pt11

description:
FFPE melanoma sample
SAMPLE 6

source_name: melanoma tissue 6


title: MG27, Estradiol, Era, Chipseq


title: 29_blood_control_mother

source_name: blood, control mother

value: M

value: low


title: 23_blood_control_mother

value: high


title: Mm_thymus_B6_P28_AF4_rep3


title: whole uterus, ac4C immunoprecipitation

description: Library name: mouse-uterus-ac4c


title: Pt10

description:
FFPE melanoma sample
SAMPLE 5

source_name: melanoma tissue 5

value: Responder


title: MG25, Estradiol, Era, Chipseq


title: 26_blood_maltreated_mother

source_name: blood, maltreated mother


title: MG28, Vehicle, Era, Chipseq


title: Il7rKO

first: James

last: Gardner

address: 513 Parnassus Ave

institute: University of California, San Francisco

description: Library name: Sample 2

data_processing:
Demultiplexing, barcode processing, gene aggregation were performed using the Cell Ranger Software (v8.0.1) Downsteam analysis was performed in Python (v3.10.12) using scanpy(v1.10.2) and scVI-tools (v1.1.5).
Assembly: mm10
Supplementary files format and content: h5 file containing raw feature matrix output from Cell Ranger
Supplementary files format and content: h5ad file containing an AnnData object with processed count data. Raw and scVI normalized counts are stored as layers. Cell and gene metadata are stored in the '.obs' and '.var' attribute.

source_name: pooled lymph nodes

extract_protocol:
Mouse lymph nodes (mesenteric, cervical, brachial, axillary, inguinal, and para-aortic) were procured and pooled in digestion medium consisting of RPMI 1640 with 2% foetal bovine serum (FBS) (Sigma-Aldrich), with deoxyribonuclease (DNase) (100 µg/mL; Roche) and LiberaseTM (96 µg/mL; Roche), minced and agitated at 37°C with gentle agitation for 30 min, and passed through a 70-micron filter. Cells were then sorted for live, tdTmt+ MHCII+ cells and processed for single-cell analysis.
10x Chromium V3 3' Protocol

value: pooled lymph nodes

value: lymphocytes


title: 22_blood_control_mother


title: Mm_thymus_B6_P28_AF4_rep1


title: 25_blood_maltreated_mother


title: 21_blood_maltreated_mother


title: WT

description: Library name: Sample 1


title: MG23, Estradiol, Era, Chipseq


title: Mm_thymus_B6_P28_cmF4_rep4


title: Pt2

description:
FFPE melanoma sample
SAMPLE 2

source_name: melanoma tissue 2


title: DTR_Positive

description: Library name: Sample 2


title: MG21, Vehicle, FOXM1, Chipseq


title: Mm_thymus_B6_P28_cmF1_rep2


title: MG22, Vehicle, FOXM1, Chipseq


title: MG24, Estradiol, Era, Chipseq


title: MG20, Vehicle, FOXM1, Chipseq


title: 20_blood_control_mother


title: Mm_thymus_B6_P28_cmF1_rep3


title: 15_blood_control_mother


title: Mm_thymus_B6_P28_cmF1_rep1


title: Mm_thymus_Foxn1KO_2

description:
Library name: Nu_2
10x Genomics snRNAseq

data_processing:
Raw data were processed with CellRanger (v8.0.1)
Reduction of background signal was performed on unfiltered CellRanger output with Cellbender (v0.3.0)
Assembly: mm10
Supplementary files format and content: H5 files contain barcode and gene information as well as counts. The contents of the cellbender H5 files are documented at https://cellbender.readthedocs.io/en/latest/reference/index.html#output-h5-file-format

molecule: nuclear RNA

extract_protocol:
Dissected tissues were transferred into a 1.5 ml Eppendorf tube containing 150 µl of freshly prepared ice-cold lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630, 0.1% Tween-20, 1% BSA), supplemented with 1 U/µl of Protector RNase inhibitors (Roche, 3335402001). The tissues were homogenized by pressing down with a circular motion using an RNAse-free disposable pestle for 1.5 ml tubes (Fisher Scientific, 12141364) until the majority of clumps were homogenized. Nuclei quality was assessed under a phase-contrast microscope. Subsequently, 500 µl of ice-cold wash buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA) with 0.2 U/µl of Protector RNase inhibitors was added, mixed by inversion, and spun quicky to collect liquid from the cap of the tube. The nuclei suspension was then filtered through a 70 µm Flowmi Cell Strainer (H13680-0070, Bel-Art) and centrifuged at 300g for 5 minutes at 4°C. The supernatant was removed, and nuclei pellet was resuspended in 200 µl of resuspension buffer (0.5% BSA in PBS, supplemented with 0.2 U/µl of Protector RNase inhibitors) and filtered again through a 40 µm Flowmi Cell Strainer (H13680-0040, Bel-Art). Nuclei were quantified by Trypan blue staining using the Countess 3 automated cell counter (Thermo Fisher Scientific). To exclude fat droplets form the count, only the Trypan blue-positive nuclei were counted. Each nuclei suspension was normalized to a concentration of 800 nuclei/µl using resuspension buffer.
The Chromium GEM-X Single Cell 3’ v4 protocol (CG000731, Rev B) was followed starting from step 1.1 according to the manufacturer’s guidelines. The Chromium GEM-X Single Cell 3’ Kit v4 (PN-1000686) and the Chromium GEM-X Single Cell 3’ Chip Kit v4 (PN-1000690) were used to process each sample. A total of 36.6 µl of normalized nuclei suspension was added to the master mix to target a recovery of 20,000 nuclei. The ready GEM-X chip was loaded onto a 10x Genomics Chromium Xo instrument, and final libraries were completed as per 10x Genomics guidelines.

value: Thymus Cells, isolated nuclei

value: BALB/cByJ

tag: jax id

value: 5 wk


title: DTR_Negative

description: Library name: Sample 1


title: MG19, Vehicle, FOXM1, Chipseq


title: Mm_thymus_B6_P28_cmF4_rep3

value: thymus


title: MG18, Vehicle, FOXM1, Chipseq


title: Mm_thymus_Foxn1KO_1

description:
Library name: Nu_1
10x Genomics snRNAseq


title: 17_blood_maltreated_mother


title: Mm_thymus_B6_P28_cmF4_rep2

value: Epcam+CD45- TECs


title: Mm_thymus_Foxn1KO_3

description:
Library name: Nu_3
10x Genomics snRNAseq


title: Mm_thymus_Foxn1het_3

description:
Library name: Ht_3
10x Genomics snRNAseq


title: MG17, Estradiol, FOXM1, Chipseq


title: 16_blood_control_mother


title: Mm_thymus_B6_P28_cmF4_rep1


title: Mm_thymus_Foxn1het_2

description:
Library name: Ht_2
10x Genomics snRNAseq


title: MG16, Estradiol, FOXM1, Chipseq


title: Pt7

description:
FFPE melanoma sample
SAMPLE 4

source_name: melanoma tissue 4


title: MG29, Vehicle, Era, Chipseq


title: Mm_thymus_Foxn1het_1

description:
Library name: Ht_1
10x Genomics snRNAseq


title: 14_blood_maltreated_mother


title: MG15, Estradiol, FOXM1, Chipseq


title: Mm_thymus_B6_P28_cmdtgF1F4_rep5


title: Mm_thymus_B6_P28_cmdtgF1F4_rep4


title: MG14, Estradiol, FOXM1, Chipseq


title: 18_blood_control_mother

description: MethylationEPIC BeadChip DNA methylation data obtained from genomic DNA extracted from whole blood of a rhesus macaque infant with a control mother.


title: CX3_Ctrl_Cort

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Library name: CX3_Ctrl_Cort_HTO

data_processing:
Seurat v4.0.3 with default parameters was used to perform sctransform (SCT) normalization, integration and Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction. The FindClusters function was used for cell clustering. To improve clustering, all samples were analyzed in an integrated analysis, based on canonical correlation analysis (CCA).
Assembly: mm10
Supplementary files format and content: Seurat output files: adata_CX3_Microglia_clusters.h5ad, adata_CX3_Neurons_clusters.h5ad, adata_CX3_astro_clusters.h5ad, adata_CX3_cell_types.h5ad, adata_CX3_oligo_clusters.h5ad
Supplementary files format and content: feature_README.txt

source_name: Brain

extract_protocol:
All samples were handled and processed under Air Clean PCR Workstation. Frozen brain tissue was dissociated using a Dounce homogenizer with 1X lysis buffer (Nuclei PURE Lysis Buffer, Sigma L9286). Nuclei suspension is filtered using a 35 um Cell Strainer and centrifuged at 600g for 5 min at 4 ºC. Pellet was resuspended in wash buffer [1X SCC (Invitrogen, cat no AM9770)  20 mM DTT, 1% BSA and RNAse inhibitor (Ambion, cat no AM2682)] and centrifuged at 600g for 5 min at 4 ºC. Nuclei were stained with DAPI at 1 mg/1 mL (Invitrogen, cat no D1306 and DAPI+ nuclei were FACS-sorted with a BD FACS Aria with a 100-μm nozzle and a sheath pressure 20 psi. Sorted nuclei were centrifuged in 5mL tubes in a swinging bucket centrifuge at 600g for 5min. RIN was determined using BioAnalyzer.
The single-nuclei RNA-Seq of FACS-sorted nuclei suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Samples were multiplexed together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO) following previously published protocol 67. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package 68. Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis.

value: Brain

tag: cell compartment

value: nuclei

value: Cortex

value: Wild Type

tag: library type

value: HTO


title: Mm_thymus_B6_P28_cmdtgF1F4_rep3

tag: cell type

tag: strain


title: CX3_Ctrl_BS

description: Library name: CX3_Ctrl_BS_HTO

value: Brainstem


title: Mm_thymus_B6_P28_cmdtgF1F4_rep2

tag: treatment


title: 13_blood_control_mother

value: F


title: MG13, Estradiol, FOXM1, Chipseq

tag: cell line


title: 11_blood_maltreated_mother


title: MG11, Vehicle, FOXA2, Chipseq


title: 12_blood_maltreated_mother

value: M

value: middle


title: Mm_thymus_B6_E15_5_WT_rep4

tag: tissue

value: WT


title: 10_blood_maltreated_mother

value: high


title: CX3_VE_BS

description: Library name: CX3_VE_BS_HTO


title: Mm_thymus_B6_E15_5_WT_rep3


title: MG12, Vehicle, FOXA2, Chipseq


title: Normal mammary gland from wild type B6 mice

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

description:
Library name: B6-Normal_mammary_gland
10x Genomics

data_processing:
Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only the Pass-Filter (PF) reads were used for further analysis. After sample demultiplexing, raw PF reads were processed through the CellRanger software (10X Genomics Inc., CA) to obtain the gene expression levels in single cells and quality control matrices for each sample.
Downstream analysis was performed using Seurat packages.
Assembly: mm10
Supplementary files format and content: tab-seperarated values/barcode files and matrix files

source_name: Mammary gland

extract_protocol:
Single cell suspension samples were examined on Attune flow cytometer for cell density and viability. For each sample, 15,000 sorted cells were resuspended in 15 ul of PBS containing 0.5% BSA for library preparation.
Around 15,000 cells from each sample were loaded into each channel of the 10X Genomics Chromium X system using the Chromium Single Cell 3’ v3.1 Reagent Kits (10X Genomics Inc., CA) to generate and amplify cDNA from individual cells. The amplified cDNA samples were purified with Ampure XP magnetic beads (Beckman Coulter, CA), quantified by Qubit fluorometer (Invitrogen, CA), and examined on Bioanalyzer with High Sensitivity DNA chips (Agilent, CA) for size distribution. Illumina sequencing libraries were generated from the amplified cDNA samples using the Illumina Tagment DNA Enzyme and Buffer kit (Illumina, CA). These libraries were examined by Qubit and Bioanalyzer, then pooled at equal molar amount and sequenced on Illumina NovaSeq 6000 S Prime flowcells as 28+94 nt pair-end reads following the standard Illumina protocol.

treatment_protocol:
Transgenic mice and tumor sampling: Mouse mammary tumors developed from B6:MMTV-PyMT mice carrying myeloid specific Cxcr4 KO conditioned by Lysm-Cre and control tumor from Littermate without Lysm-Cre were harvested at 15 weeks of age. The pair of tumors are selected with matched sizes.
Normal mouse mammary gland sampling: Normal mammary gland from wild type C57BL/6 mice were harvested at 8 weeks of age.
Cell preparation protocol: Single cell suspensions were prepared using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035

value: Mammary gland

value: All viable cells

value: Wild type C57BL/6


title: 7_blood_control_mother


title: Mm_thymus_B6_P28_cmdtgF1F4_rep1

source_name: thymus


title: 9_blood_control_mother

value: low


title: MG10, Vehicle, FOXA2, Chipseq


title: 5_blood_control_mother


title: cortical brain tissue, B6_7_28, snRNA-seq

city: New Haven

first: Sreeganga

middle: S.

last: Chandra

address: 295 Congress Avenue

department: Departments of Neurology and Neuroscience

institute: Yale School of Medicine

description: Library name: Sample 14

data_processing:
Single-cell quality control, clustering, and cell type annotation: After quality control filtering by eliminating nuclei with less than 200 genes or more than 5 percent mitochondrial gene expression (poor quality nuclei) or more than 6,000 genes (potential doublets) per nucleus, we profiled 104,750 brain nuclei. Seurat (version 4.2.0) single cell analysis R package was used for processing the snRNA-seq data. The top 2000 most variable genes across all nuclei in each sample were identified, followed by the integration and expression scaling of all samples and dimensionality reduction using principal components analysis (PCA). Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) was then applied to visualize all cell clusters, and the classification and annotation of distinct cell types were based on known marker genes of each major brain cell type and the entire single nucleus gene expression matrix  were investigated.
Differential expression (DE) analysis: Differential expression analysis for snRNA-seq data was performed using the Wilcoxon Rank Sum test using the function FindMarkers of the Seurat package (4.1.0) in R. For all cells, the threshold for differentially expressed genes (DEGs) was set as the expression log2 fold change of Mutant/WT mice being greater than 0.2 and significantly changed (p <0.05) after Bonferroni (BF)-correction for multiple comparisons and adjustment for possible confounders, using default parameters. Adjustment was made for differences in sex, batch and read depth with MAST
For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0. The processed output files for all samples were: barcodes.tsv, features.tsv, matrix.mtx, which are attached to folders named correspondingly to the samples. After quality control filtering by eliminating nuclei with less than 200 genes or more than 5 percent mitochondrial gene expression (poor quality nuclei) or more than 6,000 genes (potential doublets) per nucleus, we profiled 104,750 brain nuclei. Seurat (version 4.2.0) single cell analysis R package was used for processing the snRNA-seq data.
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx, which are attached to folders named correspondingly to the samples. After quality control filtering by eliminating nuclei with less than 200 genes or more than 5 percent mitochondrial gene expression (poor quality nuclei) or more than 6,000 genes (potential doublets) per nucleus, we profiled 104,750 brain nuclei. Seurat (version 4.2.0) single cell analysis R package was used for processing the snRNA-seq data.

source_name: cerebral cortex

extract_protocol:
Fresh cortical tissue were dissected from left hemisphere of 12 month old WT, Gba, SNCA tg and Gba-SNCA mice after euthanasia. Single nuclei were isolated as previously described with modifications5. All procedures were carried out on ice or at 4oC. Briefly, fresh cortical tissue was homogenized in 8.4 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.5), 25 mM KCl, 10% glycerol, 1 mM EDTA (pH 8.0), and ribonuclease (RNase) inhibitors freshly added (40U/ml)] using a Wheaton Dounce tissue grinder (10 strokes with the loose pestle and 10 strokes with the tight pestle). The homogenate was carefully transferred into a 15 ml ultracentrifuge tube on top of 5.6 ml of fresh nuclei homogenization buffer cushion and centrifuged at 25,000 rpm for 60 min at 4°C in an ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.5), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (40U/ml)] and counted on a hemocytometer with Trypan Blue staining. The nuclei were centrifuged at 500g for 10 min at 4°C with a swing bucket adaptor. They were subsequently resuspended at a concentration of 700 to 1200 nuclei/μl in the nuclei resuspension buffer for the next step of 10x Genomics Chromium loading and sequencing
Droplet-based single nucleus RNA sequencing and data alignment: The snRNA-seq libraries were prepared by the Chromium Single Cell 3′ Reagent Kit v3.1 chemistry according to the manufacturer’s instructions (10x Genomics). The generated snRNA-seq libraries were sequenced using Illumina NovaSeq6000 S4 at a sequencing depth of 300 million reads per sample. For snRNA-seq of brain tissues, a custom pre-mRNA genome reference was generated with mouse genome reference (available from 10x Genomics) that included pre-mRNA sequences, and snRNA-seq data were aligned to this pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using CellRanger version 3.1.0.

value: cerebral cortex

value: WT cortical cells

value: all cerebral cortex cells


title: MG26, Estradiol, Era, Chipseq


title: Mm_thymus_B6_E15_5_WT_rep2

value: thymus

value: Epcam+CD45- TECs


title: MG8, Vehicle, FOXA2, Chipseq


title: STA_TCR, CCM, #1

city: Beijing

first: Yutong

address: Dongdan

institute: Peking Union Medical College

description:
Library name: Sample12
10x Genomics

data_processing:
The raw fastq files of the 5’ end sequencing of samples STA1, STA2, STA4, and CCM were aligned and filtered with GRCh38 as reference. Barcode counting and unique molecular identifier (UMI) counting were also performed by using counting process in Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebral cavernous malformation

extract_protocol:
The excised vascular tissue was immediately washed three times in Dulbecco’s Phosphate-Buffered Saline (DPBS) to remove blood and debris, and then transported on ice for processing within 2 hours. If immediate processing was not possible, samples were stored in 4°C DPBS (no longer than 6 hours). Under a sterile laminar flow hood, the tissue was cut into approximately 0.5 mm³ pieces and incubated in enzyme digestion solution (collagenase II 1 mg/ml, DNase 50 µg/ml, hyaluronidase 0.1 mg/ml) at 37°C for 30-60 minutes, with gentle pipetting every 10 minutes to promote dissociation. The digested suspension was filtered through a 70 µm mesh filter to remove undigested fragments and collected into 15 ml centrifuge tubes. Red blood cell contamination was removed using red blood cell lysis buffer, and cell viability was assessed using trypan blue staining. Live cells (trypan blue-negative) were sorted using flow cytometry (FACS) to ensure high-quality sequencing. Cell concentration was determined using a hemocytometer to ensure each sample contained 10⁵-10⁶ cells/ml.
Single-cell suspensions were processed using the 10X Genomics Chromium System (10x Genomics, Pleasanton, CA, USA) to create 3’ gene expression libraries with the Chromium Single Cell 3′ Reagent Kit v3. Briefly, single-cell suspensions, reagents, gel beads, and partitioning oil were loaded onto a 10X Chromium Chip B. Within the chip, each cell was encapsulated in an oil droplet containing gel beads and reagents, forming a gel bead in emulsion (GEM). Each GEM serves as an independent reaction chamber where cell lysis and reverse transcription of poly-adenylated mRNA into barcoded full-length cDNA occur, with primers incorporating a sequencing primer, a cell-specific barcode, unique molecular identifiers (UMIs), and a poly(dT) tail. All cDNA molecules were then pooled, and standard library construction steps followed, including amplification, fragmentation, end repair, adapter ligation, and sample index PCR. The libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing (PE150).

value: Cerebral cavernous malformation


title: MG9, Vehicle, FOXA2, Chipseq


title: 6_blood_maltreated_mother


title: cortical brain tissue, Het, snRNA-seq

description: Library name: Sample 15 Gba heterozygot (not used)

value: Gba heterozygot cortical cells

value: Gba heterozygote


title: Mm_thymus_B6_E15_5_WT_rep1


title: STA,_BCR CCM, #1

description:
Library name: Sample11
10x Genomics


title: cortical brain tissue, Ctr, snRNA-seq

description: Library name: Sample 13


title: MG7, Estradiol, FOXA2, Chipseq


title: Mm_thymus_B6_P28_AF4_rep4


title: 4_blood_maltreated_mother


title: cortical brain tissue, B6_control_May27, snRNA-seq

description: Library name: Sample 12


title: STA_TCR, epilepsi, #4

description:
Library name: Sample10
10x Genomics

source_name: Superficial temporal artery

value: Superficial temporal artery


title: Mm_thymus_B6_P28_RosaYFPposmCardneg_rep2

value: Epcam+CD45- YFP+mCard- TECs

value: RosaYFPposmCardneg


title: 1_blood_maltreated_mother

value: F


title: CX3_VE_Cort

description: Library name: CX3_VE_Cort_HTO

value: Brain

value: nuclei

value: Cortex

value: HTO


title: 8_blood_control_mother

value: M

value: low


title: Mm_thymus_B6_P28_Fgf7het_rep3


title: STA_BCR, epilepsi, #4

description:
Library name: Sample9
10x Genomics


title: Mm_thymus_B6_P28_RosaYFPposmCardpos_rep2

value: Epcam+CD45- YFP+mCard+ TECs

value: RosaYFPposmCardpos


title: cortical brain tissue, PD_754 , snRNA-seq

description: Library name: Sample 10

value: cerebral cortex

value: SNCA tg cortical cells

value: all cerebral cortex cells

value: SNCA tg


title: cortical brain tissue, B6_control_May20, snRNA-seq

description: Library name: Sample 11

value: WT cortical cells

value: WT


title: STA_TCR, epilepsi, #2

description:
Library name: Sample8
10x Genomics

value: Superficial temporal artery


title: MG5, Estradiol, FOXA2, Chipseq


title: 3_blood_maltreated_mother

value: middle


title: 2_blood_maltreated_mother

value: high


title: Mm_thymus_B6_P28_RosaYFPposmCardneg_rep1

value: thymus

value: Epcam+CD45- YFP+mCard- TECs

value: RosaYFPposmCardneg


title: MG2, Vehicle, IgG, Chipseq


title: MG6, Estradiol, FOXA2, Chipseq


title: STA_TCR, epilepsi, #1

description:
Library name: Sample6
10x Genomics


title: cortical brain tissue, 729_PD, snRNA-seq

description: Library name: Sample 8


title: cortical brain tissue, PD_740, snRNA-seq

description: Library name: Sample 9


title: Mm_thymus_B6_P28_RosaYFPposmCardpos_rep1


title: STA_BCR, epilepsi, #2

description:
Library name: Sample7
10x Genomics


title: MG4, Estradiol, FOXA2, Chipseq


title: cortical brain tissue, 201, snRNA-seq

description: Library name: Sample 7

value: Gba mutant cortical cells

value: Gba mutant


title: MG1, Estradiol, IgG, Chipseq


title: STA_BCR, epilepsi, #1

description:
Library name: Sample5
10x Genomics


title: MG3, Estradiol, FOXA2, Chipseq


title: STA, CCM, #1

description:
Library name: Sample4
10x Genomics

value: Cerebral cavernous malformation


title: Mm_thymus_B6_P28_Fgf7wt_rep3

value: Epcam+CD45- TECs


title: cortical brain tissue, 193_GD, snRNA-seq

description: Library name: Sample 5


title: STA, epilepsi, #4

description:
Library name: Sample3
10x Genomics


title: Mm_thymus_B6_P28_Fgf7het_rep2


title: Crnkl1 WT biol rep 2

first: Louise

last: Bicknell

address: 710 Cumberland St

description: Library name: Crnkl1WT1_2

data_processing:
Pre-processing involved adaptor and low-quality trimming (Phred score < Q20) using FASTQ-MCF
The trimmed reads were then mapped against  Zebrafish genome version GRCz11 using HISAT2 (Ver. 2.0.5)
Read counts were then retrieved first by exons and summarised per gene using FeatureCount on ENSEMBL gene annotation.
Assembly: Zebrafish genome version GRCz11
Supplementary files format and content: The differential gene expression analysis was performed using DESeq2 package, values listed in a tab-delimited txt file

organism: Danio rerio

source_name: whole embryos

growth_protocol: standard conditions for zebrafish embryos

extract_protocol:
RNA extracted using Rneasy kit (Qiagen)
Zebrafish: Truseq stranded Total RNA with Ribo Zero H/M/R Gold as per manufacturers instructions.

value: whole embryos

value: Crnkl1 WT injected


title: Zebrafish Adult Leptomeninges scRNA-seq

city: Bethesda

first: Madeleine

last: Kenton

address: 10 CENTER DR

department: NICHD

institute: NIH

description:
Library name: LP_counts
Leptomeningeal cells from 10 females, 10 males; 10X genomics

data_processing:
cellranger count v7.0.0
Assembly: Assembly: zv11
Supplementary files format and content: Supplementary files format and content: TSV value and matrix files

source_name: Leptomeninges

extract_protocol:
Cell suspension prepared from 20 leptomeningeal linings (10 from females, 10 from males) removed from zebrafish comprising ~10,000 cells. Cell suspension prepared from 25 pachymeningeal linings (12 from females, 13 from males) removed from zebrafish comprising ~10,000 cells.
10X 3.1 GEM kits following manufacturer recommendations

value: Leptomeninges


title: Mm_thymus_B6_P28_Fgf7het_rep1


title: Mm_thymus_FVB_P21_chi6.up_rep15

description:
recovery phase
AN128

value: FVB

value: ca. P21


title: Zebrafish Adult Pachymeninges scRNA-seq

description:
Library name: DM_counts
Pachymeningeal cells from 12 females, 13 males; 10X genomics

source_name: Pachymeninges

value: Pachymeninges


title: Crnkl1 WT biol rep 3

description: Library name: Crnkl1WT1_3


title: STA, epilepsi, #1

description:
Library name: Sample1
10x Genomics


title: cortical brain tissue, 192_GD, snRNA-seq

description: Library name: Sample 4

value: cerebral cortex

value: all cerebral cortex cells


title: cortical brain tissue, 184_GP, snRNA-seq

description: Library name: Sample 3

value: Gba-SNCA double mutant cortical cells

value: Gba-SNCA double mutant


title: endometrial biopsy, input control

description: Library name: human-uterus-input

data_processing:
After quality control, clean RNA-seq data were aligned to the reference genome (UCSC mm10) with Hisat2 software v2.2.1
Peaks were called uing MACS v3.0.0a7 with the significance cut-off q-value <=0.05
Assembly: hg19
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: endometrial biopsy

value: endometrial biopsy


title: STA, epilepsi, #2

description:
Library name: Sample2
10x Genomics

value: Superficial temporal artery


title: Mm_thymus_FVB_P21_chi6.up_rep14

description:
recovery phase
AN228

value: thymus


title: cortical brain tissue, 187_Mneo-L444P_A30P_May20, snRNA-seq

description: Library name: Sample 1


title: Mm_thymus_B6_P28_Fgf7wt_rep2


title: Mm_thymus_FVB_P21_chi6.up_rep13

description:
recovery phase
AN227


title: endometrial biopsy, ac4C immunoprecipitation

description: Library name: human-uterus-ac4c


title: Crnkl1 WT biol rep 1

description: Library name: Crnkl1WT1_1


title: cortical brain tissue, 191_L444P_A30P, snRNA-seq

description: Library name: Sample 2


title: Crnkl1Arg105His biol rep 3

description: Library name: Crnkl1Arg105_3

value: Crnkl1 Arg105His injected


title: PyMT tumor from littermate mouse with wildtype Cxcr4 in macrophage

description: 10x Genomics

source_name: Mammary tumor

treatment_protocol:
Transgenic mice and tumor sampling: Mouse mammary tumors developed from B6:MMTV-PyMT mice carrying myeloid specific Cxcr4 KO conditioned by Lysm-Cre and control tumor from Littermate without Lysm-Cre were harvested at 15 weeks of age. The pair of tumors are selected with matched sizes.
Cell preparation protocol: Single cell suspensions were prepared using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035

value: Mammary tumor

value: All viable intratumor single cells

value: B6:MMTV-PyMT;Cxcr4fl/fl; (no Cre)


title: cortical brain tissue, 185_GD  , snRNA-seq

description: Library name: Sample 6

value: Gba mutant cortical cells

value: Gba mutant


title: Crnkl1Arg105His biol rep 2

description: Library name: Crnkl1Arg105_2

value: whole embryos


title: Mm_thymus_B6_P28_Fgf7wt_rep1

value: Epcam+CD45- TECs


title: TPC1_siXPR1

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description: Library name: Sample 2

data_processing:
FastQC/MultiQC, Trimmomatic v0.38, mapping with HISHAT2 v2.1.0, quantification using featureCounts v2.0.0
Assembly: GRCh38
Supplementary files format and content: a csv file includes TPM values for each Sample

extract_protocol:
RNA from cell lysates was extracted using RNeasy Plus Kits (QIAGEN)
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2

treatment_protocol: Thyroid cancer cell line TPC-1 transfected with either a control siRNA or an siRNA targeting XPR1

value: siRNA targeting XPR1


title: Mm_thymus_FVB_P21_chi6.up_rep12

description:
recovery phase
AN153

value: FVB

value: ca. P21


title: TPC1_siControl

description: Library name: Sample 1

value: control siRNA


title: Crnkl1Arg105His biol rep 1

description: Library name: Crnkl1Arg105_1


title: A549 shMUC5AC 3

description: Library name: A549SAC_sh3

data_processing:
Raw sequences were processed for quality control using both FastQC and MultiQC
Alignment was done usingHISAT2
Expression quantification was done in R using "featureCounts"
Differential expression analysis was run in R using the DESeq2
Assembly: GRCh38 release 84 version of H. sapiens (human) from Ensembl
Supplementary files format and content: Supplementary files format and content: raw counts (counts_A549_samples_raw.csv)

source_name: Cell line

growth_protocol: A549-shRNA control and A549-shMUC5AC cells were cultured in RPMI medium supplimented with 10% FBS and 1X Penicillin-Streptomycin antibiotics.

extract_protocol:
RNA isolation was carried out using mirVana miRNA isolation kit and used for the RNAseq experiment.
TrueSeq RNA library prep from Illumina

value: Cell line

value: A549 lung cancer cells

value: Cancer


title: Dr_thymus_foxn1-/-_rep3

data_processing:
Transcriptomes were analyzed on the Galaxy platform.
Adapters were trimmed with TrimGalore! (version 0.4.3.1).
Reads were aligned to the reference genome with Hisat2  (version 2.1.0).
Counts were generated with featureCounts (version 1.6.1.0).
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

extract_protocol:
Thymus tissue was explanted and placed into TRI reagent (Sigma-Aldrich). RNA was extracted following standard protocols.
Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.

value: thymus cells


title: Intratumoral macrophage from mouse #775 with wild type Cxcr4 macrophage

description:
Partek_EL-CXCR4cKO_TAM_Bulk_RNA_Normalization_Normalized_counts.txt
3000__MP_Ctrl_tumor_775

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence file (FASTQ) were analyzed using Partek® Flow® software package. Raw reads were aligned using STAR 2.7.8a, followed by quantification to annotation model GRCm38 – Ensembl Transcripts release 110. After noise filtering, counts were normalized as CPM+1e-4
Assembly: mm10
Supplementary files format and content: Processed macrophage and bulk tumor data files are tab delimited text files with value of Log2(CPM+1e-4)

extract_protocol:
Primary tumor samples were snap frozen and homogenized. Total RNA were extracted using RNAeasy mini-prep kit from Qiagen
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

treatment_protocol:
Transgenic mice and tumor sampling: Mouse mammary tumors developed from B6:MMTV-PyMT mice carrying myeloid specific Cxcr4 KO conditioned by Lysm-Cre and control tumor from Littermate without Lysm-Cre were harvested at 15 weeks of age. The pairs of tumors are selected with matched sizes.
Tumor associated macrophage FACS protocol: Single cell suspensions were prepared from mammary tumors using mechanical dissociation followed by enzymatic digestion with Collagenase D and Dnase I solution as details described in Jappinen et al., 2019, Nature communications Single cell suspension were stained with F4/80 and CD11b for FACS.

value: Macrophage

tag: sorting markers


title: Mm_thymus_FVB_P21_chi6.up_rep10

description:
recovery phase
AN233

value: thymus

tag: genotype


title: Mm_thymus_FVB_P21_chi6.up_rep11

description:
recovery phase
AN152


title: Mm_thymus_FVB_P21_chi6.up_rep9

description:
recovery phase
AN232


title: Intratumoral macrophage from mouse #720 with wild type Cxcr4 macrophage

description:
Partek_EL-CXCR4cKO_TAM_Bulk_RNA_Normalization_Normalized_counts.txt
3000__MP_Ctrl_tumor_720

value: Mammary tumor


title: A549 shMUC5AC 1

description: Library name: A549SAC_sh1


title: Dr_thymus_foxn1-/-_rep2


title: Dr_thymus_foxn1-/-_rep1


title: Intratumoral macrophage from mouse #867 with Cxcr4 KO in macrophage

description:
Partek_EL-CXCR4cKO_TAM_Bulk_RNA_Normalization_Normalized_counts.txt
3000__MP_cKO_tumor_867


title: Intratumoral macrophage from mouse #706 with wild type Cxcr4 macrophage

description:
Partek_EL-CXCR4cKO_TAM_Bulk_RNA_Normalization_Normalized_counts.txt
3000__MP_Ctrl_tumor_706


title: Mm_thymus_B6_P28_AF4_rep2


title: Dr_thymus_foxn1+/+_rep3


title: Mm_thymus_FVB_P21_chi6.up_rep8

description:
recovery phase
AN230


title: A549 ctrl shRNA 3

description: Library name: A549_SCV3

value: Ctrl


title: Intratumoral macrophage from mouse #746 with Cxcr4 KO in macrophage

description:
Partek_EL-CXCR4cKO_TAM_Bulk_RNA_Normalization_Normalized_counts.txt
3000__MP_cKO_tumor_746


title: Mm_thymus_FVB_P21_chi6.up_rep7

description:
recovery phase
AN229


title: Dr_thymus_foxn1+/+_rep2


title: Mm_thymus_FVB_P21_chi6.up_rep6

description:
recovery phase
AN147b


title: Intratumoral macrophage from mouse #725 with Cxcr4 KO in macrophage

description:
Partek_EL-CXCR4cKO_TAM_Bulk_RNA_Normalization_Normalized_counts.txt
3000__MP_cKO_tumor_725


title: A549 ctrl shRNA 1

description: Library name: A549_SCV1


title: Mm_thymus_FVB_P21_chi6.up_rep5

description:
recovery phase
AN150


title: PyMT tumor from mouse #720 with wild type Cxcr4 macrophage

description:
Partek_EL-CXCR4cKO_Whole_Tumor_bulk_RNA_Normalization_Normalized_counts.txt
3000__Ctrl_tumor_720

value: whole tumor

value: B6:MMTV-PyMT;Cxcr4fl/fl; (no Cre)


title: 5_control_CEREBELLUM

data_processing:
FastQ files of 2x100bp paired-end reads were quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 2012).
Samples were with high quality reads (Phred score >= 30) were aligned tothe Human reference genome (GRCh38/hg38) using STARaligner(version 2.7)55
Gene quantification was performed using feature counts from the Subread package in R56
Aligned reads were visualized using IGV (version 2.8.9).
Gene expression levels were normalized and log2 transformed using the Trimmed Mean of M-values (TMM) method
Differential expression analysis was performed using the edgeR package in R57. Significantly differentially expressed genes were selected with controlled False Positive Rate (B&H method) at 5% (FDR <= 0.05). Upregulated genes were selected at a minimum log2fold change of 2 and downregulated genes at a minimum log2fold change of -2
Heatmaps were drawn on the normalized expression matrix using the pheatmap package in R. Euclidean distance similarity metric and complete linkage algorithm were used for hierarchical clustering
Gene ontology (GO) and pathway (WikiPathways, KEGG, Reactome) analysis using g:profiler webtool was performed on the list of upregulated genes (log2>= 2 and FDR <=0.05) ordered by importance58. GO terms and pathways were selected based on an FDR <= 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts

source_name: brain

extract_protocol:
RNA was extracted from frozen tissue using the Qiagen all-prep DNA/RNA mini kit (80204) according to the manufacturer’s instructions
500 ng of total RNA was used for polyA selection and Truseq library preparation according to the instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2), with 8 cycles of PCR
TruSeq RNA Sample Prep Kit v.2

value: brain

value: Cerebellum

value: Control


title: A549 shMUC5AC 2

description: Library name: A549SAC_sh2


title: A375 CTL-tolerant persister cells

city: La Jolla

first: Matthew

last: Hangauer

address: 9500 Gilman Drive #0869

department: Dermatology

institute: University of California, San Diego

description:
Library name: Sample 2
10x genomics

data_processing:
Reads were aligned, samples aggregated, and expression quantified using 10x pipeline cellranger-3.1.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: A375 melanoma

growth_protocol: A375 cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% antibiotic-antimycotic in a 5% CO2 atmosphere at 37 degrees Celsius.

extract_protocol:
A375 cells were washed with PBS, trypsinized with 0.25% trypsin, pelleted at 300xg for 4 minutes, and resuspended in PBS.
Libraries were constructed using the 10x Chromium Single Cell 3' v3 kit per manufacturer protocol.

treatment_protocol: A375 cells were cocultured with NY-ESO-1 CTLs for 15 days in RPMI 1640 medium supplemented with 10% FBS, 1% antibiotic-antimycotic, and 7.5 ng/mL recombinant IL-2. NY-ESO-1 CTLs were replenished in fresh media every 3 days.

value: A375 melanoma

value: Melanoma cells

value: 15 days of NY-ESO-1 CTL coculture


title: Mm_thymus_FVB_P21_chi6.up_rep4

description:
recovery phase
AN149

data_processing:
Transcriptomes were analyzed on the Galaxy platform.
Adapters were trimmed with TrimGalore! (version 0.4.3.1).
Reads were aligned to the reference genome with Hisat2  (version 2.1.0).
Counts were generated with featureCounts (version 1.6.1.0).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

value: Epcam+CD45- TECs

value: FVB

value: ca. P21


title: 5_histio_BRAINSTEM

value: Brainstem

value: Histiocytosis


title: PyMT tumor from mouse #706 with wild type Cxcr4 macrophage

description:
Partek_EL-CXCR4cKO_Whole_Tumor_bulk_RNA_Normalization_Normalized_counts.txt
3000__Ctrl_tumor_706


title: Mm_thymus_FVB_P21_chi6.up_rep3

description:
recovery phase
AN241


title: PyMT tumor from mouse #746 with Cxcr4 KO in macrophage

description:
Partek_EL-CXCR4cKO_Whole_Tumor_bulk_RNA_Normalization_Normalized_counts.txt
3000__cKO_tumor_746


title: A375 parental cells

description:
Library name: Sample 1
10x genomics

value: Untreated


title: Mm_thymus_FVB_P21_chi6.up_rep2

description:
recovery phase
AN243

value: thymus


title: NIH3T3_chrRNA-seq_FCS_15min_rep3

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

institute: IGMM

description:
Serum (FCS 15%) stimulated for 15 minutes
NIH3T3_chrRNA_FCS_stimulated_merge_scaled_pos_bin50.wig
NIH3T3_chrRNA_FCS_stimulated_merge_scaled_neg_bin50.wig

data_processing:
Mnase-seq , DNAse-seq and ChIP-seq samples were aligned to human genome (hg19, GRCh37) using Bowtie 2 aligner. Samples were then treated using PASHA pipeline to produce wig files (Fenouil et al. 2016). Uniquely aligned tags were elongated after estimating optimal elongation size in silico for single ended sequencing or between the pairs for paired end sequencing, enabling to use the original fragment length for further processing. Signals were scaled according to the mean signal. The number of tags covering each nucleotide of the genome was computed and averaged in bins of 10 or 50 nucleotides. For MNase-seq datasets, signals were smoothed on 5 bins.
RNA-seq samples were aligned to human genome (hg19, GRCh37)  and ERCC  reference using tophat2 aligner.
TT-seq samples were aligned to human genome (hg19, GRCh37)  and Drosophila melanogaster (DM6)  reference using tophat2 aligner.
Assembly: hg19
Supplementary files format and content: wig

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamin (2 mg/ml) at 37°C and 5% CO2.  NIH-3T3 cells were grown in DMEM supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/L) and glutamin (2.9 mg/L) at 37°C and 5% CO2.

extract_protocol:
Fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter. For sequencing of nucleosomal DNA in Raji cells, 35 million cells were resuspended in 350μl Solution I (150 mM sucrose, 80 mM KCl, 5 mM K2HPO4, 5 mM MgCl2, 0.5 mM CaCl2, 35 mM HEPES pH 7.4) and NP40 was added to a final concentration of 0.2%. Cell membranes were permeabilized for five min at 37°C. MNase was prepared at 50, 25, 12, 6 or 3 units in 0.5L of Solution II (150 mM sucrose, 50 mM Tris pH 8, 50 mM NaCl, 2 mM CaCl2) and incubated with 50 µL of cellular preparation, corresponding to 5. million cells, for exactly 10 min at 37°C. The reactions were stopped by adding of EDTA to a final concentration of 10 mM. The cells were lysed using 1.45L of SDS Lysis Buffer (1% SDS, 10 mM EDTA pH 8, 50 mM Tris pH 8), with 10 min incubation at 4°C. 200μl aliquots were taken for purification and the remaining extracts were stored at -80°C. An equal volume of TE (200ul) was added to the aliquots, followed by subsequent 2 hour treatments with each 0.2µg/L final concentrations of RNase A and Proteinase K at 37°C and 55°C, respectively. DNA was extracted by two subsequent phenol:chloroform:isoamylalcohol (25:24:1) extractions, further purified using QIAquick PCR purifications colums (Qiagen, Germany). Nucleosomal digestion was verified by running 500ng of DNA on a 1.5% agarose gel as well as on DNA high-sensitivity 2100 Bioanalyzer chips (Agilent, USA). Digestions showing 75% of mononucleomes (running at 150bp) were selected for library preparations. Chromatin RNA fraction was prepared from ∼20 million Raji cells. Cells were washed with ice-cold PBS twice. The cells were lysed with ice-cold 4 ml of HLB/NP40 buffer (10 mM Tris-Hcl, pH 7.5, 10 mM NaCl, 0.5% NP40, and 2.5 mM MgCl2) and incubated on ice for 5 min. After the incubation, 1 ml of ice-cold HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2, and 10% Sucrose) was under-laid and then the nuclei were collected under 1,400 rcf centrifuge at 4°C for 5 min. Isolated nuclei were resuspended in 125 μl of NUN1 solution (20 mM Tri-HCl, pH 8.0, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol) followed by 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40). Fifteen minutes incubation was carried out on ice with mixing by max speed vortex for 5 s every ∼4 min and then chromatin pellets were precipitatd under 15,000 rcf centrifuge at 4°C for 10 min. Chromatin pellet was resuspended in 500 μl NUN2 buffer. Chromatin were precipitated under 15,000 rcf centrifuge at 4°C for 10 min, then Chromatin RNAs were extracted by 500 μl of Trizol reagent (Life technologies). The RNA extraction steps were repeated three times with rigorous treatment with TurboDNase in beetween. For DNase I sensitivity mapping, nuclei were prepared from 5 millions Raji cells per sample and incubated for 10 min at 37 °C with limiting concentrations of the DNA endonuclease DNase I (Sigma) supplemented with Ca2+ and Mg2+. A dose response experiment of 16 samples was performed with 2X dilution of the DNaseI between samples in cascade. Digestion was stopped by the addition of EDTA, and the samples were treated with proteinase K. The small fragments (<500 bp in length) were recovered on agrose gel from the sample in which a smear just started to appear using Quiagen gel purification kit and librairies were prepared using illumina Truseq kit. G4access was performed in K562 and NIH3T3 cells. Cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). For each experiment, 5 millions cells per titration point were re-suspended in 50 μL of prewarmed permeabilization buffer (150 mM of sucrose, 80 mM KCl, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) supplemented with 0.2% (v/v) NP40 and incubated for 5 minutes at 37ºC prior digestion. MNase digestions, were then performed by adding a volume of 500 μL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) supplemented with either 3, 6, 12, 25 or 50U of MNase (Merck, 10107921001). Digestions were incubated at 37ºC for 10 min and stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. Samples were then incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Tris.HCl pH 8). Before DNA purification, 1 mL of water was added to dilute the SDS and the samples were incubated with 5 µL of RNAse A (ThermoFisher, EN0531) at 37 ºC for 2 hours and with 8 µL of proteinase K (Euromedex, 09-0911) at 56 ºC for 2 hours to complete the lysis. To then quality control the MNase digestions: 125 μL of each sample were cleaned-up using QIAquick PCR Purification Kit (QIAGEN, 28106) and assessed by agarose gel and Bioanalyzer. At this step, for efficient G4access, samples should present ~30% (+/-5%) of mono-nucleosomes. Importantly, this assessment should be performed on purified DNA that does not contain the subnucleosomal fraction, using a bioanalyzer equipment. The remaining of the samples was then purified by phenol-chloroform and ethanol precipitation for subsequent steps. We recommend that, when implementing this method, a wide range of MNase concentrations shall be tested in a first round of preparative experiments to narrow down the condition in which the critical fraction of 30% of mononucleosome shall be obtained. Our experiences showed this fraction is on average optimal for best G4 sequence recovery. The 0-100 bp size-selected fragments from MNase digestions that have ~30% of mono-nucleosomes were subjected to DNA library preparation. In parallel, genomic DNA libraries were sonicated by Bioruptor® Pico sonicator (Diagenode) to obtain DNA fragments of ~150 bp to be used later as reference data sets for bioinformatic analyses. Paired-end libraries were constructed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645S) using a starting material of 50 ng. DNA fragments were treated with end-repair, A-tailing and ligation of Illumina-compatible adapters. Clean-up of adaptor-ligated DNA was performed by using CleanNGS beads (CNGS-0050) with a bead:DNA ratio of 2:1. The purified products were amplified with 8 cycles of PCR. Finally, samples were cleaned up with a bead:DNA ratio of 0.8:1 to remove the free sequencing adapters.  TT-seq experiments were performed in biological duplicates using 47 millions Raji cells treated with 10 μM pyridostatin (PDS; Sigma SML0678) or H2O (Control) for 10 minutes. Newly synthetised RNAs were labelled with 500µM 4-Thiouridine (4SU; Sigma T4509) for 10min at 37°C at the time of the treatment. In parallel, 60 x106 drosophila S2R+ cells were labelled for 10min with 500µM 4SU. Cells were then harvested by centrifugation and Total RNA was isolated with QIAzol reagent (QIAGEN) according to the manufacturer’s instructions. Drosophila RNA was used as spike-in and added to Raji TotRNAs (1:40 ratio). TotRNAs were fragmented (two-times 105µg in 120µL) using a Covaris sonicator M220 (7°C, Power 75W, Duty factor 1%, burst 200) to generate RNA fragments of 200bp to 10kb. 4SU-labeled RNA from 210µg of Fragmented RNA was biotinylated, pulled-down using streptavidin beads and eluted with freshly prepared 100mM DTT. 4sU-labeled RNA (TT-seq) were treated with RNase-free DNase I, purified with miRNeasy MinElute spin column and eluted in 15µL Nuclease-free water. Prior to library preparation, samples were quantified with Nanodrop and quality was assessed by Bioanalyzer Nano RNA ChIP. Ribosomal RNA were depleted from samples using NEBNext rRNA Depletion Kit V2 (NEB ; E7400) and sequencing libraries were prepared with NEBNext Ultra II Directional Kit (NEB, E7760) according to manufacturer’s instructions.
ChIP-seq, RNA-seq
Mnase-seq, DNase-seq and ChIP-seq librairies were prepared using Illumina's ChIP Sample Prep Kit according to standard protocol. ChrRNA-seq librairies were prepared using Illuminas's "TruSeq® Stranded Total RNA Library Prep Gold (ref. 20020599)" kit according to standard protocol. TT-seq librairies were prepared using NEBnext Utra II Directional Kit.

treatment_protocol: For the α-amanitin experiments, cells were treated with 2.5 µg/mL at the indicated times. For the Pyridostatin experiments, cells were treated with 10 µM pyridistatin. For Triptolide treatment,  Raji cells were treated for 2h with 1 µM. For serum stimulation, cells were starved overnight in DMEM/0.3% FCS before stimulation with 15%FCS for 15minutes.

value: Fibroblast

value: Embryo

tag: experiment

value: RNA-seq

tag: spike-in cell line

value: ERCC

tag: chip antibody

value: ChrRNA

value: Overnight starvation in DMEM+0.3% FCS+15 minutes stimulation with 15%FCS

tag: concentration

value: 15% FCS

tag: duration

value: 15 minutes


title: Mm_thymus_FVB_P21_chi6.up_rep1

description:
recovery phase
AN160

extract_protocol:
Preparations of single TECs were prepared from explanted thymi. Negative enrichment via MACS sorting with anti-CD45 beads (Miltenyi) was performed. Enriched TECs were purified by FACS and sorted directly into TRI reagent (Sigma-Aldrich). RNA was extracted following standard protocols.
Libraries were constructed with the NEBNext Ultra RNA Library Prep kit or the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.

tag: age


title: A549 ctrl shRNA 2

description: Library name: A549_SCV2

value: Cell line

value: A549 lung cancer cells

value: Cancer

value: Ctrl


title: ORG_C_ET1_18_L1_R1_001_5Al9O19Z1EWd

city: Bologna

first: Silvia

last: Cetrullo

state: BO

address: Via Irnerio 48

department: DIBINEM

country: Italy

institute: University of Bologna

description:
Library name: Sample6
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_C_ET1_18_L1_R1_001_5Al9O19Z1EWd

data_processing:
QIAGEN RNA-seq Analysis Portal 5.1
3' adapter trimming and UMI reads collpsing with QIAGEN RNA-seq Analysis Portal 5.1 ((Minimum length of miRNA: 15, Maximum length of miRNA: 55, UMI length: 12, Maximum size of small UMI groups: 1, Common sequence: AACTGTAGGCACCATCAAT, Maximum differences in common sequence: 1)
QIAGEN RNA-seq Analysis Portal 5.1 were used for this step. Trimmed sequences were aligned to miRBase_v22 database for identification and counting ((Minimum supporting count: 1, Prioritized species: H.sapiens, Allow length-based isomiRs: Yes, Additional upstream bases: 2, Additional downstream bases: 2, Missing upstream bases: 2, Missing downstream bases: 2, Maximum mismatches: 2, Strand specific: Yes, Minimum sequence length: 18, Maximum sequence length: 25, Annotation records: miRBASE).
QIAGEN RNA-seq Analysis Portal 5.1 were used for this step.
Assembly: miRBase_v22
Supplementary files format and content: "HF miRNA raw counts for GEO all samples.csv": csv file which includes raw counts for all samples
Supplementary files format and content: "HF miRNA CPM for GEO_all samples.csv" csv file which includes TMM-normalized CPM for all samples

source_name: hiPSCs-derived cardiac organoids

growth_protocol: Cells were seeded at a density of 10,000 cells per well in ultra-low attachment 96-well plates and centrifuged at 100g for 3 minutes. The following day, the medium was refreshed with Essential 8 Flex medium. After 24 hours, differentiation was initiated (day 1) using RPMI 1640/B-27 (minus insulin) supplemented with 4 µM CHIR99021, 0.36 pM BMP4, and 0.08 pM Activin A for 24 hours. On day 3, 2 µM Wnt-C59 was added and maintained for 48 hours. On day 7, insulin was introduced into the RPMI 1640/B-27 medium. On day 8, organoids were exposed to 2 µM CHIR99021 for 1 hour in RPMI 1640/B-27 medium. Medium changes were performed every 48 hours until the start of the treatments on day 14.

extract_protocol:
Total RNA was extracted from 4 organoids per experimental condition using the RNA miRNeasy micro kit (#217084, Qiagen)
RNA library preparation was conductuced by the QIAseq miRNA Library Illumina kit (#331502, Qiagen) accordingly to the manufacturer's protocol

treatment_protocol: The hypertrophic response was initiated by administering ET-1 at a final concentration of 10 nM for 24 hours.

value: hiPSCs-derived cardiac organoids

value: #18944 Thermo Fisher

value: Human Episomal iPSC line

value: 10 nM Endothelin-1


title: ORG_D_ET1_20_L1_R1_001_GPWhZL3l09py

description:
Library name: Sample7
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_D_ET1_20_L1_R1_001_GPWhZL3l09py


title: 3_histio_BRAINSTEM

value: brain

value: Brainstem

value: Histiocytosis


title: Mm_thymus_FVB_P21_chi6.down_rep9

description:
collapse phase
AN234

value: thymus

value: Epcam+CD45- TECs

value: FVB

value: ca. P21

tag: condition


title: NIH3T3_chrRNA-seq_FCS_15min_rep2

value: Fibroblast

value: Embryo

value: RNA-seq

value: ERCC

value: ChrRNA

value: Overnight starvation in DMEM+0.3% FCS+15 minutes stimulation with 15%FCS

value: 15% FCS


title: Dr_thymus_foxn1+/+_rep1

value: thymus cells


title: 3_histio_CEREBELLUM

value: Cerebellum


title: ORG_B_ET1_16_L1_R1_001_s9m69qRY5PXC

description:
Library name: Sample5
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_B_ET1_16_L1_R1_001_s9m69qRY5PXC

value: hiPSCs-derived cardiac organoids

value: #18944 Thermo Fisher

value: Human Episomal iPSC line

value: 10 nM Endothelin-1


title: Mm_thymus_FVB_P21_chi6.down_rep8

description:
collapse phase
AN159

value: thymus


title: NIH3T3_chrRNA-seq_FCS_15min_rep1

value: 15 minutes


title: PyMT tumor from mouse with Cxcr4 KO in macrophage

description: 10x Genomics

value: Mammary tumor

value: All viable intratumor single cells


title: Mm_thymus_FVB_P21_chi6.down_rep7

description:
collapse phase
AN157

value: Epcam+CD45- TECs

value: FVB

value: ca. P21


title: ORG_F_ET1_24_L1_R1_001_y4QWi3NvG31K

description:
Library name: Sample8
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_F_ET1_24_L1_R1_001_y4QWi3NvG31K


title: 4_histio_BRAINSTEM

value: brain

value: Brainstem

value: Histiocytosis


title: 4_histio_HIPPOCAMPUS

value: Hippocampus


title: NIH3T3_chrRNA-seq_Starved_rep2

description:
Starved
NIH3T3_chrRNA_Starved_merge_scaled_pos_bin50.wig
NIH3T3_chrRNA_Starved_merge_scaled_neg_bin50.wig

value: Fibroblast

value: Embryo

value: RNA-seq

value: ERCC

value: ChrRNA

value: Overnight starvation in DMEM+0.3% FCS


title: 5_histio_CORTEX

value: Cortex


title: 4_histio_CORTEX


title: 3_histio_BRAINSTEM2


title: PyMT tumor from mouse #725 with Cxcr4 KO in macrophage

description:
Partek_EL-CXCR4cKO_Whole_Tumor_bulk_RNA_Normalization_Normalized_counts.txt
3000__cKO_tumor_725

value: whole tumor


title: 1_histio_BRAINSTEM2


title: ORG_A_CTRL_13_L1_R1_001_p5CXTrWx9Hxt

description:
Library name: Sample1
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_A_CTRL_13_L1_R1_001_p5CXTrWx9Hxt

value: hiPSCs-derived cardiac organoids

value: #18944 Thermo Fisher

value: Human Episomal iPSC line

value: untreated control


title: Mm_thymus_FVB_P21_chi6.down_rep4

description:
collapse phase
AN59

value: thymus

value: Epcam+CD45- TECs

value: FVB

value: ca. P21


title: NIH3T3_chrRNA-seq_Starved_rep3


title: NIH3T3_G4access_FCS_15min_rep3

description:
Serum (FCS 15%) stimulated for 15 minutes
NIH3T3_G4access_FCS_merge_bin10.wig

tag: spike-in reference organisme

value: Drosophila melanogaster

value: Overnight starvation in DMEM+0.3% FCS+15 minutes stimulation with 15%FCS

value: 15% FCS

value: 15 minutes


title: Mm_thymus_FVB_P21_chi6.down_rep6

description:
collapse phase
AN156


title: ORG_D_CTRL_19_L1_R1_001_QCSuCP1eiF9E

description:
Library name: Sample3
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_D_CTRL_19_L1_R1_001_QCSuCP1eiF9E


title: Mm_thymus_FVB_P21_chi6.down_rep3

description:
collapse phase
AN148


title: NIH3T3_chrRNA-seq_Starved_rep1

value: Fibroblast

value: Embryo

value: RNA-seq

value: ERCC


title: NIH3T3_G4access_FCS_15min_rep2


title: 1_histio_BRAINSTEM

value: brain

value: Brainstem

value: Histiocytosis


title: sgRBM15_rep3_merge

city: Shanghai

first: Chen

last: Wang

address: Xianxia Rd 1111, Changning District

department: Department of Gastroenterology

institute: Shanghai Jiaotong University School of Medicine Affiliated Tongren Hospital

description: sgRBM15_rep3 (FPKM)

data_processing:
Raw data were aligned using HISAT2 v2.2.1 against the hg38 version of the human genome.
For quantification of RNA-seq data, read counts and fragments per kilobase million (FPKM) values for each sample were calculated using StringTie v2.0.4.
Assembly: hg38
Supplementary files format and content: FPKM values for each sample

growth_protocol: The human colorectal cancer cell line HCT15 was cultured in RPMI-1640 medium supplemented with 1% penicillin/streptomycin and 10% FBS at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA from control HCT15 and RBM15-knockout HCT15 cell lines was extracted using TRIzol.
RNA sequencing (RNA-seq) libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina and subjected to a paired-end 150 bp sequencing run on the Illumina NovaSeq 6000.

value: human colorectal cancer cells

value: RBM15 Knockout


title: 1_histio_HIPPOCAMPUS

value: Hippocampus


title: sgRBM15_rep2_merge

description: sgRBM15_rep2 (FPKM)


title: ORG_A_ET1_14_L1_R1_001_DYdlHgfMTRUO

description:
Library name: Sample4
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_A_ET1_14_L1_R1_001_DYdlHgfMTRUO

value: hiPSCs-derived cardiac organoids

value: #18944 Thermo Fisher

value: Human Episomal iPSC line

value: 10 nM Endothelin-1


title: NIH3T3_G4access_FCS_15min_rep1

value: Drosophila melanogaster

value: Overnight starvation in DMEM+0.3% FCS+15 minutes stimulation with 15%FCS


title: Mm_thymus_FVB_P21_chi6.down_rep2

description:
collapse phase
AN237

value: thymus

value: Epcam+CD45- TECs

value: FVB

value: ca. P21


title: sgRBM15_rep1_merge

description: sgRBM15_rep1 (FPKM)


title: 1_histio_CORTEX

value: Cortex


title: Mm_thymus_FVB_P21_chi6.down_rep1

description:
collapse phase
AN235


title: ORG_B_CTRL_15_L1_R1_001_F8KWfOPm4qVL

description:
Library name: Sample2
Column name in "HF miRNA raw counts for GEO_all samples.csv" and "HF miRNA CPM for GEO all samples.csv": ORG_B_CTRL_15_L1_R1_001_F8KWfOPm4qVL

value: untreated control


title: Mm_thymus_B6_P1_WT_rep2

value: WT


title: Mm_thymus_B6_P28_Foxn1KO_rep4


title: Mm_thymus_B6_P1_WT_rep1


title: sgctrl_1_merge

description: sgctrl_rep1 (FPKM)


title: M2633-Ctrl-BS-2mo

data_processing:
FastQ files of 2x100bp paired-end reads were quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 2012).
Samples were with high quality reads (Phred score >= 30) were aligned tothe Mouse reference genome mm10 using STARaligner(version 2.7)55
Gene quantification was performed using feature counts from the Subread package in R56
Aligned reads were visualized using IGV (version 2.8.9).
Gene expression levels were normalized and log2 transformed using the Trimmed Mean of M-values (TMM) method
Differential expression analysis was performed using the edgeR package in R57. Significantly differentially expressed genes were selected with controlled False Positive Rate (B&H method) at 5% (FDR <= 0.05). Upregulated genes were selected at a minimum log2fold change of 2 and downregulated genes at a minimum log2fold change of -2
Heatmaps were drawn on the normalized expression matrix using the pheatmap package in R. Euclidean distance similarity metric and complete linkage algorithm were used for hierarchical clustering
Gene ontology (GO) and pathway (WikiPathways, KEGG, Reactome) analysis using g:profiler webtool was performed on the list of upregulated genes (log2>= 2 and FDR <=0.05) ordered by importance58. GO terms and pathways were selected based on an FDR <= 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains raw counts

source_name: brain brainstem

growth_protocol: For targeting of BRAF(V600E) mutation to microglia progenitors, we genetically targeted EMPs by pulse-labelling  Cx3cr1CreER;Braf LSL-V600E E9.5 embryos ( with a single injection of 37.5 mg per kg (body weight) of 4-hydroxytamoxifen  into pregnant females.

extract_protocol:
RNA isolation was performed with Qiagen all-prep DNA/RNA mini kit (80204) according to the manufacturer’s instructio
total RNA underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 cycles) (Illumina).  An average of 29 million paired reads were generated per sample, the percent of mRNA bases per sample ranged from 47% to 85%, and ribosomal reads averaged 0.4%.
SMART-Seq v4 Ultra Low Input RNA Kit

value: brain brainstem

value: tissue

value: microglia

value: Braf WT; CX3 HET

value: 2 months


title: sgctrl_3_merge

description: sgctrl_rep3 (FPKM)

value: human colorectal cancer cells


title: Mm_thymus_FVB_P21_chi6.down_rep5

description:
collapse phase
AN155


title: M2633-Ctrl-Cort-2mo

source_name: brain cortex

value: brain cortex


title: NIH3T3_G4access_Starved_rep2

description:
Starved
NIH3T3_G4acces_starved_merge_bin10.wig

value: Fibroblast

value: Embryo

value: Overnight starvation in DMEM+0.3% FCS


title: 2_control_CORTEX2

value: brain

value: Control


title: NIH3T3_G4access_Starved_rep1

value: Drosophila melanogaster


title: 2_control_BRAINSTEM

value: Brainstem


title: Mm_thymus_B6_P28_Foxn1KO_rep3

value: thymus

value: Epcam+CD45- TECs