title: WT 1928z-VDJ Day 16 Rep-2


title: SUVKO 1928z-antibody capture Day 16 Rep-1

status: Public on Nov 03 2023

type: SRA

city: New York

first: Michel

last: Sadelain

address: 1275 York Avenue, Box 182

country: USA

institute: Memorial Sloan Kettering Cancer Cener

library_source: other

data_processing:
library strategy: CITE-seq
The scRNA-seq reads were aligned to the human transcriptome (GRCh38) and unique molecular identifier (UMI) counts quantified to generate a gene-barcode matrix using Cell Ranger pipeline (10X Genomics, version cellranger-5.0.1). CITE-seq antibody expression matrices were generated using the Cell Ranger pipeline (10X Genomics, version cellranger-5.0.1).  TCR reads were aligned to the GRCh38 reference genome and consensus TCR annotation was performed using Cell Ranger vdj pipeline (10X Genomics, version cellranger-5.0.1).
Assembly: hg38
Supplementary files format and content: R object file in .rds format

molecule: protein

organism: Homo sapiens

source_name: T cells

growth_protocol: CAR T cells were generated from healthy donors (Day 0) or flow sorted from tumor bearing mice at Day 9 or Day 16.

extract_protocol:
Pre-infusion T cells (day 0), and flow-sorted CAR T cells from mouse bone marrow (day 9 and 16) were stained for 30 minutes at room temperature with a custom panel of 101 Total-Seq-C antibodies (Biolegend), and washed 3x using the HT1000 laminar wash system (Curiox). Cells were then counted using the Cellaca MX High-throughput Automated Cell Counter as described in the manufacturer’s protocol (Nexcelom) and loaded on the 10x Chromium Next GEM Chip K Kit.
TCR CDR3 sequences were enriched using the human V(D)J T cell enrichment. Libraries were prepared according to manufacturer’s protocol (5’ V2 kit, 10x Genomics) and sequenced on a NovaSeq 6000 System using the S4 2x 150 kit (Illumina).

tag: tissue

value: T cells

tag: cell type

value: Primary T cells

tag: genotype

value: SUVKO


title: WT 1928z-antibody capture Day 16 Rep-2

value: WT


title: WT 1928z-antibody capture Day 16 Rep-1


title: Negative control.20

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

library_source: transcriptomic single cell

data_processing:
Read alignment with STAR (v.2.7.9a)
all downstream analyses were performed in R(v4.0.3)
Sum of exonic and intronic TPM values  were calculated using the scater package (v1.18.6).
Assembly: GRCm39 and Gencode vM27
Supplementary files format and content: comma delimited text, matrix of combined exonic/introinc TPMs

molecule: polyA RNA

organism: Mus musculus

growth_protocol: All animal procedures were approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and European Union animal law (license number: BMWF-66.018/0007-II/3b/2012 and BMWFW-66.018/0006-WF/V/3b/2017). Experimental mice were bred and maintained according to regulations approved by institutional animal care and use committee, institutional ethics committee and the guidelines of the preclinical facility (PCF) at IST Austria. Mice were housed at 21±1°C ambient temperature and 40–55% humidity in 12 hrs dark/light cycles. All mouse lines were kept in mixed C57/Bl6, FVB and CD1 genetic background. In some experiments, wild-type CD1 mice were also used. Both male and female littermates of the desired genotypes were used randomly. Mice were used at an age range from 2 – 8 months for breeding and from E9.5 to P30 for experiments. All efforts were made to minimize the number of animals used following the 3R principles.

extract_protocol:
The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (doi: 10.7554/eLife.52951; doi: 10.1038/nprot.2017.120) and optimized for speed and coverage of sparsely labelled cells of MADM clones. For details see publication.
cDNA libraries from E10 clones were prepared followed by Smart-seq2 protocol (doi: 10.1038/nprot.2014.006) using custom reagents (VBCF GmbH, Vienna)

treatment_protocol: MADM clone induction in the SC was adapted from previously described protocols (doi: 10.3791/61147; doi: 10.1016/j.neuron.2010.09.027).


title: SUVKO 1928z-scRNA Day 16 Rep-2

data_processing:
Primary Cells
The scRNA-seq reads were aligned to the human transcriptome (GRCh38) and unique molecular identifier (UMI) counts quantified to generate a gene-barcode matrix using Cell Ranger pipeline (10X Genomics, version cellranger-5.0.1). CITE-seq antibody expression matrices were generated using the Cell Ranger pipeline (10X Genomics, version cellranger-5.0.1).  TCR reads were aligned to the GRCh38 reference genome and consensus TCR annotation was performed using Cell Ranger vdj pipeline (10X Genomics, version cellranger-5.0.1).
Assembly: hg38
Supplementary files format and content: R object file in .rds format


title: SUVKO 1928z-scRNA Day 16 Rep-1


title: PS28.4

source_name: dSC

value: dSC

value: Neuron


title: WT 1928z-scRNA Day 16 Rep-2


title: WT 1928z-scRNA Day 16 Rep-1


title: PS29.7


title: SUVKO 1928z-VDJ Day 9 Rep-2


title: 251hsv_2

city: Xiamen

first: Yipeng

last: Rao

address: Xiangan Campus, Xiamen University, Xiangan Road, Xiangan District, Xiamen City, Fujian Province, China

country: China

institute: national insititute of diagnostics and vaccine development in infectious diseases（xiamen university）

library_source: transcriptomic

data_processing:
RNA-seq analysis was performed by GeneWiz.
Quality Control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances .We used scripts in house to enrich significantdifferential expression gene in KEGG pathways.
Assembly: hg38
Supplementary files format and content: rawreads, FPKMs

molecule: total RNA

extract_protocol:
Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.). 1 μg total RNA was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: U-251 MG cells were seeded at a density of 1 × 106 in 6-well plates and allowed to attach for 24 h. The next day, cells were pretreated for 4 h with LRRK2i (10 μM) or the vehicle. After pretreatment, the cells were infected with oHSV-GFP at an MOI of 0.5 or mock-infected. Four hours after infection, biological triplicates for each group were collected using Tripure Isolation Reagent (Roche).

tag: cell line

value: Glioma cell

tag: treatment

value: control

tag: infection

value: oHSV-GFP at an MOI of 0.5 infected


title: SUVKO 1928z-VDJ Day 16 Rep-2


title: PS29.6


title: 251hsv_3


title: WT 1928z-VDJ Day 9 Rep-2


title: PS29.5

source_name: sSC

value: sSC


title: 3B1A cells, CDDP, biol rep2

city: Ciudad de Mexico

first: Rodolfo

middle: Luis

last: Chavez-Dominguez

state: Ciudad de Mexico

address: Calz. de Tlalpan 4502

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

data_processing:
The quality of sequenced raw reads was examined using the FastQC (v0.11.9) and MultiQC (v1.6).
Then, raw reads were filtered and trimmed to eliminate sequence adapters and to preserve high-quality reads using Trimmomatic (v0.38) and Cutadapt (v2.7), respectively.
Trimmed reads were aligned and mapped to GRCh38 human genome using STAR (v2.7.3a) and abundance estimation of mapped reads were calculated using RSEM (v1.3.1).
Raw counts were normalized using the Trimmed Mean of M-values (TMM) method of edgeR (v3.32.1).
Assembly: GRCh38 release 95.
Supplementary files format and content: Tab-delimited text file includes raw counts estimated by RSEM for each sample.

source_name: Non-small cell lung cancer

growth_protocol: All cell lines were cultured in RPMI-1640 medium (Sigma) supplemented with fetal bovine serum (10 %) and antibiotics. Cells were cultured in humidified atmosphere with 5 % of CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using the RNAeasy kit (Qiagen, Germany) from cisplatin-persistent and untreated cells. For library preparation, we employed 2µg of RNA per sample.
RNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) and following manufacturer’s directions.

treatment_protocol: All cell lines were exposed for 24 h to cisplatin (Sigma) and employing a concentration inducing at least 70 % of cytotoxicity.

value: Non-small cell lung cancer

value: Cisplatin


title: 3B1A cells, CDDP, biol rep3


title: WT 1928z-VDJ Day 9 Rep-1


title: PS30.2


title: SUVKO 1928z-antibody capture Day 9 Rep-2


title: 3B1A cells, CDDP, biol rep1


title: PS29.4


title: SUVKO 1928z-antibody capture Day 9 Rep-1


title: WT 1928z-antibody capture Day 9 Rep-2


title: SUVKO 1928z-VDJ Day 0 Rep-4


title: 3B1A cells, CT, biol rep1

value: Control


title: SUVKO 1928z-VDJ Day 0 Rep-3


title: WT 1928z-scRNA Day 9 Rep-2


title: WT 1928z-antibody capture Day 9 Rep-1


title: SUVKO 1928z-VDJ Day 9 Rep-1


title: PS28.2


title: WT 1928z-scRNA Day 9 Rep-1


title: PS29.1


title: SUVKO 1928z-scRNA Day 9 Rep-2


title: Negative control.19


title: PS28.1


title: PS29.3


title: PS28.3


title: WT 1928z-VDJ Day 0 Rep-4


title: H1573 cells, CDDP, biol rep2


title: SUVKO 1928z-VDJ Day 0 Rep-1


title: PS29.2


title: 3B1A cells, CT, biol rep3


title: 3B1A cells, CT, biol rep2


title: SUVKO 1928z-scRNA Day 9 Rep-1


title: H1573 cells, CDDP, biol rep1


title: H1573 cells, CT, biol rep3


title: WT 1928z-VDJ Day 0 Rep-3


title: H1573 cells, CDDP, biol rep3


title: SUVKO 1928z-VDJ Day 0 Rep-2


title: WT 1928z-VDJ Day 0 Rep-2


title: H1573 cells, CT, biol rep2


title: WT 1928z-VDJ Day 0 Rep-1


title: SUVKO 1928z-antibody capture Day 0 Rep-4


title: SUVKO 1928z-antibody capture Day 0 Rep-2


title: SUVKO 1928z-antibody capture Day 0 Rep-1


title: PS27.9


title: H1299 cells, CDDP, biol rep3


title: PS27.10

source_name: PAG

value: PAG


title: H1573 cells, CT, biol rep1


title: WT 1928z-antibody capture Day 0 Rep-3


title: PS27.7


title: SUVKO 1928z-antibody capture Day 0 Rep-3


title: SUVKO 1928z-scRNA Day 0 Rep-2


title: PS27.6


title: PS27.8


title: H1299 cells, CT, biol rep3


title: H1299 cells, CDDP, biol rep1


title: SUVKO 1928z-scRNA Day 0 Rep-3


title: WT 1928z-antibody capture Day 0 Rep-2


title: H1299 cells, CT, biol rep2


title: WT 1928z-antibody capture Day 0 Rep-4


title: SUVKO 1928z-scRNA Day 0 Rep-4


title: H1299 cells, CDDP, biol rep2


title: H1299 cells, CT, biol rep1


title: WT 1928z-scRNA Day 0 Rep-1


title: SUVKO 1928z-scRNA Day 0 Rep-1


title: PS27.5


title: PS27.4


title: WT 1928z-scRNA Day 0 Rep-2


title: PS27.3


title: WT 1928z-scRNA Day 0 Rep-3


title: A549 cells, CDDP, biol rep3


title: WT 1928z-antibody capture Day 0 Rep-1


title: PS27.2


title: MHHNB11 cells treated with Veh144, replicate

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
CRISPR KO screens were analyzed using Mageck-Vispr/0.5.7
Supplementary files format and content: Mageck default output describing resulting RRA scores

molecule: other

source_name: Peripheral Nervous System

extract_protocol: sgRNAs for the human CRISPR KO library were first designed using CRISPick . The top 30 sgRNAs for each gene then underwent an additional round of filtering using in-house off-target analysis to identify highly unique sgRNAs. Up to 6 sgRNAs per gene were selected for the library along with non-targeting controls making up ~10% of the final library.

treatment_protocol: 72H treatments

value: Peripheral Nervous System

value: Neuroblastoma


title: MHHNB11 cells treated with JQAD1, replicate


title: MHHNB11 cells treated with Retinoic acid, replicate

value: Retinoic acid


title: PS27.1


title: A549 cells, CDDP, biol rep2


title: MHHNB11 cells treated with Vincristine, replicate

value: Vincristine


title: WT 1928z-scRNA Day 0 Rep-4

value: T cells

value: Primary T cells


title: MHHNB11 cells treated with Topotecan, replicate

value: Topotecan


title: MHHNB11 cells treated with Phosphoramide mustard, replicate

value: PM


title: MHHNB11 cells treated with Doxorubicin, replicate

value: Doxorubicin


title: A549 cells, CDDP,  biol rep1

value: WT


title: MHHNB11 cells treated with Etoposide, replicate

value: Etoposide


title: A549 cells, CT, biol rep2


title: PS26.9

value: dSC

value: Neuron


title: MHHNB11 cells treated with Cisplatin, replicate


title: PS26.10


title: Negative control.18


title: A549 cells, CT, biol rep3

value: Non-small cell lung cancer


title: A549 cells, CT, biol rep1


title: PS26.8


title: HCC1143_pooledrep_H1

city: St Lucia

first: Rebecca

last: Lane

state: QLD

address: Cnr College and Cooper Rds

department: Australian Institute for Bioengineering and Nanotechnology (AIBN)

country: Australia

institute: The University of Queensland

data_processing:
Data processing and demultiplexing was performed using Illumina bcl2fastq software v2.16, consensus reads were then generated using Gencore v0.15.0 (Chen et al. 2019).
Reads were mapped against the Genome Reference Consortium Human genome build 38 release 84 (GRCh38.84) using HiSat2 v2.1.0 with the following parameters: hisat2-align-s --trim5 2 --trim3 9 --no-softclip -p 14
A matrix of read counts was produced from sorted BAM files using the Rsubread package in the R software environment. Subsequent data normalisation and testing for differential expression was performed using the DESeq2 package (Love et al. 2014) in the R software environment.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HCC1143 cell-derived EVs

growth_protocol: Cells were maintained in a mixture of Medium 171 supplemented with Mammary Epithelial Growth Factor (MEGS 1X),1X GlutaMAX, 16g/L Phenol Red and 1% FBS depleted of extracellular vesicles by overnight ultracentrifugation. For MCF7, T47D and BT483 cells, medium was supplemented with 10ug/mL insulin (bovine pancreatic origin).

extract_protocol:
RNA was extracted from EV samples using the RNA/Protein Purification Kit (Norgen Biotek) as per manufacturer instruction. Extracted RNA was treated with 10 units RNAse free DNAase 1 (Qiagen).
10ng RNA was used for library preparation. rRNA was depleted from samples using the Fast Select rRNA Removal Reagent (Qiagen). cDNA was prepared using the NEBNext Ultra II Directional Library Prep Kit for Illumina (New England Biosciences). End repair, adaptor ligation and 15x cycles of PCR amplification were performed using the xGen Prism DNA Library Prep Kit with xGen UDI Primer Pairs used to barcode samples (Integrated DNA Technologies). Following size selection with Speed Beads magnetic particles (Cytiva) to remove unincorporated adaptors, library was reamplified for a further 9x cycles of PCR using universal p5/p7 primers.

treatment_protocol: For EV production, cells were seeded to T175 flasks, and medium (15mL) was collected and replacted 72, 96 and 120 hours after seeding respectively. Collected medium was pooled and concentrated using Amicon Ultra-15 50kDa MWCO columns to <0.5mL, and EVs were isolated by size exclusion chromatography (SEC) on a home-packed Sepharose 4B column. EV-enriched fractions were concentrated to <50uL using Amicon Ultra-0.5 10kDa MWCO columns.

value: breast carcinoma

tag: breast cancer subtype

value: ER-/PR-/HER2- (TNBC)

tag: material type

value: extracellular vesicles (EVs)


title: PS26.7

value: sSC


title: Ge518 GDC mi222 n2

city: Lyon

first: Erika

last: COSSET

state: Rhône

address: 28 Rue Laennec

country: France

institute: Centre de Recherche en Cancérologie de Lyon

data_processing:
The sequencing quality control was done with FastQC v.0.11.5.
sequences were aligned with STAR aligner v.2.5.3a
Picard tools for QC metrics
table counts were generated with HTSeq v0.6p1
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.18.1
Normalization of counts edgeR
Assembly: UCSC human GRCh38/hg38
Supplementary files format and content: tab delimited txt file containing normalized counts (CPM) for Ge518 cell lines normalized per library size (edgeR)

source_name: Transfected GBM cells

extract_protocol:
Isolation of total RNA was carried out by using RNeasy kit from Qiagen according to the manufacturer’s instructions and as previously described [18]
TruSeq RNA Seq Library preparation kit. As per manufacturer recommendations

treatment_protocol: Eight GSCs from different subtypes Ge269, 518, 835, (mesenchymal subtype) 738, 898, (proneural subtype) 885, (neural subtype) 904, 970.2 (classical subtype) were cultured in DMEM/F12 with Glutamax supple- mented with B27 supplement and b-FGF, EGF both at 10 ng/ml and 1% penicillin/streptomycin, as previously described [18]. Of note, Ge970.2 is a PDC line with a low rate of growth which precludes its use for all readouts. To generate GBM PDCs, we transferred the GSCs to, and maintained them in, Dulbecco’s modified Eagle’s medium (DMEM)-high glucose/glutamax, 10% fetal bovine serum (FBS), and 1% penicillin/streptomycin (GDC medium). All PDC lines were validated to be mycoplasma negative before experiments.

value: Transfected GBM cells

value: Glioblastoma Cells

value: Wild Type

value: miRNA 222


title: Ge518 GDC mi222 n1


title: Ge518 GDC mi340 n2

value: miRNA 340


title: Ge518 GDC mi340 n1


title: Ge518 GDC mi340 n3


title: PS26.6


title: Ge518 GDC mi17-3p n2

value: miRNA 17- 3-p


title: MHHNB11 cells treated with Veh72, replicate

value: Peripheral Nervous System

value: Neuroblastoma


title: Ge518 GDC mi17-3p n1


title: BT483_pooledrep_F2

source_name: BT483 cell-derived EVs


title: Ge518 GDC miCtrl n1

value: Control


title: PS26.4


title: MDAMB231_pooledrep_E1

source_name: MDAMB231 cell-derived EVs

value: ER-/PR-/HER2 - (TNBC)


title: Ge518 GDC miCtrl n3


title: BT483_singlerep_E2


title: PS26.5


title: hUC-MSC passage 7

city: Guangzhou, Guangdong

first: Longhui

last: Deng

address: No. 1 Helix 4th Road, International Biological Island

institute: Guangzhou SALIAI Stemcell Science and Technology Co., Ltd.

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence by cutadapt v3.7
Sequence reads were mapped to a human genome (hg38) by STAR v2.7.0f
Gene counts were estimated by HTSeq v0.13.5.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts values for each Sample

source_name: umbilical cord-derived mesenchymal stem cells

extract_protocol:
Total RNA was extracted from cultured cells using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT

tag: passage


title: BT474_pooledrep_F1

source_name: BT474 cell-derived EVs


title: MCF7_pooledrep_C2

source_name: MCF7 cell-derived EVs


title: SKBR3_pooledrep_G1

source_name: SKBR3 cell-derived EVs


title: hUC-MSC passage 6

value: umbilical cord-derived mesenchymal stem cells


title: Ge518 GDC mi222 n3


title: hUC-MSC passage 5


title: PS26.1

value: Neuron


title: hUC-MSC passage 4


title: T47D_pooledrep_C1

source_name: T47D cell-derived EVs

value: breast carcinoma


title: Ge518 GDC mi17-3p n3


title: Tumor sample 19, scRNA-seq

city: Aurora

first: John

last: DeSisto

state: CO

department: Pediatrics

institute: University of Colorado

description: 10X v.3 chemistry

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed using CellRanger  v3.0.1
Assembly: Reads were mapped to GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: high grade glioma - pediatric

extract_protocol: 10X v.3 chemistry

value: high grade glioma - pediatric


title: HS578T_pooledrep_A2

source_name: HS578T cell-derived EVs

value: extracellular vesicles (EVs)


title: PS26.3

value: sSC


title: Ge518 GDC miCtrl n2

value: Transfected GBM cells


title: Tumor sample 18, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 17, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 16, scRNA-seq

description: 10X v.3 chemistry


title: Negative control.17


title: BT474_singlerep_A1


title: PS25.3

value: dSC


title: Tumor sample 13, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 14, scRNA-seq

description: 10X v.3 chemistry


title: PS25.4

value: PAG


title: PS25.2


title: Tumor sample 12, scRNA-seq

description: 10X v.3 chemistry


title: PS25.1


title: Tumor sample 15, scRNA-seq

description: 10X v.3 chemistry


title: Negative control.11


title: PS16.4


title: PS16.3


title: Tumor sample 11, scRNA-seq

description: 10X v.3 chemistry


title: PS16.2


title: Tumor sample 8, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 7, scRNA-seq

description: 10X v.3 chemistry


title: PS25.5


title: Tumor sample 6, scRNA-seq

description: 10X v.3 chemistry


title: PS16.1


title: Tumor sample 4, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 10, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 5, scRNA-seq

description: 10X v.3 chemistry


title: PS24.14


title: PS24.15


title: PS26.2


title: PS15.9


title: Tumor sample 9, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 19, bulkRNA-seq

description:
1463_B
1463_B

data_processing:
data were mapped to the human genome (hg19) by gSNAP
expression (FPKM) was derived by Cufflinks
differential expression was analyzed with ANOVA in R
Assembly: hg19

extract_protocol: Libraries were prepared by using the TruSeq Library Preparation Kit v2 (Agilent).


title: Tumor sample 3, scRNA-seq

description: 10X v.3 chemistry


title: Tumor sample 1, scRNA-seq

description: 10X v.3 chemistry


title: PS24.13


title: PS15.8


title: PS24.12


title: Glast/Sun1-GFP control, retina

city: Ann Arbor

first: Thanh

last: Hoang

state: MI

address: 1000 Wall St, Brehm Building , Room 7426

department: Ophthalmology

institute: University of Michigan

description:
Combined_scRNA_filtered_feature_bc_matrix.h5
Cell barcodes  ID with -1 are from control

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V4 was used to perform downstream analysis following the standard pipeline.
Assembly: mm10

source_name: Retinas

extract_protocol: scRNA-Seq following 10x V3.1 guideline

value: Retinas

value: Wild type control


title: PS15.7


title: Negative control.16


title: PS24.11

source_name: dSC


title: Tumor sample 17, bulkRNA-seq

description:
1437
1437


title: Tumor sample 16, bulkRNA-seq

description:
1431
1431


title: PS15.6


title: PS15.5

source_name: sSC


title: Glast/Rbpj/Sun1-GFP knockout, retina

description:
Combined_scRNA_filtered_feature_bc_matrix.h5
Cell barcodes  ID with -2 are from Rbpj KO

value: Rbpj deletion


title: PS24.10


title: Tumor sample 15, bulkRNA-seq

description:
1421
1421


title: PS15.4


title: liver_KO_IL6-4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were quality checked with fastqc and no urther preprocessing was needed
Reads were aligned to the mm10 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm10
Supplementary files format and content: matrix of raw counts for all samples

source_name: liver

extract_protocol:
RNA was obtained with the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s protocol
RNA was used to generate an Illumina sequencing library using the Illumina Stranded mRNA Ligation LP kit according to the manufacturer’s protocol

treatment_protocol: mice wer treated with tamoxifen for 5 days (1 mg in 1:8 ethanol:oil) to induce Hnf4a deletion in transgenic animals. Three days after the final injection mice were treated with PBS or IL6 (5 mg/kg). Livers were isolated for RNA extratction after 24h and stored in RNAlater

value: liver

value: HNF4A KO


title: liver_KO_IL6-3


title: Tumor sample 2, scRNA-seq

description: 10X v.3 chemistry


title: PS24.9


title: liver_KO_IL6-2


title: PS24.8


title: Tumor sample 14, bulkRNA-seq

description:
1414
1414


title: liver_KO_IL6-1


title: PS15.2


title: PS15.3


title: PS24.7


title: Tumor sample 13, bulkRNA-seq

description:
1241
1241


title: liver_WT_IL6-1


title: liver_WT_IL6-4


title: PS14b.3


title: Negative control.10


title: Tumor sample 11, bulkRNA-seq

description:
1196
1196


title: PS24.6


title: Tumor sample 7, bulkRNA-seq

description:
1107
1107


title: liver_WT_IL6-2


title: PS15.1


title: PS14a.6

source_name: PAG


title: PS14a.7


title: Tumor sample 12, bulkRNA-seq

description:
1214
1214


title: liver_WT_IL6-3


title: PS24.4


title: Tumor sample 10, bulkRNA-seq

description:
1190
1190


title: Tumor sample 9, bulkRNA-seq

description:
1187
1187


title: PS24.5


title: Negative control.15


title: PS14a.8


title: liver_KO_PBS-3

value: PBS


title: PS24.2


title: PS24.1


title: Tumor sample 6, bulkRNA-seq

description:
968
968


title: PS14a.5


title: PS24.3


title: Tumor sample 5, bulkRNA-seq

description:
954
954


title: liver_KO_PBS-1


title: PS14a.4


title: Tumor sample 8, bulkRNA-seq

description:
1144
1144


title: liver_KO_PBS-2


title: liver_WT_PBS-4


title: Tumor sample 1, bulkRNA-seq

description:
834
834


title: liver_WT_PBS-3


title: PS23.2


title: PS14a.3


title: PS14b.2


title: PS23.1


title: PS23.3


title: hESCs, LDN_300

first: Michigan

middle: CDB

last: Bioinformatics

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

data_processing:
BCL Convert Conversion Software v3.9.3 (Illumina)
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et  al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment  options followed ENCODE standards for RNA-seq.
Assembly: GRCh38 (ENSEMBL)
Supplementary files format and content: gene_FPKM: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: gene_counts: tab-delimited text files include Raw Counts values for each Sample

source_name: dose response sample (7230-ST)

growth_protocol: Human pluripotent stem cells were grown in defined pluripotency maintenance media mTeSR1 at low density with 0.1% ROCK inhibitor in an incubator at 37C and 5% CO2

extract_protocol:
For time series samples (7072-ST), RNA extraction and DNase treatment were done with the Invitrogran RNAqueous micro kit per the kit instructions. For dose response samples (7230-ST), RNA extraction and DNase treatment were performed with the QIAGEN RNeasy micro kit according to manufacturer’s instructions.
For time series samples (7072-ST), the University of Michigan Advanced Genomics Core performed library preparation for mRNAs with ribosomal RNA depletion. For dose response samples (7230-ST), the University of Michigan Advanced Genomics Core performed library preparation for messenger RNA with polyA selection.

treatment_protocol: Cells were treated with 100 ng/mL BMP4 + 5 uM IWP-2 and a variable dose of LDN-193189 as specified above to induce BMP signaling at different levels. Treatments were diluted in mTeSR1 growth media with 0.1% ROCK inhibitor

value: human embryonic stem cells

value: GFP::SMAD4 fusion

tag: time

value: 5 hr


title: PS14b.1

value: Neuron


title: liver_WT_PBS-2

value: WT


title: PS22.11


title: hESCs, LDN_100


title: PS14a.1


title: PS22.10


title: PS14a.2


title: Midbrain Fzd10 lineage

data_processing:
Raw sequening data was processed with the Cell Ranger pipeline (v7.0.0, 10X Genomics)  with transcriptome version: mm10-2020-A, including intronic information
Supplementary files format and content: hdf5 file, filtered feature barcode matrix

source_name: Dorsal midbrain

extract_protocol:
Embryonic dorsal midbrains were dissected at E12.5, E14.5 and E16.5 by first cutting the skin and skull to expose the dorsal part of the brain. An incision was made between the forebrain-midbrain boundary and another one between the midbrain-hindbrain boundary with fine surgical scissors. Two horizontal cuts were then made through the aqueduct to free the dorsal midbrains. In total, 9, 8, and 3 dorsal midbrains were pooled for each of E12.5, E14.5 and E16.5 time points, respectively. The subsequent preparation procedures of single-cell suspension from these tissues were adapted and modified from previous protocols (). For details see publication. Single-cell suspensions were incubated with Zombie NIR fixable viability dye (Biolegend) and viable GFP+ cells were sort-purified immediately using a SH800 Cell Sorter (Sony). In total, 33,000 labelled cells were collected from each embryonic time point.
cDNA libraries were generated from pooled embryonic dorsal midbrain samples containing Fzd10-lineage cells using the Chromium Controller and the Next GEM Single Cell 3’ Reagent Kit (v3.1, 10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: To selectively label and isolate cells of the Fzd10-lineage in the embryonic dorsal midbrain, Fzd10-CreER+/- mice were crossed with mTmG reporter line to generate mTmG;Fzd10-CreER+/- embryos. Timed pregnant females received intraperitoneal (IP) injections of TM (1 mg/mouse dissolved in corn oil) at E10.5. Upon Cre activation, a switch of fluorescent color from red (tdT) to green (GFP), according to the mTmG principle (doi: 10.1002/dvg.20335) was observed in the embryonic midbrain cells. Dorsal midbrain from these mTmG;Fzd10-CreER+/- embryos were isolated at E12.5, E14.5 and E16.5 for scRNA-seq experiments.

value: Dorsal midbrain

value: Fzd10 lineage


title: hESCs, LDN_10

value: 100ng/mL BMP4 + 5uM IWP2 + RI + 10 nM LDN-193189


title: Pten KO

extract_protocol:
To isolate P0 dorsal midbrains, mice were first decapitated and the brains dissected from the skull. After removing the cortices to expose the midbrain, two cuts were made with sharp razor blades: one between the forebrain-SC boundary and another between the SC-inferior colliculus boundary. Both cuts were angled to meet at the aqueduct thus avoiding contamination from ventral midbrain regions. In total, 26 Control-MADM and 24 Pten-MADM dorsal midbrains were separately pooled. The subsequent preparation procedures of single-cell suspension from these tissues were adapted and modified from previous protocols  (10.1016/j.xpro.2020.100215). For details see publication. Single-cell suspensions were incubated with Zombie NIR fixable viability dye (Biolegend) and viable GFP+ cells were sort-purified immediately using a SH800 Cell Sorter (Sony). In total, 14,000 and 12,000 labelled cells were sorted from P0 time point of Control-MADM and Pten-MADM, respectively.
cDNA libraries were generated from Control-MADM, Pten-MADM dorsal midbrain samples using the Chromium Controller and the Next GEM Single Cell 3’ Reagent Kit (v3.1, 10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: To generate MADM genetic mosaic mice for Pten gene, we followed previously established protocols (doi: 10.1016/j.xpro.2021.100939; 10.1016/j.celrep.2021.109274). In brief, the Pten-flox allele was recombined onto Chr.19 containing the MADM-19TG cassette to generate MADM-19TG/TG,Pten-flox stocks. Next, MADM-19TG/TG,Pten-flox were crossed with MADM-19GT/GT;Nestin-Cre+/- to generate Control-MADM (MADM-19GT/TG;Nestin-Cre+/-) and Pten-MADM (MADM-19GT/TG,Pten-flox;Nestin-Cre+/-) mice. Upon Cre recombinase-mediated interchromosomal recombination for reconstitution of fluorescent MADM markers, all (red tdT+, green GFP+ and yellow tdT+/GFP+) cells in Control-MADM were wild-type (Pten+/+) whereas in Pten-MADM red tdT+ cells were wild-type (Pten+/+), green GFP+ cells homozygous mutant (Pten-/-) and yellow tdT+/GFP+ cells heterozygous (Pten+/-) in an otherwise unlabeled Pten+/- environment.

value: Nestin lineage


title: PS13a.4

value: sSC


title: hESCs, NoTreat

value: mTeSR


title: Pten Control


title: PS22.9

value: dSC


title: hESCs, LDN_0

value: 100ng/mL BMP4 + 5uM IWP2 + RI + 0 nM LDN-193189


title: PS13b.4

value: PAG


title: N2a, siMbnl1_cMBNL1, rep3

city: Worcester

first: Suna

last: Jung

state: MA

address: 373 Plantation street. Suit 204

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
normcnt_DESeq2_input_suna_revision_2023.txt
A3SS.MATS.JC_4.txt
A5SS.MATS.JC_4.txt
MXE.MATS.JC_4.txt
RI.MATS.JC_4.txt
SE.MATS.JC_4.txt

data_processing:
CASAVA (version/parameters are internal Novogene information) was used for brain tissue.
Fastqc (v0.11.8) and Trimmomatic (v0.39) was to generate sequence quality reports and trim/filter the sequences respectively.
The reads mapped to rRNA by Bowtie2 (v2.3.5) were further filtered out
The cleaned reads were aligned to the mouse reference genome (Ensembl GRCm38) using STAR (v2.6.1) , and gene expression was quantified by RSEM (v1.3.1)
Both expression normalization and differentially expressed gene (DEG) analysis was performed using DESeq2 (v1.16.1).Allternative splicing analysis was performed using rMATS software (v3.0.9)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene expression level for each Sample
Supplementary files format and content: tab-delimited text files include level of exon inclusion for each Sample

growth_protocol: Mouse N2a cells were cultured in Dulbecco’s Modified Eagels Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
TRIzol was added to the cell pellets, and Direct-zol RNA microprep kit (Zymo Research, R2062) was used for RNA extraction and quality was analyzed by fragment analyzer.
NEBNext Ultra II Directional RNA Library Prep Kit was used for Library preparation. RNA sequencing were performed with NovaSeq 6000 sequencer.

treatment_protocol: Non targeting control siRNA, siRNA targeting Fmr1 or Mbnl1 was used. Control plasmid pcDNA or FLAG-nuclear or cytoplasmic MBNL1 was co-transfected using Lipofectamine 3000.

value: Neuroblastoma

value: siMbnl1, FLAG-cytosolic MBNL1


title: PS22.8


title: hESCs, Hour_0_rep2

source_name: time series sample (7072-ST)

value: 100ng/mL BMP4 + 5uM IWP2 + RI

value: 0 hr


title: hESCs, LDN_30

value: human embryonic stem cells

value: GFP::SMAD4 fusion

value: 100ng/mL BMP4 + 5uM IWP2 + RI + 30 nM LDN-193189


title: liver_WT_PBS-1

value: liver

value: WT

value: PBS


title: PS22.12

value: Neuron


title: hESCs, Hour_42

value: 42 hr


title: PS13b.3

value: sSC


title: N2a, siMbnl1_cMBNL1, rep2


title: N2a, siMbnl1_cMBNL1, rep1


title: PS13b.2


title: hESCs, Hour_20

value: 20 hr


title: PS13a.3


title: hESCs, Hour_28

value: 28 hr


title: PS22.7

value: dSC


title: PS13b.1


title: N2a, siFmr1_nMBNL1, rep1

description:
normcnt_DESeq2_input_suna_revision_2023.txt
A3SS.MATS.JC_3.txt
A5SS.MATS.JC_3.txt
MXE.MATS.JC_3.txt
RI.MATS.JC_3.txt
SE.MATS.JC_3.txt

value: siFmr1, FLAG-nuclear MBNL1


title: PS22.5


title: PS22.4


title: N2a, siFmr1_nMBNL1, rep3

value: Neuroblastoma


title: PS13a.1


title: hESCs, Hour_4

value: 4 hr


title: PS22.3


title: hESCs, Hour_12

value: 100ng/mL BMP4 + 5uM IWP2 + RI

value: 12 hr


title: PS22.2


title: hESCs, Hour_0_rep1

value: human embryonic stem cells

value: 0 hr


title: Negative control.9


title: N2a, siMbnl1_pcDNA, rep2

description:
normcnt_DESeq2_input_suna_revision_2023.txt
A3SS.MATS.JC_2.txt
A5SS.MATS.JC_2.txt
MXE.MATS.JC_2.txt
RI.MATS.JC_2.txt
SE.MATS.JC_2.txt

value: siMbnl1, pcDNA


title: PS12b.2


title: PS22.1


title: PS13a.2


title: N2a, siFmr1_nMBNL1, rep2


title: PS21.2

value: PAG


title: PS22.6


title: N2a, siFmr1_pcDNA, rep3

description:
normcnt_DESeq2_input_suna_revision_2023.txt
A3SS.MATS.JC_1.txt
A5SS.MATS.JC_1.txt
MXE.MATS.JC_1.txt
RI.MATS.JC_1.txt
SE.MATS.JC_1.txt

value: siFmr1, pcDNA


title: PS12b.1


title: N2a, siMbnl1_pcDNA, rep1


title: genomic DNA from BLOOD75

type: genomic

city: A Coruña

first: Rosa

last: Fernandez

state: None / N/A

address: Campus Elviña

department: Psychology

country: Spain

institute: University of A Coruña

hyb_protocol: bisulphite converted DNA was amplified  fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing:
Partek® Genomics Suite® v7.19.1018
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: women

tag: genetic sex

tag: group

value: CW

tag: age

tag: onset

value: no

tag: smoking

value: current

tag: drugs

value: never

value: pre


title: N2a, siFmr1_pcDNA, rep2


title: PS12a.2

tag: tissue

value: dSC

value: Neuron


title: N2a, siFmr1_pcDNA, rep1

tag: cell type

value: Neuroblastoma


title: N2a, siNT_pcDNA, rep3

value: siNT, pcDNA


title: PS20.5

tag: genotype


title: PS12a.1


title: genomic DNA from BLOOD73


title: genomic DNA from BLOOD74


title: PS12a.3

value: sSC


title: PS21.1


title: PS20.4


title: PS20.2


title: PS11.6


title: PS11.7


title: N2a, siNT_pcDNA, rep2

tag: cell line


title: genomic DNA from BLOOD68

tag: treatment


title: genomic DNA from BLOOD71


title: PS20.3


title: genomic DNA from BLOOD70

tag: ethnic

value: white


title: genomic DNA from BLOOD69


title: genomic DNA from BLOOD72


title: Cardiac Macrophages Infarct 3

city: Bronx

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

description: 10x Genomics

data_processing:
Cell Ranger (v 3.0.1) were used to align reads of scRNA-seq data to the mouse reference genome (mm10) and transcriptome (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Mouse cardiac interstitial cells from healthy (control) or infarcted (7 days post-infarction) 12-16 week-old mice heart were obtained by enzymatic digestion. Briefly, heart tissue was minced and placed into a cocktail of Liberase TH (125 µg/mL) (Roche) and DNase (20 U/ml) (Sigma) in HBSS++ solution (Hanks balanced salt solution, Gibco) for 10 min at 37°C in an orbital shaker. After enzymatic incubation, tissue was mechanically digested by slowly pipetting to reach a single cell suspension. The supernatant was filtered through a cell strainer (40 μm, nylon; Falcon), the digestion was repeated once or twice with the remaining pieces, and the supernatants were pooled together. The total time for enzymatic digestion was around 30-45 min. Cell suspension was centrifuged for 20 min at 200g with centrifuge brakes deactivated to remove cell debris. Erythrocytes were removed using RBC lysis buffer (eBioscience). Cell suspension was then centrifuged at 500g for 5 min at 4°C, and resuspended in 100 µL of PBS containing 2% FBS and 2.5mM EDTA (sorting buffer). Cells in single cell suspensions were blocked with anti-mouse CD16/CD32 (1:250, BD Biosciences) for 15 minutes at 4°C. In order to identify neutrophils, the cell suspension was incubated for 30 minutes at 4°C in the dark with anti-Ly6G- PerCP/Cyanine5.5 (1:100, BioLegend). Cell suspension was washed twice with PBS/5% FBS, centrifuged at 500g for 5 min at 4°C, and the final pellet was resuspended in 200 µL of sorting buffer. Standard, strict forward scatter width versus area criteria were used to discriminate doublets and gate only singleton cells. Non-neutrophils (Ly6G-) were gated to identify EGFP+ macrophages, which were sorted with the FACSAria Sorter (BD Biosciences) in 1X PBS, 2% FBS.
Single cell RNA-seq libraries were constructed using the Chromium System from 10X Genomics. Single Cell 3' Reagent Kit v3.1 (Single index) was employed for all the samples according to the manufacter's instructions. Briefly, the total of EGFP+/Ly6G- events were sorted in 1X PBS/2% FBS, and the number of cells was quantified in a Neubauer chamber. A maximum of 17,000 cells were loaded at a concentration of 1,000 cells/µL on a Chromium Controller instrument (10X Genomics) to generate single-cell gel bead-in-emulsions (GEMs). In this step, each cell was encapsulated with primers containing a fixed Illumina Read 1 sequence, followed by a cell-identifying 16 bp 10X barcode, a 12 bp Unique Molecular Identifier (UMI) and a poly-dT sequence. A subsequent reverse transcription yielded full-length, barcoded cDNA. This cDNA was then released from the GEMs, PCR-amplified and purified with magnetic beads (SPRIselect, Beckman Coulter). Enzymatic Fragmentation and Size Selection was used to optimize cDNA size prior to library construction. Illumina paired-end adaptor sequences (P5 beginning and P7 end) were added and the resulting library was amplified via end repair, A-tailing, adaptor ligation and PCR. Library quality control and quantification was performed using Qubit 2.0 Fluorometer (ThermoFisher Scientific) and Agilent's 4200 TapeStation System (Agilent), respectively. The libraries were also quantified by real time PCR (KAPA biosystems). Sequencing was performed in a Novaseq 6000 (Illumina) at the recommended configuration (Read1: 150bp; Index i7: 8bp each; Read2: 150bp) at an average depth of 50,000 reads/cell. Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command.

value: Heart

value: Macrophages

value: Surgery (left coronary artery ligation)


title: genomic DNA from BLOOD67


title: PS20.1

data_processing:
Read alignment with STAR (v.2.7.9a)
all downstream analyses were performed in R(v4.0.3)
Sum of exonic and intronic TPM values  were calculated using the scater package (v1.18.6).
Assembly: GRCm39 and Gencode vM27
Supplementary files format and content: comma delimited text, matrix of combined exonic/introinc TPMs

extract_protocol:
The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (doi: 10.7554/eLife.52951; doi: 10.1038/nprot.2017.120) and optimized for speed and coverage of sparsely labelled cells of MADM clones. For details see publication.
cDNA libraries from E10 clones were prepared followed by Smart-seq2 protocol (doi: 10.1038/nprot.2014.006) using custom reagents (VBCF GmbH, Vienna)


title: PS11.5


title: PS11.8


title: genomic DNA from BLOOD66


title: PS11.4


title: Cardiac Macrophages Infarct 1

description: 10x Genomics


title: genomic DNA from BLOOD65


title: N2a, siNT_pcDNA, rep1


title: PS11.3

value: PAG


title: Cardiac Macrophages Infarct 2

description: 10x Genomics


title: Negative control.14


title: N2a, siMbnl1_pcDNA, rep3

value: siMbnl1, pcDNA


title: PS19.11


title: genomic DNA from BLOOD64

value: women


title: PS19.10


title: PS11.2


title: genomic DNA from BLOOD63

value: CW


title: PS19.9


title: Fstl1–/– lung_E18.5

city: Tianjin

first: Wen

last: Ning

address: 94 Weijin Rd

institute: Nankai univercity

description: 10x Genomics

data_processing:
Raw sequencing data (FASTQ format) were aligned to the mouse reference genome (mm10) using the 10X software package CellRanger 6.0
Assembly: mm10
Supplementary files format and content: Seurat object for the gene expressions

source_name: lung

extract_protocol:
Lung specimens were cut into small pieces and then incubated in 2 mL of digestion enzymes [collagenase type IV and dispase II (2 mg/mL)] for 30 min at 37 °C. Flow cytometry was performed to remove cell debris and adhered cells.
Library was performed using 10 x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1)

value: lung


title: genomic DNA from BLOOD62

value: no


title: PS10.4


title: genomic DNA from BLOOD61

value: never


title: WT lung_E18.5

description: 10x Genomics


title: PS19.6


title: PS20.6


title: PS10.3


title: Pericytes 7 days infarction n=3 (1 heart)

description:
10x Genomics
Heart5

data_processing:
Cell Ranger (v 7.0.1) were used to align reads of scRNA-seq data to the mouse reference genome (mm10) and transcriptome (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mouse cardiac interstitial cells from healthy (control) or infarcted (7 days post-infarction) 8-10 week old mice heart were obtained by enzymatic digestion. Erythrocytes were removed using RBC lysis buffer. NG2 lineage cells, Tomato+/CD31-/CD45- cardiac pericytes were FACS-sorted in 1X PBS, 2% FBS.
Single cell RNA-seq libraries were constructed using the Chromium System from 10X Genomics. Single Cell 3' Reagent Kit v3.1 (Dual index) was employed for all the samples according to the manufacter's instructions.

value: Pericytes

value: NG2creER+:R26tdTomato fl/fl

tag: strain background

value: 5 days Tamoxifen

tag: surgery

value: Left coronary artery ligation


title: PS19.8

value: dSC

value: Neuron


title: PS19.7


title: PS11.1


title: Cardiac Macrophages Baseline 1

description: 10x Genomics

value: No surgery


title: Pericytes 7 days infarction n=1 (2 hearts)

description:
10x Genomics
Heart1n2

value: Heart


title: PS19.5

value: sSC


title: genomic DNA from BLOOD59

value: men

value: CM

value: current

value: pre


title: Pericytes Control n=1 (2 hearts)

description:
10x Genomics
Control1n2


title: PS10.2

value: PAG


title: PS19.4


title: genomic DNA from BLOOD58


title: genomic DNA from BLOOD60


title: Negative control.8


title: PS09.4


title: PS10.1


title: Pericytes Control n=2 (2 hearts)

description:
10x Genomics
Control3n4


title: PS19.2


title: PS19.3


title: genomic DNA from BLOOD57


title: PCHiC_48h_bioRep2

city: Tallahassee

first: Peter

last: Fraser

state: FL

address: 319 stadium Drive

institute: Florida State University

library_source: genomic

data_processing:
Hi-C and PCHi-C data were processed using Hi-CUP(v0.7.2) pipeline
Hi-C data was further analysed by Homer and HiC-Explorer
CHICAGO (v1.12.0) pipeline was used to call the significant interactions with CHiCAGO score cut off 5. ChiCdiff package was used to indentify significantly differential interactions. E82
Assembly:  mm10
Supplementary files format and content: HiC interaction matrix hic format(merge biological and technical replicates for each time point) and PCHi-C Significant interactions washU format(merge biological and technical replicates merge biological and technical replicates for each time point)

source_name: C10 (CEBPalpha-ER )

growth_protocol: C10 (CEBPα-ER ) cells were cultured in RPMI 1640 (ThermoFisher, 11875-093) medium supplemented with 10% heat-inactivated FBS (ThermoFisher, A3840202), 1% Penicillin-Streptomycin (ThermoFisher, 15140122), and 50µM 2-Mercaptoethanol (ThermoFisher, 31350010).

extract_protocol:
Cell nuclei were digested by HindIII restriction enzyme, followed by overhangs repair, in-nucleus ligation, and reverse cross-linking overnight. The ligated DNA was extracted using cold ethanol and sodium acetate
Methods for Hi-C and PCHi-C libraries preparation were described in Schoenfelder S et al. J Vis Exp 2018 and He et al. Epigenetics Chromatin 2022. For PCHi-C, SureSelectXT Custom 3-5.9Mb (Agilent, 5190-4831) and SSEL TE Reagent Kit, ILM PE FULL Adaptor (Agilent, 931108) were used for enriching the Hi-C fragments that are associated with promoters.
PCHi-C

treatment_protocol: C10 (CEBPα-ER ) cell differentiation was induced by treatment of 100 nM of β-estradiol (Sigma, E2758-250MG), 10nM IL-3(PEPRO TECH, 213-13), and CSF-1(PEPRO TECH, 315-02)

value: C10 (CEBPalpha-ER )

value: HAFTL derived C10 (CEBPalpha-ER ) cells

value: CEBPalpha-ER transgene

value: Pre-B differentiation


title: Pericytes 7 days infarction n=2 (2 hearts)

description:
10x Genomics
Heart3n4

value: Pericytes

value: NG2creER+:R26tdTomato fl/fl


title: genomic DNA from BLOOD54

value: no

value: never


title: Negative control.13


title: genomic DNA from BLOOD55


title: Negative control.7


title: genomic DNA from BLOOD56


title: PS09.3

value: dSC

value: Neuron


title: PS19.1


title: PS09.2


title: PS18.17


title: PCHiC_12h_bioRep1


title: genomic DNA from BLOOD53


title: PS09.1


title: PCHiC_1h_bioRep2


title: PS18.16


title: genomic DNA from BLOOD52


title: PS08.3


title: genomic DNA from BLOOD51


title: PCHiC_0h_bioRep2


title: PS18.15


title: PCHiC_1h_bioRep1


title: genomic DNA from BLOOD49

value: women

value: TM

value: early


title: genomic DNA from BLOOD50

value: men

value: CM


title: PS18.14

value: sSC


title: PS18.13


title: PS08.1


title: PCHiC_0h_bioRep1


title: PCHiC_48h_bioRep1


title: HiC_48h_bioRep2

extract_protocol:
Cell nuclei were digested by HindIII restriction enzyme, followed by overhangs repair, in-nucleus ligation, and reverse cross-linking overnight. The ligated DNA was extracted using cold ethanol and sodium acetate
Methods for Hi-C and PCHi-C libraries preparation were described in Schoenfelder S et al. J Vis Exp 2018 and He et al. Epigenetics Chromatin 2022. For PCHi-C, SureSelectXT Custom 3-5.9Mb (Agilent, 5190-4831) and SSEL TE Reagent Kit, ILM PE FULL Adaptor (Agilent, 931108) were used for enriching the Hi-C fragments that are associated with promoters.


title: PS18.12


title: PCHiC_12h_bioRep2


title: PS07.4


title: genomic DNA from BLOOD48

value: current

value: pre


title: PS07.3


title: HiC_48h_bioRep1

value: C10 (CEBPalpha-ER )

value: HAFTL derived C10 (CEBPalpha-ER ) cells


title: PS18.11


title: genomic DNA from BLOOD47


title: HiC_12h_bioRep2

value: CEBPalpha-ER transgene

value: Pre-B differentiation


title: genomic DNA from BLOOD46


title: HiC_12h_bioRep1


title: PS07.1


title: PS18.10


title: PS08.2

value: PAG


title: genomic DNA from BLOOD44


title: PS18.9


title: HiC_1h_bioRep2


title: genomic DNA from BLOOD43

value: late


title: Negative control.4


title: Negative control.6


title: HiC_1h_bioRep1


title: Negative control.5


title: PS18.7


title: PS18.8


title: PS18.6


title: genomic DNA from BLOOD42

value: never


title: PS06.2


title: PS18.5


title: genomic DNA from BLOOD41

value: previously


title: PS06.1

value: Neuron


title: PS07.2


title: genomic DNA from BLOOD40

value: women


title: RNA_48h_bioRep3

description:
RNA_TPM.txt.gz
S12

data_processing:
Trim Galore (0.6.2) pipeline was used to remove adapters and short reads from the data.
FastQC program was used to check the quality of the data
Trimmed reads were mapped to mouse reference genome (mm10) using Hisat2 (2.1.0) with default parameters
Read count extraction and normalization were performed using RSEM
Assembly:  mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

extract_protocol:
RNA was harvested using RNAseay mini kit (Qiagen, Cat#74104) . 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina(E7770S) and NEBNext NEBNext® Multiplex Oligos for Illumina® (E7335) following manufacturer's protocols.


title: PS18.4


title: PS05.4


title: genomic DNA from BLOOD45

value: TM


title: RNA_48h_bioRep2

description:
RNA_TPM.txt.gz
S8


title: PS18.3


title: genomic DNA from BLOOD39

value: early


title: PS05.3

value: dSC


title: RNA_48h_bioRep1

description:
RNA_TPM.txt.gz
S7


title: genomic DNA from BLOOD38

value: CW

value: no


title: PS18.2

value: sSC


title: PS05.2


title: HiC_0h_bioRep2


title: RNA_12h_bioRep3

description:
RNA_TPM.txt.gz
S11


title: PS18.1


title: genomic DNA from BLOOD37

value: pre


title: genomic DNA from BLOOD36


title: Negative control.12


title: PS04.10


title: RNA_12h_bioRep1

description:
RNA_TPM.txt.gz
S5

value: C10 (CEBPalpha-ER )


title: RNA_12h_bioRep2

description:
RNA_TPM.txt.gz
S6

value: HAFTL derived C10 (CEBPalpha-ER ) cells


title: PS17.15


title: HiC_0h_bioRep1

value: CEBPalpha-ER transgene


title: genomic DNA from BLOOD34


title: genomic DNA from BLOOD35


title: PS04.8


title: PS17.14


title: PS04.9


title: PS17.13


title: RNA_1h_bioRep3

description:
RNA_TPM.txt.gz
S10

value: Pre-B differentiation


title: RNA_1h_bioRep2

description:
RNA_TPM.txt.gz
S4


title: genomic DNA from BLOOD33


title: genomic DNA from BLOOD32


title: PS17.12


title: PS04.7


title: genomic DNA from BLOOD31

value: unknown


title: PS04.5


title: RNA_0h_bioRep2

description:
RNA_TPM.txt.gz
S2


title: PS05.1


title: PS17.10


title: genomic DNA from BLOOD30

value: men

value: CM


title: RNA_0h_bioRep1

description:
RNA_TPM.txt.gz
S1


title: PS04.4


title: PS17.9


title: PS04.3


title: genomic DNA from BLOOD29

value: never


title: Spleen-shPrmt9, scRNAseq

city: Monrovia

first: Ling

last: Li

state: CA

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

description: 10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger (V6.1.1)'s default settings
Assembly: mm10
Supplementary files format and content: text files containing the raw gene expression count

source_name: Spleen

extract_protocol:
BM and spleen cells in Ctrl and Prmt9-KD mice administered Dox in drinking water over 7 days were collected for analysis. Cells were resuspended as single cells in the presence of 0.4% BSA and loaded onto a 10x Genomics Chromium instrument to generate an emulsion of single-cell gel beads (GEMs). Approximately 5,000-10,000 cells were loaded per channel.
scRNA-seq libraries were prepared using the Chromium™ Single Cell 3′ Library & Gel Bead Kit v2 (PN-120237), Single Cell 3′ Chip Kit v2 (PN-120236) and i7 Multiplex Kit (PN-120262) (10x Genomics, Pleasanton, CA, USA), following the Single Cell 3′ Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A).
Libraries were sequencedon an Illumina HiSeq 4000 system (SY-401–4001, Illumina) as 2 × 150 paired-end reads, one full lane per sample, for >90% sequencing saturation.

value: Spleen cells

value: Spleen

tag: strain

value: 6-8 weeks old


title: PS17.8

first: Florian

last: Pauler

value: Neuron


title: genomic DNA from BLOOD28


title: PS04.2


title: Spleen-Ctrl, scRNAseq

description: 10x Genomics


title: PS17.7


title: genomic DNA from BLOOD26


title: genomic DNA from BLOOD27

value: current


title: RNA_1h_bioRep1

description:
RNA_TPM.txt.gz
S3

tag: time


title: PS17.6


title: PS04.1

value: dSC


title: RNA_0h_bioRep3

description:
RNA_TPM.txt.gz
S9


title: PS03.6


title: PS17.11


title: PS04.6


title: genomic DNA from BLOOD25

tag: gender

value: no


title: genomic DNA from BLOOD24

tag: genetic sex


title: PS17.4

value: sSC


title: N2a, siFmr1, rep3

description:
RNAseq.DE.log2FC_N2a.tsv
N2a.A3SS.MATS.JC.txt
N2a.A5SS.MATS.JC.txt
N2a.MXE.MATS.JC.txt
N2a.RI.MATS.JC.txt
N2a.SE.MATS.JC.txt

extract_protocol:
For RNA extraction, TRIzol was added to the tissue powder and homogenized with Dounce tissue homogenizer. The RNA was treated with TurboDNase (Invitrogen, AM2238) to remove genomic DNA contamination. For peripheral tissues and N2a cells, total RNA was extracted and the integrity analyzed by a fragment analyzer.
For peripheral tissues and N2a cells, total RNA was extracted and the integrity analyzed by a fragment analyzer. Library preparation and RNA sequencing were performed by Novogene (CA, USA). For brain samples, polyadenylated mRNA was enriched using Nextflex Poly(A) Beads (NEXTflex, Bioo Scientific Corp, 512980) and cDNA libraries were prepared using a NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific Corp, NOVA-5130-03D).

treatment_protocol: siRNA targeting Fmr1 was transfected using Lipofectamine 3000.

value: Neuroblastoma


title: PS03.5


title: PS03.4


title: N2a, siFmr1, rep2


title: BM-shPrmt9, scRNAseq

description: 10x Genomics

source_name: Bone marrow

value: Bone marrow cells

value: Bone marrow


title: genomic DNA from BLOOD23

tag: group

value: pre


title: PS03.3


title: PS17.2


title: N2a, siFmr1, rep1


title: genomic DNA from BLOOD22

value: women

value: TM

tag: age

value: late


title: N2a, siNT, rep2

value: siNT


title: PS03.2


title: PS17.1


title: genomic DNA from BLOOD21

value: men

tag: onset

value: never


title: genomic DNA from BLOOD20

value: early

tag: smoking

value: white


title: N2a, siNT, rep1


title: PS03.1

value: Neuron


title: Testis, Fmr1 KO, rep3

description:
RNAseq.DE.log2FC_TE.tsv
TE.A3SS.MATS.JC.txt
TE.A5SS.MATS.JC.txt
TE.MXE.MATS.JC.txt
TE.RI.MATS.JC.txt
TE.SE.MATS.JC.txt

source_name: Testis

value: Testis

value: Fmr1 KO


title: BM-Ctrl, scRNAseq

description: 10x Genomics

value: 6-8 weeks old


title: PS02.6

value: dSC


title: genomic DNA from BLOOD19

tag: drugs


title: PS02.5

tag: tissue


title: Testis, Fmr1 KO, rep2


title: genomic DNA from BLOOD18


title: PS02.4

value: sSC

tag: cell type


title: PS17.3

tag: genotype


title: genomic DNA from BLOOD17

value: current


title: Testis, WT, rep3

value: WT


title: genomic DNA from BLOOD16

value: pre


title: genomic DNA from BLOOD15

value: women


title: Testis, WT, rep2


title: PS02.3


title: Testis, WT, rep1


title: PS02.1


title: genomic DNA from BLOOD14

value: TM


title: Muscle, Fmr1 KO, rep3

description:
RNAseq.DE.log2FC_MU.tsv
MU.A3SS.MATS.JC.txt
MU.A5SS.MATS.JC.txt
MU.MXE.MATS.JC.txt
MU.RI.MATS.JC.txt
MU.SE.MATS.JC.txt

source_name: Muscle

value: Muscle


title: genomic DNA from BLOOD13

value: late


title: PS01.1


title: Muscle, Fmr1 KO, rep2


title: Ob_L2-CRD_27: Pancreatic_islets_HFD_39wk_CRD_2d_rep5

type: RNA

city: Nuthetal

first: Richard

last: Kehm

address: Arthur-Scheunert-Allee 114-116

department: Molecular Toxicology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep5
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
Ob_L2-CRD_27

hyb_protocol: Agilent Gene Expression Hybridization Kit was used according to manufacturer´s instructions. Approximately 600 ng of each cRNA was hybrized on 6x80K microarray at 65°C for 17 minutes using Agilent´s recommended hybridization chamber and oven. After hybridization, microarrays were washed twice, first with Agilent gene expression wash buffer 1 at room temperature for one minute and second with preheated (37°C) Wash Buffer 2 also for one minute.

scan_protocol: Fluorescence signals were detected by SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron.

data_processing: The scanned images were analyzed with Agilent´s Feature Extraction software version 11 to read and process TIFF files, using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: Pancreatic islets, HFD, 39wk + CRD, 2d

label_protocol: Low-input QuickAmp Labeling Kit (Agilent technologies) was used to genereate fluorescent complementary RNA (cRNA). CRNA was labelled with Cyanine 3-CTP (Cy3) and fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following manufacturer's instructions First strand synthesis was conducted by using oligo-dT primer or a mixture of radnom primer/oligo-dT primer. After second strand synthesis, in vitro transcription for cRNA synthesis was performed.

growth_protocol: Mice were housed in open cages of 4-5 animals at a controlled environment (20±2°C, 12/12 h light/dark cycle) with ad libitum access to diets and water.

extract_protocol: RNA extraction was performed by using RNeasy Mini Kit (Quiagen) according to manufacturer´s instructions. Subsequently, DNAase digestion was carried out with nuclease-free DNase (Qiagen), purified using the NucleoSpin RNA Clean-up Kit (Macherey-Nagel). RNA extracts underwent a quality control with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) using RNA 6000 Pico Kit for total RNA samples. Samples with a minimal RNA integrity number (RIN) of > 8.0 were included in microarray analysis.

treatment_protocol: Islet isolation from mice before and after 2 days of CRD feeding was performed as follows. After perfusion by injection of 3 ml Collagenase Type IV from Clostridium histolyticum diluted in Hank´s buffered salt solution (plus 25 mM HEPES, 0,5% BSA) into the common bile duct, the pancreas was digested in 2 ml of collagenase for 10-15 min at 37°C. After mechanical tissue disruption by using a 18G needle, islets were separated from exocrine tissue by manual selection in RPMI 1640 (plus 10% FCS, 2% L-Glutamine, 1% penicillin/streptomycin) and frozen at -80°C.

value: Pancreas

value: male

value: 39 weeks + 2 days

value: B6.V-Lep ob/ob

tag: feeding


title: Ob_L2-CRD_21: Pancreatic_islets_HFD_39wk_CRD_2d_rep3

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep3
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
Ob_L2-CRD_21


title: PS02.2

city: Klosterneuburg

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)

value: Neuron


title: Ob_L2-CRD_25: Pancreatic_islets_HFD_39wk_CRD_2d_rep4

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep4
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
Ob_L2-CRD_25


title: Ob_L2-CRD_20: Pancreatic_islets_HFD_39wk_CRD_2d_rep2

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep2
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
Ob_L2-CRD_20


title: Ob_L2-CRD_18: Pancreatic_islets_HFD_39wk_CRD_2d_rep1

description:
Pancreatic_islets_HFD_39wk_CRD_2d_rep1
Gene expression after 39 weeks of HFD feeding followed by 2-day CRD intervention
Ob_L2-CRD_18


title: Testis, Fmr1 KO, rep1

value: Testis


title: genomic DNA from BLOOD12

value: men

value: never

value: white

tag: treatment


title: Negative control.3


title: Negative control.2


title: genomic DNA from BLOOD10

value: CM

value: no

tag: ethnic


title: Muscle, WT, rep3

value: WT


title: PS01.2

value: sSC


title: Muscle, Fmr1 KO, rep1

value: Fmr1 KO


title: genomic DNA from BLOOD11

value: pre


title: Muscle, WT, rep2

value: Muscle


title: genomic DNA from BLOOD9


title: Negative control.1


title: Muscle, WT, rep1


title: genomic DNA from BLOOD8


title: Ob_L0-HFD_26: Pancreatic_islets_HFD_39wk_rep2

description:
Pancreatic_islets_HFD_39wk_rep2
Gene expression after 39 weeks of HFD feeding
Ob_L0-HFD_26

source_name: Pancreatic islets, HFD, 39wk

value: 39 weeks

value: 39 weeks of HFD feeding


title: Ob_L0-HFD_29: Pancreatic_islets_HFD_39wk_rep5

description:
Pancreatic_islets_HFD_39wk_rep5
Gene expression after 39 weeks of HFD feeding
Ob_L0-HFD_29

value: Pancreas

value: male


title: Ob_K2-CRD_35: Pancreatic_islets_HFD_18wk_CRD_2d_rep4

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep4
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
Ob_K2-CRD_35

source_name: Pancreatic islets, HFD, 18wk + CRD, 2d

value: 18 weeks + 2 days

value: B6.V-Lep ob/ob


title: PS17.5

value: Neuron


title: Ob_L0-HFD_28: Pancreatic_islets_HFD_39wk_rep4

description:
Pancreatic_islets_HFD_39wk_rep4
Gene expression after 39 weeks of HFD feeding
Ob_L0-HFD_28


title: Ob_L0-HFD_25: Pancreatic_islets_HFD_39wk_rep1

description:
Pancreatic_islets_HFD_39wk_rep1
Gene expression after 39 weeks of HFD feeding
Ob_L0-HFD_25


title: Ob_K2-CRD_36: Pancreatic_islets_HFD_18wk_CRD_2d_rep5

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep5
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
Ob_K2-CRD_36


title: Ob_L0-HFD_27: Pancreatic_islets_HFD_39wk_rep3

description:
Pancreatic_islets_HFD_39wk_rep3
Gene expression after 39 weeks of HFD feeding
Ob_L0-HFD_27


title: genomic DNA from BLOOD7

value: men


title: Ob_K2-CRD_34: Pancreatic_islets_HFD_18wk_CRD_2d_rep3

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep3
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
Ob_K2-CRD_34


title: Liver, Fmr1 KO, rep3

description:
RNAseq.DE.log2FC_LV.tsv
LV.A3SS.MATS.JC.txt
LV.A5SS.MATS.JC.txt
LV.MXE.MATS.JC.txt
LV.RI.MATS.JC.txt
LV.SE.MATS.JC.txt

source_name: Liver

value: Liver


title: A20 fl/fl DPI10 EAE rep 1

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

data_processing:
Quality control on the sequencing data was performed with the FastQC tool (version 0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA sequencing reads were aligned to the ENSEMBL Mus_musculus.GRCm38 reference genome. The corresponding annotation (ENSEMBL v76) was also retrieved from ENSEMBL FTP website.
The STAR aligner (version 2.6.1a) was used to perform mapping to the reference genome.
Alignments were processed with the featureCounts function of the Rsubread package (version 2.10.0) using the annotation file also used for supporting the alignment.
The exploration, modeling, and interpretation of the expression data followed the protocols defined by Ludt et. al (2022).
Exploratory data analysis was performed with the pcaExplorer package (version 2.22.0).
Differential expression analysis was performed with DESeq2 package (version 1.36.0), setting the false discovery rate (FDR) cutoff to 0.05. Accurate estimation of the effect sizes (described as log2 fold change) was performed using the apeglm shrinkage estimator (version 1.18.0).
Gene expression profiles were plotted as heatmaps (color-coded standardized z-scores for the expression values, after regularized logarithm transformation) to enable comparison across samples, created with the GeneTonic package.
For functional annotation of Gene Ontology (GO) and analysis of KEGG pathway enrichment, the web-based DAVID 2021 tool was used.
Assembly: GRCm38
Supplementary files format and content: comma-delimited text file includes the expression values for all genes as a count matrix, used for the statistical modeling

source_name: Spinal cord

extract_protocol:
RNA was isolated from 500 sorted endothelial cells with the Qiagen RNeasy Plus Micro Kit
RNA was quantified with a Qubit 2.0 fluorometer (Thermo Fisher Scientific) and RNA quality was assessed on a Bioanalyzer 2100 (Agilent) using a RNA 6000 Pico chip (Agilent).
Samples with an RNA integrity number (RIN) of > 8 were used for full-length cDNA synthesis using the SMART-Seqâ v4 Ultraâ Low Input Kit (Takara).
1 ng of the resulting cDNA was used for library preparation with a Nextera XT DNA Sample Prep Kit according to the manufacturer's instructions (Illumina).
Quantity was assessed using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay

value: Spinal cord

value: Endothelial cells

value: A20 fl/fl x SLC Cre -

value: Tamoxifen + MOG/CFA + PTx


title: A20 fl/fl DPI10 EAE rep 2


title: Liver, Fmr1 KO, rep2


title: genomic DNA from BLOOD6

value: CM

value: no

value: never

value: white


title: Liver, WT, rep2

value: WT


title: A20 fl/fl DPI10 EAE rep 3


title: Liver, Fmr1 KO, rep1

value: Fmr1 KO


title: Liver, WT, rep3


title: A20∆BEC naive rep 1

value: A20 fl/fl x SLC-Cre +

value: Tamoxifen


title: A20∆BEC naive rep 2


title: A20∆BEC naive rep 3


title: genomic DNA from BLOOD4

value: women

value: CW

value: pre


title: Ob_K2-CRD_30: Pancreatic_islets_HFD_18wk_CRD_2d_rep2

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep2
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
Ob_K2-CRD_30

value: Pancreas

value: male

value: 18 weeks + 2 days

value: B6.V-Lep ob/ob


title: A20fl/fl naive rep 3

value: Spinal cord

value: Endothelial cells

value: A20 fl/fl x SLC Cre -


title: Ob_K0-HFD_36: Pancreatic_islets_HFD_18wk_rep4

description:
Pancreatic_islets_HFD_18wk_rep4
Gene expression after 18 weeks of HFD feeding
Ob_K0-HFD_36

source_name: Pancreatic islets, HFD, 18wk

value: 18 weeks

value: 18 weeks of HFD feeding


title: Ob_K0-HFD_35: Pancreatic_islets_HFD_18wk_rep3

description:
Pancreatic_islets_HFD_18wk_rep3
Gene expression after 18 weeks of HFD feeding
Ob_K0-HFD_35


title: genomic DNA from BLOOD5

value: no

value: never

value: white


title: Ob_K0-HFD_37: Pancreatic_islets_HFD_18wk_rep5

description:
Pancreatic_islets_HFD_18wk_rep5
Gene expression after 18 weeks of HFD feeding
Ob_K0-HFD_37


title: Ob_K2-CRD_29: Pancreatic_islets_HFD_18wk_CRD_2d_rep1

description:
Pancreatic_islets_HFD_18wk_CRD_2d_rep1
Gene expression after 18 weeks of HFD feeding followed by 2-day CRD intervention
Ob_K2-CRD_29


title: genomic DNA from BLOOD2


title: genomic DNA from BLOOD1


title: A20fl/fl naive rep 1


title: A20fl/fl naive rep 2


title: Cerebellum, Fmr1 KO, rep3

description:
RNAseq.DE.log2FC_Brain.tsv
CB.A3SS.MATS.JC.txt
CB.A5SS.MATS.JC.txt
CB.MXE.MATS.JC.txt
CB.RI.MATS.JC.txt
CB.SE.MATS.JC.txt

source_name: Cerebellum

value: Cerebellum

value: Fmr1 KO


title: bsf_31

status: Public on Nov 02 2023

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
Bloodstream form obtained from cell culture
count_table_bsf_processed
count_table_bsf_unprocessed

data_processing:
After demultiplexing, data quality was examined using FastQC (version 0.11.7). Illumina adaptors were removed using cutadapt (version 3.2). For the separately generated and processed BSF data, the quality check and adapter trimming was performed using bbduk (version 38.96). Trimmed reads were mapped to the TREU927 (version 48) genome with the ERCC spike-in sequences included, using RNASTAR (version 2.6.1b) as well as kallisto | bustools specifically for BSF data. Read counts for each gene were determined using featureCounts (version 2.0.1) and genes with ≥ 5 aligned reads were considered detected. For MCF, 4h, 12h, 24h and 7d, only those scRNAseq datasets with > 200 and < 1000 detected genes and a library size between 2 x 105 and 2 x 106 reads were considered for analysis. For BSF, the upper threshold of < 1000 genes per scRNAseq dataset was raised to < 2100 due to the overall higher number of detected genes. This difference between the BSF data and the other data sets was considered in all downstream analyses. Principal component analysis (PCA) was performed selecting the 1000 genes with the highest variance. The following libraries were excluded from the analysis due to BARP gene expression: "0h_1_B5_1", "0h_1_G2", "0h_1_C5_1". Differential gene expression analysis was conducted with DESeq2 (version 1.30.0) and SCDE (version 2.18.0; only used in early vs. late analysis). Features with an absolute log2 fold change > 2 and adjusted P value < 0.01 (DEseq2) or a z-score > 1.96 (SCDE) were considered as differentially expressed, respectively.
For the filtered table: The matrix contains pre-normalised counts of 11,707 genes across 31 cells. A library size cut-off of 2.5e06 has been applied to it. The raw data have been aligned and quantified using STAR and featureCounts.
For the unprocessed table: The matrix contains pre-normalised counts of 11,707 genes across 32 cells. The raw data have been aligned and quantified using STAR and featureCounts.
Assembly: Genome_build: Tbrucei TREU927 version 48 and human GRCh38
Supplementary files format and content: matrix

organism: Trypanosoma brucei

source_name: Bloodstream form

extract_protocol:
After natural infection, skin equivalents were cultured for another 4 h, 12 h, 24 h, and 7 d, respectively. In addition, freshly collected MCFs obtained from tsetse flies and cultured BSFs were used. Skin equivalents were dissociated and single viable parasites were sorted based on their tdTomato and Calcein AM signal with a FACSAria III cytometer (BD Biosciences) into 48-well plates containing 2.6 µl of 1x lysis buffer (Takara) supplemented with 0.01 µl of RNase inhibitor (40 U/µl; Takara). Immediately after sorting, cells were placed on ice for 5 min and stored at -80 °C.
After natural infection, skin equivalents were cultured for another 4 h, 12 h, 24 h, and 7 d, respectively. In addition, freshly collected MCFs obtained from tsetse flies and cultured BSFs were used. Skin equivalents were dissociated and single viable parasites were sorted based on their tdTomato and Calcein AM signal with a FACSAria III cytometer (BD Biosciences) into 48-well plates containing 2.6 µl of 1x lysis buffer (Takara) supplemented with 0.01 µl of RNase inhibitor (40 U/µl; Takara). Immediately after sorting, cells were placed on ice for 5 min and stored at -80 °C. Library preparation and sequencing was carried out as described previously (Muller et al., 2018). Briefly, 0.2 µl of a 1:20 x 106 dilution of ERCC Spike-in Control Mix 1 (Thermo Fisher Scientific) were added to the lysates of single parasites and libraries were prepared using SMART-Seq v.4 Ultra Low Input RNA Kit (Takara) using a quarter of the reagent volumes recommended by the manufacturer. 27 cycles were used for PCR amplification and cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter) using 15 μl of elution buffer (Takara). Library quantification was performed with a Qubit 3 Fluorometer with dsDNA Hs Assay kit (Life Technologies) and the quality of the libraries was assessed using a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). 0.5 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using a quarter of the recommended volumes, 10 min for tagmentation at 55 °C and 1 min extension time during PCR amplification. Libraries were pooled and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina’s NextSeq 500.

value: Bloodstream form


title: bsf_32


title: genomic DNA from BLOOD3

value: women

value: CW


title: bsf_28


title: bsf_29


title: bsf_22


title: bsf_27


title: bsf_26


title: bsf_20


title: bsf_25


title: bsf_23


title: bsf_30


title: bsf_19


title: bsf_21


title: Liver, WT, rep1

value: Liver

value: WT


title: Ob_K0-HFD_34: Pancreatic_islets_HFD_18wk_rep2

description:
Pancreatic_islets_HFD_18wk_rep2
Gene expression after 18 weeks of HFD feeding
Ob_K0-HFD_34

value: Pancreas

value: male


title: bsf_17


title: bsf_18


title: Ob_K0-HFD_30: Pancreatic_islets_HFD_18wk_rep1

description:
Pancreatic_islets_HFD_18wk_rep1
Gene expression after 18 weeks of HFD feeding
Ob_K0-HFD_30

value: B6.V-Lep ob/ob


title: bsf_16


title: bsf_15


title: bsf_11


title: bsf_12


title: bsf_14


title: bsf_10


title: bsf_9


title: bsf_8


title: bsf_24


title: bsf_7


title: bsf_6


title: bsf_5


title: bsf_4


title: bsf_1


title: bsf_13


title: bsf_2


title: bsf_3


title: Ol73_4w_H

city: ÅS

first: Gerrit

last: Timmerhaus

address: Osloveien 1

country: Norway

institute: Nofima AS

hyb_protocol: standard Agilent protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Salmo salar

source_name: olfactory organ

label_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

extract_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: time point

value: 4 weeks

value: high H2S concentration


title: Ol65_4w_L

value: low H2S concentration


title: Ol64_4w_L


title: Ol74_4w_H


title: Ol70_4w_L


title: Ol67_4w_L


title: Ol76_4w_H


title: Ol80_4w_H


title: Ol68_4w_L


title: Ol71_4w_L


title: Ol62_4w_C

value: control


title: Ol55_4w_C


title: Ol47_2w_H

value: 2 weeks


title: Ol77_4w_H


title: Ol49_2w_H


title: Ol53_2w_H


title: Ol43_2w_L


title: Ol58_4w_C


title: Ol44_2w_L


title: Ol46_2w_H


title: Ol52_2w_H


title: Ol79_4w_H


title: Ol41_2w_L


title: Ol40_2w_L


title: Ol50_2w_H


title: Ol59_4w_C


title: Ol61_4w_C


title: Ol56_4w_C


title: 8K,rep1

city: La Jolla

first: Songpeng

last: Zu

address: 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Paired-end sequencing reads were demultiplexed and the cell index transferred to the read name. Sequencing reads were aligned to mm10 reference genome using bwa.
We combined the sequencing reads to fragments with the function make_fragment_file in SnapATAC2. , and for each fragment we followed the quality controls: 1) Keep only fragments with quality scores MAPQ > 30; 2) remove PCR duplicates. Reads were also sorted based on cell barcodes in read names, and shifted +4 bp for positive strand and -5 bp for negative strand to correct the 9-bp duplication induced from Tn5 transposase.
We used the function filter_cells in SnapATAC2 to calculate TSSenrichment (TSSe). Nuclei with >=1,000 uniquely mapped fragments and TSSe >= 10 were filtered for each of 234 samples by following the ENCODE ATAC-seq data standards and process pipeline(https://www.encodeproject.org/atac-seq/). We used the function filter_cells in SnapATAC2 to filter out cells.
We applied a modified version of Scrublet to remove potential doublets for every sample independently using SnapATAC2. Firstly, we used the function of add_tile_matrix to add the 500-bp genomic bin features, then used the function of select_features to filter out the features with the frequencies along the samples lower than 0.5% or higher than 99.5%. Then applied the function of scrublet in SnapATAC2 to get the doublet scores. The parameter expected_doublet_rate is set to 0.08, which is based on our previous experiment on the snATAC-seq pipeline. Barcodes with the scrublet scores larger than 0.5 will be treated as potential doublets, and then removed from our analysis.
Assembly: Genome_build: mm10 (GRCm38)
Supplementary files format and content: SnapATAC2 HDF5 matrix files (cells with the raw fragments, 500bp bmat)

source_name: brain

extract_protocol:
Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56-63 day old mice and sectioned into 600 µm coronal sections along the anterior-posterior axis in ice-cold dissection media. Specific brain regions were dissected according to the Allen Brain Reference Atlas (Wang, Q. et al. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell (2020). https://doi.org:10.1016/j.cell.2020.04.007). For each region, dissected brain tissues were pooled from 2-31 male C57BL/6J mice  to obtain enough nuclei for single nucleus ATAC-seq for each biological replica, and two biological replicas were performed.
Brain nuclei were pelleted with a swinging bucket centrifuge (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei pellets were resuspended in 1 ml nuclei permeabilization buffer (5% BSA, 0.2% IGEPAL-CA630, 1 mM DTT and cOmpleteTM, EDTA-free protease inhibitor cocktail (Roche) in PBS) and pelleted again (500g, 5 min, 4 °C; 5920R, Eppendorf). Nuclei were resuspended in 500 μl high-salt tagmentation buffer (36.3 mM Tris-acetate (pH 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% dimethylformamide) and counted using a haemocytometer. Concentration was adjusted to 1,000–4,500 nuclei per 9 μl, and 1,000–4,500 nuclei were dispensed into each well of a 96-well plate. For tagmentation, 1 μl barcoded Tn5 transposomes26 were added using a BenchSmart 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 μl of 40 mM EDTA was added to each well with a BenchSmart 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 μl 2× sort buffer (2% BSA, 2 mM EDTA in PBS) were added using a BenchSmart 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 μM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 nuclei were sorted per well into eight 96-well plates (total of 768 wells, 30,720 nuclei total, 15,360 nuclei per sample) containing 10.5 μl EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). If processing two samples per day, tagmentation was performed with different sets of barcodes in separate 96 well plates. After tagmentation nuclei from individual plates were pooled together. Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After the addition of 1 μl 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). Then, 1 μl 12.5% Triton X-100 was added to each well to quench the SDS. Next, 12.5 μl NEBNext High-Fidelity 2 × PCR Master Mix (NEB) were added and samples were amplified by PCR (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72 °C 60 s) × 11 or 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life Technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries generated with indexing version 1 were sequenced on a HiSeq2500 sequencer (Illumina) using custom sequencing primers, 25% spike-in library and following read lengths: 50 + 43 + 37 + 50 (Read1 + Index1 + Index2 + Read2). Libraries generated with indexing version 2 were sequenced on a Libraries were sequenced on a HiSeq 4000 (Illumina) or a NovaSeq 6000 (Illumina) with these settings:  50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

value: brain

tag: tissue region

value: HY

tag: number of_animals_pooled

tag: Sex

value: Male

value: 8-9 weeks old

tag: library type

value: ATAC-seq


title: 7J,rep2

tag: strain


title: 6H,rep1


title: 8K,rep2


title: 6H,rep2


title: 15B,rep1

value: CB


title: Ol35_2w_C


title: Ol38_2w_L


title: 10H,rep2

value: MB


title: Ol34_2w_C


title: 7J,rep1


title: 16C,rep2

value: MY


title: 13E,rep1

value: Pons


title: 14D,rep2


title: 12F,rep2


title: Ol28_2w_C


title: Ol32_2w_C


title: Ol37_2w_L


title: Ol31_2w_C


title: 13E,rep2


title: B9.F.KO

city: Houston

first: Caleb

middle: A

last: Wood

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: NanoString Neuropathology probes.

scan_protocol: Scanned in a NanoString nCounter.

data_processing: Samples were processed by NanoString under standard procedures (MAN-C0035-08) and mRNA detected with the mouse Neuropathology nCounter gene panel (NanoString, XT-CSO-MNROP1-12). Expression data was analyzed by NanoString using nSolver software (version 4.0). Functional analysis was performed using Cytoscape (v3.9.1) and stringApp (v2.0.0). Differentially expressed genes were first identified using the cutoff p < 0.05. Genes were then clustered using functional interactions using stringApp with a confidence cutoff of 0.50, and the largest initial cluster was selected for visualization. The top functional enrichment pathways from either GO Cellular component or GO Biological Process were plotted in Prism (v10.0.1) using FDR values calculated in stringApp.

source_name: Brain cortex

label_protocol: RNA samples were hybridized with the NanoString nCounter Mouse Neuropathology panel and processed according to the NanoString manual MAN-10023-11.

growth_protocol: Mice were maintained in accordance with institutional and IACUC polices. Access to food and water was ad libitum.

extract_protocol: Animals between 2.5-3.5 mo of age (n=6 per genotype) were euthanized with CO2, brains removed, and tissue hemisected along the midline to isolate the rostral aspect of the frontal cortex.  Approximately 40-50 mg of frontal cortex tissue per sample was snap frozen on dry ice and stored at -80 oC until use. RNA extraction was done with the PureLink RNA Mini Kit (Life Technologies, 12183018A) paired with the PureLink DNase Set (Fisher, 12185010) to eliminate DNA contamination. RNA integrity was determined by the 260/280 ratio with a Nanodrop spectrometer and stored at -80 oC until use.

treatment_protocol: Samples were untreated prior to extraction aside from genetic manipulation.

value: F

tag: mouseline

value: TMEM106B tm2c x TMEM106B tm2c

value: KO

value: brain cortex

value: 12 wks


title: Ol29_2w_C


title: B8.F.KO

tag: age


title: B7.M.WT

value: M

value: WT


title: B6.F.WT


title: 17A,rep1


title: 14B,rep2


title: B5.M.WT


title: 18B,rep1


title: B4.M.KO


title: B3.M.KO


title: 15C,rep1


title: 13C,rep2


title: B2.M.WT


title: 17B,rep1


title: B11.F.WT


title: B1.F.KO


title: 12J,rep2


title: 13F,rep2


title: 14A,rep1


title: 13F,rep1


title: B10.F.WT


title: B12.M.KO


title: 17A,rep2


title: A9.F.KI

value: TMEM106B T186S x B6

value: KI


title: 11G,rep1

value: brain


title: 12G,rep1

value: Male


title: 11J,rep1

value: 8-9 weeks old


title: A8.F.WT


title: 16C,rep1

value: ATAC-seq


title: 12G,rep2


title: A6.F.KI


title: 16A,rep1

value: CB


title: A3.F.WT


title: A5.M.WT


title: A7.F.KI


title: 10D,rep2

value: HPF


title: A4.M.KI


title: A12.M.WT


title: A2.F.WT


title: 17B,rep2

value: MY


title: 12J,rep1

value: Pons


title: A10.M.KI


title: A1.M.KI


title: 15B,rep2


title: 15C,rep2


title: 18A,rep2


title: MCF10A_HSF1_rep2

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

institute: University of Bergen

data_processing:
Raw RNA-Seq reads were aligned to human genome hg38 in a Bash environment using hisat2 v 2.0.5. with Ensembl genes transcriptome reference. Aligned files were processed using Samtools (v. 1.13).
Reads aligned in the coding regions of the genome were counted using FeatureCounts (v. 1.6.5).
Read counts were normalized using DESeq2 (v. 1.32.0) , then normalized expression values were subject to differential analysis (mean-based fold change) in the R/Bioconductor programming environment.
Assembly: hg38
Supplementary files format and content: text, counts of reads per gene
Supplementary files format and content: text, DESeq2 normalized vailes and fold changes

growth_protocol: MCF10A were cultured in DMEM/F12 medium supplemented with 5% horse serum, 5 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF, and cholera toxin.

extract_protocol:
Total RNA was isolated using the Direct-ZolTM RNA MiniPrep Kit (Zymo Research) and digested with DNase I (Worthington Biochemical Corporation)
Illumina Total RNA Prep with Ribo-Zero Plus was used (according to the manufacturer's protocol) to prepare cDNA libraries.

tag: cell line

value: non-tumorigenic human breast epithelial

value: HSF1 overexpression


title: 16A,rep2


title: MCF10A_WT_rep2


title: MCF10A_HSF1_rep1


title: 10J,rep2

value: MB


title: COVID19_37

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Standard Illumina Protocol

data_processing:
R
Normalized by ssNoob normalization average beta values

label: Cy5 and Cy3

extract_protocol: Genomic DNA was extracted and purified from the different samples using Qiagen DNeasy Kit according to standard instructions

value: lung

tag: condition


title: COVID19_36


title: COVID19_34


title: COVID19_35


title: 14D,rep1


title: COVID19_32


title: COVID19_31

value: Female


title: COVID19_30


title: 18B,rep2


title: COVID19_33


title: 6G,rep2

value: STR


title: COVID19_28


title: COVID19_29


title: A11.M.WT

value: M

value: WT

value: brain cortex

value: 12 wks


title: 12H,rep2

value: brain

value: Male


title: COVID19_27


title: 7D,rep2

value: OLF

value: 8-9 weeks old

value: ATAC-seq


title: COVID19_26


title: 11H,rep2


title: 9E,rep1


title: 12C,rep2

value: Isocortex


title: 13C,rep1


title: COVID19_24


title: 14A,rep2


title: MCF10A_WT_rep1


title: 12H,rep1


title: COVID19_23


title: 8D,rep1


title: 11K,rep2


title: 9Kb,rep2

value: TH


title: 9Ka,rep2


title: COVID19_21


title: COVID19_20


title: COVID19_19


title: COVID19_18


title: 11H,rep1


title: COVID19_15


title: 7D,rep1


title: COVID19_14


title: 8L,rep2


title: COVID19_13


title: 8G,rep2


title: COVID19_25


title: COVID19_11


title: 12C,rep1


title: COVID19_10


title: COVID19_08


title: COVID19_09


title: COVID19_07


title: COVID19_06


title: COVID19_22


title: 7E,rep2


title: 6G,rep1


title: 7F,rep2

value: PAL


title: 9F,rep2


title: 11K,rep1


title: 9Kb,rep1


title: COVID19_03


title: COVID19_16


title: 14B,rep1

value: CB


title: COVID19_04


title: COVID19_02


title: 11J,rep2

value: MB


title: COVID19_01

value: lung


title: COVID19_12


title: Control_17

value: Control


title: 18A,rep1


title: 11G,rep2


title: Control_16


title: Control_18

value: Female


title: 10J,rep1


title: 10H,rep1


title: Control_15


title: Control_14


title: 8G,rep1


title: COVID19_05


title: 12F,rep1


title: 10D,rep1

value: HPF


title: Control_13


title: Control_12


title: Control_11


title: 9F,rep1


title: Control_09


title: Control_07


title: Control_08


title: 8L,rep1


title: Control_05


title: Control_06


title: 7E,rep1


title: Control_03


title: 9E,rep2


title: 9Ka,rep1


title: Control_04


title: 6F,rep2


title: Control_02


title: 8D,rep2


title: 7F,rep1


title: 9L,rep1

value: HY


title: R1-AD1 FLAGHAH3F3A cells, HA Ab, rep2

city: Gainesville

first: Alberto

last: Riva

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads were mapped to the GRCh38 human genome reference using Bowtie2.
ChIP-Seq peak calling was performed with MACS v2.2.7.1. with default parameters.
Assembly: GRCh38
Supplementary files format and content: MACS output file containing peak locations and fold enrichment.

source_name: R1-AD1 FLAGHA-H3F3A

growth_protocol: Cells were propogated in RPMI-1640 medium suplemented with 10% FBS, 1X penicillin/streptomycin at  5% CO2, 37C . Cells were plated in RPMI-1640 without phenol-red, suplemented with 10%CSS, 72 h before the experiment.

extract_protocol:
Cells were fixed with 1% formaldehyde in PBS for 10 min at RT, quenched with glycine (f.c. 0.125 M) for 5 min. After cell lysis chromatin was sheared by Diagenode Bioraptor Pico with peak enrichment at 200 bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

treatment_protocol: Cells were treated with 1 nM R1881 for 4, 12 or 24 hours

value: R1-AD1 FLAGHA-H3F3A

value: Prostate cancer

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene

tag: chip antibody

value: HA (BioLegend, # 901502)

value: EtOH


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, HA Ab, rep 2


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 12 h, HA Ab, rep1


title: R1-AD1 FLAGHA-H3F3A cells, R1881, 4 h, HA Ab, rep 1


title: R1-AD1 FLAGHA-H3F3A cells, HA Ab, rep1


title: Control_10

tag: tissue


title: Mouse, Db 12 (ATAC-seq)

city: Shanghai

first: Anxiang

last: Cai

state: None Selected

address: No.1630 dongfang road, pudong new district

institute: Department of Nephrology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China

data_processing:
Library quality was checked using the High Sensitivity DNA Analysis Kit (Agilent, 5067-4626). Last, 2 X 150 paired-end sequencing was performed on an Illumina Nova seq (Illumina, San Diego, CA).
Alignment and peak-calling of ATAC sequencing data were performed using the ENCODE-DCC ATAC-Seq pipeline. Briefly, data were aligned to the mouse reference genome (mm10) using Bowtie2. Aligned data were filtered for PCR duplicates, blacklisted regions, and shifted +4bp for the + strand and -5bp for the - strand. Peaks were called using MACS2. Differential peak calling was performed using Diffbind. Motif enrichment was performed using Hypergeometric Optimization of the Motif EnRichment program (HOMER) version 4.1.
Assembly: mm10
Supplementary files format and content: bed, MACS calling peaks

source_name: Kidney

extract_protocol:
Briefly, a total of 20,000 cells per sample was washed twice with 50 µL of cold Dulbecco's Phosphate-Buffered Saline and re-suspended in 50 µL of lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 µL of transposition reaction mix of TruePrep DNA Library Prep Kit V2 for Illumina. Samples were then incubated at 37°C for 30 min. DNA was isolated using the QIAquick PCR Purification Kit (QIAGEN, 28106).
ATAC-seq libraries were first subjected to five cycles of pre-amplification using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, M0541S). To determine the suitable number of cycles required for the second round of PCR, the library was assessed by qPCR using NEBNext High-Fidelity 2X PCR Master Mix with SYBR Green I Nucleic Acid Gel Stain (Thermo Fisher Scientific, S7563) and then PCR amplified for the appropriate number of cycles. Libraries were purified with the QIAquick PCR Purification Kit.

value: Kidney

value: db/db

value: Dapagliflozin


title: HIRA_4h_2

description: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, rep2

data_processing:
Reads were mapped to the GRCh38 human genome reference using Bowtie2.
ATAC peak calling was performed with MACS v2.2.7.1. with parameters appropriate for ATAC-Seq data.
Assembly: GRCh38
Supplementary files format and content: MACS output file containing peak locations and fold enrichment.

source_name: R1-AD1 FLAGHA-H3F3A, HIRA KO

extract_protocol:
Samples were prepared using ATAC-seq kit from Active Motif (Active Motif, CA, #53150) according to the manual.
Samples were prepared using ATAC-seq kit from Active Motif (Active Motif, CA, #53150) according to the manual.

treatment_protocol: Cells were treated with 1 nM R1881 for 4 or 12 h

value: R1-AD1 FLAGHA-H3F3A, HIRA KO

tag: cell type

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, HIRA KO


title: Mouse, Db 11 (ATAC-seq)

tag: genotype


title: HIRA_4h_1

description: R1-AD1 FLAGHA-H3F3A cells, HIRA KO, rep1


title: Mouse, Db 10 (ATAC-seq)


title: Mouse, Db 9 (ATAC-seq)


title: DAXX_4h_2

description: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, rep2

source_name: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: R1-AD1 FLAGHA-H3F3A, DAXX KO

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene, DAXX KO


title: Mouse, Db 8 (ATAC-seq)


title: DAXX_4h_1

description: R1-AD1 FLAGHA-H3F3A cells, DAXX KO, rep1


title: AR_4h_2

description: R1-AD1 FLAGHA-H3F3A cells, AR KO, rep2

source_name: R1-AD1 FLAGHA-H3F3A, AR KO

value: R1-AD1 FLAGHA-H3F3A, AR KO

value: FLAG-HA knock-in 5' ORF of H3F3A gene, AR KO


title: Mouse, Db 6 (ATAC-seq)

value: Normal


title: Mouse, Db 7 (ATAC-seq)


title: AR_4h_1

description: R1-AD1 FLAGHA-H3F3A cells, AR KO, rep1


title: Mouse, Db 4 (ATAC-seq)


title: IC4_4h_2

description: R1-AD1 FLAGHA-H3F3A, EtOH, biol rep 2

value: Prostate cancer cells


title: Mouse, Db 5 (ATAC-seq)


title: 6F,rep1

value: brain

value: PAL

value: Male

value: 8-9 weeks old

value: ATAC-seq


title: Control_01

value: lung

value: Control


title: 9L,rep2

value: HY


title: HIRA_CNT_2

value: Prostate cancer

value: EtOH


title: Mouse, Db 3 (ATAC-seq)

value: Kidney

value: db/db


title: IC4_4h_1

description: R1-AD1 FLAGHA-H3F3A, EtOH, biol rep 1

value: R1-AD1 FLAGHA-H3F3A

value: AR WT, FLAG-HA knock-in 5' ORF of H3F3A gene


title: Mouse, Db 2 (ATAC-seq)