title: gd15_Nrf2KO3, pancreatic isltes, pregnant (gestational day 15), tamoxifen treatment

city: Duarte

first: Sharon

last: Baumel Alterzon

address: 1500 East Duarte road

department: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute

institute: City of Hope

description: Library name: gd15_Nrf2KO3

data_processing:
Read quality was determined by using fastqc (version 0.11.9). All samples passed the quality assessment and were proceesed for read alignment to ENSEMBL Mus musculus GRcm39/mm39 by using star aligner (version 2.7.10a) amd samtools (version 1.17) for creating the bam files. Raw gene counts were finally generated by using subread (version 2.0.1).
Assembly: GRcm39/mm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: pancreatic Islets

growth_protocol: Two-month-old female mice where fed ad libitum with a standard chow diet.

extract_protocol:
Mouse pancreatic islets were isolated after collagenase P (Sigma-Aldrich 11213865001) injection through the pancreatic duct, followed by digestion and separation by density gradient using Histopaque-1077 (Sigma-Aldrich 10771). Total RNA was extracted from pancreatic islets by using the RNeasy Micro Kit (QIAGEN, Germantown, MD, USA)
RNA was quantified by Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and integrity checked with TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). rRNA depletion libraries were prepared using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany) and NEBNext Ultra II RNA Library Preparation Kit for Illumina HiSeq (NEB, Ipswich, MA, USA). Libraries were validated using the Agilent TapeStation 4200 and quantified by Qubit 2.0 Fluorometer and quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Samples were sequenced with a 2x150bp paired-end configuration

treatment_protocol: Female mice were injected intraperitoneally for 5 consecutive days with either corn oil or 75 mg/kg tamoxifen (no. T5648; Sigma-Aldrich) dissolved in corn oil. For the pregnant groups, after injections, both corn oil and tamoxifen injected females were left to recover for 30 days to allow tamoxifen washout (in tamoxifen-treated animals) before mating.

value: pancreatic Islets

value: beta cells-specific Nrf2-KO

tag: treatment

value: tamoxifen


title: gd15_Nrf2KO2, pancreatic isltes, pregnant (gestational day 15), tamoxifen treatment

status: Public on Mar 07 2025

type: SRA

state: California

country: USA

description: Library name: gd15_Nrf2KO2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: batch


title: gd15_control4, pancreatic isltes, pregnant (gestational day 15), vehicle treatment

description: Library name: gd15_control4

value: wild type

value: vehicle (oil)


title: gd15_Nrf2KO1, pancreatic isltes, pregnant (gestational day 15), tamoxifen treatment

description: Library name: gd15_Nrf2KO1


title: gd15_control1, pancreatic isltes, pregnant (gestational day 15), vehicle treatment

description: Library name: gd15_control1


title: 3803_WC_3

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

data_processing:
Raw sequencing reads were aligned to the hg19 genome reference using our in-house pipeline (https://github.com/ndu-UCSD/LJI_RNA_SEQ_PIPELINE_V2). Briefly, FASTQ files were merged and filtered using fastp (v0.20.1), reads were aligned using STAR (v2.7.3a) and further processed using SAMtools (v0.1.19–44428cd), bamCoverage (v3.3.1), and Qualimap (v.2.2.2-dev). From this pipeline, raw counts and transcripts per million (TPM) reads were provided as output. Lowly expressed genes were removed for subsequent analysis (<=10 raw read counts). Differential expression was assessed using the DESeq2 Bioconductor package (v1.36.0)(56) in an R v4.2.1 environment with gene expression called differential with an FDR<0.05. Before fold change calculations, the 5% TPM quantile was calculated per gene and batch year (2021 and 2022) to prevent inflated fold change estimates caused by measurements close to zero. For genes of which the 5% quantile was equal to zero, TPM+0.1 was applied before fold change calculations. Spearman correlation analysis was performed using the correlation package (v0.8.4)(57). Pathway enrichment analysis was performed using Metascape and the Gene Ontology (GO) gene sets(58). Motif enrichment analysis was performed using HOMER findMotifs.pl (v4.11.1) with all genes with at least 10 raw counts as background(59).
Assembly: hg38
Supplementary files format and content: "2021 2022 PBMC gene expression raw_count.csv" contains raw count values per sample and gene
Supplementary files format and content: "2021 2022 PBMC gene expression tpm.csv" contains TPM values per sample and gene

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
2 million PBMC were lysed using QIAzol Lysis Reagent (Qiagen). Samples were stored at -80C until RNA extraction. RNA was extracted using the miRNeasy Mini Kit (Qiagen) including DNase treatment according to the manufacturer's instructions. The Smart-seq2 protocol was used to perform full-length bulkRNAseq. Briefly, RNA was captured using oligo-poly(dT)-30 primers and reverse transcription was performed using 50-template switching oligos (LNA technologies, Exicon). cDNA was pre-amplified using PCR and purified twice by magnetic beads (volume ratio 0.6x and 0.8x Ampure-XP magnetic beads, Beckman Coulter). cDNA was measured using capillary electrophoresis (Fragment analyzer, Advance analytical).
0.5 ng of cDNA was used to generate indexed Illumina libraries (Nextera XT library preparation kit, Illumina). Each library's fragment size was measured by capillary electrophoresis (Fragment analyzer, Advance analytical) and was quantified (Picogreen, Thermofisher). Libraries were pooled at equal molar concentration and sequenced paired-end to a minimum depth of 15 million reads with each a length of 100 base pairs.

value: Blood

value: PBMC

tag: infancy vaccine

value: wP

tag: donor

tag: days post_booster


title: np_Nrf2KO5, pancreatic isltes, Nrf2-KO, tamoxifen treatment

description: Library name: np_Nrf2KO5


title: np_Nrf2KO6, pancreatic isltes, Nrf2-KO, tamoxifen treatment

description: Library name: np_Nrf2KO6


title: np_Nrf2KO4, pancreatic isltes, Nrf2-KO, tamoxifen treatment

description: Library name: np_Nrf2KO4


title: np_control4, pancreatic isltes, non-pregnant, vehicle treatment

description: Library name: np_control4


title: np_control5, pancreatic isltes, non-pregnant, vehicle treatment

description: Library name: np_control5


title: np_control2, pancreatic isltes, non-pregnant, vehicle treatment

description: Library name: np_control2


title: np_control6, pancreatic isltes, non-pregnant, vehicle treatment

description: Library name: np_control6


title: MG Cell SLX-20064.i729_i521,batch3

city: Paris

first: Calvin

last: Rodrigues

address: 26 Rue d Ulm

department: CdR

country: France

institute: Institut Curie

library_source: transcriptomic single cell

data_processing:
Reads were trimmed with trim Galore (v0.6.5) in order to remove adapter sequences and Ns nucleotides from both side of the read.
Cleaned reads were aligned onto a concatenated genome (the Mouse reference genome GRCm38 (mm10)  + fasta file with the ERCC spike-in sequences) with STAR (v2.7.7a). ERCC spike-in and gene quantification was performed using HTSeq (0.13.5), generating raw gene counts matrices.
ENSEMBL gene ids were converted to gene symbols using biomart (v2.56.1), using mouse genome annotation GRCm38, using the following settings: (biomart = 'genes', dataset = 'mmusculus_gene_ensembl',version = 102).
Single cell Gene counts and metadata were imported and analyzed in R (v4.3.0) using Seurat (4.3.0.1). 3 batches of single cell RNA-Seq data were first processed individually, and then integrated.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited files with raw gene counts, metadata
Supplementary files format and content: RDS file, Seurat object (Integrated batch 1,2,3)

source_name: Mammary gland

extract_protocol:
Single cells were index-sorted individually by FACS (BDFacs ARIA) into wells of a 96-well PCR plate containing 2.3 µl of lysis buffer (200U/µL SUPERase-IN (LifeTechnologies), 10% Triton X100, RNAse free H2O). scRNA-seq SMARTseq2 was performed as previously described (Picelli et al., 2014). The Illumina Nextera XT DNA kit was used to prepare libraries that were sequenced on the Illumina HiSeq 4000 (single end 50bp reads for batch 1 and 2, paired-end 50bp for batch 3 ).
Illumina Nextera XT DNA kit, library was constructed following manufacturer recommendations.

value: Mammary gland

value: Intermediate GFP+

tag: genotype


title: MG Cell SLX-20064.i729_i522,batch3


title: MG Cell SLX-20064.i729_i520,batch3


title: MG Cell SLX-20064.i729_i517,batch3


title: MG Cell SLX-20064.i729_i516,batch3


title: MG Cell SLX-20064.i728_i522,batch3


title: MG Cell SLX-20064.i729_i518,batch3


title: MG Cell SLX-20064.i729_i513,batch3

value: Basal Cell GFP-


title: MG Cell SLX-20064.i728_i521,batch3


title: gd15_control3, pancreatic isltes, pregnant (gestational day 15), vehicle treatment

description: Library name: gd15_control3


title: gd15_Nrf2KO4, pancreatic isltes, pregnant (gestational day 15), tamoxifen treatment

description: Library name: gd15_Nrf2KO4


title: gd15_control2, pancreatic isltes, pregnant (gestational day 15), vehicle treatment

description: Library name: gd15_control2


title: MG Cell SLX-20064.i728_i518,batch3


title: MG Cell SLX-20064.i729_i515,batch3

value: Basal Cell GFP+


title: MG Cell SLX-20064.i727_i521,batch3


title: MG Cell SLX-20064.i727_i518,batch3


title: MG Cell SLX-20064.i728_i517,batch3


title: MG Cell SLX-20064.i727_i516,batch3


title: MG Cell SLX-20064.i727_i520,batch3


title: MG Cell SLX-20064.i728_i516,batch3


title: MG Cell SLX-20064.i727_i522,batch3


title: MG Cell SLX-20064.i728_i515,batch3


title: MG Cell SLX-20064.i728_i513,batch3


title: MG Cell SLX-20064.i727_i517,batch3


title: MG Cell SLX-20064.i728_i520,batch3


title: MG Cell SLX-20064.i727_i515,batch3


title: MG Cell SLX-20064.i727_i513,batch3


title: MG Cell SLX-20064.i726_i522,batch3


title: MG Cell SLX-20064.i726_i520,batch3


title: MG Cell SLX-20064.i726_i521,batch3


title: MG Cell SLX-20064.i726_i518,batch3


title: MG Cell SLX-20064.i724_i522,batch3


title: MG Cell SLX-20064.i726_i517,batch3


title: MG Cell SLX-20064.i726_i513,batch3


title: MG Cell SLX-20064.i726_i516,batch3


title: MG Cell SLX-20064.i726_i515,batch3


title: MG Cell SLX-20064.i724_i517,batch3


title: MG Cell SLX-20064.i723_i517,batch3


title: MG Cell SLX-20064.i723_i522,batch3


title: MG Cell SLX-20064.i724_i521,batch3


title: MG Cell SLX-20064.i724_i520,batch3


title: MG Cell SLX-20064.i724_i513,batch3


title: MG Cell SLX-20064.i722_i522,batch3


title: MG Cell SLX-20064.i724_i515,batch3


title: MG Cell SLX-20064.i724_i518,batch3


title: MG Cell SLX-20064.i724_i516,batch3


title: MG Cell SLX-20064.i723_i520,batch3


title: MG Cell SLX-20064.i722_i521,batch3


title: MG Cell SLX-20064.i723_i518,batch3


title: MG Cell SLX-20064.i723_i516,batch3


title: MG Cell SLX-20064.i723_i513,batch3


title: MG Cell SLX-20064.i723_i521,batch3


title: MG Cell SLX-20064.i722_i520,batch3


title: MG Cell SLX-20064.i722_i518,batch3


title: MG Cell SLX-20064.i722_i517,batch3


title: MG Cell SLX-20064.i723_i515,batch3


title: MG Cell SLX-20064.i722_i516,batch3

value: Intermediate GFP-


title: MG Cell SLX-20064.i721_i520,batch3


title: MG Cell SLX-20064.i722_i515,batch3

value: Luminal cell GFP+


title: MG Cell SLX-20064.i721_i522,batch3


title: MG Cell SLX-20064.i721_i518,batch3


title: MG Cell SLX-20064.i722_i513,batch3

value: Luminal cell GFP-


title: MG Cell SLX-20064.i721_i521,batch3


title: MG Cell SLX-20064.i719_i515,batch3


title: MG Cell SLX-20064.i721_i516,batch3


title: MG Cell SLX-20064.i719_i513,batch3


title: MG Cell SLX-20064.i720_i518,batch3


title: MG Cell SLX-20064.i720_i516,batch3


title: MG Cell SLX-20064.i720_i521,batch3


title: MG Cell SLX-20064.i721_i513,batch3


title: MG Cell SLX-20064.i721_i515,batch3


title: MG Cell SLX-20064.i721_i517,batch3


title: MG Cell SLX-20064.i719_i521,batch3


title: MG Cell SLX-20064.i720_i522,batch3


title: MG Cell SLX-20064.i720_i520,batch3


title: MG Cell SLX-20064.i719_i516,batch3


title: MG Cell SLX-20064.i719_i522,batch3


title: MG Cell SLX-20064.i720_i515,batch3


title: MG Cell SLX-20064.i720_i513,batch3


title: MG Cell SLX-20064.i719_i520,batch3


title: MG Cell SLX-20064.i720_i517,batch3


title: MG Cell SLX-20064.i719_i517,batch3


title: MG Cell SLX-20064.i719_i518,batch3


title: MG Cell SLX-20064.i718_i522,batch3


title: MG Cell SLX-20064.i718_i520,batch3


title: MG Cell SLX-20064.i718_i521,batch3


title: MG Cell SLX-20064.i718_i517,batch3


title: MG Cell SLX-20064.i718_i518,batch3


title: MG Cell SLX-20064.i718_i516,batch3


title: MG Cell SLX-20064.i718_i515,batch3


title: MG Cell SLX-20064.i718_i513,batch3


title: MG Cell SLX-20064.i716_i521,batch3


title: MG Cell SLX-20064.i715_i511,batch3


title: MG Cell SLX-20064.i716_i516,batch3


title: MG Cell SLX-20064.i716_i522,batch3


title: MG Cell SLX-20064.i716_i513,batch3


title: MG Cell SLX-20064.i716_i518,batch3


title: MG Cell SLX-20064.i715_i505,batch3


title: MG Cell SLX-20064.i715_i516,batch3


title: MG Cell SLX-20064.i715_i508,batch3


title: MG Cell SLX-20064.i715_i520,batch3


title: MG Cell SLX-20064.i715_i507,batch3


title: MG Cell SLX-20064.i715_i510,batch3


title: MG Cell SLX-20064.i715_i518,batch3


title: MG Cell SLX-20064.i716_i517,batch3


title: MG Cell SLX-20064.i714_i520,batch3


title: MG Cell SLX-20064.i715_i517,batch3


title: MG Cell SLX-20064.i715_i513,batch3


title: MG Cell SLX-20064.i715_i506,batch3


title: MG Cell SLX-20064.i715_i503,batch3


title: MG Cell SLX-20064.i715_i515,batch3


title: MG Cell SLX-20064.i715_i502,batch3


title: MG Cell SLX-20064.i716_i520,batch3


title: MG Cell SLX-20064.i716_i515,batch3


title: MG Cell SLX-20064.i714_i518,batch3


title: MG Cell SLX-20064.i714_i517,batch3


title: MG Cell SLX-20064.i714_i516,batch3


title: MG Cell SLX-20064.i714_i515,batch3


title: MG Cell SLX-20064.i714_i511,batch3


title: MG Cell SLX-20064.i714_i508,batch3


title: MG Cell SLX-20064.i714_i510,batch3


title: MG Cell SLX-20064.i714_i505,batch3


title: MG Cell SLX-20064.i714_i507,batch3


title: MG Cell SLX-20064.i712_i520,batch3


title: MG Cell SLX-20064.i714_i506,batch3


title: MG Cell SLX-20064.i712_i518,batch3


title: MG Cell SLX-20064.i714_i503,batch3


title: MG Cell SLX-20064.i712_i506,batch3


title: MG Cell SLX-20064.i712_i503,batch3


title: MG Cell SLX-20064.i712_i511,batch3


title: MG Cell SLX-20064.i712_i517,batch3


title: MG Cell SLX-20064.i712_i505,batch3


title: MG Cell SLX-20064.i712_i513,batch3


title: MG Cell SLX-20064.i712_i507,batch3


title: MG Cell SLX-20064.i711_i518,batch3


title: MG Cell SLX-20064.i712_i502,batch3


title: MG Cell SLX-20064.i711_i517,batch3


title: MG Cell SLX-20064.i712_i508,batch3


title: MG Cell SLX-20064.i714_i513,batch3


title: MG Cell SLX-20064.i711_i513,batch3


title: MG Cell SLX-20064.i711_i511,batch3


title: MG Cell SLX-20064.i712_i510,batch3


title: MG Cell SLX-20064.i711_i515,batch3


title: MG Cell SLX-20064.i711_i510,batch3


title: MG Cell SLX-20064.i711_i520,batch3


title: MG Cell SLX-20064.i712_i515,batch3


title: MG Cell SLX-20064.i711_i516,batch3


title: MG Cell SLX-20064.i711_i508,batch3


title: MG Cell SLX-20064.i711_i507,batch3


title: MG Cell SLX-20064.i714_i502,batch3


title: MG Cell SLX-20064.i711_i503,batch3


title: MG Cell SLX-20064.i710_i520,batch3


title: MG Cell SLX-20064.i711_i502,batch3


title: MG Cell SLX-20064.i710_i517,batch3


title: MG Cell SLX-20064.i710_i518,batch3


title: MG Cell SLX-20064.i710_i507,batch3


title: MG Cell SLX-20064.i710_i505,batch3


title: MG Cell SLX-20064.i710_i502,batch3


title: MG Cell SLX-20064.i710_i511,batch3


title: MG Cell SLX-20064.i711_i505,batch3


title: MG Cell SLX-20064.i707_i510,batch3


title: MG Cell SLX-20064.i707_i516,batch3


title: MG Cell SLX-20064.i710_i510,batch3


title: MG Cell SLX-20064.i710_i503,batch3


title: MG Cell SLX-20064.i707_i520,batch3


title: MG Cell SLX-20064.i710_i513,batch3


title: MG Cell SLX-20064.i707_i513,batch3


title: MG Cell SLX-20064.i707_i515,batch3


title: MG Cell SLX-20064.i707_i517,batch3


title: MG Cell SLX-20064.i707_i508,batch3


title: MG Cell SLX-20064.i707_i507,batch3


title: MG Cell SLX-20064.i707_i506,batch3


title: MG Cell SLX-20064.i707_i511,batch3


title: MG Cell SLX-20064.i710_i516,batch3


title: MG Cell SLX-20064.i707_i518,batch3


title: MG Cell SLX-20064.i710_i506,batch3


title: MG Cell SLX-20064.i707_i503,batch3


title: MG Cell SLX-20064.i710_i515,batch3


title: MG Cell SLX-20064.i711_i506,batch3


title: MG Cell SLX-20064.i707_i502,batch3


title: MG Cell SLX-20064.i710_i508,batch3


title: MG Cell SLX-20064.i707_i505,batch3


title: MG Cell SLX-20064.i706_i518,batch3


title: MG Cell SLX-20064.i706_i520,batch3


title: MG Cell SLX-20064.i712_i516,batch3


title: MG Cell SLX-20064.i706_i516,batch3


title: MG Cell SLX-20064.i706_i517,batch3


title: MG Cell SLX-20064.i706_i515,batch3


title: MG Cell SLX-20064.i706_i511,batch3


title: MG Cell SLX-20064.i706_i505,batch3


title: MG Cell SLX-20064.i706_i507,batch3


title: MG Cell SLX-20064.i705_i503,batch3


title: MG Cell SLX-20064.i706_i502,batch3


title: MG Cell SLX-20064.i705_i506,batch3


title: MG Cell SLX-20064.i705_i505,batch3


title: MG Cell SLX-20064.i704_i520,batch3


title: MG Cell SLX-20064.i706_i506,batch3


title: MG Cell SLX-20064.i706_i513,batch3


title: MG Cell SLX-20064.i705_i520,batch3


title: MG Cell SLX-20064.i705_i510,batch3


title: MG Cell SLX-20064.i706_i510,batch3


title: MG Cell SLX-20064.i706_i503,batch3


title: MG Cell SLX-20064.i705_i517,batch3


title: MG Cell SLX-20064.i705_i508,batch3


title: MG Cell SLX-20064.i705_i513,batch3


title: MG Cell SLX-20064.i705_i511,batch3


title: MG Cell SLX-20064.i705_i507,batch3


title: MG Cell SLX-20064.i705_i516,batch3


title: MG Cell SLX-20064.i705_i518,batch3


title: MG Cell SLX-20064.i706_i508,batch3


title: MG Cell SLX-20064.i704_i517,batch3


title: MG Cell SLX-20064.i704_i516,batch3


title: MG Cell SLX-20064.i704_i518,batch3


title: MG Cell SLX-20064.i705_i515,batch3


title: MG Cell SLX-20064.i704_i513,batch3


title: MG Cell SLX-20064.i704_i515,batch3


title: MG Cell SLX-20064.i704_i511,batch3


title: MG Cell SLX-20064.i704_i510,batch3


title: MG Cell SLX-20064.i704_i505,batch3


title: MG Cell SLX-20064.i703_i518,batch3


title: MG Cell SLX-20064.i704_i503,batch3


title: MG Cell SLX-20064.i703_i517,batch3


title: MG Cell SLX-20064.i703_i516,batch3


title: MG Cell SLX-20064.i704_i507,batch3


title: MG Cell SLX-20064.i704_i502,batch3


title: MG Cell SLX-20064.i703_i520,batch3


title: MG Cell SLX-20064.i703_i513,batch3


title: MG Cell SLX-20064.i703_i515,batch3


title: MG Cell SLX-20064.i703_i508,batch3


title: MG Cell SLX-20064.i703_i507,batch3


title: MG Cell SLX-20064.i703_i510,batch3


title: MG Cell SLX-20064.i703_i511,batch3


title: MG Cell SLX-20064.i705_i502,batch3


title: MG Cell SLX-20064.i703_i505,batch3


title: MG Cell SLX-20064.i703_i503,batch3


title: MG Cell SLX-20064.i703_i506,batch3


title: MG Cell SLX-20064.i703_i502,batch3


title: MG Cell SLX-20064.i702_i520,batch3


title: MG Cell SLX-20064.i702_i516,batch3


title: MG Cell SLX-20064.i702_i518,batch3


title: MG Cell SLX-20064.i702_i515,batch3


title: MG Cell SLX-20064.i702_i517,batch3


title: MG Cell SLX-20064.i702_i511,batch3


title: MG Cell SLX-20064.i702_i510,batch3


title: MG Cell SLX-20064.i702_i513,batch3


title: MG Cell SLX-20064.i702_i508,batch3


title: MG Cell SLX-20064.i704_i506,batch3


title: MG Cell SLX-20064.i704_i508,batch3


title: MG Cell SLX-20064.i701_i520,batch3


title: MG Cell SLX-20064.i702_i507,batch3


title: MG Cell SLX-20064.i702_i505,batch3


title: MG Cell SLX-20064.i702_i502,batch3


title: MG Cell SLX-20064.i701_i518,batch3


title: MG Cell SLX-20064.i701_i517,batch3


title: MG Cell SLX-20064.i701_i511,batch3


title: MG Cell SLX-20064.i701_i513,batch3


title: MG Cell SLX-20064.i701_i516,batch3


title: MG Cell SLX-20064.i701_i515,batch3


title: MG Cell SLX-20064.i701_i510,batch3


title: MG Cell SLX-20064.i701_i508,batch3


title: MG Cell SLX-20064.i701_i507,batch3


title: MG Cell SLX-20064.i701_i503,batch3


title: MG Cell SLX-20064.i701_i505,batch3


title: MG Cell SLX-20064.i701_i506,batch3


title: MG Cell SLX-20064.i701_i502,batch3


title: MG Cell SLX-14936.i729_i521,batch2


title: MG Cell SLX-14936.i729_i517,batch2


title: MG Cell SLX-20064.i702_i506,batch3


title: MG Cell SLX-14936.i729_i515,batch2


title: MG Cell SLX-14936.i729_i520,batch2


title: MG Cell SLX-14936.i729_i516,batch2


title: MG Cell SLX-14936.i729_i508,batch2


title: MG Cell SLX-14936.i729_i507,batch2


title: MG Cell SLX-14936.i729_i522,batch2


title: MG Cell SLX-14936.i729_i505,batch2


title: MG Cell SLX-14936.i729_i506,batch2


title: MG Cell SLX-14936.i729_i511,batch2


title: MG Cell SLX-14936.i728_i518,batch2


title: MG Cell SLX-14936.i729_i510,batch2


title: MG Cell SLX-14936.i728_i522,batch2


title: MG Cell SLX-14936.i728_i521,batch2


title: MG Cell SLX-14936.i729_i502,batch2


title: MG Cell SLX-14936.i729_i518,batch2


title: MG Cell SLX-14936.i729_i513,batch2


title: MG Cell SLX-14936.i728_i516,batch2


title: MG Cell SLX-14936.i729_i503,batch2


title: MG Cell SLX-14936.i728_i515,batch2


title: MG Cell SLX-14936.i728_i520,batch2


title: MG Cell SLX-20064.i702_i503,batch3


title: MG Cell SLX-14936.i728_i513,batch2


title: MG Cell SLX-14936.i728_i511,batch2


title: MG Cell SLX-14936.i728_i510,batch2


title: MG Cell SLX-14936.i728_i517,batch2


title: MG Cell SLX-14936.i728_i508,batch2


title: MG Cell SLX-14936.i728_i507,batch2


title: MG Cell SLX-14936.i728_i503,batch2


title: MG Cell SLX-14936.i727_i517,batch2


title: MG Cell SLX-14936.i728_i506,batch2


title: MG Cell SLX-14936.i727_i521,batch2


title: MG Cell SLX-14936.i727_i513,batch2


title: MG Cell SLX-14936.i727_i511,batch2


title: MG Cell SLX-14936.i727_i516,batch2


title: MG Cell SLX-14936.i726_i522,batch2


title: MG Cell SLX-14936.i728_i505,batch2


title: MG Cell SLX-14936.i727_i502,batch2


title: MG Cell SLX-14936.i727_i515,batch2


title: MG Cell SLX-14936.i727_i506,batch2


title: MG Cell SLX-14936.i726_i520,batch2


title: MG Cell SLX-14936.i727_i505,batch2


title: MG Cell SLX-14936.i726_i518,batch2


title: MG Cell SLX-14936.i727_i518,batch2


title: MG Cell SLX-14936.i726_i516,batch2


title: MG Cell SLX-14936.i727_i503,batch2


title: MG Cell SLX-14936.i727_i508,batch2


title: MG Cell SLX-14936.i727_i507,batch2


title: MG Cell SLX-14936.i726_i513,batch2


title: MG Cell SLX-14936.i726_i517,batch2


title: MG Cell SLX-14936.i727_i520,batch2


title: MG Cell SLX-14936.i726_i515,batch2


title: MG Cell SLX-14936.i726_i511,batch2


title: MG Cell SLX-14936.i726_i510,batch2


title: MG Cell SLX-14936.i728_i502,batch2


title: MG Cell SLX-14936.i727_i510,batch2


title: MG Cell SLX-14936.i726_i521,batch2


title: MG Cell SLX-14936.i726_i508,batch2


title: MG Cell SLX-14936.i727_i522,batch2


title: MG Cell SLX-14936.i726_i505,batch2


title: MG Cell SLX-14936.i726_i507,batch2


title: MG Cell SLX-14936.i726_i503,batch2


title: MG Cell SLX-14936.i726_i502,batch2


title: MG Cell SLX-14936.i724_i522,batch2


title: MG Cell SLX-14936.i724_i518,batch2


title: MG Cell SLX-14936.i724_i517,batch2


title: MG Cell SLX-14936.i724_i521,batch2


title: MG Cell SLX-14936.i724_i516,batch2


title: MG Cell SLX-14936.i724_i520,batch2


title: MG Cell SLX-14936.i724_i511,batch2


title: MG Cell SLX-14936.i724_i515,batch2


title: MG Cell SLX-14936.i724_i505,batch2


title: MG Cell SLX-14936.i724_i507,batch2


title: MG Cell SLX-14936.i724_i506,batch2


title: MG Cell SLX-14936.i724_i502,batch2


title: MG Cell SLX-14936.i724_i508,batch2


title: MG Cell SLX-14936.i723_i522,batch2


title: MG Cell SLX-14936.i724_i503,batch2


title: MG Cell SLX-14936.i723_i521,batch2


title: MG Cell SLX-14936.i726_i506,batch2


title: MG Cell SLX-14936.i723_i518,batch2


title: MG Cell SLX-14936.i723_i520,batch2


title: MG Cell SLX-14936.i723_i517,batch2


title: MG Cell SLX-14936.i724_i510,batch2


title: MG Cell SLX-14936.i724_i513,batch2


title: MG Cell SLX-14936.i723_i516,batch2


title: MG Cell SLX-14936.i723_i513,batch2


title: MG Cell SLX-14936.i723_i511,batch2


title: MG Cell SLX-14936.i723_i507,batch2


title: MG Cell SLX-14936.i723_i510,batch2


title: MG Cell SLX-14936.i723_i508,batch2


title: MG Cell SLX-14936.i723_i515,batch2


title: MG Cell SLX-14936.i723_i505,batch2


title: MG Cell SLX-14936.i723_i503,batch2


title: MG Cell SLX-14936.i723_i502,batch2


title: MG Cell SLX-14936.i722_i522,batch2


title: MG Cell SLX-14936.i722_i520,batch2


title: MG Cell SLX-14936.i722_i521,batch2


title: MG Cell SLX-14936.i722_i518,batch2


title: MG Cell SLX-14936.i722_i517,batch2


title: MG Cell SLX-14936.i722_i507,batch2


title: MG Cell SLX-14936.i722_i506,batch2


title: MG Cell SLX-14936.i722_i503,batch2


title: MG Cell SLX-14936.i721_i521,batch2


title: MG Cell SLX-14936.i722_i513,batch2


title: MG Cell SLX-14936.i722_i515,batch2


title: MG Cell SLX-14936.i721_i511,batch2


title: MG Cell SLX-14936.i721_i515,batch2


title: MG Cell SLX-14936.i722_i516,batch2


title: MG Cell SLX-14936.i722_i505,batch2


title: MG Cell SLX-14936.i722_i510,batch2


title: MG Cell SLX-14936.i721_i522,batch2


title: MG Cell SLX-14936.i722_i511,batch2


title: MG Cell SLX-14936.i721_i517,batch2


title: MG Cell SLX-14936.i721_i510,batch2


title: MG Cell SLX-14936.i722_i502,batch2


title: MG Cell SLX-14936.i723_i506,batch2


title: MG Cell SLX-14936.i721_i508,batch2


title: MG Cell SLX-14936.i721_i516,batch2


title: MG Cell SLX-14936.i721_i520,batch2


title: MG Cell SLX-14936.i722_i508,batch2


title: MG Cell SLX-14936.i721_i506,batch2


title: MG Cell SLX-14936.i721_i507,batch2


title: MG Cell SLX-14936.i721_i513,batch2


title: MG Cell SLX-14936.i721_i505,batch2


title: MG Cell SLX-14936.i721_i502,batch2


title: MG Cell SLX-14936.i720_i522,batch2


title: MG Cell SLX-14936.i720_i520,batch2


title: MG Cell SLX-14936.i720_i521,batch2


title: MG Cell SLX-14936.i720_i518,batch2


title: MG Cell SLX-14936.i720_i517,batch2


title: MG Cell SLX-14936.i720_i515,batch2


title: MG Cell SLX-14936.i720_i516,batch2


title: MG Cell SLX-14936.i720_i511,batch2


title: MG Cell SLX-14936.i720_i508,batch2


title: MG Cell SLX-14936.i720_i513,batch2


title: MG Cell SLX-14936.i721_i518,batch2


title: MG Cell SLX-14936.i720_i510,batch2


title: MG Cell SLX-14936.i720_i507,batch2


title: MG Cell SLX-14936.i719_i520,batch2


title: MG Cell SLX-14936.i719_i517,batch2


title: MG Cell SLX-14936.i720_i503,batch2


title: MG Cell SLX-14936.i720_i506,batch2


title: MG Cell SLX-14936.i719_i522,batch2


title: MG Cell SLX-14936.i719_i521,batch2


title: MG Cell SLX-14936.i719_i518,batch2


title: MG Cell SLX-14936.i720_i502,batch2


title: MG Cell SLX-14936.i721_i503,batch2


title: MG Cell SLX-14936.i719_i515,batch2


title: MG Cell SLX-14936.i719_i516,batch2


title: MG Cell SLX-14936.i719_i511,batch2


title: MG Cell SLX-14936.i719_i513,batch2


title: MG Cell SLX-14936.i719_i508,batch2


title: MG Cell SLX-14936.i719_i507,batch2


title: MG Cell SLX-14936.i720_i505,batch2


title: MG Cell SLX-14936.i719_i506,batch2


title: MG Cell SLX-14936.i719_i505,batch2


title: MG Cell SLX-14936.i719_i510,batch2


title: MG Cell SLX-14936.i719_i503,batch2


title: MG Cell SLX-14936.i718_i522,batch2


title: MG Cell SLX-14936.i718_i520,batch2


title: MG Cell SLX-14936.i719_i502,batch2


title: MG Cell SLX-14936.i718_i521,batch2


title: MG Cell SLX-14936.i718_i518,batch2


title: MG Cell SLX-14936.i718_i517,batch2


title: MG Cell SLX-14936.i718_i515,batch2


title: MG Cell SLX-14936.i718_i513,batch2


title: MG Cell SLX-14936.i718_i511,batch2


title: MG Cell SLX-14936.i718_i507,batch2


title: MG Cell SLX-14936.i718_i508,batch2


title: MG Cell SLX-14936.i718_i506,batch2


title: MG Cell SLX-14936.i718_i503,batch2


title: MG Cell SLX-14936.i718_i502,batch2


title: MG Cell SLX-14936.i716_i522,batch2


title: MG Cell SLX-14936.i718_i510,batch2


title: MG Cell SLX-14936.i716_i521,batch2


title: MG Cell SLX-14936.i716_i511,batch2


title: MG Cell SLX-14936.i716_i510,batch2


title: MG Cell SLX-14936.i716_i508,batch2


title: MG Cell SLX-14936.i716_i518,batch2


title: MG Cell SLX-14936.i716_i505,batch2


title: MG Cell SLX-14936.i716_i506,batch2


title: MG Cell SLX-14936.i716_i515,batch2


title: MG Cell SLX-14936.i716_i507,batch2


title: MG Cell SLX-14936.i716_i520,batch2


title: MG Cell SLX-14936.i716_i513,batch2


title: MG Cell SLX-14936.i716_i516,batch2


title: MG Cell SLX-14936.i716_i502,batch2


title: MG Cell SLX-14936.i716_i503,batch2


title: MG Cell SLX-14936.i715_i511,batch2


title: MG Cell SLX-14936.i718_i516,batch2


title: MG Cell SLX-14936.i715_i507,batch2


title: MG Cell SLX-14936.i715_i505,batch2


title: MG Cell SLX-14936.i715_i510,batch2


title: MG Cell SLX-14936.i715_i508,batch2


title: MG Cell SLX-14936.i718_i505,batch2


title: MG Cell SLX-14936.i715_i503,batch2


title: MG Cell SLX-14936.i715_i502,batch2


title: MG Cell SLX-14936.i716_i517,batch2


title: MG Cell SLX-14936.i714_i511,batch2


title: MG Cell SLX-14936.i715_i506,batch2


title: MG Cell SLX-14936.i714_i506,batch2


title: MG Cell SLX-14936.i714_i505,batch2


title: MG Cell SLX-14936.i714_i507,batch2


title: MG Cell SLX-14936.i714_i510,batch2


title: MG Cell SLX-14936.i712_i506,batch2


title: MG Cell SLX-14936.i712_i503,batch2


title: MG Cell SLX-14936.i714_i502,batch2


title: MG Cell SLX-14936.i711_i506,batch2


title: MG Cell SLX-14936.i712_i510,batch2


title: MG Cell SLX-14936.i711_i511,batch2


title: MG Cell SLX-14936.i711_i508,batch2


title: MG Cell SLX-14936.i711_i503,batch2


title: MG Cell SLX-14936.i712_i508,batch2


title: MG Cell SLX-14936.i711_i510,batch2


title: MG Cell SLX-14936.i712_i511,batch2


title: MG Cell SLX-14936.i712_i502,batch2


title: MG Cell SLX-14936.i712_i505,batch2


title: EGFR-RFP Screen Bulk

city: South San Francisco

first: Kirill

last: Bersuker

state: CA

address: 1130 Veterans Blvd.

institute: Calico Life Sciences

description: Library name: EGFR-RFP Screen Bulk

library_source: genomic

data_processing:
MAGeCK v0.5.9.4 was used to normalize the read counts by the median sgRNA count values, calculate fold changes and determine statistical significance.
Assembly: GenCODE Release 21 corresponding to Genome assembly version GRCh38
Supplementary files format and content: .Txt files showing MAGeCK scores, fold changes, and statistical significance values when comparing gene respresentation in samples from sorted but bulk samples.
Supplementary files format and content: .Txt files showing normalized counts for individual sgRNAs isolated from sorted and bulk samples.
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: Ovarian cancer

growth_protocol: For the EGFR-RFP and Her2-GFP BiDAC screens, RTK-FP Cas9 cells were seeded in 5-layer flasks (Corning) at a density of 11 million cells per flask. After 72 hrs, the cells were infected with the Avana sgRNA library43 at a multiplicity of infection of 0.3 and treated with 5 g/ml of Polybrene transfection reagent (Fisher Scientific). The media was changed after 24 hrs, and cells were incubated for an additional 24 hrs. 48 hrs after infection, cells were treated with 2 g/ml of puromycin to initiate selection. 48 hrs after addition of puromycin, the puromycin-containing media was replaced with fresh media lacking puromycin and the cells were allowed to recover for an additional 72 hrs. After recovery and 9 days following infection, cells were treated with 1 M of Lap-VHL and incubated for 24 hrs in BiDAC. Prior to FACS, 60 x 106 cells were removed to serve as a non-sorted control. For enrichment by FACS, cells were harvested by trypsinization in TrypsinLE and resuspended in FACS buffer composed of PBS containing 2% FBS. The top 0.5-1% RTK-FP-expressing cells were sorted using a Bigfoot Cell Sorter (Thermo Fisher Scientific), comprising a total of 750 x 103 cells. After collection, cells were pelleted and frozen at -80°C.

extract_protocol:
To prepare genomic DNA, sorted cells were mixed with 5 x 106 non-infected RTK-FP cells to increase recovery, and the sorted and unsorted cell pellets were resuspended in 100 mL of TE buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA) per 5 x 106 cells. 900 mL of Lysis Buffer containing 10 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% SDS and 0.2 mg/mL Proteinase K (Thermo Fisher Scientific) was added to 100 mL of cells. Cell lysates were incubated at 56°C and vortexed vigorously every 15 min, followed by an additional overnight incubation. After the incubation, 5M NaCl was added to lysates to yield final concentration of 0.2M NaCl. A phenol chloroform extractions was performed using MaXtract tubes (Qiagen) by mixing lysates with an equal volume of Phenol:Chloroform:Isoamyl alcohol 25:24:1 (Life Technologies), followed by centrifugation at 1500 x g and extraction by an equal volume of chloroform. The aqueous phase was treated with 25 mg/mL of RNAse A (PureLink, Life Technologies) for 1 hr at 37°C with periodic mixing followed by a second phenol chloroform extraction. The aqueous phase was combined 1:30 v/v with 3M Sodium acetate, pH 5.2 and the DNA was precipitated with 2.5 volumes of ethanol for 1 hr at room temperature. Precipitated DNA was pelleted by centrifugation at 4,000 x g for 1 hr at 4°C in a swinging bucket centrifuge. The DNA pellet was washed 3 times with 75% ethanol, allowed to dry and resuspended in 200 mL of water per 5 x 106 lysed cells. DNA was further solubilized by incubation for 1 hr at 55°C followed by passage 10-20 times through a 28-gauge needle. DNA purity was assessed using a NanoDrop spectrophotometer and its concentration was determined using Qubit Fluorometric Quantification (Thermo Fisher Scientific).
Genomic sgRNA libraries were prepared by PCR amplification of all DNA extracted from sorted cells and 70 mg of DNA extracted from the unsorted control samples using common primers. 4 ml of the PCR products was used as a template for another round of PCR with barcoded primers. The products were purified using SPRIselect beads (Beckman Coulter), and their purity and concentration was determined using the 2100 Bioanalyzer instrument (Agilent)

value: Ovarian cancer

tag: cell line

value: Unsorted RTK-FP cells

value: Lap-VHL


title: MG Cell SLX-14936.i714_i503,batch2


title: EGFR-RFP Screen Sorted

description: Library name: EGFR-RFP Screen Sorted

value: RTK-FP cells sorted for high EGFR-RFP


title: MG Cell SLX-14936.i711_i505,batch2


title: MG Cell SLX-14936.i711_i502,batch2


title: MG Cell SLX-14936.i712_i507,batch2


title: MG Cell SLX-14936.i714_i508,batch2


title: MG Cell SLX-14936.i710_i511,batch2


title: MG Cell SLX-14936.i711_i507,batch2


title: Her2-GFP Screen Bulk

description: Library name: Her2-GFP Screen Bulk


title: MG Cell SLX-14936.i710_i510,batch2


title: MG Cell SLX-14936.i710_i508,batch2


title: miRNA_Control shRNA R2

city: Exeter

first: Akshay

last: Bhinge

address: Stocker Road

department: CBS

country: United Kingdom

institute: Living Systems Institute, University of Exeter

description:
Library name: J10
microRNA

data_processing:
Adapters were removed using cutadapt and reads were mapped to hg19 using bowtie2.
Differential gene expression analysis was performed using mirdeep2.
Assembly: hg19
Supplementary files format and content: tab-separated miRNA counts

source_name: iPSC-derived

growth_protocol: Healthy iPSCs were grown on matrigel in StemFlex and dissociated into small colonies with 0.1 mM EDTA when 70% confluent. Cells were plated as colonies in a 1:6 split.

extract_protocol:
Total RNA was harvested using Qiazol
Libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. Doxycycline 1ug/ml was added to the media at day 20 to induce NES nanobody expression. Samples were collected at day 40.

value: iPSC-derived

value: motor neurons

value: Control Knockdown

value: differentiation into motor neurons


title: MG Cell SLX-14936.i710_i507,batch2


title: MG Cell SLX-14936.i710_i505,batch2


title: miRNA_Control shRNA R1

description:
Library name: J08
microRNA


title: MG Cell SLX-14936.i710_i506,batch2


title: MG Cell SLX-14936.i710_i503,batch2


title: MG Cell SLX-14936.i710_i502,batch2


title: miRNA_TDP43 shRNA R3

description:
Library name: J11
microRNA

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. Doxycycline 1ug/ml was added to the media at day 20 to induce control nanobody expression. Samples were collected at day 40.

value: TDP43 knockdown


title: miRNA_AAVS1 NES R3

description:
Library name: J06
microRNA

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. MNs were transduced with AAV expressing the NES nanobody at day 20. Samples were collected at day 40.

value: NES


title: MG Cell SLX-14936.i707_i511,batch2

value: Mammary gland


title: miRNA_AAVS1 NES R2

description:
Library name: J04
microRNA


title: miRNA_AAVS1 control R2

description:
Library name: J03
microRNA

treatment_protocol: iPSCs were plated as colonies onto Matrigel and treated with neuronal differentiation media (DMEM/F12:Neurobasal in a 1:1 ratio, HEPES 10mM, N2 supplement 1%, B27 supplement 1%, L-glutamine 1%, ascorbic acid 5uM) supplemented with SB431542 (40uM), CHIR9921 (3uM) and LDN8312 (0.2uM) from day 0 till day 4. Cells were caudalized by treatment with 0.1uM retinoic acid starting at day 2 and ventralized with 1uM purmorphamine starting at day 4 and continued till day 8. On day 8, motor neuron progenitors (MNPs) were re-plated onto poly-D-lysine/laminin coated wells. Differentiation was induced by treating the cells with N2B27 media supplemented with retinoic acid, purmorphamine and DAPT 10uM. DAPT treatment was stopped at day 13 and media was changed to N2B27 supplemented with BDNF 10ng/ml, GDNF 10ng/ml. MNs were transduced with AAV expressing the control nanobody at day 20. Samples were collected at day 40.

value: Control


title: MG Cell SLX-14936.i707_i503,batch2


title: MG Cell SLX-14936.i707_i505,batch2


title: miRNA_TDP43 shRNA R2

description:
Library name: J09
microRNA


title: AAVS1 NES R3

description:
Library name: sample12
polyA purified total RNA

data_processing:
Adapters were removed using cutadapt and reads were mapped to hg19 using STAR.
Differential gene expression analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: tab-separated gene counts

extract_protocol:
Total RNA was harvested using Qiazol and polyA tailed RNA was purified using the NEB kit E7490.
Libraries were constructed using the NEBNext UltraII RNA library protocol.


title: miRNA_TDP43 shRNA R1

description:
Library name: J07
microRNA


title: MG Cell SLX-14936.i707_i502,batch2


title: MG Cell SLX-14936.i707_i508,batch2

value: Intermediate GFP+


title: AAVS1 NES R2

description:
Library name: sample10
polyA purified total RNA


title: miRNA_AAVS1 control R1

description:
Library name: J01
microRNA


title: MG Cell SLX-14936.i707_i506,batch2

value: Basal Cell GFP+


title: Her2-GFP Screen Sorted

description: Library name: Her2-GFP Screen Sorted

value: RTK-FP cells sorted for high Her2-GFP


title: miRNA_AAVS1 NES R1

description:
Library name: J02
microRNA


title: MG Cell SLX-14936.i707_i510,batch2

value: Luminal cell GFP+


title: MG Cell SLX-14936.i707_i507,batch2


title: MG Cell SLX-14936.i706_i511,batch2


title: miRNA_AAVS1 control R3

description:
Library name: J05
microRNA


title: AAVS1 control R3

description:
Library name: sample11
polyA purified total RNA


title: AAVS1 control R2

description:
Library name: sample9
polyA purified total RNA


title: AAVS1 NES R1

description:
Library name: sample8
polyA purified total RNA


title: AAVS1 control R1

description:
Library name: sample7
polyA purified total RNA


title: MG Cell SLX-14936.i706_i510,batch2


title: E8 Control nanobody R1

description:
Library name: E8_C_R1
polyA purified total RNA


title: E8 NES nanobody R2

description:
Library name: E8_N_R2
polyA purified total RNA


title: MG Cell SLX-14936.i706_i503,batch2


title: MG Cell SLX-14936.i706_i505,batch2


title: MG Cell SLX-14936.i706_i502,batch2

value: Luminal cell GFP-


title: MG Cell SLX-14936.i705_i511,batch2


title: E8 Control nanobody R2

description:
Library name: E8_C_R2
polyA purified total RNA


title: E5 NES nanobody R2

description:
Library name: E5_N_R2
polyA purified total RNA


title: MG Cell SLX-14936.i705_i505,batch2


title: MG Cell SLX-14936.i706_i506,batch2


title: MG Cell SLX-14936.i705_i507,batch2


title: E8 NES nanobody R1

description:
Library name: E8_N_R1
polyA purified total RNA


title: MG Cell SLX-14936.i705_i510,batch2


title: MG Cell SLX-14936.i705_i503,batch2


title: Hela, sg5UTR2-MBD-Rep1

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed using Trimmomatic (v0.38).
The resulting clean data was then aligned with Bowtie2 (v2.3.4.1) to the human reference genome GRCh38 using parameter “-very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 2000”.
The bigwig files for visualization were generated using deeptools (3.1.3) with uniquely mapped reads.
Assembly: GRCh38
Supplementary files format and content: The bigwig files of each Sample .

source_name: cervical

extract_protocol:
Chromatin Immunoprecipitation (ChIP) was performed using the standard protocol provided in the ChIP Assay Kit (Beyotime, P2078). Briefly, 5×106 Hela cells expressing the indicated constructs were crosslinked with 1% formaldehyde at 37°C for 10 minutes. Cells were then lysed, and the chromatin was sonicated to achieve fragment sizes ranging from 200 to 800 bp. The supernatant was incubated overnight at 4°C with 1 μg of MycTag, Flag, CHD4 antibodies or rabbit IgG as a negative control. The immunoprecipitated DNA was captured using A/G agarose beads, followed by phenol-chloroform extraction and ethanol precipitation to purify the DNA.
The ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V4 (Vazyme, ND610) according to the manufacturer’s instructions. For library construction, 50 ng of ChIP DNA was subjected to PCR amplification for 12 cycles.

value: cervical

value: Hela

value: Human cervical cancer

tag: chip antibody

value: anti-Flag (Proteintech, 80010-1-RR), 1ug for 2e6 cells


title: MG Cell SLX-14936.i705_i508,batch2


title: Hela, sg5UTR2-MBD-Rep2


title: E5 Control nanobody R1

description:
Library name: E5_C_R1
polyA purified total RNA

value: iPSC-derived


title: MG Cell SLX-14936.i706_i507,batch2


title: MG Cell SLX-14936.i705_i506,batch2


title: Hela, sg5UTR2-dCas9-Rep1

value: anti-MycTag (Proteintech, 16286-1-AP), 1ug for 2e6 cells


title: MG Cell SLX-14936.i706_i508,batch2


title: MG Cell SLX-14936.i705_i502,batch2


title: Hela, sg5UTR2-dCas9-Rep2


title: E5 Control nanobody R2

description:
Library name: E5_C_R2
polyA purified total RNA

value: motor neurons


title: Hela, sg5UTR1-MBD-Rep2


title: E5 NES nanobody R1

description:
Library name: E5_N_R1
polyA purified total RNA

value: differentiation into motor neurons


title: MG Cell SLX-14936.i704_i511,batch2


title: Hela, sg5UTR1-MBD-Rep1


title: MG Cell SLX-14936.i704_i510,batch2


title: Hela, sg5UTR1-dCas9-Rep1


title: Hela, CHD4-Rep2

value: untreated

value: anti-CHD4 (Proteintech, 14173-1-AP), 1ug for 2e6 cells


title: MG Cell SLX-14936.i704_i507,batch2

value: Mammary gland


title: MG Cell SLX-14936.i704_i508,batch2


title: Hela, 6xsgL1-MBD-Rep2


title: MG Cell SLX-14936.i704_i506,batch2


title: MG Cell SLX-14936.i703_i511,batch2


title: Hela, 6xsgL1-MBD-Rep1


title: Hela, sg5UTR1-dCas9-Rep2


title: Hela, shNC-3_1

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed using Trimmomatic (v0.38).
The filtered reads were aligned against the human reference genome GRCh38 using STAR (v2.7.10a)
Genes were quantified using HTSeq-count (v0.11.2) in intersection-strict mode.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample .

extract_protocol:
Cells were collected for RNA extraction using RNAiso plus (TAKARA) following the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: shNC (control)


title: Hela, 6xsgL1-dCas9-Rep1


title: Hela, shNC-2_1


title: MG Cell SLX-14936.i703_i506,batch2


title: MG Cell SLX-14936.i703_i505,batch2


title: MG Cell SLX-14936.i704_i505,batch2


title: Hela, shNC-1_1


title: MG Cell SLX-14936.i703_i507,batch2


title: MG Cell SLX-14936.i704_i503,batch2


title: Hela, CHD4-Rep1


title: MG Cell SLX-14936.i703_i510,batch2

value: Intermediate GFP+


title: Hela, 6xsgL1-dCas9-Rep2


title: MG Cell SLX-14936.i703_i508,batch2


title: Hela, shCHD4-2


title: MG Cell SLX-14936.i704_i502,batch2


title: MG Cell SLX-14936.i703_i503,batch2


title: Hela, shCHD4-3


title: Hela, shCHD4-1


title: MG Cell SLX-14936.i703_i502,batch2


title: MG Cell SLX-14936.i702_i510,batch2


title: HemSC150-Control Day 4

city: Boston

first: Joyce

last: Bischoff

state: MA

address: 300 Longwood Ave, Karp Research Building 12.212

department: Vascular Biology Program

institute: Boston Children's Hospital

data_processing:
Low-quality reads were trimmed using trimmomatic v0.39 (-threads 20 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Only the high-quality trimmed reads were aligned to the human reference genome (hg38) using STAR v2.7.2b.
The reads counts were calculated by featureCounts software.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: hemangioma

growth_protocol: To induce endothelial differentiation using VEGF-B, HemSC were seeded on fibronectin-coated plates (0.01 μg fibronectin/cm2) at a density of 20,000 cells/cm2 in EGM-2 media. After 18 - 24 hours, cells were starved for 16 hours in 2% BSA/serum-free EBM-2 media. Cells were washed with EBM-2 once. The medium was replaced by differentiation media that consisted of serum-free EBM-2 containing 1× insulin transferrin-selenium, 1:100 linoleic acid–albumin, 1 μM dexamethasone, and 100 μM ascorbic acid-2-phosphate. The medium was replaced with fresh differentiation medium containing 10 ng/mL VEGF-B every two days.

extract_protocol:
Total cellular RNA was extracted from cells with a RNeasy Micro Extraction Kit (QIAGEN). RNA integrity was >9.0.
TruSeq stranded mRNA LT Sample Prep Kit

treatment_protocol: A stock solution of 10 mM R(+) propranolol hydrochloride (MilliporeSigma) was made in DMSO. 20 μM R(+) propranolol was added to HemSC cultures for two hours. Cells were lysed for total RNA isolation and library preparation.

value: hemangioma

value: 3 months

value: HemSC

value: male

value: PBS


title: HemSC150-R+prop Day 4

value: R+propranolol


title: MG Cell SLX-14936.i702_i505,batch2

value: Luminal cell GFP+


title: MG Cell SLX-14936.i702_i508,batch2

value: Basal Cell GFP+


title: HemSC171-R+prop

tag: age

value: 5 months

tag: gender

value: female


title: HemSC169-R+prop

value: 2 months


title: MG Cell SLX-14936.i702_i502,batch2

value: Luminal cell GFP-


title: MG Cell SLX-14936.i701_i508,batch2


title: MG Cell SLX-14936.i701_i510,batch2


title: MG Cell SLX-14936.i701_i507,batch2


title: MG Cell SLX-14936.i701_i506,batch2


title: HemSC125-Control Day 4

value: 4 months


title: MG Cell SLX-14936.i702_i503,batch2


title: HemSC150-R+prop


title: HemSC165-R+prop

value: 6 months


title: HemSC169-Control


title: HemSC165-Control


title: MG Cell SLX-14936.i701_i505,batch2

value: Mammary gland


title: HemSC167-R+prop


title: MG Cell SLX-14936.i701_i511,batch2


title: HemSC167-Control


title: HemSC167-R+prop Day 4


title: MG Cell SLX-14936.i701_i503,batch2


title: MG Cell SLX-14936.i702_i511,batch2


title: HemSC167-Control Day 4


title: MG Cell SLX-14936.i702_i507,batch2


title: HemSC125-R+prop Day 4


title: HemSC171-Control


title: MG Cell SLX-14936.i702_i506,batch2


title: HemSC150-Control


title: MG Cell SLX-14936.i701_i502,batch2


title: HemSC125-R+prop


title: HemSC125-Control


title: 6787_BP_6

value: Blood

value: PBMC

value: aP


title: MG Cell SLX-14935.i729_i521,batch1

value: Intermediate GFP+


title: MG Cell SLX-14935.i729_i520,batch1


title: 6787_BP_7


title: MG Cell SLX-14935.i729_i517,batch1


title: MG Cell SLX-14935.i729_i522,batch1


title: MG Cell SLX-14935.i729_i518,batch1


title: MG Cell SLX-14935.i729_i513,batch1


title: MG Cell SLX-14935.i729_i515,batch1


title: 6787_BP_2


title: 6787_BP_1


title: 6787_BP_3


title: MG Cell SLX-14935.i729_i516,batch1


title: MG Cell SLX-14935.i729_i511,batch1


title: 6787_BP_4


title: 6679_BP_7


title: 6679_BP_6


title: MG Cell SLX-14935.i729_i508,batch1


title: MG Cell SLX-14935.i729_i510,batch1


title: 6679_BP_5


title: MG Cell SLX-14935.i729_i507,batch1


title: MG Cell SLX-14935.i729_i506,batch1


title: 6679_BP_3


title: 6679_BP_4


title: 6679_BP_2


title: MG Cell SLX-14935.i729_i505,batch1


title: 6787_BP_5


title: MG Cell SLX-14935.i729_i503,batch1


title: MG Cell SLX-14935.i729_i502,batch1


title: 6678_BP_7


title: 6678_BP_6


title: MG Cell SLX-14935.i728_i522,batch1


title: MG Cell SLX-14935.i728_i518,batch1


title: 6678_BP_4


title: MG Cell SLX-14935.i728_i521,batch1


title: 6678_BP_3


title: 6678_BP_2


title: MG Cell SLX-14935.i728_i517,batch1


title: 6495_BP_7


title: MG Cell SLX-14935.i728_i520,batch1


title: MG Cell SLX-14935.i728_i513,batch1


title: MG Cell SLX-14935.i728_i515,batch1


title: MG Cell SLX-14935.i728_i516,batch1


title: 6495_BP_6


title: 6678_BP_1


title: MG Cell SLX-14935.i728_i510,batch1


title: 6495_BP_5


title: MG Cell SLX-14935.i728_i511,batch1


title: 6495_BP_4


title: MG Cell SLX-14935.i728_i508,batch1


title: 6495_BP_3


title: MG Cell SLX-14935.i728_i506,batch1


title: 6495_BP_1


title: 6679_BP_1


title: MG Cell SLX-14935.i728_i507,batch1


title: MG Cell SLX-14935.i728_i505,batch1


title: 6495_BP_2


title: 6485_BP_7

value: wP


title: MG Cell SLX-14935.i728_i503,batch1


title: 6485_BP_6


title: MG Cell SLX-14935.i727_i522,batch1


title: 6485_BP_4


title: MG Cell SLX-14935.i728_i502,batch1


title: 6485_BP_3


title: 6485_BP_5


title: MG Cell SLX-14935.i727_i521,batch1


title: 6678_BP_5


title: MG Cell SLX-14935.i727_i520,batch1


title: 6483_BP_7


title: 6485_BP_1


title: MG Cell SLX-14935.i727_i517,batch1


title: 6483_BP_6


title: MG Cell SLX-14935.i727_i516,batch1


title: 6485_BP_2


title: MG Cell SLX-14935.i727_i513,batch1


title: MG Cell SLX-14935.i727_i515,batch1


title: MG Cell SLX-14935.i727_i511,batch1


title: 6483_BP_3


title: 6483_BP_2


title: 6483_BP_4


title: MG Cell SLX-14935.i727_i510,batch1


title: MG Cell SLX-14935.i727_i507,batch1


title: 6483_BP_1


title: MG Cell SLX-14935.i727_i508,batch1


title: 6482_BP_7


title: MG Cell SLX-14935.i727_i506,batch1


title: 6482_BP_5


title: 6482_BP_6


title: 6482_BP_3


title: MG Cell SLX-14935.i727_i503,batch1


title: MG Cell SLX-14935.i727_i518,batch1


title: MG Cell SLX-14935.i727_i505,batch1


title: 6482_BP_4


title: MG Cell SLX-14935.i726_i522,batch1


title: 6482_BP_2


title: MG Cell SLX-14935.i727_i502,batch1


title: 6482_BP_1


title: 6483_BP_5


title: MG Cell SLX-14935.i726_i518,batch1


title: MG Cell SLX-14935.i726_i520,batch1


title: MG Cell SLX-14935.i726_i517,batch1


title: MG Cell SLX-14935.i726_i521,batch1


title: 6389_BP_6


title: MG Cell SLX-14935.i726_i516,batch1


title: MG Cell SLX-14935.i726_i515,batch1


title: 6389_BP_2


title: 6389_BP_3


title: 6389_BP_4


title: MG Cell SLX-14935.i726_i511,batch1


title: 6389_BP_1


title: MG Cell SLX-14935.i726_i513,batch1


title: MG Cell SLX-14935.i726_i510,batch1


title: 6388_BP_7


title: MG Cell SLX-14935.i726_i508,batch1


title: 6388_BP_5


title: 6388_BP_6


title: MG Cell SLX-14935.i726_i506,batch1


title: MG Cell SLX-14935.i726_i507,batch1


title: 6388_BP_4


title: MG Cell SLX-14935.i726_i503,batch1


title: MG Cell SLX-14935.i726_i505,batch1


title: 6389_BP_7


title: 6388_BP_2


title: 6388_BP_3


title: MG Cell SLX-14935.i726_i502,batch1


title: 6389_BP_5


title: 6385_BP_7


title: MG Cell SLX-14935.i724_i521,batch1


title: 6385_BP_5


title: MG Cell SLX-14935.i724_i520,batch1


title: 6388_BP_1


title: MG Cell SLX-14935.i724_i522,batch1


title: MG Cell SLX-14935.i724_i518,batch1


title: 6385_BP_4


title: 6385_BP_3


title: MG Cell SLX-14935.i724_i517,batch1


title: MG Cell SLX-14935.i724_i516,batch1


title: 6385_BP_2


title: MG Cell SLX-14935.i724_i515,batch1


title: 6308_BP_7


title: MG Cell SLX-14935.i724_i513,batch1


title: 6385_BP_1


title: MG Cell SLX-14935.i724_i508,batch1


title: 6308_BP_4


title: MG Cell SLX-14935.i724_i506,batch1


title: MG Cell SLX-14935.i724_i507,batch1


title: 6308_BP_2


title: 6385_BP_6


title: 6308_BP_3


title: MG Cell SLX-14935.i724_i505,batch1


title: MG Cell SLX-14935.i724_i503,batch1


title: 6308_BP_1


title: 6281_BP_7


title: 6281_BP_6


title: MG Cell SLX-14935.i723_i522,batch1


title: MG Cell SLX-14935.i723_i521,batch1


title: 6281_BP_5


title: MG Cell SLX-14935.i724_i502,batch1


title: 6281_BP_4


title: MG Cell SLX-14935.i723_i518,batch1


title: 6281_BP_2


title: MG Cell SLX-14935.i723_i520,batch1


title: MG Cell SLX-14935.i723_i517,batch1


title: 6281_BP_3


title: 6281_BP_1


title: 6280_BP_7


title: MG Cell SLX-14935.i723_i515,batch1


title: 6308_BP_6


title: MG Cell SLX-14935.i724_i510,batch1


title: MG Cell SLX-14935.i724_i511,batch1


title: 6308_BP_5


title: MG Cell SLX-14935.i723_i513,batch1


title: 6280_BP_4


title: 6280_BP_3


title: 6280_BP_2


title: MG Cell SLX-14935.i723_i507,batch1


title: 6280_BP_1


title: MG Cell SLX-14935.i723_i510,batch1


title: 6280_BP_5


title: MG Cell SLX-14935.i723_i506,batch1


title: MG Cell SLX-14935.i723_i505,batch1


title: 6279_BP_7


title: 6279_BP_5


title: MG Cell SLX-14935.i723_i502,batch1


title: MG Cell SLX-14935.i723_i503,batch1


title: MG Cell SLX-14935.i723_i516,batch1


title: 6279_BP_4


title: MG Cell SLX-14935.i722_i522,batch1


title: MG Cell SLX-14935.i722_i521,batch1


title: 6279_BP_2


title: MG Cell SLX-14935.i722_i518,batch1


title: 6279_BP_1


title: MG Cell SLX-14935.i722_i520,batch1


title: 6275_BP_7


title: 6275_BP_6


title: 6280_BP_6


title: MG Cell SLX-14935.i722_i517,batch1


title: MG Cell SLX-14935.i723_i511,batch1


title: MG Cell SLX-14935.i723_i508,batch1


title: MG Cell SLX-14935.i722_i516,batch1


title: 6275_BP_5


title: 6275_BP_4


title: 6279_BP_6


title: 6275_BP_3


title: MG Cell SLX-14935.i722_i511,batch1


title: 6275_BP_2


title: MG Cell SLX-14935.i722_i510,batch1


title: 6275_BP_1


title: 6279_BP_3


title: 6097_BP_5


title: 6097_BP_7


title: MG Cell SLX-14935.i722_i505,batch1


title: MG Cell SLX-14935.i722_i507,batch1


title: MG Cell SLX-14935.i722_i506,batch1


title: 6097_BP_4


title: MG Cell SLX-14935.i722_i503,batch1


title: 6097_BP_3


title: MG Cell SLX-14935.i721_i522,batch1


title: B5S9

type: RNA

city: Munich

first: Ruoqing

last: Feng

address: Feodor-Lynen-Strasse 17

country: Germany

description: panel of 496 genes was measured by MERFISH

hyb_protocol: The gene panel used in this study included 496 protein-coding genes, complemented by 54 blank probes. Within this gene panel, a diverse array of transcripts comprising recognized markers for glial and immune cell types was included based on previously published literature. Sections were post-fixed with 4%PFA in PBS for 15 min at room temperature, washed three times with PBS and then permeabilized in 70% ethanol at 4 °C overnight. For hybridization with the gene panel, samples were washed with Sample Prep Wash Buffer (Vizgen) and then incubated in Formamide Hybridization Buffer at 37 °C for 30 min before adding 50 μl of the gene panel mix on top of the tissue. Sections were hybridized at 37 °C for 36 to 48 h, washed, and embedded into a polyacrylamide gel according to the manufacturer’s instructions. Samples were cleared with Clearing Premix containing Proteinase K, washed and stained with DAPI and polyT reagent for 15 min at room temperature.

scan_protocol: A low-resolution mosaic was acquired using a x10 objective and regions of interest were selected for high-resolution imaging with a x60 lens. For high-resolution imaging, the focus was locked to the fiducial fluorescent beads on the coverslip. Seven 1.5-μm-thick Z-planes were imaged for each field of view. Raw images were decoded to RNA spots with spatial coordinates and gene IDs using the Merlin software (Vizgen) on the MERSCOPE instrument.

data_processing:
Cell segmentation was performed using the Cellpose algorithm based in the DAPI nuclear and polyT total RNA staining channels.
Encoded MERFISH images were processed according to manufacturer's pipeline (https://vizgen.com/technology/#merfish). The output of this pipeline are spatial positions of individual transcripts and segmented single cells based on DAPI and poly-A stainings. Single cell expression tables are produced by counting individual transcripts within segmented cell boundaries.

source_name: Optic Nerves

growth_protocol: All animal experiments were approved by the Governments of Lower Franconia, Würzburg, Germany and of Upper Bavaria, Munich, Germany (AZ 55.2 DMS 2532-2-1; AZ 55.2 DMS 2532-2-399; AZ 55.2 DMS 2532-2-907; AZ 55.2 DMS 2532-2-1029; AZ 55.2 DMS 2532-2-1191). Mice were kept at the animal facility of the Centre for Experimental Molecular Medicine, University of Würzburg, or the German Center for Neurodegenerative Diseases (DZNE) in Munich under barrier conditions and at a constant cycle of 12 h in the light (<300 lux) and 12 h in the dark. Colonies were maintained at 20-24 °C and 40-60% humidity, with free access to food and water.

extract_protocol: Optic nerves were cut tangentially or longitudinally and 10-µm-thick sections were collected onto glass slides supplied by Vizgen.

treatment_protocol: PLX5622 (provided by Plexxikon Inc., Berkeley, CA, USA) was prepared as a 300 ppm drug chow to dose ~ 54 mg PLX5622/kg body weight when given ad libitum. This was based on our previous long-term treatment approaches in which we observed efficient microglia depletion without obvious neurological side effects61,62. Control mice received normal chow without the pharmacological inhibitor. Mice were treated for 6, 12, or 24 months with daily monitoring concerning certain burden criteria and phenotypic abnormalities. The treatment started before obvious aging-related pathology in mice at 18, 12, or 0 months of age (by treatment of lactating mothers post-partum and continued treatment of pups post-weaning).

value: Male

tag: strain

value: wild type

value: Aging; 24 mounths


title: MG Cell SLX-14935.i721_i521,batch1


title: MG Cell SLX-14935.i721_i520,batch1

value: Luminal cell GFP+


title: MG Cell SLX-14935.i722_i502,batch1


title: 6097_BP_2


title: MG Cell SLX-14935.i721_i518,batch1

value: Basal Cell GFP+


title: B5S7

institute: German Center for Neurodegenerative Diseases (DZNE)

value: Adult; 12 mounths

value: control food


title: 6097_BP_1


title: B5S2


title: MG Cell SLX-14935.i722_i513,batch1


title: MG Cell SLX-14935.i722_i515,batch1


title: MG Cell SLX-14935.i721_i517,batch1


title: 6096_BP_7


title: B4S9


title: MG Cell SLX-14935.i721_i515,batch1


title: MG Cell SLX-14935.i722_i508,batch1


title: B4S6


title: 6097_BP_6


title: MG Cell SLX-14935.i721_i513,batch1


title: 6096_BP_6


title: 6096_BP_5


title: 6096_BP_4


title: MG Cell SLX-14935.i721_i510,batch1


title: MG Cell SLX-14935.i721_i508,batch1


title: MG Cell SLX-14935.i721_i507,batch1


title: B4S3


title: MG Cell SLX-14935.i721_i511,batch1


title: B4S5


title: MG Cell SLX-14935.i721_i506,batch1


title: MG Cell SLX-14935.i721_i505,batch1


title: B4S2


title: MG Cell SLX-14935.i721_i502,batch1


title: B3S3


title: 6096_BP_2


title: MG Cell SLX-14935.i720_i522,batch1


title: MG Cell SLX-14935.i720_i521,batch1


title: 6096_BP_3


title: B3S2


title: 4657_BP_9


title: MG Cell SLX-14935.i720_i520,batch1


title: MG Cell SLX-14935.i720_i518,batch1


title: MG Cell SLX-14935.i721_i516,batch1


title: MG Cell SLX-14935.i721_i503,batch1


title: MG Cell SLX-14935.i720_i517,batch1


title: 6096_BP_1


title: MG Cell SLX-14935.i720_i516,batch1


title: B3S1


title: 4657_BP_8


title: 4657_BP_7


title: MG Cell SLX-14935.i720_i515,batch1


title: MG Cell SLX-14935.i720_i513,batch1


title: MG Cell SLX-14935.i720_i510,batch1


title: MG Cell SLX-14935.i720_i508,batch1


title: 4657_BP_6


title: TUM_347

type: genomic

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

description: 5K BAC CGH array data for bladder samples

hyb_protocol: The IntegraChipTM microarray was designed by the CIT-CGH consortium (Olivier Delattre Laboratory, Curie Institute, Paris; Charles Theillet Laboratory, CRLC Val d'Aurelle, Montpellier; Stanislas du Manoir Laboratory, IGBMC, Strasbourg) and the company IntegraGenTM (http://www.integragen.com). Bacterial artificial chromosome (BAC) clones were chosen to obtain a systematic coverage of the genome, and detailed coverage of regions containing genes previously implicated in carcinogenesis. The median gap between two successive clones is 600 kb. Four replicate spots were deposited on the slides. For each sample, 500-600 ng of sonicated DNA was labelled by Random-Priming (Bioprime Labelling kit, Invitrogen, Carlsberg, CA, USA) according to the suppliers\x{2019} instructions, but for 18h. For tumour DNA, final concentrations of nucleotides were 0.02 mM of dCTP-Cy5 (Amersham Biosciences), 0.1 mM of dATP, dGTP, dTTP and 0.025 mM dCTP. For control DNA, 0.04 dCTP-Cy3 (Amersham Biosciences), 0.2 mM of dATP, dGTP, dTTP and 0.05 mM dCTP. Labelled DNAs were purified using MicroSpin-G50 columns (Amersham Biosciences). COT Human DNA (70 \x{03bc}g, Roche Diagnostics) and Salmon Testes DNA (30 \x{03bc}g, Sigma Chemical Co.) were added to the mixed tumour and reference DNAs. They were subsequently concentrated using a microcon YM-30 (Millipore) and resuspended to obtain 200 \x{03bc}l of hybridization solution (final concentration: 50% formamide, 0.8 x SCC, 10% W/V dextran sulfate, 2% SDS, pH=7). Finally, the probes were pre-annealed for 3 hours at 37°C. Every step was carried out in the HS 4800 hybridization station (Tecan). Slide pre-treatment included rinsing with 2 x SSC, 0.1% SDS at 30 °C for 30s, 2 x SSC at 30 °C for 30s and drying. After probe injection, hybridization was performed for 68h at 37°C under low agitation. Four post-hybridization washes were carried out: 50% formamide, 2 x SSC, 0.1% SDS at 45 °C for 37 s, 4 times; 2 x SSC, 0.1% SDS at 45 °C for 37 sec, 4 times; 4 x SSC, 0.1 Tween 20 at 45 °C for 37 sec, 4 times; slides were finally nitrogen dried and scanned using a ScanArray 4000 (Packard Bioscience). Images were quantified using UCSF Spot 2.1cc (Jain et al., 2002).

scan_protocol: ScanArray 4000 (Packard Bioscience)

data_processing: data processed with GLAD algorithm (Hupé et al, Bioinformatics, 2004). hg18  liftover  by rtracklayer 1.48.0  hg38 version of the genome used

source_name: Bladder tumor samples TUM_347

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A.  DNA was then extracted using a standard phenol-chloroform protocol

tag: disease state

value: bladder cancer


title: MG Cell SLX-14935.i720_i511,batch1

value: Luminal cell GFP-


title: MG Cell SLX-14935.i720_i507,batch1


title: 4657_BP_4


title: 4657_BP_5


title: MG Cell SLX-14935.i720_i505,batch1


title: MG Cell SLX-14935.i720_i506,batch1


title: MG Cell SLX-14935.i720_i503,batch1


title: TUM_346

source_name: Bladder tumor samples TUM_346


title: MG Cell SLX-14935.i720_i502,batch1


title: MG Cell SLX-14935.i719_i522,batch1


title: TUM_345

source_name: Bladder tumor samples TUM_345


title: MG Cell SLX-14935.i719_i518,batch1


title: 4656_BP_8


title: MG Cell SLX-14935.i719_i517,batch1


title: 4657_BP_3


title: TUM_294

source_name: Bladder tumor samples TUM_294


title: 4656_BP_9


title: TUM_293

source_name: Bladder tumor samples TUM_293


title: MG Cell SLX-14935.i719_i521,batch1


title: TUM_290

source_name: Bladder tumor samples TUM_290


title: MG Cell SLX-14935.i719_i520,batch1


title: MG Cell SLX-14935.i719_i515,batch1


title: MG Cell SLX-14935.i719_i511,batch1


title: MG Cell SLX-14935.i719_i510,batch1


title: MG Cell SLX-14935.i719_i508,batch1


title: 4656_BP_5


title: 4656_BP_4


title: TUM_289

source_name: Bladder tumor samples TUM_289


title: 4656_BP_3


title: TUM_283

source_name: Bladder tumor samples TUM_283


title: TUM_285

source_name: Bladder tumor samples TUM_285


title: MG Cell SLX-14935.i719_i507,batch1


title: 4656_BP_7


title: MG Cell SLX-14935.i719_i503,batch1


title: MG Cell SLX-14935.i719_i516,batch1


title: MG Cell SLX-14935.i719_i506,batch1


title: 4654_BP_9


title: TUM_281

source_name: Bladder tumor samples TUM_281


title: MG Cell SLX-14935.i719_i502,batch1


title: MG Cell SLX-14935.i718_i522,batch1


title: 4654_BP_8

source_name: Blood


title: MG Cell SLX-14935.i718_i521,batch1

source_name: Mammary gland


title: 4656_BP_6


title: TUM_280

source_name: Bladder tumor samples TUM_280


title: MG Cell SLX-14935.i718_i520,batch1


title: MG Cell SLX-14935.i719_i513,batch1


title: 4654_BP_7


title: MG Cell SLX-14935.i718_i518,batch1


title: TUM_274

source_name: Bladder tumor samples TUM_274


title: TUM_269

source_name: Bladder tumor samples TUM_269


title: TUM_273

source_name: Bladder tumor samples TUM_273


title: MG Cell SLX-14935.i718_i517,batch1


title: 4654_BP_6


title: MG Cell SLX-14935.i719_i505,batch1


title: MG Cell SLX-14935.i718_i516,batch1


title: MG Cell SLX-14935.i718_i515,batch1


title: MG Cell SLX-14935.i718_i511,batch1


title: MG Cell SLX-14935.i718_i513,batch1


title: TUM_258

source_name: Bladder tumor samples TUM_258


title: MG Cell SLX-14935.i718_i508,batch1


title: 4654_BP_3


title: MG Cell SLX-14935.i718_i510,batch1


title: TUM_276

source_name: Bladder tumor samples TUM_276


title: 1788_BP_7


title: MG Cell SLX-14935.i718_i506,batch1


title: MG Cell SLX-14935.i718_i507,batch1


title: MG Cell SLX-14935.i718_i505,batch1


title: 1788_BP_6


title: MG Cell SLX-14935.i718_i502,batch1


title: MG Cell SLX-14935.i718_i503,batch1


title: TUM_252

source_name: Bladder tumor samples TUM_252


title: MG Cell SLX-14935.i716_i522,batch1


title: 1788_BP_5


title: MG Cell SLX-14935.i716_i521,batch1


title: TUM_255

source_name: Bladder tumor samples TUM_255


title: TUM_254

source_name: Bladder tumor samples TUM_254


title: 1788_BP_4


title: MG Cell SLX-14935.i716_i520,batch1


title: MG Cell SLX-14935.i716_i518,batch1


title: TUM_253

source_name: Bladder tumor samples TUM_253


title: TUM_193

source_name: Bladder tumor samples TUM_193


title: 4654_BP_5


title: 4654_BP_4


title: TUM_256

source_name: Bladder tumor samples TUM_256


title: MG Cell SLX-14935.i716_i516,batch1


title: MG Cell SLX-14935.i716_i517,batch1


title: 1788_BP_2


title: MG Cell SLX-14935.i716_i515,batch1


title: MG Cell SLX-14935.i716_i513,batch1


title: 1788_BP_3


title: TUM_194

source_name: Bladder tumor samples TUM_194


title: TUM_192

source_name: Bladder tumor samples TUM_192


title: TUM_190

source_name: Bladder tumor samples TUM_190


title: MG Cell SLX-14935.i716_i511,batch1


title: MG Cell SLX-14935.i716_i510,batch1


title: MG Cell SLX-14935.i716_i508,batch1


title: iPSC, WT, Day20, biolrep2

city: Philadelphia

first: Jennifer

middle: Melissa

last: Kalish

state: PA

address: 3501 Civic Center Blvd, CTRB 3028

institute: Children's Hospital of Philadelphia

data_processing:
Sequence reads were trimmed for adaptor sequences/low quality reads using trimgalore (v0.6.10) with quality Phred score cutoff of 20
Trimmed reads were then aligned to GRCh38/hg38 using hisat2 (v2.2.1) with ASCII chars equal to the Phred quality plus 33
Read counts were extracted using featureCounts (v2.0.1)
Variance stabilizing transformation was performed using the DESeq2 package in R
Assembly: GRCh38/hg38
Supplementary files format and content: comma separated values file of raw counts for each sample
Supplementary files format and content: comma separated values file of variance stabilizing transformed counts for each sample

growth_protocol: iPSCs were cultured in mTESR plus media with primocin and pen-strep

extract_protocol:
RNA extraction was performed using AllPrep DNA/RNA Micro Kit (QIAGEN). 300 ng RNA was used for library preparation.
Libraries were prepared using the Illumina Stranded Total RNAseq library prep kit

treatment_protocol: Hepatocyte differentiation was performed using the STEMdiffTM hepatocyte kit (Stem Cell Technologies), according to the manufacturer’s instructions

value: induced pluripotent stem cells

tag: genetic modification

value: wild-type

value: hepatocyte differentiation

tag: time

value: Day 20


title: MG Cell SLX-14935.i716_i507,batch1

value: Mammary gland


title: iPSC, WT, Day15, biolrep2

value: Day 15


title: MG Cell SLX-14935.i716_i503,batch1


title: TUM_188

source_name: Bladder tumor samples TUM_188


title: MG Cell SLX-14935.i716_i505,batch1

source_name: Mammary gland


title: MG Cell SLX-14935.i716_i506,batch1


title: TUM_185

source_name: Bladder tumor samples TUM_185


title: MG Cell SLX-14935.i715_i511,batch1


title: iPSC, WT, Day20, biolrep1


title: TUM_187

source_name: Bladder tumor samples TUM_187


title: iPSC, WT, Day15, biolrep1


title: MG Cell SLX-14935.i715_i508,batch1


title: TUM_182

source_name: Bladder tumor samples TUM_182


title: 1788_BP_1

source_name: Blood

value: Blood

value: PBMC


title: TUM_181

source_name: Bladder tumor samples TUM_181


title: MG Cell SLX-14935.i715_i506,batch1


title: iPSC, WT, Day0, biolrep2

value: Day 0


title: MG Cell SLX-14935.i715_i507,batch1


title: iPSC, WT, Day0, biolrep1


title: TUM_180

source_name: Bladder tumor samples TUM_180


title: MG Cell SLX-14935.i715_i505,batch1


title: MG Cell SLX-14935.i715_i503,batch1


title: MG Cell SLX-14935.i715_i502,batch1


title: iPSC, IC2del-3H5, Day20, biolrep2

value: IC2 deletion


title: TUM_179

source_name: Bladder tumor samples TUM_179


title: iPSC, IC2del-3H5, Day20, biolrep1


title: MG Cell SLX-14935.i714_i511,batch1


title: MG Cell SLX-14935.i716_i502,batch1


title: MG Cell SLX-14935.i714_i508,batch1


title: iPSC, IC2del-3H5, Day15, biolrep2


title: MG Cell SLX-14935.i715_i510,batch1

value: Intermediate GFP+


title: MG Cell SLX-14935.i714_i507,batch1


title: MG Cell SLX-14935.i714_i506,batch1


title: iPSC, IC2del-3H5, Day15, biolrep1


title: MG Cell SLX-14935.i714_i505,batch1


title: iPSC, IC2del-3H5, Day0, biolrep2


title: TUM_178

source_name: Bladder tumor samples TUM_178


title: MG Cell SLX-14935.i712_i511,batch1


title: iPSC, IC2del-3H5, Day0, biolrep1


title: TUM_175

source_name: Bladder tumor samples TUM_175


title: MG Cell SLX-14935.i714_i502,batch1


title: TUM_172

source_name: Bladder tumor samples TUM_172


title: TUM_170

source_name: Bladder tumor samples TUM_170


title: MG Cell SLX-14935.i712_i508,batch1


title: iPSC, IC2del-3D1, Day20, biolrep2


title: MG Cell SLX-14935.i712_i510,batch1


title: MG Cell SLX-14935.i712_i507,batch1


title: MG Cell SLX-14935.i712_i506,batch1


title: MG Cell SLX-14935.i712_i505,batch1

value: Luminal cell GFP+


title: TUM_169

source_name: Bladder tumor samples TUM_169


title: MG Cell SLX-14935.i714_i510,batch1

value: Basal Cell GFP+


title: TUM_139

source_name: Bladder tumor samples TUM_139


title: TUM_142

source_name: Bladder tumor samples TUM_142


title: MG Cell SLX-14935.i714_i503,batch1


title: TUM_132

source_name: Bladder tumor samples TUM_132


title: TUM_112

source_name: Bladder tumor samples TUM_112


title: MG Cell SLX-14935.i712_i503,batch1

source_name: Mammary gland


title: MG Cell SLX-14935.i712_i502,batch1


title: MG Cell SLX-14935.i711_i511,batch1


title: iPSC, IC2del-3D1, Day15, biolrep2


title: iPSC, IC2del-3D1, Day15, biolrep1


title: MG Cell SLX-14935.i711_i510,batch1


title: MG Cell SLX-14935.i711_i506,batch1


title: MG Cell SLX-14935.i711_i508,batch1


title: iPSC, IC2del-3D1, Day0, biolrep1


title: MG Cell SLX-14935.i711_i507,batch1


title: MG Cell SLX-14935.i711_i503,batch1


title: iPSC, IC2del-3D1, Day20, biolrep1


title: MG Cell SLX-14935.i711_i505,batch1


title: SJPHALL020_R scRNA-seq

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

data_processing:
Single-cell RNA-seq data were aligned and quantified using the Cell Ranger (v5.0.1) pipeline against the human genome.
Assembly: hg38
Supplementary files format and content: Standard cellranger output format including Market Exchange format for  feature-barcode matrix and tab-separated value (tsv) format for barcode and feature sequences

source_name: primary sample

extract_protocol:
Chromium scRNA-seq Next GEM Single Cell 5' v2 (10X Genomics)
TruSeq Read 1 and TruSeq Read 2; Sequencing Read: Read 1: 26 cycles, i7 Index: 10 cycles, i5 Index: 10 cycles, Read 2: 90 cycles

value: primary leukemia sample

value: untreated


title: MG Cell SLX-14935.i710_i511,batch1


title: SJPHALL021_D scRNA-seq


title: MG Cell SLX-14935.i710_i510,batch1


title: TUM_105

source_name: Bladder tumor samples TUM_105

value: bladder cancer


title: SJPHALL020_D scRNA-seq


title: TUM_108

source_name: Bladder tumor samples TUM_108


title: MG Cell SLX-14935.i710_i507,batch1


title: SJPHALL010_D scRNA-seq


title: TUM_75

source_name: Bladder tumor samples TUM_75


title: TUM_72

source_name: Bladder tumor samples TUM_72


title: MG Cell SLX-14935.i710_i505,batch1


title: TUM_68

source_name: Bladder tumor samples TUM_68


title: MG Cell SLX-14935.i710_i506,batch1


title: MG Cell SLX-14935.i710_i503,batch1


title: TUM_65

source_name: Bladder tumor samples TUM_65


title: MG Cell SLX-14935.i711_i502,batch1


title: TUM_67

source_name: Bladder tumor samples TUM_67


title: MG Cell SLX-14935.i710_i502,batch1


title: TUM_63

source_name: Bladder tumor samples TUM_63


title: iPSC, IC2del-3D1, Day0, biolrep2


title: MG Cell SLX-14935.i707_i510,batch1


title: MG Cell SLX-14935.i707_i511,batch1

value: Luminal cell GFP-


title: SJPHALL006_D scRNA-seq


title: MG Cell SLX-14935.i707_i508,batch1


title: MG Cell SLX-14935.i710_i508,batch1


title: SJPHALL004_D scRNA-seq


title: SJMLL009_D scRNA-seq


title: TUM_44

source_name: Bladder tumor samples TUM_44


title: MG Cell SLX-14935.i707_i506,batch1


title: MG Cell SLX-14935.i707_i505,batch1


title: MG Cell SLX-14935.i707_i503,batch1


title: TUM_40

source_name: Bladder tumor samples TUM_40


title: MG Cell SLX-14935.i707_i502,batch1


title: SJPHALL007_D scRNA-seq


title: MG Cell SLX-14935.i706_i511,batch1


title: SJINF022043_D1 scRNA-seq


title: SJHYPO146_D scRNA-seq


title: MG Cell SLX-14935.i706_i510,batch1


title: MG Cell SLX-14935.i706_i507,batch1


title: MG Cell SLX-14935.i706_i508,batch1


title: MG Cell SLX-14935.i706_i506,batch1


title: SJHYPO143_D scRNA-seq


title: MG Cell SLX-14935.i706_i505,batch1


title: SJHYPO124_D scRNA-seq


title: TUM_55

source_name: Bladder tumor samples TUM_55


title: MG Cell SLX-14935.i706_i502,batch1


title: TUM_36

source_name: Bladder tumor samples TUM_36


title: MG Cell SLX-14935.i706_i503,batch1


title: MG Cell SLX-14935.i707_i507,batch1


title: TUM_37

source_name: Bladder tumor samples TUM_37


title: TUM_33

source_name: Bladder tumor samples TUM_33


title: SJMLL006_D scRNA-seq


title: TUM_30

source_name: Bladder tumor samples TUM_30


title: TUM_25

source_name: Bladder tumor samples TUM_25


title: MG Cell SLX-14935.i705_i510,batch1

source_name: Mammary gland


title: SJHYPO120_D scRNA-seq

source_name: primary sample


title: MG Cell SLX-14935.i705_i511,batch1


title: MG Cell SLX-14935.i705_i508,batch1


title: MG Cell SLX-14935.i705_i506,batch1


title: TUM_38

source_name: Bladder tumor samples TUM_38


title: SJHYPO117_D scRNA-seq


title: SJHYPO021982_D1 scRNA-seq


title: SJHYPER022017_D1 scRNA-seq


title: TUM_17

source_name: Bladder tumor samples TUM_17


title: MG Cell SLX-14935.i705_i505,batch1


title: MG Cell SLX-14935.i705_i502,batch1


title: SJE2A067_D scRNA-seq


title: TUM_14

source_name: Bladder tumor samples TUM_14


title: SJE2A066_D scRNA-seq


title: MG Cell SLX-14935.i704_i506,batch1


title: MG Cell SLX-14935.i704_i507,batch1


title: MG Cell SLX-14935.i704_i508,batch1


title: BAT BDJ1KO TN rep3

city: Shanghai

first: Kong

last: Xingxing

address: Songhu Road 2005

department: School of Life Sciences

institute: Fudan University

data_processing:
The clean reads were mapped to the reference genome (mm10) using STAR (2.7.10a).
Quantification of gene expression was calculated using RSEM (v1.2.28).
Differential expression analysis between groups was conducted using the DESeq2(1.3.40) with adjust P value < 0.05 and |FC|>1.5. GO enrichment analysis and KEGG pathway analysis was performed by clusterProfiler (4.2.2) with different expression genes.
Assembly: mm10
Supplementary files format and content: csv files include counts values for each samples

source_name: BAT

extract_protocol:
Brown adipose tissues(BAT) from BAT-specific DJ-1 knockout (BDJ1KO) mice and flox mice which were housed at room temperature or 29°C for 8 weeks extracted for RNA sequencing.
cDNA libraries for each sample were constructed as reported previously (Yao et al., 2022).
Libraries were sequenced on BGIseq500 platform (BGI, China), using 150 bp paired-end reads aimed at 30 million reads per sample.

value: BAT

value: BAT DJ1KO

value: 29 degreeC housing


title: MG Cell SLX-14935.i704_i510,batch1


title: BAT BDJ1KO TN rep2


title: MG Cell SLX-14935.i705_i507,batch1


title: SJBALL255_D scRNA-seq


title: BAT BDJ1KO TN rep1


title: MG Cell SLX-14935.i704_i502,batch1


title: TUM_7

source_name: Bladder tumor samples TUM_7


title: MG Cell SLX-14935.i704_i505,batch1


title: TUM_23

source_name: Bladder tumor samples TUM_23


title: MG Cell SLX-14935.i704_i503,batch1


title: MG Cell SLX-14935.i703_i508,batch1


title: SJBALL243_D scRNA-seq


title: MG Cell SLX-14935.i705_i503,batch1


title: MG Cell SLX-14935.i703_i510,batch1


title: MG Cell SLX-14935.i703_i511,batch1


title: BAT WT TN rep4

value: WT


title: MG Cell SLX-14935.i704_i511,batch1

value: Mammary gland


title: MG Cell SLX-14935.i703_i506,batch1


title: MG Cell SLX-14935.i703_i507,batch1


title: SJE2A063_D scRNA-seq


title: TUM_8

source_name: Bladder tumor samples TUM_8


title: SJBALL182_R scRNA-seq


title: SJBALL211_D scRNA-seq


title: MG Cell SLX-14935.i703_i505,batch1


title: MG Cell SLX-14935.i703_i503,batch1


title: BAT WT TN rep1


title: MG Cell SLX-14935.i703_i502,batch1


title: MG Cell SLX-14935.i702_i511,batch1


title: SJBALL113_D scRNA-seq


title: MG Cell SLX-14935.i702_i510,batch1


title: MG Cell SLX-14935.i702_i508,batch1


title: SJBALL104_D scRNA-seq


title: BAT BDJ1KO RT rep4

value: room temperature housing


title: SJBALL087_D scRNA-seq


title: BAT BDJ1KO RT rep3


title: SJBALL081_D scRNA-seq


title: MG Cell SLX-14935.i702_i507,batch1


title: MG Cell SLX-14935.i702_i503,batch1


title: MG Cell SLX-14935.i702_i502,batch1


title: BAT BDJ1KO RT rep2


title: MG Cell SLX-14935.i702_i506,batch1


title: MG Cell SLX-14935.i701_i511,batch1


title: BAT BDJ1KO RT rep1


title: BAT WT TN rep3


title: MG Cell SLX-14935.i701_i510,batch1


title: BAT WT TN rep2


title: SJBALL031267_D1 scRNA-seq


title: SJBALL182_D scRNA-seq


title: MG Cell SLX-14935.i701_i507,batch1


title: BAT WT RT rep3


title: MG Cell SLX-14935.i701_i508,batch1


title: MG Cell SLX-14935.i701_i506,batch1


title: BAT WT RT rep4


title: SJBALL031144_D1 scRNA-seq


title: SJBALL031168_D1 scRNA-seq


title: BAT WT RT rep2


title: MG Cell SLX-14935.i701_i503,batch1


title: MG Cell SLX-14935.i701_i505,batch1


title: MG Cell SLX-14935.i701_i502,batch1


title: BAT WT RT rep1


title: MG Cell SLX-14935.i702_i505,batch1


title: AP5/AP

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Raw sequencing files were demultiplexed using in house python script.
Quality of Raw-seq data were reviewed using FastQC. Single end reads from individual libraries were aligned to the rat reference genome (mm10) using STAR aligner (Dobin, Davis et al., 2013).
From each library,  raw counts were obtained from uniquely aligned reads for all the Mus Musculus  genes (mm10; ucsc genome annotation) using the featureCounts tools from the Subread package
Differential expression analysis was performed using DESEq2 package  (absolute log2FC >= 1 and q <0.05)
Assembly: mm10
Supplementary files format and content: ReadCountsRNAseq.txt: raw readcounts
Supplementary files format and content: APvsCON.csv: DESEq2 output

source_name: Mouse placenta

growth_protocol: : C57/BL6 strain of mice were purchased from Jackson Lab, Bar Harbor, ME. Mice were maintained in 12:12-h light-dark cycles and care/treatment provided according to UCLA Animal Research Committee’s approved protocol in accordance with the guidelines set by the National Institutes of Health

extract_protocol:
placenta samples were collected at gestational day 19 (GD19) after hysterectomy and total RNA was extracted for transcriptomic profile using Zymo Direct-zol RNA miniprep kit (#R2050; Zymo research, Irvine, CA, USA) following manufacturer’s instructions.
mRNA seq libraries were prepared with Kapa Stranded RNA sequencing kit with Ribo-erase (# KK8483; Kapa Biosystem, Cape Town, South Africa) following manufacturer’s protocol. . Sample qualities were assessed by Agilent RNA Bioanalyzer chip traces before pooled and sequenced with an Illumina HiSeq 4000.

treatment_protocol: The Airborne PM sourced from SRM 1649b, obtained from the National Institute of Standards and Technology in Gaithersburg, MD, USA, was suspended in sterile phosphate buffered saline (PBS) to reach a concentration of 15 μg/μl. Following thorough mixing and sonication for a minimum of 15 minutes using an ultrasonic vibration instrument, pregnant mice were dosed with 300 µg/day of the suspended solution.

value: Mouse placenta

tag: Sex

value: Female

tag: study group

value: intra-nasal instilled air pollutants


title: SJBALL031281_D1 scRNA-seq

tag: treatment


title: SJBALL031128_D1 scRNA-seq

tag: cell type


title: AP4/AP

tag: tissue


title: D5

city: Beijing

first: Xiaoping

last: Wang

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

description: Library name: Sample8

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Sus_scrofa_GCF_000003025.6.gtf
Supplementary files format and content: xls files include raw counts for each Sample

organism: Sus scrofa

source_name: Heart

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen). 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Heart

value: Doxorubicin


title: AP3/AP


title: AP2/AP


title: SJBALL031052_D1 scRNA-seq


title: D3

description: Library name: Sample6


title: C4/CON

value: Control


title: SJBALL031087_D1 scRNA-seq


title: D4

description: Library name: Sample7


title: C3/CON


title: AP1/AP


title: C2/CON


title: D2

description: Library name: Sample5


title: C1/CON


title: SJBALL030975_D1 scRNA-seq


title: D1

description: Library name: Sample4


title: SJBALL030971_D1 scRNA-seq


title: SJBALL030923_D1 scRNA-seq


title: SJBALL030871_D1 scRNA-seq


title: C2

description: Library name: Sample2

value: Vehicle


title: C3

description: Library name: Sample3


title: SJBALL030762_D1 scRNA-seq

value: primary leukemia sample


title: C1

description: Library name: Sample1


title: KO3.RNAseq_3

city: San Diego

first: Samiksha

last: Mahapatra

address: 9452 Medical Center Dr

institute: University of California San Diego

description:
Library name: KO3
RNA-seq

data_processing:
NovaSeq S4 PE100 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using STAR 2.7 index for alignment into fastq files.
Fastq files were imported into the RNA-seq pipeline of Partek FLow, version 9.0.20.0202 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 93 2020-02-03). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Assembly: mm10
Supplementary files format and content: text file includes normalized counts for each sample

source_name: Mouse adipocytes

growth_protocol: P0 neonatal fibroblasts differentiated in culture in Adipocyte differentiation medium (Stem Cell Technologies)

extract_protocol:
GeneJet RNA Purification kit (Thermo Scientific K0732) and then samples were quantified via Nanodrop
RNA-seq libraries were prepared with Illumina RNA Library Prep Kit (Illumina) then multiplexed

value: Mouse adipocytes

value: Nelfb KO

value: P0 fibroblasts differentiated in adipocyte media for 14 days


title: SJBALL030734_D1 scRNA-seq

value: untreated


title: KO2.RNAseq_2

description:
Library name: KO2
RNA-seq


title: TUM_346

description: Gene expression data from bladder tumor

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG,  Brainarray Custom CDF EntrezG version 22,

label: biotin

source_name: Bladder tumor samples TUM_346

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

extract_protocol: Tumor RNA was extracted using Qiazol (Qiagen, Courtaboeuf, France) according to the manufacturer instructions and purified using miRNeasy Mini kit (Qiagen).

treatment_protocol: Bladder tumors were directly snap frozen in liquid nitrogen after resection and stored at -80°C. DNA, RNA and proteins were obtained following a triple extraction protocol

value: bladder cancer


title: SJBALL030821_D1 scRNA-seq


title: SJBALL030718_D1 scRNA-seq


title: KO1.RNAseq_1

description:
Library name: KO1
RNA-seq


title: TUM_347

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_347


title: SJBALL030491_D1 scRNA-seq


title: TUM_345

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_345


title: TUM_290

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_290


title: TUM_289

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_289


title: TUM_294

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_294


title: TUM_285

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_285


title: TUM_276

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_276


title: CTL2.RNAseq_2

description:
Library name: CTL2
RNA-seq

value: CTL


title: TUM_283

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_283


title: TUM_280

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_280


title: TUM_293

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_293


title: SJBALL030434_D1 scRNA-seq

source_name: primary sample


title: TUM_281

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_281


title: TUM_274

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_274


title: TUM_269

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_269


title: TUM_273

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_273


title: SJBALL030662_D1 scRNA-seq


title: SJBALL030379_D1 scRNA-seq


title: SJBALL030414_D1 scRNA-seq


title: A-II-801

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: A-II-801

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Excel file includes FPM values for each Sample.

source_name: aorta

extract_protocol:
The isolated small intestine are quickly put into RNA later (Invitrogen, Waltham, Massachusetts, USA) and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

value: aorta

value: Sirt6 KO

value: Ang II


title: TUM_256

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_256


title: TUM_255

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_255


title: TUM_254

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_254


title: CTL3.RNAseq_3

description:
Library name: CTL3
RNA-seq

source_name: Mouse adipocytes


title: A-II-800

description: Library name: A-II-800


title: SJBALL030344_D1 scRNA-seq


title: SJBALL030370_D1 scRNA-seq


title: CTL1.RNAseq_1

description:
Library name: CTL1
RNA-seq


title: A-II-797

description: Library name: A-II-797


title: TUM_253

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_253


title: SJBALL030285_D1 scRNA-seq


title: A-II-809

description: Library name: A-II-809

value: WT


title: TUM_194

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_194


title: TUM_258

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_258


title: A-II-806

description: Library name: A-II-806


title: TUM_252

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_252


title: SJBALL030276_D1 scRNA-seq


title: TUM_193

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_193


title: A-II-803

description: Library name: A-II-803


title: SJBALL030254_D1 scRNA-seq


title: TUM_190

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_190


title: TUM_188

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_188


title: TUM_185

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_185


title: TUM_192

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_192


title: TUM_181

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_181


title: TUM_182

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_182


title: TUM_180

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_180


title: A-II-798

description: Library name: A-II-798

source_name: aorta


title: A-II-799

description: Library name: A-II-799


title: SJBALL030313_D1 scRNA-seq

source_name: primary sample


title: TUM_179

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_179


title: SJBALL030247_D1 scRNA-seq


title: TUM_175

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_175


title: TUM_172

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_172


title: SJBALL030216_D1 scRNA-seq


title: Con-825

description: Library name: Con-825

value: saline


title: Con-823

description: Library name: Con-823


title: TUM_187

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_187


title: SJBALL030145_D1 scRNA-seq


title: SJBALL030127_D1 scRNA-seq


title: Con-821

description: Library name: Con-821


title: TUM_170

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_170


title: Con-822

description: Library name: Con-822


title: SJBALL030123_R1 scRNA-seq


title: Con-819

description: Library name: Con-819


title: SJBALL030123_D1 scRNA-seq


title: TUM_178

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_178


title: TUM_139

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_139


title: TUM_169

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_169


title: Con-817

description: Library name: Con-817


title: SJBALL030095_D1 scRNA-seq


title: SJBALL030090_D1 scRNA-seq


title: TUM_142

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_142


title: TUM_132

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_132


title: TUM_112

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_112


title: SJBALL030072_D1 scRNA-seq


title: TUM_105

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_105


title: TUM_67

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_67


title: TUM_65

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_65


title: TUM_75

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_75


title: TUM_68

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_68


title: TUM_72

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_72


title: TUM_55

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_55


title: TUM_63

description: Gene expression data from bladder tumor

source_name: Bladder tumor samples TUM_63