title: Tet2dRBD-KI ESC Tet2dRBD-RIP IP repl1


title: WT ESC 5hmC-RIP IP repl 2

status: Public on Jul 16 2020

type: SRA

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

library_source: transcriptomic

data_processing:
The raw sequencing data were first analyzed using FastQC. Low complexity reads were removed using AfterQC tool with default parameters. Further, to get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences using bowtie2. The rRNA and tRNA sequences were downloaded from https://www.ncbi.nlm.nih.gov/nuccore using "Mus musculus"[Organism] AND (biomol_rrna[PROP] OR biomol_trna[PROP] as search parameters. Reads that were unmapped to tRNA and rRNA sequences were then further processed using Trimmomatic with default parameters to remove adapter sequences. The resulting fastq data was again analyzed using FastQC to ensure no further processing is needed.
Preprocessed reads were then mapped against the mouse reference genome using STAR algorithm with RefSeq reference transcriptome (download on March 2012). 5hmC-enriched regions (peaks) were identified by applying MACS2 peak-calling tool on immunoprecipitated (IP) samples using their input counterpart for estimating background noise (q-value < 0.05). Of note, the expected genome size MACS2 parameter was set as the sum of all transcripts length including exons and introns (counting a single time regions shared by several transcripts) and the summits positions were identified using --call-summits MACS2 option. To avoid identification of extremely large enriched regions, peaks were, then, resized to 100bp from both size of the identified summit.
Genome_build: mm9
Supplementary_files_format_and_content: Peak positions (100bp around both side of the summits) in bed format

molecule: total RNA

organism: Mus musculus

source_name: Embryonic Stem Cells

growth_protocol: Mouse ESCs (WT, KI or TKO) were grown under standard culture conditions. Briefly, cells were cultured on 0.1% gelatin-coated tissue culture plates in high-glucose DMEM medium containing 15% FBS, 1mM sodium pyruvate, 1% nonessential amino acids, 1% glutaMAX, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.1 mM b-mercaptoethanol and 1000 unit/ml recombinant mouse leukemia inhibitory factor.

extract_protocol:
Total RNA from WT ESCs, TKO ESCs and WT EBs were extracted with either the RNeasy Mini or Maxi kit or TRIzol according to the manufacturer's instructions. Genomic DNA was eliminated by DNase treatment.
hMeRIP-seq: The procedure was performed in ESCs as described in Dominissi et al., 2012. Briefly, 1 mg of total RNA was sonicated to an average size of 200-300bp. RNA was then precipitated in ethanol, resuspended in RNase-free ddH2O and the fragmentation efficiency was checked on a Bioanalyzer RNA chip. For immunoprecipitation, RNA fragments were denatured by heating at 70  C for 5 min, chilled on ice for 5 min, then incubated overnight at 4  C with or without 12.5 ug of anti-5hmC antibody, in freshly prepared 1X IP buffer (50 mM Tris-HCl pH=7.4, 750 mM NaCl and 0.5% Igepal CA-630, RNasin 400 U/ml and RVC 2 mM) supplemented with protease inhibitors. Samples were then incubated at 4  C for 2.5h with 60 ul equilibrated Dynabeads Protein G, washed three times for 5 min with 1 ml IP buffer, and eluted by addition of 1 ml TriPure Reagent followed by RNA extraction according to the manufacturer's instructions.
Library preparation was performed as described in Delatte et al., 2016. Briefly, 5 to 10 ng dsDNA was subjected to 5' and 3' protruding end repair, followed by the addition of non-templated adenines to the 3' ends of the blunted DNA fragments, which allows ligation of Illumina multiplex adapters. The DNA fragments were then size selected so as to remove all unligated adapters and to sequence 200-300-bp fragments. 18 cycles of PCR were carried out to amplify the library. DNA was quantified by fluorometry with the Qubit 2.0 and DNA integrity was assessed with a 2100 bioanalyzer. 6 pM of DNA library spiked with 1% PhiX viral DNA was clustered on cBot and then sequenced.

treatment_protocol: (EB only) Embryoid body formation: Embryoid bodies (EBs) were formed from ESCs following the published standard protocol from Miriam Bibel et al. 2007, nature protocols. Briefly, ESCs were trypsinized, resuspend in ES medium without LIF and count the cells. Then 4 × 106 ESCs were seeded onto bacteriological Greiner Petri dishes in 15 ml ES medium without LIF. EBs were maintained in ES medium without LIF for 4 days before collection for further analysis. (KI only) Mouse ESCs (WT) producing tagged Tets were generated with the CRISPR-Cas9n nuclease system. Briefly, sgRNAs were designed to target the stop codons of Tet1 and Tet2 (for C-terminal tags) using the guidelines described in MIT’s online tool. They were cloned into the pX461 vector. Lipofectamine™ 3000 was used according to the manufacturer's instructions (Thermo Fisher Scientific, catalogue number L3000015) to co-transfect ESCs with an sgRNA-containing plasmid and a template containing triple tags (Flag+HA+Twin-Strep from the pINTO-N3 vector3, flanked by homologous arms with or without RBD for Tet2. Twenty-four hours after transfection, GFP-positive ESCs were selected by cell sorting and seeded into 96-well plates. One week later, clones were picked and analysed for the Flag tag by western blotting, and the CRISPR-Cas9n-targeted genomic regions were PCR-amplified and sequenced in clones producing tagged Tet2, or Tet2ΔRBD.

tag: sample type

tag: rip antibody

value: anti-5hmC antibody

tag: cell type

value: ESC

tag: genotype

value: WT


title: Tet2-KI ESC Tet2-RIP Input repl3

data_processing:
The raw sequencing data were first analyzed using FastQC. Low complexity reads were removed using AfterQC tool with default parameters. Further, to get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences using bowtie2. The rRNA and tRNA sequences were downloaded from https://www.ncbi.nlm.nih.gov/nuccore using "Mus musculus"[Organism] AND (biomol_rrna[PROP] OR biomol_trna[PROP] as search parameters. Reads that were unmapped to tRNA and rRNA sequences were then further processed using Trimmomatic with default parameters to remove adapter sequences. The resulting fastq data was again analyzed using FastQC to ensure no further processing is needed.
The processed data were then mapped to mouse genome with RefSeq reference transcriptome (download on March 2012) using RSEM tool. TPM was computed from the RSEM expression counts and pseudocount of 1 TPM was added to compute fold change of IP over Input.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM (with 1TPM pseudocount) values

molecule: polyA RNA

growth_protocol: Mouse ESCs (WT) were grown under standard culture conditions. Briefly, cells were cultured on 0.1% gelatin-coated tissue culture plates in high-glucose DMEM medium containing 15% FBS, 1mM sodium pyruvate, 1% nonessential amino acids, 1% glutaMAX, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.1 mM b-mercaptoethanol and 1000 unit/ml recombinant mouse leukemia inhibitory factor.

extract_protocol:
Total RNA from WT ESCs were extracted with either the RNeasy Mini or Maxi kit or TRIzol according to the manufacturer's instructions. Genomic DNA was eliminated by DNase treatment.
Library preparation was performed as described in Delatte et al., 2016. Briefly, 5 to 10 ng dsDNA was subjected to 5' and 3' protruding end repair, followed by the addition of non-templated adenines to the 3' ends of the blunted DNA fragments, which allows ligation of Illumina multiplex adapters. The DNA fragments were then size selected so as to remove all unligated adapters and to sequence 200-300-bp fragments. 18 cycles of PCR were carried out to amplify the library. DNA was quantified by fluorometry with the Qubit 2.0 and DNA integrity was assessed with a 2100 bioanalyzer. 6 pM of DNA library spiked with 1% PhiX viral DNA was clustered on cBot and then sequenced on a HiScanSQ module.

treatment_protocol: Mouse ESCs (WT) producing tagged Tets were generated with the CRISPR-Cas9n nuclease system as described previously2. Briefly, sgRNAs were designed to target the stop codons of Tet1 and Tet2 (for C-terminal tags) using the guidelines described in MIT’s online tool. They were cloned into the pX461 vector. Lipofectamine™ 3000 was used according to the manufacturer's instructions (Thermo Fisher Scientific, catalogue number L3000015) to co-transfect ESCs with an sgRNA-containing plasmid and a template containing triple tags (Flag+HA+Twin-Strep from the pINTO-N3 vector3, flanked by homologous arms for Tet1 and by homologous arms with or without RBD for Tet2. Twenty-four hours after transfection, GFP-positive ESCs were selected by cell sorting and seeded into 96-well plates. One week later, clones were picked and analysed for the Flag tag by western blotting, and the CRISPR-Cas9n-targeted genomic regions were PCR-amplified and sequenced in clones producing tagged Tet1, Tet2, or Tet2ΔRBD.

tag: experiment type


title: Tet2dRBD-KI ESC Tet2dRBD-RIP IP repl3

value: anti-Flag antibody


title: Tet2-KI ESC Tet2-RIP IP repl4


title: Tet2-KI ESC Tet2-RIP Input repl2


title: Tet2-KI ESC Tet2-RIP Input repl1


title: Tet2-KI ESC Tet2-RIP IP repl2


title: Tet2-KI ESC Tet2-RIP IP repl3


title: Tet2-KI ESC Tet2-RIP IP repl1


title: Tet1-KI ESC Tet1-RIP IP repl2


title: Tet1-KI ESC Tet1-RIP IP repl1


title: Tet1-KI ESC Tet1-RIP Input repl2


title: WT ESC polyA RNAseq repl3

data_processing:
The raw sequencing data were first analyzed using FastQC. Low complexity reads were removed using AfterQC tool with default parameters. Further, to get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences using bowtie2. The rRNA and tRNA sequences were downloaded from https://www.ncbi.nlm.nih.gov/nuccore using "Mus musculus"[Organism] AND (biomol_rrna[PROP] OR biomol_trna[PROP] as search parameters. Reads that were unmapped to tRNA and rRNA sequences were then further processed using Trimmomatic with default parameters to remove adapter sequences. The resulting fastq data was again analyzed using FastQC to ensure no further processing is needed.
Raw read count were obtained using HTseq tool and normalized in TPM.
Genome_build: mm9
Supplementary_files_format_and_content: read counts in TPM

growth_protocol: Wild type (WT) and Tet1,2,3 triple knock-out (TKO) mouse ESCs were grown under standard culture conditions. Briefly, cells were cultured on 0.1% gelatin-coated tissue culture plates in high-glucose DMEM medium containing 15% FBS, 1mM sodium pyruvate, 1% nonessential amino acids, 1% glutaMAX, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.1 mM b-mercaptoethanol and 1000 unit/ml recombinant mouse leukemia inhibitory factor.

extract_protocol:
RNA from ESCs were extracted with either the RNeasy Mini or Maxi kit or TRIzol according to the manufacturer's instructions. Genomic DNA was eliminated by DNase treatment.
(WT) Poly-A enriched mRNA sequencing was performed on the Illumina Hiseq 2000 platform following library preparation using the TruSeq Stranded mRNA Library Prep Kit (which includes the polyA-enrichment step). (amanitin 0 and 4h) total RNAs from α-amanitin treated and untreated control cells were extracted and underwent ribosomal RNA depletion.100-200M strand-specific pair-end reads of 150bp were generated per sample.

treatment_protocol: (aminitin 0h and 4h) WT and TKO ESCs were treated with 10 μg/ml α-amanitin or with an equal volume of vehicle (water) as a control for 0 or 4 h, respectively.


title: WT ESC polyA RNAseq repl1


title: Tet1-KI ESC Tet1-RIP Input repl1


title: WT ESC polyA RNAseq repl2


title: S17171_M7_Emx_Cx_P0_mat

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

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

data_processing:
Raw reads were delivered as BAM files and converted to fastq format using bamToFastq (bedtools suite v2.26.0) for alignment. Reads within transcripts were counted using STAR_2.5.0c with an index prepared from GRCm38 and Gencode M16 gene annotation. Note that for optimal representation of the long non-coding RNA Meg3 the spliced ENSMUST00000143836.7 transcript was modified to represent a single exon transcript. Parameters used for STAR alignment: --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts.
Raw counts from STAR alignment were used to analyse the data with Seurat (v3.1.4)
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Read counts in transcripts as reported by STAR as tab delimited text

growth_protocol: All mouse colonies were maintained in accordance with protocols approved by institutional animal care and use committee, institutional ethics committee and the preclinical core facility (PCF) at IST Austria. Experiments were performed under a license approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and EU animal laws. Mouse lines used: Emx1-Cre (JAX stock # 005628); MADM-7-GT (JAX stock # 021457), MADM-7-TG (JAX stock # 021458)

extract_protocol:
Single cells were sorted into 96 well plates (Bio-Rad) containing 4µl lysis buffer (0.2% Triton X-100, 2U/µl RNase Inhibitor [Clonetech]) per well.
sorted cells were directly processed without RNA extraction using Smart-Seq2 (VBCF GmbH Vienna or Biomedical Sequencing Facility (BSF) at CeMM Vienna)

treatment_protocol: Animals were sacrificed and brain areas of interest were dissected. Single cell suspensions were prepared by using Papain containing L-cysteine and EDTA (vial 2, Worthington), DNase I (vial 3, Worthington), Ovomucoid protease inhibitor (vial 4, Worthington), EBSS (Thermo Fisher Scientific), DMEM/F12 (Thermo Fisher Scientific), FBS and HS. All vials from Worthington kit were reconstituted according to the manufacturer’s instructions using EBSS. The dissected brain areas were directly placed into Papain-DNase solution (20units/ml papain and 1000 units DNase). Enzymatic digestion was performed for 30min at 37°C in a shaking water bath. Next, solution 2 (EBSS containing 0.67mg Ovomucoid protease inhibitor and 166.7 U/ml DNase I) was added, the whole suspension was thoroughly mixed and centrifuged for 5min at 1000rpm at RT. Supernatant was removed and cell pellet was resuspended in solution 2. Trituration with p1000 pipette was performed to mechanically dissolve any remaining tissue parts. DMEM/F12 was added to the cell suspension as a washing solution, followed by a centrifugation step of 5min with 1500rpm at RT. Cells were resuspended in media (DMEM/F12 containing 10% FBS and 10% HS) and kept on ice until sorted. Right before sorting, cell suspension was filtered using a 40µm cell strainer. FACS was performed on a BD FACS Aria III using 100 nozzle and keeping sample and collection devices at 4°C. Duplet exclusion was performed to ensure sorting of true single cells. GFP+ (green), tdTomato+ (red), and GFP+/tdTomato+ (yellow) cells were collected.

value: Emx1 lineage

tag: tissue

value: Neocortex

tag: madm insertion

tag: strain

tag: cre-driver

tag: upd

value: mat

tag: age


title: S17170_M7_Emx_Cx_P0_mat


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title: 72479_M7_Emx_Cx_P42_pat

value: pat


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title: 72449_M7_Emx_Cx_P42_pat


title: NPC E2A knockout-4, rep2

city: Beijing

first: Yang

last: Li

address: Xueyuan Road 38,Haidian District

country: China

institute: Peking University

data_processing:
HCS2.2.58 and RTA v1.18 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, including those containing more than 10% of unknown nucleotides or more than 50% of low-quality (Q-value no larger than 20%) bases. Then they were filtered against rRNA database to remove potential rRNA contamination.
Reads that passed the above filtration and quality control were mapped to GRCh38 genome, by using TopHat2 software (version 2.0.3) with custom parameters -N 2 -r 50 --mate-std-dev 80. And the transcripts were reconstructed by RABT (reference annotation based transcripts) tool in Cufflink software (version 2.0.1) with default parameters. Transcripts from different replications were merged by Cuffmerge tool in Cufflink software, then transcripts from the treatment group and the control group sampled from the same tissue were further merged by Cuffmerge tool.
Gene abundances were quantified by RSEM software (version 1.1.20) with command line parameters suggested by Trpnell C, et al Nature protocol, 2012, 7(3): 562-578. The gene expression level was normalized by using Reads Per Kilobase of transcript per Million mapped reads (RPKM) method, where the number of reads mapped to the specific gene was normalized by the total number of reads that mapped to reference genes and the number of bases on this specific gene.
Genome_build: GRCh38 genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

organism: Homo sapiens

source_name: Neural progenitor cells

growth_protocol: hESCs (H1; WiCell Research Institute, Madison, WI) were maintained and expanded on plates coated with growth-factor-reduced Matrigel (Corning, NY, USA) in serum-free, defined TeSR-E8 medium (STEMCELL Technologies, Vancouver, Canada). To initiate neural differentiation, hESC were plated onto Matrigel-coated 12-well plates at 95–100% cell confluence, and then cultured in Neural induction medium (STEMCELL Technologies, Vancouver, Canada), changing to fresh culture medium every two days.Cells were passaged by non-enzymatic dissociation using 0.5 mM EDTA (CELLAPY Technologies, BeiJing, China).

extract_protocol:
Cells were harvested, flash frozen on dry ice. Total RNA was extracted by using TruSeq RNA Library Prep Kit v2 under the manufacturer's guideline
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E2A KO hESCs were generated with CPRISPR-Cas9 genome editing technology.

value: Embryonic stem cells (H1) derived neural progenitor cells

tag: treatment

value: untreated


title: NPC E2A knockout-1, rep2


title: NPC wild type, rep3


title: 72425_M7_Emx_Cx_P42_mat


title: 72445_M7_Emx_Cx_P42_pat


title: 72434_M7_Emx_Cx_P42_pat


title: 72442_M7_Emx_Cx_P42_mat


title: NPC E2A knockout-4, rep3


title: 72430_M7_Emx_Cx_P42_pat


title: NPC wild type, rep2


title: 72424_M7_Emx_Cx_P42_mat


title: NPC E2A knockout-1, rep1


title: NPC E2A knockout-1, rep3


title: ESC (H1) E2A knockout, rep3

source_name: Embryonic stem cells

growth_protocol: hESCs (H1; WiCell Research Institute, Madison, WI) were maintained and expanded on plates coated with growth-factor-reduced Matrigel (Corning, NY, USA) in serum-free, defined TeSR-E8 medium (STEMCELL Technologies, Vancouver, Canada). Cells were passaged by non-enzymatic dissociation using 0.5 mM EDTA (CELLAPY Technologies, BeiJing, China).

value: Embryonic stem cells (H1)


title: NPC wild type, rep1


title: 72422_M7_Emx_Cx_P42_mat


title: 72423_M7_Emx_Cx_P42_mat


title: ESC (H1) E2A knockout, rep2


title: NPC E2A knockout-4, rep1


title: 72420_M7_Emx_Cx_P42_mat


title: 72421_M7_Emx_Cx_P42_mat


title: NPC-H3K27me3-E2AKO-NPC

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers (see Section V.). bigWig files also provide the peak metrics in the Active Motif analysis program described below.
The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS/MACS2 (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009). MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II). Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background).
Genome_build: GRCh38 genome
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: E2AKO neural progenitor cells - H3K27me3

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: antibody

value: H3K27me3 ( Active Motif #39155)


title: ESC (H1) wild type, rep3


title: 72419_M7_Emx_Cx_P42_pat


title: 72416_M7_Emx_Cx_P42_pat


title: 72417_M7_Emx_Cx_P42_pat


title: 72418_M7_Emx_Cx_P42_pat


title: NPC-H3K4me3-WT-NPC

source_name: Wild type neural progenitor cells - H3K4me3

value: H3K4me3 ( Active Motif #39159)


title: ESC (H1) E2A knockout, rep1


title: 72413_M7_Emx_Cx_P42_pat


title: NPC-Input

source_name: Neural progenitor cells - input DNA


title: ESC (H1) wild type, rep2


title: ESC (H1) wild type, rep1


title: 72412_M7_Emx_Cx_P42_pat


title: NPC-H3K27me3-WT-NPC

source_name: Wild type neural progenitor cells - H3K27me3


title: 72414_M7_Emx_Cx_P42_pat


title: NPC-H3K4me3-E2AKO-NPC

source_name: E2AKO neural progenitor cells - H3K4me3


title: 72411_M7_Emx_Cx_P42_mat


title: 72410_M7_Emx_Cx_P42_mat


title: ESC (H1) Input

source_name: Embryonic stem cells - input DNA

treatment_protocol: Untreated


title: 72409_M7_Emx_Cx_P42_mat


title: E2A-ESC

source_name: Embryonic stem cells - E2A

value: E2A (Santa Cruz, sc-349)


title: 72406_M7_Emx_Cx_P42_mat


title: 72415_M7_Emx_Cx_P42_pat


title: 72405_M7_Emx_Cx_P42_mat


title: KO2

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

country: USA

institute: RPCI

data_processing:
trimmed reads are mapped to the UCSC mus musculus genome sequence (version GRCm38) using a methylation-aware mapper, bismark. Bismark stores bisulfite read mapping and methylation calling in the SAM format
DMC analysis is performed in the CpG context. Samples are filtered by coverage (minimum 5), normalized, merged (only bases that are covered in all samples in the comparison are included), and subjected to DMC identification. The identified DMCs are annotated against the RefSeq genes (exons, introns, and promoters), and the CpG islands/shores.
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph

source_name: Mammary gland

extract_protocol: Libraries were prepared by DNA end polishing, adaptor ligation, library amplification using indexed primers and library purification

treatment_protocol: DNA was isolated from cells from WT and KO mouse mammary glands and concentration was measured with Picogreen fluorescence method. The samples were subjected to enzymatic digestion (MSP1+TaqI), library preparation, bisulfite conversion (Methylamp DNA Bisulfite Conversion Kit, Epigentek), Bioanalyzer QC, KAPA library quantification, and multiplex next generation sequencing on an Illumina HiSeq4000.

value: Tet2 knockout (KO)


title: 72407_M7_Emx_Cx_P42_mat


title: KO1


title: WT-RNA-seq-Rep2

city: Tianjin

first: Niannian

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

description: RNA-seq  of  RA induced differentiation  Embryonic stem cells

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture-C were cut into two pieces in the DpnII sites
All the reads were mapped to mm10 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes count.txts values for each Sample, Capture-C signal peaks for three Baits

growth_protocol: Mouse ESCs E14 was cultured as the previous scheme with a few modifications. ESCs were grown in culture dishes coated with 0.1% gelatin (Sigma, Lot # SLBQ9498V) in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, Lot # 8119213) supplemented with 15% fetal bovine serum (FBS, AusGeneX, Lot # FBS00717-1), 100 nM nonessential amino acids (100x, Gibco, Lot # 2027433), 200 mM L-Glutamate (100x, Gibco, Lot # 2085472), 1% Penicillin-streptomycin (Gibco, Lot # 2029632), 50 μM β-mercaptoethanol (Sigma, Cas # 60-24-2), 10 ng/mL LIF (ESGRO, Lot # ESG1107), 1 μM PD0325901 (a MEK inhibitor, MedChemExpress, Lot # HY-10254) and 3 μM CHIR99021 (a GSK inhibitor, MedChemExpress, Lot # HY-10182). The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
1. For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions. 2. For Capture-C：Briefly, cells were fixed with 1% (vol/vol) formaldehyde for 10 min at room temperature, quenched with 125 mM glycine in PBS, and then lysed in cold lysis buffer (10 mM Tris–HCl, pH7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.2% NP-40, 1× complete protease inhibitor cocktail (Roche)). Chromatin was digested with DpnII (New England Biolabs) at 37°C overnight. Fragments were then diluted and ligated with T4 DNA ligase (Takara) at 16°C overnight. Cross-linking was reversed by overnight incubation at 60°C with proteinase K (Bioline). Then 3C libraries were purified by phenol-chloroform followed by chloroform extraction and ethanol-precipitated at −80°C overnight. Sequencing libraries were prepared from 10μg of the 3C library by sonication to an average size of 200 ~300 bp and indexed using NEBnext reagents (New England Biolabs), according to the manufacturer's protocol. Enrichment of 2μg of an indexed library incubated with 3uM of a pool of biotinylated oligonucleotides (probe sequences are listed in Supplementary Table 7) was performed using the SeqCap EZ Hybridization reagent kit (#05634261001, Roche/NimbleGen), following the manufacturer's instructions. Two rounds of capture employing 48~72 and 24 hr hybridizations, respectively, were used. Correct library size was confirmed by agarose gel electrophoresis, and DNA concentrations were determined using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). All sequencing was performed on Hi-Seq 2500 platforms using paired 150 bp protocols (Illumina).
The Capture-C libraray was constructed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: To induce ESCs differentiation, cells were gently washed with 1x phosphate buffer saline solution (PBS), dissociated and replanted at an appropriate density on gelatin-coated plates in LIF/2i withdrawal medium supplemented with 2µm RA (Solarbio®, Lot # 1108F031). The culture medium was replaced at the given point-in-time.

tag: cell line

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation


title: CBE-KO-RNA-seq-Rep1

description: RNA-seq  of  RA induced differentiation CBE-KO Embryonic stem cells

value: CBE-KO


title: CBE-KO-RNA-seq-Rep2


title: WT3

value: Tet2 wild-type


title: WT-RNA-seq-Rep1

value: WT


title: 72403_M7_Emx_Cx_P42_pat


title: WT2


title: 72402_M7_Emx_Cx_P42_pat


title: 72401_M7_Emx_Cx_P42_pat


title: WT1


title: RNAseq OCM1 sgRNA-NC_rep3

city: Shanghai

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

data_processing:
Illumina HiSeq 4000 software used for basecalling.
WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Genome_build: Hg19
Supplementary_files_format_and_content: All_Differentially_Expressed_Transcripts.xlsx: Expression of transcripts.

source_name: melanoma cells

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

value: ocular melanoma cells


title: RNAseq OCM1 sgRNA-NC_rep2


title: 72399_M7_Emx_Cx_P42_pat

value: Emx1 lineage


title: RNAseq OCM1 sgRNA-2_rep3


title: 72398_M7_Emx_Cx_P42_pat

value: Neocortex


title: RNAseq OCM1 sgRNA-2_rep2


title: 72397_M7_Emx_Cx_P42_pat


title: RNAseq OCM1 sgRNA-1_rep3


title: 72396_M7_Emx_Cx_P42_pat


title: 72395_M7_Emx_Cx_P42_mat

value: mat


title: RNAseq OCM1 sgRNA-1_rep2


title: 72404_M7_Emx_Cx_P42_mat


title: 72394_M7_Emx_Cx_P42_mat


title: ChIP-seq H3K4me3 in human aortic valve interstitial cells (input)

city: Québec

first: Patrick

last: Mathieu

state: QC

address: 2725 Ch Ste-Foy

country: Canada

institute: Quebec Heart and Lung Institute

data_processing:
FASTQ files from sequencing experiments were mapped to the UCSC genome build hg19 using Bowtie2 with default parameters. BigWIG were generated by using bamcoverage tool.
Genome_build: hg19
Supplementary_files_format_and_content: BigWIG files correspond to the output from the bamcoverage tool.

source_name: Human aortic valve interstitial cells from non-mineralized aortic valves

extract_protocol:
Human aortic valve interstitial cells were isolated from control non-mineralized aortic valves obtained from patients undergoing heart transplantation. The protocol was approved by the local ethical committee and informed consent was obtained from the subjects. Aortic leaflets were cut into pieces and incubated in 0.3% type I collagenase (Invitrogen, Thermo Fisher Scientific, ON, Canada) at 37°C for 45 minutes, then filtered through a 70 µm mesh, centrifuged for 5 minutes at 1,500 rpm and resuspended in complete media (DMEM, 10% FBS with L-glutamine and sodium pyruvate). Cells were used between passages 3 to 7. Nuclear extracts from VICs were immunoprecipitated with antibodies against H3K4me3, H3K4me1 (Cell Signaling Technology, New England Biolabs, ON, Canada) or H3K27Ac (Abcam, ON, Canada) pre-bound to protein G Dynabeads (Life Technologies, Thermo Fisher Scientific, ON, Canada). DNA was purified using DNA clean up & concentrator kit (Zymo Research, Cedarlane, Canada).
Libraries were constructed using the QIAseq Ultralow Input Library Kit (Qiagen, ON, Canada) according to manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq4000 (UCSD IGM Genomics Facility, CA, USA).

value: aortic valve interstitial cells

value: input


title: 72392_M7_Emx_Cx_P42_mat


title: ChIP-seq H3K4me3 in human aortic valve interstitial cells


title: 72391_M7_Emx_Cx_P42_mat


title: ChIP-seq H3K4me1 in human aortic valve interstitial cells (input)


title: ChIP-seq H3K27ac in human aortic valve interstitial cells (input)


title: ChIP-seq H3K4me1 in human aortic valve interstitial cells


title: 72389_M7_Emx_Cx_P42_mat


title: ATAC-seq in human aortic valve interstitial cells

data_processing:
FASTQ files from sequencing experiments were mapped to the UCSC genome build hg19 using Bowtie2 with default parameters. BigWIG were generated by using bamcoverage tool and peaks were called using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: The BigWIG file corresponds to the output from the bamcoverage tool.

extract_protocol:
Human aortic valve interstitial cells were isolated from control non-mineralized aortic valves obtained from patients undergoing heart transplantation. The protocol was approved by the local ethical committee and informed consent was obtained from the subjects. Aortic leaflets were cut into pieces and incubated in 0.3% type I collagenase (Invitrogen, Thermo Fisher Scientific, ON, Canada) at 37°C for 45 minutes, then filtered through a 70 µm mesh, centrifuged for 5 minutes at 1,500 rpm and resuspended in complete media (DMEM, 10% FBS with L-glutamine and sodium pyruvate). Cells were used between passages 3 to 7. Nuclei from approximatively 2.5-4 x 105 cells were prepared as previously described (Shashikant T, et al. 2018, BMC Genomics).
Libraries were first amplified for 5 cycles using custom-synthesized index primers and then a second amplification was performed. The appropriate number of additional PCR cycles was determined using quantitative real-time PCR by plotting the Rn value (fluorescent signal from SYBR Green I) versus cycle number and determining the cycle number corresponding to one-third of the maximum fluorescent intensity. Libraries were PCR-amplified for 4-7 cycles. After PCR amplification, libraries were purified using DNA clean up & concentrator kit (Zymo Research, Cedarlane, Canada)Library quality was assessed on a BioAnalyser (Agilent, ON, Canada) using Agilent High Sensitivity DNA kit (Agilent, ON, Canada). Sequencing was performed on an Illumina HiSeq4000 (UCSD IGM Genomics Facility, CA, USA).


title: 72337_M7_Emx_Cx_P42_pat

value: pat


title: 72388_M7_Emx_Cx_P42_mat


title: THP-1_825_DMSO_I

city: Heidelberg

first: Stefan

last: Fröhling

address: Im Neuenheimer Feld 460

country: Germany

institute: German Cancer Research Center ans National Center for Tumor Diseases

description: shLIMK1_2, biological replicate 1

data_processing:
Basecalling was done with Illumina's Real-Time Analysis (RTA) software version 2.7.7. Base qualities were encoded by Phred+33.
Demultiplexing of sample barcodes and conversion to fastq was performed using bcl2fastq 2.19.0.316.
Reads were aligned against hg19 (hs37.d5) reference genome using STAR-2.5.2b with SAMtools version 0.1.19.
Read summarization was done using the featureCounts function of Subread version 1.5.1.
A custom script was used to calculate RPKM and TPM expression values (https://github.com/DKFZ-ODCF/RNAseqWorkflow/blob/master/resources/analysisTools/rnaseqworkflow/featureCountsDexseq_2_FpkmTpm). For total library abundance calculations, all genes on chromosomes X, Y, MT and rRNA and tRNA genes were omitted as they are likely to introduce library size estimation biases.
Genome_build: hg19_GRCh37
Supplementary_files_format_and_content: tsv format; one file per sample containing read counts, TPM, FPKM values for forward & reverse reads; "num_reads_rv" and "TPM_rv" were used for subsequent differential expression analysis

source_name: acute myeloid leukemia cell line

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum and 1 % penicillin/streptomycin. Cells were lentivirally transduced with shRNA constructs and puromycin-selected for 72 hours. RNA was isolated eight days post transduction.

extract_protocol:
RNeasy Mini Plus Kit (Qiagen)
Illumina TruSeq Stranded RNA Library Prep Kit

treatment_protocol: Cells were treated with trace amount of DMSO (0.0025 %) from day four to day eight of the experiment.

value: blood

value: leukocyte/monocyte


title: THP-1_635_DMSO_II

description: shLIMK1_1, biological replicate 2


title: 72335_M7_Emx_Cx_P42_pat


title: THP-1_825_DMSO_II

description: shLIMK1_2, biological replicate 2


title: THP-1_635_DMSO_I

description: shLIMK1_1, biological replicate 1


title: 72334_M7_Emx_Cx_P42_pat


title: THP-1_Scr_DMSO_II

description: non-targeting control shRNA (NTC), biological replicate 2

value: non-targeting control shRNA (NTC)


title: 72336_M7_Emx_Cx_P42_pat


title: 72332_M7_Emx_Cx_P42_pat


title: 72393_M7_Emx_Cx_P42_mat


title: THP-1_Scr_DMSO_I

description: non-targeting control shRNA (NTC), biological replicate 1


title: 72331_M7_Emx_Cx_P42_pat


title: 72390_M7_Emx_Cx_P42_mat


title: 72408_M7_Emx_Cx_P42_mat


title: ChIP-seq H3K27ac in human aortic valve interstitial cells


title: s_MDA231_PAR_1

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

institute: VIB

data_processing:
Reads from generated FASTQ files were quality checked, trimmed with CutAdapr v1.6, and mapped to the human reference genome (hg19) using STAR2.5.0.a. The expression count matrix of uniquely mapped reads was computed with HTseq v0.5.3.
Expression count matrix was processed through DESeq2 v1.22.1 pipeline in Bioconductor, resulting in generation of normalized count matrix (provided as processed data file).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: Parental cell line

growth_protocol: Parental cancer cell lines (Par) and their metastatic leptomenigeal derivatives (LeptoM, and their genetically manipulated counterparts) were cultured as described previously (Boire 2017). Approximately 1x10*6 cells were seeded into 100 mm dish. Two days later, cells were lysed in RNA lysis buffer (RLT).

extract_protocol:
RNA was extracted from lysates using Rneasy Mini columns (Qiagen).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, #RS-122-2102), with 8 cycles of PCR.

treatment_protocol: Lipocalin-2 (LCN2) knock-down cell were generated by transduction of LeptoM cells with two independed lentiviral hairpins (shLCN2_1 and shLCN2_2), and compared to control hairpin (shCTL)

tag: derivative

value: Parental

tag: hairpin

tag: primary tumor type

value: breast cancer

value: Parental cells


title: 72330_M7_Emx_Cx_P42_mat


title: s_MDA231_PAR_2


title: 72329_M7_Emx_Cx_P42_mat


title: s_MDA231_LeptoM_shCTL_2

source_name: Control leptomeningeal metastatic cells

value: LeptoM

value: shCTL

value: leptomeningeal metastatic cells


title: 72328_M7_Emx_Cx_P42_mat


title: 72327_M7_Emx_Cx_P42_mat


title: s_MDA231_LeptoM_shLCN2_2_2

source_name: LCN2-depleted leptomeningeal metastatic cells (shRNA2)


title: 72326_M7_Emx_Cx_P42_mat


title: s_MDA231_LeptoM_shLCN2_2_1


title: 72400_M7_Emx_Cx_P42_pat


title: 72325_M7_Emx_Cx_P42_mat


title: s_MDA231_LeptoM_shLCN2_1_1

source_name: LCN2-depleted leptomeningeal metastatic cells (shRNA1)


title: 72324_M7_Emx_Cx_P42_mat


title: 72323_M7_Emx_Cx_P42_pat


title: s_PC9_PAR2

value: lung cancer


title: 72321_M7_Emx_Cx_P42_pat


title: s_PC9_PAR1


title: 72322_M7_Emx_Cx_P42_pat


title: 72333_M7_Emx_Cx_P42_pat


title: s_PC9_LeptoM_shCTL_2


title: 72320_M7_Emx_Cx_P42_pat


title: 72319_M7_Emx_Cx_P42_pat


title: 72318_M7_Emx_Cx_P42_pat


title: s_PC9_LeptoM_shLCN2_2_2


title: s_MDA231_LeptoM_shCTL_1


title: s_PC9_LeptoM_shLCN2_2_1


title: 72317_M7_Emx_Cx_P42_pat


title: 72316_M7_Emx_Cx_P42_mat


title: s_PC9_LeptoM_shLCN2_1_1


title: s_MDA231_LeptoM_shLCN2_1_2


title: C17_I_10x_TCR

city: La Jolla

first: John

last: Chang

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: UCSD

description:
TCR RNA
5' VDJ sequencing (10X genomics)

data_processing:
Library strategy: VDJ-seq
data were processed by cellranger 2.1.0 with default parameter, using mm10 as reference.
Raw cell-reads were then loaded to R using the cellrangerRkit package. The pre-filtered VDJ information table (all_contig_annotations.csv, output by cellranger) were loaded at the same time. A cell was considered “valid” if it satisfied the following criteria: (1) Cell has enough RNA reads to pass the Cell Ranger threshold. (2) Cell has productive full-length BCR or TCR detected. Only valid cells were kept for downstream analysis in both the scRNA-seq and scTCR-seq/scBCR-seq datasets. The scRNA-seq dataset was then further filtered based on gene numbers and mitochondria gene counts tototal counts ratio. Only cells with > 400 genes,UMI > 0,and 0.5% ~ 30% of their UMIs mappingto mitochondria genes were kept for downstream analysis.
All the VDJ data that don't have the following flag of cellranger were filtered: 1. the is_cell flag, 2. the full-length flag and 3. the productive flag.
For the 5' scRNA-seq and 5' VDJ-seq, the first 16 bp of R1 is the cell barcode and the next 10bp (17-26bp) is the UMI.
Genome_build: hg38
Supplementary_files_format_and_content: cell-gene UMI table: UMI table with each row represent a cell and each column represent a gene.   BCR table: table containing BCR information, including V/D/J/C genes and CDR3  TCR table:  table containing TCR information, including V/D/J/C genes and CDR3

source_name: Ileum immune cell

growth_protocol: No growth procedure was required.

extract_protocol:
Human Peripheral Blood Mononuclear Cell Isolation  Blood was collected in BD Vacutainer CPT tube and centrifuged at 400 x g for 25 minutes. The buffy coat layer was removed, washed, and counted. Cells were resuspended in freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI [RPMI +10%(v/v) fetal bovine serum (FBS) +100 U/mL penicillin/100 μg/mL streptomycin], 50%(v/v) FBS), placed into a freezing container (Mr. Frosty), and stored at -80°C. Cells were recovered, washed, and filtered, and labeled with anti-human CD45. CD45+ immune cells were sorted on a FACSAria2 (BD Biosciences).     Human Intestinal Cell Isolation  Four intestinal biopsies were obtained with endoscopic biopsy forceps from the rectum or ileum and collected in a conical tube with Hank’s buffered saline solution (HBSS). Intestinal biopsies were transferred into freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI, 50%(v/v) FBS) and stored at -80°C. Biopsies were recovered, incubated in HBSS on a shaker, then incubated twice in HBSS + 5 mM dithiothreitol (DTT) with shaking, then washed in HBSS. Intestinal biopsies were mechanically dissociated, then placed into 10 mL of digestion mixture (complete RPMI + 1.5 mg/mL Collagenase type VIII + 50 µg/mL DNase I) on a rocker at 37°C for 20 minutes, filtered and stained with anti-human CD45. CD45+ immune cells were sorted on a FACSAria2 (BD Biosciences).
Single cell libraries were prepared according to the protocol for 10X Genomics for Single Cell V(D)J + 5’ Gene Expression. Approximately 20,000 sorted CD45+ cells were loaded and partitioned into Gel Bead In-Emulsions (GEM). scRNA libraries were sequenced on a HiSeq4000 (Illumina). The B and T cell receptor libraries were amplified according to the manufacturer’s protocol and sequenced on a NovaSeqS4 (Illumina).

treatment_protocol: These details are included in extraction protocol.

tag: subject #

tag: subject status

value: control

value: ileum

tag: cell subtype surface markers

tag: cell subtype

value: immune cells


title: C18_I_10x_TCR


title: C18_PBMC_10x_TCR

source_name: Blood immune cell

value: PBMC


title: E2A-NPC

source_name: Neural progenitor cells - E2A

tag: cell type

value: Embryonic stem cells (H1) derived neural progenitor cells

value: E2A (Santa Cruz, sc-349)

value: untreated


title: 72313_M7_Emx_Cx_P42_mat

value: Emx1 lineage

tag: tissue

value: Neocortex

value: mat


title: C17_PBMC_10x_TCR


title: 72310_M7_Emx_Cx_P42_mat

tag: madm insertion


title: C18_R_10x_TCR

source_name: Rectum immune cell

value: rectum


title: 72312_M7_Emx_Cx_P42_mat

tag: strain


title: 72311_M7_Emx_Cx_P42_mat

tag: cre-driver


title: C12_PBMC_10x_TCR


title: C12_R_10x_TCR


title: s_PC9_LeptoM_shCTL_1


title: C9_R_10x_TCR


title: 72309_M7_Emx_Cx_P42_mat

tag: upd


title: C18_I_10x_BCR

description:
BCR RNA
5' VDJ sequencing (10X genomics)


title: 72306_M7_Emx_Cx_P42_pat

value: pat

tag: age


title: 72307_M7_Emx_Cx_P42_pat


title: 72314_M7_Emx_Cx_P42_mat


title: s_PC9_LeptoM_shLCN2_1_2


title: 72308_M7_Emx_Cx_P42_pat


title: C17_I_10x_BCR


title: 72304_M7_Emx_Cx_P42_pat


title: 72303_M7_Emx_Cx_P42_pat


title: C17_PBMC_10x_BCR


title: 72302_M7_Emx_Cx_P42_pat


title: 72305_M7_Emx_Cx_P42_pat


title: 72301_M7_Emx_Cx_P42_pat


title: C18_R_10x_BCR


title: C17_R_10x_BCR


title: 72300_M7_Emx_Cx_P42_mat


title: C17_R_10x_TCR


title: 72299_M7_Emx_Cx_P42_mat


title: 72297_M7_Emx_Cx_P42_mat


title: 72298_M7_Emx_Cx_P42_mat


title: C12_PBMC_10x_BCR


title: C33_I_10x_scRNA

description:
RNA
5' Transcriptome sequencing (10X genomics)

data_processing:
data were processed by cellranger 2.1.0 with default parameter, using mm10 as reference.
Raw cell-reads were then loaded to R using the cellrangerRkit package. The pre-filtered VDJ information table (all_contig_annotations.csv, output by cellranger) were loaded at the same time. A cell was considered “valid” if it satisfied the following criteria: (1) Cell has enough RNA reads to pass the Cell Ranger threshold. (2) Cell has productive full-length BCR or TCR detected. Only valid cells were kept for downstream analysis in both the scRNA-seq and scTCR-seq/scBCR-seq datasets. The scRNA-seq dataset was then further filtered based on gene numbers and mitochondria gene counts tototal counts ratio. Only cells with > 400 genes,UMI > 0,and 0.5% ~ 30% of their UMIs mappingto mitochondria genes were kept for downstream analysis.
All the VDJ data that don't have the following flag of cellranger were filtered: 1. the is_cell flag, 2. the full-length flag and 3. the productive flag.
For the 5' scRNA-seq and 5' VDJ-seq, the first 16 bp of R1 is the cell barcode and the next 10bp (17-26bp) is the UMI.
Genome_build: hg38
Supplementary_files_format_and_content: cell-gene UMI table: UMI table with each row represent a cell and each column represent a gene.   BCR table: table containing BCR information, including V/D/J/C genes and CDR3  TCR table:  table containing TCR information, including V/D/J/C genes and CDR3


title: C9_R_10x_BCR


title: 72296_M7_Emx_Cx_P42_mat


title: 72295_M7_Emx_Cx_P42_mat


title: C30_I_10x_scRNA


title: C21_I_10x_scRNA


title: C19_I_10x_scRNA


title: C18_I_10x_scRNA


title: 72294_M7_Emx_Cx_P42_mat


title: 72293_M7_Emx_Cx_P42_mat


title: 72292_M7_Emx_Cx_P42_pat


title: C21_PBMC_10x_scRNA


title: 72289_M7_Emx_Cx_P42_pat


title: 72291_M7_Emx_Cx_P42_pat


title: C12_R_10x_BCR


title: C33_PBMC_10x_scRNA


title: 72288_M7_Emx_Cx_P42_pat


title: 72286_M7_Emx_Cx_P42_pat


title: C17_PBMC_10x_scRNA


title: U44_PBMC_10x_scRNA

value: UC


title: 72285_M7_Emx_Cx_P42_pat


title: U41_PBMC_10x_scRNA


title: C19_PBMC_10x_scRNA


title: 72283_M7_Emx_Cx_P42_mat


title: 72282_M7_Emx_Cx_P42_mat


title: 72284_M7_Emx_Cx_P42_mat


title: C18_PBMC_10x_scRNA


title: C17_I_10x_scRNA


title: 72281_M7_Emx_Cx_P42_mat


title: 72280_M7_Emx_Cx_P42_mat


title: U34_PBMC_10x_scRNA


title: C30_PBMC_10x_scRNA


title: U5_PBMC_10x_scRNA


title: U4_PBMC_10x_scRNA


title: C12_PBMC_10x_scRNA


title: 72278_M7_Emx_Cx_P42_mat


title: C16_PBMC_10x_scRNA


title: C18_PBMC_10x_BCR


title: 72287_M7_Emx_Cx_P42_pat


title: U35_PBMC_10x_scRNA


title: U45_PBMC_10x_scRNA


title: 72276_M7_Emx_Cx_P42_pat


title: 72277_M7_Emx_Cx_P42_mat


title: C30_R_10x_scRNA


title: 72315_M7_Emx_Cx_P42_mat


title: 72274_M7_Emx_Cx_P42_pat


title: C21_R_10x_scRNA


title: C18_R_10x_scRNA


title: 72290_M7_Emx_Cx_P42_pat


title: 72273_M7_Emx_Cx_P42_pat


title: C17_R_10x_scRNA


title: U45_R_10x_scRNA


title: 72270_M7_Emx_Cx_P42_pat


title: 72271_M7_Emx_Cx_P42_pat


title: 72279_M7_Emx_Cx_P42_mat


title: U44_R_10x_scRNA


title: U41_R_10x_scRNA


title: 72269_M7_Emx_Cx_P42_pat


title: 72268_M7_Emx_Cx_P42_mat


title: 72267_M7_Emx_Cx_P42_mat


title: U34_R_10x_scRNA


title: 72265_M7_Emx_Cx_P42_mat


title: U5_R_10x_scRNA


title: 72264_M7_Emx_Cx_P42_mat


title: 72275_M7_Emx_Cx_P42_pat


title: C16_R_10x_scRNA


title: 72266_M7_Emx_Cx_P42_mat


title: U4_R_10x_scRNA


title: C12_R_10x_scRNA


title: 72263_M7_Emx_Cx_P42_mat


title: 72262_M7_Emx_Cx_P42_mat


title: 72261_M7_Emx_Cx_P42_mat


title: C19_R_10x_scRNA


title: C9_R_10x_scRNA


title: Repo_2_RNAseq

city: Kansas City

first: Mehmet Neset

last: Ozel

state: MO

institute: Stowers Institute for Medical Research

data_processing:
RNA-Seq reads were trimmed using Trimmomatic version 0.32
RNA-Seq reads were aligned using STAR version 2.5.2
RNA-Seq reads were counted using htseq version 0.6.1
Genome_build: ENSEMBL-release-81-BDGP6
Supplementary_files_format_and_content: .csv includes htseq counts for each sample.

organism: Drosophila melanogaster

source_name: Optic lobe neurons

extract_protocol:
We identified lines for individual cell types and crossed each Gal4 line to UAS-Red Stinger to label the nuclei of the specific neuronal type. Dissected brains were dissociated and cells expressing the transgene were sorted on the basis of their fluorescent signal using FACS (FACS Aria III). Cells were sorted directly into extraction buffer and we extracted total RNA using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). We assessed RNA quality by Bioanalyzer using RNA 6000 Pico chips (Agilent). Smart-Seq v4 Ultra Low Input RNA Kit was used to generate full-length double stranded cDNA with 300 to 500 pg of total RNA input.
Libraries were prepared using Illumina Nextera XT DNA Library Prep Kit and sequenced on the Illumina HiSeq 2500 System. Three barcoded libraries were pooled per sequencing lane and paired-end 100 bp reads were generated.

value: glia

tag: developmental stage

value: 3-day old adults

value: Canton-S


title: Repo_3_RNAseq


title: 72260_M7_Emx_Cx_P42_pat


title: 72259_M7_Emx_Cx_P42_pat


title: 72258_M7_Emx_Cx_P42_pat


title: Elav-8B_RNAseq

value: neurons


title: Elav-10B_RNAseq


title: U35_R_10x_scRNA


title: Elav-4B_RNAseq


title: Pm2_3_RNAseq


title: 72255_M7_Emx_Cx_P42_pat


title: Pm2_2_RNAseq


title: 72253_M7_Emx_Cx_P42_pat


title: Pm2_1_RNAseq


title: 72252_M7_Emx_Cx_P42_mat


title: T4_2_RNAseq


title: 72251_M7_Emx_Cx_P42_mat


title: 72250_M7_Emx_Cx_P42_mat


title: T4_1_RNAseq


title: T4_3_RNAseq


title: 72249_M7_Emx_Cx_P42_mat


title: 72247_M7_Emx_Cx_P42_mat


title: 72246_M7_Emx_Cx_P42_mat


title: 72257_M7_Emx_Cx_P42_pat


title: 72256_M7_Emx_Cx_P42_pat


title: 72254_M7_Emx_Cx_P42_pat


title: 72212_M7_Emx_Cx_P42_mat


title: 72245_M7_Emx_Cx_P42_mat


title: 72213_M7_Emx_Cx_P42_mat


title: 72211_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1219 CBCS_N1219

type: RNA

city: Houston

first: Arjun

last: Bhattacharya

state: TX

address: 1155 Pressler Street

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: 3 uL of Reporter CodeSet, 5 uL of hybridization buffer, up to 5 uL (25-100 ng) of sample RNA, and 2 uL of Capture ProbeSet was combined for the hybridization reaction. The reactions were incubated at 65 degrees C for at least 16 hours and at most 48 hours and temperature was ramped down to 4 degrees C for processing the following day. Hybridization was run on Prep Station Serial # 0910B0040, Prep Station Serial # 1602D0412. Details provided: https://www.nanostring.com/download_file/view/1808/3822

scan_protocol: NanoString cartridges were scanned using the nCounter MAX Analysis System (NanoString Digital Analyzer Serial # 1605C0377)

data_processing: The raw data were scaled by upper quantile normalization (Bullard et al., 2010, PMID 20167110). One dimension of unwanted technical variation was estimated using Remove Unwanted Variation (Gagnon-Bartsch et al., 2012, PMID 22101192) and removed from the variance-stabilized expression matrix using the limma package (Ritche et al., 2015, PMID 25605792).

source_name: primary breast tumor

label_protocol: NanoString nCounter technology

growth_protocol: Samples were recruited by the Carolina Breast Cancer Study, a population-based cohort of breast cancer patients from North Carolina, up-sampled for African American women (Newman et al., 1995, PMID 7612904).

extract_protocol: A study pathologist reviewed hemtoxylin and eosin for each tumor, selected a representative tumor block, and selected tumor areas for coring. Ten 10 uM sections were cut from blocks after coring, and an additional section was obtained and reviewed for tumor cellularity (Troester et al., 2018, PMID 28859290). RNA was isolated from cores using Qiagen RNeasy formalin-fixed, paraffin-embedded kit and protocol (Troester et al., 2018, PMID 28859290).

treatment_protocol: Blood samples, medical record documentation, and paraffin-embedded tumor specimens are obtained for all breast cancer patients (Newman et al., 1995, PMID 7612904).

value: primary breast tumor

tag: study phase

tag: estrogen receptor status

value: Positive

tag: pam50 molecular subtype

value: LumB


title: 72209_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1218 CBCS_N1218


title: 72210_M7_Emx_Cx_P42_mat


title: 72248_M7_Emx_Cx_P42_mat


title: R1388_UGG_Mock: mock-infected renal progenitors, biological rep3

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

description: Gene expression data from renal progenitors infected with pLVX-IRES-ZsGreen1-mock

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 h at 45 °C on GeneChip® Clariom S. GeneChip® cartridges were washed and stained with GeneChip®  Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters.

data_processing: Data analysis has been carried out through the commercial software Partek Genomics Suite (version 6.6) and were normalized by Robust Multichip Average (RMA)

label: biotin

source_name: cell culture of human renal progenitor

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT Plus Kit (Affymetrix; Thermo Fisher Scientific, Inc.). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix, starting from 5.5 ug of ssDNA.

growth_protocol: Renal progenitor cells were generated by plating processed human kidney on coated plastic in EGM-MV media (Lonza) supplemented with 20% FBS (Hyclone)

extract_protocol: Total RNA was extracted using the RNeasy Microkit (Qiagen, Hilden, Germany).

treatment_protocol: Human renal progenitors were infected with pLVX-IRES-ZsGreen1-mock or pLVX-IRES-ZsGreen1-NICD1 lentivirusvirus-containing supernatant with a multiplicity of infection of 15 as well as fresh EGM-MV media, in the presence of 8 μg/mL of polybrene (Sigma-Aldrich).

value: Renal progenitor cells

tag: gender

value: male

tag: development stage

value: adulthood


title: R1388_UGG_NICD1: NICD1-infected renal progenitors, biological rep3

description: Gene expression data from renal progenitors infected with pLVX-IRES-ZsGreen1-NICD1


title: R1388_GIA_Mock: mock-infected renal progenitors, biological rep1


title: R1388_GRE_NICD1: NICD1-infected renal progenitors, biological rep2


title: 72208_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1216 CBCS_N1216

value: Weak Positive / Borderline

value: Basal


title: 72206_M7_Emx_Cx_P42_pat

value: Emx1 lineage

value: Neocortex


title: 72207_M7_Emx_Cx_P42_mat

value: mat


title: 72272_M7_Emx_Cx_P42_pat

value: pat


title: Ruvseq_Patient 1217 CBCS_N1217

value: Negative


title: R1388_GRE_Mock: mock-infected renal progenitors, biological rep2


title: Repo_1_RNAseq

value: glia


title: Ruvseq_Patient 1215 CBCS_N1215


title: Ruvseq_Patient 1214 CBCS_N1214


title: 72204_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1213 CBCS_N1213


title: 72205_M7_Emx_Cx_P42_pat


title: 72203_M7_Emx_Cx_P42_pat


title: 72202_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1211 CBCS_N1211


title: Ruvseq_Patient 1209 CBCS_N1209


title: 72201_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1210 CBCS_N1210

value: LumA


title: 72200_M7_Emx_Cx_P42_pat


title: 72199_M7_Emx_Cx_P42_mat


title: 72198_M7_Emx_Cx_P42_mat


title: 72194_M7_Emx_Cx_P42_mat


title: 72195_M7_Emx_Cx_P42_mat


title: 72196_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1207 CBCS_N1207


title: Ruvseq_Patient 1212 CBCS_N1212


title: 72192_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1205 CBCS_N1205


title: Ruvseq_Patient 1203 CBCS_N1203

value: Unknown


title: Ruvseq_Patient 1204 CBCS_N1204


title: 72191_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1202 CBCS_N1202


title: 72190_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1200 CBCS_N1200


title: Ruvseq_Patient 1201 CBCS_N1201


title: 72189_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1199 CBCS_N1199


title: 72197_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1198 CBCS_N1198


title: 72188_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1197 CBCS_N1197


title: 72187_M7_Emx_Cx_P42_pat


title: 72186_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1196 CBCS_N1196


title: Ruvseq_Patient 1195 CBCS_N1195


title: 72193_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1194 CBCS_N1194


title: Ruvseq_Patient 1208 CBCS_N1208


title: Ruvseq_Patient 1193 CBCS_N1193


title: 72184_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1206 CBCS_N1206

value: Normal


title: 72183_M7_Emx_Cx_P42_mat


title: 72185_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1191 CBCS_N1191

value: primary breast tumor


title: Ruvseq_Patient 1192 CBCS_N1192


title: Ruvseq_Patient 1190 CBCS_N1190


title: 72180_M7_Emx_Cx_P42_mat


title: 72181_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1188 CBCS_N1188


title: Ruvseq_Patient 1189 CBCS_N1189


title: 72179_M7_Emx_Cx_P42_mat


title: 72177_M7_Emx_Cx_P42_mat


title: 72178_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1187 CBCS_N1187


title: 72176_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1185 CBCS_N1185


title: Ruvseq_Patient 1184 CBCS_N1184

value: Positive


title: 72175_M7_Emx_Cx_P42_pat


title: 72174_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1182 CBCS_N1182


title: Ruvseq_Patient 1181 CBCS_N1181


title: 72173_M7_Emx_Cx_P42_pat


title: 72182_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1180 CBCS_N1180


title: Ruvseq_Patient 1183 CBCS_N1183


title: Ruvseq_Patient 1179 CBCS_N1179


title: 72170_M7_Emx_Cx_P42_pat


title: 72172_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1178 CBCS_N1178


title: 72171_M7_Emx_Cx_P42_pat


title: 72169_M7_Emx_Cx_P42_pat


title: 72168_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1176 CBCS_N1176


title: Ruvseq_Patient 1177 CBCS_N1177


title: 72166_M7_Emx_Cx_P42_mat


title: 72165_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1175 CBCS_N1175

value: LumB


title: Ruvseq_Patient 1186 CBCS_N1186


title: 72167_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1173 CBCS_N1173


title: Ruvseq_Patient 1174 CBCS_N1174


title: 72163_M7_Emx_Cx_P42_mat


title: 72164_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1171 CBCS_N1171


title: Ruvseq_Patient 1172 CBCS_N1172


title: Ruvseq_Patient 1170 CBCS_N1170


title: 72162_M7_Emx_Cx_P42_mat


title: 72159_M7_Emx_Cx_P42_pat


title: 72160_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1169 CBCS_N1169


title: 72161_M7_Emx_Cx_P42_mat


title: 72158_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1168 CBCS_N1168


title: Ruvseq_Patient 1166 CBCS_N1166


title: Ruvseq_Patient 1167 CBCS_N1167


title: 72155_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1164 CBCS_N1164


title: 72153_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1163 CBCS_N1163


title: 72152_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1162 CBCS_N1162


title: Ruvseq_Patient 1161 CBCS_N1161


title: 72154_M7_Emx_Cx_P42_pat


title: 72151_M7_Emx_Cx_P42_mat


title: 72150_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1160 CBCS_N1160


title: 72149_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1157 CBCS_N1157


title: Ruvseq_Patient 1158 CBCS_N1158


title: 72157_M7_Emx_Cx_P42_pat


title: 72156_M7_Emx_Cx_P42_pat


title: 72146_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1155 CBCS_N1155


title: 72145_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1154 CBCS_N1154


title: 72143_M7_Emx_Cx_P42_pat


title: 72142_M7_Emx_Cx_P42_pat


title: 72144_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1153 CBCS_N1153


title: Ruvseq_Patient 1159 CBCS_N1159


title: Ruvseq_Patient 1151 CBCS_N1151


title: 72140_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1152 CBCS_N1152


title: Ruvseq_Patient 1149 CBCS_N1149


title: 72141_M7_Emx_Cx_P42_pat


title: 72138_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1150 CBCS_N1150


title: Ruvseq_Patient 1148 CBCS_N1148


title: 72147_M7_Emx_Cx_P42_mat


title: 72148_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1147 CBCS_N1147


title: 72137_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1156 CBCS_N1156


title: Ruvseq_Patient 1145 CBCS_N1145


title: Ruvseq_Patient 1144 CBCS_N1144


title: 72136_M7_Emx_Cx_P42_mat


title: 72135_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1165 CBCS_N1165


title: Ruvseq_Patient 1143 CBCS_N1143


title: Ruvseq_Patient 1142 CBCS_N1142


title: 72134_M7_Emx_Cx_P42_mat


title: 72139_M7_Emx_Cx_P42_pat


title: 72132_M7_Emx_Cx_P42_mat


title: 72133_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1140 CBCS_N1140


title: Ruvseq_Patient 1139 CBCS_N1139


title: 72131_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 1146 CBCS_N1146


title: 72127_M7_Emx_Cx_P42_pat


title: 72128_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1141 CBCS_N1141


title: Ruvseq_Patient 1138 CBCS_N1138


title: 72126_M7_Emx_Cx_P42_pat


title: 72125_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1137 CBCS_N1137


title: 72124_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1134 CBCS_N1134


title: Ruvseq_Patient 1135 CBCS_N1135


title: Ruvseq_Patient 1136 CBCS_N1136


title: 72123_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1133 CBCS_N1133


title: 72122_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1132 CBCS_N1132


title: Ruvseq_Patient 1131 CBCS_N1131


title: 72121_M7_Emx_Cx_P42_pat


title: Ruvseq_Patient 1130 CBCS_N1130


title: Ruvseq_Patient 1129 CBCS_N1129


title: 72130_M7_Emx_Cx_P42_mat


title: 72129_M7_Emx_Cx_P42_mat


title: 72115_M7_Emx_Cx_E15_pat


title: 72116_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1128 CBCS_N1128


title: 72113_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1127 CBCS_N1127


title: 72111_M7_Emx_Cx_E15_pat


title: 72112_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1125 CBCS_N1125


title: Ruvseq_Patient 1126 CBCS_N1126


title: Ruvseq_Patient 1124 CBCS_N1124


title: 72109_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1122 CBCS_N1122


title: 72110_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1123 CBCS_N1123


title: 72107_M7_Emx_Cx_E15_mat


title: 72106_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1121 CBCS_N1121


title: Ruvseq_Patient 1120 CBCS_N1120


title: 72108_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1119 CBCS_N1119


title: Ruvseq_Patient 1117 CBCS_N1117


title: 72114_M7_Emx_Cx_E15_pat


title: 72103_M7_Emx_Cx_E15_mat


title: 72105_M7_Emx_Cx_E15_mat


title: 72104_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1115 CBCS_N1115


title: Ruvseq_Patient 1114 CBCS_N1114


title: Ruvseq_Patient 1116 CBCS_N1116


title: 72101_M7_Emx_Cx_E15_pat


title: 72100_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1113 CBCS_N1113


title: Ruvseq_Patient 1118 CBCS_N1118


title: Ruvseq_Patient 1111 CBCS_N1111


title: Ruvseq_Patient 1112 CBCS_N1112


title: Ruvseq_Patient 1110 CBCS_N1110


title: 72095_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1109 CBCS_N1109


title: Ruvseq_Patient 1107 CBCS_N1107


title: Ruvseq_Patient 1108 CBCS_N1108


title: Ruvseq_Patient 1106 CBCS_N1106


title: 72093_M7_Emx_Cx_E15_mat


title: 72092_M7_Emx_Cx_E15_mat


title: 72102_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1105 CBCS_N1105


title: Ruvseq_Patient 1104 CBCS_N1104


title: 72091_M7_Emx_Cx_E15_mat


title: 72090_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1103 CBCS_N1103


title: 72099_M7_Emx_Cx_E15_pat


title: 72097_M7_Emx_Cx_E15_pat


title: 72088_M7_Emx_Cx_E15_mat


title: 72098_M7_Emx_Cx_E15_pat


title: 72089_M7_Emx_Cx_E15_mat


title: 72094_M7_Emx_Cx_E15_mat


title: 72087_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1101 CBCS_N1101


title: Ruvseq_Patient 1102 CBCS_N1102


title: Ruvseq_Patient 1100 CBCS_N1100


title: 72086_M7_Emx_Cx_E15_pat


title: 72085_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1099 CBCS_N1099


title: 72096_M7_Emx_Cx_E15_pat


title: 72083_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1098 CBCS_N1098


title: Ruvseq_Patient 1096 CBCS_N1096


title: Ruvseq_Patient 1097 CBCS_N1097


title: 72081_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1095 CBCS_N1095


title: 72082_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1094 CBCS_N1094


title: 72080_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1092 CBCS_N1092


title: Ruvseq_Patient 1093 CBCS_N1093


title: 72079_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1091 CBCS_N1091


title: 72078_M7_Emx_Cx_E15_mat


title: 72076_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1090 CBCS_N1090


title: Ruvseq_Patient 1088 CBCS_N1088


title: Ruvseq_Patient 1089 CBCS_N1089


title: 72075_M7_Emx_Cx_E15_mat


title: 72074_M7_Emx_Cx_E15_mat


title: 72084_M7_Emx_Cx_E15_pat


title: 72073_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1087 CBCS_N1087


title: 72072_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1086 CBCS_N1086


title: Ruvseq_Patient 1084 CBCS_N1084


title: 72071_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1083 CBCS_N1083


title: 72069_M7_Emx_Cx_E15_pat


title: 72070_M7_Emx_Cx_E15_pat


title: 72068_M7_Emx_Cx_E15_pat


title: 72067_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1082 CBCS_N1082


title: 72066_M7_Emx_Cx_E15_pat


title: 72077_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1080 CBCS_N1080


title: Ruvseq_Patient 1081 CBCS_N1081


title: Ruvseq_Patient 1079 CBCS_N1079


title: 72065_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1078 CBCS_N1078


title: 72064_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1076 CBCS_N1076


title: 72063_M7_Emx_Cx_E15_mat


title: 72062_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1085 CBCS_N1085


title: 72060_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1075 CBCS_N1075


title: Ruvseq_Patient 1074 CBCS_N1074


title: Ruvseq_Patient 1072 CBCS_N1072


title: 72059_M7_Emx_Cx_E15_mat


title: 72061_M7_Emx_Cx_E15_mat


title: 72058_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1070 CBCS_N1070


title: 72056_M7_Emx_Cx_E15_mat


title: 72057_M7_Emx_Cx_E15_mat


title: 72055_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1069 CBCS_N1069


title: Ruvseq_Patient 1077 CBCS_N1077


title: 72053_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1068 CBCS_N1068


title: Ruvseq_Patient 1067 CBCS_N1067


title: Ruvseq_Patient 1066 CBCS_N1066


title: 72052_M7_Emx_Cx_E15_pat


title: 72051_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1065 CBCS_N1065


title: Ruvseq_Patient 1063 CBCS_N1063


title: 72050_M7_Emx_Cx_E15_pat


title: 72049_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1064 CBCS_N1064


title: Ruvseq_Patient 1061 CBCS_N1061


title: Ruvseq_Patient 1062 CBCS_N1062


title: Ruvseq_Patient 1073 CBCS_N1073


title: 72047_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1071 CBCS_N1071


title: 72048_M7_Emx_Cx_E15_pat


title: 72046_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1059 CBCS_N1059


title: 72045_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1058 CBCS_N1058


title: Ruvseq_Patient 1060 CBCS_N1060


title: Ruvseq_Patient 1057 CBCS_N1057


title: 72044_M7_Emx_Cx_E15_mat


title: 72043_M7_Emx_Cx_E15_mat


title: 72041_M7_Emx_Cx_E15_mat


title: 72042_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1055 CBCS_N1055


title: 72039_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1052 CBCS_N1052


title: Ruvseq_Patient 1054 CBCS_N1054


title: 72040_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1050 CBCS_N1050


title: 72037_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1053 CBCS_N1053


title: Ruvseq_Patient 1051 CBCS_N1051


title: 72035_M7_Emx_Cx_E15_pat


title: 72036_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1049 CBCS_N1049


title: 72033_M7_Emx_Cx_E15_pat


title: 72034_M7_Emx_Cx_E15_pat


title: 72032_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1048 CBCS_N1048


title: Ruvseq_Patient 1056 CBCS_N1056


title: Ruvseq_Patient 1047 CBCS_N1047


title: 72031_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1044 CBCS_N1044


title: Ruvseq_Patient 1042 CBCS_N1042


title: Ruvseq_Patient 1043 CBCS_N1043


title: 72029_M7_Emx_Cx_E15_mat


title: 72054_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1041 CBCS_N1041


title: Ruvseq_Patient 1045 CBCS_N1045


title: 72027_M7_Emx_Cx_E15_mat


title: 72038_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1040 CBCS_N1040


title: 72025_M7_Emx_Cx_E15_mat


title: 72026_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1039 CBCS_N1039


title: 72019_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1038 CBCS_N1038


title: 72030_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1036 CBCS_N1036


title: 72018_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1035 CBCS_N1035


title: 72016_M7_Emx_Cx_E15_mat


title: 72017_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1034 CBCS_N1034


title: 72015_M7_Emx_Cx_E15_mat


title: 72028_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1032 CBCS_N1032


title: Ruvseq_Patient 1033 CBCS_N1033


title: 72014_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1031 CBCS_N1031


title: 72013_M7_Emx_Cx_E15_mat


title: 72012_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1030 CBCS_N1030


title: 72011_M7_Emx_Cx_E15_pat


title: 72024_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1029 CBCS_N1029


title: Ruvseq_Patient 1027 CBCS_N1027


title: Ruvseq_Patient 1037 CBCS_N1037


title: 72010_M7_Emx_Cx_E15_pat


title: 72009_M7_Emx_Cx_E15_pat


title: 72008_M7_Emx_Cx_E15_pat


title: 72007_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1046 CBCS_N1046


title: Ruvseq_Patient 1023 CBCS_N1023


title: 72006_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1025 CBCS_N1025


title: Ruvseq_Patient 1024 CBCS_N1024


title: Ruvseq_Patient 1026 CBCS_N1026


title: 72005_M7_Emx_Cx_E15_mat


title: 72004_M7_Emx_Cx_E15_mat


title: 72002_M7_Emx_Cx_E15_mat


title: 72003_M7_Emx_Cx_E15_mat


title: 72001_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1020 CBCS_N1020


title: Ruvseq_Patient 1018 CBCS_N1018


title: Ruvseq_Patient 1019 CBCS_N1019


title: Ruvseq_Patient 1022 CBCS_N1022


title: Ruvseq_Patient 1028 CBCS_N1028


title: 71998_M7_Emx_Cx_E15_pat


title: 72000_M7_Emx_Cx_E15_mat


title: 71999_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1021 CBCS_N1021


title: Ruvseq_Patient 1017 CBCS_N1017


title: Ruvseq_Patient 1016 CBCS_N1016


title: Ruvseq_Patient 1014 CBCS_N1014


title: Ruvseq_Patient 1015 CBCS_N1015


title: 71995_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1013 CBCS_N1013


title: 71996_M7_Emx_Cx_E15_pat


title: 71993_M7_Emx_Cx_E15_pat


title: 71994_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1012 CBCS_N1012


title: Ruvseq_Patient 1011 CBCS_N1011


title: Ruvseq_Patient 1009 CBCS_N1009


title: Ruvseq_Patient 1010 CBCS_N1010


title: Ruvseq_Patient 1008 CBCS_N1008


title: 71991_M7_Emx_Cx_E15_pat


title: 71997_M7_Emx_Cx_E15_pat


title: 71992_M7_Emx_Cx_E15_pat


title: 71987_M7_Emx_Cx_E15_mat


title: 71990_M7_Emx_Cx_E15_mat


title: 71988_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1006 CBCS_N1006


title: Ruvseq_Patient 1005 CBCS_N1005


title: Ruvseq_Patient 1004 CBCS_N1004


title: 71986_M7_Emx_Cx_E15_mat


title: 71984_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 1001 CBCS_N1001


title: Ruvseq_Patient 1002 CBCS_N1002


title: 71983_M7_Emx_Cx_E15_mat


title: 71982_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1003 CBCS_N1003


title: Ruvseq_Patient 999 CBCS_N999


title: Ruvseq_Patient 998 CBCS_N998


title: Ruvseq_Patient 1000 CBCS_N1000


title: Ruvseq_Patient 997 CBCS_N997


title: 71981_M7_Emx_Cx_E15_pat


title: 71980_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 1007 CBCS_N1007


title: 71989_M7_Emx_Cx_E15_mat


title: 71978_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 994 CBCS_N994


title: 71979_M7_Emx_Cx_E15_pat


title: 71976_M7_Emx_Cx_E15_pat


title: 71985_M7_Emx_Cx_E15_mat


title: 71974_M7_Emx_Cx_E15_mat


title: 71975_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 992 CBCS_N992


title: Ruvseq_Patient 993 CBCS_N993


title: Ruvseq_Patient 991 CBCS_N991


title: Ruvseq_Patient 990 CBCS_N990


title: Ruvseq_Patient 996 CBCS_N996


title: 71972_M7_Emx_Cx_E15_mat


title: 71970_M7_Emx_Cx_E15_mat


title: 71968_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 988 CBCS_N988


title: Ruvseq_Patient 987 CBCS_N987


title: 71969_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 989 CBCS_N989


title: 71977_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 995 CBCS_N995


title: Ruvseq_Patient 986 CBCS_N986


title: 71966_M7_Emx_Cx_E15_pat


title: 71967_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 984 CBCS_N984


title: Ruvseq_Patient 982 CBCS_N982


title: 71965_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 985 CBCS_N985


title: 71964_M7_Emx_Cx_E15_pat


title: 71963_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 981 CBCS_N981


title: 71973_M7_Emx_Cx_E15_mat


title: 71962_M7_Emx_Cx_E15_pat


title: 71961_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 979 CBCS_N979


title: 71971_M7_Emx_Cx_E15_mat


title: 71960_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 978 CBCS_N978


title: 71959_M7_Emx_Cx_E15_pat


title: 71958_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 980 CBCS_N980


title: Ruvseq_Patient 976 CBCS_N976


title: Ruvseq_Patient 977 CBCS_N977


title: Ruvseq_Patient 983 CBCS_N983


title: 71956_M7_Emx_Cx_E15_mat


title: 71957_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 974 CBCS_N974


title: Ruvseq_Patient 975 CBCS_N975


title: Ruvseq_Patient 973 CBCS_N973


title: 71955_M7_Emx_Cx_E15_mat


title: 71954_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 972 CBCS_N972


title: 71953_M7_Emx_Cx_E15_mat


title: 71952_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 971 CBCS_N971


title: 71951_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 969 CBCS_N969


title: Ruvseq_Patient 968 CBCS_N968


title: Ruvseq_Patient 970 CBCS_N970


title: 71950_M7_Emx_Cx_E15_pat


title: 71949_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 966 CBCS_N966


title: Ruvseq_Patient 967 CBCS_N967


title: Ruvseq_Patient 965 CBCS_N965


title: Ruvseq_Patient 964 CBCS_N964


title: 71944_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 962 CBCS_N962


title: Ruvseq_Patient 963 CBCS_N963


title: 71946_M7_Emx_Cx_E15_pat


title: 71943_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 961 CBCS_N961


title: Ruvseq_Patient 960 CBCS_N960


title: 71942_M7_Emx_Cx_E15_mat


title: 71941_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 959 CBCS_N959


title: 71940_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 958 CBCS_N958


title: Ruvseq_Patient 956 CBCS_N956


title: 71939_M7_Emx_Cx_E15_mat


title: 71938_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 955 CBCS_N955


title: 71948_M7_Emx_Cx_E15_pat


title: 71937_M7_Emx_Cx_E15_mat


title: 71935_M7_Emx_Cx_E15_mat


title: 71947_M7_Emx_Cx_E15_pat


title: 71945_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 953 CBCS_N953


title: Ruvseq_Patient 951 CBCS_N951


title: Ruvseq_Patient 952 CBCS_N952


title: 71936_M7_Emx_Cx_E15_mat


title: 71934_M7_Emx_Cx_E15_pat


title: 71931_M7_Emx_Cx_E15_pat


title: 71929_M7_Emx_Cx_E15_pat


title: 71930_M7_Emx_Cx_E15_pat


title: 71932_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 948 CBCS_N948


title: 71933_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 957 CBCS_N957


title: Ruvseq_Patient 949 CBCS_N949


title: Ruvseq_Patient 947 CBCS_N947


title: Ruvseq_Patient 954 CBCS_N954


title: Ruvseq_Patient 946 CBCS_N946


title: 71927_M7_Emx_Cx_E15_pat


title: 71917_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 945 CBCS_N945


title: Ruvseq_Patient 943 CBCS_N943


title: 71916_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 941 CBCS_N941


title: 71914_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 942 CBCS_N942


title: Ruvseq_Patient 950 CBCS_N950


title: 71915_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 940 CBCS_N940


title: Ruvseq_Patient 939 CBCS_N939


title: 71912_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 938 CBCS_N938


title: Ruvseq_Patient 937 CBCS_N937


title: 71913_M7_Emx_Cx_E15_pat


title: 71928_M7_Emx_Cx_E15_pat


title: 71911_M7_Emx_Cx_E15_pat


title: 71910_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 944 CBCS_N944


title: 71909_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 936 CBCS_N936


title: Ruvseq_Patient 934 CBCS_N934


title: 71907_M7_Emx_Cx_E15_mat


title: 71908_M7_Emx_Cx_E15_mat


title: 71906_M7_Emx_Cx_E15_mat


title: R1388_GIA_NICD1: NICD1-infected renal progenitors, biological rep1

value: Renal progenitor cells


title: Ruvseq_Patient 933 CBCS_N933


title: Ruvseq_Patient 931 CBCS_N931


title: Ruvseq_Patient 932 CBCS_N932


title: Ruvseq_Patient 930 CBCS_N930


title: 71904_M7_Emx_Cx_E15_mat


title: 71903_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 928 CBCS_N928


title: 71901_M7_Emx_Cx_E15_pat


title: 71902_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 929 CBCS_N929


title: Ruvseq_Patient 927 CBCS_N927


title: 71900_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 926 CBCS_N926


title: 71898_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 924 CBCS_N924


title: 71896_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 935 CBCS_N935


title: Ruvseq_Patient 925 CBCS_N925


title: 71899_M7_Emx_Cx_E15_pat


title: 71894_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 922 CBCS_N922


title: 71893_M7_Emx_Cx_E15_mat


title: 71905_M7_Emx_Cx_E15_mat


title: 71892_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 923 CBCS_N923


title: 71897_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 921 CBCS_N921


title: 71891_M7_Emx_Cx_E15_mat


title: 71890_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 920 CBCS_N920


title: 71889_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 917 CBCS_N917


title: Ruvseq_Patient 915 CBCS_N915


title: Ruvseq_Patient 916 CBCS_N916


title: 71888_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 919 CBCS_N919


title: 71887_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 918 CBCS_N918


title: 71886_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 914 CBCS_N914


title: 71895_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 912 CBCS_N912


title: 71885_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 913 CBCS_N913


title: 71884_M7_Emx_Cx_E15_pat


title: 71883_M7_Emx_Cx_E15_pat


title: 71882_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 910 CBCS_N910


title: Ruvseq_Patient 911 CBCS_N911


title: Ruvseq_Patient 909 CBCS_N909


title: 71879_M7_Emx_Cx_E15_mat


title: 71881_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 908 CBCS_N908


title: Ruvseq_Patient 907 CBCS_N907


title: Ruvseq_Patient 906 CBCS_N906


title: 71878_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 905 CBCS_N905


title: Ruvseq_Patient 904 CBCS_N904


title: 71877_M7_Emx_Cx_E15_mat


title: 71875_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 903 CBCS_N903


title: Ruvseq_Patient 899 CBCS_N899


title: Ruvseq_Patient 901 CBCS_N901


title: Ruvseq_Patient 900 CBCS_N900


title: 71873_M7_Emx_Cx_E15_mat


title: 71874_M7_Emx_Cx_E15_mat


title: 71871_M7_Emx_Cx_E15_pat


title: 71872_M7_Emx_Cx_E15_pat


title: 71880_M7_Emx_Cx_E15_mat


title: 71870_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 898 CBCS_N898


title: Ruvseq_Patient 897 CBCS_N897


title: 71869_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 895 CBCS_N895


title: Ruvseq_Patient 894 CBCS_N894


title: 71867_M7_Emx_Cx_E15_pat


title: 71866_M7_Emx_Cx_E15_pat


title: 71868_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 893 CBCS_N893


title: 71876_M7_Emx_Cx_E15_mat


title: 71865_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 892 CBCS_N892


title: Ruvseq_Patient 891 CBCS_N891


title: Ruvseq_Patient 902 CBCS_N902


title: 71864_M7_Emx_Cx_E15_mat


title: 71863_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 890 CBCS_N890


title: Ruvseq_Patient 889 CBCS_N889


title: Ruvseq_Patient 888 CBCS_N888


title: 71861_M7_Emx_Cx_E15_mat


title: 71860_M7_Emx_Cx_E15_mat


title: 71862_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 896 CBCS_N896


title: Ruvseq_Patient 887 CBCS_N887


title: Ruvseq_Patient 886 CBCS_N886


title: Ruvseq_Patient 884 CBCS_N884


title: Ruvseq_Patient 885 CBCS_N885


title: 71857_M7_Emx_Cx_E15_mat


title: 71858_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 882 CBCS_N882


title: 71859_M7_Emx_Cx_E15_mat


title: 71856_M7_Emx_Cx_E15_pat


title: 71855_M7_Emx_Cx_E15_pat


title: 71854_M7_Emx_Cx_E15_pat


title: 71853_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 883 CBCS_N883


title: Ruvseq_Patient 880 CBCS_N880


title: 71852_M7_Emx_Cx_E15_pat


title: 71851_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 881 CBCS_N881


title: 71850_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 875 CBCS_N875


title: Ruvseq_Patient 877 CBCS_N877


title: 71849_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 874 CBCS_N874


title: Ruvseq_Patient 878 CBCS_N878


title: 71847_M7_Emx_Cx_E15_mat


title: 71848_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 873 CBCS_N873


title: Ruvseq_Patient 871 CBCS_N871


title: 71844_M7_Emx_Cx_E15_mat


title: 71845_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 870 CBCS_N870


title: 71842_M7_Emx_Cx_E15_mat


title: 71841_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 879 CBCS_N879


title: Ruvseq_Patient 868 CBCS_N868


title: Ruvseq_Patient 867 CBCS_N867


title: Ruvseq_Patient 872 CBCS_N872


title: Ruvseq_Patient 869 CBCS_N869


title: 71839_M7_Emx_Cx_E15_pat


title: 71840_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 876 CBCS_N876


title: 71843_M7_Emx_Cx_E15_mat


title: 71838_M7_Emx_Cx_E15_pat


title: 71837_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 864 CBCS_N864


title: Ruvseq_Patient 865 CBCS_N865


title: Ruvseq_Patient 866 CBCS_N866


title: Ruvseq_Patient 863 CBCS_N863


title: 71836_M7_Emx_Cx_E15_pat


title: 71835_M7_Emx_Cx_E15_pat


title: 71846_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 862 CBCS_N862


title: Ruvseq_Patient 861 CBCS_N861


title: Ruvseq_Patient 860 CBCS_N860


title: 71834_M7_Emx_Cx_E15_pat


title: 71833_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 859 CBCS_N859


title: Ruvseq_Patient 858 CBCS_N858


title: 71832_M7_Emx_Cx_E15_mat


title: 71831_M7_Emx_Cx_E15_mat


title: 71830_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 857 CBCS_N857


title: Ruvseq_Patient 856 CBCS_N856


title: 71829_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 855 CBCS_N855


title: 71828_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 854 CBCS_N854


title: 71826_M7_Emx_Cx_E15_mat


title: 71827_M7_Emx_Cx_E15_mat


title: 71818_M7_Emx_Cx_E15_mat


title: 71817_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 851 CBCS_N851


title: 71825_M7_Emx_Cx_E15_mat


title: 71816_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 848 CBCS_N848


title: 71815_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 846 CBCS_N846


title: Ruvseq_Patient 850 CBCS_N850


title: 71813_M7_Emx_Cx_E15_mat


title: 71812_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 844 CBCS_N844


title: 71814_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 845 CBCS_N845


title: Ruvseq_Patient 843 CBCS_N843


title: Ruvseq_Patient 842 CBCS_N842


title: 71810_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 853 CBCS_N853


title: Ruvseq_Patient 852 CBCS_N852


title: Ruvseq_Patient 841 CBCS_N841


title: Ruvseq_Patient 849 CBCS_N849


title: 71808_M7_Emx_Cx_E15_pat


title: 71807_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 839 CBCS_N839


title: 71811_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 847 CBCS_N847


title: 71805_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 837 CBCS_N837


title: Ruvseq_Patient 836 CBCS_N836


title: 71806_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 835 CBCS_N835


title: Ruvseq_Patient 834 CBCS_N834


title: 71803_M7_Emx_Cx_E15_mat


title: 71802_M7_Emx_Cx_E15_mat


title: 71804_M7_Emx_Cx_E15_mat


title: 71801_M7_Emx_Cx_E15_mat


title: 71809_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 833 CBCS_N833


title: 71800_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 832 CBCS_N832


title: Ruvseq_Patient 840 CBCS_N840


title: 71798_M7_Emx_Cx_E15_mat


title: 71797_M7_Emx_Cx_E15_pat


title: 71796_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 838 CBCS_N838


title: 71795_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 828 CBCS_N828


title: Ruvseq_Patient 829 CBCS_N829


title: Ruvseq_Patient 827 CBCS_N827


title: Ruvseq_Patient 826 CBCS_N826


title: Ruvseq_Patient 825 CBCS_N825


title: 71793_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 824 CBCS_N824


title: Ruvseq_Patient 823 CBCS_N823


title: 71799_M7_Emx_Cx_E15_mat


title: 71792_M7_Emx_Cx_E15_pat


title: 71794_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 830 CBCS_N830


title: 71791_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 822 CBCS_N822


title: 71789_M7_Emx_Cx_E15_mat


title: 71788_M7_Emx_Cx_E15_mat


title: 71790_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 831 CBCS_N831


title: 71787_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 819 CBCS_N819


title: Ruvseq_Patient 818 CBCS_N818


title: 71786_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 817 CBCS_N817


title: 71785_M7_Emx_Cx_E15_mat


title: 71784_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 816 CBCS_N816


title: 71782_M7_Emx_Cx_E15_mat


title: 71783_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 815 CBCS_N815


title: 71781_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 814 CBCS_N814


title: Ruvseq_Patient 813 CBCS_N813


title: 71780_M7_Emx_Cx_E15_pat


title: 71778_M7_Emx_Cx_E15_pat


title: 71779_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 821 CBCS_N821


title: Ruvseq_Patient 810 CBCS_N810


title: Ruvseq_Patient 820 CBCS_N820


title: Ruvseq_Patient 812 CBCS_N812


title: Ruvseq_Patient 808 CBCS_N808


title: Ruvseq_Patient 809 CBCS_N809


title: 71777_M7_Emx_Cx_E15_pat


title: 71776_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 811 CBCS_N811


title: 71775_M7_Emx_Cx_E15_pat


title: 71774_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 806 CBCS_N806


title: 71773_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 807 CBCS_N807


title: Ruvseq_Patient 805 CBCS_N805


title: Ruvseq_Patient 804 CBCS_N804


title: 71772_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 803 CBCS_N803


title: 71771_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 802 CBCS_N802


title: 71769_M7_Emx_Cx_E15_mat


title: 71770_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 801 CBCS_N801


title: 71768_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 800 CBCS_N800


title: 71766_M7_Emx_Cx_E15_mat


title: 71767_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 799 CBCS_N799


title: 71765_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 798 CBCS_N798


title: 71763_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 796 CBCS_N796


title: Ruvseq_Patient 794 CBCS_N794


title: 71759_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 792 CBCS_N792


title: 71760_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 793 CBCS_N793


title: Ruvseq_Patient 795 CBCS_N795


title: 71757_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 790 CBCS_N790


title: Ruvseq_Patient 789 CBCS_N789


title: 71756_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 787 CBCS_N787


title: Ruvseq_Patient 791 CBCS_N791


title: 71755_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 786 CBCS_N786


title: 71753_M7_Emx_Cx_E15_mat


title: 71764_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 785 CBCS_N785


title: Ruvseq_Patient 784 CBCS_N784


title: Ruvseq_Patient 788 CBCS_N788


title: 71761_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 783 CBCS_N783


title: Ruvseq_Patient 797 CBCS_N797


title: 71752_M7_Emx_Cx_E15_mat


title: 71762_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 782 CBCS_N782


title: 71758_M7_Emx_Cx_E15_pat


title: 71750_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 781 CBCS_N781


title: 71748_M7_Emx_Cx_E15_pat


title: 71749_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 780 CBCS_N780


title: 71747_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 779 CBCS_N779


title: 71746_M7_Emx_Cx_E15_pat


title: 71745_M7_Emx_Cx_E15_pat


title: 71754_M7_Emx_Cx_E15_mat


title: 71744_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 777 CBCS_N777


title: Ruvseq_Patient 775 CBCS_N775


title: 71751_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 776 CBCS_N776


title: Ruvseq_Patient 774 CBCS_N774


title: 71742_M7_Emx_Cx_E15_pat


title: 71741_M7_Emx_Cx_E15_mat


title: 71740_M7_Emx_Cx_E15_mat


title: 71738_M7_Emx_Cx_E15_mat


title: 71739_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 771 CBCS_N771


title: Ruvseq_Patient 772 CBCS_N772


title: Ruvseq_Patient 770 CBCS_N770


title: 71737_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 773 CBCS_N773


title: 71736_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 778 CBCS_N778


title: 71735_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 767 CBCS_N767


title: 71734_M7_Emx_Cx_E15_mat


title: Ruvseq_Patient 768 CBCS_N768


title: Ruvseq_Patient 766 CBCS_N766


title: 71733_M7_Emx_Cx_E15_pat


title: 71743_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 765 CBCS_N765


title: 71732_M7_Emx_Cx_E15_pat


title: 71731_M7_Emx_Cx_E15_pat


title: 71729_M7_Emx_Cx_E15_pat


title: 71730_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 764 CBCS_N764


title: Ruvseq_Patient 763 CBCS_N763


title: 71728_M7_Emx_Cx_E15_pat


title: Ruvseq_Patient 769 CBCS_N769


title: Ruvseq_Patient 759 CBCS_N759


title: Ruvseq_Patient 758 CBCS_N758


title: 71726_M7_Emx_Cx_E15_pat


title: 71727_M7_Emx_Cx_E15_pat


title: 71577_M7_Emx_Cx_P42_mat


title: 71576_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 760 CBCS_N760


title: Ruvseq_Patient 757 CBCS_N757


title: Ruvseq_Patient 755 CBCS_N755


title: 71575_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 754 CBCS_N754


title: 71574_M7_Emx_Cx_P42_mat


title: 71573_M7_Emx_Cx_P42_mat


title: Ruvseq_Patient 753 CBCS_N753


title: Ruvseq_Patient 750 CBCS_N750


title: Ruvseq_Patient 751 CBCS_N751


title: Ruvseq_Patient 752 CBCS_N752


title: Ruvseq_Patient 749 CBCS_N749


title: Ruvseq_Patient 762 CBCS_N762


title: 46234: M12_Emx_OB_patUPD

data_processing:
Raw reads were delivered as BAM files and converted to fastq format using bamToFastq (bedtools suite v2.26.0) for alignment. Reads were aligned to mm10 and gencode vM16 annotation using STAR  with  --clip5pNbases 12 --outFilterMultimapNmax 1 --outSAMmode BAM --quantMode TranscriptomeSAM GeneCounts. The resulting BAM file was used to count unique reads aligning to the trascriptome, and the number of “raw” reads resulting in 10 million reads aligning to the transcriptome was determined. This number of reads was randomly extracted from the raw reads using DownsampleSam from the picard toolkit (v.2.16.0). These reads were used to count reads per gene, using STAR with --outFilterMultimapNmax 1 --outSAMtype None --outSAMmode None --quantMode GeneCounts --clip5pNbases 12 parameters.
Differential expression between maternal and paternal UPD cells in all cell types was calculated using DESeq2 v1.16.1. Results are given as supplementary file.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Read counts in transcripts as reported by STAR as tab delimited text
Supplementary_files_format_and_content: Excel spreadsheet with differential expression analysis between matUPD and patUPD sample as reported by DESeq2. Cell type given in column headers.

growth_protocol: All mouse colonies were maintained in accordance with protocols approved by institutional animal care and use committee, institutional ethics committee and the preclinical core facility (PCF) at IST Austria. Experiments were performed under a license approved by the Austrian Federal Ministry of Science and Research in accordance with the Austrian and EU animal laws. Mouse lines used: MADM-7-GT (JAX stock # 021457), MADM-7-TG (JAX stock # 021458), MADM-11-GT (JAX stock # 013749), MADM-11-TG (JAX stock # 013751), MADM-12-GT (JAX stock # 021460), MADM-12-TG (JAX stock # 021461), Emx1-Cre (JAX stock # 005628), Nkx2.1-Cre (JAX stock # 008661)

extract_protocol:
Samples in isolation Buffer (IB; Lexogen) were processed according to the SPLIT kit instructions (Lexogen). All other samples were incubated for 30min at 37°C. Total volume was filled to 250µl using RNase-free H2O (Thermo Fisher Scientific) followed by addition of 750µl Trizol LS (Thermo Fisher Scientific). Samples were mixed by 5 times inverting. After a 5min incubation step at RT, the entire solution was transferred into a MaXtract tube (Qiagen). 200µl chloroform (Sigma-Aldrich) was added, followed by 3 times 5sec vortexing and 2min incubation at RT. Samples were centrifuged for 2min with 12000rpm at 18°C. Supernatant was transferred to a new tube and isopropanol (Sigma-Aldrich) was added in a 1:1 ratio. For better visibility of the RNA pellet 1µl GlycoBlue (Thermo Fisher Scientific) was added and entire solution was mixed by vortexing (3x 5sec). Samples were left for precipitation o/n at -20°C. After precipitation samples were centrifuged for 20min with 14000rpm at 4°C. Supernatant was removed and RNA pellet was washed with 70% ethanol, followed by a 5min centrifugation step (14000rpm at 4°C). RNA pellet was resuspended in an appropriate amount of RNase-free H2O. RNA quality was analyzed using Bioanalyzer RNA 6000 Nano (Agilent) and RNA 6000 Pico kit (Agilent) following the manufacturer’s instructions.
cDNA libraries were prepared using QuantSeq 3’mRNA library preparation kit (Lexogen) following the manufacturer’s instructions. In order to amplify libraries correctly RT-PCR was performed as indicated in the protocol using PCR Add-on kit (Lexogen). cDNA library size distribution was analyzed using Bioanalyzer DNA High Sensitivity kit (Agilent) according to the manufacturer’s instructions. cDNA library concentration was measured using Qubit. Libraries were pooled according to library length and concentration.

treatment_protocol: P0 animals were sacrificed and brain areas of interest (neocortex, hippocampus and olfactory bulb) were dissected. Single cell suspensions were prepared by using Papain containing L-cysteine and EDTA (vial 2, Worthington), DNase I (vial 3, Worthington), Ovomucoid protease inhibitor (vial 4, Worthington), EBSS (Thermo Fisher Scientific), DMEM/F12 (Thermo Fisher Scientific), FBS and HS. All vials from Worthington kit were reconstituted according to the manufacturer’s instructions using EBSS. The dissected brain areas were directly placed into Papain-DNase solution (20units/ml papain and 1000 units DNase). Entire litters were pooled in order to obtain sufficient material for RNA extraction. Enzymatic digestion was performed for 30min at 37°C in a shaking water bath. Next, solution 2 (EBSS containing 0.67mg Ovomucoid protease inhibitor and 166.7 U/ml DNase I) was added, the whole suspension was thoroughly mixed and centrifuged for 5min at 1000rpm at RT. Supernatant was removed and cell pellet was resuspended in solution 2. Trituration with p1000 pipette was performed to mechanically dissolve any remaining tissue parts. DMEM/F12 was added to the cell suspension as a washing solution, followed by a centrifugation step of 5min with 1500rpm at RT. Cells were resuspended in media (DMEM/F12 containing 10% FBS and 10% HS) and kept on ice until sorted. Right before sorting, cell suspension was filtered using a 40µm cell strainer. FACS was performed on a BD FACS Aria III using 100 nozzle and keeping sample and collection devices at 4°C. Duplet exclusion was performed to ensure sorting of true single cells. GFP+ (green), tdTomato+ (red), and GFP+/tdT+ (yellow) cells were collected. Cells were sorted directly into either Isolation Buffer (IB; Lexogen) if more than 2000 sorted cells/per color were expected or if samples yielded fewer labeled cells into custom made lysis buffer (30nM TRIS pH 8, 10nM EDTA pH 8, 1% SDS and 200 µg/µL Proteinase K).

value: Olfactory bulb

tag: color

value: red


title: 46237: M12_Emx_OB_wt

value: yellow

value: wt


title: 46236: M12_Emx_OB_matUPD

value: Emx1 lineage

value: green


title: Ruvseq_Patient 748 CBCS_N748


title: 47889: M12_Emx_OB_patUPD


title: 46233: M12_Emx_OB_wt


title: Ruvseq_Patient 747 CBCS_N747


title: 46232: M12_Emx_OB_matUPD

value: mat