title: GC077040_TACGCTGC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: 2xcr+pik3ca-3

status: Public on Oct 09 2019

type: SRA

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

description: 2xcr+pik3ca Rep3, with over-expression of wildtype PIK3CA

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using HISAT2 (Galaxy tool version2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

molecule: total RNA

organism: Mus musculus

source_name: mouse GBM model relying on in utero electroporation (IUE) and CRISPR-Cas9 mediated knockout of NF1 and p53 (termed 2xCR), and coelectroporation of pGlast-PBase plasmid with a PBCAG-GFPt2aLuc and PBCAG-PIK3CA(WT) constructs

growth_protocol: All mouse gliomas were generated in the CD-1 IGS mouse background as previously described (PMID: 28166219). In utero electroporation was performed on embryonic day 15. Previously generated CRISPR constructs were used to knockout NF1, PTEN, and TRP53 (each at 1.5μg per μl) (PMID: 28166219).

extract_protocol:
tissue samples were harvested with the aid of a fluorescence microscope from end stage tumors, dissecting out the GFP-positive tumor tissue, minced into ~30mg pieces, snap frozen on dry ice, and stored at -80°C. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, #74134) according to the manufacturer’s protocol. Samples were prepared in biological replicates, n ≥ 3 per genotype. RNA integrity (RIN ≥ 8.0) was confirmed using the High Sensitivity RNA Analysis Kit (AATI, DNF-472-0500) on a 12-Capillary Fragment Analyzer.
Illumina sequencing libraries with 6-bp single indices were constructed from 1 μg total RNA using the TruSeq Stranded mRNA LT kit (Illumina, RS-122-2101). The resulting library was validated using the Standard Sensitivity NGS Fragment Analysis Kit (AATI, DNF-473-0500) on a 12-Capillary Fragment Analyzer. Equal concentrations (2nM) of libraries were pooled and subjected to sequencing of approximately 20 million reads per sample using the Mid Output v2 kit (Illumina, FC-404-2001) on a Illumina NextSeq550 following the manufacturer’s instructions.

treatment_protocol: PIK3CA alleles were genomically integrated and overexpressed through the piggyBac (PB) transposase (PBase) system. The pGlast-PBase plasmid (at 2.0μg per μl) was coelectroporated with a PBCAG-PIK3CA* construct (1.0μg per μl).

tag: strain

value: ICR (CD-1) outbred

tag: tissue

value: mouse GBM model

tag: genotype/variation

value: over-expression of wildtype PIK3CA


title: 2xcr+pik3ca-2

description: 2xcr+pik3ca Rep2, with over-expression of wildtype PIK3CA


title: GC077040_TAAGGCGA-GCGTAAGA_recurring_nodular_sc

city: Edinburgh

first: Jana

last: Travnickova

address: Crewe Road South

department: MRC Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: MRC Human Genetics Unit & Cancer Research UK EC

description: NexteraXT library preparation

data_processing: Sequence quality was checked using FastQC (version 0.11.4). Raw reads were trimmed, using Cutadapt to remove Smart-Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 (Ensembl V92, 20178) including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment-based mode.

molecule: polyA RNA

organism: Danio rerio

source_name: mitfa:GFP cell from recurring_nodular triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from recurring tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA -  Nextera XT

tag: genotype

value: GFP+ cell from recurring_nodular triple melanoma


title: GC077040_GTAGAGGA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_superficial triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from regressed tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA -  Nextera XT

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077040_GTAGAGGA-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_GTAGAGGA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_nodular triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from primary tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA -  Nextera XT


title: 2xcr+pik3ca-1

description: 2xcr+pik3ca Rep1, with over-expression of wildtype PIK3CA


title: 2xcr-3

description: 2xcr Rep3, with Cherry control

source_name: mouse GBM model relying on in utero electroporation (IUE) and CRISPR-Cas9 mediated knockout of NF1 and p53 (termed 2xCR), and coelectroporation of pGlast-PBase plasmid with a PBCAG-GFPt2aLuc and PBCAG-Cherry constructs

value: Cherry control


title: GC077040_GTAGAGGA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_GTAGAGGA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_nodular triple melanoma

value: GFP+ cell from regressed_nodular triple melanoma


title: GC077040_GGACTCCT-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: 2xcr-2

description: 2xcr Rep2, with Cherry control


title: GC077041_ACTCGCTA-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_superficial triple melanoma

value: GFP+ cell from primary_superficial triple melanoma


title: GC077040_GGACTCCT-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: 2xcr-1

description: 2xcr Rep1, with Cherry control


title: GC077040_TAAGGCGA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077040_GGACTCCT-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077040_GGACTCCT-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_GGACTCCT-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077040_GCTCATGA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_TAAGGCGA-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_GCTCATGA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077040_TAAGGCGA-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_GCTCATGA-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: MDA-MB-231_RNA_CRISPRctrl_Rep2

city: Chapel Hill

first: Travis

last: Ptacek

state: NC

address: 5109 Neuroscience Research Building

institute: UNC Neuroscience Center Bioinformatics Core

data_processing:
Illumina Casava software used for base calling
Quality filtering was performed using FASTX v0.0.14 fastq_quality_filter for reads with 90% of bases having a quality of 20+
Reads aligned to reference genome using STAR v2.5.2b
Gene expression quantified using salmon v0.8.1
Differential gene expression tested using DESeq v1.22.2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of VST normalized counts from DESeq2 for all genes and samples

organism: Homo sapiens

extract_protocol:
Rneasy kit with on column Dnase digestion (Qiagen)
TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions

tag: cell line

tag: treatment


title: GC077040_GCTCATGA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077040_GCTCATGA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: MDA-MB-231_RNA_ADSL_sgRNA6_Rep2


title: MDA-MB-231_RNA_CRISPRctrl_Rep3


title: MDA-MB-231_RNA_ADSL_sgRNA6_Rep3


title: MDA-MB-231_RNA_ADSL_sgRNA6_Rep1


title: GC077040_CTCTCTAC-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_CTCTCTAC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: MDA-MB-231_RNA_ADSL_sgRNA5_Rep3


title: MDA-MB-231_RNA_CRISPRctrl_Rep1


title: GC077040_CTCTCTAC-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_CTCTCTAC-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077040_CTCTCTAC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: MDA-MB-231_RNA_ADSL_sgRNA5_Rep2


title: GC077040_CGTACTAG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: MDA-MB-231_RNA_ADSL_sgRNA5_Rep1


title: GC077040_GCTCATGA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_CGAGGCTG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_GCTCATGA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_CGAGGCTG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_CGAGGCTG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077040_CGAGGCTG-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077040_ATGCGCAG-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077040_ATCTCAGG-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_CGAGGCTG-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_ATCTCAGG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_ATCTCAGG-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_ATCTCAGG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_AGGCAGAA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_AGGCAGAA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: HO1_2: primary hepatic organoids

city: PALO ALTO

first: YUAN

last: GUAN

state: CA

address: 1701 Page Mill Road

institute: Stanford University

data_processing:
Adapter sequences and low-quality bases at the end of the reads were then removed using the Cutadapt software
The reads were then aligned to human exon sequences (Build GRCh38) using STAR
The expression level of each gene for each cell were then quantified using the FeatureCounts tool
the counts-per-million (CPM) values were generated using scater package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited file containing the log2-transformed CPM values

source_name: > day 21

growth_protocol: Diffenretiation protocol detail describe in manuscript. Briefly, we collected samples from different stages during iPSC toward hepatic organoids.

extract_protocol:
SMART-SEQ2
Nextera XT DNA Sample Preparation kit

value: primary hepatic organoids


title: LIVER1: normal liver tissue

source_name: tissue

value: normal liver tissue


title: iPSC: iPSCs

source_name: day 0

value: iPSCs


title: GC077040_CTCTCTAC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: HO1_1: primary hepatic organoids


title: GC077040_CTCTCTAC-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: LIVER2: normal liver tissue


title: PHH: primary human hepatocyte

source_name: primary cells

value: primary human hepatocyte


title: GC077040_AGGCAGAA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: HB: hepatoblast

source_name: day 9

value: hepatoblast


title: GC077040_AAGAGGCA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_AAGAGGCA-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_AAGAGGCA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077040_AAGAGGCA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC056865_GCTCATGA-TCGACTAG_regressed_sc

description: NexteraXT library preparation

data_processing:
Sequence quality was checked using FastQC (version 0.11.4). Raw reads were trimmed, using Cutadapt to remove Smart-Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 (Ensembl V92, 20178) including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment-based mode.
Illumina  software used for basecalling.
Sequence quality was checked using FastQC (version 0.11.3)
Reads were aligned to the zebrafish genome (GRCz11) using STAR (STAR_2.5.1b) with the default parameters or using Salmon in the alignment-based mode
The quality of the resulting alignment to the transcriptome (Ensembl annotation version GRCz11) has been checked using RNASeqQC (v1.1.8.1)
Raw counts of reads covering the transcriptome (Ensembl annotation version GRCz11) was obtained using htseq-count (0.6.1) with the “-s reverse” option.
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: tab-delimited filed of raw counts at gene level for each sample

source_name: mitfa:GFP cells from regressed triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from regression site, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: GFP+ cell from regressed triple melanoma


title: GC056865_GGACTCCT-TTCTAGCT_regressed_sc

description: NexteraXT library preparation


title: GC077040_AAGAGGCA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077040_AAGAGGCA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: DM: secondary hepatic organoids in differentiation medium

source_name: > day 62


title: GC056865_ACTCGCTA-TTCTAGCT_regressed_sc

description: NexteraXT library preparation


title: GC056829_TGCAGCTA-CGTCTAAT_regressed_sc

description: NexteraXT library preparation


title: GC056829_TGCAGCTA-CCTAGAGT_primary_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cells from primary triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from primary tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: GFP+ cell from primary triple melanoma


title: GC056829_TGCAGCTA-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: GC077040_AGGCAGAA-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC056829_TCCTGAGC-GAGCCTTA_regressed_sc

description: NexteraXT library preparation


title: GC056829_TAGCGCTC-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: GC056829_TCGACGTC-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: GC056829_TAGGCATG-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: GC056829_TAGCGCTC-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: GC056829_TAGGCATG-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: GC056829_TACGCTGC-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: GM: secondary hepatic organoids in growth medium


title: GC056829_TACGCTGC-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: GC056829_TAGCGCTC-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: TATCoc_Rep3 [CocT3]

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
20190214_RatNeuro_cpm_AVG(glmFit)
CocT3

data_processing:
Indexed sequences were checked by FastQC | version: 0.11.5
Trimed adapter by TrimGalore-0.4.5
Reads were mapped to the Rattus_6.0_r93 reference genome using STAR | version 2.5 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes Rattus_norvegicus.Rnor_6.0.93.gtf were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -T 10
Genome_build: Rattus_6.0_r93
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

organism: Rattus norvegicus

source_name: neuro cells TAT+Cocaine

growth_protocol: Rat primary cortical cultures were maintain  in Neurobasal mediim supplemented with B-27 and 1% penicillin-strptomycin and 2mM L-glutamine.The cells were plated in 6-well plate.

extract_protocol:
Total RNA was extracted using Quick-RNA MicroPrep Kit(ZYMO) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)

treatment_protocol: Rat primary cortical cultures were treated with 60ng/ml TAT for 48 hours and then treated with 25um Cocaine for another 24 hours. RK33 was added at the same time with TAT.

tag: cell type

value: primary cortical culture

value: treated with TAT 60ng/ml+ 25um Cocaine

value: sprague dawley


title: GC056829_TAGCGCTC-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: TATCoc_Rep1 [CocT1]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
CocT1


title: TATCoc_Rep2 [CocT2]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
CocT2


title: Coc_Rep3 [Coc3]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
Coc3

source_name: neuro cells Cocaine

value: treated with 25um Cocaine


title: Coc_Rep2 [Coc2]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
Coc2


title: GC056829_TACGCTGC-GAGCCTTA_regressed_sc

description: NexteraXT library preparation


title: GC056829_TACGCTGC-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: GC056829_TACGCTGC-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_TACGCTGC-CGTCTAAT_regressed_sc

description: NexteraXT library preparation


title: Coc_Rep1 [Coc1]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
Coc1


title: GC056829_TCGACGTC-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_TCCTGAGC-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: GC056829_TAAGGCGA-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: GC056829_TAAGGCGA-GAGCCTTA_regressed_sc

description: NexteraXT library preparation


title: TAT_Rep3 [T3]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
T3

source_name: neuro cells TAT

value: treated with TAT 60ng/ml


title: GC056829_TAAGGCGA-CGTCTAAT_regressed_sc

description: NexteraXT library preparation


title: GC056829_TAAGGCGA-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_GTAGAGGA-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: TAT_Rep2 [T2]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
T2


title: GC056829_GGAGCTAC-GAGCCTTA_regressed_sc

description: NexteraXT library preparation


title: GC056829_GTAGAGGA-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_GGAGCTAC-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: Control_Rep3 [C3]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
C3

source_name: neuro cells Control

value: no treatment


title: TAT_Rep1 [T1]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
T1


title: GC056829_GGAGCTAC-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: GC056829_GGAGCTAC-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: GC056829_GGAGCTAC-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_GGACTCCT-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_GGACTCCT-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: GC056829_GGACTCCT-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: Control_Rep1 [C1]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
C1


title: Control_Rep3

description:
20180621_Rat.cpm_AVG(glmFit)
Control3


title: Control_Rep2

description:
20180621_Rat.cpm_AVG(glmFit)
Control2


title: Control_Rep2 [C2]

description:
20190214_RatNeuro_cpm_AVG(glmFit)
C2


title: GC056829_GCTCATGA-CTATTAAG_regressed_sc

description: NexteraXT library preparation


title: GC056829_GCTCATGA-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: Control_Rep1

description:
20180621_Rat.cpm_AVG(glmFit)
Control1


title: 10dpp Dazl SKO mouse testes

city: Shanghai

first: Haixin

last: Li

state: Shanghai

address: 36 Yunxin Rd

department: Shanghai Tenth People's Hospital, School of Medicine

country: China

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR with parameters --twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5, count by RSEQC.
Reads were assembled by StringTie, FPKM value of each sample were calculated by StringTie, expression level of each gene was assessed by formula log2(FPKM+1). The significant difference was defined as |log2FoldChange| >= 1 and P-value <= 1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2(FPKM+1) values and GO analysis for each sample

source_name: testes

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 10 dpp

value: testes

value: Dazl SKO


title: GC056829_GCTCATGA-CGTCTAAT_regressed_sc

description: NexteraXT library preparation


title: GC056829_GCTCATGA-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: GC056829_GCTCATGA-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: 10dpp wild type mouse testes

value: wild type


title: RK_Rep2

description:
20180621_Rat.cpm_AVG(glmFit)
RK2

source_name: neuro cells RK33

value: treated with 6um RK33


title: GC056829_GCGTAGTA-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: RK_Rep3

description:
20180621_Rat.cpm_AVG(glmFit)
RK3


title: RK_Rep1

description:
20180621_Rat.cpm_AVG(glmFit)
RK1


title: GC056829_GTAGAGGA-GAGCCTTA_regressed_sc

description: NexteraXT library preparation


title: GC056829_GCGTAGTA-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: TATRK_Rep3

description:
20180621_Rat.cpm_AVG(glmFit)
TAT_RK3

source_name: neuro cells TAT +RK33

value: treated with TAT 60ng/ml+6um RK33


title: GC056829_GCGTAGTA-CGTCTAAT_regressed_sc

description: NexteraXT library preparation


title: F522_M1152_69h

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

description: Sample was taken after 69h after inoculation of 4.5 mL spore suspension.

data_processing:
Sequencing lane combination
Mapped with HISAT2, v2.1.0
Gene counts were computed using featureCounts -s 2 -t transcript -g gene_name --minOverlap 10 --fracOverlap 0.9, v1.6.0
Quantile-normalization using MayDay - Seasight (Pseudocount, log2 transformation, quantile normalization)
Genome_build: GCF_000203835.1 v32
Supplementary_files_format_and_content: tsv, containing the normalized counts per timepoint and biological replicate

organism: Streptomyces coelicolor A3(2)

source_name: F522 69h sample of S. coelicolor strain M1152

extract_protocol:
Lysates were extracted using RNAprotect Bacteria (Qiagen) kit and RNeasy mini kit (Qiagen)
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) following the instructions according to NED. Breifly, 1µg of RNA was subject to rRNA depletion using Ribo-Zero rRNA Removal Kit Bacteria (Illumina). The resulting tRNA was used to construct the cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB).

tag: timepoint

tag: fermenter

tag: phosphate

value: depleted


title: F522_M1152_65h

description: Sample was taken after 65h after inoculation of 4.5 mL spore suspension.

source_name: F522 65h sample of S. coelicolor strain M1152


title: TATRK_Rep2

description:
20180621_Rat.cpm_AVG(glmFit)
TAT_RK2


title: GC056829_GCGTAGTA-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_GCGTAGTA-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: TATRK_Rep1

description:
20180621_Rat.cpm_AVG(glmFit)
TAT_RK1


title: TAT_Rep3

description:
20180621_Rat.cpm_AVG(glmFit)
TAT3


title: F522_M1152_53h

description: Sample was taken after 53h after inoculation of 4.5 mL spore suspension.

source_name: F522 53h sample of S. coelicolor strain M1152


title: TAT_Rep2

description:
20180621_Rat.cpm_AVG(glmFit)
TAT2


title: GC056829_CTCTCTAC-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: TAT_Rep1

description:
20180621_Rat.cpm_AVG(glmFit)
TAT1


title: F522_M1152_49h

description: Sample was taken after 49h after inoculation of 4.5 mL spore suspension.

source_name: F522 49h sample of S. coelicolor strain M1152


title: F522_M1152_45h

description: Sample was taken after 45h after inoculation of 4.5 mL spore suspension.

source_name: F522 45h sample of S. coelicolor strain M1152

value: medium


title: GC056829_CTCTCTAC-CTATTAAG_regressed_sc

description: NexteraXT library preparation


title: GC056829_CTCTCTAC-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: F522_M1152_41h

description: Sample was taken after 41h after inoculation of 4.5 mL spore suspension.

source_name: F522 41h sample of S. coelicolor strain M1152

value: rich


title: Intestinal progenitor cells, LPesgtsNRNAi3

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116st and 85ave

department: MMI

country: Canada

institute: University of Alberta

data_processing:
Qualtiy control of raw reads with FastQC
Read trimming with Trimmomatic
Aligned to the Drosophila transcriptome using HISAT2
Conversion of BAM files to SAM files using Samtools
Counts for each sampek were determined with Rsubread then compiled into one document proir to differential analysis via edgeR
Genome_build: bdgp6
Supplementary_files_format_and_content: tab delimited files for raw counts (Rsubread output) and differential expression (edgeR output) for valid comparisons

organism: Drosophila melanogaster

source_name: adult female intestinal progenitor cells

growth_protocol: adult virgin female drosophila were raised for 5 days at 25C, monoassociated with L brevis or L plantarum overnight (or kept germ free) then trasnferred to 29C for an additional 5 days before intestine dissection

extract_protocol:
Intestines were dissected and immediately placed in DEPC PBS on ice. After 100 guts per sample were collected for a replicate of three (approx. 2 hour dissection time) guts were dissociated into a single cell solution using elastase (1mg/mL) before running through the FACS machine. Small GFP+ cells were gated upon and selected for collection into DEPC PBS. The RNA was extracted from the progenitor cells using standard Trizol methods.
Library construction was performed at the Lunenfeld-Tanenbaum Research Facility (LTRI) using standard Illumina protocols

tag: developmental stage

value: adult

tag: gender

value: female

value: esgts/NRNAi

tag: microbiome

value: L. plantarum

value: intestinal progenitor cells


title: F522_M1152_61h

description: Sample was taken after 61h after inoculation of 4.5 mL spore suspension.

source_name: F522 61h sample of S. coelicolor strain M1152


title: Intestinal progenitor cells, LPesgtsNRNAi2


title: F522_M1152_33h

description: Sample was taken after 33h after inoculation of 4.5 mL spore suspension.

source_name: F522 33h sample of S. coelicolor strain M1152


title: F522_M1152_57h

description: Sample was taken after 57h after inoculation of 4.5 mL spore suspension.

source_name: F522 57h sample of S. coelicolor strain M1152


title: GC056829_CGTACTAG-GTAAGGAG_primary_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cells from primary triple melanoma

value: GFP+ cell from primary triple melanoma


title: Intestinal progenitor cells, LPesgtsNRNAi1


title: GC056829_CTCTCTAC-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: Intestinal progenitor cells, LPesgts3

value: esgts


title: GC056829_CGTACTAG-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_CGGAGCCT-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: Intestinal progenitor cells, LPesgts2


title: F521_M1152_69h

source_name: F521 69h sample of S. coelicolor strain M1152


title: GC056829_CGGAGCCT-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: F521_M1152_61h

source_name: F521 61h sample of S. coelicolor strain M1152


title: Intestinal progenitor cells, LPesgts1


title: GC056829_CGGAGCCT-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: F521_M1152_57h

source_name: F521 57h sample of S. coelicolor strain M1152


title: GC056829_CGGAGCCT-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: Intestinal progenitor cells, LBesgtsNRNAi3

value: L. brevis


title: F521_M1152_53h

source_name: F521 53h sample of S. coelicolor strain M1152


title: Intestinal progenitor cells, LBesgtsNRNAi2


title: F521_M1152_65h

source_name: F521 65h sample of S. coelicolor strain M1152


title: F521_M1152_49h

source_name: F521 49h sample of S. coelicolor strain M1152


title: F521_M1152_45h

source_name: F521 45h sample of S. coelicolor strain M1152


title: Intestinal progenitor cells, LBesgtsNRNAi1


title: GC056829_CGATCAGT-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: Intestinal progenitor cells, LBesgts3


title: GC056829_CGGAGCCT-AAGGAGTA_regressed_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cells from regressed triple melanoma

value: GFP+ cell from regressed triple melanoma


title: GC056829_CGATCAGT-CTATTAAG_regressed_sc

description: NexteraXT library preparation


title: Intestinal progenitor cells, LBesgts2


title: F521_M1152_33h

source_name: F521 33h sample of S. coelicolor strain M1152


title: F521_M1152_41h

source_name: F521 41h sample of S. coelicolor strain M1152


title: GC056829_CGATCAGT-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_CGAGGCTG-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: GC056829_CGAGGCTG-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: Intestinal progenitor cells, GFesgtsNRNAi2

value: Germ Free


title: Intestinal progenitor cells, LBesgts1


title: Brain_PD_parietal_oxBS_9

type: genomic

city: Grand Rapids

first: Alison

middle: I

last: Bernstein

state: MI

address: 400 Monroe Ave NW

department: Translational Neuroscience

institute: Michigan State University

description: oxidative bisulfite treatment

hyb_protocol: Hybridized to Illumina EPIC BeadChip according to manufacturer's protocol.

scan_protocol: Illumina iScan platform

data_processing: Data processing was performed in R (version 3.5.3). For PD EPIC array data, probes were first filtered based on a detection p-value > 0.05 in any sample. Next, samples with a high percentage (>10%) of failed probes were removed prior to analysis. In the PD data, no samples were excluded due to a high percentage of failed probes. Cross-reactive probes and probes containing SNPs were removed based upon previous identification. A comparison of technical replicates revealed consistent results across arrays in both datasets. After removal of technical artifacts, dye-bias correction was performed with ssNoob within minfi. The proportion of neuronal vs. glial cells in each sample was estimated with CETS. For PD data, the oxBS.MLE function in the ENmix package was used to calculate maximum likelihood estimates (MLE) of 5-mC and 5-hmC beta values for each probe, and batch effects were assessed using the ChAMP package. After beta value estimation, we filtered out samples where mean 5-mC or 5-hmC beta value < 0.1. This beta value > 0.1 cutoff was instituted due to increased variability of beta values at such low levels. As a final step, we removed probes that had any missing 5-mC or 5-hmC values to ensure complete modeling.

molecule: genomic DNA

source_name: postmortem brain, Parkinson's disease, parietal, oxidative bisulfite treatment

label_protocol: TrueMethyl Array kit (Cambridge Epigenetix)

extract_protocol: Qiagen DNeasy Blood & Tissue Kits (Cat. # 69504)

treatment_protocol: Sodium bisulfite treatment (n=18) and oxidative bisulfite treatment (n=18)

tag: Sex

value: Male

tag: age of pd onset

tag: age at death

tag: race

value: White

tag: pmi

tag: pathology

value: Parkinson's Disease

value: brain


title: GC056829_CGAGGCTG-CCTAGAGT_primary_sc

description: NexteraXT library preparation

tag: genotype

tag: tissue


title: F519_M1152_61h

source_name: F519 61h sample of S. coelicolor strain M1152

tag: strain

value: depleted


title: Intestinal progenitor cells, GFesgtsNRNAi1

source_name: adult female intestinal progenitor cells

tag: cell type


title: Brain_PD_parietal_oxBS_7

description: oxidative bisulfite treatment


title: GC056829_CCTAAGAC-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: F519_M1152_57h

source_name: F519 57h sample of S. coelicolor strain M1152


title: Intestinal progenitor cells, GFesgts2


title: Brain_PD_parietal_oxBS_8

description: oxidative bisulfite treatment


title: Intestinal progenitor cells, GFesgtsNRNAi3


title: Brain_PD_parietal_oxBS_5

description: oxidative bisulfite treatment


title: Intestinal progenitor cells, GFesgts1


title: Brain_control_parietal_oxBS_3

description: oxidative bisulfite treatment

source_name: postmortem brain, control, parietal, oxidative bisulfite treatment

value: Hispanic


title: GC056829_CCTAAGAC-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: F519_M1152_69h

source_name: F519 69h sample of S. coelicolor strain M1152


title: F519_M1152_49h

source_name: F519 49h sample of S. coelicolor strain M1152


title: GC056829_CCTAAGAC-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: F519_M1152_65h

source_name: F519 65h sample of S. coelicolor strain M1152


title: larva_9hpe_day_night8_28

city: Brisbane

first: Tahsha

last: Say

state: QLD

address: The University of Queensland

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

description: Transcriptomic data for 43 individual larvae of the sponge Amphimedon queenslandica aged 1 and 9 hours post emergence (hpe) that were exposed to one of three experimental light regimes.

data_processing:
Raw CEL-Seq reads were processed using a publicly available pipeline (https://github.com/yanailab/CEL-Seq-pipeline).
The demultiplexed reads were mapped to the Amphimedon queenslandica Aqu2.1 gene models (Fernandez-Valverde et al., 2015) and read counts were generated. The identifiers in the processed data (e.g. Aqu2.1.39671_001) are searchable in the EnsemblMetazoa database (http://metazoa.ensembl.org/Amphimedon_queenslandica/Info/Index).
Supplementary_files_format_and_content: Tab-delimited text file including raw count values for each sample.

organism: Amphimedon queenslandica

source_name: single larva

extract_protocol:
RNA was isolated from individual Amphimedon queenslandica larvae using TRIzol as previously described (Jindrich et al., 2017).
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

treatment_protocol: Larvae were collected within a 30-minute window beginning at 11 am and were distributed into 0.22 μm filtered sea water, under one of three experimental light regimes, by 0.5 hours post emergence (hpe). The light regimes were (1) natural day-night, (2) constant dark (using LEE filter model 299, 1.2 neutral density, allowing 6.6% transmission of ambient daylight), and (3) constant light (full spectrum Lumilux T5 HE tube). For RNA-sequencing, two timepoints (1 and 9 hpe) were chosen to represent precompetent and competent larvae, respectively.

tag: developmental time point (hours post emergence)

tag: light regime

value: day-night


title: Brain_control_parietal_oxBS_1

description: oxidative bisulfite treatment


title: Brain_PD_parietal_oxBS_6

description: oxidative bisulfite treatment


title: Brain_control_parietal_oxBS_2

description: oxidative bisulfite treatment


title: F519_M1152_53h

source_name: F519 53h sample of S. coelicolor strain M1152

tag: timepoint

tag: fermenter


title: F519_M1152_45h

source_name: F519 45h sample of S. coelicolor strain M1152

tag: phosphate

value: medium


title: F519_M1152_41h

source_name: F519 41h sample of S. coelicolor strain M1152

value: rich


title: larva_9hpe_day_night7_27


title: GC056829_ATGCGCAG-GAGCCTTA_regressed_sc

description: NexteraXT library preparation


title: Brain_PD_cingulate_oxBS_9

description: oxidative bisulfite treatment

source_name: postmortem brain, Parkinson's disease, cingulate, oxidative bisulfite treatment


title: larva_9hpe_day_night6_26


title: Brain_PD_cingulate_oxBS_4

description: oxidative bisulfite treatment


title: Brain_PD_cingulate_oxBS_7

description: oxidative bisulfite treatment


title: GC056829_ATGCGCAG-CTATTAAG_regressed_sc

description: NexteraXT library preparation


title: F518_M145_57h

data_processing:
Sequencing lane combination
Mapped with HISAT2, v2.1.0
Gene counts were computed using featureCounts -s 2 -t transcript -g gene_name --minOverlap 10 --fracOverlap 0.9
Quantile-normalization using MayDay - Seasight (Pseudocount, log2 transformation, quantile normalization)
Genome_build: GCF_000203835.1 v32
Supplementary_files_format_and_content: tsv, containing the normalized counts per timepoint and fermenter

source_name: F518 57h sample of S. coelicolor strain M145


title: Brain_control_cingulate_oxBS_2

description: oxidative bisulfite treatment

source_name: postmortem brain, control, cingulate, oxidative bisulfite treatment


title: larva_9hpe_day_night4_25


title: Brain_PD_cingulate_oxBS_8

description: oxidative bisulfite treatment


title: F518_M145_53h

source_name: F518 53h sample of S. coelicolor strain M145


title: GC056829_ATGCGCAG-TCGACTAG_primary_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cells from primary triple melanoma


title: Brain_PD_cingulate_oxBS_6

description: oxidative bisulfite treatment


title: larva_9hpe_day_night5_43


title: Brain_PD_cingulate_oxBS_5

description: oxidative bisulfite treatment


title: Brain_PD_parietal_oxBS_4

description: oxidative bisulfite treatment

source_name: postmortem brain, Parkinson's disease, parietal, oxidative bisulfite treatment


title: GC056829_ATCTCAGG-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: F519_M1152_33h

source_name: F519 33h sample of S. coelicolor strain M1152


title: GC056829_ATGCGCAG-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_ATCTCAGG-GTAAGGAG_primary_sc

description: NexteraXT library preparation


title: Brain_control_cingulate_oxBS_3

description: oxidative bisulfite treatment


title: F518_M145_49h

source_name: F518 49h sample of S. coelicolor strain M145


title: Brain_PD_parietal_BS_9

description: bisulfite treatment

source_name: postmortem brain, Parkinson's disease, parietal, bisulfite treatment


title: GC056829_ATCTCAGG-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: GC056829_ATGCGCAG-AAGGAGTA_regressed_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cells from regressed triple melanoma


title: larva_9hpe_constant_light7_42

value: light


title: Brain_PD_parietal_BS_7

description: bisulfite treatment


title: GC056829_AGGCAGAA-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: F518_M145_45h

source_name: F518 45h sample of S. coelicolor strain M145


title: larva_9hpe_constant_light6_41


title: larva_9hpe_day_night2_23


title: larva_9hpe_day_night1_22


title: GC056829_ACTGAGCG-TCGACTAG_primary_sc

description: NexteraXT library preparation


title: F518_M145_41h

source_name: F518 41h sample of S. coelicolor strain M145


title: larva_9hpe_day_night3_24


title: Brain_control_cingulate_oxBS_1

description: oxidative bisulfite treatment


title: F518_M145_33h

source_name: F518 33h sample of S. coelicolor strain M145


title: larva_9hpe_constant_light5_40

source_name: single larva


title: F518_M145_29h

description: Sample was taken after 29h after inoculation of 4.5 mL spore suspension.

source_name: F518 29h sample of S. coelicolor strain M145


title: F518_M145_37h

description: Sample was taken after 37h after inoculation of 4.5 mL spore suspension.

source_name: F518 37h sample of S. coelicolor strain M145


title: GC056829_ACTGAGCG-CTATTAAG_regressed_sc

description: NexteraXT library preparation


title: F517_M145_57h

source_name: F517 57h sample of S. coelicolor strain M145


title: GC056829_ACTGAGCG-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: Brain_PD_parietal_BS_6

description: bisulfite treatment


title: larva_9hpe_constant_light2_37


title: Brain_PD_parietal_BS_4

description: bisulfite treatment


title: larva_9hpe_constant_light1_36


title: GC056829_ACTGAGCG-AAGGAGTA_regressed_sc

description: NexteraXT library preparation


title: larva_9hpe_constant_light4_39


title: Control_3

city: Ciudad de Mexico

first: Erika Alejandra

last: Cabrera-Reyes

state: Cd. de Mexico

address: AV. Universidad 300

country: Mexico

institute: UNAM

data_processing:
The alignment was carried out the rat genome downloaded from NCBI: GCF_000001895.5_Rnor_6.0_genomic.fna.gz, using the smalt program with its default values.
For all the samples, alienation exceeding 93% was obtainedthe NCBI gff, GCF_000001895.5_Rnor_6.0_genomic.gff.gz, filtering only the genes and the matrix result was introduced to the IDEAmex (Integrated Differential Expresion Analysis multiExperiment) site using a FDR (False Discovery Range) of 0.05 and a LogFoldChange of 1.
For functional clusterin, was ran DAVID v6.7 (the Database for Annotation, Visualization and Integrated Discovery)
For the correlations and networks, were perform in Phyton Python 3.5 (matplotlib, numpy, matplotlib.pyplot, pandas networkx, seaborn) and Cytoscape 3.6.1.

source_name: Hippocampus

extract_protocol:
Hipocampuus were removed, flash put into RNAlater, and RNA was harvested using RNeasy Micro Kit Qiagen . Illumina NextSeq 500, TruSeq Stranded mRNA Library Prep (Cat#20020595) was used with 2 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols fir RNA-Seq

treatment_protocol: Treatement were administrated intraperitoneally, PRL groups 3, 6, 24 hours (500µg/kg) or control group (Solutin saline), at 9:00 a.m.

value: Wistar

value: Hippocampus

tag: age

value: 11 weeks


title: GC056829_ACTCGCTA-TCGACTAG_primary_sc

description: NexteraXT library preparation

value: GFP+ cell from primary triple melanoma


title: Brain_control_parietal_BS_3

description: bisulfite treatment

source_name: postmortem brain, control, parietal, bisulfite treatment


title: Brain_PD_parietal_BS_8

description: bisulfite treatment


title: Brain_PD_cingulate_BS_8

description: bisulfite treatment

source_name: postmortem brain, Parkinson's disease, cingulate, bisulfite treatment


title: F517_M145_53h

source_name: F517 53h sample of S. coelicolor strain M145


title: Control_2


title: GC056829_ACTCGCTA-CGTCTAAT_regressed_sc

description: NexteraXT library preparation


title: larva_9hpe_constant_light3_38


title: GC056829_AAGAGGCA-TCGACTAG_primary_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cells from primary triple melanoma


title: larva_9hpe_constant_dark7_35

value: dark


title: GC056829_ACTCGCTA-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: F517_M145_45h

source_name: F517 45h sample of S. coelicolor strain M145


title: Brain_control_parietal_BS_2

description: bisulfite treatment


title: larva_9hpe_constant_dark6_34


title: PRL500_24hr_3


title: Brain_control_parietal_BS_1

description: bisulfite treatment


title: GC056829_AAGAGGCA-CTCTCTAT_primary_sc

description: NexteraXT library preparation


title: Brain_PD_parietal_BS_5

description: bisulfite treatment


title: F517_M145_41h

source_name: F517 41h sample of S. coelicolor strain M145


title: PRL500_24hr_2


title: F518_M145_21h

description: Sample was taken after 21h after inoculation of 4.5 mL spore suspension.

source_name: F518 21h sample of S. coelicolor strain M145


title: F517_M145_37h

source_name: F517 37h sample of S. coelicolor strain M145


title: Brain_PD_cingulate_BS_5

description: bisulfite treatment


title: Brain_PD_cingulate_BS_9

description: bisulfite treatment


title: F517_M145_33h

source_name: F517 33h sample of S. coelicolor strain M145


title: F517_M145_49h

source_name: F517 49h sample of S. coelicolor strain M145


title: GC056829_AAGAGGCA-AAGGAGTA_regressed_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cells from regressed triple melanoma

value: GFP+ cells from regressed triple melanoma


title: PRL500_24hr_1


title: F517_M145_29h

source_name: F517 29h sample of S. coelicolor strain M145


title: larva_9hpe_constant_dark5_33

source_name: single larva


title: PRL500_6hr_2


title: GC056865_TCCTGAGC-TCGACTAG_control_psbulk

description: NexteraXT library preparation

source_name: mitfa:GFP cells from control

extract_protocol:
FACS sorting of 50 GFP+ living cells from control, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: GFP+ cells from control


title: larva_9hpe_constant_dark2_30


title: GC056829_AAGAGGCA-CCTAGAGT_primary_sc

description: NexteraXT library preparation


title: PRL500_6hr_3


title: Brain_PD_cingulate_BS_7

description: bisulfite treatment

value: Male


title: larva_9hpe_constant_dark3_31


title: larva_9hpe_constant_dark4_32


title: GC056865_TAAGGCGA-TCGACTAG_control_psbulk

description: NexteraXT library preparation


title: larva_1hpe_day_night7_07


title: Brain_PD_cingulate_BS_4

description: bisulfite treatment

value: White


title: F517_M145_21h

source_name: F517 21h sample of S. coelicolor strain M145


title: Brain_PD_cingulate_BS_6

description: bisulfite treatment

value: Parkinson's Disease


title: F516_M145_53h

source_name: F516 53h sample of S. coelicolor strain M145


title: PRL500_3hr_2

source_name: Hippocampus


title: Brain_control_cingulate_BS_1

description: bisulfite treatment

source_name: postmortem brain, control, cingulate, bisulfite treatment

value: brain


title: Brain_control_cingulate_BS_3

description: bisulfite treatment


title: F516_M145_57h

source_name: F516 57h sample of S. coelicolor strain M145

value: depleted


title: larva_1hpe_day_night6_06


title: larva_1hpe_day_night5_05


title: larva_9hpe_constant_dark1_29


title: PRL500_3hr_1


title: GC056865_GCGTAGTA-TCGACTAG_control_psbulk

description: NexteraXT library preparation


title: F516_M145_49h

source_name: F516 49h sample of S. coelicolor strain M145


title: Control_1


title: PRL500_6hr_1


title: GC056865_GGAGCTAC-TCGACTAG_control_psbulk

description: NexteraXT library preparation


title: Brain_control_cingulate_BS_2

description: bisulfite treatment


title: GC056865_CTCTCTAC-TCGACTAG_regressed_psbulk

description: NexteraXT library preparation

extract_protocol:
FACS sorting of 5 GFP+ living cells from regression site, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads


title: F516_M145_45h

source_name: F516 45h sample of S. coelicolor strain M145


title: larva_1hpe_day_night4_04


title: larva_1hpe_day_night3_03


title: Input H3K27ac ChIP-seq

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

library_source: genomic

data_processing:
Reads were mapped using  Bowtie -m 2 (v.1.0.0) to galGal4. Read counts were obtained using subread (v.1.4.5) FeatureCounts
Ranking of super-enhancer was performed using the ROSE algorithm.
Peak calling was performed using MACS2, de novo motif search was performed using Homer (v.4.7)
Genome_build: galGal4
Supplementary_files_format_and_content: read counts (txt file).

organism: Gallus gallus

source_name: dorsal neural tube microdissection

growth_protocol: Fertilised wild-type chicken eggs were obtained from Henry Stewart & Co (Norfolk), staged according to Hamburger and Hamilton (1951) (24). All experiments were performed on chicken embryos younger than 12 days of development, and as such were not regulated by the Animals (Scientific Procedures) Act 1986.

extract_protocol:
FAC-sorted cells were cross-linked with 1% formaldehyde for 9mins. Fixation was quenched with 125mM of glycine for 5min. Cross-linker was washed out by 3x pellet washes with 1xPBS ((supplemented with 1X PI (protease inhibitors)), 1mM DTT and 0.2mM PMSF) centrifuging at 2000g for 4mins at 4°C. Pellets were re-suspended in isotonic nuclei extraction buffer ((NEB: 0.5% NP40, 0.25% Triton-X, 10mM Tris-HCl-pH 7.5, 3mM CaCl2, 0.25M sucrose, 1mM DTT, 0.2mM PMSF, 1X PI. Cell nuclei were expulsed with 20 strokes using pestle B in a glass homogeniser, pelleted and washed with 1xPBS (with 1X PI, 1mM DTT and 0.2mM PMSF). Nuclei were lysed in SDS lysis buffer (0.7% SDS, 10mM EDTA, 50mM Tris-HCl (pH 7.5), 1x PI). Cross-linked chromatin was sonicated at 11A 10x (10s on 30s off) followed by 6A 8x (30s on 30s off) using a probe sonicator, to achieve 300-800bp fragments. Pre-blocked Protein A Dynabeads were incubated with antibody (H3K27ac, Abcam Ab4729, Brd4, Bethyl Laboratories A301-985A). Sonicated DNA-protein complexes were applied to beads overnight at 4°C. IgG antibody (Millipore 12-370) was used as control and an input sample was taken. Samples were washed 8x with RIPA buffer (50mM Hepes-KOH (pH 8.0), 500mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x PI) and 1x NaCl TE wash (1x TE, 50mM NaCl) at 4°C. Chromatin was eluted from the beads with SDS ChIP elution buffer (50mM Tris-HCl (pH 7.5), 10mM EDTA, 1% SDS). Cross-linking was reversed overnight at 65°C at 1300 rpm. Cellular RNA was digested with RNaseA (0.2mg/ml) at 37°C for 1 hour, and cellular proteins were removed with Proteinase-K (0.4mg/ml) at 55°C for 1 hour. Samples were purified by standard phenol-chloroform extraction and ethanol precipitation. ChIP’d DNA was amplified using published protocol (47) for small cell number ChIP. Three biological replicates for each stage and antibody were obtained.
Libraries were prepared using NEBNext Ultra DNATM library prep kit following manufacturers protocol. ChIP libraries were sequenced using 50bp paired-end reads using Illumina Hiseq2500 platform.

treatment_protocol: Dissected cranial regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37°C for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37°C for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion. We collected ~300 and ~600 NC cells per embryo at 5-6ss and 8-10ss respectively.

tag: developmental stage

value: stage 8-10ss

value: neural crest

value: dorsal neural tube microdissection

tag: amplification

value: NEBNext Ultra DNATM

tag: chip antibody


title: Input BRD4 ChIP-seq

value: stage 6-10ss


title: GC056865_CGGAGCCT-TCGACTAG_control_psbulk

description: NexteraXT library preparation


title: F516_M145_41h

source_name: F516 41h sample of S. coelicolor strain M145


title: F516_M145_37h

source_name: F516 37h sample of S. coelicolor strain M145


title: H3K27ac-8-10ss ChIP-seq

value: H3K27ac (Abcam Ab4729)


title: GC056865_CGAGGCTG-TTCTAGCT_primary_psbulk

description: NexteraXT library preparation

source_name: mitfa:GFP cells from primary triple melanoma

extract_protocol:
FACS sorting of 50 GFP+ living cells from primary tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: GFP+ cells from primary triple melanoma


title: H3K27ac-seq-5-6ss ChIP-seq

value: stage 5-6ss


title: larva_1hpe_day_night2_02

value: day-night


title: GC056865_AGGCAGAA-TCGACTAG_control_psbulk

description: NexteraXT library preparation


title: GC056865_CGTACTAG-TCGACTAG_control_psbulk

description: NexteraXT library preparation


title: F516_M145_29h

source_name: F516 29h sample of S. coelicolor strain M145

value: rich


title: BRD4-ChIP-seq

value: Brd4 (Bethyl Laboratories, A301-985A)


title: GC056865_ACTGAGCG-TTCTAGCT_primary_psbulk

description: NexteraXT library preparation


title: F516_M145_33h

source_name: F516 33h sample of S. coelicolor strain M145

value: medium


title: larva_1hpe_day_night1_01


title: larva_1hpe_constant_light6_20

value: light


title: GC056865_ACTCGCTA-TCGACTAG_control_psbulk

description: NexteraXT library preparation

value: GFP+ cells from control


title: erythrocytes rep2 Capture-C

data_processing:
Library strategy: Capture-C
All the below steps except normalization were done with CCseqBasic tool, or its predecessors ( http://userweb.molbiol.ox.ac.uk/public/telenius/CCseqBasicManual/ )
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser.pl)
Removal of ploidy regions and off target capture (custom scripts)
Counting reads per dpnII fragment (CCanalyser.pl)
Normalizing the counts to 100 000 reported interacting fragments for each capture site, combining all capture sites to a single file (custom scripts)
Genome_build: galGal4
Supplementary_files_format_and_content: Normalized read counts per dpnII fragment, custom format : chr:str-stp \t count \t count \t count .. etc (one column per capture site)

extract_protocol:
Neural crest cells were obtained by microddisecting dorsal neural tubes (5-10ss).
Red blood cells were obtained by peripheral blood collection at 10dpf.
NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for generation of the 3C libraries: cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in MilliQ dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an ethanol precipitation and a wash with 70% ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%.  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next sample preparation reagent kits, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using  the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using the Illumina MiSeq (150bp paired end reads). The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage). Oligonucleotide capture technology was then used to pull down the restricion fragments containing the promoters of the genes of interest and their interacting partners, which were subsequently idendified by high throughput sequencing.  The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.
Capture-C (high resolution targeted Hi-C-seq)

value: red blood cells

value: peripheral blood collection

tag: assay

value: Capture-C


title: 14

city: Washington

first: John

middle: Russell

last: Bracht

state: DC

address: 4400 Massachusetts Ave NW

department: Biology

institute: American University

description: RNA was ribosome-depleted and sequencing library constructed using KAPA Total Stranded preparation kit (Cat# KK8484).

data_processing:
Tophat2 v. 2.1.1 alignment to genome, along with a reference gene set produced by Maker v. 2.31.8
Stringtie v. 1.3.4 assembly of new transcripts
Stringtie v. 1.3.4 merging of transcripts
Ballgown v. 2.12.0 to filter out genes < 5 FPKM across all 12 samples
Ballgown v. 2.12.0 to return all FPKM for all transcripts and statistical tests for enriched genes
Genome_build: SWDT00000000
Supplementary_files_format_and_content: Excel table of FPKM values across transcripts.

organism: Halicephalobus mephisto

source_name: mixed population 40 degrees C

growth_protocol: Worms grown for 2-4 weeks at target temperature prior to harvest.

extract_protocol:
Total RNA was extracted with Zymo Duet DNA/RNA Miniprep Plus following manufacturer's instructions.
For Illumina RNA, stranded RNA-seq libraries were generated using the KAPA Total Stranded preparation kit with an average insert size of 175 bp.

treatment_protocol: Worms grown at three different temperatures in incubators.

tag: group

value: mixed population 40 degrees C


title: 12


title: GC056829_TAGGCATG-TCGACTAG_primary_psbulk

description: NexteraXT library preparation


title: erythrocytes rep1 Capture-C


title: larva_1hpe_constant_light7_21


title: larva_1hpe_constant_light4_18


title: 11


title: larva_1hpe_constant_light3_17


title: SAMPLE 1: genomic DNA from primitive brain tumor

city: Paris

first: Julien

last: Masliah-Planchon

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: iScan Control Software

label: Cy5 and Cy3

source_name: Brain tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from the frozen tumor using phenol-chloroform procedure

tag: gender

value: Female

value: Brain tumor


title: GC056829_TAGGCATG-CTCTCTAT_primary_psbulk

description: NexteraXT library preparation


title: 10


title: F516_M145_21h

source_name: F516 21h sample of S. coelicolor strain M145


title: larva_1hpe_constant_light2_16

source_name: single larva


title: GC056829_GGACTCCT-TCGACTAG_primary_psbulk

description: NexteraXT library preparation

source_name: mitfa:GFP cells from primary  triple melanoma

value: GFP+ cells from primary  triple melanoma


title: M8R


title: dorsal_neural_tubes_5-6ss rep1 Capture-C

value: neural crest

value: dorsal neural tube microdissection

value: NEBNext Ultra DNATM


title: dorsal_neural_tubes_5-6ss rep2 Capture-C

value: stage 5-6ss


title: larva_1hpe_constant_light1_15


title: GC056829_GGACTCCT-CTCTCTAT_primary_psbulk

description: NexteraXT library preparation

value: GFP+ cells from primary triple melanoma


title: VRTN_ChIPSeq

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

data_processing:
ChIP-seq reads were mapped to the human genome (GRCh38.p5) using BEDtools.
Only the alignments with fewer than two mismatches were considered for enriched-region (peak) identification (peak calling) using the Model-based Analysis of ChIP-seq (MACS) algorithm.
MEME 4.6.1 software was used to identify the VRTN binding motif.
PeakAnalyzer software was used for peak annotation and the analysis of the nearest downstream gene.
Genome_build: the human genome (GRCh38.p5)
Supplementary_files_format_and_content: wig files were generated with MACS algorithm.

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in high-glucose DMEM (Gibco) supplemented with 10% fetal bovine serum (Hyclone) and an antibiotic solution

extract_protocol:
ChIP samples were prepared from VRTN-overexpressing HEK293T cells using the SimpleChIP Enzymatic Chromatin IP kit (CST) according to the manufacturer’s instructions. The cells were harvested and chemically cross-linked with 1% formaldehyde for 10 minutes at 16-20°C. The cell nuclei were released via sonication using an Ultrasonic Processor (SONXI). The collected nuclei were digested with micrococcal nuclease (CST) for 20 minutes at 37 °C. Sheared chromatin was incubated with Anti-FLAG M2 Affinity Gel (Sigma) for 4 hours. Immunoprecipitated DNA was treated with RNase A (CST) and purified with the SimpleChIP kit (CST).
A sequencing library was constructed from enriched DNA fragments using the TruSeq ChIP Library Prep kit (Illumina). Final DNA libraries were validated and sequenced at 50 bp per sequence read using a HiSeq 2000 sequencer (Illumina) at a depth of approximately 20 million sequences.

treatment_protocol: The full-length coding sequence of pig VRTN was subcloned into pNTAP-2×flag expression vectors. HEK293T cells were transfected with pNTAP-2×flag-VRTN.

tag: cell line

value: Human Embryonic Kidney

tag: passages

value: Anti-FLAG M2 Affinity Gel (Sigma)


title: larva_1hpe_constant_dark7_14

value: dark


title: M6R

source_name: mixed population 38 degrees C

value: mixed population 38 degrees C


title: GC056829_CGTACTAG-CTCTCTAT_control_psbulk

description: NexteraXT library preparation

source_name: mitfa:GFP cells from control

tag: genotype

tag: tissue

value: GFP+ cells from control


title: dorsal_neural_tubes_5-6ss rep3 Capture-C

value: stage 8-10ss


title: M7R


title: GC056829_TAAGGCGA-CTCTCTAT_control_psbulk

description: NexteraXT library preparation


title: M2R


title: larva_1hpe_constant_dark5_12


title: M1R


title: Mock Immunoprecipitated DNA without antibody from a pool sample of Mis12- and Dsn1-mCherry Mucor circinelloides strains

city: Murcia

first: Carlos

last: Pérez-Arques

state: Murcia

address: Campus Universitario Espinardo, Facultad de Biología

department: Genética y Microbiología

country: Spain

institute: Universidad de Murcia

data_processing:
Quality-checked with FASTQC v0.11.8 and adapter removal with Trim Galore! v0.6.2
Reads aligned with BWA v0.7.8
Peak calling with MACS2 v.2.1.1
Genome_build: Mucor circinelloides f. lusitanicus MU402 reference genome Muccir1_3
Supplementary_files_format_and_content: Normalize BW files of aligned reads were generated with deepTools v3.2.1 bamCompare

organism: Mucor lusitanicus

source_name: Pregerminated spores

growth_protocol: 10^7 spores/mL of these strains were germinated in 100 ml of liquid YPG pH 4.5 medium, shaking at 250 rpm at 26ºC for 3 hours

extract_protocol:
150 mg of ground pelleted cells was resuspended in ChIP lysis Buffer. Sonication with Bioruptor (Diogenode) with 50 cycles of pulses of 30s ON/OFF to obtain 100-300 bp fragments. Clarification by centrifugation. Immunoprecipitation with Red Fluorescent Protein (RFP)-Trap Magnetic Agarose (MA) beads (Chromotek) to the IP samples and with MA beads (Chromotek) to the binding control. Washing and de-crosslinking. RNase A and Proteinase K treatment. DNA purification by phenol:chloroform
TruSeq ChIP Library Prep Kit

treatment_protocol: Cells were fixed by adding formaldehyde at a final concentration of 1% for 20 minutes. The fixation was quenched by adding glycine to a final concentration of 135 mM.

value: Pregerminated spores

tag: strain

value: Mis12- and Dsn1-mCherry (MU842 and MU846)

tag: culture medium

value: liquid YPG  pH 4.5

tag: culture duration

value: 3 hours

tag: cross-linking

value: Formaldehyde 1% 20 min

tag: dna-shearing

value: Bioruptor 50 cycles of 30 seconds ON/OFF

tag: antibody

value: MA beads without antibody (Chromotek)

tag: dna fragments size


title: larva_1hpe_constant_dark4_11

tag: developmental time point (hours post emergence)

tag: light regime


title: M5R

source_name: mixed population 25 degrees C

value: mixed population 25 degrees C


title: larva_1hpe_constant_dark3_10


title: Input DNA from Mis12-mCherry Mucor circinelloides strain

value: Mis12-mCherry (MU842)

value: none (input)


title: M4R


title: GC056829_AGGCAGAA-CTATTAAG_regressed_psbulk

description: NexteraXT library preparation

source_name: mitfa:GFP cells from regressed triple melanoma

extract_protocol:
FACS sorting of 10 GFP+ living cells from regression site, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: GFP+ cells from regressed triple melanoma


title: M3R


title: Immunoprecipitated DNA from Dsn1-mCherry Mucor circinelloides strain

value: Dsn1-mCherry (MU846)

value: RFP-Trap MA beads (Chromotek)


title: larva_1hpe_constant_dark6_13

value: dark


title: Immunoprecipitated DNA from Mis12-mCherry Mucor circinelloides strain


title: HEK293T transfected with pNTAP-2×flag-VRTN, biological replicate 2

type: RNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G.

data_processing: Netaffx build 36 was used for the analysis.  The data were analyzed with Affymetrix Expression Console Software (version 1.0)  using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Gene expression data from HEK293T transfected with pNTAP-2xflag-VRTN vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The full-length coding sequence of pig VRTN was subcloned into pNTAP-2×flag expression vectors. HEK293T cells were transfected with pNTAP-2×flag-VRTN or empty vectors.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Total RNA was isolated from cells 24 hours after transfection using TRIzol reagent (Invitrogen).

tag: transfection


title: HEK293T transfected with pNTAP-2×flag empty vector, biological replicate 3

source_name: Gene expression data from HEK293T transfected with pNTAP-2xflag vector

value: pNTAP-2×flag empty vector


title: HEK293T transfected with pNTAP-2×flag empty vector, biological replicate 2


title: HEK293T transfected with pNTAP-2×flag empty vector, biological replicate 1


title: HEK293T transfected with pNTAP-2×flag-VRTN, biological replicate 3


title: Input DNA from Dsn1-mCherry Mucor circinelloides strain


title: larva_1hpe_constant_dark2_09


title: HEK293T transfected with pNTAP-2×flag-VRTN, biological replicate 1


title: larva_1hpe_constant_dark1_08


title: WT_adult_2

status: Public on Oct 08 2019

city: Sheffield

first: Noemie

last: Hamilton

state: Great Britain

address: Western Bank

department: Department of Infection, Immunity and Cardiovascular Disease

institute: University of Sheffield

hyb_protocol: .Incubate at 60C for exactly 30 min to fragment the RNA.  .Add Buffer to stop the fragmentation reaction:  2x Hybridization Buffer to the 1x22K and 1x44K array formats  2x GEx Hybridization Buffer HI-RPM to the 1x244K, 2x105K, 4x44K and 8x15K array  formats. Hybridize the arrays in an ozone free room (room 0.224).

scan_protocol: Genome-wide expression profiling was performed using the Zebrafish (v3) Gene Expression 4x44K Microarray (Agilent G2519F) containing 43803 probes according to the manufacturer’s instructions.

data_processing: The probe sequences for this array platform were re-annotated using the ReAnnotator pipeline (Arloth et al., 2015) against reference genome danRer11 in order to obtain updated gene symbols.  Scanned raw data were normalised using quantile normalisation, and then filtered using the ReAnnotator results so that only probes matching the exons of their target gene were retained. In the case of genes with more than 1 probe, the probe with the highest inter-quartile range was chosen as the representative probe for the gene.

source_name: WT sibling zebrafish adult brain 1year old

label_protocol: Agilent Low Input Quick Amp Labeling Kit generates fluorescent cRNA (complimentary RNA) with a sample input RNA range between 25 ng and 200 ng of total RNA or a minimum of 5 ng of poly A+ RNA for one- color processing. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- labeled CTP. Amplification is typically at least a 100- fold from total RNA to cRNA with the use of this kit.

growth_protocol: All zebrafish were maintained following standard protocols (Nüsslein-Volhard and Dham, 2002). Tanks were maintained at 28°C with a continuous re-circulating water supply and a daily light/dark cycle of 14/10 hours.

extract_protocol: RNA was isolated from pooled dechorionated embryos at 28 hour post fertilisation (hpf), 3 day post fertilisation (hpf) and dissected whole adult brains using TRIzol (Invitrogen), following the manufacturer’s protocol. The integrity of the RNA was confirmed using the Agilent 2100 BioAnalyzer, using only samples with an RNA integrity number of at least 8.

tag: genotype/variation

value: wild type

tag: developmental stage

value: adult

tag: tissu

value: Brain


title: WT_hpf_2

source_name: WT sibling zebrafish whole embryos at 28hpf

value: 28 dpf

value: whole embryo


title: WT_dpf_1

source_name: WT sibling zebrafish whole embryos at 3dpf

value: 3 dpf


title: WT_hpf_1


title: WT_adult_1


title: WT_adult_3


title: larva_1hpe_constant_light5_19

value: light


title: WT_dpf_3


title: PRL500_3hr_3

source_name: Hippocampus

value: Wistar

value: Hippocampus

tag: age

value: 11 weeks


title: M_hpf_1

source_name: rnaset2 zebrafish  mutant whole embryos at 28hpf

value: rnaset2 mutant


title: M_hpf_3


title: M_adult_3

source_name: rnaset2 zebrafish  mutant adult brain 1year old


title: M_hpf_1.1


title: 44-Chr16wt

city: Safed

first: Evan

last: Elliott

state: Galilee

address: Henrietta Szold Street, 8

department: Neurobiology

country: Israel

institute: Bar Ilan University

data_processing:
Mapping to genome performed by Tophat2 version 2.0.13 (running Bowtie2 version 2.1.0.0)
For differential expression analysis, we used the script cuffdiff v2.2.1
Genome_build: mm9

source_name: Dorsal Striatum

extract_protocol:
Dorsal striatum was removed from mice brains using 13 gauge needle of 2mm slices in area of dorsal striatum.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: asd model

value: Wild type littermate

value: postnatal week 8


title: 45-Chr16wt


title: 43-Chr16wt


title: WT_dpf_2


title: 46-Chr16df


title: M_dpf_3

source_name: rnaset2 zebrafish  mutant whole embryos at 3dpf


title: WT_hpf_1.1


title: WT_hpf_3


title: M_dpf_1


title: 48-Chr16df


title: 47-Chr16df


title: wild-type, biological rep 2

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions • Hybridization at 45°C for 16 hrs at 60rpm • Fluidics washing is FS450_00002

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with robust multiarray average algorithm (Affymetrix): RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: wild-type, hippcampus

label_protocol: Fragmented, biotinylated cDNAs were prepared from 300 ng total RNA. Samples were amplified and labelled using the Ambion® WT Expression Kit, combined with the GeneChip® WT Terminal Labeling and Controls Kit according to the manufacturers instructions.

growth_protocol: Mouse hippocampus dissected from day P/N 21 mice

extract_protocol: total RNA isolation was performed using the RNeasy Mini Kit from Qiagen. Additionally, a DNase treatment was made during the isolation procedure.

treatment_protocol: not applicable

value: P/N day 21

value: hippocampus

tag: genotype

value: wild-type

tag: gender

value: male


title: 41-Shank3ko

tag: strain

value: Shank3b KO


title: quadruple knockout (Tnc, Tnr, Bcan, Ncan), biological rep 1

source_name: Tnc -/-, Tnr -/-, Bcan -/-, Ncan -/-, hippocampus

tag: tissue


title: quadruple knockout (Tnc, Tnr, Bcan, Ncan), biological rep 2


title: wild-type, biological rep 3


title: wild-type, biological rep 1


title: M_adult_1

value: adult


title: quadruple knockout (Tnc, Tnr, Bcan, Ncan), biological rep 3


title: M_dpf_2


title: M_hpf_2


title: M_adult_2

value: Brain


title: 39-Shank3wt


title: 38-Shank3wt


title: 37-Shank3wt


title: 42-Shank3ko


title: 34-Caspr2ko

value: Caspr2 KO


title: 35-Caspr2ko


title: 29-BTBR

value: BTBR

value: BTBR T +tf/J


title: 28-BTBR


title: 30-BTBR


title: 31-Caspr2wt


title: 32-Caspr2wt


title: 26-C57


title: 33-Caspr2wt


title: 25-C57


title: 40-Shank3ko


title: 36-Caspr2ko


title: cont1_GC

city: WEST NEWTON

first: David

last: Levitan

state: MA

address: 56 south gate park

institute: Brandeis University

data_processing:
Reads are trimmed and then aligned to the mouse genome using TopHat
Sam files are converted to binary format using Sam-tools and visualized at the sequence level using IGV
Script written in python and R statistical package are used to convert unique reads to gene expression values and to filter genes by relative expression and statistical significance. These are plotted using web-based software written in JavaScript.
Genome_build: mm10
Supplementary_files_format_and_content: Fastq

source_name: gustatory cortex Thy1YFPH neurons

growth_protocol: Two groups of 4 mice received either 30 minutes access to 0.5% saccharin which was followed by I.P injection of 0.15M lithium chloride (2% body weight) or 30 minutes of saccharin followed by saline I.P injection

extract_protocol:
Total RNA was extracted from sorted cells using Pico-pure RNA isolation kit (Thermo fisher).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: post natal day 60-80

tag: region

value: gustatory cortex

tag: treatment

value: saline I.P injection


title: cont4_BLA

source_name: basolateral amygdala Thay1YFPH neurons

value: basolateral amygdala


title: cont1_BLA


title: cont2_BLA


title: CTA3_GC

value: I.P injection of 0.15M lithium chloride


title: cont4_GC


title: CTA3_BLA


title: CTA2_GC


title: CTA1_GC


title: cont3_GC


title: CTA4_GC


title: CTA4_BLA


title: cont3_BLA


title: CTA1_BLA


title: cont2_GC


title: 27-C57

value: postnatal week 8


title: erythrocytes rep3 Capture-C

source_name: dorsal neural tube microdissection

value: red blood cells

value: peripheral blood collection

tag: amplification

value: NEBNext Ultra DNATM

tag: assay

value: Capture-C


title: R201C #2

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

description:
gnas_r201c_2
Primary cells from mice, culture after transduction for 72-hours.

data_processing:
Low-quality reads and nucleotide was trimmed by using trimmomatic, and then were aligned to mouse mm10 assembly by using STAR.
The bam files were processed by using igvtools to generate Wig file and converted to BigWig file by using WigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: HSCs expressing GNAS-R201C lentiviral vector

growth_protocol: HSCs were isolated from wild-type mice and transduced with lentiviral vectors. 72-hours later, GFP+ Sca-1+ c-Kit+ CD48- CD150+ HSCs were purified for RNA extraction.

extract_protocol:
NucleoSpin RNA XS Kit (Machery-Nagel).
SMARTer kit (Clontech), HiSeq 1x50 (Illumina).

tag: strain/background

tag: cell type

value: hematopoietic stem cells (HSCs)

tag: lentiviral vector


title: R201C #3

description:
gnas_r201c_3
Primary cells from mice, culture after transduction for 72-hours.


title: GNAS #3

description:
gnas_wt_3
Primary cells from mice, culture after transduction for 72-hours.

source_name: HSCs expressing GNAS wild-type lentiviral vector

value: GNAS wild-type


title: R201C #1

description:
gnas_r201c_1
Primary cells from mice, culture after transduction for 72-hours.


title: Colo357_2G8

city: Dallas

first: Yuqing

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UTSouthwestern Medical Center

description: DifferentialExpression_Ctrl-VS-Treated_gene_CODING_KNOWN_counts_normalized.counts.CPM.tab

data_processing:
RNA concentration was determined by a Qubit fluorometer (Thermo Fisher Scientific) and then prepared with TruSeq Stranded Total RNA Sample Prep Kit (Illumina).
Samples were quantified, normalized, and sequenced on the Illumina HiSeq 2500 with at least 25 million reads per sample.
FASTQ files were aligned to mouse mm10 reference transcriptome.
A differential expression analysis was performed using edgeR and statistical cutoffs of FDR ≤ 0.01, log2CPM ≥ 0 and FC cutoffs of −1.5 ≥ FC ≥ 1.5 were used to identify statistically significant transcripts.
Data analysis was performed using an IPA tool (Qiagen).
Genome_build: Grcm38
Supplementary_files_format_and_content: Tab separated files, normalized counts

source_name: xenograft tumor tissues

extract_protocol:
Tumor tissues were harvested in RLT lysis buffer and purified according to instructions of the RNeasy Plus Kit (QIAGEN). An Agilent 2100 Bioanalyzer was used to determine RNA quality, and only samples with an RNA integrity number score of 7 or higher were used. The samples were subjected to RNA sequencing.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Eight-week-old NOD SCID or NSG mice were orthotopically injected with MiaPaCa-2 and Colo357 cells. Mice were randomized to receive Control or 2G8 (30 mg/kg, 2X/week) 10 days after injection and treated for 3 weeks.

value: NOD SCID

value: tumor

tag: injected cell line


title: MiaPaca-2_2G8 2

value: MiaPaca


title: MiaPaca-2_Ctrl 1

value: control


title: GNAS #2

description:
gnas_wt_2
Primary cells from mice, culture after transduction for 72-hours.


title: MiaPaca-2_Ctrl 2


title: MiaPaca-2_2G8 1


title: CTA2_BLA

value: brain


title: GNAS #1

description:
gnas_wt_1
Primary cells from mice, culture after transduction for 72-hours.


title: Colo357_Ctrl


title: GFP #3

description:
pmnd_3
Primary cells from mice, culture after transduction for 72-hours.

source_name: HSCs expressing control lentiviral vector


title: GFP #2

description:
pmnd_2
Primary cells from mice, culture after transduction for 72-hours.


title: BE(2)-C lncNB siRNA-2 transfected replicate 3

city: Kensington

first: Pei

last: Liu

address: C25 Lowy Cancer Research Centre

institute: CCIA

description: MYCN-amplified neuroblastoma cells

hyb_protocol: 2.3 ug of fragmented, labeled cDNA was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridisation Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_0007.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner.

data_processing: Results from the microarray experiment were analyzed in R (http://www.r-project.org/) and normalized independently with the RMA method for the HuGene-2_st and Clariom_S platforms. The probes with the same gene annotations were extracted from the two platforms. Then, the extracted and normalized data were combined, and adopted as the input of the package 'RankProd' for multiply origins data analysis (meta-analysis). The output p-values were adjusted with the 'BH' method to obtain the adjust p-values.

source_name: BE(2)-C cells

label_protocol: We used the Affymerix GeneChip WT Plus Reagent Kit: Manual Target Preparation for GeneChip Whole Transcript Expression Arrays (Affymetrix_WT_Plus_User_Guide). 100 ng of total RNA was used for input.

growth_protocol: BE(2)-C neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen, Hamburg, Germany) according to the manufacturer's instructions.

treatment_protocol: BE(2)-C neuroblastoma cells were transfected with control siRNA, lncNB1 siRNA-1 or lncNB1 siRNA-2 for 40 hours.

value: BE(2)-C cells

tag: genotype/variation

value: lncNB1 siRNA-2


title: BE(2)-C lncNB siRNA-1 transfected replicate 3

description: MYCN-amplified neuroblastoma cells

value: lncNB1 siRNA-1


title: BE(2)-C lncNB siRNA-1 transfected replicate 2

description: MYCN-amplified neuroblastoma cells


title: BE(2)-C lncNB siRNA-2 transfected replicate 2

description: MYCN-amplified neuroblastoma cells


title: BE(2)-C lncNB siRNA-2 transfected replicate 1

description: MYCN-amplified neuroblastoma cells


title: BE(2)-C control siRNA transfected replicate 2

description: MYCN-amplified neuroblastoma cells

value: Control siRNA


title: GFP #1

description:
pmnd_1
Primary cells from mice, culture after transduction for 72-hours.


title: P14

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using hisat2 v2.0.5
Raw counts and Fragments Per Kilobase Million(FPKM) were calculated by stringtie v1.3.3
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files include raw counts and FPKM values for each Sample ...

source_name: Polycystic ovary syndrome

extract_protocol:
After collected, the ovarian granulosa cells were put in liquid nitrogen quickly, and preserved in low temperature environment. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from granulosa cells following a manufacturer’s protocol. Total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running an 1% agarose gel electrophoresis, stained with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit from KAPA®.

value: ovarian granulosa cells

tag: disease state

value: Polycystic ovary syndrome


title: Single cell fibroblast TS1B_C66

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

description:
Single cell fibroblast
processed.data.trisomic_diploid.tar.gz

data_processing:
[Single cell RNA-seq]  RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 10 million reads and/or cells with <10% of expressed genes (total number of 56680 genes) were excluded from the analyses.
[Allele specific expression]  Cellular Allelic Specific Expression (ASE) of each heterozygous site was calculated in the diploid and trisomic fraction of the genome of each single cell per individual using two different formulas (provided in the manuscript). In both cases, ASE values range from 0 to 1 (Supplementary Figure 5). We consider 0≤ASE≤0.1 as the signature of monoallelic expression of the Alternative allele (euploid) or Single allele (trisomic). Conversely 0.9≤ASE≤1 indicates monoallelic expression of the Reference allele in the case of diploid cells or of the Double allele in the case of (trisomic cells). ASE from 0.1 to 0.9 is an indicator of biallelic expression.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: processed.data.trisomic_diploid.tar.gz, twin1B.10x.processed.csv, twin2A.10x.processed.csv

growth_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described

extract_protocol:
Single-cell capture was performed using the C1 single-cell auto prep system (Fluidigm) following the manufacturer’s procedure. The integrated fluidic circuit used for the study is the C1™ Single-Cell mRNA Seq IFC, 17–25 μm with a capacity of 96 chambers. During the capture, all 96 chambers were inspected under an inverted phase contrast microscope; only chambers containing a non-damaged single cell were considered for downstream analysis. SMARTer Ultra Low RNA kit for Illumina sequencing (version 2, Clontech) was used for the cell lysis and cDNA synthesis.
Libraries were prepared with 0.3 ng of pre-amplified cDNA using Nextera XT DNA kit (Illumina)
Libraries were sequenced on an Illumina HiSeq2000 sequencer as 100 bp single ended reads. RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 10 million reads and/or cells with <10% of expressed genes (total number of 56680 genes) were excluded from the analyses.

value: primary skin fibroblast

tag: trisomy type

tag: cell line

value: fibroblast


title: Single cell fibroblast TS1B_C68

treatment_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described


title: N25

source_name: Normal

value: normal


title: N21


title: Single cell fibroblast TS1B_C81


title: BE(2)-C lncNB siRNA-1 transfected replicate 1

description: MYCN-amplified neuroblastoma cells


title: BE(2)-C control siRNA transfected replicate 3

description: MYCN-amplified neuroblastoma cells


title: Single cell fibroblast TS1B_C55


title: Single cell fibroblast TS1B_C85


title: Single cell fibroblasts twin1B

description: Single cell fibroblast


title: Single cell fibroblasts twin2A

description: Single cell fibroblast


title: N20


title: Single cell fibroblast TS1B_C63


title: P16


title: P15


title: Single cell fibroblast TS1B_C45


title: Single cell fibroblast TS1B_C32


title: Single cell fibroblast TS1B_C35


title: Single cell fibroblast TS1B_C41


title: BE(2)-C control siRNA transfected replicate 1

description: MYCN-amplified neuroblastoma cells


title: Single cell fibroblast TS1B_C31


title: Single cell fibroblast TS1B_C30


title: Single cell fibroblast TS1B_C23


title: Single cell fibroblast TS1B_C16


title: Single cell fibroblast TS1B_C13


title: Single cell fibroblast TN2A_C94


title: Single cell fibroblast TS1B_C03


title: Single cell fibroblast TN2A_C96


title: Single cell fibroblast TN2A_C67bis


title: Single cell fibroblast TS1B_C11


title: Single cell fibroblast TN2A_C70bis


title: Single cell fibroblast TN2A_C81


title: Single cell fibroblast TN2A_C43


title: Single cell fibroblast TN2A_C84


title: Single cell fibroblast TN2A_C40


title: Single cell fibroblast TN2A_C37


title: Single cell fibroblast TN2A_C46


title: Single cell fibroblast TN2A_C28


title: Single cell fibroblast TN2A_C34


title: Single cell fibroblast TN2A_C26bis


title: Single cell fibroblast CAP34_C91


title: Single cell fibroblast CAP34_C93


title: Single cell fibroblast CAP34_C96


title: Single cell fibroblast CAP34_C90


title: Single cell fibroblast CAP34_C78


title: Single cell fibroblast TN2A_C91


title: Single cell fibroblast CAP34_C76


title: Single cell fibroblast CAP34_C67


title: Single cell fibroblast CAP34_C73


title: Single cell fibroblast TS1B_C05


title: Single cell fibroblast TS1B_C12


title: Single cell fibroblast CAP34_C66


title: Single cell fibroblast CAP34_C55


title: Single cell fibroblast CAP34_C57


title: Single cell fibroblast CAP34_C53


title: Single cell fibroblast CAP34_C47


title: Single cell fibroblast CAP34_C26


title: Single cell fibroblast CAP34_C34


title: Single cell fibroblast CAP34_C36


title: Single cell fibroblast CAP34_C21


title: Single cell fibroblast CAP34_C05


title: Single cell fibroblast CAP34_C30


title: Single cell fibroblast CAP34_C23


title: Single cell fibroblast CAP34_C03


title: Single cell fibroblast CAP34_C10


title: Single cell fibroblast CAP34_C19


title: Single cell fibroblast CAP34_C13


title: Single cell fibroblast CAP34_C09


title: Single cell fibroblast CAP34_C22


title: Single cell fibroblast CAP33_C93


title: Single cell fibroblast CAP33_C84


title: Single cell fibroblast CAP33_C80


title: Single cell fibroblast CAP34_C01


title: Single cell fibroblast CAP33_C77


title: Single cell fibroblast CAP34_C14


title: Single cell fibroblast CAP33_C70


title: Single cell fibroblast CAP33_C59


title: Single cell fibroblast CAP33_C64


title: Single cell fibroblast CAP33_C52


title: Single cell fibroblast CAP33_C61


title: Single cell fibroblast CAP33_C50


title: Single cell fibroblast CAP33_C39


title: Single cell fibroblast CAP33_C23


title: Single cell fibroblast CAP33_C16


title: Single cell fibroblast CAP33_C05


title: Single cell fibroblast CAP25_C96


title: Single cell fibroblast CAP25_C90


title: Single cell fibroblast CAP25_C87


title: Single cell fibroblast CAP25_C85


title: Single cell fibroblast CAP25_C81


title: Single cell fibroblast CAP25_C79


title: Single cell fibroblast CAP25_C61


title: Single cell fibroblast CAP25_C63


title: Single cell fibroblast CAP25_C73


title: Single cell fibroblast CAP25_C70


title: Single cell fibroblast CAP25_C49


title: Single cell fibroblast CAP25_C42


title: Single cell fibroblast CAP25_C39


title: Single cell fibroblast CAP25_C41


title: Single cell fibroblast CAP25_C35


title: Single cell fibroblast CAP25_C28


title: Single cell fibroblast CAP25_C24


title: Single cell fibroblast CAP25_C25


title: Single cell fibroblast CAP25_C30


title: Single cell fibroblast CAP25_C14


title: Single cell fibroblast CAP33_C27


title: Single cell fibroblast CAP25_C13


title: Single cell fibroblast CAP25_C09


title: Single cell fibroblast CAP25_C08


title: Single cell fibroblast CAP25_C01


title: Single cell fibroblast CAP25_C84


title: Single cell fibroblast CAP25_C45


title: Single cell fibroblast CAP34_C89


title: Single cell fibroblast CAP34_C88


title: Single cell fibroblast CAP34_C84


title: Single cell fibroblast CAP34_C85


title: Single cell fibroblast CAP34_C83


title: Single cell fibroblast CAP34_C80


title: Single cell fibroblast CAP34_C71


title: Single cell fibroblast CAP34_C70


title: Single cell fibroblast CAP34_C79


title: Single cell fibroblast CAP34_C72


title: Single cell fibroblast CAP34_C77


title: Single cell fibroblast CAP34_C74


title: Single cell fibroblast CAP34_C64


title: Single cell fibroblast CAP34_C82


title: Single cell fibroblast CAP34_C51


title: Single cell fibroblast CAP34_C46


title: Single cell fibroblast CAP25_C29


title: Single cell fibroblast CAP34_C52


title: Single cell fibroblast CAP34_C48


title: Single cell fibroblast CAP34_C43


title: Single cell fibroblast CAP34_C50


title: Single cell fibroblast CAP34_C68


title: Single cell fibroblast CAP25_C06


title: Single cell fibroblast CAP34_C95


title: Single cell fibroblast CAP34_C41


title: Single cell fibroblast CAP34_C42


title: Single cell fibroblast CAP34_C35


title: Single cell fibroblast CAP34_C40


title: Single cell fibroblast CAP34_C33


title: Single cell fibroblast CAP34_C32


title: Single cell fibroblast CAP34_C31


title: Single cell fibroblast CAP34_C28


title: Single cell fibroblast CAP34_C27


title: Single cell fibroblast CAP34_C25


title: Single cell fibroblast CAP34_C24


title: Single cell fibroblast CAP34_C18


title: Single cell fibroblast CAP34_C20


title: Single cell fibroblast CAP34_C17


title: Single cell fibroblast CAP34_C15


title: Single cell fibroblast CAP34_C16


title: Single cell fibroblast CAP34_C11


title: Single cell fibroblast CAP33_C78


title: Single cell fibroblast CAP33_C92


title: Single cell fibroblast CAP34_C07


title: Single cell fibroblast CAP34_C08


title: Single cell fibroblast CAP33_C74


title: Single cell fibroblast CAP33_C67


title: Single cell fibroblast CAP34_C06


title: Single cell fibroblast CAP33_C75


title: Single cell fibroblast CAP33_C69


title: Single cell fibroblast CAP33_C53


title: Single cell fibroblast CAP33_C65


title: Single cell fibroblast CAP33_C38


title: Single cell fibroblast CAP33_C63


title: Single cell fibroblast CAP33_C68


title: Single cell fibroblast CAP33_C32


title: Single cell fibroblast CAP34_C29


title: Single cell fibroblast CAP33_C26


title: Single cell fibroblast CAP33_C29


title: Single cell fibroblast CAP33_C33


title: Single cell fibroblast CAP33_C20


title: Single cell fibroblast CAP33_C15


title: Single cell fibroblast CAP34_C12


title: Single cell fibroblast CAP33_C11


title: Single cell fibroblast CAP33_C07


title: Single cell fibroblast CAP33_C01


title: Single cell fibroblast CAP25_C78


title: Single cell fibroblast CAP25_C93


title: Single cell fibroblast CAP25_C80


title: Single cell fibroblast CAP25_C69


title: Single cell fibroblast CAP25_C58


title: Single cell fibroblast CAP25_C68


title: Single cell fibroblast CAP25_C67


title: Single cell fibroblast CAP25_C55


title: Single cell fibroblast CAP25_C33


title: Single cell fibroblast CAP25_C23


title: Single cell fibroblast CAP25_C43


title: Single cell fibroblast CAP25_C38


title: Single cell fibroblast CAP25_C44


title: Single cell fibroblast CAP25_C22


title: Single cell fibroblast CAP25_C20


title: Single cell fibroblast CAP33_C19


title: Single cell fibroblast CAP25_C19


title: Single cell fibroblast CAP25_C21


title: Single cell fibroblast CAP25_C17


title: Single cell fibroblast CAP25_C11


title: Single cell fibroblast CAP25_C16


title: Single cell fibroblast CAP25_C12


title: Single cell fibroblast CAP25_C10


title: Single cell fibroblast CAP25_C75


title: Single cell fibroblast CAP25_C05


title: Single cell fibroblast CAP25_C04


title: Single cell fibroblast CAP25_C64


title: Single cell fibroblast CAP37_C94


title: Single cell fibroblast CAP25_C51


title: Single cell fibroblast CAP37_C93


title: Single cell fibroblast CAP25_C27


title: Single cell fibroblast CAP37_C90


title: Single cell fibroblast CAP37_C89


title: Single cell fibroblast CAP37_C78


title: Single cell fibroblast CAP37_C71


title: Single cell fibroblast CAP37_C77


title: Single cell fibroblast CAP37_C64


title: Single cell fibroblast CAP37_C69


title: Single cell fibroblast CAP37_C63


title: Single cell fibroblast CAP37_C61


title: Single cell fibroblast CAP37_C56


title: Single cell fibroblast CAP37_C57


title: Single cell fibroblast CAP37_C51


title: Single cell fibroblast CAP25_C07


title: Single cell fibroblast CAP37_C49


title: Single cell fibroblast CAP37_C43


title: Single cell fibroblast CAP37_C42


title: Single cell fibroblast CAP37_C27


title: Single cell fibroblast CAP25_C02


title: Single cell fibroblast CAP37_C25


title: Single cell fibroblast CAP37_C18


title: Single cell fibroblast CAP37_C16


title: Single cell fibroblast CAP37_C11


title: Single cell fibroblast CAP37_C07


title: Single cell fibroblast CAP37_C01


title: Single cell fibroblast CAP37_C03


title: Single cell fibroblast CAP26_C96


title: Single cell fibroblast CAP26_C82


title: Single cell fibroblast CAP26_C81


title: Single cell fibroblast CAP26_C88


title: Single cell fibroblast CAP26_C80


title: Single cell fibroblast CAP26_C73


title: Single cell fibroblast CAP26_C71