title: Floral nectary presecretory replicate1 (1)

description: FL pre 1 Rep.1


title: Bracteal nectary presecretory control replicate2 (1)

status: Public on Apr 19 2018

type: SRA

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

country: USA

institute: University of Minnesota Duluth

description: B pre 3C Rep.1

library_source: transcriptomic

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn, normalized by upper-quartile count and reference length
Contigs aligned to cotton reference proteins
Cotton reference proteins annotated with closest Arabidopsis thaliana match
Genome_build: Cotton: https://www.ncbi.nlm.nih.gov/assembly/GCF_000987745.1/
Genome_build: Arabidopsis used Araport 11 build 201606
Supplementary_files_format_and_content: Cotton_protein_counts.txt - file with upper quartile and mRNA-length normalized counts

molecule: total RNA

organism: Gossypium hirsutum

source_name: Bracteal nectary presecretory control

growth_protocol: Seeds for Gossipium hirsutum cv. TM1 were chipped and germinated in 8cm x 8cm x 10 cm pots filled with a soil mixture of 3-parts LC8 soil to 1-part sand. Plants were grown in Environmental Growth Chambers kept at 12h light 26 °C /12h dark 22 °C cycle. Seedlings were transplanted into two-gallon (2A) pots after reaching approximately 30 cm in height. Upon transplanting, 10 g of Osmocote Pro 19-5-8 was mixed into the previously described soil mixture per pot. Plants were water each day and once per week with a 10% fertilizer solution of Scotts Excel 21-5-20 all purpose water soluble fertilizer and Scotts Excel 15-5-15 Cal-Mag water soluble fertilizer. All tissues were collected from plants after the first flower bloomed, approximately ten weeks after sowing, between the times of 1000 and 1500.

extract_protocol:
RNA isolation: For a single biological replicate, approximately five nectaries were transferred with a clean forcep to a 2 ml Lysing matrix A tube (MP Biomedicals, Ref # 6910-500) containing a ceramic bead, resting in a liquid nitrogen bath. The tubes were quickly transferred to a QuickPrep adaptor (containing dry ice) and attached to the FastPrep 24™-5G  (MP Biomedicals) benchtop homogenizer. The tissue were subjected to 5 to 6 homogenizing runs of 40 seconds each at 6 m/sec, with each run interjected with a period of immersing the tubes in liquid nitrogen and refilling the adaptor with dry ice. Post-pulverization, 600µl of the RNA lysis buffer of the Quick-RNA™ MiniPrep kit (Zymo Research, Cat# R1054) was quickly added to the Lysing matrix tube and the tubes were vortexed. This was followed by addition of 50µl of the Plant RNA Isolation Aid (Thermo Fisher Scientific Cat#AM9690; erstwhile Ambion) and a quick vortex to aid removal of common plant contaminants such as polyphenolics and polysaccharides. Quick-RNA™ MiniPrep kit directions were followed for RNA isolation. Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. All libraries were pooled and sequenced across two and a half lanes, then sequencing was repeated for quality concerns. This generated ≥24 M reads for each sample and the average quality scores were above Q30.
Illumina's Truseq RNA Preparation v2 kit (RS-122-2001)

tag: tissue

value: Near bracteal nectary tissue

tag: Stage

value: presecretory control


title: Single Cell Epcam_neg GC049234_TAGCGCTC-TTATGCGA

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

country: Belgium

institute: Université Libre de Bruxelles (ULB)

description: SmartSEQ2 scRNAseq

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated matrix containing raw transcript counts

organism: Mus musculus

source_name: YFP+/Epcam- FACS skin squamous cell carcinoma

growth_protocol: Skin tumours from Lgr5CreER/KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ were dissected, minced and digested in collagenase type I (Sigma) at 3.5mg/ml during 1 hour at 37ºC on a rocking plate protected from light. Collagenase activity was blocked by the addition of EDTA (5mM) and then the cells were rinsed in PBS supplemented with 10% FBS and the cell suspensions were filtered through a 70um cell strainers (BD Bioscience). Tumour cells were first incubated with APCCy7 conjugated anti-Epcam antibody (rat, clone G8.8, BD Cat#624073, dilution 1:50) during 30 min at 4ºC protected from light and after BD lyoplate screening panel for mouse cells (BD, Cat#562208), containing 176 anti-mouse monoclonal antibodies and 18 isotype controls, was applied. Living single tumour cells were selected by forward and side scatter, doublets discrimination and by DAPI dye exclusion. The expression of the markers was analyzed in YFP+Epcam+ and YFP+Epcam- tumour cells (negative, homogeneously expressed or heterogeneously expressed). Fluorescence-activated  cell  sorting  and  analysis  were erformed  using FACSAria and LSRFortessa, using FACSDiva software (BD Bioscience). Sorted cells were collected in culture medium  (for in  vivo transplantation experiments), lysis buffer (for RNA extraction) or in PBS supplemented with 3% FBS (for ATAC).

extract_protocol:
Single cell transcriptomes were generated using a modified Smartseq-2 protocol. 1µL lysis buffer in 384 well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer, 2.5mM dNTPs, 2.5µM oligo-dT30-VN and ERCC controls at a final dilution of 1:400 million.
Reverse transcription and PCR was performed according to the Smartseq-2 protocol with reduced volumes: 1μl of reverse B372transcription mix instead of 5.7μl and 3μl PCR Master mix instead of 12.5μl. cDNA was amplified for 24 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8x ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 30μl buffer EB (Qiagen) and transferred to 384_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermofisher) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit. After initial quality control 24 samples were discarded with cDNA yields of less than 21ng. Next generation sequencing library preparation was performed using a Nextera XT DNA library preparation kit with volumes reduced by one-tenth (Illumina) using an acoustic dispenser. In brief, 100pg of cDNA in a volume of 500nL was tagmented by adding 1.5μl Tn5-buffer mix and incubating for 10 min at 55°C. Tagmented samples were barcoded with Nextera index sets A - D and amplified with 11 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6x ratio. Library pools were eluted in buffer EB and quality control performed using an Agilent 2100 BioAnalyser and High Sensitiviy DNA chip before adjusting to a concentration of 4nM. The diluted pools were quantified using a KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before a final dilution to 2nM. The pool of 384 samples was sequenced on 1 lane of a HiSeq4000 with 1x50bp read length.
scRNAseq

tag: library type

value: Nextera XT


title: Floral nectary secretory control replicate3 (1)

description: FL sec 3C Rep.1

source_name: Floral nectary secretory control

value: Near floral nectary tissue

value: secretory control


title: Single Cell Epcam_neg GC049234_CCTAAGAC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Foliar nectary presecretory replicate2 (1)

description: FO pre 2 Rep.1

source_name: Foliar nectary presecretory

value: Foliar nectary tissue

value: presecretory


title: Single Cell Epcam_neg GC049234_AAGAGGCA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AAGAGGCA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCGACGTC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TGCAGCTA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAAGGCGA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTGAGCG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGATCAGT-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGCGCTC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TACGCTGC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCGTAGTA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGAGCTAC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: C646_untreated_rep2

type: RNA

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Control probes were excluded before data processing. Scanned signal intensity (gMedianSignal) was log2-transformed. Quantile normalization was performed to sampe-wise comparison

organism: Homo sapiens

source_name: C646(-) human keratinocytes

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Normal human keratinocytes (Cascade Biologies, Portland, OR, USA) were maintained in keratinocytes growth (KGM) GOLD medium (Lonza, Based, Switzerland)

extract_protocol: Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

treatment_protocol: siRNA transfection was performed with ON-TARGETplus SMARTpool siRNA (Life Technologies) using Lipofectamine RNAimax (Life Technologies).

tag: treatment

value: untreated

tag: cell type

value: primary keratinocytes (Lonza)


title: PRKO GC, biological rep1

city: St Lucia

first: Lisa

last: Akison

state: QLD

address: Sir William MacGregor Building

department: Biomedical Sciences

country: Australia

institute: University of Queensland

description: Gene expression data from granulosa cells collected from progesterone receptor knockouts (PRKO) at 8h post-hCG

hyb_protocol: Following fragmentation and biotinylation, samples were hybridised at 45C for 16-18 h on Affymetrix Mouse Gene 1.0 ST arrays. Arrays were washed and then stained using a fluorescently-labelled antibody using the GeneChip® Fluidics Station 450/250.

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

data_processing: Microarray data were analysed using Partek Genomics Suite software (Partek Inc.). Background correction was performed by robust multichip averaging followed by probe affinity adjustment for the variable G-C content of probes. Quantile normalisation was performed to remove systematic variations resulting from array preparation or sample hybridization conditions. A mean probe-set summary was obtained by averaging the intensity values for the multiple probes representing an individual gene.

label: biotin

source_name: Mouse granulosa cells, PRKO genotype, 8h post-hCG

label_protocol: Biotinylated cRNA were prepared using the GeneChip® Whole-Transcript (WT) cDNA Synthesis and Amplification kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: All mice were injected i.p. with 5IU of equine chorionic gonadotropin and 5IU of human chorionic gonadotropin prior to collection of granulosa cells. Granulosa cells were collected at 8h post-hCG.

extract_protocol: Granulosa cells were homogenised in 1 ml Tri Reagent (Sigma-Aldrich Pty. Ltd.) using a Precellys 24 tissue homogeniser (Sapphire Bioscience). Total RNA was extracted using a modified Tri Reagent protocol, which included an overnight precipitation step at -20C and the addition of 1 μl Ambion GlycoBlue (15 mg/ml; Applied Biosystems) during precipitation.

tag: genotype

value: PRKO


title: PR+/- GC, biological rep1

description: Gene expression data from granulosa cells collected from heterozygous progesterone receptor mutants (PR+/-) at 8h post-hCG

source_name: Mouse granulosa cells, PR+/- genotype, 8h post-hCG


title: PRKO GC, biological rep4


title: C646_treated_rep1

source_name: C646(+) human keratinocytes


title: Single Cell Epcam_neg GC049234_ATCTCAGG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: C646_treated_rep2


title: PRKO COC, biological rep3

description: Gene expression data from cumulus oocyte complexes collected from progesterone receptor knockouts (PRKO) at 8h post-hCG

source_name: Mouse cumulus oocyte complex, PRKO genotype, 8h post-hCG

growth_protocol: All mice were injected i.p. with 5IU of equine chorionic gonadotropin and 5IU of human chorionic gonadotropin prior to collection of cumulus oocyte complexes. Cumulus oocye complexes were collected at 8h post-hCG.

extract_protocol: Cumulus oocyte complexes were homogenised in 500 μl Tri Reagent (Sigma-Aldrich Pty. Ltd.) using a Precellys 24 tissue homogeniser (Sapphire Bioscience). Total RNA was extracted using a modified Tri Reagent protocol, which included an overnight precipitation step at -20C and the addition of 1 μl Ambion GlycoBlue (15 mg/ml; Applied Biosystems) during precipitation.


title: PR+/- GC, biological rep5


title: PRKO COC, biological rep4


title: PRKO GC, biological rep5


title: PRKO GC, biological rep3


title: PR+/- GC, biological rep2


title: PR+/- GC, biological rep4


title: PR+/- GC, biological rep3


title: C646_untreated_rep1


title: PRKO GC, biological rep2


title: PRKO COC, biological rep1


title: PRKO COC, biological rep2


title: PR+/- COC, biological rep3

description: Gene expression data from cumulus oocyte complexes collected from heterozygous progesterone receptor mutants (PR+/-) at 8h post-hCG

source_name: Mouse cumulus oocyte complex, PR+/- genotype, 8h post-hCG


title: PR+/- COC, biological rep2


title: PR+/- COC, biological rep4


title: Single Cell Epcam_neg GC049234_AAGAGGCA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GCTCATGA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GGACTCCT-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: PR+/- COC, biological rep1


title: 0 cell negative control GC049234_TAAGGCGA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_AGGCAGAA-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGTACTAG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. UMUC17 BladCL

city: Santa Monica

first: HSIAOWANG

last: CHEN

state: CA

address: 2825 Santa Monica Blvd

department: Medicine

institute: UCLA

hyb_protocol: In comparison of expression between each Bladder cancer cell line and a reference mix pool composed of equal amount of all the Bladder cancer cell lines list under column Sample name. 825 ng each of labeled reference mix  (BladCLRefMix28,cy3 label) and individual Bladder cancer cell  line(cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent G2505C scanner with extended dynamic range. Images were quantified using Agilent Feature Extraction Software version 12.0.0 refer to raw data file column.

data_processing:
Agilent Feature Extraction Software was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used  to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extracted data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging.
In Rosetta analysis, setting for cluster Algoritm is list here and applies to both sample experiment and sequence.  Algorithm=Agglomerative, Algorithm parameters: Heuristic criteria=Average link, Similarity measure metric type=Cosine correlation.
In Rosetta analysis, setting for statistical cuts is list here to generate the heatmap.  Thresholds=equal or bigger than 1.5 fold change with P-vaule no bigger than 0.01. No further statistical cuts nor FDR applied. Significant different expressed genes are obtained then by ANOVA and is based on three catagories of miR-21 levels in these 28 Bladder Cancer cell lines.  The three catagories are denoted as high, medium and low to indicates the qPCR levels of miR-21.

source_name: BladCLRefMix

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions.

growth_protocol:
Bladder cancer cell lines were cultured in recommended media following manufacture's instruction.
All cell line cultures used for arrays were harvested at 50-70% confluency, centrifuged, and quick frozen.
All cell lines were verified by mtDNA sequence and validate to be authentical prior to use.

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's protocol.

tag: sample type

value: reference mix pool

source_name: UMUC17 BladCL

tag: cell line

value: Bladder cancer Cell line


title: BladCLRefMix vs. UMUC5 BladCL

source_name: UMUC5 BladCL


title: BladCLRefMix vs. UMUC15 BladCL

source_name: UMUC15 BladCL


title: BladCLRefMix vs. UMUC13 BladCL

source_name: UMUC13 BladCL


title: Single Cell Epcam_neg GC049234_CGATCAGT-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGAGGCTG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. T24 BladCL

source_name: T24 BladCL


title: BladCLRefMix vs. UMUC3 BladCL

source_name: UMUC3 BladCL


title: BladCLRefMix vs. Scabber BladCL

source_name: Scabber BladCL

value: Scabber


title: BladCLRefMix vs. SW780 BladCL

source_name: SW780 BladCL


title: Single Cell Epcam_neg GC049234_TCGACGTC-ACTGCATA

description: SmartSEQ2 scRNAseq

source_name: YFP+/Epcam- FACS skin squamous cell carcinoma


title: BladCLRefMix vs. HT1376 BladCL

source_name: HT1376 BladCL


title: Single Cell Epcam_neg GC049234_TGCAGCTA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATGCGCAG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CCTAAGAC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. J82 BladCL

source_name: J82 BladCL


title: BladCLRefMix vs. TCCSUP BladCL

source_name: TCCSUP BladCL

value: TCCSUP


title: Single Cell Epcam_neg GC049234_ACTGAGCG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. HBCLS-2 BladCL

source_name: HBCLS-2 BladCL


title: BladCLRefMix vs. HT1197 BladCL

source_name: HT1197 BladCL


title: BladCLRefMix vs. SW1710 BladCL

source_name: SW1710 BladCL


title: BladCLRefMix vs. BC-3C BladCL

source_name: BC-3C BladCL


title: BladCLRefMix vs. UMUC11 BladCL

source_name: BladCLRefMix

source_name: UMUC11 BladCL


title: Single Cell Epcam_neg GC049234_TAGCGCTC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-AAGGAGTA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CGGAGCCT-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. HB-CLS1 BladCL

source_name: HB-CLS1 BladCL


title: BladCLRefMix vs. UMUC14 BladCL

source_name: UMUC14 BladCL


title: BladCLRefMix vs. UMUC4 BladCL

source_name: UMUC4 BladCL


title: Single Cell Epcam_neg GC049234_GGAGCTAC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ATCTCAGG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. UMUC1 BladCL

source_name: UMUC1 BladCL


title: BladCLRefMix vs. RT112 BladCL

source_name: RT112 BladCL


title: BladCLRefMix vs. KU19-19 BladCL

source_name: KU19-19 BladCL


title: Single Cell Epcam_neg GC049234_AAGAGGCA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. CLS439 BladCL

source_name: CLS439 BladCL


title: BladCLRefMix vs. UMUC9 BladCL

source_name: UMUC9 BladCL


title: Single Cell Epcam_neg GC049234_GCGTAGTA-ACTGCATA

description: SmartSEQ2 scRNAseq

source_name: YFP+/Epcam- FACS skin squamous cell carcinoma


title: Single Cell Epcam_neg GC049234_GGACTCCT-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TCCTGAGC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. UMUC7 BladCL

source_name: UMUC7 BladCL


title: Single Cell Epcam_neg GC049234_TACGCTGC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_TAGGCATG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_ACTCGCTA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. RT4 BladCL

source_name: RT4 BladCL


title: Single Cell Epcam_neg GC049234_GCTCATGA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_GTAGAGGA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: SUB HFD 2

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
Pair-end reads from each sample were aligned to the mouse genome (mm10 build) using TopHat (version 2.0.9).
Differential expression between high-fat diet and normal chow samples was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 2.1.1).
Differentially expressed genes are those that have a log2 fold change of > 1 or < -1 and a q-value < 0.05 when compared to the control condition.
We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 1 in any of the condition.
Genome_build: mm10
Supplementary_files_format_and_content: Expression value in terms of fpkm

molecule: polyA RNA

source_name: inguinal adipocytes

growth_protocol: Male mice on the C57BL/6 background were kept at the Duke-NUS animal facilities.

extract_protocol:
Adipose tissues were excised from mice and immediately minced in a collagenase solution comprising 0.2% collagenase (C6885, Sigma) and 2% BSA dissolved in Hanks’ balanced salt solution (HBSS, Gibco). Minced tissues were transferred to a 50ml tube and incubated at 37ºC for 20min (for EPI and ING) or 40min (for BAT) at 500rpm. 10ml complete DMEM was subsequently added. Cell resuspensions were filtered through 100μm strainers, spun at 2000rpm for 5min, and washed once with PBS. The floating adipocyte layer and the pelleted SVF fraction were collected separately.
Total RNA was extracted using Qiagen kit. 1ug of total RNA was used for each RNA-Seq library preparation according to the manufacturer's instructions (New England Biolab), and sequencing was done on HiSeq 2000 (Illumina).

treatment_protocol: Mice were fed regular chow diet or high fat diet (Research Diets, #D12492) for 16 weeks commenced upon weaning at 3 weeks of age.

value: inguinal adipocytes

tag: diet

value: high fat diet

tag: strain


title: Single Cell Epcam_neg GC049234_CGAGGCTG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_neg GC049234_CTCTCTAC-ACTGCATA

description: SmartSEQ2 scRNAseq


title: BladCLRefMix vs. 5637 BladCL

source_name: 5637 BladCL


title: SUB ND 2

value: normal diet


title: SUB ND 0


title: SUB ND 1


title: SUB HFD 0


title: BladCLRefMix vs. UMUC10 BladCL

source_name: UMUC10 BladCL


title: EPI ND 1

source_name: epididymal adipocytes

value: epididymal adipocytes


title: EPI ND 0


title: EPI HFD 2


title: EPI HFD 1


title: SUB HFD 1


title: DAOY-NERT2_HIF1a siRNA and subjected to hypoxia

city: Solna

first: Urban

last: Lendahl

address: Berzelius väg 35

department: CMB

country: Sweden

institute: Karolinska Institutet

description:
hypsiH1
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_GTTTCG_AR021
Cells transfected with HIF1a siRNA and subjected to hypoxia

data_processing:
The quality of the cDNA libraries was tested on an Agilent 2100 bioanalyzer.
The libraries were sequenced on an Illumina HiSeq 2000 system, and the reads were aligned to the human genome (assembly hg19) and a transcriptome database (RefSeq and Ensembl) using bowtie, as described in Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25.
RPKM values were generated using rpkmforgenes, as described in Ramsköld D et al., An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 2009; 5: 1–11.
Genome_build: hg19
Supplementary_files_format_and_content: .txt tab seperated matrix files containing: Gene IDs (ID1, column 1), ENSEMBL IDs (ID2, column2) and RPKM values (column 3)

extract_protocol: TrueSeq RNA kit from Illumina was used according to the manufacturers’ protocol.

treatment_protocol: Cells were transfected with Ctrl siRNA, HIF1a siRNA or HIF2a siRNA and treated  +/- hypoxia  for 48h,  +/- induction of Notch signaling by TMX for 48 h.

tag: cell line background

value: DAOY

value: human primary medulloblastoma cell line

tag: transfected with

value: HIF1a siRNA

tag: oxygen level

value: hypoxia


title: Single Cell Epcam_neg GC049234_AGGCAGAA-ACTGCATA

description: SmartSEQ2 scRNAseq

value: Nextera XT


title: DAOY-NERT2_HIF2a siRNA, treated with Tamoxifen (TMX) to induce Notch signaling, and subjected to hypoxia

description:
hypTMXsiH2
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_ATTCCT_AR027
Cells transfected with HIF2a siRNA, treated with Tamoxifen (TMX) to induce Notch signaling, and subjected to hypoxia

value: HIF2a siRNA

tag: treated with


title: SSEA1_Neg_Male_2

city: Cambridge

first: Rahul

last: Karnik

state: MA

address: 419 Broadway

library_source: genomic

data_processing:
Reads were aligned to the mm9 build of the mouse genome using bsmap.
CpG level methylation calls were calculated using the mcall program from the MOABS package.
Genome_build: mm9
Supplementary_files_format_and_content: Column headings are: #chrom,start,end,ratio,totalC,methC,strand,next,Plus,totalC,methC,Minus,totalC,methC,localSeq

molecule: genomic DNA

growth_protocol: iPSCs were feeder-depleted before isolation for RRBS.

extract_protocol:
gDNA for reduced representation bisulfite sequencing (RRBS) was isolated using the DNeasy QIAGEN Blood and Tissue kit (Cat. 69504).
RRBS libraries were prepared as described in Boyle et al, Genome Biology, 2012 (PMC ID: PMC3491420)

tag: Sex

value: male


title: Single Cell Epcam_neg GC049234_CGTACTAG-ACTGCATA

description: SmartSEQ2 scRNAseq


title: EPI ND 2


title: Single Cell Epcam_pos GC049234_ACTGAGCG-GTAAGGAG

description: SmartSEQ2 scRNAseq

source_name: YFP+/Epcam+ FACS skin squamous cell carcinoma


title: Single Cell Epcam_pos GC049234_CCTAAGAC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: DAOY-NERT2_HIF1a siRNA, treated with Tamoxifen (TMX) to induce Notch signaling, and subjected to hypoxia

description:
hypTMXsiH1
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_ACTGAT_AR025
Cells transfected with HIF1a siRNA, treated with Tamoxifen (TMX) to induce Notch signaling, and subjected to hypoxia


title: 50 cell positive control GC049234_TAAGGCGA-ACTGCATA

description: SmartSEQ2 scRNAseq


title: DAOY-NERT2_control siRNA, treated with Tamoxifen (TMX) to induce Notch signaling, and subjected to hypoxia

description:
hypTMXsiC
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_GAGTGG_AR023
Cells transfected with control siRNA, treated with Tamoxifen (TMX) to induce Notch signaling, and subjected to hypoxia

value: control siRNA


title: Single Cell Epcam_pos GC049234_TCGACGTC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: DAOY-NERT2_HIF2a siRNA and subjected to hypoxia

description:
hypsiH2
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_CGTACG_AR022
Cells transfected with HIF2a siRNA and subjected to hypoxia


title: EPI HFD 0


title: Single Cell Epcam_pos GC049234_TGCAGCTA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_ATGCGCAG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: iPS_Female_8

value: female

value: iPSC


title: Single Cell Epcam_pos GC049234_CGATCAGT-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: BAT ND

source_name: interscapular brown adipocytes

value: interscapular brown adipocytes


title: iPS_Female_6


title: BAT HFD


title: SSEA1_Pos_Male_2


title: Single Cell Epcam_pos GC049234_CGGAGCCT-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: DAOY-NERT2_control siRNA maintained in normoxia

description:
O2siC
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_ATCACG_AR001
Cells transfected with control siRNA maintained in normoxia

value: normoxia


title: iPS_Female_3


title: Single Cell Epcam_pos GC049234_GCGTAGTA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_GGAGCTAC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: DAOY-NERT2_HIF2a siRNA, maintained in normoxia and treated with Tamoxifen (TMX) to induce Notch signaling

description:
O2TMXsiH2
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_GGCTAC_AR011
Cells transfected with HIF2a siRNA, maintained in normoxia and treated with Tamoxifen (TMX) to induce Notch signaling


title: MEF_Male_5

value: MEF


title: DAOY-NERT2_control siRNA and subjected to hypoxia

description:
hypsiC
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_GTGGCC_AR020
Cells transfected with control siRNA and subjected to hypoxia


title: P30+--2

city: paris

first: Jessica

last: Apulei

address: 11 place marcelin berthelot

country: France

institute: Collège de France

data_processing:
Reads were filtered and mapped with Bowtie using the following parameters -n 2 -l 28 -e 70 -k 2 –best.
Unmapped reads were removed and expression levels for Ensembl-annoted genes were estimated using htseq-count with the following parameters –m union –s yes –t exon.
Differentially expressed genes between ages and genotypes samples were obtained using DESeq package version 1.8.3.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing genes expression level

source_name: Layer IV of visual cortex

extract_protocol:
Total RNA was extracted using Qiiagen RNeasy Lipid Tissue Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
Layer IV were manually dissected, flash frozen on dry ice, and RNA was harvested using Rneasy Lipid Tissue Mini Kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Layer IV visual cortex

tag: age

value: post natal day 30


title: P30++-1

tag: tissue


title: iPS_Male_4


title: DAOY-NERT2_HIF1a siRNA, maintained in normoxia and treated with Tamoxifen (TMX) to induce Notch signaling

description:
O2TMXsiH1
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_TAGCTT_AR010
Cells transfected with HIF1a siRNA, maintained in normoxia and treated with Tamoxifen (TMX) to induce Notch signaling


title: MEF_Male_4


title: D2.0R on BME at Day 5 replicate c

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
The HiSeq Real Time Analysis software RTA 1.18 was used for processing image files
The Illumina CASAVA_v1.8.4 was used for demultiplex and converting binary base calls and qualities to fastq format
The sequencing reads were trimmed adapters and low quality bases using Trimmomatic (version 0.30
Trimmed reads were aligned to mouse mm9 reference genome (NCBIM37 /UCSC mm9) and Ensembl annotation version 67 using TopHat_v2.0.8
Aligned reads were analysed using PartekFlow software for differential expression and gene enrichment analysis. Comparisons used Partek Gene Specific Analysis (GSA) algorithm and multiple comparisons were corrected using False Discovery Rate (FDR), which was set at 0.05.
Genome_build: Mm9
Supplementary_files_format_and_content: gene quantifiaciton files

source_name: Breast cancer

growth_protocol: Cell culture surfaces were coated with either BME or BME + COL. Cells were resuspended in DMEM low glucose supplemented with 2% FBS and 2% Cultrex or 2% FBS supplemented with Cultrex + COL. Cells were grown for either 1 or 5 days at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s instructions. The quality and quantity of extracted total RNA was assessed using TapeStation 2200 (Agilent)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Grown on BME

tag: days in culture


title: D2.0R on BME at Day 5 replicate b


title: iPS_Male_2


title: Single Cell Epcam_pos GC049234_TAGCGCTC-GTAAGGAG

description: SmartSEQ2 scRNAseq

tag: library type


title: iPS_Male_1

tag: cell type


title: D2.0R on BME at Day 5 replicate a


title: DAOY-NERT2_control siRNA, maintained in normoxia and treated with Tamoxifen (TMX) to induce Notch signaling

description:
O2TMXsiC
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_GATCAG_AR009
Cells transfected with control siRNA, maintained in normoxia and treated with Tamoxifen (TMX) to induce Notch signaling


title: Normal tubulointerstitium control 5

city: Mexico City

first: Juan

middle: Manuel

last: Mejia-Vilet

state: Mexico City

address: 15 Vasco de Quiroga, Seccion XVI

department: Nephrology

country: Mexico

institute: Instituto Nacional de Nutrición Salvador Zubirán

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM5T

hyb_protocol: See manufacturer instructions at https://www.nanostring.com/products/gene-expression-panels/ncounter-immunology-panels

data_processing: Technical, Biological, Batch and Quantile normalization

source_name: tubulointerstitium kidney donor

label_protocol: Continuous sample labeling

growth_protocol: Formalin-fixed paraffin embeded tissues

extract_protocol: Laser microdissection from FFPE samples

treatment_protocol: No specific treatment

value: donor kidney tissue tubulointerstitium

tag: lupus nephritis class

value: normal kidney tissue

tag: gender

tag: 12 month response


title: iPS_Female_9


title: DAOY-NERT2_HIF2a siRNA maintained in normoxia

description:
O2siH2
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_ACTTGA_AR008
Cells transfected with HIF2a siRNA maintained in normoxia

value: DAOY

value: human primary medulloblastoma cell line


title: Normal tubulointerstitium control 4

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM4T

scan_protocol: See manufacturer instructions at https://www.nanostring.com/products/gene-expression-panels/ncounter-immunology-panels


title: iPS_Female_7


title: DAOY-NERT2_HIF1a siRNA maintained in normoxia

description:
O2siH1
Run00194_L7_1_130712_SN893_0194_BD24FTACXX_TTAGGC_AR003
Cells transfected with HIF1a siRNA maintained in normoxia

value: HIF1a siRNA


title: iPS_Female_5


title: Single Cell Epcam_pos GC049234_AAGAGGCA-GTAAGGAG

description: SmartSEQ2 scRNAseq

value: Nextera XT


title: Single Cell Epcam_pos GC049234_TACGCTGC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Normal tubulointerstitium control 2

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM2T


title: P30+--1


title: P100++-2

value: post natal day 100


title: P100++-1


title: D2.0R on BME + COL at Day 5 replicate b

value: Grown on BME + COL


title: D2.0R on BME + COL at Day 5 replicate c


title: Single Cell Epcam_pos GC049234_ACTCGCTA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Normal tubulointerstitium control 3

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM3T


title: P30++-2


title: Single Cell Epcam_pos GC049234_ATCTCAGG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_CTCTCTAC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: D2.0R on BME + COL at Day 5 replicate a


title: Single Cell Epcam_pos GC049234_GCTCATGA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Normal tubulointerstitium control 9

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM9T


title: Single Cell Epcam_pos GC049234_TAGGCATG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Patient 19 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P19AT

source_name: tubulointerstitium first biopsy

value: kidney tissue tubulointerstitium

value: class 3+5

value: complete


title: Patient 17 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P17AT

value: class 4+5

value: female


title: Normal tubulointerstitium control 8

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM8T


title: Normal tubulointerstitium control 7

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM7T

value: male


title: Normal tubulointerstitium control 10

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM10T


title: Single Cell Epcam_pos GC049234_GTAGAGGA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Patient 12 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P12BT

source_name: tubulointerstitium repeated biopsy


title: Single Cell Epcam_pos GC049234_CGAGGCTG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Normal tubulointerstitium control 6

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM6T


title: D2.0R on BME at Day 1 replicate c


title: Single Cell Epcam_pos GC049234_GGACTCCT-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: D2.0R on BME at Day 1 replicate b


title: 12h_KO_replicate2

city: Jupiter

first: Adam

last: Getzler

state: FL

address: 130 Scripps Way

institute: TSRI-FL

description: Tn5 transposase treated nuclei DNA

data_processing:
Bowtie
samtools
MACS2
Homer
HT-Seq Count
DESEQ2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: HT-Seq Count raw conuts

source_name: 12H Runx3 KO CD8 CD8+ T-cells

extract_protocol:
Treated with 50uL of Tn5 transposase reaction mixture( Nextera DNA Sample Prep Kit)
Created libraries using Nextra DNA Sample Kit, as per Buenrostro et al, 2015

tag: time point


title: Patient 19 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P19BT


title: D2.0R on BME at Day 1 replicate a


title: 24h_KO_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 24H Runx3 KO CD8 CD8+ T-cells

tag: strain


title: 12h_WT_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 12H WT CD8 CD8+ T-cells


title: Patient 17 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P17BT

value: class 4

value: partial


title: Normal tubulointerstitium control 1

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitum from a normal kidney donor
NM1T


title: Patient 08 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P08BT


title: Single Cell Epcam_pos GC049234_TCCTGAGC-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: 6h_KO_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 6H Runx3 KO CD8 CD8+ T-cells


title: 24h_WT_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 24H WT CD8 CD8+ T-cells


title: Patient 18 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P18AT

value: class 3


title: Patient 12 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P12AT


title: Patient 18 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P18BT


title: Patient 05 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P05AT


title: Patient 09 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P09BT


title: 2h_KO_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 2H Runx3 KO CD8 CD8+ T-cells


title: 6h_WT_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 6H WT CD8 CD8+ T-cells


title: Single Cell Epcam_pos GC049234_TCGACGTC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 08 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P08AT


title: Single Cell Epcam_pos GC049234_TAAGGCGA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_AGGCAGAA-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Patient 14 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P14AT


title: Patient 14 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P14BT


title: Single Cell Epcam_pos GC049234_TGCAGCTA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 05 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P05BT


title: Patient 11 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P11BT


title: 2h_WT_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 2H WT CD8 CD8+ T-cells


title: Patient 09 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P09AT


title: Single Cell Epcam_pos GC049234_CGATCAGT-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 11 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P11AT


title: Single Cell Epcam_pos GC049234_CGTACTAG-GTAAGGAG

description: SmartSEQ2 scRNAseq


title: Patient 7 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P07BT


title: 0h_KO_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 0H Runx3 KO CD8 CD8+ T-cells


title: Patient 7 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P07AT


title: Single Cell Epcam_pos GC049234_CCTAAGAC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 16 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P16BT


title: 0h_WT_replicate2

description: Tn5 transposase treated nuclei DNA

source_name: 0H WT CD8 CD8+ T-cells


title: Single Cell Epcam_pos GC049234_ACTGAGCG-TATCCTCT

description: SmartSEQ2 scRNAseq

source_name: YFP+/Epcam+ FACS skin squamous cell carcinoma


title: 24h_KO_replicate1

description: Tn5 transposase treated nuclei DNA


title: Patient 16 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P16AT


title: Patient 13 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P13BT


title: Single Cell Epcam_pos GC049234_TAGCGCTC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 3 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P03BT


title: 24h_WT_replicate1

description: Tn5 transposase treated nuclei DNA


title: Single Cell Epcam_pos GC049234_ATGCGCAG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: 12h_KO_replicate1

description: Tn5 transposase treated nuclei DNA


title: 12h_WT_replicate1

description: Tn5 transposase treated nuclei DNA


title: 6h_KO_replicate1

description: Tn5 transposase treated nuclei DNA


title: 6h_WT_replicate1

description: Tn5 transposase treated nuclei DNA


title: 2h_WT_replicate1

description: Tn5 transposase treated nuclei DNA


title: 2h_KO_replicate1

description: Tn5 transposase treated nuclei DNA


title: 0h_WT_replicate1

description: Tn5 transposase treated nuclei DNA


title: 0h_KO_replicate1

description: Tn5 transposase treated nuclei DNA


title: Single Cell Epcam_pos GC049234_GGAGCTAC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_TACGCTGC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_CGGAGCCT-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_ACTCGCTA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 19 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P19BG

source_name: glomeruli repeated biopsy

value: kidney tissue glomeruli


title: Normal glomeruli control 8

description:
glomerulirawdata.xls
LCM glomeruli from a normal kidney donor
NM8G

source_name: glomeruli kidney donor

value: donor kidney tissue glomeruli

value: normal kidney tissue


title: Patient 17 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P17BG


title: Patient 12 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P12AG

source_name: glomeruli first biopsy


title: Single Cell Epcam_pos GC049234_GCGTAGTA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 3 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P03AT


title: Patient 1 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P01AT


title: Patient 1 tubulointerstitium biopsy B

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a repeated lupus nephritis flare
P01BT


title: Normal glomeruli control 7

description:
glomerulirawdata.xls
LCM glomeruli from a normal kidney donor
NM7G


title: Patient 17 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P17AG


title: Patient 19 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P19AG


title: Patient 09 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P09BG


title: Patient 12 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P12BG


title: Normal glomeruli control 5

description:
glomerulirawdata.xls
LCM glomeruli from a normal kidney donor
NM5G


title: Normal glomeruli control 10

description:
glomerulirawdata.xls
LCM glomeruli from a normal kidney donor
NM10G


title: Normal glomeruli control 9

description:
glomerulirawdata.xls
LCM glomeruli from a normal kidney donor
NM9G


title: Patient 18 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P18BG


title: Naive replicate2

data_processing:
Bowtie2
HT-Seq Count
DESEQ2
Genome_build: UCSC mm9
Supplementary_files_format_and_content: HT-Seq Count raw conuts

source_name: Naïve CD8+ T cells

extract_protocol:
oligo(dT) priming and SMART-Seq v5 ultra low input RNA KIT
Strand specific paired end libraries were made using the TruSeq stranded total RNA kit. Samples were DNAseI treated.

value: Naive CD8+ T cells


title: Patient 09 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P09AG


title: Single Cell Epcam_pos GC049234_ATCTCAGG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_GTAGAGGA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 13 tubulointerstitium biopsy A

description:
tubulointerstitiumrawdata.xls
LCM tubulointerstitium from a first lupus nephritis flare
P13AT

source_name: tubulointerstitium first biopsy


title: Single Cell Epcam_pos GC049234_GCTCATGA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Normal glomeruli control 6

description:
glomerulirawdata.xls
LCM glomeruli from a normal kidney donor
NM6G


title: Patient 18 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P18AG


title: Naive replicate1


title: TE replicate2

source_name: Sorted Day 8 Post LCMV-Arm Infection CD8+ T cells

value: Flow Sorted CD127- KLRG1+ CD8+ T cells


title: Patient 08 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P08AG


title: Single Cell Epcam_pos GC049234_GGACTCCT-TATCCTCT

description: SmartSEQ2 scRNAseq

value: Nextera XT


title: TE replicate1


title: Patient 08 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P08BG


title: Single Cell Epcam_pos GC049234_TCCTGAGC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_TAGGCATG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_CGTACTAG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: MP replicate3

value: Flow Sorted CD127+ KLRG1- CD8+ T cells


title: Single Cell Epcam_pos GC049234_AGGCAGAA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_CTCTCTAC-TATCCTCT

description: SmartSEQ2 scRNAseq


title: MP replicate2


title: TE replicate3


title: Single Cell Epcam_pos GC049234_CGAGGCTG-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 05 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P05BG


title: Patient 05 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P05AG


title: Patient 14 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P14BG


title: Single Cell Epcam_pos GC049234_AAGAGGCA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 14 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P14AG


title: MP replicate1


title: Patient 11 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P11BG


title: Patient 7 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P07BG


title: Patient 11 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P11AG


title: Patient 7 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P07AG


title: Runx3 KO Day 8 TE replicate 2 read1

data_processing:
Star Aligner
HT-Seq Count
DESEQ2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: HT-Seq Count raw conuts

source_name: Sorted Day 8 Post LCMV-Arm Infection P14 cells


title: Runx3 KO Day 8 MP replicate 2 read1


title: 0 cell negative control GC049234_TAAGGCGA-TATCCTCT

description: SmartSEQ2 scRNAseq


title: Patient 16 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P16BG


title: Single Cell Epcam_pos GC049234_TCGACGTC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Wild Type Day 8 TE replicate 2 read1


title: Runx3 KO Day 8 EE replicate 2 read1

value: Flow Sorted CD127- KLRG1- CD8+ T cells


title: Wild Type Day 8 MP replicate 2 read1


title: Wild Type Day 8 EE replicate 2 read1


title: Single Cell Epcam_pos GC049234_TGCAGCTA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Patient 16 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P16AG


title: Single Cell Epcam_pos GC049234_ACTGAGCG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_CCTAAGAC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Patient 13 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P13BG


title: Patient 13 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P13AG


title: Patient 3 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P03BG


title: Runx3 KO Day 8 MP replicate 1 read1


title: Single Cell Epcam_pos GC049234_CGATCAGT-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Patient 3 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P03AG


title: Runx3 KO Day 8 TE replicate 1 read1


title: Runx3 KO Day 8 EE replicate 1 read1


title: Patient 1 glomeruli biopsy B

description:
glomerulirawdata.xls
LCM glomeruli from a repeated lupus nephritis flare
P01BG


title: Patient 1 glomeruli biopsy A

description:
glomerulirawdata.xls
LCM glomeruli from a first lupus nephritis flare
P01AG


title: Wild Type Day 8 MP replicate 1 read1


title: Single Cell Epcam_pos GC049234_ATGCGCAG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_CGGAGCCT-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_TACGCTGC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Wild Type Day 8 TE replicate 1 read1


title: Single Cell Epcam_pos GC049234_TAGCGCTC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Staphylococcus epidermidis Ctr and α-MG

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

description: RNA-seq (Drop-seq-like)

data_processing:
Sequencing in 75 cycles produced 20 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 55 bp Read 2 (sequence derived from the bacterial mRNA).
The data was analyzed using the Drop-seq Tools (Macosko et al., 2015). The sequencing reads were aligned against the strain S. epidermidis RP62A (ATCC 35984) genome using the STAR aligner (Dobin et al., 2013). The pipeline prodused the Digital Gene Expression matrix (DGE).
The edgeR, a Bioconductor package (Robinson et al., 2010) was used to obtain the list of differentially expressed genes.
Se_Ctrl_1: barcode: ATTACTCGATCG
Se_Ctrl_2: barcode: TCCGGAGATCGA
Se_Ctrl_3: barcode: CGCTCATTCGAT
Se_α-MG_1 : barcode: GAGATTCCGATC
Se_α-MG_2: barcode: ATTCAGAACGAG
Se_α-MG_3: barcode: GAATTCGTACTA
Genome_build: ASM1192v1
R1 read: Barcode, R2 read: Biological read
Supplementary_files_format_and_content: Digital Gene Expression (DGE): tab-delimited text file containing UMI read counts for each sample

organism: Staphylococcus epidermidis

source_name: log growth phase

growth_protocol: Staphylococcus epidermidis RP62A (ATCC 35984) was routinely grown in Luria-Bertani (LB) and was maintained in LB with 30% glycerol at -80 °C. For the experiment the overnight cultures of S. epidermidis were diluted 1:100 in LB and were grown to mid-log phase ( ̴ 2.5 × 108 CFU/ml) at 37 °C.

extract_protocol:
After incubation, 2 volume of RNAprotect Bacteria Reagent (Qiagen) was added to one volume of bacterial cultures. Then, the cells were pelleted by centrifugation, resuspended in 200 µl of TE buffer containing 15 mg/ml of lysozyme and 10 µl of proteinase K and incubated at 37°C for 30 min. After incubation, zirconia beads (50 mg; 0.1 mm) were added to lyse the cells using FastPrep 24 instrument (Qbiogene) and the total RNA was extracted using RNeasy Mini kit (Qiagen). To remove genomic DNA, on-column DNA digestion was done using RNase-Free DNase set (Qiagen). The RNA integrity was analyzed using LabChip GXII Touch HT (PerkinElmer). The ribosomal RNA (rRNA) was depleted using Ribo-Zero rRNA Removal kit for Gram-positive bacteria (Illumina).
Sequencing library was prepared as described before (Macosko et al., 2015) with modifications. Reverse transcription of mRNA was performed using specially designed primers. Similarly to the method described in (Macosko et al., 2015), all the primers shared a common sequence that served as a PCR handle. Additionally, the primers contained known 12 bp barcode (unique for each sample) and different random unique molecular identifiers (UMIs) (Macosco et al., 2015). The poly(T) regions of the oligos were replaced by random hexamers to enable the capturing of the bacterial mRNA particles. The reverse transcription, PCR amplification of the cDNA and tagmentation were performed as described in (Macosko et al., 2015). Paired-end sequencing was performed on NextSeq500 sequencer (Illumina) using the sequencing primers described in (Macosko et al., 2015) in Biomedicum Functional Genomics Unit (FuGU; Helsinki)

treatment_protocol: α-MG was purchased from Sigma-Aldrich (Catalogue no.: M3824) and stock solution of 1 mg/mL was prepared in methanol. Bacterial cells were treated with 0.7 MIC (0.875 µg/ml) of α-MG or 0.1 % methanol (solvent control) for 10 min.

tag: genotype

value: wt


title: Single Cell Epcam_pos GC049234_GCGTAGTA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Runx3 KO Day 5 KLRG1hi replicate 2

source_name: Sorted Day 5 Post LCMV-Arm Infection P14 cells

value: Flow Sorted KLRG1+ CD8+ T cells


title: Runx3 KO Day 5 KLRG1lo replicate 2

value: Flow Sorted KLRG1- CD8+ T cells


title: Single Cell Epcam_pos GC049234_ACTCGCTA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Wild Type Day 8 EE replicate 1 read1


title: Single Cell Epcam_pos GC049234_ATCTCAGG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: delneo_257453510010_1_1

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: The Agilent Gene Expression Hybridisation Kit (Agilent Technologies) was used for hybridisation. 600 ng of each cRNA were hybridised on 8x60K microarrays at 65°C for 17 h according to Agilent's recommendations. Microarrays were washed with the Agilent Gene Expression Wash Buffer 1 for 1 minute at ambient temperature followed washing with preheated (37°C) Gene Expression Wash Buffer 2 for 1 minute.

scan_protocol: Detection of fluorescence signals was done using the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron, generating a 20 bit TIFF file.

data_processing: Agilent’s Feature Extraction software version 11 is used to read and process the TIFF file..The raw data was pre-processed in Partek Genomic Suite

source_name: Flox

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) was used according to the manufacturers instructions to generate fluorescent cRNA (complementary RNA). A random primer/oligo-dT primer mixture (WT primer) was used for 1st strand synthesis and after 2nd strand synthesis cRNA labelled with cyanine 3-CTP was generated by in vitro transcription.

extract_protocol: RNA was prepared from mouse liver (25 mg) using the RNA Tissue Miniprep System (Promega) according to the manufacturers instructions including an on-column DNase digestion. RNA quality was checked using the 2100 Bioanalyzer (Agilent Technologies) with the RNA 6000 Pico Kit for total RNA samples. RNA quantity was checked using the Nanodrop 2000 spectrophotometer (Thermo Scientific).

value: delneo

tag: label for publication

value: CerS2 Flox

value: 6 weeks

tag: genetic background

tag: array

tag: position of subarray


title: Single Cell Epcam_pos GC049234_GGAGCTAC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: delneo_257453510010_2_2

value: male


title: Wild Type Day 5 KLRG1hi replicate 2

tag: genotype/variation


title: delneo_257453510009_2_2

tag: age


title: Single Cell Epcam_pos GC049234_GCTCATGA-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Wild Type Day 5 KLRG1lo replicate 2


title: delHox_257453510010_1_4

source_name: Del

value: delHox

value: CerS2 Del


title: cut day 4

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

institute: MDC-Berlin

data_processing:
Paired-end reads, one containing the cellular and the molecular barcodes and the other containing an RNA fragment, were joined in a bam file using picard-tools v 1.95.
Reads were then sorted using samtools 1.3.
Reads were then tagged with the cell and the molecular barcodes (UMIs), trimmed at the 5’end to remove adapter sequences and at the 3’end to remove polyA tails using Dropseq tools v 1.12
Reads were mapped to the S. mediterranea dd_Smed_v6 transcriptome assembly using STAR v 2.5 1b
Reads mapped to different transcripts were aggregated and assigned to the corresponding gene, counting reads mapping to different transcripts only once.
Dropseq tools v 1.12 were used to correct synthesis errors affecting the last position of the cell barcode and assign mapped reads to genes included in the transcriptome
To define the number of cells, we plotted the cumulative fraction of reads assigned to each cellular barcoded for each of the barcodes sequenced ordered decreasingly and identified the inflection point of the curve using the R package dropbead (https://github.com/rajewsky-lab/dropbead)
The final DGE for each of the samples was obtained using DigitalExpression from drop-seq tools using all mapped reads and counting the number of unique UMIs assigned to each gene in each of the selected cells
Genome_build: Schmidtea mediterranea dd_Smed_v6 transcriptome assembly
Supplementary_files_format_and_content: DGE files contain a matrix in which columns are cells and rows are genes, and in each position it contains the amount of UMIs assigned to each gene in each cell of the sample

organism: Schmidtea mediterranea

source_name: bulk population whole cells

growth_protocol: 20ºC Artificial Montjuic Water

extract_protocol:
trypsin dissociation and cell filtering, whole cells selected by hoechst and calcein content
Macosko et al. 2015 Cell. Online Dropseq Protocol-v 3.1
Drop-seq

treatment_protocol: RNAi (dsRNA injected 5 days prior to sample collection) or wild type

tag: run name

value: cut d4

value: regeneration day 4

tag: fixation method

value: methanol

tag: developmental stage

value: adult


title: delneo_257453510009_2_1

tag: condition


title: Single Cell Epcam_pos GC049234_GTAGAGGA-CTCTCTAT

description: SmartSEQ2 scRNAseq

tag: library type


title: BA0018_07_a_Genomic DNA from AR24Q (SH-SY5Y cell)

type: genomic

city: Nagoya

first: Naohide

last: Kondo

state: Aichi

address: 65 Tsurumai-chou, Showa-ku

department: Neurology

country: Japan

institute: Nagoya University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software.  The file unmethylated_and_methylated_signal.txt contains the raw signal. Signal A is the unmethylated signal and Signal B is methylated signal. This file includes the Full Report and thus also contains un-normalized Average Beta  and other statistics. A peak-based correction method was used to normalize the Average Beta values.

label: Cy3, Cy5

source_name: SH-SY5Y cells stably expressing human androgen receptor(AR) containing 24 glutamines (normal repeats)

label_protocol: Standard Illumina Protocol

growth_protocol: Standard growth protocol of SH-SY5Y and treated with dihidrotestosterone before harvesting cells.

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Dihidrotestosterone treatment 48h before harvesting cells.

tag: cell line

tag: cag repeats

value: 24 (normal)

tag: treatment

value: dihydrotestosterone


title: Runx3 KO Day 5 KLRG1hi replicate 1

tag: cell type


title: Runx3 KO Day 5 KLRG1lo replicate 1

tag: strain


title: BA0018_06_a_Genomic DNA from AR97Q (SH-SY5Y cell)

source_name: SH-SY5Y cells stably expressing human androgen receptor(AR) containing 97 glutamines (abnormal repeats)

value: 97 (abnormal)


title: BA0018_05_a_Genomic DNA from AR97Q (SH-SY5Y cell)


title: Single Cell Epcam_pos GC049234_AAGAGGCA-CTCTCTAT

description: SmartSEQ2 scRNAseq

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated matrix containing raw transcript counts

extract_protocol:
Single cell transcriptomes were generated using a modified Smartseq-2 protocol. 1µL lysis buffer in 384 well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer, 2.5mM dNTPs, 2.5µM oligo-dT30-VN and ERCC controls at a final dilution of 1:400 million.
Reverse transcription and PCR was performed according to the Smartseq-2 protocol with reduced volumes: 1μl of reverse B372transcription mix instead of 5.7μl and 3μl PCR Master mix instead of 12.5μl. cDNA was amplified for 24 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8x ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 30μl buffer EB (Qiagen) and transferred to 384_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermofisher) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit. After initial quality control 24 samples were discarded with cDNA yields of less than 21ng. Next generation sequencing library preparation was performed using a Nextera XT DNA library preparation kit with volumes reduced by one-tenth (Illumina) using an acoustic dispenser. In brief, 100pg of cDNA in a volume of 500nL was tagmented by adding 1.5μl Tn5-buffer mix and incubating for 10 min at 55°C. Tagmented samples were barcoded with Nextera index sets A - D and amplified with 11 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6x ratio. Library pools were eluted in buffer EB and quality control performed using an Agilent 2100 BioAnalyser and High Sensitiviy DNA chip before adjusting to a concentration of 4nM. The diluted pools were quantified using a KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before a final dilution to 2nM. The pool of 384 samples was sequenced on 1 lane of a HiSeq4000 with 1x50bp read length.
scRNAseq

value: Nextera XT


title: cut day 0

value: regeneration day 0


title: Single Cell Epcam_pos GC049234_CGAGGCTG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: cut day 2

value: regeneration day 2


title: delHox_257453510009_2_3

tag: gender


title: Wild Type Day 5 KLRG1lo replicate 1

value: Flow Sorted KLRG1- CD8+ T cells


title: delHox_257453510010_1_2

tag: label for publication


title: Wild Type Day 5 KLRG1hi replicate 1

value: Flow Sorted KLRG1+ CD8+ T cells


title: Single Cell Epcam_pos GC049234_TAGGCATG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Single Cell Epcam_pos GC049234_CTCTCTAC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: Runx3 deficient replicate 2

source_name: Day 6 100U IL2 CD8+ T-cells

extract_protocol:
Chromatin associated RNA was extracted in TRIZoL reagent
Strand specific paired end libraries were made using the TruSeq stranded total RNA kit. Samples were DNAseI treated and rRNA depleted

tag: retrovirus

value: pMigR-Cre

tag: molecule

value: Nascent RNA


title: BA0018_01_a_Genomic DNA from AR24Q (SH-SY5Y cell)


title: Single Cell Epcam_pos GC049234_GGACTCCT-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: BA0018_02_a_Genomic DNA from AR24Q (SH-SY5Y cell)


title: Wild type replicate 2

value: PMigR-Empty


title: Single Cell Epcam_pos GC049234_TCCTGAGC-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: WT_257453510009_1_4

source_name: WT

value: WT

value: CerS2 WT

value: 6 weeks

value: male

tag: genetic background

tag: array

tag: position of subarray


title: WT_257453510009_1_2

tag: age


title: WT_257453510010_2_3


title: delHox_257453510010_1_3

value: delHox

value: CerS2 Del


title: Single Cell Epcam_pos GC049234_AGGCAGAA-CTCTCTAT

description: SmartSEQ2 scRNAseq

source_name: YFP+/Epcam+ FACS skin squamous cell carcinoma


title: Runx3 deficient replicate 1

tag: genotype/variation


title: Runx3 Overexpression replicate 2

value: pMigR-Runx3 cDNA


title: WT_257453510010_2_4


title: Single Cell Epcam_pos GC049234_CGTACTAG-CTCTCTAT

description: SmartSEQ2 scRNAseq


title: HA_257453510010_2_1

source_name: H/A

value: HA

value: CerS2 H/A


title: Wild type replicate 1


title: ELL2 cko +LPS 3

city: Pittsburgh

first: Christine

last: Milcarek

state: PA

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

description: SST RMA expression value from Affymetrix Expression Console

hyb_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.

data_processing: CHP files were generated from CEL files using Expression Console from Affymetrix, using SST-RMA analysis algorithm.

source_name: ELL2 -/- cko

growth_protocol: Primary splenic B cells were isolated from each mouse using MACS columns.

extract_protocol: RNA was isolated from B cells at noted timepoints via Macherey Nagel Nucleospin RNA kits.

treatment_protocol: Unstimulated cells were processed immediately.  Stimulated cells were cultured in media + LPS for 72 hours before processing.

value: B cell

tag: agent

value: LPS

value: ELL2 -/- cko


title: Runx3 Overexpression replicate 1


title: BA0018_04_a_Genomic DNA from AR97Q (SH-SY5Y cell)

value: 97 (abnormal)

value: dihydrotestosterone


title: ELL2 cko -LPS 3

scan_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.


title: input DP ChIP-seq

status: Public on Apr 18 2018

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

description: DP input control

data_processing:
Duplicated reads were removed before mapping.
Experimental and input control fastaq tags were aligned to the mouse reference genome (mm9) using Bowtie 0.12.9. Alignment parameters used:-a -v 2 -m 3 --best --strata
All reads mapping with their best alignment score at more than 3 sites in the genome were discarded.
Confident peaks were called using MACS (version 1.4.2), with FDR<= 1% and the default p value (1E-5).
Genome_build: mm9
Supplementary_files_format_and_content: file format: bed; content: confident peaks (as called by MACS).

source_name: Rag1 -/- with TCRb transgene, thymocytes

growth_protocol: Bone marrow and spleen cells were isolated from 6 to 14 wk old C57BL/6 mice, including both males and females. DN Thymocytes were obtained from 4- to 8-wk-old Rag1-/- mice. DP Thymocytes were obtained from 4- to 8-wk-old Rag1-/- mice carrying a rearranged TCRb transgene.

extract_protocol:
For bone marrow subset purification we used B6.RAG1-/-mice to obtain pro-B cells.  B6.RAG-/-+ mice bearing a rearranged IgM transgene were used to obtain pre-B cells. For pro-B IL7, RAG1-/- pro-B cells were cultured with IL7 for 7 days.
For each sample 1 - 10 ng of IP material or input control sample was prepared into sequencing libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturers protocol. Samples were amplified using 18 cycles of PCR and then size selected on 2% EX agarose gels (Thermo Fisher) and bands cut at 300bps (+ 25 bps) and cleaned up using DNA Clean & Concentrator-25  (Zymo Research). The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.

tag: tissue

value: CD4+CD8+ (DP) thymocytes


title: Rad21 DP ChIP-seq

description: Rad21 DP ChIP-seq


title: WT +LPS 2

source_name: wild type

label_protocol: All samples were treated as per Affymetrix standard protocol by the University of Pittsburgh Genomics Core.

value: wild type


title: ELL2 cko +LPS 1


title: ELL2 cko +LPS 2


title: HA_257453510009_1_3

tag: condition


title: Rad21 DN ChIP-seq

description: Rad21 DN ChIP-seq

source_name: Rag1 -/- thymocytes

value: CD4-CD8- (DN) thymocytes


title: ELL2 cko -LPS 2


title: HA_257453510009_1_1


title: HA_257453510009_2_4


title: Rad21 pre-B ChIP-seq

description: Rad21 pre-B ChIP-seq

source_name: RAG-/-µ+ pre-B cells

value: Pre-B cells


title: CTCF pre-B ChIP-seq

description: CTCF pre-B ChIP-seq


title: input pro-B IL7 ChIP-seq

description: Pro-B IL7 input control

source_name: RAG1-/- pro-B cells cultured with IL7

value: Pro-B cells


title: WT -LPS 3


title: WT +LPS 3


title: WT +LPS 4


title: ELL2 cko -LPS 4


title: WT -LPS 2


title: CTCF pro-B IL7 ChIP-seq

description: CTCF IL7 ChIP-seq


title: ELL2 cko -LPS 1


title: WT +LPS 1