title: A5_023_SU2_T

description:
B12_030_SU4_N_CAGCCTCG_GCGTAAGA_S176_R1_001.fastq.gz
B12_030_SU4_N_CAGCCTCG_GCGTAAGA_S176_R2_001.fastq.gz


title: A1_023_SU2_T

status: Public on Jan 28 2020

type: SRA

city: Stanford

first: Gunsagar

middle: Singh

last: Gulati

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

country: USA

institute: Stanford University

description:
B12_020_SU20_T_GTAGCTCC_CCTAGAGT_S134_R1_001.fastq.gz
B12_020_SU20_T_GTAGCTCC_CCTAGAGT_S134_R2_001.fastq.gz

library_source: transcriptomic

data_processing:
Bcl2fastq2 v2.18 (Illumina) was used to extract the data and generate FASTQ files for each sample by using unique barcode combinations from the Nextera preparation. Raw FASTQ reads were then aligned to GENCODE v25 reference transcripts (GRCh38.p7) with Salmon v0.7.2 using the --seq-bias flag and otherwise default parameters. Salmon results were merged into a single gene-level TPM matrix using the R package, tximport v1.4.0. Low quality cells, identified as cells expressing <1,000 detectable genes, were excluded from further analysis. Using Seurat, clusters were identified by running ‘FindClusters’ on the first 10 principal components of the data with the resolution parameter set to 0.6. Cell labels for known epithelial subpopulations were assigned according to the expression of previously described marker genes (KRT14high, MYLKhigh = basal, MMP7high, RARRES1high = luminal progenitor, MUC1high, AREGhigh = mature luminal). Clusters with similar expression patterns of epithelial marker genes were merged and clusters lacking expression of expected markers were eliminated. These steps resulted in three remaining clusters that distinguished basal (tumor: n = 294, normal: n = 366), luminal progenitor (tumor: n = 213, normal: n = 319), and mature luminal cells (tumor: n = 354, normal: n = 356). The final expression matrix was filtered to focus on protein-coding genes approved by the HUGO Gene Nomenclature Committee (n = 19,031 genes).
Genome_build: GENCODE v25 (GRCh38.p7)
Supplementary_files_format_and_content: Tab-delimited text files include (1) Transcripts per million (TPM) values for each single cell (2) Metadata for each single cell

molecule: total RNA

organism: Homo sapiens

source_name: Breast

extract_protocol:
6 tumor biopsies from patients with luminal-like breast cancer and 2 tumor biopsies from patients with basal-like breast cancer were obtained from the primary site during surgical resection of breast tumors at Stanford Hospital and City of Hope National Medical Center. Samples were mechanically dissociated into < 1-2 mm3 pieces with a razor blade and then digested at 37 oC with 1500 U collagenase and 500 U hyaluronidase in Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM Glutamax (Invitrogen), and an antibiotic/antimycotic mix containing 120 μg/ml penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin-B (PSA) for 4-6 hrs with hourly pipetting for 5 min. After digestion, cells were treated with ACK lysis buffer to deplete red blood cells and then incubated with 10 U dispase to further dissociate the tissue into single cells and 1000 U DNase I to prevent cell clumping. Cells were filtered through a 70 μm nylon mesh and washed with staining buffer containing 2% fetal bovine serum (FBS) and PSA in Hank’s Balanced Salt Solution (HBBS). Single cell suspensions of fresh breast tissue were then stained with fluorescent antibodies to prepare for FACS. To reduce nonspecific antibody binding, single cells were blocked with 10 μg/mL rat IgG on ice for 10 minutes. Cells were then stained, in the dark, on ice for 30 minutes. FACS was performed with a 130 μm nozzle on a BD FACSAria II with BD FACSDiva software. Side scatter and forward scatter profiles (area and width) were used to eliminate debris and cell doublets. Dead cells were eliminated by excluding 4’,6-diamidino-2-phenylindole (DAPI) positive cells. Breast epithelial cells were enriched by negative gating of lineage cells expressing CD45, CD31, CD3, CD16, or CD64. Human breast basal cells were then gated as CD49fhighEPCAMmed-low, luminal progenitors as CD49fhighEPCAMhigh, and mature luminal cells as CD49flowEPCAMhigh. Single human breast cells were then sorted into 96-well plates of lysis buffer.
cDNA libraries were constructed using a modified Smart-seq2 protocol and machine-automated pipeline by the Stanford Functional Genomic Facility (SFGF), as described previously (PMIDs: 24385147 and 30241615). Notably, 27 cycles of PCR amplification were required to obtain cDNA amounts within range of the recommended concentrations (0.05 – 0.32 ng/μL) for downstream tagmentation. Wells with over-amplified cDNA were diluted. Libraries were prepared using the Nextera XT DNA Library Prep (Illumina) kit and sequenced on a NextSeq 500 (Illumina) to obtain 2x76 or 2x151 bp paired-end reads.

tag: patient

tag: clinical subtype

value: Luminal

tag: tissue

value: Tumor

tag: celltype by seurat cluster

value: Mature luminal

tag: er status

tag: pr status

tag: her status


title: A3_023_SU2_T

description:
B12_022_SU2_N_ACTGATCG_AAGGCTAT_S286_R1_001.fastq.gz
B12_022_SU2_N_ACTGATCG_AAGGCTAT_S286_R2_001.fastq.gz


title: G5_022_SU2_N

description:
B12_008_SU20_N_GCTCATGA_TCTTACGC_S275_R1_001.fastq.gz
B12_008_SU20_N_GCTCATGA_TCTTACGC_S275_R2_001.fastq.gz

value: Adjacent normal

value: Luminal progenitor


title: G9_022_SU2_N

description:
B12_018_SU20_N_TAGCTGCA_AAGGCTAT_S287_R1_001.fastq.gz
B12_018_SU20_N_TAGCTGCA_AAGGCTAT_S287_R2_001.fastq.gz


title: G3_022_SU2_N

description:
B12_004_SU2_N_ATGCGCAG_TATGCAGT_S90_R1_001.fastq.gz
B12_004_SU2_N_ATGCGCAG_TATGCAGT_S90_R2_001.fastq.gz

value: Basal


title: G6_022_SU2_N

description:
B12_016_SU20_N_CTGCGCAT_CCTAGAGT_S138_R1_001.fastq.gz
B12_016_SU20_N_CTGCGCAT_CCTAGAGT_S138_R2_001.fastq.gz


title: G10_022_SU2_N

description:
B11_062_COH69_T_GTCTTAGG_GCGTAAGA_S189_R1_001.fastq.gz
B11_062_COH69_T_GTCTTAGG_GCGTAAGA_S189_R2_001.fastq.gz


title: F8_022_SU2_N

description:
B11_061_COH69_T_TCATGAGC_GTAAGGAG_S107_R1_001.fastq.gz
B11_061_COH69_T_TCATGAGC_GTAAGGAG_S107_R2_001.fastq.gz


title: C1_023_SU2_T

description:
B12_043_SU9_T_TAGCTGCA_CTCTCTAT_S23_R1_001.fastq.gz
B12_043_SU9_T_TAGCTGCA_CTCTCTAT_S23_R2_001.fastq.gz


title: F6_022_SU2_N

description:
B11_060_SU21_T_CTAGTACG_GAGCCTTA_S314_R1_001.fastq.gz
B11_060_SU21_T_CTAGTACG_GAGCCTTA_S314_R2_001.fastq.gz


title: F2_022_SU2_N

description:
B11_058_SU21_T_CTGCGCAT_CCTAGAGT_S138_R1_001.fastq.gz
B11_058_SU21_T_CTGCGCAT_CCTAGAGT_S138_R2_001.fastq.gz


title: E7_022_SU2_N

description:
B11_040_SU9_N_TAGCTGCA_CTCTCTAT_S23_R1_001.fastq.gz
B11_040_SU9_N_TAGCTGCA_CTCTCTAT_S23_R2_001.fastq.gz


title: E9_022_SU2_N

description:
B11_043_SU9_T_ACTGATCG_CTCTCTAT_S22_R1_001.fastq.gz
B11_043_SU9_T_ACTGATCG_CTCTCTAT_S22_R2_001.fastq.gz


title: F1_022_SU2_N

description:
B11_051_SU21_N_TCGCCTTA_AAGGAGTA_S193_R1_001.fastq.gz
B11_051_SU21_N_TCGCCTTA_AAGGAGTA_S193_R2_001.fastq.gz


title: E3_022_SU2_N

description:
B11_036_SU17_N_ACTGATCG_GCGTAAGA_S190_R1_001.fastq.gz
B11_036_SU17_N_ACTGATCG_GCGTAAGA_S190_R2_001.fastq.gz


title: E4_022_SU2_N

description:
B11_037_SU17_T_TAGCTGCA_CTCTCTAT_S23_R1_001.fastq.gz
B11_037_SU17_T_TAGCTGCA_CTCTCTAT_S23_R2_001.fastq.gz


title: E12_022_SU2_N

description:
B11_035_SU17_N_GCAGCGTA_GTAAGGAG_S113_R1_001.fastq.gz
B11_035_SU17_N_GCAGCGTA_GTAAGGAG_S113_R2_001.fastq.gz


title: E8_022_SU2_N

description:
B11_041_SU9_N_TACTACGC_GTAAGGAG_S111_R1_001.fastq.gz
B11_041_SU9_N_TACTACGC_GTAAGGAG_S111_R2_001.fastq.gz


title: F3_022_SU2_N

description:
B11_059_SU21_T_TAGCGAGT_CTATTAAG_S229_R1_001.fastq.gz
B11_059_SU21_T_TAGCGAGT_CTATTAAG_S229_R2_001.fastq.gz


title: F11_022_SU2_N

description:
B11_057_SU21_T_CCTGAGAT_TTCTAGCT_S84_R1_001.fastq.gz
B11_057_SU21_T_CCTGAGAT_TTCTAGCT_S84_R2_001.fastq.gz


title: E5_022_SU2_N

description:
B11_038_SU17_T_GCTCAGGA_CTAAGCCT_S244_R1_001.fastq.gz
B11_038_SU17_T_GCTCAGGA_CTAAGCCT_S244_R2_001.fastq.gz


title: D8_022_SU2_N

description:
B11_032_SU4_T_GAGCGCTA_GAGCCTTA_S331_R1_001.fastq.gz
B11_032_SU4_T_GAGCGCTA_GAGCCTTA_S331_R2_001.fastq.gz


title: D6_022_SU2_N

description:
B11_029_SU4_N_CGCTCAGT_TTCTAGCT_S92_R1_001.fastq.gz
B11_029_SU4_N_CGCTCAGT_TTCTAGCT_S92_R2_001.fastq.gz


title: D4_022_SU2_N

description:
B11_028_SU4_N_TTCTGCCT_TCGACTAG_S27_R1_001.fastq.gz
B11_028_SU4_N_TTCTGCCT_TCGACTAG_S27_R2_001.fastq.gz


title: D3_022_SU2_N

description:
B11_023_SU2_T_CAGCCTCG_TCTCTCCG_S344_R1_001.fastq.gz
B11_023_SU2_T_CAGCCTCG_TCTCTCCG_S344_R2_001.fastq.gz


title: F10_022_SU2_N

description:
B11_044_SU9_T_TGCCTCTT_GTAAGGAG_S105_R1_001.fastq.gz
B11_044_SU9_T_TGCCTCTT_GTAAGGAG_S105_R2_001.fastq.gz


title: D2_022_SU2_N

description:
B11_022_SU2_N_GTCTTAGG_AAGGCTAT_S285_R1_001.fastq.gz
B11_022_SU2_N_GTCTTAGG_AAGGCTAT_S285_R2_001.fastq.gz


title: E1_022_SU2_N

description:
B11_034_SU17_N_TAGCTGCA_CTCTCTAT_S23_R1_001.fastq.gz
B11_034_SU17_N_TAGCTGCA_CTCTCTAT_S23_R2_001.fastq.gz


title: D11_022_SU2_N

description:
B11_021_SU20_T_GCTCAGGA_CTATTAAG_S220_R1_001.fastq.gz
B11_021_SU20_T_GCTCAGGA_CTATTAAG_S220_R2_001.fastq.gz


title: D1_022_SU2_N

description:
B11_016_SU20_N_GCAGCGTA_CCTAGAGT_S137_R1_001.fastq.gz
B11_016_SU20_N_GCAGCGTA_CCTAGAGT_S137_R2_001.fastq.gz


title: C9_022_SU2_N

description:
B11_010_SU20_N_TGCAGCTA_TAAGGCTC_S359_R1_001.fastq.gz
B11_010_SU20_N_TGCAGCTA_TAAGGCTC_S359_R2_001.fastq.gz


title: C12_022_SU2_N

description:
B1_054_SU21_N_TAGCGAGT_CTCTCTAT_S13_R1_001.fastq.gz
B1_054_SU21_N_TAGCGAGT_CTCTCTAT_S13_R2_001.fastq.gz


title: C2_022_SU2_N

description:
B1_060_SU21_T_AGGCTCCG_CGTCTAAT_S304_R1_001.fastq.gz
B1_060_SU21_T_AGGCTCCG_CGTCTAAT_S304_R2_001.fastq.gz


title: C5_022_SU2_N

description:
B11_008_SU20_N_GTAGAGGA_TCTTACGC_S274_R1_001.fastq.gz
B11_008_SU20_N_GTAGAGGA_TCTTACGC_S274_R2_001.fastq.gz


title: C4_022_SU2_N

description:
B11_004_SU2_N_TACGCTGC_TATGCAGT_S89_R1_001.fastq.gz
B11_004_SU2_N_TACGCTGC_TATGCAGT_S89_R2_001.fastq.gz


title: C1_022_SU2_N

description:
B1_051_SU21_N_TACTACGC_GCGTAAGA_S183_R1_001.fastq.gz
B1_051_SU21_N_TACTACGC_GCGTAAGA_S183_R2_001.fastq.gz


title: B12_022_SU2_N

description:
B1_044_SU9_T_TAGCTGCA_TTCTAGCT_S95_R1_001.fastq.gz
B1_044_SU9_T_TAGCTGCA_TTCTAGCT_S95_R2_001.fastq.gz


title: B11_022_SU2_N

description:
B1_043_SU9_T_TAGCGAGT_CTCTCTAT_S13_R1_001.fastq.gz
B1_043_SU9_T_TAGCGAGT_CTCTCTAT_S13_R2_001.fastq.gz


title: A2_022_SU2_N

description:
B1_039_SU9_N_CAGCCTCG_GAGCCTTA_S320_R1_001.fastq.gz
B1_039_SU9_N_CAGCCTCG_GAGCCTTA_S320_R2_001.fastq.gz


title: B1_022_SU2_N

description:
B1_041_SU9_N_AGGAGTCC_GTAAGGAG_S101_R1_001.fastq.gz
B1_041_SU9_N_AGGAGTCC_GTAAGGAG_S101_R2_001.fastq.gz


title: G2_019_SU20_T

description:
B1_034_SU17_N_TAGCGAGT_CTCTCTAT_S13_R1_001.fastq.gz
B1_034_SU17_N_TAGCGAGT_CTCTCTAT_S13_R2_001.fastq.gz

value: Pos


title: F6_019_SU20_T

description:
B1_030_SU4_N_GTCTTAGG_ACTGCATA_S165_R1_001.fastq.gz
B1_030_SU4_N_GTCTTAGG_ACTGCATA_S165_R2_001.fastq.gz


title: G1_019_SU20_T

description:
B1_032_SU4_T_TGCCTCTT_GAGCCTTA_S321_R1_001.fastq.gz
B1_032_SU4_T_TGCCTCTT_GAGCCTTA_S321_R2_001.fastq.gz


title: F3_019_SU20_T

description:
B1_022_SU2_N_GAGCGCTA_AAGGCTAT_S283_R1_001.fastq.gz
B1_022_SU2_N_GAGCGCTA_AAGGCTAT_S283_R2_001.fastq.gz


title: F4_019_SU20_T

description:
B1_023_SU2_T_GCTCAGGA_TCTCTCCG_S340_R1_001.fastq.gz
B1_023_SU2_T_GCTCAGGA_TCTCTCCG_S340_R2_001.fastq.gz


title: G3_019_SU20_T

description:
B1_035_SU17_N_GTAGAGAG_GTAAGGAG_S103_R1_001.fastq.gz
B1_035_SU17_N_GTAGAGAG_GTAAGGAG_S103_R2_001.fastq.gz


title: F5_019_SU20_T

description:
B1_028_SU4_N_CTGCGCAT_CTCTCTAT_S18_R1_001.fastq.gz
B1_028_SU4_N_CTGCGCAT_CTCTCTAT_S18_R2_001.fastq.gz


title: E6_019_SU20_T

description:
B1_013_SU20_T_TCATGAGC_CTCTCTAT_S11_R1_001.fastq.gz
B1_013_SU20_T_TCATGAGC_CTCTCTAT_S11_R2_001.fastq.gz


title: C7_022_SU2_N

description:
B11_009_SU20_N_GGAGCTAC_ATAGCCTT_S326_R1_001.fastq.gz
B11_009_SU20_N_GGAGCTAC_ATAGCCTT_S326_R2_001.fastq.gz


title: E4_019_SU20_T

description:
B10_061_COH69_T_TCCTCTAC_GTAAGGAG_S106_R1_001.fastq.gz
B10_061_COH69_T_TCCTCTAC_GTAAGGAG_S106_R2_001.fastq.gz


title: E11_019_SU20_T

description:
B10_054_SU21_N_ACTGATCG_CTCTCTAT_S22_R1_001.fastq.gz
B10_054_SU21_N_ACTGATCG_CTCTCTAT_S22_R2_001.fastq.gz


title: E1_019_SU20_T

description:
B10_052_SU21_N_AGGCTCCG_AAGGCTAT_S280_R1_001.fastq.gz
B10_052_SU21_N_AGGCTCCG_AAGGCTAT_S280_R2_001.fastq.gz


title: E2_019_SU20_T

description:
B10_057_SU21_T_TCATGAGC_TTCTAGCT_S83_R1_001.fastq.gz
B10_057_SU21_T_TCATGAGC_TTCTAGCT_S83_R2_001.fastq.gz


title: F10_019_SU20_T

description:
B1_019_SU20_T_TCATGAGC_TCGACTAG_S35_R1_001.fastq.gz
B1_019_SU20_T_TCATGAGC_TCGACTAG_S35_R2_001.fastq.gz


title: E10_019_SU20_T

description:
B10_051_SU21_N_GACGTCGA_GCGTAAGA_S192_R1_001.fastq.gz
B10_051_SU21_N_GACGTCGA_GCGTAAGA_S192_R2_001.fastq.gz


title: D2_019_SU20_T

description:
B10_044_SU9_T_CAGCCTCG_GTAAGGAG_S104_R1_001.fastq.gz
B10_044_SU9_T_CAGCCTCG_GTAAGGAG_S104_R2_001.fastq.gz


title: D4_019_SU20_T

description:
B1_004_SU2_N_CTCTCTAC_TATGCAGT_S79_R1_001.fastq.gz
B1_004_SU2_N_CTCTCTAC_TATGCAGT_S79_R2_001.fastq.gz


title: C5_019_SU20_T

description:
B10_041_SU9_N_GTAGCTCC_GTAAGGAG_S110_R1_001.fastq.gz
B10_041_SU9_N_GTAGCTCC_GTAAGGAG_S110_R2_001.fastq.gz


title: E3_019_SU20_T

description:
B10_060_SU21_T_TCGCCTTA_GAGCCTTA_S313_R1_001.fastq.gz
B10_060_SU21_T_TCGCCTTA_GAGCCTTA_S313_R2_001.fastq.gz


title: C4_019_SU20_T

description:
B10_040_SU9_N_ACTGATCG_CTCTCTAT_S22_R1_001.fastq.gz
B10_040_SU9_N_ACTGATCG_CTCTCTAT_S22_R2_001.fastq.gz


title: F7_019_SU20_T

description:
B1_031_SU4_T_TAGCGAGT_CTAAGCCT_S253_R1_001.fastq.gz
B1_031_SU4_T_TAGCGAGT_CTAAGCCT_S253_R2_001.fastq.gz


title: C3_019_SU20_T

description:
B10_039_SU9_N_GCAGCGTA_GAGCCTTA_S329_R1_001.fastq.gz
B10_039_SU9_N_GCAGCGTA_GAGCCTTA_S329_R2_001.fastq.gz


title: A11_022_SU2_N

description:
B1_037_SU17_T_TAGCGAGT_CTCTCTAT_S13_R1_001.fastq.gz
B1_037_SU17_T_TAGCGAGT_CTCTCTAT_S13_R2_001.fastq.gz


title: E8_019_SU20_T

description:
B1_017_SU20_N_GCAGCGTA_AAGGAGTA_S209_R1_001.fastq.gz
B1_017_SU20_N_GCAGCGTA_AAGGAGTA_S209_R2_001.fastq.gz


title: F1_019_SU20_T

description:
B1_021_SU20_T_CTGCGCAT_AAGGAGTA_S210_R1_001.fastq.gz
B1_021_SU20_T_CTGCGCAT_AAGGAGTA_S210_R2_001.fastq.gz


title: C1_019_SU20_T

description:
B10_037_SU17_T_ACTGATCG_CTCTCTAT_S22_R1_001.fastq.gz
B10_037_SU17_T_ACTGATCG_CTCTCTAT_S22_R2_001.fastq.gz


title: B8_019_SU20_T

description:
B10_036_SU17_N_GTCTTAGG_GCGTAAGA_S189_R1_001.fastq.gz
B10_036_SU17_N_GTCTTAGG_GCGTAAGA_S189_R2_001.fastq.gz


title: B5_019_SU20_T

description:
B10_035_SU17_N_AGGCTCCG_GTAAGGAG_S112_R1_001.fastq.gz
B10_035_SU17_N_AGGCTCCG_GTAAGGAG_S112_R2_001.fastq.gz


title: B3_019_SU20_T

description:
B10_034_SU17_N_ACTGATCG_CTCTCTAT_S22_R1_001.fastq.gz
B10_034_SU17_N_ACTGATCG_CTCTCTAT_S22_R2_001.fastq.gz


title: A9_019_SU20_T

description:
B10_017_SU20_N_TAGCTGCA_AAGGAGTA_S215_R1_001.fastq.gz
B10_017_SU20_N_TAGCTGCA_AAGGAGTA_S215_R2_001.fastq.gz


title: B1_019_SU20_T

description:
B10_018_SU20_N_GTCTTAGG_AAGGCTAT_S285_R1_001.fastq.gz
B10_018_SU20_N_GTCTTAGG_AAGGCTAT_S285_R2_001.fastq.gz


title: A5_019_SU20_T

description:
B10_013_SU20_T_CGCTCAGT_CTCTCTAT_S20_R1_001.fastq.gz
B10_013_SU20_T_CGCTCAGT_CTCTCTAT_S20_R2_001.fastq.gz


title: A7_019_SU20_T

description:
B10_016_SU20_N_AGGCTCCG_CCTAGAGT_S136_R1_001.fastq.gz
B10_016_SU20_N_AGGCTCCG_CCTAGAGT_S136_R2_001.fastq.gz


title: A4_019_SU20_T

description:
B10_008_SU20_N_AAGAGGCA_TCTTACGC_S273_R1_001.fastq.gz
B10_008_SU20_N_AAGAGGCA_TCTTACGC_S273_R2_001.fastq.gz


title: A2_019_SU20_T

description:
B10_007_SU58_T_CGTACTAG_AGCTAGAA_S218_R1_001.fastq.gz
B10_007_SU58_T_CGTACTAG_AGCTAGAA_S218_R2_001.fastq.gz


title: A12_019_SU20_T

description:
B10_004_SU2_N_CGGAGCCT_TATGCAGT_S88_R1_001.fastq.gz
B10_004_SU2_N_CGGAGCCT_TATGCAGT_S88_R2_001.fastq.gz


title: G7_020_SU20_T

description:
A9_043_SU9_T_TGCCTCTT_CTCTCTAT_S9_R1_001.fastq.gz
A9_043_SU9_T_TGCCTCTT_CTCTCTAT_S9_R2_001.fastq.gz


title: G2_020_SU20_T

description:
A9_040_SU9_N_TGCCTCTT_CTCTCTAT_S9_R1_001.fastq.gz
A9_040_SU9_N_TGCCTCTT_CTCTCTAT_S9_R2_001.fastq.gz


title: F9_020_SU20_T

description:
A9_037_SU17_T_TGCCTCTT_CTCTCTAT_S9_R1_001.fastq.gz
A9_037_SU17_T_TGCCTCTT_CTCTCTAT_S9_R2_001.fastq.gz


title: E9_020_SU20_T

description:
A9_035_SU17_N_TTCTGCCT_GTAAGGAG_S99_R1_001.fastq.gz
A9_035_SU17_N_TTCTGCCT_GTAAGGAG_S99_R2_001.fastq.gz


title: H3_020_SU20_T

description:
A9_054_SU21_N_TGCCTCTT_CTCTCTAT_S9_R1_001.fastq.gz
A9_054_SU21_N_TGCCTCTT_CTCTCTAT_S9_R2_001.fastq.gz


title: H1_020_SU20_T

description:
A9_051_SU21_N_TCATGAGC_GCGTAAGA_S179_R1_001.fastq.gz
A9_051_SU21_N_TCATGAGC_GCGTAAGA_S179_R2_001.fastq.gz


title: E3_020_SU20_T

description:
A9_034_SU17_N_TGCCTCTT_CTCTCTAT_S9_R1_001.fastq.gz
A9_034_SU17_N_TGCCTCTT_CTCTCTAT_S9_R2_001.fastq.gz


title: D6_020_SU20_T

description:
A9_028_SU4_N_TACTACGC_CTCTCTAT_S15_R1_001.fastq.gz
A9_028_SU4_N_TACTACGC_CTCTCTAT_S15_R2_001.fastq.gz


title: E2_020_SU20_T

description:
A9_033_SU4_T_CGCTCAGT_TCTCTCCG_S356_R1_001.fastq.gz
A9_033_SU4_T_CGCTCAGT_TCTCTCCG_S356_R2_001.fastq.gz


title: D4_020_SU20_T

description:
A9_019_SU20_T_GTAGAGAG_TCGACTAG_S31_R1_001.fastq.gz
A9_019_SU20_T_GTAGAGAG_TCGACTAG_S31_R2_001.fastq.gz


title: C8_020_SU20_T

description:
A9_017_SU20_N_GTAGCTCC_AAGGAGTA_S206_R1_001.fastq.gz
A9_017_SU20_N_GTAGCTCC_AAGGAGTA_S206_R2_001.fastq.gz


title: C5_020_SU20_T

description:
A9_016_SU20_N_CATGCCTA_CCTAGAGT_S126_R1_001.fastq.gz
A9_016_SU20_N_CATGCCTA_CCTAGAGT_S126_R2_001.fastq.gz


title: C3_020_SU20_T

description:
A9_013_SU20_T_CAGCCTCG_CTCTCTAT_S8_R1_001.fastq.gz
A9_013_SU20_T_CAGCCTCG_CTCTCTAT_S8_R2_001.fastq.gz


title: B3_020_SU20_T

description:
A9_005_SU2_T_ACTCGCTA_ATTAGACG_S157_R1_001.fastq.gz
A9_005_SU2_T_ACTCGCTA_ATTAGACG_S157_R2_001.fastq.gz


title: B2_020_SU20_T

description:
A9_004_SU2_N_AGGCAGAA_TATGCAGT_S75_R1_001.fastq.gz
A9_004_SU2_N_AGGCAGAA_TATGCAGT_S75_R2_001.fastq.gz


title: B12_020_SU20_T

description:
A8_062_COH69_T_CAGCCTCG_GCGTAAGA_S176_R1_001.fastq.gz
A8_062_COH69_T_CAGCCTCG_GCGTAAGA_S176_R2_001.fastq.gz


title: A7_020_SU20_T

description:
A8_060_SU21_T_TCATGAGC_CGTCTAAT_S299_R1_001.fastq.gz
A8_060_SU21_T_TCATGAGC_CGTCTAAT_S299_R2_001.fastq.gz


title: A11_020_SU20_T

description:
A8_058_SU21_T_AGGAGTCC_CCTAGAGT_S125_R1_001.fastq.gz
A8_058_SU21_T_AGGAGTCC_CCTAGAGT_S125_R2_001.fastq.gz


title: G8_020_SU20_T

description:
A9_044_SU9_T_GAGCGCTA_TTCTAGCT_S91_R1_001.fastq.gz
A9_044_SU9_T_GAGCGCTA_TTCTAGCT_S91_R2_001.fastq.gz


title: H5_021_SU20_T

description:
A8_052_SU21_N_GCTCAGGA_AAGGCTAT_S268_R1_001.fastq.gz
A8_052_SU21_N_GCTCAGGA_AAGGCTAT_S268_R2_001.fastq.gz


title: H4_021_SU20_T

description:
A8_051_SU21_N_TCCTCTAC_GCGTAAGA_S178_R1_001.fastq.gz
A8_051_SU21_N_TCCTCTAC_GCGTAAGA_S178_R2_001.fastq.gz


title: G7_021_SU20_T

description:
A8_043_SU9_T_CAGCCTCG_CTCTCTAT_S8_R1_001.fastq.gz
A8_043_SU9_T_CAGCCTCG_CTCTCTAT_S8_R2_001.fastq.gz


title: G4_021_SU20_T

description:
A8_040_SU9_N_CAGCCTCG_CTCTCTAT_S8_R1_001.fastq.gz
A8_040_SU9_N_CAGCCTCG_CTCTCTAT_S8_R2_001.fastq.gz


title: G2_021_SU20_T

description:
A8_038_SU17_T_TACTACGC_CTATTAAG_S231_R1_001.fastq.gz
A8_038_SU17_T_TACTACGC_CTATTAAG_S231_R2_001.fastq.gz


title: G10_021_SU20_T

description:
A8_035_SU17_N_CTAGTACG_GTAAGGAG_S98_R1_001.fastq.gz
A8_035_SU17_N_CTAGTACG_GTAAGGAG_S98_R2_001.fastq.gz


title: G3_021_SU20_T

description:
A8_039_SU9_N_GCTCAGGA_GAGCCTTA_S316_R1_001.fastq.gz
A8_039_SU9_N_GCTCAGGA_GAGCCTTA_S316_R2_001.fastq.gz


title: G1_021_SU20_T

description:
A8_037_SU17_T_CAGCCTCG_CTCTCTAT_S8_R1_001.fastq.gz
A8_037_SU17_T_CAGCCTCG_CTCTCTAT_S8_R2_001.fastq.gz


title: F9_021_SU20_T

description:
A8_034_SU17_N_CAGCCTCG_CTCTCTAT_S8_R1_001.fastq.gz
A8_034_SU17_N_CAGCCTCG_CTCTCTAT_S8_R2_001.fastq.gz


title: F6_021_SU20_T

description:
A8_031_SU4_T_CAGCCTCG_CTAAGCCT_S248_R1_001.fastq.gz
A8_031_SU4_T_CAGCCTCG_CTAAGCCT_S248_R2_001.fastq.gz


title: F3_021_SU20_T

description:
A8_030_SU4_N_AGGCTCCG_ACTGCATA_S160_R1_001.fastq.gz
A8_030_SU4_N_AGGCTCCG_ACTGCATA_S160_R2_001.fastq.gz


title: E7_019_SU20_T

description:
B1_016_SU20_N_TGCCTCTT_CCTAGAGT_S129_R1_001.fastq.gz
B1_016_SU20_N_TGCCTCTT_CCTAGAGT_S129_R2_001.fastq.gz


title: E8_021_SU20_T

description:
A8_023_SU2_T_TTCTGCCT_TCTCTCCG_S339_R1_001.fastq.gz
A8_023_SU2_T_TTCTGCCT_TCTCTCCG_S339_R2_001.fastq.gz


title: E6_021_SU20_T

description:
A8_016_SU20_N_AGGAGTCC_CCTAGAGT_S125_R1_001.fastq.gz
A8_016_SU20_N_AGGAGTCC_CCTAGAGT_S125_R2_001.fastq.gz


title: E5_021_SU20_T

description:
A8_013_SU20_T_GTAGAGAG_CTCTCTAT_S7_R1_001.fastq.gz
A8_013_SU20_T_GTAGAGAG_CTCTCTAT_S7_R2_001.fastq.gz


title: E7_021_SU20_T

description:
A8_018_SU20_N_GTAGAGAG_AAGGCTAT_S271_R1_001.fastq.gz
A8_018_SU20_N_GTAGAGAG_AAGGCTAT_S271_R2_001.fastq.gz


title: E2_021_SU20_T

description:
A8_004_SU2_N_CGTACTAG_TATGCAGT_S74_R1_001.fastq.gz
A8_004_SU2_N_CGTACTAG_TATGCAGT_S74_R2_001.fastq.gz


title: C2_019_SU20_T

description:
B10_038_SU17_T_TTCTGCCT_CTAAGCCT_S243_R1_001.fastq.gz
B10_038_SU17_T_TTCTGCCT_CTAAGCCT_S243_R2_001.fastq.gz


title: D7_021_SU20_T

description:
A7_061_COH69_T_GTCTTAGG_TTCTAGCT_S93_R1_001.fastq.gz
A7_061_COH69_T_GTCTTAGG_TTCTAGCT_S93_R2_001.fastq.gz


title: H6_021_SU20_T

description:
A8_054_SU21_N_CAGCCTCG_CTCTCTAT_S8_R1_001.fastq.gz
A8_054_SU21_N_CAGCCTCG_CTCTCTAT_S8_R2_001.fastq.gz


title: D6_021_SU20_T

description:
A7_060_SU21_T_TCCTCTAC_CGTCTAAT_S298_R1_001.fastq.gz
A7_060_SU21_T_TCCTCTAC_CGTCTAAT_S298_R2_001.fastq.gz


title: D4_021_SU20_T

description:
A7_057_SU21_T_TTCTGCCT_TTCTAGCT_S75_R1_001.fastq.gz
A7_057_SU21_T_TTCTGCCT_TTCTAGCT_S75_R2_001.fastq.gz


title: C8_021_SU20_T

description:
A7_054_SU21_N_GTAGAGAG_CTCTCTAT_S7_R1_001.fastq.gz
A7_054_SU21_N_GTAGAGAG_CTCTCTAT_S7_R2_001.fastq.gz


title: C6_021_SU20_T

description:
A7_043_SU9_T_GTAGAGAG_CTCTCTAT_S7_R1_001.fastq.gz
A7_043_SU9_T_GTAGAGAG_CTCTCTAT_S7_R2_001.fastq.gz


title: C7_021_SU20_T

description:
A7_044_SU9_T_GCAGCGTA_TTCTAGCT_S89_R1_001.fastq.gz
A7_044_SU9_T_GCAGCGTA_TTCTAGCT_S89_R2_001.fastq.gz


title: C3_021_SU20_T

description:
A7_039_SU9_N_TTCTGCCT_GAGCCTTA_S315_R1_001.fastq.gz
A7_039_SU9_N_TTCTGCCT_GAGCCTTA_S315_R2_001.fastq.gz


title: B7_021_SU20_T

description:
A7_037_SU17_T_GTAGAGAG_CTCTCTAT_S7_R1_001.fastq.gz
A7_037_SU17_T_GTAGAGAG_CTCTCTAT_S7_R2_001.fastq.gz


title: F1_021_SU20_T

description:
A8_028_SU4_N_GTAGCTCC_CTCTCTAT_S14_R1_001.fastq.gz
A8_028_SU4_N_GTAGCTCC_CTCTCTAT_S14_R2_001.fastq.gz


title: B6_021_SU20_T

description:
A7_035_SU17_N_TCGCCTTA_GTAAGGAG_S97_R1_001.fastq.gz
A7_035_SU17_N_TCGCCTTA_GTAAGGAG_S97_R2_001.fastq.gz


title: B4_021_SU20_T

description:
A7_031_SU4_T_GTAGAGAG_CTAAGCCT_S247_R1_001.fastq.gz
A7_031_SU4_T_GTAGAGAG_CTAAGCCT_S247_R2_001.fastq.gz


title: B11_021_SU20_T

description:
A7_029_SU4_N_GCTCAGGA_TTCTAGCT_S76_R1_001.fastq.gz
A7_029_SU4_N_GCTCAGGA_TTCTAGCT_S76_R2_001.fastq.gz


title: B1_021_SU20_T

description:
A7_028_SU4_N_TAGCGAGT_CTCTCTAT_S13_R1_001.fastq.gz
A7_028_SU4_N_TAGCGAGT_CTCTCTAT_S13_R2_001.fastq.gz


title: A5_021_SU20_T

description:
A7_020_SU20_T_ACTGATCG_GTAAGGAG_S118_R1_001.fastq.gz
A7_020_SU20_T_ACTGATCG_GTAAGGAG_S118_R2_001.fastq.gz


title: A11_021_SU20_T

description:
A7_016_SU20_N_GCTCAGGA_CCTAGAGT_S124_R1_001.fastq.gz
A7_016_SU20_N_GCTCAGGA_CCTAGAGT_S124_R2_001.fastq.gz


title: A10_021_SU20_T

description:
A7_008_SU20_N_TGCAGCTA_ACTCTAGG_S263_R1_001.fastq.gz
A7_008_SU20_N_TGCAGCTA_ACTCTAGG_S263_R2_001.fastq.gz


title: G8_003_SU58_T

description:
A7_005_SU2_T_GCTCATGA_ATTAGACG_S155_R1_001.fastq.gz
A7_005_SU2_T_GCTCATGA_ATTAGACG_S155_R2_001.fastq.gz

value: Neg


title: G6_003_SU58_T

description:
A7_004_SU2_N_TAAGGCGA_TATGCAGT_S73_R1_001.fastq.gz
A7_004_SU2_N_TAAGGCGA_TATGCAGT_S73_R2_001.fastq.gz


title: G12_003_SU58_T

description:
A6_062_COH69_T_CATGCCTA_GCGTAAGA_S174_R1_001.fastq.gz
A6_062_COH69_T_CATGCCTA_GCGTAAGA_S174_R2_001.fastq.gz


title: G11_003_SU58_T

description:
A6_060_SU21_T_TGCCTCTT_CGTCTAAT_S297_R1_001.fastq.gz
A6_060_SU21_T_TGCCTCTT_CGTCTAAT_S297_R2_001.fastq.gz


title: C5_021_SU20_T

description:
A7_041_SU9_N_TAGCTGCA_TTCTAGCT_S95_R1_001.fastq.gz
A7_041_SU9_N_TAGCTGCA_TTCTAGCT_S95_R2_001.fastq.gz


title: G10_003_SU58_T

description:
A6_057_SU21_T_CTAGTACG_TTCTAGCT_S74_R1_001.fastq.gz
A6_057_SU21_T_CTAGTACG_TTCTAGCT_S74_R2_001.fastq.gz


title: F9_001_SU58_N

description:
A6_054_SU21_N_CATGCCTA_CTCTCTAT_S6_R1_001.fastq.gz
A6_054_SU21_N_CATGCCTA_CTCTCTAT_S6_R2_001.fastq.gz


title: F8_003_SU58_T

description:
A6_053_SU21_N_CTAGTACG_GAGCCTTA_S314_R1_001.fastq.gz
A6_053_SU21_N_CTAGTACG_GAGCCTTA_S314_R2_001.fastq.gz


title: F7_003_SU58_T

description:
A6_051_SU21_N_CAGCCTCG_GCGTAAGA_S176_R1_001.fastq.gz
A6_051_SU21_N_CAGCCTCG_GCGTAAGA_S176_R2_001.fastq.gz


title: F12_003_SU58_T

description:
A6_044_SU9_T_AGGCTCCG_TTCTAGCT_S88_R1_001.fastq.gz
A6_044_SU9_T_AGGCTCCG_TTCTAGCT_S88_R2_001.fastq.gz


title: E1_020_SU20_T

description:
A9_030_SU4_N_GCAGCGTA_ACTGCATA_S161_R1_001.fastq.gz
A9_030_SU4_N_GCAGCGTA_ACTGCATA_S161_R2_001.fastq.gz


title: C4_021_SU20_T

description:
A7_040_SU9_N_GTAGAGAG_CTCTCTAT_S7_R1_001.fastq.gz
A7_040_SU9_N_GTAGAGAG_CTCTCTAT_S7_R2_001.fastq.gz


title: D8_021_SU20_T

description:
A7_062_COH69_T_GTAGAGAG_GCGTAAGA_S175_R1_001.fastq.gz
A7_062_COH69_T_GTAGAGAG_GCGTAAGA_S175_R2_001.fastq.gz


title: E9_003_SU58_T

description:
A6_036_SU17_N_CCTGAGAT_GCGTAAGA_S180_R1_001.fastq.gz
A6_036_SU17_N_CCTGAGAT_GCGTAAGA_S180_R2_001.fastq.gz


title: A3_021_SU20_T

description:
A7_017_SU20_N_CCTGAGAT_AAGGAGTA_S204_R1_001.fastq.gz
A7_017_SU20_N_CCTGAGAT_AAGGAGTA_S204_R2_001.fastq.gz


title: A4_021_SU20_T

description:
A7_019_SU20_T_AGGAGTCC_TCGACTAG_S29_R1_001.fastq.gz
A7_019_SU20_T_AGGAGTCC_TCGACTAG_S29_R2_001.fastq.gz


title: D11_003_SU58_T

description:
A6_034_SU17_N_CATGCCTA_CTCTCTAT_S6_R1_001.fastq.gz
A6_034_SU17_N_CATGCCTA_CTCTCTAT_S6_R2_001.fastq.gz


title: F10_001_SU58_N

description:
A6_040_SU9_N_CATGCCTA_CTCTCTAT_S6_R1_001.fastq.gz
A6_040_SU9_N_CATGCCTA_CTCTCTAT_S6_R2_001.fastq.gz


title: G5_007_SU58_T

description:
A6_029_SU4_N_TTCTGCCT_TTCTAGCT_S75_R1_001.fastq.gz
A6_029_SU4_N_TTCTGCCT_TTCTAGCT_S75_R2_001.fastq.gz


title: G2_007_SU58_T

description:
A6_028_SU4_N_CCTGAGAT_CTCTCTAT_S12_R1_001.fastq.gz
A6_028_SU4_N_CCTGAGAT_CTCTCTAT_S12_R2_001.fastq.gz


title: G9_007_SU58_T

description:
A6_031_SU4_T_CATGCCTA_CTAAGCCT_S246_R1_001.fastq.gz
A6_031_SU4_T_CATGCCTA_CTAAGCCT_S246_R2_001.fastq.gz


title: G11_007_SU58_T

description:
A6_023_SU2_T_TCGCCTTA_TCTCTCCG_S337_R1_001.fastq.gz
A6_023_SU2_T_TCGCCTTA_TCTCTCCG_S337_R2_001.fastq.gz


title: F11_007_SU58_T

description:
A5_061_COH69_T_GAGCGCTA_TTCTAGCT_S91_R1_001.fastq.gz
A5_061_COH69_T_GAGCGCTA_TTCTAGCT_S91_R2_001.fastq.gz


title: G6_007_SU58_T

description:
A6_030_SU4_N_GTAGCTCC_ACTGCATA_S158_R1_001.fastq.gz
A6_030_SU4_N_GTAGCTCC_ACTGCATA_S158_R2_001.fastq.gz


title: F3_007_SU58_T

description:
A5_062_COH69_T_AGGAGTCC_GCGTAAGA_S173_R1_001.fastq.gz
A5_062_COH69_T_AGGAGTCC_GCGTAAGA_S173_R2_001.fastq.gz


title: G8_021_SU20_T

description:
A8_044_SU9_T_CTGCGCAT_TTCTAGCT_S90_R1_001.fastq.gz
A8_044_SU9_T_CTGCGCAT_TTCTAGCT_S90_R2_001.fastq.gz


title: F9_007_SU58_T

description:
A6_005_SU2_T_GTAGAGGA_ATTAGACG_S154_R1_001.fastq.gz
A6_005_SU2_T_GTAGAGGA_ATTAGACG_S154_R2_001.fastq.gz


title: E9_007_SU58_T

description:
A5_060_SU21_T_CAGCCTCG_CGTCTAAT_S296_R1_001.fastq.gz
A5_060_SU21_T_CAGCCTCG_CGTCTAAT_S296_R2_001.fastq.gz


title: E2_007_SU58_T

description:
A5_054_SU21_N_AGGAGTCC_CTCTCTAT_S5_R1_001.fastq.gz
A5_054_SU21_N_AGGAGTCC_CTCTCTAT_S5_R2_001.fastq.gz


title: E12_007_SU58_T

description:
A5_051_SU21_N_GTAGAGAG_GCGTAAGA_S175_R1_001.fastq.gz
A5_051_SU21_N_GTAGAGAG_GCGTAAGA_S175_R2_001.fastq.gz


title: G10_007_SU58_T

description:
A6_016_SU20_N_TTCTGCCT_CCTAGAGT_S123_R1_001.fastq.gz
A6_016_SU20_N_TTCTGCCT_CCTAGAGT_S123_R2_001.fastq.gz


title: F10_003_SU58_T

description:
A6_043_SU9_T_CATGCCTA_CTCTCTAT_S6_R1_001.fastq.gz
A6_043_SU9_T_CATGCCTA_CTCTCTAT_S6_R2_001.fastq.gz


title: E11_007_SU58_T

description:
A5_044_SU9_T_TACTACGC_TTCTAGCT_S87_R1_001.fastq.gz
A5_044_SU9_T_TACTACGC_TTCTAGCT_S87_R2_001.fastq.gz


title: E8_003_SU58_T

description:
A6_035_SU17_N_GACGTCGA_TTCTAGCT_S96_R1_001.fastq.gz
A6_035_SU17_N_GACGTCGA_TTCTAGCT_S96_R2_001.fastq.gz


title: D5_007_SU58_T

description:
A5_040_SU9_N_AGGAGTCC_CTCTCTAT_S5_R1_001.fastq.gz
A5_040_SU9_N_AGGAGTCC_CTCTCTAT_S5_R2_001.fastq.gz


title: D2_007_SU58_T

description:
A5_038_SU17_T_CCTGAGAT_CTATTAAG_S228_R1_001.fastq.gz
A5_038_SU17_T_CCTGAGAT_CTATTAAG_S228_R2_001.fastq.gz


title: D11_007_SU58_T

description:
A5_037_SU17_T_AGGAGTCC_CTCTCTAT_S5_R1_001.fastq.gz
A5_037_SU17_T_AGGAGTCC_CTCTCTAT_S5_R2_001.fastq.gz


title: D6_007_SU58_T

description:
A5_042_SU9_T_TCATGAGC_GCGTAAGA_S179_R1_001.fastq.gz
A5_042_SU9_T_TCATGAGC_GCGTAAGA_S179_R2_001.fastq.gz


title: D10_007_SU58_T

description:
A5_035_SU17_N_TAGCTGCA_TTCTAGCT_S95_R1_001.fastq.gz
A5_035_SU17_N_TAGCTGCA_TTCTAGCT_S95_R2_001.fastq.gz


title: C9_007_SU58_T

description:
A5_034_SU17_N_AGGAGTCC_CTCTCTAT_S5_R1_001.fastq.gz
A5_034_SU17_N_AGGAGTCC_CTCTCTAT_S5_R2_001.fastq.gz


title: C6_007_SU58_T

description:
A5_031_SU4_T_AGGAGTCC_CTAAGCCT_S245_R1_001.fastq.gz
A5_031_SU4_T_AGGAGTCC_CTAAGCCT_S245_R2_001.fastq.gz


title: D12_019_SU20_T

description:
B10_043_SU9_T_GTCTTAGG_CTCTCTAT_S21_R1_001.fastq.gz
B10_043_SU9_T_GTCTTAGG_CTCTCTAT_S21_R2_001.fastq.gz


title: C4_007_SU58_T

description:
A5_030_SU4_N_TAGCGAGT_ACTGCATA_S157_R1_001.fastq.gz
A5_030_SU4_N_TAGCGAGT_ACTGCATA_S157_R2_001.fastq.gz


title: C2_007_SU58_T

description:
A5_023_SU2_T_GACGTCGA_GAGCCTTA_S336_R1_001.fastq.gz
A5_023_SU2_T_GACGTCGA_GAGCCTTA_S336_R2_001.fastq.gz


title: C11_007_SU58_T

description:
A5_019_SU20_T_TTCTGCCT_TCGACTAG_S27_R1_001.fastq.gz
A5_019_SU20_T_TTCTGCCT_TCGACTAG_S27_R2_001.fastq.gz


title: B9_007_SU58_T

description:
A5_017_SU20_N_TCCTCTAC_AAGGAGTA_S202_R1_001.fastq.gz
A5_017_SU20_N_TCCTCTAC_AAGGAGTA_S202_R2_001.fastq.gz


title: E4_007_SU58_T

description:
A5_057_SU21_T_TCGCCTTA_TTCTAGCT_S73_R1_001.fastq.gz
A5_057_SU21_T_TCGCCTTA_TTCTAGCT_S73_R2_001.fastq.gz


title: B10_007_SU58_T

description:
A5_015_SU20_T_TTCTGCCT_TTCTAGCT_S75_R1_001.fastq.gz
A5_015_SU20_T_TTCTGCCT_TTCTAGCT_S75_R2_001.fastq.gz


title: G9_008_SU20_N

description:
A5_013_SU20_T_AGGAGTCC_CTCTCTAT_S5_R1_001.fastq.gz
A5_013_SU20_T_AGGAGTCC_CTCTCTAT_S5_R2_001.fastq.gz


title: G6_008_SU20_N

description:
A4_062_COH69_T_GCTCAGGA_GCGTAAGA_S172_R1_001.fastq.gz
A4_062_COH69_T_GCTCAGGA_GCGTAAGA_S172_R2_001.fastq.gz


title: G8_008_SU20_N

description:
A5_005_SU2_T_AAGAGGCA_ATTAGACG_S153_R1_001.fastq.gz
A5_005_SU2_T_AAGAGGCA_ATTAGACG_S153_R2_001.fastq.gz


title: E10_007_SU58_T

description:
A5_043_SU9_T_AGGAGTCC_CTCTCTAT_S5_R1_001.fastq.gz
A5_043_SU9_T_AGGAGTCC_CTCTCTAT_S5_R2_001.fastq.gz


title: G2_008_SU20_N

description:
A4_052_SU21_N_GACGTCGA_CTAAGCCT_S264_R1_001.fastq.gz
A4_052_SU21_N_GACGTCGA_CTAAGCCT_S264_R2_001.fastq.gz


title: G11_008_SU20_N

description:
A4_051_SU21_N_CATGCCTA_GCGTAAGA_S174_R1_001.fastq.gz
A4_051_SU21_N_CATGCCTA_GCGTAAGA_S174_R2_001.fastq.gz


title: G3_008_SU20_N

description:
A4_054_SU21_N_GCTCAGGA_CTCTCTAT_S4_R1_001.fastq.gz
A4_054_SU21_N_GCTCAGGA_CTCTCTAT_S4_R2_001.fastq.gz


title: D1_007_SU58_T

description:
A5_036_SU17_N_TCATGAGC_GCGTAAGA_S179_R1_001.fastq.gz
A5_036_SU17_N_TCATGAGC_GCGTAAGA_S179_R2_001.fastq.gz


title: G10_008_SU20_N

description:
A4_043_SU9_T_GCTCAGGA_CTCTCTAT_S4_R1_001.fastq.gz
A4_043_SU9_T_GCTCAGGA_CTCTCTAT_S4_R2_001.fastq.gz


title: F7_008_SU20_N

description:
A4_039_SU9_N_GACGTCGA_CGTCTAAT_S312_R1_001.fastq.gz
A4_039_SU9_N_GACGTCGA_CGTCTAAT_S312_R2_001.fastq.gz


title: G7_008_SU20_N

description:
A5_004_SU2_N_TGCAGCTA_CTCCTTAC_S71_R1_001.fastq.gz
A5_004_SU2_N_TGCAGCTA_CTCCTTAC_S71_R2_001.fastq.gz


title: D1_008_SU20_N

description:
A4_035_SU17_N_ACTGATCG_TTCTAGCT_S94_R1_001.fastq.gz
A4_035_SU17_N_ACTGATCG_TTCTAGCT_S94_R2_001.fastq.gz


title: C9_008_SU20_N

description:
A4_034_SU17_N_GCTCAGGA_CTCTCTAT_S4_R1_001.fastq.gz
A4_034_SU17_N_GCTCAGGA_CTCTCTAT_S4_R2_001.fastq.gz


title: C8_008_SU20_N

description:
A4_031_SU4_T_GCTCAGGA_CTAAGCCT_S244_R1_001.fastq.gz
A4_031_SU4_T_GCTCAGGA_CTAAGCCT_S244_R2_001.fastq.gz


title: C12_007_SU58_T

description:
A5_021_SU20_T_TCCTCTAC_AAGGAGTA_S202_R1_001.fastq.gz
A5_021_SU20_T_TCCTCTAC_AAGGAGTA_S202_R2_001.fastq.gz


title: C3_007_SU58_T

description:
A5_029_SU4_N_CTAGTACG_TTCTAGCT_S74_R1_001.fastq.gz
A5_029_SU4_N_CTAGTACG_TTCTAGCT_S74_R2_001.fastq.gz


title: C7_008_SU20_N

description:
A4_021_SU20_T_TGCCTCTT_AAGGAGTA_S201_R1_001.fastq.gz
A4_021_SU20_T_TGCCTCTT_AAGGAGTA_S201_R2_001.fastq.gz


title: F11_008_SU20_N

description:
A4_036_SU17_N_TCCTCTAC_GCGTAAGA_S178_R1_001.fastq.gz
A4_036_SU17_N_TCCTCTAC_GCGTAAGA_S178_R2_001.fastq.gz


title: C3_008_SU20_N

description:
A4_013_SU20_T_GCTCAGGA_CTCTCTAT_S4_R1_001.fastq.gz
A4_013_SU20_T_GCTCAGGA_CTCTCTAT_S4_R2_001.fastq.gz


title: C4_008_SU20_N

description:
A4_016_SU20_N_TCGCCTTA_CCTAGAGT_S121_R1_001.fastq.gz
A4_016_SU20_N_TCGCCTTA_CCTAGAGT_S121_R2_001.fastq.gz


title: C2_008_SU20_N

description:
A4_008_SU20_N_CGATCAGT_ACTCTAGG_S262_R1_001.fastq.gz
A4_008_SU20_N_CGATCAGT_ACTCTAGG_S262_R2_001.fastq.gz


title: C12_008_SU20_N

description:
A4_005_SU2_T_CGAGGCTG_ATTAGACG_S152_R1_001.fastq.gz
A4_005_SU2_T_CGAGGCTG_ATTAGACG_S152_R2_001.fastq.gz


title: C10_008_SU20_N

description:
A3_061_COH69_T_GCAGCGTA_TTCTAGCT_S89_R1_001.fastq.gz
A3_061_COH69_T_GCAGCGTA_TTCTAGCT_S89_R2_001.fastq.gz


title: C11_008_SU20_N

description:
A3_062_COH69_T_TTCTGCCT_GCGTAAGA_S171_R1_001.fastq.gz
A3_062_COH69_T_TTCTGCCT_GCGTAAGA_S171_R2_001.fastq.gz


title: C1_021_SU20_T

description:
A7_038_SU17_T_GTAGCTCC_CTATTAAG_S230_R1_001.fastq.gz
A7_038_SU17_T_GTAGCTCC_CTATTAAG_S230_R2_001.fastq.gz


title: F8_008_SU20_N

description:
A4_041_SU9_N_CGCTCAGT_TTCTAGCT_S92_R1_001.fastq.gz
A4_041_SU9_N_CGCTCAGT_TTCTAGCT_S92_R2_001.fastq.gz


title: B3_008_SU20_N

description:
A3_052_SU21_N_TAGCTGCA_CTAAGCCT_S263_R1_001.fastq.gz
A3_052_SU21_N_TAGCTGCA_CTAAGCCT_S263_R2_001.fastq.gz


title: B12_008_SU20_N

description:
A3_043_SU9_T_TTCTGCCT_CTCTCTAT_S3_R1_001.fastq.gz
A3_043_SU9_T_TTCTGCCT_CTCTCTAT_S3_R2_001.fastq.gz


title: B11_008_SU20_N

description:
A3_041_SU9_N_GAGCGCTA_TTCTAGCT_S91_R1_001.fastq.gz
A3_041_SU9_N_GAGCGCTA_TTCTAGCT_S91_R2_001.fastq.gz


title: B9_008_SU20_N

description:
A3_060_SU21_T_CATGCCTA_CGTCTAAT_S294_R1_001.fastq.gz
A3_060_SU21_T_CATGCCTA_CGTCTAAT_S294_R2_001.fastq.gz


title: B10_008_SU20_N

description:
A3_040_SU9_N_TTCTGCCT_CTCTCTAT_S3_R1_001.fastq.gz
A3_040_SU9_N_TTCTGCCT_CTCTCTAT_S3_R2_001.fastq.gz


title: C5_008_SU20_N

description:
A4_018_SU20_N_TTCTGCCT_AAGGCTAT_S267_R1_001.fastq.gz
A4_018_SU20_N_TTCTGCCT_AAGGCTAT_S267_R2_001.fastq.gz


title: B4_008_SU20_N

description:
A3_054_SU21_N_TTCTGCCT_CTCTCTAT_S3_R1_001.fastq.gz
A3_054_SU21_N_TTCTGCCT_CTCTCTAT_S3_R2_001.fastq.gz


title: C6_008_SU20_N

description:
A4_019_SU20_T_CTAGTACG_TCGACTAG_S26_R1_001.fastq.gz
A4_019_SU20_T_CTAGTACG_TCGACTAG_S26_R2_001.fastq.gz


title: A9_008_SU20_N

description:
A3_039_SU9_N_TAGCTGCA_CGTCTAAT_S311_R1_001.fastq.gz
A3_039_SU9_N_TAGCTGCA_CGTCTAAT_S311_R2_001.fastq.gz


title: A7_008_SU20_N

description:
A3_038_SU17_T_TCCTCTAC_CTATTAAG_S226_R1_001.fastq.gz
A3_038_SU17_T_TCCTCTAC_CTATTAAG_S226_R2_001.fastq.gz


title: A10_008_SU20_N

description:
A3_034_SU17_N_TTCTGCCT_CTCTCTAT_S3_R1_001.fastq.gz
A3_034_SU17_N_TTCTGCCT_CTCTCTAT_S3_R2_001.fastq.gz


title: A11_008_SU20_N

description:
A3_035_SU17_N_GTCTTAGG_TTCTAGCT_S93_R1_001.fastq.gz
A3_035_SU17_N_GTCTTAGG_TTCTAGCT_S93_R2_001.fastq.gz


title: G4_009_SU20_N

description:
A3_032_SU4_T_GCTCAGGA_GAGCCTTA_S316_R1_001.fastq.gz
A3_032_SU4_T_GCTCAGGA_GAGCCTTA_S316_R2_001.fastq.gz


title: A4_008_SU20_N

description:
A3_036_SU17_N_TGCCTCTT_GCGTAAGA_S177_R1_001.fastq.gz
A3_036_SU17_N_TGCCTCTT_GCGTAAGA_S177_R2_001.fastq.gz


title: G3_009_SU20_N

description:
A3_031_SU4_T_TTCTGCCT_CTAAGCCT_S243_R1_001.fastq.gz
A3_031_SU4_T_TTCTGCCT_CTAAGCCT_S243_R2_001.fastq.gz


title: G10_009_SU20_N

description:
A3_028_SU4_N_TGCCTCTT_CTCTCTAT_S9_R1_001.fastq.gz
A3_028_SU4_N_TGCCTCTT_CTCTCTAT_S9_R2_001.fastq.gz


title: F8_009_SU20_N

description:
A3_023_SU2_T_TAGCTGCA_GAGCCTTA_S335_R1_001.fastq.gz
A3_023_SU2_T_TAGCTGCA_GAGCCTTA_S335_R2_001.fastq.gz


title: B2_008_SU20_N

description:
A3_051_SU21_N_AGGAGTCC_GCGTAAGA_S173_R1_001.fastq.gz
A3_051_SU21_N_AGGAGTCC_GCGTAAGA_S173_R2_001.fastq.gz


title: E7_009_SU20_N

description:
A3_013_SU20_T_TTCTGCCT_CTCTCTAT_S3_R1_001.fastq.gz
A3_013_SU20_T_TTCTGCCT_CTCTCTAT_S3_R2_001.fastq.gz


title: F1_009_SU20_N

description:
A3_017_SU20_N_TGCCTCTT_AAGGAGTA_S201_R1_001.fastq.gz
A3_017_SU20_N_TGCCTCTT_AAGGAGTA_S201_R2_001.fastq.gz


title: F7_009_SU20_N

description:
A3_021_SU20_T_CAGCCTCG_AAGGAGTA_S200_R1_001.fastq.gz
A3_021_SU20_T_CAGCCTCG_AAGGAGTA_S200_R2_001.fastq.gz


title: E5_009_SU20_N

description:
A3_010_SU20_N_TAGCGCTC_TAAGGCTC_S355_R1_001.fastq.gz
A3_010_SU20_N_TAGCGCTC_TAAGGCTC_S355_R2_001.fastq.gz


title: E8_009_SU20_N

description:
A3_016_SU20_N_GACGTCGA_GTAAGGAG_S120_R1_001.fastq.gz
A3_016_SU20_N_GACGTCGA_GTAAGGAG_S120_R2_001.fastq.gz


title: E11_009_SU20_N

description:
A3_004_SU2_N_CCTAAGAC_CTCCTTAC_S69_R1_001.fastq.gz
A3_004_SU2_N_CCTAAGAC_CTCCTTAC_S69_R2_001.fastq.gz


title: D6_009_SU20_N

description:
A2_060_SU21_T_AGGAGTCC_CGTCTAAT_S293_R1_001.fastq.gz
A2_060_SU21_T_AGGAGTCC_CGTCTAAT_S293_R2_001.fastq.gz


title: E2_009_SU20_N

description:
A3_005_SU2_T_CTCTCTAC_ATTAGACG_S151_R1_001.fastq.gz
A3_005_SU2_T_CTCTCTAC_ATTAGACG_S151_R2_001.fastq.gz


title: D4_009_SU20_N

description:
A2_054_SU21_N_CTAGTACG_CTCTCTAT_S2_R1_001.fastq.gz
A2_054_SU21_N_CTAGTACG_CTCTCTAT_S2_R2_001.fastq.gz


title: D1_009_SU20_N

description:
A2_052_SU21_N_ACTGATCG_CTAAGCCT_S262_R1_001.fastq.gz
A2_052_SU21_N_ACTGATCG_CTAAGCCT_S262_R2_001.fastq.gz


title: B5_021_SU20_T

description:
A7_034_SU17_N_GTAGAGAG_CTCTCTAT_S7_R1_001.fastq.gz
A7_034_SU17_N_GTAGAGAG_CTCTCTAT_S7_R2_001.fastq.gz


title: D7_009_SU20_N

description:
A2_061_COH69_T_AGGCTCCG_TTCTAGCT_S88_R1_001.fastq.gz
A2_061_COH69_T_AGGCTCCG_TTCTAGCT_S88_R2_001.fastq.gz


title: D5_009_SU20_N

description:
A2_057_SU21_T_GACGTCGA_TATCCTCT_S72_R1_001.fastq.gz
A2_057_SU21_T_GACGTCGA_TATCCTCT_S72_R2_001.fastq.gz


title: A1_019_SU20_T

description:
A9_060_SU21_T_CCTGAGAT_CGTCTAAT_S300_R1_001.fastq.gz
A9_060_SU21_T_CCTGAGAT_CGTCTAAT_S300_R2_001.fastq.gz


title: F7_010_SU20_N

description:
A2_034_SU17_N_CTAGTACG_CTCTCTAT_S2_R1_001.fastq.gz
A2_034_SU17_N_CTAGTACG_CTCTCTAT_S2_R2_001.fastq.gz


title: C9_009_SU20_N

description:
A2_043_SU9_T_CTAGTACG_CTCTCTAT_S2_R1_001.fastq.gz
A2_043_SU9_T_CTAGTACG_CTCTCTAT_S2_R2_001.fastq.gz


title: C3_009_SU20_N

description:
A2_040_SU9_N_CTAGTACG_CTCTCTAT_S2_R1_001.fastq.gz
A2_040_SU9_N_CTAGTACG_CTCTCTAT_S2_R2_001.fastq.gz


title: C7_009_SU20_N

description:
A2_041_SU9_N_CTGCGCAT_TTCTAGCT_S90_R1_001.fastq.gz
A2_041_SU9_N_CTGCGCAT_TTCTAGCT_S90_R2_001.fastq.gz


title: F6_010_SU20_N

description:
A2_031_SU4_T_CTAGTACG_CTAAGCCT_S242_R1_001.fastq.gz
A2_031_SU4_T_CTAGTACG_CTAAGCCT_S242_R2_001.fastq.gz


title: B4_009_SU20_N

description:
A2_039_SU9_N_ACTGATCG_CGTCTAAT_S310_R1_001.fastq.gz
A2_039_SU9_N_ACTGATCG_CGTCTAAT_S310_R2_001.fastq.gz


title: B11_009_SU20_N

description:
A2_035_SU17_N_CGCTCAGT_TTCTAGCT_S92_R1_001.fastq.gz
A2_035_SU17_N_CGCTCAGT_TTCTAGCT_S92_R2_001.fastq.gz


title: F3_009_SU20_N

description:
A3_018_SU20_N_CTAGTACG_AAGGCTAT_S266_R1_001.fastq.gz
A3_018_SU20_N_CTAGTACG_AAGGCTAT_S266_R2_001.fastq.gz


title: C2_020_SU20_T

description:
A9_008_SU20_N_TAAGGCGA_TCTTACGC_S265_R1_001.fastq.gz
A9_008_SU20_N_TAAGGCGA_TCTTACGC_S265_R2_001.fastq.gz


title: F4_010_SU20_N

description:
A2_030_SU4_N_TCATGAGC_ACTGCATA_S155_R1_001.fastq.gz
A2_030_SU4_N_TCATGAGC_ACTGCATA_S155_R2_001.fastq.gz


title: E6_010_SU20_N

description:
A2_022_SU2_N_AGGCTCCG_AAGGCTAT_S280_R1_001.fastq.gz
A2_022_SU2_N_AGGCTCCG_AAGGCTAT_S280_R2_001.fastq.gz


title: E8_010_SU20_N

description:
A2_028_SU4_N_CAGCCTCG_CTCTCTAT_S8_R1_001.fastq.gz
A2_028_SU4_N_CAGCCTCG_CTCTCTAT_S8_R2_001.fastq.gz


title: E5_010_SU20_N

description:
A2_019_SU20_T_GACGTCGA_CTCTCTAT_S24_R1_001.fastq.gz
A2_019_SU20_T_GACGTCGA_CTCTCTAT_S24_R2_001.fastq.gz


title: E3_010_SU20_N

description:
A2_018_SU20_N_TCGCCTTA_AAGGCTAT_S265_R1_001.fastq.gz
A2_018_SU20_N_TCGCCTTA_AAGGCTAT_S265_R2_001.fastq.gz


title: D8_010_SU20_N

description:
A2_016_SU20_N_TAGCTGCA_GTAAGGAG_S119_R1_001.fastq.gz
A2_016_SU20_N_TAGCTGCA_GTAAGGAG_S119_R2_001.fastq.gz


title: C8_010_SU20_N

description:
A12_054_SU21_N_CCTGAGAT_CTCTCTAT_S12_R1_001.fastq.gz
A12_054_SU21_N_CCTGAGAT_CTCTCTAT_S12_R2_001.fastq.gz


title: B9_010_SU20_N

description:
A12_051_SU21_N_GTAGCTCC_GCGTAAGA_S182_R1_001.fastq.gz
A12_051_SU21_N_GTAGCTCC_GCGTAAGA_S182_R2_001.fastq.gz


title: C7_010_SU20_N

description:
A12_053_SU21_N_CAGCCTCG_GAGCCTTA_S320_R1_001.fastq.gz
A12_053_SU21_N_CAGCCTCG_GAGCCTTA_S320_R2_001.fastq.gz


title: B7_010_SU20_N

description:
A12_044_SU9_T_ACTGATCG_TTCTAGCT_S94_R1_001.fastq.gz
A12_044_SU9_T_ACTGATCG_TTCTAGCT_S94_R2_001.fastq.gz


title: B6_010_SU20_N

description:
A12_043_SU9_T_CCTGAGAT_CTCTCTAT_S12_R1_001.fastq.gz
A12_043_SU9_T_CCTGAGAT_CTCTCTAT_S12_R2_001.fastq.gz


title: F7_021_SU20_T

description:
A8_032_SU4_T_GTAGAGAG_GAGCCTTA_S319_R1_001.fastq.gz
A8_032_SU4_T_GTAGAGAG_GAGCCTTA_S319_R2_001.fastq.gz


title: G9_004_SU2_N

description:
A12_039_SU9_N_GTAGAGAG_GAGCCTTA_S319_R1_001.fastq.gz
A12_039_SU9_N_GTAGAGAG_GAGCCTTA_S319_R2_001.fastq.gz


title: A3_010_SU20_N

description:
A12_040_SU9_N_CCTGAGAT_CTCTCTAT_S12_R1_001.fastq.gz
A12_040_SU9_N_CCTGAGAT_CTCTCTAT_S12_R2_001.fastq.gz


title: B11_010_SU20_N

description:
A12_041_SU9_N_GCTCAGGA_GTAAGGAG_S100_R1_001.fastq.gz
A12_041_SU9_N_GCTCAGGA_GTAAGGAG_S100_R2_001.fastq.gz


title: E12_010_SU20_N

description:
A2_017_SU20_N_CAGCCTCG_AAGGAGTA_S200_R1_001.fastq.gz
A2_017_SU20_N_CAGCCTCG_AAGGAGTA_S200_R2_001.fastq.gz


title: D7_010_SU20_N

description:
A2_004_SU2_N_ACTGAGCG_CTCCTTAC_S68_R1_001.fastq.gz
A2_004_SU2_N_ACTGAGCG_CTCCTTAC_S68_R2_001.fastq.gz


title: G8_004_SU2_N

description:
A12_035_SU17_N_CATGCCTA_GTAAGGAG_S102_R1_001.fastq.gz
A12_035_SU17_N_CATGCCTA_GTAAGGAG_S102_R2_001.fastq.gz


title: F12_010_SU20_N

description:
A2_029_SU4_N_TAGCTGCA_TATCCTCT_S71_R1_001.fastq.gz
A2_029_SU4_N_TAGCTGCA_TATCCTCT_S71_R2_001.fastq.gz


title: G6_004_SU2_N

description:
A12_034_SU17_N_CCTGAGAT_CTCTCTAT_S12_R1_001.fastq.gz
A12_034_SU17_N_CCTGAGAT_CTCTCTAT_S12_R2_001.fastq.gz


title: G5_004_SU2_N

description:
A12_030_SU4_N_CGCTCAGT_ACTGCATA_S164_R1_001.fastq.gz
A12_030_SU4_N_CGCTCAGT_ACTGCATA_S164_R2_001.fastq.gz


title: F4_005_SU2_T

description:
A12_016_SU20_N_CAGCCTCG_CCTAGAGT_S128_R1_001.fastq.gz
A12_016_SU20_N_CAGCCTCG_CCTAGAGT_S128_R2_001.fastq.gz


title: G12_004_SU2_N

description:
A12_028_SU4_N_GCAGCGTA_CTCTCTAT_S17_R1_001.fastq.gz
A12_028_SU4_N_GCAGCGTA_CTCTCTAT_S17_R2_001.fastq.gz


title: G10_004_SU2_N

description:
A12_019_SU20_T_TCCTCTAC_TCGACTAG_S34_R1_001.fastq.gz
A12_019_SU20_T_TCCTCTAC_TCGACTAG_S34_R2_001.fastq.gz


title: F2_005_SU2_T

description:
A11_060_SU21_T_GTAGCTCC_CGTCTAAT_S302_R1_001.fastq.gz
A11_060_SU21_T_GTAGCTCC_CGTCTAAT_S302_R2_001.fastq.gz


title: E9_005_SU2_T

description:
A11_054_SU21_N_TCATGAGC_CTCTCTAT_S11_R1_001.fastq.gz
A11_054_SU21_N_TCATGAGC_CTCTCTAT_S11_R2_001.fastq.gz


title: F3_005_SU2_T

description:
A12_004_SU2_N_TAGGCATG_TATGCAGT_S78_R1_001.fastq.gz
A12_004_SU2_N_TAGGCATG_TATGCAGT_S78_R2_001.fastq.gz


title: F1_005_SU2_T

description:
A11_057_SU21_T_AGGAGTCC_TTCTAGCT_S77_R1_001.fastq.gz
A11_057_SU21_T_AGGAGTCC_TTCTAGCT_S77_R2_001.fastq.gz


title: E7_005_SU2_T

description:
A11_041_SU9_N_TTCTGCCT_GTAAGGAG_S99_R1_001.fastq.gz
A11_041_SU9_N_TTCTGCCT_GTAAGGAG_S99_R2_001.fastq.gz


title: D3_010_SU20_N

description:
A12_060_SU21_T_TACTACGC_CGTCTAAT_S303_R1_001.fastq.gz
A12_060_SU21_T_TACTACGC_CGTCTAAT_S303_R2_001.fastq.gz


title: E6_005_SU2_T

description:
A11_040_SU9_N_TCATGAGC_CTCTCTAT_S11_R1_001.fastq.gz
A11_040_SU9_N_TCATGAGC_CTCTCTAT_S11_R2_001.fastq.gz


title: E3_005_SU2_T

description:
A11_037_SU17_T_TCATGAGC_CTCTCTAT_S11_R1_001.fastq.gz
A11_037_SU17_T_TCATGAGC_CTCTCTAT_S11_R2_001.fastq.gz


title: E2_005_SU2_T

description:
A11_036_SU17_N_TAGCGAGT_GCGTAAGA_S181_R1_001.fastq.gz
A11_036_SU17_N_TAGCGAGT_GCGTAAGA_S181_R2_001.fastq.gz


title: E8_005_SU2_T

description:
A11_044_SU9_T_GTCTTAGG_TTCTAGCT_S93_R1_001.fastq.gz
A11_044_SU9_T_GTCTTAGG_TTCTAGCT_S93_R2_001.fastq.gz


title: D8_005_SU2_T

description:
A11_034_SU17_N_TCATGAGC_CTCTCTAT_S11_R1_001.fastq.gz
A11_034_SU17_N_TCATGAGC_CTCTCTAT_S11_R2_001.fastq.gz


title: D6_005_SU2_T

description:
A11_031_SU4_T_TCATGAGC_CTAAGCCT_S251_R1_001.fastq.gz
A11_031_SU4_T_TCATGAGC_CTAAGCCT_S251_R2_001.fastq.gz


title: D5_005_SU2_T

description:
A11_030_SU4_N_GAGCGCTA_ACTGCATA_S163_R1_001.fastq.gz
A11_030_SU4_N_GAGCGCTA_ACTGCATA_S163_R2_001.fastq.gz


title: E1_005_SU2_T

description:
A11_035_SU17_N_AGGAGTCC_GTAAGGAG_S101_R1_001.fastq.gz
A11_035_SU17_N_AGGAGTCC_GTAAGGAG_S101_R2_001.fastq.gz


title: D2_005_SU2_T

description:
A11_020_SU20_T_CTAGTACG_CCTAGAGT_S122_R1_001.fastq.gz
A11_020_SU20_T_CTAGTACG_CCTAGAGT_S122_R2_001.fastq.gz


title: D1_005_SU2_T

description:
A11_013_SU20_T_TCCTCTAC_CTCTCTAT_S10_R1_001.fastq.gz
A11_013_SU20_T_TCCTCTAC_CTCTCTAT_S10_R2_001.fastq.gz


title: D3_005_SU2_T

description:
A11_022_SU2_N_CTGCGCAT_AAGGCTAT_S282_R1_001.fastq.gz
A11_022_SU2_N_CTGCGCAT_AAGGCTAT_S282_R2_001.fastq.gz


title: C9_004_SU2_N

description:
A11_008_SU20_N_AGGCAGAA_TCTTACGC_S267_R1_001.fastq.gz
A11_008_SU20_N_AGGCAGAA_TCTTACGC_S267_R2_001.fastq.gz


title: D2_004_SU2_N

description:
A11_016_SU20_N_GTAGAGAG_CCTAGAGT_S127_R1_001.fastq.gz
A11_016_SU20_N_GTAGAGAG_CCTAGAGT_S127_R2_001.fastq.gz


title: C8_005_SU2_T

description:
A11_004_SU2_N_GGACTCCT_TATGCAGT_S77_R1_001.fastq.gz
A11_004_SU2_N_GGACTCCT_TATGCAGT_S77_R2_001.fastq.gz


title: C7_005_SU2_T

description:
A1_054_SU21_N_TCGCCTTA_CTCTCTAT_S1_R1_001.fastq.gz
A1_054_SU21_N_TCGCCTTA_CTCTCTAT_S1_R2_001.fastq.gz


title: C4_005_SU2_T

description:
A1_051_SU21_N_TTCTGCCT_GCGTAAGA_S171_R1_001.fastq.gz
A1_051_SU21_N_TTCTGCCT_GCGTAAGA_S171_R2_001.fastq.gz


title: C7_004_SU2_N

description:
A1_052_SU21_N_GTCTTAGG_CTAAGCCT_S261_R1_001.fastq.gz
A1_052_SU21_N_GTCTTAGG_CTAAGCCT_S261_R2_001.fastq.gz


title: C8_004_SU2_N

description:
A1_059_SU21_T_AGGCTCCG_AAGGAGTA_S208_R1_001.fastq.gz
A1_059_SU21_T_AGGCTCCG_AAGGAGTA_S208_R2_001.fastq.gz


title: C3_005_SU2_T

description:
A1_043_SU9_T_TCGCCTTA_CTCTCTAT_S1_R1_001.fastq.gz
A1_043_SU9_T_TCGCCTTA_CTCTCTAT_S1_R2_001.fastq.gz


title: C2_004_SU2_N

description:
A1_040_SU9_N_TCGCCTTA_CTCTCTAT_S1_R1_001.fastq.gz
A1_040_SU9_N_TCGCCTTA_CTCTCTAT_S1_R2_001.fastq.gz


title: C12_004_SU2_N

description:
A1_039_SU9_N_GTCTTAGG_CGTCTAAT_S309_R1_001.fastq.gz
A1_039_SU9_N_GTCTTAGG_CGTCTAAT_S309_R2_001.fastq.gz


title: C10_004_SU2_N

description:
A1_031_SU4_T_TCGCCTTA_CTAAGCCT_S241_R1_001.fastq.gz
A1_031_SU4_T_TCGCCTTA_CTAAGCCT_S241_R2_001.fastq.gz


title: C3_004_SU2_N

description:
A1_041_SU9_N_GCAGCGTA_TTCTAGCT_S89_R1_001.fastq.gz
A1_041_SU9_N_GCAGCGTA_TTCTAGCT_S89_R2_001.fastq.gz


title: C11_004_SU2_N

description:
A1_035_SU17_N_GAGCGCTA_TTCTAGCT_S91_R1_001.fastq.gz
A1_035_SU17_N_GAGCGCTA_TTCTAGCT_S91_R2_001.fastq.gz


title: C1_004_SU2_N

description:
A1_034_SU17_N_TCGCCTTA_CTCTCTAT_S1_R1_001.fastq.gz
A1_034_SU17_N_TCGCCTTA_CTCTCTAT_S1_R2_001.fastq.gz


title: B9_004_SU2_N

description:
A1_029_SU4_N_ACTGATCG_TATCCTCT_S70_R1_001.fastq.gz
A1_029_SU4_N_ACTGATCG_TATCCTCT_S70_R2_001.fastq.gz


title: B9_005_SU2_T

description:
A1_030_SU4_N_TCCTCTAC_ACTGCATA_S154_R1_001.fastq.gz
A1_030_SU4_N_TCCTCTAC_ACTGCATA_S154_R2_001.fastq.gz


title: B6_005_SU2_T

description:
A1_028_SU4_N_GTAGAGAG_CTCTCTAT_S7_R1_001.fastq.gz
A1_028_SU4_N_GTAGAGAG_CTCTCTAT_S7_R2_001.fastq.gz


title: B6_004_SU2_N

description:
A1_023_SU2_T_ACTGATCG_GAGCCTTA_S334_R1_001.fastq.gz
A1_023_SU2_T_ACTGATCG_GAGCCTTA_S334_R2_001.fastq.gz


title: B5_005_SU2_T

description:
A1_019_SU20_T_TAGCTGCA_CTCTCTAT_S23_R1_001.fastq.gz
A1_019_SU20_T_TAGCTGCA_CTCTCTAT_S23_R2_001.fastq.gz


title: B4_005_SU2_T

description:
A1_017_SU20_N_GTAGAGAG_AAGGAGTA_S199_R1_001.fastq.gz
A1_017_SU20_N_GTAGAGAG_AAGGAGTA_S199_R2_001.fastq.gz


title: B5_004_SU2_N

description:
A1_018_SU20_N_GACGTCGA_CTAAGCCT_S264_R1_001.fastq.gz
A1_018_SU20_N_GACGTCGA_CTAAGCCT_S264_R2_001.fastq.gz


title: D3_004_SU2_N

description:
A11_021_SU20_T_AGGCTCCG_AAGGAGTA_S208_R1_001.fastq.gz
A11_021_SU20_T_AGGCTCCG_AAGGAGTA_S208_R2_001.fastq.gz


title: B2_005_SU2_T

description:
A10_061_COH69_T_GACGTCGA_TTCTAGCT_S96_R1_001.fastq.gz
A10_061_COH69_T_GACGTCGA_TTCTAGCT_S96_R2_001.fastq.gz


title: B2_004_SU2_N

description:
A10_060_SU21_T_TAGCGAGT_CGTCTAAT_S301_R1_001.fastq.gz
A10_060_SU21_T_TAGCGAGT_CGTCTAAT_S301_R2_001.fastq.gz


title: B3_004_SU2_N

description:
A1_013_SU20_T_TCGCCTTA_CTCTCTAT_S1_R1_001.fastq.gz
A1_013_SU20_T_TCGCCTTA_CTCTCTAT_S1_R2_001.fastq.gz


title: B3_005_SU2_T

description:
A1_016_SU20_N_ACTGATCG_GTAAGGAG_S118_R1_001.fastq.gz
A1_016_SU20_N_ACTGATCG_GTAAGGAG_S118_R2_001.fastq.gz


title: B12_004_SU2_N

description:
A1_005_SU2_T_TAGGCATG_ATTAGACG_S150_R1_001.fastq.gz
A1_005_SU2_T_TAGGCATG_ATTAGACG_S150_R2_001.fastq.gz


title: B11_004_SU2_N

description:
A10_058_SU21_T_GTAGAGAG_CCTAGAGT_S127_R1_001.fastq.gz
A10_058_SU21_T_GTAGAGAG_CCTAGAGT_S127_R2_001.fastq.gz


title: A9_004_SU2_N

description:
A1_004_SU2_N_TAGCGCTC_CTCCTTAC_S67_R1_001.fastq.gz
A1_004_SU2_N_TAGCGCTC_CTCCTTAC_S67_R2_001.fastq.gz


title: A8_004_SU2_N

description:
A10_044_SU9_T_CGCTCAGT_TTCTAGCT_S92_R1_001.fastq.gz
A10_044_SU9_T_CGCTCAGT_TTCTAGCT_S92_R2_001.fastq.gz


title: B10_004_SU2_N

description:
A10_054_SU21_N_TCCTCTAC_CTCTCTAT_S10_R1_001.fastq.gz
A10_054_SU21_N_TCCTCTAC_CTCTCTAT_S10_R2_001.fastq.gz


title: A9_005_SU2_T

description:
A10_051_SU21_N_CCTGAGAT_GCGTAAGA_S180_R1_001.fastq.gz
A10_051_SU21_N_CCTGAGAT_GCGTAAGA_S180_R2_001.fastq.gz


title: A6_005_SU2_T

description:
A10_041_SU9_N_CTAGTACG_GTAAGGAG_S98_R1_001.fastq.gz
A10_041_SU9_N_CTAGTACG_GTAAGGAG_S98_R2_001.fastq.gz


title: A7_004_SU2_N

description:
A10_042_SU9_T_AGGCTCCG_GCGTAAGA_S184_R1_001.fastq.gz
A10_042_SU9_T_AGGCTCCG_GCGTAAGA_S184_R2_001.fastq.gz


title: A5_005_SU2_T

description:
A10_040_SU9_N_TCCTCTAC_CTCTCTAT_S10_R1_001.fastq.gz
A10_040_SU9_N_TCCTCTAC_CTCTCTAT_S10_R2_001.fastq.gz


title: A4_005_SU2_T

description:
A10_037_SU17_T_TCCTCTAC_CTCTCTAT_S10_R1_001.fastq.gz
A10_037_SU17_T_TCCTCTAC_CTCTCTAT_S10_R2_001.fastq.gz


title: A2_004_SU2_N

description:
A10_030_SU4_N_CTGCGCAT_ACTGCATA_S162_R1_001.fastq.gz
A10_030_SU4_N_CTGCGCAT_ACTGCATA_S162_R2_001.fastq.gz


title: A3_004_SU2_N

description:
A10_031_SU4_T_TCCTCTAC_CTAAGCCT_S250_R1_001.fastq.gz
A10_031_SU4_T_TCCTCTAC_CTAAGCCT_S250_R2_001.fastq.gz


title: A12_004_SU2_N

description:
A10_029_SU4_N_GTAGAGAG_TTCTAGCT_S79_R1_001.fastq.gz
A10_029_SU4_N_GTAGAGAG_TTCTAGCT_S79_R2_001.fastq.gz


title: A3_005_SU2_T

description:
A10_034_SU17_N_TCCTCTAC_CTCTCTAT_S10_R1_001.fastq.gz
A10_034_SU17_N_TCCTCTAC_CTCTCTAT_S10_R2_001.fastq.gz


title: A1_004_SU2_N

description:
A10_008_SU20_N_CGTACTAG_TCTTACGC_S266_R1_001.fastq.gz
A10_008_SU20_N_CGTACTAG_TCTTACGC_S266_R2_001.fastq.gz


title: A11_004_SU2_N

description:
A10_021_SU20_T_TACTACGC_AAGGAGTA_S207_R1_001.fastq.gz
A10_021_SU20_T_TACTACGC_AAGGAGTA_S207_R2_001.fastq.gz


title: A1_005_SU2_T

description:
A10_015_SU20_T_GCTCAGGA_TTCTAGCT_S76_R1_001.fastq.gz
A10_015_SU20_T_GCTCAGGA_TTCTAGCT_S76_R2_001.fastq.gz


title: A10_004_SU2_N

description:
A10_004_SU2_N_TCCTGAGC_TATGCAGT_S76_R1_001.fastq.gz
A10_004_SU2_N_TCCTGAGC_TATGCAGT_S76_R2_001.fastq.gz


title: T076F

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: Female, age 59, Hispanic, diabetic

data_processing:
Raw sequence data was processed by the on-instrument Real Time Analysis software (v.2.4.11) to basecall files.
Basecall files were converted to de-multiplexed FASTQ files with the Illumina supplied scripts in the BCL2FASTQ software (v2.17).
The quality of reads was determined with the FASTQC software to evaluate per base sequence quality, duplication rates, and overrepresented k-mers.
Illumina adapters were trimmed from the ends of the reads using the Trim Galore! Package.
Reads were aligned to the human reference genome (hg19) with the STAR aligner (v2.5.0a).
Gene count quantification was performed using the GeneCounts function within STAR against the GENCODE v19 human transcript .gtf file.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is a matrix of raw counts per gene for every gene in the GENCODE v19 gtf file as computed by the STAR GeneCounts Function.

source_name: Juxta-anastomotic AVF

growth_protocol: Not applicable

extract_protocol:
RNAlater-preserved samples were ground in liquid nitrogen and isolated with Trizol (Thermo Fisher Scientific) followed by column purification (EZNA Total RNA Kit I, Omega Bio-tek).
500 ng of total RNA was used as input for the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero to generate ribosomal RNA-depleted sequencing libraries. Each sample had a unique barcode to allow multiplexing, and was sequenced to >40 million raw reads in a single end 75 bp sequencing run on the Illumina NextSeq500.

treatment_protocol: Not applicable

tag: individual

value: Patient 19

tag: outcome

value: Failed


title: B1_004_SU2_N

description:
A10_057_SU21_T_GCTCAGGA_TTCTAGCT_S76_R1_001.fastq.gz
A10_057_SU21_T_GCTCAGGA_TTCTAGCT_S76_R2_001.fastq.gz


title: T036F

description: Female, age 62, non-Hispanic Black, diabetic

value: Patient 16


title: T027F

description: Female, age 67, non-Hispanic Black, non-diabetic

value: Patient 15


title: T073M

description: Male, age 49, Hispanic, diabetic

value: Patient 12


title: T389M

description: Male, age 40, non-Hispanic Black, diabetic

value: Patient 14


title: T372M

description: Male, age 85, Hispanic, diabetic

value: Patient 13


title: T390F

description: Female, age 65, Hispanic, diabetic

value: Patient 11

value: Matured


title: A7_005_SU2_T

description:
A10_043_SU9_T_TCCTCTAC_CTCTCTAT_S10_R1_001.fastq.gz
A10_043_SU9_T_TCCTCTAC_CTCTCTAT_S10_R2_001.fastq.gz

value: Luminal


title: T173M

description: Male, age 62, Hispanic, non-diabetic

value: Patient 21 (no vein pair)


title: T394F

description: Female, age 60, non-Hispanic Black, diabetic

value: Patient 10


title: T382F

description: Female, age 42, non-Hispanic Black, non-diabetic

value: Patient 9


title: T072M

description: Male, age 80, non-Hispanic Black, non-diabetic

value: Patient 5


title: T362M

description: Male, age 66, non-Hispanic Black, diabetic

value: Patient 6


title: T052M

description: Male, age 81, Hispanic, non-diabetic

value: Patient 4


title: T093F

description: Female, age 23, Hispanic, non-diabetic

value: Patient 7


title: T171F

description: Female, age 67, non-Hispanic Black, diabetic

value: Patient 8


title: A5_004_SU2_N

description:
A10_039_SU9_N_CATGCCTA_GAGCCTTA_S318_R1_001.fastq.gz
A10_039_SU9_N_CATGCCTA_GAGCCTTA_S318_R2_001.fastq.gz

value: Adjacent normal

value: Basal


title: B2_019_SU20_T

description:
B10_030_SU4_N_CATGCCTA_GCGTAAGA_S174_R1_001.fastq.gz
B10_030_SU4_N_CATGCCTA_GCGTAAGA_S174_R2_001.fastq.gz

value: Tumor

value: Luminal progenitor

value: Pos


title: T024M

description: Male, age 51, non-Hispanic Black, no diabetes

value: Patient 2


title: V013F

source_name: Basilic vein

value: Patient 16

value: Failed


title: V062F

description: Female, age 59, Hispanic, diabetic

value: Patient 19


title: T039M

description: Male, age 46, Hispanic, diabetic

value: Patient 20 (no vein pair)

value: Matured


title: T032M

description: Male, age 45, non-Hispanic Black, diabetes

value: Patient 1


title: V058F

description: Female, age 58, non-Hispanic Black, diabetic

value: Patient 18


title: V056M

description: Male, age 49, Hispanic, diabetic

value: Patient 12


title: V011F

value: Patient 15


title: T071F


title: V165M

description: Male, age 85, Hispanic, diabetic

value: Patient 13


title: V399F

description: Female, age 65, Hispanic, diabetic

value: Patient 11


title: V401M

value: Patient 14


title: V167M

value: Patient 6


title: V385F

value: Patient 9


title: V066F

description: Female, age 23, Hispanic, non-diabetic

value: Patient 7


title: V035M

description: Male, age 81, Hispanic, non-diabetic

value: Patient 4


title: V155F

value: Patient 8


title: V390F

value: Patient 10


title: V006M

description: Male, age 45, non-Hispanic Black, diabetic


title: V015M

description: Male, age 57, non-Hispanic Black, non-diabetic

value: Patient 3 (no AVF pair)


title: V012M

description: Male, age 51, non-Hispanic Black, non-diabetic

value: Patient 2


title: V034F

description: Female, age 79, non-Hispanic Black, non-diabetic

value: Patient 17 (no AVF pair)

value: Failed


title: D20_TGFb_3

city: Bruce

first: Reena

last: Ghildyal

state: ACT

address: Kirinari St

country: Australia

institute: University of Canberra

data_processing:
QC was performed with the fastQC tool
Sequenced reads were trimmed using the Trimmomatic tool (Lohse et al, 2012), then mapped to hg19 whole genome using Rsubread (Y et al, 2013).
Genome_build: hg19
Supplementary_files_format_and_content: raw counts and voom normalized

source_name: WI-38 cell line

extract_protocol:
Media was removed from cells and RNA was harvested using Trizol reagent. New England Biolabs Ultra Directional RNA library Prep Kit (Cat# E7420) was used with 1ug of total RNA for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: WI-38 fibroblast cell line

tag: passages

value: 5 to 6


title: D20_TGFb_1


title: D20_TGFb_2


title: D20_noTGFb_3


title: D20_noTGFb_2


title: E18.5 placenta/decidua female 144hr polyIC4

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1340 Jefferson Park Ave

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
cutadapt v1.15 (--nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 15)
STAR aligner v2.5.4
unitas v1.7.3 (–species_miR_only –species mus_musculus)
Genome_build: mm10
Supplementary_files_format_and_content: unitas miR and tRF count file (decimal come from fractionated reads if multi-mapping happens)

organism: Mus musculus

growth_protocol: C57BL/6 mice were obtained from Taconic Biosciences and housed in specific pathogen-free conditions.

extract_protocol:
Embryonic tissues were harvested for individual fetal mouse at indicated time points relative to the E12.5 injection and snap frozen for storage at -80°C. RNA was purified from homogenized tissues with Trizol Reagent (Invitrogen) according to manufacturer's protocol.
Small RNA-sequencing libraries were prepared following NEBNext Small RNA library kit (NEB #E7300). Briefly, 0.2-1 μg total RNA was ligated with 3’ pre-adenylated adaptors and then 5’ adaptors. After reverse transcription and PCR amplification with indexed-adaptors, each library was size selected on 8% TBE-PAGE gel to enrich for 15-50 nt insert.

treatment_protocol: Each pregnant dam was weighed and administered 20mg/kg poly(I:C) potassium salt (Millipore Sigma) or saline by i.p. injections on both E11.5 and E12.5.

tag: strain

tag: tissue type

value: placenta/decidua

tag: Sex

value: female

tag: time point


title: D1_noTGFb_3

value: 2 to 3


title: D20_noTGFb_1


title: D1_noTGFb_2


title: D1_noTGFb_1


title: D1_TGFb_2


title: E18.5 placenta/decidua female 144hr control4


title: D1_TGFb_1


title: E18.5 placenta/decidua female 144hr control3


title: E18.5 placenta/decidua male 144hr control3

value: male


title: E18.5 placenta/decidua female 144hr control2


title: E18.5 placenta/decidua female 144hr polyIC2


title: E18.5 placenta/decidua male 144hr control4


title: V063M

value: Patient 5

value: Matured


title: E18.5 placenta/decidua male 144hr polyIC2


title: E18.5 placenta/decidua male 144hr polyIC3


title: E18.5 placenta/decidua male 144hr polyIC4


title: E18.5 placenta/decidua female 144hr control1


title: E18.5 placenta/decidua male 144hr control2


title: E18.5 placenta/decidua female 144hr polyIC1


title: E14.5 placenta/decidua female 48hr control3


title: E14.5 placenta/decidua male 48hr control3


title: D1_TGFb_3


title: E18.5 placenta/decidua male 144hr control1


title: E14.5 placenta/decidua female 48hr polyIC1


title: E14.5 placenta/decidua male 48hr polyIC3


title: E14.5 placenta/decidua female 48hr polyIC3


title: E14.5 placenta/decidua male 48hr polyIC2


title: E14.5 placenta/decidua female 48hr polyIC2


title: E14.5 placenta/decidua male 48hr control1


title: E18.5 placenta/decidua female 144hr polyIC3


title: E18.5 placenta/decidua male 144hr polyIC1


title: E13.5 placenta/decidua female 24hr control3


title: E14.5 placenta/decidua female 48hr control2


title: E14.5 placenta/decidua male 48hr control2


title: E14.5 placenta/decidua male 48hr polyIC1


title: E13.5 placenta/decidua male 24hr polyIC2


title: E14.5 placenta/decidua female 48hr control1


title: E13.5 placenta/decidua female 24hr polyIC3


title: E13.5 placenta/decidua male 24hr polyIC3


title: E13.5 placenta/decidua male 24hr control2


title: E13.5 placenta/decidua female 24hr polyIC2


title: E13.5 placenta/decidua male 24hr control1


title: E13.5 placenta/decidua female 24hr control2


title: E13.5 placenta/decidua male 24hr polyIC1


title: E13.5 placenta/decidua female 24hr control1


title: E12.5 placenta/decidua male 12hr polyIC2


title: E12.5 placenta/decidua male 12hr control2


title: E12.5 placenta/decidua male 12hr polyIC1


title: E12.5 placenta/decidua female 12hr polyIC1


title: E12.5 placenta/decidua female 12hr control2


title: E12.5 placenta/decidua male 12hr control1


title: E12.5 placenta/decidua male 6hr polyIC3

source_name: E12.5 placenta/decidua male 6hr polyIC3


title: E12.5 placenta/decidua female 12hr control1


title: E12.5 placenta/decidua female 6hr polyIC3


title: E12.5 placenta/decidua male 6hr control3


title: E12.5 placenta/decidua female 6hr control3


title: E13.5 placenta/decidua female 24hr polyIC1


title: E12.5 placenta/decidua female 6hr polyIC2


title: E12.5 placenta/decidua female 6hr control2


title: E13.5 placenta/decidua male 24hr control3


title: E12.5 placenta/decidua male 6hr polyIC2

source_name: E12.5 placenta/decidua male 6hr polyIC2


title: E12.5 placenta/decidua female 6hr control1


title: E12.5 placenta/decidua male 6hr polyIC1

source_name: E12.5 placenta/decidua male 6hr polyIC1


title: E12.5 placenta/decidua female 6hr polyIC1


title: E12.5 placenta/decidua male 6hr control1


title: E12.5 placenta/decidua male 3hr polyIC3

source_name: E12.5 placenta/decidua male 3hr polyIC3


title: E12.5 placenta/decidua female 12hr polyIC2


title: E12.5 placenta/decidua female 3hr polyIC3


title: E12.5 placenta/decidua female 3hr control3


title: E12.5 placenta/decidua female 3hr polyIC2


title: E12.5 placenta/decidua male 3hr control3


title: E12.5 placenta/decidua female 3hr control2


title: E12.5 placenta/decidua male 3hr polyIC2

source_name: E12.5 placenta/decidua male 3hr polyIC2


title: E12.5 placenta/decidua male 3hr control2


title: E12.5 placenta/decidua male 3hr polyIC1

source_name: E12.5 placenta/decidua male 3hr polyIC1


title: E12.5 placenta/decidua female 3hr control1


title: E12.5 placenta/decidua male 3hr control1


title: E13.5 fetal liver female control3

source_name: E13.5 fetal liver female control3

value: fetal liver


title: E12.5 placenta/decidua male 6hr control2


title: E13.5 fetal liver male control2

source_name: E13.5 fetal liver male control2


title: E13.5 fetal liver male control3

source_name: E13.5 fetal liver male control3


title: E13.5 fetal brain male control3

source_name: E13.5 fetal brain male control3

value: fetal brain


title: E13.5 fetal liver male control1

source_name: E13.5 fetal liver male control1


title: E13.5 fetal liver female control1

source_name: E13.5 fetal liver female control1


title: E13.5 fetal brain male control2

source_name: E13.5 fetal brain male control2


title: E13.5 fetal brain female control2

source_name: E13.5 fetal brain female control2


title: E13.5 fetal brain male control1

source_name: E13.5 fetal brain male control1


title: E13.5 fetal brain female control1

source_name: E13.5 fetal brain female control1


title: E12.5 placenta/decidua female 3hr polyIC1


title: E13.5 fetal liver female control2

source_name: E13.5 fetal liver female control2


title: E13.5 fetal brain female control3

source_name: E13.5 fetal brain female control3


title: SJMMNORM048218 [WT_female_day20]

city: Memphis

first: Jackowski

last: Suzanne

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to the genome using STAR 2.5.2b
Genome_build: Mus musculus GRCm38.p5
Supplementary_files_format_and_content: STAR raw gene count output
column 1: gene ID
column 2: counts for unstranded RNA-seq
column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes)
column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)
column 4 is used for further analysis in upcoming manuscript

source_name: wild type_female_day20

extract_protocol:
Organs were quickly excised from euthanized animals and immediately flash frozen in liquid nitrogen (LN2)
Libraries were prepared according to TruSeq Stranded mRNA from Illumina.

tag: strain background

tag: genotype/variation

value: wild type

value: Back left brain

tag: day


title: SJMMNORM048220 [WT_male_day20]

source_name: wild type_male_day20


title: SJMMNORM048215 [WT_male_day10]

source_name: wild type_male_day10


title: SJMMNORM048221 [WT_male_day20]


title: SJMMNORM048219 [WT_male_day20]


title: SJMMNORM048214 [WT_male_day10]


title: SJMMNORM048213 [WT_male_day10]


title: SJMMNORM048217 [WT_female_day20]


title: SJMMNORM048212 [WT_female_day10]

source_name: wild type_female_day10


title: SJMMNORM048216 [WT_female_day20]


title: SJMMNORM048211 [WT_female_day10]


title: 3.0 Gy irradiated , biological rep1

type: RNA

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the robust multichip average (RMA) method, using the statistical language R (R-3.3.2) and Bioconductor 3.3.

label: biotin

source_name: Whole blood from a mouse 24h after 3.0 Gy irradiation

label_protocol: Biotinylated cRNA was obtained from 200 ng of purified total RNA using a GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated and purified using RNeasy Protect Animal Blood Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Collected whole blood sample was immediately treated with RNAprotect Animal Blood Tube (QIAGEN, Hilden, Germany) according to the manufacturer's protocol.

tag: gender

value: Female

value: Whole blood

tag: age

value: 8 weeks

tag: treatment

value: 3.0 Gy irradiated


title: 3.0 Gy irradiated , biological rep4

tag: tissue


title: 0.5 Gy irradiated , biological rep3

source_name: Whole blood from a mouse 24h after 0.5 Gy irradiation

value: 0.5 Gy irradiated


title: 0.5 Gy irradiated , biological rep1


title: 3.0 Gy irradiated , biological rep2


title: 0.5 Gy irradiated , biological rep4


title: Control, biological rep5

source_name: Whole blood from a control mouse 24h after 0 Gy irradiation

value: Control


title: 1.0 Gy irradiated , biological rep3

source_name: Whole blood from a mouse 24h after 1.0 Gy irradiation

value: 1.0 Gy irradiated


title: SJMMNORM048210 [WT_female_day10]


title: SJMMPKAN048209 [KO_male_day20]

value: Pank1-/-Syn-Pank2-/- double knockout mice (dKO)


title: Control, biological rep2


title: SJMMPKAN048207 [KO_male_day20]


title: SJMMPKAN048205 [KO_female_day20]

value: female


title: SJMMPKAN048206 [KO_female_day20]


title: 1.0 Gy irradiated , biological rep2


title: Control, biological rep1


title: SJMMPKAN048208 [KO_male_day20]


title: SJMMPKAN048203 [KO_male_day10]


title: SJMMPKAN048202 [KO_male_day10]


title: Control, biological rep4


title: SJMMPKAN048200 [KO_female_day10]


title: SJMMPKAN048199 [KO_female_day10]


title: Control, biological rep3


title: 3.0 Gy irradiated , biological rep3


title: 0.5 Gy irradiated , biological rep2


title: 1.0 Gy irradiated , biological rep4


title: 1.0 Gy irradiated , biological rep1


title: SJMMPKAN048198 [KO_female_day10]


title: c-Kit+ NK (2)

city: Seoul

first: Chang-Yuil

last: Kang

address: 29-102, Seoul National University, Shillim-dong, Gwanak-gu

country: South Korea

institute: Seoul National University

description: c-Kit NK.txt

data_processing:
Illumina HCS 2.2.70 software used for sequencing and base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic 0.32, then mapped to mm10 whole genome using HISAT2 version 2.0.5 and Bowtie2 2.2.6.
Transcripts were assembled and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated using StringTie version 1.3.3b.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Spleen

extract_protocol:
Total RNAs were extracted using Trizol (Invitrogen) plus Rneasy micro kit (Qiagen). SMARTer Ultra Low Input RNA Kit (Clontech) was used for cDNA synthesis and amplification.
NGS libraries were prepared with a TruSeq RNA Library Prep Kit (Illumina).

value: BALB/c

value: Spleen

tag: cell phenotype


title: c-Kit-CD24- NK (2)

description: c-Kit&CD24 NK.txt

source_name: Bone marrow

value: Bone marrow


title: c-Kit+ NK (1)

description: c-Kit NK.txt


title: c-Kit+CD24+ NK (2)

description: c-Kit&CD24 NK.txt


title: c-Kit+CD24+ NK (1)

description: c-Kit&CD24 NK.txt


title: SJMMPKAN048204 [KO_female_day20]


title: c-Kit- NK (1)

description: c-Kit NK.txt


title: c-Kit- NK (2)

description: c-Kit NK.txt


title: SJMMPKAN048201 [KO_male_day10]

value: male


title: 43-Oligo

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

data_processing:
Total RNA was sequenced on Illumina HiSeq 2500 (1x50 base paire, single-read). For the base-calling, Illumina Bal2fastq program, version 1.8.4 was used
Sequence reads were aligned to the mouse mm10 reference genome using TopHat 2.1.0.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated with Cufflinks version 2.2.1.0 and normalized expression levels were determined by Cuffnorm version 2.2.1.1
Significant changes in transcript expression were determined with Cuffdiff version 2.2.1.3
Genome_build: mus musculus mm10 (GRCm38)
Supplementary_files_format_and_content: RNA-Seq

growth_protocol: Naïve CD4 T cells were cultured with plate-bound anti-CD3e(10ug/ml) and anti-CD28(1ug/ml) and Th17 polarizing cytokines (IL-6 20ng/ml, TGFb1 2.5ng/ml, IL-23 10ng/ml) for 48h

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing according to Illumina's instructions

treatment_protocol: vehicle (DMSO) or oligomycin (2.5ng/ml)

value: Oligo


title: 43-DMSO

value: DMSO


title: 17-Oligo


title: 17-DMSO


title: 42-Oligo


title: c-Kit+CD24+ NK 24h M-Med

description: c-Kit&CD24 NK.txt

value: 20ng/ml IL-3, 20ng/ml IL-6, 50ng/ml SCF for 24hours


title: c-Kit-CD24- NK (1)

description: c-Kit&CD24 NK.txt


title: c-Kit+ NK 24h GM

description: c-Kit NK.txt

value: 20ng/ml GM-CSF for 24hours


title: 42-DMSO


title: monocytes for Patient EMG-EC-057

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

description:
RNA-seq sample from a HIV-1 controller
rawcounts and TPM

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline.
STAR and RSEM were used to align to HG38 and to calculate the raw counts for genes, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and TPM in csv

source_name: monocytes

growth_protocol: ALL patient samples used for the RNAseq analysis were obtained ex vivo without any in vitro culture

extract_protocol:
Total RNA was extracted from the 4 cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 550 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the GRCh38 human genome database.

treatment_protocol: There is no treatment for the patient samples used in the RNAseq study.

value: peripheral blood

tag: cohort

value: NonNeut


title: monocytes for Patient EMG-EC-059

value: Neut


title: monocytes for Patient EMG-EC-055


title: monocytes for Patient EMG-EC-060


title: monocytes for Patient EMG-EC-058


title: snouty/wt E9.5 rep3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: mixture of probe for wt1 and wt2 against 3rd replicate of snouty

hyb_protocol: Slides were hybridized with a mixture of Cy3 and Cy5 labeled aRNA probes. Hybridizations were performed at 63C overnight under standard conditions (3X SSC, 0.2 mg/ml salmon sperm DNA, 25 mM HEPES, 0.25% SDS) and slides were washed at room temperature successively with 0.6X SSC/0.03% SDS and then 0.06X SSC prior to scanning.

scan_protocol: Microarray images were acquired with a GenePix 4000B scanner (Axon Instruments, Foster City, CA). For image analysis GenePix pro 6.0 software was used (Axon Instruments).

data_processing: Data files were uploaded to Acuity version 4.0 (Molecular Devices), where the raw data were log-transformed, normalized using Lowess normalization, filtered for quality spots (RgnR2[635/532]>0.5; F532median - B532 >= 150; F635median - B635 >= 150; problematic or flagged spots removed). Mean values from dye-swap experiments were used for further analysis. Oligonucleotide probes were mapped to genes and transcripts defined in Flybase (version FB2009_07, r5.20, released August 10, 2009) (http://flybase.org/) (Tweedie et al. 2009).

source_name: E9.5 Embryo,snouty3

label_protocol: Concentration and quality of RNA were determined on the Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA). For array analysis, labeled aRNA was prepared starting with ≤ 1 µg of total RNA using the Amino Allyl MessageAmp II aRNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) according to the manufacturer’s specifications.  5 µg amino allyl-modified aRNA was coupled with Cy dyes (CyDye Post-Labeling Reactive Dye Pack, GE Heathcare, RPN 5661). Labeling reactions were quenched with hydroxylamine, and uncoupled dye material removed with aRNA Filter Cartridges supplied in the MessageAmp II kit.  Labeled aRNA was fragmented to 60-200 nts using Ambion RNA Fragmentation Reagents (P/N AM8740) according to manufacturer’s instructions.

growth_protocol: The snouty mouse line used in this study was generated and maintained as described in Sandell, L. L. et al. A phenotype-driven ENU mutagenesis screen identifies novel alleles with functional roles in early mouse craniofacial development. Genesis 49, 342–359 (2011)

extract_protocol: Total RNA was extracted from littermate embryos using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Mouse embryos were extracted at embryonic day 9.5.

tag: replicate

tag: Stage

tag: genotype

source_name: E9.5 Embryo,wt1,wt2

value: wt


title: monocytes for Patient EMG-EC-052


title: monocytes for Patient EMG-EC-053


title: snouty/wt E9.5 rep2

description: 1 wt against 1 snouty mutant

source_name: E9.5 Embryo,snouty2

source_name: E9.5 Embryo,wt2


title: monocytes for Patient EMG-EC-054


title: snouty/wt E9.5 rep1

description: 1 wt against 1 snouty mutant

source_name: E9.5 Embryo,snouty1

source_name: E9.5 Embryo,wt1


title: monocytes for Patient EMG-EC-061


title: monocytes for Patient EMG-EC-048


title: monocytes for Patient EMG-EC-044


title: monocytes for Patient EMG-EC-040


title: monocytes for Patient EMG-EC-051


title: monocytes for Patient EMG-EC-043


title: monocytes for Patient EMG-EC-041


title: monocytes for Patient EMG-EC-050


title: monocytes for Patient EMG-EC-046


title: monocytes for Patient EMG-EC-042


title: monocytes for Patient EMG-EC-038


title: monocytes for Patient EMG-EC-037


title: monocytes for Patient EMG-EC-035


title: monocytes for Patient EMG-EC-034


title: monocytes for Patient EMG-EC-030


title: monocytes for Patient EMG-EC-031


title: monocytes for Patient EMG-EC-029


title: monocytes for Patient EMG-EC-028


title: monocytes for Patient EMG-EC-032


title: monocytes for Patient EMG-EC-027


title: monocytes for Patient EMG-EC-026


title: monocytes for Patient EMG-EC-015


title: monocytes for Patient EMG-EC-013


title: monocytes for Patient EMG-EC-022


title: monocytes for Patient EMG-EC-021


title: monocytes for Patient EMG-EC-020


title: monocytes for Patient EMG-EC-016


title: monocytes for Patient EMG-EC-017


title: monocytes for Patient EMG-EC-039


title: monocytes for Patient EMG-EC-011


title: NBD008_NBD014

type: genomic

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

description: Biological replicate 5, Choroid Plexus Papiloma, Atoh1-Cre;MycT58A/MycT58A

hyb_protocol: Hybridization was carried out in an Agilent oven at 65°C for 40 hours at 20 rpm; after hybridization, slides were washed sequentially according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) with protocol CGH_105_Jan09 and LOWESS normalization.

molecule: genomic DNA

label_protocol: 1.5μg of genomic DNA was labeled using the Agilent ULS Labeling kit

growth_protocol: Transgenic mice were monitored for tumor growth. Animals were sacrificed and tumor tissues were collected when mice show sign of tumor development including weight loss, ataxia, hydrocephalus.

extract_protocol: DNA was extracted from mouse normal choroid plexus or tumors using Dneasy Blood and Tissue Kit (QIAGEN)

tag: sample type

value: Male tail reference for MycT58A/MycT58A;p53fl/fl

value: Choroid Plexus Papiloma


title: monocytes for Patient EMG-EC-009


title: monocytes for Patient EMG-EC-012


title: monocytes for Patient EMG-EC-047


title: monocytes for Patient EMG-EC-007


title: monocytes for Patient EMG-EC-008


title: monocytes for Patient EMG-EC-006


title: monocytes for Patient EMG-EC-003


title: NBD005_NBD014

description: Biological replicate 2, Choroid Plexus Papiloma, Atoh1-Cre;MycT58A/MycT58A


title: monocytes for Patient EMG-EC-014


title: monocytes for Patient EMG-EC-002


title: NBD001_NBD016

description: Biological replicate 1, Choroid plexus, MycT58A/MycT58A;p53fl/fl

value: Mixed tail reference for MycT58A/MycT58A;p53fl/fl (no sex information)

value: Choroid plexus


title: monocytes for Patient EMG-EC-001


title: DCs for Patient EMG-EC-059

source_name: DCs


title: DCs for Patient EMG-EC-060


title: DCs for Patient EMG-EC-055


title: NBD013_NBD015

description: Biological replicate 5, Choroid Plexus Carcinoma, Atoh1-Cre;MycT58A/MycT58A;p53fl/fl

value: Female tail reference for MycT58A/MycT58A;p53fl/fl

value: Choroid Plexus Carcinoma


title: NBD003_NBD016

description: Biological replicate 3, Choroid plexus, MycT58A/MycT58A;p53fl/fl


title: NBD012_NBD014

description: Biological replicate 4, Choroid Plexus Carcinoma, Atoh1-Cre;MycT58A/MycT58A;p53fl/fl


title: DCs for Patient EMG-EC-054


title: DCs for Patient EMG-EC-053


title: NBD010_NBD015

description: Biological replicate 2, Choroid Plexus Carcinoma, Atoh1-Cre;MycT58A/MycT58A;p53fl/fl


title: DCs for Patient EMG-EC-058


title: DCs for Patient EMG-EC-049


title: BLM013_BLM000

description: Biological replicate 4, Choroid Plexus Carcinoma, Blbp-Cre;MycT58A/MycT58A;p53fl/-

value: Male tail reference for Blbp-Cre;MycT58A/MycT58A;p53fl/-


title: DCs for Patient EMG-EC-051


title: DCs for Patient EMG-EC-052


title: DCs for Patient EMG-EC-061


title: DCs for Patient EMG-EC-048


title: DCs for Patient EMG-EC-047


title: DCs for Patient EMG-EC-046


title: DCs for Patient EMG-EC-045


title: DCs for Patient EMG-EC-043


title: DCs for Patient EMG-EC-044


title: NBD006_NBD015

description: Biological replicate 3, Choroid Plexus Papiloma, Atoh1-Cre;MycT58A/MycT58A


title: NBD002_NBD016

description: Biological replicate 2, Choroid plexus, MycT58A/MycT58A;p53fl/fl


title: DCs for Patient EMG-EC-042


title: monocytes for Patient EMG-EC-004


title: BLM012_BLM000

description: Biological replicate 3, Choroid Plexus Carcinoma, Blbp-Cre;MycT58A/MycT58A;p53fl/-


title: DCs for Patient EMG-EC-056


title: BLM014_BLM021

description: Biological replicate 5, Choroid Plexus Carcinoma, Blbp-Cre;MycT58A/MycT58A;p53fl/-

value: Female tail reference for Blbp-Cre;MycT58A/MycT58A;p53fl/-


title: DCs for Patient EMG-EC-041


title: monocytes for Patient EMG-EC-019


title: BLM010_BLM021

description: Biological replicate 1, Choroid Plexus Carcinoma, Blbp-Cre;MycT58A/MycT58A;p53fl/-


title: Liver of salmon fed with a taurocholate supplemented plant diet, fish 1

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with GenePix 4100A DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1 and GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Liver of salmon fed with a fish meal based diet, pool of 10 fish

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol using Agilent Quick Amp Labelling Kit

growth_protocol: Salmon (initial average weight 362 ± 95g) was kep in tanks with sea water

extract_protocol: RNA was isolated using TRIzol® (Invitrogen), and purified with PureLink RNA mini kits

treatment_protocol: The fish were fed continuously and approximately 20% in excess of expected feed intake a plant based diet with and without 1.5% cholesterol

value: liver

tag: diet

value: fish meal

value: taurocholate supplemented plant diet


title: DCs for Patient EMG-EC-038


title: DCs for Patient EMG-EC-036


title: Liver of salmon fed with a taurocholate supplemented plant diet, fish 2


title: NBD004_NBD015

description: Biological replicate 1, Choroid Plexus Papiloma, Atoh1-Cre;MycT58A/MycT58A


title: NBD007_NBD014

description: Biological replicate 4, Choroid Plexus Papiloma, Atoh1-Cre;MycT58A/MycT58A


title: DCs for Patient EMG-EC-035

description:
RNA-seq sample from a HIV-1 controller
rawcounts and TPM


title: DCs for Patient EMG-EC-034


title: Liver of salmon fed with a taurine supplemented plant diet, fish 4

value: taurine supplemented plant diet


title: DCs for Patient EMG-EC-032


title: DCs for Patient EMG-EC-033


title: Liver of salmon fed with a taurine supplemented plant diet, fish 2


title: Liver of salmon fed with a choline supplemented plant diet, fish 4

value: choline supplemented plant diet


title: DCs for Patient EMG-EC-031

value: peripheral blood


title: DCs for Patient EMG-EC-040


title: Liver of salmon fed with a taurocholate supplemented plant diet, fish 4


title: Liver of salmon fed with a taurine supplemented plant diet, fish 3


title: Liver of salmon fed with a taurocholate supplemented plant diet, fish 5


title: Liver of salmon fed with a taurine supplemented plant diet, fish 1


title: Liver of salmon fed with a choline supplemented plant diet, fish 5


title: DCs for Patient EMG-EC-039


title: DCs for Patient EMG-EC-050


title: DCs for Patient EMG-EC-030


title: Liver of salmon fed with a choline supplemented plant diet, fish 3


title: DCs for Patient EMG-EC-028

value: NonNeut


title: DCs for Patient EMG-EC-027

value: Neut


title: BLM011_BLM000

description: Biological replicate 2, Choroid Plexus Carcinoma, Blbp-Cre;MycT58A/MycT58A;p53fl/-


title: NBD011_NBD015

description: Biological replicate 3, Choroid Plexus Carcinoma, Atoh1-Cre;MycT58A/MycT58A;p53fl/fl


title: NDUFB10_H2O2_1: bulk RNA seq

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

description: H2O2 treated, NDUFB10-knockdown, biology replication 1

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Single-cell RNA-seq: The template switch oligo (TSO) and poly(A) tail sequences were trimmed from the raw single-cell RNA-seq data, and then the reads with adapters and low-quality bases were removed to obtain clean reads. The clean reads were mapped against the Ensembl Macaca fascicularis reference genome (version: Macaca_fascicularis_5.0) using Tophat (version: 2.0.12). Only the uniquely mapped reads according to UMI numbers were counted using HTSeq, i.e., reads with the same UMI sequence were counted only once.
Bulk RNA-seq: Raw RNA-seq sequencing data were removed adapters and low-quality bases to obtain the clean reads, and then clean reads were mapped against UCSC human reference hg19 using Tophat (version: 2.0.12), and uniquely mapped reads were counted using HTSeq. Gene expression levels were quantified with RPKM (reads per kilobase million).
Genome_build: Macaca_fascicularis_5.0
Genome_build: hg19
Supplementary_files_format_and_content: Single-cell RNA-seq: UMI_count.txt files include the UMI count values of Ensembl genes
Supplementary_files_format_and_content: Bulk RNA-seq: expression.txt files include the read count and RPKM

molecule: polyA RNA

source_name: Human granulosa cell line

extract_protocol:
Single-cell RNA-seq: Single-cell RNA-seq libraries were constructed according to the STRT-seq protocol with modifications, as previously described. Briefly, individual oocytes or somatic cells were picked into lysis buffer by mouth pipetting. Then, the mRNA in lysates was reverse transcribed with SuperScript II reverse transcriptase (Thermo Fisher Scientific, 18064-071), and an 8 nt cell-specific barcode was added to the cDNA from each cell. Absolute counting of molecules was performed with the 8 nt unique molecular identifiers (UMIs). The synthesized cDNAs from cells with different barcodes were pooled together and amplified with 19-21 (somatic cells) or 13 (oocytes) cycles, followed by fragmentation with Covaris S2 (Thermo Fisher) and enrichment of fragments of interest via Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher, 65001). The enriched fragments were constructed into libraries using a KAPA Hyper Prep Kit (KAPA, KK8504) and sequenced on an Illumina HiSeq 4000 platform with a 150-bp paired-end read length by Novogene.
Bulk RNA-seq: Total RNA was extracted from one million cells using TRIzol reagent (Invitrogen). 3 ug per sample were constructed into libraries through NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530L) following manufacturer’s manuals. Sequencing data were generated via on Illumina HiSeq 4000 platform with 150-bp paired-end read length by Novogene.

value: Human granulosa cell line

tag: cell type

value: Granulosa cells


title: NDUFB10_H2O2_2: bulk RNA seq

description: H2O2 treated, NDUFB10-knockdown, biology replication 2


title: DCs for Patient EMG-EC-026


title: Liver of salmon fed with a choline supplemented plant diet, fish 2


title: DCs for Patient EMG-EC-025


title: Liver of salmon fed with a choline supplemented plant diet, fish 1


title: NC_H2O2_2: bulk RNA seq

description: H2O2 treated, negative control, biology replication 2


title: NDUFB10_B_1: bulk RNA seq

description: Untreated, NDUFB10-knockdown, biology replication 1


title: Liver of salmon fed with a taurocholate supplemented plant diet, fish 3


title: NC_H2O2_1: bulk RNA seq

description: H2O2 treated, negative control, biology replication 1


title: DCs for Patient EMG-EC-022


title: DCs for Patient EMG-EC-024


title: DCs for Patient EMG-EC-029


title: DCs for Patient EMG-EC-023


title: NC_B_2: bulk RNA seq

description: Untreated, negative control, biology replication 2


title: DCs for Patient EMG-EC-021


title: NC_B_1: bulk RNA seq

description: Untreated, negative control, biology replication 1


title: IDH1_B_2: bulk RNA seq

description: Untreated, IDH1-knockdown, biology replication 2


title: IDH1_H2O2_1: bulk RNA seq

description: H2O2 treated, IDH1-knockdown, biology replication 1


title: DCs for Patient EMG-EC-057


title: p284R_5_M2

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

country: United Kingdom

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

data_processing:
FastQ files were quality-checked (FastQC) and any residual adaptor sequences were removed (TrimGalore).
Reads were then aligned to the reference genome (mm10, UCSC) using HISAT2.
Differential gene expression analysis was performed on read count files using the limma package in R with the Voom transformation.
Supplementary_files_format_and_content: read counts and cpm data

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages from 6-10 week old Faminp.254I, Faminp.254V and Faminp.284R mice (as described in Cader et. al 2016) were cultured for 6 days and polarised towards an M0, M1 or M2 phenotype.

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit (QIAGEN, 74104) in accordance with the manufacturer's instructions.
Strand-specific single-end sequencing libraries were prepared using TruSeq Stranded mRNA kit (Illumina Inc.). Eleven libraries were sequenced at a time in one lane on an Illumina HiSeq3000 (1x50 base pairs).

tag: strain

tag: phenotype

value: M2 polarised


title: DCs for Patient EMG-EC-018


title: DCs for Patient EMG-EC-019


title: p284R_5_M0


title: DCs for Patient EMG-EC-020


title: NBD009_NBD014

description: Biological replicate 1, Choroid Plexus Carcinoma, Atoh1-Cre;MycT58A/MycT58A;p53fl/fl

value: Male tail reference for MycT58A/MycT58A;p53fl/fl


title: DCs for Patient EMG-EC-017


title: IDH1_H2O2_2: bulk RNA seq

description: H2O2 treated, IDH1-knockdown, biology replication 2


title: NDUFB10_B_2: bulk RNA seq

description: Untreated, NDUFB10-knockdown, biology replication 2


title: IDH1_B_1: bulk RNA seq

description: Untreated, IDH1-knockdown, biology replication 1


title: p254I_5_M0


title: p254I_5_M1

value: M1 polarised


title: DCs for Patient EMG-EC-016


title: p254V_5_M2


title: H30550_NEXTflex_blocked

city: Kiel

first: Simonas

last: Juzenas

address: Am Botanischen Garten 11

department: Institute of Clinical Molecular Biology

country: Germany

institute: Christian-Albrechts-University of Kiel

data_processing:
TruSeq data: “cutadapt -a TG- GAATTCTCGGGTGCCAAGG -m 18 -q 20 –discard-untrimmed”; and with the following parameters for NEXTflex data: “cutadapt -u 4 -a NNNNTGGAATTCTCGGGTGCCAAGG -m 18 -q 20 –discard-untrimmed”.
For TruSeq and NEXTflex data: miraligner -sub 1 -trim 3 -add 3 -s hsa -freq
Genome_build: miRBase v22
Supplementary_files_format_and_content: tab-delimited text files include miRNA and iso-miRNA counts for each sample

source_name: peripheral blood

extract_protocol:
PAXgene Blood miRNA Kit (Qiagen)
TruSeq® Small RNA Library Prep Kit (Illumina) and NEXTFLEX® Small RNA-Seq Kit v3 (Perkin Elmer)

value: M

tag: protocol

value: modified

value: blood


title: H30546_NEXTflex_blocked


title: H30545_NEXTflex_blocked

value: F


title: p254I_5_M2


title: DCs for Patient EMG-EC-015


title: DCs for Patient EMG-EC-014


title: p284R_5_M1


title: H30543_NEXTflex_blocked


title: H30541_NEXTflex_blocked


title: DCs for Patient EMG-EC-013


title: p284R_4_M0


title: p254V_4_M2


title: p284R_4_M1


title: p254I_4_M0


title: p254I_4_M1


title: p254V_4_M1


title: p254V_5_M0


title: H30546_NEXTflex_unblocked

value: standard


title: p254I_4_M2


title: p284R_4_M2


title: p254V_4_M0


title: DCs for Patient EMG-EC-010


title: p284R_3_M2


title: H30545_NEXTflex_unblocked


title: p284R_3_M1


title: p254V_5_M1


title: DCs for Patient EMG-EC-009


title: p284R_3_M0


title: DCs for Patient EMG-EC-012


title: H30543_NEXTflex_unblocked


title: H30550_NEXTflex_unblocked


title: p254I_3_M2


title: p254I_3_M0


title: DCs for Patient EMG-EC-011


title: H30541_NEXTflex_unblocked


title: p254I_3_M1


title: DCs for Patient EMG-EC-007


title: p254V_3_M2


title: H30550_TruSeq_unblocked


title: p254V_3_M0


title: p284R_2_M1


title: H30549_TruSeq_unblocked


title: p254V_3_M1


title: p284R_2_M2


title: p284R_2_M0


title: DCs for Patient EMG-EC-006


title: DCs for Patient EMG-EC-004


title: DCs for Patient EMG-EC-005


title: p254I_2_M2


title: DCs for Patient EMG-EC-003


title: H30547_TruSeq_unblocked


title: p254I_2_M0


title: p254I_2_M1


title: DCs for Patient EMG-EC-008


title: p254V_2_M2


title: DCs for Patient EMG-EC-002


title: p254V_2_M1


title: p254V_2_M0


title: H30543_TruSeq_unblocked


title: H30542_TruSeq_unblocked


title: p284R_1_M2


title: p284R_1_M1


title: p284R_1_M0


title: CD4 for Patient EMG-EC-061


title: H30548_TruSeq_unblocked


title: H30541_TruSeq_unblocked


title: p254I_1_M2


title: p254I_1_M1


title: H30550_TruSeq_blocked


title: CD4 for Patient EMG-EC-060


title: p254V_1_M2


title: CD4 for Patient EMG-EC-059


title: H30544_TruSeq_unblocked


title: DCs for Patient EMG-EC-037


title: p254V_1_M0


title: H30549_TruSeq_blocked


title: CD4 for Patient EMG-EC-058


title: H30548_TruSeq_blocked


title: DCs for Patient EMG-EC-001


title: CD4 for Patient EMG-EC-057


title: CD4 for Patient EMG-EC-055


title: H30547_TruSeq_blocked


title: H30544_TruSeq_blocked


title: p254V_1_M1


title: H30543_TruSeq_blocked


title: CD4 for Patient EMG-EC-050


title: CD4 for Patient EMG-EC-052


title: p254I_1_M0


title: CD4 for Patient EMG-EC-051


title: H30542_TruSeq_blocked


title: CD4 for Patient EMG-EC-054


title: H30541_TruSeq_blocked


title: CD4 for Patient EMG-EC-039


title: CD4 for Patient EMG-EC-048


title: CD4 for Patient EMG-EC-040


title: CD4 for Patient EMG-EC-047


title: CD4 for Patient EMG-EC-038


title: CD4 for Patient EMG-EC-053


title: CD4 for Patient EMG-EC-037


title: R_CSE_Drug_Rep4

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

department: Biology

country: Canada

institute: University of Waterloo

data_processing:
Samples were sequenced on the Illumina HiSeq 2500 instrument with 125 bp paired-end reads to a minimum depth of 30 million reads per sample.
Reads were de-multiplexed and trimmed at The Centre for Applied Genomics and BCL files generated from the Illumina sequencer were converted to fastq files prior to our receivement of the reads.
Quality control was performed using FastQC (v.0.11.7) and Prinseq (v.0.20.4).
Sequences were aligned to the human reference genome (hg19) using HISAT2 (v.2.1.0)
Sequences were assembled into full transcriptomes using StringTie (v.1.3.3b). Samtools (v.1.9) was used to convert and sort HISAT2 output into sorted bam files for use by StringTie.
StringTie was also used to calculate transcript abundances for downstream differential expression analysis using the Ballgown package in R (v. 3.4.3.).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: cannabis smoke extract (CSE) with drug: formoterol/budesonide

growth_protocol: Calu-3 cells, an immortalized human lung adenocarcinoma cell line, were obtained from ATCC (HTB-55, Lot: 61449062) and maintained in Eagle’s Minimum Essential Medium (EMEM, Millipore Sigma) supplemented with 10mM HEPES (Millipore Sigma), 10% FBS (Millipore Sigma), and Antibiotic-Antimycotic (Gibco®, ThermoFisher Scientific). Calu-3 cells were cultured in vented 75cm^2 tissue culture flasks (Sarstedt) and used between passages 10-20. Calu-3 cells were seeded onto either 4.7cm^2 or 0.3cm^2 polyester Transwell® permeable supports with a pore size of 0.4μm (Corning) and grown for 20 days to allow the Calu-3 cells to semi-differentiate into a pseudo-stratified epithelium. BS was removed from Calu-3 cultures 24 hours prior to the start of the exposures.

extract_protocol:
Total RNA was extracted using a RNeasy Plus Kit (QIAGEN, Valencia, CA) according to the manufacturer's instructions.
cDNA was prepared at The Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Ontario, Canada).

treatment_protocol: For exposures, fresh FBS free EMEM culture media was added to basal chambers and CSE or TSE media diluted with fresh FBS free EMEM culture media was added to the apical chambers for 24 hours. For intervention conditions, budesonide 100nM (Cayman Chemical) and formoterol 10nM (Cayman Chemical) was added to the exposure medias before being applied to Calu-3 cells for 24 hours.

tag: cell line

value: Lung epithelium


title: CD4 for Patient EMG-EC-042


title: CD4 for Patient EMG-EC-044


title: CD4 for Patient EMG-EC-043


title: CD4 for Patient EMG-EC-046