title: MPP3 population

description: PMA-RNA-seq in MPP3

source_name: Multipotent precursors 3


title: MPP1 96 rep2

status: Public on Dec 24 2016

type: SRA

city: New Haven

first: Sherman

last: Weissman

state: CT

address: 1 Gilbert street

department: Genetics

country: USA

institute: Yale University

description: single-cell RNA-seq in MPP1 biorep2

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were mapped to the mouse genome (mm9 from UCSC database) by Tophat (v1.3.3) with “–r 100” option
Gene expression values were then calculated by Cufflinks (v1.2.1), using RefSeq genes as reference annotation with “-G” option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RefSeq gene id, gene symbol, chromosome and FPKM value for each sample

molecule: total RNA

organism: Mus musculus

source_name: Multipotent precursors 1

growth_protocol: Bone Marrow cells were isolated from 6-8 weeks C57BL6 mice

extract_protocol:
Total RNA was isolated with Smart-seq protocol for single-cell RNA-seq and Pan et al. 2013 protocol for bulk RNA-seq
library preparation was conducted using standard Tru-Seq Illumina kits.

treatment_protocol: 18 different populations of mouse BM cells were sorted by FACS AriaII (BD Biosciences) from the Yale cell sorter Core Facility.

tag: marker

tag: barcodes

value: TCCTGAGC-TATCCTCT

tag: cell count

tag: well id


title: HSC population

description: PMA-RNA-seq in HSC

source_name: Hematopoietic stem cells


title: MPP1 90 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TCCTGAGC-ACTGCATA


title: MPP1 91 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TCCTGAGC-AGAGTAGA


title: MPP1 93 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TCCTGAGC-CTCTCTAT


title: MPP1 95 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TCCTGAGC-TAGATCGC


title: MPP1 92 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TCCTGAGC-CTAAGCCT


title: MPP1 94 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TCCTGAGC-GTAAGGAG


title: MPP1 89 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TCCTGAGC-AAGGAGTA


title: MPP1 88 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-TATCCTCT


title: MPP1 86 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-GTAAGGAG


title: MPP1 87 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-TAGATCGC


title: MPP1 85 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-CTCTCTAT


title: preGM population

description: PMA-RNA-seq in preGM

source_name: pre-granulocyte-macrophage


title: MPP1 84 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-CTAAGCCT


title: MPP1 77 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-CTCTCTAT


title: MPP1 80 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-TATCCTCT


title: MPP1 76 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-CTAAGCCT


title: MPP1 81 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-AAGGAGTA


title: MPP1 79 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-TAGATCGC


title: MPP1 82 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-ACTGCATA


title: MPP1 83 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAGGCATG-AGAGTAGA


title: MPP1 74 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-ACTGCATA


title: MPP1 75 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-AGAGTAGA


title: MPP1 71 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-TAGATCGC


title: MPP1 73 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-AAGGAGTA


title: MPP1 68 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-CTAAGCCT


title: MPP1 69 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-CTCTCTAT


title: MPP1 70 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-GTAAGGAG


title: MPP1 67 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-AGAGTAGA


title: MPP1 66 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-ACTGCATA


title: MPP1 58 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-ACTGCATA


title: MPP1 59 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-AGAGTAGA


title: MPP1 60 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-CTAAGCCT


title: MPP1 65 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-AAGGAGTA


title: MPP1 62 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-GTAAGGAG


title: MPP1 56 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-TATCCTCT


title: MPP1 57 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-AAGGAGTA


title: MPP1 78 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: TAAGGCGA-GTAAGGAG


title: MPP1 55 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-TAGATCGC


title: MPP1 54 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-GTAAGGAG


title: MPP1 72 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GTAGAGGA-TATCCTCT


title: MPP1 53 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-CTCTCTAT


title: MPP1 51 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-AGAGTAGA


title: MPP1 52 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-CTAAGCCT


title: MPP1 45 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-CTCTCTAT


title: MPP1 48 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-TATCCTCT


title: MPP1 47 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-TAGATCGC


title: MPP1 46 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-GTAAGGAG


title: MPP1 44 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-CTAAGCCT


title: MPP1 43 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-AGAGTAGA


title: MPP1 64 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-TATCCTCT


title: MPP1 61 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-CTCTCTAT


title: MPP1 39 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-TAGATCGC


title: MPP1 41 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-AAGGAGTA


title: MPP1 42 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CTCTCTAC-ACTGCATA


title: MPP1 38 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-GTAAGGAG


title: MPP1 63 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GGACTCCT-TAGATCGC


title: MPP1 40 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-TATCCTCT


title: MPP1 37 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-CTCTCTAT


title: MPP1 36 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-CTAAGCCT


title: MPP1 32 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-TATCCTCT


title: MPP1 34 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-ACTGCATA


title: MPP1 33 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-AAGGAGTA


title: MPP1 31 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-TAGATCGC


title: MPP1 30 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-GTAAGGAG


title: MPP1 35 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGTACTAG-AGAGTAGA


title: MPP1 50 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-ACTGCATA


title: MPP1 49 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: GCTACGCT-AAGGAGTA


title: MPP1 29 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-CTCTCTAT


title: MPP1 27 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-AGAGTAGA


title: MPP1 26 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-ACTGCATA


title: MPP1 28 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-CTAAGCCT


title: MPP1 25 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CGAGGCTG-AAGGAGTA


title: MPP1 23 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-TAGATCGC


title: MPP1 22 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-GTAAGGAG


title: MPP1 21 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-CTCTCTAT


title: MPP1 19 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-AGAGTAGA


title: MPP1 18 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-ACTGCATA


title: MPP1 17 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-AAGGAGTA


title: MPP1 16 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-TATCCTCT


title: MPP1 15 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-TAGATCGC


title: MPP1 12 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-CTAAGCCT


title: MPP1 10 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-ACTGCATA


title: MPP1 13 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-CTCTCTAT


title: MPP1 9 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-AAGGAGTA


title: MPP1 8 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-TATCCTCT


title: MPP1 7 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-TAGATCGC


title: MPP1 3 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-AGAGTAGA


title: MPP1 2 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-ACTGCATA


title: MPP1 4 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-CTAAGCCT


title: MPP1 6 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-GTAAGGAG


title: MPP1 1 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-AAGGAGTA


title: MPP1 96 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-TATCCTCT


title: MPP1 24 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-TATCCTCT


title: MPP1 94 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-GTAAGGAG


title: MPP1 11 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-AGAGTAGA


title: MPP1 20 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: CAGAGAGG-CTAAGCCT


title: MPP1 14 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AGGCAGAA-GTAAGGAG


title: MPP1 91 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-AGAGTAGA


title: MPP1 93 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-CTCTCTAT


title: MPP1 92 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-CTAAGCCT


title: MPP1 90 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-ACTGCATA


title: MPP1 88 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-TATCCTCT


title: MPP1 84 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-CTAAGCCT


title: MPP1 85 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-CTCTCTAT


title: MPP1 89 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-AAGGAGTA


title: MPP1 83 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-AGAGTAGA


title: MPP1 82 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-ACTGCATA


title: MPP1 79 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-TAGATCGC


title: MPP1 78 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-GTAAGGAG


title: MPP1 77 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-CTCTCTAT


title: MPP1 81 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-AAGGAGTA


title: MPP1 75 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-AGAGTAGA


title: MPP1 76 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-CTAAGCCT


title: MPP1 72 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-TATCCTCT


title: MPP1 74 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-ACTGCATA


title: MPP1 73 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-AAGGAGTA


title: MPP1 69 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-CTCTCTAT


title: MPP1 70 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-GTAAGGAG


title: MPP1 71 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-TAGATCGC


title: MPP1 68 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-CTAAGCCT


title: MPP1 86 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-GTAAGGAG


title: MPP1 87 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAGGCATG-TAGATCGC


title: MPP1 67 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-AGAGTAGA


title: MPP1 65 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-AAGGAGTA


title: MPP1 66 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GTAGAGGA-ACTGCATA


title: MPP1 64 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-TATCCTCT


title: MPP1 62 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-GTAAGGAG


title: MPP1 80 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TAAGGCGA-TATCCTCT


title: MPP1 59 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-AGAGTAGA


title: MPP1 58 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-ACTGCATA


title: MPP1 55 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-TAGATCGC


title: MPP1 54 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-GTAAGGAG


title: MPP1 53 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-CTCTCTAT


title: MPP1 52 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-CTAAGCCT


title: MPP1 51 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-AGAGTAGA


title: MPP1 47 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-TAGATCGC


title: MPP1 48 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-TATCCTCT


title: MPP1 45 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-CTCTCTAT


title: MPP1 50 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-ACTGCATA


title: MPP1 63 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-TAGATCGC


title: MPP1 49 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-AAGGAGTA


title: MPP1 46 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-GTAAGGAG


title: MPP1 44 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-CTAAGCCT


title: MPP1 40 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-TATCCTCT


title: MPP1 38 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-GTAAGGAG


title: MPP1 43 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-AGAGTAGA


title: MPP1 61 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-CTCTCTAT


title: MPP1 41 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-AAGGAGTA


title: MPP1 36 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-CTAAGCCT


title: MPP1 42 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CTCTCTAC-ACTGCATA


title: MPP1 37 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-CTCTCTAT


title: MPP1 57 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-AAGGAGTA


title: MPP1 34 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-ACTGCATA


title: MPP1 33 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-AAGGAGTA


title: MPP1 56 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GCTACGCT-TATCCTCT


title: MPP1 35 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-AGAGTAGA


title: MPP1 31 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-TAGATCGC


title: MPP1 29 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-CTCTCTAT


title: MPP1 28 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-CTAAGCCT


title: MPP1 26 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-ACTGCATA


title: MPP1 24 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-TATCCTCT


title: MPP1 25 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-AAGGAGTA


title: MPP1 23 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-TAGATCGC


title: MPP1 22 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-GTAAGGAG


title: MPP1 39 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGTACTAG-TAGATCGC


title: MPP1 27 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-AGAGTAGA


title: MPP1 20 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-CTAAGCCT


title: MPP1 21 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-CTCTCTAT


title: MPP1 17 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-AAGGAGTA


title: MPP1 19 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-AGAGTAGA


title: MPP1 16 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-TATCCTCT


title: MPP1 13 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-CTCTCTAT


title: MPP1 11 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-AGAGTAGA


title: MPP1 15 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-TAGATCGC


title: MPP1 10 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-ACTGCATA


title: MPP1 18 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CAGAGAGG-ACTGCATA


title: MPP1 32 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-TATCCTCT


title: MPP1 60 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: GGACTCCT-CTAAGCCT


title: MPP1 12 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-CTAAGCCT


title: MPP1 7 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-TAGATCGC


title: MPP1 9 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-AAGGAGTA


title: MPP1 6 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-GTAAGGAG


title: MPP1 8 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-TATCCTCT


title: MPP1 5 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-CTCTCTAT


title: MPP1 30 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: CGAGGCTG-GTAAGGAG


title: MPP1 3 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-AGAGTAGA


title: MPP1 1 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-AAGGAGTA


title: MPP1 2 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-ACTGCATA


title: MPP1 14 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AGGCAGAA-GTAAGGAG


title: HSC 96 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-TATCCTCT


title: HSC 91 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-AGAGTAGA


title: HSC 92 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-CTAAGCCT


title: HSC 87 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-TAGATCGC


title: HSC 94 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-GTAAGGAG


title: HSC 95 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-TAGATCGC


title: HSC 84 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-CTAAGCCT


title: HSC 82 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-ACTGCATA


title: HSC 86 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-GTAAGGAG


title: HSC 90 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-ACTGCATA


title: HSC 88 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-TATCCTCT


title: HSC 81 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-AAGGAGTA


title: HSC 85 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-CTCTCTAT


title: HSC 79 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-TAGATCGC


title: HSC 80 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-TATCCTCT


title: HSC 78 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-GTAAGGAG


title: HSC 83 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAGGCATG-AGAGTAGA


title: HSC 77 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-CTCTCTAT


title: MPP1 4 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: AAGAGGCA-CTAAGCCT


title: HSC 75 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-AGAGTAGA


title: HSC 76 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-CTAAGCCT


title: HSC 89 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-AAGGAGTA


title: HSC 74 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-ACTGCATA


title: HSC 93 rep2

description: single-cell RNA-seq in HSC biorep2

value: TCCTGAGC-CTCTCTAT


title: HSC 72 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-TATCCTCT


title: HSC 73 rep2

description: single-cell RNA-seq in HSC biorep2

value: TAAGGCGA-AAGGAGTA


title: HSC 71 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-TAGATCGC


title: HSC 70 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-GTAAGGAG


title: HSC 69 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-CTCTCTAT


title: HSC 68 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-CTAAGCCT


title: HSC 67 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-AGAGTAGA


title: HSC 66 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-ACTGCATA


title: HSC 65 rep2

description: single-cell RNA-seq in HSC biorep2

value: GTAGAGGA-AAGGAGTA


title: HSC 63 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-TAGATCGC


title: HSC 64 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-TATCCTCT


title: HSC 62 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-GTAAGGAG


title: HSC 61 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-CTCTCTAT


title: HSC 60 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-CTAAGCCT


title: HSC 53 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-CTCTCTAT


title: HSC 59 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-AGAGTAGA


title: HSC 58 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-ACTGCATA


title: HSC 56 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-TATCCTCT


title: HSC 57 rep2

description: single-cell RNA-seq in HSC biorep2

value: GGACTCCT-AAGGAGTA


title: HSC 48 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-TATCCTCT


title: HSC 49 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-AAGGAGTA


title: HSC 51 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-AGAGTAGA


title: HSC 47 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-TAGATCGC


title: HSC 50 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-ACTGCATA


title: HSC 46 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-GTAAGGAG


title: HSC 45 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-CTCTCTAT


title: HSC 44 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-CTAAGCCT


title: HSC 43 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-AGAGTAGA


title: HSC 42 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-ACTGCATA


title: HSC 41 rep2

description: single-cell RNA-seq in HSC biorep2

value: CTCTCTAC-AAGGAGTA


title: HSC 40 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-TATCCTCT


title: HSC 38 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-GTAAGGAG


title: HSC 39 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-TAGATCGC


title: HSC 37 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-CTCTCTAT


title: HSC 55 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-TAGATCGC


title: HSC 36 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-CTAAGCCT


title: HSC 54 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-GTAAGGAG


title: HSC 33 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-AAGGAGTA


title: HSC 28 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-CTAAGCCT


title: HSC 32 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-TATCCTCT


title: HSC 35 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-AGAGTAGA


title: HSC 29 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-CTCTCTAT


title: MPP1 95 rep1

description: single-cell RNA-seq in MPP1 biorep1

value: TCCTGAGC-TAGATCGC


title: HSC 30 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-GTAAGGAG


title: HSC 24 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-TATCCTCT


title: HSC 23 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-TAGATCGC


title: HSC 27 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-AGAGTAGA


title: HSC 52 rep2

description: single-cell RNA-seq in HSC biorep2

value: GCTACGCT-CTAAGCCT


title: HSC 21 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-CTCTCTAT


title: HSC 26 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-ACTGCATA


title: HSC 34 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGTACTAG-ACTGCATA


title: HSC 20 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-CTAAGCCT


title: HSC 18 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-ACTGCATA


title: MPP1 5 rep2

description: single-cell RNA-seq in MPP1 biorep2

value: AAGAGGCA-CTCTCTAT


title: HSC 25 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-AAGGAGTA


title: HSC 13 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-CTCTCTAT


title: HSC 14 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-GTAAGGAG


title: HSC 17 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-AAGGAGTA


title: HSC 15 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-TAGATCGC


title: HSC 16 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-TATCCTCT


title: HSC 12 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-CTAAGCCT


title: HSC 11 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-AGAGTAGA


title: HSC 10 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-ACTGCATA


title: HSC 8 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-TATCCTCT


title: HSC 9 rep2

description: single-cell RNA-seq in HSC biorep2

value: AGGCAGAA-AAGGAGTA


title: HSC 6 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-GTAAGGAG


title: HSC 7 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-TAGATCGC


title: HSC 4 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-CTAAGCCT


title: HSC 22 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-GTAAGGAG


title: HSC 31 rep2

description: single-cell RNA-seq in HSC biorep2

value: CGAGGCTG-TAGATCGC


title: HSC 2 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-ACTGCATA


title: HSC 3 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-AGAGTAGA


title: HSC 1 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-AAGGAGTA


title: HSC 95 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-TAGATCGC


title: HSC 5 rep2

description: single-cell RNA-seq in HSC biorep2

value: AAGAGGCA-CTCTCTAT


title: HSC 94 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-GTAAGGAG


title: HSC 96 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-TATCCTCT


title: HSC 92 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-CTAAGCCT


title: HSC 91 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-AGAGTAGA


title: HSC 90 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-ACTGCATA


title: HSC 19 rep2

description: single-cell RNA-seq in HSC biorep2

value: CAGAGAGG-AGAGTAGA


title: HSC 93 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-CTCTCTAT


title: HSC 89 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-AAGGAGTA


title: HSC 88 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-TATCCTCT


title: HSC 87 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-TAGATCGC


title: HSC 84 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-CTAAGCCT


title: HSC 86 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-GTAAGGAG


title: HSC 82 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-ACTGCATA


title: HSC 83 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-AGAGTAGA


title: HSC 80 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-TATCCTCT


title: HSC 85 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-CTCTCTAT


title: HSC 79 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-TAGATCGC


title: HSC 81 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-AAGGAGTA


title: HSC 76 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-CTAAGCCT


title: HSC 75 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-AGAGTAGA


title: HSC 74 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-ACTGCATA


title: HSC 77 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-CTCTCTAT


title: HSC 73 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-AAGGAGTA


title: HSC 69 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-CTCTCTAT


title: HSC 67 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-AGAGTAGA


title: HSC 66 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-ACTGCATA


title: HSC 68 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-CTAAGCCT


title: HSC 65 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-AAGGAGTA


title: HSC 78 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-GTAAGGAG


title: HSC 72 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-TATCCTCT


title: HSC 64 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-TATCCTCT


title: HSC 61 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-CTCTCTAT


title: HSC 63 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-TAGATCGC


title: HSC 60 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-CTAAGCCT


title: HSC 71 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-TAGATCGC


title: HSC 58 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-ACTGCATA


title: HSC 57 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-AAGGAGTA


title: HSC 62 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-GTAAGGAG


title: HSC 56 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-TATCCTCT


title: HSC 55 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-TAGATCGC


title: HSC 54 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-GTAAGGAG


title: HSC 52 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-CTAAGCCT


title: HSC 51 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-AGAGTAGA


title: HSC 70 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-GTAAGGAG


title: HSC 49 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-AAGGAGTA


title: HSC 48 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-TATCCTCT


title: HSC 47 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-TAGATCGC


title: HSC 45 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-CTCTCTAT


title: HSC 44 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-CTAAGCCT


title: HSC 46 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-GTAAGGAG


title: HSC 41 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-AAGGAGTA


title: HSC 40 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-TATCCTCT


title: HSC 59 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-AGAGTAGA


title: HSC 43 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-AGAGTAGA


title: HSC 36 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-CTAAGCCT


title: HSC 34 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-ACTGCATA


title: HSC 33 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-AAGGAGTA


title: HSC 37 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-CTCTCTAT


title: HSC 38 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-GTAAGGAG


title: HSC 42 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-ACTGCATA


title: HSC 30 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-GTAAGGAG


title: HSC 39 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-TAGATCGC


title: HSC 31 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-TAGATCGC


title: HSC 32 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-TATCCTCT


title: HSC 29 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-CTCTCTAT


title: HSC 53 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-CTCTCTAT


title: HSC 50 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-ACTGCATA


title: HSC 28 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-CTAAGCCT


title: HSC 26 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-ACTGCATA


title: HSC 25 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-AAGGAGTA


title: HSC 24 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-TATCCTCT


title: HSC 22 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-GTAAGGAG


title: HSC 20 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-CTAAGCCT


title: HSC 18 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-ACTGCATA


title: HSC 23 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-TAGATCGC


title: HSC 19 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-AGAGTAGA


title: HSC 17 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-AAGGAGTA


title: HSC 35 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-AGAGTAGA


title: HSC 16 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-TATCCTCT


title: HSC 14 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-GTAAGGAG


title: HSC 15 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-TAGATCGC


title: HSC 13 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-CTCTCTAT


title: HSC 12 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-CTAAGCCT


title: HSC 11 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-AGAGTAGA


title: HSC 10 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-ACTGCATA


title: HSC 6 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-GTAAGGAG


title: HSC 4 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-CTAAGCCT


title: HSC 27 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-AGAGTAGA


title: HSC 8 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-TATCCTCT


title: HSC 1 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-AAGGAGTA


title: HSC 5 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-CTCTCTAT


title: HSC 9 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-AAGGAGTA


title: HSC 3 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-AGAGTAGA


title: HSC 96 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-TATCCTCT


title: HSC 95 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-TAGATCGC


title: HSC 93 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-CTCTCTAT


title: HSC 92 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-CTAAGCCT


title: HSC 21 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-CTCTCTAT


title: HSC 94 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-GTAAGGAG


title: HSC 89 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-AAGGAGTA


title: HSC 88 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-TATCCTCT


title: HSC 90 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-ACTGCATA


title: HSC 85 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-CTCTCTAT


title: HSC 91 rep1

description: single-cell RNA-seq in HSC biorep1

value: TCCTGAGC-AGAGTAGA


title: HSC 87 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-TAGATCGC


title: HSC 7 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-TAGATCGC


title: HSC 84 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-CTAAGCCT


title: HSC 83 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-AGAGTAGA


title: HSC 2 rep1 (Technical replicate)

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-ACTGCATA


title: HSC 81 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-AAGGAGTA


title: HSC 82 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-ACTGCATA


title: HSC 79 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-TAGATCGC


title: HSC 78 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-GTAAGGAG


title: HSC 77 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-CTCTCTAT


title: HSC 76 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-CTAAGCCT


title: HSC 75 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-AGAGTAGA


title: HSC 74 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-ACTGCATA


title: HSC 73 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-AAGGAGTA


title: HSC 71 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-TAGATCGC


title: HSC 72 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-TATCCTCT


title: HSC 68 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-CTAAGCCT


title: HSC 69 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-CTCTCTAT


title: HSC 70 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-GTAAGGAG


title: HSC 86 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAGGCATG-GTAAGGAG


title: HSC 67 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-AGAGTAGA


title: HSC 65 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-AAGGAGTA


title: HSC 63 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-TAGATCGC


title: HSC 62 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-GTAAGGAG


title: HSC 64 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-TATCCTCT


title: HSC 58 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-ACTGCATA


title: HSC 60 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-CTAAGCCT


title: HSC 59 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-AGAGTAGA


title: HSC 56 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-TATCCTCT


title: HSC 80 rep1

description: single-cell RNA-seq in HSC biorep1

value: TAAGGCGA-TATCCTCT


title: HSC 57 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-AAGGAGTA


title: HSC 53 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-CTCTCTAT


title: HSC 55 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-TAGATCGC


title: HSC 54 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-GTAAGGAG


title: HSC 51 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-AGAGTAGA


title: HSC 50 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-ACTGCATA


title: HSC 49 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-AAGGAGTA


title: HSC 47 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-TAGATCGC


title: HSC 46 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-GTAAGGAG


title: HSC 41 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-AAGGAGTA


title: HSC 45 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-CTCTCTAT


title: HSC 42 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-ACTGCATA


title: HSC 43 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-AGAGTAGA


title: HSC 44 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-CTAAGCCT


title: HSC 40 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-TATCCTCT


title: HSC 39 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-TAGATCGC


title: HSC 66 rep1

description: single-cell RNA-seq in HSC biorep1

value: GTAGAGGA-ACTGCATA


title: HSC 38 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-GTAAGGAG


title: HSC 61 rep1

description: single-cell RNA-seq in HSC biorep1

value: GGACTCCT-CTCTCTAT


title: HSC 36 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-CTAAGCCT


title: HSC 35 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-AGAGTAGA


title: HSC 37 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-CTCTCTAT


title: HSC 52 rep1

description: single-cell RNA-seq in HSC biorep1

value: GCTACGCT-CTAAGCCT


title: HSC 32 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-TATCCTCT


title: HSC 33 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-AAGGAGTA


title: HSC 30 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-GTAAGGAG


title: HSC 28 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-CTAAGCCT


title: HSC 29 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-CTCTCTAT


title: HSC 27 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-AGAGTAGA


title: HSC 48 rep1

description: single-cell RNA-seq in HSC biorep1

value: CTCTCTAC-TATCCTCT


title: HSC 26 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-ACTGCATA


title: HSC 24 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-TATCCTCT


title: HSC 23 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-TAGATCGC


title: HSC 31 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-TAGATCGC


title: HSC 25 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGAGGCTG-AAGGAGTA


title: HSC 19 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-AGAGTAGA


title: HSC 21 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-CTCTCTAT


title: HSC 15 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-TAGATCGC


title: HSC 17 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-AAGGAGTA


title: HSC 11 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-AGAGTAGA


title: HSC 13 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-CTCTCTAT


title: HSC 12 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-CTAAGCCT


title: HSC 8 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-TATCCTCT


title: HSC 18 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-ACTGCATA


title: HSC 7 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-TAGATCGC


title: HSC 9 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-AAGGAGTA


title: HSC 5 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-CTCTCTAT


title: HSC 34 rep1

description: single-cell RNA-seq in HSC biorep1

value: CGTACTAG-ACTGCATA


title: HSC 10 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-ACTGCATA


title: HSC 6 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-GTAAGGAG


title: HSC 3 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-AGAGTAGA


title: HSC 16 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-TATCCTCT


title: HSC 2 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-ACTGCATA


title: Testis 6

city: Bar Harbor

first: Elizabeth

last: Snyder

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Trimming: fastx v0.13, fastx_trimmer -f 7
Alignment: tophat v2.0.13, -r 100
Variant calling: GATK UnifiedGenotyper, --filter_reads_with_N_cigar -stand_call_conf 0 -stand_emit_conf 0 -mbq 25 -rf MappingQuality -mmq 20
Generate table: GATK GenomeAnalysisTK, -F CHROM -F POS -F REF -F ALT -F QUAL -F AC -F AF -F AN -F DP -F DS -F FS -F MQ -F MQ0 -F MQRankSum -F GT -F AD --allowMissingData
Filtering for single variants, shared by all samples, within exons: custom awk scripts
Samtools, mpileup,  -A -Q 25 -q 20 -d 500
Genome_build: mm10
Supplementary_files_format_and_content: pileup

source_name: Testis

growth_protocol: All experimental mice used in this study were cared for in accordance with the “Guide for the Care and Use of Experimental Animals” established by the National Institutes of Health (NIH) and all protocols approved by the Jackson Laboratory Animal Care and Use Committee. Animals were maintained in a 12 h light and 12 h dark cycle vivarium in the Research Animal Facility at The Jackson Laboratory.  Autoclaved NIH31 diet (6% fat) and HCl acidified water (pH 2.8-3.2) were provided ad libitum.

extract_protocol:
Total RNA extraction via the mirVana RNA isolation kit (Life Technologies, Grand Island, NY) was performed per manufacturers, including DNase treatment.
RNA sequencing libraries for 100 bp paired-end sequencing were produced using the TruSeq RNA Sample prep Kit v2 Set A and B (Illumina, San Diego, CA).

tag: strain

tag: tissue

value: Testis

tag: age

value: 25 dpp

tag: genotype

value: wildtype


title: HSC 22 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-GTAAGGAG


title: HSC 4 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-CTAAGCCT


title: Testis 2


title: Testis 4


title: HSC 20 rep1

description: single-cell RNA-seq in HSC biorep1

value: CAGAGAGG-CTAAGCCT


title: Testis 5


title: HSC 1 rep1

description: single-cell RNA-seq in HSC biorep1

value: AAGAGGCA-AAGGAGTA


title: HSC 14 rep1

description: single-cell RNA-seq in HSC biorep1

value: AGGCAGAA-GTAAGGAG


title: Adar2-KO

status: Public on Dec 23 2016

city: Urbana

first: Prasanth

last: Kannanganattu

state: IL

address: 601S Goodwin Avenue

department: Cell and Developmental Biology

institute: UIUC

data_processing:
Sequenced reads were aligned to mm9 genome using STAR v2.4.0d with default parameters.
Duplicate reads were removed by SAMtools rmdup, version 0.1.19.
Differentially expressed genes were identified using GFOLD, version 1.1.4.
RNA editing events in known editing sites were counted by SAMtools mpileup.The known list of A-to-I RNA editing sites was downloaded from Rigorously Annotated Database of A-to-I RNA Editing (version 2) (Ramaswami & Li, 2014)
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are tab-delimited text files. Gene expression file (WTvsKO.txt) was created by GFOLD, including RPKM values for each sample. Other two text files (WT_editing.txt and KO_editing.txt) contain RNA editing level information. First eight columns show annotations of known editing sites (from RADAR database); last three columns show the number of mapped reads, number of editing reads, and editing level.

source_name: Mouse embryonic Fibroblasts

growth_protocol: Cultured cells in DMEM + 10%Fetal Bovine Serum + Penicillin-Streptomycin

extract_protocol:
Adar2-WT and Adar2-KO cells were grown in culture. RNA was isolated using Rneasy mini kit (Cat#74104, Qiagen)
Libraries are constructed with the TruSeq Sample Prep or Nextera kits from Illumina.


title: Pin KO / Htt WT rep2

city: Novara

first: Francesca

last: Persichetti

state: Italy

address: via Solaroli 17

department: Scienze della Salute

country: Italy

institute: Universita' del Piemonte Orientale

description: Sample 7 – 9211

data_processing:
RNA-seq quality control eas executed with FastQC
genome mapping was done with STAR aligner
mapped reads were counted with HTSeq
DGE analysis was executed with the EdgeR package
Functional annotation, category and pathway analysis was executed with the R/Bioconductor clusterProfiler and Ingenuity Pathway Analysis
Genome_build: mm9
Supplementary_files_format_and_content: htt1_pin_matrix.txt file containing average tag counts for the three replicates of each phenotype

source_name: Striatum

extract_protocol:
Total RNA was harvested with Triazol reagent
Libraries were constructed with the Illumina TruSeq RNA kits
50 base pair single reads

value: Striatum

value: Pin KO / Htt WT

value: 12 months


title: Pin KO / Htt WT rep3

description: Sample 11 – 9246


title: Pin WT / Htt KI rep2

description: Sample 3 – 9299

value: Pin WT / Htt KI


title: mRNA_Col_RiobosomeMBP_2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

country: China

institute: Fudan University

data_processing:
Basecalls performed using Illumina CASAVA
Sequence reads were mapped to the Arabidopsis genome TAIR10 (www.arabidopsis.org) using Tophat2 V2.0.13 with parameters -g 1 -N 1
Read mapped to each gene were counted by a homemade Perl script
Normalized read counts of each gene were calculated using R package DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files including raw read counts and normalized read counts for each gene

organism: Arabidopsis thaliana

source_name: 12-day seedlings

growth_protocol: Arabidopsis seedlings were grown in a growth chamber (Percival) at 23℃ with 16h light

extract_protocol:
1. RibosomeFP and RibosomeMBP RNA extractioin    2g Arabidopsis seedlings was ground in liquid nitrogen. The powder was suspended in 8 ml extraction buffer (pH 8.5) containing 0.2 M Tris, 0.1 M KCl, 70 mM Mg-acetate, 50 mM EGTA, 0.25 M sucrose, 10 mM DTT, 50ug/ml cycloheximide, 50ug/ml chloramphenicol and 50 U/ml SUPERase In RNase inhibitor (Ambion). Membranes were pelleted by centrifugation at 30000 g in Thickwall SW28 tubes (Beckman Coulter) for 30 min at 4℃. The supernatant was transferred into a new tube and kept in ice. The membrane pellet was carefully resuspended in extraction buffer containing 1% v/v TritonX-100 to solubilize membranes. Both fractions subjected to 30000g centrifugation for 30 min to remove any residual membrane. The supernatants were loaded on the top of 8mL sucrose cushion solution (0.4M Tris-Cl, pH9.0, 0.2M KCl,0.005M EGTA, 0.035M MgCl2,1.75M sucrose, 5mM DTT, 50mg/ml cycloheximide, and 50mg/ml chloramphenicol ), and free polysome (FP) and membrane bond polysome (MBP) were obtained by centrifuging 170000g in a TYPE0 Ti tube (Beckman Coulter) at 4℃ for 3 hours. FP and MBP RNAs were isolated by Tri Reagent (Molecular Research Center).    2. Cytosol and microsome RNA extraction    2g seedlings were ground in liquid nitrogen and the powder was suspended with 7mL MEB buffer (100mM Tris-Cl, pH7.5, 5mM EGTA, 15mM MgCl2, 5mM DTT, 0.3M sucrose, 50U/ml SUPPERase In RNase inhibitor (Ambion), 50ug/ml cycloheximide, 50ug/ml chloramphenicol, and a complete proteinase inhibitor cocktail (Roche)), filtered by 2 lays of mirocloth and centrifuged at 10000g twice to remove debris. The supernatant was centrifuged at 100,000g in SW41 rotor (Beckman coulter) for 1 hour at 4℃. 1mL supernatant was transferred into new tube, and 5mL Tri Reagent was added to isolate Cytosol RNA. The microsome pellet was dissolved with 1mL Tri Reagent to isolate microsome RNA.
mRNA libraries were constructed with NEBNext® mRNA Library Prep kit (NEB, #6110s). Briefly, mRNA was purified from 5ug total RNA with Dynabeads® mRNA Purification Kit (Thermo Fisher, #61006), and hydrolyzed with RNA fragmentation reagent (Thermofisher, #AM8740). About 200nt RNA fragments was purified with Agencourt RNAClean XP Beads (Beckman Coulter, #63987), and reverse transcription was conducted with random primer. Adenine tail was added to the 3' end of the cDNA followed by DNA adaptor ligation to both ends. Finally, the mRNA library was amplified with primers complementary to the adaptor sequences.

tag: ecotype

value: WT


title: Pin WT / Htt WT rep3

description: Sample 10 – 9256

value: Pin WT / Htt WT


title: Pin KO / Htt KI rep3

description: Sample 1 – 9355

value: Pin KO / Htt KI


title: mRNA_Col_RiobosomeMBP_1


title: Pin KO / Htt KI rep1

description: Sample 6 – 9278


title: Pin KO / Htt KI rep2

description: Sample 2 – 9312


title: Adar2-WT


title: Pin WT / Htt WT rep2

description: Sample 12 – 9247


title: Pin KO / Htt WT rep1

description: Sample 4 – 9125


title: Pin WT / Htt KI rep1

description: Sample 5 – 9235


title: Pin WT / Htt WT rep1

description: Sample 9 – 9197


title: Testis 3


title: Testis 1


title: mRNA_Col_RiobosomeMBP_3


title: mRNA_Col_Cytosol_3


title: mRNA_Col_Microsome_2


title: mRNA_Col_RiobosomeFP_2


title: mRNA_Col_Microsome_3


title: mRNA_Col_Cytosol_2


title: mRNA_Col_Cytosol_1


title: sRNA_Col_MBP_3

data_processing:
Basecalls performed using Illumina CASAVA
Sequence reads were trimmed and size selected (18-42nt) using cutadapt v1.9.1, and then filtered to remove rRNA, tRNA, snoRNA, etc using bowtie with parameters -v 2 -k1.
Remained reads were mapped to the Arabidopsis genome TAIR10 (www.arabidopsis.org) using ShortStack v3.4 with parameters --bowtie_m 1000 --ranmax 50 --mmap u --mismatches 0.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files including mapped unique sequences and counts

extract_protocol:
1. Total RNA extraction.   (sRNA_Col_Total_1, sRNA_Col_Total_2, sRNA_Col_Total_3, sRNA_ago1-27_Total_1, sRNA_ago1-27_Total_2, sRNA_ago1-27_Total_3, sRNA_ago1-36_Total_1, sRNA_ago1-36_Total_2, sRNA_ago1-36_Total_3)    12 day seedlings of Col, ago1-27 and ago1-36 were ground in liquid nitrogen, and RNAs were extracted by Tri Reagent (Molecular Research Center) following the manufactory's instruction.    2. Microsome RNA extraction.   (sRNA_Col_Microsome_1, sRNA_Col_Microsome_2, sRNA_Col_Microsome_3, sRNA_ago1-27_Microsome_1, sRNA_ago1-27_Microsome_2)    2g seedlings of Col and ago1-27 were ground in liquide nitrogen, and the powder was suspended with 7mL MEB buffer containing 100mM Tris-Cl, pH7.5, 5mM EGTA, 15mM MgCl2, 5mM DTT, 0.3M sucrose, 50U/ml SUPERase In RNase inhibitor (Ambion), 50ug/ml cycloheximide, 50ug/ml chloramphenicol, and complete set of proteinase inhibitor cocktail (Roche).The slurry was filtered by 2 layers of mirocloth (Merk Millipore) and centrifuged at 10000g twice to remove debris. The supernatant was loaded on the top of 20% and 60% sucrose step gradients dissolved in MEB buffer, and centrifuged at 100,000g in SW41 rotor (Beckman coulter) for 1 hour at 4℃. The microsome fraction was recovered from the interface of the two layers of sucrose gradients, diluted by 10 times of MEB and precipitated by centrifuge. RNAs were isolated from these samples by Tri Reagent (Molecular Research Center).    3. Total polysome RNA extraction.   (sRNA_Col_TP_1, sRNA_Col_TP_2, sRNA_Col_TP_3)    1g Col seedlings was ground in liquid nitrogen, and the powder was resuspended with 8mL polysome extraction buffer (0.2M Tris-Cl, pH9.0, 0.2M KCl, 0.025M EGTA, 0.035M MgCl2, 0.2% Brij-35, 0.2% Triton X-100, 0.2% Igepal CA630, 0.2% Tween 20, 0.2% polyoxyethylene 10 tridecyl ether, 5mM DTT, 1mM PMSF, 50mg/ml cycloheximide, 50mg/ml chloramphenicol, , and 50U/ml SUPPERase In(Ambion)). The slurry was clarified by 10000g centrifugation twice at 4℃, and the supernatant was loaded on the top of sucrose cushion solution (0.4M Tris-Cl, pH9.0, 0.2M KCl, 0.005M EGTA, 0.035M MgCl2, 1.75M sucrose, 5mM DTT, 50mg/ml cycloheximide and 50mg/ml chloramphenicol), and centrifuged at 170000g for 3 hours at 4℃ to obtain the total polysome (TP). RNA was isolated by Tri Reagent.     4. MBP RNA extraction  (sRNA_Col_MBP_1, sRNA_Col_MBP_2, sRNA_Col_MBP_3)    2g seedlings was ground in liquid nitrogen, and the powder was suspended in 7ml microsome extraction buffer (MEB) consisting of 100mM Tris-Cl, pH7.5, 5mM EGTA, 15mM MgCl2, 5mM DTT, 0.3M sucrose, 50U/ml SUPPERase In (Ambion), 50mg/ml cycloheximide, 50mg/ml chloramphenicol, and complete proteinase inhibitor cocktail (Roche). The slurry was filtered with 2 layers of miracloth (Merk Millipore), and centrifuged at 10,000 g for 15 min at 4℃ to remove debris. The supernatant was loaded on the top of a 2.5ml 0.6M/2.5ml 1.7M sucrose step gradient and centrifuged at 140,000 g in a Beckman SW41 rotor for 1 hr at 4℃. The microsome fraction, which sediments to the 0.6M/1.7M layer interface, was carefully transferred into a new tube. The microsome fraction was diluted 10 times by MEB and centrifuged at 140,000 g for 0.5 hour to pellet the microsomes. The microsomes were dissolved in 8ml polysome extraction buffer (PEB) consisting of 0.2M Tris-Cl, pH9.0, 0.2M KCl, 0.025M EGTA, 0.035M MgCl2, 0.2% Brij-35, 0.2% Triton X-100, 0.2% Igepal CA630, 0.2% Tween 20, 0.2% polyoxyethylene 10 tridecyl ether, 5mM DTT, 1mM PMSF, 50mg/ml cycloheximide, 50mg/ml chloramphenicol and 0.5mg/ml heparin. Next, the microsome lysate were loaded onto the top of an 8ml 1.75M sucrose cushion solution (0.4M Tris-Cl, pH9.0, 0.2M KCl, 0.005M EGTA, 0.035M MgCl2, 1.75M sucrose, 5mM DTT, 50mg/ml cycloheximide and 50mg/ml chloramphenicol) and centrifuged at 170,000 g in a Beckman rotor Type70 Ti for 3h at 4℃ to obtain the MBP pellet. MBP RNA was isolated by Tri Reagent (Molecular Research Center).    5. ER associated RNA isolation   (sRNA_Col_ER_IP)    1g Arabidopsis seedlings expressing YFP-SEC12 was ground in liquid nitrogen, and the powder was suspended with 2mL IP buffer containing 50mM Tris-HCL, pH7.5, 150mM NaCL, 0.3M sucrose, 10% glycerol, and complete proteinase inhibitor cocktail (Roche). The slurry was clarified by 10000g centrifugation after gently shaking for 50 min at 4℃, and the supernatant was preleared by adding 30ul dynabeads proteinA (Life) for 30 1 hour. The beads was removed by centrifugation and the plant extract was incubated with 40ul anti-GFP antibody (Clotech) for 2 hours at 4℃ with gentle shaking. After washing with IP buffer 4 times the beads was subjected to RNA isolation by Tri Reagent (Molecular Research Center).
sRNA libraries were constructed with NEBNext® Multiplex Small RNA Library kit (NEB, #E7300S). Briefly, 30ug total RNA was resolved on 15% Ura PAGE, and 20-25nt small RNAs were recovered by gel purification. 3' and 5' adaptors were ligated to the small RNAs, and reverse transcription was conducted with the RT primer complementary to the 3' adaptor. Finally, the libraries were amplified with the primers complementary to the 5' and 3' adaptor sequences.


title: sRNA_Col_ER_IP


title: Pin WT / Htt KI rep3

description: Sample 8 – 9354


title: mRNA_Col_RiobosomeFP_3


title: mRNA_Col_RiobosomeFP_1


title: mRNA_Col_Microsome_1


title: sRNA_Col_MBP_2


title: sRNA_Col_TP_2


title: sRNA_Col_TP_3


title: sRNA_Col_MBP_1


title: sRNA_Col_TP_1


title: sRNA_ago1-36_Total_3


title: sRNA_ago1-36_Total_1


title: sRNA_ago1-36_Total_2


title: sRNA_Col_Microsome_3


title: sRNA_ago1-27_Microsome_1


title: sRNA_ago1-27_Total_3


title: sRNA_ago1-27_Microsome_2


title: sRNA_Col_Microsome_1


title: sRNA_ago1-27_Total_1


title: NoDice(4-25)-PKR expressing dDcr2 LoqsD R2D2 Rip

city: Durham

first: Edward

middle: Matthew

last: Kennedy

state: NC

address: Department of Molecular Genetics and Microbiology, Box 3025

department: Molecular Genetics and Microbiology

institute: Duke University

description:
RISC-associated small RNA
Dicer-deficient NoDice(4-25) HEK-293T cells with PKR knockout. Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):E6945-54. doi: 10.1073/pnas.1513421112

data_processing:
Initial reads were quality filtered with Cassava 1.8.2.
Reads >15 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33| fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15 –c | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, miRBase v. 20 annotations of miRNA hairpins or mature miRNA sequences (Kozomara and Griffiths-Jones, 2014), Ensembl noncoding RNA database release 70 (Flicek et al., 2014), human functional RNA database version 3.4 (Mituyama et al., 2009), the vector or viral sequence of interest, and finally human genome 19.  No mismatches were allowed for alignments to the different references except the human genome for which two mismatches were allowed.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and the strand (+ or -) that the read aligns to.  In this specific case it is aligned to the insert of the pCD-Rluc constuct which generates the dsRNA described in this work.

organism: Homo sapiens

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and Gentamicin

extract_protocol:
RISC-bound miRNAs 48 transfection were isolated by immunoprecipitation using a monoclonal antibody that recognizes all human Argonaute proteins (Abcam: AB 57113), TRIzol, Illumina TruSeq kit
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

tag: rna substrate investigated

value: pCD-Rluc

tag: cell line

tag: illumina index number


title: sRNA_Col_Microsome_2


title: RAT_PLA_1h_1

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

institute: PICB

description: small RNA expression data from RA rats after 1 hour placebo therapy

data_processing:
Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively.
The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie.
quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno.
The txt files for miRNA expression from mirDeep2 were used for further analysis.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample

organism: Rattus norvegicus

source_name: Muscle tissue from PLA  after 1 hour therapy, replicate 1

growth_protocol: Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC.

extract_protocol:
Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies).
Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)

treatment_protocol: Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction.

value: Wistar

tag: gender

value: Female

value: RAT Sub-epidermidis muscle tissue


title: RAT_AP_34d_1

description: small RNA expression data from RA rats after 34 days acupuncture therapy

source_name: Muscle tissue from AP after 34 days therapy, replicate 1


title: RAT_PLA_1h_2

source_name: Muscle tissue from PLA after 1 hour therapy, replicate 2


title: sRNA_Col_Total_3


title: sRNA_ago1-27_Total_2


title: sRNA_Col_Total_2


title: RAT_PLA_34d_2

description: small RNA expression data from RA rats after 34 days placebo therapy

source_name: Muscle tissue from PLA after 34 days therapy, replicate 2


title: RAT_AP_1h_2

description: small RNA expression data from RA rats after 1 hour acupuncture therapy

source_name: Muscle tissue from AP after 1 hour therapy, replicate 2


title: RAT_PLA_34d_1

source_name: Muscle tissue from PLA after 34 days therapy, replicate 1


title: RAT_AP_34d_2

source_name: Muscle tissue from AP after 34 days therapy, replicate 2


title: sRNA_Col_Total_1


title: NoDice(4-25)-PKR expressing dDcr2 R2D2 Rip


title: RAT_AP_1h_1

source_name: Muscle tissue from AP after 1 hour therapy, replicate 1


title: RAT_RA_T0_2

description: small RNA expression data from RA rats before therapy

source_name: Muscle tissue from RA before therapy, replicate 2


title: NoDice(4-25)-PKR expressing dDcr2 Rip

source_name: NoDice(4-25)-PKR expressing dDcr2 Rip


title: NoDice(4-25)-PKR Neg Rip

source_name: NoDice(4-25)-PKR Neg Rip


title: RAT_RA_T0_1

source_name: Muscle tissue from RA before therapy, replicate 1


title: NoDice(4-25)-PKR expressing dDcr2 R2D2 Deep

description:
Total small RNA
Dicer-deficient NoDice(4-25) HEK-293T cells with PKR knockout. Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):E6945-54. doi: 10.1073/pnas.1513421112

extract_protocol:
small RNAs (<200 nt) purified using the mirVana Kit (Ambion)
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.


title: NoDice(4-25)-PKR expressing dDcr2 LoqsD Deep


title: NoDice(4-25)-PKR expressing dDcr2 LoqsD Rip


title: HtVm3

city: Uppsala

first: Göran

last: Arnqvist

address: Norbyvägen 18D

department: Ecology and Genetics

country: Sweden

institute: Uppsala University

data_processing:
Quality trimming: RNA reads quality assessed using FastQC v.0.11.2. Illumina adapter sequences removed with cutadapt v.1.2.1. Low quality reads were trimmed with Trimmomatic v.0.3
Transcriptome was de novo assembled with Trinity 2.0.6. Reads from each library were aligned to the assembly using Bowtie v.0.12.6.
Gene Open Reading Frames were predicted using Transdecoder v.2.0.1. and ORF's >100 aminoacids were retained.
Each library were sequenced on two lanes (i.e. as technical replicates), which were subsequently pooled to maximize the coverage. The raw data is available separately for each technical replicate.
Supplementary_files_format_and_content: Txt file matrix of the raw read counts of predicted genes and transcripts, for all samples. The technical replicates are pooled.

organism: Callosobruchus maculatus

source_name: Virgin male head and thorax, replicate 3

extract_protocol:
Beetles (strain South India) were flash frozen and abdomen removed from the thorax on ice. Total RNA was harvested using Rneasy (Qiagen). The RNA-seq libraries were prepared using the Illumina TruSeq stranded mRNA sample preparation kit according to the manufacturer’s guidelines
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Please see the manuscript for details.

value: Head and thorax

tag: reproductive status

value: Virgin

tag: Sex

value: male


title: HtVm2

source_name: Virgin male head and thorax, replicate 2


title: NoDice(4-25)-PKR expressing dDcr2 LoqsD R2D2 Deep


title: HtVm1

source_name: Virgin male head and thorax, replicate 1


title: NoDice(4-25)-PKR expressing N-terminally trunctated human Dicer N1 Deep


title: popZ-del26_ZitP-N

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
Base calling: HiSeq Control Software 2.0.12.0, RTA 1.17.21.3, CASAVA-1.8.2
Alignment: BWA, samtools (via Galaxy plattform)
Peak calling: SeqMonk software (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1;
Supplementary_files_format_and_content: The processed data files report the coverage, expressed as a percentage of reads per probe, for the peak region covering the origin of replication of Caulobacter crescentus.Column1: location of the peak; column 2 percentage of reads per probe

molecule: genomic DNA

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus

growth_protocol: Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract).

extract_protocol:
Mid-log phase cells were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1%  formaldehyde at room temperature for 10 min and on ice for 30 min thereafter, washed  thrice in phosphate buffered saline (PBS) and lysed in a Ready-Lyse lysozyme solution  (Epicentre, Madison, WI) according to the manufacturer`s instructions. Lysates were  sonicated (Sonifier Cell Disruptor B-30; Branson Sonic Power. Co., Danbury, CT) on ice  using 10 bursts of 20 sec at output level 4.5 to shear DNA fragments to an average length  of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. Lysates were  normalized by protein content, diluted to 1 mL using ChIP buffer (0.01% SDS, 1.1%  Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl plus protease  inhibitors (Roche) and pre-cleared with 80 μL of protein-A agarose (Roche, Switzerland)  and 100 uμg BSA. Ten % of the supernatant was removed and used as total chromatin  input DNA as described before (Radhakrishnan et al., 2008).  Two microliters of polyclonal antibodies were added to the remains of the  supernatant, incubated overnight at 4°C with 80 μL of protein-A agarose beads pre  saturated with BSA, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2  mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1%  Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) and LiCl buffer  (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH  8.1) and twice with TE buffer (10 mM Tris-HCl (pH 8.1) and 1 mM EDTA). The  protein•DNA complexes were eluted in 500 μL freshly prepared elution buffer (1% SDS,  0.1 M NaHCO3), supplemented with NaCl to a final concentration of 300 mM and  incubated overnight at 65°C to reverse the crosslinks. The samples were treated with 2 μg  of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA  extracted using phenol:chloroform:453 isoamyl alcohol (25:24:1), ethanol-precipitated  using 20 ug glycogen as carrier and re-suspended in 100uL of water. For deep  sequencing (ChIP-seq) total chromatin input DNA was not saved.
DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland

tag: antibody

value: α-ZitP(N-TER) antibody


title: CysNO treatment: Treat_2

city: Daegu

first: Sang-Uk

last: Lee

address: 80 Daehakro, Bukgu

country: South Korea

institute: Kyungpook National University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: MSU7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: Leaf

growth_protocol: Sterilized seeds were germinated on sterile wet tissue papers and grown under 16h of light and 8h of dark at 23◦C

extract_protocol:
RNA was extracted from triplicate leaf samples of treated and control plants using RNeasy® Plant Mini Kit (Qiagen) according to standard protocol provided by the manufacturer.
RNA was purified using miRNeasy Kit (Qiagen), following the manufacturer’s instructions. Quality of RNA was analyzed by Agilent 2100 Bioanalyzer QC and samples with RIN(RNA Integrity Number) 7 ≥ and 28s/18s ratio 1.0 ≥ were used for c DNA synthesis. Library was prepared using TruSeq RNA library prep kit (Illumina) for 100bp paired-end sequencing.  Briefly, poly A tailed transcript RNA was isolated using oligo(dT) selection from 2µg total RNA and ramdomly fragmented by Mg 2+  ion treatment. The fragmented mRNA was subjected to cDNA synthesis through random hexamer priming. End-repair, A-tailing and Adapter ligation was conducted for Blunt-end producing and Adapter genernation. After that c DNA was amplified by PCRcDNA libraries were quantified by KAPA library quantification kit (Illumina). Samples were sequenced using Hiseq-2500 sequencer (Illumina)

treatment_protocol: 7 days grown seedling plants were irrigated with different concentration of CysNO solution and the optimized concentration (5mM CysNO) were used for RNA-Seq analysis.buffer (1mM HCl) only

tag: Stage

value: Seedling

value: Dongjin


title: popZ-KE_ZitP-N

value: popZ-mCherry(KE)


title: HtMm3

source_name: Mated male head and thorax, replicate 3

value: Mated


title: HtVf2

source_name: Virgin female head and thorax, replicate 2

value: female


title: popZ-KE_ZitP-C

value: α-ZitP(C-TER) antibody


title: CysNO treatment: Control_2


title: HtMm2

source_name: Mated male head and thorax, replicate 2


title: NoDice(4-25)-PKR Neg Deep

source_name: NoDice(4-25)-PKR Neg Deep


title: popZ-del26_ZitP-C


title: HtVf1

source_name: Virgin female head and thorax, replicate 1


title: ΔpopZ ZitP_ChIPseq

description: α-ZitP(C-TER) antibody

source_name: ΔpopZ ZitP ChIPseq

value: delta-popZ


title: CysNO treatment: Control_1


title: NoDice(4-25)-PKR expressing N-terminally trunctated human Dicer N1 Rip


title: ΔzitP ZitP_ChIPseq

description:
no peaks
α-ZitP(C-TER) antibody

source_name: ΔzitP ZitP ChIPseq

value: delta-zitP


title: NoDice(4-25)-PKR expressing dDcr2 Deep

source_name: NoDice(4-25)-PKR expressing dDcr2 Deep


title: HtVf3

source_name: Virgin female head and thorax, replicate 3


title: WT mcherry-PopZ_ChIPseq

description: α-RFP(C-TER) antibody (RFP TRAP, chromoTech)

source_name: WT mcherry-PopZ ChIPseq

value: parB::cfp-parB; popZ::mcherry-popZ


title: HtMm1

source_name: Mated male head and thorax, replicate 1


title: WT ZitP_ChIPseq 2

description: α-ZitP(N-TER) antibody

source_name: WT ZitP ChIPseq

value: wild type


title: HtMf3

source_name: Mated female head and thorax, replicate 3


title: WT ZitP_ChIPseq 1

description: α-ZitP(C-TER) antibody


title: WT ParB_ChIPseq

description: α-ParB antibody

source_name: WT ParB ChIPseq


title: HtMf2

source_name: Mated female head and thorax, replicate 2


title: CysNO treatment: Treat_1


title: AVm3

source_name: Virgin male abdomen, replicate 3

value: Abdomen


title: Y3E_24

city: Beijing

first: xiaoling

last: zhang

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of microbiology chinese academy of sciences

data_processing:
Illumina Casava software was used for base calling.
Sequenced reads were trimmed for adaptor sequences, masked for low-complexity or low-quality sequences, and then mapped to the reference genome Lactobacillus acetotolerans NBRC 13120 using tophap
Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated by cufflink
Genome_build: Lactobacillus acetotolerans NBRC 13120
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all sample

organism: Lactobacillus acetotolerans

source_name: 24 hours after 12% (v/v) ethanol treatment rep2

growth_protocol: L. acetotolerans F28 was cultured at 30℃ in MRS5 broth medium (MRS broth medium with pH value is 5)

extract_protocol:
Total RNA were extracted and purified using the Bacterial RNA kit (OMEGATM) according to the protocol provided by the manufacturer.
The cDNA libraries were constructed using NEBNextUltraTM RNA library Prep Kit and submitted for sequencing using Illumina Hiseq 4000.

treatment_protocol: L. acetotolerans F28 cells were cultured till OD600≈1 and treated with 12% (v/v) ethanol or water  for 3 and 24 hours

tag: time

value: post ethanol treatment hour 24


title: Y4E_24

source_name: 24 hours after 12% (v/v) ethanol treatment rep3


title: Y1E_24

source_name: 24 hours after 12% (v/v) ethanol treatment rep1


title: HtMf1

source_name: Mated female head and thorax, replicate 1


title: Y4_24

source_name: 24 hours after 12% (v/v) water treatment rep3

value: post water treatment hour 24


title: AVm1

source_name: Virgin male abdomen, replicate 1


title: AVf3

source_name: Virgin female abdomen, replicate 3


title: Y1_24

source_name: 24 hours after 12% (v/v) water treatment rep1


title: Y3_24

source_name: 24 hours after 12% (v/v) water treatment rep2


title: AVf2

source_name: Virgin female abdomen, replicate 2


title: Y4E_3

source_name: 3 hours after 12% (v/v) ethanol treatment rep3

value: post ethanol treatment hour 3


title: AVf1

source_name: Virgin female abdomen, replicate 1

value: Virgin


title: AMm3

source_name: Mated male abdomen, replicate 3

value: male


title: Y3E_3

source_name: 3 hours after 12% (v/v) ethanol treatment rep2


title: AMm2

source_name: Mated male abdomen, replicate 2


title: Y1E_3

source_name: 3 hours after 12% (v/v) ethanol treatment rep1


title: AMf3

source_name: Mated female abdomen, replicate 3


title: AMm1

source_name: Mated male abdomen, replicate 1


title: Y3_3

source_name: 3 hours after 12% (v/v) water treatment rep2

value: post water treatment hour 3


title: AMf2

source_name: Mated female abdomen, replicate 2


title: AMf1

source_name: Mated female abdomen, replicate 1


title: Y1_3

source_name: 3 hours after 12% (v/v) water treatment rep1


title: Day 2 adult P-granule(-); UNC-119::GFP(+) gonads #3

status: Public on Dec 22 2016

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing:
Raw sequences were mapped to transcriptome version WS220 using Tophat2.  Only reads with one unique mapping were allowed; otherwise default options were used.  Reads mapping to ribosomal RNAs were removed from further analysis.
The Bioconductor package DESeq2 was used for differential expression analysis. A Benjamini-Hochberg multiple hypothesis corrected p-value cutoff of 0.05 was used as a significance cutoff.
Normalized read counts per gene were obtained with DESeq2, size factor normalization was used.
Genome_build: WS220
Supplementary_files_format_and_content: Wormbase ID, WS220 Gene names, gene sequence, transcript type, gene category designation, and Differential expression comparison data (Mean expression, log2(Fold Change), BH adjusted p-value) and read counts per gene averaged over replicates for control samples, RNAi samples and mutant samples.

organism: Caenorhabditis elegans

source_name: dissected gonads

growth_protocol: C. elegans strains were maintained at 15° or 20° on OP50 bacteria as described (Brenner 1974).

extract_protocol:
Total RNA was extracted using Trizol reagent and ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (Cat. #E6310).
Libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina sequencing (Cat. #E7530). Libraries were sequenced at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley using the Illumina HiSeq 2000, 2500, or 4000 platforms.

treatment_protocol: For experiments using RNAi, synchronized unc-119::gfp L1 worms (P0) were placed on HT115 bacteria containing empty RNAi vector (control) or expressing double strand RNA that targets P granules (i.e., pgl-1, pgl-3, glh-1, and glh-4) or targets pgl-1 or pgl-1; pgl-3 (Updike et al. 2014; Campbell and Updike 2015) at 24° (Day 0).  Three days later, F1 larvae were transferred to new control or P-granule RNAi plates and returned to 24°.  The majority of these F1 larvae were at the L1 or L2 stage at the time of transfer.  The next day (Day 4), L4 worms were visually identified by their size and the presence of a white crescent at their vulva.  Gonads were dissected from L4 control worms and L4 P-granule RNAi worms and cut at the gonad bend with 30½ gauge needles in egg buffer (27.5 mM HEPES, 130 mM NaCl, 2.2 mM MgCl2, 2.2 mM CaCl2, and 0.528 mM KCl) containing 0.5% Tween-20 and 1 mM levamisole.  Sterility could not be assessed in L4 worms.  However, greater than 80% sterility was observed in P-granule RNAi adults that were aged from the population of worms from which L4 gonads were collected.  For Day 1 adults, worms were allowed to age one day past the L4 stage and then dissected.  For Day 2 adults, worms were allowed to age two days past the L4 stage and then dissected.  In Day 2 adults, gonads that visually expressed the unc-119::gfp transgene were collected as a separate sample from those that did not detectably express unc-119::gfp.  For adult control gonads, gonads were dissected from fully fertile worms and cut at the gonad bend.  For adult P-granule RNAi worms, gonads were collected only from sterile worms, as judged by the lack of embryos in the uterus.  Large P-granule RNAi gonads were cut at the gonad bend; stunted P-granule RNAi gonads were collected in their entirety.  Once dissected, gonad arms were collected in Trizol, and total RNA was extracted.  For control samples, 75 to 100 gonads were collected per replicate.  For P-granule RNAi samples, 125 to 150 gonads were collected per replicate. Three biological replicates were performed for each treatment and time point. For experiments using P-granule mutants, wild-type (control), pgl-1 single mutants, or glh-1 single mutant adults (isolated from glh-1(gk100)/hT2g balanced parents) were allowed to lay eggs overnight on OP50 bacteria at 24°.  The day after the egg lay, the adults were removed and the F1 progeny were returned to 24° for two days.  Day 1 adult gonads were dissected, collected into Trizol, and total RNA was extracted.  Only distal gonad arms were collected from fertile wild-type worms or sterile P-granule mutant worms, as judged by the lack of embryos in the uterus.  Three biological replicates were performed for the wild-type and pgl-1 samples, and two biological replicates were performed for the glh-1 sample.

value: edIs6[unc-119p::unc-119::gfp + rol-6] IV

tag: RNAi treatment

value: P-granule RNAi

tag: temperature


title: Day 2 adult P-granule(-); UNC-119::GFP(+) gonads #2


title: AVm2

source_name: Virgin male abdomen, replicate 2


title: Day 2 adult P-granule(-); UNC-119::GFP(-) gonads #3


title: Day 2 adult P-granule(-); UNC-119::GFP(+) gonads #1


title: Day 2 adult P-granule(-); UNC-119::GFP(-) gonads #2


title: Day 1 adult control gonads #3

value: empty vector RNAi


title: AtTric1&2 dko rosette leaves

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

description:
3 replicates
Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to growth chambers at 22C, following a 16 h photoperiod. At 5 day old seedlings were transferred to soil and rosette leaves collected at 4 weeks.
rosettes_col0vdko_tair.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, then mapped to the tair10 whole genome using bowtie v2.2.0-beta7 and tophat v2.2.0 with the parameters:–b2-sensitive –r 0 –mate-std-dev 100 –g 1 –G .
Transcript abundance was estimated by FPKM (fragment per Kilobase of exon per million fragments mapped) using Cufflinks pipeline (version 2.2.0) and RNAseq data was analysed using Cuffdiff 2.2.0 under default parameters.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, as part of Cuffdiff output

source_name: Arabidopsis rosette leaves from 4-week old AtTric1&2 dko mutant plants.

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich) with an on-column DNase treatment according to the manufacturer’s instructions.
RNA-seq libraries were generated using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to manufacturer’s instructions (Illumina).

treatment_protocol: 22 degrees with light intensity of 80nmol quanta m-2s-1 in a 16-photoperiod

value: rosette leaf

value: AtTric1&2 dko mutants

value: 4-week old plants

tag: treatment/conditions


title: Day 1 adult P-granule(-); UNC-119::GFP(-) gonads #2

tag: strain


title: Day 2 adult P-granule(-); UNC-119::GFP(-) gonads #1


title: Day 1 adult control gonads #1


title: Day 2 adult control gonads #2


title: 1 µM retinoic acid (2 hours), rep1

city: La Jolla

first: Gregg

last: Duester

address: 10901 N. Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina’s Basespace was used to convert bcl files to FASTQ files and de-multiplex the samples
Sequenced reads were assessed with FastQC v0.11, then mapped to mm10 whole genome using TopHat2 v2.0.13 and Bowtie2 v2.2.5.0 with --b2-sensitive option and default parameters
Partek Genomics Suite v6.6 was applied for quantification based on RefSeq transcript model (2015-08-04)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count and RPKM values for each Sample

source_name: neuromesodermal progenitor cells

growth_protocol: Neuromesodermal progenitor cells were derived from mouse embryonic stem cells that were treated with bFGF for 2 days, then treated with bFGF and WNT agonist (CHIR99021) for 1 day.

extract_protocol:
Total RNA was extracted using the Ambion mirVana miRNA Isolation Kit.
1ug of Total RNA was used to construct multiplexed Libraries using Illumina's Truseq Stranded Total RNA Kit. First, the Total RNA was subjected to ribodepletion process to remove rRNA. The remaining RNA is purified, fragmented, Reverse transcribed, adapter ligated and finally PCR amplified to enrich the DNA fragments.

treatment_protocol: Cells were treated with either DMSO control (2 hours), 25 nM retinoic acid (2 hours), or 1 µM retinoic acid (2 hours).

tag: tissue

value: embryonic stem cell

tag: agent

value: 1 µM retinoic acid


title: DMSO control (2 hours), rep2

value: DMSO control


title: 25 nM retinoic acid (2 hours), rep2

value: 25 nM retinoic acid


title: L4 larval control gonads #1

tag: genotype


title: AtTric1&2 dko seedlings

description:
3 replicates
Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to growth chambers at 22C, following a 16 h photoperiod. Tissue was collected at 2 weeks.
seedling_col0vdko_tair.txt

source_name: Arabidopsis seedlings, 2-weeks old, AtTric1&2 dko mutants.

value: whole seedling

tag: age

value: 2-week old plants

value: 22 degrees with light intensity of 80nmol quanta m-2s-1 in a 16-photoperiod


title: Aerobic, glucose, rep2

city: Seoul

first: kucsbl

last: submitter

state: Seoul

address: Anamdong 5-ga, Seongbuk-gu

department: Department of Biotechnology

institute: Korea University

description: AsuRPKM.csv

data_processing:
Low quality (Q<30) reads were trimmed at the 5' and 3' ends using the ShortRead package.
Quality controlled read data were aligned on the reference genome sequence using Bowtie2.
DESeq and edgeR package in the Bioconductor/R packages were used for making RPKM values.
Genome_build: Actinobacillus succinogenes strain 130Z (NCBI RefSeq ID: NC_009655.1)
Supplementary_files_format_and_content: CSV file of normalized RPKM value from edgeR for every samples

organism: Actinobacillus succinogenes 130Z

source_name: Mid-exponential growth phase

extract_protocol:
TruSeq RNA Sample Preparation Kit (Illumina) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: oxygen

value: Aerobic

tag: substrate

value: Glucose


title: WT(Col0) seedlings

source_name: Arabidopsis seedlings, 2-weeks old, WT(Col0).

growth_protocol: Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to growth chambers at 22C, following a 16 h photoperiod.


title: Aerobic, glucose, rep3

description: AsuRPKM.csv


title: Aerobic, glucose, rep1

description: AsuRPKM.csv


title: Aerobic, fumarate, rep2

description: AsuRPKM.csv

value: Fumarate with glycerol


title: Day 1 adult control gonads #2


title: Aerobic, fumarate, rep1

description: AsuRPKM.csv


title: Anaerobic, glucose, rep1

description: AsuRPKM.csv

value: Anaerobic


title: WT(Col0) rosette leaves

source_name: Arabidopsis rosette leaves from 4-week old WT(Col0) plants.


title: 1 µM retinoic acid (2 hours), rep2


title: Y4_3

source_name: 3 hours after 12% (v/v) water treatment rep3

value: post water treatment hour 3


title: 25 nM retinoic acid (2 hours), rep1


title: Anaerobic, fumarate, rep3

description: AsuRPKM.csv


title: DMSO control (2 hours), rep1


title: Aerobic, fumarate, rep3

description: AsuRPKM.csv


title: L4 larval P-granule(-); UNC-119::GFP(-) gonads #2

value: edIs6[unc-119p::unc-119::gfp + rol-6] IV

value: P-granule RNAi


title: HIV-1-infected CEM-SS total small RNA replicate 1

description: Total small RNA

data_processing:
Initial reads were quality filtered with Cassava 1.8.2.
Reads>15 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33|  fastx_clipper -a TruSeq-Index# -l 15 –c | fastq_to_fasta –Q 33 | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, miRBase v. 20 annotations of miRNA hairpins or mature miRNA sequences, Ensembl noncoding RNA database release 70, human functional RNA database version 3.4, the viral sequence of interest, and finally human genome 19.  Reverse complement alignments were only allowed for the human and viral genomes.  No mismatches or were allowed except for the human genome for which two mismatches were allowed.
miRNA sequences were given a -5p or -3p designation if they aligned to the 5′ or 3′ stem region, respectively, of the miRNA precursor, as annotated in miRbase.  miRNAs that represented ≥0.1% of the total miRNA population in both cellular and virion libraries were considered significant.
Genome_build: human genome 19
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and the strand (+ or -) that the read aligns to.

source_name: CEM-SS cell line (#776, AIDS Reagent Program)

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and Gentamicin.

extract_protocol:
Total RNA was isolated using TRIzol for cells and purified virons.
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

tag: illumina index number

tag: cell line

value: CEM-SS


title: Anaerobic, glucose, rep2

description: AsuRPKM.csv


title: HIV-1-infected CEM-SS total small RNA replicate 2

description: Total small RNA


title: Anaerobic, fumarate, rep2

description: AsuRPKM.csv


title: Anaerobic, glucose, rep3

description: AsuRPKM.csv