title: HMVII-NC-1


title: hESC_CHD7 KO_RNA-seq_rep1

status: Public on Oct 10 2021

type: SRA

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

country: USA

institute: Massachusetts General Hospital

description: rRNA depleted

library_source: transcriptomic

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 reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count for each gene

molecule: total RNA

organism: Homo sapiens

source_name: hESCs

growth_protocol: Human ES cell line H9 was cultured and maintained in mTesR1 medium (Stem Cell Technologies).

extract_protocol:
RNA was extracted from cells using TRI Reagent (Molecular Research Center, Inc) and further purified using Zymo RNA clean and concentrator-5 kit (Zymo Research) with DNase I treatment. DNA was extracted using phenol/chloroform followed by ethanol precipitation.
Sequencing libraries were prepared as described previously in Bowman SK et al. (2013).

treatment_protocol: Cells were treated with 4-Thiouridine for 16 hours and with LNA-GapmeRs for 24 hours, respectively, before harvesting for further experiments.

tag: cell line

tag: treatment

value: Untreated

tag: genotype


title: hESC_HERVH KD_RNA-seq_rep2

description: rRNA depleted

value: LNA-GapmeRs treated

value: wild type (CHD7-HA)


title: hESC_WT_PAR-CLIP_rep1

data_processing:
Library strategy: PARCLIP-seq
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 reference genome hg19 using BWA
Normalized genome coverage bigWig files were generated by deeptools bamCoverage
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

value: 4-Thiouridine treated

value: wild type

tag: antibody

value: CHD7 (Abcam, ab31824)


title: hESC_CHD7 KO_p300 CnR_rep2

library_source: genomic

data_processing:
Library strategy: CUT&RUN-seq
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 reference genome hg19 using BWA
Normalized genome coverage bigWig files were generated by deeptools bamCoverage
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

tag: chip antibody


title: hESC_CHD7 KO_p300 CnR_rep1


title: hESC_HERVH KO_H3K4me1 CnR_rep2

value: Deletion of HERVH element on Chr2


title: hESC_WT_PAR-CLIP_input1

value: IgG (Abcam, ab37415)


title: hESC_CHD7 KO_H3K4me1 CnR_rep1


title: hESC_HERVH KD_H3K4me1 CnR_rep2


title: hESC_HERVH KO_H3K4me1 CnR_rep1


title: hESC_WT_p300 CnR_rep2


title: hESC_HERVH KD_H3K4me1 CnR_rep1


title: hESC_WT_RNA-seq_rep1

description: rRNA depleted


title: hESC_WT_p300 CnR_rep1


title: hESC_HERVH KO_H3K27ac CnR_rep4


title: hESC_CHD7 KO_H3K4me1 CnR_rep2


title: hESC_WT_H3K4me1 CnR_rep2


title: hESC_HERVH KD_H3K27ac CnR_rep3


title: hESC_WT_H3K4me1 CnR_rep1


title: hESC_HERVH KO_H3K27ac CnR_rep2


title: hESC_HERVH KD_H3K27ac CnR_rep4


title: hESC_CHD7 KO_H3K27ac CnR_rep4


title: hESC_HERVH KD_H3K27ac CnR_rep1


title: hESC_HERVH KD_H3K27ac CnR_rep2


title: hESC_CHD7 KO_H3K27ac CnR_rep3


title: hESC_HERVH KO_H3K27ac CnR_rep1


title: hESC_CHD7 KO_H3K27ac CnR_rep2


title: hESC_HERVH KO_H3K27ac CnR_rep3


title: hESC_WT_H3K27ac CnR_rep4


title: hESC_CHD7 KO_H3K27ac CnR_rep1


title: hESC_HERVH KO_CHD7 CnR_rep4


title: hESC_WT_H3K27ac CnR_rep1


title: hESC_HERVH KO_CHD7 CnR_rep1


title: hESC_CHD7 KO_CHD7 CnR_rep1


title: hESC_HERVH KO_CHD7 CnR_rep3


title: hESC_WT_H3K27ac CnR_rep2


title: hESC_CHD7 KO_CHD7 CnR_rep2


title: hESC_WT_CHD7 CnR_rep1


title: hESC_WT_CHD7 CnR_rep2


title: hESC_HERVH KD_ATAC-seq_rep2

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 reference genome hg19 using BWA
Normalized genome coverage bigWig files were generated by deeptools bamCoverage
Genome_build: hg19
Supplementary_files_format_and_content: bigWig


title: hESC_CHD7 KO_ATAC-seq_rep1


title: hESC_HERVH KD_ATAC-seq_rep1


title: Casodex-DHT-100k

city: Guangzhou

first: Xin

last: Chen

address: No. 100 Waihuan Xi Road, GuangzhouHigher Education Mega Center, Panyu District

country: China

institute: Guangdong University of Technology

description:
Casodex-DHT-100k
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt

data_processing:
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters.
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: VCaP_casodex_gene_fpkm.txt: Tab-delimited text file includes FPKM values for single cells with sufficient and unbiased sequencing reads.

source_name: VCaP

growth_protocol: VCaP human prostate cancer cell lines were obtained from ATCC and maintained in DMEM media (Gibco). The media was supplemented with 10% fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.

extract_protocol: Nextera XT Index Kit v2.

treatment_protocol: VCaP cells were transferred into phenol-red free DMEM media (Gibco), 1 day prior to DHT stimulation. The media was supplemented with 10% charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were induced with either ethanol (vehicle) or DHT following DMSO (vehicle) or Casodex pre-treatment, before being dissociated and triturated into single-cell suspensions for single-cell analyses.

value: VCaP

tag: cell type

value: Prostate cancer cell line

value: Caso-DHT

tag: time


title: Casodex-EtOH-100k

description:
Casodex-EtOH-100k
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt

value: Caso-EtOH


title: C2-H8_S124

description:
C2-H8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: hESC_WT_H3K27ac CnR_rep3


title: hESC_HERVH KD_CHD7 CnR_rep2


title: hESC_HERVH KD_CHD7 CnR_rep1


title: hESC_WT_CHD7 CnR_rep3


title: hESC_WT_ATAC-seq_rep2


title: C2-H10_S90

description:
C2-H10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: hESC_CHD7 KO_CHD7 CnR_rep3


title: hESC_HERVH KO_ATAC-seq_rep2


title: hESC_HERVH KD_CHD7 CnR_rep3


title: C2-H11_S60

description:
C2-H11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: hESC_HERVH KO_ATAC-seq_rep1


title: hESC_HERVH KO_CHD7 CnR_rep2


title: DMSO-EtOH-100k

description:
DMSO-EtOH-100k
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt

value: DMSO-EtOH


title: hESC_CHD7 KO_ATAC-seq_rep2


title: C2-H9_S106

description:
C2-H9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: hESC_WT_ATAC-seq_rep1


title: C2-H5_S78

description:
C2-H5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-H12_S135

description:
C2-H12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G6_S61

description:
C2-G6
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-H2_S81

description:
C2-H2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: DMSO-DHT-100k

description:
DMSO-DHT-100k
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt

value: DMSO-DHT


title: C2-H4_S63

description:
C2-H4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G9_S95

description:
C2-G9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-H7_S111

description:
C2-H7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G5_S120

description:
C2-G5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G1_S54

description:
C2-G1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-H1_S129

description:
C2-H1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G4_S67

description:
C2-G4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G2_S100

description:
C2-G2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G12_S69

description:
C2-G12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-F2_S134

description:
C2-F2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E7_S49

description:
C2-E7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D9_S58

description:
C2-D9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-F7_S94

description:
C2-F7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E1_S73

description:
C2-E1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E2_S55

description:
C2-E2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D5_S101

description:
C2-D5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G3_S96

description:
C2-G3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D11_S119

description:
C2-D11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D6_S70

description:
C2-D6
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D12_S115

description:
C2-D12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-F9_S86

description:
C2-F9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-F5_S116

description:
C2-F5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E11_S110

description:
C2-E11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-G11_S71

description:
C2-G11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D3_S56

description:
C2-D3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E8_S114

description:
C2-E8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E4_S75

description:
C2-E4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D8_S82

description:
C2-D8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E3_S52

description:
C2-E3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-C4_S92

description:
C2-C4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-C9_S84

description:
C2-C9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-C10_S74

description:
C2-C10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-F3_S66

description:
C2-F3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-C8_S80

description:
C2-C8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E5_S76

description:
C2-E5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B5_S85

description:
C2-B5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-F12_S50

description:
C2-F12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-E12_S65

description:
C2-E12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-F6_S64

description:
C2-F6
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B2_S88

description:
C2-B2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B4_S79

description:
C2-B4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B10_S91

description:
C2-B10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B1_S57

description:
C2-B1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-A4_S105

description:
C2-A4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-H9_S108

description:
C1-H9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-D1_S93

description:
C2-D1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-C1_S83

description:
C2-C1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B8_S68

description:
C2-B8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-H8_S133

description:
C1-H8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B3_S62

description:
C2-B3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-C5_S77

description:
C2-C5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-H1_S31

description:
C1-H1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-C6_S51

description:
C2-C6
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B6_S87

description:
C2-B6
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G3_S112

description:
C1-G3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G4_S10

description:
C1-G4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-B11_S130

description:
C2-B11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-A2_S72

description:
C2-A2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-A11_S89

description:
C2-A11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G1_S103

description:
C1-G1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G11_S128

description:
C1-G11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-A6_S53

description:
C2-A6
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-A1_S125

description:
C2-A1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-H7_S2

description:
C1-H7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F9_S30

description:
C1-F9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F8_S43

description:
C1-F8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-H5_S1

description:
C1-H5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F5_S20

description:
C1-F5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F4_S29

description:
C1-F4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F12_S22

description:
C1-F12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G7_S16

description:
C1-G7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F10_S44

description:
C1-F10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C2-A10_S59

description:
C2-A10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F1_S21

description:
C1-F1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G12_S36

description:
C1-G12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E5_S17

description:
C1-E5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-H4_S26

description:
C1-H4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G8_S99

description:
C1-G8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G9_S48

description:
C1-G9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E12_S3

description:
C1-E12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F6_S24

description:
C1-F6
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F7_S41

description:
C1-F7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G5_S132

description:
C1-G5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-G2_S12

description:
C1-G2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-F3_S98

description:
C1-F3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D10_S7

description:
C1-D10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-C7_S47

description:
C1-C7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-C5_S34

description:
C1-C5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E3_S46

description:
C1-E3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E10_S39

description:
C1-E10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D4_S25

description:
C1-D4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D8_S45

description:
C1-D8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D5_S28

description:
C1-D5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-C1_S35

description:
C1-C1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E7_S32

description:
C1-E7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B4_S102

description:
C1-B4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B9_S6

description:
C1-B9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D12_S123

description:
C1-D12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D3_S107

description:
C1-D3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E11_S15

description:
C1-E11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E1_S127

description:
C1-E1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E4_S23

description:
C1-E4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B8_S117

description:
C1-B8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-C4_S97

description:
C1-C4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D1_S11

description:
C1-D1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B7_S13

description:
C1-B7
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B5_S27

description:
C1-B5
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B12_S113

description:
C1-B12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-C3_S37

description:
C1-C3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-D9_S18

description:
C1-D9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-C11_S8

description:
C1-C11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-A9_S42

description:
C1-A9
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B10_S109

description:
C1-B10
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B2_S104

description:
C1-B2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-C2_S5

description:
C1-C2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B11_S118

description:
C1-B11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-A8_S40

description:
C1-A8
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-E2_S33

description:
C1-E2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-B3_S4

description:
C1-B3
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-A4_S14

description:
C1-A4
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-A12_S19

description:
C1-A12
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-A11_S38

description:
C1-A11
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-A1_S122

description:
C1-A1
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: C1-A2_S9

description:
C1-A2
PolyA RNA
processed data file: VCaP_casodex_gene_fpkm.txt


title: VCaP_normal_H6

description:
PolyA RNA
processed data file: LNCaP_normal_growing_time_course_fpkm.txt

data_processing:
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters.
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: LNCaP_normal_growing_time_course_fpkm.txt: Tab-delimited text file includes FPKM values for single cells.

growth_protocol: VCaP and LNCaP human prostate cancer cell lines were obtained from ATCC and maintained in DMEM and RPMI 1640 media (Gibco), respectively. Both media were supplemented with 10% fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.

treatment_protocol: For time course induction, LNCaP cells were transferred into phenol-red free RPMI media (Gibco), 3 days prior to DHT stimulation. The media were supplemented with 10% charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were treated with either ethanol (vehicle) or DHT at 4 time points (0h, 3h, 6h and 12 h), before being dissociated and triturated into single-cell suspensions for single-cell analyses. For normal growing cells, there's no treatment to them.

value: normal growing, no treatment


title: VCaP_normal_H3


title: VCaP_normal_G9


title: VCaP_normal_G8


title: VCaP_normal_G4


title: VCaP_normal_H4


title: VCaP_normal_G3


title: VCaP_normal_H1


title: VCaP_normal_F8


title: VCaP_normal_F10


title: VCaP_normal_C5


title: VCaP_normal_G1


title: VCaP_normal_D5


title: VCaP_normal_C2


title: VCaP_normal_F1


title: VCaP_normal_D1


title: VCaP_normal_B12


title: VCaP_normal_B11


title: VCaP_normal_B8


title: VCaP_normal_A9


title: VCaP_normal_B9


title: VCaP_normal_A8


title: VCaP_normal_C11


title: VCaP_normal_B7


title: VCaP_normal_A7


title: VCaP_normal_100k_bulk


title: VCaP_normal_A12


title: LNCaP_normal_H10

source_name: LNCaP

value: LNCaP


title: LNCaP_normal_E9


title: LNCaP_normal_G10


title: LNCaP_normal_G2


title: VCaP_normal_F3


title: LNCaP_normal_G7


title: LNCaP_normal_E12


title: LNCaP_normal_F7


title: LNCaP_normal_E10


title: LNCaP_normal_E4


title: LNCaP_normal_D8


title: LNCaP_normal_D3


title: LNCaP_normal_E6


title: LNCaP_normal_C4


title: LNCaP_normal_C3


title: LNCaP_normal_E7


title: LNCaP_normal_D7


title: LNCaP_normal_B2


title: LNCaP_normal_E11


title: LNCaP_normal_C10


title: LNCaP_normal_D10


title: VCaP_normal_A2


title: LNCaP_normal_B5


title: LNCaP_normal_A6


title: LNCaP_normal_B3


title: LNCaP_12_h_H6

value: DHT


title: VCaP_normal_A1


title: LNCaP_12_h_H7


title: LNCaP_normal_A3


title: LNCaP_12_h_H4


title: LNCaP_normal_C12


title: LNCaP_12_h_F3


title: LNCaP_12_h_H12


title: LNCaP_normal_A4


title: LNCaP_12_h_G2


title: LNCaP_12_h_F11


title: LNCaP_12_h_E9


title: LNCaP_normal_B4


title: LNCaP_12_h_H11


title: LNCaP_12_h_E11


title: LNCaP_12_h_D7


title: LNCaP_12_h_D5


title: LNCaP_normal_C8


title: LNCaP_12_h_C5


title: LNCaP_12_h_D10


title: LNCaP_12_h_F1


title: LNCaP_normal_A5


title: LNCaP_normal_100k_bulk


title: LNCaP_12_h_D2


title: LNCaP_12_h_C3


title: LNCaP_12_h_C4


title: LNCaP_12_h_D11


title: LNCaP_12_h_G9


title: LNCaP_12_h_C1


title: LNCaP_12_h_E7


title: LNCaP_12_h_C10


title: LNCaP_12_h_C12


title: LNCaP_12_h_D8


title: LNCaP_12_h_B7


title: LNCaP_12_h_B4


title: LNCaP_12_h_B2


title: LNCaP_12_h_A8


title: LNCaP_12_h_A3


title: LNCaP_6_h_G3


title: LNCaP_12_h_A6


title: LNCaP_12_h_A1


title: LNCaP_6_h_G2


title: LNCaP_6_h_H11


title: LNCaP_6_h_H2


title: LNCaP_6_h_H7


title: LNCaP_6_h_F11


title: LNCaP_6_h_G7


title: LNCaP_6_h_E11


title: LNCaP_6_h_D7


title: LNCaP_6_h_E4


title: LNCaP_6_h_D9


title: LNCaP_6_h_E8


title: LNCaP_6_h_D5


title: LNCaP_6_h_C6


title: LNCaP_6_h_C7


title: LNCaP_6_h_D3


title: LNCaP_6_h_C4


title: LNCaP_6_h_D12


title: LNCaP_6_h_E2


title: LNCaP_6_h_C2


title: LNCaP_6_h_E1


title: LNCaP_12_h_100_k_bulk


title: LNCaP_6_h_B7


title: LNCaP_6_h_B2


title: LNCaP_6_h_B5


title: LNCaP_6_h_B12


title: LNCaP_6_h_A9


title: LNCaP_6_h_A1


title: LNCaP_6_h_A7


title: LNCaP_6_h_A8


title: LNCaP_6_h_100k_bulk


title: LNCaP_3_h_H8


title: LNCaP_3_h_H6


title: LNCaP_6_h_F4


title: LNCaP_3_h_H4


title: LNCaP_3_h_H1


title: LNCaP_3_h_G1


title: LNCaP_3_h_G10


title: LNCaP_3_h_F7


title: LNCaP_3_h_F8


title: LNCaP_3_h_G4


title: LNCaP_3_h_F2


title: LNCaP_3_h_F6


title: LNCaP_3_h_E12


title: LNCaP_3_h_E3


title: LNCaP_3_h_E6


title: LNCaP_3_h_D6


title: LNCaP_3_h_F1


title: LNCaP_3_h_E10


title: LNCaP_3_h_F9


title: LNCaP_3_h_D11


title: LNCaP_3_h_C11


title: LNCaP_3_h_D2


title: LNCaP_3_h_C12


title: LNCaP_3_h_C10


title: LNCaP_3_h_C5


title: LNCaP_3_h_D1


title: LNCaP_3_h_D4


title: LNCaP_3_h_A5


title: LNCaP_3_h_B4


title: LNCaP_3_h_B10


title: LNCaP_3_h_100k_bulk


title: LNCaP_3_h_A4


title: LNCaP_3_h_A3


title: LNCaP_0_h_H5


title: LNCaP_0_h_G12


title: LNCaP_0_h_G11


title: LNCaP_0_h_G6


title: LNCaP_0_h_G8


title: LNCaP_0_h_H2


title: LNCaP_3_h_D10


title: LNCaP_0_h_F9


title: LNCaP_0_h_F7


title: LNCaP_0_h_H10


title: LNCaP_0_h_F6


title: LNCaP_0_h_F12


title: LNCaP_0_h_G4


title: LNCaP_0_h_E12


title: LNCaP_0_h_C7


title: LNCaP_0_h_C2


title: LNCaP_0_h_F2


title: LNCaP_0_h_D12


title: LNCaP_0_h_D9


title: LNCaP_0_h_F10


title: LNCaP_0_h_C6


title: LNCaP_0_h_A7


title: LNCaP_0_h_B8


title: LNCaP_0_h_A5


title: LNCaP_0_h_B5


title: LNCaP_0_h_A12


title: LNCaP_0_h_A11


title: LNCaP_0_h_100_k_bulk


title: LNCaP_0_h_C8


title: LNCaP_0_h_B11


title: RHV103

description:
Time course
PolyA RNA
processed data file: vcap_time_course_single_cell_FPKM.txt

data_processing:
For processing the HT samples, demultiplexing was performed using Fluidigm’s HT Demultiplexer Perl script.
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters.
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKM values for each single cell.

treatment_protocol: VCaP cells were transferred into phenol-red free DMEM media (Gibco), 1day prior to DHT stimulation. The media was supplemented with 10% charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were treated with either ethanol (vehicle) or DHT at 4 time points (0h, 3h, 6h and 12 h), before being dissociated and triturated into single-cell suspensions for single-cell analyses.


title: LNCaP_0_h_A10


title: LNCaP_0_h_E6


title: RHV097


title: RHV095


title: RHV104


title: RHV094


title: RHV098


title: RHV100


title: RHV093


title: LNCaP_0_h_A4


title: LNCaP_0_h_B9


title: RHV099


title: RHV102


title: RHV085


title: RHV084


title: RHV083


title: Day 21, 0μM paraquat

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
The start of the iCRISPR scaffold sequence (GTTTAAGAGCTAT) within each read was identified, and the 19 bases immediately preceding this sequence extracted.
The resulting 19 base reads were mapped using Bowtie to a custom genome comprising the sgRNA library sequences, without allowing mismatches.
The number of reads mapped to each sgRNA was quantified using Seqmonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing counts for each guide RNA across all samples, together with the targeted gene name and sgRNA ID. Gene names starting 'NT_sgRNA' indicate non-targeting guide RNAs.

source_name: Jurkat T cells

growth_protocol: Jurkat cells were maintained in supplemented Roswell Park Memorial Institute 1640 (RPMI-1640) medium with 10% FBS and 1 × GlutaMAX™ (35050061; Gibco).

extract_protocol:
Genomic DNA was isolated as previously described (doi:10.1016/j.cell.2015.02.038)
Next-generation sequencing (NGS) libraries were generated in one round by PCR to amplify the guide RNA sequences and add sequencing adapters, from 2.5 μg gDNA in 22 cycles with Q5 polymerase following the manufacturer's protocol. PCR products were concentrated (D4031; Zymo Research), size was selected by gel electrophoresis, and purified (D4005; Zymo Research). Libraries were sequenced on a 75bp single end HiSeq 2500 RapidRun
OTHER:CRISPR screen

treatment_protocol: Jurkat-Cas9 cells were transduced with VSV-G pseudotyped lentivirus in the presence of 4 ng/mL polybrene (H9268; Sigma-Aldrich®), by spinfection at 1500 g for 99 min at 32°C. Transduced cells were selected with 0.75 μg/mL puromycin from day 2 to day 5 post-transduction. On day 6, cells were cultured in 0, 50, or 200 μM paraquat (856177; Sigma-Aldrich®) for 14 or 21 days. Cells were harvested at the start and end of paraquat exposure. The representation of the library was maintained at >1000 cells per sgRNA in all conditions.

tag: days in culture

tag: paraquat concentration (μm)


title: Day 21, 50μM paraquat


title: RHV096


title: RHV082


title: Day 14, 0μM paraquat


title: RHV080


title: RHV091


title: RHV079


title: RHV088


title: Day 14, 50μM paraquat


title: Day 0, 0μM paraquat


title: VCaP_Input

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie v0.12.9 with default parameters
SAM to BAM conversion and sorting was performed using samtools v1.9.0
The duplicated reads were marked using Picard MarkDuplicates v2.20.0 utility
Peak calling was performed using MACS1.4 with pvalue < 1e-4
The alignment coverage was calculated and converted into bigwig format using deeptools v3.4.3 bamCoverage utility and visualized into IGV v2.7.2 (Genome Build: hg19)
Genome_build: hg19
Supplementary_files_format_and_content: .bed files representing the peaks in text formate
Supplementary_files_format_and_content: .bw files store alignment coverage in binary foramte

source_name: prostate cancer cells

growth_protocol: The prostate cancer cell line VCaP  was obtained from ATCC and maintained in DMEM media (Gibco),  supplemented with 10 % fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.

extract_protocol: NEBNext Ultra II DNA library Prep Kit for Illumina

treatment_protocol: VCaP cells were transferred into phenol-red free DMEM and RPMI media (Gibco), 1day  prior to DHT stimulation. The media were supplemented with 10 % charcoal/dextran-stripped FBS (Hyclone). VCaP cells were treated with either ethanol (vehicle) or 100nM DHT for 2h, before being harvested for ChIP assay.

value: prostate cancer cells

value: untreated


title: VCaP_CREB3L2_DHT

value: treated with DHT (100nM) for 2 hours


title: RHV077


title: RHV087


title: Day 21, 200μM paraquat


title: RHV092


title: RHV101


title: Day 14, 200μM paraquat


title: LNCaP_6_h_E5


title: RHV090


title: RHV089


title: RHV086


title: RHV073


title: RHV072


title: Exp4_xrn1Deg_30min_RNA

city: Seattle

first: David

last: Wiener

state: Washington

department: School of Oceanography

institute: University of Washington

data_processing:
For mRNAseq libraries, paired-end reads were aligned with STAR v2.5.3a
Each read gene assignment was done with the intersect function from bedtools
TMM normalization and RPKM calculation was performed using the EdgeR package
Genome_build: SacCer3
Supplementary_files_format_and_content: csv files RNA abundance measured by RNAseq

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: All vegetative growth points were growing cells at 30°C at 190 rpm in YPD 2% after reaching OD600 = ~0.5. To induce synchronous meiotic entry, cells were grown for 24 h in YPD 4%at 30°C, diluted in BYTA  to OD600 = 0.2 and grown for another 16 h at 30°C, 200 rpm. Cells were then washed twice with water, re-suspended in SPO at OD600 = 2.0 and incubated at 30°C at 190 rpm. For the return to growth experiment cells were removed from SPO at indicated timepoints and resuspended in YPD 2% for RNA extraction. Xrn1 degron system was activated by adding 500μM auxin/Indole-3-acetic acid(IAA) + 50μM CuSo4 to the inducible strain at OD600 = ~0.5. Overexpression of Ccr4 was caused by activating the Cup1 promoter with 50μM CuSo4 to the inducible strain at OD600 = 0.5. Cells were isolated from each media at the indicated times and collected by 2 min centrifugation at 3000 g

extract_protocol:
NucleoSpin RNA mini kit (Macherey-Nagel, 740955.50)
3' adapter ligation,Ribodepletion,Fragmentation, cDNA synthesis, second adapter ligation and enrichment

tag: strain


title: Exp4_xrn1Deg_0min_RNA


title: Exp5_ccr4Over_60min_RNA


title: RHV069


title: Exp2_7Hr_5min_RtG_rep2_RNA

value: WT


title: Exp2_7Hr_5min_RtG_rep1_RNA


title: RHV078


title: Exp2_7Hr_RtG_rep2_RNA


title: RHV065


title: RHV081


title: LNCaP_6_h_G12


title: RHV075


title: RHV063


title: RHV062


title: Exp5_ccr4Over_0min_RNA


title: Exp2_7Hr_20min_RtG_rep2_RNA


title: Exp4_xrn1Deg_Ct_RNA


title: VCaP_CREB3L2_ETOH

value: treated with Ethanol for 2 hours


title: Exp2_1Hr_5min_RtG_rep1_RNA


title: RHV070


title: RHV067


title: RHV074


title: RHV076


title: RHV068


title: Exp2_1Hr_20min_RtG_rep2_RNA


title: Exp5_ccr4Over_Ct_RNA


title: RHV057


title: RHV066


title: Exp2_1Hr_20min_RtG_rep1_RNA


title: Exp1_9Hr_rep1_RNA


title: RHV071


title: RHV061


title: Exp1_8Hr_rep1_RNA


title: Exp2_1Hr_RtG_rep2_RNA


title: RHV058


title: Exp2_7Hr_20min_RtG_rep1_RNA


title: RHV059


title: Exp2_7Hr_RtG_rep1_RNA


title: Exp2_1Hr_RtG_rep1_RNA


title: Exp2_1Hr_5min_RtG_rep2_RNA


title: Exp1_9Hr_rep2_RNA


title: Exp1_6Hr_rep1_RNA


title: RHV053


title: RHV056


title: RHV055


title: RHV050


title: RHV064


title: RHV049


title: Exp1_7Hr_rep2_RNA


title: RHV048


title: Exp1_4Hr_rep2_RNA


title: Exp1_5Hr_rep1_RNA


title: Exp1_7Hr_rep1_RNA


title: RHV045


title: Exp1_3Hr_rep1_RNA


title: Exp1_2Hr_rep2_RNA


title: RHV044


title: Exp1_2Hr_rep1_RNA


title: RHV042


title: RHV060


title: Exp1_1Hr_rep2_RNA


title: Exp1_1Hr_rep1_RNA


title: RHV039


title: RHV038


title: Exp1_5Hr_rep2_RNA


title: RHV054


title: Exp5_ccr4Over_0min_mPAT

data_processing:
Library strategy: mPAT-seq
For RNA identification, read 1 was aligned with STAR v2.5.3a 60 to the SacCer3 reference genome with default parameters but limiting the intron length to 1000 nt (‘–alignIntronMax 1000’ parameter).
 Reads were assigned to genes using the ‘closest’ function from bedtools v2.26.0 61 and reads that were further than 500nt away from the open reading frame end were filtered.
For poly(A) quantification, two filters were applied. 1) A minimum of 4 adenosines at the beginning of the read 2 was required. 2) Reads that aligned perfectly to the genome (STAR  --alignEndsType EndToEnd ", "--alignIntronMax 1,--outFilterMismatchNmax 3) were removed from the analysis to avoid genomic encoded adenosines.
Quantification of poly(A) tail length was performed with a sliding window strategy beginning from the end of read 2, using a 5 nt window and a 1 nt offset, with a requirement that at least 4 of the 5 nucleotides in the window are adenosines; The 5’ end of the poly(A) tail was defined as the 3’-most adenosine within the first window in which this condition was not fulfilled. A minimum of 30 poly(A) tags per gene were required for further analyses.
Genome_build: SacCer3
Supplementary_files_format_and_content: csv files containing poly(A) tail length average,Poly(A) tags per genes

extract_protocol:
NucleoSpin RNA mini kit (Macherey-Nagel, 740955.50)
PolyA Selection,Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment


title: RHV052


title: Exp1_8Hr_rep2_RNA


title: RHV051


title: RHV036


title: RHV047


title: RHV046


title: Exp1_6Hr_rep2_RNA


title: Exp4_xrn1Deg_30min_mPAT


title: Exp1_4Hr_rep1_RNA


title: Exp4_xrn1Deg_0min_mPAT


title: RHV041


title: RHV043


title: Exp1_0Hr_rep1_RNA


title: Exp1_0Hr_rep2_RNA


title: Exp5_ccr4Over_60min_mPAT


title: Exp5_ccr4Over_Ct_mPAT


title: RHV037


title: Exp1_3Hr_rep2_RNA


title: RHV028


title: RHV035


title: RHV030


title: RHV027


title: Exp2_7Hr_5min_RtG_rep1_mPAT


title: RHV040


title: Exp2_7Hr_20min_RtG_rep1_mPAT


title: RHV034


title: Exp4_xrn1Deg_Ct_mPAT


title: RHV032


title: Exp2_1Hr_20min_RtG_rep1_mPAT


title: Exp2_1Hr_20min_RtG_rep2_mPAT


title: Exp2_7Hr_20min_RtG_rep2_mPAT


title: RHV033


title: Exp2_7Hr_5min_RtG_rep2_mPAT


title: Exp2_7Hr_RtG_rep2_mPAT


title: Exp2_7Hr_RtG_rep1_mPAT


title: RHV021


title: RHV029


title: RHV031


title: Tbx1 cKO E8.5

city: Bronx

first: Hiroko

last: Nomaru

state: NY

address: 1300 Morris Park ave

department: Genetics

institute: Albert Einstein College of Medicine

description: scRNA-seq

data_processing:
Cell Ranger (v 3.1.0) was used to align reads of scRNA-seq data to the mouse reference genome (mm10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

organism: Mus musculus

source_name: pharyngeal mesoderm

extract_protocol:
After dissected out, the tissues were incubated in trypsin-EDTA. Then GFP positive DAPI negative cells were sorted and then the cells were loaded in a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using Chromium Single Cell 3’ Library & Gel Bead Kit v2.
RNA libraries were prepared for sequencing using standard 10x Genomics protocols.

value: Swiss Webster

tag: tissue

value: Upper half of the body

tag: developmental stage


title: Exp2_1Hr_RtG_rep2_mPAT


title: RHV022


title: RHV023


title: Exp2_1Hr_5min_RtG_rep1_mPAT


title: RHV020


title: RHV026


title: RHV024


title: RHV025


title: Exp2_1Hr_5min_RtG_rep2_mPAT


title: RHV019


title: RHV018


title: RHV016


title: Tbx1 Ctrl E8.5

description: scRNA-seq


title: F-7

type: RNA

city: Jinan

first: Qian

last: Zhang

address: JingLiu Road

department: Center for Reproductive Medicine

institute: Shandong Provincial Hospital Affiliated to Shandong University

description: Endometrial MiRNA expressions at the time of embryo implantation from RIF patients

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min.b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon).

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: endometrial tissues

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps: a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C.c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: endometrial tissues

tag: disease

value: recurrent implantation failure (RIF)

tag: Sex

value: Female


title: NgWt_2

city: Berlin

first: Xiaoyan

last: Wei

address: Thielallee 63

country: Germany

institute: Free University of Berlin

data_processing:
Mapping was performed using STAR 2.4.2a software with mouse genome (mm9).
Read counts were generated with R Studio function Summarize Overlaps and normalized to RPKM based on the number of uniquely mapped reads.
Differential expression analysis was performed with DESeq2 using default settings.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: muscle from forelimbs

extract_protocol: Sequencing libraries was prepared following Roche’s “KAPA stranded mRNA Seq” library preparation protocol. 11 cycles of PCR were used for libraries amplification followed by sequencing with an Illumina HiSeq 4000 system.

treatment_protocol: Total RNA from E15.5 fore limb muscle tissue was isolated using the RNeasy Micro Kit (Qiagen). RNA quantity and quality was tested on a Qubit®Fluorometer (Invitrogen) and a Bioanalyzer 2100 (Agilent).

value: muscle

value: Wild type control


title: Exp2_1Hr_RtG_rep1_mPAT


title: Mesp1Cre-Tbx1cKO E9.5

data_processing:
Cell Ranger (v 3.1.0) were used to align reads of scRNA-seq data to the mouse reference genome (mm10).
Supplementary_files_format_and_content: barcodes, features, mtx

extract_protocol:
After dissected out, the tissues were incubated in trypsin-EDTA. Then GFP positive DAPI negative cells were sorted and then the cells were loaded in a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using Chromium Single Cell 3’ Library & Gel Bead Kit v2
RNA libraries were prepared for sequencing using standard 10xGenomics protocols

value: pharyngeal apparatus and heart


title: F-29


title: F-17


title: F-32


title: NgWt_1


title: RHV015

value: VCaP

value: Prostate cancer cell line


title: F-14


title: F-6


title: F-5


title: NgKo_3

value: Noggin-deficient


title: F-22


title: C-18

description: Endometrial MiRNA expressions at the time of embryo implantation from controls

value: control


title: NgKo_2


title: RHV014

value: DHT


title: RHV013


title: RHV012


title: C-13


title: C-11


title: NgKo_1


title: C-8


title: C-16


title: C-10


title: RHV011


title: Mesp1E10.5

data_processing: Cell Ranger (v 3.1.0) were used to align reads of scRNA-seq data to the mouse reference genome (mm10).

value: Pharyngeal apparatus and heart


title: C-7


title: C-4


title: C-2


title: HT1912011246_VCaP_6h_COL20_S40_L002

description:
HT
PolyA RNA
processed data file: VCaP_HT_genes_fpkm.txt


title: Mesp1E8.0


title: C-6


title: RHV010


title: U2OS_TH59-DB_rep2

city: Mishima

first: Satoru

last: Ide

address: 1111 Yata

country: Japan

institute: National Institute of Genetics

data_processing:
Illumina Miseq reporter software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by CUTADAPT and PRINSEQ using a composite set of Illumina adapters, a minimum quality score of 20 and a minimum length of 25, and then mapped to hg38 whole genome using Hisat2 with parameters -p 12 -no--mixed --no-discordant --un-conc
Fragments Per Kilobase of trannscript per Megabase of library size (FPKM) were calculated using Cufflinks and featureCounts. In short, the mapped fragments in TH59-DB pulled-down fractions were assembled into transcripts and annotated using Cufflinks software. The number of fragments falling in this transcript were counted and normalized by the size of the transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample

source_name: ALT-positive cell line U2-OS

growth_protocol: HeLa1.3 and U2-OS cells were grown in DMEM medium containing 10% FBS at 37°C (5% CO2).

extract_protocol:
To extract RNA, the input and isolated chromatin with masked TH59-DB and TH59-DB were incubated in de-crosslinking buffer (32 mM Tris-HCl pH 8.0, 320 μg/mL Protease K, 0.8% SDS) for 6 hr at 65°C. An equal volume of acidic phenol was added, then vortexed, and incubated for 5 min at room temperature. After adding an equal volume of chloroform: isoamyl alcohol (24:1, v/v) and centrifuging at 16,000 g for 5 min at 4°C, the upper aqueous phase was transferred to a new tube. This step was repeated. One-tenth volume of 3 M sodium acetate, glycogen, and double volume of ethanol were added and incubated overnight at -80°C. After centrifugation at 20,000 g for 30 min at 4ºC, the pellet was retained, washed with 70% ethanol, and dried up. The dried pellet was dissolved in diethylpyrocarbonate (DEPC)-treated water (36415-54, Nakarai) and kept at -80°C until use.
RNA libraries were synthesized by the SMARTer Stranded Total RNA-Seq Kit v2 (634411, Takara).

treatment_protocol: The cells were washed with PBS and crosslinked with 3.7% formaldehyde in PBS for 30 min at room temperature.  Following the chromatin sample preparation, the region-specific chromatin isolation were  performed by TH59-DB and masked TH59-DB (negative control) probes.

value: ALT-positive cell line U2-OS

value: Osteosarcoma epithelial cell

tag: pull-down fraction

value: performed by TH59-DB


title: U2OS_Input_rep2

value: Input


title: U2OS_masked_TH59-DB_rep2

value: performed by masked_TH59-DB


title: HeLa_TH59-DB_DNA-seq

data_processing:
Illumina Miseq reporter software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by CUTADAPT and PRINSEQ using a composite set of Illumina adapters, a minimum quality score of 20 and a minimum length of 25, and then mapped to hg38 whole genome using Bowtie2 with parameters -p 12 -no--mixed --no-discordant --un-conc.
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph files were generated  for each Sample

source_name: Telomerase positive cell line HeLa1.3

extract_protocol:
To extract DNA, the pull-down chromatin fractions were incubated in de-crosslinking buffer (50 mM Tris-HCl pH 8.0, 200 μg/mL Protease K, 2% SDS) overnight at 65°C. An equal volume of phenol: chloroform: isoamyl alcohol (25:24:1,v/v) (311-90151, Wako) was added and vortexed, and centrifuge at 16,000 g for 5 min at room temperature. The upper aqueous phase was transferred to a new tube. This step was repeated. One-tenth volume of 3 M sodium acetate, glycogen, and the double volume of ethanol were added and incubated for 2 hr at -80°C. After centrifugation at 20,000 g for 30 min at 4ºC, the pellet was retained, washed with 70% ethanol, and dried up. The dried pellet was dissolved in 10 μg/mL RNase A in DNA dilution buffer attached to DNA SMART ChIP-Seq Kit (634865, Takara). After incubation for 1 hr at 37°C, DNA was purified by the phenol-chloroform extraction and ethanol precipitation to remove RNase A.
DNA libraries were synthesized by the DNA SMART ChIP Seq Kit (634865, Takara).

treatment_protocol: The cells were washed with PBS and crosslinked with 3.7% formaldehyde in PBS for 30 min at room temperature.  Following the chromatin sample preparation, the region-specific chromatin isolation were  performed by TH59-DB probe.

value: Telomerase positive cell line HeLa1.3

value: epithelial cell


title: HT1912011246_VCaP_6h_COL18_S38_L002


title: HeLa_masked_TH59-DB_rep2


title: HT1912011246_VCaP_6h_COL19_S39_L002


title: Exp3_Wt_Mei_ZeroRNA

description: SK1 strain

data_processing:
Paired-end reads were aligned with STAR v2.5.3a
Each read gene assignment was done with the intersect function from bedtools
TMM normalization and RPKM calculation was performed using the EdgeR package
Coverage per position was calculated with a in house script
3'Bias was calculated either as the ratio of the last 100nt coverage divided by the first 100nt coverage or as the ratio of the last 10%nt coverage divided by the first 10%nt coverage
Genome_build: SacCer3
Supplementary_files_format_and_content: csv files RNA abundance measured by RNAseq. 3' Bias calculation per gene.

extract_protocol:
NucleoSpin RNA mini kit (Macherey-Nagel, 740955.50)
Fragmentation, 3' adapter ligation,Ribosomal Depletion, cDNA synthesis, second adapter ligation and enrichment
Ribo-RNAseq

value: WT


title: Exp3_xrn1_Veg_ZeroRNA

description: SK1 strain

value: xrn1 delta/delta


title: HeLa_TH59-DB_rep2


title: HeLa_Input_rep2


title: Exp3_Wt_Veg_ZeroRNA

description: SK1 strain


title: U2OS_TH59-DB_rep1


title: HT1912011246_VCaP_6h_COL17_S37_L002


title: U2OS_masked_TH59-DB_rep1


title: U2OS_Input_rep1


title: U2OS_TH59-DB_DNA-seq


title: HT1912011246_VCaP_6h_COL16_S36_L002


title: HeLa_masked_TH59-DB_rep1


title: HeLa_TH59-DB_rep1


title: HeLa_Input_rep1


title: HT1912011246_VCaP_6h_COL15_S35_L002


title: HT1912011246_VCaP_6h_COL14_S34_L002


title: HT1912011246_VCaP_6h_COL13_S33_L002


title: Exp3_xrn1_Mei_RNA


title: Exp3_pop2_Mei_RNA


title: Exp3_xrn1_Pre_RNA


title: Exp3_ccr4_Mei_RNA


title: HT1912011246_VCaP_6h_COL11_S31_L002


title: Serum_22

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

hyb_protocol: EV miRNAs were profiled with the NanoString nCounter® Human v3 miRNA Expression Assay Kit (NanoString, Seattle, WA, USA) at the Genomics Shared Resource at the Ohio State University Comprehensive Cancer Center according to the manufacturer and as previously reported (Tank et al., 2018).

data_processing: The nSolver (Wohlfarth et al., 2017) analysis platform was used to assess the quality of the nCounter data and process the data for further analysis. Normalization was done using NanoString’s three ligation control probes. Bioconductor package sva was used to remove batch effects from combining five different assay kits (Leek et al., 2012). Principal component analysis (PCA) was used to visualize variation in differentially expressed miRNAs (DEmiRNAs) across samples. Probes were excluded from further analysis if their average count across all samples fell below the geometric mean plus one standard deviation (geomean +  1SD) of all negative controls. Differential miRNA expression between control and ALS groups in each tissue was evaluated using a two-tailed t-test, as used in NanoString nSolver v4.0 analysis software.

source_name: exosome

extract_protocol: ExoChip captured EVs were lysed and flushed with Qiazol (QIAGEN, Hilden, Germany) at a flowrate of 20 μL/min. Total RNA was extracted following a standard phenol/chloroform protocol and Norgen columns (Norgen Biotek Corp, Thorold, ON, Canada) as indicated by the manufacturer. The samples were eluted in 50 µL of DNAse- and RNAse-free water and stored at -80 °C.

value: Serum

tag: casegroup

value: Ctrl

value: Male

tag: cartridge


title: Serum_21

scan_protocol: EV miRNAs were profiled with the NanoString nCounter® Human v3 miRNA Expression Assay Kit (NanoString, Seattle, WA, USA) at the Genomics Shared Resource at the Ohio State University Comprehensive Cancer Center according to the manufacturer and as previously reported (Tank et al., 2018).


title: Serum_17

value: Female


title: Serum_19


title: Serum_18


title: Exp3_pop2_Pre_RNA


title: Serum_16


title: HT1912011246_VCaP_3h_COL10_S30_L002

tag: cell line

value: VCaP

value: Prostate cancer cell line


title: Exp3_ccr4_Pre_RNA


title: Exp3_xrn1_Veg_RNA


title: Serum_20


title: HT1912011246_VCaP_3h_COL09_S29_L002

tag: treatment

value: DHT


title: Serum_13

value: ALS


title: Serum_15


title: Exp3_ccr4_Veg_RNA

tag: genotype


title: HT1912011246_VCaP_6h_COL12_S32_L002


title: Exp3_pop2_Veg_RNA


title: HT1912011246_VCaP_3h_COL08_S28_L002


title: Exp3_Wt_Mei_RNA


title: HT1912011246_VCaP_3h_COL07_S27_L002


title: Serum_11


title: Serum_10


title: Exp3_Wt_Pre_RNA


title: Serum_14


title: HT1912011246_VCaP_3h_COL06_S26_L002


title: Exp3_Wt_Veg_RNA


title: HT1912011246_VCaP_3h_COL05_S25_L002


title: Serum_07


title: Serum_08


title: Exp3_xrn1_Pre_mPAT


title: Exp3_xrn1_Mei_mPAT


title: Serum_12


title: HT1912011246_VCaP_3h_COL04_S24_L002


title: HT1912011246_VCaP_3h_COL03_S23_L002


title: Serum_03


title: Serum_06


title: Serum_02


title: Serum_01


title: Frontal Cortex_20

value: Frontal Cortex


title: Serum_04


title: Frontal Cortex_19


title: Exp3_xrn1_Veg_mPAT


title: HT1912011246_VCaP_3h_COL02_S22_L002


title: Exp3_pop2_Mei_mPAT


title: Frontal Cortex_16


title: HT1912011246_VCaP_3h_COL01_S21_L002


title: Serum_09


title: Serum_05


title: Frontal Cortex_17


title: Exp3_pop2_Pre_mPAT


title: HT1912011246_VCaP_12h_COL20_S20_L001


title: Frontal Cortex_13


title: Frontal Cortex_12


title: Exp3_pop2_Veg_mPAT


title: Frontal Cortex_14


title: Exp3_ccr4_Mei_mPAT


title: HT1912011246_VCaP_12h_COL19_S19_L001


title: Exp3_ccr4_Veg_mPAT


title: Exp3_ccr4_Pre_mPAT


title: HT1912011246_VCaP_12h_COL18_S18_L001


title: HT1912011246_VCaP_12h_COL17_S17_L001


title: Exp3_Wt_Pre_mPAT


title: Frontal Cortex_10


title: HT1912011246_VCaP_12h_COL16_S16_L001


title: HT1912011246_VCaP_12h_COL15_S15_L001


title: Exp3_Wt_Mei_mPAT


title: Frontal Cortex_11


title: Frontal Cortex_18


title: Frontal Cortex_08


title: Exp3_Wt_Veg_mPAT


title: Frontal Cortex_07


title: Frontal Cortex_09


title: Frontal Cortex_06


title: Lung, SA (SAMPLE 21)

city: Silver Spring

first: Hang

last: Xie

state: Maryland

address: 10993 New Hampshire Ave WO 52/72 Rm 1324

institute: US Food and Drug Administration, Center for Biologics Evaluation and Research

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://dataanalysis.qiagen.com/pcr/arrayanalysis.php?wuid=b4d56157-c14b-4fd9-a99c-8ddecd502e64&logindata=&customerdata=&customeremail=&platform=catalogArray&format=X
Normalization was performed using GUSB as the internal housekeeping gene.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
non-normalized_data.txt reports raw signals
normalized_data.txt reports normalized signal (against housekeeping gene).
Fold_Change.txt file reports test/control (i.e., NY/Naive) ratios.

label: SYBR Green

source_name: Lung, Test4

label_protocol: Reverse transcription was performed using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Quantitative real-time PCR were performed in Stratagene MX3000p using RT² Profiler™ PCR Array Mouse Hypoxia Signaling Pathway kit (QIAgen) following the Manufacturer’s instructions. The cycling conditions are: hold for 10 min at 95°C, followed by 40 cycles of 15 s at 95°C and 60 s at 60°C.

extract_protocol: Total RNA was extracted using QIAgen RNeasy Plus Mini Kit

value: K18-hACE2 transgenic

value: Whole lung homogenate

tag: infection

tag: activation agent

value: SA infection

value: dpi 3 after SA infection

tag: group


title: Frontal Cortex_15


title: Exp1_9Hr_rep2_mPAT


title: HT1912011246_VCaP_12h_COL13_S13_L001

tag: cell type

tag: time


title: Frontal Cortex_05


title: HT1912011246_VCaP_12h_COL12_S12_L001


title: HT1912011246_VCaP_12h_COL14_S14_L001


title: Exp1_9Hr_rep1_mPAT


title: HT1912011246_VCaP_12h_COL11_S11_L001


title: Exp1_8Hr_rep2_mPAT


title: Lung, CA (SAMPLE 17)

source_name: Lung, Test3

value: CA infection

value: dpi 3 after CA infection


title: Lung, SA (SAMPLE 20)


title: Lung, SA (SAMPLE 19)


title: Frontal Cortex_03


title: Frontal Cortex_02


title: Lung, SA (SAMPLE 18)


title: HT1912011246_VCaP_0h_COL09_S9_L001


title: Frontal Cortex_01


title: Exp1_7Hr_rep1_mPAT

value: WT


title: HT1912011246_VCaP_0h_COL07_S7_L001


title: Lung, CA (SAMPLE 16)


title: Exp1_8Hr_rep1_mPAT


title: HT1912011246_VCaP_0h_COL08_S8_L001


title: Spinal Cord_16

value: Spinal Cord


title: Spinal Cord_17


title: Lung, CA (SAMPLE 15)


title: Exp1_6Hr_rep1_mPAT


title: HT1912011246_VCaP_0h_COL06_S6_L001


title: HT1912011246_VCaP_0h_COL05_S5_L001


title: Exp1_6Hr_rep2_mPAT


title: HT1912011246_VCaP_0h_COL04_S4_L001


title: Lung, NY (SAMPLE 11)

source_name: Lung, Test2

value: NY infection

value: dpi 3 after NY infection


title: Lung, CA (SAMPLE 14)


title: Spinal Cord_18

value: Ctrl

value: Male


title: Exp1_4Hr_rep2_mPAT


title: Lung, NY (SAMPLE 10)


title: Lung, NY (SAMPLE 12)


title: HT1912011246_VCaP_0h_COL02_S2_L001

value: VCaP


title: Frontal Cortex_04

value: Female


title: Exp1_4Hr_rep1_mPAT


title: Lung, NY (SAMPLE 13)


title: Lung, WA (SAMPLE 9)

source_name: Lung, Test1

value: WA infection

value: dpi 3 after WA infection


title: Spinal Cord_15


title: Exp1_3Hr_rep2_mPAT


title: HT1912011246_VCaP_0h_COL10_S10_L001

value: Prostate cancer cell line

value: DHT


title: Spinal Cord_13


title: HT1912011246-VCaP_0h-COL10_S8_L002


title: Exp1_5Hr_rep1_mPAT


title: Spinal Cord_14


title: HT1912011246_VCaP_0h_COL03_S3_L001


title: HT1912011246-VCaP_0h-COL09_S5_L002


title: Lung, WA (SAMPLE 8)

value: K18-hACE2 transgenic

value: Whole lung homogenate


title: Exp1_2Hr_rep2_mPAT


title: HT1912011246_VCaP_0h_COL01_S1_L001


title: Exp1_3Hr_rep1_mPAT


title: Spinal Cord_09

value: ALS


title: Spinal Cord_10


title: Lung, WA (SAMPLE 5)


title: Spinal Cord_11


title: HT1912011246-VCaP_0h-COL08_S9_L002


title: Exp1_1Hr_rep1_mPAT


title: Lung, WA (SAMPLE 6)


title: Spinal Cord_12


title: Exp1_0Hr_rep2_mPAT


title: HT1912011246-VCaP_0h-COL05_S12_L002


title: Lung, WA (SAMPLE 7)


title: Exp1_1Hr_rep2_mPAT


title: HT1912011246-VCaP_0h-COL07_S10_L002


title: Exp1_5Hr_rep2_mPAT


title: Lung, Naive (SAMPLE 4)

source_name: Lung, Control

value: control

value: naïve

value: no infection

value: Control


title: Lung, Naive (SAMPLE 1)


title: Lung, Naive (SAMPLE 3)


title: Spinal Cord_08

value: Spinal Cord


title: Lung, Naive (SAMPLE 2)


title: HT1912011246-VCaP_0h-COL06_S11_L002


title: Spinal Cord_07


title: Exp1_2Hr_rep1_mPAT

value: WT


title: HT1912011246-VCaP_0h-COL02_S3_L002


title: Spinal Cord_05


title: root tip, DMSO control, scRNA-seq

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description: Root tips of 6-d-old-seedlings Arabidopsis thailiana Col-0, treated with DMSO for 2h

data_processing:
Demultiplexing; Cell Ranger mkfastq; version 3.1.0
Read alignment + counting; Cell Ranger count; version 3.1.0
Genome_build: TAIR 10; Ensembl Plants, release 40
Supplementary_files_format_and_content: h5 file containing filtered count matrix  (output Cell Ranger count)

organism: Arabidopsis thaliana

source_name: root tip

growth_protocol: All seeds were surface sterilized, sown on solid 1⁄2 MS plates without sucrose, and stratified for 24h at 4°C two days before they were grown at 22°C in continuous light conditions.

extract_protocol:
Root tips of 6-d-old seedlings were cut and incubated in protoplasting Solution B [1.5% (wt/vol) cellulysin and 0.1% (wt/vol) pectolyase in Solution A (600 mM mannitol, 2 mMMgCl2, 0.1% [wt/vol] BSA, 2 mMCaCl2, 2 mMMes, 10mMKCl, pH 5.5)] for approximately 1 h at room temperature. Cells were filtered through a 70 μm cell strainer and spun down at 200 × g for 6 min; resuspended in Solution A, filtered through a 40 μm cell strainer and stained for live/dead using 4′,6- diamidino-2-phenylindole (DAPI) at 14 μM final concentration. Cells were sorted on a BD Aria II, and protoplasts not containing the DAPI signal were selected for further analysis.
Sorted cells were centrifuged at 4°C at 400g and resuspended in solution A to yield an estimated concentration of 1000 cells/μl. Cellular suspensions were loaded on a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit (V3 chemistry, 10X Genomics) according to the manufacturer’s instructions.

treatment_protocol: 6-day-old seedlings were transferred to 10 µM 6-Benzylaminopurine (BAP) supplemented medium or an equal volume of Dimethyl sulfoxide (DMSO) as mock treatment and continued growth for 2 hours

tag: ecotype

tag: age

value: wild type


title: Tbx1 cKO E9.5

description: scRNA-seq

tag: strain

value: Swiss Webster

tag: tissue

value: Pharyngeal apparatus and heart


title: root tip, CK treatment, scRNA-seq

description: Root tips of 6-d-old-seedlings Arabidopsis thailiana Col-0, treated with 10 uM BAP for 2h

value: 6-Benzylaminopurine (BAP)


title: Spinal Cord_03

value: Female


title: HT1912011246-VCaP_0h-COL04_S4_L002

source_name: VCaP

value: VCaP


title: Exp1_0Hr_rep1_mPAT


title: Spinal Cord_01


title: HT1912011246-VCaP_0h-COL01_S6_L002

value: Prostate cancer cell line


title: Spinal Cord_06


title: Spinal Cord_02


title: Spinal Cord_04


title: Mouse4 Villus 6

status: Public on Oct 09 2021

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description:
bulk RNA seq Mouse#4 V6 (tip)
M4_V6

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1) and read 2 (R2))
each mice zones (V1-V6) was Pooled to a total of 4 pools. pooled samples were demultiplexed using i7+SCRB specific barcode (attaced).
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Jejunum - FACS sorted

growth_protocol: C57bl6 male mice were fed regular chow ad libitum

extract_protocol:
Isolation of jejunual enterocytes was as prevously described (Moor et al, Cell 2018) followed by staining with CD73+CD26 antibodies to evaluate spatial location along villus axis. Cells were obtained via FACS sorting.
mcSCRBseq protocol was used (Bagnoli et al, Nat Commun. 2018)

treatment_protocol: Mice were sacrificed by cervical dislocation

value: Jejunum

tag: tissue region

value: tip

value: post natal 10 weeks

tag: gender

value: male


title: GF CD3- Leukocytes

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
The standard 10X Genomics cellranger (version 3.1.0) pipeline was used to extract Fastqs and 10X Genomics cellranger (version 3.1.0) pipeline was used to perform data processing. Sequenced reads were aligned to the 10X Genomics provided mouse reference sequence (refdata-cellranger-mm10-3.0.0).
Genome_build: mm10
Supplementary_files_format_and_content: 10X Genomics cellranger counts (barcodes, matrix  and features)

source_name: tumor

extract_protocol:
One week post-implantation, EL4 tumors were mechanically disrupted prior to enzymatic digestion with 0.5% FCS RPMI containing 1mg/ml DNase and 200U collagenase IV for 1 hour at 37C. The digested tissue was then passed through a 40um filter followed by 5min of red blood cell lysis with ACK. Cell hashing with barcoded CD45 antibodies were used to pool biological replicates. Samples were then sorted as either LiveCD45+CD3- (CD3- leukocytes) or LiveCD45+CD3-CD19-NK1.1-TCRb-TCRgd-Ter119- (myeloid).
Samples were spun and washed with PBS + 0.04% BSA twice. Sample concentration and viability were assessed after processing using the LunaFL fluorescent cell counter. Cells were loaded at 1200 cells/ul with a targeted recovery of 8000 cells. Cell partitioning completed successfully with uniform emulsion consistency and the reverse transcription PCR was run overnight. All subsequent steps of library preparation and Quality Control were performed as described in the 10X Genomics 3’ Single Cell User Guide.

value: tumor

tag: microbiota status

value: GF

tag: sorting strategy


title: Mesp1E8.25

value: Upper half of the body

tag: developmental stage


title: Mouse4 Villus 5

description:
bulk RNA seq Mouse#4 V5 (middle-tip)
M4_V5

value: middle-tip


title: HT1912011246-VCaP_0h-COL03_S7_L002

data_processing:
For processing the HT samples, demultiplexing was performed using Fluidigm’s HT Demultiplexer Perl script.
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters.
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKM values for each single cell.

extract_protocol: Nextera XT Index Kit v2.

tag: cell line

value: DHT


title: SPF Myeloid

value: SPF


title: Mouse4 Villus 3

description:
bulk RNA seq Mouse#4 V3 (bottom-middle)
M4_V3

value: bottom-middle


title: Mouse3 Villus 6

description:
bulk RNA seq Mouse#3 V6 (tip)
M3_V6


title: Mouse3 Villus 5

description:
bulk RNA seq Mouse#3 V5 (middle-tip)
M3_V5


title: Mouse4 Villus 2

description:
bulk RNA seq Mouse#4 V2 (bottom)
M4_V2

value: bottom


title: Mouse3 Villus 4

description:
bulk RNA seq Mouse#3 V4 (middle)
M3_V4

value: middle


title: Mouse4 Villus 4

description:
bulk RNA seq Mouse#4 V4 (middle)
M4_V4


title: Mouse4 Villus 1

description:
bulk RNA seq Mouse#4 V1 (most bottom)
M4_V1

value: most bottom


title: Mouse3 Villus 2

description:
bulk RNA seq Mouse#3 V2 (bottom)
M3_V2


title: Mouse2 Villus 6

description:
bulk RNA seq Mouse#2 V6 (tip)
M2_V6


title: Mouse2 Villus 4

description:
bulk RNA seq Mouse#2 V4 (middle)
M2_V4


title: SPF CD3- Leukocytes


title: Mouse1 Villus 6

description:
bulk RNA seq Mouse#1 V6 (tip)
M1_V6


title: Mouse3 Villus 3

description:
bulk RNA seq Mouse#3 V3 (bottom-middle)
M3_V3


title: Mouse1 Villus 2

description:
bulk RNA seq Mouse#1 V2 (bottom)
M1_V2


title: Mouse3 Villus 1

description:
bulk RNA seq Mouse#3 V1 (most bottom)
M3_V1


title: Mouse2 Villus 2

description:
bulk RNA seq Mouse#2 V2 (bottom)
M2_V2


title: GF Myeloid


title: Mouse2 Villus 1

description:
bulk RNA seq Mouse#2 V1 (most bottom)
M2_V1


title: Mouse1 Villus 4

description:
bulk RNA seq Mouse#1 V4 (middle)
M1_V4


title: Mouse2 Villus 5

description:
bulk RNA seq Mouse#2 V5 (middle-tip)
M2_V5


title: Mouse1 Villus 3

description:
bulk RNA seq Mouse#1 V3 (bottom-middle)
M1_V3


title: Mouse2 Villus 3

description:
bulk RNA seq Mouse#2 V3 (bottom-middle)
M2_V3


title: Mouse1 Villus 5

description:
bulk RNA seq Mouse#1 V5 (middle-tip)
M1_V5


title: Mouse1 Villus 1

description:
bulk RNA seq Mouse#1 V1 (most bottom)
M1_V1


title: MUC12138_control_2

city: Neuherberg

first: Joel

middle: Anton

last: Schick

address: Ingolstädter Landstr. 1

department: TOXI

institute: HMGU

data_processing:
Differential gene expression analysis was performed on rRNA-depleted samples with TopHat and Cufflinks using default settings on Galaxy and mouse genome version mm10
TopHat alignment to the file gencode.vM12.lncRNA_transcripts.fa was performed to determine percent transcript mapping to long non-coding RNA
Cuffdiff was used to calculate FPKM levels for each gene with Cuffdiff gene level determinations with the default settings
Htseq-count
DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file

source_name: mouse fibroblasts

growth_protocol: MF cells were cultured in DMEM supplemented with 10% FBS Superior, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA were extracted using the RNeasy Mini Kit (Qiagen)
For library preparation, 1 µg of total RNA per sample was used. RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).
Strand-specific RNA libraries were sequenced as 150 bp paired-end runs on an Illumina HiSeq4000 platform.

value: immortalized mouse fibroblasts

value: wild type


title: MUC12139_control_3


title: HO + Callus 10X-scRNA-seq

city: Houston

first: Alan

middle: R

last: Davis

email: adavis3269@gmail.com, ardavis@bcm.edu

state: TX

address: One Baylor Plaza

department: Center for Cell and Gene Therapy

institute: Baylor College of Medicine

data_processing:
Data were processed using the Seurat protocol
Pseudotime tranjectories were determined using Monocle 3
Genome_build: mm9
Supplementary_files_format_and_content: Matrix files with the RNA transcript present in each cluster for HO and fracture callus

source_name: Mouse muscle + fracture callus

extract_protocol:
HO and callus were each bar-coded at the single-cell level, which were then combined before preparing the RNA. RNA was extracted with trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina/10X Genomics protocols

treatment_protocol: Injected with cells transduced with AdBmp2 or the mice were fractured in the femur using a "drill hole technique"

value: Heterotopic ossification (HO)

value: Fracture callus

value: post natal day 21


title: MUC12137_control_1


title: MUC12134_Ms4a15_1

value: Ms4a15 OE


title: MUC12135_Ms4a15_2


title: control daf-7(e1372) rep1

city: Baltimore

first: Margaret

last: Starostik

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
GeneExpressionMatrix-RSEM-ExpectedCounts.txt
GeneExpressionMatrix-NormalizedCounts.txt
daf-16(0)_vs_control-DifferentialExpression.txt

data_processing:
Basecalling and base call quality were performed using Illumina’s Real-Time Analysis (RTA) software, and CIDRSeqSuite 7.1.0 was used to convert compressed bcl files into compressed fastq files.
Using Trimmomatic v. 0.39, Illumina adapters were clipped from raw mRNA-seq reads, followed by quality trimming (LEADING: 5; TRAILING: 5; SLIDINGWINDOW:4:15) (Bolger et al. 2014). Reads with a minimum length of 36 bases were retained (MINLEN: 36).
Processed reads were aligned to C. elegans reference genome WBcel235 using STAR v. 2.4.2a with default parameters and --twopassMode Basic (Dobin et al. 2013).
RSEM v. 2.1 was used to quantify gene abundance based on mapped reads (Li and Dewey 2011).
Outlier samples were identified by assessing the quality of raw and processed reads with FastQC v. 0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and by Principal Component Analysis (PCA) on log2-transformed normalized gene expression counts generated using DESeq2 v. 1.30.0 (Love et al. 2014).
Differential gene expression analysis was performed using DESeq2 with a significance threshold of FDR ≤ 0.05 and absolute value of log2-transformed fold changes of at least 2.
Genome_build: WBcel235
Supplementary_files_format_and_content: GeneExpressionMatrix-RSEM-ExpectedCounts.txt is a tab-delimited file with gene-level RSEM expected counts for all samples.
GeneExpressionMatrix-NormalizedCounts.txt is a tab-delimited file with normalized gene-level counts.
daf-16(0)_vs_control-DifferentialExpression.txt is a tab-delimited file containing differential expression results along with normalized gene-level counts for samples analyzed.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Synchronized populations of VT2317 daf-16(mgDf50); daf-7(e1372) and control CB1372 daf-7(e1372) dauer larvae were obtained by incubating embryos isolated by sodium-hypochlorite treatment at 24˚C for 52 hours. Because some daf-16; daf-7 animals grown under these conditions fail to enter dauer (Nika et al. 2016), dauer larvae from both strains were handpicked into M9 solution, washed twice, and then pelleted to a volume of 100µl packed worms. TRIzol reagent (Invitrogen) was added to the samples at a 10:1 ratio of TRIzol to worm pellet. The samples were then frozen in dry-ice/ethanol. Two biological replicates were obtained for each strain for mRNA-seq.

extract_protocol:
Total RNA isolation from dauer sample was conducted using TriReagent (Ambion) protocol with the following modifications: pelleted C. elegans in TRI-Reagent were subjected to three freeze/thaw/vortex cycles prior to BCP addition to improve extraction efficiency, isopropanol precipitation was conducted in the presence of glycogen for 1hr at -80°C, RNA was pelleted by centrifugation at 4°C for 30min at 20,000 x g; the pellet was washed three times in 70% ethanol and resuspended in water. BioAnalyzer assay (Agilent Technologies) was used for quality control of the RNA sequencing samples prior to library creation, with a minimum RIN of 8.5.
Libraries were constructed using the TruSeq RNA Library Prep Kit v2 (Illumina). The DNA concentration and fragment size of sequencing libraries were analyzed using the BioAnalyzer assay (Agilent Technologies). High-throughput sequencing was performed on the Illumina HiSeq 2500 platform to generate paired-end reads of 100 bp.

value: whole worm

value: dauer larvae

tag: replicate


title: daf-16(mgDf50); daf-7(e1372) rep 3

tag: genotype


title: control daf-7(e1372) rep 3

description:
GeneExpressionMatrix-RSEM-ExpectedCounts.txt
GeneExpressionMatrix-NormalizedCounts.txt


title: control daf-7(e1372) rep2


title: MUC12136_Ms4a15_3


title: daf-16(mgDf50); daf-7(e1372) rep1


title: daf-16(mgDf50); daf-7(e1372) rep2


title: 120 minutes

city: San Diego

first: Rohan

last: Balakrishnan

state: Ca

address: 9500 Gilman drive

department: Physics

institute: UCSD

data_processing:
Demultiplexed reads were trimmed for adapter sequences using Cutadapt (DOI:10.14806/ej.17.1.200).
Reads were aligned to the E. coli MG1655 U00096.3 genome using bowtie v2.2.6.
Read counts were obtained using Python HTSeq-count (HTSeq v0.6.1p2).
Genome_build: E.coli MG1655 U00096.3
Supplementary_files_format_and_content: compiled_reads.txt: Tab-delimited text file with read counts for each gene across the 6 samples.

organism: Escherichia coli K-12

source_name: Glucose to acetate growth transition, 120 minutes

growth_protocol: E. coli NCM3722 was grown on MOPS minimal media with 30 mM acetate and 0.61 mM glucose.

extract_protocol:
Cells were pelleted and RNA was extracted using the TRIzol method.
rRNA was removed using Ribo-Zero and libraries were constructed using the TruSeq kit (Illumina).

treatment_protocol: Cells were sampled at different time intervals as described above.

value: WT

tag: condition

value: glucose to acetate growth transition

tag: time point

value: 120 minutes following glucose run-out


title: 60 minutes

source_name: Glucose to acetate growth transition, 60 minutes

value: 60 minutes following glucose run-out


title: 5 minutes

source_name: Glucose to acetate growth transition, 5 minutes

value: 5 minutes following glucose run-out


title: 15 minutes

source_name: Glucose to acetate growth transition, 15 minutes

value: 15 minutes following glucose run-out


title: Pre-shift

source_name: Glucose to acetate growth transition, pre-shift

value: Exponential growth with glucose consumption


title: Post-shift

source_name: Glucose to acetate growth transition, post-shift

value: Exponential growth with acetate consumption


title: Embryo 72hpf_20160727_bath study 72hpf stripB 15-04-16_ _08.RCC

city: Moscow

first: Leonid

last: Uroshlev

address: Gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics RAS

description: This sample was filtered out of the analysis and contains no processed data.

hyb_protocol: Hybridize with both Reporter and Capture probes. NanoString manufacturer's protocol

scan_protocol: nCounter analysis system

data_processing: We removed cells with poor total counts of test probes other than those of housekeeping genes (rpl13 and kanamycin), assuming that most of them related to cell types expressing other cell markers than those represented in our panel. In addition, we removed data for probes (genes) that displayed expression in only a small number of cells. We used the NanoStringNorm R package, and removed a number of cells with poor norm factors and noisy background.  Normalization was performed using the sum of probes (kanamycin spike-in and rpl13 internal controls) as the reference housekeeping class with ‘mean and 2sd’ selected for the background.  We filtered the expression matrix nullifying elements with values less than 30 and imputed for dropouts using drImpute. In total about 20% of zero counts have been imputed into meaningful quantitative values.

label: NanoString manufacturer's protocol

organism: Danio rerio

source_name: Neural Crest

label_protocol: NanoString manufacturer's protocol

growth_protocol: Embryos were obtained from natural crosses and staged according to Kimmel et al. System water is made up from Reverse Osmosis water, with synthetic sea salt added at an amount such that the conductivity of the water is kept at approximately 800uS. Average water quality data are as follows: pH: 7.30, general Hardness: 160mg/l CaCO3, Ammonia: 0 mg/l NH3, Nitrite: 0 mg/l NO2, Nitrate: < 10 mg/l NO3- and Conductivity: around 800μS/cm. Light cycle is 14 hours light/10 hours dark (Lights on at 08:00, off at 22:00 daily). All fish were in general good health and no specific diseases were observed throughout the colony. The fish were fed Paramecium from 5-15dpf, followed by Ziegler Larval AP100 powder from day 16 – 22dpf. From 23dpf onwards they are fed Sparos Zebrafeed and Brine Shrimp. Fish euthanized by schedule 1 killing were given an overdose of an anaesthetic (5 drops of 0.48% MS-222 added to a petridish of water)

extract_protocol: To extract RNA from Trizol stocks we used Direct-zol™ RNA MicroPrep (Cat.# R2062, ZymoResearch, USA) according the manufacturer’s protocol. The total RNA was extracted in 10 ml, measured using Nanodrop-2000, and tested with Experion™ RNA HighSens Analysis Kits (Cat.# 700-7105, Bio-Rad ) using the Experion™ Automated Electrophoresis System (Bio-Rad). 5 ml of total RNA from either melanocytes or iridophore (50-60 ng/ml) was used directly for NanoString expression analysis

tag: age (hpf)

value: decapitated embryos


title: Embryo 30hpf_20170602_bath study 30hpf 06-04-17 strip b plate 1_ _08.RCC


title: Embryo 30hpf_20170602_bath study 30hpf 06-04-17 strip a plate 1_ _02.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 8_08.RCC

value: pa rt of body:de wholembryos


title: Exp1_7Hr_rep2_mPAT

data_processing:
Library strategy: mPAT-seq
For RNA identification, read 1 was aligned with STAR v2.5.3a 60 to the SacCer3 reference genome with default parameters but limiting the intron length to 1000 nt (‘–alignIntronMax 1000’ parameter).
 Reads were assigned to genes using the ‘closest’ function from bedtools v2.26.0 61 and reads that were further than 500nt away from the open reading frame end were filtered.
For poly(A) quantification, two filters were applied. 1) A minimum of 4 adenosines at the beginning of the read 2 was required. 2) Reads that aligned perfectly to the genome (STAR  --alignEndsType EndToEnd ", "--alignIntronMax 1,--outFilterMismatchNmax 3) were removed from the analysis to avoid genomic encoded adenosines.
Quantification of poly(A) tail length was performed with a sliding window strategy beginning from the end of read 2, using a 5 nt window and a 1 nt offset, with a requirement that at least 4 of the 5 nucleotides in the window are adenosines; The 5’ end of the poly(A) tail was defined as the 3’-most adenosine within the first window in which this condition was not fulfilled. A minimum of 30 poly(A) tags per gene were required for further analyses.
Genome_build: SacCer3
Supplementary_files_format_and_content: csv files containing poly(A) tail length average,Poly(A) tags per genes

source_name: Yeast cells

extract_protocol:
NucleoSpin RNA mini kit (Macherey-Nagel, 740955.50)
PolyA Selection,Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 6_06.RCC

value: wild type


title: Embryo 30hpf_20170602_bath study 30hpf 06-04-17 strip a plate 1_ _04.RCC


title: Embryo 72hpf_20160727_bath study 72hpf stripA 15-04-16_ _11.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 2_02.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 1_01.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 11_11.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 4_04.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 5_05.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 3_03.RCC


title: Embryo 30hpf_20160902_bath study 30hpf 13-04 samples 49-60_ _07.RCC


title: Embryo 30hpf_20160902_bath study 30hpf 13-04 samples 49-60_ _04.RCC


title: Embryo 30hpf_20170602_bath study 30hpf 06-04-17 strip a plate 1_ _09.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 9_09.RCC


title: Embryo 24hpf_20170609_bath study 24hpf 05-05-17 strip e tails_ _05.RCC

value: tails


title: Embryo 72hpf_20160727_bath study 72hpf stripA 15-04-16_ _08.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 9_09.RCC


title: Embryo 72hpf_20160811_bath study 72hpf 15-04-16 samples 41-52_   _05.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 7_07.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 8_08.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 6_06.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 5_05.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 7_07.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 3_03.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 4_04.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 10 _10.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 1_01.RCC


title: Embryo 72hpf_20160916_bath study stripA 12-09-16_ _05.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 12_12.RCC


title: Embryo 21hpf_20160525_bath study 21 hpf -07- samples 1-12_ 12_12.RCC


title: Embryo 72hpf_20160916_bath study stripA 12-09-16_ _06.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 10 _10.RCC


title: Embryo 48hpf_20160527_bath study 48hpf plate1 1-12_ 11_11.RCC


title: Embryo 72hpf_20160916_bath study stripA 12-09-16_ _03.RCC


title: Embryo 72hpf_20160916_bath study stripA 12-09-16_ _04.RCC


title: Embryo 72hpf_20160916_bath study stripA 12-09-16_ _01.RCC


title: Embryo 72hpf_20160916_bath study stripA 12-09-16_ _02.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 strip B_ _12.RCC

value: whole embryo


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 strip B_ _02.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 strip B_ _10.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 strip B_ _03.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 stripA_ _10.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 strip B_ _01.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 stripA_ _09.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 stripA_ _01.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 stripA_ _02.RCC


title: Embryo 30hpf_20170509_bath study 30hpf 06-04-17 strip a plate 2_ _07.RCC


title: Embryo 30hpf_20160816_bath study 30hpf 13-04 samples 25-36_  _03.RCC


title: Embryo 24hpf_20161013_bath study 24hpf 22-09-16 stripA_ _05.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 4_04.RCC

value: whole embryos


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 7_07.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 5_05.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 9_09.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 3_03.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 1_01.RCC


title: Embryo 21hpf_20160809_bath study 21hpf 06-04-16 samples 13-24 _ 1_06.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 10 _10.RCC


title: Embryo 21hpf_20160809_bath study 21hpf 06-04-16 samples 25-36_ 1_11.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 11_11.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 12_12.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _11.RCC

value: sox10 m618 mutants


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _12.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _08.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _09.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _05.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _06.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _03.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _10.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _07.RCC


title: Embryo 60hpf_20161018_bath study 60hpf 29-09-16 stripC_  _11.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _02.RCC


title: Embryo 18hpf_20160726_bath study 18hpf strip A 1-12 25-05-16_ _12.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _01.RCC


title: Embryo 18hpf_20160524_bath study 18hpf plate1 1-12_ 2_02.RCC


title: Embryo 60hpf_20161018_bath study 60hpf 29-09-16 stripC_  _10.RCC


title: Embryo 60hpf_20161018_bath study 60hpf 29-09-16 stripC_  _09.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_48_12.RCC


title: Embryo 21hpf_20160809_bath study 21hpf 06-04-16 samples 13-24 _ 1_02.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_46_10.RCC


title: Embryo 60hpf_20161014_bath study 60hpf 29-09-16 IP strip b_ _01.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_47_11.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_44_08.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_45_09.RCC


title: Embryo 30hpf_20170609_bath study 30hpf 16-03-17 strip 3 plate 3_ _04.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_39_03.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_43_07.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_40_04.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_37 low volume supplied_01.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_38_02.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_41_05.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_36_12.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_ 35_11.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_27_03.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_29_05.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_25_01.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_ 34 very low volume of sample supplied_10.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_ 32_08.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_ 31_07.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_ 30_06.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 9_09.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 8_08.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 5_05.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 3_03.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 6_06.RCC


title: Embryo 18hpf_20160513_bath study 18hpf plate 2 37-48_ 42_06.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_28_04.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 1_01.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 23_11.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 11_11.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 22_10.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_26_02.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 10 _10.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 12_12.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_24_12.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 17_05.RCC


title: Embryo 18hpf_20160510_bath study 18hpf plate 2 25-36_ 33_09.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 16_04.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 20_08.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 21_09.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 15_03.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 18_06.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 2_02.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 4_04.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 14_02.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 13_01.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 19_07.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 22_10.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 16_04.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 17_05.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 18_06.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate 2 13-24_ 19_07.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 14_02.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 13_01.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_30_06.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_31_07.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_ 26_02.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_ 34_10.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_32_08.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_ 35_11.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_28_04.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_29_05.RCC


title: Embryo 72hpf_20160819_bath study 72hpf 15-04 samples 65-76_66_02.RCC


title: Embryo 48hpf_20160602_bath 48hpf new 25-36_25_01.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 9_09.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 8_08.RCC


title: Embryo 48hpf_20160602_bath study new 48hpf 13-24_ 24_12.RCC


title: Embryo 72hpf_20160819_bath study 72hpf 15-04 samples 65-76_70_06.RCC


title: Embryo 18hpf_20160504_bath study 18hpf plate2_ 7_07.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 7_07.RCC


title: Embryo 72hpf_20160819_bath study 72hpf 15-04 samples 65-76_72_08.RCC


title: Embryo 72hpf_20160819_bath study 72hpf 15-04 samples 65-76_74_10.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 6_06.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 5_05.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 3_03.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 4_04.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 11_11.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 1_01.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 10 _10.RCC


title: Embryo 72hpf_20160819_bath study 72hpf 15-04 samples 65-76_68_04.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_48_12.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_47_11.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_43_07.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_42_06.RCC


title: Embryo 21hpf_20160525_bath study 21hpf -03-  1-12_ 12_12.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_45_09.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_44_08.RCC


title: Embryo 72hpf_20160819_bath study 72hpf 15-04 samples 65-76_71_07.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_40_04.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_37_01.RCC


title: Embryo 48hpf_20160608_bath 48hpf 07-04 37-48_41_05.RCC


title: Embryo 30hpf_20170531_bath study 30hpf 16-03-17 plate 3 strip d_ _06.RCC


title: Embryo 30hpf_20170531_bath study 30hpf 16-03-17 plate 3 strip d_ _11.RCC


title: Embryo 18hpf_20160726_bath study 2-5ul unlabelled stripb 25-05-16_ _04.RCC


title: Embryo 24hpf_20170601_bath study 24hpf 05-05-17 strip b tails_ _06.RCC


title: Embryo 30hpf_20170531_bath study 30hpf 16-03-17 strip c plate 3_ _08.RCC


title: Embryo 30hpf_20170531_bath study 30hpf 16-03-17 strip c plate 3_ _01.RCC


title: Embryo 30hpf_20170531_bath study 30hpf 16-03-17 strip c plate 3_ _10.RCC


title: Embryo 30hpf_20170531_bath study 30hpf 16-03-17 plate 3 strip d_ _04.RCC


title: Embryo 24hpf_20170601_bath study 24hpf 27-04-17 strip a tails_ _03.RCC


title: Embryo 24hpf_20170601_bath study 24hpf 27-04-17 strip a tails_ _06.RCC


title: Embryo 24hpf_20170601_bath study 24hpf 27-04-17 strip a tails_ _12.RCC


title: Embryo 48hpf_20160324_bath study 8_ 47_11.RCC


title: Embryo 24hpf_20170601_bath study 24hpf 27-04-17 strip a tails_ _07.RCC


title: Embryo 48hpf_20160324_bath study 8_ 46_10.RCC


title: Embryo 48hpf_20160324_bath study 8_ 44_08.RCC


title: Embryo 48hpf_20160324_bath study 8_ 45_09.RCC


title: Embryo 48hpf_20160324_bath study 8_ 43_07.RCC


title: Embryo 48hpf_20160324_bath study 8_ 38_02.RCC


title: Embryo 48hpf_20160324_bath study 8_ 41_05.RCC


title: Embryo 48hpf_20160324_bath study 8_ 42_06.RCC


title: Embryo 48hpf_20160324_bath study 8_ 40_04.RCC


title: Embryo 30hpf_20170531_bath study 30hpf 16-03-17 plate 3 strip d_ _02.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 33_09.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 36_12.RCC


title: Embryo 48hpf_20160324_bath study 8_ 37_01.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 31_07.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 32_08.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 29_05.RCC


title: Embryo 48hpf_20160324_bath study 8_ 48_12.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 28_04.RCC


title: Embryo 30hpf_20161025_bath study 72hpf and 30hpf mitf _ _12.RCC


title: Embryo 72hpf_20161007_bath study 72hpf mc-ip 15-09-16 strip e_ _08.RCC


title: Embryo 30hpf_20161025_bath study 72hpf and 30hpf mitf _ _11.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 26_02.RCC


title: Embryo 48hpf_20160324_bath study 7 48hpf_ 25_01.RCC


title: Embryo 30hpf_20161025_bath study 72hpf and 30hpf mitf _ _09.RCC


title: Embryo 72hpf_20161005_bath study IP 15-09-16 strip B_ _01.RCC


title: Embryo 72hpf_20160805_bath study IP 12-07-16 samples 1-12_ 10 _10.RCC


title: Embryo 30hpf_20161025_bath study 72hpf and 30hpf mitf _ _10.RCC


title: Embryo 72hpf_20160728_bath study MC mixed 12-07-16_ 12_12.RCC


title: Embryo 72hpf_20161006_bath study 72hpf mc-ip 15-09-16 strip D_ _05.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _12.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _11.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _07.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _09.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _10.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _03.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _01.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 samples 25-36_ _02.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 13-24_ _12.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 13-24_ _09.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 13-24_ _10.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 13-24_ _02.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 13-24_ _01.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _11.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _09.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _06.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _07.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _03.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _02.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _05.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _04.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 8_08.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 5_05.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 4_04.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 3_03.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 1_01.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 12_12.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 10 _10.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 24_12.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 13-24_ _06.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 22_10.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 21_09.RCC


title: Embryo 24hpf_20160908_bath study 24hpf 06-04 13-24_ _05.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 18_06.RCC


title: Embryo 30hpf_20160818_bath study 30hpf 15-05 samples 1-12_  _10.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 16_04.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 20_08.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 19_07.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 15_03.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 7_07.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf_ 9_09.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 14_02.RCC


title: Embryo 48hpf_20160407_bath study new 48hpf 2_ 13_01.RCC


title: Embryo 21hpf_20160802_bath study 21hpf 22-03-16 sample 13-24 _ _11.RCC