title: young_C57BL6_LTHSC_127

description:
young_LT_HSC_127
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_105

status: Public on Sep 30 2015

type: SRA

city: Cambridge

first: Monika

middle: Sylwia

last: Kowalczyk

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute

description:
LT_HSC_old_plate3_biol_rep_TCL_G3
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

library_source: transcriptomic

data_processing:
Paired-end 25bp reads were mapped to the UCSC mouse transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters. TPM values as defined by RSEM were added a value of 1 (to avoid zeros) and then log2-transformed.
We filtered out cells in which less than 2500 UCSC genes were detected above a log2(TPM+1) threshold of 2. We excluded genes whose log2(TPM+1) was lower than 4 in the aggregared data for each of the 6 populations, and those UCSC genes that were not associated with a HUGO gene Symbol, leaving 7823 genes for the final dataset.
Genome_build: mm9
Supplementary_files_format_and_content: GEO_HSC_single_data.xlsx is an Excel sheet that contain the log-transformed expression levels, log2(TMP+1) of 8422 mouse transcripts in 1429 single cells and in six population averages, including young and old LT-HSCs, ST-HSCs and MPPs. The first row contains cell ID (a unique index for each single cell) or "pop" for the population averages. The second row indicates the type of population (age and cell type) that the cell (or population average) belongs to. The first and second columns include gene symbols and UCSC transcript names, respectively. (The processed data file only represents samples that were of sufficient quality to analyze)

molecule: total RNA

organism: Mus musculus

source_name: hematopoietic stem and progenitor cells

growth_protocol: cells were profiled immediately

extract_protocol:
for single cells - direct lysis; for populations we used PrepEase (Affymetrix) according to manufacturers protocol.
cDNA from each sample was prepared using the SMARTer cDNA synthesis (Clontech). RNA libraries were prepared for sequencing using Nextera XT (Illumina).

tag: strain

tag: age

value: 22 months old

tag: cell type

value: long term hematopoietic stem cell


title: young_C57BL6_LTHSC_125

description:
young_LT_HSC_125
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

value: 2-3 months old


title: young_C57BL6_LTHSC_128

description:
young_LT_HSC_128
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_131

description:
young_LT_HSC_131
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_132

description:
young_LT_HSC_132
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_103

description:
LT_HSC_old_plate3_biol_rep_TCL_A11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_124

description:
young_LT_HSC_124
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_129

description:
young_LT_HSC_129
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: Ak2

city: omaha

first: Paras

middle: Kumar

last: Mishra

state: Nebraska

address: DRC1 Room 5047

department: Cellular and Integrative Physiology

institute: University of Nebraska medical center

data_processing:
Illumina HCS v2.05 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat 2 aligner in basespace.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks 2 and differential expression was done using cuffdiff 2.1.1 in basespace.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

source_name: Heart tissue (Akita)

extract_protocol:
RNA was isolated from fresh heart tissue using mirVana kit.
RNA libraries were prepared for sequencing using TruSeq RNA sample prepration kit from Illumina. 1μg of RNA was used to construct the library. QC was done by bioanalyzer and quantified by Qubit. 6PM strating quantity was used for further sequencing. 100 base single read run after o-botclustering was performed on Illumina HiSeq 2500.

tag: genotype

value: Mutation in Insulin 2 gene. Type 1 diabetic model.

value: Male (12 week)

tag: tissue

value: heart

tag: genetic background


title: old_C57BL6_LTHSC_biol_replicate_102

description:
LT_HSC_old_plate3_biol_rep_TCL_E11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_123

description:
young_LT_HSC_123
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_120

description:
young_LT_HSC_120
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_101

description:
LT_HSC_old_plate3_biol_rep_TCL_B11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_100

description:
LT_HSC_old_plate3_biol_rep_TCL_H11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_99

description:
LT_HSC_old_plate3_biol_rep_TCL_D11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_98

description:
LT_HSC_old_plate3_biol_rep_TCL_F11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_121

description:
young_LT_HSC_121
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_122

description:
young_LT_HSC_122
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_119

description:
young_LT_HSC_119
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_126

description:
young_LT_HSC_126
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_117

description:
young_LT_HSC_117
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_95

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_118

description:
young_LT_HSC_118
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_97

description:
LT_HSC_old_plate3_biol_rep_TCL_G11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_93

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_94

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_113

description:
young_LT_HSC_113
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_114

description:
young_LT_HSC_114
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_91

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_92

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_115

description:
young_LT_HSC_115
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_111

description:
young_LT_HSC_111
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_89

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_112

description:
young_LT_HSC_112
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_88

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_110

description:
young_LT_HSC_110
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_109

description:
young_LT_HSC_109
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_107

description:
young_LT_HSC_107
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_85

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_106

description:
young_LT_HSC_106
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_86

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_84

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_104

description:
young_LT_HSC_104
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_82

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_105

description:
young_LT_HSC_105
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_103

description:
young_LT_HSC_103
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_96

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_83

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_81

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_102

description:
young_LT_HSC_102
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_79

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_80

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_90

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F04
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_101

description:
young_LT_HSC_101
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_78

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_99

description:
young_LT_HSC_99
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_97

description:
young_LT_HSC_97
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: WT5

source_name: Heart tissue (Wild type)

value: Wild type


title: young_C57BL6_LTHSC_98

description:
young_LT_HSC_98
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_77

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_100

description:
young_LT_HSC_100
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_108

description:
young_LT_HSC_108
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_87

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A06
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_74

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_94

description:
young_LT_HSC_94
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_73

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_75

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_96

description:
young_LT_HSC_96
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_72

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_93

description:
young_LT_HSC_93
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_92

description:
young_LT_HSC_92
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_69

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_70

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_90

description:
young_LT_HSC_90
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_71

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_91

description:
young_LT_HSC_91
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_89

description:
young_LT_HSC_89
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_76

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H01
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_68

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_88

description:
young_LT_HSC_88
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_67

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_66

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_87

description:
young_LT_HSC_87
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_64

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_85

description:
young_LT_HSC_85
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_65

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_63

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_95

description:
young_LT_HSC_95
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_84

description:
young_LT_HSC_84
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_116

description:
young_LT_HSC_116
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_61

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_82

description:
young_LT_HSC_82
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_60

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_59

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_80

description:
young_LT_HSC_80
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_81

description:
young_LT_HSC_81
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_77

description:
young_LT_HSC_77
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_79

description:
young_LT_HSC_79
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_56

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_55

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_76

description:
young_LT_HSC_76
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_54

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_57

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_86

description:
young_LT_HSC_86
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_53

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_75

description:
young_LT_HSC_75
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_73

description:
young_LT_HSC_73
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_51

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_71

description:
young_LT_HSC_71
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_50

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_72

description:
young_LT_HSC_72
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_49

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_83

description:
young_LT_HSC_83
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_58

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_62

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E05
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_46

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_47

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_45

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_70

description:
young_LT_HSC_70
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_68

description:
young_LT_HSC_68
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_78

description:
young_LT_HSC_78
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_66

description:
young_LT_HSC_66
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_65

description:
young_LT_HSC_65
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_48

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_52

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H09
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_64

description:
young_LT_HSC_64
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_42

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_74

description:
young_LT_HSC_74
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_43

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_44

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_62

description:
young_LT_HSC_62
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_39

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_61

description:
young_LT_HSC_61
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_67

description:
young_LT_HSC_67
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_59

description:
young_LT_HSC_59
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_38

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_60

description:
young_LT_HSC_60
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_37

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_58

description:
young_LT_HSC_58
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_63

description:
young_LT_HSC_63
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_36

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_69

description:
young_LT_HSC_69
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_56

description:
young_LT_HSC_56
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_34

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_57

description:
young_LT_HSC_57
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_35

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_55

description:
young_LT_HSC_55
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_32

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_33

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_31

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_40

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C02
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_30

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_52

description:
young_LT_HSC_52
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_51

description:
young_LT_HSC_51
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_29

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_50

description:
young_LT_HSC_50
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_28

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_49

description:
young_LT_HSC_49
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_48

description:
young_LT_HSC_48
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_25

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_26

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_47

description:
young_LT_HSC_47
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_46

description:
young_LT_HSC_46
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_24

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_104

description:
LT_HSC_old_plate3_biol_rep_TCL_C11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_45

description:
young_LT_HSC_45
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_54

description:
young_LT_HSC_54
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_41

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G07
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_44

description:
young_LT_HSC_44
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_23

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_53

description:
young_LT_HSC_53
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_42

description:
young_LT_HSC_42
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_20

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_22

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_21

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_40

description:
young_LT_HSC_40
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_43

description:
young_LT_HSC_43
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_41

description:
young_LT_HSC_41
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_19

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_39

description:
young_LT_HSC_39
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_38

description:
young_LT_HSC_38
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_17

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_16

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_18

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F08
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_37

description:
young_LT_HSC_37
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_36

description:
young_LT_HSC_36
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_14

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_13

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_12

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_33

description:
young_LT_HSC_33
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_34

description:
young_LT_HSC_34
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_11

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_10

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_32

description:
young_LT_HSC_32
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_9

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_8

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_C11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_31

description:
young_LT_HSC_31
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_6

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_E11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_7

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_5

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_B11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_26

description:
young_LT_HSC_26
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_30

description:
young_LT_HSC_30
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_15

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_A03
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_4

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_H11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_2

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_F11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_23

description:
young_LT_HSC_23
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_24

description:
young_LT_HSC_24
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_3

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_25

description:
young_LT_HSC_25
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: old_C57BL6_LTHSC_biol_replicate_1

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_G11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_22

description:
young_LT_HSC_22
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_35

description:
young_LT_HSC_35
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_21

description:
young_LT_HSC_21
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_20

description:
young_LT_HSC_20
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_19

description:
young_LT_HSC_19
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_18

description:
young_LT_HSC_18
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_28

description:
young_LT_HSC_28
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_16

description:
young_LT_HSC_16
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_29

description:
young_LT_HSC_29
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_15

description:
young_LT_HSC_15
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_27

description:
young_LT_HSC_27
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_14

description:
young_LT_HSC_14
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_11

description:
young_LT_HSC_11
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_12

description:
young_LT_HSC_12
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_10

description:
young_LT_HSC_10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_13

description:
young_LT_HSC_13
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_8

description:
young_LT_HSC_8
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_7

description:
young_LT_HSC_7
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_6

description:
young_LT_HSC_6
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_2

description:
young_LT_HSC_2
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_1

description:
young_LT_HSC_1
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_3

description:
young_LT_HSC_3
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: young_C57BL6_LTHSC_5

description:
young_LT_HSC_5
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: NIPS_1_2

city: LYON

first: MARMIGERE

last: FREDERIC

address: 32/34 Av. Tony Garnier

department: Institut de génomique fonctionelle de Lyon

country: France

institute: CNRS

library_source: genomic

data_processing:
Demultiplexing and alignment were performed using Illumina's sequencing analysis software (CASAVA 1.8.2) that performs alignment to mouse genome (mm10) and keeps only the reads that align to unique positions in the genome.
In NIPS_1_2 library, 58 149 472 passing-filter (PF) clusters were detected, 42 816 709 reads passing-filter were uniquely aligned to the mm10 reference and 3 279 530 reads had distinct coordinates. In SCGM_1_2 library, 62 059 483 passing-filter (PF) clusters were detected, 18 116 859 reads passing-filter were uniquely aligned to the mm10 reference and 1 300 875 reads had distinct coordinates.
ChIP-enriched genomic regions were defined using Model-based Analysis of ChIP-Seq (MACS 1.4.2).
The list of regions were annotated with the closest genes (maximal distance allowed from transcription start or transcription end is 20kb) using CisGenome 1.2 software. The gene annotation was retrieved from UCSC (refFlat file) on October 10, 2012 and gene IDs from gene2refseq.gz file (NCBI; October 30, 2012).
Genome_build: mm10
Supplementary_files_format_and_content: peak file was generated using MACS software

molecule: genomic DNA

source_name: NIPS

extract_protocol:
Two times 20 SCGs from E16 C57Bl6 embryos were dissected, fixed by adding PBS/PFA 1% for 10 min and precipitated independantly. Chromatin was isolated and sheared by sonication (16 cycles composed by 30’ pulses following by 30’ without pluses on a BIORUPTOR® STANDARD) to obtain a smear between 250 and 1000 bp. After immunoprecipitation, DNA was  purified using the iPure kit (Diagenode, C03010012) according to the manufacturer’s instructions and the two samples were pulled.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Superior cervical ganglion

value: Embryonic day 16

tag: chip antibody


title: SCGM_1_2

source_name: SCGM

value: Anti-Meis Millipore 05-779


title: D18 Adipogenic Differentiation

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19, mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

organism: Homo sapiens

source_name: Adipose-derived mesenchymal stromal cells

extract_protocol:
RNA was isolated using the miRNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: Healthy donor

tag: passage

value: Passage 6-8

tag: Sex

value: Female


title: FOXM1_ChIPSeq

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with the --very-sensitive-local parameter
read coverage at each genome was calculated using a custom Perl script
any position with less than 4 read coverage was removed
translation into BigWig format using UCSC tool wigToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from BAM files via Wig files using a custom Perl script and the wigToBigWig tool; scores represent read coverage at each genomic position (where >= 4).

source_name: HMEC–TERT

growth_protocol: Primary HMEC cells which were previously immortalised by retroviral expression of hTERT were maintained in M87A medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 300–500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Primary HMEC cells immortalised by retroviral expression of hTERT

tag: passages


title: E2F1_ChIPSeq


title: input DNA


title: Day -1 Osteogenic Differentation (2D)


title: Day 21 Osteogenic Differentation (2D)


title: Day 14 Osteogenic Differentation (2D)


title: Day 7 Osteogenic Differentation (3D)


title: young_C57BL6_LTHSC_17

description:
young_LT_HSC_17
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: MYBL2_ChIPSeq


title: Day 21 Osteogenic Differentation (3D)


title: Day 7 Osteogenic Differentation (2D)


title: Day 3 Osteogenic Differentation (3D)


title: Day 14 Osteogenic Differentation (3D)


title: young_C57BL6_LTHSC_9

description:
young_LT_HSC_9
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: Day 0 Osteogenic Differentation (3D)


title: young_C57BL6_LTHSC_4

description:
young_LT_HSC_4
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx


title: DMSO AMSCs B


title: DMSO AMSCs A


title: Day 0 Osteogenic Differentation (2D)


title: 2µM GSK126 AMSCs B


title: ADM_Methylation

city: Wu Xi

first: Dong-Xu

last: He

address: Jiangnan University

department: Jiangnan University

country: China

institute: National Engineering Laboratory for Cereal Fermentation Technology

description: processed_data_file: DMR 1.xls

data_processing:
Basecalls performed using CASAVA software
Clean reads were obtained after removal of adaptor sequences, and removal of reads having greater than 10% of unknown bases as well as removal of reads with low quality bases (base with quality value ≤ 5) greater than 50% in a read.
The mapped read counts for each gene were normalized for RNA length and for the total read number in each lane using the reads per kilobase per million (RPKM) method.
For RRBS, Genomic DNA from the above 3 samples were extracted and were subjected to RRBS library preparation.
The libraries were sequenced using an Illumina Hiseq 2000 analyzer according to the manufacturer’s instructions.
Raw sequencing data was processed by the Illumina base-calling pipeline. Low-quality reads containing more than 30% ‘N’s or with more than 10% of the sequence having a low quality value (quality value <20) per read, were omitted from the data analysis.
The sequencing reads were aligned to the human genomic reference sequence (Hg19) in an unbiased way for bisulfite sequencing data: (1) all the observed cytosines were replaced by thymines and the guanines were replaced by adenosines in silico, forming two “alignment form” references; (2) observed cytosines on the forward read of each read pair were replaced by thymines, and observed guanines on the reverse read of each read pair were replaced by adenosines, in silico; (3) the “alignment form” reads were then mapped to the “alignment form” reference using the Short Oligonucleotide Alignment Program (SOAP) (http://soap.genomics.org.cn).
The uniquely mapped reads that contained at least one enzyme digestion site in the ends were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample or different methylated region measurement.

growth_protocol: Cells were cultured in RPMI supplemented with 10% FBS, 100 μg/mL penicillin, and 100 U/mL streptomycinsupplemented with L-glutamine, MEM nonessential amino acids, gentamicin sulfate, and 10% FBS.

extract_protocol:
For RRBS, Genomic DNA was digested with MspI enzymes (NEB) and blunt-ended. Then dA was added, followed by methylated-adapter ligation. To obtain DNA fractions of 40-120 bp and 120-220 bp ranges of MspIdigested products, two ranges of 160-240 bp and 240-340 bp adapter-ligated fractions were excised from a 2% agarose gel, respectively. Bisulfite conversion was conducted using a ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO), following the manufacturer’s instructions. The final libraries were generated by PCR amplification using JumpStart™ Taq DNA Polymerase (Sigma). RRBS libraries were analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies).
Total DNA and RNA was isolated.

treatment_protocol: MCF-7 cells were treated with stepwise increasing concentrations of adriamycin (ADM) and paclitaxel (PTX) over 8 mo.

tag: cell line

value: breast

value: breast cancer

tag: treatment

value: treated with ADM


title: PTX_Methylation

description: processed_data_file: DMR 1.xls

value: treated with PTX


title: WT_Methylation

description: processed_data_file: DMR 1.xls

source_name: MCF-7_treated_with_growth medium

value: treated with growth medium


title: PTX_RNAseq

description: processed_data_file: RNA-Seq rpkm.xlsx

extract_protocol:
For RNA-Seq, The total RNA samples were first treated with DNase I to degrade any possible DNA contamination. Then the mRNA was enriched by using the oligo (dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments (about 200 bp). Then the first strand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, Agilent2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used to qualify and quantify of the sample library. The library products were ready for sequencing via Illumina HiSeq2000.
Total DNA and RNA was isolated.


title: WT_RNAseq

description: processed_data_file: RNA-Seq rpkm.xlsx


title: ADM_RNAseq

description: processed_data_file: RNA-Seq rpkm.xlsx


title: 2µM GSK126 AMSCs A


title: wz255_input

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 50bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-7 for ChIP-seq data. DFilter was run with bs=100, ks=50 for FAIRE data and bs=50, ks=30, refine, nonzero for ChIP data.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using genomecov utility from bedtools; intersect.bed files contain peaks called by both peak calling algorithms

source_name: Human prostate tumor

growth_protocol: Fresh frozen post-operative prostate needle biopsies from normal (pathologically validated tumor-free region from the peripheral zone) and tumor samples were obtained from prostatectomy specimens at the Netherlands Cancer Institute (Amsterdam, the Netherlands). The androgen-blockade resistant tumor samples (Transurethral resection of the prostate (TURP)) and lymph node metastases were obtained from the Erasmus University Medical Center (Rotterdam, the Netherlands). The study was performed in accordance with the Code of Conduct of the Federation of Medical Scientific Societies in the Netherlands and has been approved by the local medical ethics committees.

extract_protocol:
FAIRE experiments were performed as described (Giresi PG et al. Methods 2009;48(3):233-9): fresh frozen tissues were crosslinked with 1% formaldehyde for 20 min. Cells were washed, nuclei isolated. Chromatin was sonicated and cleared by centrifugation. The soluble chromatin was subjected to three consecutive phenol-chloroform-isoamyl alcohol (25:24:1) extractions. The samples were reverse crosslinked overnight at 65C and purified by ethanol precipitation. Purified samples were treated with RNase A and proteinase K and repurified by PCR purification kit. Chromatin Immunoprecipitation was performed as described (Zwart W et al. BMC Genomics 2013;14:232): 10ug of antibody was used, with 100ml of Protein A magnetic beads. Antibody used was AR-N20 (sc-618; Santa Cruz). DNA was amplified as described (Ross-Innes CS et al. Nature 2012;481(7381):389-93).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: tumor sections or biopsies were cryosectioned; 10x30um sections were used

value: primary prostate tumor

tag: antibody

value: none (input)

tag: tumor id


title: wz256_input


title: wz248_input

value: lymph node metastasis

value: mix LN


title: wz242_AR_TURP

value: resistant prostate tumor (TURP)

value: anti-AR (sc-618, Santa Cruz)

tag: gleason score

tag: initial psa (ng/ml)


title: wz243_AR_TURP


title: DMSO AMSCs C


title: wz247_input

value: mix TURP


title: wz229_AR_primary


title: wz241_AR_TURP


title: wz363_FAIRE_Met

value: none (FAIRE)


title: 2µM GSK126 AMSCs C

value: Healthy donor


title: wz361_FAIRE_Met


title: wz228_AR_primary


title: wz359_FAIRE_TURP


title: wz253_AR_primary


title: wz365_FAIRE_primary


title: wz252_AR_primary


title: wz362_FAIRE_Met


title: wz367_FAIRE_TURP


title: wz251_AR_primary


title: wz368_FAIRE_TURP


title: wz360_FAIRE_primary


title: wz366_FAIRE_primary


title: wz371_FAIRE_normal

source_name: Human prostate tissue

value: normal prostate tissue


title: wz364_FAIRE_primary


title: ZFHX3_bait2_TATNF

city: Nijmegen

first: Shuang-Yin

last: Wang

address: Geert Grooteplein 28

department: Molecular Biology

institute: RIMLS

description: 4C PCR product. Barcode: CACACAGTCAGGAAAGAGATC

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Illumina RTA 1.6.47.1 used for basecalling of GAII data.
Library strategy: ChIP-seq. The reads were aligned to build version hg19 of the human genome using bwa (version 0.6.2) with default parameters. Only unique mapped reads were kept for downstream analysis. Reads from PCR duplicates were also removed. MACS (version 1.4.2), was used to identify regions of ChIP-seq enrichment over background using parameters -p 1e-9 –nomodel.
Library strategy: ChIA-PET. The first 72bp of each sequenced read carries the complete ChIA-PET ligation product (linker plus genomic DNA) was taken for the further analysis after trimming the ends of each read.  Subsequently, single end sequenced reads were split at the linker ligation junction (linkerA/B-|-linkerA/B) and flipped to make the data compatible (similar to paired end sequencing reads) for the ChIA-PET data analysis pipeline (doi:10.1186/gb-2010-11-2-r22).
Library strategy: 4C-seq. The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank DpnII sites (fragment ends). Repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse genome hg19.
Genome_build: hg19

source_name: HeLa B2 cells

growth_protocol: HeLa B2 cells were maintained as described in previous study (doi:10.1101/gr.118042.110). Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% charcoal stripped fetal calf serum (FCS) for 72-96 hours before subsequent treatment and/or harvesting.

extract_protocol: Libraries were prepared according to Illumina's instructions.

value: HeLa

tag: treatment protocol

value: 1μM of Triamcinolonacetonide (T6501, Sigma-Aldrich) with 10ng/ml Tumor necrosis factor α (T0157, Sigma-Aldrich) for the last 1 hour.


title: ZFHX3_bait3_TATNF


title: wz382_FAIRE_normal


title: ZFHX3_bait1_DMSO_rep1

description: 4C PCR product. Barcode: GCAAATAGGACCTAATGTGATC


title: ZFHX3_bait1_TATNF_rep1


title: ZFHX3_bait1_TATNF_rep2


title: SULF1_TATNF_rep3

description: 4C PCR product. Barcode: ATGGACCTGCATTTGAGATC


title: ZBTB16_TATNF_rep1

description: 4C PCR product. Barcode: ACAGTGATTTGAGGGGATC


title: ZBTB16_DMSO_rep2


title: ZFHX3_bait1_DMSO_rep2


title: SULF1_TATNF_rep1


title: ZBTB16_DMSO_rep1


title: ZBTB16_TATNF_rep2


title: PTPN1_TATNF_rep1

description: 4C PCR product. Barcode: AGCCTTCAACAAGAGGATC


title: SULF1_TATNF_rep2


title: PTPN1_TATNF_rep2


title: KLF6_bait2_TATNF_rep3

description: 4C PCR product. Barcode: CGATGACTTTCAAGGTGATC


title: SULF1_DMSO_rep3


title: SULF1_DMSO_rep2


title: KLF6_bait2_DMSO_rep1


title: wz383_FAIRE_normal


title: SULF1_DMSO_rep1


title: KLF6_bait2_DMSO_rep2


title: KLF6_bait2_DMSO_rep3


title: PTPN1_DMSO_rep2


title: KLF6_bait2_TATNF_rep2


title: wz369_FAIRE_normal


title: KLF6_bait2_TATNF_rep1


title: KLF6_bait1_DMSO_rep2

description: 4C PCR product. Barcode: GTCTCTGGCACGTAATGATC


title: KLF6_bait1_TATNF_rep1

description: 4C PCR product. Barcode: TCTCTGGCACGTAATGATC


title: KLF6_bait1_DMSO_rep1


title: FKBP5_enh_DMSO_rep2

description: 4C PCR product. Barcode: ATTACTGGGTCATGAGGATC


title: FKBP5_enh_TATNF_single

description: 4C PCR product. Barcode: TTACTGGGTCATGAGGATC


title: FKBP5_enh_TA_single

value: 1μM of Triamcinolonacetonide (T6501, Sigma-Aldrich)


title: FKBP5_enh_DMSO_rep1


title: FKBP5_enh_TNF_single

value: 10ng/ml Tumor necrosis factor α (T0157, Sigma-Aldrich) for 1 hour.


title: PTPN1_DMSO_rep1


title: FKBP5_enh_TATNF_rep1


title: DUSP1_TATNF_rep1

description: 4C PCR product. Barcode: GGCATTCATTGCCAGTGATC


title: DUSP1_TATNF_rep2

description: 4C PCR product. Barcode: GCATTCATTGCCAGTGATC


title: BIRC3_enh2_TATNF_rep1

description: 4C PCR product. Barcode: ACAGAATCAGTGGGTTGATC


title: DUSP1_DMSO_rep2


title: BIRC3_enh2_TATNF_rep2


title: DUSP1_DMSO_rep1


title: BIRC3_enh2_DMSO_rep1


title: FKBP5_enh_TATNF_rep2


title: BIRC3_enh2_DMSO_rep2


title: KLF6_bait1_TATNF_rep2


title: BIRC3_enh1_TATNF_rep2

description: 4C PCR product. Barcode: AAATCTCAACTGTTGGGATC


title: H3K4me3_TA+TNFα

value: H3K4me3 (C15410003, Diagenode)


title: BIRC3_enh1_TATNF_rep1


title: old_C57BL6_LTHSC_biol_replicate_27

description:
LT_HSC_old_plate2_biol_rep_TCL_plate1_D10
single cell RNA-Seq
processed data file: GEO_HSC_single_data.xlsx

tag: strain

tag: age

value: 22 months old

value: long term hematopoietic stem cell


title: BIRC3_enh1_DMSO_rep2


title: FKBP5_enh_DMSO_single


title: H3K27ac_DMSO

value: H3K27ac (C15410196, Diagenode)


title: BIRC3_enh1_DMSO_rep1


title: H3K4me3_DMSO


title: DNaseI_TA+TNFα


title: H3K27ac_TA+TNFα


title: DNaseI_DMSO


title: ChIAPET_RNAPII_TA+TNFα

value: RNA Pol II (MMS-126R-500, Covance)


title: ChIAPET_P300_DMSO

value: P300 (sc-585x, Santa Cruz biotechnology)


title: ChIAPET_P300_TA+TNFα


title: ChIAPET_RNAPII_DMSO_rep2

description: 2514_3850_ChIAPET_RNAPII_DMSO_HeLaB2.tsv


title: H3K4me1_DMSO

value: H3k4me1 (C15410194, Diagenode)


title: ChIAPET_RNAPII_DMSO_rep1


title: White  feather bulbs (W-w1)

city: Wuhan

first: Sheila

middle: Nabwire

last: Apopo

state: Hubei

address: No.1,Shizishan Street · Hongshan District

department: Animal Science

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequence quality was assessed with FastQC software . To obtain clean reads, low quality reads, adapter sequences and reads shorter than 18 nt were eliminated using our own perl scripts, then mapped to duck  genome using bowtie v0.12.2 with default options.
The Anas platyrhynchos genome reference and precursor of duck miRNA were downloaded from the Ensembl database. Chicken mature miRNAs and precursor miRNA were obtained from miRBase version 21. Clean sequence reads were analysed by miRDeep2 software version 2.1.2. MiRDeep2 software  was used to identify known and novel miRNA. Afterwards, the expression level of each miRNA was normalized to follow the formula: Normalized expression (NE) =Actual miRNA count/Total count of clean reads x 1,000,000.
Genome_build: BGI_duck_1.0, INSDC Assembly GCA_000355885.1
Supplementary_files_format_and_content: Individual tables for each sample containing raw counts of sequencing reads and normalized abundance measurements for the identified known and novel miRNAs

organism: Anas platyrhynchos

source_name: pure white plumage duck

extract_protocol:
Black and white feather bulbs were removed and  placed into 2-mL tubes containing 1 mL of TRIzol reagent (Invitrogen, San Diego, CA). Total RNA was extracted using TRIzol reagent as per the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina HiSeq 2000

tag: breed

value: Kaiya

value: Feather bulbs

value: 12 months

tag: plumage color

value: pure white


title: black feather bulbs (B-wb)

source_name: white-black plumage duck

value: Kaiya-Liancheng F2

tag: tissue

value: white-black


title: White  feather bulbs (W-w2)

value: Liancheng


title: White feather bulbs(W-wb)


title: PE_midgut

city: Changsha City

first: XingLI

last: Xu

address: Furong District

institute: Hunan Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw sequence data preprocess and assembly were performed by using CLC Genomics Workbench (CLC bio, Aarhus, Denmark). All raw reads were trimmed according to their quality score. The sequences with low quality, adapter sequences, ambiguous bases and containing less than 20 nucleotides were removed from further analysis before contig assembly. After clean up, de novo sequence assembly was performed on all remaining reads with a contig scaffolding algorithm with a minimum contig length of 200 bp or longer.
Comparison of unigene in the two Haemaphysalis flava midgut (MG) Illumina libraries was performed by the following process: Based on the number of reads of each unigene from two MG libraries, RPKM method (reads per kilobase of exon model per million mapped reads) was used to quantify gene expression levels of each gene. In this study, DEGseq, an R package for identifying differentially expressed genes from RNA-seq data was applied to determine the significance of difference in gene expression between FE and PE.
Genome_build: Assembled sequences.  The fasta file of assembled sequences are available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values and raw fragment counts for each Sample.

molecule: polyA RNA

organism: Haemaphysalis flava

source_name: midgut

extract_protocol:
Total RNA was extracted with Trizol Reagent (Invitrogen, Carlsbad, CA, USA).
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: MGs were dissected and stored in liquid nitrogen until RNA extraction

value: midgut

tag: Stage

value: partially engorged Haemaphysalis flava ticks


title: Black feather bulbs (B-b)

source_name: pure black plumage duck

value: Cui Hei

value: pure black


title: control ChIP

status: Public on Sep 29 2015

city: Heidelberg

first: Ingrid

last: Lohmann

address: Im Neuenheimer Feld 230

country: Germany

institute: COS, University Heidelberg

data_processing:
ChIP-seq reads were mapped with Bowtie.
Peak-calling was performed with MACS.
Genome_build: Drosophila melanogaster release 5.29
Supplementary_files_format_and_content: .csv files containing detected peak positions.

organism: Drosophila melanogaster

source_name: wild-type embryos

growth_protocol: Wild-type (Oregon R) Drosophila melanogaster flies were aloud to lay eggs on apple-juice agar plates with yeast paste at 25°C. After 4.5h of egg deposition, plates were changed and incubated for additional 5h at 25°C to obtain embryos of the desired stages 9 to 12.

extract_protocol:
The ChIP protocol of Sandmann et al, Nature Protocols, 2006 was used to isolate gDNA fragments.
Illumina standard library protocol.

treatment_protocol: For ChIP, a specific anti-Deformed (guinea pig, gift from W. McGinnis) or mock guinea pig IgG antibodies were used.

tag: developmental stage

value: 5 to 9.5 hours

tag: genotype

value: wild type

value: Oregon R


title: ChIPSeq Vehicle treated_APOBEC3B

city: London

first: Luca

last: Magnani

address: DuCane road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows. Alignments were done using Bowtie 1.0.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using default settings.
Genome_build: Hg 19
Supplementary_files_format_and_content: Wig files

source_name: MCF7 cells

growth_protocol: MCF-7 cells were cultured in DMEM containing 10%FCS. For ChIP-seq study, the cells were cultured in DMEM lacking phenol-red, supplemented with 10% dextran-coated charcoal-stripped FCS for 72 hours. Estrogen (100 nM) or Ethanol  was added and cells were fixed  and sonicated for ChIP after 45 minutes.

extract_protocol:
Lysates were clarified from sonicated nuclei and APOBEC3B--DNA complexes were isolated with antibody.
Libraries were prepared according to NEB DNA UltraKit's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated using Ampure SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the H-Seq2000 following the manufacturer's protocols.

tag: cell type

value: breast cancer cell line

tag: treated with

value: Ethanol (vehicle)

tag: chip antibody

value: Rabbit polyclonal APOBEC3B antiserum prepared by immunising with overlapping peptides


title: H3K4me1_TA+TNFα

tag: cell line

value: HeLa

value: 1μM of Triamcinolonacetonide (T6501, Sigma-Aldrich) with 10ng/ml Tumor necrosis factor α (T0157, Sigma-Aldrich) for the last 1 hour.

value: H3k4me1 (C15410194, Diagenode)


title: ChIPSeq Vehicle treated_Input


title: ChIPSeq Estrogen treated_APOBEC3B

value: Estrogen (100 nM)


title: Deformed ChIP


title: FE_midgut

value: fully engorged Haemaphysalis flava ticks


title: P2

city: Tianjin

first: Lingyi

last: Chen

address: 94 Weijin Road

institute: Nankai University

data_processing:
By base calling, the original image data produced by the sequencer is transferred into sequences, which are defined as "raw reads" (or "raw data") and saved as ".fastq" files. As the raw reads may contain low quality reads and or adaptor sequences, preprocessing is necessary before starting further analysis. Normally, data cleaning (or data filtering) is performed to obtain "clean reads" (or "clean data") for further analysis.
As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean data). The procedure include following steps:1. Remove reads with adaptor sequences.  2. Remove reads in which the percentage of unknown bases (N) is greater than 10%.  3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality.
Clean reads are the high quality sequences after data cleaning, on which all following analyses are based.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2[1]. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample(see 3.2.7.2 for details). The related information of gene is also provided (Coverage, Symbol, Description and so on).
Genome_build: mm9
Supplementary_files_format_and_content: Text files include RPKM values for each Sample

source_name: iErk1; Erk KO ESCs cultured without Dox for 96 hours

extract_protocol:
Trizol and Qiagen RNeasy kit
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products were sequenced via Illumina HiSeqTM 2000 (SE50).

tag: background strain

value: mouse embryonic stem cells (ESCs)

tag: genotype/variation

value: iErk1; Erk KO


title: P2_PD

source_name: iErk1; Erk KO ESCs cultured without Dox for 96 hours, and treated with PD0325901 in the last 48 hours


title: P1

source_name: iErk1; Erk KO ESCs cultured without Dox for 48 hours


title: P0

source_name: iErk1; Erk KO ESCs cultured with Dox


title: KH2_PD

source_name: KH2 ESCs treated with PD0325901 for 48 hours


title: Hypoxia short-130 rep3

city: Boston

first: Thomas

last: BERTERO

address: 77 Av Louis Pasteur

department: Cardiology

institute: Brigham and women hospital, Harvard Medical School

description: treated with short-130

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), a quality control tool for high throughput sequence data, was used for checking q-scores and reads were not trimmed prior to alignments.
The data were aligned against UCSC mouse genome version mm10 using STAR aligner (Dobin, A. et al., Bioinformatics, 2013).
From BAM files, gene-level counts of uniquely mapped reads were computed using SAMTools (Li H. et al, Bioinformatics, 2009) and HTSeq v0.5.4p5 (Anders S. et al, bioRxiv preprint, 2014).
Gene level counts were then normalized with the R/Bioconductor package limma (Smyth, G. K., Springer, 2005) using the voom (Law CW, et al. Genome Biology, 2014) /variance stabilization method
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with gene counts for each sample and tab-delimited text file with normalized Log2 transformed data matrix

source_name: Hypoxia short-130 rep3

extract_protocol:
Lungs were removed, flash frozen on liquid nitrogen, and RNA was harvested using Qiazol reagent. Illumina’s TruSeq RNA Sample Preparation v2 kit was used to construct libraries. Briefly, 150ng of total RNA input was used. The libraries were quantified using KAPA library quantification kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: Lung

value: 8 weeks old


title: Hypoxia short-NC rep3

description: treated with short-NC

source_name: Hypoxia short-NC rep3

value: short-NC


title: Hypoxia short-130 rep2

description: treated with short-130

source_name: Hypoxia short-130 rep2


title: Hypoxia short-130 rep1

description: treated with short-130

source_name: Hypoxia short-130 rep1


title: Hypoxia short-NC rep1

description: treated with short-NC

source_name: Hypoxia short-NC rep1


title: Hypoxia short-NC rep2

description: treated with short-NC

source_name: Hypoxia short-NC rep2


title: Normoxia rep3

description: treated with PBS

source_name: Normoxia rep3

value: PBS


title: Normoxia rep2

description: treated with PBS

source_name: Normoxia rep2


title: Normoxia rep1

description: treated with PBS

source_name: Normoxia rep1


title: Sample0018_LS_L007_R1_001

city: New York

first: Joel

middle: M

last: Correa da Rosa

state: New York

address: 1230 York Avenue

department: CTSA

institute: Rockefeller University

data_processing:
Samples were sequenced on the Illumina Genome Analyzer llx platform
Sequencing was carried out for 100 cycles and raw sequecing data was processed using the onboard SCS/RTA software version 2,8yielding 100 bp reads.
Genome_build: hg19
Supplementary_files_format_and_content: RNASeqMappingCounts: generated by the easyRNASeq package in R
Supplementary_files_format_and_content: TableSeqGenes: LogFC

source_name: lesional skin sample

extract_protocol:
Total RNA from paired lesional and non-lesional skin samples was reverse trancribed and amplified by using Ovation RNA-Seq FFPE system go generate cDNA library(NuGEN Technologies, Inc.)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lesional skin

tag: gender

value: M


title: Sample0018_NL_L007_R1_001

source_name: non-lesional skin sample

value: non-lesional skin


title: Sample0016_LS_L006_R1_001

value: F


title: Sample0014_NL_L006_R1_001


title: Sample0014_LS_L006_R1_001


title: Sample0013_LS_L005_R1_001


title: Sample1000_NL_L004_R1_001


title: Sample0800_LS_L004_R1_001


title: Sample0011_NL_L005_R1_001


title: Sample0016_NL_L006_R1_001


title: KH2

source_name: KH2 ESCs

value: wild type


title: Sample0600_NL_L003_R1_001


title: Sample0600_LS_L003_R1_001


title: Sample0500_LS_L003_R1_001


title: Sample0500_NL_L003_R1_001


title: 3'READs HBL tot_rep1.1

city: Oxford

first: Jonathan

last: Neve

address: South Parks Road

department: Biochemistry

institute: Oxford University

data_processing:
Alignment with bowtie2
Selection for poly(A) supporting reads containing 2 or more non-genomically encoded A's
Conversion to bigwig file
Normalisation of bigwig files to reads per million
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing the normalised (RPM) data

source_name: 3'READs HBL tot

growth_protocol: 10% FCS in DMEM

extract_protocol:
3'READS (Hoque, Nature Methods, 2013)
Trizol

treatment_protocol: Dicer depleted over 5 days when stated

tag: cell line/type

value: HBL melanocyte cells

tag: subcellular fraction

value: whole cell

tag: dicer knockdown

value: No


title: 3'READs HBL tot_rep1.2


title: Sample0400_NL_L002_R1_001

tag: age


title: Sample0400_LS_L002_R1_001


title: 3'READs HBL nuc_rep1.2

source_name: 3'READs HBL nuc

value: nuclear


title: Sample0300_NL_L002_R1_001


title: 3'READs HBL nuc_rep1.1


title: Sample0200_LS_L001_R1_001


title: Sample0013_NL_L005_R1_001


title: Sample0200_NL_L001_R1_001


title: 3'READs HBL cyto_rep1.2

source_name: 3'READs HBL cyto

value: cytoplasmic


title: Sample0100_LS_L001_R1_001


title: Sample0011_LS_L005_R1_001


title: Sample1000_LS_L004_R1_001


title: Sample0800_NL_L004_R1_001


title: Sample0008_NL_L002_R1_001


title: 3'READs HBL cyto_rep1.1


title: 3'READs Dicerkd tot_rep2.2

description:
2_5dT2
Fastq of 2_5dT1 and 2_5dT2 merged
processed data files are available on the 'rep1-1' sample records

source_name: 3'READs Dicerkd tot

value: HEK293 cells

value: Yes


title: 3'READs Dicerkd tot_rep2.1

description:
2_5dT1
Fastq of 2_5dT1 and 2_5dT2 merged


title: Sample0005_LS_L001_R1_001


title: Sample0005_NL_L001_R1_001


title: Sample0006_LS_L002_R1_001


title: Sample0008_LS_L002_R1_001


title: Sample0006_NL_L002_R1_001


title: Sample0004_NL_L001_R1_001


title: Sample0003_LS_L008_R1_001


title: 3'READs Dicerkd cyto_rep2.2

description:
2_5dC2
Fastq of 2_5dC1 and 2_5dC2 merged
processed data files are available on the 'rep1-1' sample records

source_name: 3'READs Dicerkd cyto


title: Sample0300_LS_L002_R1_001


title: Sample0004_LS_L001_R1_001


title: Sample0001_LS_L007_R1_001


title: 3'READs Dicerkd cyto_rep2.1

description:
2_5dC1
Fastq of 2_5dC1 and 2_5dC2 merged


title: Sample0100_NL_L001_R1_001


title: Sample0010_LS_L008_R1_001


title: 3'READs tot_rep2.1

description:
2_0dT1
Fastq of 2_0dT1 and 2_0dT2 merged

source_name: 3'READs tot


title: Sample0001_NL_L007_R1_001


title: 3'READs tot_rep2.2

description:
2_0dT2
Fastq of 2_0dT1 and 2_0dT2 merged
processed data files are available on the 'rep1-1' sample records


title: 3'READs nuc_rep2.2

description:
2_0dN2
Fastq of 2_0dN1 and 2_0dN2 merged
processed data files are available on the 'rep1-1' sample records

source_name: 3'READs nuc


title: 3'READs nuc_rep2.1

description:
2_0dN1
Fastq of 2_0dN1 and 2_0dN2 merged


title: 3'READs Dicerkd tot_rep1.2

description:
5dT2
Fastq of 5dT1 and 5dT2 merged
processed data files are available on the 'rep1-1' sample records


title: Sample0010_NL_L008_R1_001


title: 3'READs cyto_rep2.1

description:
2_0dC1
Fastq of 2_0dC1 and 2_0dC2 merged

source_name: 3'READs cyto


title: 3'READs Dicerkd nuc_rep2.1

description:
2_5dN1
Fastq of 2_5dN1 and 2_5dN2 merged

source_name: 3'READs Dicerkd nuc


title: 3'READs Dicerkd nuc_rep1.2

description:
5dN2
Fastq of 5dN1 and 5dN2 merged
processed data files are available on the 'rep1-1' sample records


title: 3'READs Dicerkd nuc_rep1.1

description:
5dN1
Fastq of 5dN1 and 5dN2 merged


title: 3'READs Dicerkd cyto_rep1.2

description:
5dC2
Fastq of 5dC1 and 5dC2 merged
processed data files are available on the 'rep1-1' sample records


title: 3'READs cyto_rep2.2

description:
2_0dC2
Fastq of 2_0dC1 and 2_0dC2 merged
processed data files are available on the 'rep1-1' sample records


title: 3'READs tot_rep1.1

description:
0dT1
Fastq of 0dT1 and 0dT2 merged


title: 3'READs Dicerkd tot_rep1.1

description:
5dT1
Fastq of 5dT1 and 5dT2 merged


title: 3'READs Dicerkd cyto_rep1.1

description:
5dC1
Fastq of 5dC1 and 5dC2 merged


title: 3'READs tot_rep1.2

description:
0dT2
Fastq of 0dT1 and 0dT2 merged
processed data files are available on the 'rep1-1' sample records


title: 3'READs cyto_rep1.2

description:
0dC2
Fastq of 0dC1 and 0dC2 merged
processed data files are available on the 'rep1-1' sample records


title: PRPL-Csf3r_6130

first: Adam

last: Blaisdell

address: 522 First Avenue, SRB 307

institute: NYU School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Samples with reads spanning multiple lanes were merged.
The sequencing reads were aligned to the mouse genome (UCSC build mm10) using the STAR aligner.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
HTSeq was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
Counts were normalized and tested for differential expression with the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

extract_protocol:
4-week-old mice were sacrificed in accordance with IACUC approved protocol.  Uteri were harvested and digested in Hank’s Balanced Salt Solution (HBSS) containing 0.28 Wünsch units/ml Liberase TM Research Grade (Roche Life Science) and 30 μg/ml DNAase I (Roche), then incubated for 30 min at 37°C with intermittent trituration.
Tissues were washed and then resuspended in FACS buffer (PBS, 1% FBS, 5 mM EDTA) and incubated at 37°C for an additional 15 min, after which they were filtered through 70 μm nylon mesh.
Samples were then stained with fluorescent-conjugated antibodies to CD45 and CD326 for 20 min on ice.  Samples were washed in FACS buffer and then resuspended in FACS buffer containing 7-AAD.
CD45-CD326+7-AAD- (live epithelial) cells were sorted on a BC MoFlo.  RNA was then isolated using a Qiagen RNeasy Mini Kit according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: 4 weeks

value: uterine epithelial cells

tag: cell subtype

value: neutrophil-deficient


title: 3'READs cyto_rep1.1

description:
0dC1
Fastq of 0dC1 and 0dC2 merged


title: 3'READs Dicerkd nuc_rep2.2

description:
2_5dN2
Fastq of 2_5dN1 and 2_5dN2 merged
processed data files are available on the 'rep1-1' sample records


title: PRPL-Csf3r_6129


title: PRPL-Csf3r_6127


title: PRPL-Csf3r_6126


title: PRPL_6149

value: Pgr(cre/+)Pten(lox/lox)

value: neutrophil-sufficient


title: G4-3: 2% green tea powder group Repeat3

city: hefei

first: xing

middle: yong

last: chen

state: anhui

address: 130 West Changjiang Road

department: School Of Animal Science And Technology

institute: Anhui Agricultural University

data_processing:
data were sequenced on a 454 GS FLX+ system (Roche, USA)
Raw pyrosequencing reads were filtered according to barcode and primer sequences using a combination of tools from Mothur (version 1.34.0; http://www.mothur.org).
The high-quality reads were clustered into operational taxonomic units (OTUs) using Mothur.
The OTUs that reached at a 97% nucleotide similarity level were used for alpha diversity (Shannon and Simpson,), richness (ACE and Chao1), Good’s coverage, Venn diagram, and rarefaction curve analysis using Mothur.
Taxonomy-based analyses were performed by classifying each sequence using the Naive Bayesian Classifier Bayesian Classifier program of the Michigan State University Center for Microbial Ecology Ribosomal Database Project (RDP) database (http://rdp.cme.msu.edu/) with a 80% bootstrap score.
Genome_build: Microbial Ecology Ribosomal Database Project (RDP) database (http://rdp.cme.msu.edu/)
Supplementary_files_format_and_content: tab-delimited text files include Microbial phylotypes classification for each sample

organism: chicken gut metagenome

source_name: Ileum contents

growth_protocol: The experiment was performed in a broiler unit consisting of 4 rooms with 11.86 m2 per room. Four hundred of AA male broilers at 1-d-old were purchased from a commercial company (Anhui Hewei Agricultural Company, Ltd, China) and allocated into the four rooms randomly with 100 broilers per room. All broilers were reared on the floor with 10-cm layer of wood shavings. Both feed and water were provided ad libitum throughout the study. Continuous artificial lighting was maintained for 23 h/d throughout the experiment. Room temperature was maintained electrically and at 34  during the first 3 d and was gradually reduced by 2.5℃ per week.

extract_protocol:
The ileum were thawed and the contents were gently scraped from the ileal walls. Genomic DNA was extracted from each of the 12 samples using the Bacterial Genomic DNA Extraction Kit (Tiangen Biotech, Co., LTD, China).
The bacterial genomic DNA was amplified with the 343F (5‘-TACGGRAGGCAGCAG-3‘) and 798R (5‘-AGGGTATCTAATCCT-3‘) primers, which are specific for the V3-V4 hyper-variable regions of the 16S rRNA gene. Each primer incorporated FLX Titanium adapters and a sample barcode at the 5’ end of the forward primer to allow all samples to be mixed in the 1/4 454 FLX+ sequencing run

tag: host

value: Gallus gallus (chicken)


title: G4-2: 2% green tea powder group Repeat2


title: PRPL_6144


title: PRPL_6148


title: G4-1: 2% green tea powder group Repeat1


title: 3'READs nuc_rep1.2

description:
0dN2
Fastq of 0dN1 and 0dN2 merged
processed data files are available on the 'rep1-1' sample records


title: male pupa

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

data_processing:
Sequenced reads were aligned onto the corresponding reference (unpublished, assembly will published under PRJNA270386) using TopHat v1.0.12 with default parameters except -r 20 --mate-std-dev 10 -I 10000 --segment-mismatches 3 --segment-length 24 --solexa1.3-quals；
bam files are dealed to wig files by /tophat-1.4.1.Linux_x86_64/wiggles
Supplementary file display the rpkm files. rpkm are calculated based on bam files from tophit aliger using custom programes. identifiers in the RPKM files are the gene identifier in the corresponding reference.

organism: Papilio machaon

source_name: whole body

extract_protocol:
total RNA is extracted by TRIzol Reagent
For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.

tag: developmental stage

value: pupa

tag: Sex

value: male


title: 3st-instar larva

value: 3st-instar larva


title: 4st-instar larva

value: 4st-instar larva


title: G2-2: 0.5% green tea powder group Repeat2


title: male adult

value: adult


title: female adult

value: female


title: G3-1: 1.0% green tea powder group Repeat1


title: G1-3: control group Repeat3


title: female pupa


title: G2-1: 0.5% green tea powder group Repeat1


title: G2-3: 0.5% green tea powder group Repeat3


title: HEK293 nuclear RNA seq

source_name: HEK293 nuclear RNA seq

extract_protocol:
PolyA+ RNA and prepared with Ion Proton whole transcriptome v2 kit
Trizol

value: No


title: 1st-instar larva

value: 1st-instar larva


title: G1-2: control group Repeat2


title: 3'READs nuc_rep1.1

description:
0dN1
Fastq of 0dN1 and 0dN2 merged

value: nuclear


title: HEK293 cytoplasmic RNA seq

source_name: HEK293 cytoplasmic RNA seq

value: HEK293 cells

value: cytoplasmic


title: 5st-instar larva

value: 5st-instar larva


title: G3-3: 1.0% green tea powder group Repeat3


title: Sample0003_NL_L008_R1_001

tag: tissue

value: non-lesional skin

value: M


title: G3-2: 1.0% green tea powder group Repeat2


title: egg

value: egg


title: PolyA-Seq CD8 T cell

status: Public on Sep 28 2015

city: Bar Harbor

first: Shengdong

last: Ke

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
We required a minimum quality score of 20 at these index and barcode positions in addition to an average score of 20 for the remaining positions.
The remaining read sequences (actual RNA tags) were mapped to the reference genome (mm9 and hg18) by novoalign program (http://www.novocraft.com) with no more than 2 mismatches (substitutions, insertions or deletions) allowed per read. A minimum of 20nt matches was required and only those reads mapped uniquely to the genome (single hits) were kept. To remove PCR duplicates, we collapsed reads mapped to the same genomic locations (the same start and end) into a single read if they have the same barcode sequence; on the other side, reads mapped to the same location but with distinct barcodes were kept. This step removed PCR duplicates while retaining genuinely unique reads representing independent RNA fragments (the same analysis pipeline for m6A IP, CLIP and its input RNA fragments). To ensure reads unambiguously mapped in the genome, we further mapped the reads by two additional alignment programs (bowtie2 and tophat2). Different from bowtie2 and novoalign, tophat2 allowed mapping across exon-exon junctions. The mapping parameters for bowtie2: -k 4 and for tophat2: --library-type fr-firststrand -p 10, with other parameters in default setting. We kept reads uniquely mapped in the genome by all three programs and the reads which were not mappable by novoalign and bowtie2 but uniquely mapped to exon-exon junctions by tophat2 (requiring at least 4nt overlap on each exon).
Similar to previous m6A publications ((Meyer et al., 2012) (Batista et al., 2014)), we searched for the enriched m6A peak regions by scanning the genome using 20nt sliding windows, and evaluating the statistical significance of enrichment by Fisher Exact Test (m6A IP vs. input). Benjamini-Hochberg was implemented to adjust the p value to False Discovery Rate (FDR) for multiple testing. We identified a window as being sigificantly m6A enriched when its FDR was less than 0.05 and the fold of enrichment (m6A IP vs. input) was at least 4 fold in at least 2 out 3 biological replicates. Significantly m6A enriched 20nt windows were concatenated if they were adjacent to each other. Because we did size selection for 20nt~80nt RNA fragments, the resulted m6A peak regions would be mostly 40nt~200nt. We filtered out m6A peak regions less than 40nt. In some cases, m6A peak regions were longer than 200nt, suggesting multiple m6A sites within those peak regions. Thus we split them into multiple m6A peak regions with the minimum number of m6A peaks that could form such a concatenated window.
PolyA-Seq experiments for mouse brain, liver, human CD8 T cells and A549 cells (control vs knockdown) were performed according to Derti A et al (Derti et al., 2012). We followed a similar PolyA-Seq data analysis pipeline as previous publications ((Shepard et al., 2011) (Almada et al., 2013)). The sequenced library reads was first filtered by trimming T’s off the beginning of reads and removing reads that have a string of 12 or more T’s, and then aligned to the reference genomes (mm9 for mouse brain and liver, hg18 for human CD8 T cells and hg19 for A549 cells) by tophat2 with default settings. Only uniquely mapped reads were kept for downstream analysis. Reads that had more than five consecutive A’s or more than six A’s in the 10nt immediately downstream from the poly(A) junction were removed as they were likely due to internal priming. We then clustered reads that were within 50nt from each other by bedtools merge, and kept the polyA sites (i.e. read clusters) that had at least 4 reads total, with reads drawn from at least 2 biological replicates.
Genome_build: mm9, hg18
Supplementary_files_format_and_content: bed: m6A peak region and precise m6A site; wig: polyA site locations

source_name: CD8 T cell

growth_protocol: Human A549 cells were plated in 100mm dishes with regular DMEM (with 10% FBS+1x Penstrap) at 20% confluency. Using Lipofectamine® RNAiMAX Transfection Reagent (Cat. # 13778-150, Invitrogen Life Technologies), siRNAs were transfected. One additional siRNA boost was delivered at 48 hours following transfection. Cells were harvested at 96 hours after transfection. From Adult C57BL/6 mice, adult livers were collected and brains were harvested at postnatal day 2. All mice procedures were performed in accordance with the Section for Comparative Medicine at Oslo University Hospital and the Norwegian Animal Research Authority.

extract_protocol:
Total RNAs were isolated from cells and mouse tissues according to manufacturer’s instructions using TRIzol reagent (Cat.# 15596, Life Technologies), then was resuspended in RNA-free water, digested with RQ1 RNase-Free DNase (Cat. # M6101, Promega) for 20 min at 37°C and then subject to phenol/chloroform extraction and ethanol precipitation. The resulted total RNA pallet was resuspended in RNA-free water. PolyA+ RNAs were selected using Dynabeads® mRNA Purification Kit (Cat.# 61006, Invitrogen) according to the manufacturer’s protocol.
The PolyA+ RNA was fragmented to 20~80nt nucleotide fragments by alkaline hydrolysis (1mM EDTA, 6mM Na2CO3, 44mM NaHCO3, pH~9.3) at 95°C for 18 minutes, then the RNA fragments precipitated following standard ethanol precipitation. Dynabeads Protein A beads (250ul, Cat. # 10008D, Life Technologies) was pretreated with BSA (Cat. # B9000S, NEB) for 45 minutes at room temperature to reduce background. Anti-m6A rabbit polyclonal antibody (25ug, Cat. # 202003, Synaptic Systems) was then conjugated to Dynabeads Protein at room temperature for 1 hour. The fragmented polyA+ RNAs (3ug) were subject to PAGE selection for 20nt~80nt size and then incubated with the antibody in 1x PXL buffer (1x PBS, 0.1% SDS, 0.5% Sodium Deoxycholate and 0.5% NP-40) supplemented with 2% RNasin® Plus RNase Inhibitor (Cat. # N2615, Promega) for 2 hours at 4°C.  After incubation, the bead and antibody was washed 5 times by 4 different wash buffers: first twice by ice cold Nelson Low Salt Buffer (15mM Tris pH7.5 and 5mM EDTA), once by ice cold Nelson High Salt Buffer (15mM Tris pH7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Sodium Deoxycholate, 0.1% SDS and 1M NaCl), once by ice cold Nelson Stringent Wash Buffer (15mM Tris pH7.5, 5mM EDTA, 2.5mM EGTA, 1% Triton X-100, 1% Sodium Deoxycholate, 0.1% SDS, 120mM NaCl and 25mM KCl) and last wash by ice cold NT-2 Buffer (50mM Tris pH7.4, 150mM NaCl, 1mM MgCl2 and 0.05% NP-40). After the stringent wash series, the bead and antibody was split into two halves: one half performed m6A-CLIP leg, and the other half had its bounded RNA eluted with 0.5mg/mL N6-methyladenosine sodium salt (Cat. # M2780, Sigma-Aldrich) at 4°C for 1 hour (m6A-IP leg).  The eluted RNA was ethanol precipitated and re-suspended in RNase-free water for downstream cDNA library preparation. The eluted RNA from m6A-IP step and the input RNA fragments were first treated with T4 PNK to remove its 3’phospho group and then ligated to 68 pmol pre-adenylated DNA linker (L32N from IDT) with T4 RNA ligase2, truncated KQ (Cat. # M0373L, NEB) overnight at 16°C. This ligation mixture was subject to 8% PAGE purification to harvest the ligated product. The purified RNAs from m6A-IP, m6A-CLIP and their input RNA fragments were all subject to the same BrdU-CLIP cDNA library preparation. The detailed BrdU-CLIP cDNA library protocol was described previously (Weyn-Vanhentenryck et al., 2014).
m6A-CLIP/IP

tag: cell type

value: CD8 T cell

tag: strain

tag: antibody


title: PolyA-Seq Brain

source_name: Brain

value: whole brain


title: m6A-CLIP/IP CD8 T cell

value: m6A antibody (Synaptic Systems, 202003)


title: m6A-CLIP/IP A549 Cell

source_name: A549 Cell

value: cancer cell line A549


title: 2st-instar larva

value: 2st-instar larva


title: PolyA-Seq Liver

source_name: Liver

value: whole liver


title: PolyA-Seq A549 Cell


title: Vehicle rep3

first: Chenyi

last: Xue

state: NY

institute: Columbia University

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) each read is uniquely mapped, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp
Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000 --library-type fr-firststrand". Annotation from RefSeq genes and lincRNA annotation from either Gencode or the stringent set of lincRNAs from Cabili et al. 2011 were provided.
Genome_build: hg19
Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output.
Supplementary_files_format_and_content: Normoxia_vs_Hypoxia_Gencode_gene_exp.diff contains differential expression results from normoxia and hypoxia treated samples. RefSeq genes and lincRNAs from Gencode were included. sample_1 = normoxia, sample_2 = hypoxia
Supplementary_files_format_and_content: Normoxia_vs_Hypoxia_Rinn_gene_exp.diff contains differential expression results from normoxia and hypoxia treated samples. RefSeq genes and the stringent set of lincRNAs from Cabili et al. 2011 were included. sample_1 = normoxia, sample_2 = hypoxia
Supplementary_files_format_and_content: Vehicle_vs_Cytokine_Gencode_gene_exp.diff contains differential expression results from vehicle and cytokine treated samples. RefSeq genes and lincRNAs from Gencode were included. sample_1 = vehicle, sample_2 = cytokine
Supplementary_files_format_and_content: Vehicle_vs_Cytokine_Rinn_gene_exp.diff contains differential expression results from vehicle and cytokine treated samples. RefSeq genes and the stringent set of lincRNAs from Cabili et al. 2011 were included. sample_1 = vehicle, sample_2 = cytokine

source_name: PTEC

extract_protocol:
RNA isolated from cells using miRNeasy kit (Qiagen), RIN > 9.5 (Agilent 2100 Bioanalyzer)
mRNA Illumina protocol with following exceptions: 6 minutes fragmentation time, 12 cycles of PCR

treatment_protocol: Hypoxia (0.1% O2) or cytokine treatment (cocktail of 50 ng/mL IL6, 50 ng/mL TNF-α, and 20 ng/mL IFN-γ) for 12 hours

value: Control

value: proximal tubular epithelial cells


title: Hypoxia rep3

value: Hypoxia treated


title: Cytokine rep1

value: Cytokine treated


title: Cytokine rep2


title: Vehicle rep2


title: Vehicle rep1


title: Cytokine rep3


title: at-seed-ler_wt_x_col_osd1_adm_2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

data_processing:
TopHat v2.0.10; tophat2 -p 20 -g 1 -a 10 -i 40 -I 5000 -F 0 -r 130 -o
GFOLD
Genome_build: TAIR10
Supplementary_files_format_and_content: Gene counts, rpkm

organism: Arabidopsis thaliana

source_name: AT F1-Seed  wt Landsberg x osd1 adm Columbia

growth_protocol: Plants were grown in a growth cabinet under long day photoperiods (16 h light and 8 h dark) at 22°C. After 10 days, seedlings were transferred to soil and plants were grown in a growth chamber at 60% humidity and daily cycles of 16 h light at 22°C and 8 h darkness at 18°C.

extract_protocol:
For RNA sequencing, seeds from 20 siliques of Ler x Col, Ler x osd1, Ler x adm osd1, Ler x suvh7 osd1, and Ler x peg2 osd1 were harvested at 6 DAP into RNA later (Sigma-Aldrich) in duplicates and homogenized (Silamat S5; IvoclarVivadent) using glass beads (1.25-1.55 mm; Carl Roth). RNA was extracted following a modified protocol for the RNAqueous kit (Ambion, Life Technologies). RNA was purified by Qiagen RNeasy Plant Mini Kit (Qiagen) after residual DNA removed by 2 uL DNaseI (Thermo-Scientific).
The library was prepared using the Truseq RNA Sample Preparation Kit (Illumina)

treatment_protocol: For all crosses, designated female plants were emasculated and the pistils were hand-pollinated two days after emasculation.

value: seed

tag: genotype

value: wt Landsberg x osd1 adm Columbia


title: Normoxia rep3


title: Normoxia rep2


title: Hypoxia rep2


title: at-seed-ler_wt_x_col_osd1_2

source_name: AT F1-Seed  wt Landsberg x osd1 Columbia

value: wt Landsberg x osd1 Columbia


title: Hypoxia rep1


title: at-seed-ler_wt_x_col_osd1_peg2_2

source_name: AT F1-Seed  wt Landsberg x osd1 peg2 Columbia

value: wt Landsberg x osd1 peg2 Columbia


title: Resistant line DKK Bcat ChIP

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the mm10 mouse genome using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Normalised read counts for B-catenin ChIPs were generated with GenomicTools
Genome_build: mm10
Supplementary_files_format_and_content: bed files from MACS2 for BRD4 and H3K27ac ChIP
Supplementary_files_format_and_content: text file of normalised B-catenin ChIP read counts in 100bp bins around BRD4 peaks from sensitive line

source_name: Resistant line

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with murine IL-3 (10 ng/mL), 20% fetal calf serum, penicillin (100 units/mL), streptomycin (100 ug/mL), amphotericin B (250ng/mL) and gentamycin (50 ug/mL)

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: Cell lines were grown in 0.1% DMSO or 600nM of I-BET151

value: haematopoietic progenitors

tag: condition

value: Resistant + DKK

tag: chip antibody

value: B-catenin


title: G1-1: control group Repeat1

value: Gallus gallus (chicken)


title: at-seed-ler_wt_x_col_osd1_1


title: Resistant line Bcat ChIP

value: Resistant


title: Sensitive line Bcat ChIP

source_name: Sensitive line

value: Sensitive


title: Sensitive line H3K27ac ChIP


title: Normoxia rep1

tag: treatment


title: Resistant line BRD4 ChIP


title: Resistant line H3K27ac ChIP


title: at-seed-ler_wt_x_col_wt_2

source_name: AT F1-Seed  wt Landsberg x wt Columbia

value: wt Landsberg x wt Columbia


title: at-seed-ler_wt_x_col_osd1_peg2_1


title: m6A-CLIP/IP Liver

value: m6A antibody (Synaptic Systems, 202003)


title: Sensitive line BRD4 ChIP