title: bladder_cancer_turbt_sample_123 [GNDX-MGH-QCFCG123]


title: RHC7262

status: Public on Mar 23 2019

type: SRA

city: Singapore

first: Huipeng

last: Li

address: 60 Biopolis St, #02-01

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description:
sample 644
mRNA
QC: PASSED

library_source: transcriptomic

data_processing:
scRNAseq FASTQ files were aligned to hg19 human genome assembly using STAR 2.5.2a and GENCODEv19 gene models. The STAR parameters were set as follows: --outFilterMultimapNmax=1, --outFilterMismatchNmax=999, --outFilterMismatchNoverLmax=0.04, --outFilterIntronMotifs=RemoveNoncanonical, --alignSJoverhangMin=8, --alignSJDBoverhangMin=1, --alignIntronMax=1000000, --alignMatesGapMax=1000000. Gene FPKM was calculated using RSEM 1.2.31 with the default parameters. Targeted DNA FASTQ files were aligned to the human_g1k_v37_decoy.fasta from GATK bundle 2.8 using BWA 0.7.12. SNPs and INDELS were called using the “gatk_haplotype_caller” with default parameters.
scRNAseq QC: (BAMMR) were calculated as the number of uniquely mapped reads in the aligned BAM file. The rate of exonic reads (ROER) represents the ratio between exonic reads and all mapped reads in the BAM file. The number of detected genes (NODG) was calculated as the total number of genes with FPKM >0. scRNAseq data with NODG ≥3,000 and ROER ≥5% were selected for downstream analysis.
Targeted DNA QC: Variations (SNPs and INDELs) from all sequenced cells were combined into one table using VCFtools. 8 variations were selected for downstream analysis based on the criteria that they were detected in at least 5% of all sequenced cells. Since GATK does not report allelic depth information for the 8 variations in all cells, SAMtools (version 1.3) mpileup was used to extract the allelic depth and total depth for each cell. Targeted DNA data with total depth >=500 for all the 8 selected mutations were chosen for further analysis. The allelic frequency (AF) was calculated as the ratio between the dominant alternative allelic depth and the total depths (DP). A variation was labelled as positive for a cell if its AF>=0.005 and DP>=500 in that cell.
Out of 546 cells sequenced, 507 (20 cells in DMSO condition were also excluded from the downstream analysis) cells with both the scRNAseq data and targeted DNA data passing the QC were selected for downstream analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Comma-separated files include raw FPKM values of all cells that passed QC.
Supplementary_files_format_and_content: cell_gene_FPKM.csv
Supplementary_files_format_and_content: cell_mutation_AF.csv
Supplementary_files_format_and_content: cell_mutation_DP.csv

molecule: total RNA

organism: Homo sapiens

source_name: PC9 lung cancer cell line

growth_protocol: Human PC9 cell line was maintained in RPMI supplemented with 10% FBS, 200 nM L-glutamine and 1% penicillin – streptomycin (Gibco).

extract_protocol:
The isolation of single cells followed by cDNA synthesis were carried out using the Fluidigm C1 Auto-prep system following the manufacturer's recommended protocol.
The library preparation was carried out following the manufacturer’s recommendation using the Nextera XT Sample Preparation kit (Illumina) with minor modifications and one quarter of the recommended volume.
The cDNA libraries were sequenced on the NextSeq (Illumina) platform for 76 bp single read sequencing run, while the gDNA libraries were sequenced on the MiSeq (Illumina) platform for 250 bp paired-end sequencing run.

treatment_protocol: The parental TKI responsive PC9 cell line was treated with DMSO or 0.1 µM Gefitinib for 48 hours prior to harvesting for single cell analysis. In order to generate TKI-resistant cell lines, Gefitinib was added to the media in a progressively increasing dose from 0.1 µM to 6.4 µM for a period of 3 months.

tag: cell line

tag: cell type

value: lung cancer cell line

tag: cell id

tag: cell line group

tag: batch


title: AHP125

description:
sample 111
Targeted DNA
QC: PASSED

library_source: genomic

molecule: genomic DNA


title: RHC7261

description:
sample 643
mRNA
QC: PASSED


title: RHC7260

description:
sample 642
mRNA
QC: PASSED


title: RHC7259

description:
sample 641
mRNA
QC: PASSED


title: AHP123

description:
sample 109
Targeted DNA
QC: PASSED


title: AHP122

description:
sample 108
Targeted DNA
QC: FAILED


title: RHC7258

description:
sample 640
mRNA
QC: PASSED


title: AHP121

description:
sample 107
Targeted DNA
QC: PASSED


title: RHC7257

description:
sample 639
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_122 [GNDX-MGH-QCFCG122]

type: RNA

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After pathologic review, tissue was harvested from formalin-fixed, paraffin-embedded tumor blocks by 1mm punch under RNAse-free conditions. Total RNA was extracted and purified using RNeasy FFPE kit (Qiagen, Valencia, CA)

tag: age

tag: Sex

value: Female

tag: cstage


title: bladder_cancer_turbt_sample_121 [GNDX-MGH-QCFCG121]

value: Male


title: bladder_cancer_turbt_sample_120 [GNDX-MGH-QCFCG120]


title: bladder_cancer_turbt_sample_117 [GNDX-MGH-QCFCG117]


title: bladder_cancer_turbt_sample_119 [GNDX-MGH-QCFCG119]


title: AHP119

description:
sample 105
Targeted DNA
QC: FAILED


title: AHP124

description:
sample 110
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_118 [GNDX-MGH-QCFCG118]


title: AHP117

description:
sample 103
Targeted DNA
QC: PASSED


title: AHP118

description:
sample 104
Targeted DNA
QC: FAILED


title: AHP116

description:
sample 102
Targeted DNA
QC: PASSED


title: RHC7255

description:
sample 637
mRNA
QC: PASSED


title: RHC7253

description:
sample 635
mRNA
QC: PASSED


title: RHC7254

description:
sample 636
mRNA
QC: PASSED


title: AHP114

description:
sample 100
Targeted DNA
QC: PASSED


title: RHC7252

description:
sample 634
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_115 [GNDX-MGH-QCFCG115]


title: AHP120

description:
sample 106
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_113 [GNDX-MGH-QCFCG113]


title: AHP113

description:
sample 99
Targeted DNA
QC: PASSED


title: AHP115

description:
sample 101
Targeted DNA
QC: PASSED


title: RHC7250

description:
sample 632
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_114 [GNDX-MGH-QCFCG114]


title: bladder_cancer_turbt_sample_116 [GNDX-MGH-QCFCG116]


title: RHC7256

description:
sample 638
mRNA
QC: PASSED


title: AHP112

description:
sample 98
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_110 [GNDX-MGH-QCFCG110]


title: bladder_cancer_turbt_sample_108 [GNDX-MGH-QCFCG108]


title: bladder_cancer_turbt_sample_112 [GNDX-MGH-QCFCG112]


title: bladder_cancer_turbt_sample_109 [GNDX-MGH-QCFCG109]


title: RHC7249

description:
sample 631
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_111 [GNDX-MGH-QCFCG111]


title: RHC7248

description:
sample 630
mRNA
QC: PASSED


title: AHP111

description:
sample 97
Targeted DNA
QC: PASSED


title: AHP110

description:
sample 96
Targeted DNA
QC: PASSED


title: AHP109

description:
sample 95
Targeted DNA
QC: PASSED


title: AHP108

description:
sample 94
Targeted DNA
QC: PASSED


title: RHC7246

description:
sample 628
mRNA
QC: PASSED


title: RHC7245

description:
sample 627
mRNA
QC: PASSED


title: AHP107

description:
sample 93
Targeted DNA
QC: PASSED


title: RHC7244

description:
sample 626
mRNA
QC: PASSED


title: RHC7247

description:
sample 629
mRNA
QC: PASSED


title: RHC7251

description:
sample 633
mRNA
QC: PASSED


title: RHC7243

description:
sample 625
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_104 [GNDX-MGH-QCFCG104]


title: bladder_cancer_turbt_sample_107 [GNDX-MGH-QCFCG107]


title: bladder_cancer_turbt_sample_106 [GNDX-MGH-QCFCG106]


title: bladder_cancer_turbt_sample_103 [GNDX-MGH-QCFCG103]


title: RHC7242

description:
sample 624
mRNA
QC: PASSED


title: AHP105

description:
sample 91
Targeted DNA
QC: PASSED


title: RHC7241

description:
sample 623
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_105 [GNDX-MGH-QCFCG105]


title: AHP104

description:
sample 90
Targeted DNA
QC: PASSED


title: RHC7240

description:
sample 622
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_102 [GNDX-MGH-QCFCG102]


title: AHP103

description:
sample 89
Targeted DNA
QC: PASSED


title: AHP106

description:
sample 92
Targeted DNA
QC: PASSED


title: RHC7238

description:
sample 620
mRNA
QC: PASSED


title: AHP102

description:
sample 88
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_101 [GNDX-MGH-QCFCG101]


title: bladder_cancer_turbt_sample_100 [GNDX-MGH-QCFCG100]


title: AHP101

description:
sample 87
Targeted DNA
QC: PASSED


title: AHP100

description:
sample 86
Targeted DNA
QC: FAILED


title: AHP099

description:
sample 85
Targeted DNA
QC: PASSED


title: RHC7236

description:
sample 618
mRNA
QC: PASSED


title: RHC7237

description:
sample 619
mRNA
QC: FAILED


title: AHP098

description:
sample 84
Targeted DNA
QC: PASSED


title: RHC7235

description:
sample 617
mRNA
QC: PASSED


title: RHC7234

description:
sample 616
mRNA
QC: PASSED


title: RHC7239

description:
sample 621
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_97 [GNDX-MGH-QCFCG97]


title: AHP096

description:
sample 82
Targeted DNA
QC: FAILED


title: RHC7224

description:
sample 614
mRNA
QC: FAILED

value: parental


title: bladder_cancer_turbt_sample_96 [GNDX-MGH-QCFCG96]


title: AHP097

description:
sample 83
Targeted DNA
QC: PASSED


title: AHP094

description:
sample 80
Targeted DNA
QC: PASSED


title: RHC7222

description:
sample 612
mRNA
QC: PASSED


title: RHC7223

description:
sample 613
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_99 [GNDX-MGH-QCFCG99]


title: AHP095

description:
sample 81
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_95 [GNDX-MGH-QCFCG95]


title: bladder_cancer_turbt_sample_94 [GNDX-MGH-QCFCG94]


title: RHC7220

description:
sample 610
mRNA
QC: FAILED


title: bladder_cancer_turbt_sample_92 [GNDX-MGH-QCFCG92]


title: AHP091

description:
sample 77
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_98 [GNDX-MGH-QCFCG98]


title: RHC7219

description:
sample 609
mRNA
QC: PASSED


title: AHP090

description:
sample 76
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_90 [GNDX-MGH-QCFCG90]


title: RHC7225

description:
sample 615
mRNA
QC: FAILED


title: AHP089

description:
sample 75
Targeted DNA
QC: PASSED


title: RHC7217

description:
sample 607
mRNA
QC: PASSED


title: RHC7221

description:
sample 611
mRNA
QC: PASSED


title: AHP088

description:
sample 74
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_91 [GNDX-MGH-QCFCG91]


title: bladder_cancer_turbt_sample_89 [GNDX-MGH-QCFCG89]


title: AHP087

description:
sample 73
Targeted DNA
QC: PASSED


title: RHC7216

description:
sample 606
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_87 [GNDX-MGH-QCFCG87]


title: bladder_cancer_turbt_sample_86 [GNDX-MGH-QCFCG86]


title: bladder_cancer_turbt_sample_85 [GNDX-MGH-QCFCG85]


title: AHP086

description:
sample 72
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_88 [GNDX-MGH-QCFCG88]


title: bladder_cancer_turbt_sample_83 [GNDX-MGH-QCFCG83]


title: bladder_cancer_turbt_sample_84 [GNDX-MGH-QCFCG84]


title: RHC7218

description:
sample 608
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_82 [GNDX-MGH-QCFCG82]


title: bladder_cancer_turbt_sample_81 [GNDX-MGH-QCFCG81]


title: AHP085

description:
sample 71
Targeted DNA
QC: PASSED


title: RHC7213

description:
sample 603
mRNA
QC: FAILED


title: RHC7214

description:
sample 604
mRNA
QC: FAILED


title: AHP084

description:
sample 70
Targeted DNA
QC: FAILED


title: RHC7212

description:
sample 602
mRNA
QC: PASSED


title: RHC7211

description:
sample 601
mRNA
QC: FAILED


title: RHC7215

description:
sample 605
mRNA
QC: PASSED


title: RHC7210

description:
sample 600
mRNA
QC: PASSED


title: RHC7209

description:
sample 599
mRNA
QC: PASSED


title: AHP083

description:
sample 69
Targeted DNA
QC: FAILED


title: AHP080

description:
sample 66
Targeted DNA
QC: PASSED


title: AHP078

description:
sample 64
Targeted DNA
QC: PASSED


title: AHP081

description:
sample 67
Targeted DNA
QC: PASSED


title: RHC7207

description:
sample 597
mRNA
QC: PASSED


title: AHP079

description:
sample 65
Targeted DNA
QC: PASSED


title: RHC7206

description:
sample 596
mRNA
QC: PASSED


title: AHP077

description:
sample 63
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_79 [GNDX-MGH-QCFCG79]


title: bladder_cancer_turbt_sample_76 [GNDX-MGH-QCFCG76]


title: AHP082

description:
sample 68
Targeted DNA
QC: PASSED


title: AHP076

description:
sample 62
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_93 [GNDX-MGH-QCFCG93]


title: RHC7205

description:
sample 595
mRNA
QC: FAILED


title: bladder_cancer_turbt_sample_77 [GNDX-MGH-QCFCG77]


title: bladder_cancer_turbt_sample_78 [GNDX-MGH-QCFCG78]


title: bladder_cancer_turbt_sample_74 [GNDX-MGH-QCFCG74]


title: AHP075

description:
sample 61
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_80 [GNDX-MGH-QCFCG80]


title: RHC7203

description:
sample 593
mRNA
QC: FAILED


title: bladder_cancer_turbt_sample_72 [GNDX-MGH-QCFCG72]


title: bladder_cancer_turbt_sample_75 [GNDX-MGH-QCFCG75]


title: bladder_cancer_turbt_sample_73 [GNDX-MGH-QCFCG73]


title: bladder_cancer_turbt_sample_71 [GNDX-MGH-QCFCG71]


title: RHC7202

description:
sample 592
mRNA
QC: FAILED


title: AHP073

description:
sample 59
Targeted DNA
QC: PASSED


title: RHC7204

description:
sample 594
mRNA
QC: FAILED


title: bladder_cancer_turbt_sample_70 [GNDX-MGH-QCFCG70]


title: AHP072

description:
sample 58
Targeted DNA
QC: PASSED


title: RHC7201

description:
sample 591
mRNA
QC: FAILED


title: AHP071

description:
sample 57
Targeted DNA
QC: PASSED


title: RHC7200

description:
sample 590
mRNA
QC: FAILED


title: bladder_cancer_turbt_sample_69 [GNDX-MGH-QCFCG69]


title: RHC7199

description:
sample 589
mRNA
QC: FAILED


title: AHP070

description:
sample 56
Targeted DNA
QC: PASSED


title: AHP074

description:
sample 60
Targeted DNA
QC: PASSED


title: RHC7198

description:
sample 588
mRNA
QC: FAILED


title: AHP069

description:
sample 55
Targeted DNA
QC: PASSED


title: RHC7197

description:
sample 587
mRNA
QC: FAILED


title: AHP068

description:
sample 54
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_68 [GNDX-MGH-QCFCG68]


title: bladder_cancer_turbt_sample_64 [GNDX-MGH-QCFCG64]


title: AHP067

description:
sample 53
Targeted DNA
QC: PASSED


title: RHC7195

description:
sample 585
mRNA
QC: FAILED


title: AHP066

description:
sample 52
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_65 [GNDX-MGH-QCFCG65]


title: bladder_cancer_turbt_sample_67 [GNDX-MGH-QCFCG67]


title: RHC7194

description:
sample 584
mRNA
QC: FAILED


title: bladder_cancer_turbt_sample_63 [GNDX-MGH-QCFCG63]


title: AHP065

description:
sample 51
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_62 [GNDX-MGH-QCFCG62]


title: RHC7193

description:
sample 583
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_66 [GNDX-MGH-QCFCG66]


title: AHP064

description:
sample 50
Targeted DNA
QC: PASSED


title: AHP062

description:
sample 48
Targeted DNA
QC: PASSED


title: RHC7191

description:
sample 581
mRNA
QC: FAILED


title: RHC7190

description:
sample 580
mRNA
QC: PASSED


title: AHP063

description:
sample 49
Targeted DNA
QC: PASSED


title: RHC7192

description:
sample 582
mRNA
QC: FAILED


title: bladder_cancer_turbt_sample_61 [GNDX-MGH-QCFCG61]


title: bladder_cancer_turbt_sample_59 [GNDX-MGH-QCFCG59]


title: RHC7196

description:
sample 586
mRNA
QC: FAILED


title: AHP061

description:
sample 47
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_60 [GNDX-MGH-QCFCG60]


title: RHC7189

description:
sample 579
mRNA
QC: FAILED


title: AHP060

description:
sample 46
Targeted DNA
QC: PASSED


title: RHC7188

description:
sample 578
mRNA
QC: PASSED


title: AHP059

description:
sample 45
Targeted DNA
QC: PASSED


title: RHC7186

description:
sample 576
mRNA
QC: PASSED


title: RHC7187

description:
sample 577
mRNA
QC: PASSED


title: AHP057

description:
sample 43
Targeted DNA
QC: PASSED


title: AHP058

description:
sample 44
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_58 [GNDX-MGH-QCFCG58]


title: bladder_cancer_turbt_sample_57 [GNDX-MGH-QCFCG57]


title: bladder_cancer_turbt_sample_56 [GNDX-MGH-QCFCG56]


title: bladder_cancer_turbt_sample_55 [GNDX-MGH-QCFCG55]


title: bladder_cancer_turbt_sample_54 [GNDX-MGH-QCFCG54]


title: RHC7185

description:
sample 575
mRNA
QC: PASSED


title: AHP093

description:
sample 79
Targeted DNA
QC: PASSED


title: AHP055

description:
sample 41
Targeted DNA
QC: PASSED


title: RHC7184

description:
sample 574
mRNA
QC: PASSED


title: AHP054

description:
sample 40
Targeted DNA
QC: PASSED


title: AHP056

description:
sample 42
Targeted DNA
QC: PASSED


title: AHP053

description:
sample 39
Targeted DNA
QC: PASSED


title: RHC7181

description:
sample 571
mRNA
QC: PASSED


title: RHC7183

description:
sample 573
mRNA
QC: PASSED


title: RHC7182

description:
sample 572
mRNA
QC: PASSED


title: AHP092

description:
sample 78
Targeted DNA
QC: PASSED


title: RHC7180

description:
sample 570
mRNA
QC: PASSED


title: AHP052

description:
sample 38
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_52 [GNDX-MGH-QCFCG52]


title: bladder_cancer_turbt_sample_51 [GNDX-MGH-QCFCG51]


title: bladder_cancer_turbt_sample_48 [GNDX-MGH-QCFCG48]


title: AHP051

description:
sample 37
Targeted DNA
QC: PASSED


title: AHP050

description:
sample 36
Targeted DNA
QC: FAILED


title: AHP049

description:
sample 35
Targeted DNA
QC: PASSED


title: RHC7178

description:
sample 568
mRNA
QC: PASSED


title: RHC7177

description:
sample 567
mRNA
QC: PASSED


title: AHP048

description:
sample 34
Targeted DNA
QC: PASSED


title: RHC7176

description:
sample 566
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_45 [GNDX-MGH-QCFCG45]


title: AHP047

description:
sample 33
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_47 [GNDX-MGH-QCFCG47]


title: bladder_cancer_turbt_sample_50 [GNDX-MGH-QCFCG50]


title: RHC7175

description:
sample 565
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_53 [GNDX-MGH-QCFCG53]


title: RHC7174

description:
sample 564
mRNA
QC: PASSED


title: AHP046

description:
sample 32
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_46 [GNDX-MGH-QCFCG46]


title: bladder_cancer_turbt_sample_49 [GNDX-MGH-QCFCG49]


title: bladder_cancer_turbt_sample_44 [GNDX-MGH-QCFCG44]


title: AHP045

description:
sample 31
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_42 [GNDX-MGH-QCFCG42]


title: RHC7173

description:
sample 563
mRNA
QC: PASSED


title: AHP044

description:
sample 30
Targeted DNA
QC: PASSED


title: RHC7179

description:
sample 569
mRNA
QC: PASSED


title: RHC7172

description:
sample 562
mRNA
QC: FAILED


title: AHP043

description:
sample 29
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_41 [GNDX-MGH-QCFCG41]


title: RHC7171

description:
sample 561
mRNA
QC: PASSED


title: AHP042

description:
sample 28
Targeted DNA
QC: PASSED


title: AHP041

description:
sample 27
Targeted DNA
QC: PASSED


title: RHC7170

description:
sample 560
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_40 [GNDX-MGH-QCFCG40]


title: RHC7169

description:
sample 559
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_43 [GNDX-MGH-QCFCG43]


title: bladder_cancer_turbt_sample_38 [GNDX-MGH-QCFCG38]


title: RHC7168

description:
sample 558
mRNA
QC: PASSED


title: bladder_cancer_turbt_sample_37 [GNDX-MGH-QCFCG37]


title: RHC7167

description:
sample 557
mRNA
QC: PASSED


title: AHP039

description:
sample 25
Targeted DNA
QC: PASSED


title: AHP038

description:
sample 24
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_35 [GNDX-MGH-QCFCG35]


title: RHC7208

description:
sample 598
mRNA
QC: PASSED


title: AHP037

description:
sample 23
Targeted DNA
QC: FAILED


title: AHP036

description:
sample 22
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_36 [GNDX-MGH-QCFCG36]


title: AHP035

description:
sample 21
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_39 [GNDX-MGH-QCFCG39]


title: Kit-W/sh Sample 1 [preneoplastic]

city: Ribeirao Preto

first: Vinicius

last: Kannen

state: SP

address: Av Café, s/ N°

department: DACTB

country: Brazil

institute: Universidade de São Paulo

description:
Kit-W/sh_S1
mRNA

data_processing:
Checking of the Fastq read data quality, alignment of reads to the mouse genome (NCBI37.p3/mm9) and data normalization using DEseq2 method were carried out in the online Qiagen software GeneGlobe Data Analysis Center.
To identify differentially expressed genes between KitB6 and KitW/sh mouse groups, we performed a supervised analysis using the t-test. Genes with p < 0.05 were selected. The analysis was performed in R, and the plots were generated using the R package 'fmsb.'
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Processed data files are in .txt format and correspond to gene count tables.

organism: Mus musculus

source_name: Preneoplastic colon

extract_protocol:
Following tumors harvesting and freezing steps, RNA extraction was performed with Qiagen RNeasy (#74106) and Qiagen RNase-free DNase kits (#79254).
QIAseq Targeted RNAseq Mouse Immuno-Oncology panel (#333005) and QIAseq Targeted RNA 96-Index I (#333117) were used to generate cDNA libraries.

treatment_protocol: Sporadic colorectal tumors were detected in mice that underwent 6 intraperitoneal (i.p.) injections of azoxymethane (AOM) throughout 6 wks and were euthanatized (CO2 chamber) following other 18 wks. Preneoplastic colon samples were detected in mice that underwent 3 intraperitoneal (i.p.) injections of azoxymethane (AOM) throughout 3 wks and were euthanatized (CO2 chamber) following other 3 wks.

tag: strain/background

value: W-SASH

tag: tissue

value: Preneoplastic colon

value: postnatal week 14


title: Kit-B6 Sample 3 [preneoplastic]

description:
Kit-B6_S3
C57BL/6
mRNA


title: bladder_cancer_turbt_sample_34 [GNDX-MGH-QCFCG34]


title: Kit-B6 Sample 2 [preneoplastic]

description:
Kit-B6_S2
C57BL/6
mRNA


title: AHP040

description:
sample 26
Targeted DNA
QC: PASSED


title: AHP034

description:
sample 20
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_32 [GNDX-MGH-QCFCG32]


title: Kit-W/sh Sample 2 [preneoplastic]

description:
Kit-W/sh_S2
mRNA


title: bladder_cancer_turbt_sample_33 [GNDX-MGH-QCFCG33]


title: AHP032

description:
sample 18
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_31 [GNDX-MGH-QCFCG31]


title: bladder_cancer_turbt_sample_30 [GNDX-MGH-QCFCG30]


title: Kit-W/sh Sample 6 [tumor]

description:
Kit-W/sh_S6
mRNA

source_name: Colon tumors

value: Colon tumor

value: postnatal week 32


title: Kit-W/sh Sample 5 [tumor]

description:
Kit-W/sh_S5
mRNA


title: AHP031

description:
sample 17
Targeted DNA
QC: PASSED


title: AHP030

description:
sample 16
Targeted DNA
QC: PASSED


title: Kit-W/sh Sample 4 [tumor]

description:
Kit-W/sh_S4
mRNA


title: Kit-W/sh Sample 3 [tumor]

description:
Kit-W/sh_S3
mRNA


title: AHP029

description:
sample 15
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_29 [GNDX-MGH-QCFCG29]


title: bladder_cancer_turbt_sample_28 [GNDX-MGH-QCFCG28]


title: Kit-W/sh Sample 2 [tumor]

description:
Kit-W/sh_S2
mRNA


title: Kit-W/sh Sample 1 [tumor]

description:
Kit-W/sh_S1
mRNA


title: AHP028

description:
sample 14
Targeted DNA
QC: FAILED


title: AHP027

description:
sample 13
Targeted DNA
QC: PASSED


title: Kit-B6 Sample 1 [preneoplastic]

description:
Kit-B6_S1
C57BL/6
mRNA


title: Kit-B6 Sample 6 [tumor]

description:
Kit-B6_S6
C57BL/6
mRNA


title: bladder_cancer_turbt_sample_27 [GNDX-MGH-QCFCG27]


title: AHP033

description:
sample 19
Targeted DNA
QC: PASSED


title: Kit-B6 Sample 5 [tumor]

description:
Kit-B6_S5
C57BL/6
mRNA


title: bladder_cancer_turbt_sample_25 [GNDX-MGH-QCFCG25]


title: AHP025

description:
sample 11
Targeted DNA
QC: PASSED


title: AHP024

description:
sample 10
Targeted DNA
QC: PASSED


title: Kit-B6 Sample 4 [tumor]

description:
Kit-B6_S4
C57BL/6
mRNA


title: AHP026

description:
sample 12
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_26 [GNDX-MGH-QCFCG26]


title: AHP023

description:
sample 9
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_24 [GNDX-MGH-QCFCG24]


title: Kit-B6 Sample 1 [tumor]

description:
Kit-B6_S1
C57BL/6
mRNA


title: Kit-B6 Sample 2 [tumor]

description:
Kit-B6_S2
C57BL/6
mRNA


title: bladder_cancer_turbt_sample_22 [GNDX-MGH-QCFCG22]


title: bladder_cancer_turbt_sample_23 [GNDX-MGH-QCFCG23]


title: bladder_cancer_turbt_sample_19 [GNDX-MGH-QCFCG19]


title: AHP022

description:
sample 8
Targeted DNA
QC: PASSED


title: AHP020

description:
sample 6
Targeted DNA
QC: PASSED


title: AHP021

description:
sample 7
Targeted DNA
QC: PASSED


title: bladder_cancer_turbt_sample_20 [GNDX-MGH-QCFCG20]


title: bladder_cancer_turbt_sample_18 [GNDX-MGH-QCFCG18]


title: AHP019

description:
sample 5
Targeted DNA
QC: PASSED


title: LN18 1mM dbcAMP_24h RNA-seq

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

country: China

institute: sysu

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
RNA-seq for Sample 1-15:Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample 1-5 were the RNA-seq data of DBTRG-05MG treated with dbcAMP at 0/6/12/24/48 hours. Sample 6-10 were the RNA-seq data of U87 treated with dbcAMP at 0/6/12/24/48 hours. Sample 11-15 were the RNA-seq data of LN18 treated with dbcAMP at 0/6/12/24/48 hours.

tag: treatment

value: 1mM dbcAMP_24h


title: LN18 1mM dbcAMP_48h RNA-seq

value: 1mM dbcAMP_48h


title: LN18 1mM dbcAMP_12h RNA-seq

value: 1mM dbcAMP_12h


title: bladder_cancer_turbt_sample_16 [GNDX-MGH-QCFCG16]


title: AHP018

description:
sample 4
Targeted DNA
QC: PASSED


title: AHP017

description:
sample 3
Targeted DNA
QC: PASSED


title: AHP016

description:
sample 2
Targeted DNA
QC: PASSED


title: LN18 1mM dbcAMP_6h RNA-seq

value: 1mM dbcAMP_6h


title: input DNA

city: Santander

first: Miguel

middle: Angel

last: Lafarga

address: Avd,. Cardenal Herrera Oria sn

department: Department of Anatomy and Cell Biology

country: Spain

institute: Faculty of Medicine

data_processing:
Unaligned single read sequences obtained in bam format were initially converted to fastq with bamToFastq from bedtools.
Reads were aligned to the RGSC6.0/rn6 rat genome with Bowtie (v1)
Enriched areas were sought on aligned reads with the MACS peak caller (Model-based Analysis of ChIP-Seq) version 2.1.0.20150420
ChIP samples were compared to the input sample as control to increase specificity.
Called peaks/enriched areas were converted to bigWig format (with bedGraphToBigWig) for visualization at the UCSC genome browser.
Unaligned sequencing reads are presented in bam format. Called peaks -as obtained by MACS analysis with the --bdg option subsequent to alignment with Bowtie- are presented in bedGraph format
Genome_build: RGSC 6.0/rn6
Supplementary_files_format_and_content: bigwig

organism: Rattus norvegicus

source_name: input

growth_protocol: Young male Sprague-Dawley rats were routinary housed with a 12h light/dark cycle and had free access to food and and water.

extract_protocol:
Small tissue fragments of the cerebral cortex were treated with the formaldehyde solution for cross-linking, lysate tissue samples were sonicate in a Covaris ultrasound device and the extracted DNA processed for ChIP
An average of 9.8 ng of fragmented DNA per sample (range: 8.2-11.1 ng) was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated libraries were completed by limited-cycle PCR (10 cycles) and extracted with a [single] double-sided SPRI size selection. Median fragment size was 450 bp from which 120bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2000 instrument by following manufacturer's protocols.

treatment_protocol: DNA damage was induced by X-Ray irradiation. Animal received a single dose of 4Gy focused on the head and were sacrificed 15 days post-irradiation. Non-irrdiated animals were used as controls

tag: strain

value: Sprague-Dawley

value: cerebral cortex

value: cortical neurons

tag: stress

value: control

tag: chip antibody


title: bladder_cancer_turbt_sample_14 [GNDX-MGH-QCFCG14]


title: bladder_cancer_turbt_sample_12 [GNDX-MGH-QCFCG12]


title: bladder_cancer_turbt_sample_11 [GNDX-MGH-QCFCG11]


title: IR treated_2 gH2AX

source_name: IR treated

value: IR

value: H2AX phosphSer139 (Upstate, catalog#, 05-636, lot# 2977883)


title: AHP015

description:
sample 1
Targeted DNA
QC: PASSED

value: lung cancer cell line


title: bladder_cancer_turbt_sample_21 [GNDX-MGH-QCFCG21]

value: Male


title: U87 1mM dbcAMP_24h RNA-seq


title: Control gH2AX

source_name: Control


title: bladder_cancer_turbt_sample_13 [GNDX-MGH-QCFCG13]

value: Female


title: U87 1mM dbcAMP_12h RNA-seq


title: IR treated_1 gH2AX


title: U87 1mM dbcAMP_6h RNA-seq


title: 564Y_2

city: Shenyang

first: Zhiyong

last: Liu

institute: Shenyang Agriculture University

data_processing:
Libraries were sequenced on an Illumina 2500 Hiseq platform (San Diego, CA, USA)
The reference genome and gene model annotation files were downloaded from the genome website （http://brassicadb.org/brad/index.php, V1.5）. An index of the reference genome was built.using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12.
Gene expression levels were calculated based on reads per kb per million reads. Differential expression analysis of 6 samples (three biological replicates per condition) was performed using DESeq R package v.1.10.1 (Mortazavi et al., 2008). The false discovery rate (FDR) method was used to determine the threshold P value in multiple tests to identify DEGs; an adjusted log2 ratio ≥ 5 and FDR ≤ 0.001 were set as the threshold for differential expression.
Genome_build: the genome website （http://brassicadb.org/brad/index.php）
Supplementary_files_format_and_content: RPKM values for each Sample

organism: Brassica rapa subsp. chinensis

source_name: the aboveground parts

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
In total, of 3 μg RNA per sample from four time points each with three independent biological replicates were used to construct 6 cDNA libraries designated as 564_1, 564_2, 564_3, 564Y_1, 564Y_2 and 564Y_3.

value: the aboveground parts

tag: developmental stage

value: trifoliate

tag: genotype

value: mutant


title: DBTRG 1mM dbcAMP_48h RNA-seq

value: DBTRG


title: bladder_cancer_turbt_sample_10 [GNDX-MGH-QCFCG10]


title: bladder_cancer_turbt_sample_17 [GNDX-MGH-QCFCG17]


title: U87 1mM dbcAMP_0h RNA-seq

value: 1mM dbcAMP_0h


title: bladder_cancer_turbt_sample_9 [GNDX-MGH-QCFCG9]


title: bladder_cancer_turbt_sample_7 [GNDX-MGH-QCFCG7]


title: 564Y_1


title: U87 1mM dbcAMP_48h RNA-seq

value: 1mM dbcAMP_48h


title: bladder_cancer_turbt_sample_8 [GNDX-MGH-QCFCG8]


title: dVncR

city: Birmingham

first: Sang-Sang

last: Park

state: AL

address: 845 19th ST S

department: Medicine

country: USA

institute: UAB

hyb_protocol: Each 3,500ng of Cy5-labeled cRNA was fragmented at 60°C for 30 min (Agilent Gene Expression Hybridization Kit) and then hybridized to Streptoccocus pneumoniae 6 × 7K oligo microarray slide (MYcroarray.com) at 52°C for 17 h. After hybridization, the arrays were washed consecutively by using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Axon DNA Scanner (GenePix 4000B).

data_processing:
The scanned images were analyzed with GenePix4.0 software (Axon, Inc) to obtain background subtracted Signal intensities.
The Normalized and prenormalized value calculation of 1-color experiment.
1. Normalization step-1 : Data Transformation: Set measurement less than 5.0 to 5.0
GS uses log values-therefore, no zeros or –ves allowed. To change double click on “Data Transformations”. Already set at changing “0.01 to 0.01”.
In case of 1-color, GS manual said “5.0 to 5.0”. So, change the cutoff value as GS manual.
This option sets any measurements less than a specified cutoff value to the cutoff value. The cutoff value in 1-color data is 5.0.
2. Normalization step-2 : Per chip Normalization to 50% (global normalization)
Removes non biological error (systematic error) i.e. variation across chips (e.g. different hybridization efficiencies for different chips can account
for apparent large differences in signal value).  50% is calculated independently for each chip. What is the 50%? Using all the genes on a chip,
GS calculates the median (50%) intensity.
→ Prenormalized value was calculated in this step.
Prenornalized value = Gene A raw value / Chip 1 median
3. Normalization step-3 : divide with control samples
Normalized value =  Prenormalized Gene A value in test sample / Prenomalized Gene A value in control sanpleNormalization step-3 : divide with control samples
Control value = Chip 1 median * prenormalized Gene A value in control sample

organism: Streptococcus pneumoniae D39

source_name: dVncR

label_protocol: The Low Input Quick Amp Labeling Kit (Agilent Technologies Inc.) was used for labeling and hybridization. The sample was labeled with the aid of T7 RNA polymerase in the presence of Cy5-CTP. The Cy5-labeled cRNAs were purified using RNeasy MiniElute Cleanup kit (Qiagen). The yield and label incorporation efficiencies were measured with the aid of a spectrophotometer (NanoDrop Lite, Thermo Fisher Scientific, Inc).

growth_protocol: Streptococcus pneumoniae D39 and its isogenic vncR mutant were cultured in THY media until OD550=0.3.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

treatment_protocol: Bacterial culture was supplemented with 10% human serum and incubated further for 3 and 10 min at 37 °C.

tag: genotype/variation

value: vncR mutant

tag: agent

tag: time


title: dVncR+serum-10min

value: serum


title: dVncR+serum-3min


title: 564_3

value: wild type


title: bladder_cancer_turbt_sample_6 [GNDX-MGH-QCFCG6]


title: DBTRG 1mM dbcAMP_12h RNA-seq

tag: cell type

value: 1mM dbcAMP_12h


title: 564_2


title: D39+serum-10min


title: D39+serum-3min


title: 564_1


title: DBTRG 1mM dbcAMP_6h RNA-seq

value: 1mM dbcAMP_6h


title: bladder_cancer_turbt_sample_5 [GNDX-MGH-QCFCG5]


title: D39

value: control


title: DBTRG 1mM dbcAMP_24h RNA-seq

value: 1mM dbcAMP_24h


title: DBTRG 1mM dbcAMP_0h RNA-seq


title: bladder_cancer_turbt_sample_2 [GNDX-MGH-QCFCG2]


title: LN18 1mM dbcAMP_0h RNA-seq


title: bladder_cancer_turbt_sample_3 [GNDX-MGH-QCFCG3]


title: bladder_cancer_turbt_sample_4 [GNDX-MGH-QCFCG4]


title: bladder_cancer_turbt_sample_1 [GNDX-MGH-QCFCG1]


title: S22

status: Public on Mar 22 2019

city: York

first: Katherine

last: Newling

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

description:
Mus musculus C57BL/6 miR-132 -/-
S10_to_S25_FPKMs.txt

data_processing:
Illumina HiSeq 3000 sequencing
Reads were trimmed using Cutadapt v.1.8.3
Reads were aligned to mouse genome GRCm38 using HISAT2 v 2.0.5
Transcriptomes were assembled and gene expression quantified using the Tuxedo pipeline (version 2.2.1). Transcriptome assembly, merging, quantification and normalisation to fragments per kilobase per million mapped reads (FPKM) were performed using Cufflinks, Cuffmerge, Cuffquant and Cuffnorm, respectively.
Differential expression was performed using paired and independent T-tests follwed by Benjamini-Hochberg FDR correction
Genome_build: Mouse genome GRCm38.p4
Supplementary_files_format_and_content: S01_to_S09_FPKMs.txt and S10_to_S25_FPKMs.txt contain Cuffnorm output including FPKM values for each sample

source_name: spleen and lymph nodes

growth_protocol: Purified CD4 T cells were stimulated with 10μg/ml plate bound anti-CD3ε (clone 145-2C11) and 2μg/ml soluble anti-CD28 (37.51) in RPMI 1640 as before in flat bottom 96 well plates. For Th1 polarisation, cells were also treated with 15ng/ml recombinant mouse IL-12 and 5μg/ml anti-IL-4 (11B11)

extract_protocol:
RNA was extracted from tissue samples or purified cell populations using QIAzol and miRNeasy RNA extraction kits (QIAGEN) according to manufacturer’s instructions. Tissue samples were first dissociated in QIAzol using a Tissuelyser LT with stainless steel beads (all QIAGEN, UK).
RNA yield was quantified and checked for quality using a Nanodrop spectrophotometer before quality control and further quantification using an Agilent bioanalyser prior to RNAseq

treatment_protocol: For ex vivo stimulation of CD4+ T cells from infected spleens, cells were first stimulated in complete RPMI for 4 hours at 37oC with 500ng/ml PMA, 1μg/ml ionomycin

value: CD4+ T cells following in vitro stimulation for 18h under Th1 conditions


title: S12

description:
Mus musculus C57BL/6 WT
S10_to_S25_FPKMs.txt

value: Naive sorted CD4+ T cells prior to stimulation


title: S15


title: S19


title: S21


title: S16


title: S14


title: S17


title: S24


title: S18


title: S25


title: S13


title: S20


title: S10


title: S09

description:
L.Donovani infected Mus musculus C57BL/6 miR-132 -/-
S01_to_S09_FPKMs.txt

source_name: spleen

value: CD4+ T cells


title: S08


title: S06


title: S04

description:
L.Donovani infected Mus musculus C57BL/6 WT
S01_to_S09_FPKMs.txt


title: S05


title: S23


title: S02


title: Ovcar3 shIDH1 #1 rep3 (G400_2_3)

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Fastq was generated by FASTQ Generaton App on BaseSpace (Illumina)
Quality and adapter/polyA trimming by BBDuk (bbmap/36_49)
Read alignment using HISAT2/2.1.0. SAM files were generated.
Raw read count was computed using hteq/0.11.2 by supplementing Ensembl gene annotation (GRCm38.78)
Filtered genes that don't have at least 1 read count in 3 samples
Genome_build: hg38
Supplementary_files_format_and_content: csv file of EdgeR data withh raw read counts and CPM (copy per million) gene expression matrix

source_name: Ovcar3 shIDH1 #1

extract_protocol:
RNA was isolated by phenol extraction and purified using Zymo RNA Clean and Concentrator Kit
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment closed to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The processed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
RNAseq (QuantSeq 3'mRNA-Seq)

tag: cell line

value: high grade serous ovarian cancer (HGSOC) cell line


title: S11


title: S07


title: Ovcar3 Control rep3 (G400_1_3)

source_name: Ovcar3 Control


title: Ovcar3 Control rep2 (G400_1_2)


title: Ovcar3 shIDH1 #1 rep2 (G400_2_2)


title: Ovcar3 shIDH1 #1 rep1 (G400_2_1)


title: Ovcar3 Control rep1 (G400_1_1)


title: S03


title: bladder_cancer_turbt_sample_15 [GNDX-MGH-QCFCG15]

value: Male


title: S01


title: H-1303_P5_4w_SCB-DMSO-free 2

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human cell

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software GX13.1 (Agilent) using default parameters.

source_name: H-1303, passage 5, cryopreserved with STEM-CELLBANKER DMSO Free for 4 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ADSCs were maintained in MesenPRO RS Medium (Invitrogen), according to the manufacturer’s instructions. UC-MSCs were maintained using Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum (ATCC, PCS-500-040) plus Mesenchymal Stem Cell Basal Medium for Adipose, Umbilical and Bone Marrow-derived MSCs (ATCC, PCS-500-030), according to the manufacturer’s instructions. Yub621c and Yub625 were cultured in 1x Penicillin-Streptomycin (gibco)-containing MesenPRO RS Medium (Invitrogen), according to the manufacturer’s instructions. NHAC-kn and H-1303 were maintained using CGM Chondrocyte Growth Medium BulletKit (Lonza, CC-3216) and Chondrocyte ReagentPack Subculture Reagents (Lonza, CC-3233), according to the manufacturer’s instructions.

extract_protocol: Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Each viable cells were suspended in either STEM-CELLBANKER (ZENOAQ), STEM-CELLBANKER DMSO Free (ZENOAQ), or 10% DMSO (SIGMA, D2650) in 20% Fetal Bovine Serum, MSC-Qualified (FBS) (Invitrogen) containing culture medium. The cell suspension was dispensed into a cryopreservation tube (Corning, 430488) and was frozen in a BICELL freezing vessel (Nippon freezer) at -80℃ for overnight, and was transferred into a liquid nitrogen tank or -150°C refrigerator for more than 4 weeks or 1 year. The frozen cells were quickly thaw in a 37°C water bath and were plated into culture vessel. When the cell confluency becomes 60–90 %, the cells were subcultured. The cell confluency becomes 70–90 % again, then the cells were harvested for DNA microarray analysis.

tag: cell characters

value: normal chondrocytes

tag: cell provider

value: Articular Engineering

tag: cell line name

value: Human Chondrocytes, Cryopreserved, Primary, CDD-H-2610

tag: cell lot

tag: passage number

tag: cryoprotectant medium

value: STEM-CELLBANKER DMSO Free

tag: cryopreservation period

value: 4 weeks


title: cirrhotic liver treated with CVX-060, biological rep3

city: Belvaux

first: Gaia

last: Zaffaroni

address: avenue du Swing, 6

country: Luxembourg

institute: Luxembourg Centre for Systems Biomedicine

description: CVX-060 was diluted in 500 l of saline solution and injected intravenously via the tail vein.

hyb_protocol: Following fragmentation, 10 ug of fragmented and labeled cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.

scan_protocol: Arrays were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneCHip Scanner 3000 System.Data was analyzed with Expression Console Software using RMA analysis.

data_processing: CEL files were analyzed using the functions rma and mas5calls contained in the R Bioconductor package affy (1.56.0) and LIMMA package (3.38.2), with R-3.4.0.

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl4, treated with CVX-062

label_protocol: 150ng of each RNA sample were processed according to 3’IVT PLUS chemistry. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: See overall design in the Series section

extract_protocol: Total RNA was extracted from frozen liver tissue with Trizol reagent according to the manufacturer's instructions (Invitrogene, Carlsbad, CA)

tag: type

value: treated

tag: strain

value: Wistar

tag: tissue

value: whole liver

tag: treatment

value: Once a week with 10 mg/kg of CVX-060 (Pfizer, Inc., New York, NY, USA) for 4 weeks.


title: TC71 biological replicate B

city: Bologna

first: Annalisa

last: Astolfi

address: via massarenti 11

department: "Giorgio Prodi" Cancer Research center

country: Italy

institute: University of Bologna

description: TC71 biological replicate B, untreated

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

data_processing: Gene Spring GX v.14.9 ExonRMA16

label_protocol: Samples were labeled using labeling kit materials provided by Affymetrix

growth_protocol: A total of 500,000 cells were seeded in six-well plates in complete medium.

extract_protocol: Total RNA from cell lines was extracted with a TRIzol extraction kit (Life Technologies, Grand Island, NY). Nucleic acid quality and quantity were assessed with a NanoDrop spectrophotometer (NanoDrop Technologies)

treatment_protocol: Exosomes in equal amounts (10 µg/5,000 cells), purified from CD99-silenced EWS cell lines, were incubated in serum-free conditions with recipient cells (TC-71) at 37°C.


title: cirrhotic liver treated with CVX-060, biological rep1

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl4, treated with CVX-060

treatment_protocol: See overall design in the Series section


title: cirrhotic liver, biological rep5

description: vehicle treatment

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl8

value: diseased

value: Once a week with vehicle solution


title: cirrhotic liver, biological rep4

description: vehicle treatment

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl7


title: cirrhotic liver, biological rep2

description: vehicle treatment

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl5


title: cirrhotic liver treated with CVX-060, biological rep2

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl4, treated with CVX-061


title: cirrhotic liver, biological rep1

description: vehicle treatment

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl4


title: H-1303_P5_4w_SCB-DMSO-free 1

description: Gene expression in human cell


title: TC71 biological replicate A

description: TC71 biological replicate A, untreated


title: cirrhotic liver, biological rep3

description: vehicle treatment

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl6


title: H-1303_P5_4w_SCB 2

description: Gene expression in human cell

source_name: H-1303, passage 5, cryopreserved with STEM-CELLBANKER for 4 weeks

value: STEM-CELLBANKER


title: TC71+exoTCsiCD99 biological replicate D

description: TC71+exoTCsiCD99 biological replicate D, treated with exoTCsiCD99


title: Kit-B6 Sample 3 [tumor]

description:
Kit-B6_S3
C57BL/6
mRNA

source_name: Colon tumors

tag: strain/background

value: Colon tumor

tag: age

value: postnatal week 32


title: cirrhotic liver treated with CVX-060, biological rep4

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl4, treated with CVX-063


title: H-1303_P5_4w_control 1

description: Gene expression in human cell

source_name: H-1303, passage 5, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 4 weeks


title: H-1303_P5_0d_non-frozen 2

description: Gene expression in human cell

source_name: H-1303, passage 5, non-frozen

value: 0 day


title: H-1303_P5_4w_control 2

description: Gene expression in human cell

value: 10% DMSO in 20% Fetal Bovine Serum containing culture medium


title: NHAC-kn_P6_4w_SCB 2

description: Gene expression in human cell

source_name: NHAC-kn, passage 6, cryopreserved with STEM-CELLBANKER for 4 weeks

value: articular chondrocyte from adult knee

value: Lonza

value: NHAC-kn - Human Articular Chondrocytes - Knee, CC-2550


title: NHAC-kn_P6_4w_SCB-DMSO-free 1

description: Gene expression in human cell

source_name: NHAC-kn, passage 6, cryopreserved with STEM-CELLBANKER DMSO Free for 4 weeks


title: H-1303_P5_4w_SCB 1

description: Gene expression in human cell

value: normal chondrocytes

value: Articular Engineering

value: Human Chondrocytes, Cryopreserved, Primary, CDD-H-2610


title: NHAC-kn_P6_4w_SCB 1

description: Gene expression in human cell

value: 4 weeks


title: TC71+exoTCsiCD99 biological replicate C

description: TC71+exoTCsiCD99 biological replicate C, treated with exoTCsiCD99


title: NHAC-kn_P6_4w_SCB-DMSO-free 2

description: Gene expression in human cell

value: STEM-CELLBANKER DMSO Free


title: H-1303_P5_0d_non-frozen 1

description: Gene expression in human cell


title: 564Y_3

source_name: the aboveground parts

value: the aboveground parts

tag: developmental stage

value: trifoliate

tag: genotype

value: mutant


title: NHAC-kn_P6_4w_control 1

description: Gene expression in human cell

source_name: NHAC-kn, passage 6, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 4 weeks


title: NHAC-kn_P6_0d_non-frozen 2

description: Gene expression in human cell

source_name: NHAC-kn, passage 6, non-frozen


title: Yub625_P10_4w_SCB-DMSO-free 2

description: Gene expression in human cell

source_name: Yub625, passage 10, cryopreserved with STEM-CELLBANKER DMSO Free for 4 weeks

value: cartilage-derived mesenchymal stem cells

value: RIKEN Bio Resource Center


title: Yub625_P11_0d_non-frozen 2

description: Gene expression in human cell

source_name: Yub625, passage 11, non-frozen


title: UC-MSC_P7_1y_SCB 1

description: Gene expression in human cell

source_name: UC-MSC, passage 7, cryopreserved with STEM-CELLBANKER for 1 year

value: umbilical cord-derived mesenchymal stem cell

value: ATCC

value: Umbilical Cord-Derived Mesenchymal Stem Cells, PCS-500-010

value: STEM-CELLBANKER

value: 1 year


title: NHAC-kn_P6_4w_control 2

description: Gene expression in human cell

value: articular chondrocyte from adult knee

value: Lonza

value: 10% DMSO in 20% Fetal Bovine Serum containing culture medium


title: Yub625_P10_4w_control 1

description: Gene expression in human cell

source_name: Yub625, passage 10, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 4 weeks


title: Yub621c_P15_1y_SCB 2

description: Gene expression in human cell

source_name: Yub621c, passage 15, cryopreserved with STEM-CELLBANKER for 1 year


title: Yub621c_P15_1y_control 1

description: Gene expression in human cell

source_name: Yub621c, passage 15, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 1 year


title: ADSC_P6_1y_control 1

description: Gene expression in human cell

source_name: ADSC, passage 6, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 1 year

value: adipose-derived stem cells

value: invitrogen

value: STEMPRO Human Adipose-Derived Stem Cells, R7788-115


title: NHAC-kn_P6_0d_non-frozen 1

description: Gene expression in human cell

value: NHAC-kn - Human Articular Chondrocytes - Knee, CC-2550

value: 0 day


title: ADSC_P6_1y_control 2

description: Gene expression in human cell


title: UC-MSC_P7_4w_SCB 1

description: Gene expression in human cell

source_name: UC-MSC, passage 7, cryopreserved with STEM-CELLBANKER for 4 weeks

value: 4 weeks


title: UC-MSC_P7_0d_non-frozen 1

description: Gene expression in human cell

source_name: UC-MSC, passage 7, non-frozen


title: UC-MSC_P7_1y_SCB 2

description: Gene expression in human cell


title: UC-MSC_P7_4w_SCB 2

description: Gene expression in human cell

source_name: UC-MSC, passage 7. cryopreserved with STEM-CELLBANKER for 4 weeks


title: ADSC_P6_1y_SCB 1

description: Gene expression in human cell

source_name: ADSC, passage 6, cryopreserved with STEM-CELLBANKER for 1 year


title: ADSC_P6_4w_SCB 1

description: Gene expression in human cell

source_name: ADSC, passage 6, cryopreserved with STEM-CELLBANKER for 4 weeks


title: UC-MSC_P7_4w_control 2

description: Gene expression in human cell

source_name: UC-MSC, passage 7, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 4 weeks


title: cirrhotic liver treated with CVX-060, biological rep5

source_name: male Wistar rats, whole liver, cirrhosis induced with CCl4, treated with CVX-064

value: treated

value: Wistar

value: whole liver

value: Once a week with 10 mg/kg of CVX-060 (Pfizer, Inc., New York, NY, USA) for 4 weeks.


title: UC-MSC_P7_0d_non-frozen 2

description: Gene expression in human cell

value: umbilical cord-derived mesenchymal stem cell

value: ATCC


title: ADSC_P6_1y_SCB 2

description: Gene expression in human cell

value: STEM-CELLBANKER


title: ADSC_P6_4w_control 2

description: Gene expression in human cell

source_name: ADSC, passage 6, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 4 weeks


title: UC-MSC_P7_4w_control 1

description: Gene expression in human cell

value: Umbilical Cord-Derived Mesenchymal Stem Cells, PCS-500-010


title: Luminal Foxp1-knockout Rep3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: LUM-C

data_processing:
100bp single-end reads were generated using the Illumina CASAVA pipeline version 1.8.2.
Reads were aligned to the mouse genome by Rsubread version 1.26.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Luminal Foxp1-knockout

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy kit.
RNA libraries were prepared for sequencing on an Illumina HiSeq 2000 using Illumina’s TruSeq RNA v2 sample preparation protocol.

value: Mammary epithelium

tag: cell type

value: Luminal epithelial cell

value: Foxp1 Knockout


title: UC-MSC_P7_1y_control 2

description: Gene expression in human cell

source_name: UC-MSC, passage 7, cryopreserved with 10% DMSO in 20% Fetal Bovine Serum containing culture medium for 1 year

value: 1 year


title: ADSC_P6_4w_SCB 2

description: Gene expression in human cell

value: adipose-derived stem cells

value: invitrogen


title: UC-MSC_P7_1y_control 1

description: Gene expression in human cell

value: 10% DMSO in 20% Fetal Bovine Serum containing culture medium


title: Yub625_P11_0d_non-frozen 1

description: Gene expression in human cell

value: cartilage-derived mesenchymal stem cells

value: RIKEN Bio Resource Center

value: 0 day


title: ADSC_P6_4w_control 1

description: Gene expression in human cell

value: STEMPRO Human Adipose-Derived Stem Cells, R7788-115

value: 4 weeks


title: Luminal Control Rep3

description: LUM-C-CT

source_name: Luminal Control

value: Foxp1 Control


title: Luminal Control Rep2

description: LUM-B-CT


title: Basal Control Rep3

description: DP-C-CT

source_name: Basal Control

value: Basal epithelial cell


title: Luminal Control Rep1

description: LUM-A-CT


title: Basal Foxp1-knockout Rep2

description: DP-B

source_name: Basal Foxp1-knockout


title: Basal Control Rep2

description: DP-B-CT


title: Basal Foxp1-knockout Rep1

description: DP-A


title: Luminal Foxp1-knockout Rep1

description: LUM-A


title: Basal Control Rep1

description: DP-A-CT


title: Luminal Foxp1-knockout Rep2

description: LUM-B


title: Basal Foxp1-knockout Rep3

description: DP-C


title: P2 tumor b

type: genomic

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

country: Switzerland

institute: University Hospital Bern

hyb_protocol: Sodium bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged on BeadArray Reader with standard recommended Illumina scanner settings

data_processing: GenomeStudio GX software v1.1.0 and R(2.14.0) with methylumi library (2.0.13)

label: Cy5 and Cy3

source_name: Primary tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from colorectal tissue was extracted and purified from patient samples using QIAamp DNA mini kit (Qiagen) according to standard instructions. An RNAse A treatment was included in the protocol according to the manufacturer’s protocol. Genomic DNA from blood samples was extracted with the NucleoSpin Blood L Kit (Macherey-Nagel). 2 μg of the extracted DNA was sodium bisulfite converted using the EZ DNA Methylation Kit (Zymo).

value: CRC

value: non-CIMP

tag: gender

value: Female

tag: colonic location

value: Right

tag: stage (uicc)

value: IV

tag: patient number


title: P2 tumor a


title: P2 normal b

source_name: Cancer-associated mucosa

value: CAM


title: P3 tumor a

value: III


title: P2 normal a


title: P2 blood b

source_name: Blood

value: Blood


title: P1 blood a

value: CIMP

value: Male

value: II


title: P2 blood a


title: P3 tumor b


title: P3 normal b


title: P3 normal a


title: P1 tumor b


title: P1 normal b


title: P1 normal a


title: P1 blood b


title: P3 blood b


title: Sample 17 rs11614913[T]

city: Reykjavik

first: Olafur

middle: Andri

last: Stefansson

address: Sturlugata 8

department: Population Genomics

country: Iceland

institute: deCODE / Amgen Inc

data_processing:
RTA (real-time analysis) was used to generate .bcl files
bcl2fastq was used to generate fastq files
Kallisto was used for quantification of RNA transcript expression using Ensembl v87 cDNA sequences as reference transcriptome.
Genome_build: Hg38
Supplementary_files_format_and_content: tsv files generated by Kallisto; target_id represents ensembl transcript Ids and est_counts represents their estimated count.

growth_protocol: DMEM with 10% fetal calf serum, 50units/mL penicillin and 50ug/mL streptomycin

extract_protocol:
RNA from sorted cells was isolated using RNeasy plus mini kit (Qiagen 74136) following the manufacturer’s protocol. After isolation, RNAsecure (ThermoFisher AM7006) was added to the RNA and samples heated for 10 minutes at 60°C. Samples cooled down on ice and then placed in -80°C.
The preparation of poly(A)+ cDNA sequencing libraries and RNA sequencing were carried out as described before in Styrkarsdottir, U. Nat Genet 2017 and Sigurdsson et al Nat Communications 2017.

treatment_protocol: On the day of transfection, medium was replaced with 3 ml of the identical media as before without antibiotics. For each transfected well, 3.3 µg of Mir_Empty, Mir196A2_WT or Mir196A_Mut plasmids were diluted in 155 µl Opti-Mem (ThermoFisher 31985047) and 9.9 µl Fugene HD (Promega E2312). Incubated at room temperature for 10 min before 150 µl of transfection mix was added to the appropriate well. Forty eight hours after transfection, cells were harvested for cell sorting. Cells were released from the plate surface with TrypLE Express (ThermoFisher 12605010) and then washed with 2% FBS (ThermoFisher 10500064) in dPBS (ThermoFisher 14190144). After washing, cells were diluted in 1 ml of 2% FBS in dPBS with 1:1000 DAPI (Sigma D9542). Live cells were then positively sorted for the expression of GFP using a Sony SH800S cell sorter, giving a purity of >85% transfected cells. Cells were first gated by size with FSC Area/SSC Area and doublets were excluded by gating at FSC Height/FSC Area. Unstained cells were then used to specify the gating for negative cells. DAPI stained cells were also used to define the live/dead gate.

value: embryonic kidney

tag: transfection


title: Sample 16 rs11614913[C]


title: Sample 13 empty vector

value: empty vector


title: Sample 14 empty vector


title: Sample 9 rs11614913[C]


title: Sample 15 rs11614913[T]


title: Sample 7 rs11614913[C]


title: Sample 8 rs11614913[C]


title: Sample 11 empty vector


title: Sample 18 empty vector


title: Sample 10 rs11614913[T]


title: P1 tumor a


title: P3 blood a


title: Sample 12 rs11614913[T]


title: Sample 6 empty vector


title: Sample 3 empty vector


title: Sample 4 rs11614913[C]


title: Sample 5 rs11614913[T]


title: Sample 2 rs11614913[C]


title: Sample 1 rs11614913[T]


title: H9.KO.2o repl3

city: Cambridge

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Trim Galore! v0.4.0 with parameters "--stringency 3 -e 0.2 -a TGGAATTCTCGGGTGCCAAGGA" was used to remove sequencing adapters.
Bismark v0.14.4 with parameters "-n 2 -l 50 --un --ambiguous --bowtie1 --chunkmbs 2048" was used to align the reads to the hg38 reference genome.
Seqtk with parameters "-e 3" was used to remove last three bases from unaligned and ambigous reads followed by re-alignment by Bismark.
Ngsutils v0.5.9 in the "junction" mode was used to extract splice junctions; unaligned reads from the previous alignment attempt were aligned to them using Bismark. The aligned reads were coverted back to genomic coordinates using bamutils in "convertregion" mode. 'N' in the cigar string was replaced with 'D' for compatibility with bismark_methylation_extractor.
Samtools merge was used to combine aligned reads from all steps. Reads with >1/3 methylated cytosines were discarded.
bismark_methylation_extractor with the "--bedGraph --counts --CX_context" options was used to extract methylated cytosines.
Genome_build: hg38
Supplementary_files_format_and_content: The bismark coverage reports are tab delimited and contain methylation level at each covered cytosine in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: H9 cells

growth_protocol: H9 cells were grown on matrigel coated plates in essential 8 medium, passaged as clumps after dissociation using EDTA in PBS, HEK293 cells were grown in DMEM media completed with 10% fetal bovine serum and glutamax.

extract_protocol:
15 μg of total RNA was extracted using Trizol (ThermoFisher) and DNase (Ambion) then Ribo‐Zero (Illumina) treated (3 times treatment of 5 ug and then pooled). The remaining RNA fraction was bisulfite‐treated according to Pollex, T., Hanna, K., & Schaefer, M. (2010). Detection of cytosine methylation in RNA using bisulfite sequencing. Cold Spring Harbor Protocols, 2010(10). Briefly, ribosomal depleted RNA was mixed with 42.5 μl of 40% sodium bisulfite pH 5.0 and 17.5 μl of DNA protection buffer (EpiTect Bisulfite Kit, Qiagen). The reaction mixture was incubated for three cycles of 5 min at 70°C followed by 1 h at 60°C and then desalted with Micro Bio‐spin 6 chromatography columns (Bio‐Rad). RNA was desulphonated by adding an equal volume of 1 M Tris (pH 9.0) to the reaction mixture and incubated for 1 h at 37°C, followed by ethanol precipitation. Bisulfite converted RNA was treated with T4 PNK (New England Biolabs) to repair both 5’ and 3’ ends for library preparation. Repaired RNA quality and concentration was measured on a Bioanalyzer 2100 RNA nano‐chip (Agilent).
About 100 ng of RNA was used to generate Bisulfite‐seq libraries. Libraries were performed according to TruSeq Small RNA preparation kit (Illumina). RNA adapters were then ligated, reverse‐transcribed followed by 18‐cycle PCR amplification before sequencing.

value: human embryonic stem cells

tag: genotype/variation

value: Crispr /Cas9 mediated (HDR) deletion of EXON 2 of NSUN6, clone 2, puromycin selection

tag: cell line

tag: batch


title: H9.KO.2o repl2


title: H9.KO.1o repl2

value: Crispr /Cas9 mediated (HDR) deletion of EXON 2 of NSUN6, clone 1 puromycin selection


title: H9.KO.2o repl4


title: H9.WT.1o repl3

value: WT H9 cell line


title: H9.WT.1o repl4


title: H9.KO.1o repl3


title: H9.KO.2o repl1


title: H9.WT.1o repl2


title: H9.KO.1o repl1


title: H9.WT.1o repl1


title: sRNAseq of paf1+ [paf1wt _609X1]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
paf1wt _609X1

data_processing:
Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17. Illumina or Qiagen 3' adaptors were trimmed using cutadapt with parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie 1.0.0 with parameters -M 1 -v 0 --best --strata. Bowtie sam out put was converted to bam using samtools (v1.3.1). Bam files were converted to bed using bedtools bamtobed (v2.25.0), Bed files were used to calculate strand-specific coverage using bedtools genomecov (v2.25.0) and resulting bedgraph files were normalized to 1 million genome mapping reads (RPM) and converted to bigWig format using bedGraphToBigWig (v4).
smallRNA-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17. Illumina or Qiagen 3' adaptors were trimmed using cutadapt with parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie 1.0.0 with parameters -M 1 -v 0 --best --strata. Bowtie sam out put was converted to bam using samtools (v1.3.1). Bam files were converted to bed using bedtools bamtobed (v2.25.0), Bed files were used to calculate strand-specific coverage using bedtools genomecov (v2.25.0) and resulting bedgraph files were normalized to 1 million genome mapping reads (RPM) and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
Genome_build: Spombe.ASM294v2.24
Supplementary_files_format_and_content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV.

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures was grown exponentially in YES media at 30 degrees celsius

extract_protocol:
Total RNA was isolated from exponentially growing cells using the hot phenol method (Leeds, 1991). The RNA was fractionated using RNeasy Midi columns (Qiagen) following the „RNA cleanup protocol“ provided by the manufacturer. The flow-through fraction was precipitated („small RNA“ fraction). 25 μg of the "small RNA" fraction were separated on a 17.5% PAGE and the 18 – 28 nt population was purified.
The isolated small RNA populations were prepared for sequencing using the Illumina® TruSeq small RNA preparation protocol (Cat.# RS-930-1012).


title: sRNAseq of mst2D::ura3+ [mst2D _823X12]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
mst2D _823X12

value: h- leu1-32, ura4-D18, shade6-250/natMX ade6-706 or -210 trp1+::ade6+ mst2D::ura3


title: sRNAseq of leo1D::kanMX [leo1D _609X2]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
leo1D _609X2

value: h- , leu1-32,  ura4-D18, leo1D::kanMX


title: sRNAseq of paf1-Q264Stop::LEU2 [paf1Q264Stop _696X2]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
paf1Q264Stop _696X2

value: h- leu1-32 ura4-D18 ade6-704  trp1+::ade6+ shade6-250/natMX paf1-sms8::LEU2


title: sRNAseq of paf1-Q264Stop::kanMX [paf1Q264Stop _696X3]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
paf1Q264Stop _696X3

value: h+ leu1-32 ura4-D18 ade6-M210 trp1+::ade6+ paf1-sms8::kanMX


title: sRNAseq of paf1-Q264Stop::kanMX [paf1Q264Stop _696X4]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
paf1Q264Stop _696X4


title: sRNAseq of F10 pedigree 2 spore 15, paf1-Q264Stop

description:
F10p2s15_paf1Q264Stop_845X15
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG

value: h-  leu1-32 ura4-D18 ade6-M210 trp1+::ade6+ paf1-Q264Stop::kanMX


title: sRNAseq of paf1-Q264Stop::LEU2 [paf1Q264Stop _325X8]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
paf1Q264Stop _325X8


title: sRNAseq of paf1-Q264Stop::LEU2 [paf1Q264Stop _696X1]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
paf1Q264Stop _696X1


title: sRNAseq of F10 pedigree 2 spore 13, paf1-Q264Stop

description:
F10p2s13_paf1Q264Stop_845X13
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of paf1+ [paf1wt _325X3]

description:
3' adapter sequence: TGGAATTCTCGGGTGCCAAGG
paf1wt _325X3

value: h+ leu1-32 ade6-210 ura4-DS/E imr1L(NcoI)::ura4+ otr1R(SphI)::ade6+


title: H9.KO.1o repl4


title: sRNAseq of F10 pedigree 2 spore 12, paf1-Q264Stop

description:
F10p2s12_paf1Q264Stop_845X12
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 11, paf1-Q264Stop

description:
F10p2s11_paf1Q264Stop_845X11
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG

value: h+ leu1-32 ura4-D18 ade6-M210 trp1+::ade6+ paf1-Q264Stop::kanMX


title: sRNAseq of F10 pedigree 2 spore 9, paf1-Q264Stop

description:
F10p2s9_paf1Q264Stop_845X9
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 8, paf1-Q264Stop

description:
F10p2s8_paf1Q264Stop_845X8
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 7, paf1-Q264Stop

description:
F10p2s7_paf1Q264Stop_845X7
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 14, paf1-Q264Stop

description:
F10p2s14_paf1Q264Stop_845X14
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 5, paf1-Q264Stop

description:
F10p2s5_paf1Q264Stop_845X5
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 6, paf1-Q264Stop

description:
F10p2s6_paf1Q264Stop_845X6
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 1, paf1-Q264Stop

description:
F10p2s1_paf1Q264Stop_845X1
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 2, paf1-Q264Stop

description:
F10p2s2_paf1Q264Stop_845X2
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 2 spore 2, paf1-Q264Stop

description:
F4p2s21_paf1Q264Stop_779X10
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG

value: h? leu1-32 ura4-D18 ade6-M210 trp1+::ade6+ paf1-Q264Stop::kanMX


title: sRNAseq of F4 pedigree 2 spore 3, paf1-Q264Stop

description:
F4p2s20_paf1Q264Stop_779X9
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 4, paf1-Q264Stop

description:
F10p2s4_paf1Q264Stop_845X4
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 2 spore 4, paf1-Q264Stop

description:
F4p2s5_paf1Q264Stop_779X8
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 2 spore 7, paf1-Q264Stop

description:
F4p2s12_paf1Q264Stop_779X5
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 2 spore 8, paf1-Q264Stop

description:
F4p2s9_paf1Q264Stop_779X4
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 2 spore 1, paf1-Q264Stop

description:
F4p2s22_paf1Q264Stop_779X11
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 spore 1, paf1+

description:
F1s22_paf1wt_776X22
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG

value: SPB389 x SPB390


title: sRNAseq of F1 spore 4, paf1+

description:
F1s25_paf1wt_776X25
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 10, paf1-Q264Stop

description:
F10p2s10_paf1Q264Stop_845X10
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F10 pedigree 2 spore 3, paf1-Q264Stop

description:
F10p2s3_paf1Q264Stop_845X3
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 2 spore 9, paf1-Q264Stop

description:
F4p2s8_paf1Q264Stop_779X3
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 23, paf1-Q264Stop

description:
F1p4s31_paf1Q264Stop_776X31
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG

value: h? leu1-32 ura4-D18 ade6-M210/704 trp1+::ade6+ paf1-Q264Stop::kanMX


title: sRNAseq of F4 pedigree 2 spore 6, paf1-Q264Stop

description:
F4p2s15_paf1Q264Stop_779X6
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 2 spore 5, paf1-Q264Stop

description:
F4p2s16_paf1Q264Stop_779X7
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 spore 7, paf1+

description:
F1s28_paf1wt_776X28
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 spore 2, paf1+

description:
F1s23_paf1wt_776X23
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 spore 6, paf1+

description:
F1s27_paf1wt_776X27
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 20, paf1-Q264Stop

description:
F1p4s20_paf1Q264Stop_776X20
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 18, paf1-Q264Stop

description:
F1p4s18_paf1Q264Stop_776X18
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 17, paf1-Q264Stop

description:
F1p4s17_paf1Q264Stop_776X17
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 22, paf1-Q264Stop

description:
F1p4s30_paf1Q264Stop_776X30
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 spore 3, paf1+

description:
F1s24_paf1wt_776X24
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 14, paf1-Q264Stop

description:
F1p4s14_paf1Q264Stop_776X14
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 15, paf1-Q264Stop

description:
F1p4s15_paf1Q264Stop_776X15
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 21, paf1-Q264Stop

description:
F1p4s21_paf1Q264Stop_776X21
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 16, paf1-Q264Stop

description:
F1p4s16_paf1Q264Stop_776X16
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 11, paf1-Q264Stop

description:
F1p4s11_paf1Q264Stop_776X11
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 10, paf1-Q264Stop

description:
F1p4s10_paf1Q264Stop_776X10
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 19, paf1-Q264Stop

description:
F1p4s19_paf1Q264Stop_776X19
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 7, paf1-Q264Stop

description:
F1p4s7_paf1Q264Stop_776X7
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 spore 8, paf1+

description:
F1s29_paf1wt_776X29
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 13, paf1-Q264Stop

description:
F1p4s13_paf1Q264Stop_776X13
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 5, paf1-Q264Stop

description:
F1p4s5_paf1Q264Stop_776X5
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 12, paf1-Q264Stop

description:
F1p4s12_paf1Q264Stop_776X12
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 4, paf1-Q264Stop

description:
F1p4s4_paf1Q264Stop_776X4
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 8, paf1-Q264Stop

description:
F1p4s8_paf1Q264Stop_776X8
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 3, paf1-Q264Stop

description:
F1p4s3_paf1Q264Stop_776X3
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 9, paf1-Q264Stop

description:
F1p4s9_paf1Q264Stop_776X9
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 1 spore 1, paf1-Q264Stop

description:
F4p1s8_paf1Q264Stop_696X10
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F1 pedigree 4 spore 1, paf1-Q264Stop

description:
F1p4s1_paf1Q264Stop_776X1
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 1 spore 2, paf1-Q264Stop

description:
F4p1s7_paf1Q264Stop_696X9
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 1 spore 3, paf1-Q264Stop

description:
F4p1s6_paf1Q264Stop_696X8
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 1 spore 6, paf1-Q264Stop

description:
F4p1s3_paf1Q264Stop_696X5
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 1 spore 4, paf1-Q264Stop

description:
F4p1s5_paf1Q264Stop_696X7
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: sRNAseq of F4 pedigree 1 spore 5, paf1-Q264Stop

description:
F4p1s4_paf1Q264Stop_696X6
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 1, input

data_processing:
Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
smallRNA-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17. Illumina or Qiagen 3' adaptors were trimmed using cutadapt with parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie 1.0.0 with parameters -M 1 -v 0 --best --strata. Bowtie sam out put was converted to bam using samtools (v1.3.1). Bam files were converted to bed using bedtools bamtobed (v2.25.0), Bed files were used to calculate strand-specific coverage using bedtools genomecov (v2.25.0) and resulting bedgraph files were normalized to 1 million genome mapping reads (RPM) and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
Genome_build: Spombe.ASM294v2.24
Supplementary_files_format_and_content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV.

extract_protocol:
Exponentially growing S.pombe cell culture (50ml YES, OD = 1) was fixed with 1% formaldehyde and lysed. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol. For a detailed protocol, see Kowalik et al., 2015.
For multiplex ChIP sequencing, samples were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L) and NEBNext Multiplex Oligos for Illumina (E7600S).

value: h-  leu1-32 ura4-D18 ade6-M210 trp1+::ade6si3 paf1-Q264Stop::kanMX

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6+imp paf1-sms8::kanR


title: sRNAseq of F1 pedigree 4 spore 2, paf1-Q264Stop

description:
F1p4s2_paf1Q264Stop_776X2
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: ChIPseq of paf1+ ade6+, replicate 1, input


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 1, Pol II

extract_protocol:
Exponentially growing S.pombe cell culture (50ml YES, OD = 1) was fixed with 1% formaldehyde and lysed. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol. For chromatin immunoprecipitation (ChIP), RNA polymerase II mouse monoclonal antibody from Covance (8WG16) was used. For a detailed protocol, see Kowalik et al., 2015.
For multiplex ChIP sequencing, samples were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L) and NEBNext Multiplex Oligos for Illumina (E7600S).


title: sRNAseq of F1 pedigree 4 spore 6, paf1-Q264Stop

description:
F1p4s6_paf1Q264Stop_776X6
3'_adapter_sequence: TGGAATTCTCGGGTGCCAAGG


title: ChIPseq of paf1+ ade6+imp, replicate 1, Pol II

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6si3

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6+imp


title: ChIPseq of paf1+ ade6+imp, replicate 1, H3K36me3

extract_protocol:
Exponentially growing S. pombe cell culture (50ml YES, OD = 1) was fixed with 1% formaldehyde and lysed. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol. For chromatin immunoprecipitation (ChIP), H3K36me3-specific polyclonal rabbit antibody from abcam (ab9050) was used. For a detailed protocol, see Kowalik et al., 2015.
For multiplex ChIP sequencing, samples were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L) and NEBNext Multiplex Oligos for Illumina (E7600S).


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 1, H3K36me3


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 1, H3 total

extract_protocol:
Exponentially growing S. pombe cell culture (50ml YES, OD = 1) was fixed with 1% formaldehyde and lysed. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol. For chromatin immunoprecipitation (ChIP), histone H3-specific rabbit polyclonal antibody from Abcam (ab1791) was used. For a detailed protocol, see Kowalik et al., 2015.
For multiplex ChIP sequencing, samples were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L) and NEBNext Multiplex Oligos for Illumina (E7600S).


title: ChIPseq of paf1+ ade6+, replicate 1, H3K36me3


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 3, input


title: ChIPseq of paf1+ ade6+, replicate 1, H3 total


title: ChIPseq of paf1+ ade6+imp, replicate 1, input


title: ChIPseq of paf1+ ade6+imp, replicate 1, H3 total


title: ChIPseq of paf1+ ade6+imp, replicate 3, input


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 2, input


title: ChIPseq of paf1+ ade6+, replicate 3, input


title: ChIPseq of paf1+ ade6+imp, replicate 2, input


title: ChIPseq of paf1+ ade6+imp, replicate 3, Pol II


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 3, Pol II


title: ChIPseq of paf1+ ade6+, replicate 2, input


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 2, Pol II


title: ChIPseq of paf1+ ade6+imp, replicate 2, Pol II


title: ChIPseq of paf1+ ade6+, replicate 2, Pol II


title: KO iNKT

city: Adelaide

first: Damon

middle: John

last: Tumes

state: South Australia

address: North Terrace

department: Centre for Cancer Biology

institute: University of South Australia

data_processing:
Reads were aligned using Bowtie 2 (version 2.0.0) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) were calculated using Cufflinks (version 2.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is supplied as text files and data is expressed as fragments per kilobase of exon per million mapped reads (FPKM)

source_name: Ezh2fl/fl CD4-Cre

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) and RNA was extracted from the aqueous phase (after addition of chloroform) with Picopure columns.
TruSeq RNA Sample Prep Kit v2 (Illumina) was used for cDNA library construction, according to the manufacturer's protocol.

treatment_protocol: Cells were sorted by fluorescence activated cell sorting. Invariant NKT cells were sorted using antibodies for T cell receptor beta and PBS-57-loaded CD1d tetramers. CD44hi CD4+ T cells were sorted using antibodies for T cell receptor beta, CD44 and CD4.

tag: strain background

value: Ezh2fl/fl CD4-Cre

value: Spleen

value: invariant natural killer T cells


title: WT CD44hi

source_name: WT

value: WT

value: CD44-high CD4+ T cells


title: KO CD44hi


title: WT iNKT


title: ChIPseq of paf1+ ade6+, replicate 3, Pol II

tag: strain


title: ChIPseq of paf1+ ade6+imp, replicate 3, H3K36me3


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 3, H3K36me3


title: ChIPseq of paf1+ ade6+imp, replicate 2, H3K36me3


title: brain mononuclear cell sample from CD47 null mice

city: Maebashi

first: Hiroshi

last: Ohnishi

state: Gunma

address: 3-39-22 Showa-machi

department: Department of Laboratory Sciences

institute: Gunma University Graduate School of Health Sciences

description: Gene expression data from CD47 null mouse brain mononuclear cells

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45˚C on the GeneChip Mouse Genome 430 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

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

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: cells isolated from brain

label_protocol: Total RNAs from seven (wild-type) and six (CD47 knockout) different genotype-matched animals were pooled and labelled. Biotinylated cRNA were synthesized by Ovation Pico WTA systemV2 (NuGEN, San Carlos, CA) and Encore Biotin Module (NuGEN) from 20 ng of total RNA prepared from the brain mononuclear cells.

growth_protocol: Mice were housed in an air-conditioned room under specific pathogen–free conditions with a 12-h-light, 12-h-dark cycle.

extract_protocol: Total RNAs were prepared from brain mononuclear cells by the use of Sepasol RNA I (Nacalai Tesque) and an RNeasy Mini kit (Qiagen, Hilden, Germany). Extraction and purification of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Whole brains were dissected from genotype-matched male mice euthanised by cervical dislocation after deep anaesthesia. Whole brain tissues were rinsed in ice-cold Hank’s Balanced Salt Solution (HBSS; Gibco, Grand Island, NY) and then homogenised in HBSS containing collagenase type 2 (37.5 U/ml; Worthington) and DNase I (45 U/ml; Sigma). Homogenates were then incubated at 37°C for 30 min, gently triturated with a Pasteur pipette, and incubated at 37°C for 10 min. Undigested material was removed by filtration through a 70-μm cell strainer (BD Biosciences), and the remaining cells were centrifuged at 1,100 ×g for 5 min at 18°C. Collected cells were then suspended in 8 ml of 1×HBSS containing 70% Percoll (GE Healthcare Life Science, Uppsala, Sweden), and then 4–5 ml of each was placed into a 15 ml tube. Cell suspensions were then overlaid consecutively with 4 ml HBSS containing 37% Percoll and 1 ml PBS. The resulting gradient was centrifuged at 200 ×g for 40 min at 18°C, after which cells at the interface of the bottom 2 layers (70%/37%) were collected as brain mononuclear cells.

tag: tissue

value: brain mononuclear cells

value: CD47 null

value: 12-16 weeks of age

value: male


title: synovium, CAIA+MA, biological rep5

city: Atsugi

first: Kyoko

last: Shimazu

state: Kanagawa

address: 5-1-3 Midorigaoka

department: Innovation Center

institute: Nippon Flour Mills Co., Ltd.

description: Gene expression data from synovium in CAIA mouse administrated Maslinic acid.

hyb_protocol: The biotinylated cRNA was then fragmented and hybridized to a GeneChip Mouse genome 430 2.0 Array (Thermo Fisher Scientific) at 45°C for 16 h.

scan_protocol: The array was washed and stained using a GeneChip Fluidics Station 450 (Thermo Fisher Scientific). Fluorescence signals were scanned using a GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The Affymetrix GeneChip Command Console program (Thermo Fisher Scientific) was used to convert the array images into intensity values for each probe (CEL files).The CEL files were normalized using the distribution free weighted method (DFW) in the statistical packages R (version 3.2.1 or 3.2.2) and Bioconductor (version 3.2) . A total of 5044 probe sets with NetAffx (ver. 2014/10) annotation grade E or R were excluded from the subsequent analyses.

source_name: synovium, CAIA+MA

label_protocol: The cDNA was synthesized from 100 ng of purified total RNA, and biotinylated cRNA was transcribed using T7 RNA polymerase and purified using the GeneChip 3’IVT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: Five-week-old male DBA/1J mice were housed under conventional conditions (24°C ± 1°C, 50% ± 10% relative humidity with a 12 h light/dark cycle). The mice were fed the AIN-93G diet, where fat is provided by corn instead of soy, and were provided ad libitum access to the diet and water for 24 h.

extract_protocol: The left hind legs were collected, treated with RNAlater solution (Thermo Fisher Scientific Inc., Waltham, MA, USA), stored at 4°C overnight, and then removed from the reagent and stored at -80°C. Synoviums were collected from the legs by cleaning of the surrounding muscle and skin, and total RNA was isolated using Isogen reagent (Nippon Gene Co., Ltd., Tokyo, Japan) and then purified using the RNeasy Mini Kit (Qiagen K.K., Tokyo, Japan)

treatment_protocol: After a week of acclimatization, the mice were divided into three groups: untreated (CT), CAIA (CA), and CAIA plus MA treatment (CA + MA). MA was suspended in corn oil and orally administered to CA + MA mice daily at a dose of 200 mg/kg of body weight. The other two groups were administrated corn oil instead of MA. CAIA was induced by intraperitoneal injection with 1 mg of a type II collagen mAb (Chondrex, Inc., Redmond, WA, USA) on day 8 and 25 µg of LPS (Chondrex) on day 11. Mice were sacrificed on day 12.

value: synovium

value: 8 weeks


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 2, H3K36me3


title: ChIPseq of paf1+ ade6+, replicate 3, H3K36me3


title: brain mononuclear cell sample from wild-type mice

description: Gene expression data from wild-type mouse brain mononuclear cells

value: wild-type

value: 10-15 weeks of age


title: synovium, CAIA+MA, biological rep2


title: synovium, CAIA+MA, biological rep4


title: ChIPseq of paf1+ ade6+, replicate 2, H3K36me3


title: synovium, CAIA+MA, biological rep3


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 3, H3 total

value: h-  leu1-32 ura4-D18 ade6-M210 trp1+::ade6si3 paf1-Q264Stop::kanMX


title: ERG_Input_HUVEC

city: London

first: Graeme

middle: Miles

last: Birdsey

address: Hammersmith Hospital, Du Cane Road

department: National Heart and Lung Institute

institute: Imperial College London

data_processing:
ChIP-seq reads were identified using Illumina’s Genome Analyzer 2.
ChIP-seq reads were aligned with Bowtie2 to the hg19 reference genome.
Only tags that map uniquely, with no more than 2 mismatches and pass quality control filtering are used subsequently.
Bigwig generated using bedGraphToBigWig from UCSC.
Peak calling was performed with MACS2 using default settings.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bedgraph: bedGraph files.

source_name: human umbilical vein endothelial cells

growth_protocol: Cells were seeded in pre-coated culture dishes with 1% gelatin and cultured in commercial EGM2 media from Lonza.

extract_protocol:
Fixed whole cell lysate was sheared by sonication and subsequently incubated with the ERG antibody to isolate bound DNA fragments.
Libraries were prepared with TruSeq ChIP Sample Prep Kit (Illumina).

treatment_protocol: Untreated

value: Pooled HUVEC

tag: passage

value: 4 to 6

tag: treatment

value: control

tag: chip antibody


title: synovium, CAIA, biological rep5

description: Gene expression data from synovium in CAIA mouse

source_name: synovium, CAIA

tag: age


title: ChIPseq of paf1-Q264Stop ade6+imp, replicate 2, H3 total

tag: genotype

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6+imp paf1-sms8::kanR


title: white matter sample from wild-type mice

description: Gene expression data from wild-type mouse white matter

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on the GeneChip Mouse Genome 430 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

source_name: brain white matter

label_protocol: Total RNAs from four (wild-type) and five (CD47 knockout) different genotype-matched animals were pooled and labelled. Biotinylated cRNA were synthesized by GeneChip 3' IVT Expression Kit（Affymetrix) from 250 ng of the pooled total RNA sample according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNAs were prepared from the tissues by the use of Sepasol RNA I (Nacalai Tesque) and an RNeasy Mini kit (Qiagen, Hilden, Germany). Extraction and purification of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues were dissected from genotype-matched male mice euthanised by cervical dislocation after deep anaesthesia. Tissues were rinsed with PBS, frozen in liquid nitorgen, and then stored in deep freezer (-80°C ) until the RNA extraction.

value: optic nerve and optic tract

value: 13-15 weeks of age


title: synovium, CAIA, biological rep4


title: ChIPseq of paf1+ ade6+imp, replicate 3, H3 total

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6si3

value: h- leu1-32 ura4-D18 ade6-M210 trp1+::ade6+imp


title: ERG_HUVEC

tag: cell type

value: ERG (sc-354X, Santa Cruz Biotechnology)


title: synovium, CAIA, biological rep1

tag: gender


title: ChIPseq of paf1+ ade6+, replicate 3, H3 total


title: ChIPseq of paf1+ ade6+imp, replicate 2, H3 total