title: F3 sample 238

value: F3 eQTL population sample 238

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 239

status: Public on Jul 14 2023

type: SRA

city: Gent

first: Marilou

last: Vandenhole

address: Coupure links 653

department: Department of Plants and Crops

country: Belgium

institute: UGent

library_source: transcriptomic

data_processing:
Reads were aligned to the genome with STAR (version 2.7.3a)
BAM files were sorted with samtools (version 1.9).
Raw read counts were obtained with htseq-count (version 2.0.1) using the Tetranychus_urticae_2022_12 genome annotation.
Assembly: Bulk segregant analysis scaffolded Tetranychus urticae reference genome reported by Wybouw et al. 2019 (GENETICS; 211: 1409–1427: doi: 10.1534/genetics.118.301803).
Supplementary files format and content: Processed data files consist of raw read counts per sample (from htseq-count output).

molecule: total RNA

organism: Tetranychus urticae

source_name: whole organism

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using IlluminaTruseq stranded mRNA library prep (carried out at Fasteris, Switzerland)

tag: tissue

value: whole organism

tag: genotype

value: F3 eQTL population sample 239

tag: treatment


title: F3 sample 236

value: F3 eQTL population sample 236


title: F3 sample 235

value: F3 eQTL population sample 235


title: F3 sample 234

value: F3 eQTL population sample 234


title: F3 sample 233

value: F3 eQTL population sample 233


title: F3 sample 228

value: F3 eQTL population sample 228


title: F3 sample 227

value: F3 eQTL population sample 227


title: F3 sample 230

value: F3 eQTL population sample 230


title: F3 sample 232

value: F3 eQTL population sample 232


title: F3 sample 229

value: F3 eQTL population sample 229


title: F3 sample 231

value: F3 eQTL population sample 231


title: F3 sample 226

value: F3 eQTL population sample 226


title: F3 sample 275

value: F3 eQTL population sample 275


title: F3 sample 223

value: F3 eQTL population sample 223


title: F3 sample 224

value: F3 eQTL population sample 224


title: F3 sample 222

value: F3 eQTL population sample 222

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 220

value: whole organism

value: F3 eQTL population sample 220


title: F3 sample 221

value: F3 eQTL population sample 221


title: F3 sample 216

value: F3 eQTL population sample 216


title: F3 sample 214

value: F3 eQTL population sample 214


title: F3 sample 218

value: F3 eQTL population sample 218


title: F3 sample 215

value: F3 eQTL population sample 215


title: F3 sample 217

value: F3 eQTL population sample 217


title: F3 sample 212

value: F3 eQTL population sample 212


title: F3 sample 207

value: F3 eQTL population sample 207


title: F3 sample 211

value: F3 eQTL population sample 211


title: F3 sample 213

value: F3 eQTL population sample 213


title: F3 sample 208

value: F3 eQTL population sample 208


title: F3 sample 206

value: F3 eQTL population sample 206


title: F3 sample 210

value: F3 eQTL population sample 210


title: F3 sample 205

value: F3 eQTL population sample 205


title: F3 sample 209

value: F3 eQTL population sample 209

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 204

value: whole organism

value: F3 eQTL population sample 204


title: F3 sample 202

value: F3 eQTL population sample 202


title: F3 sample 199

value: F3 eQTL population sample 199


title: F3 sample 200

value: F3 eQTL population sample 200


title: F3 sample 225

value: F3 eQTL population sample 225


title: F3 sample 198

value: F3 eQTL population sample 198


title: F3 sample 197

value: F3 eQTL population sample 197


title: F3 sample 201

value: F3 eQTL population sample 201


title: F3 sample 196

value: F3 eQTL population sample 196


title: F3 sample 194

value: F3 eQTL population sample 194


title: F3 sample 219

value: F3 eQTL population sample 219


title: F3 sample 195

value: F3 eQTL population sample 195


title: F3 sample 193

value: F3 eQTL population sample 193


title: F3 sample 191

value: F3 eQTL population sample 191


title: F3 sample 189

value: F3 eQTL population sample 189


title: F3 sample 187

value: F3 eQTL population sample 187

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 186

value: whole organism

value: F3 eQTL population sample 186


title: F3 sample 185

value: F3 eQTL population sample 185


title: F3 sample 190

value: F3 eQTL population sample 190


title: F3 sample 184

value: F3 eQTL population sample 184


title: F3 sample 203

value: F3 eQTL population sample 203


title: F3 sample 182

value: F3 eQTL population sample 182


title: F3 sample 183

value: F3 eQTL population sample 183


title: F3 sample 181

value: F3 eQTL population sample 181


title: F3 sample 179

value: F3 eQTL population sample 179


title: F3 sample 180

value: F3 eQTL population sample 180


title: F3 sample 178

value: F3 eQTL population sample 178


title: F3 sample 176

value: F3 eQTL population sample 176


title: F3 sample 171

value: F3 eQTL population sample 171


title: F3 sample 172

value: F3 eQTL population sample 172


title: F3 sample 175

value: F3 eQTL population sample 175


title: F3 sample 177

value: F3 eQTL population sample 177

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 173

value: whole organism

value: F3 eQTL population sample 173


title: F3 sample 174

value: F3 eQTL population sample 174


title: F3 sample 192

value: F3 eQTL population sample 192


title: F3 sample 170

value: F3 eQTL population sample 170


title: F3 sample 166

value: F3 eQTL population sample 166


title: F3 sample 168

value: F3 eQTL population sample 168


title: F3 sample 169

value: F3 eQTL population sample 169


title: F3 sample 165

value: F3 eQTL population sample 165


title: F3 sample 188

value: F3 eQTL population sample 188


title: F3 sample 167

value: F3 eQTL population sample 167


title: F3 sample 163

value: F3 eQTL population sample 163


title: F3 sample 164

value: F3 eQTL population sample 164


title: F3 sample 160

value: F3 eQTL population sample 160


title: F3 sample 159

value: F3 eQTL population sample 159


title: F3 sample 157

value: F3 eQTL population sample 157


title: F3 sample 158

value: F3 eQTL population sample 158

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 162

value: whole organism

value: F3 eQTL population sample 162


title: F3 sample 161

value: F3 eQTL population sample 161


title: F3 sample 155

value: F3 eQTL population sample 155


title: F3 sample 156

value: F3 eQTL population sample 156


title: F3 sample 152

value: F3 eQTL population sample 152


title: F3 sample 151

value: F3 eQTL population sample 151


title: F3 sample 153

value: F3 eQTL population sample 153


title: F3 sample 148

value: F3 eQTL population sample 148


title: F3 sample 149

value: F3 eQTL population sample 149


title: F3 sample 146

value: F3 eQTL population sample 146


title: F3 sample 145

value: F3 eQTL population sample 145


title: F3 sample 144

value: F3 eQTL population sample 144


title: F3 sample 142

value: F3 eQTL population sample 142


title: F3 sample 139

value: F3 eQTL population sample 139


title: F3 sample 143

value: F3 eQTL population sample 143


title: F3 sample 140

value: F3 eQTL population sample 140

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 138

value: whole organism

value: F3 eQTL population sample 138


title: F3 sample 147

value: F3 eQTL population sample 147


title: F3 sample 137

value: F3 eQTL population sample 137


title: F3 sample 136

value: F3 eQTL population sample 136


title: F3 sample 141

value: F3 eQTL population sample 141


title: F3 sample 135

value: F3 eQTL population sample 135


title: F3 sample 134

value: F3 eQTL population sample 134


title: F3 sample 127

value: F3 eQTL population sample 127


title: F3 sample 131

value: F3 eQTL population sample 131


title: F3 sample 150

value: F3 eQTL population sample 150


title: F3 sample 132

value: F3 eQTL population sample 132


title: F3 sample 130

value: F3 eQTL population sample 130


title: F3 sample 125

value: F3 eQTL population sample 125


title: F3 sample 126

value: F3 eQTL population sample 126


title: F3 sample 154

value: F3 eQTL population sample 154


title: F3 sample 120

value: F3 eQTL population sample 120

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 124

value: whole organism

value: F3 eQTL population sample 124


title: F3 sample 122

value: F3 eQTL population sample 122


title: F3 sample 121

value: F3 eQTL population sample 121


title: F3 sample 133

value: F3 eQTL population sample 133


title: F3 sample 129

value: F3 eQTL population sample 129


title: F3 sample 118

value: F3 eQTL population sample 118


title: F3 sample 112

value: F3 eQTL population sample 112


title: F3 sample 111

value: F3 eQTL population sample 111


title: F3 sample 113

value: F3 eQTL population sample 113


title: F3 sample 114

value: F3 eQTL population sample 114


title: F3 sample 128

value: F3 eQTL population sample 128


title: F3 sample 109

value: F3 eQTL population sample 109


title: F3 sample 108

value: F3 eQTL population sample 108


title: F3 sample 119

value: F3 eQTL population sample 119


title: F3 sample 115

value: F3 eQTL population sample 115


title: F3 sample 106

value: F3 eQTL population sample 106

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 116

value: whole organism

value: F3 eQTL population sample 116


title: F3 sample 117

value: F3 eQTL population sample 117


title: F3 sample 105

value: F3 eQTL population sample 105


title: F3 sample 104

value: F3 eQTL population sample 104


title: F3 sample 123

value: F3 eQTL population sample 123


title: F3 sample 102

value: F3 eQTL population sample 102


title: F3 sample 103

value: F3 eQTL population sample 103


title: F3 sample 101

value: F3 eQTL population sample 101


title: F3 sample 99

value: F3 eQTL population sample 99


title: F3 sample 100

value: F3 eQTL population sample 100


title: F3 sample 98

value: F3 eQTL population sample 98


title: F3 sample 97

value: F3 eQTL population sample 97


title: F3 sample 110

value: F3 eQTL population sample 110


title: F3 sample 96

value: F3 eQTL population sample 96


title: F3 sample 93

value: F3 eQTL population sample 93


title: F3 sample 94

value: F3 eQTL population sample 94

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 107

value: whole organism

value: F3 eQTL population sample 107


title: F3 sample 95

value: F3 eQTL population sample 95


title: F3 sample 92

value: F3 eQTL population sample 92


title: F3 sample 91

value: F3 eQTL population sample 91


title: F3 sample 90

value: F3 eQTL population sample 90


title: F3 sample 83

value: F3 eQTL population sample 83


title: F3 sample 85

value: F3 eQTL population sample 85


title: F3 sample 89

value: F3 eQTL population sample 89


title: F3 sample 79

value: F3 eQTL population sample 79


title: F3 sample 80

value: F3 eQTL population sample 80


title: F3 sample 87

value: F3 eQTL population sample 87


title: F3 sample 86

value: F3 eQTL population sample 86


title: F3 sample 82

value: F3 eQTL population sample 82


title: F3 sample 81

value: F3 eQTL population sample 81


title: F3 sample 77

value: F3 eQTL population sample 77


title: F3 sample 76

value: F3 eQTL population sample 76

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 88

value: whole organism

value: F3 eQTL population sample 88


title: F3 sample 72

value: F3 eQTL population sample 72


title: F3 sample 78

value: F3 eQTL population sample 78


title: F3 sample 75

value: F3 eQTL population sample 75


title: F3 sample 73

value: F3 eQTL population sample 73


title: F3 sample 71

value: F3 eQTL population sample 71


title: F3 sample 70

value: F3 eQTL population sample 70


title: F3 sample 69

value: F3 eQTL population sample 69


title: F3 sample 65

value: F3 eQTL population sample 65


title: F3 sample 68

value: F3 eQTL population sample 68


title: F3 sample 66

value: F3 eQTL population sample 66


title: F3 sample 67

value: F3 eQTL population sample 67


title: F3 sample 64

value: F3 eQTL population sample 64


title: F3 sample 62

value: F3 eQTL population sample 62


title: F3 sample 61

value: F3 eQTL population sample 61


title: F3 sample 58

value: F3 eQTL population sample 58

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 57

value: whole organism

value: F3 eQTL population sample 57


title: F3 sample 59

value: F3 eQTL population sample 59


title: F3 sample 53

value: F3 eQTL population sample 53


title: F3 sample 49

value: F3 eQTL population sample 49


title: F3 sample 54

value: F3 eQTL population sample 54


title: F3 sample 51

value: F3 eQTL population sample 51


title: F3 sample 55

value: F3 eQTL population sample 55


title: F3 sample 56

value: F3 eQTL population sample 56


title: F3 sample 50

value: F3 eQTL population sample 50


title: F3 sample 52

value: F3 eQTL population sample 52


title: F3 sample 47

value: F3 eQTL population sample 47


title: F3 sample 48

value: F3 eQTL population sample 48


title: F3 sample 46

value: F3 eQTL population sample 46


title: F3 sample 43

value: F3 eQTL population sample 43


title: F3 sample 42

value: F3 eQTL population sample 42


title: F3 sample 74

value: F3 eQTL population sample 74

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 45

value: whole organism

value: F3 eQTL population sample 45


title: F3 sample 38

value: F3 eQTL population sample 38


title: F3 sample 41

value: F3 eQTL population sample 41


title: F3 sample 40

value: F3 eQTL population sample 40


title: F3 sample 39

value: F3 eQTL population sample 39


title: F3 sample 37

value: F3 eQTL population sample 37


title: F3 sample 63

value: F3 eQTL population sample 63


title: F3 sample 60

value: F3 eQTL population sample 60


title: F3 sample 36

value: F3 eQTL population sample 36


title: F3 sample 35

value: F3 eQTL population sample 35


title: F3 sample 34

value: F3 eQTL population sample 34


title: F3 sample 32

value: F3 eQTL population sample 32


title: F3 sample 44

value: F3 eQTL population sample 44


title: F3 sample 33

value: F3 eQTL population sample 33


title: F3 sample 30

value: F3 eQTL population sample 30


title: F3 sample 25

value: F3 eQTL population sample 25

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 27

value: whole organism

value: F3 eQTL population sample 27


title: F3 sample 26

value: F3 eQTL population sample 26


title: F3 sample 31

value: F3 eQTL population sample 31


title: F3 sample 29

value: F3 eQTL population sample 29


title: F3 sample 23

value: F3 eQTL population sample 23


title: F3 sample 21

value: F3 eQTL population sample 21


title: F3 sample 20

value: F3 eQTL population sample 20


title: F3 sample 19

value: F3 eQTL population sample 19


title: F3 sample 16

value: F3 eQTL population sample 16


title: F3 sample 17

value: F3 eQTL population sample 17


title: F3 sample 14

value: F3 eQTL population sample 14


title: F3 sample 15

value: F3 eQTL population sample 15


title: F3 sample 18

value: F3 eQTL population sample 18


title: F3 sample 12

value: F3 eQTL population sample 12


title: F3 sample 9

value: F3 eQTL population sample 9


title: F3 sample 10

value: F3 eQTL population sample 10

value: Grown on bean (Phaseolus vulgaris) as host plant


title: F3 sample 8

value: whole organism

value: F3 eQTL population sample 8


title: F3 sample 11

value: F3 eQTL population sample 11


title: F3 sample 6

value: F3 eQTL population sample 6


title: F3 sample 7

value: F3 eQTL population sample 7


title: F3 sample 28

value: F3 eQTL population sample 28


title: F3 sample 24

value: F3 eQTL population sample 24


title: F3 sample 3

value: F3 eQTL population sample 3


title: F3 sample 4

value: F3 eQTL population sample 4


title: F3 sample 5

value: F3 eQTL population sample 5


title: F3 sample 22

value: F3 eQTL population sample 22


title: DAOY si-circ_63706 rep1

city: St. Petersburg

first: Ranjan

middle: J.

last: Perera

state: FL

address: 600 Fifth Street S.

department: Department of Oncology,

country: USA

institute: Johns Hopkins University School of Medicine

data_processing:
Illumina Truseq adapters and polyA/polyT sequences were trimmed using Cutadapt version 2.3.
Trimmed reads were aligned to human genome version hg38 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 adopting alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
RSEM version 1.3.1 was used to obtain gene level estimated counts and transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes TPM (Transcripts Per Million) values for each sample.

organism: Homo sapiens

source_name: DAOY

growth_protocol: DAOY cells were cultured in DMEM with 10% serum and 1% glutamate/penicillin/streptomycin.

extract_protocol:
Total RNA was prepared from cell line and orthotopic xenograft using a Direct-zol RNA Miniprep kit (Zymo Research). The quality of RNA was determined with the Agilent 2100 Bioanalyzer Nano Assay (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with 20 nM siRNA targeting each gene or control non-targeting siRNA (negative control siRNA) (AM4611, Applied Biosystems, Foster City, CA) for 48 h using Lipofectamine RNAiMAX (Thermo Fisher Scientific).

tag: cell line

value: DAOY

tag: cell type

value: Human medulloblastoma cell line


title: DAOY si-circ_63706 rep2


title: F3 sample 2

value: F3 eQTL population sample 2


title: DAOY si-NC rep2

value: si-NC


title: DAOY si-circ_63706 rep3


title: F3 sample 13

value: F3 eQTL population sample 13


title: input,enhancers, olig-repSTARR-seq,Rps12, rep2

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

description:
150bp
olig_repSTARR_seq_Rps12_raw_and_norm_counts.tsv

data_processing:
Paired-end sequencing reads were demultiplexed using the standard illumina i5 and i7  indexes and mapped Drosophila Melanogaster (dm3) genome and subsequently to the artificial Drosophila Pseudoobscura BAC genome (spike-in), using Bowtie v.1.2.2. PE 36bp reads with a maximal insert size of 2 kb and up to three mismatches were kept. The olig screens were demultiplexed and mapped to a synthetic reference genome containing the 249bp sequences with both wildtype and mutant enhancers, only exact matches were kept and subsequently to the artificial Drosophila Pseudoobscura BAC genome (spike-in).
For the genome-wide screen enhancers were detected macs25 callpeak using –nomodel and –fe-cutoff 4 as additional parameters. Enhancers were called on all 12 samples separately, and their genomic coordinates were merged into one enhancer backbone file. Rep-STARR-seq reads falling into these enhancers were quantified for every sample, obtaining a raw counts matrix. The raw counts matrix was then normalized using the spike-in normalization factors and the normalized matrix was used to perform differential enhancer activity analysis.
We quantified the differences in enhancer activites between the Gal4-GFP (control) samples and our Gal4-CoRs using EdgeR with two biological replicates.
Assembly: For the genome-wide screens: BDGP R5/dm3 For the disigned oligo library we generated a custom assembly
Supplementary files format and content: Spike-in normalized reads matrix for all samples
Supplementary files format and content: genomic coverage of rep-STARR-seq for every sample in bigWig format

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured in Schneider’s Medium (Gibco; cat. no. 21720-024) supplemented with 10% heat inactivated FBS (Sigma; cat. no. F7524)

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy Mini Prep Kit.
mRNAs were enriched with Dynabeads Oligo-dT25 (Invitrogen), followed by a DNA digest with Turbo DNase (Ambion).
mRNAs were cleaned up with AMPure XP DNA beads (Agencourt; ratio sample/beads 1:1.8) and then reverse transcribed with Superscript III (50°C for 60 min, 70°C for 15 min; Invitrogen 18080085) and a primer binding within the poly-A site of candidate mRNAs (reverse_transcription_rv: CTCATCAATGTATCTTATCATGTCTG).
Next, RNA was digested with Rnase A (Thermo) for 1 h at 37°C, followed by bead cleanup of the remaining DNA (ratio sample/beads 1:1.4).
All subsequent PCR reactions were prepared using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2602). A junction PCR was performed with a primer binding only in correctly spliced candidate mRNAs junction_primer_fw: AAGCCACCATGGAAAAG*G*C*C*A*T, junction_primer_rv: TATCATGTCTGCTCGAAG*C*G*G (98°C for 45s, (98°C for 15s,  65°C for 30 s, 72°C for 45 s)X15, followed by bead cleanup (ratio sample/beads 1:0.9).
Sequencing ready PCR: candidate fragments were amplified (98°C 45 s, followed by 6-15 cycles, 98°C 15 s, 65°C 30 s, 72°C 30s) with the following primers: i5: aatgatacggcgaccaccgagatctacacXXXXXXXXacactctttccctacacgacgctcttccgatct (XXXXXXXX indicates the position of the index sequence for NGS) and the reverse primer TruSeq IDX with approptiate barcode for demultiplexing individual samples. PCR products were purified by Agencourt AMPure XP DNA beads (ratio sample/beads 1:0.8), pooled, and subjected to NGS.
After another beads cleanup we measured each sample and made and equimolar mixture that was subjected to sequencing

treatment_protocol:
per OC-400, 200million Drosophila S2 cell lines were transfected with a pre-mixed rep-STARR-seq library (20ug) + Gal4-CoR expression vector (20ug) + spike-in (0.2ug). 2 OC 400 were used per gw rep-STARR-seq sample and one OC 400 was used for the BAC and designed oligonucleotide libraries.
24h after transfection, the cells were havested and the same samples pooled to then be processed like regular STARR-seq (Arnold et al., 2013)

tag: enhancer library

value: designed 249bp enhancers

tag: core-promoter

value: PCR amplyfied the enhancers from the cloned rep-STARR-seq oligo library (used for performing the screens


title: DAOY si-NC rep1


title: input,enhancers, olig-repSTARR-seq, DSCP, rep2

description:
150bp
olig_repSTARR_seq_DSCP_raw_and_norm_counts.tsv

value: DSCP


title: olig-repSTARR-seq, Rps12, Sin3A, rep2

value: Schneider S2

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: olig-repSTARR-seq, Rps12, Rbf2, rep2


title: Individual B, clone 4, passage 39, adipogenic medium

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

data_processing:
Basecalling was performed by Illumina CASAVA.
Reads were aligned against the Human Genome assembly GRCh38 using STAR with default settings (version 2.5).
HTSeq-count (version 0.9) was used to generate raw gene counts
Assembly: GRCh38
Supplementary files format and content: Matrix table (tab delimited) with raw gene counts for every gene and every sample

source_name: human induced pluripotent stem cell derived cardiomyocytes

growth_protocol: Purified hiPSC-Cms were maintained in culture for additional 30 days in either basal or adipogenic medium in Matrigel coated 12-well plates. Basal medium was composed of High Glucose DMEM, 2% Hyclone Fetal Bovine Defined, 1% non-essential Amino Acids, 1% Penicillin/Streptomycin and 0.09% beta-mercapto-ethanol.

extract_protocol:
Total RNA was extracted from CStCs using Direct-zol RNA Kit (Zymo Research), according to manufacturer’s instructions. The concentration and purity of the isolated total RNA was assessed by Nanodrop and Qubit, while the integrity was evaluated using the Experion RNA StdSens Analysis Kit (Bio- Rad). High quality RNA, with A260/A280 > 1.8, A260/A230 ranging from 1.8 up to 2.02 and RQI > 9.5, were used for subsequent library preparation.
500 ng of RNA for each sample were used for the preparations of the libraries, using the QuantSeq 3' mRNA-Seq Library Prep FWD (Lexogen). Samples were sequenced using the platform HiSeq2500, following the protocol SR1000.

treatment_protocol: Adipogenic differentiation was stimulated using an adipogenic medium composed of the basal medium supplemented with 50 ug/ml Insulin, 0.5 uM Dexamethasone, 0.25 mM 3-isobutyl-1 methylxanthine, 200 uM Indomethacin and 4 uM Rosiglitazone.

tag: individual

value: CTR (I-2)

tag: clone

tag: phenotype

value: CTRL

value: adipogenic medium


title: olig-repSTARR-seq, Rps12, Rbf2, rep1


title: olig-repSTARR-seq, Rps12, Rbf, rep1


title: Individual G, clone 1, passage 17, adipogenic medium

value: human induced pluripotent stem cell derived cardiomyocytes

value: ASY


title: Individual D, clone 3, passage 33, adipogenic medium


title: Individual B, clone 5, passage 32, basal medium

value: basal medium


title: Individual D, clone 3, passage 31, adipogenic medium


title: Individual E, clone 8, passage 26, adipogenic medium

value: ACM


title: olig-repSTARR-seq, Rps12, CtBP, rep1


title: olig-repSTARR-seq, Rps12, CoRest, rep2


title: F3 sample 1

value: whole organism

value: F3 eQTL population sample 1

value: Grown on bean (Phaseolus vulgaris) as host plant


title: Individual C, clone 2, passage 28, adipogenic medium


title: olig-repSTARR-seq, Rps12, CoRest, rep1


title: input,enhancers, olig-repSTARR-seq, Rps12, rep1


title: olig-repSTARR-seq, Rps12, GFP, rep2


title: Individual A, clone 8, passage 30, adipogenic medium


title: olig-repSTARR-seq, Rps12, GFP, rep1


title: olig-repSTARR-seq, Rps12, Sin3A, rep1


title: input,enhancers, olig-repSTARR-seq, DSCP, rep1


title: Individual B, clone 4, passage 39, basal medium


title: olig-repSTARR-seq, DSCP, Sin3A, rep2


title: olig-repSTARR-seq, Rps12, Rbf, rep2


title: olig-repSTARR-seq, Rps12, CtBP, rep2


title: olig-repSTARR-seq, DSCP, Rbf2, rep2


title: olig-repSTARR-seq, DSCP, Rbf2, rep1


title: Individual D, clone 3, passage 33, basal medium


title: Individual G, clone 1, passage 17, basal medium


title: Individual B, clone 5, passage 32, adipogenic medium


title: Individual E, clone 8, passage 26, basal medium


title: Individual D, clone 3, passage 31, basal medium


title: Individual C, clone 14, passage 26, adipogenic medium


title: Individual C, clone 2, passage 28, basal medium


title: olig-repSTARR-seq, DSCP, CtBP, rep2


title: Individual A, clone 5, passage 30, adipogenic medium


title: olig-repSTARR-seq, DSCP, Sin3A, rep1


title: olig-repSTARR-seq, DSCP, CtBP, rep1


title: Individual C, clone 14, passage 26, basal medium


title: olig-repSTARR-seq, DSCP, CoRest, rep1


title: olig-repSTARR-seq, DSCP, CoRest, rep2


title: Individual A, clone 8, passage 30, basal medium


title: Individual A, clone 5, passage 30, basal medium


title: olig-repSTARR-seq, DSCP, GFP, rep1


title: olig-repSTARR-seq, DSCP, GFP, rep2


title: rnaseq_581_PBS

city: New York City

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 581

data_processing:
The raw reads were trimmed with Trimmomatic [PMID: 24695404] and then mapped to human reference genome GRCh38 analysis set reference genome with the pseudoautosomal region masked on chromosome Y with the STAR aligner [PMID: 23104886]. This yielded for each sample a BAM file of mapped paired-end reads sorted by genomic coordinates. From these files, reads that mapped to multiple loci or to the mitochondrial genome were removed using samtools [PMID: 19505943] and duplicated reads were removed with PICARD. Quality control metrics were reported with phantompeakqualtools [PMID: 22955991] and Picard.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values (files count_matrix), normalized count values () and annotations of peaks (files peaks_description_38.tsv

source_name: hiPSC-derived neurons

growth_protocol: hiPSCs were reprogrammed from HFs using Cytotune Sendai viruses (ThermoFisher Scientific). hiPSC colonies were initially expanded on mEFs in hiPSC media (DMEM/F12, 20% KO-Serum Replacement (v/v), 1% (v/v) GlutaMAX, 1% (v/v) nonessential amino acids (NEAA), 55 μM β‐mercaptoethanol (β‐me) (all ThermoFisher Scientific) and 20 ng ml-1 FGF2 (R & D Systems, 233-FB-10)); individual hiPSC lines were validated as previously described [PMID:29263384]. Mycoplasma detection kit (Lonza); all cells used in this study and were found to be negative. NPCs were derived as previously described [PMID:24686136] and maintained at high density on growth factor reduced Matrigel (BD Biosciences) coated plates in NPC media (Dulbecco’s Modiﬁed Eagle Medium/Ham’s F12 Nutrient Mixture (ThermoFisher Scientific), 1x N2, 1x B27-RA (ThermoFisher Scientific) and 20 ng ml−1 FGF2 and split 1:3 every week with Accutase (Millipore, Billerica, MA, USA).

extract_protocol:
Patients with children-oset schizophrenia (COS), unaffected family members, and unrelated controls were recruited into a longitudinal study by Dr Judith Rapoport at the NIMH [23689535, 25510512]. The Rapoport laboratory generously provided fibroblasts that were reprogrammed.
ATAC-seq was performed using an established protocol [PMID:25559105] with minor modifications. Following cell lysis, iPSC-derived neuronal nuclei were stained with DAPI (Thermoscientific) and sorted using a FACSAria flow cytometer (BD Biosciences). 75,000 nuclei were used as input for each ATAC-seq reaction and the resulting libraries sequenced at the New York Genome Center as 50bp paired-end reads on a HiSeq 2500 (Illumina).    RNA was isolated from approximately density-matched plates (initially seeded with ~200,000 NPCs per well) using TRIzol (Thermo Fisher), according to the manufacturer’s instructions. The RNA Integrity Number (RIN) was determined using an RNA Nano chip (Agilent Technologies) on the Agilent 2100 Bioanalyzer. All samples have high RIN (mean ± standard deviation: 9.53 ± 0.22). 500 ng of total RNA was used as input material for library preparation using the TruSeq Stranded Total RNA Sample Prep Kit (LT) (Illumina, USA) according to manufacturer’s instructions. Individual libraries were indexed as recommended by Illumina.

treatment_protocol: At day -2, hiPSC-NPCs were seeded as 4-6x105 cells / well in a 24-well plate coated with Matrigel. At day -1, cells were transduced with rtTA (Addgene 20342), NGN2 (Addgene 99378) and gRNA (Addgene 99374) lentiviruses via spinfection. Medium was switched to non-viral medium three hours post-spinfection. At Day 0, 1 μg/ml dox was added to induce NGN2-expression. At Day 1, transduced hiPSC-NPCs were treated with corresponding antibiotics to the lentiviruses (300 ng/ml puromycin for NGN2-Puro in order to increase the purity of transduced hiPSC-NPCs. At day 11, full medium change withdrew residual dox completely.50% of the medium was replaced with fresh neuronal medium (lacking dox once every second day. At day 11, full medium change withdrew residual dox completely. At day 13, NGN2-excitatory neurons were treated with 200 nM Ara-C to reduce the proliferation of non-neuronal cells in the culture, followed by half medium change by day 17. At Day 17, Ara-C was completely withdrawn by full medium change, followed by half medium changes until the neurons were fixed or harvested day 21-24. Neurons were treated with 50nM KCl (or PBS vehicle control) for the final one or six hours prior to harvest.

tag: person id

tag: agent

value: PBS 6hr

tag: gender

value: Male

tag: ethnicity

value: White

tag: diagnosis

value: Children-onset schizophrenia

value: hiPSC-derived neurons


title: olig-repSTARR-seq, DSCP, Rbf, rep1

value: designed 249bp enhancers

value: DSCP

value: Schneider S2


title: rnaseq_690_KCl_1hr

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 690

value: KCl 1hr

value: Control


title: RNA-seq, CD8+ T cells, Slamf6+, AC484-treated, Replicate B

city: Cambridge

first: Robert

last: Manguso

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq (v2.20.0)
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Trimmed reads were quantified by pseudoalignment to mm10 using Kallisto (v0.46.0)
RNA-seq transcript counts were quantified using the tximport (v1.24.0) R package
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Subcutaneous tumours

extract_protocol:
Subcutaneous B16 tumours were implanted on the back mice. On day 19 after tumours were injected, tumors were collected, weighed and chpped before chemical and mechanical digestions with Tumour Dissociation Kit II (Myltenyi) and gentleMACS DIssociator (Myltenyi) using the m-TDK-1 program. Immune cells were isolated by density centrifugation with Lympholyte (Cederlane Labs) followed by positive selection for CD8a+ cells (Myltenyi). CD8+ cells were pooled into samples from 5-11 tumours, depending on cell counte recovered. Live cells were sorted into Tim3+ (10,000 cells) and Slamf6+ (1,000 cells) populations with two pooled samples per treatment condition. RNA was harvested using Rneasy micro kit (Qiagen). PolyA RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module
First-strand Illumina-barcoded ibraries were constructed using the NEBNext Ultra II Directional RNA Kit. During the library construction Ilumina R2 primer sequence, P7 sequences and a sample index were added.

value: Subcutaneous tumours

value: B16 melanoma

value: CD8 + Slamf6 +


title: rnaseq_581_KCl_6hr

value: KCl 6hr


title: RNA-seq, CD8+ T cells, Slamf6+, aPD1-treated, Replicate B


title: rnaseq_690_KCl_6hr


title: RNA-seq, CD8+ T cells, Slamf6+, AC484-treated, Replicate A


title: RNA-seq, CD8+ T cells, Slamf6+, Untreated, Replicate B

value: untreated


title: olig-repSTARR-seq, DSCP, Rbf, rep2

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: RNA-seq, CD8+ T cells, Slamf6+, Untreated, Replicate A


title: rnaseq_581_KCl_1hr


title: rnaseq_553_PBS

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 553


title: rnaseq_553_KCl_6hr


title: RNA-seq, CD8+ T cells, Tim3+, AC484-treated, Replicate B

value: CD8 + Tim3 +


title: RNA-seq, CD8+ T cells, Tim3+, AC484-treated, Replicate A


title: RNA-seq, CD8+ T cells, Tim3+, aPD1-treated, Replicate B


title: rnaseq_499_KCl_6hr

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 499


title: rnaseq_499_PBS

value: PBS 6hr


title: RNA-seq, CD8+ T cells, Tim3+, aPD1-treated, Replicate A


title: RNA-seq, CD8+ T cells, Tim3+, Untreated, Replicate B


title: rnaseq_553_KCl_1hr

value: Male


title: rnaseq_499_KCl_1hr

value: White


title: rnaseq_3234_PBS

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 3234

value: Indian (non-hispanic)


title: rnaseq_3234_KCl_6hr

value: hiPSC-derived neurons


title: RNA-seq, CD8+ T cells, Tim3+, Untreated, Replicate A


title: rnaseq_3234_KCl_1hr


title: B16, PTPN2/N1 DKO, AC484 + IFNg, Replicate 3

data_processing:
Read data were adapter and quality trimmed using trimmomatic v0.36
Trimmed reads were quantified by pseudoalignment to mm10 using kallisto v0.46.0
RNA-seq counts were quantified using the program tximport
Assembly: mm10
Supplementary files format and content: raw counts, tab delimited text file

source_name: melanoma tumour

growth_protocol: Control and Ptpn2/1 dual deletion B16 cells were seeded at a density of 250,000 cells per well in a 12-well plate

extract_protocol:
RNA was isolated from cell pellets using the QIAGEN RNEasy Mini kit according to the manufacturer’s instructions. PolyA RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module
First-strand Illumina-barcoded ibraries were constructed using the NEBNext Ultra II Directional RNA Kit. During the library construction Ilumina R2 primer sequence, P7 sequences and a sample index were added.

treatment_protocol: Cells were stimulated with IFNγ (10 ng ml-1), AC484 (10 µM) or both. After 24 hours, cell pellets were collected for transcriptional profiling

value: melanoma tumour

value: B16F10 melanoma

value: tumour

value: PTPN2/N1 DKO C57BL/6

tag: strain

value: CTRL


title: B16, PTPN2/N1 DKO, AC484 + IFNg, Replicate 2


title: B16, PTPN2/N1 DKO, AC484 + IFNg, Replicate 1


title: rnaseq_3130_PBS

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 3130

value: Control


title: rnaseq_3130_KCl_6hr


title: B16, PTPN2/N1 DKO, IFNg, Replicate 3


title: B16, PTPN2/N1 DKO, IFNg, Replicate 2


title: rnaseq_3084_PBS

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 3084

value: Afro-american


title: rnaseq_3130_KCl_1hr

value: KCl 1hr


title: B16, PTPN2/N1 DKO, IFNg, Replicate 1


title: rnaseq_3084_KCl_6hr

value: KCl 6hr


title: rnaseq_690_PBS


title: B16, PTPN2/N1 DKO, CTRL, Replicate 3


title: rnaseq_3084_KCl_1hr


title: B16, PTPN2/N1 DKO, CTRL, Replicate 2


title: rnaseq_2962_PBS

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 2962

value: Children-onset schizophrenia


title: B16, PTPN2/N1 DKO, CTRL, Replicate 1


title: rnaseq_2962_KCl_6hr


title: B16, PTPN2/N1 DKO, AC484, Replicate 3


title: B16, PTPN2/N1 DKO, AC484, Replicate 2


title: rnaseq_2620_PBS

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 2620


title: B16, PTPN2/N1 DKO, AC484, Replicate 1


title: rnaseq_2962_KCl_1hr


title: rnaseq_2620_KCl_6hr


title: rnaseq_2620_KCl_1hr


title: RNA-seq, CD8+ T cells, Slamf6+, aPD1-treated, Replicate A

value: Subcutaneous tumours

value: B16 melanoma

value: CD8 + Slamf6 +


title: B16, AC484 + IFNg, Replicate 2

value: WT


title: rnaseq_2513_KCl_6hr

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 2513

value: Male

value: White


title: rnaseq_2513_PBS

value: PBS 6hr

value: hiPSC-derived neurons


title: B16, AC484 + IFNg, Replicate 1

value: melanoma tumour

value: B16F10 melanoma


title: B16, IFNg, Replicate 3

value: tumour


title: B16, CTRL, Replicate 2

value: CTRL


title: B16, CTRL, Replicate 1


title: B16, IFNg, Replicate 2


title: B16, CTRL, Replicate 3


title: B16, IFNg, Replicate 1


title: B16, AC484, Replicate 3


title: rnaseq_1442_PBS

description: hiPSC-derived neurons, assay: RNA-seq, subject: Homo sapiens, treatment: 1442


title: rnaseq_1442_KCl_1hr


title: rnaseq_1442_KCl_6hr


title: atacseq_690_PBS

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 690

library_source: genomic

molecule: genomic DNA

value: Control


title: atacseq_690_KCl_1hr


title: B16, AC484, Replicate 2


title: atacseq_581_PBS

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 581


title: B16, AC484, Replicate 1


title: B16, AC484 + IFNg, Replicate 3


title: atacseq_581_KCl_6hr


title: rnaseq_2513_KCl_1hr


title: atacseq_553_KCl_6hr

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 553


title: atacseq_553_PBS


title: atacseq_553_KCl_1hr


title: atacseq_690_KCl_6hr


title: F3 sample 84

value: whole organism

value: F3 eQTL population sample 84

value: Grown on bean (Phaseolus vulgaris) as host plant


title: cSCC Kindlin-1 Nulls (mouse number 242L)

city: Edinburgh

first: Denise Giovana

last: Carrasco Gonzalez

state: --- Select One ---

address: Crewe Road, Western General Hospital Campus (ECRC)

department: ECRC

country: United Kingdom

institute: University of Edinburgh

data_processing:
RNA-Sequencing (RNA-Seq) was performed on Kin1-/- and Kin1-WT tumor samples (n = 3 tumors) using single-read sequencing on the Illumina Next-Generation Sequencing platform (via GATC Biotech, London, United Kingdom).
48 million NULL reads and 26 million WT reads respectively were mapped to the mouse mm9 reference genome using Tophat2 (Trapnell, 2013) that aligns the reads across splice junctions independently of gene annotations.
Overall alignment rates were around 30% due to variable mapping rates across the replicates in each condition, possibly due to sample quality problems.
Differential expression was analysed by cuffdiff (Trapnell, 2013) and by DESeq2 (Anders and Huber, 2010) to obtain lists of differentially expressed genes by two alternative statistical techniques.
Genes with a q value (p value adjusted for multiple testing) of less than 0.05 were considered differentially expressed, but other potentially relevant genes showing sizable fold changes were also further investigated.
Assembly: mm9
Supplementary files format and content: tsv file with raw counts for each sample
Supplementary files format and content: Compiled files (Excel) with differential expression

source_name: Tumor

extract_protocol:
Total RNA was extracted from cSCC tumors with RNeasy kit (Qiagen) according to manufacturer’s instructions.
Cluster 3.0 (C Clustering Library, version 1.54)

value: Tumor

value: Cutaneous squamous cell carcinoma (cSCC)

value: Kindlin-1 Null


title: cSCC Kindlin-1 wild type-WT cells (mouse number 238L)

value: Kindlin-1 WT


title: cSCC Kindlin-1 Nulls (mouse number 242R)


title: cSCC Kindlin-1 Nulls (mouse number 240R)


title: cSCC Kindlin-1 wild type-WT (mouse number 239R)


title: cSCC Kindlin-1 wild type-WT cells (mouse number 238R)


title: atacseq_3234_KCl_6hr

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 3234

value: KCl 6hr

value: Indian (non-hispanic)


title: atacseq_499_KCl_1hr

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 499

value: KCl 1hr

value: Male

value: White

value: Children-onset schizophrenia


title: atacseq_581_KCl_1hr

value: hiPSC-derived neurons


title: atacseq_3130_PBS

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 3130

value: PBS 6hr


title: atacseq_499_KCl_6hr


title: atacseq_3130_KCl_1hr


title: atacseq_3234_PBS


title: atacseq_3234_KCl_1hr


title: atacseq_3130_KCl_6hr


title: atacseq_3084_PBS

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 3084

value: Afro-american


title: 11ctrl

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
Cmtr1+/loxP; AlbCreERT2+/-
MD_ctrl1_D2_b1

data_processing:
For gene expression profiling the reads were sorted into individual libraries based on the barcodes and mapped either to the mouse or human transcriptome (Ensembl release 102) with STAR v2.7.10a and then the corresponding BAM files were processed by salmon v1.8.0 (salmon quant with options -l A  --validateMappings --gcBias)(Patro et al., 2017). The DESeq function of DESeq2_1.34.0 bioconductor package (Love et al., 2014) was used to obtain log2 fold changes of gene expression and the adjusted p-values. Log2 fold change of 1 and adjusted p-value 0.05 was used as a threshold for statistical significance.
Ribosome profiling libraries were mapped to rRNAs and the remaining fraction of reads was aligned by STAR v2.7.10a (--alignEndsType EndToEnd) either to the mouse or human genome (Ensembl release 102). Metagene analysis of the ribosome fragments phasing was done by metagene count function of the plastid package v0.6.1. RiboCode toolkit v1.2.13 was used to detect longest translated ORFs (-l yes). Count tables of the longest translated ORFs for further differential translation efficiency analysis were made by ORFcount program from the RiboCode toolkit. First and last 10 translated codons were masked from counting (-f 10 -l 10). Hidden noise was inferred by sva bioconductor package and 2 surrogate variables (SV1 and SV2) were included into model. Differential translational efficiency analysis was done by DESeq function from DESeq2 bioconductor package with the following parameters specified: test=”LRT”, reduced = ~SV1 + SV2 + assay + condition. Model design was as follows: ~SV1 + SV2 + assay + condition + assay:condition.
Assembly: Ensembl release 102
Supplementary files format and content: RNA-seq and ribosome profiling supplementary files contain tables with DESeq2-specific differential gene expression parameters (baseMean, log2 fold change, adjusted p-value, etc.).

source_name: Liver

growth_protocol: The Cmtr1 floxed mouse was generated at the Transgenic Mouse Facility of University of Geneva, while the Cmtr1 and Cmtr2 knockout models were generated by the Knockout Mouse Project (KOMP). The Alb-CreERT2 mouse  specifically expresses using the Albumin (Alb) promoter the tamoxifen-inducible CreERT2 in hepatocytes. As described by the authors , a cassette consisting of an IRES with coding sequence for Cre-ERT2 was inserted (knock-in) downstream of the stop codon, in the 3′ UTR of the serum albumin (Alb) gene. The Alb-CreERT2 mouse was a gift from David Gatfield, University of Lausanne, Switzerland. The Cmtr1loxP/loxP mice were crossed with Alb-CreERT2KI/KI mice. In another cross, the Cmtr1+/- mice were crossed with the Alb-CreERT2KI/KI mice. Using the these lines we prepared the conditional knockouts (cKO) (Cmtr1loxP/- ; Alb-CreERT2KI/+ mice) and control (Cmtr1loxP/+; Alb-CreERT2KI/+) animals.

extract_protocol:
HAP1 cell pellets were directly mixed with the TRIzol reagent (Invitrogen, Cat. No. 15596026), flash frozen and kept at -70°C. They were then processed according to the manufacture’s protocol. To remove genomic DNA, approximately 10 µg of the extracted RNA was treated with TurboDNase (Invitrogen, Cat. No. AM2238) for 30 minutes and then cleaned by RNA Clean and Concentrator kit (Zymo Research, Cat. No. R1017). For total RNA purification from mouse livers we used multiple biological replicates (n=4) of mouse liver from control (Cmtr1loxP/+; Alb-Cre-ERT2) and Cmtr1 cKO (Cmtr1loxP/-; Alb-Cre-ERT2) animals after tamoxifen injections. Approximately 0.5 g tissue was taken and placed in a 50 mL conical tube (Sarstedt, Cat. No. 62.547.254) with 5 mL of extraction buffer. [Preparation of the extraction buffer: 250 g guanidium thiocyanate (ITW Reagents, Cat. No. A1107), 17.6 mL sodium citrate, 0.75 M, pH 7.0 (Sigma-Aldrich, Cat. No. C8532) and 320 mL water were mixed at 60°C. Add 1/10 volume of sodium acetate, 2 M, pH 4.0 (Merck, Cat. No. 1.06268 ); 1/100 volume β-mercaptoethanol (Sigma, M3148), before use.] Homogenize using a douncer (Kinematica AG, Cat. No. PT 2500E) in the 50 ml conical tube for 20 s until no fragments are left, and then add 5 mL phenol-H2O, mix well and stand on ice. Add 2 mL chloroform (VWR, Cat. No. 8.22265.2500 ): isoamyl alcohol (Merck, Cat. No. W205702 ) (49:1), mix well, stand on ice for 15 min, and transfer all the solution to a 15 mL TPP centrifuge tube (Thermo Fisher, Cat. No. 91016). Spin down for 20 min at 4000 rpm at 4°C, transfer the upper phase (approximately 5 ml) to a new 15 mL TPP tube. Then add 1 volume (~5ml) of phenol-chloroform: isoamyl alcohol (48:2) mix. Shake well to mix. Spin down for 15 min at 4000 rpm at 4°C, transfer upper phase (approximately 4 ml) to a new 15 mL TPP tube. Add 4 mL isopropanol to precipitate the nucleic acids, and leave it at −20°C for 25 min. After this, spin down at 5000rpm, 15min at 4°C, remove all the solution, and completely dry the tube by keeping it up-side down on a tissue to remove all the liquid. Add 6 mL 4M lithium chloride (Merck, Cat. No. 1.05679) to resuspend the precipitate. The volume used depends on the size of the pellet. Shake till the pellet completely dissolves. Note that the pellet contains DNA along with the RNA. Leave on ice for 5 min, and spin down at 4500 rpm for 15 min at 4°C, remove all the solution and dry the tube completely. Add 7 mL 75% ethanol to resuspend the precipitate and leave it at room temperature for 10 min. Spin down at 4500 rpm for 15 min, remove all the solution and dry the tube completely with a tissue. A pellet will be visible if the amount of RNA is abundant.. Add 75% ethanol and keep sample on ice or at -20°C for longer time. Repeat the 75% ethanol step once again. And dry the tubes at room temperature for 45min by keeping them open. Dissolve the RNA precipitation with ~700 ul DEPC treated water to a proper concentration. Dissolve RNA by gently pipetting. After a short spin, measure concentration and transfer RNA into a new 1.5ml tube. Store it under -80°C.
RNA-seq library: Library preparation for embryos form the heterozygous (HET) Cmtr1+/- crosses (n=4) was performed at the Genomics Core Facility (GeneCore, EMBL Heidelberg) using 50 ng (for E6.5 embryos) and 200 ng (for E7.5 embryos) of total RNA with stranded rRNAminus RNAseq protocol and sequenced on NextSeq 500, HI, 75SE (85SE). Library preparation and sequencing of a second batch of embryos from the heterozygous (HET) Cmtr1+/- crosses or Cmtr2+/- crosses was performed at iGE3 facility at the University of Geneva. We used 50 ng (for E6.5 embryos) and 200 ng (for E7.5 embryos) of total RNA for the Smarter Ribodepletion kit. The prepared libraries were sequenced on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva). Libraries were prepared with total RNA (500 ng) from human HAP1 WT and CMTR1 KO (n=4) cells at the Genomics Core Facility (GeneCore, EMBL Heidelberg) sequencing facility using the stranded rRNAminus RNAseq protocol and sequenced on the HiSeq2000. Ribosome profiling: ribosome protected fragments (RPFs) were size-selected (25-34 nt) by electrophoresis using a 15% TBE-Urea polyacrylamide gel electrophoresis (PAGE) and two RNA markers, 25-mer (OP-RNA25) and 34-mer (OP-RNA34) (Table S1). After dephosphorylation with T4 Polynucleotide Kinase (NEB, #M0201S) the adapter Linker-1 (OP-RNA45) was ligated to the 3′ end of the RPF using T4 RNA Ligase 2 (NEB, #M0242S). The ligated products were purified using 10% TBE-Urea PAGE. Ribosomal RNA was removed using RiboCop rRNA Depletion Kit V2 H/M/R (Lexogen #144) for mouse liver samples or using the Ribo-Zero Plus rRNA Depletion kit (Illumina, #20040892) for HAP1 cell samples. The adapter Linker-1 was used for priming reverse transcription (RT) with the RT primer Ni-Ni-9 (OP27) using ProtoScript® II Reverse Transcriptase (NEB, #M0368S). RT products were purified using 10% TBE-Urea PAGE. The cDNA was circularized with CircLigase™ II ssDNA Ligase (Epicentre, #CL9021K). The final libraries were generated by PCR using forward index primer NI-N-2 (OP28) and reverse index primers. Amplified libraries were purified using 8% TBE-PAGE and analyzed with TapeStation. Libraries were sequenced on an Illumina HiSeq 4000, single-reads, 1x 50 bp, 8 libraries in a pool.

tag: type

value: gene expression profiling

tag: age

value: Day2 expt-1stbatch

value: control


title: atacseq_499_PBS

tag: tissue


title: atacseq_3084_KCl_6hr

value: Control


title: 13c1cKOliv

description:
Cmtr1-/loxP; AlbCreERT2+/-
MD_cKO3_D2_b1

tag: genotype

value: cKO


title: 12c1cKOliv

description:
Cmtr1-/loxP; AlbCreERT2+/-
MD_cKO2_D2_b1


title: 12ctrl

description:
Cmtr1+/loxP; AlbCreERT2+/-
MD_ctrl2_D2_b1


title: 11c1cKOliv

description:
Cmtr1-/loxP; AlbCreERT2+/-
MD_cKO1_D2_b1


title: 14c1cKOliv

description:
Cmtr1-/loxP; AlbCreERT2+/-
MD_cKO4_D2_b1


title: E7-5_WT4

description:
Cmtr1+/+
MD_WT4

source_name: Embryo

value: WT


title: E7-5_WT3

description:
Cmtr1+/+
MD_WT3


title: E7-5_WT2

description:
Cmtr1+/+
MD_WT2


title: atacseq_3084_KCl_1hr


title: 14ctrl

description:
Cmtr1+/loxP; AlbCreERT2+/-
MD_ctrl3_D2_b1


title: E7-5_WT1

description:
Cmtr1+/+
MD_WT1


title: atacseq_2962_PBS

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 2962


title: E7-5_KO4

description:
Cmtr1-/-
MD_KO4

value: KO


title: E7-5_KO3

description:
Cmtr1-/-
MD_KO3


title: atacseq_2962_KCl_1hr


title: atacseq_2962_KCl_6hr


title: atacseq_2620_KCl_6hr

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 2620


title: atacseq_2620_PBS


title: E7-5_KO2

description:
Cmtr1-/-
MD_KO2


title: E7-5_KO1

description:
Cmtr1-/-
MD_KO1


title: E6-5_WT3

description:
Cmtr1+/+
MD_WT3


title: E6-5_WT4

description:
Cmtr1+/+
MD_WT4


title: atacseq_2513_PBS

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 2513


title: atacseq_2620_KCl_1hr


title: atacseq_2513_KCl_6hr


title: atacseq_2513_KCl_1hr


title: E6-5_WT1

description:
Cmtr1+/+
MD_WT1


title: atacseq_1442_PBS

description: hiPSC-derived neurons, assay: ATAC-seq, subject: Homo sapiens, treatment: 1442


title: atacseq_1442_KCl_1hr


title: E6-5_KO4

description:
Cmtr1-/-
MD_KO4


title: atacseq_1442_KCl_6hr


title: E6-5_KO2

description:
Cmtr1-/-
MD_KO2


title: MLLT6/AF17 G2 rep1

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: KK22-CP-MAF9-YFP-Cas9-MLLT6-G2-REP1_S20_R1_001

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the mouse reference genome joint with Drosophilia spike-ins using HiSAT2 and reads were assigned to genes using htseq-count.
Differential expression was calculated using DESeq2
Genome_build: Joint Mm10 and Dm3
Supplementary_files_format_and_content: Raw gene counts from htseq

source_name: AML

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 2mM Glutamax, 100IU/ml Penicillin, 100 ug/ml Streptomycin and 10%HI-FCS in 5% CO2 37degrees.

extract_protocol: Qiagen RNA purification kit

treatment_protocol: MLLAF9 Cas9 cells (10x10^6 per cell line) were infected with lentiviral sgRNA libraries at a multiplicity of infection of 0.3. Infected cells were selected with 2ug/ml puromycin for 72hrs, commencing 48hrs after transduction. RNA was harvested 9 days post infection

tag: cell line

tag: time point

value: day 9 post infection harvest


title: E6-5_KO3

description:
Cmtr1-/-
MD_KO3


title: MLLT6/AF17 G2 rep3

description: KK22-CP-MAF9-YFP-Cas9-MLLT6-G2-REP3_S36_R1_001


title: MLLT6/AF17 G2 rep2

description: KK22-CP-MAF9-YFP-Cas9-MLLT6-G2-REP2_S28_R1_001


title: MLLT6/AF17 G1 rep3

description: KK22-CP-MAF9-YFP-Cas9-MLLT6-G1-REP3_S35_R1_001


title: E6-5_KO1

description:
Cmtr1-/-
MD_KO1


title: 26S0R_B73_top-crown_rep3

city: Changchun

first: Chunmei

last: Xue

state: Jilin Province

address: No. 5333 Xi’an Road, Lvyuan District

country: China

institute: Jilin University

description: 11211_5751_108472_H7WVVBGXC_cx_maize_H05_3_26_S_0_R_TC_GATTGT

data_processing:
3′ RNA libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) and were sequenced on Illumina NextSeq500 platform at the Cornell Genomic Facility.
Raw reads were cleaned up with bbduk (sourceforge.net/projects/bbmap/) to trim the adapter, poly-A and poly-G according to the instruction of 3′ RNA libraries preparation kit. The purified reads were mapped to Zea mays B73 reference genome V4 (http://plants.ensembl.org/index.html) with STAR
The Differentially Expressed Genes (DEGs) were identified in R program (https://www.r-project.org/) with EdgeR package
Genome_build: B73 reference genome V4 (http://plants.ensembl.org/index.html)
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for every gene and every sample; Tab-delimited text files include CPM values for each Sample.

organism: Zea mays

source_name: top-crown tissues

growth_protocol: Before treatment on three-leaf stage, the maize in growth chamber with temperature 26℃, photoperiod 14h/10h (day/night), light irradiance 250μmol·m-2·s-1 and humidity 50-70%

extract_protocol:
RNA was harvested by using the Trizol Reagent (Invitrogen, Carlsbad, CA) and further purified by RNA Clean and Concentrator-5 (Zymo Research, Tustin, CA, USA; catalog number R1014).
3′ RNA libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) and were sequenced on Illumina NextSeq500 platform at the Cornell Genomic Facility.

treatment_protocol: Normal condition (26℃ shoot + 26℃ root), whole-plant chilling (4℃ shoot + 4℃ root) for 24 hours, shoot-only chilling (4℃ shoot + 26℃ root) for 24 hours, root-only chilling (26℃ shoot + 0℃ root) for 24 hours

value: top-crown tissues

tag: treatment

tag: Stage

value: three-leaf stage

tag: ecotype


title: 26S0R_B73_bottom-crown_rep3

description: 11211_5751_108473_H7WVVBGXC_cx_maize_A06_3_26_S_0_R_BC_CTCTCG

source_name: bottom-crown tissues

value: bottom-crown tissues

value: root-only chilling (26℃ shoot + 0℃ root) for 24 hours


title: 26S0R_B73_bottom-crown_rep2

description: 11211_5751_108457_H7WVVBGXC_cx_maize_A04_2_26_S_0_R_BC_TTTATG


title: 26S0R_B73_bottom-crown_rep1

description: 11211_5751_108440_H7WVVBGXC_cx_maize_H01_1_26_S_0_R_BC_TGTGCA


title: 26S0R_B73_top-crown_rep1

description: 11211_5751_108439_H7WVVBGXC_cx_maize_G01_1_26_S_0_R_TC_CTAGTC


title: MLLT6/AF17 G1 rep2

description: KK22-CP-MAF9-YFP-Cas9-MLLT6-G1-REP2_S27_R1_001


title: E6-5_WT2

description:
Cmtr1+/+
MD_WT2


title: 26S0R_B73_root_rep3

description: 11211_5751_108471_H7WVVBGXC_cx_maize_G05_3_26_S_0_R_root_CAACAG

source_name: root tissues

value: root tissues


title: MLLT6/AF17 G1 rep1

description: KK22-CP-MAF9-YFP-Cas9-MLLT6-G1-REP1_S19_R1_001


title: MLLT1/ENL G2 rep3

description: KK22-CP-MAF9-YFP-Cas9-ENL-G2-REP3_S38_R1_001


title: 26S0R_B73_root_rep1

description: 11211_5751_108438_H7WVVBGXC_cx_maize_F01_1_26_S_0_R_root_GTGTAG


title: MLLT1/ENL G2 rep2

description: KK22-CP-MAF9-YFP-Cas9-ENL-G2-REP2_S30_R1_001


title: MLLT1/ENL G2 rep1

description: KK22-CP-MAF9-YFP-Cas9-ENL-G2-REP1_S22_R1_001


title: 26S0R_B73_leaf_rep3

description: 11211_5751_108470_H7WVVBGXC_cx_maize_F05_3_26_S_0_R_leaf_ACCGTG

source_name: leaf tissues

value: leaf tissues


title: MLLT1/ENL G1 rep3

description: KK22-CP-MAF9-YFP-Cas9-ENL-G1-REP3_S37_R1_001


title: 26S0R_B73_leaf_rep2

description: 11211_5751_108454_H7WVVBGXC_cx_maize_F03_2_26_S_0_R_leaf_GGAGGT


title: MLLT1/ENL G1 rep2

description: KK22-CP-MAF9-YFP-Cas9-ENL-G1-REP2_S29_R1_001


title: 26S0R_B73_leaf_rep1

description: 11211_5751_108437_H7WVVBGXC_cx_maize_E01_1_26_S_0_R_leaf_ACATTA


title: MLLT1/ENL G1 rep1

description: KK22-CP-MAF9-YFP-Cas9-ENL-G1-REP1_S21_R1_001


title: 4S26R_B73_bottom-crown_rep3

description: 11211_5751_108481_H7WVVBGXC_cx_maize_A07_3_4_S_26_R_BC_GTGCCA

value: shoot-only chilling (4℃ shoot + 26℃ root) for 24 hours


title: 26S0R_B73_top-crown_rep2

description: 11211_5751_108456_H7WVVBGXC_cx_maize_H03_2_26_S_0_R_TC_CCGCAA


title: MLLT10 G2 rep2

description: KK22-CP-MAF9-YFP-Cas9-MLLT10-G2-REP2_S26_R1_001


title: 4S26R_B73_bottom-crown_rep1

description: 11211_5751_108444_H7WVVBGXC_cx_maize_D02_1_4_S_26_R_BC_ATGAAC


title: 4S26R_B73_bottom-crown_rep2

description: 11211_5751_108465_H7WVVBGXC_cx_maize_A05_2_4_S_26_R_BC_AGATAG


title: 4S26R_B73_top-crown_rep3

description: 11211_5751_108480_H7WVVBGXC_cx_maize_H06_3_4_S_26_R_TC_AATAGC


title: MLLT10 G1 rep3

description: KK22-CP-MAF9-YFP-Cas9-MLLT10-G1-REP3_S33_R1_001


title: DOT1L KO -rep3

description: KK22-CP-MAF9-YFP-Cas9-DOT1L-5-1-REP3_S32_R1_001


title: MLLT10 G1 rep1

description: KK22-CP-MAF9-YFP-Cas9-MLLT10-G1-REP1_S17_R1_001


title: MLLT10 G1 rep2

description: KK22-CP-MAF9-YFP-Cas9-MLLT10-G1-REP2_S25_R1_001


title: 4S26R_B73_root_rep2

description: 11211_5751_108463_H7WVVBGXC_cx_maize_G04_2_4_S_26_R_root_ACCTAC


title: 4S26R_B73_root_rep3

description: 11211_5751_108479_H7WVVBGXC_cx_maize_G06_3_4_S_26_R_root_GCATGG


title: 4S26R_B73_top-crown_rep1

description: 11211_5751_108443_H7WVVBGXC_cx_maize_C02_1_4_S_26_R_TC_TTAACT


title: DOT1L KO -rep2

description: KK22-CP-MAF9-YFP-Cas9-DOT1L-5-1-REP2_S24_R1_001


title: 26S0R_B73_root_rep2

description: 11211_5751_108455_H7WVVBGXC_cx_maize_G03_2_26_S_0_R_root_CACACT


title: 4S26R_B73_leaf_rep3

description: 11211_5751_108478_H7WVVBGXC_cx_maize_F06_3_4_S_26_R_leaf_CTCCAT


title: 4S26R_B73_root_rep1

description: 11211_5751_108442_H7WVVBGXC_cx_maize_B02_1_4_S_26_R_root_CGGTTA


title: DOT1L KO -rep1

description: KK22-CP-MAF9-YFP-Cas9-DOT1L-5-1-REP1_S15_R1_001


title: NT- rep3

description: KK22-CP-MAF9-YFP-Cas9-mNTG2-REP3_S31_R1_001


title: 4S26R_B73_leaf_rep1

description: 11211_5751_108441_H7WVVBGXC_cx_maize_A02_1_4_S_26_R_leaf_TCAGGA


title: NT - rep2

description: KK22-CP-MAF9-YFP-Cas9-mNTG2-REP2_S23_R1_001


title: NT - rep1

description: KK22-CP-MAF9-YFP-Cas9-mNTG2-REP1_S14_R1_001


title: 4S26R_B73_leaf_rep2

description: 11211_5751_108462_H7WVVBGXC_cx_maize_F04_2_4_S_26_R_leaf_TGGATT


title: 4S4R_B73_bottom-crown_rep2

description: 11211_5751_108461_H7WVVBGXC_cx_maize_E04_2_4_S_4_R_BC_GCGAAT

value: whole-plant chilling (4℃ shoot + 4℃ root) for 24 hours


title: Menin inhibitor treated -H3K79me2 ChIP-seq

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with cutadapt.
K562 ChIP-seq reads were aligned to the GRCh37.73 ensembl genome assembly using BWA. MLLAF9 ChIP-seq reads were aligned to the Mm10 genome assembly using BWA.
Sam files were converted into Bam files using samtools. Tdf files were generated using igvtools.
Peak calling was performed using MACS2.
Genome_build: GRCh37.73 and Mm10
Supplementary_files_format_and_content: Bed files

extract_protocol:
ChIP DNA was purified using qiagen PCR clean up columns
Library prep was performed on ChIP DNA using rubicon kit

treatment_protocol: K562 and MLLAF9 Cas9 cells (10x10^6 per cell line) were infected with lentiviral sgRNA libraries at a multiplicity of infection of 0.3. Infected cells were selected with 2ug/ml puromycin for 72hrs, commencing 48hrs after transduction. ~ 100x10^6 cells were fixed/sonicated and ChIP performed at indicated timepoints from approx- 20-30 million cells per ChIP

tag: cell type

value: menin inhibtor treatment 48hrs

tag: antibody


title: MLLT10 G2 rep1

description: KK22-CP-MAF9-YFP-Cas9-MLLT10-G2-REP1_S18_R1_001


title: 4S4R_B73_bottom-crown_rep1

description: 11211_5751_108449_H7WVVBGXC_cx_maize_A03_1_4_S_4_R_BC_TCTTAA


title: MLLT10 G2 rep3

description: KK22-CP-MAF9-YFP-Cas9-MLLT10-G2-REP3_S34_R1_001


title: Menin inhibitor treated - FLAG MLLAF9 ChIP-seq

value: FLAG clone M1 F3040 mouse


title: 4S4R_B73_top-crown_rep2

description: 11211_5751_108460_H7WVVBGXC_cx_maize_D04_2_4_S_4_R_TC_GCTCGA


title: DMSO H3K79me2

value: DMSO treatment 72hrs


title: 4S26R_B73_top-crown_rep2

description: 11211_5751_108464_H7WVVBGXC_cx_maize_H04_2_4_S_26_R_TC_CGAAGG


title: 4S4R_B73_top-crown_rep3

description: 11211_5751_108476_H7WVVBGXC_cx_maize_D06_3_4_S_4_R_TC_ACAGAT


title: 4S4R_B73_bottom-crown_rep3

description: 11211_5751_108477_H7WVVBGXC_cx_maize_E06_3_4_S_4_R_BC_TAGGCT


title: DOT1L inhibitor treated - H3K79me2 ChIP-seq

value: DOT1L inhibitor treatment 72hrs


title: 4S4R_B73_top-crown_rep1

description: 11211_5751_108448_H7WVVBGXC_cx_maize_H02_1_4_S_4_R_TC_TACCTT


title: 4S4R_B73_root_rep3

description: 11211_5751_108475_H7WVVBGXC_cx_maize_C06_3_4_S_4_R_root_AAGACA


title: 4S4R_B73_root_rep2

description: 11211_5751_108459_H7WVVBGXC_cx_maize_C04_2_4_S_4_R_root_CAAGCA


title: 4S4R_B73_root_rep1

description: 11211_5751_108446_H7WVVBGXC_cx_maize_F02_1_4_S_4_R_root_AATCCG


title: 4S4R_B73_leaf_rep3

description: 11211_5751_108474_H7WVVBGXC_cx_maize_B06_3_4_S_4_R_leaf_TGACAC


title: DMSO FLAG-MLLAF9 ChIP-seq

value: DMSO treatment 48hrs


title: DOT1L KO guide 1- H3K79me2 ChIP-seq

value: DOT1L KO guide 1 9 days


title: MLLT10 KO guide 1 - H3K79me2 ChIP-seq

value: MLLT10 KO guide1 9 days


title: DOT1L KO guide 2- H3K79me2 ChIP-seq

value: DOT1L KO guide 2 9 days


title: MLLT10 KO guide 2 - H3K79me2 ChIP-seq

value: MLLT10 KO guide2 9 days


title: Control guide - H3K79me2 ChIP-seq

value: Control guide - 9 days


title: 4S4R_B73_leaf_rep2

description: 11211_5751_108458_H7WVVBGXC_cx_maize_B04_2_4_S_4_R_leaf_AACGCC

value: three-leaf stage


title: MLLAF9 H3K79me2 CRISPR-ChIP day 9

description: Custom targeted epigenetic library

data_processing:
Library strategy: CRISPR-seq
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
The RSA algorithm was used to rank the genes for which targeting sgRNA were significantly enriched in the sorted populations compared to the control unsorted populations grown in parallel.
Supplementary_files_format_and_content: Guide Counts file

extract_protocol:
Genomic DNA was extracted using Blood and tissue genomic DNA kit, Qiagen
One-step PCR was performed, containing adaptors for Illumina sequencing.

treatment_protocol: K562 and MLLAF9 Cas9 cells (100x10^6 per cell line) were infected with the pooled lentiviral sgRNA libraries at a multiplicity of infection of 0.3. Infected cells were selected with 2ug/ml puromycin for 72hrs, commencing 48hrs after transduction. ~ 100x10^6 cells were fixed/sonicated and ChIP performed at day 6 (H3K4me3) and day 9 (H3K79me2).

value: day 9


title: 4S4R_B73_leaf_rep1

description: 11211_5751_108445_H7WVVBGXC_cx_maize_E02_1_4_S_4_R_leaf_CCTAAG


title: 26S26R_B73_bottom-crown_rep3

description: 11211_5751_108469_H7WVVBGXC_cx_maize_E05_3_26_S_26_R_BC_TGGCGA

value: bottom-crown tissues

value: normal condition (26℃ shoot + 26℃ root)


title: 26S26R_B73_bottom-crown_rep2

description: 11211_5751_108453_H7WVVBGXC_cx_maize_E03_2_26_S_26_R_BC_GAGTCC


title: 26S26R_B73_bottom-crown_rep1

description: 11211_5751_108436_H7WVVBGXC_cx_maize_D01_1_26_S_26_R_BC_TGCACG


title: R27_F_TI_AGN_5

type: RNA

city: Charlottesville

first: Loren

last: Erickson

state: Virginia

address: 345 Crispell Drive

department: Department of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

hyb_protocol: Hybridization to Affymetrix Clariom D (NZM2328 and R27 female mice) or GeneChip Mouse 430 v2.0 (NZM2328 male) arrays was carried out by standard Affymetrix protocols.

scan_protocol: Arrays were scanned according to standard Affymetrix protocol.

data_processing:
Processing of raw microarray data was carried out with the R/Bioconductor package oligo. Affymetrix CEL files were background corrected and normalized using the robust multiarray average (RMA) method. Normalized data was transformed intot log2 intensity values and formatted as R expression set objects (e-sets). E-sets were annotated using chip definition files corresponding to each array.
The RMA-normalization of raw CEL files yielded 72,688 probe intensity values and the transcript annotation file from the Affymetrix Clariom D website used to label the probes (MTA-1_0.r3.na36.mm10.a1.transcript-modified.csv) contained 73,033 probe identifiers. After merging these datasets and removing unannotated probes with no gene symbol annotation, we arrived at the 40,161 remaining probe intensity values.

label: biotin

source_name: Kidney tubulointerstitial tissue (acute stage)

label_protocol: RNA was labeled with biotin by standard Affymetrix protocol.

growth_protocol: Mice were sacrificed at 8-9 weeks of age for the control group and 26-38 weeks for diseased mice. Glomerulonephritis (GN) was assessed using proteinuria test strips.

extract_protocol: Total RNA was isolated from LMD-derived cells using PicoPure RNA isolation kit (Applied Biosysytems Cat #:KIT0204) according to the manufacturer's instructions.

treatment_protocol: Kidneys of control and GN mice were harvested and the stage of GN was confirmed by histological classification. Snap frozen kidney sections were cut by Cryostat to 5-micron thickness and placed on dry ice. The sections were fixed in ethanol followed by hematoxylin and eosin (H&E) staining. Laser microdissection (LMD) was used to isolated kidney glomeruli and tubulointerstitial tissue.

value: Female

value: Kidney tubulointerstitial tissue


title: MLLAF9 screen control

description: Custom targeted epigenetic library


title: 26S26R_B73_top-crown_rep3

description: 11211_5751_108468_H7WVVBGXC_cx_maize_D05_3_26_S_26_R_TC_CGCAAC

value: top-crown tissues


title: R27_F_TI_AGN_1


title: IRAK2-overexpressing cells_Biological replicate 2

city: Madrid

first: Elba

last: del Val

state: Madrid

address: Plaza Ramón y Cajal s/n

department: Microbiología y Parasitología

country: Spain

institute: Universidad Complutense de Madrid

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scaner were analyzed using GCRMA algorithm from Bioconductor software

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: Following affymetrix labelling instructions

growth_protocol: Yeast cells were incubated for 18 h at 30 °C in SR medium. They were then diluted to OD=0.3 in SG medium and grown for 6h at 30 °C.

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

treatment_protocol: The expression of human genes from plasmids was controlled by the galactose promoter, so that when we changed the sugar source from the medium to galactose, its expression was induced, in this case for 6h. Samples were then collected.


title: IRAK2-overexpressing cells_Biological replicate 3


title: R27_F_TI_AGN_2


title: 26S26R_B73_top-crown_rep2

description: 11211_5751_108452_H7WVVBGXC_cx_maize_D03_2_26_S_26_R_TC_TATGTC


title: R27_F_Glom_AGN_3

source_name: Kidney glomeruli (acute stage)

value: Kidney glomeruli


title: IRAK1-overexpressing cells_Biological replicate 3


title: R27_F_TI_AGN_4


title: R27_F_TI_CTL_1

source_name: Kidney tubulointerstitial tissue (Pre-disease)


title: R27_F_TI_CTL_3


title: R27_F_Glom_AGN_1


title: IRAK2-overexpressing cells_Biological replicate 1


title: R27_F_TI_CTL_4


title: NZM2328_F_TI_CGN_6

source_name: Kidney tubulointerstitial tissue (chronic stage)


title: 26S26R_B73_top-crown_rep1

description: 11211_5751_108435_H7WVVBGXC_cx_maize_C01_1_26_S_26_R_TC_ACCAGT


title: R27_F_Glom_CTL_4

source_name: Kidney glomeruli (Pre-disease)


title: R27_F_Glom_AGN_5


title: NZM2328_F_TI_CGN_5


title: R27_F_Glom_AGN_4


title: R27_F_Glom_CTL_3


title: 26S26R_B73_root_rep3

description: 11211_5751_108467_H7WVVBGXC_cx_maize_C05_3_26_S_26_R_root_GTTACC

value: root tissues


title: R27_F_TI_AGN_3


title: 26S26R_B73_root_rep2

description: 11211_5751_108451_H7WVVBGXC_cx_maize_C03_2_26_S_26_R_root_ATACTG


title: R27_F_TI_CTL_2


title: IRAK1-overexpressing cells_Biological replicate 2


title: NZM2328_F_TI_CGN_4


title: R27_F_Glom_AGN_2


title: 26S26R_B73_root_rep1

description: 11211_5751_108434_H7WVVBGXC_cx_maize_B01_1_26_S_26_R_root_GATCAC


title: IRAK1-overexpressing cells_Biological replicate 1


title: 26S26R_B73_leaf_rep3

description: 11211_5751_108466_H7WVVBGXC_cx_maize_B05_3_26_S_26_R_leaf_TTGGTA

value: leaf tissues


title: R27_F_Glom_CTL_2


title: 26S26R_B73_leaf_rep2

description: 11211_5751_108450_H7WVVBGXC_cx_maize_B03_2_26_S_26_R_leaf_GTCAGG


title: NZM2328_F_TI_CGN_3


title: R27_F_Glom_CTL_1


title: 26S26R_B73_leaf_rep1

description: 11211_5751_108433_H7WVVBGXC_cx_maize_A01_1_26_S_26_R_leaf_CAGCGT


title: IRAK4(KD)-overexpressing cells_Biological replicate 2


title: AGA22: Macrophages differentiated in the presence of GW3965 and GSK2033 #1

first: Miguel

middle: A

last: Vega

address: Ramiro de Maeztu 9

institute: CIB (CSIC)

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml M-CSF to generate M-CSF-polarized macrophages.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: At the beginning of the differentiaton prtocol, monocytes were treated with LXR agonist GW3965 (1 μM, Tocris), LXR antagonist GSK2033 (1 μM, Tocris), GW3965 and GSK2033, or dimethyl sulfoxide (DMSO) as vehicle.

value: Monocyte-derived GM-CSF macrophages

value: GW3965 and GSK2033


title: AGA21: Macrophages differentiated in the presence of GSK2033 #3


title: AGA23: Macrophages differentiated in the presence of GW3965 and GSK2033 #2


title: NZM2328_F_TI_CGN_1


title: AGA24: Macrophages differentiated in the presence of GW3965 and GSK2033 #3


title: NZM2328_F_TI_TGN_5

source_name: Kidney tubulointerstitial tissue (transitional stage)


title: AGA19: Macrophages differentiated in the presence of GSK2033 #1


title: NZM2328_F_TI_CGN_2


title: IRAK4-overexpressing cells_Biological replicate 1


title: NZM2328_F_TI_TGN_2


title: IRAK4(KD)-overexpressing cells_Biological replicate 1


title: IRAK4(KD)-overexpressing cells_Biological replicate 3


title: AGA20: Macrophages differentiated in the presence of GSK2033 #2


title: IRAK4-overexpressing cells_Biological replicate 2


title: IRAK4-overexpressing cells_Biological replicate 3


title: NZM2328_F_TI_TGN_4


title: NZM2328_F_TI_TGN_3


title: AGA18: Macrophages differentiated in the presence of GW3965 #3


title: NZM2328_F_TI_AGN_3


title: WT_RP527

description:
Cmtr2+/+
RP527

source_name: HAP1 cells

value: ribosome profiling

value: cell culture

value: control (input)


title: NZM2328_F_TI_AGN_1


title: AGA17: Macrophages differentiated in the presence of GW3965 #2


title: NZM2328_F_TI_TGN_1


title: WT_RP528

description:
Cmtr2+/+
RP528


title: AGA16: Macrophages differentiated in the presence of GW3965 #1


title: WT_RP526

description:
Cmtr2+/+
RP526


title: WT_RP525

description:
Cmtr2+/+
RP525


title: Control cells_Biological replicate 2

value: control


title: NZM2328_F_TI_AGN_2


title: Control cells_Biological replicate 3


title: NZM2328_F_TI_CTL_3


title: Control cells_Biological replicate 1


title: KO_RP532

description:
Cmtr2-/-
RP532

value: cKO (input)


title: AGA13: Macrophages differentiated in the presence of DMSO #1

value: DMSO


title: NZM2328_F_TI_CTL_2


title: KO_RP531

description:
Cmtr2-/-
RP531


title: KO_RP529

description:
Cmtr2-/-
RP529


title: NZM2328_M_Glom_AGN_6

data_processing: Processing of raw microarray data was carried out with the R/Bioconductor package oligo. Affymetrix CEL files were background corrected and normalized using the robust multiarray average (RMA) method. Normalized data was transformed intot log2 intensity values and formatted as R expression set objects (e-sets). E-sets were annotated using chip definition files corresponding to each array.

value: Male


title: NZM2328_M_Glom_AGN_5


title: M-MØ macrophage MCTO donor1 rep1

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from two healthy donors and one MTO patient over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

value: Monocyte-derived M-CSF macrophages

tag: disease state

value: MCTO


title: AGA15: Macrophages differentiated in the presence of DMSO #3


title: WT_RPF228

description:
Cmtr2+/+
RPF228

value: control (footprints)


title: NZM2328_F_Glom_CGN_6

source_name: Kidney glomeruli (chronic stage)

value: Female


title: M-MØ macrophage MCTO donor1 rep2


title: NZM2328_M_Glom_AGN_4


title: NZM2328_F_Glom_CGN_5


title: M-MØ macrophage healthy donor2 rep1

value: healthy


title: NZM2328_M_Glom_AGN_3

value: Kidney glomeruli


title: NZM2328_F_TI_CTL_1

value: Kidney tubulointerstitial tissue


title: AGA14: Macrophages differentiated in the presence of DMSO #2


title: KO_RP530

description:
Cmtr2-/-
RP530


title: WT_RPF227

description:
Cmtr2+/+
RPF227


title: NZM2328_F_Glom_CGN_2


title: WT_RPF226

description:
Cmtr2+/+
RPF226


title: M-MØ macrophage healthy donor1 rep1


title: NZM2328_F_Glom_CGN_4


title: NZM2328_M_Glom_AGN_2


title: NZM2328_F_Glom_CGN_3


title: WT_RPF225

description:
Cmtr2+/+
RPF225


title: NZM2328_M_Glom_AGN_1


title: NZM2328_F_Glom_CGN_1


title: HSC_LentiA8_2

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Total RNA from samples was extracted to create an RNA-seq library, which was analyzed by BGI USA (Cambridge, MA) using a BGISEQ-500 sequencer.
Raw sequencing reads were cleaned by removing reads containing aptamer or poly-N sequences, and reads with low-quality base ratios.
Afterwards, clean reads were obtained and stored in FASTQ format. Clean reads were mapped to the reference genome using the HISAT2 (v2.0.4)/Bowtie2 (v2.2.5) tool.
Gene expression levels were calculated by RESM software and normalized to determine gene expression.
Assembly: mm10
Supplementary files format and content: FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: hematopoietic stem cells

extract_protocol:
Total RNA was extracted using the TRIZOL following the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using DNBSEQ following manufacturer's protocols.

value: hematopoietic stem cells

value: Cas9 knockout S100A8


title: HSC_LentiA8_3


title: HSC_LentiA8_1


title: KO_RPF232

description:
Cmtr2-/-
RPF232

value: cKO (footprints)


title: NZM2328_M_Glom_CTL_3


title: NZM2328_M_Glom_CTL_2


title: KO_RPF230

description:
Cmtr2-/-
RPF230

value: ribosome profiling


title: 12hap1WT

description:
Cmtr1+/+
MD_WT2

value: gene expression profiling

value: cell culture

value: WT


title: KO_RPF229

description:
Cmtr2-/-
RPF229


title: 14hap1WT

description:
Cmtr1+/+
MD_WT4


title: 13hap1WT

description:
Cmtr1+/+
MD_WT3


title: NZM2328_F_Glom_TGN_3

source_name: Kidney glomeruli (transitional stage)


title: HSC_Ctrl_1

value: Vector control


title: 11hap1WT

description:
Cmtr1+/+
MD_WT1


title: HSC_Ctrl_2


title: NZM2328_F_Glom_TGN_5


title: KO_RPF231

description:
Cmtr2-/-
RPF231


title: NZM2328_F_Glom_TGN_1


title: OM14

city: Milwaukee

first: Satoshi

last: Shimada

state: WI

address: 8701 Watertown plank road

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction: The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly:  ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: all_compare.xls

organism: Rattus norvegicus

extract_protocol:
RNA were extracted from snap frozen tissues by Trizol reagent and cleaned up by RNAeasy MinElute Cleanup kit (Qiagen)
mRNA library preparation (polyA enrichment) (Novogene, Plant and Animal Eukaryptic mRNA-seq with reference (WBI-quantification)

value: Sprague-Dawley

value: Right kidney outer medulla


title: NZM2328_F_Glom_TGN_4


title: HSC_OEA8_69_3

value: Overexpression point mutation (69) S100A8


title: HSC_Ctrl_3


title: NZM2328_F_Glom_AGN_3


title: HSC_OEA8_69_2


title: NZM2328_F_Glom_TGN_2


title: OM13


title: NZM2328_F_Glom_AGN_2


title: NZM2328_M_Glom_CTL_1

value: Male


title: 13hap1KO

description:
Cmtr1-/-
MD_KO3

value: KO


title: NZM2328_F_Glom_AGN_1

value: Female


title: OM15


title: 12hap1KO

description:
Cmtr1-/-
MD_KO2


title: 14hap1KO

description:
Cmtr1-/-
MD_KO4


title: NZM2328_F_Glom_CTL_3


title: OM11


title: UP_UAS_STARR-seq, Rbf, rep1

description:
50bp
normalized_counts_BAC_screens.tsv

data_processing:
Paired-end sequencing reads were demultiplexed using the standard illumina i5 and i7  indexes and mapped Drosophila Melanogaster (dm3) genome and subsequently to the artificial Drosophila Pseudoobscura BAC genome (spike-in), using Bowtie v.1.2.2. PE 36bp reads with a maximal insert size of 2 kb and up to three mismatches were kept. The olig screens were demultiplexed and mapped to a synthetic reference genome containing the 249bp sequences with both wildtype and mutant enhancers, only exact matches were kept and subsequently to the artificial Drosophila Pseudoobscura BAC genome (spike-in).
For the genome-wide screen enhancers were detected macs25 callpeak using –nomodel and –fe-cutoff 4 as additional parameters. Enhancers were called on all 12 samples separately, and their genomic coordinates were merged into one enhancer backbone file. Rep-STARR-seq reads falling into these enhancers were quantified for every sample, obtaining a raw counts matrix. The raw counts matrix was then normalized using the spike-in normalization factors and the normalized matrix was used to perform differential enhancer activity analysis.
We quantified the differences in enhancer activites between the Gal4-GFP (control) samples and our Gal4-CoRs using EdgeR with two biological replicates.
Assembly: For the genome-wide screens: BDGP R5/dm3 For the disigned oligo library we generated a custom assembly
Supplementary files format and content: Spike-in normalized reads matrix for all samples
Supplementary files format and content: genomic coverage of rep-STARR-seq for every sample in bigWig format

treatment_protocol:
per OC-400, 200million Drosophila S2 cell lines were transfected with a pre-mixed rep-STARR-seq library (20ug) + Gal4-CoR expression vector (20ug) + spike-in (0.2ug).  2 OC 400 were used per gw rep-STARR-seq sample and one OC 400 was used for the BAC and designed oligonucleotide libraries.
24h after transfection, the cells were havested and the same samples pooled to then be processed like regular STARR-seq (Arnold et al., 2013)

tag: enhancer library

value: 32 BAC sheared ~750bp

tag: core-promoter

value: Mixed DSCP and Rps12

value: Schneider S2

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: HSC_OEA8_69_1

value: hematopoietic stem cells


title: 11hap1KO

description:
Cmtr1-/-
MD_KO1


title: HSC_OEA8_67_3

value: Overexpression point mutation (67) S100A8


title: OM12


title: OM10


title: UP_UAS_STARR-seq, CtBP, rep2

description:
50bp
normalized_counts_BAC_screens.tsv


title: 5-Uninfected Apical-out

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

data_processing:
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume
Paired-end reads were directionally mapped to the genomic loci of the human genome (GRCh38/hg38) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Assembly: GRCh38/hg38
Supplementary files format and content:
Gene expression file generated by cuffdiff analysis
differential gene expression between infected and uninfected samples; gene count and fpkm
*_count: the estimated count of fragments or reads mapped to a particular feature (e.g., gene, transcript) in a given sample; an estimate of the expression level of that feature.
*_count_variance: the estimated variance of the count for a particular feature in a sample; the variability or dispersion in the count measurement for that feature.
*_count_uncertainty_var: the uncertainty variance associated with the count estimate for a specific feature in a sample; the level of uncertainty in the count measurement, taking into account various sources of variability.
*_count_dispersion_var: the dispersion variance associated with the count estimate for a particular feature in a sample. Dispersion refers to the degree of heterogeneity or variability in the expression levels across samples. The dispersion variance reflects the amount of dispersion associated with the count measurement for that feature.

source_name: iPSC-derived alveolar organoids

extract_protocol:
Total RNA was isolated from  iPSC-derived alveolar organoids by using Tri reagent
The Illumina Stranded mRNA Prep kit was employed for library preparation, following the manufacturer's reference guide and checklist (Document # 1000000124518 v02). In Summary, 100 ng of total RNA input is used for each library prep. First step, the Oligo(dT) magnetic beads purify and capture the mRNA molecules containing polyA tails. The purified mRNA is fragmented and copied into first strand complimentary DNA (cDNA) using reverse transcriptase and random primers. In a second strand cDNA synthesis step, dUTP replaces dTTP to achieve strand specificity. Then, add adenine (A) and thymine (T) bases to fragment ends and ligate adapters. The resulting products are purified with magnetic beads. Then, add indexes to the anchor-ligated DNA fragments with PCR. The resulting products are purified and selectively amplified for sequencing on an Illumina system.

value: Uninfected

value: iPSC-derived alveolar organoids

tag: tissue type

value: Apical-out


title: 6-Infected Apical-out

value: SARS-CoV-2 WA1 infected


title: UP_UAS_STARR-seq, CtBP, rep1

description:
50bp
normalized_counts_BAC_screens.tsv

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy Mini Prep Kit.
mRNAs were enriched with Dynabeads Oligo-dT25 (Invitrogen), followed by a DNA digest with Turbo DNase (Ambion).
mRNAs were cleaned up with AMPure XP DNA beads (Agencourt; ratio sample/beads 1:1.8) and then reverse transcribed with Superscript III (50°C for 60 min, 70°C for 15 min; Invitrogen 18080085) and a primer binding within the poly-A site of candidate mRNAs (reverse_transcription_rv: CTCATCAATGTATCTTATCATGTCTG).
Next, RNA was digested with Rnase A (Thermo) for 1 h at 37°C, followed by bead cleanup of the remaining DNA (ratio sample/beads 1:1.4).
All subsequent PCR reactions were prepared using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2602). A junction PCR was performed with a primer binding only in correctly spliced candidate mRNAs junction_primer_fw: AAGCCACCATGGAAAAG*G*C*C*A*T, junction_primer_rv: TATCATGTCTGCTCGAAG*C*G*G (98°C for 45s, (98°C for 15s,  65°C for 30 s, 72°C for 45 s)X15, followed by bead cleanup (ratio sample/beads 1:0.9).
Sequencing ready PCR: candidate fragments were amplified (98°C 45 s, followed by 6-15 cycles, 98°C 15 s, 65°C 30 s, 72°C 30s) with the following primers: i5: aatgatacggcgaccaccgagatctacacXXXXXXXXacactctttccctacacgacgctcttccgatct (XXXXXXXX indicates the position of the index sequence for NGS) and the reverse primer TruSeq IDX with approptiate barcode for demultiplexing individual samples. PCR products were purified by Agencourt AMPure XP DNA beads (ratio sample/beads 1:0.8), pooled, and subjected to NGS.
After another beads cleanup we measured each sample and made and equimolar mixture that was subjected to sequencing


title: NZM2328_F_Glom_CTL_2

tag: gender

value: Kidney glomeruli


title: HSC_OEA8_67-2


title: HSC_OEA8_67_1


title: OM9

tag: strain

value: Sprague-Dawley


title: 4-Infected Sheared

value: Sheared


title: UP_UAS_STARR-seq, GFP, rep2

description:
50bp
normalized_counts_BAC_screens.tsv


title: OM8

value: Right kidney outer medulla


title: HSC_OEA8_Ctrl_3

value: Overexpression control


title: 3-Uninfected Sheared


title: NZM2328_F_Glom_CTL_1


title: HSC_OEA8_Ctrl_2


title: 2-Infected Apical-in

value: Apical-in


title: OM7


title: OM6


title: 1-Uninfected Apical-in


title: UP_UAS_STARR-seq, GFP, rep1

description:
50bp
normalized_counts_BAC_screens.tsv


title: UE_UAS_STARR-seq, Rbf, rep2

description:
50bp
normalized_counts_BAC_screens.tsv


title: HSC_OEA8_Ctrl_1


title: UE_UAS_STARR-seq, Rbf, rep1

description:
50bp
normalized_counts_BAC_screens.tsv


title: UE_UAS_STARR-seq, CtBP, rep2

description:
50bp
normalized_counts_BAC_screens.tsv


title: TE9_sgNAT10-2-input

city: Guangzhou

first: Wei

last: Wei

state: -- None selected --

address: 越秀区中山二路

institute: 中山大学附属第一医院

description:
ac4C-rip-seq
small RNA

data_processing:
library strategy: ac4C-rip-seq
Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. After adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2.

source_name: esophagus

growth_protocol: TE-9 cells were cultured in DMEM with 10% fetal bovine serum, 1% streptomycin and 1% Penicillin. Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37°C.

extract_protocol:
RNA was extracted according to TRIzol protocol.Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to the NEBNext® Small RNA Library Prep Set.

treatment_protocol: TE-9 cells were  stable knockout of NAT10. TE-9 cells with normal expression of NAT10 were used as control.Total RNAs were isolated using Trizol reagent following the manufacturer’s instructions. Small RNAs (17-200nt) were then purified using The RNA Clean and Concentrator-25 kit. 20 μg small RNAs were incubated with 5 μl anti-ac4C antibody  or IgG for 2 hours. The immunoprecipitated RNAs were isolated using Trizol reagent. The input small RNAs and immunoprecipitated small RNAs were treated with AlkB and AlkB-D135S and then used for cDNA library construction with Multiplex Small RNA Library Prep Set for Illumina Kitand subjected to high-throughput sequencing.

value: esophagus

value: esophageal epithelial

value: demethylated by ALKB


title: OM4

source_name: OMLS

value: LS


title: OM3


title: rHSC_GA_1

value: GA treatment 24 hours


title: TE9_NC2-ac4C

description:
ac4C-rip-seq
small RNA

value: WT


title: UE_UAS_STARR-seq, GFP, rep2

description:
50bp
normalized_counts_BAC_screens.tsv

value: 32 BAC sheared ~750bp

value: Mixed DSCP and Rps12

value: Schneider S2

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: rHSC_Ctrl_3

value: hematopoietic stem cells

value: Normal Culture


title: rHSC_GA_3


title: TE9_NC2-IgG

description:
ac4C-rip-seq
small RNA


title: OM1

value: Sprague-Dawley


title: OM2


title: UE_UAS_STARR-seq, CtBP, rep1

description:
50bp
normalized_counts_BAC_screens.tsv


title: rHSC_Ctrl_2


title: TE9_NC2-input

description:
ac4C-rip-seq
small RNA


title: C15

value: Right kidney cortex


title: C14


title: OM5

value: Right kidney outer medulla


title: rHSC_Ctrl_1


title: TE9_NC1-ac4C

description:
ac4C-rip-seq
small RNA


title: rHSC_GA_2


title: TE9_sgNAT10-1-input

description:
ac4C-rip-seq
small RNA


title: DE_UAS_STARR-seq, Rbf, rep2

description:
50bp
normalized_counts_BAC_screens.tsv


title: Day 7 OT-I T cells, HTO

city: Aurora

first: Ross

middle: M

last: Kedl

state: CO

address: 12800 E. 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: HTO library: read 1 contains cell barcode and UMI; read 2 contains Hashtag Antibody Derived tag reads

library_source: transcriptomic single cell

data_processing:
Reads from scRNA-seq were aligned to mm10 or hashtag oligo sequences and collapsed into unique molecular identifier (UMI) counts using the 10x Genomics Cell Ranger software (version 2.1.0) to generate the the output files:  matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz
Assembly: mm10
Supplementary files format and content: CellRanger output files: matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz

source_name: spleen

extract_protocol:
T cells were isolated on day 7 post immunization using FACS sorting of CD45.1+ CD8+ cells. Cells from an individual condition (adjuvant, LM or VV) were stained with an unique oligo-tagged anti-CD45 “hashtag” antibody (Biolegend) and then combined into one sample. 20,000 hashtagged OT-I cells were loaded into Single Cell A chips (10x Genomics) and partitioned into Gel Bead In-Emulsions in a Chromium Controller (10x Genomics.)
Gene expression and HTO libraries were prepared according to the protocols provided by the 10x Genomics Chromium Single Cell 3' Reagent Kits v2 User Guide by the CU Anchutz Genomics Core.

value: spleen

value: CD8+ T cell

value: OT-I

value: mixed sample(adjuvant, listeria monocytogenes, vaccinia virus)

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3


title: C13

tag: tissue


title: Day 7 OT-I T cells, GEX

description: GEX (3' mRNA) library: read 1 contains cell barcode and UMI; read 2 contains transcript

tag: genotype

value: mRNA


title: TE9_NC1-IgG

description:
ac4C-rip-seq
small RNA

value: esophagus

tag: cell line

value: esophageal epithelial

value: WT

value: demethylated by ALKB


title: UE_UAS_STARR-seq, GFP, rep1

description:
50bp
normalized_counts_BAC_screens.tsv

value: 32 BAC sheared ~750bp

value: Mixed DSCP and Rps12

value: Schneider S2

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: TE9_NC1-input

description:
ac4C-rip-seq
small RNA


title: DE_UAS_STARR-seq, CtBP, rep2

description:
50bp
normalized_counts_BAC_screens.tsv


title: DE_UAS_STARR-seq, GFP, rep3

description:
50bp
normalized_counts_BAC_screens.tsv