title: MNase-seq: wild-type, DMSO, rep 3

value: SPT6-3xFLAG, SPT6-V5-AID, POB3


title: MNase-seq: spt6Δ2-238, IAA, rep 2

status: Public on Nov 25 2024

type: SRA

city: Boston

first: James

middle: L

last: Warner

state: MA

address: 77 Avenue Louis Pasteur, Room 358

department: Genetics

country: USA

institute: Harvard Medical School

library_source: genomic

data_processing:
Reads were aligned to the S.cerevisiae and S. pombe genomes using Bowtie2 (Langmead and Salzburg 2012) and sorted using samtools (Danecek et al. 2021).
Spike-in normalization factors were calculated using a custom python script (https://github.com/winston-lab/warner_mnase_seq) using the number of reads mapping to the S. pombe genome.
Spike-in normalized nucleosome dyad postion coverage tracks were generated using deeptools bamCoverage (Ramirez et al 2016) and the '--MNase' optional argument.
Assembly: S. cerevisiae R64.2.1/sacCer3
Supplementary files format and content: Spike-in normalized coverage tracks generated using deeptools (Ramirez et al 2016) are provided in BIGWIG format (files ending .bw).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in SC-Trp at 30°C wth shaking to an OD600 of ≈ 0.6 prior to treament.

extract_protocol:
Cell pellets were processed for MNase digestion as described in (McKnight et al 2021). Briefly, cells were fixed with 1% formaldehyde for 15 minutes and quenched with glycine. Cells were spheroplasted using Zymolyase 100T until >90% of the cells were spheroplasts as assessed by microscopy. Micrococcal nuclease and Exonucelase III were added to each sample and the reactions were incubated at 37°C for exactly 15 minutes. Digestion was halted by the addition of EDTA and EGTA. Each sample was mixed mith S. pombe mononucleosomal DNA (strain FWP570) at a ratio of 1 ng S. pobe DNA / 1.5 x 10^7 S. cerevisiae cells. Mononucleosomal DNA was isolated and used to construct libraries.
Libraries were constructed using the NEBNext Ultra II DNA library Prep Kit for Illumina (New England Biolabs) following manufacturer specifications.

treatment_protocol: Cultures were diluted in SC-Trp to OD600 = 0.3 and treated with either DMSO (final concentration 0.05% v/v) or 3-indoleacetic acid (IAA, final concentration 25 μM) for 90 minutes at 30°C with shaking.

tag: cell line

tag: plasmid

tag: genotype

tag: treatment

value: 3-indoleacetic acid


title: MNase-seq: wild-type, IAA, rep 1


title: MNase-seq: empty vector, IAA, rep 2

value: empty vector, SPT6-V5-AID, POB3


title: MNase-seq: empty vector, IAA, rep 1


title: MNase-seq: wild-type, DMSO, rep 2

value: DMSO


title: Exp.Sample.29

status: Public on Nov 15 2024

city: Baltimore

first: Michael

last: Considine

state: Maryland

address: 550 North Broadway

institute: Johns Hopkins University

description: Expr, Non-Progressor, Her2

library_source: transcriptomic

data_processing:
Fastq files were generated using bcl2fastq v2.20.0.422.
Reads were aligned to the human genome GRCh38 using the splice-aware STAR aligner v.2.4.2a (20)
Gene-level quantification of expression was performed with the package DESeq2 (21), using GENCODE v.27 as reference annotations
MntJULiP was used with default argumentsto determine differential splicing events at the intron level and to estimate the splicing ratios of individual introns
Supplementary files format and content: tab delimited text file includes normalized values
Supplementary files format and content: tab delimited text file includes splice values
Assembly: human genome GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: breast

extract_protocol:
Nucleic Acids were extracted using AllPrep DNA/RNA FFPE kit (Qiagen, Valencia, CA) Extracted RNA was quantified by Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA) and stored at -80°C.
50ng of total RNA were used for library construction using TruSeq RNA Exome kits (Illumina, RS-301-2001)

tag: tissue

value: breast

tag: classification

value: Non-Progressor

tag: age

tag: race

value: WHITE

tag: expressioncluster

tag: methylationcluster

tag: hormonetreatment

value: Untreated

tag: radiationtreatment

value: Treated


title: MNase-seq: empty vector, DMSO, rep 1


title: MNase-seq: empty vector, DMSO, rep 2


title: MNase-seq: wild-type, IAA, rep 3


title: MNase-seq: wild-type, IAA, rep 2


title: Exp.Sample.25

description: Expr, Non-Progressor, Normal

value: Normal


title: Exp.Sample.55

description: Expr, Progressor, LumA

value: Progressor

value: LumA


title: Exp.Sample.28

description: Expr, Progressor, Her2

value: LumB


title: Exp.Sample.192

description: Expr, Non-Progressor, Normal


title: MNase-seq: empty vector, DMSO, rep 3


title: Exp.Sample.191

description: Expr, Non-Progressor, Normal


title: Exp.Sample.190

description: Expr, Non-Progressor, LumB

value: Lum B

value: HISPANIC WHITE


title: Exp.Sample.175

description: Expr, Non-Progressor, LumA


title: Exp.Sample.170

description: Expr, Non-Progressor, Normal


title: Exp.Sample.174

description: Expr, Non-Progressor, Her2


title: Exp.Sample.187

description: Expr, Non-Progressor, LumA

value: Lum A


title: MNase-seq: wild-type, DMSO, rep 1


title: Exp.Sample.183

description: Expr, Non-Progressor, LumB


title: Exp.Sample.162

description: Expr, Non-Progressor, Normal


title: Exp.Sample.167

description: Expr, Non-Progressor, LumA


title: Exp.Sample.150

description: Expr, Non-Progressor, Basal

value: Basal


title: Exp.Sample.169

description: Expr, Non-Progressor, Normal

value: BLACK


title: Exp.Sample.148

description: Expr, Non-Progressor, Normal


title: Exp.Sample.144

description: Expr, Non-Progressor, LumB


title: Exp.Sample.136

description: Expr, Non-Progressor, Her2


title: Exp.Sample.130

description: Expr, Non-Progressor, LumB


title: Exp.Sample.128

description: Expr, Non-Progressor, LumA


title: Exp.Sample.146

description: Expr, Non-Progressor, LumA


title: Exp.Sample.132

description: Expr, Non-Progressor, LumA


title: Exp.Sample.143

description: Expr, Non-Progressor, LumA


title: Exp.Sample.124

description: Expr, Non-Progressor, LumA


title: Exp.Sample.160

description: Expr, Non-Progressor, LumA


title: Exp.Sample.126

description: Expr, Non-Progressor, LumA


title: Exp.Sample.134

description: Expr, Non-Progressor, LumB


title: Exp.Sample.154

description: Expr, Non-Progressor, Basal


title: Exp.Sample.110

description: Expr, Non-Progressor, LumB


title: Exp.Sample.113

description: Expr, Non-Progressor, LumA


title: Exp.Sample.115

description: Expr, Non-Progressor, LumA


title: Exp.Sample.120

description: Expr, Non-Progressor, Her2


title: Exp.Sample.117

description: Expr, Non-Progressor, Normal


title: Exp.Sample.107

description: Expr, Non-Progressor, LumA


title: Exp.Sample.109

description: Expr, Non-Progressor, LumA


title: Exp.Sample.97

description: Expr, Non-Progressor, LumB


title: Exp.Sample.95

description: Expr, Non-Progressor, Her2


title: Exp.Sample.91

description: Expr, Non-Progressor, LumA


title: Exp.Sample.104

description: Expr, Non-Progressor, Her2


title: Exp.Sample.88

description: Expr, Non-Progressor, LumB


title: Exp.Sample.86

description: Expr, Non-Progressor, Her2


title: Exp.Sample.152

description: Expr, Non-Progressor, LumA


title: Exp.Sample.84

description: Expr, Non-Progressor, Basal


title: Exp.Sample.80

description: Expr, Non-Progressor, LumA


title: Exp.Sample.78

description: Expr, Non-Progressor, LumA


title: Exp.Sample.76

description: Expr, Non-Progressor, Normal


title: Exp.Sample.74

description: Expr, Non-Progressor, LumB


title: Exp.Sample.62

description: Expr, Non-Progressor, Her2


title: Exp.Sample.65

description: Expr, Non-Progressor, LumB


title: Exp.Sample.54

description: Expr, Non-Progressor, LumA


title: Exp.Sample.50

description: Expr, Non-Progressor, LumA


title: Exp.Sample.60

description: Expr, Non-Progressor, LumB


title: Exp.Sample.56

description: Expr, Non-Progressor, LumB


title: Exp.Sample.45

description: Expr, Non-Progressor, LumA


title: Exp.Sample.38

description: Expr, Non-Progressor, LumB


title: Exp.Sample.52

description: Expr, Non-Progressor, Basal


title: Exp.Sample.40

description: Expr, Non-Progressor, LumB


title: Exp.Sample.33

description: Expr, Non-Progressor, Her2


title: Exp.Sample.36

description: Expr, Non-Progressor, Her2


title: Exp.Sample.22

description: Expr, Non-Progressor, LumB


title: Exp.Sample.182

description: Expr, Progressor, Her2


title: Exp.Sample.171

description: Expr, Progressor, Normal


title: Exp.Sample.177

description: Expr, Progressor, Basal


title: Exp.Sample.186

description: Expr, Progressor, Her2


title: Exp.Sample.180

description: Expr, Progressor, Normal


title: Exp.Sample.168

description: Expr, Progressor, Normal


title: Exp.Sample.166

description: Expr, Progressor, LumA


title: Exp.Sample.67

description: Expr, Non-Progressor, LumA


title: Exp.Sample.153

description: Expr, Progressor, LumB

value: Asian/other


title: Exp.Sample.149

description: Expr, Progressor, LumA


title: Exp.Sample.161

description: Expr, Progressor, LumA


title: Exp.Sample.82

description: Expr, Non-Progressor, Basal


title: Exp.Sample.131

description: Expr, Progressor, Her2


title: Exp.Sample.70

description: Expr, Non-Progressor, Basal


title: Exp.Sample.145

description: Expr, Progressor, Normal


title: Exp.Sample.142

description: Expr, Progressor, Her2


title: Exp.Sample.129

description: Expr, Progressor, Her2


title: Exp.Sample.135

description: Expr, Progressor, LumA


title: Exp.Sample.119

description: Expr, Progressor, LumA


title: Exp.Sample.31

description: Expr, Non-Progressor, LumA


title: Exp.Sample.137

description: Expr, Progressor, Her2


title: Exp.Sample.125

description: Expr, Progressor, Her2


title: Exp.Sample.116

description: Expr, Progressor, LumB


title: Exp.Sample.114

description: Expr, Progressor, Normal


title: Exp.Sample.112

description: Expr, Progressor, LumA


title: Exp.Sample.94

description: Expr, Progressor, LumB


title: Exp.Sample.96

description: Expr, Progressor, Basal


title: Exp.Sample.92

description: Expr, Progressor, Normal


title: Exp.Sample.108

description: Expr, Progressor, Basal


title: Exp.Sample.163

description: Expr, Progressor, Her2


title: Exp.Sample.90

description: Expr, Progressor, LumB


title: Exp.Sample.87

description: Expr, Progressor, LumB


title: Exp.Sample.151

description: Expr, Progressor, Basal


title: Exp.Sample.83

description: Expr, Progressor, Her2


title: Exp.Sample.85

description: Expr, Progressor, Her2


title: Exp.Sample.75

description: Expr, Progressor, Her2


title: Exp.Sample.77

description: Expr, Progressor, LumB


title: Exp.Sample.72

description: Expr, Progressor, LumA


title: Exp.Sample.68

description: Expr, Progressor, Her2


title: Exp.Sample.66

description: Expr, Progressor, LumB


title: Exp.Sample.53

description: Expr, Progressor, Her2


title: Exp.Sample.49

description: Expr, Progressor, LumA


title: Exp.Sample.81

description: Expr, Progressor, LumB


title: Exp.Sample.44

description: Expr, Progressor, LumA


title: Exp.Sample.47

description: Expr, Progressor, Basal


title: Exp.Sample.106

description: Expr, Progressor, LumB


title: Exp.Sample.41

description: Expr, Progressor, Basal


title: Exp.Sample.32

description: Expr, Progressor, Normal


title: Exp.Sample.23

description: Expr, Progressor, Her2


title: Exp.Sample.26

description: Expr, Progressor, LumA


title: Exp.Sample.16

description: Expr, Progressor, Her2


title: Meth.Sample.162

type: genomic

description: Meth, Control, Normal

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the FunNorm algorithm using minfi in R

label: Cy3 and Cy5

label_protocol: Bisulfite-treated genomic DNA was restored using the Illumina Infinium HumanMethylation450K BeadChip Kit (WG-314-1003)

extract_protocol: Nucleic Acids were extracted using AllPrep DNA/RNA FFPE kit (Qiagen, Valencia, CA) Extracted DNA was quantified by Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA) and stored at -80°C

value: Non-progressor


title: Exp.Sample.19

description: Expr, Progressor, LumA


title: Exp.Sample.24

description: Expr, Progressor, Her2


title: Exp.Sample.79

description: Expr, Progressor, LumA


title: Exp.Sample.73

description: Expr, Progressor, LumB


title: Meth.Sample.132

description: Meth, Control, LumA


title: Meth.Sample.114

description: Meth, Case, Normal


title: Meth.Sample.3

description: Meth, Control, NA


title: Meth.Sample.52

description: Meth, Control, Basal


title: Exp.Sample.64

description: Expr, Progressor, LumA


title: Meth.Sample.27

description: Meth, Control, NA


title: Meth.Sample.79

description: Meth, Case, LumA


title: Meth.Sample.105

description: Meth, Normal, NA


title: Exp.Sample.121

description: Expr, Progressor, LumA


title: Meth.Sample.8

description: Meth, Control, NA


title: Meth.Sample.155

description: Meth, Case, NA


title: Meth.Sample.53

description: Meth, Case, Her2


title: Meth.Sample.34

description: Meth, Case, NA


title: Meth.Sample.59

description: Meth, Case, NA


title: Meth.Sample.156

description: Meth, Control, NA


title: Exp.Sample.37

description: Expr, Progressor, LumB


title: Meth.Sample.131

description: Meth, Case, Her2


title: Meth.Sample.87

description: Meth, Case, LumB


title: Meth.Sample.158

description: Meth, Control, NA


title: Meth.Sample.70

description: Meth, Control, Basal


title: Meth.Sample.13

description: Meth, Control, NA


title: Meth.Sample.147

description: Meth, Case, NA


title: Meth.Sample.120

description: Meth, Control, Her2


title: Meth.Sample.148

description: Meth, Control, Normal


title: Meth.Sample.63

description: Meth, Case, NA


title: Meth.Sample.19

description: Meth, Case, LumA


title: Meth.Sample.48

description: Meth, Control, NA


title: Meth.Sample.154

description: Meth, Control, Basal


title: Meth.Sample.49

description: Meth, Case, LumA


title: Meth.Sample.80

description: Meth, Control, LumA


title: Meth.Sample.18

description: Meth, Control, NA


title: Meth.Sample.98

description: Meth, Case, NA


title: Meth.Sample.71

description: Meth, Normal, NA


title: Meth.Sample.106

description: Meth, Case, LumB


title: Meth.Sample.159

description: Meth, Case, NA


title: Meth.Sample.165

description: Meth, Control, NA


title: Meth.Sample.15

description: Meth, Control, NA


title: Meth.Sample.88

description: Meth, Control, LumB


title: Meth.Sample.39

description: Meth, Case, NA


title: Meth.Sample.175

description: Meth, Control, LumA


title: Meth.Sample.97

description: Meth, Control, LumB


title: Meth.Sample.54

description: Meth, Control, LumA


title: Meth.Sample.55

description: Meth, Case, LumA


title: Meth.Sample.90

description: Meth, Case, LumB


title: Meth.Sample.170

description: Meth, Control, Normal


title: Exp.Sample.111

description: Expr, Progressor, LumB


title: Meth.Sample.50

description: Meth, Control, LumA


title: Meth.Sample.17

description: Meth, Case, NA


title: Meth.Sample.77

description: Meth, Case, LumB


title: Meth.Sample.62

description: Meth, Control, Her2


title: Meth.Sample.192

description: Meth, Control, Normal


title: Meth.Sample.92

description: Meth, Case, Normal


title: Meth.Sample.161

description: Meth, Case, LumA


title: Exp.Sample.138

description: Expr, Non-Progressor, Normal


title: Meth.Sample.149

description: Meth, Case, LumA


title: Meth.Sample.86

description: Meth, Control, Her2


title: Meth.Sample.14

description: Meth, Control, NA


title: Meth.Sample.135

description: Meth, Case, LumA


title: Meth.Sample.82

description: Meth, Control, Basal


title: Meth.Sample.177

description: Meth, Case, Basal


title: Meth.Sample.76

description: Meth, Control, Normal


title: Meth.Sample.2

description: Meth, Case, NA


title: Meth.Sample.181

description: Meth, Control, NA


title: Meth.Sample.112

description: Meth, Case, LumA


title: Meth.Sample.113

description: Meth, Control, LumA


title: Meth.Sample.25

description: Meth, Control, Normal


title: Meth.Sample.172

description: Meth, Control, NA


title: Meth.Sample.122

description: Meth, Case, NA


title: Meth.Sample.44

description: Meth, Case, LumA


title: Meth.Sample.145

description: Meth, Case, Normal


title: Meth.Sample.133

description: Meth, Case, NA


title: Meth.Sample.94

description: Meth, Case, LumB


title: Meth.Sample.100

description: Meth, Control, NA


title: Meth.Sample.51

description: Meth, Case, NA


title: Meth.Sample.69

description: Meth, Normal, NA


title: Meth.Sample.180

description: Meth, Case, Normal


title: Meth.Sample.33

description: Meth, Control, Her2


title: Meth.Sample.1

description: Meth, Control, NA

value: ALs not in DCIS_Splice_PAM50


title: Meth.Sample.11

description: Meth, Control, NA

value: breast


title: Meth.Sample.178

description: Meth, Control, NA


title: Meth.Sample.72

description: Meth, Case, LumA


title: Meth.Sample.109

description: Meth, Control, LumA


title: Meth.Sample.37

description: Meth, Case, LumB


title: Meth.Sample.24

description: Meth, Case, Her2


title: Meth.Sample.166

description: Meth, Case, LumA


title: Meth.Sample.103

description: Meth, Normal, NA


title: Meth.Sample.29

description: Meth, Control, Her2


title: Meth.Sample.85

description: Meth, Case, Her2


title: Meth.Sample.40

description: Meth, Control, LumB


title: Meth.Sample.5

description: Meth, Control, NA


title: Meth.Sample.91

description: Meth, Control, LumA


title: Meth.Sample.7

description: Meth, Case, NA


title: Meth.Sample.183

description: Meth, Control, LumB


title: Meth.Sample.81

description: Meth, Case, LumB


title: Meth.Sample.153

description: Meth, Case, LumB


title: Meth.Sample.179

description: Meth, Control, NA

value: asian/other


title: Meth.Sample.121

description: Meth, Case, LumA

value: WHITE


title: Meth.Sample.66

description: Meth, Case, LumB

value: Untreated


title: Meth.Sample.46

description: Meth, Control, NA

value: Treated


title: Meth.Sample.173

description: Meth, Case, NA


title: Meth.Sample.26

description: Meth, Case, LumA


title: Meth.Sample.73

description: Meth, Case, LumB


title: Meth.Sample.67

description: Meth, Control, LumA


title: Meth.Sample.152

description: Meth, Control, LumA


title: Meth.Sample.22

description: Meth, Control, LumB


title: Meth.Sample.10

description: Meth, Case, NA


title: Meth.Sample.174

description: Meth, Control, Her2


title: Meth.Sample.32

description: Meth, Case, Normal

value: Normal


title: Exp.Sample.184

description: Expr, Progressor, Basal

value: Progressor


title: Meth.Sample.169

description: Meth, Control, Normal


title: Meth.Sample.119

description: Meth, Case, LumA

value: LumA


title: Meth.Sample.123

description: Meth, Case, NA


title: Meth.Sample.136

description: Meth, Control, Her2


title: Meth.Sample.74

description: Meth, Control, LumB

value: LumB


title: Meth.Sample.182

description: Meth, Case, Her2


title: Meth.Sample.107

description: Meth, Control, LumA


title: Meth.Sample.193

description: Meth, Control, NA


title: Meth.Sample.164

description: Meth, Case, NA


title: Meth.Sample.56

description: Meth, Control, LumB


title: Meth.Sample.21

description: Meth, Case, NA


title: Meth.Sample.116

description: Meth, Case, LumB


title: Meth.Sample.84

description: Meth, Control, Basal


title: Meth.Sample.102

description: Meth, Case, NA


title: Meth.Sample.95

description: Meth, Control, Her2


title: Meth.Sample.65

description: Meth, Control, LumB


title: Meth.Sample.150

description: Meth, Control, Basal


title: Meth.Sample.137

description: Meth, Case, Her2


title: Meth.Sample.189

description: Meth, Control, NA


title: Meth.Sample.146

description: Meth, Control, LumA


title: Meth.Sample.176

description: Meth, Control, NA


title: Meth.Sample.30

description: Meth, Case, NA


title: Meth.Sample.57

description: Meth, Control, NA


title: Meth.Sample.4

description: Meth, Case, NA


title: Meth.Sample.83

description: Meth, Case, Her2


title: Meth.Sample.184

description: Meth, Case, Basal


title: Meth.Sample.35

description: Meth, Case, LumB


title: Meth.Sample.187

description: Meth, Control, LumA


title: Meth.Sample.68

description: Meth, Case, Her2


title: Exp.Sample.35

description: Expr, Progressor, LumB


title: Meth.Sample.138

description: Meth, Control, Normal


title: Meth.Sample.186

description: Meth, Case, Her2


title: Meth.Sample.20

description: Meth, Case, NA


title: Meth.Sample.134

description: Meth, Control, LumB


title: Meth.Sample.110

description: Meth, Control, LumB


title: Meth.Sample.31

description: Meth, Control, LumA


title: Meth.Sample.16

description: Meth, Case, Her2


title: Meth.Sample.9

description: Meth, Case, NA


title: Meth.Sample.43

description: Meth, Case, NA


title: Meth.Sample.125

description: Meth, Case, Her2


title: Meth.Sample.168

description: Meth, Case, Normal


title: Meth.Sample.96

description: Meth, Case, Basal


title: Meth.Sample.130

description: Meth, Control, LumB


title: Meth.Sample.60

description: Meth, Control, LumB


title: Meth.Sample.115

description: Meth, Control, LumA


title: Meth.Sample.61

description: Meth, Case, NA


title: Meth.Sample.6

description: Meth, Case, NA


title: Meth.Sample.42

description: Meth, Case, NA


title: Meth.Sample.188

description: Meth, Control, NA


title: Meth.Sample.190

description: Meth, Control, LumB

value: Lum B


title: Meth.Sample.47

description: Meth, Case, Basal


title: Meth.Sample.128

description: Meth, Control, LumA


title: Meth.Sample.127

description: Meth, Case, NA


title: Meth.Sample.104

description: Meth, Control, Her2


title: Meth.Sample.171

description: Meth, Case, Normal


title: Meth.Sample.36

description: Meth, Control, Her2


title: Meth.Sample.89

description: Meth, Case, NA


title: Meth.Sample.101

description: Meth, Normal, NA


title: Meth.Sample.41

description: Meth, Case, Basal


title: Meth.Sample.45

description: Meth, Control, LumA


title: Meth.Sample.111

description: Meth, Case, LumB


title: Meth.Sample.160

description: Meth, Control, LumA

value: HISPANIC WHITE


title: Meth.Sample.163

description: Meth, Case, Her2


title: Meth.Sample.23

description: Meth, Case, Her2


title: Meth.Sample.129

description: Meth, Case, Her2


title: Meth.Sample.191

description: Meth, Control, Normal


title: Meth.Sample.126

description: Meth, Control, LumA


title: Meth.Sample.124

description: Meth, Control, LumA


title: Meth.Sample.93

description: Meth, Control, NA


title: Meth.Sample.75

description: Meth, Case, Her2


title: Meth.Sample.12

description: Meth, Case, NA


title: Meth.Sample.185

description: Meth, Control, NA


title: Meth.Sample.167

description: Meth, Control, LumA


title: Meth.Sample.99

description: Meth, Normal, NA


title: Meth.Sample.118

description: Meth, Normal, NA


title: Meth.Sample.64

description: Meth, Case, LumA


title: Meth.Sample.142

description: Meth, Case, Her2


title: Meth.Sample.28

description: Meth, Case, Her2


title: Meth.Sample.194

description: Meth, Normal, NA


title: Meth.Sample.157

description: Meth, Case, NA


title: Meth.Sample.108

description: Meth, Case, Basal


title: Meth.Sample.78

description: Meth, Control, LumA


title: Meth.Sample.117

description: Meth, Control, Normal


title: Meth.Sample.58

description: Meth, Control, NA


title: Meth.Sample.38

description: Meth, Control, LumB


title: ilmn_ZR_75_1_rep2

status: Public on Oct 22 2024

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
We used pbccs to generate highly accurate HiFi reads using raw subreads through circular consensus sequencing (CCS). These high-quality reads were then processed using lima to demultiplex the sequences based on barcodes and to remove cDNA primers. The isoseq-refine tool was subsequently applied for polyA tail trimming and concatemer removal, resulting in Full-Length Non-Chimeric (FLNC) reads. The FLNC reads were aligned to the reference genome using minimap2, employing the splice preset optimized for long-read spliced alignment After alignment, samtools was used to sort and index the BAM files. For transcript isoform quantification, we utilized bambu, operating in both discovery and quantification modes.
Assembly: hg38
Supplementary files format and content: processed data were quantification in tsv, csv, and txt format

source_name: Breast

extract_protocol:
Cells were collected and lysed in TRIzol reagent (ThermoFisher). The lysate was mixed with chloroform and phase-separated in a phaselock gel tube heavy (Quantabio) by centrifugation. The aqueous phase containing RNA was then mixed with one volume of 100% ethanol, and column-purified using Zymo QuickRNA Miniprep kit with in-column DNase treatment per the manufacturer’s protocol. RNA integrity (RIN  ≥ 9) was confirmed using the 4200 Tapestation System (Agilent) prior to library construction.
Long-read RNA-seq libraries were constructed using the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, PacBio Iso-Seq Express Oligo Kit and SMRTbell express template prep kit 3.0 according to the manufacturer’s protocol. Short-read RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-seq kit v3 (TaKaRa Bio) following the manufacturer’s instructions.

value: Breast


title: Sample patient pool 1

status: Public on Oct 30 2024

city: Bethesda

first: Elise

middle: M

last: O'Connell

state: MD

address: 4 Center Drive

department: Laboratory of Parasitic Diseases

institute: National Institute of Allergy and Infectious Diseases

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Initial processing of the two samples included removal of cells with a low number of unique molecular identifier (UMI) counts using Cellranger v7.1.0 with default parameters. Demuxlet was used with matching exome SNP data to call cell genotypes and multiplet annotations.
The remainder of the single cell RNA sequencing (scRNA) analysis was performed with Seurat v4.1.0. Cell type identification was completed using a combination of SingleR with the Novershtern hematopoietic database and canonical immune cell markers. Sample S1 was filtered for cells containing greater than 200 and less than 4000 detected genes, less than 5% total mitochondrial gene expression, and singlet calls by demuxlet. Sample S2 was filtered for cells containing greater than 200 and less than 4000 detected genes, less than 10% total mitochondrial gene expression, and singlet calls by demuxlet. The final total numbers of cells in S1 and S2 were 668 and 1,336, respectively.
Pooled patient samples were deconvoluted using the genotype calls in S1 and S2 and early and late samples identified. Samples S1 and S2 were then re-integrated using Seurat and standard scRNA analysis was completed using 20 principal components to visualize the UMAP diagrams. After unsupervised clustering, iTregs were defined as the CD4+ T Cell cluster that contained a majority of cells with 0 FoxP3 expression and greater than 0 CTLA4 expression. nTregs were defined as the CD4+ T cell cluster that contained a majority of cells with greater than 0 FoxP3 expression.
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, and demuxlet csv files

molecule: polyA RNA

source_name: CSF

extract_protocol:
Single cell capture, cDNA amplification, and library construction were completed using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, cat#1000127, 1000128) according to manufacturer’s protocols. SPRIselect Reagent (Beckman Coulter, cat#B23317) was used for cDNA clean up, and quality control steps were completed using Bioanalyzer High Sensitivity DNA Kits (Agilent, cat#5067-4626).
Two 10x Genomics Single Cell Chromium 3' mRNA libraries were made (S1 and S2) and sequenced as part of one Illumina NovaSeq S1 run. Each sample had a sequencing yield of greater than 399 million reads. The sequencing run was performed using recommended parameters with 28 cycles + 90 cycles asymmetric run.

value: CSF


title: Sample patient pool 2

description: 10x Genomics


title: Meth.Sample.151

description: Meth, Case, Basal

value: Basal


title: Meth.Sample.143

description: Meth, Control, LumA


title: Meth.Sample.197

description: Meth, Normal, NA


title: Meth.Sample.141

description: Meth, Control, NA


title: Meth.Sample.140

description: Meth, Case, NA

value: Lum A


title: Meth.Sample.139

description: Meth, Case, NA


title: Meth.Sample.196

description: Meth, Normal, NA


title: ilmn_PANC1tr_rep1

source_name: Pancreas

value: Pancreas


title: ilmn_MDA_453_rep2


title: ilmn_MDA_231u_rep2


title: ilmn_SW620_rep2

source_name: Colon

value: Colon


title: ilmn_PC3_rep1

source_name: Prostate

value: Prostate


title: ilmn_MDA_231u_rep1


title: ilmn_MDA_453_rep1


title: ilmn_MCF7_rep1


title: ilmn_SW480tr_rep1


title: ilmn_SW480tr_rep2


title: ilmn_ZR_75_1_rep1


title: ilmn_PANC1tr_rep2


title: ilmn_MCF7_rep2


title: ilmn_PC3_rep2


title: ilmn_K562_rep2

source_name: Bone

value: Bone


title: ilmn_MP2_rep1

value: MIA PaCa-2


title: ilmn_MP2_rep2


title: ilmn_HEPG2_rep2

source_name: Liver

value: Liver


title: ilmn_LS174Ttr_rep2

value: LS 174T


title: ilmn_HEPG2_rep1


title: ilmn_HEK293_rep2

source_name: Embryonic Kidney

value: Embryonic Kidney


title: ilmn_HEK293_rep1


title: ilmn_LS174Ttr_rep1


title: ilmn_LNCaP_rep2

value: LNCaP


title: ilmn_LNCaP_rep1


title: ilmn_HS707A_rep2


title: ilmn_HS707A_rep1


title: ilmn_H23_rep2

source_name: Lung

value: Lung


title: ilmn_H23_rep1


title: ilmn_HCT116_rep2


title: ilmn_K562_rep1


title: ilmn_HCC44_rep2


title: ilmn_HCC44_rep1


title: ilmn_SW620_rep1


title: ilmn_C42B_rep1


title: ilmn_C42B_rep2


title: ilmn_BxPC3_rep2


title: ilmn_A549_rep2


title: ilmn_BxPC3_rep1


title: ilmn_Colo320_rep1


title: ilmn_H358_rep2


title: ilmn_H1299_rep1


title: ilmn_H358_rep1


title: ilmn_HCT116_rep1


title: pb_SW620_rep2


title: ilmn_Colo320_rep2


title: pb_ZR_75_1_rep1


title: ilmn_A549_rep1


title: pb_SW480tr_rep1


title: ilmn_H1299_rep2


title: pb_MP2_rep2


title: pb_SW480tr_rep2


title: pb_SW620_rep1


title: ilmn_A2058_rep1

source_name: Skin

value: Skin


title: ilmn_A375tr_rep1


title: pb_MDA_453_rep1


title: pb_PANC1tr_rep1


title: pb_PC3_rep1


title: pb_MDA_453_rep2


title: pb_MDA_231u_rep1


title: pb_MDA_231u_rep2


title: pb_MP2_rep1


title: pb_MCF7_rep1


title: ilmn_A375tr_rep2


title: ilmn_A2058_rep2


title: pb_LS174Ttr_rep1


title: pb_LS174Ttr_rep2


title: pb_LNCaP_rep2


title: pb_K562_rep1


title: pb_HEPG2_rep1


title: pb_HS707A_rep1


title: pb_K562_rep2


title: pb_HS707A_rep2


title: pb_LNCaP_rep1


title: pb_HEK293_rep1


title: pb_PANC1tr_rep2


title: pb_H358_rep2


title: pb_HCT116_rep1


title: pb_HCC44_rep2


title: pb_HCT116_rep2


title: pb_PC3_rep2


title: pb_H358_rep1


title: pb_H23_rep1


title: pb_HCC44_rep1


title: pb_H23_rep2


title: pb_Colo320_rep1


title: pb_MCF7_rep2


title: pb_HEPG2_rep2


title: pb_Colo320_rep2


title: pb_H1299_rep1


title: pb_H1299_rep2


title: pb_BxPC3_rep1


title: pb_C42B_rep1


title: pb_HEK293_rep2


title: pb_A549_rep2


title: pb_A549_rep1


title: pb_A2058_rep2


title: pb_A375tr_rep2


title: pb_A2058_rep1


title: RNF2_EED_DIST_E12_5_REP1

status: Public on Oct 21 2024

city: Montréal

first: Fanny

last: GUERARD-MILLET

state: Quebec

address: 110 AVENUE DES PINS OUEST

country: Canada

institute: IRCM

data_processing:
Mouse (GRCm38.p6) genome FASTA and GTF files were downloaded from the Ensembl Website (http://useast.ensembl.org/info/about/publications.html) on October 4th 2022. Adapter sequences were removed from reads using robtools (https://github.com/francoisrobertlab/robtools) with the command “robtools trimmomatic --trimmers "ILLUMINACLIP:adapters.fa:2:30:10 HEADCROP:10 SLIDINGWINDOW:4:15 TRAILING:20 MINLEN:40"” which requires Trimmomatic. Reads were aligned to the genome using STAR (https://github.com/alexdobin/STAR ) using the command “STAR --readFilesCommand zcat --readFilesIn "$sample"-paired_R1.fastq.gz "$sample"-paired_R2.fastq.gz --genomeDir mouse-star-index --genomeLoad NoSharedMemory --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --outSAMheaderHD @HD VN:1.4 SO:unsorted --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFileNamePrefix "$sample".star/"$sample"_“ where “$sample” is replaced by the sample name. STAR version 2.7.9a was used. The number of fragments per transcript were counted using RSEM (http://deweylab.github.io/RSEM/ ) with the command “rsem-calculate-expression --alignments --paired-end "$sample".star/"$sample"_Aligned.toTranscriptome.out.bam rsem-index/Mus_musculus "$sample".rsem/"$sample"” where “$sample” is replaced by the sample name. RSEM version 1.3.3 was used.
Assembly: mm10

organism: Mus musculus

source_name: distal forelimb

extract_protocol:
RNA was extracted from dissected proximal and distal limb buds from 2 independent pools of wild type limb buds (n=2) and from two independent pools of mutant limb buds (n=2). The extraction was performed using the RNAeasy Plus mini kit. Next, mRNA enrichment, library preparation and flow-cell preparation for sequencing were performed by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations. Sequencing was done on a Nextseq500 instrument with a paired-end 50 cycles protocol.
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina in a 50 cycles paired-end configuration.

value: distal forelimb


title: RNF2_PROX_E12_5_REP1

source_name: proximal forelimb

value: proximal forelimb


title: RNF2_DIST_E12_5_REP2


title: pb_A375tr_rep1


title: pb_BxPC3_rep2


title: RNF2_DIST_E12_5_REP1


title: RNF2_EED_DIST_E12_5_REP2


title: EED_DIST_E12_5_REP2


title: EED_DIST_E12_5_REP1


title: EED_PROX_E12_5_REP1


title: purified EVs from m005 cell line, bulk RNA-seq

status: Public on Oct 01 2024

city: Rehovot

first: Rony

last: Chanoch

state: Israel

address: Weizmann Institute of Science, 234 Herzl Street

country: Israel

institute: Weizmann Instititue

description:
Smart-Seq2
EV_TPM.txt

data_processing:
Utilized CellRanger for initial alignment, filtering, and quantification of single-cell RNA-seq data.
Assembly: GRCh38, mm10
Supplementary files format and content: tab-separated tpm and metadata files, and space-separated raw counts file.

source_name: Mouse glioblastoma

extract_protocol:
Dissociated organoids were pooled together by model and resuspended in ice cold PBS with 1% BSA for fluorescence-activated cell sorting (FACS). Each sample was co-stained for 30 minutes with CellTrace Calcein Violet, AM (Thermo Fisher Scientific) and TO-PRO-3 (Thermo Fisher Scientific) live and dead cell markers, respectively. For each glioblastoma-cortical organoid FACS experiment, an age and batch matched cortical organoid was run as a negative gating control. GFP/tdT positive and negative fractions from each model were collected into separate 1.5 mL microcentrifuge tubes, with a minimum goal of 25,000 cells per collection tube. Sorting was performed with a FACS Aria Fusion Special Order System (Becton Dickinson). The sorting was limited to under 90 minutes per sample, and the collection tubes were maintained at 4° C for the sort duration, to minimize FACS artifacts on the downstream scRNA-seq results. Sorted, viable cell populations were immediately transferred to droplet-based (10x) single-cell RNA sequencing pipelines.
For the 10X experiments, GFP/tdT positive and negative pools were centrifuged at 250 RCF for 5 mins, and the resulting cell pellets were resuspended in PBS + 0.04% BSA at a target concentration of 1 million cells per mL. The scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G, and 10x Chromium Controller (10x Genomics) according to the 10X Single Cell 3′ v3.1 protocol. The GFP/tdT positive and negative cell populations were separately profiled for each glioblastoma-cortical organoid model. We loaded approximately 10,000 single cells to the Chromium Controller with a targeted recovery of 6,000 cells per cell population. Single cells, reagents and single gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized droplets and subjected to reverse transcription. Droplets were broken and the barcoded cDNAs were purified with DynaBeads and amplified by 12 cycles of PCR (98°C for 3 min; [98°C for 15 s, 63°C for 20 s, 72°C for 1 min] x 12; 72°C for 1 min). 3′ gene expression cDNA were size-selected and separated with SPRIselect Reagent (Beckman Coulter), and then fragmented, end-repaired, ligated with index adaptors. Quality control of the resulting libraries was performed with the Bioanalyzer High Sensitivity DNA Analysis (Agilent). The constructed gene expression libraries were paired-end sequenced using a NextSeq 2000 sequencer (Illumina). Smart-seq2 whole transcriptome amplification, library construction, and sequencing were performed as previously published.

value: Mouse glioblastoma


title: BS-5856

status: Public on Oct 11 2024

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
We initiated our analysis by aligning the raw fastq files to the customized mouse genome reference mm10, which included the Rfp sequence. This alignment process was executed using CellRanger v5.0.0 by 10X Genomics. Following alignment, we used the CellRanges algorithm to filter count matrices. Cells with less than 400 genes, fewer than 1000 UMI (unique molecular identifier), or over 25% mitochondrial gene expression were excluded. Subsequent data processing and analysis were conducted using the Seurat v4.2.2 R package. The data was normalized using the NormalizeData function, utilizing the normalization.method = 'LogNormalize' parameter. For dimensionality reduction, we focused on the top 2,000 variable features, using functions such as FindVariableFeatures, ScaleData, and RunPCA. Ultimately, we generated UMAPs based on the top 15 principal components (PCs).
To subcluster the immune compartment, we employed the R package Harmony to address batch effects stemming from technical variations across replicates. De novo clustering was carried out using the Louvain algorithm at multiple resolutions (0.2, 0.4, 0.8, 2, 3, 5, 8) within the KNN graph space. For high-level cell type annotation, we iteratively and semi-supervisedly assigned de novo discovered clusters to cell types based on the expression of established marker genes defining each cluster. The annotation of cell subtypes at a lower level followed a similar approach to the high-level annotation, with additional assistance from de novo marker discovery utilizing the Seurat FindMarkers function and Wilcoxon Rank Sum test.
To identify clusters enriched with doublets, we searched for cell clusters that exhibited the expression of canonical markers for two or more distinct cell types and a higher count of genes/UMI. These identified clusters were subsequently excluded from further analysis.
Cell-level proliferation analysis was performed using the Seurat function CellCycleScoring, which utilized a curated list of murine cell cycle genes. Subsequently, cells were categorized as 'cycling' or 'non-cycling' based on whether their S-phase score or G2M-score exceeded a threshold of 0.10 for the tumor compartment and immune compartment.
To identify modules of co-expressed genes, we employed the R package scWGCNA (https://github.com/smorabit/scWGCNA). Initially, we computed metacells, each comprising 100 cells (k=100), utilizing the construct_metacells function. For module identification, we utilized the blockwiseConsensusModules function with the following parameter settings: softPower=14, deepSplit=1, and mergeCutHeight=0.20 for the tumor analysis, and softPower=12, deepSplit=4, and mergeCutHeight = 0.20 for the microglia analysis. It's important to note that only the top 10,000 variable genes were included in this analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tumor

extract_protocol:
Tumors were dissected from the brain, minced into pieces < 1 mm3, and digested with an enzymatic mixture that includes papain (0.94 mg/ml, Worthington, LS003120), EDTA (0.18 mg/ml, Sigma, E6758), cysteine (0.18 mg/ml, Sigma, A8199), and DNase I (60 μg/ml, Roche, 11284932001) in 2 ml HBSS (Gibco, 14175-095). Tumor tissues were kept at 37°C for 15 minutes with occasional agitation. The digestion was terminated with the addition of 2 ml Ovomucoid (0.7 mg/ml, Worthington, LS003086). Following digestion, single cells were passed through a 70 μm cell strainer, centrifuged, and resuspended in 30% Percoll (GE Healthcare, 17-0891-01) solution containing 10% FBS (Hyclone SH30396.03). Cells were separated by centrifugation at 800g for 15 minutes at 4°C. The pellet was resuspended in RBC lysis buffer (BioLegend, 420301) for 1 min at 37°C before they were centrifuged at 450g for 5 min. The pellet was resuspend in PBS and immediately dilvered for GEM preparation.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (ThermoFisher) analyses

value: brain tumor


title: MGH143 GCO, GFPpos (FACS), scRNA-seq

description:
10X genomics (3' SC)
HUMAN_MODELS_TPM.txt
HUMAN_MODELS_METADATA.txt

source_name: Glioblastoma-cortical organoid (GCO)

value: Glioblastoma-cortical organoid (GCO)


title: EED_PROX_E12_5_REP2


title: MGG87 GCO, tdTpos (FACS), scRNA-seq


title: RNF2_PROX_E12_5_REP2


title: MGG75 GCO, GFPneg (FACS), scRNA-seq


title: BS-H3-1K27M-20210804

description: 10x Genomics


title: RNF2_EED_PROX_E12_5_REP1


title: MGG70 GCO, GFPneg (FACS), scRNA-seq


title: 5718-20210810-BS-H3-1K27M

description: 10x Genomics


title: RNF2_EED_PROX_E12_5_REP2


title: MGG87 GCO, tdTneg (FACS), scRNA-seq


title: MGH143 GCO, GFPneg (FACS), scRNA-seq


title: MGG65 GCO, GFPneg (FACS), scRNA-seq


title: MGG70 GCO, GFPpos (FACS), scRNA-seq


title: MGG23_11A GCO, GFPpos and GFPneg gene expression

description:
10X genomics (3' SC + FB) gene expression
HUMAN_MODELS_TPM.txt
HUMAN_MODELS_METADATA.txt


title: MGG65 GCO, GFPpos (FACS), scRNA-seq


title: MGG23_PGP1 GCO, GFPpos (FACS), scRNA-seq


title: MGG23_PGP1 GCO, GFPneg (FACS), scRNA-seq


title: MGG23_H1 GCO, GFPneg (FACS), scRNA-seq


title: MGG23_11A GCO, GFPpos and GFPneg feature barcoding

description:
10X genomics (3' SC + FB) Feature barcoding: GFPpos (TotalSeq(tm)-B0253 anti-human Hashtag 3 Antibody -- GTCAACTCTTTAGCG); GFPneg:  (TotalSeq(tm)-B0254 anti-human Hashtag 4 Antibody -- TGATGGCCTATTGGG)
HUMAN_MODELS_TPM.txt
HUMAN_MODELS_METADATA.txt


title: MGG23_H1 GCO, GFPpos (FACS), scRNA-seq


title: MGG101 GCO, GFPpos and GFPneg feature barcoding

description:
10X genomics (3' SC + FB) feature barcoding: GFPpos (TotalSeq(tm)-B0253 anti-human Hashtag 3 Antibody -- TTCCGCCTCTCTTTG); GFPneg:  (TotalSeq(tm)-B0254 anti-human Hashtag 4 Antibody -- AGTAAGTTCAGCGTA)
HUMAN_MODELS_TPM.txt
HUMAN_MODELS_METADATA.txt


title: MGG125 GCO, GFPpos (FACS), scRNA-seq


title: MGG75 GCO, GFPpos (FACS), scRNA-seq


title: MGG123 GCO, GFPpos (FACS), scRNA-seq


title: MGG125 GCO, GFPneg (FACS), scRNA-seq


title: MGG123 GCO, GFPneg (FACS), scRNA-seq


title: MGG101 GCO, GFPpos and GFPneg gene expression


title: DMS-MaPseq of E. coli TOP10, in vitro refolded, 37°C (mRNA)

status: Public on Sep 24 2024

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

data_processing:
*library strategy: DMS-MaPseq
Following sequencing, paired-end reads were clipped of sequencing adapters using Cutadapt v4.4 (parameters: -A AGATCGGAAG -a AGATCGGAAG -m 100:100 -O 1), and merged using PEAR v0.9.11 (parameters: -n 100 -q 20 -u 0 -e -y 10G -z). Merged reads were then combined with R1 and the reverse-complemented R2 for read pairs that could not be merged. Next, a comprehensive annotation of E. coli transcriptional units with experimentally-determined TSSs was built by aggregating 5’ UTR information from RegulonDB and transcriptional units from EcoCyc (available from https://www.incarnatolab.com/datasets/EcoliEnsembles_Borovska_2024.php), and the corresponding sequences were extracted from the E. coli str. K-12 substr. MG1655 genome (GenBank: U00096.3). Reads were then mapped to this reference using the rf-map tool of the RNA Framework v2.8.3 and Bowtie2 v2.3.5.1, after clipping terminal bases with Phred quality < 20, discarding reads containing internal Ns, and trimming the 6 5’-most bases to account for possible mispriming artifacts (parameters: -cq5 20 -ctn -cmn 0 -cl 50 -mp "--very-sensitive-local --nofw" -b5 6). Alignments in SAM format were sorted and converted to BAM format using Samtools v1.15.1. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage) and MM files (containing a map of mutated positions per read). Aligned reads spanning less than 100 nt of a transcript, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -wl 2000 -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1 -mpr 2). DMS-MaPseq data from total RNA, used for the calibration of folding parameters, was analyzed with minor changes to the above protocol. Briefly, reads were mapped to a reference composed only of the 16S and 23S rRNA sequences. The minimum length spanned by reads was decreased to 90 nt (as total RNA DMS-MaPseq experiments were sequenced as single-read 100 bp, in contrast to rRNA-depleted DMS-MaPseq experiments that were sequenced as paired-end 150 bp) and reads harboring < 2 mutations were also retained (parameters: -m -ds 90 -es -na -ni -dc 3 -ow -me 0.1 -md 1).
Assembly: U00096.3
Supplementary files format and content: Wiggle files of bulk raw DMS-MaPseq mutation frequencies

molecule: cytoplasmic RNA

organism: Escherichia coli

growth_protocol: E. coli K-12 MG1655 derivative strains DH5α and TOP10 (DH10b) were streaked on LB plates, and a single colony was picked, inoculated in 4 mL LB broth, and grown overnight at 37°C with shaking. The day after, the culture was diluted to an OD600 = 0.05 in 25 mL LB broth and grown at 37°C until OD600 ≈ 0.5 (~2 h). For cold-shock, 2 mL of this culture were mixed with 2 mL of LB broth pre-chilled to 0°C in a water-ice slurry, then incubated at 10°C for 20 min.

extract_protocol:
For in cell treatments, cell pellets were resuspended in 62.5 μl Resuspension Buffer [20 mM Tris-HCl pH 8.0; 80 mM NaCl; 10 mM EDTA pH 8.0], supplemented with 100 μg/mL final Lysozyme (cat. L6876, Merck) and 20 U SUPERase•In™ RNase Inhibitor (cat. A2696, ThermoFisher Scientific), by vigorous vortexing. Samples were incubated at room temperature for 1 min, followed by addition of 62.5 μl Lysis Buffer [0.5% Tween-20; 0.4% Sodium deoxycholate; 2 M NaCl; 10 mM EDTA]. Samples were then inverted 5-10 times and incubated at room temperature for 2 min, followed by additional 2 min on ice. 1 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific) was then added, samples were vigorously vortexed for 15 sec, and RNA was extracted as per manufacturer instructions.
Prior to library preparation, highly abundant short RNA species, such as tRNAs, were depleted on Monarch® RNA Cleanup columns by loading a 1:1:1 mixture of total RNA in nuclease-free water, RNA binding buffer and 100% ethanol. rRNA depletion was performed on 1.1 μg total RNA using the RiboCop for Bacteria kit (cat. 126, Lexogen), with two minor changes to the manufacturer’s protocol: denaturation temperature was increased to 95°C, and probe annealing temperature was lowered to 55°C. Following rRNA depletion, RNA was cleaned up on Monarch® RNA Cleanup columns, eluted in 8 μl nuclease-free water, and supplemented with 2 μl 100 μM random hexamers, 2 μl dNTPs (10 mM each) and 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2]. Samples were then incubated at 94°C for 5.5 min, to simultaneously denature and fragment the RNA to a median size of 200 nt, and immediately transferred to ice for 1 min. Samples were then supplemented with 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50) and 25 ng/μl Actinomycin D (to increase strand-specificity; cat. A1410, Merck), and then incubated at 25°C for 10 min, 57°C for 1 h, and 60°C for 1 h. TGIRT-III was degraded by adding 2 μg Proteinase K and incubating at 37°C for 20 min. Proteinase K was inactivated by addition of Protease Inhibitor Cocktail (cat. P8340, Merck). cDNA-RNA hybrids were then converted to dsDNA using the NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (cat. E7550, New England Biolabs), by incubating at 16°C for 1 h. DsDNA was then cleaned up with 1.8 volumes NucleoMag NGS Clean-up and Size Select beads (cat. 744970, Macherey Nagel), and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (cat. E7645S, New England Biolabs), as per manufacturer instructions.

treatment_protocol: For dimethyl sulfate (DMS; cat. D186309, Merck) probing, DMS from a fresh 1:4 dilution in ethanol (~2.64 M) was added to the bacteria at a final concentration of 200 mM. Probing was conducted for 2 min at 37°C, or for 30 min at 10°C (to achieve comparable modification efficiencies), with moderate shaking (800 RPM). For in vitro refolded samples, RNA was first extracted from exponentially growing bacteria, then denatured at 95°C for 2 min, snap-cooled on ice for 2 min, then mixed with ice cold RNA Folding Buffer [25 mM HEPES pH 7.5; 200 mM KCl] and incubated at 37°C for 15 min. MgCl2 was then added to 5 mM final, and RNA was further incubated for 15 min at 37°C before proceeding to probing with 200 mM final DMS for 2 min at 37°C. Reactions were then quenched by addition of 1 volume 1 M DTT. For in cell treatments, bacteria were collected by centrifugation at 17,000g for 1 min. Supernatant was discarded, the pellet was washed twice with 0.5 M DTT, and then immediately subjected to RNA extraction. For in vitro samples, RNA was directly cleaned up on Monarch RNA Cleanup Kit (10 µg) columns.

tag: strain


title: MDA-231 GCO, GFPneg (FACS), scRNA-seq

source_name: MDA-MB-231-cortical organoid (GCO)

value: MDA-MB-231-cortical organoid (GCO)


title: DMS-MaPseq of E. coli DH5a, exponential phase, 10°C cold-shock (mRNA)

data_processing:
Following sequencing, paired-end reads were clipped of sequencing adapters using Cutadapt v4.4 (parameters: -A AGATCGGAAG -a AGATCGGAAG -m 100:100 -O 1), and merged using PEAR v0.9.11 (parameters: -n 100 -q 20 -u 0 -e -y 10G -z). Merged reads were then combined with R1 and the reverse-complemented R2 for read pairs that could not be merged. Next, a comprehensive annotation of E. coli transcriptional units with experimentally-determined TSSs was built by aggregating 5’ UTR information from RegulonDB and transcriptional units from EcoCyc (available from https://www.incarnatolab.com/datasets/EcoliEnsembles_Borovska_2024.php), and the corresponding sequences were extracted from the E. coli str. K-12 substr. MG1655 genome (GenBank: U00096.3). Reads were then mapped to this reference using the rf-map tool of the RNA Framework v2.8.3 and Bowtie2 v2.3.5.1, after clipping terminal bases with Phred quality < 20, discarding reads containing internal Ns, and trimming the 6 5’-most bases to account for possible mispriming artifacts (parameters: -cq5 20 -ctn -cmn 0 -cl 50 -mp "--very-sensitive-local --nofw" -b5 6). Alignments in SAM format were sorted and converted to BAM format using Samtools v1.15.1. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage) and MM files (containing a map of mutated positions per read). Aligned reads spanning less than 100 nt of a transcript, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -wl 2000 -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1 -mpr 2). DMS-MaPseq data from total RNA, used for the calibration of folding parameters, was analyzed with minor changes to the above protocol. Briefly, reads were mapped to a reference composed only of the 16S and 23S rRNA sequences. The minimum length spanned by reads was decreased to 90 nt (as total RNA DMS-MaPseq experiments were sequenced as single-read 100 bp, in contrast to rRNA-depleted DMS-MaPseq experiments that were sequenced as paired-end 150 bp) and reads harboring < 2 mutations were also retained (parameters: -m -ds 90 -es -na -ni -dc 3 -ow -me 0.1 -md 1).
Assembly: U00096.3
Supplementary files format and content: Wiggle files of bulk raw DMS-MaPseq mutation frequencies
Library strategy: DMS-MaPseq

extract_protocol:
Cell pellets were resuspended in 62.5 μl Resuspension Buffer [20 mM Tris-HCl pH 8.0; 80 mM NaCl; 10 mM EDTA pH 8.0], supplemented with 100 μg/mL final Lysozyme (cat. L6876, Merck) and 20 U SUPERase•In™ RNase Inhibitor (cat. A2696, ThermoFisher Scientific), by vigorous vortexing. Samples were incubated at room temperature for 1 min, followed by addition of 62.5 μl Lysis Buffer [0.5% Tween-20; 0.4% Sodium deoxycholate; 2 M NaCl; 10 mM EDTA]. Samples were then inverted 5-10 times and incubated at room temperature for 2 min, followed by additional 2 min on ice. 1 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific) was then added, samples were vigorously vortexed for 15 sec, and RNA was extracted as per manufacturer instructions.
Prior to library preparation, highly abundant short RNA species, such as tRNAs, were depleted on Monarch® RNA Cleanup columns by loading a 1:1:1 mixture of total RNA in nuclease-free water, RNA binding buffer and 100% ethanol. rRNA depletion was performed on 1.1 μg total RNA using the RiboCop for Bacteria kit (cat. 126, Lexogen), with two minor changes to the manufacturer’s protocol: denaturation temperature was increased to 95°C, and probe annealing temperature was lowered to 55°C. Following rRNA depletion, RNA was cleaned up on Monarch® RNA Cleanup columns, eluted in 8 μl nuclease-free water, and supplemented with 2 μl 100 μM random hexamers, 2 μl dNTPs (10 mM each) and 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2]. Samples were then incubated at 94°C for 5.5 min, to simultaneously denature and fragment the RNA to a median size of 200 nt, and immediately transferred to ice for 1 min. Samples were then supplemented with 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor, 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50) and 25 ng/μl Actinomycin D (to increase strand-specificity; cat. A1410, Merck), and then incubated at 25°C for 10 min, 57°C for 1 h, and 60°C for 1 h. TGIRT-III was degraded by adding 2 μg Proteinase K and incubating at 37°C for 20 min. Proteinase K was inactivated by addition of Protease Inhibitor Cocktail (cat. P8340, Merck). cDNA-RNA hybrids were then converted to dsDNA using the NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (cat. E7550, New England Biolabs), by incubating at 16°C for 1 h. DsDNA was then cleaned up with 1.8 volumes NucleoMag NGS Clean-up and Size Select beads (cat. 744970, Macherey Nagel), and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (cat. E7645S, New England Biolabs), as per manufacturer instructions.

treatment_protocol: For dimethyl sulfate (DMS; cat. D186309, Merck) probing, DMS from a fresh 1:4 dilution in ethanol (~2.64 M) was added to the bacteria at a final concentration of 200 mM. Probing was conducted for 2 min at 37°C, or for 30 min at 10°C (to achieve comparable modification efficiencies), with moderate shaking (800 RPM). Reactions were then quenched by addition of 1 volume 1 M DTT, after which bacteria were collected by centrifugation at 17,000g for 1 min. Supernatant was discarded, the pellet was washed twice with 0.5 M DTT, and then immediately subjected to RNA extraction.


title: MDA-231 GCO, GFPpos (FACS), scRNA-seq


title: DMS-MaPseq of E. coli TOP10, exponential phase, 10°C cold-shock (mRNA)


title: m005 GCO, GFPneg (FACS), scRNA-seq

description:
10X genomics (3' SC)
M005_TPM.txt
M005_METADATA.txt

source_name: mus musculus

value: mus musculus


title: DMS-MaPseq of E. coli TOP10, exponential phase, 37°C (mRNA)


title: DMS-MaPseq of E. coli TOP10, exponential phase, ex vivo, 37°C (total RNA)


title: DMS-MaPseq of E. coli DH5a, in vitro refolded, 37°C (mRNA)


title: DMS-MaPseq of E. coli TOP10, exponential phase, in vivo, 37°C (total RNA)


title: purified EVs from 11A cortical organoids, bulk RNA-seq

description:
Smart-Seq2
EV_TPM.txt

source_name: Cortical organoid

value: Cortical organoid


title: DMS-MaPseq of E. coli DH5a, exponential phase, ex vivo, 37°C (total RNA)


title: RPWE_KRAB_Tam_1_S16

status: Public on Sep 03 2024

city: New York

first: Xuanrong

last: Chen

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Data was processed using nf-core/rnaseq (v3.10) of the nf-core collection of workflows. The pipeline was executed with Nextflow v22.10.4 with the following command:  nextflow run nf-core/rnaseq -r 3.10 --input samplesheet.csv --genome GRCh37 -profile singularity
Briefly, raw FASTQ files were aligned to the GRCh37 genome and quantified by salmon (v 1.9.0). Differential gene expression was obtained in R with DESeq2(1.28.0) package.
Assembly: GRCh37
Supplementary files format and content: tab-delimited TSV file contains gene counts values for each sample

source_name: ectopic Repressive MACC construct (KRAB) expressed RWPE1 cell line

growth_protocol: RWPE-1 cells (ATCC CRL-11609) were maintained in Keratinocyte SFM (1X) medium supplemented with human recombinant epidermal growth factor (rEGF) and bovine pituitary extract and incubated at 37°C and 5% CO2. RWPE-1 MACC cells were selected and maintained in 3 μg/mL Blasticidin-containing medium.

extract_protocol:
RWPE-1 MACC cells were stimulated with either vehicle (EtOH) or Tamoxifen (Sigma-Aldrich; cat. T176) and harvested for RNA-seq in biological replicates. Total RNA was extracted, and DNaseI treated by RNeasy Mini Kit (Qiagen; cat. 74104). Nanodrop quantified RNA was checked by Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies). Samples with RNA integrity number > 10 were used for library preparation (Illumina Stranded mRNA Prep kit) and sequenced on Illumina NovaSeq 6000 at the WCM Genomics Core.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit following manufacturer's protocols.

treatment_protocol: RWPE-1 MACC cells were stimulated with 1.25uM Tamoxifen or vehicle 48 hours in biological replicates.

tag: cell type

value: human prostate epithelial cell line

value: Ectopic expression of Repressive MACC construct (KRAB)

value: 1.5uM Tamoxifen


title: RPWE_KRAB_Tam_3_S18

value: ectopic Repressive MACC construct (KRAB) expressed RWPE1 cell line


title: RPWE_KRAB_Tam_2_S17


title: RPWE_VP64_Tam_2_S11

source_name: ectopic Activating MACC construct (VP64) expressed RWPE1 cell line

value: Ectopic expression of Activating MACC construct (VP64)


title: RPWE_KRAB_Veh_2_S14

value: Vehicle


title: RPWE_VP64_Tam_1_S10

value: ectopic Activating MACC construct (VP64) expressed RWPE1 cell line


title: RPWE_VP64_Veh_3_S9


title: DMS-MaPseq of E. coli DH5a, exponential phase, 37°C (mRNA)


title: DMS-MaPseq of E. coli DH5a, exponential phase, in vivo, 37°C (total RNA)


title: RPWE_VP64_Veh_2_S8


title: RPWE_VP64_Tam_3_S12


title: RPWE_3X_Tam_3_S6

source_name: ectopic Neutral MACC construct (3X) expressed RWPE1 cell line

value: Ectopic expression of the neutral MACC construct (3X)


title: RPWE_3X_Tam_1_S4

value: ectopic Neutral MACC construct (3X) expressed RWPE1 cell line


title: RPWE_3X_Veh_2_S2


title: Young Femur Stromal Haem

status: Public on Aug 22 2024

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: BD Rhapsody

data_processing:
STAR version 2.7.10a was used to generate a reference genome index for GRCm39, with Gencode annotations vM29, subset to lncRNA and protein-coding genes.
FASTQ reads were mapped against the reference genome index using STAR with the settings “--soloType CB_UMI_Complex --soloCellFilter None --outSAMtype BAM SortedByCoordinate --soloFeatures GeneFull_Ex50pAS --soloCBmatchWLtype 1MM  --soloUMIlen 8 --soloCBwhitelist BD_CLS1.txt BD_CLS2.txt BD_CLS3.txt --runRNGseed 1 --soloMultiMappers EM --readFilesCommand zcat --outSAMattributes NH HI AS nM NM MD jM jI MC ch CB UB GX GN sS CR CY UR UY”.
Libraries using standard BD Rhapsody beads were mapped using the adapter parameters “--soloAdapterSequence NNNNNNNNNACTGGCCTGCGANNNNNNNNNGGTAGCGGTGACA --soloCBposition 2_0_2_8 2_21_2_29 3_1_3_9 --soloUMIposition 3_10_3_17”, libraries with BD Rhapsody enhanced beads with --soloAdapterSequence NNNNNNNNNGTGANNNNNNNNNGACA --soloCBposition 2_0_2_8 2_13_2_21 3_1_3_9 --soloUMIposition 3_10_3_17”.
Raw counts were imported as AnnData objects. We removed low complexity barcodes with the knee plot method, and further filtered out cells with a mitochondrial mRNA content, as well as unusually high total and gene counts using manually determined cutoffs for each sample. Doublets were scored with scrublet.
Finally, each sample’s gene expression matrix was normalized using scran (1.22.1) with Leiden clustering input at resolution 0.5.
Assembly: mm39
Supplementary files format and content: Tab-separated values and MatrixMarket files

source_name: Femur bone marrow

extract_protocol:
Mice from each age group were euthanized and skull and femur were harvested. Skulls were chopped with scissors in FACS buffer before crushed with mortar and pestle; femurs were crushed without chopping. BM stromal samples were dissociated with Collagenase I (Gibco, Cat# 17100-017, 2 mg/ml) and Collagenase IV (Gibco, Cat# 17104-019, 2 mg/ml) in PBS for 20 minutes at 37°C with intermittent shaking. Cell suspensions were strained through a 40 mm mesh filter and washed with FACS buffer. Cells were resuspended and incubated with biotinylated rat monoclonal anti-hematopoietic lineage antibody cocktail (Miltenyi-Biotec, Cat# 130-092-613, 1:50 dilution). Cells were washed, resuspended in FACS buffer with mouse monoclonal anti-Biotin MicroBeads (Miltenyi-Biotec, Cat# 130-105-637, 1:50 dilution) and incubated before being loaded into a magnetic-associated cell sorting (MACS) column (Miltenyi-Biotec, Cat# 130-042-201) for Lin-depletion. Lin-negative cells were further incubated with rat monoclonal anti-CD45 MicroBeads (Miltenyi-Biotec, Cat# 130-052-301, 1:50 dilution), rat monoclonal anti-CD117 MicroBeads (Miltenyi-Biotec, Cat# 130-091-224, 1:50 dilution), biotinylated rat monoclonal anti-CD71 (Biolegend, Cat# 113803, 1:100). Cells were washed, resuspended in FACS buffer with mouse monoclonal anti-Biotin MicroBeads (Miltenyi-Biotec, Cat# 130-105-637, 1:50 dilution) and incubated before being loaded into a magnetic-associated cell sorting (MACS) column (Miltenyi-Biotec, Cat# 130-042-201) for further hematopoietic depletion.
Single cell suspensions were processed with BD Rhapsody Express system according to the manufacturer's instructions. Then, single cell whole transcriptome libraries were prepared using BD Rhapsody WTA Reagent kit (BD Biosciences).

value: Femur bone marrow

tag: developmental stage

value: Young

value: HSPCs and stromal cells

tag: Sex

value: Female


title: RPWE_3X_Veh_3_S3


title: RPWE_KRAB_Veh_3_S15


title: RPWE_3X_Veh_1_S1


title: m005 GCO, GFPpos (FACS), scRNA-seq

value: Glioblastoma-cortical organoid (GCO)


title: RPWE_KRAB_Veh_1_S13


title: RPWE_3X_Tam_2_S5


title: MIA PaCa-2/SR, MCB-294,rep1

status: Public on Jul 30 2024

city: 上海市

first: 新婷

last: 夏

state: 上海市

address: 东川路500号

department: 生命科学学院

country: China

institute: 华东师范大学

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
Clean reads were aligned to the Human genome hg38 using STAR. StringTie.
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the R package DESeq2 with the likelihood ratio test option.
Assembly: GRCH38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample .

source_name: MIA paca II/SR

growth_protocol: Mice were housed in an animal facility with a 12-hour day/night light cycle, temperature maintained at 25°C and humidity at 60%. Mice were maintained under pathogen-free conditions, with food and water were provided ad libitum.

extract_protocol:
Total RNA samples were extracted with RNA TRIzol Reagent (Magen) according to the manufacture’s manual.
For RNA-sequencing, 1μg of total RNA was used for library construction. Sequencing libraries were generated using VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina®. The libraries were sequenced as 150bp paired-end reads using Illumina Novaseq6000 according to the manufacturer's instructions by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

treatment_protocol: MIA and MIA/SR were treated with MCB-294 (30 nM, 3h) or MCB-36 (100 nM, 12h), and then harvested for bulk RNAseq.

value: MIA paca II/SR

value: Pancreatic cancer

tag: time


title: MIA PaCa-2/SR, rep3

tag: cell line


title: MIA PaCa-2/SR, MCB-36,rep1


title: MIA PaCa-2/SR, rep2


title: MIA PaCa-2, rep2

source_name: MIA paca II

value: MIA paca II


title: MIA PaCa-2, rep3


title: RNA_DMSO1

status: Public on Jul 10 2024

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

country: Japan

institute: RIKEN

description: RNAseq_and_rRNA_depletion_with_Ribo-Zero_Ribo-Calibration

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms

source_name: cultures

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer.
Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer.
The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice.
S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer.
E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker.
For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.
0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)

value: cultures

value: Human Embryonic Kidney cells293

tag: rrna depletion

value: Ribo zero and Ribo-Filterout

value: DMSO


title: RNA_RocA3μM2

value: 3 uM RocA


title: RNA_DMSO2

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-Zero, Ribo-FilterOut_Ribo-Calibration


title: RNA_RocA3μM1


title: VUILD91_Less-affected_TMA4-Run2_3mm

status: Public on Jun 04 2024

type: other

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

hyb_protocol: A total of 343 unique genes were included in the analysis of this dataset. 246 genes came from an early version of the Xenium human lung base panel (PD_336) and 97 genes from a custom designed panel (CVEVZD). The custom panel was curated based on human lung single cell analysis data (Habermann et al. 2020), selecting for genes useful in cell type identification and/or with suspected involvement in IPF. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation (Davis et al. 2014). Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. The data in this paper was acquired on instrument software version 1.1.2.4 and analysis version xenium-1.1.0.2. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

data_processing:
Transcript-based niche embedding files (node_meta.csv and .npy files) were genetared using GraphSAGE.
Information about output files can be found here:
https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/understanding-xenium-outputs
Supplementary files format and content: HE_annotations.tar: This file contains geojson polygons of pathology annotations of regions mentioned in the paper for each sample as well as a csv assigning cells to the annotations they fall within.

molecule: other

source_name: Lung, less affected

label_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000580).

growth_protocol: A 5um section of each archived lung FFPE block was H&E stained and presented to a physician who identified areas of interest and labeled them as less or more fibrotic (LF or MF) relative to the sample. TMA blocks were designed in a 3x3 or 2x2 pattern for 3mm and 5mm cores, respectively. Sample cores were punched and placed manually using a “Quick-Ray Manual Tissue Microarrayer Full Set” and “Quick-Ray Molds”, according to the manufacturer’s directions. Empty core spaces were filled with core punches taken from blank paraffin blocks (VWR 76548-194). Once complete, blocks are placed face down on a clean glass slide and briefly heated in a warm drawer (~45°C) to slightly melt the paraffin together and even the block face. TMA blocks were then cooled to room temperature, removed from the slide, sealed, and stored at 4°C.

extract_protocol: Sectioning was performed at 5um on a Leica RM2135 with a water float temperature of 40°C. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were then stored in a sealed dessicator at room temperature for up to a maximum of 10 days.

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free.

tag: gender

value: M

tag: ethnicity

value: European

tag: tobacco

value: N

tag: status

value: Disease

value: Lung

tag: tma

tag: run

tag: punch size

tag: clinical diagnosis

value: IPF

tag: sample type


title: VUILD91_More-affected_TMA4-Run2_3mm

source_name: Lung, more affected

tag: age

tag: tissue


title: VUILD78_More-affected_TMA4-Run2_3mm

value: F

value: IPAF


title: pb_ZR_75_1_rep2

source_name: Breast

value: Breast


title: MIA PaCa-2/SR, MCB-294,rep3

tag: genotype

value: MIA paca II/SR

tag: cell type

tag: treatment


title: MIA PaCa-2/SR, MCB-36,rep3

value: Pancreatic cancer

tag: time


title: VUILD48-2_Less-affected_TMA2-Run1_3mm

value: Y

value: NSIP


title: VUILD110_Less-affected_TMA3-Run2_5mm

value: CTD-ILD


title: Young Skull Stromal Haem

description: BD Rhapsody

source_name: Skull bone marrow

value: Skull bone marrow

tag: developmental stage

value: Young

value: HSPCs and stromal cells

tag: strain

tag: Sex

value: Female


title: VUILD115_More-affected_TMA3-Run2_5mm

tag: gender

value: M

tag: ethnicity

value: European

value: cHP


title: VUILD96_More-affected_TMA1-Run1_3mm

value: African American

tag: tobacco

value: N

tag: status

value: Disease

value: Lung

value: Sarcoidosis


title: MIA PaCa-2/SR, rep1

tag: cell line

value: MIA paca II/SR

value: Vehicle


title: MIA PaCa-2/SR, MCB-294,rep2

value: Pancreatic cancer


title: VUILD102_Less-affected_TMA1-Run1_3mm

value: Y

tag: tma

tag: run

tag: punch size

value: IPF


title: RPWE_VP64_Veh_1_S7

value: ectopic Activating MACC construct (VP64) expressed RWPE1 cell line

value: human prostate epithelial cell line

value: Ectopic expression of Activating MACC construct (VP64)


title: MIA PaCa-2, rep1

value: MIA paca II


title: VUILD107_More-affected_TMA1-Run1_3mm

tag: age

value: M

tag: clinical diagnosis

tag: sample type


title: VUILD106_More-affected_TMA3-Run1_5mm

value: European

tag: tissue


title: VUILD96_Less-affected_TMA1-Run1_3mm

value: F


title: VUILD105-2_More-affected_TMA2-Run1_3mm


title: VUILD104-1_More-affected_TMA2-Run1_3mm


title: VUHD116A_Control_TMA1-Run1_3mm

source_name: Lung, control

value: Control


title: VUILD78_Less-affected_TMA4-Run2_3mm

value: N

value: IPAF


title: TILD175_More-affected_TMA4-Run2_3mm

value: American Indian

value: Disease

value: Lung


title: VUHD069_Control_TMA2-Run1_3mm

value: African American


title: THD0011_Control_TMA4-Run2_3mm


title: VUHD095_Control_TMA2-Run1_3mm


title: TILD117_Less-affected_TMA4-Run2_3mm

value: ILD


title: Meth.Sample.195

description: Meth, Normal, NA

source_name: breast

value: breast

tag: classification

value: Normal

tag: race

tag: expressioncluster

tag: methylationcluster

tag: hormonetreatment

tag: radiationtreatment


title: VUHD113_Control_TMA2-Run1_3mm

tag: gender

tag: ethnicity


title: THD0008_Control_TMA3-Run2_5mm

tag: tobacco

value: Y

tag: status


title: VUILD102_More-affected_TMA1-Run1_3mm

tag: tma

value: IPF


title: pb_C42B_rep2

source_name: Prostate

value: Prostate

tag: cell line


title: S. Typhi strain 4048/82 [9-Typhi 4048-82_2]

status: Public on Apr 05 2024

type: RNA

first: Adonis

last: D'Mello

address: Health Science Facility III, 670 W Baltimore St 3rd floor

institute: IGS- University of Maryland Baltimore

description: Chronic

data_processing: Data were processed using the NanoString nSolver software v4.0 comparing acute vs. uninfected and chronic vs uninfected conditions, using within chip uninfected controls and recommended settings (including initial QC, negative control count thresholding using mean +/- 2 standard deviations, positive control normalization using default settings but excluding housekeeping genes with counts below 100 as well as G6PD and GAPDH that were found to vary in expression in our assays, and calculation of expression ratios of acute or chronic vs. uninfected). After normalization, expression values were compiled into a single matrix for differential expression (DE) analysis. DE genes were estimated using R packages Limma, with chip-to-chip variation modeled into the analysis. DE genes meeting a p-value<0.01 were used to identify enriched Gene Ontologies for biological processes using the R package ClusterProfiler v4.0.

source_name: Gallbladder organoid

growth_protocol: S. Typhi isolated from acutely infected patients include strains Ty2, the parent strain of the oral typhoid vaccine strain Ty21a, and 5 strains obtained from public hospitals in Santiago, Chile. S. Typhi isolated from chronically infected patients include strains Quailes, and 6 strains obtained from Santiago public hospitals. Luria-Bertani (LB) agar Lennox (Difco Laboratories, Detroit, MI, USA) was prepared according to the package instructions and used to grow S. Typhi strains overnight at 37oC. Gallbladder stem cell (SC) isolation, culture, and establishment of the HODGM model were performed according to previous protocols with few modifications. Briefly, gallbladder tissues were rinsed with chelation buffer (2% sorbitol, 1% D-sucrose, 1% bovine serum albumin fraction V (BSA), 10 g/ml Gentamicin and 250 ng/ml Amphotericin in Dulbecco's Phosphate buffered saline) (Sigma-Aldrich-Aldrich, St Louis, MO, USA)), minced, and incubated with PBS/ 2 mM EDTA for 30 minutes to release SC clusters. The SC clusters were then co-cultured with 3T3-J2 -irradiated mouse embryonic fibroblasts in 6-well plates coated with Matrigel and containing intestinal Organoid Culture Medium (DMEM/F-12 medium supplemented with 10% L-WRN conditioned medium, 100 U/mL penicillin, 100 µg/mL streptomycin, 50 µg/mL gentamicin, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 M MEM-Non-Essential Amino-Acids, 10 mM HEPES buffer, 5 g/ml insulin (Sigma-Aldrich-Aldrich, St Louis, MO, USA), 0.4 g/ml 3,3',5-triiodo-L-thyronine (T3, Sigma-Aldrich), 1.8  10-4 M adenine (Sigma-Aldrich), 5 g/ml transferrin (Sigma-Aldrich), 10-10 M cholera toxin (Sigma-Aldrich), 500 nM A-83-01 (Sigma-Aldrich), 10 µM Y-27632 Rock inhibitor (Biogems, Westlake Village, CA), 50 ng/mL epidermal growth factor (EGF) recombinant human protein (ThermoFisher, Waltham, MA, USA), 0.4 g Hydrocortisone (Sigma-Aldrich), 1 µM Jagged-1 peptide (AnaSpec, Fremont, CA, USA), and 10 mM Nicotinamide (Sigma-Aldrich)). After 10-15 days, SC colonies were dissociated with Trypsin-EDTA (0.25%) (Invitrogen), and 500,000 SC were plated onto 0.4μm transwells coated with Matrigel and containing 200,000 -irradiated fibroblasts. Monolayers were cultured to confluence and subsequently differentiated for 3-4 days in differentiation media (intestinal Organoid Culture Medium without L-WRN conditioned medium and Nicotinamide) under an air-liquid interface (ALI).

extract_protocol: RNA was isolated from transwell membranes according to previous protocols with few modifications. Briefly, membranes were cut, added into power ceramic beads tubes (Qiagen, Valencia, CA) containing 1 mL RNA RLT Buffer (RNeasy Micro kit, Qiagen, Valencia, CA, USA), and beaten in a Bullet Blender Homogenizer for 30 seconds; total cellular RNA was then isolated according to the manufacturer's instructions. RNA concentrations were measured on a NanoDrop 1000 spectrophotometer (Thermo Fisher) and 75ng of RNA per sample were used for assaying on the NanoString nCounter platform, using the Human Immunology V2 Panel to profile 579 genes covering the core pathways and processes of the immune response.

treatment_protocol: The HODGM models were incubated for 5 hours at 37oC in DMEM media (without antibiotics) in the presence of one of the 13 S. Typhi strains isolated from acutely (n=6) and chronically (n=7) infected patients at a multiplicity of infection (MOI) of 50. HODGM models with media only were used as controls. After 5 hours, supernatants were collected for the detection of cytokines. Cells were also collected from the transwell membrane to prepare whole-cell lysates and/or to extract mRNA.

value: Epithelial

tag: ChIP

tag: agent

value: 13 S. Typhi strains


title: S. Typhi strain 4048/82 [9-Typhi 4048-82_3]

description: Chronic


title: S. Typhi strain 3129/82 [8-Typhi 3129-82]

description: Chronic


title: S. Typhi strain 3555/82 [7-Typhi6-GB05242022]

description: Chronic


title: VUHD116B_Control_TMA1-Run1_3mm

tag: run

tag: punch size

tag: clinical diagnosis


title: S. Typhi strain 4048/82 [9-Typhi8-GB05242022]

description: Chronic

tag: tissue


title: S. Typhi strain 4048/82 [9-Typhi8-GB05242022_2]

description: Chronic


title: S. Typhi strain 4048/82 [9-Typhi 4048-82_1]

description: Chronic


title: S. Typhi strain 3555/82 [7-Typhi6-GB05242022_2]

description: Chronic


title: S. Typhi strain 3129/82 [8-Typhi7-GB05242022]

description: Chronic


title: S. Typhi strain 4060/82 [6-Typhi5-GB05242022_2]

description: Chronic


title: S. Typhi strain 3555/82 [7-Typhi 3555-82]

description: Chronic


title: S. Typhi strain 4060/82 [6-Typhi 4060-82_2]

description: Chronic


title: S. Typhi strain 3129/82 [8-Typhi7-GB05242022_2]

description: Chronic


title: S. Typhi strain 4060/82 [6-Typhi 4060-82_1]

description: Chronic


title: S. Typhi strain 4060/82 [6-Typhi5-GB05242022]

description: Chronic


title: PHL1-Healthy control-SITTE1

status: Public on Apr 04 2024

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality control was peformed using fastQC ( v0.11.8) and multiQC (v 1.9)
Alignment, filtering and gene quantification was performed using 10x cellranger v5.0.0; the alignment was perfomed against the H Sapiens reference genome (GRCh38.p13)
Normalization of expression was levels was performed with SCTransform (Hafemeister and Satija, 2019)
Clustering was performed using SLM algorithm from the FindClusters function from Seurat (Satija, 2021)
Differential Expression was perfored using the Wilcoxon Rank Sum test  from FindMarkers function from Seurat (Satija, 2021)
Assembly: GRCh38.p13
Supplementary files format and content: Raw and norrmalised count matrices, in csv format.
Supplementary files format and content: Seurat object, rds format.

source_name: liver biopsy

extract_protocol:
Tissue lysis by dounce homogenisation and nuclei isolation by flow cytometry using scatter properties and DAPI staining to label nuclei.
Single-nuclei RNA-seq libraries were prepared using the following: Chromium Single Cell 3′ Library & Gel Bead Kit v3.1, Chromium Chip G Kit and Chromium Single Cell 3' Reagent Kits v3.1 User Guide (Manual Part CG000316 Rev A; 10X Genomics). For each sample 16k nuclei were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing nuclei cells. RNA from the barcoded nuclei for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-nuclei libraries were performed according to the manufacturer’s protocol with 19 PCR cycles in cDNA amplification step. cDNA quality and quantity was measured with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape) after which 25% of material was used for gene expression library preparation. Library quality was confirmed with Agilent TapeStation 4200 (High Sensitivity D1000 ScreenTape to evaluate library sizes) and Qubit 4.0 Flourometer  (ThermoFisher Qubit™ dsDNA HS Assay Kit to evaluate dsDNA quantity). Each sample was normalized and pooled in equal molar concentration. To confirm concentration pool was qPCRed using KAPA Library Quantification Kit on QuantStudio 6 Flex before sequencing. Pool was sequenced on Illumina NovaSeq6000 sequencer with following parameters: 28 bp, read 1; 10 bp, i5 index; 10bp, i7 index; 90 bp, read 2

treatment_protocol: Biopsies were snap frozen in liquid nitrogen

value: liver

tag: disease status

value: Healthy control

tag: patient id

tag: liver lobe

value: Caudate

value: M

tag: saf score

value: healthy control

tag: age


title: rRNA Depleted totalRNA from liver from untreated SHR rats (replicate 1b, sequencing batch 3)

status: Public on Oct 23 2023

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1b_batch3
SHR_1b_control_3

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Filter transcripts/genes from RSEM filtered transcriptome results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: Rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA was collected from liver using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).
rRNA depleted stranded totalRNA

treatment_protocol: Tissue frozen in RNA later.

tag: strain

value: SHR/OlaIpcv

tag: batch

tag: treatment


title: PCL17-end stage-SITTE11

value: end stage

value: Left

tag: gender


title: rRNA Depleted totalRNA from liver from untreated  rats (replicate 3, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: WAG_3_batch17
WAG_3

value: WAG/RijCrl


title: Uninfected cells [Reference_2]


title: S. Typhi strain 2262/83 [3-Typhi 2262-83_1]

description: Acute


title: purified EVs from m005_11A GCOs, bulk RNA-seq

description:
Smart-Seq2
EV_TPM.txt

source_name: mus musculus

value: mus musculus

value: Glioblastoma-cortical organoid (GCO)


title: S. Typhi strain 1366/83 [5-Typhi 1366-83]

description: Acute


title: S. Typhi strain 2262/83 [3-Typhi 2262-83_3]

description: Acute


title: S. Typhi strain 1994/83 [4-Typhi3-GB05242022]

description: Acute


title: S. Typhi strain 2262/83 [3-Typhi2-GB05242022_2]

description: Acute


title: Uninfected cells [Reference_3]


title: rRNA Depleted totalRNA from liver from untreated  rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: WAG_1_batch16
WAG_1


title: Uninfected cells [Reference_GB05242022]


title: S. Typhi strain 2262/83 [3-Typhi 2262-83_2]

description: Acute


title: S. Typhi strain 2262/83 [3-Typhi2-GB05242022]

description: Acute


title: S. Typhi strain 1994/83 [4-Typhi 1994-83]

description: Acute


title: S. Typhi strain 1366/83 [5-Typhi4-GB05242022]

description: Acute


title: S. Typhi strain 2251/83 [2-Typhi1-GB05242022_2]

description: Acute


title: rRNA Depleted totalRNA from liver from untreated HXB24 rats (replicate 1, sequencing batch 2)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: HXB24_1_batch2
HXB24_1


title: Uninfected cells [Reference_GB05242022_2]


title: S. Typhi strain 2251/83 [2-Typhi 2251-83_1]

description: Acute


title: S. Typhi strain 1994/83 [4-Typhi3-GB05242022_2]

description: Acute


title: rRNA Depleted totalRNA from liver from untreated  rats (replicate 2, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: WAG_2_batch17
WAG_2


title: S. Typhi strain 2251/83 [2-Typhi1-GB05242022]

description: Acute


title: Uninfected cells [Reference_1]


title: MIA PaCa-2/SR, MCB-36,rep2

tag: genotype

value: MIA paca II/SR

tag: cell type

value: Pancreatic cancer

tag: time


title: rRNA Depleted totalRNA from liver from untreated SHR rats (replicate 1b, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1b_batch18
SHR_1b_control_18


title: rRNA Depleted totalRNA from liver from untreated SHR rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1_batch16
SHR_1_control_16


title: rRNA Depleted totalRNA from liver from untreated SHR rats (replicate 1b, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1b_batch17
SHR_1b_control_17


title: rRNA Depleted totalRNA from liver from untreated SHR rats (replicate 1b, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1b_batch16
SHR_1b_control_16


title: S. Typhi strain 1366/83 [5-Typhi4-GB05242022_2]

description: Acute

tag: ChIP

tag: agent


title: rRNA Depleted totalRNA from liver from untreated PVG rats (replicate 3, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: PVG_3_batch18
PVG_3

value: PVG/Seac


title: rRNA Depleted totalRNA from liver from untreated M520 rats (replicate 2, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: M520_2_batch17
M520_2


title: rRNA Depleted totalRNA from liver from untreated MWF rats (replicate 2, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: MWF_2_batch18
MWF_2

value: MWF/Hsd


title: rRNA Depleted totalRNA from liver from untreated MWF rats (replicate 3, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: MWF_3_batch17
MWF_3


title: rRNA Depleted totalRNA from liver from untreated LEXF10A rats (replicate 2, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEXF10A_2_batch16
LEXF10A_2


title: rRNA Depleted totalRNA from liver from untreated M520 rats (replicate 3, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: M520_3_batch17
M520_3


title: rRNA Depleted totalRNA from liver from untreated M520 rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: M520_1_batch16
M520_1


title: rRNA Depleted totalRNA from liver from untreated LEXF1C rats (replicate 3, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEXF1C_3_batch17
LEXF1C_3


title: rRNA Depleted totalRNA from liver from untreated GK rats (replicate 3, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: GK_3_batch18
GK_3

value: GK/FarMcwi


title: rRNA Depleted totalRNA from liver from untreated LEXF1C rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEXF1C_1_batch16
LEXF1C_1


title: rRNA Depleted totalRNA from liver from untreated MWF rats (replicate 1, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: MWF_1_batch18
MWF_1


title: rRNA Depleted totalRNA from liver from untreated PVG rats (replicate 1, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: PVG_1_batch17
PVG_1


title: rRNA Depleted totalRNA from liver from untreated LEXF1C rats (replicate 2, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEXF1C_2_batch16
LEXF1C_2


title: rRNA Depleted totalRNA from liver from untreated FXLE20 rats (replicate 3, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE20_3_batch17
FXLE20_3


title: rRNA Depleted totalRNA from liver from untreated LEXF10A rats (replicate 3, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEXF10A_3_batch17
LEXF10A_3


title: rRNA Depleted totalRNA from liver from untreated PVG rats (replicate 2, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: PVG_2_batch18
PVG_2


title: rRNA Depleted totalRNA from liver from untreated FXLE20 rats (replicate 2, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE20_2_batch16
FXLE20_2


title: rRNA Depleted totalRNA from liver from untreated GK rats (replicate 2, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: GK_2_batch18
GK_2


title: rRNA Depleted totalRNA from liver from untreated LH rats (replicate 3, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LH_3_batch18
LH_3

value: LH/MavRrrc


title: rRNA Depleted totalRNA from liver from untreated LH rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LH_1_batch16
LH_1

value: liver


title: rRNA Depleted totalRNA from liver from untreated LH rats (replicate 2, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LH_2_batch17
LH_2


title: rRNA Depleted totalRNA from liver from untreated GK rats (replicate 1, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: GK_1_batch17
GK_1


title: rRNA Depleted totalRNA from liver from untreated FXLE20 rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE20_1_batch16
FXLE20_1


title: rRNA Depleted totalRNA from liver from untreated LEXF10A rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: LEXF10A_1_batch16
LEXF10A_1


title: rRNA Depleted totalRNA from liver from untreated FXLE15 rats (replicate 1, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE15_1_batch16
FXLE15_1


title: S. Typhi strain 2251/83 [2-Typhi 2251-83_2]

description: Acute

value: Epithelial

value: 13 S. Typhi strains


title: rRNA Depleted totalRNA from liver from untreated FXLE15 rats (replicate 2, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE15_2_batch16
FXLE15_2


title: rRNA Depleted totalRNA from liver from untreated FXLE15 rats (replicate 3, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE15_3_batch17
FXLE15_3


title: rRNA Depleted totalRNA from liver from untreated FXLE12 rats (replicate 4, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE12_4_batch16
FXLE12_4


title: rRNA Depleted totalRNA from liver from untreated FXLE12 rats (replicate 2, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE12_2_batch17
FXLE12_2


title: rRNA Depleted totalRNA from liver from untreated FHH rats (replicate 3, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FHH_3_batch18
FHH_3

value: FHH/EurMcwi


title: rRNA Depleted totalRNA from liver from untreated FHH rats (replicate 2, sequencing batch 17)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FHH_2_batch17
FHH_2


title: rRNA Depleted totalRNA from liver from untreated BN rats (replicate 3, sequencing batch 18)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: BN_3_batch18
BN_3

value: BN/NHsdMcwi


title: rRNA Depleted totalRNA from liver from untreated FXLE12 rats (replicate 3, sequencing batch 16)

description:
rRNA depleted totalRNA
HRDPv6 Sample Name: FXLE12_3_batch16
FXLE12_3