title: Case 167

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R01C01


title: Case 165

status: Public on Jan 16 2024

type: genomic

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Hyderabad

address: Jawahar nagar

department: Biological Sciences

country: India

institute: Birla Institute of Technology and Science

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R12C01

hyb_protocol: DNA is incubated overnight at 37 degrees

scan_protocol: Scanning is done with in 72 hrs after the process is completed.BeadChip positions in the scanner is noted down.

data_processing:
Data is loaded with the standard cluster file first and then re clustering is done. Control summery, B allele frequency and log R ratio is observed to evaluate the data quality
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: DNA quality is checked by Picogreen a dye very specific for binding DNA, Quality check is done by UV spectrophotometer at 260/280 ratio.After the quantification  the samples are normalized to 50ng/ul (12ul). A gel check is also performed to check the normalization on 0.8% Agarose Gel.

extract_protocol: Extraction of genomic DNA from blood was performed using proteinase K and repeated phenol-chloroform extraction. The DNA samples were purified with ZR 96 well DNA   clean up kit supplied by zymo research. The elution is done twice with 40+30 ul respectively

tag: gender

value: Male


title: Case 168

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110046_R01C02

value: Female


title: CD8__P27

type: SRA

city: Heidelberg

first: Bruno

last: Steinkraus

state: Baden-Württemberg

address: Im Neuenheimer Feld 583

country: Germany

institute: HUMMINGBIRD DIAGNOSTICS GMBH

library_source: transcriptomic

data_processing:
Raw sequence reads were adapter trimmed and depleted of PCR duplicates based on the UMIs.
Only sequences that had at least one read in at least three samples per blood component type and that were longer than 17 nucleotides were kept.
For 25 cellular fractions (4.6% of derivatives, 25/539) the purification process did not meet the prespecified quality standard (purity > 70% as determined by flow cytometry). These samples were excluded from further analyses. See 'quality filter for processed data'
As additional quality control, the normalized data of the blood component samples was converted to a two-dimensional T-distributed Stochastic Neighbor Embedding (t-SNE) space. When plotting the two embedding vectors against each other, four samples did not cluster with the samples of the same blood component type (0.8% of derivatives, 4/514) and were excluded from further analysis. See 'quality filter for processed data'
The pre-processed sRNA sequences were annotated using the annotation pipelines unitas  and SPORTS. In case of multi-assignments, the annotation was prioritized in the following manner: miRNA > tRNA > rRNA > YRNA > snoRNA > lncRNA > snRNA > piRNA.
Assembly: hg38
Supplementary files format and content: csv files including log2-transformed RPM values per small RNA name for all blood component samples (1 file) and for all whole blood samples (1 file)

molecule: total RNA

source_name: peripheral blood cells

extract_protocol:
The fractional blood derivatives as well as the whole blood samples were directly lysed in Qiazol. For RNA isolation the miRNeasy Serum/Plasma mini kit was combined with minElute columns.
Dual indexed sRNA libraries with unique molecular identifiers (UMIs) adaptors were generated using the QIAseq miRNA Library Kit.

tag: tissue

value: peripheral blood cells

tag: cell type

value: CD8+ T cells


title: CD8__P29


title: Case 166

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R12C02


title: CD8__P30


title: Case 162

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R09C01


title: Control 157

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R09C02


title: CD8__P25


title: CD8__P28


title: CD8__P26


title: CD8__P24


title: Case 161

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R08C01


title: Case 160

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R07C02


title: CD8__P23


title: Case 159

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R07C01


title: CD8__P22


title: Control 155

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R06C02


title: CD8__P20


title: Case 158

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R06C01


title: Case 157

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R05C01


title: CD8__P18


title: Control 153

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R04C02


title: CD8__P19


title: CD8__P17

tag: quality filter_for_processed_data

value: does NOT pass cellsorting purity filter


title: Case 156

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R04C01


title: CD8__P15


title: CD8__P16


title: Control 152

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R03C02


title: CD8__P14


title: Case 155

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R03C01


title: Control 156

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R08C02


title: Control 151

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R02C02


title: Case 154

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R02C01


title: CD4__P52

value: CD4+ T cells


title: CD4__P51


title: CD4__P50


title: CD4__P49


title: Control 149

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R12C02


title: Case 153

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R01C01


title: CD4__P48


title: Control 154

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R05C02


title: Case 151

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R11C01


title: Control 148

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R11C02


title: CD8__P21


title: CD4__P45


title: Control 146

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R09C02


title: CD4__P44


title: CD8__P13


title: CD4__P46


title: Case 149

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R09C01


title: CD4__P43


title: CD4__P41


title: CD4__P39


title: CD4__P42


title: Control 145

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R08C02


title: Control 150

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110026_R01C02


title: CD4__P40


title: Control 144

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R07C02


title: Case 147

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R07C01


title: Case 152

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R12C01


title: CD4__P37


title: Case 148

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R08C01


title: CD4__P36


title: Control 143

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R06C02


title: CD4__P35


title: CD4__P38


title: CD4__P34


title: Case 150

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R10C01


title: Case 144

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R04C01


title: Case 146

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R06C01


title: CD4__P47


title: Control 147

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R10C02


title: CD4__P33


title: Control 140

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R03C02


title: Control 142

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R05C02


title: CD4__P32


title: CD4__P31


title: CD4__P30


title: CD4__P29


title: Case 142

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R02C01


title: Case 143

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R03C01


title: Control 139

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R02C02


title: CD4__P27


title: CD4__P25


title: Case 140

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R12C02


title: Case 141

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R01C01


title: CD4__P24


title: Control 141

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R04C02


title: Case 138

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R11C02


title: CD4__P21


title: CD4__P22


title: Case 137

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R10C02


title: CD4__P20


title: Case 136

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R10C01


title: CD4__P19


title: Case 132

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R08C01


title: CD4__P18


title: Case 133

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R08C02


title: CD4__P17


title: CD4__P16


title: Control 138

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R01C02


title: Case 134

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R09C01


title: Case 130

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R07C01


title: CD4__P15


title: CD4__P28


title: Case 145

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
207041110024_R05C01


title: Case 139

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R12C01


title: CD4__P23


title: CD4__P14


title: Basophils__P50

value: Basophils


title: CD4__P26


title: Case 129

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R06C02


title: Case 128

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R06C01


title: Case 127

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R05C02


title: Basophils__P49


title: CD4__P13


title: Case 126

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R05C01


title: Case 125

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R04C02


title: Basophils__P48


title: Case 124

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R04C01


title: Case 131

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R07C02


title: Basophils__P46


title: Case 123

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R03C02


title: Case 135

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R09C02


title: Case 121

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R02C02


title: Case 120

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R02C01


title: Case 122

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R03C01


title: Basophils__P45


title: Basophils__P42


title: Basophils__P43


title: Basophils__P41


title: Case 118

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R01C01


title: Case 119

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590006_R01C02


title: Control 137

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R12C02


title: Basophils__P38


title: Basophils__P39


title: Control 135

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R11C02


title: Control 136

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R12C01


title: Basophils__P35


title: Basophils__P33


title: Basophils__P47


title: Basophils__P37

value: does NOT pass t-SNE filter


title: Basophils__P34


title: Basophils__P32


title: Basophils__P30


title: Control 132

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R10C01


title: Control 131

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R09C02


title: Control 129

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R08C02


title: Control 133

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R10C02


title: Control 130

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R09C01


title: Basophils__P28


title: Control 127

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R07C02


title: Control 126

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R07C01


title: Basophils__P27


title: Basophils__P25


title: Basophils__P26


title: Control 125

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R06C02


title: Control 124

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R06C01


title: Basophils__P29


title: Basophils__P24


title: Basophils__P23


title: Control 134

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R11C01


title: Control 123

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R05C02


title: Control 122

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R05C01


title: Basophils__P22


title: Basophils__P21


title: Basophils__P20


title: Basophils__P31


title: Control 120

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R04C01


title: Control 119

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R03C02


title: Basophils__P19


title: Control 121

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R04C02


title: Basophils__P17


title: Control 118

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R03C01


title: Control 117

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R02C02


title: Control 128

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R08C01


title: Control 115

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R01C02


title: Basophils__P16


title: Basophils__P18


title: Control 116

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R02C01


title: Basophils__P13


title: Control 113

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R12C02


title: B_cells__P51

value: B cells


title: B_cells__P50


title: Control 112

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R11C02


title: B_cells__P49


title: B_cells__P48


title: Case 117

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R12C01


title: Control 111

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R11C01


title: Control 110

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R10C02


title: B_cells__P47


title: Control 108

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R09C02


title: B_cells__P44


title: Control 107

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R09C01


title: B_cells__P46


title: B_cells__P42


title: B_cells__P43


title: Control 106

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R08C02


title: Control 104

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R07C02


title: Control 103

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R07C01


title: B_cells__P40


title: Control 105

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R08C01


title: B_cells__P41


title: B_cells__P39


title: Control 114

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590004_R01C01


title: Control 102

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R06C02


title: B_cells__P52


title: Control 101

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R06C01


title: B_cells__P37


title: Control 100

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R05C02


title: B_cells__P38


title: Control 98

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R04C02


title: B_cells__P36


title: Control 97

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R04C01


title: B_cells__P45


title: B_cells__P34


title: Control 109

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R10C01


title: B_cells__P33


title: Control 96

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R03C02


title: B_cells__P32


title: Control 94

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R02C02


title: Control 93

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R02C01


title: Control 95

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R03C01


title: B_cells__P31


title: B_cells__P29


title: Case 116

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R01C02


title: B_cells__P28


title: B_cells__P26


title: Case 113

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R12C01


title: B_cells__P27


title: B_cells__P25


title: Case 114

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R12C02


title: Case 115

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R01C01


title: B_cells__P24


title: Case 111

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R10C02


title: B_cells__P23


title: Case 109

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R09C02


title: Case 110

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R10C01


title: Case 112

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R11C01


title: B_cells__P35


title: Case 108

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R09C01


title: B_cells__P20


title: B_cells__P22


title: Control 99

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590002_R05C01


title: B_cells__P21


title: Case 107

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R08C02


title: B_cells__P19


title: B_cells__P30


title: Case 105

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R07C02


title: Case 106

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R08C01


title: B_cells__P18


title: Case 103

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R06C02


title: Case 104

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R07C01


title: B_cells__P16


title: B_cells__P17


title: B_cells__P15


title: Case 102

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R06C01


title: B_cells__P14


title: Case 99

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R04C02


title: Case 101

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R05C02


title: Case 98

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R04C01


title: Case 97

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R03C02


title: Case 100

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R05C01


title: Case 93

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R01C02


title: Case 92

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R01C01


title: Control 92

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R12C01


title: Case 95

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R02C02


title: COR-3722-D1

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

country: USA

institute: Cornell University

library_source: transcriptomic single cell

data_processing:
cellranger mkfastq was used to generate fastq files by the sequencing facility
Because some samples were sequenced on different (or multiple) Illumina sequencers with different read lengths, all reads were trimmed for analysis and for upload to GEO (R1=28bp, R2=55bp). Samples are annotated with the number of different sequencer models used (NextSeq, HiSeq, and NovaSeq) and final fastq files are annotated by the instrument that generated the majority of reads.
cellranger count (v6) was used to generate raw count tables (h5 files), with the following parameters: --expect-cells=5000 --r1-length=28 --r2-length=55 --nosecondary
Assembly: 10x Genomics reference: refdata-gex-GRCh38-2020-A
Supplementary files format and content: h5

source_name: PBMCs

extract_protocol:
Whole blood was collected in EDTA tubes before and 24h after a cardiopulmonary exercise test (CPET) for each subject in the study. PBMCs were isolated with SepMate tubes  and cryopreserved with 1-10 x10^6 cells per vial. Frozen PBMCs were recovered following the 10x Genomics Demonstrated Protocol: Fresh Frozen Human Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing (CG00039) and resuspended in 1x PBS containing 0.04% BSA. For a target of 5,000 cells per final library, 8,000 cells were loaded onto the 10x Chromium chip.
Libraries were constructed using the Chromium Single Cell 3ʹ v3 kit (10x Genomics)

value: PBMCs

tag: collection day

tag: disease state

value: control

tag: Sex

value: M

tag: age bin

tag: chromium batch

value: batch 14

tag: number of sequencer models used


title: Case 94

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R02C01


title: Control 91

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R11C01


title: Case 96

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
205927590001_R03C01


title: Control 90

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R10C01


title: Case 89

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R10C02


title: Case 91

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R12C02


title: Case 88

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R09C02


title: Case 90

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R11C02


title: Case 87

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R08C02


title: Control 88

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R08C01


title: Control 89

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R09C01


title: Case 86

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R07C02


title: Control 87

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R07C01


title: Case 85

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R06C02


title: Case 84

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R05C02


title: Control 86

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R06C01


title: Control 85

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R05C01


title: Case 83

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R04C02


title: B_cells__P13


title: Control 83

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R03C01


title: Control 84

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R04C01


title: Control 82

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R02C02


title: Control 80

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R01C02


title: Control 81

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R02C01


title: Control 79

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570045_R01C01


title: GD1951_control_female_t1

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Total RNA Total RNA was isolated from PBMCs collected at all sampling timepoints following preparation into single cell suspension using theQiagen RNeasy Plus Mini Kit (74136)
RNA-seq libraries were prepared usingNew England Biolab’s NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L), Globin & rRNA Depletion Kit (E7750X), Ultra II Directional RNA Library Prep Kitfor Illumina (E7760L), andMultiplex Oligosfor Illumina (E6440L)according to the manufacturer’s instructions. Libraries were pooled at equimolar concentrations and sequenced using Illumina’s NextSeq 2000 on one P2-100 kit (2004681)and four P3-100 kits (20040559).

value: Blood

value: Peripheral Blood Mononuclear Cells

tag: genotype

value: BALB/c

tag: treatment

value: female

tag: timepoint


title: Case 82

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R12C02


title: GD1950_10 _mg_ IL12ns_female_t2

value: 10 mg IL12ns


title: Case 80

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R11C02

value: Male


title: Case 79

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R11C01

value: Female


title: GD1948_0.1 _mg_ IL12ns_male_t1

value: 0.1 mg IL12ns

value: male


title: GD1949_10 _mg_ IL12ns_male_t2


title: Case 77

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R10C01


title: Case 78

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R10C02


title: GD1947_10 _mg_ IL12ns_male_t2


title: GD1944_control_female_t4


title: Case 75

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R09C01


title: GD1945_control_female_t7


title: Case 73

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R08C01


title: Case 74

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R08C02


title: GD1941_control_female_t1


title: GD1943_control_female_t4


title: Case 72

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R07C02


title: GD1939_control_male_t4


title: GD1940_control_male_t7


title: GD1938_control_male_t2


title: Case 81

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R12C01


title: MQ, DKO, RNA, stimulated 2h, r2

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

description: mRNA

data_processing:
Raw reads were mapped to mm9 reference genome using hisat 2 (parameter: hisat2 --known-splicesite-infile --rna-strandness R -k 1).
Reads mapped to chrM and unassembled "random" contigs were removed (sed '/chrM/d;/random/d;/chrUn/d').
Read counts were extracted and normalized using SeqMonk software.
Assembly: mm9
Supplementary files format and content: tab-deliminaed text files include raw read counts

source_name: Bone marrow

growth_protocol: Bone marrow precursors were grown in BMDM media (20% FBS, 10% CMG condition medium [containing M-CSF], 1x Pen-Strep [GIBCO, #15140-122], 1x L-Glutamine [GIBCO, #25030-081], 0.5 mM sodium pyruvate [GIBCO, #11360-070] in Dubecco’s Modified Eagle Medium) for 6 days to obtain mature BMDMs prior to stimulation. J2 immortalized bone marrow-derived macrophages were grown in BMDM media to stimulation.

extract_protocol:
Total RNA was extracted from BMDMs or macrophage cells using TRIzol reagent (ThermoFisher #15596018) followed by Qiagen RNAeasy plus mini kit (QIAGEN #74136) according to the manufacturer's instructions.
Libraries were prepared with Illumina TruSeq RNA Library Preparation Kit 2.0 (Illumina #RS-122-2001) according to the manufacturer's instructions.

treatment_protocol: BMDMs from C57/B16 mice and J2 immortalized macrophage cells were stimulated with lipid-A for 0, 15, 30, 60 or 120 minutes.

tag: strain

value: Bone marrow

tag: cell line

value: J2 vitus transformed cell line

value: bone marrow-derived macrophages

value: Rela-/-Rel-/-

value: 2 hours


title: Case 71

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R07C01


title: GD1937_control_male_t1

value: control


title: GD1936_control_male_t4


title: GD1935_control_male_t2


title: MQ, DKO, RNA, stimulated 2h, r1

description: mRNA


title: MQ, DKO, RNA, unstimulated, r1

description: mRNA

value: unstimulated


title: GD1934_control_male_t1


title: GD1946_10k_ngkgday_ IL-12_male_t1

value: 10k ng/kg/day IL-12


title: MQ, WT, RNA, stimulated 2h, r1

description: mRNA

value: wildtype


title: MQ, DKO, RNA, unstimulated, r2

description: mRNA


title: MQ, WT, RNA, unstimulated, r2

description: mRNA


title: MQ, WT, RNA, stimulated 2h, r2

description: mRNA


title: GD1932_10k_ngkgday_ IL-12_female_t2

value: Blood

value: Peripheral Blood Mononuclear Cells


title: GD1933_10k_ngkgday_ IL-12_female_t4

value: BALB/c

value: female


title: GD1942_control_female_t2


title: MQ, WT, RNA, unstimulated, r1

description: mRNA


title: Case 76

description:
Genomic DNA extracted from individuals was genotyped using Infinium Psych Array V 1.3 (Illumina).
203900570044_R09C02


title: GD1929_10k_ngkgday_ IL-12_female_t1


title: EnDel_120

library_source: genomic

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 3000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23 and all fastq files were mapped using Bowtie2.
The reads were excluded from downstream analysis if unmapped to index genome, multiple alignments, in duplicate, aligned to mitochondrial genome. or contiguous sequences.
Genomic sites enriched with aligned reads were identified and called peaks by using MACS2. The called peaks from each sample were merged to generate a combined probe list using HOMER.
All the sorted bam files were imported into seqMonk for quantification. Raw reads among each combined probe site were converted to reads per kilobases of the probe and per million reads of total read counts (RPKM).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample were generated from sorted bam files using HOMER to represent the reads coverage genome-widely.

source_name: macrophage cell line

growth_protocol: J2 immortalized bone-marrow derived macrophages were grown in CMG media containing FBS prior to stimulation.

extract_protocol:
50,000 macrophages were centrifuged and washed with PBS once. The cell pellet was resuspended with cold hypotonic lysis buffer. The lysate was centrifuged and the supernatant was discarded. The crude nuclei were treated with transposition reaction mix (50ul) containing 2.5ul Tn5 transposase (Nextera) and incubated in a 37oC thermomixer with 1000RPM mixing for 30 minutes. The transposed DNA was then cleaned up with a Qiagen Minelute PCR Purification Kit.
The transposed DNA was amplified by a non-saturating PCR containing primer 1 and barcode primer 2 provided in the published protocols by Buenristro et al. The amplified DNA was size selected on the gel from 100bp to 1000bp and purified with a Qiagen QIAquick Gel Extraction Kit. The selected DNA library was quantified by Qubit and Agilent Bioanalyzer High-Sensitivity DNA Analysis Kit.

treatment_protocol: Immortalized macrophages were stimulated with lipid-A for 0, 15, 30, 60 or 120 minutes.

value: macrophage cell line

value: enhancer deletion clones

tag: lipid a stimulation

value: stimulated

tag: treatment time

value: 120 minutes


title: GD1927_10k_ngkgday_ IL-12_female_t1


title: GD1928_10k_ngkgday_ IL-12_female_t2


title: EnDel_15

value: 15 minutes


title: EnDel_60

value: 60 minutes


title: EnDel_30

value: 30 minutes


title: GD1926_10k_ngkgday_ IL-12_female_t4


title: GD1925_10k_ngkgday_ IL-12_female_t2


title: GD1922_10k_ngkgday_ IL-12_male_t2

value: male


title: GD1924_10k_ngkgday_ IL-12_male, t6


title: GD1923_10k_ngkgday_ IL-12_male_t4


title: EnDel_0

value: 0 minute


title: GD1921_10k_ngkgday_ IL-12_male_t1


title: DKO_r2_120

value: Rela-/-Rel-/-


title: DKO_r1_30


title: DKO_r1_60


title: DKO_r2_30

value: unstimulated


title: DKO_r2_15


title: GD1930_10k_ngkgday_ IL-12_female_t4

value: 10k ng/kg/day IL-12


title: GD1919_10k_ngkgday_ IL-12_male_t4


title: DKO_r1_15


title: GD1917_10k_ngkgday_ IL-12_male_t1


title: DKO_r2_0


title: GD1916_10k_ngkgday_ IL-12_male_t6


title: DKO_r1_0


title: GD1915_10k_ngkgday_ IL-12_male_t5


title: WT_120 _r2

value: wildtype


title: DKO_r1_120


title: GD1918_10k_ngkgday_ IL-12_male_t2

value: Blood


title: GD1913_10k_ngkgday_ IL-12_male_t2

value: Peripheral Blood Mononuclear Cells


title: WT_60 _r2


title: WT_120 _r1


title: DKO_r2_60


title: WT_60 _r1


title: GD1931_10k_ngkgday_ IL-12_female_t1

value: BALB/c


title: GD1911_control_female_t2

value: control

value: female


title: GD1920_10k_ngkgday_ IL-12_male_t6


title: GD1910_control_female_t2


title: GD1909_control_female_t7


title: WT_30 _r2

value: macrophage cell line


title: WT_15 _r1

value: stimulated


title: WT_0 _r2


title: GD1907_control_female_t2


title: GD1906_control_male_t2


title: WT_15 _r2


title: GD1905_control_male_t1


title: WT_0 _r1


title: GD1904_control_male_t7


title: GD1903_0.1 _mg_ IL12ns_female_t5

value: 0.1 mg IL12ns


title: GD1914_10k_ngkgday_ IL-12_male_t4


title: Embryo, 14-15 stage, H3K27ac E7, ChIP-seq, rep2

city: Ciudad de Buenos Aires

first: Nicolas

last: Frankel

state: Buenos Aires

address: Ciudad Universitaria

department: FMBC

country: Argentina

institute: CONICET

data_processing:
Adapters were removed from fastq files with bbduk.sh.
Adapter-corrected reads were aligned to the D. melanogaster reference genome dm6 using BWA, producing SAM files.
SAM were compressed to BAM format using samtools.
Duplicate reads in BAM files were identified and marked using MarkDuplicates from the Picard suite.
BAM files were filtered based on MAPQ values (>=20) and sam flags 4, 256, 1024 and 2048 with samtools. Only properly paired reads were retained (sam flag 2).
BAM files corresponding to the H3K27ac ChIP-seq of 7 cells and E10 cells of the embryo were merged after removing duplicates and subsampling to the size of the smaller dataset.
H3K27ac experiments were normalized with bamCompare from the DeepTools suite (Ramírez et al. 2016) with --scaleFactorsMethod SES and a bin size of 1 to generate a bigWig H3K27ac normalized signal file of the X chromosome.
Assembly: dm6
Supplementary files format and content: bigWig signal file with the H3K27ac signal across the X chromosome in 14-15 stage D. melanogaster embryos.

organism: Drosophila melanogaster

source_name: Embryo (14-15 stage)

extract_protocol:
Stage 14-15 embryos from a line containing E10::GFP and 7::DsRed transgenes (Preger-Ben Noon, Davis, and Stern 2016) were cross-linked, dissociated and isolated nuclei were immunostained with anti-GFP and anti-DsRed antibodies and the appropriate secondary antibodies. The E10::GFP and 7::DsRed nuclei, which constitute the majority of svb expressing nuclei, were then isolated by fluorescence activated cell sorter (FACS). Chromatin from 250,000 nuclei of each cell sub-populations (n=3) was isolated and used for ChIP with anti-H3K27ac and anti-H3 antibodies (Abcam) using the iDeal ChIP-seq kit (Diagenode).
Libraries were prepared using the Ovation Ultralow V2 DNA-Seq library preparation kit (NuGen) according to the manufacturer instructions. Libraries were sequenced on a NextSeq 550 system (Illumina) with 50 bp SE reads.

value: Embryo (14-15 stage)

value: svb positive cells (enhancer E7)


title: Embryo, 14-15 stage, H3 E7, ChIP-seq, rep2


title: Embryo, 14-15 stage, H3 E7, ChIP-seq, rep1


title: Embryo, 14-15 stage, H3K27ac E7, ChIP-seq, rep1


title: Embryo, 14-15 stage, H3 E10, ChIP-seq, rep2

value: svb positive cells (enhancer E10)


title: GD1900_0.1 _mg_ IL12ns_female_t7


title: GD1901_0.1 _mg_ IL12ns_female_t1


title: GD1899_0.1 _mg_ IL12ns_female_t2


title: Embryo, 14-15 stage, H3 E10, ChIP-seq, rep1


title: GD1898_0.1 _mg_ IL12ns_female_t1


title: Embryo, 14-15 stage, H3K27ac E10, ChIP-seq, rep3


title: Embryo, 14-15 stage, H3K27ac E10, ChIP-seq, rep2


title: GD1908_control_female_t5


title: WT_30 _r1

value: 30 minutes


title: GD1897_0.1 _mg_ IL12ns_female_t7


title: GD1896_0.1 _mg_ IL12ns_female_t2


title: Embryo, 14-15 stage, H3K27ac E10, ChIP-seq, rep1


title: Pupal abdominal epidermis, ATAC-seq, rep2

data_processing:
Adapters were removed from fastq files with bbduk.sh.
Adapter-corrected reads were aligned to the D. melanogaster reference genome dm6 using BWA, producing SAM files.
SAM files were compressed to BAM format using samtools.
Duplicate reads in BAM files were identified and marked using MarkDuplicates from the Picard suite.
BAM files were filtered based on MAPQ values (>=20) and sam flags 4, 256, 1024 and 2048 with samtools. Only properly paired reads were retained (sam flag 2).
ATAC-seq experiments were normalized using S3norm to generate bigWig signal files of the regulatory region of svb. Signal was averaged base-by-base across all 3 replicates.
MACS2 was used to call peaks across the genome by merging all 3 replicates and using the following parameters: -g dm -f BAM --keep-dup all --shift -50 --extsize 100 --nomodel.
Assembly: dm6
Supplementary files format and content: narrowPeak (bed) file of genome-wide open chromatin regions of the abdominal pupal epidermis.
Supplementary files format and content: bigWig file of the chromatin accessibility signal in the cis-regulatory region of the svb gene.

source_name: Pupal abdominal epidermis

extract_protocol:
For each replicate (n=3) we removed abdominal cuticles from 50 pupae 38-45 hAPF. We carefully removed internal organs with forceps in cold PBS, to retain only epidermal cells, which are attached to the cuticle.
We followed the Omni-ATAC protocol (Corces et al. 2017) but using a lysis buffer based on IGEPAL detergent (Lysis Buffer: 10 mM Tris-HCl, pH=7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Library concentration was quantified with a KAPA Library Quantification Kit (Roche) and quality control was performed with the High-Sensitivity DNA Analysis kit in a Bioanalyzer 2100 (Agilent).

value: Pupal abdominal epidermis

value: Epidermal cells

value: WT


title: Pupal abdominal epidermis, ATAC-seq, rep1


title: Pupal abdominal epidermis, ATAC-seq, rep3


title: GD1895_0.1 _mg_ IL12ns_female_t1


title: GD1894_0.1 _mg_ IL12ns_female_t7


title: GD1893_0.1 _mg_ IL12ns_female_t5


title: GD1892_0.1 _mg_ IL12ns_male_t5

value: male


title: GD1902_0.1 _mg_ IL12ns_female_t2


title: GD1891_0.1 _mg_ IL12ns_male_t1


title: Ctrl, MLP1/2 mutant, MeDIP, 2hr, 0X, rep2

city: UNIVERSITY PARK

first: Lu

last: Bai

state: PENNSYLVANIA

address: 406 SOUTH FREAR, UNIVERSITY PARK

department: BMB

institute: Penn State University

data_processing:
Paired-end reads of 50 bp or 150 bp were processed with fastp (version 0.23.2) to remove low quality reads. Processed reads were aligned to S. cerevisiae genome (sacCer3) with BWA (version 0.7.17). Aligned bam files were deduplicated with Picard MarkDuplicates (version 3.0.0). bigwig files were generated by deeptools bamCoverage (version 3.5.1) for visualization purposes. To detect differentially methylated NDRs, aligned reads on each NDR were counted by Subread featureCounts (version 2.0.3) using a list of NDR coordinates generated from a previous study, with the following parameters “-p -O”. Fold change and P-value were generated by DEseq2 (1.38.0) without outliers filtering. log2 (Fold Change) > 0.7 and the adjusted P-value < 0.05 were used as the cutoff for identifying differentially methylated regions.
Assembly: sacCer3
Supplementary files format and content: table generated by DEseq2
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in 50 mL synthetic media with/without methionine at 30°C to OD660 = 0.3.

extract_protocol:
Standard MeDIP protocol for preparation of methylated genomic DNA
MeDIP-Seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L). Next generation sequencing was performed on NextSeq 2000 (Illumina).

treatment_protocol: β-estradiol (Sigma, 50-28-2) was added to a final concentration of 2 nM for 1/2 hrs, allowing the LacI-NLS-M.CviPI fusion protein to express. For MATa and MATalpha viewpoint, glucose (D) or galactose(G) was added according to the experimental conditions.

tag: chip antibody

tag: condition

value: 2hr, 2nM Beta-estradiol

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, MLP2::HygoMX, MLP1::KanMX


title: GD1912_control_female_t7

tag: tissue

value: Blood

tag: cell type

value: Peripheral Blood Mononuclear Cells


title: GD1888_0.1 _mg_ IL12ns_male_t2

value: BALB/c


title: HiC, YBP2, +E2, rep1

data_processing:
150 bp paired-end reads were aligned to S. cerevisiae genome (sacCer3) and analyzed with HiC-pro.
Assembly: sacCer3
Supplementary files format and content: cool file of Hi-C dataset

growth_protocol: Yeast strains were grown in 200 mL synthetic media without methionine to OD660 = 0.3.

extract_protocol:
Standard Hi-C protocol was used for the preparation of Hi-C samples
Hi-C libraries were prepared with NEBNext Ultra II DNA Library Prep Kit. Next generation sequencing was performed on NextSeq 2000.

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, YBP2::256XLacO::HIS3

value: methionine depletion, 2nM Beta-estradiol for 2hrs.


title: HiC, Ctrl, +E2, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2


title: GD1886_0.1 _mg_ IL12ns_male_t5

value: 0.1 mg IL12ns


title: HiC, YBP2, -E2, rep1

value: methionine depletion, without Beta-estradiol


title: HiC, Ctrl, -E2, rep1


title: GD1889_0.1 _mg_ IL12ns_male_t2


title: GD1885_0.1 _mg_ IL12ns_male_t2


title: GD1884_10 _mg_ IL12ns_female_t5

value: 10 mg IL12ns

value: female


title: GD1882_10 _mg_ IL12ns_female_t1


title: YBP2, MLP1/2 mutant, MeDIP, 2hr, 256X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, MLP2::HygoMX, MLP1::KanMX, YBP2::256XLacO::HIS3


title: GD1883_10 _mg_ IL12ns_female_t2


title: GD1881_10 _mg_ IL12ns_female_t5


title: GD1880_10 _mg_ IL12ns_female_t1


title: YBP2, MLP1/2 mutant, MeDIP, 2hr, 256X, rep1


title: Ctrl, MLP1/2 mutant, MeDIP, 2hr, 0X, rep1


title: NC-RNA-1

city: Changsha

first: Mengqi

last: Nie

address: Xiangya Road

country: China

institute: Xiangya Hospital of Central South University

data_processing:
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model. Differential expression was assessed by DEseq/DESeq2/edgeR/DEGseq using read counts as input.
The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05. All the differentially expressed genes were used for heat map analysis and KEGG ontology enrichment analyses. For KEGG enrichment analysis, a P-value < 0.05 was used as the threshold to determine significant enrichment of the gene sets.
Assembly: Pre-processing of sequencing reads / Quality Control. 1) Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: :TRAILING:20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes. 2) Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52). Quantification of gene expression level . Paired-end reads were aligned to the mouse reference genome mm10/hg19/rn6 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene. Differential expression analysis. The statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(foldchange)| > 1 using theDEseq/DESeq2/edgeR/DEGseq software. Finally, a hierarchical clustering analysis was performed using the R language package gplots according to the RPKM values of differential genes in different groups. And colors represent different clustering information, such as the similar expression pattern in the same group, including similar functions or participating in the same biological process. GO terms and KEGG pathway enrichment analysis. In order to identify the Gene Ontology (GO) annotations and pathways in which differentially expressed genes were enriched, GO term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the “clusterProfiler”package in RBioconductor /KOBAS3.0 software. In the present study, the clusterProfiler package in R Bioconductor/ KOBAS3.0 was used to identify and visualize the GO terms and KEGG pathways enriched by all differentially expressed genes. Co-expression network of differentially expressed lncRNAs/mRNAs. To investigate the potential functions of differentially expressed lncRNAs and the interactions between mRNAsand lncRNAs, we constructed alncRNA/mRNA transcripts co-expression network. The co-expression networkwas constructed by calculating the Pearson correlation coefficient and P value between multiple genes. Inour study, the transcripts were filtered using a COR of >0.85 and a P-value of <0.05. Then we chose XXXXX DEmRNA transcripts that were enriched in reproduction-related pathways and all DE lncRNAs to construct a coexpressionnetwork, theco-expression network was illustrated using Cytoscape software. Analysis of the protein-protein interaction (PPI) network of DEGs. In order to explore the correlation between these DEGs, the interaction network of protein-protein internet (PPI) was constructed using the STRING database and visualized in Cytoscape software.
Supplementary files format and content: NC-RNA--A-RNA.all.gene.xls

source_name: Adipose

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA).
The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: Adipose

value: Adipose-derived stem cell

value: Adipose-derived mesenchymal stem cells


title: A-RNA-1

value: CEFFE


title: NC-RNA-2


title: GD1878_10 _mg_ IL12ns_female_t5


title: A-RNA-2


title: NC-RNA-3


title: GD1879_10 _mg_ IL12ns_female_t2


title: CEBPAnonbZIPinf_11

city: Taipei

first: Fengming

last: Tien

state: Taiwan

address: No.7, Chungshan south road

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Trimming of adaptor sequences and removal of reads of low quality were performed using cutadapt (v2.3).
Quantified reads were aligned to the human genome (GRCh38.p12) by STAR (v2.6.1a)(24) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: bone marrow

extract_protocol:
Total RNA were extracted using RNeasy kit (Qiagen) and reverse trasncribed using Superscript II RT (Invitrogen).
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer's recommendations.

value: bone marrow

value: bone marrow mononuclear cells

value: CEBPAnonbZIPinf

value: pretreatment diagnostic


title: GD1890_0.1 _mg_ IL12ns_male_t5

value: Blood

value: Peripheral Blood Mononuclear Cells

value: BALB/c

value: male


title: GD1877_10 _mg_ IL12ns_female_t3


title: GD1887_0.1 _mg_ IL12ns_male_t1

value: 0.1 mg IL12ns


title: CEBPAnonbZIPinf_09


title: A-RNA-3


title: GD1876_10 _mg_ IL12ns_female_t1


title: GD1875_10 _mg_ IL12ns_male_t5


title: CEBPAnonbZIPinf_07


title: CEBPAnonbZIPinf_08


title: GD1874_10 _mg_ IL12ns_male_t3


title: CEBPAnonbZIPinf_05


title: GD1872_10 _mg_ IL12ns_male_t3


title: GD1873_10 _mg_ IL12ns_male_t5


title: GD1871_10 _mg_ IL12ns_male_t2


title: GD1870_10 _mg_ IL12ns_male_t1


title: CEBPAnonbZIPinf_03


title: CEBPAnonbZIPinf_04


title: GD1869_10 _mg_ IL12ns_male_t3


title: CEBPAnonbZIPinf_02


title: CEBPAwt_89

value: CEBPAwt


title: GD1867_10 _mg_ IL12ns_male_t5

value: 10 mg IL12ns


title: CEBPAnonbZIPinf_01


title: GD1868_10 _mg_ IL12ns_male_t1


title: CEBPAnonbZIPinf_10


title: CEBPAwt_88


title: GD1866_10 _mg_ IL12ns_male_t1


title: CEBPAwt_86


title: GD1193_control_female_t6

value: control

value: female


title: CEBPAwt_85


title: GD1191_control_female_t3


title: GD1192_control_female_t5


title: CEBPAwt_84


title: CEBPAnonbZIPinf_06


title: GD1188_control_female_t3


title: CEBPAwt_82


title: GD1190_control_female_t6


title: GD1189_control_female, t5


title: CEBPAwt_81


title: GD1187_control_male_t6


title: CEBPAwt_80


title: GD1186_control_male_t5


title: CEBPAwt_79


title: GD1185_control_male_t3


title: GD1184_control_male_t7


title: CEBPAwt_78


title: CEBPAwt_76


title: CEBPAwt_77


title: GD1183_control_male_t6


title: CEBPAwt_74


title: GD1180_10k_ngkgday_ IL-12_female_t7

value: 10k ng/kg/day IL-12


title: GD1181_control_male_t3


title: CEBPAwt_75


title: GD1179_10k_ngkgday_ IL-12_female_t6


title: CEBPAwt_72


title: GD1178_10k_ngkgday_ IL-12_female_t5


title: CEBPAwt_83


title: GD1177_10k_ngkgday_ IL-12_female_t3


title: CEBPAwt_71


title: GD1176_10k_ngkgday_ IL-12_female_t6


title: CEBPAwt_69


title: CEBPAwt_73


title: CEBPAwt_70


title: CEBPAwt_68


title: GD1174_10k_ngkgday_ IL-12_female_t3


title: GD1175_10k_ngkgday_ IL-12_female_t5


title: CEBPAwt_66


title: GD1173_10k_ngkgday_ IL-12_female_t7


title: CEBPAwt_67


title: CEBPAwt_65


title: GD1170_10k_ngkgday_ IL-12_female_t5


title: GD1182_control_male_t5


title: GD1171_10k_ngkgday_ IL-12_female_t7


title: GD1169_10k_ngkgday_ IL-12_female_t3


title: CEBPAwt_62


title: CEBPAwt_63


title: GD1168_10k_ngkgday_ IL-12_male_t7


title: GD1167_10k_ngkgday_ IL-12_male_t7


title: CEBPAwt_60


title: CEBPAwt_61


title: GD1165_10k_ngkgday_ IL-12_male_t3


title: GD1164_10k_ngkgday_ IL-12_male_t5


title: CEBPAwt_57


title: CEBPAwt_58


title: GD1172_10k_ngkgday_ IL-12_female_t6


title: CEBPAwt_56


title: CEBPAwt_54


title: GD1162_10k_ngkgday_ IL-12_male_t7


title: GD1160_control_female_t6


title: CEBPAwt_53


title: GD1159_control_female_t3


title: CEBPAwt_55


title: GD1163_10k_ngkgday_ IL-12_male_t3


title: GD1161_10k_ngkgday_ IL-12_male_t3


title: CEBPAwt_64


title: GD1158_control_female_t4


title: CEBPAwt_52


title: CEBPAwt_87


title: CEBPAwt_51


title: CEBPAwt_50


title: GD1156_control_male_t5


title: CEBPAwt_48


title: CEBPAwt_47


title: GD1154_control_male_t3


title: GD1157_control_male_t6


title: GD1166_10k_ngkgday_ IL-12_male_t5


title: CEBPAwt_59


title: CEBPAwt_46


title: GD1152_0.1 _mg_ IL12ns_female_t3


title: CEBPAwt_45


title: CEBPAwt_44


title: GD1151_0.1 _mg_ IL12ns_female_t6


title: GD1150_0.1 _mg_ IL12ns_female_t5


title: CEBPAwt_43


title: GD1149_0.1 _mg_ IL12ns_female_t6


title: CEBPAwt_42


title: GD1148_0.1 _mg_ IL12ns_female_t4


title: CEBPAwt_41


title: CEBPAwt_40


title: GD1145_0.1 _mg_ IL12ns_female_t4


title: GD1147_0.1 _mg_ IL12ns_female_t3


title: CEBPAwt_39


title: GD1146_0.1 _mg_ IL12ns_female_t6


title: CEBPAwt_37


title: CEBPAwt_49


title: GD1144_0.1 _mg_ IL12ns_female_t3


title: GD1143_0.1 _mg_ IL12ns_male_t7


title: GD1153_0.1 _mg_ IL12ns_female_t4


title: GD1142_0.1 _mg_ IL12ns_male_t4


title: CEBPAwt_35


title: GD1155_control_male_t4


title: GD1141_0.1 _mg_ IL12ns_male_t7


title: CEBPAwt_34


title: CEBPAwt_36


title: GD1140_0.1 _mg_ IL12ns_male_t6


title: GD1139_0.1 _mg_ IL12ns_male_t3


title: CEBPAwt_33


title: CEBPAwt_32


title: GD1138_0.1 _mg_ IL12ns_male_t7


title: CEBPAwt_31


title: GD1137_0.1 _mg_ IL12ns_male_t6


title: CEBPAwt_30


title: CEBPAwt_38


title: GD1136_0.1 _mg_ IL12ns_male_t4


title: CEBPAwt_28


title: GD1134_0.1 _mg_ IL12ns_male_t6


title: CEBPAwt_29


title: CEBPAwt_26


title: CEBPAwt_24


title: CEBPAwt_23


title: CEBPAwt_27


title: GD1133_0.1 _mg_ IL12ns_male_t4


title: GD1131_10 _mg_ IL12ns_female_t7


title: CEBPAwt_25


title: CEBPAwt_22


title: GD1128_10 _mg_ IL12ns_female_t3


title: GD1129_10 _mg_ IL12ns_female_t4


title: GD1127_10 _mg_ IL12ns_female_t6


title: CEBPAwt_21


title: CEBPAwt_19


title: CEBPAwt_20


title: GD1132_0.1 _mg_ IL12ns_male_t3


title: CEBPAwt_17


title: GD1124_10 _mg_ IL12ns_female_t6


title: GD1125_10 _mg_ IL12ns_female_t7


title: CEBPAwt_18


title: GD1126_10 _mg_ IL12ns_female_t4


title: GD1123_10 _mg_ IL12ns_female_t4


title: CEBPAwt_16


title: GD1122_10 _mg_ IL12ns_female_t3


title: GD1135_0.1 _mg_ IL12ns_male_t3


title: CEBPAwt_15


title: GD1121_10 _mg_ IL12ns_female_t7


title: CEBPAwt_14


title: CEBPAwt_13


title: GD1130_10 _mg_ IL12ns_female_t6


title: GD1119_10 _mg_ IL12ns_male_t6


title: CEBPAwt_12


title: GD1118_10 _mg_ IL12ns_male_t4


title: GD1117_10 _mg_ IL12ns_male_t7


title: CEBPAwt_09


title: CEBPAwt_10


title: GD1116_10 _mg_ IL12ns_male_t6


title: CEBPAwt_11


title: GD1115_10 _mg_ IL12ns_male_t4


title: CEBPAwt_08


title: GD1112_10 _mg_ IL12ns_male_t4


title: GD1113_10 _mg_ IL12ns_male_t6


title: CEBPAwt_05


title: CEBPAwt_04


title: CD22+ Eos sample 3

city: New Haven

first: Vassily

middle: Igor

last: Kutyavin

state: CT

address: 1 Gilbert St

department: Immunobiology

institute: Yale University

data_processing:
First 14 bp of read 2 (UMI, linker, and adapter sequences) were trimmed by Trimmomatic (v. 0.39)
Trimmed sequence reads were pseudoaligned to GrCM38/mm10 using Kallisto (v. 0.46.1)
Normalized count tables were generated with DESeq2 (v. 1.38.2)
Assembly: Genome build: mm10
Supplementary files format and content: tab-delimited text files include normalized count values for each sample

source_name: Eosinophil

growth_protocol: Mice were maintained with free access to standard chow under a regular 12h light/12h dark cycle at a constant temperature of 22°C.

extract_protocol:
The cells were lysed in Tri Reagent (Sigma-Aldrich) and processed according to the manufacturer's protocol until the phase separation. The aqueous phase was collected and RNA was extracted with a Direct-zol RNA Microprep Kit (Zymo Research) according to the manufacturer's instructions, including the DNase step.
Sequencing libraries were constructed with SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio) according to the manufacturer’s instructions. 3 ng of total RNA was used as input.

tag: population

value: Eosinophil

value: wild type


title: CEBPAwt_06


title: CD22+ Eos sample 1


title: CEBPAwt_07


title: GD1120_10 _mg_ IL12ns_male_t7


title: CEBPAwt_02


title: CD22+ Eos sample 4


title: CEBPAwt_01


title: a4b7- CD22- Eos sample 4


title: a4b7- CD22- Eos sample 3


title: CEBPAbZIPinf_36

value: CEBPAbZIPinf


title: CD22+ Eos sample 2


title: CEBPAwt_03

value: bone marrow


title: CEBPAbZIPinf_35

value: bone marrow mononuclear cells


title: CEBPAbZIPinf_34


title: a4b7- CD22- Eos sample 1


title: a4b7- CD22- Eos sample 2


title: a4b7+ Eos sample 4


title: CEBPAbZIPinf_32


title: a4b7+ Eos sample 3


title: CEBPAbZIPinf_31


title: GD1114_10 _mg_ IL12ns_male_t7


title: a4b7+ Eos sample 2


title: a4b7+ Eos sample 1


title: CEBPAbZIPinf_29


title: YP_18_Total_KES30_rep2

city: Chicago

first: Mee-Ngan

middle: F.

last: Yap

state: IL

address: 320 E Superior St

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

data_processing:
CASAVA-1.8.2 basecalling
Raw FastQ sequencing data were processed on local instance of Galaxy platform..  Sequence libraries were pre-processed by clipping the adaptor sequence (5’CTGTAGGCACCATCAAT3’) and trimming the sequences by discarding the first base and all those extending beyond the 50th base.  The sequencing reads were mapped to the rRNA reference genome with Bowtie2.
The unaligned output files from Bowtie 2 (rRNA-less sequences) were mapped to the S. aureus NCTC 8325 (GeneBank CP000253) with Bowtie v.0.12.0. The alignment .map files were used as inputs for the modified Python scripts to obtain normalized read density in "reads per million mapped reads" (RPM) at each nucleotide positions. Original Python scripts have been published in Ref: Becker et al (2013)Nature Protoc 8: 2212-2239
mRNA abundance were determined by Cufflinks in FPKM (Fragments Per Kilobase of transcript per Million mapped reads)
Differential gene expression was measured by Cuffdiff. Geometric library normalization and pooled dispersion estimation methods were employed with a 0.05 false discovery rate and a minimum alignment count of 10.
Genome_build: GenBank: CP000255.1
Supplementary_files_format_and_content: Tab-delimited text files include normalized-read densities (RPM) at each nucleotide position

organism: Staphylococcus aureus

source_name: YP_18_Total_KES30_bacterial cells

growth_protocol: S. aureus cells were grown in 1 liter of  tryptic soy broth until mid-log phase (OD600 ~0.8-1.0) at 37°C

extract_protocol:
Bacterial cells were disrupted by cryomilling on a Retch MM400 (15 mm grinding balls, 10 ml jars) for 6 set of 3 min cycles at 15 Hz. Ref: Oh et al (2011) Cell 147: 1295-1308
Cell lysates were subjected to micrococcal S7 nuclease digestion, and  70S monosomes were collected by 10-40% sucrose density gradient. Total mRNA (alkaline hydrolysis) and the monosomal mRNAs (26-42 nt) were isolated by hot-phenol/chloroform method.
The fragmented mRNAs and ribosome footprint mRNAs (RPFs) were ligated to a universal linker. Following rRNA subtraction, PAGE purification, reverse transcription, cDNA circularization, and multiplexing PCR amplification, the cDNA libraries were sequenced on Illumina HiSeq 2000

treatment_protocol: Unlike other Ribo-seq protocols, translation inhibitor was not added to the culture.To preserve ribosome occupancy on its mRNA template, cells were rapidly collected via vacuum filtration through 0.45 µm nitrocelluloase membrane.

tag: genotype/variation

value: KES30 (m6A2058-modified ribosomes)

tag: growth phase

value: Exponentially grown

tag: cdna type

value: Total mRNAs


title: YP16_Total_KES30_rep1

source_name: YP16_Total_KES30_bacterial cells


title: CEBPAbZIPinf_27

value: pretreatment diagnostic


title: CEBPAbZIPinf_28


title: YP15_RPF_KES30_rep2

source_name: YP15_RPF_KES30_bacterial cells

value: Ribosome-protected mRNA fragments (RPFs)


title: YP13_RPF_KES30_rep1

source_name: YP13_RPF_KES30_bacterial cells


title: CEBPAbZIPinf_25


title: YP10_RPF_KES34_rep3

source_name: YP10_RPF_KES34_bacterial cells

value: KES34 (unmodified ribosomes)


title: CEBPAbZIPinf_24


title: YP12_Total_KES34_rep3

source_name: YP12_Total_KES34_bacterial cells


title: CEBPAbZIPinf_23


title: YP8_Total_KES34_rep2

source_name: YP8_Total_KES34_bacterial cells


title: YP4_Total_KES34_rep1

source_name: YP4_Total_KES34_bacterial cells


title: YP2_RPF_KES34_rep1

source_name: YP2_RPF_KES34_bacterial cells


title: CEBPAbZIPinf_30


title: CEBPAbZIPinf_33


title: YP6_RPF_KES34_rep2

source_name: YP6_RPF_KES34_bacterial cells


title: Liver DSS Day 20 -3

city: Bethesda

first: Chuan

last: Wu

state: MD

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

data_processing:
All analyses were performed in Partek® Flow® software, version 5.0 (Copyright 2016, Partek Inc., St. Louis, MO).
FASTQ files were uploaded into Partek Flow software for processing, aligned using STAR aligner, and quantified to transcriptome (Partek E/M using mm10 – Ensembl Transcripts release 94 as the reference index)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: WT

value: DSS

tag: time

value: Day 20


title: CEBPAbZIPinf_21


title: CEBPAbZIPinf_19


title: CEBPAbZIPinf_20


title: CEBPAbZIPinf_18


title: CEBPAbZIPinf_17


title: CEBPAbZIPinf_16


title: Liver DSS Day 10 -3

value: Day 10


title: Liver DSS Day 20 -1


title: CEBPAbZIPinf_15


title: CEBPAbZIPinf_26


title: Liver DSS Day 10 -1


title: Liver DSS Day 0 -3

value: Day 0


title: CEBPAbZIPinf_13


title: Liver DSS Day 10 -2


title: CEBPAbZIPinf_22


title: CEBPAbZIPinf_12


title: Liver DSS Day 0 -2


title: Hepatectomy SI Crypt-2

source_name: Small intestine

value: Small intestine

value: Crypt

value: Hepatectomy


title: CEBPAbZIPinf_10

value: bone marrow

value: CEBPAbZIPinf


title: CEBPAbZIPinf_11

value: bone marrow mononuclear cells


title: Liver DSS Day 0 -1


title: Liver DSS Day 20 -2


title: Hepatectomy SI IEC-2

value: IEC


title: Hepatectomy SI IEC-1


title: CEBPAbZIPinf_06


title: CEBPAbZIPinf_04


title: CEBPAbZIPinf_08


title: Sham SI Crypt-2

value: Sham


title: Hepatectomy SI Crypt-1


title: CEBPAbZIPinf_07

value: pretreatment diagnostic


title: Sham SI IEC-1


title: Sham SI IEC-2


title: CEBPAbZIPinf_05


title: Sham SI Crypt-1


title: CEBPAbZIPinf_01


title: CEBPAbZIPinf_02


title: CEBPAbZIPinf_03


title: CEBPAbZIPinf_14


title: IgG_T1

city: San Francisco

first: Angelo

last: Pelonero

state: CA

address: 1650 Owens Street

department: Cardiovascular Disease Institute

institute: Gladstone Institutes (UCSF)

description:
WTC11 hIPSCs differentiated to cardiac progenitor cells (CPCs) with CUT&RUN performed on day 6
BRD4_Epicypher_T1rep1+2_mean_SEACR_FDR1e-2.bed
H3K27me3_T1rep1+2_mean_SEACR_FDR1e-2.bed
H3K4me3_T1+T2reps_mean_SEACR_FDR1e-2.bed

data_processing:
library strategy: Cleavage Under Target & Release (CUT&RUN)
Illumina Casava v1.8 was used for base-calling.
All Cut & Run raw data was initially processed using the nfcore Cut & Run pipeline (nf-core/cutandrun v2.0) with standard settings, aligned to hg38.
Peaks were called outside of nfcore framework using Sparse Enrichment Analysis for CUT&RUN (SEACR v1.3) with an FDR threshold of 1e-2
Assembly: hg38
Supplementary files format and content: Bed files of SEACR peak calls from IgG subtracted and averaged samples (FDR threshold 0.01)

source_name: day 6 human iPSC-derived cardiac progenitor cells

extract_protocol:
Nuclei were isolated with Nuclear extraction buffer [20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM Spermidine (Sigma #05292–1ml-F), 0.1% Triton X-100, 20% Glycerol and 1× protease and phosphatase inhibitor (Thermo Fisher #78442)]. To aid in nuclear capture, isolated nuclei were incubated with activated Concanavalin A beads (Bangs Laboratories #Bp531) for 15 minutes at room temperature followed by incubation with the desired primary antibody (1:100 dilution) overnight.
Libraries were prepares using a commercially available CUT&RUN kit (Epicypher #14-1048).

value: WTC11 hIPSCs


title: IgG_T2

description:
WTC11 hIPSCs differentiated to cardiac progenitor cells (CPCs) with CUT&RUN performed on day 6
BRD4_FLAG_T2rep1+2_mean_SEACR_FDR1e-2.bed


title: H3K4me3_T2

description:
WTC11 hIPSCs differentiated to cardiac progenitor cells (CPCs) with CUT&RUN performed on day 6
H3K4me3_T1+T2reps_mean_SEACR_FDR1e-2.bed


title: CAVD2_DP

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

institute: Stanford University

description: CD34+/c-kit+ endothelial cells from diseased aortic valve leaflet 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
RPKM was counted by using HtSeq
Assembly: hg38

source_name: Diseased aortic valve leaflet 2

growth_protocol: Endothelial cells were grown in EGM2 (Lonza) and cultured on 0.2% gelatin-coated plates

extract_protocol:
Using Direct-zol RNA Microprep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: calcific aortic valve disease

value: aortic valve leaflet

tag: age

value: 3 passages following initial stripping from the valve leaflet

value: CD34+/c-kit+ endothelial cells


title: CAVD2_DN

description: CD34-/c-kit- endothelial cells from diseased aortic valve leaflet 2

value: CD34-/c-kit- endothelial cells


title: CAVD1_DP

description: CD34+/c-kit+ endothelial cells from diseased aortic valve leaflet 1

source_name: Diseased aortic valve leaflet 1


title: CAVD1_DN

description: CD34-/c-kit- endothelial cells from diseased aortic valve leaflet 1


title: CNTRL2_DP

description: CD34+/c-kit+ endothelial cells from control aortic valve leaflet 2

source_name: Control aortic valve leaflet 2

value: control


title: CEBPAbZIPinf_09

source_name: bone marrow

tag: genotype

tag: treatment


title: H3K4me3_T1


title: H3K27me3_T1_2

description:
WTC11 hIPSCs differentiated to cardiac progenitor cells (CPCs) with CUT&RUN performed on day 6
H3K27me3_T1rep1+2_mean_SEACR_FDR1e-2.bed


title: H3K27me3_T1_1


title: BRD4_FLAG_T2_2


title: CNTRL2_DN

description: CD34-/c-kit- endothelial cells from control aortic valve leaflet 2


title: CNTRL1_DP

description: CD34+/c-kit+ endothelial cells from control aortic valve leaflet 1

source_name: Control aortic valve leaflet 1


title: CNTRL1_DN

description: CD34-/c-kit- endothelial cells from control aortic valve leaflet 1


title: BRD4_Epicycpher_T1_1

description:
WTC11 hIPSCs differentiated to cardiac progenitor cells (CPCs) with CUT&RUN performed on day 6
BRD4_Epicypher_T1rep1+2_mean_SEACR_FDR1e-2.bed


title: BRD4_FLAG_T2_1


title: HeLa-HBO1-KO, H3K9la, CHIP, rep1

city: Tianjin

first: wang

middle: si

last: yu

address: No. 22, Meteorological Tai Road, Heping District

institute: Tianjin Medical University

data_processing:
Sequencing quality was evaluated by FastQC version (v0.11.9). All reads were aligned to the human genome build hg38 using the Bowtie2 (v2.4.5) with the default parameters.
Duplicate reads were removed using Picard tools (version 2.27.4). Then Samtools version (1.15.1) was used to convert and sort files to bam format.
Uniquely mapped reads were normalized using deepTools (version 3.5.1) with the parameters --normalizeUsing RPKM --binSize 50 to visualize CUT&Tag signals at specific genomic loci by IGV (version 2.15.1)
Peaks were identified for each sample and biological replicate using MACS2 (version 2.2.7.1) with command line options “macs2 callpeak -q 0.05 -g hs -f BAM --nomodel”.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: cervix

growth_protocol: Cells were cultured with DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were cultured at 37 °C at 5% CO2.

extract_protocol:
HeLa cells were collected and counted for incubation with pre-treated ConA beads. Subsequently, cells are resuspended in an Antibody Buffer and incubated overnight at 4 °C with the corresponding primary antibody of HBO1 or H3K9la. The secondary antibodies were diluted in appropriate proportions and incubate them with the cells at room temperature. Subsequently, pA/G-Tnp transposons were rotated and incubated with the samples for 1h to activate the translocase fragment DNA and extract DNA.
DNA library was constructed with TruePreP Index Kit V2 for Illumina. The library was purified by VAHTS DNA Clean Beads and sequenced by Illumina novaseq 150PE.

value: cervix

value: HeLa

value: Human cervical cancer cell


title: HeLa, H3K9la, CHIP, rep2

value: WT


title: HeLa-HBO1-KO, H3K9la, CHIP, rep2


title: IP_NONO_Eto

city: würzburg

first: Kaspar

last: Burger

address: Am Hubland

institute: University of Würzburg

library_source: other

data_processing:
Paired-end sequencing reads from eCLIP experiments were initially trimmed using a custom Python script to identify the unique molecular identifier(UMI).
These trimmed reads were then aligned to the human genome (hg38, ensemble v100) using the Burrows–Wheeler Aligner (BWA, 0.7.17-r1188).
Next, we removed PCR duplicates using Picard’s MarkDuplicates (v2.23.3-1) with UMI-aware deduplication.
Finally, enriched protein binding regions were identified by MACS2 callpeak (v.2.2.7) with parameters ‘-g hs -s 58 -B --keep-dup all --nomodel --extsize 50 --d-min 5 --scale-to small –B’, of IP against size-matched(SM) INPUT samples.
Visualizations of the region were rendered from the PCR-deduplicated .bam files using the Integrative Genomics Viewer(IGV).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: eCLIP-seq

molecule: other

extract_protocol:
Cells cultured in the absence or presence of etoposide were washed with PBS, subjected to UV irradiation (200 mJ/cm2), scraped and resuspended in ice-cold PBS, pelleted (1200 rpm, 5 min) and stored at -80 °C. The pellet was lysed (20 min, 4°C) in eCLIP lysis buffer (50 mM tris-HCl pH7.4, 150 mM NaCl, 1 mM EDTA, 1% IGEPAL CA-630, 0.5% sodium deoxycholate, 0.25 mM of TCEP) and sonicated. Subsequently, a limited RNase I (Invitrogen) digest (10 min, 22 °C) and TURBOTM DNase (Invitrogen) digest (20 min, 37 °C) was performed. For the immunoprecipitation (IP) per mg total protein, 5 µg of anti- NONO rabbit polyclonal antibody (proteintech®; cat: 11058-1-AP; lot: 0082415) was coupled to 30µl DynabeadsTM Protein G beads (Invitrogen) and incubated over night at 4 °C. The samples were washed twice in CLIP lysis buffer, twice in wash buffer (50 mM of tris-HCl pH7.4, 300 mM of NaCl, 1 mM of EDTA, 1% IGEPAL CA-630, 0.5% sodium deoxycholate, 0.25 mM of TCEP), followed by two washes in low-salt wash buffer (50 mM of tris-HCl pH7.4, 1 mM of EDTA, 0.5% IGEPAL CA-630).
Subsequent library preparation was performed as described in the eCLIP protocol (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)

value: human bone osterosarcoma epithelial cells

tag: clip antibody

value: NONO

value: etoposide


title: IP_NONO_ctrl

tag: cell line


title: EVT_D8, H3K4me1, ChIP-seq, rep2

city: Austin

first: Mijeong

last: Kim

address: 2506 Speedway, NMS 4.246

institute: The University of Texas at Austin

data_processing:
Sequenced reads were mapped to human genome (hg38) using Bowtie 2.4.5
Peaks were called using MACS3 peak caller with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: Placenta

extract_protocol:
ChIP and bioChIP were performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNAs were applied for the generation of sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (E7103L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

value: Placenta

value: Human trophoblast stem cells


title: HeLa, HBO1, CHIP, rep2


title: HeLa, HBO1, CHIP, rep1


title: EDTA_WholeBlood__P12

data_processing:
Raw sequence reads were adapter trimmed and depleted of PCR duplicates based on the UMIs.
Only sequences that had at least one read in at least three samples per blood component type and that were longer than 17 nucleotides were kept.
For 25 cellular fractions (4.6% of derivatives, 25/539) the purification process did not meet the prespecified quality standard (purity > 70% as determined by flow cytometry). These samples were excluded from further analyses. See 'quality filter for processed data'
As additional quality control, the normalized data of the blood component samples was converted to a two-dimensional T-distributed Stochastic Neighbor Embedding (t-SNE) space. When plotting the two embedding vectors against each other, four samples did not cluster with the samples of the same blood component type (0.8% of derivatives, 4/514) and were excluded from further analysis. See 'quality filter for processed data'
The pre-processed sRNA sequences were annotated using the annotation pipelines unitas  and SPORTS. In case of multi-assignments, the annotation was prioritized in the following manner: miRNA > tRNA > rRNA > YRNA > snoRNA > lncRNA > snRNA > piRNA.
Assembly: hg38
Supplementary files format and content: csv files including log2-transformed RPM values per small RNA name for all blood component samples (1 file) and for all whole blood samples (1 file)

source_name: peripheral blood

extract_protocol:
The fractional blood derivatives as well as the whole blood samples were directly lysed in Qiazol. For RNA isolation the miRNeasy Serum/Plasma mini kit was combined with minElute columns.
Dual indexed sRNA libraries with unique molecular identifiers (UMIs) adaptors were generated using the QIAseq miRNA Library Kit.

value: peripheral blood


title: EVT_D3, H3K4me1, ChIP-seq, rep2


title: EVT_D3, H3K4me1, ChIP-seq, rep1


title: EDTA_WholeBlood__P09


title: EDTA_WholeBlood__P08


title: EVT_D8, H3K4me1, ChIP-seq, rep1


title: EDTA_WholeBlood__P10


title: TSC, H3K4me1, ChIP-seq, rep1


title: TSC, H3K4me1, ChIP-seq, rep2


title: EVT_D8, Med1, ChIP-seq, rep2


title: EDTA_WholeBlood__P07


title: BRD4_Epicycpher_T1_2

value: WTC11 hIPSCs


title: SM_NONO_Eto


title: EDTA_WholeBlood__P05


title: EDTA_WholeBlood__P04


title: SM_NONO_ctrl


title: EVT_D8, Med1, ChIP-seq, rep1


title: EVT_D3, Med1, ChIP-seq, rep1


title: HeLa, H3K9la, CHIP, rep1


title: EDTA_WholeBlood__P03


title: EDTA_WholeBlood__P11


title: TSC, Med1, ChIP-seq, rep1


title: EDTA_WholeBlood__P01


title: EVT_D8, P300, ChIP-seq, rep2


title: EDTA_WholeBlood__P06


title: Thrombocytes__P12

source_name: peripheral blood cells

value: peripheral blood cells

value: Thrombocytes


title: EVT_D8, P300, ChIP-seq, rep1


title: Thrombocytes__P11


title: EVT_D3, P300, ChIP-seq, rep2


title: Thrombocytes__P10


title: EVT_D3, Med1, ChIP-seq, rep2


title: Thrombocytes__P09


title: Thrombocytes__P07


title: TSC, P300, ChIP-seq, rep2


title: EVT_D3, P300, ChIP-seq, rep1


title: Thrombocytes__P08


title: K154Q_veh_4

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
basecalling bcl2fastq version 2.20.0.422
preprocessing cutadapt version 3.7 (-q 10 -m 30 -a "A{100}" -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
alignment STAR 2.7.6a (Ensembl v100; -readFilesCommand zcat --outSAMtype BAMSortedByCoordinate --outSAMstrandField intronMotif --outSAMmultNmax 1 --outSJfilterReads Unique --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --alignIntronMax 1000000 --sjdbOverhang 99)
featurecount version 2.0.3
Assembly: GRCh38.p13
Supplementary files format and content: tab separated file comprising count values per gene and sample

growth_protocol: HepG2 GR-/- +Ty1-WT, HepG2 GR-/- +Ty1-K154R and HepG2 GR-/- +Ty1-K154Q were grown in RPMI160 containing 10% FCS and 1000 U penicillin/ 100 µg/mL streptomycin (Pen-strep) solution under standard aseptic culture conditions (5% CO2 and 37°C). GR expression in each cell line was induced by 0.3 - 1 µg/mL doxycycline treatment (to match GR protein levels) in culture medium for 24 hours followed by washout in RPMI1640/10% charcoal-stripped FCS/Pen-strep medium for another 24 hours. 6 hours before harvesting, cells were treated with 1 µM Dex or equivalent volume of ethanol as vehicle.

extract_protocol:
Cells were harvested in TRIzol (Ambion) and mixed with bromochloropropane (BCP) (10% volume of TRIzol lysate). Samples were vortexed, centrifuged at 18,000 g for 15 min at 4°C. Aqueous phase was mixed with equal volume of isopropanol and 20 µg glycogen (Thermo Fischer Scientific) followed by incubation on ice for 30 minutes. RNA was precipitated by high- speed centrifugation as above and pellet was washed twice in 70% ethanol followed by air drying. RNA was reconstituted by resuspension in nuclease-free water and agitation at 56°C for 15 minutes. Nanodrop was used to measure RNA concentration and quality. To remove any phenol or protein contamination, RNA was re-precipitated overnight at -20°C or 1 hour at -80°C in three volumes of absolute ethanol and 1/10th volume of 3 M sodium acetate pH 5, followed by washes in 70% ethanol and reconstitution in nuclease-free water. RNA integrity was measured by Bioanalyzer (Agilent Technologies). 300 ng total RNA from each sample with RIN values of at least 8.6 were processed into libraries for Illumina sequencing.
NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module following manufacturer's instructions.

treatment_protocol:
transduction of cells with doxycycline-inducible pseudotyped lentiviral constructs harboring cDNAs for Ty1-tagged WT-, K154R- and K154Q-GR respectively
induction of cells with doxycycline to express the variants of GR followed by treatment with vehicle or 1 µM Dex (in growth medium containing 10% charcoal-stripped medium) for 6 hours before harvesting

value: vehicle


title: EDTA_WholeBlood__P02

city: Heidelberg

first: Bruno

last: Steinkraus

address: Im Neuenheimer Feld 583

institute: HUMMINGBIRD DIAGNOSTICS GMBH


title: TSC, P300, ChIP-seq, rep1


title: TSC, Med1, ChIP-seq, rep2


title: K154Q_dex_4

value: dexamethasone


title: Thrombocytes__P04


title: K154R_dex_4


title: Thrombocytes__P03


title: WT_dex_4


title: Thrombocytes__P05


title: K154R_veh_4


title: WT_veh_4


title: Thrombocytes__P02


title: Thrombocytes__P01


title: K154Q_dex_3


title: Plasma_Norgen__P12

source_name: peripheral blood plasma

value: peripheral blood plasma

value: Plasma


title: K154Q_veh_3


title: Plasma_Norgen__P11


title: K154R_dex_3


title: K154R_veh_3


title: Plasma_Norgen__P09


title: Plasma_Norgen__P08


title: WT_veh_3


title: WT_dex_3


title: Plasma_Norgen__P07


title: K154Q_dex_2


title: Plasma_Norgen__P06


title: K154Q_veh_2


title: Plasma_Norgen__P05


title: K154R_veh_2


title: K154R_dex_2


title: WT_veh_2


title: Plasma_Norgen__P04


title: Plasma_Norgen__P01


title: Plasma_Norgen__P02

tag: quality filter_for_processed_data

value: does NOT pass t-SNE filter


title: WT_dex_2


title: Neutrophils__P12

value: Neutrophils


title: K154Q_dex_1


title: Neutrophils__P10


title: K154R_veh_1


title: K154R_dex_1


title: Neutrophils__P09


title: WT_dex_1


title: Neutrophils__P08


title: Neutrophils__P11


title: K154Q_veh_1


title: Plasma_Norgen__P10


title: WT_veh_1


title: COR-5587-D2

city: Ithaca

first: Jennifer

last: Grenier

address: 526 Campus Rd

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Assembly: hg38 (Ensembl genes)
Supplementary files format and content: Matrix table with raw gene counts for every annotated gene and every sample

source_name: plasma

extract_protocol:
Total RNA was isolated using the Trizol protocol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a HS RNA Qubit assay (ThermoFisher) and integrity assessed on a Fragment Analyzer (Agilent).
Directional RNA-seq libraries were prepared from 40ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Whole blood was collected in EDTA tubes before and 24h after subjects completed a cardiopulmonary exercise test (CPET). Plasma was separated from whole blood and stored frozen at -80C in 1 mL aliquots. Plasma was dilulted 3-fold in DMEM after thawing, and centrifuged at 100xg for 20 min at RT (no brake) to remove large debris. Supernatants were transfered to new tubes with wide-bore pipet and spun at 800xg for 20 min at RT (no brake) to pellet plasma particles containing platelets. Pellets were gently rinsed once with Tyrode's buffer, then resuspended in 1 mL of Tyrode's buffer. For RNA extraction, 250 uL of each sample was combined with 750 ul Trizol-LS.

value: plasma

tag: timepoint

value: control


title: Neutrophils__P06


title: COR-5587-D1


title: Plasma_Norgen__P03


title: Neutrophils__P05


title: COR-4614-D2

value: case


title: Neutrophils__P04


title: COR-4614-D1


title: Neutrophils__P03


title: Neutrophils__P02


title: COR-3013-D2


title: COR-3013-D1


title: Neutrophils__P01


title: COR-2349-D2


title: COR-1726-D2 #2


title: NK_cells__P11

value: Natural killer cells


title: COR-2349-D1


title: NK_cells__P10


title: NK_cells__P09


title: COR-1726-D1


title: NK_cells__P07


title: Neutrophils__P07


title: COR-1433-D1


title: NK_cells__P08


title: COR-1433-D2 #2


title: Brain, TSC Het, Rep3

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2213 Garland Avenue South 9465

institute: Vanderbilt University

data_processing:
Raw sequencing reads were trimmed and filtered for quality using Trimgalore v0.6.7.
Trimmed reads were aligned to the hg38 reference genome and counted using STAR v2.7.9a with the `--quantMode GeneCounts` option.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: BMEC, Astrocytes, Neurons

growth_protocol: Cells were grown for 5 days under continual perfusion.

extract_protocol:
RNA isolation was performed using the Qiagen Rneasy Mini Kit and protocol per manufacturer recommendations
Library preparation was completed using theNEBNext Ultra II Directional RNA Library Prep Kitand protocol (P/N: E7760L) per manufacturer recommendations.
RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by fragmentation using divalent cations under elevated temperature.
First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation were performed to generate the final cDNA library.

value: BMEC, Astrocytes, Neurons

value: TSC Heterozygous Mutation


title: Brain, TSC Het, Rep1


title: NK_cells__P05


title: NK_cells__P03


title: Brain, Control, Rep3

value: WT (Control)


title: NK_cells__P04


title: Monocytes__P12

value: Monocytes


title: NK_cells__P02


title: Monocytes__P11


title: NK_cells__P01


title: Monocytes__P10


title: NK_cells__P12