title: 036-0 [lib37255]

description:
lib37255
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 038-7 [lib37260]

status: Public on Apr 01 2021

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

description:
lib37260
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

library_source: transcriptomic

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using STAR aligner; duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, STAR, Samtools, and htseq-count.
Genome_build: GRCh38 release 91
Supplementary_files_format_and_content: P216-2_CD3JAANXX_190311_combined_counts.csv is a comma-separated value file. The first column contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library.

molecule: total RNA

organism: Homo sapiens

source_name: Nasal Brush Epithelial Cell

extract_protocol:
Cells were provided in RLT/1%BME; Dual RNA and DNA extraction (AllPrep Kit).
Reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

tag: cell type

value: Nasal brush epithelial cells

tag: age

value: 11 years

tag: Sex

value: Female

tag: site

tag: atopy

value: Atopic

value: TW-LA

value: Yes

tag: total number of cells counted

tag: number of ciliated epithelial cells

tag: percent ciliated epithelial cells

tag: number of non-ciliated epithelial cells

tag: percent non-ciliated epithelial cells

tag: number of leukocytes

tag: percent leukocytes

tag: fev1/fvc percent


title: 040-9 [lib37259]

description:
lib37259
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: Male

value: LW-HA

value: No


title: 037-3 [lib37266]

description:
lib37266
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 039-4 [lib37252]

description:
lib37252
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: MW-LA


title: 070-4 [lib37262]

description:
lib37262
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 023-7 [lib37251]

description:
lib37251
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 154-1 [lib37267]

description:
lib37267
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: Non-atopic


title: 042-1 [lib37264]

description:
lib37264
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 011-4 [lib37248]

description:
lib37248
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 056-8 [lib37254]

description:
lib37254
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 030-2 [lib37256]

description:
lib37256
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: LW-LA


title: 028-5 [lib37247]

description:
lib37247
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 034-1 [lib37245]

description:
lib37245
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 027-1 [lib37246]

description:
lib37246
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 016-7 [lib37244]

description:
lib37244
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 026-3 [lib37249]

description:
lib37249
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 022-8 [lib37250]

description:
lib37250
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 013-3 [lib37243]

description:
lib37243
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 008-2 [lib37241]

description:
lib37241
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 007-6 [lib37242]

description:
lib37242
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 141-5 [lib37270]

description:
lib37270
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: HW-HA-LF


title: 004-8 [lib37240]

description:
lib37240
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 069-6 [lib37257]

description:
lib37257
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 043-2 [lib37263]

description:
lib37263
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 060-8 [lib37253]

description:
lib37253
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: HW-HA


title: 047-8 [lib37265]

description:
lib37265
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 018-6 [lib37239]

description:
lib37239
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 011-7 [lib37235]

description:
lib37235
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 016-4 [lib37237]

description:
lib37237
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 015-5 [lib37236]

description:
lib37236
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 008-9 [lib37232]

description:
lib37232
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 007-0 [lib37234]

description:
lib37234
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 006-2 [lib37230]

description:
lib37230
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 014-0 [lib37231]

description:
lib37231
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 013-8 [lib37233]

description:
lib37233
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 005-8 [lib37229]

description:
lib37229
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 012-9 [lib37227]

description:
lib37227
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 010-1 [lib37228]

description:
lib37228
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 053-8 [lib37223]

description:
lib37223
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 087-5 [lib37224]

description:
lib37224
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 051-7 [lib37222]

description:
lib37222
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 054-0 [lib37221]

description:
lib37221
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 088-1 [lib37225]

description:
lib37225
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 071-2 [lib37220]

description:
lib37220
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 049-0 [lib37217]

description:
lib37217
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 041-9 [lib37218]

description:
lib37218
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 065-8 [lib37219]

description:
lib37219
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 016-0 [lib37215]

description:
lib37215
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 020-6 [lib37238]

description:
lib37238
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 063-6 [lib37216]

description:
lib37216
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 047-4 [lib37214]

description:
lib37214
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 068-9 [lib37213]

description:
lib37213
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 042-6 [lib37208]

description:
lib37208
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 077-7 [lib37212]

description:
lib37212
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 046-1 [lib37211]

description:
lib37211
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 031-4 [lib37207]

description:
lib37207
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 044-2 [lib37209]

description:
lib37209
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 067-0 [lib37226]

description:
lib37226
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 034-6 [lib37206]

description:
lib37206
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 037-9 [lib37210]

description:
lib37210
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 035-1 [lib37205]

description:
lib37205
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 014-3 [lib37201]

description:
lib37201
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 027-8 [lib37203]

description:
lib37203
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 028-4 [lib37202]

description:
lib37202
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 024-5 [lib37204]

description:
lib37204
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 034-8 [lib37198]

description:
lib37198
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 039-5 [lib37196]

description:
lib37196
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 022-1 [lib37194]

description:
lib37194
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 017-0 [lib37197]

description:
lib37197
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 036-9 [lib37199]

description:
lib37199
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 025-0 [lib37193]

description:
lib37193
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 010-4 [lib37188]

description:
lib37188
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 005-6 [lib37189]

description:
lib37189
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 013-6 [lib37191]

description:
lib37191
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 009-4 [lib37190]

description:
lib37190
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 121-4 [lib37185]

description:
lib37185
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 016-2 [lib37195]

description:
lib37195
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 002-5 [lib37186]

description:
lib37186
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 003-9 [lib37187]

description:
lib37187
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 018-9 [lib37192]

description:
lib37192
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 069-3 [lib37184]

description:
lib37184
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 108-5 [lib37182]

description:
lib37182
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 118-7 [lib37181]

description:
lib37181
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 005-3 [lib37174]

description:
lib37174
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 006-9 [lib37176]

description:
lib37176
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 010-5 [lib37173]

description:
lib37173
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 008-5 [lib37170]

description:
lib37170
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 028-2 [lib37171]

description:
lib37171
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 021-3 [lib37200]

description:
lib37200
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 007-1 [lib37166]

description:
lib37166
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 014-1 [lib37167]

description:
lib37167
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 027-6 [lib37168]

description:
lib37168
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 010-2 [lib37165]

description:
lib37165
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 018-7 [lib37164]

description:
lib37164
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 032-2 [lib37172]

description:
lib37172
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 001-1 [lib37178]

description:
lib37178
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 012-5 [lib37162]

description:
lib37162
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 002-8 [lib37161]

description:
lib37161
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 021-1 [lib37163]

description:
lib37163
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 013-9 [lib37160]

description:
lib37160
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 036-7 [lib37158]

description:
lib37158
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 004-4 [lib37159]

description:
lib37159
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 094-7 [lib37157]

description:
lib37157
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 025-9 [lib37179]

description:
lib37179
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 099-6 [lib37180]

description:
lib37180
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 126-7 [lib37154]

description:
lib37154
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 122-2 [lib37155]

description:
lib37155
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 109-0 [lib37156]

description:
lib37156
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 143-8 [lib37153]

description:
lib37153
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 134-9 [lib37147]

description:
lib37147
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 130-8 [lib37146]

description:
lib37146
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 140-1 [lib37149]

description:
lib37149
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 118-5 [lib37152]

description:
lib37152
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 125-1 [lib37145]

description:
lib37145
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 124-6 [lib37151]

description:
lib37151
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 117-1 [lib37150]

description:
lib37150
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 003-7 [lib37169]

description:
lib37169
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 142-9 [lib37148]

description:
lib37148
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 103-5 [lib37142]

description:
lib37142
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 067-2 [lib37140]

description:
lib37140
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 114-4 [lib37143]

description:
lib37143
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 070-5 [lib37139]

description:
lib37139
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 119-2 [lib37144]

description:
lib37144
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 056-1 [lib37138]

description:
lib37138
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 080-8 [lib37136]

description:
lib37136
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 081-4 [lib37134]

description:
lib37134
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 091-2 [lib37135]

description:
lib37135
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 071-4 [lib37137]

description:
lib37137
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 111-8 [lib37132]

description:
lib37132
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 088-0 [lib37133]

description:
lib37133
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 070-7 [lib37131]

description:
lib37131
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 100-0 [lib37129]

description:
lib37129
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 090-8 [lib37127]

description:
lib37127
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 093-1 [lib37126]

description:
lib37126
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 076-9 [lib37125]

description:
lib37125
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 083-3 [lib37130]

description:
lib37130
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 063-5 [lib37124]

description:
lib37124
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 134-7 [lib37118]

description:
lib37118
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 057-1 [lib37122]

description:
lib37122
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 086-8 [lib37119]

description:
lib37119
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 081-0 [lib37115]

description:
lib37115
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 062-9 [lib37141]

description:
lib37141
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 073-1 [lib37114]

description:
lib37114
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 074-8 [lib37120]

description:
lib37120
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 080-6 [lib37113]

description:
lib37113
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 091-3 [lib37111]

description:
lib37111
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 053-7 [lib37121]

description:
lib37121
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 105-5 [lib37108]

description:
lib37108
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 141-2 [lib37102]

description:
lib37102
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 099-7 [lib37106]

description:
lib37106
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 158-0 [lib37101]

description:
lib37101
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 144-9 [lib37103]

description:
lib37103
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 109-3 [lib37109]

description:
lib37109
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 106-4 [lib37107]

description:
lib37107
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 157-9 [lib37097]

description:
lib37097
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 050-0 [lib37123]

description:
lib37123
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 132-9 [lib37098]

description:
lib37098
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 134-0 [lib37096]

description:
lib37096
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 138-6 [lib37095]

description:
lib37095
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 129-1 [lib37091]

description:
lib37091
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 098-4 [lib37110]

description:
lib37110
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 131-7 [lib37099]

description:
lib37099
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 147-7 [lib37087]

description:
lib37087
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 156-7 [lib37092]

description:
lib37092
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 113-5 [lib37116]

description:
lib37116
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 130-1 [lib37090]

description:
lib37090
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 102-9 [lib37112]

description:
lib37112
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 122-7 [lib37093]

description:
lib37093
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 084-9 [lib37084]

description:
lib37084
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 076-7 [lib37083]

description:
lib37083
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 136-4 [lib37086]

description:
lib37086
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 002-4 [lib37088]

description:
lib37088
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 151-4 [lib37104]

description:
lib37104
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 139-3 [lib37094]

description:
lib37094
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 073-6 [lib37261]

description:
lib37261
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 091-0 [lib37081]

description:
lib37081
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 128-9 [lib37089]

description:
lib37089
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 160-7 [lib37100]

description:
lib37100
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 096-8 [lib37078]

description:
lib37078
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 093-4 [lib37075]

description:
lib37075
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 088-3 [lib37073]

description:
lib37073
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 095-2 [lib37074]

description:
lib37074
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 102-6 [lib37077]

description:
lib37077
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 106-1 [lib37080]

description:
lib37080
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 100-3 [lib37072]

description:
lib37072
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 092-3 [lib37071]

description:
lib37071
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 082-0 [lib37069]

description:
lib37069
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 079-8 [lib37070]

description:
lib37070
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 085-4 [lib37068]

description:
lib37068
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 075-1 [lib37067]

description:
lib37067
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 066-4 [lib37066]

description:
lib37066
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 059-0 [lib37064]

description:
lib37064
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 044-1 [lib37059]

description:
lib37059
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 058-5 [lib37058]

description:
lib37058
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 051-6 [lib37057]

description:
lib37057
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 061-9 [lib37061]

description:
lib37061
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 077-6 [lib37062]

description:
lib37062
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 042-5 [lib37056]

description:
lib37056
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 065-7 [lib37063]

description:
lib37063
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 047-3 [lib37050]

description:
lib37050
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 064-2 [lib37052]

description:
lib37052
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 049-4 [lib37049]

description:
lib37049
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 062-6 [lib37055]

description:
lib37055
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 096-6 [lib37048]

description:
lib37048
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 046-0 [lib37051]

description:
lib37051
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 069-0 [lib37060]

description:
lib37060
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 022-4 [lib37044]

description:
lib37044
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 060-3 [lib37053]

description:
lib37053
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 110-3 [lib37046]

description:
lib37046
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 111-9 [lib37047]

description:
lib37047
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 137-5 [lib37042]

description:
lib37042
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 147-0 [lib37043]

description:
lib37043
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 112-6 [lib37045]

description:
lib37045
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 156-0 [lib37040]

description:
lib37040
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 142-7 [lib37039]

description:
lib37039
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 044-2 [lib37041]

description:
lib37041
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 144-3 [lib37038]

description:
lib37038
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 054-4 [lib37054]

description:
lib37054
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 129-6 [lib37037]

description:
lib37037
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 126-2 [lib37035]

description:
lib37035
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 125-4 [lib37036]

description:
lib37036
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 103-4 [lib37033]

description:
lib37033
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 125-8 [lib37034]

description:
lib37034
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 124-3 [lib37032]

description:
lib37032
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 127-0 [lib37031]

description:
lib37031
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 110-9 [lib37030]

description:
lib37030
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 118-4 [lib37028]

description:
lib37028
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 107-5 [lib37029]

description:
lib37029
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 086-4 [lib37023]

description:
lib37023
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 120-4 [lib37027]

description:
lib37027
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 095-7 [lib37024]

description:
lib37024
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 119-7 [lib37019]

description:
lib37019
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 102-3 [lib37022]

description:
lib37022
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 108-1 [lib37021]

description:
lib37021
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 112-1 [lib37017]

description:
lib37017
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 105-2 [lib37015]

description:
lib37015
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 117-8 [lib37026]

description:
lib37026
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 085-5 [lib37014]

description:
lib37014
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 083-8 [lib37020]

description:
lib37020
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 106-8 [lib37016]

description:
lib37016
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 088-6 [lib37011]

description:
lib37011
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 094-2 [lib37018]

description:
lib37018
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 100-6 [lib37010]

description:
lib37010
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 076-2 [lib37008]

description:
lib37008
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 098-8 [lib37013]

description:
lib37013
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 087-2 [lib37009]

description:
lib37009
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 068-3 [lib37012]

description:
lib37012
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 127-7 [lib37007]

description:
lib37007
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 128-3 [lib37005]

description:
lib37005
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 113-2 [lib37025]

description:
lib37025
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 117-4 [lib37006]

description:
lib37006
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 026-9 [lib37004]

description:
lib37004
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 033-3 [lib37002]

description:
lib37002
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 017-3 [lib37000]

description:
lib37000
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 119-0 [lib37003]

description:
lib37003
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 122-0 [lib36995]

description:
lib36995
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 121-2 [lib36996]

description:
lib36996
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 114-2 [lib36993]

description:
lib36993
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 095-0 [lib36992]

description:
lib36992
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: 123-1 [lib36998]

description:
lib36998
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv


title: input_GHMT2m_A-83-01

status: Public on Feb 13 2021

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

library_source: genomic

data_processing:
Fastq files were quality checked using FastQC and trimmed using BBDuk from BBTools.
The ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 (v. 2.3.2).
Samtools (v. 1.5) was used to convert the sam files into bam files, to filter out unmapped reads and to sort the bam files.
The total number of reads used for peak calling was normalized using samtools view -s (random extraction of a specified percentage of reads).
Samtools sort was used to sort the bam files after read extraction.
Bam files were indexed using samtools index.
Bedtools (2.26.0) genomecov was used to create bedgraph files from the bam files.
Igvtools toTDF was used to create tdf files from the bedgraph files.
Peaks were called using macs2 (v. 2.1.1.20160309) with default parameters using python (v. 2.7.14).
Peak locations were further annotated using the ChIPseeker R package.
Heatmaps were generated using ngs.plot.r.
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: MEFs

growth_protocol: MEFs were cultured in DMEM/High Glucose (HyClone) containing 10% fetal bovine serum (FBS; Gemini), 1.1% Penicillin-Streptomycin (Gibco), and 1.1% GlutaMAX supplement (Gibco). Retroviral infection of MEFs was performed as previously described (Riching et al., 2018). Approximately 5 x 106 Platinum E cells (PE cells; Cell Biolabs) were plated in 10-cm dishes. 20 hours later, cells were transfected with 36 µL FuGENE 6 (Promega) and 12 µg of retroviral plasmid DNA. On the day of transfection, MEFs were thawed and plated into 60-mm dishes pre-coated with SureCoat (Cellutron). MEFs were allowed to settle overnight. Viral supernatant was collected from transfected PE cells at 24 and 48 hours, and filtered through a 0.45-μm cellulose filter. Polybrene (Sigma) was added to viral supernatant at a concentration of 6 μg/mL and added to dishes containing MEFs. Following the first collection of viral supernatant, fresh medium (DMEM/High Glucose) (HyClone) containing 10% FBS (Gemini), 1.1% Penicillin-Streptomycin (Gibco), and 1.1% GlutaMAX supplement (Gibco) was added to PE cells. Infected MEFs were maintained in induction medium composed of DMEM/High Glucose:Medium 199 (4:1, HyClone:Gibco), 10% FBS (Gemini), 5% horse serum (Gemini), antibiotics (Gibco), 1X non-essential amino acids (Gibco), 1X essential amino acids (Gibco), 1X B-27 (Gibco), 1X insulin–selenium–transferin (Gibco), 1X MEM vitamin solution (Gibco) and 1X sodium pyruvate (Gibco) starting at 72 hours post-infection.

extract_protocol:
Chromatin from D5 control MEFs or D7 GHMT2m-reprogrammed MEFs was isolated using the Magna ChIP A/G Chromatin Immunoprecipitation kit (Millipore 17-10085) as per the manufacturer’s instructions. Briefly, 10 cm dishes of cells were crosslinked with 1% paraformaldehyde for 9 minutes at room temperature. Cells were then quenched with glycine (125 mM final concentration) for 5 minutes at room temperature. Chromatin was sheared to approximately 300 bp fragments using a Diagenode Bioruptor 300 ultrasonicator (D5 control MEFs: 15 cycles, 30 seconds on/90 seconds off, high intensity; D7 reprogrammed MEFs: 25 cycles, 30 seconds on/30 seconds off, high intensity). Chromatin was diluted 10 times and incubated overnight at 4 ˚C with 20 µL Protein A/G MagnaChIP beads (Millipore) and 8 µg anti-H3K27me3 (Millipore, 07-449) antibody in an end-over-end mixer. The next day, immunoprecipitated chromatin was washed, eluted, and reverse crosslinked with Proteinase K for 2 hours at 62 ˚C.
Libraries were prepared from 1 ng ChIP DNA using the Ovation Ultralow Library System V2 1-16 (NuGEN).

treatment_protocol: Reprogrammed MEFs were treated with DMSO (Thermo Scientific) or 0.5 μM A-83-01 (Tocris 2939) from Day 3 to Day 7

value: Mouse embryonic fibroblasts

tag: passages

tag: strain

tag: chip antibody


title: input_GHMT2m_DMSO


title: input_MEFs


title: H3K27me3_ChIP_GHMT2m_DMSO

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_ChIP_MEFs


title: H3K27me3_ChIP_GHMT2m_A-83-01


title: KSP5D23

status: Public on Jan 23 2021

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to mouse genome annotation mm10 using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Genome_build: ENSMBL mm10 release 98, Genome: Mus_musculus.GRCm38.98
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: lung

extract_protocol:
Whole lung RNA was extracted using Rneasy Midi kit from Qiagen. Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 500 ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs).
The libraries were treated with Illumina Free Adapter Blocking and  were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (300 cycles, paired end run 2x 150 bp) with an average of 6 x107 reads per RNA sample.

treatment_protocol: Lungs were collected from mice

tag: infection

value: PR8F 2*10e3 FFU i.n.

tag: time

value: 5 days post infection

tag: tissue

value: lung


title: KSP5D21


title: KSP5D25


title: KSP5D22


title: KSP5D24


title: input_GHMT2m+Smad2

tag: cell type


title: KSP5B65


title: KSP5B64


title: 126-5 [lib37001]

description:
lib37001
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: Nasal brush epithelial cells

tag: age

value: 11 years

tag: Sex

tag: site


title: 015-6 [lib36999]

description:
lib36999
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

tag: atopy

value: Atopic

tag: total number of cells counted

tag: number of ciliated epithelial cells


title: KSP5B62


title: KSP5B61


title: KSP5B63


title: KSP3D25

value: 3 days post infection


title: 118-8 [lib36997]

description:
lib36997
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

value: Female

tag: percent ciliated epithelial cells

tag: number of non-ciliated epithelial cells

tag: percent non-ciliated epithelial cells


title: KSP3D24


title: 120-8 [lib36994]

description:
lib36994
PolyA RNA
processed data file: P216-2_CD3JAANXX_190311_combined_counts.csv

tag: number of leukocytes

tag: percent leukocytes


title: H3K27me3_ChIP_GHMT2m_Smad2

tag: passages

tag: strain


title: KSP3D23

tag: infection


title: KSP3D21

tag: time


title: KSP3D22

tag: tissue


title: KSP3B65


title: KSP3B64


title: KSMD25

value: MOCK


title: KSMD22


title: KSP3B62


title: KSMD23


title: KSP3B61


title: KSMD24


title: KSMB64


title: KSMB65


title: KSMB62


title: 1875_PD1pos_week_104

status: Public on Dec 23 2020

description:
P298-1_rawGeneCts_24libs.csv
lib36297

data_processing:
The processing workflow was managed on the Galaxy platform. Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
Sequence alignment was performed using STAR aligner (v2.4.2a) with the GRCh38 reference genome and gene annotations from Ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), and HTSeq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: The file "P298-1_rawGeneCts_24libs.csv" is a comma-separated matrix. The first column describes the gene symbol for each row. The remaining columns are named according to the sample name and contain raw read counts assigned to each library. Counts have not been filtered or normalized.

source_name: CD8 T cells

extract_protocol:
Cells were thawed and sorted using a Hawks FACS sorter into SmartSeq lysis buffer
RT was performed on the lysate followed by second strand cDNA and enrichment by PCR amplification. Libraries were prepared following the Nextera XT library preparation protocol.

tag: individual id

tag: diagnosis

value: recent-onset T1D

tag: treatment

value: alefacept

value: Responder

tag: cell type

value: CD8 T cells


title: KSP3B63


title: 1875_CD57neg_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36294


title: KSMD21


title: KSMB63


title: KSMB61


title: 1875_PD1neg_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36296


title: 1875_DN_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36292


title: 1875_DP_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36293


title: 1875_PD1pos_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36291


title: 1875_CD57pos_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36289


title: Mimic ctl repeat 1

status: Public on Jan 12 2021

type: RNA

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

description:
Expression console values
HuGene2_121420H_RM4_MIMct1

hyb_protocol: Samples were hybridized with HuGene-2_0-st  arrays (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Relative expression changes assessed by Expression Console
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

source_name: HuH-7_miR1908-5p mimic ctl

label_protocol: Standard Affymetrix protocol

growth_protocol: Low glucose DMEM supplemented with 10% serum

extract_protocol: Cells were lysed with TriPure Isolation Reagent (Roche) and the total RNA was isolated using the Direct-zol RNA Miniprep Plus Kit (Zymo Research)

treatment_protocol: HuH-7 cells were transfected for 72 h with hsa-miR-1908-5p miRIDIAN microRNA Hairpin Inhibitor or a hsa-miR-1908-5p miRIDIAN Mimic (Dharmacon) to a final concentration of 9 nM using Lipofectamine® RNAiMAX Reagent. MiRIDIAN microRNA Hairpin Inhibitor/Mimic Transfection Controls coupled to Dy547 were used as controls,

tag: cell line

value: Human Hepatocyte carcinoma cell line

tag: genotype/variation

value: miR1908-5p mimic ctl


title: Inhibitor ctl repeat 3

description:
Expression console values
HuGene2_121420H_RM10_INHct3

source_name: HuH-7_miR1908-5p inhibitor ctl

value: miR1908-5p inhibitor ctl


title: 1875_CD57neg_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36288


title: Mimic repeat 1

description:
Expression console values
HuGene2_121420H_RM3_MIM1

source_name: HuH-7_miR1908-5p mimic

value: miR1908-5p mimic


title: Mimic repeat 2

description:
Expression console values
HuGene2_121420H_RM7_MIM2


title: Inhibitor ctl repeat 2

description:
Expression console values
HuGene2_121420H_RM6_INHct2


title: Inhibitor ctl repeat 1

description:
Expression console values
HuGene2_121420H_RM2_INHct1


title: Mimic ctl repeat 2

description:
Expression console values
HuGene2_121420H_RM8_MIMct2


title: Mimic ctl repeat 3

description:
Expression console values
HuGene2_121420H_RM12_MIMct3


title: Inhibitor repeat 1

description:
Expression console values
HuGene2_121420H_RM1_INH1

source_name: HuH-7_miR1908-5p inhibitor

value: miR1908-5p inhibitor


title: 5574_PD1pos_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36285


title: 5574_PD1neg_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36284


title: Inhibitor repeat 2

description:
Expression console values
HuGene2_121420H_RM5_INH2


title: Inhibitor repeat 3

description:
Expression console values
HuGene2_121420H_RM9_INH3


title: 1875_CD57pos_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36295


title: 5574_CD57neg_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36282


title: 5574_CD57pos_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36283


title: 1875_PD1neg_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36290


title: 5574_DP_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36281


title: 5574_DN_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36280


title: 4229_PD1pos_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36279


title: 1875_DP_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36287


title: 1875_DN_week_52

description:
P298-1_rawGeneCts_24libs.csv
lib36286


title: 4229_DP_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36275


title: 4229_PD1neg_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36278


title: T1DAL_CD8_S34483_w104

status: Public on Dec 10 2020

description:
lib10521
P127_rawGeneCts_116libs.csv

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0).
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were generated using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: The file "P127_rawGeneCts_116libs.csv" is a comma-separated matrix. The first column describes the gene symbol for each row. The remaining columns are named according to the sample name and contain raw read counts assigned to each library. Counts have not been filtered or normalized.

extract_protocol:
RNA was extracted from sorted cells using the Qiagen miRNeasy Micro Kit (tRNA extraction from Trizol with on-column DNase digestion).
Libraries were constructed from RNA using the Illumina TruSeq RNA Sample Preparation kit v2.

value: Recent-onset type 1 diabetes

value: Alefacept

tag: week

value: NR


title: T1DAL_CD8_S34468_w104

description:
lib10506
P127_rawGeneCts_116libs.csv

value: R


title: T1DAL_CD8_S34488_w104

description:
lib10526
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S34463_w104

description:
lib10501
P127_rawGeneCts_116libs.csv

value: P


title: 4229_DN_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36274


title: T1DAL_CD8_S34443_w104

description:
lib10481
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S34433_w104

description:
lib10471
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S34423_w104

description:
lib10461
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S34473_w104

description:
lib10511
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S34428_w104

description:
lib10466
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38648_w52

description:
lib14034
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38634_w35

description:
lib14020
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S34438_w104

description:
lib10476
P127_rawGeneCts_116libs.csv


title: 4229_CD57pos_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36277


title: T1DAL_CD8_S38644_w24

description:
lib14030
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S34458_w104

description:
lib10496
P127_rawGeneCts_116libs.csv


title: 4229_CD57neg_week_104

description:
P298-1_rawGeneCts_24libs.csv
lib36276


title: T1DAL_CD8_S38620_w0

description:
lib14006
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38626_w52

description:
lib14012
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38632_w24

description:
lib14018
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38622_w24

description:
lib14008
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38642_w0

description:
lib14028
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38628_w104

description:
lib14014
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38624_w35

description:
lib14010
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38646_w35

description:
lib14032
P127_rawGeneCts_116libs.csv


title: Mimic repeat 3

description:
Expression console values
HuGene2_121420H_RM11_MIM3


title: T1DAL_CD8_S34453_w104

description:
lib10491
P127_rawGeneCts_116libs.csv

value: PR


title: T1DAL_CD8_S38636_w52

description:
lib14022
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38630_w0

description:
lib14016
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38650_w104

description:
lib14036
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38505_w24

description:
lib13891
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38474_w24

description:
lib13860
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38523_w0

description:
lib13909
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38486_w52

description:
lib13872
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38569_w52

description:
lib13955
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38595_w0

description:
lib13981
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38555_w24

description:
lib13941
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38476_w35

description:
lib13862
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38464_w0

description:
lib13850
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38438_w104

description:
lib13824
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38512_w104

description:
lib13898
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38571_w104

description:
lib13957
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38557_w35

description:
lib13943
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38496_w0

description:
lib13882
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38596_w24

description:
lib13982
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38442_w24

description:
lib13828
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38440_w0

description:
lib13826
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38567_w35

description:
lib13953
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38536_w0

description:
lib13922
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38606_w52

description:
lib13992
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38544_w104

description:
lib13930
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38458_w24

description:
lib13844
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38540_w35

description:
lib13926
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38530_w35

description:
lib13916
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38573_w0

description:
lib13959
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38581_w104

description:
lib13967
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38585_w24

description:
lib13971
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38462_w52

description:
lib13848
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38593_w24

description:
lib13979
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38494_w52

description:
lib13880
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38478_w52

description:
lib13864
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38526_w0

description:
lib13912
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38502_w52

description:
lib13888
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38508_w35

description:
lib13894
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38600_w0

description:
lib13986
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38579_w52

description:
lib13965
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38518_w35

description:
lib13904
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38450_w24

description:
lib13836
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38452_w35

description:
lib13838
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38542_w52

description:
lib13928
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38587_w35

description:
lib13973
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38553_w0

description:
lib13939
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38472_w0

description:
lib13858
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38592_w0

description:
lib13978
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38504_w0

description:
lib13890
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38460_w35

description:
lib13846
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38448_w0

description:
lib13834
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38444_w35

description:
lib13830
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38575_w24

description:
lib13961
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38559_w52

description:
lib13945
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38480_w0

description:
lib13866
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38563_w0

description:
lib13949
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38482_w24

description:
lib13868
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38591_w104

description:
lib13977
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38583_w0

description:
lib13969
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38500_w35

description:
lib13886
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38565_w24

description:
lib13951
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38492_w35

description:
lib13878
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38510_w52

description:
lib13896
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38514_w0

description:
lib13900
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38466_w24

description:
lib13852
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38561_w104

description:
lib13947
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38538_w24

description:
lib13924
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38522_w104

description:
lib13908
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38436_w35

description:
lib13822
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38490_w24

description:
lib13876
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38488_w0

description:
lib13874
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38498_w24

description:
lib13884
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38432_w0

description:
lib13818
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38484_w35

description:
lib13870
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38602_w24

description:
lib13988
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38434_w24

description:
lib13820
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38577_w35

description:
lib13963
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38456_w0

description:
lib13842
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38516_w24

description:
lib13902
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38598_w52

description:
lib13984
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38597_w35

description:
lib13983
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38604_w35

description:
lib13990
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38534_w104

description:
lib13920
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38594_w35

description:
lib13980
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38524_w35

description:
lib13910
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38468_w35

description:
lib13854
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38454_w52

description:
lib13840
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38528_w24

description:
lib13914
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38520_w52

description:
lib13906
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38446_w52

description:
lib13832
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38608_w104

description:
lib13994
P127_rawGeneCts_116libs.csv


title: T1DAL_CD8_S38589_w52

description:
lib13975
P127_rawGeneCts_116libs.csv


title: C9_CarrierMix

status: Public on Dec 07 2020

data_processing:
The raw reads were processed in Galaxy using TopHat (with bowtie) for alignment (GRCh37 as reference genome), BAM-to-SAM, Picard Alignment Summary Metrics, and Picard RNAseq Metrics. Genes were quantified using htseq-count. Raw counts were used for downstream analysis and Fragments Per Kilobase Million (FPKM) values were used for plotting. FPKMs s for genes were obtained using edgeR
To identify differentially-expressed genes, a general linear model using negative binomial distribution with no random effects was applied using edgeR. Genes having a false discovery rate (FDR) <0.05 were considered differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: text file including a matrix table with rpkm for every gene and every sample
Supplementary_files_format_and_content: text file including a matrix table with raw gene counts for every gene and every sample

source_name: PBMC

growth_protocol: Peripheral blood was drawn into ACD VacutainerÒ tubes from participants enrolled in the study using standard phlebotomy techniques. Specimen tubes were labeled and transported at 4°C to the University of Texas Health Science Center at Houston School of Public Health for PBMC isolation. PBMCs were isolated from whole blood within 4 h of collection using Ficoll Paque plus (GE Healthcare) and frozen down in 7% DMSO in fetal bovine serum and cooled at -1°C/min in a freezing container (Nalgene, ThermoFisher Scientific). Frozen PBMCs were stored at -80°C before shipping on dry ice to Benaroya Research Institute for further processing and stimulation.

extract_protocol:
RNA was extracted from PBMCs using the RNeasy Mini Kit (Qiagen) and RNA integrity was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA). Libraries were clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v3 Cluster Kit (Illumina). Single-read sequencing was carried out on an Illumina HiScanSQ sequencer using a HiSeq SBS v3 Kit to generate 100-base single-end reads with a target of approximately 10 million reads per sample.

treatment_protocol: PBMCs were stimulated for 6 h with (1)  heat-killed S. aureus (10e7 cells/ml, InvivoGen), (2) a mixture (10e7 cells/ml) of all S. aureus isolates obtained from carrier subjects (“Carrier Mix”), or (3) un-stimulated, for the same time period. Due to the limited cell numbers that could be obtained from each pediatric donor, each treatment and control group/participant were carried out as singletons. After the incubation period, cells were washed with PBS and lysed using RLT buffer (Qiagen) supplemented with 1% β-mercaptoethanol (Sigma). Cell lysates were stored at -80°C until RNA extraction.

tag: patient

tag: carrier status

value: Carrier

tag: age

value: 10 years old

tag: Sex

value: Female

tag: libraryid

value: CarrierMix


title: T1DAL_CD8_S38470_w52

description:
lib13856
P127_rawGeneCts_116libs.csv


title: C9_HKSA

value: HKSA


title: C9_NS

value: NS


title: NC29_CarrierMix

value: Non-carrier

value: 2 years old


title: NC29_NS


title: NC25_CarrierMix

value: 4 years old

value: Male


title: C5_CarrierMix


title: NC29_HKSA


title: NC25_HKSA


title: NC25_NS


title: C5_HKSA


title: C5_NS


title: NC19_HKSA

value: 11 years old


title: NC19_CarrierMix


title: NC19_NS


title: U2OS_Lib7_B_EboGP-VSV_MOI_10

status: Public on Sep 16 2020

data_processing:
Pre-processed (Trimmomatic v. 0.33) to remove Illumina adaptor sequences, filter out sequences < 40 bp, and crop longer sequences to 50 bp.
Aligned to human genome hg19 using Bowtie v. 2.1.0.
Sequences that did not map to unique sites or showed significant mismatch or error (edit distance >2 over 50bp) were excluded from further analysis.
Reads were mapped to a known PiggyBac consensus insertion site (TTAA) at their start. Any sequence whose start was greater than three bases away from a TTAA site was excluded from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are represented in bedGraph format. Column 4 (value) represents the log10-transformed read counts at a particular occupied TTAA site. The '+' or '-' indicate whether the transposon inserted into the plus or minus strand, respectively.

source_name: mutagenized U2OS cells

growth_protocol: U2OS cells were co-transfected with PiggyBac (PB) transposon plasmid pPB-SB-CMV-puro-SD3 and the transposase p-hyPBASE. For each library, between 10^7 to 10^8 cells were transfected, cultured with the addition of 2 µg/ml puromycin for one week to select cells that had incorporated the transposon, and then used for screens of virus resistance with minimal further expansion.

extract_protocol:
After virus resistant cells were selected, genomic DNA (gDNA) was isolated from 5 to 10 X 10^6 cells using a DNeasy Blood and Tissue Kit (Qiagen).
Between 1 and 4 ug of gDNA was digested with BfaI or CviQI and purified (QIAquick PCR purification kits). Digested gDNA was ligated with barcoded P7-side adaptors using T4 DNA Ligase. Ligated gDNA fragments were then combined and amplified by nested PCR. The first round of PCR used primers corresponding to transposon sequence (KS15) and the P7-side adaptor (LP1). The linkers used were asymmetric, with the DNA barcode and P7 sequence on only one oligo, forming a 5 prime overhang, and a 3 prime dideoxy cytosine on the truncated pairing oligo to prevent strand extension. As a result, the first strand of DNA synthesis must be from the KS15 primer, resulting in amplification primarily of gDNA fragments containing transposon fragments. A second round of PCR (primers P2A and LP22) added the full Illumina P5 and P7 sequences. Library fragments were typically between 100 bp to 2 kb. Sequencing was performed using a HiScan or HiSeq platform with a custom sequencing primer (Rd1SeqP.ipdC) to generate 50 or 100 bp single end reads.
Custom sequencing primers used to sequence the transposon genome junction.

treatment_protocol: Mutagenized cells were challenged with replication-competent recombinant EboGP-VSV at MOI of 1 or 10 and propagated for up to 3 weeks with regular media changes to select virus-resistant colonies.

tag: manuscript library id

tag: sequencing library id

tag: experiment name

tag: cell line name

tag: virus moi


title: U2OS_Lib8_B_EboGP-VSV_MOI_10


title: C4_NS

value: 5 years old


title: C4_CarrierStrain


title: U2OS_Lib8_A_EboGP-VSV_MOI_10


title: U2OS_Lib7_A_EboGP-VSV_MOI_10


title: U2OS_Lib3_B_EboGP-VSV_MOI_10


title: U2OS_CIITA_C6_RNAseq

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality trimming step was applied to remove low-confidence base calls from the ends of reads.
The FASTQs were aligned to the reference genome, using TopHat v.1 and gene counts were generated using htseq-count.
QC and metrics analysis was performed, using the Picard family of tools (v1).
Differential gene expression between CIITA and control cells were determined using the BaseSpace RNA Express app, which uses STAR aligner and DE-Seq analysis tools.
Genome_build: hg19
Supplementary_files_format_and_content: gene.counts.csv is a comma-separated counts matrix. The first column contains HGNC gene symbols. The remaining columns include raw read counts assigned for each library. Gene counts have not been filtered or normalized.

source_name: Stable U2OS cell clones

extract_protocol:
Cell lysates were disrupted using QIAshredder columns and RNA was extracted using the Qiagen Rneasy mini kit, according to manufacturer's protocol.
Libraries were constructed from 100 ng of total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina) with poly (A) selection.

tag: stable integrated plasmid

value: pcDNA-CIITA


title: U2OS_pcDNA_C5_RNAseq

value: pcDNA


title: U2OS_WT_RNAseq

source_name: U2OS cell culture


title: U2OS_pcDNA_C6_RNAseq


title: U2OS_CIITA_C11_RNAseq


title: U2OS_pcDNA_C3_RNAseq


title: U2OS_CIITA_C1_RNAseq


title: U2OS_Lib2_B_EboGP-VSV_MOI_10


title: T1DAL_CD8_S38532_w52

description:
lib13918
P127_rawGeneCts_116libs.csv

tag: diagnosis

value: Recent-onset type 1 diabetes

value: Alefacept

value: NR

value: CD8 T cells


title: U2OS_Lib2_A_EboGP-VSV_MOI_10


title: U2OS_Lib5_B_EboGP-VSV_MOI_1


title: C4_HKSA

value: Carrier

tag: treatment


title: U2OS_Lib6_A_EboGP-VSV_MOI_10


title: U2OS_Lib4_EboGP-VSV_MOI_10


title: U2OS_Lib5_A_EboGP-VSV_MOI_1


title: U2OS_Lib1_A_EboGP-VSV_MOI_10, lib3165


title: U2OS_CIITA_C4_RNAseq


title: TH_0720_2_L003

status: Public on Jul 01 2020

city: San Diego

first: Zhen

last: Li

state: CA

address: 9500 Gilman Dr, CNCB122

institute: UCSD

data_processing:
Data was mapped to mouse genome assembly mm10 with Illumina SureCell RNA Single-Cell toolkit v1
Cells with less than 200 genes expressed were removed
Genome_build: mm10
Supplementary_files_format_and_content: single_cell_RNA-seq_of_CD1_mouse_E15.5.mtx: Matrix Market file of UMI counts for all cells.
Supplementary_files_format_and_content: gene.tsv: all the genes included in the analysis
Supplementary_files_format_and_content: cell.tsv: all the cells included in the analysis

source_name: mouse forebrain

extract_protocol:
Illumina® Bio-Rad® SureCell Single-Cell RNA Sequencing workflow
Illumina® Bio-Rad® SureCell Single-Cell RNA Sequencing workflow

tag: strain

value: Wild type


title: TH_0720_1_L003

description: single_cell_RNA-seq_of_CD1_mouse_E15.5.mtx


title: U2OS_Lib3_A_EboGP-VSV_MOI_10

tag: cell line


title: TH_0720_3_L003

tag: genotype/variation


title: TH_0720_2_L004


title: TH_0720_3_L004


title: TH_0720_1_L004


title: TH_0720_4_L003


title: TH_0720_4_L004


title: TH_0720_3_L002


title: TH_0720_2_L002


title: TH_0720_4_L002


title: TH_0720_1_L002


title: TH_0720_3_L001


title: U2OS_Lib6_B_EboGP-VSV_MOI_10


title: TH_0720_2_L001


title: TH_0720_4_L001


title: TH_0720_1_L001


title: S64915 [lib37850_CD2Y3ANXX]

status: Public on Apr 07 2020

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using STAR aligner; duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, STAR, Samtools, and htseq-count.
Genome_build: GRCh38 release 77
Supplementary_files_format_and_content: P290-2_CD2Y3ANXX_190408_combined_counts.csv is a comma separated value file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

molecule: polyA RNA

source_name: neutrophils_non-risk for the IRF5-SLE risk haplotype

extract_protocol:
Fresh blood was collected and granulocytes were extracted from the left over pellet after Ficoll purification by lysing RBCs with RBC lysis buffer. Granulocytes were then washed 3X with DNAse- and RNAse-free PBS and then lysed in RLT/bME buffer. After a 30min incubation at 4 degrees, RNA was isolated using the Qiagen RNA preparation kit.
Reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

tag: study group

tag: tissue

value: whole blood

tag: cell type

value: Neutrophils


title: S64914 [lib37849_CD2Y3ANXX]

value: non-risk for the IRF5-SLE risk haplotype


title: S64916 [lib37851_CD2Y3ANXX]


title: U2OS_Lib1_A_EboGP-VSV_MOI_10, lib2860


title: GmEM_Input_br2

status: Public on Jun 20 2020

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads from technical replicates were combined and peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

organism: Glycine max

source_name: embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol: Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213?218, except that the isolated nuclei were resuspended in in shearing buffer (10mM Tris pH8, 1mM EDTA, 0.1% SDS, 1mM PMSF), sonicated to achieve chromatin fragments ranging from 100 to 500 bp, and Triton X-100 and NaCl were added to chromatin to final concentrations of 1% and 150mM, respectively.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3 ug of an antibody raised against the peptide FSTQPGDHETESDVN corresponding to the amino acids 352-366 of GLYMA.08G227700.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.

treatment_protocol: Early maturation stage embryos were dissected from 6 to 7 mm seeds.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

value: embryos

tag: Stage

value: early maturation stage

tag: antibody


title: GmEM_Input_br1


title: GmEM_GLYMA.08G227700-ChIP_br2

value: anti-peptide GLYMA.08G227700


title: S64911 [lib37846_CD2Y3ANXX]

source_name: neutrophils_risk for the IRF5-SLE risk haplotype

value: risk for the IRF5-SLE risk haplotype


title: S64913 [lib37848_CD2Y3ANXX]


title: S64910 [lib37845_CD2Y3ANXX]


title: S64907 [lib37842_CD2Y3ANXX]


title: S64906 [lib37841_CD2Y3ANXX]


title: S64909 [lib37844_CD2Y3ANXX]


title: S64908 [lib37843_CD2Y3ANXX]


title: S64905 [lib37840_CD2Y3ANXX]


title: S64912 [lib37847_CD2Y3ANXX]


title: S64904 [lib37839_CD2Y3ANXX]


title: GmEM_GLYMA.08G227700-ChIP_br1


title: S64903 [lib37838_CD2Y3ANXX]


title: UPN727, START_013003 serum

status: Public on Feb 03 2020

description: Gene expression data fUPN727 cells stimulated with serum from a new onset T1D subject

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed with Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.

label: biotin

source_name: UPN727 cells stimulated with START_013003 serum

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Total RNA was extracted and amplified using either the Affymetrix Express IVT kit  or the Affymetrix IVT PLUS kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of T1D patient serum (n=40). Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl. After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)

tag: responder cells

tag: serum source - disease status

value: New onset T1D

tag: serum source - bmi

tag: serum source - age at enrollment

tag: serum source- sex

value: M

tag: serum source - baseline 2 hour auc (pmol/ml)

tag: serum source - c-peptide decay rate


title: UPN727, START_013010 serum

source_name: UPN727 cells stimulated with START_013010 serum


title: UPN727, ABATE_004005 serum

source_name: UPN727 cells stimulated with ABATE_004005 serum


title: UPN727, ABATE_006001 serum

source_name: UPN727 cells stimulated with ABATE_006001 serum


title: UPN727, START_008003 serum

source_name: UPN727 cells stimulated with START_008003 serum


title: UPN727, START_008008 serum

source_name: UPN727 cells stimulated with START_008008 serum

value: F


title: UPN727, START_001001 serum

source_name: UPN727 cells stimulated with START_001001 serum


title: UPN727, START_002003 serum

source_name: UPN727 cells stimulated with START_002003 serum


title: UPN727, START_002018 serum

source_name: UPN727 cells stimulated with START_002018 serum


title: UPN727, START_001005 serum

source_name: UPN727 cells stimulated with START_001005 serum


title: UPN727, START_013007 serum

source_name: UPN727 cells stimulated with START_013007 serum


title: UPN727, START_010005 serum

source_name: UPN727 cells stimulated with START_010005 serum


title: UPN727, START_002012 serum

source_name: UPN727 cells stimulated with START_002012 serum


title: UPN727, ABATE_002019 serum

source_name: UPN727 cells stimulated with ABATE_002019 serum


title: UPN727, START_002007 serum

source_name: UPN727 cells stimulated with START_002007 serum


title: UPN727, START_002019 serum

source_name: UPN727 cells stimulated with START_002019 serum


title: UPN727, ABATE_002008 serum

source_name: UPN727 cells stimulated with ABATE_002008 serum


title: UPN727, ABATE_007012 serum

source_name: UPN727 cells stimulated with ABATE_007012 serum


title: UPN727, ABATE_005001 serum

source_name: UPN727 cells stimulated with ABATE_005001 serum


title: UPN727, T1DAL_01710726 serum

source_name: UPN727 cells stimulated with T1DAL_01710726 serum


title: UPN727, START_003004 serum

source_name: UPN727 cells stimulated with START_003004 serum


title: UPN727, T1DAL_01710475 serum

source_name: UPN727 cells stimulated with T1DAL_01710475 serum


title: UPN727, T1DAL_01110590 serum

source_name: UPN727 cells stimulated with T1DAL_01110590 serum


title: UPN727, START_002010 serum

source_name: UPN727 cells stimulated with START_002010 serum


title: UPN727, T1DAL_01510142 serum

source_name: UPN727 cells stimulated with T1DAL_01510142 serum


title: UPN727, T1DAL_01410379 serum

source_name: UPN727 cells stimulated with T1DAL_01410379 serum


title: UPN727, T1DAL_01010340 serum

source_name: UPN727 cells stimulated with T1DAL_01010340 serum


title: UPN727, T1DAL_01010608 serum

source_name: UPN727 cells stimulated with T1DAL_01010608 serum


title: UPN727, ABATE_007005 serum

source_name: UPN727 cells stimulated with ABATE_007005 serum


title: UPN727, T1DAL_00410087 serum

source_name: UPN727 cells stimulated with T1DAL_00410087 serum


title: UPN727, T1DAL_00910199 serum

source_name: UPN727 cells stimulated with T1DAL_00910199 serum


title: UPN727, T1DAL_00110202 serum

source_name: UPN727 cells stimulated with T1DAL_00110202 serum


title: lib11768

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: CAV_sorted_cells_RNAseq_counts_for_GEO.csv is a comma-delimited matrix. The first column ("ensgene") contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. Data have not been filtered or normalized.

extract_protocol:
RNA was isolated from purified cell subsets (CD4+ T cells, CD8+ T cells, B cells and monocytes) using a Qiagen RNeasy micro kit with on-column DNase digestion
Libraries were constructed from RNA using the Illumina TruSeq RNA Sample Preparation kit v2. Libraries were clustered on flow cells using the TruSeq Single Read Cluster Kit v3.

tag: subject

tag: study

tag: baseline 2 hour auc (pmol/ml)

tag: rate of c-peptide decay

tag: bmi

tag: age at enrollment

tag: Sex

value: Male

tag: primary race

value: White

tag: secondary race

tag: ethnicity

value: Not Hispanic or Latino


title: UPN727, ABATE_005007 serum

source_name: UPN727 cells stimulated with ABATE_005007 serum

tag: responder cells


title: UPN727, ABATE_003005 serum

source_name: UPN727 cells stimulated with ABATE_003005 serum

tag: serum source - disease status


title: UPN727, ABATE_002004 serum

source_name: UPN727 cells stimulated withABATE_002004 serum

tag: serum source - bmi


title: UPN727, CAV452905251 serum

description: Gene expression data fUPN727 cells stimulated with serum from a T1D subject

source_name: UPN727 cells stimulated with T1D  xse294378780 serum

extract_protocol: Total RNA was extracted and amplified using  the Affymetrix Express IVT kit (Affymetrix, Santa Clara, CA).

tag: disease status

value: E

tag: serum source - race

value: White, Caucasian

tag: serum source - age at blood draw

value: female


title: UPN727, ABATE_003020 serum

source_name: UPN727 cells stimulated with ABATE_003020 serum

tag: serum source - age at enrollment

tag: serum source- sex

tag: serum source - baseline 2 hour auc (pmol/ml)

tag: serum source - c-peptide decay rate


title: UPN727, T1DAL_00210551 serum

source_name: UPN727 cells stimulated with T1DAL_00210551 serum


title: UPN727, ABATE_002018 serum

source_name: UPN727 cells stimulated with ABATE_002018 serum


title: UPN727, CAV171522212 serum

source_name: UPN727 cells stimulated with T1D xse294378780 serum

tag: subject


title: UPN727, CAV564853165 serum

source_name: UPN727 cells stimulated with T1D xse823857290 serum

value: D

value: male


title: UPN727, ABATE_003012 serum

source_name: UPN727 cells stimulated with ABATE_003012 serum


title: UPN727, ABATE_003003 serum

source_name: UPN727 cells stimulated with ABATE_003003 serum


title: UPN727, CAV321199696 serum

source_name: UPN727 cells stimulated with T1D xse294378780serum


title: UPN727, CAV653766700 serum

source_name: UPN727 cells stimulated with T1D xse988873004serum

value: C


title: UPN727, CAV41693360 serum

source_name: UPN727 cells stimulated with T1D xse00903601 serum

value: B

value: Black, African American


title: UPN727, CAV572112279 serum

source_name: UPN727 cells stimulated with T1D xse988873004 serum


title: UPN727, CAV709964428 serum


title: UPN727, CAV38965678 serum


title: UPN727, CAV483594755 serum


title: UPN727, CAV293627594serum


title: UPN727, CAV57322067 serum

source_name: UPN727 cells stimulated with T1D xse03040594 serum

value: A


title: UPN727, CAV89634132 serum


title: UPN727, CAV35218996 serum

source_name: UPN727 cells stimulated with T1D xse00903601serum


title: UPN727, CAV63533175 serum


title: lib11780

tag: study

tag: baseline 2 hour auc (pmol/ml)

tag: rate of c-peptide decay

tag: bmi


title: lib11747

value: START

tag: age at enrollment

tag: Sex

tag: primary race

tag: secondary race

value: Hispanic or Latino


title: lib11769

source_name: monocyte

tag: ethnicity


title: lib11738


title: lib11767

source_name: Bcell


title: lib11744


title: lib11779


title: lib11746


title: lib11730

value: Female


title: lib11755

value: Black or African American


title: lib11728


title: lib11711


title: lib11754


title: lib11710


title: lib11706


title: lib11708


title: lib11752


title: lib11693


title: lib11696


title: lib11694


title: lib11680


title: lib11753


title: lib11731


title: lib11687


title: lib11725


title: lib11666


title: lib11678


title: lib11695


title: lib11665


title: lib11729


title: lib11664


title: lib11654


title: lib11649


title: lib11638


title: lib11637


title: lib11709


title: lib11636


title: lib11624

value: Asian


title: lib11622


title: lib11679

value: Male


title: lib11606

value: White


title: lib11600

value: Not Hispanic or Latino


title: lib11607


title: lib11621


title: lib11601


title: lib11593


title: lib11580


title: lib11581


title: lib11663


title: lib11651


title: lib11652


title: lib11592


title: lib11653


title: lib11577


title: lib11563


title: lib11576


title: lib11578


title: lib11564


title: lib11623


title: lib11561


title: lib11543


title: lib11650


title: lib11558


title: lib11555


title: lib11541


title: lib11535


title: lib11540


title: lib11534


title: lib11528


title: lib11527


title: lib11526


title: lib11579


title: lib11562


title: lib11513


title: lib11500


title: lib11511


title: lib11512


title: lib11501


title: lib11499


title: lib11487


title: lib11475


title: lib11488


title: lib11489


title: lib11473


title: lib11542


title: lib11474


title: lib11469


title: lib11472


title: lib11464


title: lib11456


title: lib11455


title: lib11465


title: lib11443


title: lib11442


title: lib11432


title: lib11431


title: lib11419

value: American Indian or Alaska Native


title: lib11418


title: lib11440


title: lib11514


title: lib11417


title: lib11416


title: lib11396


title: lib11468


title: lib11393


title: lib11394


title: lib11414


title: lib6057

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: CAV_Replicate_testing_RNAseq_whole_blood_counts.csv is a comma-delimited matrix. The first column ("ensgene") contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. Data have not been filtered or normalized.

source_name: whole blood

extract_protocol:
RNA was isolated from whole blood samples preserved in Tempus blood RNA tubes (Applied Biosystems, CA) using the Total RNA Isolation chemistry on an ABI Prism 6100 (Applied Biosystems, CA) or a Thermo Scientific KingFisher (Thermo Fisher Scientific, MA).
Libraries were constructed from RNA using the Illumina TruSeq RNA Sample Preparation kit v2. Libraries were clustered on flow cells using the TruSeq Single Read Cluster Kit v3.

tag: subject - disease status

value: Type 1 Diabetes

tag: age at draw

value: White, Caucasian

tag: median cv coverage

tag: fastq total reads

tag: unpaired reads examined

tag: unpaired read duplicates


title: lib6055


title: lib6054


title: lib6056


title: lib11441


title: lib6052


title: lib6050


title: lib6049


title: lib6048

value: Screened Healthy Control


title: lib6051


title: lib6047


title: lib6045


title: lib11395


title: lib6046


title: lib6053


title: lib3946

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: CAV_Replicate_testing_RNAseq_cell_subset_counts.csv is a comma-delimited matrix. The first column ("ensgene") contains Ensembl gene IDs. The remaining columns include raw read counts assigned for each library. Data have not been filtered or normalized.


title: lib6044


title: lib6043


title: lib3947


title: lib3944

source_name: Monocytes


title: lib3943

value: Systemic Lupus Erythematosus


title: lib3945

source_name: B


title: lib11408


title: lib11409


title: lib3941


title: lib3939


title: lib3940


title: lib3938


title: lib3942


title: lib3937


title: lib3935

value: Biracial


title: lib3934


title: lib3933


title: lib3936


title: lib3929


title: lib3930


title: lib3932


title: lib3927


title: lib3931


title: lib3926


title: lib3925


title: lib3924


title: lib3923


title: lib3922


title: lib3921


title: lib3918


title: lib3915


title: lib3916


title: lib3917


title: lib3912


title: lib3913


title: lib3909


title: lib3914


title: lib3910


title: lib3906


title: lib3907


title: lib3908


title: lib3905


title: lib3928


title: lib3902


title: lib3901


title: lib3898


title: lib3903


title: lib3904


title: lib3920


title: lib3899


title: lib3919


title: lib3896


title: lib3893


title: lib3892


title: lib3900


title: lib3897


title: lib3891


title: lib3889


title: lib3888


title: lib3895


title: lib3887


title: lib3884


title: lib3885


title: lib3882


title: lib3886


title: lib3880


title: lib3881


title: lib3883


title: lib3879


title: lib3876


title: lib3878


title: lib3894


title: lib3890


title: lib3877


title: REP3 TrcrRNA

status: Public on Dec 17 2019

hyb_protocol: Samples were hybridized with HuGene-2_0-ST (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

data_processing: Relative expression changes assessed by Expression Console

growth_protocol: High glucose DMEM

extract_protocol: High Pure RNA isolation

treatment_protocol: Plasmid transfection with lipofectamine 3000 in 24 well plates; 0.5 ug plasmid 0.35 ug of  SP-dCas9-VPR (SP-dCas9 with VP64-p65-Rta; from George Church's lab through Addgene)  and 0.15 ug of either pCRU6 vector expressing either cgRNA or TracrRNA ; ratio of 1.5 lipof3000:1 ul p3000: 0.5 ug DNA

tag: grna

value: tracrRNA

tag: cell type

value: Human embryonic Kidney cells


title: WT biologic1

treatment_protocol: Plasmid transfection with lipofectamine 3000 in 24 well plates; 0.5 ug plasmid (0.35 ug of eSpCas9 (1.1)  and 0.15 ug of either pCRU6 vector expressing the cgRNAs or a TracrRNA control ; ratio of 1.5 lipof3000:1 ul p3000: 0.5 ug DNA.

tag: genotype

value: WT


title: REP 2 CG6


title: WT biologic2


title: REP2 TrcrRNA


title: Subject19_blood_CD69-

status: Public on Dec 08 2019

description: BulkRNAseqCounts.csv

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Genome_build: GRCh38

source_name: CD4 T cells from blood

extract_protocol:
Full-length cDNA was prepared from 250-1000 sorted CD4+CCR5+ cells using SMARTer Ultra Low Input RNA Kit for Sequencing - v4 according to manufacturer’s instructions (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

tag: subject id

tag: cell sort

tag: pathology score

tag: number of cells


title: Subject43_mucosa_CD69+

description: BulkRNAseqCounts.csv

source_name: CD4 T cells from oral mucosa


title: Subject56_mucosa_CD69-

description: BulkRNAseqCounts.csv


title: Subject53_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject53_blood_CD69-

description: BulkRNAseqCounts.csv


title: Subject53_mucosa_CD69-

description: BulkRNAseqCounts.csv


title: KO biologic4


title: KO biologic3


title: Subject56_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject56_blood_CD69-

description: BulkRNAseqCounts.csv


title: Subject19_mucosa_CD69-

description: BulkRNAseqCounts.csv


title: KO biologic2


title: WT biologic4


title: KO biologic1


title: REP 1 CG6


title: WT biologic3


title: Subject43_mucosa_CD69-

description: BulkRNAseqCounts.csv


title: REP1 TrcrRNA


title: REP 2 CG4


title: REP 3 CG4


title: Subject43_blood_CD69-

description: BulkRNAseqCounts.csv


title: REP 1 CG4


title: Subject19_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: REP 3 CG6


title: Subject49_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject49_blood_CD69-

description: BulkRNAseqCounts.csv


title: Subject47_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject40_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject42_mucosa_CD69-

description: BulkRNAseqCounts.csv


title: Subject40_blood_CD69-

description: BulkRNAseqCounts.csv


title: Subject40_mucosa_CD69-

description: BulkRNAseqCounts.csv


title: Subject42_blood_CD69-

description: BulkRNAseqCounts.csv


title: Subject47_blood_CD69-

description: BulkRNAseqCounts.csv


title: Subject35_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject42_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject34_mucosa_CD69+

description: BulkRNAseqCounts.csv


title: Subject34_blood_CD69-

description: BulkRNAseqCounts.csv


title: Blood CD4+ T cells

description:
10X Genomics single-cell RNA-seq
filtered_gene_bc_matrices_h5.h5
filtered_molecules.h5

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
Reads were demultiplexed and converted to FASTQs using in 10X Cell Ranger mkfastq (v. 2.0.1).
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 2.0.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 2.0.1).
UMI counts were aggregated across all samples using 10X Cell Ranger aggr (v. 2.0.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination

source_name: peripheral blood

extract_protocol:
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.
Per manufacturer instructions, droplet emulsions were broken, cDNA was amplified, and libraries were generated using enzymatic fragmentation.

treatment_protocol: Cells freshly isolated from blood and digested oral mucosal tissue were sorted into defined populations on a FACSAriaII (BD Biosciences).

tag: tissue

value: peripheral blood


title: Blood CD4+ T cells, CCR5+ CD69-


title: Oral mucosa CD4+ T cells, CCR5+

source_name: gingival oral mucosal tissue

value: gingiva


title: Oral mucosa CD4+ T cells, CCR5+ CD69-


title: Oral mucosa CD4+ T cells, CCR5+ CD69+


title: Oral mucosa CD4+ T cells, CCR5-


title: CrVg2wCD90R2

status: Public on Nov 27 2019

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment to mouse genome GRCm38 with a costumized transcriptome reference using the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Genome_build: GRCm38
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples at each time point

source_name: Mouse retina, 6-8 wk old

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90, CD45 and CD140a (conjugated to various fluorophores) (Thermo Fisher Scientific) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP co-expression. Collected cells were loading into 10X Chromium Single Cell A Chips at ~1,000 cells/ul.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: Vglut2:cre;Stp15 and C57BL/6J mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.

value: retina

tag: age

value: 6-8 wk old

value: retinal ganglion cells

tag: time point


title: CrVg2wCD45CD90R1


title: CrVg2wCD90R1


title: CrVg2wCD45CD90R2


title: Subject47_mucosa_CD69-

description: BulkRNAseqCounts.csv


title: Subject49_mucosa_CD69-

description: BulkRNAseqCounts.csv