title: GM12878 cell 100

description:
Peak_counts_GM12878_experiment1.txt.gz
067-13-Ad1-43-Ad2-75_S227


title: GM12878 cell 102

status: Public on Dec 20 2018

type: SRA

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive, CCSR 2150

country: USA

institute: Stanford University

description:
Peak_counts_GM12878_experiment1.txt.gz
067-15-Ad1-43-Ad2-73_S225

library_source: genomic

data_processing:
For ATAC-seq data: adapter sequence trimming, mapping to Hg19 using Bowtie2, and PCR duplicate removal using Picard Tools was performed. ATAC-seq peaks were called with MACS2 and reads in each peak were counted for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq counts table file; adapter trimmed, reads aligned, pcr duplicates removed, and reads in ATAC-seq peaks counted

molecule: genomic DNA

organism: Homo sapiens

source_name: GM12878 cell line

growth_protocol: GM1878 cells were grown in RPMI 1640 with 10% FBS and 1% pen/strep. Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)

extract_protocol: Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips and assayed using the single-cell ATAC-seq protocol. In a 96-well plate, 6-7 µL from a total of 15ul of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. Pooled libraries were purified and quantified using qPCR prior to sequencing.

tag: cell type

value: GM12878 cell line


title: GM12878 cell 98

description:
Peak_counts_GM12878_experiment1.txt.gz
067-11-Ad1-42-Ad2-80_S220


title: GM12878 cell 99

description:
Peak_counts_GM12878_experiment1.txt.gz
067-12-Ad1-42-Ad2-79_S219


title: GM12878 cell 97

description:
Peak_counts_GM12878_experiment1.txt.gz
067-10-Ad1-42-Ad2-81_S221


title: scATAC-D6-9

source_name: Primary epidermal keratinocyte

growth_protocol: Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)

extract_protocol: Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips and assayed using the single-cell ATAC-seq protocol. In a 96-well plate, 15 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. Pooled libraries were purified and quantified using qPCR prior to sequencing.

value: Primary epidermal keratinocyte

tag: differentiation status

value: Differentiated (Day 6)


title: scATAC-D6-95


title: scATAC-D6-96


title: scATAC-D6-94


title: scATAC-D6-93


title: scATAC-D6-92


title: scATAC-D6-88


title: scATAC-D6-91


title: scATAC-D6-8


title: scATAC-D6-89


title: scATAC-D6-90


title: scATAC-D6-87


title: scATAC-D6-86


title: BN.Whole blood PBMC cells from patient 33, visit 5 SAMPLE_315

type: RNA

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

label: biotin

molecule: total RNA

source_name: Whole blood

label_protocol: amplified cRNA was generated from 100ng RNA using the TargetAmp Nano-g Biotin-aRNA Labeling Kit (Epicentre, Madison WI)

growth_protocol: Whole blood samples were collected in PAXgene Tubes (Qiagen) as recommended

extract_protocol: Total RNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: PAXgene tubes were transferred to Wistar Genomics facility for RNA extraction

tag: nodule class

value: BN

tag: sample set

value: testing

tag: collection site

value: NYU

tag: gender

value: male

tag: smoking

value: quit

tag: race

value: Caucasian

tag: age

tag: packyears

tag: lesion size, mm

tag: cancer stage


title: BN.Whole blood PBMC cells from patient 98, visit 0 SAMPLE_309

value: UPenn


title: BN.Whole blood PBMC cells from patient na, visit 5 SAMPLE_300


title: BN.Whole blood PBMC cells from patient 62, visit 0 SAMPLE_310

value: female

value: smoker


title: BN.Whole blood PBMC cells from patient 60, visit 5 SAMPLE_307


title: BN.Whole blood PBMC cells from patient na, visit 0 SAMPLE_301


title: BN.Whole blood PBMC cells from patient 0, visit 7 SAMPLE_306

value: never


title: BN.Whole blood PBMC cells from patient 80, visit 8 SAMPLE_312


title: BN.Whole blood PBMC cells from patient 3.5, visit 5 SAMPLE_308


title: BN.Whole blood PBMC cells from patient 62, visit 1 SAMPLE_314


title: BN.Whole blood PBMC cells from patient 37.5, visit 0 SAMPLE_313


title: scATAC-D6-81


title: scATAC-D6-82


title: scATAC-D6-83


title: MN.Whole blood PBMC cells from patient 18.5, visit 8 SAMPLE_305

value: MN


title: BN.Whole blood PBMC cells from patient na, visit a SAMPLE_311


title: BN.Whole blood PBMC cells from patient 42.5, visit a SAMPLE_303


title: BN.Whole blood PBMC cells from patient na, visit 5 SAMPLE_299


title: scATAC-D6-80


title: BN.Whole blood PBMC cells from patient 46, visit 2 SAMPLE_304


title: BN.Whole blood PBMC cells from patient 15, visit 4 SAMPLE_302

value: African American


title: BN.Whole blood PBMC cells from patient 40, visit 1 SAMPLE_298

value: HFGCC


title: scATAC-D6-85


title: scATAC-D6-84


title: scATAC-D6-7


title: MN.Whole blood PBMC cells from patient 30, visit 1 SAMPLE_293


title: MN.Whole blood PBMC cells from patient 0, visit 2 SAMPLE_295


title: MN.Whole blood PBMC cells from patient 52.5, visit 3 SAMPLE_296


title: MN.Whole blood PBMC cells from patient 23, visit 8 SAMPLE_294


title: MN.Whole blood PBMC cells from patient 60, visit 5 SAMPLE_291


title: BN.Whole blood PBMC cells from patient 21, visit 6 SAMPLE_297

value: Temple


title: scATAC-D6-78


title: scATAC-D6-76


title: scATAC-D6-77


title: scATAC-D6-72


title: scATAC-D6-79


title: scATAC-D6-71


title: scATAC-D6-75


title: scATAC-D6-74


title: MN.Whole blood PBMC cells from patient 60, visit 8 SAMPLE_292


title: scATAC-D6-70


title: MN.Whole blood PBMC cells from patient 9, visit 8 SAMPLE_289


title: MN.Whole blood PBMC cells from patient 35, visit 8 SAMPLE_290


title: MN.Whole blood PBMC cells from patient 0.8, visit 6 SAMPLE_285


title: MN.Whole blood PBMC cells from patient 0, visit 2 SAMPLE_288


title: MN.Whole blood PBMC cells from patient 30, visit 1 SAMPLE_287


title: MN.Whole blood PBMC cells from patient 40, visit 5 SAMPLE_286


title: MN.Whole blood PBMC cells from patient 30, visit 2 SAMPLE_283


title: MN.Whole blood PBMC cells from patient 65, visit 9 SAMPLE_282


title: scATAC-D6-6


title: scATAC-D6-73


title: scATAC-D6-69


title: scATAC-D6-66


title: scATAC-D6-65


title: scATAC-D6-63


title: scATAC-D6-67


title: scATAC-D6-62


title: scATAC-D6-64


title: scATAC-D6-68


title: scATAC-D6-61


title: MN.Whole blood PBMC cells from patient 30, visit 7 SAMPLE_277


title: MN.Whole blood PBMC cells from patient 53, visit 3 SAMPLE_281


title: MN.Whole blood PBMC cells from patient 60, visit 2 SAMPLE_284


title: MN.Whole blood PBMC cells from patient 100, visit 6 SAMPLE_280


title: scATAC-D6-5


title: MN.Whole blood PBMC cells from patient 50, visit 3 SAMPLE_279


title: MN.Whole blood PBMC cells from patient 106, visit 1 SAMPLE_275


title: MN.Whole blood PBMC cells from patient 21.5, visit 6 SAMPLE_273


title: MN.Whole blood PBMC cells from patient 33, visit 5 SAMPLE_278


title: scATAC-D6-60


title: scATAC-D6-59


title: scATAC-D6-58


title: MN.Whole blood PBMC cells from patient 84, visit 9 SAMPLE_276


title: MN.Whole blood PBMC cells from patient 25, visit 0 SAMPLE_272


title: scATAC-D6-56


title: scATAC-D6-57


title: scATAC-D6-55


title: MN.Whole blood PBMC cells from patient 36, visit 7 SAMPLE_274


title: scATAC-D6-54


title: scATAC-D6-53


title: scATAC-D6-51


title: MN.Whole blood PBMC cells from patient 20, visit 7 SAMPLE_267


title: MN.Whole blood PBMC cells from patient 68, visit 0 SAMPLE_269


title: MN.Whole blood PBMC cells from patient 8, visit 7 SAMPLE_268


title: scATAC-D6-52


title: MN.Whole blood PBMC cells from patient 50, visit 7 SAMPLE_266


title: MN.Whole blood PBMC cells from patient 38, visit 1 SAMPLE_265


title: BN.Whole blood PBMC cells from patient 63, visit 5 SAMPLE_263


title: scATAC-D6-50


title: scATAC-D6-4


title: MN.Whole blood PBMC cells from patient 75, visit 7 SAMPLE_271


title: MN.Whole blood PBMC cells from patient 90, visit 9 SAMPLE_270


title: scATAC-D6-49


title: BN.Whole blood PBMC cells from patient 30, visit 8 SAMPLE_262


title: BN.Whole blood PBMC cells from patient 47, visit 8 SAMPLE_264


title: scATAC-D6-48


title: scATAC-D6-47


title: scATAC-D6-45


title: scATAC-D6-46


title: scATAC-D6-44


title: BN.Whole blood PBMC cells from patient 52, visit 9 SAMPLE_261


title: BN.Whole blood PBMC cells from patient 40, visit 4 SAMPLE_259


title: BN.Whole blood PBMC cells from patient 62, visit 9 SAMPLE_257


title: BN.Whole blood PBMC cells from patient 2, visit 5 SAMPLE_258


title: BN.Whole blood PBMC cells from patient 39, visit 4 SAMPLE_256


title: BN.Whole blood PBMC cells from patient 80, visit 8 SAMPLE_260


title: scATAC-D6-43


title: BN.Whole blood PBMC cells from patient 67.5, visit 9 SAMPLE_255


title: BN.Whole blood PBMC cells from patient 29, visit 6 SAMPLE_253


title: BN.Whole blood PBMC cells from patient 14, visit 5 SAMPLE_254


title: BN.Whole blood PBMC cells from patient 35.1, visit 0 SAMPLE_252


title: scATAC-D6-42


title: scATAC-D6-40


title: scATAC-D6-41


title: scATAC-D6-3


title: scATAC-D6-36


title: scATAC-D6-39


title: scATAC-D6-37


title: scATAC-D6-38


title: BN.Whole blood PBMC cells from patient 61.5, visit 6 SAMPLE_250


title: scATAC-D6-35


title: scATAC-D6-34


title: scATAC-D6-32


title: scATAC-D6-31


title: scATAC-D6-30


title: BN.Whole blood PBMC cells from patient 81, visit 5 SAMPLE_248


title: BN.Whole blood PBMC cells from patient 34, visit 4 SAMPLE_247

value: other


title: BN.Whole blood PBMC cells from patient 55.5, visit 5 SAMPLE_251


title: scATAC-D6-2

value: Primary epidermal keratinocyte


title: BN.Whole blood PBMC cells from patient 35, visit 4 SAMPLE_246


title: scATAC-D6-29

value: Differentiated (Day 6)


title: BN.Whole blood PBMC cells from patient 42, visit 5 SAMPLE_243

value: BN


title: scATAC-D6-28


title: BN.Whole blood PBMC cells from patient 0, visit 0 SAMPLE_245

value: testing


title: scATAC-D6-27


title: BN.Whole blood PBMC cells from patient 36, visit 4 SAMPLE_244

value: NYU


title: BN.Whole blood PBMC cells from patient 33, visit 2 SAMPLE_249

value: male


title: scATAC-D6-26


title: scATAC-D6-25


title: scATAC-D6-33


title: BN.Whole blood PBMC cells from patient 52.5, visit 6 SAMPLE_238

value: quit


title: BN.Whole blood PBMC cells from patient 17.5, visit 4 SAMPLE_240


title: BN.Whole blood PBMC cells from patient 108, visit 5 SAMPLE_237

value: Caucasian


title: BN.Whole blood PBMC cells from patient 27.95, visit 7 SAMPLE_241


title: BN.Whole blood PBMC cells from patient 50, visit 4 SAMPLE_239


title: BN.Whole blood PBMC cells from patient 88, visit 6 SAMPLE_242

value: Asian


title: BN.Whole blood PBMC cells from patient 51, visit 6 SAMPLE_236

value: female


title: BN.Whole blood PBMC cells from patient 36, visit 3 SAMPLE_235

value: smoker


title: BN.Whole blood PBMC cells from patient 117, visit 6 SAMPLE_233


title: scATAC-D6-24


title: scATAC-D6-23


title: scATAC-D6-21


title: scATAC-D6-20


title: BN.Whole blood PBMC cells from patient 28, visit 6 SAMPLE_231


title: scATAC-D6-1


title: scATAC-D6-19


title: BN.Whole blood PBMC cells from patient 147, visit 5 SAMPLE_234


title: BN.Whole blood PBMC cells from patient 43, visit 6 SAMPLE_229


title: scATAC-D6-17


title: scATAC-D6-16


title: scATAC-D6-15


title: scATAC-D6-13


title: scATAC-D6-14


title: scATAC-D6-22


title: BN.Whole blood PBMC cells from patient 42, visit 5 SAMPLE_230


title: BN.Whole blood PBMC cells from patient 23.75, visit 4 SAMPLE_227


title: BN.Whole blood PBMC cells from patient 40, visit 9 SAMPLE_232


title: BN.Whole blood PBMC cells from patient 32.4, visit 5 SAMPLE_224


title: BN.Whole blood PBMC cells from patient 54, visit 5 SAMPLE_225


title: scATAC-D6-12


title: scATAC-D6-11


title: scATAC-D3-9

value: Differentiated (Day 3)


title: scATAC-D6-18


title: BN.Whole blood PBMC cells from patient 86, visit 2 SAMPLE_222


title: scATAC-D3-96


title: scATAC-D3-95


title: BN.Whole blood PBMC cells from patient 15, visit 5 SAMPLE_220

value: UPenn


title: BN.Whole blood PBMC cells from patient 6, visit 2 SAMPLE_217


title: BN.Whole blood PBMC cells from patient 28.5, visit 5 SAMPLE_228


title: BN.Whole blood PBMC cells from patient 150, visit 0 SAMPLE_219


title: scATAC-D3-94


title: BN.Whole blood PBMC cells from patient 37, visit 4 SAMPLE_226


title: scATAC-D3-93


title: scATAC-D3-92


title: BN.Whole blood PBMC cells from patient 0, visit 0 SAMPLE_214

value: never


title: BN.Whole blood PBMC cells from patient 45, visit 8 SAMPLE_215


title: BN.Whole blood PBMC cells from patient 37.5, visit 1 SAMPLE_223


title: scATAC-D3-91


title: BN.Whole blood PBMC cells from patient 2.25, visit 1 SAMPLE_216


title: BN.Whole blood PBMC cells from patient 45, visit 6 SAMPLE_221


title: BN.Whole blood PBMC cells from patient 0, visit 2 SAMPLE_213


title: scATAC-D6-10


title: BN.Whole blood PBMC cells from patient 55, visit 9 SAMPLE_218


title: scATAC-D3-90


title: scATAC-D3-8


title: scATAC-D3-88


title: scATAC-D3-87


title: scATAC-D3-89


title: scATAC-D3-86


title: scATAC-D3-85


title: BN.Whole blood PBMC cells from patient 78, visit 6 SAMPLE_208


title: BN.Whole blood PBMC cells from patient 45, visit 8 SAMPLE_211


title: BN.Whole blood PBMC cells from patient 37.5, visit 5 SAMPLE_209


title: BN.Whole blood PBMC cells from patient 235, visit 8 SAMPLE_210


title: scATAC-D3-83


title: BN.Whole blood PBMC cells from patient 24, visit 6 SAMPLE_207


title: BN.Whole blood PBMC cells from patient 10, visit 2 SAMPLE_212


title: scATAC-D3-82


title: scATAC-D3-81


title: scATAC-D3-84


title: scATAC-D3-7


title: scATAC-D3-80


title: BN.Whole blood PBMC cells from patient 0, visit 7 SAMPLE_206


title: BN.Whole blood PBMC cells from patient 14.5, visit 0 SAMPLE_203

value: HFGCC


title: scATAC-D3-79


title: BN.Whole blood PBMC cells from patient 18, visit 4 SAMPLE_204


title: BN.Whole blood PBMC cells from patient 25, visit 4 SAMPLE_205


title: BN.Whole blood PBMC cells from patient 35, visit 7 SAMPLE_201

value: African American


title: BN.Whole blood PBMC cells from patient 41, visit 8 SAMPLE_202


title: BN.Whole blood PBMC cells from patient 52.5, visit 1 SAMPLE_199


title: scATAC-D3-78


title: BN.Whole blood PBMC cells from patient 30, visit 4 SAMPLE_198


title: BN.Whole blood PBMC cells from patient 20, visit 4 SAMPLE_196


title: BN.Whole blood PBMC cells from patient 24, visit 6 SAMPLE_200


title: BN.Whole blood PBMC cells from patient 56, visit 2 SAMPLE_197


title: scATAC-D3-77


title: scATAC-D3-76


title: BN.Whole blood PBMC cells from patient 140, visit 9 SAMPLE_194

value: Temple


title: scATAC-D3-75

value: Primary epidermal keratinocyte


title: scATAC-D3-74


title: scATAC-D3-71


title: scATAC-D3-73


title: scATAC-D3-72


title: scATAC-D3-6


title: BN.Whole blood PBMC cells from patient 30, visit 3 SAMPLE_195


title: scATAC-D3-69


title: scATAC-D3-65


title: scATAC-D3-66


title: scATAC-D3-68


title: scATAC-D3-70


title: BN.Whole blood PBMC cells from patient 34, visit 9 SAMPLE_192


title: BN.Whole blood PBMC cells from patient 45, visit 2 SAMPLE_193


title: MN.Whole blood PBMC cells from patient 80, visit 4 SAMPLE_190

value: MN

value: trainingB

value: other


title: scATAC-D3-62


title: MN.Whole blood PBMC cells from patient 0, visit 6 SAMPLE_189

value: NYU


title: MN.Whole blood PBMC cells from patient 0, visit 0 SAMPLE_187

value: male


title: MN.Whole blood PBMC cells from patient 40, visit 5 SAMPLE_188

value: quit


title: MN.Whole blood PBMC cells from patient 40, visit 3 SAMPLE_191

value: Caucasian


title: MN.Whole blood PBMC cells from patient 30, visit 7 SAMPLE_185


title: MN.Whole blood PBMC cells from patient 20, visit 5 SAMPLE_184


title: MN.Whole blood PBMC cells from patient 20, visit 0 SAMPLE_186


title: MN.Whole blood PBMC cells from patient 20, visit a SAMPLE_181


title: MN.Whole blood PBMC cells from patient 45, visit a SAMPLE_182


title: MN.Whole blood PBMC cells from patient 50, visit 0 SAMPLE_179


title: scATAC-D3-61


title: scATAC-D3-64


title: scATAC-D3-63


title: MN.Whole blood PBMC cells from patient 23.5, visit 5 SAMPLE_180


title: MN.Whole blood PBMC cells from patient 0.4, visit 2 SAMPLE_183


title: scATAC-D3-67


title: scATAC-D3-60


title: scATAC-D3-59


title: MN.Whole blood PBMC cells from patient 69, visit 0 SAMPLE_178


title: scATAC-D3-57


title: MN.Whole blood PBMC cells from patient 36, visit 5 SAMPLE_177


title: scATAC-D3-58


title: scATAC-D3-55


title: MN.Whole blood PBMC cells from patient 50, visit 1 SAMPLE_175


title: scATAC-D3-5


title: scATAC-D3-51


title: scATAC-D3-54


title: MN.Whole blood PBMC cells from patient 60, visit 6 SAMPLE_171


title: MN.Whole blood PBMC cells from patient 32, visit 7 SAMPLE_173


title: scATAC-D3-50


title: scATAC-D3-4


title: MN.Whole blood PBMC cells from patient 15, visit 5 SAMPLE_174


title: MN.Whole blood PBMC cells from patient 52.5, visit 3 SAMPLE_172


title: MN.Whole blood PBMC cells from patient 45, visit 2 SAMPLE_170


title: MN.Whole blood PBMC cells from patient 86, visit 2 SAMPLE_176


title: scATAC-D3-53


title: MN.Whole blood PBMC cells from patient 84, visit 8 SAMPLE_168


title: scATAC-D3-56


title: scATAC-D3-47


title: scATAC-D3-49


title: scATAC-D3-52


title: MN.Whole blood PBMC cells from patient 60, visit 5 SAMPLE_166


title: MN.Whole blood PBMC cells from patient 45, visit 2 SAMPLE_169


title: MN.Whole blood PBMC cells from patient 85, visit 0 SAMPLE_165


title: MN.Whole blood PBMC cells from patient 40, visit 0 SAMPLE_163


title: scATAC-D3-46


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_160


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_161


title: scATAC-D3-45


title: scATAC-D3-43


title: MN.Whole blood PBMC cells from patient 32, visit 2 SAMPLE_167


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_159


title: MN.Whole blood PBMC cells from patient 57, visit 0 SAMPLE_164


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_162


title: scATAC-D3-42


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_158


title: scATAC-D3-40


title: scATAC-D3-48


title: scATAC-D3-44


title: scATAC-D3-38


title: scATAC-D3-41


title: scATAC-D3-39


title: MN.Whole blood PBMC cells from patient 40, visit 4 SAMPLE_155


title: scATAC-D3-36


title: scATAC-D3-34


title: scATAC-D3-3


title: scATAC-D3-35


title: MN.Whole blood PBMC cells from patient 93, visit 8 SAMPLE_156


title: MN.Whole blood PBMC cells from patient 68, visit 8 SAMPLE_154


title: MN.Whole blood PBMC cells from patient 40, visit 1 SAMPLE_157


title: scATAC-D3-32


title: MN.Whole blood PBMC cells from patient 19.5, visit 9 SAMPLE_151


title: MN.Whole blood PBMC cells from patient 41, visit 9 SAMPLE_149


title: scATAC-D3-31


title: scATAC-D3-30


title: scATAC-D3-37


title: MN.Whole blood PBMC cells from patient 50, visit 7 SAMPLE_150


title: scATAC-D3-29


title: MN.Whole blood PBMC cells from patient 50, visit 8 SAMPLE_148


title: scATAC-D3-28


title: MN.Whole blood PBMC cells from patient 38, visit 3 SAMPLE_153


title: MN.Whole blood PBMC cells from patient 25, visit 9 SAMPLE_145


title: MN.Whole blood PBMC cells from patient 48, visit 2 SAMPLE_146


title: MN.Whole blood PBMC cells from patient 49, visit 1 SAMPLE_147


title: MN.Whole blood PBMC cells from patient 35, visit 4 SAMPLE_152


title: scATAC-D3-33


title: scATAC-D3-27


title: scATAC-D3-26


title: MN.Whole blood PBMC cells from patient 90, visit 0 SAMPLE_141


title: MN.Whole blood PBMC cells from patient 13.475, visit 2 SAMPLE_142


title: MN.Whole blood PBMC cells from patient 22.5, visit 9 SAMPLE_144


title: MN.Whole blood PBMC cells from patient 118, visit 1 SAMPLE_143


title: scATAC-D3-25


title: MN.Whole blood PBMC cells from patient 30, visit 3 SAMPLE_139


title: scATAC-D3-24


title: scATAC-D3-23


title: scATAC-D3-2


title: MN.Whole blood PBMC cells from patient 5, visit 3 SAMPLE_138


title: scATAC-D3-22


title: MN.Whole blood PBMC cells from patient 120, visit 4 SAMPLE_140


title: MN.Whole blood PBMC cells from patient 20.5, visit 6 SAMPLE_137


title: scATAC-D3-21


title: MN.Whole blood PBMC cells from patient 2, visit 4 SAMPLE_136


title: scATAC-D3-19


title: scATAC-D3-18


title: scATAC-D3-1


title: scATAC-D3-20


title: scATAC-D3-17


title: scATAC-D3-16


title: scATAC-D3-14


title: scATAC-D3-13


title: scATAC-D3-12


title: scATAC-D3-11


title: scATAC-D3-10


title: MN.Whole blood PBMC cells from patient 40, visit 9 SAMPLE_133


title: scATAC-D0-9

value: Undifferentiated (Day 0)


title: MN.Whole blood PBMC cells from patient 18, visit 0 SAMPLE_134

value: female


title: MN.Whole blood PBMC cells from patient 18.5, visit 3 SAMPLE_132

value: smoker


title: MN.Whole blood PBMC cells from patient 20.5, visit 6 SAMPLE_131


title: MN.Whole blood PBMC cells from patient 10, visit 0 SAMPLE_124


title: MN.Whole blood PBMC cells from patient 112, visit 5 SAMPLE_126


title: MN.Whole blood PBMC cells from patient 10, visit 0 SAMPLE_129


title: scATAC-D0-96


title: scATAC-D0-95


title: scATAC-D3-15

value: Differentiated (Day 3)


title: MN.Whole blood PBMC cells from patient 15, visit 3 SAMPLE_130


title: MN.Whole blood PBMC cells from patient 20, visit 1 SAMPLE_128


title: MN.Whole blood PBMC cells from patient na, visit a SAMPLE_122


title: MN.Whole blood PBMC cells from patient 150, visit 2 SAMPLE_135


title: BN.Whole blood PBMC cells from patient 49, visit 4 SAMPLE_120

value: BN

value: trainingA


title: scATAC-D0-94


title: scATAC-D0-93


title: BN.Whole blood PBMC cells from patient 12, visit 3 SAMPLE_119


title: MN.Whole blood PBMC cells from patient 52, visit 5 SAMPLE_127

value: HFGCC


title: MN.Whole blood PBMC cells from patient 90, visit 4 SAMPLE_125


title: BN.Whole blood PBMC cells from patient 75, visit 0 SAMPLE_117


title: BN.Whole blood PBMC cells from patient 26, visit a SAMPLE_118

value: African American


title: MN.Whole blood PBMC cells from patient 60, visit 5 SAMPLE_123


title: scATAC-D0-91


title: scATAC-D0-92


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_121

value: Temple

value: never


title: scATAC-D0-90

value: Primary epidermal keratinocyte


title: scATAC-D0-8


title: scATAC-D0-88


title: scATAC-D0-89


title: scATAC-D0-85


title: scATAC-D0-86


title: scATAC-D0-87


title: scATAC-D0-84


title: scATAC-D0-83


title: scATAC-D0-82


title: scATAC-D0-81


title: scATAC-D0-80


title: scATAC-D0-7


title: BN.Whole blood PBMC cells from patient 26, visit a SAMPLE_115


title: BN.Whole blood PBMC cells from patient 45, visit 4 SAMPLE_113


title: scATAC-D0-79


title: scATAC-D0-77


title: scATAC-D0-76


title: BN.Whole blood PBMC cells from patient 44, visit 6 SAMPLE_110


title: BN.Whole blood PBMC cells from patient 0, visit 6 SAMPLE_114


title: BN.Whole blood PBMC cells from patient 57, visit 3 SAMPLE_116


title: scATAC-D0-75


title: BN.Whole blood PBMC cells from patient 75, visit 0 SAMPLE_111


title: BN.Whole blood PBMC cells from patient 62.5, visit 0 SAMPLE_102


title: BN.Whole blood PBMC cells from patient 54, visit 4 SAMPLE_112


title: scATAC-D0-74


title: BN.Whole blood PBMC cells from patient na, visit 0 SAMPLE_107


title: scATAC-D0-72


title: BN.Whole blood PBMC cells from patient 38, visit 0 SAMPLE_104

value: Asian


title: BN.Whole blood PBMC cells from patient 26, visit 6 SAMPLE_101


title: scATAC-D0-73


title: BN.Whole blood PBMC cells from patient 33, visit 0 SAMPLE_106


title: BN.Whole blood PBMC cells from patient 33, visit 4 SAMPLE_108


title: BN.Whole blood PBMC cells from patient 15, visit 5 SAMPLE_103


title: BN.Whole blood PBMC cells from patient 84, visit 3 SAMPLE_109


title: scATAC-D0-70


title: BN.Whole blood PBMC cells from patient 36.6521, visit a SAMPLE_100


title: BN.Whole blood PBMC cells from patient 46, visit 4 SAMPLE_105

value: other


title: scATAC-D0-71


title: scATAC-D0-6


title: scATAC-D0-69


title: scATAC-D0-68


title: BN.Whole blood PBMC cells from patient 38, visit 5 SAMPLE_98

value: NYU


title: BN.Whole blood PBMC cells from patient na, visit 0 SAMPLE_99

value: male


title: scATAC-D0-67


title: scATAC-D0-66


title: scATAC-D0-65


title: BN.Whole blood PBMC cells from patient 42, visit 8 SAMPLE_95


title: BN.Whole blood PBMC cells from patient 33.8, visit 0 SAMPLE_96


title: BN.Whole blood PBMC cells from patient 70, visit 8 SAMPLE_93

value: quit


title: BN.Whole blood PBMC cells from patient 9, visit 1 SAMPLE_90

value: UPenn

value: Caucasian


title: BN.Whole blood PBMC cells from patient 5, visit 0 SAMPLE_91


title: scATAC-D0-63

value: Undifferentiated (Day 0)


title: BN.Whole blood PBMC cells from patient 30, visit 0 SAMPLE_89

value: female


title: scATAC-D0-62


title: BN.Whole blood PBMC cells from patient 86, visit 2 SAMPLE_92


title: scATAC-D0-64


title: BN.Whole blood PBMC cells from patient 59, visit 0 SAMPLE_94

value: smoker


title: BN.Whole blood PBMC cells from patient 22, visit 0 SAMPLE_87

value: BN


title: BN.Whole blood PBMC cells from patient 78.75, visit 7 SAMPLE_88

value: trainingA


title: BN.Whole blood PBMC cells from patient na, visit 5 SAMPLE_85


title: scATAC-D0-61


title: scATAC-D0-5


title: scATAC-D0-59


title: BN.Whole blood PBMC cells from patient na, visit a SAMPLE_83


title: scATAC-D0-55


title: scATAC-D0-57


title: scATAC-D0-56


title: scATAC-D0-54


title: scATAC-D0-60


title: scATAC-D0-58


title: scATAC-D0-52


title: BN.Whole blood PBMC cells from patient na, visit 5 SAMPLE_84


title: BN.Whole blood PBMC cells from patient na, visit 0 SAMPLE_82


title: BN.Whole blood PBMC cells from patient na, visit a SAMPLE_80


title: BN.Whole blood PBMC cells from patient 18, visit 7 SAMPLE_76

value: HFGCC


title: BN.Whole blood PBMC cells from patient na, visit 1 SAMPLE_81


title: BN.Whole blood PBMC cells from patient 26, visit 8 SAMPLE_79


title: BN.Whole blood PBMC cells from patient 25, visit 3 SAMPLE_86


title: BN.Whole blood PBMC cells from patient 66, visit 3 SAMPLE_78


title: BN.Whole blood PBMC cells from patient 52.5, visit 8 SAMPLE_74


title: BN.Whole blood PBMC cells from patient 43, visit 5 SAMPLE_77

value: African American


title: BN.Whole blood PBMC cells from patient 48, visit 5 SAMPLE_75


title: scATAC-D0-50


title: scATAC-D0-51


title: scATAC-D0-53


title: scATAC-D0-48


title: scATAC-D0-47


title: scATAC-D0-46


title: BN.Whole blood PBMC cells from patient 30, visit 5 SAMPLE_68

value: Temple


title: scATAC-D0-4


title: BN.Whole blood PBMC cells from patient 27, visit 3 SAMPLE_71


title: BN.Whole blood PBMC cells from patient 15, visit a SAMPLE_72


title: scATAC-D0-49


title: BN.Whole blood PBMC cells from patient 50, visit 0 SAMPLE_70


title: BN.Whole blood PBMC cells from patient 41, visit 3 SAMPLE_73


title: scATAC-D0-44


title: scATAC-D0-45


title: scATAC-D0-42


title: scATAC-D0-3


title: scATAC-D0-43


title: scATAC-D0-41


title: scATAC-D0-40


title: scATAC-D0-39


title: scATAC-D0-38


title: CBMS1_d0_ESC_p9_150901 (re-analysis)

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
Biological replicate 3 of 3
CBMS1_allele_specific_genetable.txt.gz

library_source: transcriptomic

data_processing:
BrdUIP, Population early-S, 100-cells, Single-cell data: sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
BrdUIP, Population early-S, 100-cells, Single-cell data: trimmed reads were mapped into mm9, hg19, CBMS1-specific (CBA/MsM) diploid genome based on mm9 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 or hg19 were removed by using picard tool and the reads overlapped with mm9, hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
BrdUIP data: we counted the reads of early and late S-phase BrdU-IP samples in sliding windows of 200 kb at 40-kb or 80-kb intervals (written in the processed data file as “w200sk40k” or “w200ks80k”, respectively) in non-overlapping 400-kb windows (“400k”) and performed rpm (reads per million) normalization. Then, the ratio of early-S to total read counts [(Early-S reads)/(Early-S reads + Late-S reads)] was calculated for each bin and their distribution converted to fit within a ± 1 scale, and this value was defined as the BrdU-IP RT score of each bin. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Population early-S data: we counted the reads of early-S and G1 in sliding windows of 200 kb at 40-kb intervals, performed rpm normalization in a manner identical to BrdU-IP data processing, and defined Log2[(Early-S reads)/(G1 reads)] as the population early-S RT score.
100-cells data: we counted the reads of 100 mid-S and G1 cells in sliding windows of 200 kb at 40-kb intervals and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on G1 data. From the mappability corrected mid-S read counts, the genome-wide median was obtained and used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the 100-cell mid-S RT score.
Single-cell data (hTERT-RPE1): For the analysis of single mid-S cells, we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the AneuFinder’s correctMappability command sfor normalizing mid-S data based on the merged G1 control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
Single-cell data (CBMS1 un-resolved): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved data: after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy" ].
Binarized unresolved data: Sample_Name_80k_100S_MAP_2HMM2_eps0.01.binary.bedGraph, Binarized CBA data: Sample_name_cba_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph, Binarized MsM data: Sample_name_msm_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
RNA-seq: allele-specific RNA-seq analysis was performed using CBA/MsM diploid genome as described in Sakata et al. Development 2017. We defined genes with allelic expression imbalance as those with the percentage of either MsM- or CBA-specific reads above 60% (or >70%) among genes that show ≥10 total reads (i.e. CBA+MsM read numbers combined) and >0.1 FPKM (fragments per kilobase of exon per million fragments mapped, in a non-allelic manner) in three biological replicates (CBMS1_allele_specific_genetable.txt).
Genome_build: hg19 / mm9 / CBMS1 diploid genome
Supplementary_files_format_and_content: bedGraph, bigWig

organism: Mus musculus

source_name: CBMS1 ESC

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013).

extract_protocol:
For BrdU-IP samples, we followed our routine protocol as described (Ryba et al., Nat. Protoc. 2011). A Sony SH800 cell sorter was used in the ultra-purity mode, fractionating early and late S-phase populations. The BrdU-IP protocol has been described in detail (Ryba et al., Nat. Protoc. 2011), except that we used a Bioruptor UCD-250 (Sonic Bio) for gDNA sonication in high output mode, with ON/OFF pulse times of 30 sec/30 sec for 6 minutes. After BrdU-IP, immunoprecipitated DNA samples were subject to WGA with a SeqPlex kit (Sigma, SEQXE).   For early S-phase population samples, 200,000 cells from the first half of S-phase were sorted by Sony SH800 cell sorter, and gDNA was isolated using a Qiagen kit (Qiagen #69504, DNeasy Blood & Tissue Kit) and fragmented to 200–300 bp with a Covaris ultrasonciator (model: S220, tube: microTUBE snap-cap) according to the manufacturer’s instructions (peak incident power: 175, duty factor: 10%, cycles per burst: 200, treatment time: 120), followed by cleanup and size selection via Agencourt AMPure XP SPRI beads (Beckman Coulter).  For single or 100 cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).  For RNA-seq samples, cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).  For RNA-seq, NGS library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain

value: CBA/MsM

value: embryonic stem cell

tag: sample state

value: Population

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: CBMS1_d0_ESC_p7_150901 (re-analysis)

description:
Biological replicate 2 of 3
CBMS1_allele_specific_genetable.txt.gz

tag: cell type


title: CBMS1_d0_ESC_p7_150813 (re-analysis)

description:
Biological replicate 1 of 3
CBMS1_allele_specific_genetable.txt.gz


title: MC12_BrdUIP_LateS_rep3

description: RT_MC12plus6TG_3rep_mean_IP_Aneu_rmdup_w200ks80k_P374_83-88_Percent_q0.05.bedGraph

value: embryonal carcinoma cell

value: BrdUIP

value: LateS


title: MC12_BrdUIP_LateS_rep2


title: MC12_BrdUIP_EarlyS_rep3


title: scATAC-D0-37

value: Primary epidermal keratinocyte

tag: differentiation status


title: BN.Whole blood PBMC cells from patient 25, visit 4 SAMPLE_67

tag: nodule class

tag: sample set

tag: collection site

value: quit


title: BN.Whole blood PBMC cells from patient 17, visit 6 SAMPLE_69

tag: gender

tag: smoking

tag: race

value: Caucasian


title: scATAC-D0-78

value: Undifferentiated (Day 0)


title: scATAC-D0-36


title: BN.Whole blood PBMC cells from patient na, visit 0 SAMPLE_66

value: male

tag: age

tag: packyears

tag: lesion size, mm


title: BN.Whole blood PBMC cells from patient 49, visit 7 SAMPLE_63

value: female

tag: cancer stage


title: BN.Whole blood PBMC cells from patient 0, visit 0 SAMPLE_61

value: BN

value: never

value: Asian


title: BN.Whole blood PBMC cells from patient 55, visit 2 SAMPLE_64

value: trainingA

value: African American


title: BN.Whole blood PBMC cells from patient 150, visit 7 SAMPLE_65

value: Temple


title: MN.Whole blood PBMC cells from patient 70, visit 5 SAMPLE_60

value: MN

value: NYU


title: BN.Whole blood PBMC cells from patient 14, visit 5 SAMPLE_62


title: MN.Whole blood PBMC cells from patient 0, visit 9 SAMPLE_59


title: scATAC-D0-33


title: scATAC-D0-35


title: scATAC-D0-31


title: scATAC-D0-34


title: MC12_BrdUIP_LateS_rep1

tag: strain

value: embryonal carcinoma cell

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: scATAC-D0-32


title: MC12_BrdUIP_EarlyS_rep1

value: BrdUIP

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: EarlyS


title: MN.Whole blood PBMC cells from patient 116, visit 6 SAMPLE_58


title: scATAC-D0-30

tag: cell type

value: Primary epidermal keratinocyte

tag: differentiation status


title: MC12_single_MidS_19

value: Single cell

value: TRUE

tag: cell cycle phase

value: MidS


title: scATAC-D0-29

value: Undifferentiated (Day 0)


title: scATAC-D0-27


title: scATAC-D0-26


title: scATAC-D0-25


title: MC12_single_MidS_17


title: MC12_BrdUIP_EarlyS_rep2


title: scATAC-D0-28


title: MN.Whole blood PBMC cells from patient 10, visit 1 SAMPLE_56

tag: nodule class

tag: sample set

tag: collection site

value: female

value: quit

value: Caucasian


title: MN.Whole blood PBMC cells from patient 0, visit 6 SAMPLE_55

tag: gender

tag: smoking

value: never

tag: race


title: MN.Whole blood PBMC cells from patient 54, visit 5 SAMPLE_57

value: trainingA

value: male

tag: age

tag: packyears

tag: lesion size, mm


title: scATAC-D0-2


title: scATAC-D0-22


title: MC12_single_MidS_16

tag: strain

tag: sample state


title: BN.Whole blood PBMC cells from patient 80, visit 8 SAMPLE_97

value: BN

tag: cancer stage


title: scATAC-D0-21


title: scATAC-D0-24


title: MC12_single_MidS_18

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)


title: MC12_single_MidS_15

tag: cell type

tag: repliscore of 40–70%


title: scATAC-D0-1

tag: differentiation status


title: scATAC-D0-20


title: MN.Whole blood PBMC cells from patient 80, visit 6 SAMPLE_54

tag: nodule class

value: MN

tag: sample set

value: African American


title: MC12_single_MidS_14

value: embryonal carcinoma cell

tag: cell cycle phase


title: scATAC-D0-15


title: scATAC-D0-18


title: MN.Whole blood PBMC cells from patient 70, visit 9 SAMPLE_52

tag: collection site

value: NYU

tag: gender

tag: smoking


title: MN.Whole blood PBMC cells from patient 30, visit a SAMPLE_53

tag: race

tag: age

tag: packyears


title: MN.Whole blood PBMC cells from patient 63.75, visit 1 SAMPLE_51

tag: lesion size, mm


title: MC12_single_G1_05

tag: strain

tag: sample state


title: scATAC-D0-16


title: MC12_single_G1_04

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: scATAC-D0-19

tag: cell type


title: MN.Whole blood PBMC cells from patient 30, visit 5 SAMPLE_49

value: UPenn

value: smoker

tag: cancer stage


title: MN.Whole blood PBMC cells from patient 43.75, visit 2 SAMPLE_50


title: scATAC-D0-17

value: Primary epidermal keratinocyte

tag: differentiation status


title: scATAC-D0-23


title: scATAC-D0-11


title: scATAC-D0-14


title: MN.Whole blood PBMC cells from patient 20, visit 2 SAMPLE_47

tag: nodule class


title: MN.Whole blood PBMC cells from patient 39, visit 5 SAMPLE_48

tag: sample set


title: MC12_single_G1_03

value: Single cell

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: scATAC-D0-13


title: scATAC-D0-12


title: MC12_single_MidS_13

value: TRUE

value: MidS


title: GM12878 bulk SPI1 Rep1

source_name: GM12878 cells

growth_protocol: GM1878 cells were grown in RPMI 1640 with 10% FBS and 1% pen/strep.

extract_protocol: Cells were sorted by FACS and 5e4 cells were pelleted and resuspended in 50ul of ATAC RSB with 0.1% NP40, 0.1% Tween-20, and 0.01%. After three minutes, 1ml of ATAC RSB with 0.1% Tween-20 was added, tubes were inverted, and nuclei were centrifuged at 500 rcf for 10 min. Supernatant was carefully removed and nuclei were resuspended in 50ul transposition mix (25ul TD buffer, 2.5ul transposase, 16.5ul PBS, 0.5ul 0.1% digitonin, 0.5ul 10% Tween-20, and 5ul water). Transposition was performed for 30 minutes at 37 C with shaking in a thermomixer at 1000 RPM. Reactions were purified with a Zymo DNA Clean & Concentrator 5 kit and library generation was performed as described.

tag: cell line

value: GM12878 cells


title: GM12878 bulk SPI1 Rep3


title: GM12878 bulk SPI1 Rep2


title: MC12_single_MidS_11


title: GM12878 bulk NT2 Rep2


title: MC12_single_MidS_12


title: GM12878 bulk NT2 Rep1


title: GM12878 bulk NT1 Rep3


title: MN.Whole blood PBMC cells from patient 42, visit 5 SAMPLE_44

tag: collection site

tag: gender

value: female

tag: smoking

value: quit

tag: race


title: scATAC-D0-10

value: Undifferentiated (Day 0)


title: MC12_single_MidS_10

tag: strain


title: MC12_single_MidS_08

tag: sample state


title: MC12_single_MidS_09

tag: xx or xo chromosomes in single cell samples


title: GM12878 bulk NT1 Rep2


title: GM12878 bulk NT1 Rep1


title: MC12_single_MidS_07

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: MC12_single_MidS_06

tag: cell type


title: MN.Whole blood PBMC cells from patient 114, visit 5 SAMPLE_45

value: trainingA

value: Caucasian

tag: age

tag: packyears

tag: lesion size, mm

tag: cancer stage


title: MN.Whole blood PBMC cells from patient 25, visit 5 SAMPLE_46

tag: nodule class

tag: sample set


title: Input_1_mM_2

first: Kathryn

last: Wellen

address: 421 Curie Blvd BRB II/III RM 632

department: Cancer Biology

institute: University of Pennsylvania

description: Drosophila cells were spiked in to serve as a reference genome

data_processing:
Sequenced reads were aligned to the human genome (hg19) and drosophila genome (dm3) using Bowtie2
Duplicate reads and mitochondria reads were removed by using SAMtools
Samples were peak-called against the paired input samples using MACS
peaks were annotated by HOMER annotatePeaks.pl
read counts (depth) were adjusted with traditional normalization (per basepair per peak (TSS), on top of the standard total mapped tag normalization of 10 million tags) or reference-adjusted normalization (per basepair per peak (TSS), on top of the total mapped tag normalization of drosophila reference)
bigWig files from each human SAM file using the HOMER make UCSC file
Genome_build: hg19; dm3
Supplementary_files_format_and_content: bigWig files normalized traditionally or with the reference genome can both be downloaded and visualized on IGV for comparison

source_name: glioblastoma

growth_protocol: LN229 cells were cultured in RPMI + 10% CS + 1% glutamine supplementation. S2 cells were cultured in Scheneider media + 10% FBS (heat inactivated)

extract_protocol:
Whole cell extracts were sonicated to shear the chromatin. The chromatin extracts containing DNA fragments were immunoprecipitated using antibodies against H3K27ac, H3, and IgG. Purified immunoprecipitated DNA were prepared for sequencing according to the NEBNext DNA Ultra II protocol.
NEBNext DNA Ultra II kit

treatment_protocol: LN229 cells were treated with 1 mM glucose, 10 mM glucose, or 1 mM glucose plus 5 mM acetate in glucose free RPMI + 10% dFBS + 1% glutamine for 24 hours prior to harvesting. S2 cells were maintained in normal growth conditions

value: human glioblastoma cell line LN229

tag: treatment

value: 1 mM glucose

tag: reference epigenome spike-in

value: Drosophila cell line S2

tag: chip antibody


title: MN.Whole blood PBMC cells from patient 0, visit 5 SAMPLE_43

value: MN

tag: collection site

tag: gender

value: never


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_41

value: UPenn

tag: smoking

tag: race


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_40


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_42


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_39


title: Tumor formation by A549+H1299 cells-30day-rep3

city: HangZhou City

first: Li

last: Xu

state: ZheJiang Province

address: BinWen Street  358#

country: China

institute: ZJTCMU

description: Tumor gene expression induced by A549+H1299 cell

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

label_protocol: total RNA from each sample was linearly amplified and labeled with Cy3-UTP.The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The animal housing facility is a barrier housing facility, and it is maintained in accordance with the national standards (Laboratory Animal-Requirements of Environment and Housing Facilities, GB 14925–2001).

extract_protocol: Total RNA of tumor tissue were isolated using Trizol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: 10 week old of thymus-free nude mice were randomly divided into different groups. 2ml saline suspension containing corresponding cells were implanted subcutaneously in the flanks of each nude mouse. During the experiment, mice drank and ate freely for 30 days. The tumor tissues were used for agilent human 4x44K gene expression assay.

tag: host mouse strain

value: thymus-free nude mouse

tag: Sex

tag: injected with

value: 14 weeks old

tag: tissue

value: tumor


title: Tumor formation by A549+H1299 cells-30day-rep2

tag: age


title: Tumor formation by A549+H1299 cells-30day-rep1


title: MC12_single_MidS_04

tag: strain

tag: cell type

value: embryonal carcinoma cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: TRUE

tag: cell cycle phase


title: Input_1plusac2

tag: cell line

tag: treatment

value: 1 mM glucose + 5 mM acetate

tag: reference epigenome spike-in

tag: chip antibody


title: Input_1_mM_1


title: MC12_single_MidS_03

value: MidS


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_38

tag: nodule class

tag: sample set

tag: collection site

tag: gender

value: female

tag: smoking

value: quit

tag: race

tag: packyears

tag: lesion size, mm

tag: cancer stage


title: Tumor formation by A549 cells-30day-rep3

description: Tumor gene expression induced by A549 cell

source_name: Tumor formation by A549 cells-30day

tag: host mouse strain

tag: Sex

tag: injected with

value: A549 cells

tag: age

tag: tissue


title: Tumor formation by A549 cells-30day-rep2


title: Input_1plusac1

tag: cell line

value: human glioblastoma cell line LN229

tag: treatment


title: MC12_single_MidS_02

tag: strain

tag: cell type

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: MC12_single_MidS_05


title: Input_10_mM_2

value: 10 mM glucose

tag: reference epigenome spike-in

tag: chip antibody


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_36

tag: nodule class

tag: sample set

value: trainingA

tag: collection site

tag: gender

value: male

tag: smoking

tag: race

value: Caucasian

tag: packyears

tag: lesion size, mm

tag: cancer stage


title: MC12_single_MidS_01

tag: strain

tag: cell type

tag: sample state


title: Input_10_mM_1

tag: cell line

tag: treatment

value: Drosophila cell line S2


title: H3_1_mM_2

value: 1 mM glucose


title: MC12_single_G1_02

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_35

tag: nodule class

value: MN

tag: sample set

tag: collection site

value: UPenn

tag: age


title: Tumor formation by A549 cells-30day-rep1

tag: host mouse strain

value: thymus-free nude mouse

tag: Sex

tag: injected with

value: 14 weeks old

tag: tissue

value: tumor


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_34

tag: gender

tag: smoking

tag: race

tag: packyears

tag: lesion size, mm

tag: cancer stage


title: MN.Whole blood PBMC cells from patient 0, visit a SAMPLE_37


title: Normal CHD4_ChIPSeq

city: Kolkata

first: Amitava

last: Sengupta

state: West Bengal

address: CN 6, Sector V, Salt Lake

department: Cancer Biology & Inflammatory Disorder Division

country: India

institute: CSIR - Indian Institute of Chemical Biology (Translational Research Unit of Excellence)

data_processing:
ChIp seq reads were aligned to hg19 genome assembly using Bowtie,with following parameters -n,-a,-S
Peaks were called using MACS1.4 version with following settings : Pvalue(0.5),mfold(10,30)
Peaks were annotated using PeakAnalyzer1.4 tool
Genome_build: GrCh37/hg19
Supplementary_files_format_and_content: Bed files were genearted using MACS1.4 version

source_name: Normal peripheral blood nuclear cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with antibody.
ChIP-seq library preparation was performed using TruSeqChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions.10ng of input ChIP-enriched DNA was used for ChIP-seq library preparation. Final libraries were checked using High Sensitivity chips in 2100 Bioanalyzer (Agilent). Average fragment size of final libraries was found to be 280 ± 8bp. Paired-end sequencing (2 x 100 bp) of these libraries were performed in HiSeq-2500 (Illumina) according to the manufacturer's protocols.

value: Peripheral blood

tag: chip antibody

value: CHD4 (Abcam, Cat. ab70469, Clone:3F2/4)

tag: cell type

value: peripheral blood nuclear cells

tag: disease state

value: normal


title: Normal KDM6A_ChIPSeq

value: KDM6A (Bethyl Laboratories, Cat. A302-374A)


title: H3_1_mM_1

tag: cell line

value: human glioblastoma cell line LN229

tag: treatment

tag: reference epigenome spike-in


title: AML patient 3 CHD4_ChIPSeq

source_name: AML patient 3 bone marrow nuclear cells

value: Bone marrow

value: bone marrow nuclear cells

value: acute myeloid leukemia


title: H3_1plusac1

value: 1 mM glucose + 5 mM acetate


title: AML patient 2 KDM6A_ChIPSeq

source_name: AML patient 2 bone marrow nuclear cells


title: Tumor formation by H1299 cells-30day-rep2

description: Tumor gene expression induced by H1299 cell

source_name: Tumor formation by H1299 cells-30day

value: female

value: H1299 cells

tag: age


title: Tumor formation by H1299 cells-30day-rep1

tag: host mouse strain


title: Tumor formation by H1299 cells-30day-rep3

tag: Sex


title: H3_1plusac2

value: Drosophila cell line S2


title: H3_10_mM_2

value: 10 mM glucose


title: MN.Whole blood PBMC cells from patient 70, visit a SAMPLE_33

tag: nodule class

value: MN

tag: sample set

value: trainingA

tag: collection site

value: HFGCC

value: smoker

value: Caucasian


title: H3_10_mM_1


title: MN.Whole blood PBMC cells from patient 57, visit 6 SAMPLE_30

tag: gender

tag: smoking

value: quit


title: MN.Whole blood PBMC cells from patient 40, visit 5 SAMPLE_28

tag: race

tag: packyears


title: AML patient 2 CHD4_ChIPSeq

tag: tissue

value: CHD4 (Abcam, Cat. ab70469, Clone:3F2/4)


title: MC12_single_G1_01

tag: strain

value: embryonal carcinoma cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: MN.Whole blood PBMC cells from patient 104, visit 5 SAMPLE_29

value: male

tag: age

tag: lesion size, mm

tag: cancer stage


title: MN.Whole blood PBMC cells from patient 0, visit 7 SAMPLE_32

tag: nodule class

tag: sample set

value: never

value: other


title: MN.Whole blood PBMC cells from patient 36, visit 9 SAMPLE_31

tag: collection site

tag: gender


title: AML patient 1 CHD4_ChIPSeq

source_name: AML patient 1 bone marrow nuclear cells

value: Bone marrow

tag: chip antibody

tag: cell type

value: bone marrow nuclear cells

tag: disease state

value: acute myeloid leukemia


title: H3K27ac_1_mM_2

tag: cell line

value: human glioblastoma cell line LN229

tag: treatment

value: 1 mM glucose

tag: reference epigenome spike-in

value: Drosophila cell line S2


title: AML patient 3 KDM6A_ChIPSeq

tag: tissue

value: KDM6A (Bethyl Laboratories, Cat. A302-374A)


title: H3K27ac_1_mM_1


title: MN.Whole blood PBMC cells from patient 74, visit 5 SAMPLE_26

value: MN

value: trainingA

value: HFGCC

tag: smoking

tag: race

tag: packyears


title: H3K27ac_1plusac2

value: 1 mM glucose + 5 mM acetate


title: H3K27ac_1plusac1


title: MN.Whole blood PBMC cells from patient 48, visit 8 SAMPLE_24

value: smoker

value: Caucasian

tag: age


title: L1

city: Wuhan

first: Xiang

last: Li

state: Hubei

address: No.152 Luoyu Road

department: School of Chemistry

institute: Central China Normal University

data_processing:
After removed reads containing adapter, the reads containing ploy-N and the low-quality reads from raw data, the clean reads all were introduced into the downstream analyses. Using a Burrows-Wheeler Alignment tool, the clean reads were aligned to the reference genome
MACS2 (model-based analysis of ChIP-Seq) was used to identify regions of IP enrichment over background.
MEME was used to detect the sequence motif.
PeakAnnotator was used to identify the nearest TSS of every peak and to obtain the distribution of peak summits on different function regions
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: bigWig files for all samples; narrow_peaks_tables containing details of all samples' peaks

source_name: Cervix

growth_protocol: HeLa cells were obtained from China Center for Type Culture Collection (CCTCC) and maintained at 37 °C in a saturating humidity atmosphere containing 5% CO2. HeLa cells were cultured in DMEM medium (Gibco; C11995500BT) supplemented with 1% penicillin/streptomycin (Gibco; 15140122), and 10% fetal bovine serum (FBS) (Gibco; 26140079).

extract_protocol:
Briefly, the cells were incubated with 1% formaldehyde for 10 min, and then incubated with 0.125 M glycine (final concentration) for 5 min. The nuclei of each sample was incubated with 0.6 μL micrococcal nuclease in MNase digestion buffer working solution for 5 min. The input DNA was prepared by treating aliquots of chromatin with NaCl, proteinase K and heat for de-crosslinking. The supernatants of experimental groups were incubated with 8 μL immunoprecipitation grade anti-human SOD1 primary antibody (Abcam; ab16831) overnight at 4 °C on a rocking platform. Following capturing the immune complex using Protein A/G Plus Agarose, the immune complexes were treated with NaCl, proteinase K and heated for de-crosslinking. Finally, DNAs were purified using Agencourt AMPure XP (Beckman Coulter; 15770600).
Illumina sequencing libraries were prepared from ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After amplification by PCR, the resulting DNA libraries were quantified and sequenced on the Illumina HiSeq platform according to the manufacturer’s instructions.

treatment_protocol: HeLa cells were seeded in 25 cm2 cell culture flask for ChIP-Seq at a density of 1×10^6 cells/flask in the DMEM culture medium. After washed with PBS, cells were first incubated for 4 h in the medium mixed respectively with or without H2O2 (0.4 mM), GSH (2 mM), and LD100 (50 μM). Then, ChIP was performed using Pierce Agarose ChIP Kit (Thermo Scientific; 26156).

value: HeLa cervical adenocarcinoma cell line

value: treated with LD100


title: L2

value: anti-human SOD1 primary antibody (Abcam; ab16831)


title: H1

value: treated with hydrogen peroxide


title: H2


title: C3

value: under normal conditons


title: L3


title: input


title: H3


title: MN.Whole blood PBMC cells from patient 90, visit 2 SAMPLE_23

value: male

value: quit

tag: lesion size, mm


title: MN.Whole blood PBMC cells from patient 20, visit 1 SAMPLE_27

tag: cancer stage


title: MN.Whole blood PBMC cells from patient 11, visit 2 SAMPLE_25

tag: nodule class

value: female

value: African American


title: H3K27ac_10_mM_1

value: human glioblastoma cell line LN229

value: 10 mM glucose

value: Drosophila cell line S2


title: MN.Whole blood PBMC cells from patient 71, visit 5 SAMPLE_20

value: MN

tag: sample set

value: trainingA


title: MN.Whole blood PBMC cells from patient 30, visit a SAMPLE_22

tag: collection site

value: HFGCC


title: AML patient 1 KDM6A_ChIPSeq

value: Bone marrow

value: KDM6A (Bethyl Laboratories, Cat. A302-374A)

value: bone marrow nuclear cells

value: acute myeloid leukemia


title: MN.Whole blood PBMC cells from patient 66, visit 2 SAMPLE_16

tag: gender

value: smoker

value: Caucasian


title: MN.Whole blood PBMC cells from patient 126, visit a SAMPLE_21


title: H3K27ac_10_mM_2

tag: chip antibody


title: C2

value: HeLa cervical adenocarcinoma cell line

value: under normal conditons

value: anti-human SOD1 primary antibody (Abcam; ab16831)


title: siMST1-2

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using Hisat2-2.0.5, which is capable of reporting split-read alignments across splice junctions and determined using Stringtie-1.3.3b software in default options.
The reference genome sequence of Homo sapiens (hg38) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

extract_protocol:
RNAs were extracted from the cell of Homo Sapiens. Poly(A) mRNA using the Illumina  TruSeq RNA Sample Prep Kit v2, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

tag: cell type

value: Cultured Human umbilical vein endothelial cell (HUVEC)

tag: genotype

value: MST1-depleted HUVEC


title: siFOXO1-3

source_name: Human umbilical vein endothelial cell (HUVEC)

value: FOXO1-depleted HUVEC


title: siMST1-3


title: C1

tag: cell line


title: MN.Whole blood PBMC cells from patient 40, visit 2 SAMPLE_18

value: female

value: African American


title: MN.Whole blood PBMC cells from patient 45, visit 5 SAMPLE_19

value: MN


title: siFOXO1-2


title: MN.Whole blood PBMC cells from patient 135, visit 8 SAMPLE_14

value: trainingA

value: quit


title: MN.Whole blood PBMC cells from patient 40, visit 2 SAMPLE_12

value: HFGCC


title: MN.Whole blood PBMC cells from patient 90, visit a SAMPLE_17

value: male


title: MN.Whole blood PBMC cells from patient 38, visit 1 SAMPLE_15


title: MN.Whole blood PBMC cells from patient 12.5, visit 2 SAMPLE_11


title: MN.Whole blood PBMC cells from patient 47, visit 5 SAMPLE_13


title: MN.Whole blood PBMC cells from patient 30, visit 6 SAMPLE_10


title: siMST1-1


title: MN.Whole blood PBMC cells from patient 35, visit 4 SAMPLE_9


title: Striatum [TG_STR_3]

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

country: Germany

institute: Saarland University

data_processing:
Read quality of RNA-seq data in fastq files was assessed using FastQC (v0.11.4) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR (v2.4.2a) allowing gapped alignments to account for splicing against the Ensembl MusMusculus genome v82
Raw counts describing gene-level abundances were derived from DESeq2 (v1.8.2) (Love et al., 2014) with default parameters.
Genome_build: Ensembl MusMusculus genome v82
Supplementary_files_format_and_content: comma seperated text file containing raw read counts per gene identified by Ensembl gene ID

source_name: Striatum

extract_protocol:
Striata were removed, flash-frozen in liquid nitrogen, and RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen). TruSeq RNA Sample Prep Kit (Illumina) was used with 500 ng of total RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Poly(A)-selected single-end sequencing libraries were generated according to the manufacturer’s instructions. All libraries were sequenced on an Illumina HiSeq 2500 platform at a depth of 12–20 million single-end reads.

tag: strain

value: striatum

value: transgenic overexpressing human SNCA

tag: environment

value: stress

value: 6 months


title: siControl-3

value: Control


title: siFOXO1-1


title: Striatum [TG_STR_2]

tag: tissue


title: Striatum [TG_STR_1]


title: siControl-2


title: Striatum [TG_SE_3]

value: standard


title: Striatum [TG_SE_4]


title: MN.Whole blood PBMC cells from patient 124, visit a SAMPLE_8

tag: smoking

value: Caucasian


title: siControl-1

value: Cultured Human umbilical vein endothelial cell (HUVEC)


title: MZ29_d1_60KPa

city: Barcelona

first: Nuria

last: Montserrat

address: Baldiri Reixac, 10-12

country: Spain

institute: Institute for Bioengineering of Catalonia (IBEC)

data_processing:
Raw reads were trimmed using skewer (0.2.2) to remove possible  adapters
Trimmed reads were  mapped to the reference genome using STAR (v2.5.3a) with default parameters
Read counts were obtained by using the STAR's parameter " --quantMode GeneCounts"
Read counts on the reverse strand were fed to R and analyzed using DESEQ2
regularized transformed log counts were calculated using the function rlog from the DESEQ2 package
Genome_build: Gencode v26 corresponding to GRCh38
Supplementary_files_format_and_content: CSV file containing regularized log transformed fragment counts

source_name: Human Blastocyst

growth_protocol: hPSCs were maintained in Essential 8 medium (Life Technologies #A1517001) in p10 culture plates coated with vitronectin (Fisher Scientific S.L. A14700) in a 37ºC incubator with 5% CO2 and were passaged every 5-6 days.

extract_protocol:
Cells were collected by scraping and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 500-750 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hPSCs were maintained in Essential 8 medium (Life Technologies #A1517001) in p10 culture plates coated with vitronectin (Fisher Scientific S.L. A14700) in a 37ºC incubator with 5% CO2 and were passaged at day 0 to 1 or 60 kPa-PA hydrogels coated with vitronectin (Fisher Scientific S.L. A14700). From day 0 to day 1 hPSCs were exposed to 8µM CHIR99021 (Sigma #SML1046-5MG) in basic differentiation medium [Advanced RPMI 1640(Life technologies #12633-012) + 1 × 1-GlutaMAX (Life Technologies #35050-038) + Penicillin/Streptomycin (Life Technologies #15140122)]

tag: developmental stage

value: Human Pluripotent Stem Cells

tag: treatment

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 60kPa in the presence of 8uM CHIR (Wnt agonist) during 24 hours


title: MZ29_d1_1KPa

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 1kPa in the presence of 8uM CHIR (Wnt agonist) during 24 hours


title: Striatum [TG_SE_1]

tag: age


title: MZ29_d0_60KPa

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 60kPa in the presence of commercial media sustaining undifferentatited conditions (E8 media) during 24 hours


title: Striatum [TG_SE_2]


title: MN.Whole blood PBMC cells from patient 47, visit 6 SAMPLE_6

value: MN

value: female

value: smoker

tag: race

value: African American

tag: packyears

tag: lesion size, mm


title: Striatum [WT_STR_2]

value: wildtype


title: Striatum [WT_STR_1]

value: striatum


title: MZ28_d1_60KPa


title: MZ29_d0_1KPa

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 1kPa in the presence of commercial media sustaining undifferentatited conditions (E8 media) during 24 hours


title: Striatum [WT_SE_2]


title: MN.Whole blood PBMC cells from patient 60, visit 7 SAMPLE_7

tag: nodule class

tag: sample set

value: trainingA

value: HFGCC

value: quit

tag: cancer stage


title: MN.Whole blood PBMC cells from patient 49, visit 6 SAMPLE_4

tag: collection site

tag: gender

value: male


title: Striatum [WT_SE_1]

tag: genotype

value: standard

value: 6 months


title: MN.Whole blood PBMC cells from patient 20, visit 7 SAMPLE_3

value: Caucasian


title: Striatum [WT_SE_3]


title: MZ28_d1_1KPa

tag: cell type

value: Human Pluripotent Stem Cells


title: MN.Whole blood PBMC cells from patient 0, visit 7 SAMPLE_5

value: never

value: Asian


title: MN.Whole blood PBMC cells from patient 30, visit 2 SAMPLE_2

value: MN


title: MZ28_d0_60KPa

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 60kPa in the presence of commercial media sustaining undifferentatited conditions (E8 media) during 24 hours


title: MN.Whole blood PBMC cells from patient 60, visit 0 SAMPLE_1

value: female


title: MZ28_d0_1KPa


title: MZ27_d1_60KPa

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 60kPa in the presence of 8uM CHIR (Wnt agonist) during 24 hours


title: Trem2 R47H KI Rep3

city: San Diego

first: Jun

last: Yin

address: 10901 N Torrey Pines Rd

department: Bioinformatics Core

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
RNA-seq sequencing reads were aligned using OSA aligner embedded in the Omicsoft ArrayStudio pipeline (Omicsoft Inc., USA). Mouse genome version GRCm38 and UCSC gene annotation was used in the alignment and quantification. Quantification was performed to the gene and transcript level based on RSEM. Normalized gene expression level was calculated by fragments per kilobase per million reads (FPKM) then quantile normalized at 70 percentile to 10 (FPKQ). Only genes with at least one sample expressed at FPKQ >= 1 were used in the following statistical analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Quantification was performed to the gene and transcript level based on RSEM. Normalized gene expression level was calculated by fragments per kilobase per million reads (FPKM) then quantile normalized at 70 percentile to 10 (FPKQ).

source_name: Bone Marrow Derived Macrophage

growth_protocol: Bone marrow cells from TREM2-/-, TREM2-/+, TREM2R47H, TREM2R47H/+ and TREM2+/+ mice were obtained from femurs and tibiae using standard protocols and seeded in DMEM supplemented with 10% heatinactivated FBS and 50ng/ml mouse CSF-1 (R&D Systems) in non-TC treated sterile petri dishes (ThermoFisher Scientific). Nonadherent cells were removed by washing with cold phosphate-buffered saline (PBS) (Gibco) on Day 5 or Day 6 in culture (unless otherwise indicated) and the adherent macrophages were harvested by gentle scraping, counted and used for futher downstream analysis.

extract_protocol:
Day 6 BMDMs were harvested from TREM2-/-, TREM2R47H and respective wild-type littermates (n=5 animals per genotype) and total RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
1-2 ug of total RNA purified from BM-derived ex vivo macrophages was used for cDNA library preparation by using a modified protocol based on the Illumina Truseq RNA Sample Preparation Kit (Illumina, San Diego, CA) and the published methods for strandspecific RNA-Seq. After poly-A selection, fragmentation, and priming, reverse transcription was carried out for 1st strand cDNA synthesis at the presence of RNaseOut (Life Technologies, Carlsbad, CA) and actinomycin-D (MP Biomedicals, Santa Ana, CA). The synthesized cDNA was further purified by using AMPure RNAClean beads (Beckman Coulter, Pasadena, CA) following the commercial instruction. A modified method by incorporation of dUTP instead of dTTP was prepared and used for the second strand synthesis. After AMPure XP bead purification (Beckman Coulter), following the standard protocol recommended by Illumina, end repairing, Atailing, and ligation of index adaptors were sequentially performed for generation of cDNA libraries. After size selection of libraries using Pippen Prep (SAGE Biosciences, Beverly, MA), the dUTPcontaining cDNA strands were destroyed by digestion of USER enzymes (New England Biolabs, Ipswich, MA) followed by a step of PCR enrichment for introduction of strand specificity. After cleaning up, the enriched cDNA libraries were analyzed in Agilent Bioanalyser and quantified by Quant-iTTM Pico-Green assays (Life Technologies) before being sequenced onto Illumina HiSeq platform. Each library generated at least 35 millions of 75bp pair-end reads for downstream analysis.

treatment_protocol: Treated with M-CSF 50ng/ml for 6 days

tag: strain

value: 4-5 months

value: TREM2 R47H KI


title: Trem2 R47H KI Rep5


title: Trem2 R47H KI Rep4


title: Trem2 R47H KI Rep2


title: Trem2 R47H KI Rep1


title: IRF37PR8CD103-4_S18

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

country: Australia

institute: University of Melbourne

description:
Batch 4 - 151106_SN7001291_0311_BHYLF2ADXX
counts.tsv

data_processing:
RNA-seq reads were aligned to the mouse genome mm10 using STAR (Dobin et al., 2013). Aligned fragments were summarised by gene (mm10 annotation from Ensembl) using featureCounts (Liao et al., 2014), ignoring those where both reads of the pair had mapping quality scores <10. Raw counts were transformed to log Counts Per Million (CPM) for visualisation. Normalisation and differential expression testing was conducted using edgeR (Robinson et al., 2010). The HTSFilter package (Rau et al., 2013) was used to remove genes with consistent low expression following normalisation and testing as suggested by the HTSFilter documentation.
For the IAV genome, RNAseq reads were aligned to a synthetic genome containing the 8 gene segments of the PR8 virus retrieved from NCBI using Tophat (Trapnell et al., 2009). Aligned reads were assigned to the appropriate viral segments using feature Counts function from Bioconductor Rsubread package (Liao et al., 2013). Differential expression analysis was performed on normalised counts in every viral segment by the total (virus and mouse) number of reads in each sample with limma package (Ritchie et al., 2015), treating every viral segment as a gene.
Genome_build: mouse genome mm10

source_name: IRF3/7-/- lung lobes, PR8 Influenza virus, 9h post intranasal

extract_protocol:
Lung lobes were processed as described in Ma et al. ~3000 cells were collected for each sample. Total RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen).
First strand cDNA synthesis and tailing by reverse transcription was performed using Clontech’s proprietary SMART (Switching Mechanism at 5’ End of RNA Template) technology. Following first strand synthesis, cDNA was amplified 13 cycles by LD PCR using blocked PCR primers. Amplified cDNA was purified using AMPure XP prior to QC using the Bioanalyser 2100 HS DNA kit (Agilent Technologies). Library preparation of purified amplified cDNA was performed following Nextera XT library preparation (Illumina). Following QC, 150pg of cDNA was tagmented (simultaneously fragmented with adaptors inserted) using Nextera transposon. Molecular barcodes were incorporated during 12 cycles of amplification followed by purification using AMPure XP. The libraries passed a quality checkpoint (Qubit and Bioanalyser HS DNA) prior to normalisation and pooling before loading onto a HiSeq 2500 (Illumina) sequencer for paired-end sequencing. The libraries were each sequenced to 10-20 million reads.
RNA-seq and library construction were performed as 4 independent batches.

value: LUNG LOBES

tag: mouse strain

tag: infection

value: PR8, 9h post infection (intranasal)


title: MZ27_d1_1KPa

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 1kPa in the presence of 8uM CHIR (Wnt agonist) during 24 hours


title: MZ27_d0_60KPa


title: WT Rep10

value: WT


title: Striatum [WT_STR_3]

tag: tissue

value: striatum

value: wildtype

tag: environment

value: stress


title: IRF37PR8CD103-3_S18

description:
Batch 3 - 151102_SN7001291_0303_BH5N3GADXX
counts.tsv


title: MZ27_d0_1KPa

tag: developmental stage

tag: treatment

value: human embryonic stem cell line ES[4] cultured in PA hydrogels of 1kPa in the presence of commercial media sustaining undifferentatited conditions (E8 media) during 24 hours


title: WT Rep9

tag: age


title: WT Rep8


title: P2_d8

data_processing:
Raw reads were trimmed using skewer (0.2.2) to remove adapters
Trimmed reads were mapped to the reference genome using STAR (v2.5.3a) with default parameters
Read counts were obtained by using the STAR's parameter " --quantMode GeneCounts"
Read counts on the reverse strand were fed to R and analyzed using DESEQ2
regularized transformed log counts were calculated using the function rlog from the DESEQ2 package
Genome_build: Gencode v26 corresponding to GRCh38
Supplementary_files_format_and_content: CSV file containing regularized log transformed fragment counts

extract_protocol:
Cells were collected by scraping and RNA was harvested using Trizol reagent. TruSeq Stranded Total RNA LT (with Ribo-Zero Human/Mouse/Rat)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hPSCs grown on vitronectin were washed twice with PBS (Life Technologies #1001-015) and dissociated into small clusters with EDTA (Sigma #E9884). Cells were then seeded onto vitronectin pre-coated culture dishes at a density of 50.000-150.000 cells per cm2 in Essential 8 Medium. After overnight culture, the differentiation was initiated (day -4) by treatment with 8µM CHIR99021 (Sigma #SML1046-5MG) in basic differentiation medium [Advanced RPMI 1640(Life technologies #12633-012) + 1 × 1-GlutaMAX (Life Technologies #35050-038) + Penicillin/Streptomycin (Life Technologies #15140122)] for 3 days. On day -1, CHIR99021 was removed by washing once with PBS and cells were exposed to 200 ng ml-1 FGF9 (PeproTech House#100-23B), 1 µ ml -1 Heparin (Sigma#H3149-10KU) and 10 ng ml-1 Activin A (Vitro S.A #338-AC-050) in basic differentiation media for 24h. On day 0, cells were mechanically dissociated into single cells and resuspended in basic differentiation medium supplemented with 3μM CHIR99021, 200 ng ml-1 FGF9 and 1µg ml-1 Heparin. Cells were then placed in 96-well, round bottom, ultra-low attachment plates at a density of 500.000 cells per well. Cells were spun down at x300g for 2 min form a pellet and then cultured at 37ºC, 5% CO2 for 2 days additional days without media change. On day 2, the pellets were transferred onto a Transwell 0.4µm pore polyester membrane (Sigma#3460) and treated with basic differentiation media supplemented with 3μM CHIR99021, 200 ng ml-1 FGF9 and 1µg ml-1 Heparin. On day 3, CHIR99021 was removed and the organoids were switched to basic differentiation media supplemented with 200 ng ml-1 FGF9 and 1µg ml-1 Heparin for another 4 days. From that point, organoids were cultured in basic differentiation medium and maintained without additional growth factors. The medium was changed every 2 or 3 days.

value: Differentiating Cells

value: ES4 cells at day 12 of differentiation

value: Human Pluripotent Stem Cells in the presence of FGF9 for 3 days (day 8 in the protocol)


title: P2_d16

value: ES4 cells at day 20 of differentiation

value: Human Pluripotent Stem Cells in the absence of growth factors and in the presence of RPMI advanced media


title: WT Rep7


title: IRF37PR8CC-4_S20


title: IRF37PR8CC-3_S20


title: WT Rep6


title: P2_d5

value: ES4 cells at day 9 of differentiation

value: Human Pluripotent Stem Cells in the presence of Wnt agonist (CHIR) and FGF9 for 3 days (day 3 in the protocol) and in the presence of only FGF9 for two more consecutive days (day 5 in the protocol)


title: P2_d0

value: ES4 cells at day 4 of differentiation

value: Human Pluripotent Stem Cells in the presence of Wnt agonist (CHIR) for 3 days (day -4 in the protocol) and 1 additional day (day -1 in the protocol) in the presence of FGF9 and Activin A


title: Trem2 KO Rep5

value: 4-5 months

value: TREM2 5bp KO


title: IRF37PR8CC-2_S20

description:
Batch 2 - 150928_SN7001291_0299_AHYLW2ADXX
counts.tsv

value: LUNG LOBES

value: PR8, 9h post infection (intranasal)


title: Trem2 KO Rep3


title: IRF37PR8CC_S20

description:
Batch 1 - 150922_SN7001291_0298_AHVL7LADXX
counts.tsv


title: IRF37PR8CD103-2_S18


title: Trem2 KO Rep4


title: P2_d-4

value: Human Pluripotent Stem Cells

value: Human Pluripotent Stem Cells in the presence of commercial media (E8) supporting undifferentiated conditions of growth and expansion


title: Trem2 KO Rep2


title: Trem2 KO Rep1


title: IRF37PR8AM-4_S17


title: P1_d8


title: P1_d16


title: WT Rep5

value: WT


title: P1_d5


title: IRF37PR8AM-3_S17


title: IRF37PR8AM-2_S17


title: P1_d0


title: WT Rep4


title: IRF37PR8AM_S17


title: IRF37PR8AECII-4_S19


title: IRF37PR8CD103_S18


title: WT Rep3


title: ESC_Yap1Flagbio_Lifminus_rep2

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Chromatin IP against Yap1

data_processing:
Illumina CASAVA software was used for base calling.
Sequenced reads were mapped to mouse mm9 genome using Bowtie2.
Peaks were called using MACS2 peak caller (nomodel, nolambda).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: embryonic stem cells

growth_protocol: Mouse J1 ES cells were grown in 0.1% gelatin-coated cell culture dishes in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 18% fetal bovine serum (FBS), MEM non-essential amino acids at the manufacturer's recommended concentration, EmbryoMax nucleosides at the manufacturer's recommended concentration, 0.1 mM ß-mercaptoethanol, 1000U/ml recombinant mouse leukemia inhibitory factor (LIF) and 50 U/ml of penicillin/streptomycin/L-glutamine.

extract_protocol:
After reaching ~80% confluency, ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution (neutralized with 125 mM glycine) J1 mouse ES cells. After sonication and extensive washing, immunoprecipitated DNA was sequenced using Illumina sequencers.
After pulldown, DNA was used to generate sequencing libraries using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (#E7645S) according to the manufacturer’s instructions.

treatment_protocol: When differentiation was indicated, cells were grown in medium without LIF for 3 days and passaged once (on day 1).

value: J1 embryonic stem (ES) cells

tag: expressing

tag: culture condition

value: Lifminus

tag: pulldown reagent

value: streptavidin-conjugated beads


title: WT Rep1


title: ESC_Yap1Flagbio_Lifminus_rep1

description: Chromatin IP against Yap1


title: WT Rep2


title: IRF37PR8AECII_S19


title: ESC_Yap1Flagbio_Lifplus

description: Chromatin IP against Yap1

value: Lifplus


title: IRF37PR8AECII-2_S19


title: ESC_BirA_Lifminus

description: Chromatin IP against Yap1

value: BirA


title: IRF37mockCD103-4_S22

source_name: IRF3/7-/- lung lobes, Allantoic fluid (Mock), 9h post intranasal


title: ESC_BirA_Lifplus

description: Chromatin IP against Yap1


title: C098_moderate chronic liver injury for 8 weeks plus severe injury for 4 weeks

city: Shanghai

first: Pu

last: You

address: 800 Xiangyin Road

institute: Second Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text file with FPKM values

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fah-/- mice were maintained on continuous NTBC in their drinking water (7.5mg/L). In severe acute liver injury (SALI), NTBC was totally withdrawn. In order to keep Fah-/- mice survive under prolonged, SALI treatments were divided into several stages. For each stage intervals between two SALI treatments, the Fah-/-mice were taken back to standard administration of NTBC for three days. Using this method let the total time-length of collective treatments of SALI equal to total time-length of CLI treatments. Mice exposed to a reduced treatment regimen of NTBC (2.5%) in the moderate chronic liver injury (MCLI) group. In the induced senescence group (MCLI8 + SALI4), Fah-/- mice were given 2.5% curative dosage NTBC for 8 weeks, and then NTBC was removed for 4 weeks.

tag: strain background

tag: genotype/variation

value: Fah-/-

value: chronic injury 8 weeks plus severe injury 4 weeks

tag: tissue type

value: liver


title: IRF37mockCD103-3_S22

value: Allantoic fluid (Mock), 9h post intranasal


title: C097_moderate chronic liver injury for 8 weeks plus severe injury for 4 weeks


title: FT8_3a_moderate chronic liver injury for 8 weeks

value: chronic injury 8 weeks


title: C096_moderate chronic liver injury for 8 weeks plus severe injury for 4 weeks


title: FT8_2a_moderate chronic liver injury for 8 weeks


title: IRF37mockCD103-2_S22


title: IRF37mockCC-4_S24


title: P1_d-4


title: FT8_1a_moderate chronic liver injury for 8 weeks


title: IRF37mockCD103_S22


title: Abf1-AA_rapamycin_90min

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor was clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert  quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Genome_build: R64
Supplementary_files_format_and_content: Bigwig files providing coverage for all samples. All values are normalized to 10,000,000 reads.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae culture

growth_protocol: For all datasets, 2L of yeast cells expressing Rpb1-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) . For Abf1 nuclear depletion , rapamycin was added to a final concentration of 1µg/ml for the times indicated . For Rap1 depletion IAA (Indole-3’-Acetic Acid, Sigma) was added to a final concentration of 100µM  for the times indicated.

extract_protocol:
See the original publication for details
Library construction is described in Candelli et al., EMBO J, 2018 and in the associated manuscript. Barcodes used for demultiplexing are as follows: NNNNNNTGCAGC   Rap1_no_ auxin;  NNNNNNGAGAGC Rap1_auxin_10min; NNNNNNCTAAGC    Rap1_auxin_20min; NNNNNNGTCAGC Abf1_no_rapa; NNNNNNACTAGC Abf1_rapa_30min; NNNNNNCGTAGC Abf1_rapa_90min

treatment_protocol: Cells were crosslinked for 50 seconds using a W5 UV crosslinking unit (UVO3). Cells were broken and extracts were prepared as described in the original publication.

value: rapamycin

tag: time point


title: FT12_3e_moderate chronic liver injury for 12 weeks

value: chronic injury 12 weeks

value: tumor


title: IRF37PR8AECII-3_S19

value: LUNG LOBES

value: PR8, 9h post infection (intranasal)


title: Rap1-AID_auxin_20min

value: auxin


title: Abf1-AA_rapamycin_30min


title: IRF37mockCC-2_S24


title: Abf1-AA_no_rapamycin

value: no treatment


title: IRF37mockCC_S24


title: FT12_2e_moderate chronic liver injury for 12 weeks


title: Rap1-AID_no_auxin


title: IRF37mockAM-4_S21


title: IRF37mockAM_S21


title: IRF37mockAM-2_S21


title: LL01181_iP66_S452_L006

city: San Francisco

first: Robert

middle: L

last: Raffai

address: 4150 Clement Street

institute: University of California, San Francisco

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of TGGAATTCTCGGGTGCCAAGG. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

source_name: Plasma

extract_protocol:
RNA was isolated using miRNeasy.
NEBNext library prep kit was used.

value: Plasma

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: Chylomicron


title: LL01186_iP71_S457_L006

value: VLDL


title: LL01184_iP69_S455_L006

value: LDL


title: IRF37mockAECII-4_S23


title: LL01182_iP67_S453_L006

value: HDL


title: IRF37mockCC-3_S24


title: hThO late

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: Gene expression in hThO

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Cellranger (v2.1.0).
All libraries were merged by aggr function of Cellranger.
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format.

source_name: human thalamic organoid

growth_protocol: ESCs were cultured on Matrigel coated cell culture dish with mTeSR1 media. hThOs were cultured in each established condition.

extract_protocol: Chromium™ Single Cell 3’ Reagent Kits

tag: status

value: Thalamus

tag: time

value: late (day 89)


title: IRF37mockAECII-2_S23

tag: mouse strain

tag: infection

value: Allantoic fluid (Mock), 9h post intranasal


title: IRF37mockAECII_S23

tag: tissue


title: hThO early

description: Gene expression in hThO

value: early (day 34)


title: IRF37mockAECII-3_S23


title: IFNPR8CD103-3_S10

source_name: IFNAR2-/- lung lobes, PR8 Influenza virus, 9h post intranasal


title: Rap1-AID_auxin_10min


title: IFNPR8CD103-2_S10


title: IFNPR8CD103_S10


title: IFNPR8CC-3_S12


title: IRF37mockAM-3_S21


title: 35S:LBD16-GR_DEX+CHX_rep3

first: Hidehiro

last: Fukaki

address: Rokko-dai 1-1

institute: Kobe University

description: Gene expression data from 5-day-old LBD16-GR roots DEX+CHX treatment (4h)

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

organism: Arabidopsis thaliana

source_name: Arabidopsis 5-day-old root

label_protocol: Sense-strand DNA target preparation was performed in combination with Ambion WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix)

growth_protocol: Arabidopsis seedlings of 35S:LBD16:GR arf7 arf19 were grown for 5 days on 1x MS agar plate under continuous light condition.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: 5-day-old seedlins of 35S:LBD16:GR arf7 arf19 were treated with/without 2 µM DEX and 10 µM CHX for 4 hours

tag: genotype

value: 5-day-old root

value: 2 µM DEX and 10 µM CHX treatment for 4 hours


title: IFNPR8CC-4_S12


title: IFNPR8CC_S12


title: IFNPR8CC-2_S12


title: IFNPR8AM-3_S9


title: IFNPR8CD103-4_S10


title: IFNPR8AM-2_S9


title: IFNPR8AM_S9


title: 35S:LBD16-GR_CHX_rep3

description: Gene expression data from 5-day-old LBD16-GR roots CHX treatment (4h)

tag: treatment

value: 10 µM CHX treatment for 4 hours


title: IFNPR8AECII-4_S11

value: LUNG LOBES


title: IFNPR8AECII-3_S11

value: PR8, 9h post infection (intranasal)


title: 35S:LBD16-GR_CHX_rep2


title: IFNPR8AECII-2_S11


title: 35S:LBD16-GR_DEX+CHX_rep2


title: 35S:LBD16-GR_DEX_rep2

description: Gene expression data from 5-day-old LBD16-GR roots DEX treatment (4h)

value: 2 µM DEX treatment for 4 hours


title: IFNPR8AECII_S11


title: 35S:LBD16-GR_mock_rep2

description: Gene expression data from 5-day-old LBD16-GR roots mock treatment (4h)

value: Mock (0.1% DMSO) treatment for 4 hours


title: IFNPR8AM-4_S9


title: 35S:LBD16-GR_mock_rep3


title: 35S:LBD16-GR_DEX_rep3


title: 35S:LBD16-GR_DEX+CHX_rep1


title: IFNmockCD103-4_S14

source_name: IFNAR2-/- lung lobes, Allantoic fluid (Mock), 9h post intranasal


title: 35S:LBD16-GR_mock_rep1


title: TM-4 EtOH5 03072011

city: MADISON

first: Donna

last: Peters

state: WI- WISCONSIN

address: 1300 UNIVERSITY AVE

department: Pathology & Laboratory Medicine

institute: UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE

description:
biological rep2
EtOH-treated  HTM TM-4 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells

hyb_protocol: Following fragmentation, 2.5ug ss cDNA was hybridized for 16 hr at 45C on GeneChip Human Array St 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were read using the GeneChip G7 Scanner

data_processing: Raw data was anlyzed using the open source software Bioconductor 2.9 in R. RMA was used for normalization of data using the AFFY package

source_name: 6-day EtOH treatment

label_protocol: Biotinylated cDNA was prepared the GeneChip WT terminal labeling kit

growth_protocol: human trabecular meshwork cells were cultured in low glucose DMEM, 15% fetal bovine serum (FBS), 1ng/ml FGF-2, 1% amphoteracin B, and 0.05% gentamicin until they reached conlfuency

extract_protocol: Total RNA was extracted using the QIAshredder and RNAeasy Plus mini kits (Qiagen, Inc) according to manufacturer's instructions. cDNA synthesis from 300ng of total RNA was done using the GeneChip WT cDNA synthesis kit

treatment_protocol: Confluent cultures were treated with  500nM dexamethasone dissolved in 0.1% EtOH or 0.1% EtOH for 6 days. Media used was DMEM containing10% FBS, 1% amphoteracin and 0.05% gentamicin. FGF-2 was not present

value: trabecular meshwork cells

tag: isolate

tag: donor age


title: 35S:LBD16-GR_DEX_rep1