title: Donor1_PMA/Ionomycin_HT SS3_Plate2_322


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_317

status: Public on Jul 02 2024

type: SRA

city: Foster City

first: Ruidong

last: Li

state: CA

address: 324 Lakeside Drive

department: Research Data Sciences

country: USA

institute: Gilead Sciences, Inc.

description:
Seurat_Object_HT_SS3.rds
TraCeR_filtered_cell_data_HT_SS3.csv
TraCeR_filtered_recombinants_HT_SS3.txt

library_source: transcriptomic single cell

data_processing:
Demultiplexed FASTQ files for cells on each plate were first merged using the merge_demultiplexed_fastq.R script provided in the zUMIs tool (v2.9.7). Then, the zUMIs.sh script was used to execute a series of steps - filtering, mapping, counting, and summarizing - to generate the gene expression count matrices and summary statistics.
The source code in the runfeatureCountFun.R script within zUMIs was modified to exclude multi-mappers (countMultiMappingReads=FALSE) and fragments that were not successfully mapped to both ends (requireBothEndsMapped=TRUE) from quantification. The read count matrix for both exonic and intronic mapping was used for downstream analysis.
To ensure consistency for benchmarking, the same genome reference sequence (genome.fa) and gene annotation information (genes.gtf) provided in cellranger reference index refdata-gex-GRCh38-2020-A was used for Smart-seq3 data analysis
Seurat (v5.0.0) was used for quality control and downstream analysis of gene expression data
To reconstruct TCR sequences from HT Smart-seq3 RNA sequencing data, we utilized the Docker image of the TraCeR tool (v0.6.0) in Docker Hub. The assemble module within TraCeR was first used to reconstruct TCR sequences for each individual cell, and the summarise module was subsequently used to generate the summary statistics and detailed information for all cells
Assembly: GRCh38
Supplementary files format and content: RDS file includes Seurat object for all cells
Supplementary files format and content: CSV file includes cell data output from TraCeR summarise analysis for all cells
Supplementary files format and content: tab-delimited TXT file includes recombinants output from TraCeR summarise analysis for all cells

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMCs from healthy donors were isolated by SepMateTM tubes (STEMCELL Technologies, Catalog#85450), following manufacturer’s instruction, and resuspended in RPMI 1640 medium (Gibco, Catalog#11875093) containing 5% human serum (Sigma, Catalog# H3667-100ML) and 1% penicillin-streptomycin and cultured in 6-well plates (3 mL/well). After overnight culture, the PBMC was resuspended and cultured at 5 × 106 cells/ml in 48-well plate and treated immediately with DMSO or phorbol-12-myristate-13-acetate (PMA) plus ionomycin (PMA/Ionomycin) cocktail (Cell stimulation cocktail, eBioscience, Catalog#00-4970) for 3 h. Then, PBMC was stained with APC mouse anti-human CD4 (SK3, BD Biosciences, Catalog#340443) and Alexa Fluor 488 mouse anti-human CD3 (UCHT1, BioLegend, Catalog#300454) before sorting. The dead cells were gated out after staining with viability dye eFluor 780 (Invitrogen, Catalog#65-0865-14). The live and single CD4+ T-cells were sorted into 96-well plates containing lysis buffer using SH800S cell sorter (Sony Biotechnology Inc, San Jose, CA) with a 100-μm nozzle.
The Smart-seq3 library preparations were performed as previously described [Hagemann-Jensen et al., Nat Biotechnol, 2020, 38:708-714] with some modifications. In addition, we developed and optimized an automated sample handling process for most steps of the Smart-seq3 protocol, including single-cell lysis, reverse transcription, and library construction by using Integra Biosciences VIAFLO 96 electronic pipetting system and Mantis liquid handler (Formulatrix, Bedford, MA, USA).

tag: tissue

value: PBMC

tag: cell type

value: CD4+ T cells

tag: donor id

value: Donor 1

tag: plate

value: Plate 2

tag: disease

value: Healthy

tag: treatment

value: PMA/Ionomycin


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_315


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_321


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_318


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_310


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_309


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_314


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_313


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_308


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_330


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_300


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_305


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_298


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_323


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_290


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_191


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_294


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_306


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_297


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_307


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_292


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_293


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_303


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_289


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_302


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_301


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_299


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_190


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_187


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_189


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_183


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_316


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_311


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_188


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_185


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_186


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_291


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_180


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_179


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_181


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_175


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_176


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_177


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_182


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_174


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_168


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_172


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_173


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_166


title: Post12_Water_R3

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

library_source: transcriptomic

data_processing:
The sequenced reads (ranging from 21.5 to 60 million read pairs per sample) were mapped on the reference transcriptional units from GDDH13 v1.1 using Salmon software (Patro et al., 2017)
Assembly: MJAX00000000.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample

molecule: total RNA

organism: Malus domestica

source_name: Young leaf

growth_protocol: Plants were grown under greenhouse conditions (natural photoperiod supplemented with artificial light if needed, 18 °C night and 20–23 °C day), in sub-irrigation devices allowing a fine monitoring of N fertilisation with contrasted nitrate concentrations (high 7 mM N or low 0.5 mM solutions) over the growing period.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plant (Macherey-Nagel GmbH & Co., Düren, Germany) according to the manufacturer's procedure.
Libraries were generated using the Illumina mRNA Stranded protocol

treatment_protocol: Plants with different N status were obtained after transfer from high N to low N solution for 12 days (N limited), and transferred back on high N (N-resupplied). Reference plants (HN) stayed on high N solution. Plants were ASM treated with 0.4g.L Bion®(50%-ASM, Syngenta) sprayed to run-off after 10 days of N limitation or 24h of N-resupply. Controlled plants were sprayed with demineralized water.

value: Young leaf

tag: genotype

value: Gala progeny

value: Water

tag: nitrogen diet

tag: nitrogen status

value: N-resupplied


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_165


title: Post12_Water_R1


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_169


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_171


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_164


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_163


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_161


title: Post12_Water_R2


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_162


title: Post12_ASM_R1

value: ASM


title: Post12_ASM_R2


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_170


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_159


title: Ante12_ASM_R2

value: N-limitted


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_178


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_158


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_160


title: Ante12_ASM_R1


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_157


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_184


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_167


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_155


title: Ante12_Water_R2


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_156


title: Ante12_Water_R1


title: Ante12_Water_R3


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_154


title: HN_ASM_R3

value: HN

value: High N


title: HN_ASM_R1


title: HN_Water_R3


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_150


title: HN_Water_R2


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_149


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_148


title: Post12_ASM_R3


title: HN_Water_R1


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1344

value: Donor 2

value: Plate 4


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_146


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_147


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1343


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_145


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1342


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1338


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_153


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_139


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_143


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_141


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_151


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_140


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_142


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_152


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1339


title: Ante12_ASM_R3


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1336


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_138


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1335


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1333


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_135


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_134


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1341


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1332


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_133


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_132


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1330


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_131


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1327


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_127


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_129


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1325


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1328


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_130


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1324


title: HN_ASM_R2


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_124


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1326


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_137


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1322


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1340


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_123


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1323


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1334


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1321


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_121


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1320


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_119


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1319


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1329


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1331


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1318


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_126


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_117


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_118


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_116


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1317


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_115


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1316


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_113


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_114


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1315


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1314


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1311


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1313


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_122


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_110


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_111


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_108


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_109


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1309


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1307


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_105


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1308


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_107


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1304


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_103


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1303


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1306


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1305


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_102


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1299


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_97


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1310


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_100


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_99


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1302


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_106


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1297


title: Donor1_DMSO_HT SS3_Plate2_382

value: DMSO


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1296

value: PBMC


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1298

value: CD4+ T cells


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_98

value: Donor 1


title: Donor1_DMSO_HT SS3_Plate2_384

value: Plate 2


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1293

value: Healthy


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1294

value: PMA/Ionomycin


title: Donor1_DMSO_HT SS3_Plate2_383


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1301


title: Donor1_DMSO_HT SS3_Plate2_381


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1291


title: Donor1_DMSO_HT SS3_Plate2_377


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1290


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1337


title: Donor1_DMSO_HT SS3_Plate2_375


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1295


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1292


title: Donor1_DMSO_HT SS3_Plate2_379


title: Donor1_DMSO_HT SS3_Plate2_380


title: Donor1_DMSO_HT SS3_Plate2_378


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1300


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1288


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_101


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1312


title: Donor1_DMSO_HT SS3_Plate2_373


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1287


title: Donor1_DMSO_HT SS3_Plate2_371


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1286


title: Donor1_DMSO_HT SS3_Plate2_374


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1285


title: Donor1_DMSO_HT SS3_Plate2_370


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1289


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1284


title: Donor1_DMSO_HT SS3_Plate2_367


title: Donor1_DMSO_HT SS3_Plate2_369


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1283


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1280


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1279


title: Donor1_DMSO_HT SS3_Plate2_372


title: Donor1_DMSO_HT SS3_Plate2_368


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1278


title: Donor1_DMSO_HT SS3_Plate2_376


title: Donor1_DMSO_HT SS3_Plate2_363


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1281


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1275


title: Donor1_DMSO_HT SS3_Plate2_361


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1274


title: Donor1_DMSO_HT SS3_Plate2_359


title: Donor1_DMSO_HT SS3_Plate2_365


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1271


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1272


title: Donor1_DMSO_HT SS3_Plate2_362


title: Donor1_DMSO_HT SS3_Plate2_364


title: Donor1_DMSO_HT SS3_Plate2_360


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1273


title: Donor1_DMSO_HT SS3_Plate2_357


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1276


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1277


title: Donor1_DMSO_HT SS3_Plate2_358


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1282


title: Donor1_DMSO_HT SS3_Plate2_356


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1270


title: Donor1_DMSO_HT SS3_Plate2_366


title: Donor1_DMSO_HT SS3_Plate2_355


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1269


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1267


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1268


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1266


title: Donor1_DMSO_HT SS3_Plate2_353


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1265


title: Donor1_DMSO_HT SS3_Plate2_350


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1264


title: Donor1_DMSO_HT SS3_Plate2_351


title: Donor1_DMSO_HT SS3_Plate2_348


title: Donor1_DMSO_HT SS3_Plate2_349


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1262


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1261


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1260


title: Donor1_DMSO_HT SS3_Plate2_347


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1259


title: Donor1_DMSO_HT SS3_Plate2_345


title: Donor1_DMSO_HT SS3_Plate2_346


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1258


title: Donor1_DMSO_HT SS3_Plate2_342


title: Donor1_DMSO_HT SS3_Plate2_354


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1257


title: Donor1_DMSO_HT SS3_Plate2_352


title: Donor1_DMSO_HT SS3_Plate2_341


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1256


title: Donor1_DMSO_HT SS3_Plate2_338


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1255


title: Donor1_DMSO_HT SS3_Plate2_337


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1254


title: Donor1_DMSO_HT SS3_Plate2_340


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1253


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1263


title: Donor1_DMSO_HT SS3_Plate2_334


title: Donor1_DMSO_HT SS3_Plate2_333


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1251


title: Donor1_DMSO_HT SS3_Plate2_335


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1252


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1250


title: Donor1_DMSO_HT SS3_Plate2_332


title: Donor1_DMSO_HT SS3_Plate2_331


title: Donor1_DMSO_HT SS3_Plate2_344


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1247


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1248


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1245


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1246


title: Donor1_DMSO_HT SS3_Plate2_327


title: Donor1_DMSO_HT SS3_Plate2_329


title: Donor1_DMSO_HT SS3_Plate2_330


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1244


title: Donor1_DMSO_HT SS3_Plate2_325


title: Donor1_DMSO_HT SS3_Plate2_322


title: Donor1_DMSO_HT SS3_Plate2_321


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1241


title: Donor1_DMSO_HT SS3_Plate2_323


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1243


title: Donor1_DMSO_HT SS3_Plate2_318


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1237


title: Donor1_DMSO_HT SS3_Plate2_319


title: Donor1_DMSO_HT SS3_Plate2_316


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1240


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1239


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1238


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1236


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title: Donor1_DMSO_HT SS3_Plate2_317


title: Donor1_DMSO_HT SS3_Plate2_313


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1232


title: Donor1_DMSO_HT SS3_Plate2_315


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1234


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1233


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1235


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1230


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1242


title: Donor1_DMSO_HT SS3_Plate2_311


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1229


title: Donor1_DMSO_HT SS3_Plate2_308


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1228


title: Donor1_DMSO_HT SS3_Plate2_307


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1227


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1226


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1225


title: Donor1_DMSO_HT SS3_Plate2_305


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1224


title: Donor1_DMSO_HT SS3_Plate2_303


title: Donor1_DMSO_HT SS3_Plate2_302


title: Donor1_DMSO_HT SS3_Plate2_301


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1223


title: Donor1_DMSO_HT SS3_Plate2_300


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1222


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1221


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1220


title: Donor1_DMSO_HT SS3_Plate2_299


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1231


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title: Donor1_DMSO_HT SS3_Plate2_310


title: Donor1_DMSO_HT SS3_Plate2_298


title: Donor1_DMSO_HT SS3_Plate2_297


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1218


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1219


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1217


title: Donor1_DMSO_HT SS3_Plate2_294


title: Donor1_DMSO_HT SS3_Plate2_295


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1215


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1214


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title: Donor1_DMSO_HT SS3_Plate2_291


title: Donor1_DMSO_HT SS3_Plate2_289


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title: Donor1_DMSO_HT SS3_Plate2_293


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1207


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1203


title: Donor1_DMSO_HT SS3_Plate2_190


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1206


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title: Donor1_DMSO_HT SS3_Plate2_186


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1204


title: Donor1_DMSO_HT SS3_Plate2_184


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1202


title: Donor1_DMSO_HT SS3_Plate2_182


title: Donor1_DMSO_HT SS3_Plate2_183


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1199


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1201


title: Donor1_DMSO_HT SS3_Plate2_180


title: Donor1_DMSO_HT SS3_Plate2_181


title: Donor1_DMSO_HT SS3_Plate2_179


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1200


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1197


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1198


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1196


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title: Donor1_DMSO_HT SS3_Plate2_172


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1195


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1190


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1189


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1191


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1188


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1192


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1193


title: Donor1_DMSO_HT SS3_Plate2_175


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1194


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1187


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title: Donor1_DMSO_HT SS3_Plate2_164


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1179


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1175


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1181


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1177


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title: Donor1_DMSO_HT SS3_Plate2_155


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title: Donor1_DMSO_HT SS3_Plate2_152


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title: Donor1_DMSO_HT SS3_Plate2_149


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1167


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1157


title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1156


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1153


title: Donor1_DMSO_HT SS3_Plate2_158


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title: Donor1_DMSO_HT SS3_Plate2_122


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title: Donor2_DMSO_HT SS3_Plate4_1337


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title: Donor2_PMA/Ionomycin_HT SS3_Plate4_1155


title: Donor2_DMSO_HT SS3_Plate4_1335


title: Donor1_DMSO_HT SS3_Plate2_127


title: Donor1_DMSO_HT SS3_Plate2_117


title: Donor1_DMSO_HT SS3_Plate2_115


title: Donor2_DMSO_HT SS3_Plate4_1333


title: Donor2_DMSO_HT SS3_Plate4_1334


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title: Donor2_DMSO_HT SS3_Plate4_1330


title: Donor2_DMSO_HT SS3_Plate4_1331


title: Donor2_DMSO_HT SS3_Plate4_1329


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title: Donor1_DMSO_HT SS3_Plate2_109


title: Donor2_DMSO_HT SS3_Plate4_1328


title: Donor2_DMSO_HT SS3_Plate4_1327


title: Donor2_DMSO_HT SS3_Plate4_1326


title: Donor1_DMSO_HT SS3_Plate2_103


title: Donor2_DMSO_HT SS3_Plate4_1323


title: Donor2_DMSO_HT SS3_Plate4_1322


title: Donor2_DMSO_HT SS3_Plate4_1324


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title: Donor1_DMSO_HT SS3_Plate2_101


title: Donor2_DMSO_HT SS3_Plate4_1321


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title: Donor2_DMSO_HT SS3_Plate4_1319


title: Donor1_DMSO_HT SS3_Plate2_99


title: Donor2_DMSO_HT SS3_Plate4_1320


title: Donor2_DMSO_HT SS3_Plate4_1317


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_288

value: Plate 1


title: Donor2_DMSO_HT SS3_Plate4_1316


title: Donor2_DMSO_HT SS3_Plate4_1315


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_286


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_285


title: Donor2_DMSO_HT SS3_Plate4_1314


title: Donor2_DMSO_HT SS3_Plate4_1313


title: Donor2_DMSO_HT SS3_Plate4_1325


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title: Donor2_DMSO_HT SS3_Plate4_1312


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_284


title: Donor2_DMSO_HT SS3_Plate4_1311


title: Donor2_DMSO_HT SS3_Plate4_1310


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title: Donor2_DMSO_HT SS3_Plate4_1304


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_277


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title: Donor2_DMSO_HT SS3_Plate4_1305


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_271


title: Donor2_DMSO_HT SS3_Plate4_1300


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_272


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_280


title: Donor2_DMSO_HT SS3_Plate4_1297


title: Donor2_DMSO_HT SS3_Plate4_1295


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_268


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_267


title: Donor2_DMSO_HT SS3_Plate4_1294


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_266


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title: Donor2_DMSO_HT SS3_Plate4_1293


title: Donor2_DMSO_HT SS3_Plate4_1291


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_264


title: Donor2_DMSO_HT SS3_Plate4_1302


title: Donor2_DMSO_HT SS3_Plate4_1301


title: Donor2_DMSO_HT SS3_Plate4_1292


title: Donor2_DMSO_HT SS3_Plate4_1290


title: Donor2_DMSO_HT SS3_Plate4_1287


title: Donor2_DMSO_HT SS3_Plate4_1288


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_263


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_260


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_257


title: Donor2_DMSO_HT SS3_Plate4_1284


title: Donor2_DMSO_HT SS3_Plate4_1283


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title: Donor2_DMSO_HT SS3_Plate4_1282


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_255


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_250


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title: Donor2_DMSO_HT SS3_Plate4_1271


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_234


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title: Donor2_DMSO_HT SS3_Plate4_1267


title: Donor2_DMSO_HT SS3_Plate4_1253


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_229


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_227


title: Donor2_DMSO_HT SS3_Plate4_1251


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_226


title: Donor2_DMSO_HT SS3_Plate4_1252


title: Donor2_DMSO_HT SS3_Plate4_1250


title: Donor2_DMSO_HT SS3_Plate4_1260


title: Donor2_DMSO_HT SS3_Plate4_1248


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title: Donor1_PMA/Ionomycin_HT SS3_Plate1_223


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_222


title: Donor2_DMSO_HT SS3_Plate4_1247


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_221


title: Donor2_DMSO_HT SS3_Plate4_1246


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_220


title: Donor2_DMSO_HT SS3_Plate4_1245


title: Donor2_DMSO_HT SS3_Plate4_1256


title: Donor2_DMSO_HT SS3_Plate4_1243


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_219


title: Donor2_DMSO_HT SS3_Plate4_1244


title: Donor1_PMA/Ionomycin_HT SS3_Plate2_125


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_218


title: Donor2_DMSO_HT SS3_Plate4_1254


title: Donor2_DMSO_HT SS3_Plate4_1242


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_217


title: Donor2_DMSO_HT SS3_Plate4_1241


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_215


title: Donor2_DMSO_HT SS3_Plate4_1240


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_214


title: Donor2_DMSO_HT SS3_Plate4_1238


title: Donor2_DMSO_HT SS3_Plate4_1239


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_212


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_211


title: Donor2_DMSO_HT SS3_Plate4_1236


title: Donor2_DMSO_HT SS3_Plate4_1235


title: Donor2_DMSO_HT SS3_Plate4_1234


title: Donor2_DMSO_HT SS3_Plate4_1237


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_207


title: Donor2_DMSO_HT SS3_Plate4_1233


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_210


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_205


title: Donor2_DMSO_HT SS3_Plate4_1232


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_209


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_206


title: Donor2_DMSO_HT SS3_Plate4_1231


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_204


title: Donor2_DMSO_HT SS3_Plate4_1230


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_213


title: Donor2_DMSO_HT SS3_Plate4_1229


title: Donor2_DMSO_HT SS3_Plate4_1228


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_202


title: Donor2_DMSO_HT SS3_Plate4_1227


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_199


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_198


title: Donor2_DMSO_HT SS3_Plate4_1226


title: Donor2_DMSO_HT SS3_Plate4_1225


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_196


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_197


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_195


title: Donor2_DMSO_HT SS3_Plate4_1223


title: Donor2_DMSO_HT SS3_Plate4_1224


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_194


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_96


title: Donor2_DMSO_HT SS3_Plate4_1222


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_93


title: Donor2_DMSO_HT SS3_Plate4_1221


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_92


title: Donor2_DMSO_HT SS3_Plate4_1218


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_203


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_95


title: Donor2_DMSO_HT SS3_Plate4_1220


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_94


title: Donor2_DMSO_HT SS3_Plate4_1219


title: Donor2_DMSO_HT SS3_Plate4_1215


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_90


title: Donor2_DMSO_HT SS3_Plate4_1216


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_87


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_89


title: Donor2_DMSO_HT SS3_Plate4_1212


title: Donor2_DMSO_HT SS3_Plate4_1214


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_88


title: Donor2_DMSO_HT SS3_Plate4_1213


title: Donor2_DMSO_HT SS3_Plate4_1211


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_85


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_193


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_86


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_84


title: Donor2_DMSO_HT SS3_Plate4_1208


title: Donor2_DMSO_HT SS3_Plate4_1209


title: Donor2_DMSO_HT SS3_Plate4_1217


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_83


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_91


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_80


title: Donor2_DMSO_HT SS3_Plate4_1205


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_82


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_81


title: Donor2_DMSO_HT SS3_Plate4_1203


title: Donor2_DMSO_HT SS3_Plate4_1204


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_79


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_78


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_77


title: Donor2_DMSO_HT SS3_Plate4_1202


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_76


title: Donor2_DMSO_HT SS3_Plate4_1200


title: Donor2_DMSO_HT SS3_Plate4_1210


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_75


title: Donor2_DMSO_HT SS3_Plate4_1201


title: Donor2_DMSO_HT SS3_Plate4_1199


title: Donor2_DMSO_HT SS3_Plate4_1198


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_73


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_74


title: Donor2_DMSO_HT SS3_Plate4_1207


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_72


title: Donor2_DMSO_HT SS3_Plate4_1195


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_70


title: Donor2_DMSO_HT SS3_Plate4_1196


title: Donor2_DMSO_HT SS3_Plate4_1197


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_71


title: Donor2_DMSO_HT SS3_Plate4_1194


title: Donor2_DMSO_HT SS3_Plate4_1206


title: Donor2_DMSO_HT SS3_Plate4_1193


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_68


title: Donor2_DMSO_HT SS3_Plate4_1192


title: Donor2_DMSO_HT SS3_Plate4_1191


title: Donor2_DMSO_HT SS3_Plate4_1190


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_67


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_65


title: Donor2_DMSO_HT SS3_Plate4_1189


title: Donor2_DMSO_HT SS3_Plate4_1188


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_63


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_62


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_64


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_61


title: Donor2_DMSO_HT SS3_Plate4_1187


title: Donor2_DMSO_HT SS3_Plate4_1186


title: Donor2_DMSO_HT SS3_Plate4_1184


title: Donor2_DMSO_HT SS3_Plate4_1185


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_59


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_60


title: Donor2_DMSO_HT SS3_Plate4_1183


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_69


title: Donor2_DMSO_HT SS3_Plate4_1181


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_58


title: Donor2_DMSO_HT SS3_Plate4_1180


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_55


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_66


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_57


title: Donor2_DMSO_HT SS3_Plate4_1179


title: Donor2_DMSO_HT SS3_Plate4_1178


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_54


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_51


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_53


title: Donor2_DMSO_HT SS3_Plate4_1175


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_50


title: Donor2_DMSO_HT SS3_Plate4_1174


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_49


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_47


title: Donor2_DMSO_HT SS3_Plate4_1173


title: Donor2_DMSO_HT SS3_Plate4_1170


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_44


title: Donor2_DMSO_HT SS3_Plate4_1169


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_56


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_46


title: Donor2_DMSO_HT SS3_Plate4_1171


title: Donor2_DMSO_HT SS3_Plate4_1182


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_42


title: Donor2_DMSO_HT SS3_Plate4_1167


title: Donor2_DMSO_HT SS3_Plate4_1168


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_45


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_43


title: Donor2_DMSO_HT SS3_Plate4_1172


title: Donor2_DMSO_HT SS3_Plate4_1165


title: Donor2_DMSO_HT SS3_Plate4_1166


title: Donor2_DMSO_HT SS3_Plate4_1164


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_41


title: Donor2_DMSO_HT SS3_Plate4_1176


title: Donor2_DMSO_HT SS3_Plate4_1177


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_52


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_38


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_37


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_39


title: Donor2_DMSO_HT SS3_Plate4_1162


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_36


title: Donor2_DMSO_HT SS3_Plate4_1161


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_34


title: Donor2_DMSO_HT SS3_Plate4_1160


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_33


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_31


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_29


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_30


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_28


title: Donor2_DMSO_HT SS3_Plate4_1157


title: Donor2_DMSO_HT SS3_Plate4_1156


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_27


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_26


title: Donor2_DMSO_HT SS3_Plate4_1158


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1536

value: Plate 3


title: Donor2_DMSO_HT SS3_Plate4_1153


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1535


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_22


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_23


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_25


title: Donor2_DMSO_HT SS3_Plate4_1163


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_35


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_21


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1534


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1532


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1533


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_20


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_19


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1531


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1529


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_18


title: Donor2_DMSO_HT SS3_Plate4_1159


title: Donor2_DMSO_HT SS3_Plate4_1154


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1530


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_13


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_17


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1527


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1528


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_15


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1526


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1524


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_12


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_10


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1525


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1523


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_11


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1522


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1521


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_9


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_7


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1519


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_5


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1517


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1520


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_6


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1518


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_14


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1514


title: Donor1_DMSO_HT SS3_Plate1_288


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1515


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1512


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1511


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_3


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_1


title: Donor1_DMSO_HT SS3_Plate1_287


title: Donor1_DMSO_HT SS3_Plate1_285


title: Donor1_DMSO_HT SS3_Plate1_286


title: Donor1_DMSO_HT SS3_Plate1_284


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1510


title: Donor1_DMSO_HT SS3_Plate1_283


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1508


title: Donor1_DMSO_HT SS3_Plate1_282


title: Donor1_PMA/Ionomycin_HT SS3_Plate1_4


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1506


title: Donor1_DMSO_HT SS3_Plate1_281


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1516


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1507


title: Donor1_DMSO_HT SS3_Plate1_280


title: Donor1_DMSO_HT SS3_Plate1_279


title: Donor1_DMSO_HT SS3_Plate1_278


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1504


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1503


title: Donor1_DMSO_HT SS3_Plate1_277


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1509


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1500


title: Donor1_DMSO_HT SS3_Plate1_276


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1502


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1501


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1498


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1499


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1497


title: Donor1_DMSO_HT SS3_Plate1_275


title: Donor1_DMSO_HT SS3_Plate1_272


title: Donor1_DMSO_HT SS3_Plate1_271


title: Donor1_DMSO_HT SS3_Plate1_270


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1496


title: Donor1_DMSO_HT SS3_Plate1_274


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1505


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1513


title: Donor1_DMSO_HT SS3_Plate1_267


title: DND_DMSO_HiChIP

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

library_source: genomic

data_processing:
Hi-ChIP data were aligned and processed using HiC-Pro pipeline version 2.11.1, and the reads in the fastq files were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 version 2.4.1.
The restriction sites ^GATC and G^ANTC across the human genome were cut and utilized by HiC-Pro using the HiC-Pro Utilities Python script “digest genome”.
HiC-Pro configuration on ligation site were set to be ^GATC and G^ANTC optimize for ARIMA kit data. The aligned data were further processed using hichipper to call interactions.
Hichipper version 2.7.9 was used to extract the valid interactions from the HiC-Pro data and generate the bedpe interaction file by utilizing anchors from peaks called by MACS2 broadPeak using the dangling-end and self-cycle Hi-ChIP read pairs with the following parameters: --keep-dup all -p 1e-9 --extsize 147 --nomodel -f bed.
Hichipper used to process interactions using the following parameters: -l 50 -mi 5000 -ma 2000000.
Assembly: hg19
Supplementary files format and content: *_allValidPairs txt file output from HiC-Pro
Supplementary files format and content: *.intra.loop_counts.bedpe bedpe file output from hichipper
Supplementary files format and content: *.anchors.bed anchor used by hichipper

molecule: genomic DNA

growth_protocol: DND-41 and MOLT-4 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Library construction from the H3K27ac Hi-ChIP-seq samples and sequencing of paired-end 100-bp-long reads by the DNBSEQ platform were performed at BGI Genomics.
Paired-end Hi-ChIP

treatment_protocol: The cells were cross-linked with formaldehyde, lysed with Hi-C buffer, and then sonicated. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. Post-ChIP DNA was tagmented with Tn5 enzyme follwed by PCR amplification library synthesis.

tag: cell line

value: T-ALL

tag: chip antibody

value: H3K27ac Antibody (Abcam; ab4729)


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1495


title: Donor1_DMSO_HT SS3_Plate1_268


title: DND_24H_ACBI_HiChIP

value: ACBI 24H


title: MOLT4_24H_ACBI_HiChIP


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1489


title: Donor1_DMSO_HT SS3_Plate1_266


title: Donor1_DMSO_HT SS3_Plate1_265


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1492


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1493


title: MOLT4_DMSO_HiChIP


title: Donor1_DMSO_HT SS3_Plate1_264


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1494


title: DND_3H_ACBI_HIChIP

value: ACBI 3H


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1491


title: MOLT4_3H_ACBI_HiChIP


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1488


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1490


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1487


title: Donor1_DMSO_HT SS3_Plate1_262


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1485


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1479


title: MOLT4_DMSO_24H_Rep1

data_processing:
RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 ACBI treated vs 2 DMSO control samples (2 ACBI treated vs 2 DMSO control with 2 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBSEQ platform were performed at the BGI Genomics.

treatment_protocol: DND-41 and MOLT-4 cells were treated with 100nM ACBI-1 or DMSO. At 24 hours post treatment, total RNA were harvested.

tag: time


title: Donor1_DMSO_HT SS3_Plate1_261


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1484


title: MOLT4_DMSO_24H_Rep2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1483


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1486


title: Donor1_DMSO_HT SS3_Plate1_263


title: MOLT4_ACBI_24H_Rep1


title: Donor1_DMSO_HT SS3_Plate1_260


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1477


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1481


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1480


title: MOLT4_ACBI_24H_Rep2


title: Donor1_DMSO_HT SS3_Plate1_259


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1478


title: DND_DMSO_24H_Rep2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1474


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1476


title: Donor1_DMSO_HT SS3_Plate1_258


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1475


title: DND_DMSO_24H_Rep1


title: DND_ACBI_24H_Rep1


title: Donor1_DMSO_HT SS3_Plate1_256


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1482


title: Donor1_DMSO_HT SS3_Plate1_269


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1470


title: DND_ACBI_24H_Rep2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1471


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1469


title: Donor1_DMSO_HT SS3_Plate1_254


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1468


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1467


title: MOLT4_DMSO_8H_Rep1

treatment_protocol: DND-41 and MOLT-4 cells were treated with 100nM ACBI-1 or DMSO. At 8 hours post treatment, total RNA were harvested.


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1464


title: MOLT4_DMSO_8H_Rep2


title: MOLT4_ACBI_8H_Rep2


title: Donor1_DMSO_HT SS3_Plate1_255


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1463


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1462


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1465


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1473


title: Donor1_DMSO_HT SS3_Plate1_252


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1472


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1461


title: MOLT4_ACBI_8H_Rep1


title: Donor1_DMSO_HT SS3_Plate1_251


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1460


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1459


title: Donor1_DMSO_HT SS3_Plate1_248


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1457


title: Donor1_DMSO_HT SS3_Plate1_249


title: DND_DMSO_8H_Rep1


title: DND_ACBI_8H_Rep2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1456


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1455


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1466


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1454


title: Donor1_DMSO_HT SS3_Plate1_247


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1453


title: Donor1_DMSO_HT SS3_Plate1_253


title: DND_ACBI_8H_Rep1


title: MOLT4_DMSO_3H_Rep2

treatment_protocol: DND-41 and MOLT-4 cells were treated with 100nM ACBI-1 or DMSO. At 3 hours post treatment, total RNA were harvested.


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1449


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1451


title: Donor1_DMSO_HT SS3_Plate1_245


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1450


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1447


title: Donor1_DMSO_HT SS3_Plate1_244


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1446


title: MOLT4_DMSO_3H_Rep1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1448


title: Donor1_DMSO_HT SS3_Plate1_243


title: DND_DMSO_8H_Rep2


title: MOLT4_ACBI_3H_Rep2


title: MOLT4_ACBI_3H_Rep1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1458


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1444


title: Donor1_DMSO_HT SS3_Plate1_242


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1443


title: DND_DMSO_3H_Rep2


title: Donor1_DMSO_HT SS3_Plate1_241


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1442


title: DND_DMSO_3H_Rep1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1441


title: Donor1_DMSO_HT SS3_Plate1_246


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1440


title: Donor1_DMSO_HT SS3_Plate1_239


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1439


title: Donor1_DMSO_HT SS3_Plate1_238


title: DND_ACBI_3H_Rep2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1445


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1437


title: DND_ACBI_3H_Rep1


title: TAM from PyMT tumor spontaneously grown in Atg5flox/flox+LysMcre mouse #2

city: Cambridge

first: Seungmin

middle: "Sam"

last: Hwang

state: MA

address: 415 Main st.

institute: Broad Institute of MIT and Harvard

data_processing:
Novogene Co., Ltd. conducted Eukaryotic RNA-seq and analysis.
Mapping reads to mouse reference genome was accomplished using STAR software.
Raw image data file from Illumina was transformed to Sequenced Reads by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Mus musculus

source_name: PyMT tumor

growth_protocol: TAMs were isolated from MMTV-PyMT tumors grown at 65-day-old mice.

extract_protocol:
Total RNA from 0.5 – 1e6 TAMs were extracted using RNA clean & concentrator kit (Zymo research).
RNA library for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit

value: PyMT tumor

value: Tumor associated macrophage (TAM)

value: Atg5 KO (MP-KO)


title: Donor1_DMSO_HT SS3_Plate1_235


title: Donor1_DMSO_HT SS3_Plate1_237


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1436

value: Donor 2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1435


title: Donor1_DMSO_HT SS3_Plate1_236

value: DMSO


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1433

value: PBMC


title: TAM from PyMT tumor spontaneously grown in Atg5flox/flox+LysMcre mouse #1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1431

value: CD4+ T cells


title: TAM from PyMT tumor spontaneously grown in Atg5flox/flox mouse #3

value: Atg5 WT (MP-WT)


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1428


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1432


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1430


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1429


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1427


title: Donor1_DMSO_HT SS3_Plate1_234

value: Donor 1


title: TAM from PyMT tumor spontaneously grown in Atg5flox/flox mouse #2


title: TAM from PyMT tumor spontaneously grown in Atg5flox/flox mouse #1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1426

value: Healthy


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1424

value: PMA/Ionomycin


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1425


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1438


title: TAM from PyMT tumor spontaneously grown in Atg5flox/flox+LysMcre mouse #3


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1434


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1423


title: TAM from MC38 tumor implanted in Atg5flox/flox+LysMcre mouse #4

data_processing:
Novogene Co., Ltd. conducted Eukaryotic RNA-seq and analysis.
Mapping reads to mouse reference genome was accomplished using STAR software.
Raw image data file from Illumina was transformed to Sequenced Reads by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: MC38 tumor

growth_protocol: TAMs were isolated from tumors grown at 21 days after implanting MC38 tumor cells.

value: MC38 tumor

value: Atg5 KO


title: Donor1_DMSO_HT SS3_Plate1_230

value: Plate 1


title: Donor1_DMSO_HT SS3_Plate1_231


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1422

value: Plate 3


title: Donor1_DMSO_HT SS3_Plate1_229


title: Donor1_DMSO_HT SS3_Plate1_228


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1421


title: Donor1_DMSO_HT SS3_Plate1_233


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1418


title: TAM from MC38 tumor implanted in Atg5flox/flox+LysMcre mouse #3


title: Donor1_DMSO_HT SS3_Plate1_227


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1419


title: TAM from MC38 tumor implanted in Atg5flox/flox+LysMcre mouse #2


title: TAM from MC38 tumor implanted in Atg5flox/flox+LysMcre mouse #1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1417


title: Donor1_DMSO_HT SS3_Plate1_225


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1413


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1416


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1415


title: Donor1_DMSO_HT SS3_Plate1_226


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1414


title: TAM from MC38 tumor implanted in Atg5flox/flox mouse #4

value: Atg5 WT


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1411


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1410


title: Donor1_DMSO_HT SS3_Plate1_222


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1412


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1409


title: TAM from MC38 tumor implanted in Atg5flox/flox mouse #3


title: Donor1_DMSO_HT SS3_Plate1_221


title: TAM from MC38 tumor implanted in Atg5flox/flox mouse #1


title: Donor1_DMSO_HT SS3_Plate1_223


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1420


title: TAM from MC38 tumor implanted in Atg5flox/flox mouse #2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1408


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1406


title: retina, rd10 P21 rep 2

city: Shanghai

first: Wenchuan

last: Zhou

address: No. 1665, Kongjiang Road

country: China

institute: Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
Assembly: Hisat2
Supplementary files format and content: Raw counts for each sample

source_name: retina

extract_protocol:
Following whole retina isolation, sample tissue was placed in 100 μl Trizol reagent within a 1.5 ml Eppendorf (Qiagen, Valencia, CA). Each sample contained 1 whole retinae.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: retina

tag: age


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1404


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1405


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1403


title: Donor1_DMSO_HT SS3_Plate1_220


title: retina, rd10 P18 rep 2


title: Donor1_DMSO_HT SS3_Plate1_219


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1402


title: Donor1_DMSO_HT SS3_Plate1_218


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1401


title: retina, rd10 P18 rep 1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1398


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1399


title: retina, rd10 P15 rep 2


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1400


title: Donor1_DMSO_HT SS3_Plate1_215


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1407


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1397


title: Donor1_DMSO_HT SS3_Plate1_214


title: retina, rd10 P21 rep 1


title: Donor1_DMSO_HT SS3_Plate1_213


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1393


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1392


title: retina, Wild-type P15 rep 2

value: wild type


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1394


title: retina, Wild-type P15 rep 1


title: Donor1_DMSO_HT SS3_Plate1_212


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1390


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1391


title: Donor1_DMSO_HT SS3_Plate1_211


title: Control group rep1

city: Tianjin

first: Yu

last: Liu

state: -- None selected --

address: 288 Nanjing Road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: 10X genomics

data_processing:
The gene count matrix was created using the Cell Ranger toolkit (version 6.1.2, https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: mm10
Supplementary files format and content: barcode.tsv.gz: list of cell barcodes; features.tsv.gz: list of gene IDs; matrix.mtx.gz: gene expression

source_name: Bone marrow

extract_protocol:
The BM cells were sorted using AriaIII as follows: DAPI-Lin-c-kit+ cells from the control mouse, DAPI-mCherry-Lin-c-kit+ cells from the AML1/ETO mouse (non-mCherry group) and DAPI-mCherry+Lin-c-kit+ cells from the AML1/ETO mouse (mCherry+ group). The cells of non-mCherry group and mCherry+ group were derived from the same AML1/ETO mouse.
10× Genomics sequencing was performed by Novogene (Beijing, China). Purified libraries were subject to NovaSeq 6000 sequencer (Illumina) for 150-bp paired-end sequencing.

value: Bone marrow

tag: strain

value: Wild-type

tag: library type

value: mRNA

tag: group

value: control


title: AML1_ETO group rep2

description: 10X genomics

value: mCherry


title: Donor1_DMSO_HT SS3_Plate1_210

value: PBMC

value: CD4+ T cells

value: DMSO


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1388

value: Donor 2

value: Healthy


title: Donor1_DMSO_HT SS3_Plate1_217

value: Donor 1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1387

value: PMA/Ionomycin


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1389


title: AML1_ETO group rep1

description: 10X genomics


title: retina, rd10 P15 rep 1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1385


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1386


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1396


title: ileum, PCN-2_1

city: Chengdu

first: Yanping

state: Sichuan

address: No.37 Guo Xue Xiang

institute: Sichuan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genemic benchwork (parameter-Quality limit:0.05)
Read count extration and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: ileum

growth_protocol: 8-week-old C57BL/6J mice were housed at  25°C in a 12-h light-dark cycle

extract_protocol:
RNA was harvest using Rneasy mini plus kit(Qiagen). 2μg RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER RNA-seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Mice were injected with 40 mg/kg prenenolone-16a-carbonitrile (PCN; in DMSO/corn oil 1:3, Cayman Chemical Company, cat 16343) intraperitoneally every 8 h for three times. Mice were sacrificed 8 h after the last administration and the Ileum tissues were collected for total RNA isolation

value: ileum

value: WT

value: PCN


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1395

value: Plate 3


title: Donor1_DMSO_HT SS3_Plate1_207

value: Plate 1


title: Donor1_DMSO_HT SS3_Plate1_209


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1383


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1382


title: Donor1_DMSO_HT SS3_Plate1_206


title: ileum, PCN-1_1


title: ileum, Veh-2_1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1379


title: Donor1_DMSO_HT SS3_Plate1_205


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1380


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1378


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1377


title: ileum, Veh-1_1


title: 7 day male CCI replicate 4

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

description: 10X Genomics

data_processing:
We used 10X Cell Ranger 6.1.2 pipeline to perform the alignment to the reference genome, UMI demultiplexing, cell barcode identification, and subsequently generated the gene-cell expression matrices
We leveraged the Seurat based integrative analysis workflow for downstream analysis. Pre-processing includes merging the replicates, and quality control at the cell and gene level. Filter criteria was determined using the median number of genes using the quality control plots.
Additionally, we filtered out cells with a high fraction of reads mapping to the mitochondrial genome (>5%).
The multiplexed "CCI7" sample was aligned using the Cell Ranger "multi" pipeline to include cell-specific levels of antibody tags (HTOs). The 3 samples within the CCI7 dataset were demultiplexed using the "HTODemux" function and the abundance of the HTO from the Antibody Capture assay, with a classification threshold of 0.99.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz - Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample.
Supplementary files format and content: barcodes.tsv.gz - Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample.
Supplementary files format and content: features.tsv.gz - Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene-count matrix for the respective sample.

source_name: 3mm piece of Cortex & Hippocampus around the injury  was cut, then split into upper & lower quandrants, the upper quadrant was used.

growth_protocol: NA, Adult C57/BL6 male mice were used (litters aged 12-15 weeks, weighing 25-30 grams; Jackson Laboratories, ME, USA).

extract_protocol:
3mm piece of Cortex & Hippocampus was cut, then split into upper & lower quandrants and the upper quadrant was placed into Collaganase IV Cocktail (10mg of DNAse, 32mg Collaganse IV, 20mg of Trypsin Soybean Inhibitor Worthington Chemicals), tissue was mechnically and enzymatically dissociated and strained into a single-cell suspension. Live cells were enriched in each sample, by removing the dead cells using Miltenyi Biotech dead cell removal kit, viability was determined and samples were loaded on a Next GEM G chip and placed into a 10x Genomics Chromium Controller
RNA libraries were prepared using Chromium Single Cell 3' Reagent Kits User Guide from 10x Genomics. Briefly, RNA was isolated and reverse transcibed into cDNA. The cDNA was then amplified and constructed into a 10x Genomics library.

value: Brain tissue

value: CCI


title: Donor1_DMSO_HT SS3_Plate1_203


title: 7 day male CCI replicate 3

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus around the injury was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1375


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1373


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1372


title: Donor1_DMSO_HT SS3_Plate1_201


title: 7 day male CCI replicate 2

description: 10X Genomics

value: 3mm piece of Cortex & Hippocampus around the injury was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1371


title: 7 day male CCI replicate 1

description: 10X Genomics


title: Donor1_DMSO_HT SS3_Plate1_199


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1370


title: Donor1_DMSO_HT SS3_Plate1_198


title: 6 month male CCI replicate 4

description: 10X Genomics

value: 3mm piece of Cortex & Hippocampus around the injury  was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor1_DMSO_HT SS3_Plate1_204


title: Donor1_DMSO_HT SS3_Plate1_197


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1365


title: 6 month male CCI replicate 3

description: 10X Genomics


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1367


title: 6 month male CCI replicate 2

description: 10X Genomics


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1374


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1368


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1376


title: Donor1_DMSO_HT SS3_Plate1_202


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1364


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1363


title: Donor1_DMSO_HT SS3_Plate1_196


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1362


title: Donor1_DMSO_HT SS3_Plate1_195


title: 6 month male CCI replicate 1

description: 10X Genomics


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1361


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1360


title: Donor1_DMSO_HT SS3_Plate1_194


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1369


title: 24 hours female Naïve replicate 3

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus was cut (same Allen-Brain bregma coordinates as CCI), then split into upper & lower quandrants, the upper quadrant was used.

value: Naive


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1359

value: PBMC


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1358

value: CD4+ T cells


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1366


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1357


title: 24 hours female Naïve replicate 1

description: 10X Genomics

value: 3mm piece of Cortex & Hippocampus was cut (same Allen-Brain bregma coordinates as CCI), then split into upper & lower quandrants, the upper quadrant was used.


title: Donor1_DMSO_HT SS3_Plate1_193

value: DMSO


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1356

value: Donor 2

value: Healthy


title: Donor1_DMSO_HT SS3_Plate1_96

value: Donor 1


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1355

value: PMA/Ionomycin


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1354


title: 24 hours male Naïve replicate 6

description: 10X Genomics


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1352


title: Donor1_DMSO_HT SS3_Plate1_95


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1351


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1353


title: Donor1_DMSO_HT SS3_Plate1_94


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1348


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1349


title: 24 hours male Naïve replicate 5

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus was cut (same Allen-Brain bregma coordinates as CCI) , then split into upper & lower quandrants, the upper quadrant was used.


title: Donor1_DMSO_HT SS3_Plate1_93


title: 24 hours female Naïve replicate 2

description: 10X Genomics


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1346


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1347


title: Donor1_DMSO_HT SS3_Plate1_92


title: Donor2_PMA/Ionomycin_HT SS3_Plate3_1345


title: 24 hours female CCI ipsilateral replicate 2

description: 10X Genomics


title: Donor1_DMSO_HT SS3_Plate1_91


title: Donor2_DMSO_HT SS3_Plate3_1536


title: 24 hours female CCI ipsilateral replicate 1

description: 10X Genomics


title: Donor2_DMSO_HT SS3_Plate3_1535


title: 24 hours male Naïve replicate 7

description: 10X Genomics


title: Donor2_DMSO_HT SS3_Plate3_1534


title: Donor1_DMSO_HT SS3_Plate1_90


title: Donor2_DMSO_HT SS3_Plate3_1533


title: 24 hours male CCI contralateral replicate 3  (same mouse as ipsilateral replicate 6)

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus on the contralateral brain from the injury was cut- a mirror-image based on Allen-Brain atlas coordinates, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_DMSO_HT SS3_Plate3_1532


title: 24 hours female CCI ipsilateral replicate 3

description: 10X Genomics


title: Donor2_DMSO_HT SS3_Plate3_1531


title: Donor1_DMSO_HT SS3_Plate1_88


title: Donor2_DMSO_HT SS3_Plate3_1529


title: Donor2_DMSO_HT SS3_Plate3_1530


title: 24 hours male CCI contralateral replicate 2  (same mouse as ipsilateral replicate 5)

description: 10X Genomics

value: 3mm piece of Cortex & Hippocampus on the contralateral brain from the injury was cut- a mirror-image based on Allen-Brain atlas coordinates, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_DMSO_HT SS3_Plate3_1527


title: Donor1_DMSO_HT SS3_Plate1_87


title: 24 hours male  CCI ipsilateral replicate 5

description: 10X Genomics


title: 24 hours male CCI ipsilateral replicate 6

description: 10X Genomics


title: Donor2_DMSO_HT SS3_Plate3_1526


title: Donor2_DMSO_HT SS3_Plate3_1525


title: Donor1_DMSO_HT SS3_Plate1_86


title: Donor2_DMSO_HT SS3_Plate3_1528


title: Donor2_DMSO_HT SS3_Plate3_1523


title: Donor1_DMSO_HT SS3_Plate1_89


title: 24 hours male CCI ipisilateral replicate  4

description: 10X Genomics


title: 24 hours male CCI contralateral replicate 1  (same mouse as ipsilateral replicate 4)

description: 10X Genomics


title: Donor2_DMSO_HT SS3_Plate3_1521


title: 24 hours male CCI replicate (ipsilateral) 3

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus around the contusion was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_DMSO_HT SS3_Plate3_1519


title: Donor1_DMSO_HT SS3_Plate1_83


title: Donor2_DMSO_HT SS3_Plate3_1522


title: Donor1_DMSO_HT SS3_Plate1_84


title: 24 hours male Naïve replicate 4

description: 10X Genomics


title: Donor1_DMSO_HT SS3_Plate1_82


title: Donor2_DMSO_HT SS3_Plate3_1518


title: Donor2_DMSO_HT SS3_Plate3_1516


title: Donor1_DMSO_HT SS3_Plate1_81


title: Donor2_DMSO_HT SS3_Plate3_1515


title: 24 hours male CCI+ HS replicate 3

description: 10X Genomics

value: 3mm piece of Cortex & Hippocampus around the contusion was cut, then split into upper & lower quandrants, the upper quadrant was used.

value: Combined Injury (CCI +HS)


title: 24 hours male repetitive closed head tbi replicate 3

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus (same Allen-Brain bregma coordinates as CCI since this injury is not focal)  was cut, then split into upper & lower quandrants, the upper quadrant was used.

value: Repetitive Closed Head Injury (weight drop model)


title: Donor2_DMSO_HT SS3_Plate3_1512

value: Plate 3


title: Donor1_DMSO_HT SS3_Plate1_80

value: Plate 1


title: Donor2_DMSO_HT SS3_Plate3_1511


title: Donor1_DMSO_HT SS3_Plate1_79


title: 24 hours male repetitive closed head tbi replicate 2

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus (same Allen-Brain bregma coordinates as CCI since this injury is not focal) was cut, then split into upper & lower quandrants, the upper quadrant was used.

value: Brain tissue


title: Donor2_DMSO_HT SS3_Plate3_1510


title: Donor2_DMSO_HT SS3_Plate3_1509


title: 24 hours male Naïve replicate 3

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus (same Allen-Brain bregma coordinates as CCI) was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_DMSO_HT SS3_Plate3_1520


title: Donor2_DMSO_HT SS3_Plate3_1508


title: Donor1_DMSO_HT SS3_Plate1_78


title: 24 hours male repetitive closed head tbi replicate 1

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus  (same Allen-Brain bregma coordinates as CCI since this injury is not focal) was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_DMSO_HT SS3_Plate3_1507

source_name: PBMC


title: 24 hours male  Naïve replicate 2

description: 10X Genomics

source_name: 3mm piece of Cortex & Hippocampus  (same Allen-Brain bregma coordinates as CCI) was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor1_DMSO_HT SS3_Plate1_77


title: Donor2_DMSO_HT SS3_Plate3_1505


title: Donor2_DMSO_HT SS3_Plate3_1504


title: 24 hours male CCI + HS replicate 2

description: 10X Genomics


title: Donor1_DMSO_HT SS3_Plate1_76


title: Donor1_DMSO_HT SS3_Plate1_75


title: Donor2_DMSO_HT SS3_Plate3_1513


title: Donor2_DMSO_HT SS3_Plate3_1502


title: 24 hours male Naïve replicate 1

description: 10X Genomics

value: 3mm piece of Cortex & Hippocampus (same Allen-Brain bregma coordinates as CCI) was cut, then split into upper & lower quandrants, the upper quadrant was used.


title: Donor2_DMSO_HT SS3_Plate3_1499


title: Donor2_DMSO_HT SS3_Plate3_1498


title: Donor2_DMSO_HT SS3_Plate3_1501


title: Donor2_DMSO_HT SS3_Plate3_1500


title: Donor2_DMSO_HT SS3_Plate3_1495


title: Donor1_DMSO_HT SS3_Plate1_74


title: Donor2_DMSO_HT SS3_Plate3_1493


title: 24 hours male CCI+HS replicate 1

description: 10X Genomics


title: Donor1_DMSO_HT SS3_Plate1_73


title: colon, PCN-6_1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genemic benchwork (parameter-Quality limit:0.05)
Read count extration and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: colon

treatment_protocol: Mice were injected with 40 mg/kg prenenolone-16a-carbonitrile (PCN; in DMSO/corn oil 1:3, Cayman Chemical Company, cat 16343) intraperitoneally every 8 h for three times. Mice were sacrificed 8 h after the last administration and the colon tissues were collected for total RNA isolation

value: colon

value: WT

value: PCN


title: Donor1_DMSO_HT SS3_Plate1_71

value: PBMC

value: CD4+ T cells


title: 24 hours male CCI replicate (ipsilateral) 1

description: 10X Genomics

value: CCI


title: Donor2_DMSO_HT SS3_Plate3_1490

value: Donor 2

value: Healthy

value: DMSO


title: Donor1_DMSO_HT SS3_Plate1_72

value: Donor 1


title: Donor2_DMSO_HT SS3_Plate3_1488


title: Donor2_DMSO_HT SS3_Plate3_1487


title: Donor2_DMSO_HT SS3_Plate3_1492


title: Donor2_DMSO_HT SS3_Plate3_1491


title: Donor1_DMSO_HT SS3_Plate1_70


title: Donor2_DMSO_HT SS3_Plate3_1489


title: colon, PCN-5_1


title: colon, Veh-6_1

value: control


title: Donor2_DMSO_HT SS3_Plate3_1496


title: Donor1_DMSO_HT SS3_Plate1_69


title: colon, Veh-5_1


title: colon, PCN-4_1


title: Donor2_DMSO_HT SS3_Plate3_1506


title: Donor1_DMSO_HT SS3_Plate1_68


title: Donor2_DMSO_HT SS3_Plate3_1485


title: colon, Veh-3_1


title: Donor2_DMSO_HT SS3_Plate3_1483


title: Donor1_DMSO_HT SS3_Plate1_67


title: Donor2_DMSO_HT SS3_Plate3_1481


title: Donor2_DMSO_HT SS3_Plate3_1486


title: Donor2_DMSO_HT SS3_Plate3_1477


title: Donor2_DMSO_HT SS3_Plate3_1476


title: Liver, CDAHFD, bio-rep3, snRNA-seq

city: DURHAM

first: Rajesh

middle: Kumar

last: Dutta

state: NC

address: 905 S LaSalle street, GSRB1, Rm-1063

department: Gastroenterology

institute: Duke University

description: 10x Genomics

data_processing:
data processed using cellranger version 5.0.1
Assembly: mm10
Supplementary files format and content: Barcodes, Features and matrix file

molecule: nuclear RNA

source_name: Liver

extract_protocol:
live nuclei were isolated from mouse liver tissue.
Libraries were prepared according to the 10X Genomics Single Cell RNA version 3

value: Liver

tag: Sex

value: Male

value: CDAHFD diet


title: Donor2_DMSO_HT SS3_Plate3_1480

tag: tissue

value: Plate 3


title: Donor2_DMSO_HT SS3_Plate3_1478

tag: cell type


title: Donor1_DMSO_HT SS3_Plate1_65

tag: donor id

value: Plate 1


title: Donor1_DMSO_HT SS3_Plate1_64

tag: plate


title: Donor2_DMSO_HT SS3_Plate3_1482

tag: disease


title: Liver, CDAHFD, bio-rep2, snRNA-seq

description: 10x Genomics

tag: treatment


title: Donor2_DMSO_HT SS3_Plate3_1475


title: Donor1_DMSO_HT SS3_Plate1_63


title: Donor2_DMSO_HT SS3_Plate3_1473


title: Donor1_DMSO_HT SS3_Plate1_66


title: Donor2_DMSO_HT SS3_Plate3_1474


title: Donor2_DMSO_HT SS3_Plate3_1472


title: Donor2_DMSO_HT SS3_Plate3_1471


title: Liver, Chow, bio-rep3, snRNA-seq

description: 10x Genomics

value: Chow diet


title: Donor2_DMSO_HT SS3_Plate3_1469


title: Donor1_DMSO_HT SS3_Plate1_61


title: Liver, Chow, bio-rep2, snRNA-seq

description: 10x Genomics


title: Donor1_DMSO_HT SS3_Plate1_60


title: Donor2_DMSO_HT SS3_Plate3_1470


title: Donor2_DMSO_HT SS3_Plate3_1466


title: Donor1_DMSO_HT SS3_Plate1_59


title: Liver, Chow, bio-rep1, snRNA-seq

description: 10x Genomics


title: Donor2_DMSO_HT SS3_Plate3_1468


title: Donor2_DMSO_HT SS3_Plate3_1465


title: ATAC-Seq iMSBmal1KO Control 4

city: Gainesville

first: Mark

middle: Robert

last: Viggars

state: Alachua

address: University of Florida, M531

department: Physiology & Aging

institute: University of Florida

data_processing:
Partek Flow
Quality score trimmed for Phred <20, 3-prime right end, min-read length 25,
Trimmed sequence reads were mapped to mm10, GRCm39 using Bowtie2, MACS2 peak calling.
Peaks were quantified, normalized using Deseq2 (median of ratios) before differential analysis to identify differentially accessible regions (DARs) between conditions (significant differences in peak heights).
Assembly: mm10 (GRCm39)
Supplementary files format and content: tab-delimited text files include average peak height per sample.

source_name: Gastrocnemius Muscle

extract_protocol:
Two whole gastrocnemius muscle (~300-350mg) were diced and then homogenized using a Polytron homogenizer in homogenization buffer (Homogenization buffer (10mM HEPES, pH 7.5, 10mM MgCl2, 60mM KCl, 300mM sucrose, 0.1mM EDTA, 0.1% Triton, 1mM DTT, complete with mini protease inhibitor mix). Homogenates were spun at 300rpm for 3 minutes and supernatant containing nuclei moved to a new tube. This was repeated 3 times. The supernatant was then filtered through a 40µm cell strainer before centrifugation at 1000g for 10 minutes. The nuclei pellet was then resuspended in 1.2ml of homogenization buffer, gently triturated and 200µl loaded on top of several 2.15M sucrose cushions (10mM HEPES, pH 7.5, 10mM MgCl2, 60mM KCl, 2.15M sucrose, 0.1mM EDTA, 0.1% Triton, 1mM DTT, complete with mini protease inhibitor mix). Nuclei samples were centrifuged at 13,500g at 4°C for 1.5 hours. Samples were aspirated and washed leaving a nuclei pellet, mainly free of cytoplasmic fragments. Nuclei were quality checked using light microscopy (intact nuclei, no blebbing, free of cytoplasmic fragments) and then counted. 50,000 nuclei were used for input into a commercially available ATAC-seq kit which includes library preparation (#53150, Active Motif, Inc., CA, USA).
Active Motif Kit,(#53150, Active Motif, Inc., CA, USA)

value: Gastrocnemius Muscle

tag: genotype

value: Cre+:iMSBmal1 fl/fl

value: Tamoxifen

value: 6 Months


title: Donor2_DMSO_HT SS3_Plate3_1464

value: PBMC

value: CD4+ T cells


title: Donor2_DMSO_HT SS3_Plate3_1462

value: Donor 2


title: Donor2_DMSO_HT SS3_Plate3_1463

value: Healthy


title: ATAC-Seq iMSBmal1KO Control 3


title: Donor1_DMSO_HT SS3_Plate1_57

value: DMSO


title: Donor1_DMSO_HT SS3_Plate1_62

value: Donor 1


title: Donor1_DMSO_HT SS3_Plate1_58


title: Donor2_DMSO_HT SS3_Plate3_1461


title: Donor2_DMSO_HT SS3_Plate3_1460


title: Donor2_DMSO_HT SS3_Plate3_1459


title: ATAC-Seq iMSBmal1KO Control 2


title: Donor2_DMSO_HT SS3_Plate3_1467


title: ATAC-Seq iMSBmal1KO Control 1


title: Donor2_DMSO_HT SS3_Plate3_1458


title: Donor1_DMSO_HT SS3_Plate1_55


title: Donor2_DMSO_HT SS3_Plate3_1457


title: ATAC-Seq Vehicle Control 3

value: Vehicle


title: Donor2_DMSO_HT SS3_Plate3_1454


title: ATAC-Seq Vehicle Control 4


title: Donor1_DMSO_HT SS3_Plate1_54


title: Donor2_DMSO_HT SS3_Plate3_1455


title: 24 hours male CCI Replicate (ipsilateral) 2

description: 10X Genomics

value: 3mm piece of Cortex & Hippocampus around the contusion was cut, then split into upper & lower quandrants, the upper quadrant was used.

value: Brain tissue

value: CCI


title: Donor1_DMSO_HT SS3_Plate1_53


title: Donor2_DMSO_HT SS3_Plate3_1456

value: Plate 3


title: Donor2_DMSO_HT SS3_Plate3_1450


title: Donor1_DMSO_HT SS3_Plate1_56

value: Plate 1


title: ATAC-Seq Vehicle Control 2


title: Donor2_DMSO_HT SS3_Plate3_1452


title: Donor2_DMSO_HT SS3_Plate3_1451


title: Donor1_DMSO_HT SS3_Plate1_52


title: ATAC-Seq Vehicle Control 1


title: Donor2_DMSO_HT SS3_Plate3_1524


title: Donor1_DMSO_HT SS3_Plate1_51


title: Liver, CDAHFD, bio-rep1, snRNA-seq

description: 10x Genomics

value: Liver

value: Male

value: CDAHFD diet


title: Donor2_DMSO_HT SS3_Plate3_1449


title: Donor2_DMSO_HT SS3_Plate3_1448


title: Gastrocnemius Muscle, iMSBmal1KO Acute Exercise 5

description: iMSBmal1KO Exercise Trained 5

data_processing:
Partek Flow
Quality score trimmed for Phred <20, 3-prime right end, min-read length 25,
Trimmed sequence reads were mapped to mm10, GRCm39. Annotated to genomes. Star alignment 2.7.8a
CPM values used in processed data file. Deseq2 median of ratios and Deseq2 differential expression analysis used.
Assembly: mm10 (GRCm39)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Trizol with Qiagen, RNEasy Kit
Illumina library kit.

value: Gastrocnemius Muscle

value: Cre+:iMSBmal1 fl/fl

value: iMSBmal1KO + Exercise

value: ZT13-1 Hour Post


title: Donor1_DMSO_HT SS3_Plate1_50

value: PBMC

value: CD4+ T cells


title: Gastrocnemius Muscle, iMSBmal1KO Acute Exercise 4

description: iMSBmal1KO Exercise Trained 4


title: Donor1_DMSO_HT SS3_Plate1_85

value: Healthy

value: DMSO


title: Gastrocnemius Muscle, iMSBmal1KO Acute Exercise 3

description: iMSBmal1KO Exercise Trained 3


title: Donor2_DMSO_HT SS3_Plate3_1453

value: Donor 2


title: Donor2_DMSO_HT SS3_Plate3_1444


title: Donor2_DMSO_HT SS3_Plate3_1446


title: Donor1_DMSO_HT SS3_Plate1_47

value: Donor 1


title: Donor1_DMSO_HT SS3_Plate1_49


title: Donor2_DMSO_HT SS3_Plate3_1443


title: Donor2_DMSO_HT SS3_Plate3_1445


title: Donor2_DMSO_HT SS3_Plate3_1442


title: Gastrocnemius Muscle, iMSBmal1KO Acute Exercise 2

description: iMSBmal1KO Exercise Trained 2


title: Gastrocnemius Muscle, iMSBmal1KO Acute Exercise 1

description: iMSBmal1KO Exercise Trained 1


title: Donor1_DMSO_HT SS3_Plate1_45


title: Donor2_DMSO_HT SS3_Plate3_1439


title: Donor1_DMSO_HT SS3_Plate1_46


title: Gastrocnemius Muscle, iMSBmal1KO Control 5

description: iMSBmal1KO Control 5

value: iMSBmal1KO + No Exercise


title: Donor2_DMSO_HT SS3_Plate3_1438


title: Donor1_DMSO_HT SS3_Plate1_44


title: Donor2_DMSO_HT SS3_Plate3_1441


title: Gastrocnemius Muscle, iMSBmal1KO Control 4

description: iMSBmal1KO Control 4


title: Donor1_DMSO_HT SS3_Plate1_43


title: Gastrocnemius Muscle, iMSBmal1KO Control 3

description: iMSBmal1KO Control 3


title: Donor2_DMSO_HT SS3_Plate3_1435


title: Donor2_DMSO_HT SS3_Plate3_1437


title: Donor2_DMSO_HT SS3_Plate3_1434


title: Donor1_DMSO_HT SS3_Plate1_42


title: Donor2_DMSO_HT SS3_Plate3_1433


title: Gastrocnemius Muscle, iMSBmal1KO Control 2

description: iMSBmal1KO Control 2


title: Donor2_DMSO_HT SS3_Plate3_1431


title: Donor2_DMSO_HT SS3_Plate3_1432


title: Donor2_DMSO_HT SS3_Plate3_1440


title: Gastrocnemius Muscle, iMSBmal1KO Control 1

description: iMSBmal1KO Control 1


title: Donor2_DMSO_HT SS3_Plate3_1429


title: Gastrocnemius Muscle, Vehicle Acute Exercise 5

description: Vehicle Acute Exercise 5

value: Vehicle + Exercise


title: Donor2_DMSO_HT SS3_Plate3_1436

value: Plate 3


title: Donor2_DMSO_HT SS3_Plate3_1428


title: Gastrocnemius Muscle, Vehicle Acute Exercise 4

description: Vehicle Acute Exercise 4


title: Donor1_DMSO_HT SS3_Plate1_38

value: Plate 1


title: Donor2_DMSO_HT SS3_Plate3_1426


title: Donor1_DMSO_HT SS3_Plate1_37


title: Donor2_DMSO_HT SS3_Plate3_1427


title: Gastrocnemius Muscle, Vehicle Acute Exercise 3

description: Vehicle Acute Exercise 3


title: Donor2_DMSO_HT SS3_Plate3_1425


title: Donor1_DMSO_HT SS3_Plate1_36


title: Gastrocnemius Muscle, Vehicle Acute Exercise 2

description: Vehicle Acute Exercise 2


title: Donor2_DMSO_HT SS3_Plate3_1424


title: Donor2_DMSO_HT SS3_Plate3_1422


title: Donor1_DMSO_HT SS3_Plate1_35


title: Donor1_DMSO_HT SS3_Plate1_41


title: Donor1_DMSO_HT SS3_Plate1_39


title: Donor2_DMSO_HT SS3_Plate3_1420


title: Donor2_DMSO_HT SS3_Plate3_1430


title: Donor2_DMSO_HT SS3_Plate3_1419


title: Donor2_DMSO_HT SS3_Plate3_1423


title: Gastrocnemius Muscle, Vehicle Control 5

description: Vehicle Control 5

value: Vehicle + No Exercise


title: Gastrocnemius Muscle, Vehicle Acute Exercise 1

description: Vehicle Acute Exercise 1


title: Donor1_DMSO_HT SS3_Plate1_33


title: Donor2_DMSO_HT SS3_Plate3_1418


title: Donor2_DMSO_HT SS3_Plate3_1417


title: Gastrocnemius Muscle, Vehicle Control 4

description: Vehicle Control 4


title: Donor2_DMSO_HT SS3_Plate3_1415


title: Gastrocnemius Muscle, Vehicle Control 3

description: Vehicle Control 3


title: Gastrocnemius Muscle, Vehicle Control 2

description: Vehicle Control 2


title: Donor2_DMSO_HT SS3_Plate3_1413


title: Donor1_DMSO_HT SS3_Plate1_30


title: Donor2_DMSO_HT SS3_Plate3_1412


title: Donor2_DMSO_HT SS3_Plate3_1421


title: Donor2_DMSO_HT SS3_Plate3_1411


title: Donor1_DMSO_HT SS3_Plate1_29


title: Donor2_DMSO_HT SS3_Plate3_1410


title: Gastrocnemius Muscle, Vehicle Control 1

description: Vehicle Control 1


title: Donor2_DMSO_HT SS3_Plate3_1409


title: Donor1_DMSO_HT SS3_Plate1_28


title: Donor2_DMSO_HT SS3_Plate3_1408


title: Donor1_DMSO_HT SS3_Plate1_34


title: Donor2_DMSO_HT SS3_Plate3_1407


title: White Adipose, Exercise Trained, Muscle-Specific Bmal1KO_3

description: WhiteadiposeCPM.xlsx

data_processing:
Partek Flow
Quality score trimmed for Phred <20, 3-prime right end, min-read length 25,
Trimmed sequence reads were mapped to mm10, GRCm39. Annotated to genomes. Star alignment 2.7.8a
CPM values used in processed data file.
Assembly: mm10 (GRCm39)
Supplementary files format and content: tab-delimited text files include CPM values for each sample. Each tissue has its own file containing the data from all 4 groups.

source_name: White Adipose

value: White Adipose

value: iMSBMal1KO + Exercise Training

value: 48-hours post


title: Donor2_DMSO_HT SS3_Plate3_1406


title: White Adipose, Exercise Trained, Muscle-Specific Bmal1KO_2

description: WhiteadiposeCPM.xlsx

value: Cre+:iMSBmal1 fl/fl


title: Donor1_DMSO_HT SS3_Plate1_26


title: Donor2_DMSO_HT SS3_Plate3_1404


title: Donor1_DMSO_HT SS3_Plate1_31


title: Donor2_DMSO_HT SS3_Plate3_1414


title: Donor2_DMSO_HT SS3_Plate3_1403


title: Donor1_DMSO_HT SS3_Plate1_25


title: White Adipose, Exercise Trained, Muscle-Specific Bmal1KO_1

description: WhiteadiposeCPM.xlsx


title: Donor1_DMSO_HT SS3_Plate1_23


title: White Adipose, Exercise Trained_3

description: WhiteadiposeCPM.xlsx

value: Vehicle + Exercise Training


title: Donor2_DMSO_HT SS3_Plate3_1401


title: Donor2_DMSO_HT SS3_Plate3_1399


title: Donor2_DMSO_HT SS3_Plate3_1400


title: Donor2_DMSO_HT SS3_Plate3_1398


title: White Adipose, Exercise Trained_2

description: WhiteadiposeCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1397


title: Donor1_DMSO_HT SS3_Plate1_21


title: Donor2_DMSO_HT SS3_Plate3_1395


title: White Adipose, Exercise Trained_1

description: WhiteadiposeCPM.xlsx


title: White Adipose, Sedentary, Muscle-Specific Bmal1KO_3

description: WhiteadiposeCPM.xlsx


title: Donor1_DMSO_HT SS3_Plate1_27


title: Donor2_DMSO_HT SS3_Plate3_1396


title: Donor1_DMSO_HT SS3_Plate1_20


title: Donor2_DMSO_HT SS3_Plate3_1405


title: Donor2_DMSO_HT SS3_Plate3_1394


title: White Adipose, Sedentary, Muscle-Specific Bmal1KO_2

description: WhiteadiposeCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1393


title: Donor1_DMSO_HT SS3_Plate1_19


title: White Adipose, Sedentary, Muscle-Specific Bmal1KO_1

description: WhiteadiposeCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1392


title: Donor2_DMSO_HT SS3_Plate3_1390


title: Donor2_DMSO_HT SS3_Plate3_1391


title: Donor1_DMSO_HT SS3_Plate1_18


title: Donor2_DMSO_HT SS3_Plate3_1389


title: Donor1_DMSO_HT SS3_Plate1_22


title: Donor2_DMSO_HT SS3_Plate3_1388


title: White Adipose, Sedentary_3

description: WhiteadiposeCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1387


title: White Adipose, Sedentary_2

description: WhiteadiposeCPM.xlsx


title: Donor1_DMSO_HT SS3_Plate1_15


title: Donor2_DMSO_HT SS3_Plate3_1385


title: White Adipose, Sedentary_1

description: WhiteadiposeCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1384


title: Lung, Exercise Trained, Muscle-Specific Bmal1KO_3

description: LungCPM.xlsx

source_name: Lung

value: Lung


title: Donor1_DMSO_HT SS3_Plate1_14

value: PBMC


title: Donor2_DMSO_HT SS3_Plate3_1383

value: CD4+ T cells


title: Donor1_DMSO_HT SS3_Plate1_13

value: Healthy


title: Donor2_DMSO_HT SS3_Plate3_1381

value: DMSO


title: Donor2_DMSO_HT SS3_Plate3_1380

value: Donor 2


title: Lung, Exercise Trained, Muscle-Specific Bmal1KO_2

description: LungCPM.xlsx


title: Donor1_DMSO_HT SS3_Plate1_12

value: Donor 1


title: Lung, Exercise Trained_3

description: LungCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1376


title: Donor2_DMSO_HT SS3_Plate3_1379


title: Donor1_DMSO_HT SS3_Plate1_10


title: Donor1_DMSO_HT SS3_Plate1_11


title: Donor2_DMSO_HT SS3_Plate3_1386


title: Donor2_DMSO_HT SS3_Plate3_1378


title: Lung, Exercise Trained, Muscle-Specific Bmal1KO_1

description: LungCPM.xlsx


title: Donor1_DMSO_HT SS3_Plate1_17


title: Lung, Exercise Trained_2

description: LungCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1374


title: Donor2_DMSO_HT SS3_Plate3_1377


title: Donor1_DMSO_HT SS3_Plate1_9


title: Donor2_DMSO_HT SS3_Plate3_1375


title: Donor2_DMSO_HT SS3_Plate3_1382


title: Donor2_DMSO_HT SS3_Plate3_1373


title: Lung, Exercise Trained_1

description: LungCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1372


title: Lung, Sedentary, Muscle-Specific Bmal1KO_3

description: LungCPM.xlsx

value: iMSBmal1KO + No Exercise


title: Donor2_DMSO_HT SS3_Plate3_1370


title: Donor1_DMSO_HT SS3_Plate1_7


title: Donor2_DMSO_HT SS3_Plate3_1369


title: Donor2_DMSO_HT SS3_Plate3_1371


title: Donor1_DMSO_HT SS3_Plate1_6


title: Lung, Sedentary, Muscle-Specific Bmal1KO_2

description: LungCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1368


title: Donor1_DMSO_HT SS3_Plate1_5


title: Donor2_DMSO_HT SS3_Plate3_1366


title: Lung, Sedentary, Muscle-Specific Bmal1KO_1

description: LungCPM.xlsx


title: Donor1_DMSO_HT SS3_Plate1_4


title: Lung, Sedentary_3

description: LungCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1367


title: Donor2_DMSO_HT SS3_Plate3_1365


title: Donor1_DMSO_HT SS3_Plate1_3


title: Donor2_DMSO_HT SS3_Plate3_1363


title: Donor2_DMSO_HT SS3_Plate3_1362


title: Donor1_DMSO_HT SS3_Plate1_2


title: Lung, Sedentary_1

description: LungCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1361


title: Donor2_DMSO_HT SS3_Plate3_1360


title: Lung, Sedentary_2

description: LungCPM.xlsx


title: Donor2_DMSO_HT SS3_Plate3_1359


title: Heart, Exercise Trained, Muscle-Specific Bmal1KO_5

description: HeartCPM.xlsx

source_name: Heart

value: Heart


title: Donor2_DMSO_HT SS3_Plate3_1358

value: Plate 3


title: Donor2_DMSO_HT SS3_Plate3_1357


title: Donor2_DMSO_HT SS3_Plate3_1356


title: Heart, Exercise Trained, Muscle-Specific Bmal1KO_4

description: HeartCPM.xlsx


title: Donor1_DMSO_HT SS3_Plate1_1

value: Plate 1


title: Donor2_DMSO_HT SS3_Plate3_1355