title: ani_G. lacustris, gradual temperature increase, 12 degrees C, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_4
differential expression file:
GlaT12annot.csv


title: ani_G. lacustris, gradual temperature increase, 12 degrees C, sample 3

status: Public on May 23 2019

type: SRA

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_3
differential expression file:
GlaT12annot.csv

library_source: transcriptomic

data_processing:
Raw reads were mapped onto transcriptome assemblies with salmon v0.9.1.
DESeq2 abundance estimation was performed with an in-house R script, which can be found at https://github.com/drozdovapb/EveEcyGlaDE.
Transcript abundances were merged with transcript annotation.
Genome_build: de novo transcriptome assembly of the corresponding species (FASTA files on series record)
Supplementary_files_format_and_content: Salmon output files as TPM (transcript per million counts, text files) and DESeq2 output files with custom annotation (*annot.csv)
Supplementary_files_format_and_content: GSE129069_update_Ecy_Eve_Gla_differential_expression_T12_T18_and_T24_to_B6.tar.gz: Differential expression for the samples fixed at 12.4, 18, and 24.4 degrees C (T12, T18, and T24, respectively) was analyzed relative to the initial control at 6 degrees C (B6) separately for each species; the species-specific assemblies EveBCdTP1_ani, EcyBCdTP1_ani, and GlaBCdTP1_ani were used. The abundance of each transcript was estimated with salmon (Patro et al., 2017, https://doi.org/10.1038/nmeth.4197), and differential expression was calculated with the DESeq2 (Love et al., 2014; https://doi.org/10.1186/s13059-014-0550-8) package for the R statistical environment (R Core Team, 2017) using scripts provided by Trinity (Haas et al., 2013, https://doi.org/10.1038/nprot.2013.084).

molecule: total RNA

organism: Gammarus lacustris

source_name: whole body

extract_protocol:
Total RNA for RNA sequencing was extracted from either a single individual or from a pool of up to 5 individuals (see individual BioSample description). Amphipods were homogenized in 1 ml of Qiazol Reagent (Qiagen) with MM400 homogenizer (Retsch). RNA isolation from the aqueous phases was performed with a Qiacube (Qiagen) and miRNeasy kit (Qiagen).
mRNA was isolated from the total RNA sample using Oligotex mRNA Mini Kit (Qiagen). The quality of RNA was checked with RNA 6000 Nano Kit on the Agilent Bioanalyzer 2100. mRNA libraries were prepared with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, # SSV21124).

treatment_protocol: Animals were acclimated at 6 degrees C for 3-5 days before the experiment. Please refer to description of individual samples for species- and sample-specific details

tag: tissue

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Bolshie Koty village, Lake No14

value: Till Luckenbach, Daria Bedulina

tag: depth

value: adult

value: littoral zone

value: Maxim Timofeyev, Daria Bedulina

tag: condition


title: ani_G. lacustris, gradual temperature increase, 18 degrees C, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_3
differential expression file:
GlaT18annot.csv


title: ani_E. cyaneus, control, 24 hours, sample 2

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_2
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv
EcyPhB24_annot.csv

organism: Eulimnogammarus cyaneus

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village


title: ani_E. cyaneus, control, 24 hours, sample 4

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_4
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv
EcyPhB24_annot.csv


title: ani_G. lacustris, gradual temperature increase, 12 degrees C, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_1
differential expression file:
GlaT12annot.csv


title: ani_G. lacustris, gradual temperature increase, 18 degrees C, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 15 days at 18 degrees C.
GlaT18_4
differential expression file:
GlaT18annot.csv


title: ani_E. cyaneus, control, 24 hours, sample 3

description:
Pooled sample of approx. 5 individuals of E. cyaneus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EcyB24_3
differential expression file:
EcyCd24_annot.csv
Ecy10LT24_annot.csv
EcyPB24_annot.csv
EcyPhB24_annot.csv


title: ani_G. lacustris, parallel control for GlaT24, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB247
differential expression file:
GlaT24annot.csv


title: ani_G. lacustris, parallel control for GlaT24, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB24_2_6
differential expression file:
GlaT24annot.csv


title: ani_G. lacustris, gradual temperature increase, 12 degrees C, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days, kept at rising (0.8 degrees C per day) temperature and fixed after 8 days at 12.4 degrees C.
GlaT12_2
differential expression file:
GlaT12annot.csv


title: ani_G. lacustris, parallel control for GlaT18, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
GlaB18_3
differential expression file:
GlaT18annot.csv


title: ani_E. verrucosus, parallel control for EveT12, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
EveB12_1
differential expression file:
EveT12annot.csv

organism: Eulimnogammarus verrucosus


title: ani_E. verrucosus, initial control for EveT, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_4
differential expression file:


title: ani_E. verrucosus, initial control for EveT, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_2
differential expression file:


title: ani_G. lacustris, parallel control for GlaT18, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
GlaB18_1
differential expression file:
GlaT18annot.csv


title: ani_G. lacustris, parallel control for GlaT18, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 15 days (parallel control for gradual temperature rise).
GlaB18_2
differential expression file:
GlaT18annot.csv


title: ani_G. lacustris, parallel control for GlaT24, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB24_1_6
differential expression file:
GlaT24annot.csv


title: ani_G. lacustris, parallel control for GlaT12, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_4
differential expression file:
GlaT12annot.csv


title: ani_G. lacustris, parallel control for GlaT12, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_2
differential expression file:
GlaT12annot.csv


title: ani_E. verrucosus, initial control for EveT, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_3
differential expression file:


title: ani_G. lacustris, parallel control for GlaT12, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_1
differential expression file:
GlaT12annot.csv


title: ani_E. verrucosus, initial control for EveT, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days (initial control).
EveB6_1
differential expression file:


title: ani_G. lacustirs, initial control for GlaT, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_2
differential expression file:


title: ani_E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_2
differential expression file:
EvePh24_annot.csv
EvePhB24_annot.csv


title: ani_E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_3
differential expression file:
EvePh24_annot.csv
EvePhB24_annot.csv


title: ani_G. lacustirs, initial control for GlaT, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_4
differential expression file:


title: ani_G. lacustirs, initial control for GlaT, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_1
differential expression file:


title: ani_G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_4
differential expression file:
GlaPh24_annot.csv
GlaPhB24_annot.csv


title: ani_E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_3
differential expression file:
EvePh3_annot.csv
EvePhB3_annot.csv


title: ani_E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_2
differential expression file:
EvePh3_annot.csv
EvePhB3_annot.csv


title: ani_G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_2
differential expression file:
GlaPh24_annot.csv
GlaPhB24_annot.csv


title: ani_E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_4
differential expression file:
EvePh3_annot.csv
EvePhB3_annot.csv


title: ani_G. lacustris, parallel control for GlaT24, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 23 days (parallel control for gradual temperature rise).
GlaB24_4_7
differential expression file:
GlaT24annot.csv


title: ani_G. lacustirs, initial control for GlaT, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days (initial control).
GlaB6_3
differential expression file:


title: ani_G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_1
differential expression file:
GlaPh24_annot.csv
GlaPhB24_annot.csv


title: ani_G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_2
differential expression file:
GlaPh3_annot.csv
GlaPhB3_annot.csv


title: ani_G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_4
differential expression file:
GlaPh3_annot.csv
GlaPhB3_annot.csv


title: ani_E. verrucosus, 0.1% acetone, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EvePB24_1
differential expression file:
EvePB24_annot.csv


title: ani_E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_1
differential expression file:
EvePh24_annot.csv
EvePhB24_annot.csv


title: ani_E. verrucosus, 1 mg/L phenanthrene, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
EveP3_1
differential expression file:
EvePh3_annot.csv
EvePhB3_annot.csv


title: ani_E. verrucosus, 0.1% acetone, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EvePB24_2
differential expression file:
EvePB24_annot.csv


title: ani_G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_3
differential expression file:
GlaPh3_annot.csv
GlaPhB3_annot.csv


title: ani_G. lacustris, 0.1% acetone, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
GlaPB24_3
differential expression file:
GlaPB24_annot.csv


title: ani_E. verrucosus, 0.1% acetone, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
EvePB24_3
differential expression file:
EvePB24_annot.csv


title: ani_E. verrucosus, LT10, 24 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_4
differential expression file:
Eve10LT24_annot.csv


title: ani_E. verrucosus, LT10, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_2
differential expression file:
Eve10LT24_annot.csv


title: ani_G. lacustris, 0.1% acetone, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
GlaPB24_1
differential expression file:
GlaPB24_annot.csv


title: ani_G. lacustris, 1 mg/L phenanthrene, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and  subjected to 1 mg/L phenanthrene for 24 hours.
GlaP24_3
differential expression file:
GlaPh24_annot.csv
GlaPhB24_annot.csv


title: ani_G. lacustris, 0.1% acetone, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 24 hours.
GlaPB24_2
differential expression file:
GlaPB24_annot.csv


title: ani_E. verrucosus, 0.1% acetone, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EvePB3_1
differential expression file:
EvePB3_annot.csv


title: ani_G. lacustris, 0.1% acetone, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
GlaPB3_1
differential expression file:
GlaPB3_annot.csv


title: ani_E. verrucosus, LT10, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_3
differential expression file:
Eve10LT24_annot.csv


title: ani_G. lacustris, LT10, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Gla10LT24_3
differential expression file:
Gla10LT24_annot.csv


title: ani_E. verrucosus, LT10, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_3
differential expression file:
Eve10LT3_annot.csv


title: ani_G. lacustris, LT10, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Gla10LT24_4
differential expression file:
Gla10LT24_annot.csv


title: ani_E. verrucosus, LT10, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_4
differential expression file:
Eve10LT3_annot.csv


title: ani_E. verrucosus, LT10, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Eve10LT24_1
differential expression file:
Eve10LT24_annot.csv


title: ani_G. lacustris, LT10, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 24 hours.
Gla10LT24_1
differential expression file:
Gla10LT24_annot.csv


title: ani_E. verrucosus, 0.1% acetone, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
EvePB3_2
differential expression file:
EvePB3_annot.csv


title: ani_G. lacustris, 1 mg/L phenanthrene, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 3 hours.
GlaP3_1
differential expression file:
GlaPh3_annot.csv
GlaPhB3_annot.csv


title: ani_E. verrucosus, LT10, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_2
differential expression file:
Eve10LT3_annot.csv


title: ani_G. lacustris, 0.1% acetone, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to 0.1% acetone (phenanthrene solvent) for 3 hours.
GlaPB3_2
differential expression file:
GlaPB3_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 24 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_4
differential expression file:
EveCd24_annot.csv


title: ani_G. lacustris, LT10, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_2
differential expression file:
Gla10LT3_annot.csv


title: ani_G. lacustris, LT10, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_1
differential expression file:
Gla10LT3_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_3
differential expression file:
EveCd24_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_1
differential expression file:
EveCd24_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and  subjected to LC10 (2.9 uM) cadmium chloride for 24 hours.
EveCd24_2
differential expression file:
EveCd24_annot.csv


title: ani_G. lacustris, LC10 cadmium, 24 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_4
differential expression file:
GlaCd24_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_4
differential expression file:
EveCd3_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_3
differential expression file:
EveCd3_annot.csv


title: ani_G. lacustris, LC10 cadmium, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_3
differential expression file:
GlaCd24_annot.csv


title: ani_G. lacustris, LC10 cadmium, 24 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_1
differential expression file:
GlaCd24_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_1
differential expression file:
EveCd3_annot.csv


title: ani_G. lacustris, LC10 cadmium, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd24_2
differential expression file:
GlaCd24_annot.csv


title: ani_G. lacustris, LC10 cadmium, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd3_3
differential expression file:
GlaCd3_annot.csv


title: ani_E. verrucosus, LC10 cadmium, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to LC10 (2.9 uM) cadmium chloride for 3 hours.
EveCd3_2
differential expression file:
EveCd3_annot.csv


title: ani_G. lacustris, LC10 cadmium, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd3_1
differential expression file:
GlaCd3_annot.csv


title: ani_G. lacustris, LC10 cadmium, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and subjected to LC10 (3.2 uM) cadmium chloride for 24 hours.
GlaCd3_2
differential expression file:
GlaCd3_annot.csv


title: ani_E. verrucosus, control, 24 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EveB24_3
differential expression file:
EveCd24_annot.csv
Eve10LT24_annot.csv
EvePB24_annot.csv
EvePhB24_annot.csv


title: ani_E. verrucosus, control, 24 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EveB24_2
differential expression file:
EveCd24_annot.csv
Eve10LT24_annot.csv
EvePB24_annot.csv
EvePhB24_annot.csv


title: ani_G. lacustris, control, 24 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
GlaB24_4
differential expression file:
GlaCd24_annot.csv
Gla10LT24_annot.csv
GlaPB24_annot.csv
GlaPhB24_annot.csv


title: ani_E. verrucosus, control, 24 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
EveB24_1
differential expression file:
EveCd24_annot.csv
Eve10LT24_annot.csv
EvePB24_annot.csv
EvePhB24_annot.csv


title: ani_E. verrucosus, control, 3 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_4
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv
EvePhB3_annot.csv


title: ani_G. lacustris, control, 24 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
GlaB24_3
differential expression file:
GlaCd24_annot.csv
Gla10LT24_annot.csv
GlaPB24_annot.csv
GlaPhB24_annot.csv


title: ani_E. verrucosus, LT10, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Eve10LT3_1
differential expression file:
Eve10LT3_annot.csv


title: ani_G. lacustris, LT10, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_3
differential expression file:
Gla10LT3_annot.csv


title: ani_G. lacustris, LT10, 3 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and subjected to LT10 (24.9 degrees C) for 3 hours.
Gla10LT3_4
differential expression file:
Gla10LT3_annot.csv


title: ani_E. verrucosus, 1 mg/L phenanthrene, 24 hours, sample 4

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and subjected to 1 mg/L phenanthrene for 24 hours.
EveP24_4
differential expression file:
EvePh24_annot.csv
EvePhB24_annot.csv


title: ani_G. lacustris, control, 24 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 24 hours (parallel control).
GlaB24_2
differential expression file:
GlaCd24_annot.csv
Gla10LT24_annot.csv
GlaPB24_annot.csv
GlaPhB24_annot.csv


title: ani_E. verrucosus, control, 3 hours, sample 3

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_3
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv
EvePhB3_annot.csv


title: ani_E. verrucosus, control, 3 hours, sample 2

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_2
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv
EvePhB3_annot.csv


title: ani_G. lacustris, control, 3 hours, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_3
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv
GlaPhB3_annot.csv


title: ani_E. verrucosus, control, 3 hours, sample 1

description:
1 individual of E. verrucosus acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
EveB3_1
differential expression file:
EveCd3_annot.csv
Eve10LT3_annot.csv
EvePB3_annot.csv
EvePhB3_annot.csv


title: ani_G. lacustris, control, 3 hours, sample 2

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_2
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv
GlaPhB3_annot.csv


title: IHEC_54

status: Public on Mar 12 2019

city: Toulouse

first: Jean-Philippe

last: Girard

address: 205 Route de Narbonne

country: France

institute: Institut de Pharmacologie et de Biologie Structurale

data_processing:
FASTQ file generated by Illumina CASAVA 1.8
Sequenced reads were trimmed for adaptors and low quality reads then mapped to the mm10 mouse genome using RSEM v1.2.18
FPKM measurements were compiled from RSEM output
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all samples

organism: Mus musculus

source_name: Lymph Node

extract_protocol:
Lymph nodes were removed from mice, dissociated into single cell suspension and High Endothelial Cells or Blood Endothelial Cells were FACS sorted. Purified cells were sorted, RNA was extracted and cDNA constructed using the Fluidigm C1 System.
Libraries were constructed using the Nextera XT kit as per the manufacturer’s instructions
Single Cell RNA-Seq

tag: strain

tag: cell type

value: High Endothelial Cell

value: Inflamed

tag: treament

value: Treated with 4% Oxazolone on Skin, Harvest Day 3


title: IHEC_53


title: ani_G. lacustris, control, 3 hours, sample 4

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_4
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv
GlaPhB3_annot.csv


title: IHEC_48


title: IHEC_62


title: IHEC_61


title: IHEC_50


title: IHEC_51


title: IHEC_52


title: IHEC_63


title: IHEC_59


title: IHEC_56


title: IHEC_58


title: IHEC_49


title: IHEC_57


title: IHEC_64


title: IHEC_55


title: IHEC_65


title: IHEC_60


title: IHEC_45


title: IHEC_46


title: IHEC_44


title: IHEC_41


title: IHEC_39


title: IHEC_42


title: IHEC_43


title: IHEC_35


title: IHEC_36


title: IHEC_47


title: IHEC_40


title: IHEC_32


title: IHEC_28


title: IHEC_34


title: IHEC_31


title: IHEC_37


title: IHEC_38


title: ani_G. lacustris, control, 3 hours, sample 1

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 3 days and kept at 6 degrees C for 3 hours (parallel control).
GlaB3_1
differential expression file:
GlaCd3_annot.csv
Gla10LT3_annot.csv
GlaPB3_annot.csv
GlaPhB3_annot.csv


title: IHEC_30


title: IHEC_29


title: IHEC_33


title: IHEC_21


title: IHEC_23


title: IHEC_25


title: IHEC_20


title: IHEC_26


title: IHEC_22


title: IHEC_27


title: IHEC_24


title: IHEC_18


title: IHEC_19


title: IHEC_17


title: IHEC_14


title: IHEC_16


title: ani_G. lacustris, parallel control for GlaT12, sample 3

description:
Pooled sample of approx. 3 individuals of G. lacustris acclimated at 6 degrees C for 5 days and kept at 6 degrees C for 8 days (parallel control for gradual temperature rise).
GlaB12_3
differential expression file:
GlaT12annot.csv


title: IHEC_15


title: IHEC_10


title: IHEC_12


title: IHEC_08


title: IHEC_06


title: HHEC_79

value: Homeostatic

value: Untreated


title: IHEC_11


title: IHEC_02


title: HHEC_72


title: IHEC_03


title: IHEC_07


title: IHEC_01


title: IHEC_13


title: HHEC_77


title: HHEC_76


title: HHEC_73


title: HHEC_74


title: IHEC_04


title: HHEC_71


title: HHEC_75


title: HHEC_69


title: HHEC_68


title: HHEC_78


title: IHEC_09


title: HHEC_67


title: HHEC_70


title: HHEC_66


title: HHEC_62


title: HHEC_64


title: HHEC_65


title: HHEC_63


title: HHEC_61


title: HHEC_60


title: HHEC_58


title: HHEC_57


title: HHEC_55


title: HHEC_56


title: HHEC_50


title: HHEC_53


title: HHEC_52


title: HHEC_49


title: HHEC_48


title: HHEC_51


title: HHEC_47


title: HHEC_44


title: HHEC_45


title: HHEC_54


title: HHEC_42


title: HHEC_41


title: HHEC_40


title: HHEC_43


title: HHEC_46


title: HHEC_39


title: HHEC_38


title: HHEC_59


title: HHEC_37


title: HHEC_35


title: HHEC_36


title: HHEC_34


title: HHEC_33


title: HHEC_32


title: HHEC_30


title: HHEC_31


title: HHEC_29


title: HHEC_28


title: HHEC_27


title: HHEC_23


title: HHEC_26


title: HHEC_24


title: HHEC_21


title: HHEC_19


title: HHEC_18


title: HHEC_22


title: HHEC_17


title: HHEC_12


title: HHEC_16


title: HHEC_15


title: HHEC_11


title: HHEC_09


title: HHEC_10


title: HHEC_20


title: HHEC_14


title: HHEC_13


title: HHEC_07


title: HHEC_06


title: HHEC_25


title: HHEC_08


title: HHEC_05


title: BEC_28

value: Blood Endothelial Cell


title: BEC_30


title: BEC_26


title: BEC_32


title: BEC_29


title: HHEC_03


title: BEC_22


title: BEC_27


title: HHEC_02


title: BEC_20


title: HHEC_01


title: BEC_25


title: BEC_19


title: BEC_17


title: BEC_16


title: BEC_18


title: BEC_14


title: BEC_21


title: BEC_15


title: BEC_13


title: BEC_12


title: BEC_11


title: HHEC_04


title: BEC_10


title: BEC_23


title: BEC_09


title: BEC_08


title: BEC_24


title: BEC_06


title: BEC_03


title: BEC_02


title: BEC_05


title: BEC_04


title: HSCs_MTP10-HDL_rep5

status: Public on Feb 21 2019

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - Location AMC

description:
MTP_5
processed data file: GSE126793_HSC-counts.txt

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM tools 1.3.1
Raw tag counts per gene were counted using HOMER2’s analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: readcounts, RPKMs

source_name: Hematopoietic stem cells

extract_protocol:
Total RNA was isolated from HSC using a Direct-zol RNA Kit (Zymo Research) kit with DNase treatment. RNA amplification and cDNA generation was preformed using Ovation RNA-Seq System V2 (NuGEN).
Libraries were constructed using Ovation Ultralow V2 DNA-Seq Library Preparation Kit following manufacturer’s instructions (NuGEN). Samples were pooled and diluted to 10 nM and sequenced on an Illumina HiSeq 4000 instrument (Illumina) to a depth of ± 20 million single-ended 50 bp reads.

tag: number of mice used

tag: agent

value: Hematopoietic stem cells


title: HSCs_PBS_rep8

description:
PBS_8
processed data file: GSE126793_HSC-counts.txt

value: PBS


title: HSCs_PBS_rep5

description:
PBS_5
processed data file: GSE126793_HSC-counts.txt


title: BEC_07


title: HSCs_MTP10-HDL_rep4

description:
MTP_4
processed data file: GSE126793_HSC-counts.txt


title: HSCs_MTP10-HDL_rep1

description:
MTP_1
processed data file: GSE126793_HSC-counts.txt


title: HSCs_MTP10-HDL_rep3

description:
MTP_3
processed data file: GSE126793_HSC-counts.txt


title: HSCs_PBS_rep4

description:
PBS_4
processed data file: GSE126793_HSC-counts.txt


title: HSCs_MTP10-HDL_rep6

description:
MTP_6
processed data file: GSE126793_HSC-counts.txt


title: BEC_01


title: HSCs_PBS_rep1

description:
PBS_1
processed data file: GSE126793_HSC-counts.txt


title: HSCs_PBS_rep2

description:
PBS_2
processed data file: GSE126793_HSC-counts.txt


title: BEC_31


title: HSCs_MTP10-HDL_rep2

description:
MTP_2
processed data file: GSE126793_HSC-counts.txt


title: HSCs_PBS_rep6

description:
PBS_6
processed data file: GSE126793_HSC-counts.txt


title: X20170513_P1_SAAABT_Post_01

status: Public on Feb 01 2019

type: RNA

city: New Haven

first: Lajos

last: Pusztai

state: CT

address: 300 George St., Suite 120

country: USA

institute: Yale University

hyb_protocol: When possible, 100 ng of RNA was hybridized to the NanoString IO360 panel (beta version) codeset and read on the nCounter platform.

scan_protocol: nCounter analysis system

data_processing: Negative (non-target binding) control probes embedded in the assay are used to evaluate the background. Positive control probes (specific for alien oligo sequences included in each reaction) are used to normalize samples to control for variations in hybridization and recovery. Finally, all samples are normalized to the geometric mean of housekeeper gene to correct for variations in sample input.

label: nanostring

organism: Homo sapiens

source_name: post-treatment breast cancer

label_protocol: NanoString manufactuerer's protocol

extract_protocol: Total RNA was isolated from 5um FFPE tumor tissue sections using the Qiagen RNeasy FFPE kit and quantified by Nanodrop

tag: er/pr status (1 if er+ or pr+; 0 if er- and pr-)

tag: pcr status (1 if pcr; 0 if residual disease or progressed before surgery)

tag: treatment arm (1 if assigned to bevacizumab (arm a); 0 if assigned to control (arm b + c))


title: X20170513_P1_SAAABY_Post_03


title: X20170513_P1_SAAABT_Pre_02

source_name: pre-treatment breast cancer


title: IHEC_05


title: X20170513_P1_SAAABY_Pre_04


title: HSCs_PBS_rep3

description:
PBS_3
processed data file: GSE126793_HSC-counts.txt


title: X20170513_P1_SAAAFF_Post_08


title: X20170513_P1_SAAAFF_Pre_09


title: X20170513_P1_SAAAGF_Pre_11


title: X20170513_P1_SAAAGF_Post_10


title: X20170513_P2_SAAAGN_Pre_04


title: X20170513_P2_SAAAGN_Post_03


title: X20170513_P2_SAAAGG_Post_01


title: X20170513_P2_SAAALY_Post_05


title: X20170513_P2_SAAANK_Post_07


title: X20170513_P2_SAAANN_Post_10


title: X20170513_P3_SAAANS_Pre_02


title: X20170513_P3_SAAANS_Post_01


title: X20170513_P2_SAAANN_Pre_11


title: X20170513_P3_SAAASA_Pre_04


title: X20170513_P3_SAAASK_Post_05


title: X20170513_P3_SAAATV_Pre_11


title: X20170513_P3_SAAATV_Post_10


title: X20170513_P4_SAAAYJ_Post_03


title: X20170513_P4_SAAATX_Post_01


title: X20170513_P4_SAAAYJ_Pre_04


title: X20170513_P4_SAABCL_Post_05


title: X20170513_P4_SAABIW_Post_08


title: X20170513_P4_SAABIW_Pre_09


title: X20170513_P2_SAAAGG_Pre_02


title: X20170513_P3_SAAASK_Pre_07


title: X20170514_P5_SAABPS.post_01


title: X20170513_P4_SAABKD_Pre_11


title: X20170513_P3_SAAASA_Post_03


title: X20170514_P5_SAABXY.post_03


title: X20170514_P5_SAABPS.pre_02


title: X20170514_P5_SAACBI.pre_07


title: X20170513_P3_SAAASZ_Post_08


title: X20170514_P5_SAACIL.post_08


title: X20170514_P5_SAACIL.pre_09


title: X20170514_P6_SAACMD.post_01


title: X20170514_P5_SAACJA.pre_11


title: X20170514_P6_SAACMD.pre_02


title: X20170514_P6_SAACTT.post_03


title: X20170514_P6_SAACTX.post_06


title: X20170514_P6_SAACTT.pre_04


title: X20170514_P6_SAACWC.post_08


title: X20170514_P6_SAACTX.pre_07


title: X20170514_P7_SAADBT.post_01


title: X20170517_P13_SAACYD.pre_01


title: X20170514_P7_SAAECM.post_03


title: X20170514_P7_SAADBT.pre_02


title: X20170514_P7_SAAEKA.pre_09


title: X20170514_P7_SAAECM.pre_04


title: X20170514_P7_SAAEKA.post_08


title: X20170514_P7_SAAEFU.pre_07


title: X20170514_P8_SAAHUV.post_01


title: X20170514_P7_SAAHGE.pre_11


title: X20170514_P8_SAAIBB.pre_04


title: X20170514_P8_SAAHUV.pre_02


title: X20170514_P8_SAAIBB.post_03


title: X20170514_P8_SAAJKX.pre_07


title: X20170514_P8_SAALRR.post_10


title: X20170514_P8_SAAKGE.post_08


title: X20170515_P9_SAALZP.post_01


title: X20170514_P7_SAAEFU.post_06


title: X20170514_P8_SAALRR.pre_11


title: X20170514_P8_SAAJKX.post_06


title: X20170514_P6_SAACWC.pre_09


title: X20170514_P8_SAAKGE.pre_09


title: X20170515_P9_SAAPPW.post_06


title: X20170515_P9_SAANIE.pre_04


title: X20170515_P9_SAANIE.post_03


title: X20170515_P9_SAALZP.pre_02


title: X20170515_P9_SAAPPW.pre_07


title: X20170515_P9_SAASDZ.pre_11


title: X20170515_P9_SAARGY.pre_09


title: X20170515_P10_SAAVBU.post_03


title: X20170515_P10_SAASVZ.pre_02


title: X20170515_P10_SAAVBU.pre_04


title: X20170515_P10_SAAZAM.post_10


title: X20170515_P10_SAAZAM.pre_11


title: X20170517_P13_SAAZPI.post_02


title: X20170517_P13_SAAZPI.pre_03


title: X20170515_P10_SAAVTI.pre_09


title: X20170515_P11_SABACY.post_06


title: X20170515_P11_SABADW.post_08


title: X20170517_P13_SABACY.pre_04


title: X20170515_P11_SAAZXY.pre_04


title: X20170515_P9_SAASDZ.post_10


title: X20170515_P9_SAARGY.post_08


title: X20170515_P10_SAASVZ.post_01


title: X20170515_P11_SABADW.pre_09


title: X20170515_P12_SABBMG.post_01


title: X20170515_P12_SABBMG.pre_02


title: X20170515_P11_SABAEM.post_10


title: X20170517_P13_SABAEM.pre_05


title: X20170515_P10_SAAVBV.post_06


title: X20170515_P12_SABCVB.pre_04


title: X20170515_P12_SABKWX.post_10


title: X20170515_P12_SABKWX.pre_11


title: PrAd_2H_MP_BR1

status: Public on Jan 21 2019

city: Bethesda

first: Luis

middle: M

last: Franco

state: MD

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description: Preadipocytes_2_hours_methylprednisolone_BR1

data_processing:
bcl to FASTQ file conversion was performed with bcl2fastq2 v. 2.20
Starting with the untrimmed FASTQ files (provided as raw files with this GEO entry), adapter-sequence trimming was performed with Cutadapt v. 1.10 on Python v. 2.7.9. Cutadapt parameters and adapter sequences: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 20
Alignment of the adapter-trimmed reads was performed with STAR v. 2.6. Reference genome assembly: GRCh38 reference assembly. Transcript annotation: GENCODE28 (gencode.v28.primary_assembly.annotation.gtf)
Generation of a matrix of aligned-read counts was performed with featureCounts, which is part of the Subread package v. 1.5.3. featureCounts parameters: -p -B -s 2 -T 8 -O -t exon -g gene_name. Transcript annotation: GENCODE28 (gencode.v28.primary_assembly.annotation.gtf)
Generation of abundance measurements (read counts) normalized by library size was performed with the R package DESeq2 v. 1.18.1, in R v. 3.5.0. Platform: x86_64-pc-linux-gnu (64-bit)
Genome_build: GRCh38
Supplementary_files_format_and_content: A file with processed data is provided: GSE112101_NormalizedReadCounts.txt. The values in the file are read counts normalized by library size by the median-of-ratios method implemented in DESeq2. The file contains a table with 58,765 rows and 13 columns. The first row is a header row and it is followed by 56,870 rows, each corresponding to one transcript. The first column has the transcript identifiers (corresponding to the GENCODE28 annotation file: gencode.v28.primary_assembly.annotation.gtf) and it is followed by 144 columns, one for each sample. A separate file with un-normalized read counts is also provided: GSE112101_RawReadCounts.txt. A file that contains the differential expression results for this dataset is provided: GSE112101_differential_expression_results.xlsx.

source_name: Human primary subcutaneous preadipocytes from adult

extract_protocol:
Total RNA was isolated by extraction with TRIzol Reagent (Thermo Fisher Scientific, Cat. No. 15596018) followed by column-based purification with the RNA Clean & Concentrator-5 kit (Zymo Research; Cat. No. R1016).
RNA libraries were prepared with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Preparation Kit (Illumina, Cat. No. RS-122-2303).

value: primary subcutaneous preadipocytes

tag: time

value: 2 hours

value: Methylprednisolone

tag: replicate number


title: Myob_6H_VH_BR1

source_name: Human primary skeletal muscle myoblasts from adult

value: primary skeletal muscle myoblasts

value: 6 hours

value: Vehicle


title: PrAd_2H_VH_BR1


title: Myob_6H_MP_BR1

description: Myoblasts_6_hours_methylprednisolone_BR1


title: Myob_2H_MP_BR1

description: Myoblasts_2_hours_methylprednisolone_BR1


title: Fibr_6H_VH_BR1

source_name: Human primary dermal fibroblasts from adult

value: primary dermal fibroblasts


title: Fibr_2H_VH_BR1


title: Fibr_2H_MP_BR1

description: Fibroblasts_2_hours_methylprednisolone_BR1


title: PrAd_6H_VH_BR1


title: PrAd_6H_MP_BR1

description: Preadipocytes_6_hours_methylprednisolone_BR1


title: Ostb_6H_MP_BR1

description: Osteoblasts_6_hours_methylprednisolone_BR1

source_name: Human primary osteoblasts from adult

value: primary osteoblasts


title: Endo_6H_VH_BR1

source_name: Human dermal microvascular endothelial cells from adult

value: dermal microvascular endothelial cells


title: Endo_6H_MP_BR1

description: Endothelial_cells_6_hours_methylprednisolone_BR1


title: Ostb_2H_MP_BR1

description: Osteoblasts_2_hours_methylprednisolone_BR1


title: Bcells_6H_MP_BR1

source_name: Peripheral blood total B cells from adult

value: Peripheral blood total B cells


title: Bcells_6H_VH_BR1


title: Bcells_2H_VH_BR1


title: Ostb_6H_VH_BR1


title: Endo_2H_MP_BR1

description: Endothelial_cells_2_hours_methylprednisolone_BR1


title: Ostb_2H_VH_BR1


title: Endo_2H_VH_BR1


title: CD4_6H_VH_BR1

source_name: Peripheral blood CD4+ T cells from adult

value: Peripheral blood CD4+ T cells


title: CD4_6H_MP_BR1

description: CD4_T_cells_6_hours_methylprednisolone_BR1


title: CD4_2H_VH_BR1


title: Bcells_2H_MP_BR1


title: Myob_2H_VH_BR1


title: Neut_6H_VH_BR1

source_name: Peripheral blood neutrophils from adult

value: Peripheral blood neutrophils


title: Fibr_6H_MP_BR1

description: Fibroblasts_6_hours_methylprednisolone_BR1


title: Neut_2H_MP_BR1

description: Neutrophils_2_hours_methylprednisolone_BR1


title: Neut_6H_MP_BR1

description: Neutrophils_6_hours_methylprednisolone_BR1


title: Mono_2H_VH_BR1

source_name: Peripheral blood monocytes from adult

value: Peripheral blood monocytes


title: Mono_6H_MP_BR1

description: Monocytes_6_hours_methylprednisolone_BR1


title: PrAd_6H_VH_BR4

description:
PrAd_6H_VH_BR4_S107_L008
Preadipocytes_6_hours_vehicle_BR4

value: Human primary subcutaneous preadipocytes

tag: exposure


title: PrAd_6H_MP_BR3

description:
PrAd_6H_MP_BR3_S102_L008
Preadipocytes_6_hours_methylprednisolone_BR3


title: PrAd_6H_MP_BR4

description:
PrAd_6H_MP_BR4_S106_L008
Preadipocytes_6_hours_methylprednisolone_BR4


title: PrAd_6H_VH_BR2

description:
PrAd_6H_VH_BR2_S99_L008
Preadipocytes_6_hours_vehicle_BR2


title: PrAd_6H_MP_BR2

description:
PrAd_6H_MP_BR2_S98_L008
Preadipocytes_6_hours_methylprednisolone_BR2


title: CD4_2H_MP_BR1

description: CD4_T_cells_2_hours_methylprednisolone_BR1


title: PrAd_2H_VH_BR4

description:
PrAd_2H_VH_BR4_S105_L008
Preadipocytes_2_hours_vehicle_BR4


title: PrAd_2H_VH_BR3

description:
PrAd_2H_VH_BR3_S101_L008
Preadipocytes_2_hours_vehicle_BR3


title: Neut_2H_VH_BR1


title: PrAd_6H_VH_BR3

description:
PrAd_6H_VH_BR3_S103_L008
Preadipocytes_6_hours_vehicle_BR3


title: PrAd_2H_MP_BR4

description:
PrAd_2H_MP_BR4_S104_L008
Preadipocytes_2_hours_methylprednisolone_BR4


title: Myob_6H_VH_BR4

description:
Myob_6H_VH_BR4_S108_L008
Myoblasts_6_hours_vehicle_BR4

value: Human primary skeletal muscle myoblasts


title: Myob_6H_VH_BR2

description:
Myob_6H_VH_BR2_S28_L002
Myoblasts_6_hours_vehicle_BR2


title: PrAd_2H_MP_BR3

description:
PrAd_2H_MP_BR3_S100_L008
Preadipocytes_2_hours_methylprednisolone_BR3


title: Myob_2H_VH_BR4

description:
Myob_2H_VH_BR4_S82_L006
Myoblasts_2_hours_vehicle_BR4


title: PrAd_2H_MP_BR2

description:
PrAd_2H_MP_BR2_S96_L008
Preadipocytes_2_hours_methylprednisolone_BR2


title: Myob_6H_MP_BR2

description:
Myob_6H_MP_BR2_S21_L002
Myoblasts_6_hours_methylprednisolone_BR2


title: Myob_2H_VH_BR2

description:
Myob_2H_VH_BR2_S14_L001
Myoblasts_2_hours_vehicle_BR2


title: Myob_6H_VH_BR3

description:
Myob_6H_VH_BR3_S56_L004
Myoblasts_6_hours_vehicle_BR3


title: Mono_2H_MP_BR1

description: Monocytes_2_hours_methylprednisolone_BR1


title: Myob_6H_MP_BR4

description:
Myob_6H_MP_BR4_S95_L007
Myoblasts_6_hours_methylprednisolone_BR4


title: Mono_6H_VH_BR1


title: Myob_2H_MP_BR4

description:
Myob_2H_MP_BR4_S63_L005
Myoblasts_2_hours_methylprednisolone_BR4


title: Myob_6H_MP_BR3

description:
Myob_6H_MP_BR3_S49_L004
Myoblasts_6_hours_methylprednisolone_BR3


title: Myob_2H_MP_BR3

description:
Myob_2H_MP_BR3_S35_L003
Myoblasts_2_hours_methylprednisolone_BR3


title: Fibr_6H_VH_BR3

description:
Fibr_6H_VH_BR3_S54_L004
Fibroblasts_6_hours_vehicle_BR3

value: Human primary dermal fibroblasts


title: Fibr_6H_VH_BR4

description:
Fibr_6H_VH_BR4_S80_L006
Fibroblasts_6_hours_vehicle_BR4


title: Myob_2H_MP_BR2

description:
Myob_2H_MP_BR2_S7_L001
Myoblasts_2_hours_methylprednisolone_BR2


title: PrAd_2H_VH_BR2

description:
PrAd_2H_VH_BR2_S97_L008
Preadipocytes_2_hours_vehicle_BR2


title: Myob_2H_VH_BR3

description:
Myob_2H_VH_BR3_S42_L003
Myoblasts_2_hours_vehicle_BR3


title: Fibr_6H_MP_BR4

description:
Fibr_6H_MP_BR4_S74_L006
Fibroblasts_6_hours_methylprednisolone_BR4


title: Fibr_6H_VH_BR2

description:
Fibr_6H_VH_BR2_S26_L002
Fibroblasts_6_hours_vehicle_BR2


title: Fibr_6H_MP_BR3

description:
Fibr_6H_MP_BR3_S47_L004
Fibroblasts_6_hours_methylprednisolone_BR3


title: Fibr_6H_MP_BR2

description:
Fibr_6H_MP_BR2_S19_L002
Fibroblasts_6_hours_methylprednisolone_BR2


title: Fibr_2H_VH_BR4

description:
Fibr_2H_VH_BR4_S68_L005
Fibroblasts_2_hours_vehicle_BR4


title: Fibr_2H_VH_BR3

description:
Fibr_2H_VH_BR3_S40_L003
Fibroblasts_2_hours_vehicle_BR3


title: Ostb_6H_VH_BR4

description:
Ostb_6H_VH_BR4_S81_L006
Osteoblasts_6_hours_vehicle_BR4

source_name: Human primary osteoblasts from child

value: Human primary osteoblasts


title: Fibr_2H_VH_BR2

description:
Fibr_2H_VH_BR2_S12_L001
Fibroblasts_2_hours_vehicle_BR2


title: Fibr_2H_MP_BR2

description:
Fibr_2H_MP_BR2_S5_L001
Fibroblasts_2_hours_methylprednisolone_BR2


title: Fibr_2H_MP_BR4

description:
Fibr_2H_MP_BR4_S61_L005
Fibroblasts_2_hours_methylprednisolone_BR4


title: Fibr_2H_MP_BR3

description:
Fibr_2H_MP_BR3_S33_L003
Fibroblasts_2_hours_methylprednisolone_BR3


title: Ostb_2H_MP_BR3

description:
Ostb_2H_MP_BR3_S34_L003
Osteoblasts_2_hours_methylprednisolone_BR3


title: Ostb_6H_MP_BR4

description:
Ostb_6H_MP_BR4_S75_L006
Osteoblasts_6_hours_methylprednisolone_BR4


title: Ostb_6H_MP_BR2

description:
Ostb_6H_MP_BR2_S20_L002
Osteoblasts_6_hours_methylprednisolone_BR2


title: Ostb_2H_VH_BR3

description:
Ostb_2H_VH_BR3_S41_L003
Osteoblasts_2_hours_vehicle_BR3


title: Ostb_2H_MP_BR4

description:
Ostb_2H_MP_BR4_S62_L005
Osteoblasts_2_hours_methylprednisolone_BR4


title: Ostb_2H_VH_BR2

description:
Ostb_2H_VH_BR2_S13_L001
Osteoblasts_2_hours_vehicle_BR2


title: Ostb_2H_VH_BR4

description:
Ostb_2H_VH_BR4_S69_L005
Osteoblasts_2_hours_vehicle_BR4


title: Ostb_2H_MP_BR2

description:
Ostb_2H_MP_BR2_S6_L001
Osteoblasts_2_hours_methylprednisolone_BR2


title: Endo_6H_VH_BR4

description:
Endo_6H_VH_BR4_S94_L007
Endothelial_cells_6_hours_vehicle_BR4

value: Human dermal microvascular endothelial cells


title: Endo_6H_VH_BR2

description:
Endo_6H_VH_BR2_S86_L007
Endothelial_cells_6_hours_vehicle_BR2


title: Endo_6H_MP_BR4

description:
Endo_6H_MP_BR4_S93_L007
Endothelial_cells_6_hours_methylprednisolone_BR4


title: Endo_6H_MP_BR3

description:
Endo_6H_MP_BR3_S89_L007
Endothelial_cells_6_hours_methylprednisolone_BR3


title: Endo_6H_MP_BR2

description:
Endo_6H_MP_BR2_S85_L007
Endothelial_cells_6_hours_methylprednisolone_BR2


title: Ostb_6H_MP_BR3

description:
Ostb_6H_MP_BR3_S48_L004
Osteoblasts_6_hours_methylprednisolone_BR3


title: Endo_2H_VH_BR4

description:
Endo_2H_VH_BR4_S92_L007
Endothelial_cells_2_hours_vehicle_BR4


title: Ostb_6H_VH_BR3

description:
Ostb_6H_VH_BR3_S55_L004
Osteoblasts_6_hours_vehicle_BR3


title: X20170515_P10_SAAVTI.post_08


title: Endo_2H_VH_BR3

description:
Endo_2H_VH_BR3_S88_L007
Endothelial_cells_2_hours_vehicle_BR3


title: Endo_2H_MP_BR4

description:
Endo_2H_MP_BR4_S91_L007
Endothelial_cells_2_hours_methylprednisolone_BR4


title: Endo_2H_VH_BR2

description:
Endo_2H_VH_BR2_S84_L007
Endothelial_cells_2_hours_vehicle_BR2


title: Endo_2H_MP_BR3

description:
Endo_2H_MP_BR3_S87_L007
Endothelial_cells_2_hours_methylprednisolone_BR3


title: Ostb_6H_VH_BR2

description:
Ostb_6H_VH_BR2_S27_L002
Osteoblasts_6_hours_vehicle_BR2


title: Endo_2H_MP_BR2

description:
Endo_2H_MP_BR2_S83_L007
Endothelial_cells_2_hours_methylprednisolone_BR2


title: Bcells_6H_VH_BR4

description:
Bcells_6H_VH_BR4_S25_L002
B_cells_6_hours_vehicle_BR4


title: Bcells_6H_VH_BR2

description:
Bcells_6H_VH_BR2_S50_L004
B_cells_6_hours_vehicle_BR2


title: Bcells_6H_VH_BR3

description:
Bcells_6H_VH_BR3_S77_L006
B_cells_6_hours_vehicle_BR3


title: Endo_6H_VH_BR3

description:
Endo_6H_VH_BR3_S90_L007
Endothelial_cells_6_hours_vehicle_BR3


title: Bcells_6H_MP_BR4

description:
Bcells_6H_MP_BR4_S18_L002
B_cells_6_hours_methylprednisolone_BR4


title: Bcells_6H_MP_BR3

description:
Bcells_6H_MP_BR3_S71_L006
B_cells_6_hours_methylprednisolone_BR3


title: Bcells_2H_VH_BR4

description:
Bcells_2H_VH_BR4_S11_L001
B_cells_2_hours_vehicle_BR4


title: Bcells_6H_MP_BR2

description:
Bcells_6H_MP_BR2_S43_L004
B_cells_6_hours_methylprednisolone_BR2


title: Bcells_2H_VH_BR3

description:
Bcells_2H_VH_BR3_S65_L005
B_cells_2_hours_vehicle_BR3


title: CD4_6H_VH_BR4

description:
CD4_6H_VH_BR4_S53_L004
CD4_T_cells_6_hours_vehicle_BR4


title: Bcells_2H_VH_BR2

description:
Bcells_2H_VH_BR2_S36_L003
B_cells_2_hours_vehicle_BR2


title: Bcells_2H_MP_BR2

description:
Bcells_2H_MP_BR2_S29_L003
B_cells_2_hours_methylprednisolone_BR2


title: Bcells_2H_MP_BR3

description:
Bcells_2H_MP_BR3_S58_L005
B_cells_2_hours_methylprednisolone_BR3


title: Bcells_2H_MP_BR4

description:
Bcells_2H_MP_BR4_S4_L001
B_cells_2_hours_methylprednisolone_BR4


title: CD4_6H_VH_BR2

description:
CD4_6H_VH_BR2_S76_L006
CD4_T_cells_6_hours_vehicle_BR2


title: CD4_6H_MP_BR3

description:
CD4_6H_MP_BR3_S17_L002
CD4_T_cells_6_hours_methylprednisolone_BR3


title: CD4_2H_VH_BR4

description:
CD4_2H_VH_BR4_S39_L003
CD4_T_cells_2_hours_vehicle_BR4


title: CD4_6H_MP_BR4

description:
CD4_6H_MP_BR4_S46_L004
CD4_T_cells_6_hours_methylprednisolone_BR4


title: CD4_6H_MP_BR2

description:
CD4_6H_MP_BR2_S70_L006
CD4_T_cells_6_hours_methylprednisolone_BR2


title: CD4_2H_VH_BR3

description:
CD4_2H_VH_BR3_S10_L001
CD4_T_cells_2_hours_vehicle_BR3


title: CD4_2H_MP_BR4

description:
CD4_2H_MP_BR4_S32_L003
CD4_T_cells_2_hours_methylprednisolone_BR4


title: Neut_6H_VH_BR4

description:
Neut_6H_VH_BR4_S78_L006
Neutrophils_6_hours_vehicle_BR4


title: CD4_2H_MP_BR3

description:
CD4_2H_MP_BR3_S3_L001
CD4_T_cells_2_hours_methylprednisolone_BR3


title: CD4_2H_VH_BR2

description:
CD4_2H_VH_BR2_S64_L005
CD4_T_cells_2_hours_vehicle_BR2


title: Neut_6H_MP_BR4

description:
Neut_6H_MP_BR4_S72_L006
Neutrophils_6_hours_methylprednisolone_BR4


title: Neut_6H_VH_BR2

description:
Neut_6H_VH_BR2_S22_L002
Neutrophils_6_hours_vehicle_BR2


title: CD4_2H_MP_BR2

description:
CD4_2H_MP_BR2_S57_L005
CD4_T_cells_2_hours_methylprednisolone_BR2


title: Neut_6H_VH_BR3

description:
Neut_6H_VH_BR3_S51_L004
Neutrophils_6_hours_vehicle_BR3


title: Neut_6H_MP_BR3

description:
Neut_6H_MP_BR3_S44_L004
Neutrophils_6_hours_methylprednisolone_BR3


title: CD4_6H_VH_BR3

description:
CD4_6H_VH_BR3_S24_L002
CD4_T_cells_6_hours_vehicle_BR3


title: Neut_6H_MP_BR2

description:
Neut_6H_MP_BR2_S15_L002
Neutrophils_6_hours_methylprednisolone_BR2


title: Neut_2H_VH_BR4

description:
Neut_2H_VH_BR4_S66_L005
Neutrophils_2_hours_vehicle_BR4


title: Neut_2H_MP_BR3

description:
Neut_2H_MP_BR3_S30_L003
Neutrophils_2_hours_methylprednisolone_BR3


title: Neut_2H_VH_BR2

description:
Neut_2H_VH_BR2_S8_L001
Neutrophils_2_hours_vehicle_BR2


title: Mono_6H_VH_BR3

description:
Mono_6H_VH_BR3_S52_L004
Monocytes_6_hours_vehicle_BR3


title: Mono_6H_VH_BR4

description:
Mono_6H_VH_BR4_S79_L006
Monocytes_6_hours_vehicle_BR4


title: Neut_2H_MP_BR4

description:
Neut_2H_MP_BR4_S59_L005
Neutrophils_2_hours_methylprednisolone_BR4


title: Neut_2H_VH_BR3

description:
Neut_2H_VH_BR3_S37_L003
Neutrophils_2_hours_vehicle_BR3


title: Mono_6H_VH_BR2

description:
Mono_6H_VH_BR2_S23_L002
Monocytes_6_hours_vehicle_BR2


title: Mono_6H_MP_BR2

description:
Mono_6H_MP_BR2_S16_L002
Monocytes_6_hours_methylprednisolone_BR2


title: Mono_6H_MP_BR3

description:
Mono_6H_MP_BR3_S45_L004
Monocytes_6_hours_methylprednisolone_BR3


title: Mono_6H_MP_BR4

description:
Mono_6H_MP_BR4_S73_L006
Monocytes_6_hours_methylprednisolone_BR4


title: Mono_2H_VH_BR3

description:
Mono_2H_VH_BR3_S38_L003
Monocytes_2_hours_vehicle_BR3


title: Mono_2H_VH_BR4

description:
Mono_2H_VH_BR4_S67_L005
Monocytes_2_hours_vehicle_BR4


title: Neut_2H_MP_BR2

description:
Neut_2H_MP_BR2_S1_L001
Neutrophils_2_hours_methylprednisolone_BR2


title: Mono_2H_MP_BR3

description:
Mono_2H_MP_BR3_S31_L003
Monocytes_2_hours_methylprednisolone_BR3


title: Mono_2H_MP_BR4

description:
Mono_2H_MP_BR4_S60_L005
Monocytes_2_hours_methylprednisolone_BR4


title: Mono_2H_MP_BR2

description:
Mono_2H_MP_BR2_S2_L001
Monocytes_2_hours_methylprednisolone_BR2


title: Mono_2H_VH_BR2

description:
Mono_2H_VH_BR2_S9_L001
Monocytes_2_hours_vehicle_BR2


title: AHJCJKADXX_US-1577492_CAGATC_L002: FA-2

status: Public on Dec 19 2018

city: Seattle

first: Charles

middle: E.

last: Murry

state: WA

address: 850 Republican St.

institute: Institute for Stem Cell & Regenerative Medicine

data_processing:
RNA-seq reads in fastq files were aligned to hg19 using Tophat (version 2.0.13).
Gene-level read counts were quantified using htseq-count 62 using Ensembl GRCh37 gene annotations.
FeatureCounts was used to do gene-level quantification.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each sample.

source_name: hPSC-CM (human pluripotent stem cell derived cardiomyoyctes)

growth_protocol: Undifferentiated human IMR90-induced pluripotent stem cells, originally derived from lung fibroblasts(Yu et al., 2007) (James A. Thomson, University of Wisconsin-Madison), were expanded using mouse embryonic fibroblast-conditioned medium supplemented with 5 ng/ml basic fibroblast growth factor. Cardiomyocytes were obtained using a protocol based on our previously reported directed differentiation method that involves the serial application of activin A and bone morphogenetic protein-4 (BMP4) under serum-free, monolayer culture conditions(Hofsteen et al., 2016). The cultures were also supplemented with the Wnt agonist CHIR 99021 in the early stages of differentiation followed by the Wnt antagonist Xav 939. After 20 days of in vitro differentiation, the cells were dispersed using 0.05% trypsin-EDTA and replated. Cultures were fed every other day thereafter with serum-free RPMI-B27 plus L-glutamine. Only cell preparations containing >80% cardiac troponin T-positive cardiomyocytes were used for the current study.  After 20 days of differentiation, the cells were treated with half dosage (52.5 µM palmitate-BSA, 40.5 µM oleic-BSA, and 22.5 µM linoleic-BSA) of fatty acids-albumin complexes in RPMI-B27 plus insulin medium for two weeks. Note that glucose was maintained at its normal media levels (11 mM).  L-carnitine was added to the medium at 120 µM, because this dipeptide is essential for fatty acid transport into mitochondria. Control hPSC-CMs were fed with the same basal medium (RPMI + B27 plus insulin) supplemented with 50 μM fatty acid-free albumin and 120 μM carnitine. Media were changed every other day. This study was mainly performed with cardiomyocytes-derived from the IMR90 hiPS cell line. However, cardiomyocytes from another hiPS cell line, WTC11(Miyaoka et al., 2014) (Wild Type C, Gladstone Institute of Cardiovascular Disease, University of California San Francisco), and an embryonic stem cell line, RUES2 (Rockfeller University, New York, NY), were also used to confirm that major findings were generally applicable. RUES2 and WTC11 undifferentiated cells were cultured with mTeSR medium and similar differentiation protocols as to IMR90 were used to obtain cardiomyocytes from these two cell lines. Only cell preparations containing >80% cardiac troponin T-positive cardiomyocytes (by flow cytometry) were used for the current investigation.

extract_protocol:
mRNA Sequencing Analysis  RNA was extracted using RNeasy mini kit (Qiagen).
RNA library was prepared using Truseq library preparation kits (Illumina) following the manufacturer’s protocols.


title: AHJCJKADXX_US-1577483_ACAGTG_L001: control-2

treatment_protocol: After 20 days of differentiation, the cells were treated with half dosage (52.5 µM palmitate-BSA, 40.5 µM oleic-BSA, and 22.5 µM linoleic-BSA) of fatty acids-albumin complexes in RPMI-B27 plus insulin medium for two weeks. Note that glucose was maintained at its normal media levels (11 mM).  L-carnitine was added to the medium at 120 µM, because this dipeptide is essential for fatty acid transport into mitochondria. Control hPSC-CMs were fed with the same basal medium (RPMI + B27 plus insulin) supplemented with 50 μM fatty acid-free albumin and 120 μM carnitine.

value: hPSC-CM (human pluripotent stem cell derived cardiomyoyctes)


title: AHJCJKADXX_US-1577475_ATCACG_L001: control-1


title: AHJCJKADXX_US-1577479_TTAGGC_L001: FA-1


title: NE_Pax6GFP_1

status: Public on Sep 08 2017

city: New York

first: Lorenz

last: Studer

state: NY

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
P1
Neuroectoderm #1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to hg19 whole genome using Tophat v1.2.  Alignments were then quantified using HTSeq and analyzed using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file

source_name: Day 12 of differentiation from hESCs

extract_protocol:
Cells were FACS sorted for reporter signal and Trizol was added to the cells and frozen.  RNA was extracted using a combination of phase lock gels and the Rneasy Mini Elute kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PAX6+ neuroectoderm


title: NE_Pax6GFP_2

description:
P2
Neuroectoderm #2


title: Growth with no caspofungin - sample 2

status: Public on Jun 16 2017

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

institute: CHU de Rennes

data_processing:
The reads were mapped against the genomic sequence of E. faecium Aus0004 (Genbank accession no. CP003351) and counted using the CLC Genomics Workbench software v10.0.1 (Qiagen).
The expression of genes in different RNA-seq samples was compared using the R package DESeq2 R package.
genome build: E. faecium Aus0004 (Genbank accession no. CP003351)
processed data files format and content: Tab-delimited text files generated using the CLC Genomics Workbench software v10.0.1 (Qiagen).

molecule: polyA RNA

organism: Enterococcus faecium

source_name: Bacteria_without caspofungin

growth_protocol: Bacterial cells of E. faecium Aus0004 bacteria were cultured at 37°C to the late-exponential-growth phase in BHI broth

extract_protocol:
Total RNA was extracted from using the ZR Fungal/Bacterial RNA Miniprep kit (Zymo Research, Irvine, CA). Residual chromosomal DNA was removed by treating samples with the TURBO DNA-free kit (Life Technologies). The Ribo-Zero Magnetic Kit Gram-Positive Bacteria (Epicentre, Madison, WI) was used according to the manufacturer’s recommendations to remove the 23S, 16S, and 5S rRNAs from the total RNA samples.
The strand-specific library preparation was performed using the NEXTflex Directional RNA-Seq Kit (dUTP-Based) (Bio Scientific, Austin, TX) and the samples were sequenced using the Illumina HiSeq 2500 platform (multiplex protocol, single-end 50-bp reads).


title: Growth with no caspofungin - sample 1


title: C2C12 myoblast GRO-seq rep 1

status: Public on Jun 13 2017

first: Jie

last: Yao

address: 615 Westlake Ave N

institute: Allen Institute

data_processing:
library strategy: GRO-seq
Basecalls performed using CASAVA version 1.8.
Reads were aligned to mm9 by Bowtie2 using the default setting.
To maximize the yield, unqualified reads were subject to trimming of 5 bp from the 3’ end and realignment at the reduced length. This process was repeated until reads were trimmed down to 21bp.
Reads mapped to rRNA and tRNA genes (track RepeatMasker in UCSC genome browser) were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: C2C12myoblast.GRO-seq.geneActivity.txt: Tab-delimited text file listing RefSeq gene activity (RPKmM) by GRO-seq in C2C12 myoblasts.

source_name: C2C12 myoblasts

growth_protocol: C2C12 cells were grown on 10 cm plates to a confluency of 80% in DMEM high glucose (Invitrogen, 11965-092), supplemented with 10% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
C2C12 myoblasts cultured to 80% confluency were washed directly on the 10 cm plate three times with ice cold 1X PBS. Four 10 cm plates were used for each nuclei isolation. Nuclei were isolated as described in Core et al (Core, Waterfall and Lis, Science 2008). Nuclei were counted, resuspended in 100 μl Storage Buffer/5x 106 nuclei and flash frozen in liquid nitrogen.  GRO-seq libraries were prepared as in Core et al (Core, Waterfall and Lis, Science 2008) with the following modifications: Total RNA in the 200 μL run-on reaction was extracted by 600 μL Trizol LS (Invitrogen, 10296-010) and subsequently extracted by 160 μL chloroform once, acid phenol-chloroform twice (equal volume) and chloroform once (equal volume).  During immunoprecipitation of BrU RNA, 1 μL SUPERaseIN (20u/μL) was added to 5 ml Binding Buffers. Anti-BrdU beads were first washed three times in Binding Buffer + 500 mM NaCl and then incubated with the Blocking Buffer. Blocked anti-BrdU Beads were washed twice with 500 μL Binding Buffer, resuspended in 400 μL Binding Buffer before adding run-on RNA. Beads were then washed once with Low Salt Buffer, once with High Salt Buffer and twice with TET Buffer. RNA end repairs steps were performed as described in the extraction protocol of GSM1480325 (Core et al, Nature Genetics, 2014).
NEXTflex small RNA sequencing kit (Bioo Scientific) was used to generate the libraries. Anti-BrdU beads (Santa Cruz, sc-32323 AC) were used to immunoprecipitate BrU RNA after the 5’- and the 3’- RNA adaptor ligation as described in Core et al (Core, Waterfall and Lis, Science 2008).

treatment_protocol: No specific treatment was performed for this study.

tag: cell line

value: mouse myoblast cell line

tag: rna source

value: nuclear run-on

tag: pull-down strategy

value: BrU

tag: antibody

value: Anti-BrdU (Santa Cruz Biotechnology, sc-32323 AC)


title: NE_Pax6GFP_3

description:
P3
Neuroectoderm #3


title: Growth with caspofungin (8 mg/L) - sample 2

source_name: Bacteria_with caspofungin


title: C2C12 myoblast GRO-seq rep 2


title: RHC2502

status: Public on Mar 20 2017

city: Singapore

first: Huipeng

last: Li

address: 60 Biopolis St, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: processed data file = cell_line_FPKM.csv

data_processing:
Raw FASTQ files were processed with Tophat-2.1.0 for alignment. Tophat parameters were tuned for single cell data. Namely, "--read-edit-dist" was set to 3, "--read-realign-edit-dist" was set to 0. hg19 was used as the genome reference. The "max-multihits" parameter was set to 1 so that only uniquely mapped reads were exported to the aligned BAM file.
Gene abundances were quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using Cuffdiff-2.2.1, with "--frag-bias-correct" parameter enabled, "--library-norm-method" set to be "classic-fpkm". To remove the systematic scaling effect of short RNAs on the FPKM values of the whole transcriptome, we masked out rRNAs, tRNAs, snRNA and snoRNAs by introducing a mask file for the "--mask-file" option of Cuffdiff. Raw count values were also exported by Cuffdiff for the QC analysis.
Genome_build: hg19
Supplementary_files_format_and_content: comma separated files include raw FPKM values of all cells that passed QC

source_name: H1_Cell line_batch2

growth_protocol: Cell lines: H1 human ES cell line was grown in mTESR medium (STEMCELL). GM12878 were grown in suspension in RPMI 1640 supplemented with 2mM L-glutamine and 15% fetal bovine serum. A549, HCT116, K562, IMR90 and H1437 cell lines were cultivated in DMEM medium supplemented with 10% fetal bovine serum and 2mM L-glutamine. Cell lines were maintained at 37 degrees, in 5% CO2 and 95% air controlled humid chamber.

extract_protocol:
Dissociated single cells were stained for viability assessment using Calcein AM and Ethidium-Homodimer-1 (Live/Dead Kit, Lifetech) before being loaded onto RNAseq IFC-C1 chips (5-10 and 10-17µm size chips). RNAseq assay was done according to the manufacturer's instructions (Fluidigm). Briefly, dissociated single cells optimal buoyancy was achieved by mixing them with Cell Suspension Buffer and Cell Wash Buffer before loading onto the IFC chips. Once the cell capture was achieved, all the IFC were imaged using  Nikon microscope. Based on bright field and Calcein AM imaging, only single cells were selected for subsequent library preparation and sequencing analysis. RNAseq protocol was conducted according to the manufacturer indications, onto C1 machines using SMARTer® Kit Designed for the C1TM System (Clontech). Briefly, after cell lysis, mRNA was isolated and converted to cDNA using modified oligo dT primers. PCR based pre-amplification of the cDNA was achieved using the Advantage 2 PCR kit (Clontech) for 21 cycles (C1 protocol). cDNAs were subsequently harvested for each single cell, individually quantified using Quant-ITTM PicoGreen® dsDNA Assay Kit (Lifetech) and checked for quality using High Sensitivity DNA Chips on a Bioanalyzer instrument (Agilent Technologies).  RNAseq assays were identically conducted from cell lines: A549 (Human Lung carcinoma cell line, ATCC), GM12878 (human B-Lymphoide cancer cell line, Coriell Institute), H1437 (Human Lung adenocarcinoma cancer cell line, ATCC), IMR90 (human fetal lung fibroblast cell line, ATCC), H1 (human embryonic cell line), K562 (human immortalised myelogenous leukemia cell line, ATCC). For GM12878 and H1 ESC cell lines, two independent experiments were conducted.
Library prep were prepared only with selected single cells showing correct cDNA concentration and quality. We used Nextera XT DNA Sample Preparation Kit (illumina) in combination with Nextera XT DNA Sample Preparation Index Kit (96 indices) (Illumina) to complete individual library preparation, according to manufacturer's instruction. We subsequently pooled up to 96 libraries for clean up using Agencourt AMPure® XP (Agencourt Bioscience Corp). Pooled and multiplexed libraries were processed on HiSeq HighOutput v3000 for 101-paired-end sequencing (Illumina).

treatment_protocol: Tumor tissues were obtained from patients diagnosed with colorectal cancer, after written informed consent was obtained, from the National Cancer Center of Singapore, Singapore General Hospital. Patients (n=11) diagnosed with stage 2-4 Colorectal Carcinoma (CRC) were selected for this study. Primary tumors were surgically removed and kept in sterile and cold RPMI medium until processing. Normal Mucosa (NM) was sampled far from neoplastic tissue. Fresh resected tissues were processed as soon as possible after surgery. Briefly, samples were minced on a plate and enzymatically digested with Collagenase IV (Gibco) and DNAse I (Worthington) for 30 min at 37 degrees celcius, with agitation. After digestion, samples were sieved on a 100µm cell strainer, washed with PBS/BSA 1%/EDTA 2mM and centrifuged for 8 min at 500g. The washing  step was repeated using a 40µm cell strainer disposal. Pelleted cells were then resuspended in PBS/EDTA 2mM and assessed for viability and size in a Countess instrument (Lifetech). Cells were counted and resuspended in Cell suspension buffer (Fluidigm) and loaded onto IFC-C1 chips as per manufacturer recommendations.

tag: sample type

value: Cell line

tag: batch


title: RHC2499


title: RHC2500


title: RHC2504


title: RHC2501


title: RHC2505


title: RHC2503


title: RHC2494


title: RHC2496


title: RHC2506

description: processed data file = cell_line_FPKM.csv,


title: RHC2492


title: RHC2498


title: RHC2493


title: RHC2490


title: RHC2491


title: RHC2497


title: Growth with caspofungin (8 mg/L) - sample 1

tag: strain


title: RHC2488


title: RHC2487


title: RHC2486


title: RHC2485


title: RHC2483


title: RHC2484


title: RHC2482


title: RHC2480


title: RHC2481


title: RHC2479


title: RHC2477


title: RHC2476


title: RHC2471


title: RHC2473


title: RHC2474


title: RHC2489


title: RHC2475


title: RHC2469


title: RHC2463


title: RHC2472


title: RHC2465


title: RHC2470


title: RHC2468


title: RHC2467


title: RHC2466


title: RHC2462


title: RHC2458


title: RHC2457


title: RHC2455


title: RHC2461


title: RHC2456


title: RHC2454


title: RHC2478


title: RHC2453


title: RHC2449


title: RHC2451


title: RHC2452


title: RHC2460


title: RHC2448


title: RHC2447


title: RHC2446


title: RHC2444


title: RHC2445


title: RHC2437


title: RHC2440


title: RHC2441


title: RHC2443


title: RHC2439


title: RHC2434


title: RHC2436


title: RHC2459


title: RHC2435


title: RHC2442


title: RHC2426


title: RHC2427


title: RHC2431


title: RHC2430


title: RHC2428


title: RHC2429


title: RHC2425


title: RHC2424


title: RHC2423


title: RHC2420


title: RHC2421


title: RHC2419


title: RHC2438


title: RHC2432


title: RHC2417


title: RHC2433


title: RHC2416


title: RHC2414


title: RHC2413


title: RHC2410


title: RHC2409


title: RHC2415


title: RHC2408


title: RHG198

source_name: GM12878_Cell line_batch2


title: RHG194


title: RHC2411


title: RHG192


title: RHG191


title: RHC2412


title: RHG195


title: RHC2422


title: RHG196


title: RHC2418


title: RHG197


title: RHG190


title: RHG189


title: RHG188


title: RHG185


title: RHG186


title: RHG184


title: RHG193


title: RHG182


title: RHG187


title: RHG183


title: RHG180


title: RHG179


title: RHG178


title: RHG177


title: RHG176


title: RHG173


title: RHG174


title: RHG175


title: RHG172


title: RHG171


title: RHG165


title: RHG168


title: RHG166


title: RHG167


title: RHG170


title: RHG164


title: RHG160


title: RHG169


title: RHG161


title: RHG163


title: RHG181


title: RHG154


title: RHG153


title: RHG158


title: RHG155


title: RHG150


title: RHG152


title: RHG156


title: RHG151


title: RHG149


title: RHG147


title: RHG159


title: RHG146


title: RHG145


title: RHG144


title: RHG143


title: RHG157


title: RHG142


title: RHG141


title: RHG139


title: RHG140


title: RHG137


title: RHG134


title: RHG136


title: RHG135


title: RHG162


title: RHG131


title: RHG129


title: RHG130


title: RHG128


title: RHG148


title: RHG125


title: RHG124


title: RHG122


title: RHG123


title: RHG120


title: RHG138


title: RHG118


title: RHG121


title: RHG117


title: RHG116


title: RHG115


title: RHG114


title: RHG113


title: RHG133


title: RHG112


title: RHG126


title: RHG127


title: RHG132


title: RHG105


title: RHG106


title: RHG111


title: RHG107


title: RHG108


title: RHT112

source_name: K562_Cell line_batch1


title: RHG103


title: RHT111


title: RHT110


title: RHT108


title: RHT102


title: RHT106


title: RHT105


title: RHT101


title: RHG110


title: RHT100


title: RHT107


title: RHT099


title: RHT096


title: RHT097


title: RHT098


title: RHT113


title: RHG109


title: RHG119


title: RHT095


title: RHG104


title: RHT094


title: RHT093


title: RHT092


title: RHT109


title: RHT087


title: RHT089


title: RHT090


title: RHT104


title: RHT088


title: RHT086


title: RHT103


title: RHT084


title: RHT082


title: RHT081


title: RHT080


title: RHT083


title: RHT079


title: RHT077


title: RHT076


title: RHT075


title: RHT073


title: RHT072


title: RHT070


title: RHT071


title: RHT091


title: RHT069


title: RHT068


title: RHT066


title: RHT062


title: RHT065


title: RHT067


title: RHT063


title: RHT061


title: RHT059


title: RHT064


title: RHT085


title: RHT060


title: RHT058


title: RHT057


title: RHT056


title: RHT052


title: RHT078


title: RHT074


title: RHT053


title: RHT055


title: RHT049


title: RHT051


title: RHT050


title: RHT048


title: RHT046


title: RHT045


title: RHT047


title: RHT043


title: RHT041


title: RHT042


title: RHT039


title: RHT040


title: RHT038


title: RHT037


title: RHT035


title: RHT036


title: RHT034


title: RHT032


title: RHT031


title: RHT030


title: RHT054


title: RHT026


title: RHT028


title: RHT025


title: RHT027


title: RHT024


title: RHT023


title: RHT022


title: RHT021


title: RHT044


title: RHT020


title: RHC146

source_name: H1_Cell line_batch1


title: RHT019


title: RHT033


title: RHT029


title: RHC145


title: RHC144


title: RHC141


title: RHC140


title: RHC142


title: RHC138


title: RHC139


title: RHC137


title: RHC133


title: RHC136


title: RHC134


title: RHC132


title: RHC127


title: RHC131


title: RHC135


title: RHC125


title: RHC128


title: RHC129


title: RHC130


title: RHC126


title: RHC121


title: RHC122


title: RHC123


title: RHC118


title: RHC124


title: RHC120


title: RHC117


title: RHC119


title: RHC115


title: RHC143


title: RHC114


title: RHC116


title: RHC111


title: RHC113


title: RHC112


title: RHC110


title: RHC109


title: RHC108


title: RHC107


title: RHC106


title: RHC103


title: RHC105


title: RHC095


title: RHC099


title: RHC096


title: RHC101


title: RHC097


title: RHC100


title: RHC102


title: RHC098


title: RHC089


title: RHC094


title: RHC090


title: RHC092


title: RHC091


title: RHC087


title: RHC088


title: RHC093


title: RHC083


title: RHC084


title: RHC082


title: RHC081


title: RHC085


title: RHC104


title: RHC079


title: RHC076


title: RHC077


title: RHC072


title: RHC075


title: RHC074


title: RHC073


title: RHC069


title: RHB1202

source_name: IMR90_Cell line_batch1


title: RHB1203


title: RHC086


title: RHC070


title: RHC071


title: RHC080


title: RHB1152


title: RHB1144


title: RHB1187


title: RHB1181


title: RHB1174


title: RHB1179


title: RHB1176


title: RHB1178


title: RHB1168


title: RHB1183


title: RHB1175


title: RHC078


title: RHB1157


title: RHB1160


title: RHB1180


title: RHH1170

source_name: HCT116_Cell line_batch1


title: RHH1171


title: RHB1125


title: RHB1133


title: RHH1172


title: RHB1139


title: RHB1138


title: RHB1136


title: RHB1143


title: RHH1169


title: RHH1168


title: RHH1167


title: RHB1130


title: RHB1134


title: RHH1156


title: RHH1153


title: RHH1157


title: RHH1154


title: RHH1144


title: RHH1150


title: RHH1158


title: RHH1136


title: RHH1137


title: RHH1142


title: RHH1140


title: RHH1138


title: RHH1159


title: RHH1164


title: RHH1165


title: RHH1166


title: RHH1146


title: RHH1149


title: RHH1147


title: RHH1143


title: RHH1145


title: RHH1141


title: RHH1161


title: RHH1135


title: RHH1133


title: RHH1132


title: RHH1148


title: RHH1151


title: RHH1129


title: RHH1127


title: RHH1128


title: RHH1126


title: RHH1130


title: RHH1124


title: RHH1119


title: RHH1120


title: RHH1122


title: RHH1125


title: RHH1117


title: RHH1115


title: RHL1146

source_name: H1437_Cell line_batch1


title: RHH1118


title: RHL1158


title: RHH1112


title: RHH1111


title: RHH1116


title: RHH1114


title: RHH1160


title: RHL1144


title: RHH1131


title: RHT018


title: RHH1121


title: RHH1123


title: RHL1115


title: RHL1119


title: RHL1133


title: RHL1117


title: RHL1120


title: RHL1135


title: RHL1136


title: RHL1111


title: RHL1103


title: RHL1102


title: RHL1105


title: RHL1104


title: RHL1100


title: RHL1109


title: RHL1077


title: RHL1094


title: RHL1096


title: RHL1076


title: RHL1088


title: RHL1078


title: RHL1095


title: RHL1110


title: RHL1072


title: RHL1073


title: RHL1074


title: RHL1106


title: RHL1067


title: RHL1071


title: RHL1099


title: RHL1075


title: RHL1049


title: RHL1050


title: RHL1059


title: RHL1027


title: RHL1030


title: RHL1066


title: RHL1032


title: RHL1063


title: RHL1033


title: RHL1019


title: RHL1014


title: RHL1061


title: RHL1022


title: RHL1062


title: RHL1013


title: RHL1057


title: RHL1011


title: RHL1003


title: RHL1004


title: RHL1016


title: RHL1042


title: RHL1010


title: RHL999


title: RHL1001


title: RHL1005


title: RHL997


title: RHL996


title: RHL1020


title: RHL1012


title: RHL1015


title: RHL993


title: RHB1209

source_name: GM12878_Cell line_batch1


title: RHB1185


title: RHB1189


title: RHB1193


title: RHB1200


title: RHB1196


title: RHB1204


title: RHB1199


title: RHB1172


title: RHB1208


title: RHB1171


title: RHB1206


title: RHB1169


title: RHB1188


title: RHB1163


title: RHB1201


title: RHB1197


title: RHB1173


title: RHB1167


title: RHB1158


title: RHB1165


title: RHL995


title: RHB1162


title: RHB1146


title: RHB1147


title: RHB1141


title: RHB1140


title: RHB1207


title: RHB1205


title: RHB1137


title: RHB1132


title: RHB1124


title: RHB1116


title: RHB1118


title: RHA094

source_name: A549_Cell line_batch1


title: RHA098


title: RHA096


title: RHA093


title: RHA088


title: RHA090


title: RHA091


title: RHA095


title: RHA089


title: RHA087


title: RHA082


title: RHA083


title: RHA085


title: RHA081


title: RHA084


title: RHA086


title: RHA080


title: RHA079


title: RHB1129


title: RHB1123


title: RHA099


title: RHB1122


title: RHA078


title: RHA097


title: RHB1153


title: RHA092


title: RHA077


title: RHA076


title: RHA074


title: RHA073


title: RHA075


title: RHA072


title: RHA068


title: RHA065


title: RHA064


title: RHA069


title: RHA067


title: RHA063


title: RHA062


title: RHA059


title: RHA058


title: RHA057


title: RHA060


title: RHA056


title: RHA061


title: RHA055


title: RHA053


title: RHA054


title: RHA070


title: RHA046


title: RHA048


title: RHA049


title: RHA047


title: RHA050


title: RHA045


title: RHA052


title: RHA044


title: RHA071


title: RHA051


title: RHA066


title: RHA043


title: RHA042


title: RHA037


title: RHA036


title: RHA038


title: RHA039


title: RHA029


title: RHA040


title: RHA034


title: RHA041


title: RHA035


title: RHA032


title: RHA033


title: RHA030


title: RHA031


title: RHA025


title: RHA027


title: RHA021


title: RHA022


title: RHA023


title: RHA020


title: RHA028


title: RHA024


title: RHA016


title: RHA018


title: RHC6176

description: processed data file = All_normal_mucosal_cells_FPKM.csv

source_name: CRC11_Normal Mucosa

tag: patient id

value: Primary CRC patient tissue sample

tag: tissue type

value: Normal Mucosa

tag: primary tissue sample id

tag: patient gender

value: Male

tag: tnm

tag: tumor grade

tag: stage ajcc

value: I


title: RHA015


title: RHA017


title: RHC6187


title: RHC6174


title: RHC6173


title: RHC6166


title: RHC6135


title: RHC6114

description: processed data file = All_normal_mucosal_cells_FPKM.csv, normal_mucosal_epithelial_cells_FPKM.csv


title: RHC6149


title: RHC6106


title: RHC6144


title: RHC6161


title: RHC6105


title: RHC6156


title: RHC6108


title: RHC6151


title: RHC6155


title: RHC6113


title: RHC6103


title: RHC6099


title: RHC6095


title: RHC6094


title: RHC6093


title: RHC6092


title: RHC6091


title: RHC6163


title: RHC6090


title: RHC6089


title: RHC6085


title: RHC6081


title: RHC6079


title: RHC6078


title: RHC6087


title: RHC6077


title: RHC6073


title: RHC6060


title: RHC6058


title: RHC6057


title: RHC6053


title: RHC6074


title: RHC6052


title: RHC6041

description: processed data file = All_CRC_tumor_cells_FPKM.csv

source_name: CRC11_Colorectal Tumor

value: Colorectal Tumor


title: RHC6054


title: RHC6049


title: RHC6039


title: RHC6033


title: RHC6030


title: RHC6022


title: RHC6010


title: RHC6004


title: RHC6076


title: RHC5995


title: RHC5999


title: RHC6075


title: RHC5991


title: RHC5967


title: RHC5952

source_name: CRC10_Normal Mucosa

value: Female

value: IIA


title: RHC6063


title: RHC5949


title: RHC5948


title: RHC5950


title: RHC5982


title: RHC6056


title: RHC5947


title: RHC5941


title: RHC5937


title: RHC5943


title: RHC5935


title: RHC5931


title: RHC5934


title: RHC5930

source_name: CRC10_Colorectal Tumor


title: RHC5932


title: RHC5926


title: RHC5929


title: RHC5925


title: RHC5924


title: RHC5922


title: RHC5920


title: RHC5918


title: RHC5914


title: RHC5915


title: RHC5936


title: RHC5913


title: RHC5909


title: RHC5908

description: processed data file = All_CRC_tumor_cells_FPKM.csv, CRC_tumor_epithelial_cells_FPKM.csv


title: RHC5912


title: RHC5907


title: RHC5905


title: RHC5904


title: RHC5906


title: RHC5903


title: RHC5902


title: RHC5901


title: RHC5899


title: RHC5900


title: RHC5895


title: RHC5898


title: RHC5894


title: RHC5892


title: RHC5893


title: RHC5891


title: RHC5896


title: RHC5890


title: RHC5923


title: RHC5888


title: RHC5889


title: RHC5887


title: RHC5885


title: RHC5886


title: RHC5910


title: RHC5884


title: RHC5881


title: RHC5879


title: RHC5880


title: RHC5874


title: RHC5875


title: RHC5876


title: RHC5870


title: RHC5869


title: RHC5862


title: RHC5864


title: RHC5861


title: RHC5859


title: RHC5857


title: RHC5867


title: RHC5866


title: RHC5860


title: RHC5938


title: RHC5831


title: RHC5816


title: RHC5815


title: RHC5814


title: RHC5811


title: RHC5834


title: RHC5810


title: RHC5878


title: RHC5840


title: RHC5871


title: RHC5801


title: RHC5790


title: RHC5785


title: RHC5783


title: RHC5768


title: RHC5863


title: RHC5765


title: RHC5764


title: RHC5844


title: RHC5718

source_name: CRC09_Colorectal Tumor

value: IIIB


title: RHC5716


title: RHC5711


title: RHC5714


title: RHC5710


title: RHC5827


title: RHC5702


title: RHC5704


title: RHC5701


title: RHC5699


title: RHC5665


title: RHC5647


title: RHC5666


title: RHC5698


title: RHC5646


title: RHC5658


title: RHC5808


title: RHC5644


title: RHC5643


title: RHC5633


title: RHC5761


title: RHC5629


title: RHC5637


title: RHC5628


title: RHC5632


title: RHC5627


title: RHC5624


title: RHC5707


title: RHC5623


title: RHC5626


title: RHC5620


title: RHC5616


title: RHC5614


title: RHC5613


title: RHC5611


title: RHC5608


title: RHC5606


title: RHC5612


title: RHC5605


title: RHC5607


title: RHC5602


title: RHC5604


title: RHC5601


title: RHC5598


title: RHC5600


title: RHC5599


title: RHC5592


title: RHC5597


title: RHC5622


title: RHC5586


title: RHC5594


title: RHC5578


title: RHC5610


title: RHC5576


title: RHC5615


title: RHC5577


title: RHC5582


title: RHC5585


title: RHC5571


title: RHC5570


title: RHC5574


title: RHC5569


title: RHC5568


title: RHC5617


title: RHC5566


title: RHC5567


title: RHC5565


title: RHC5563


title: RHC5562


title: RHC5580


title: RHC5561


title: RHC5558


title: RHC5560


title: RHC5557


title: RHC5553


title: RHC5555


title: RHC5550


title: RHC5554


title: RHC5549


title: RHC5575


title: RHC5547


title: RHC5552


title: RHC5551


title: RHC5546


title: RHL2879

source_name: CRC08_Normal Mucosa


title: RHC5544


title: RHL2880


title: RHC5564


title: RHL2875


title: RHL2867


title: RHL2868


title: RHL2864


title: RHL2856


title: RHL2854


title: RHL2853


title: RHL2852


title: RHL2850


title: RHL2845


title: RHL2844


title: RHL2837


title: RHL2824


title: RHL2840


title: RHL2816


title: RHL2834


title: RHL2819


title: RHL2821


title: RHL2799


title: RHL2789

source_name: CRC08_Colorectal Tumor


title: RHL2788


title: RHL2871


title: RHL2791


title: RHL2873


title: RHL2863


title: RHL2786


title: RHL2855


title: RHL2779


title: RHL2773


title: RHL2780


title: RHL2770


title: RHL2781


title: RHL2769


title: RHL2847


title: RHL2768


title: RHL2767


title: RHL2766


title: RHL2809


title: RHL2763


title: RHL2765


title: RHL2759


title: RHL2755


title: RHL2752


title: RHL2753


title: RHL2760


title: RHL2806


title: RHL2747


title: RHL2733


title: RHL2749


title: RHL2738


title: RHL2723


title: RHL2718


title: RHL2724


title: RHL2717


title: RHL2704


title: RHL2701


title: RHL2679


title: RHL2672


title: RHC4815

source_name: CRC07_Colorectal Tumor


title: RHC4813


title: RHL2716


title: RHC4811


title: RHC4807


title: RHL2762


title: RHC4804


title: RHC4800


title: RHC4801


title: RHC4789


title: RHC4810


title: RHC4797


title: RHC4784


title: RHL2758


title: RHC4787


title: RHC4780


title: RHC4788


title: RHC4781


title: RHC4775


title: RHC4776


title: RHC4774


title: RHC4772


title: RHC4769


title: RHC4771


title: RHC4768


title: RHC4767


title: RHC4763


title: RHC4761


title: RHC4758


title: RHC4760


title: RHC4757


title: RHC4755


title: RHC4751


title: RHC4747


title: RHC4746


title: RHC4745


title: RHC4947

source_name: CRC06_Colorectal Tumor


title: RHC4944


title: RHC4938


title: RHC4743


title: RHC4937


title: RHC4940


title: RHC4935


title: RHC4945


title: RHC4924


title: RHC4926


title: RHC4925


title: RHC4915


title: RHC4916


title: RHC4911


title: RHC4921


title: RHC4922


title: RHC4910


title: RHC4902


title: RHC4900


title: RHC4881


title: RHC4880


title: RHC4878


title: RHC4879


title: RHC4886


title: RHC4890


title: RHC4877


title: RHC4874


title: RHC4872


title: RHC4861


title: RHC4931


title: RHC4862


title: RHC4864


title: RHC4859


title: RHC5010

source_name: CRC06_Normal Mucosa


title: RHC4871


title: RHC5008


title: RHC5002


title: RHC5003


title: RHC4993


title: RHC4992


title: RHC4897


title: RHC4887


title: RHC4986


title: RHC4996


title: RHC4999


title: RHC4995


title: RHC4984


title: RHC4975


title: RHC4980


title: RHC4970


title: RHC4971


title: RHC4981


title: RHC4968


title: RHC4963


title: RHC4866


title: RHC4961


title: RHC4115

source_name: CRC05_Normal Mucosa


title: RHC4951


title: RHC4117


title: RHC4956


title: RHC4114


title: RHC4112


title: RHC4111


title: RHC4990


title: RHC4108


title: RHC4110


title: RHC4107


title: RHC4089


title: RHC4104


title: RHC5005


title: RHC4087


title: RHC4100


title: RHC4099


title: RHC4083

source_name: CRC05_Colorectal Tumor


title: RHC4079


title: RHC4080


title: RHC4075


title: RHC4076


title: RHC4073


title: RHC4085


title: RHC4068


title: RHC4067


title: RHC4066


title: RHC4061


title: RHC4062


title: RHC4059


title: RHC4058


title: RHC4065


title: RHC4057


title: RHC4055


title: RHC4053


title: RHC4052


title: RHC4050


title: RHC4046


title: RHC4051


title: RHC4045


title: RHC4034


title: RHC4048


title: RHC4031


title: RHC4028


title: RHC4070


title: RHC4072


title: RHC4030


title: RHC4196

source_name: CRC04_Colorectal Tumor


title: RHC4026


title: RHC4183

source_name: CRC04_Normal Mucosa


title: RHC4174


title: RHC4165


title: RHC4169


title: RHC4160


title: RHC4159


title: RHC4161


title: RHC4155


title: RHC4144


title: RHC4148


title: RHC4131


title: RHC4142


title: RHC4130


title: RHC4128


title: RHC4124


title: RHC4123


title: RHC4122


title: RHC4289


title: RHC4297


title: RHC4300


title: RHC4298


title: RHC4285


title: RHC4273


title: RHC4276


title: RHC4257


title: RHC4277


title: RHC4286


title: RHC4227


title: RHC4240


title: RHC4220


title: RHC4141


title: RHC4008

source_name: CRC03_Normal Mucosa


title: RHC4021

source_name: CRC03_Colorectal Tumor


title: RHC4014


title: RHC4005


title: RHC4134


title: RHC4003


title: RHC3947


title: RHC3944


title: RHC3962


title: RHC4304


title: RHC3934


title: RHC3926


title: RHC4274


title: RHC3914


title: RHC3924


title: RHC3912


title: RHC4266


title: RHC3906


title: RHC3910


title: RHC3909


title: RHC3907


title: RHC3905


title: RHC3904


title: RHC3903


title: RHC4007


title: RHC3919

source_name: CRC02_Colorectal Tumor


title: RHC3922


title: RHC3925


title: RHC3923


title: RHC3902


title: RHC3901


title: RHC3911


title: RHC3915


title: RHC3898


title: RHC3927


title: RHC3891


title: RHC3900


title: RHC3920


title: RHC3894


title: RHC3890


title: RHC3885


title: RHC3886


title: RHC3882


title: RHC3895


title: RHC3884


title: RHC3883


title: RHC3881


title: RHC3875


title: RHC3879


title: RHC3872


title: RHC3871


title: RHC3876


title: RHC3874


title: RHC3869


title: RHC3866


title: RHC3870


title: RHC3897


title: RHC3863


title: RHC3851


title: RHC3849


title: RHC3843


title: RHC3846


title: RHC3850


title: RHC3855


title: RHC3862


title: RHC3848


title: RHC3847


title: RHC3854


title: RHC3839


title: RHC3838


title: RHC3852


title: RHC3641

source_name: CRC01_Colorectal Tumor

value: IIC


title: RHC3835


title: RHC3836


title: RHC3837


title: RHC3640


title: RHC3865


title: RHC3856


title: RHC3633


title: RHC3635


title: RHC3868


title: RHC3638


title: RHC3840


title: RHC3878


title: RHC3864


title: RHC3844


title: RHC3845


title: RHC3629


title: RHC3621


title: RHC3619


title: RHC3617


title: RHC3609


title: RHC3608


title: RHC3599


title: RHC3628


title: RHC3625


title: RHC3598


title: RHC3602


title: RHC3600


title: RHC3596


title: RHC3597


title: RHC3593


title: RHC3589


title: RHC3584


title: RHC3590


title: RHC3582


title: RHC3585


title: RHC3581


title: RHC3579


title: RHC3570


title: RHC3569


title: RHC3567


title: RHC3568


title: RHC3606


title: RHC3562


title: RHC3565


title: RHC3563


title: RHC3556


title: RHC3552


title: RHC3591


title: RHC3594


title: RHC3553


title: RHC3546


title: RHC3557


title: RHC3577