title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01G)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03H)

status: Public on Sep 11 2018

type: RNA

city: Bethesda

first: Myrtle

last: Davis Millin

state: MD

address: 31 Center Drive

country: USA

institute: The National Cancer Institute

description: The rat was administered an intravenous (iv) infusion dose, given over a 30-minute interval, of oxaliplatin or corresponding vehicle formulation (D5W).  Thirty (30) minutes after iv administration of oxaliplatin or corresponding vehicle formulation, sorafenib, sunitinib, or the respective vehicle formulation was administered po.  IV infusion doses were administered at a flow rate of approximately 4 mL/kg/30 minute infusion.  The actual infusion rates were based on the mean body weight of animals dosed on each day of dosing.  PO doses were administered in a dose volume of 10 mL/kg.

hyb_protocol: 11 μg of purified cRNA was applied to Affymetrix GeneChip Rat Genome 230 2.0 Arrays, and incubated at 45°C for 16 hours. Following hybridization, arrays were washed and stained using standard Affymetrix procedures.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 using factory PMT settings. Data extraction was completed with Expression Console software using a target scaling of 500.

data_processing: Data analysis was performed using the Bioconductor R package using the affyQCReport, simpleaffy and arrayQualityMetrics packages. The raw data was normalized using the robust multichip average (RMA) algorithm (Irizarry et. al. Biostatistics, 2003) with log2 transformation.

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Oxaliplatin (30 minute infusion) followed by F68/PG/PEG400 (po)

label_protocol: Total RNA samples were converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: Rats used in this study were procured with an indwelling femoral vein cannula.  Prior to dosing on day 1, the catheter of each rat was checked for patency. Rats with patent catheters were randomly assigned to one of 8 treatment groups. On day 1, the rats weighed between 251.5–336.2 grams. Teklad Certified Rodent Diet 2016C (Harlan; Madison, WI) and tap water (Birmingham public water supply) were provided ad libitum to the rats prior to and throughout the study. The animals were individually housed in solid-bottom polycarbonate cages on stainless steel racks in a room maintained at a temperature of 70-79°F and a relative humidity of 44-66%. Room lights were controlled by an automatic timer set to provide a 12/12 light:dark cycle

extract_protocol: RNA isolation from individual tissues was accomplished using an RNeasy microarray kit (QIAGEN Inc.). After extraction, the RNA concentration of each sample was determined using a RiboGreen assay. The RNA Integrity Number (RIN) of each sample was determined using an Agilent 2100 Bioanalyzer with 2100 Expert Software. Only samples with a RIN of 7.5 or higher were deemed acceptable for gene expression analysis.

treatment_protocol: At 1, 6, or 24 hours after the completion of dosing, rats were euthanized by CO2 asphyxiation. Immediately after euthanasia, tissues of interest were collected for RNA isolation.  Kidney (left), heart (apex, with left and right ventricles), liver (left lateral and median lobes).   Samples collected for RNA isolation were cut into sections ≤ 2 mm in thickness and immediately placed into pre-filled tubes containing RNAlater® (Applied Biosystems; Foster City, CA).  After collection into RNAlater®, tissues were maintained refrigerated (approximately 4-5 °C) for at least 24 hours and then stored at or below -20 °C.

tag: strain

value: Sprague-Dawley

tag: Sex

value: Male

tag: age

value: 8 weeks

tag: tissue

value: Kidney

tag: compound given 1st

value: Oxaliplatin

tag: dose (mg/kg) compound given 1st

tag: compound given 2nd

tag: dose (mg/kg) compound 2nd

tag: time

value: 1 hr


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06E)

source_name: D5W  (30 minute infusion) followed by Sunitinib (po)

value: Liver

value: Sunitinib

value: 6 hr


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06B)

source_name: Oxaliplatin (30 minute infusion) followed by Sunitinib (po)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02G)

value: Heart


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02D)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01G)

source_name: Oxaliplatin (30 minute infusion) followed by sterile water (po)

value: sterile water

value: 24 hr


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06D)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07H)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03H)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07F)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04C)

source_name: Oxaliplatin (30 minute infusion) followed by Sorafenib (po)

value: Sorafenib


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06D)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02H)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01A)

source_name: D5W (30 minute infusion) followed by sterile water (po)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04F)

source_name: D5W  (30 minute infusion) followed by Sorafenib (po)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03B)

source_name: D5W (30 minute infusion) followed by F68/PG/PEG400 (po)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04C)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01D)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06A)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01C)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05C)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02A)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07E)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05A)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03F)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08G)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03H)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01G)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02B)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08F)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02D)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04G)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02E)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03E)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08D)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06A)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03B)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04F)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02H)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07C)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03C)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02A)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04C)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01D)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01A)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07B)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02H)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08F)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08C)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03F)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05H)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02A)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01D)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05G)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04F)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02B)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04G)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03B)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01H)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04D)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06H)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08C)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01A)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04C)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02E)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01G)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03F)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03C)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02H)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05E)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05D)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06H)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04C)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01A)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05G)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01H)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02B)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03F)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04G)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01E)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01G)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08A)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04A)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04D)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06E)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06F)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02F)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01D)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02H)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 24 hr(s) (A905GDKR_02B)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05D)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02E)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 6 hr(s) (A905GDKN_05B)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01D)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05A)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07G)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01H)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04G)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07F)


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01A)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (A905GDKR_03C)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04D)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 1 hr(s) (A905GDKN_01B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03F)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06E)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04A)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 6 hr(s) (A905GDKP_06B)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08H)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03C)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08G)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 6 hr(s) (A905GDKN_06C)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01E)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02E)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05A)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04D)


title: D5W (30 min infusion) followed by sterile water (po) in Heart for 1 hr(s) (A905GDKS_01A)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Kidney for 1 hr(s) (A905GDKP_02B)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07D)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 24 hr(s) (A905GDKO_04A)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 1 hr(s) (A905GDKN_02C)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04G)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03F)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04H)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07F)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01H)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 6 hr(s) (A905GDKS_06B)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 6 hr(s) (A905GDKS_08G)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Heart for 1 hr(s) (A905GDKS_04G)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07C)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 1 hr(s) (A905GDKP_03C)


title: D5W (30 min infusion) followed by sterile water (po) in Liver for 24 hr(s) (A905GDKL_01B)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02F)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Heart for 1 hr(s) (A905GDKS_02B)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (A905GDKL_03G)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (A905GDKS_07C)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 6 hr(s) (A905GDKP_05H)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 6 hr(s) (A905GDKP_08D)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03D)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 6 hr(s) (A905GDKN_08E)


title: D5W  (30 min infusion) followed by Sunitinib (po) in Kidney for 24 hr(s) (A905GDKO_02F)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 6 hr(s) (A905GDKP_07A.T2)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 24 hr(s) (A905GDKR_01E)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Heart for 24 hr(s) (A905GDKR_04A)


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Kidney for 1 hr(s) (A905GDKP_01H)


title: Oxaliplatin (30 min infusion) followed by Sorafenib (po) in Kidney for 1 hr(s) (A905GDKP_04D)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 1 hr(s) (A905GDKN_04E)


title: Oxaliplatin (30 min infusion) followed by Sunitinib (po) in Liver for 24 hr(s) (A905GDKL_02C)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (A905GDKN_07A)


title: D5W  (30 min infusion) followed by Sorafenib (po) in Liver for 24 hr(s) (A905GDKL_04H)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (A905GDKN_03G)


title: D5W (30 min infusion) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (A905GDKS_03C)


title: Oxaliplatin (30 min infusion) followed by F68/PG/PEG400 (po) in Kidney for 24 hr(s) (A905GDKO_03G)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (7M77)

description: The rat was administered a single bolus intravenous (iv) dose of temsirolimus or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of temsirolimus or vehicle formulation, sorafenib, sunitinib, or respective vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent body weight taken.

growth_protocol: Rats used in this study were procured with an indwelling femoral vein cannula.  Prior to dosing on day 1, the catheter of each rat was checked for patency. Rats with patent catheters were randomly assigned to one of 8 treatment groups. On day 1, the rats weighed between 197.6–274.4 grams. Teklad Certified Rodent Diet 2016C (Harlan; Madison, WI) and tap water (Birmingham public water supply) were provided ad libitum to the rats prior to and throughout the study. The animals were individually housed in solid-bottom polycarbonate cages on stainless steel racks in a room maintained at a temperature of 70-79°F and a relative humidity of 44-66%. Room lights were controlled by an automatic timer set to provide a 12/12 light:dark cycle

treatment_protocol: At 1, 6, or 24 hours after the completion of dosing, rats were euthanized by CO2 asphyxiation. Immediately after euthanasia, tissues of interest were collected for RNA isolation.  Bone marrow (left femur), heart (apex, with left and right ventricles), liver (left lateral and median lobes).   Samples of the heart and liver collected for RNA isolation were cut into sections ≤ 2 mm in thickness and immediately placed into pre-filled tubes containing RNAlater® (Applied Biosystems; Foster City, CA).  Bone marrow was flushed from bone using RNAlater®.  After collection into RNAlater®, tissues were maintained refrigerated (approximately 4-5 °C) for at least 24 hours and then stored at or below -20 °C.

value: 7-8 weeks

value: Bone Marrow


title: Oxaliplatin (30 min infusion) followed by sterile water (po) in Heart for 6 hr(s) (A905GDKS_05H)


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 1 hr(s) (3M31)

value: Temsirolimus


title: D5W (30 min infusion) followed by sterile water (po) in Kidney for 24 hr(s) (A905GDKO_01B)


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M63)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M23)


title: Jejunal explant_NIV_2µM_rep4

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 INRA Sus scrofa  v1 GE microarray (8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 36 out of 44 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 44737 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 44736 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: Jejunal explant

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Jejunal explants obtained from 5 week old crossbred castrated male piglets were incubated in complete Williams medium at 39°C

extract_protocol: The explants were lysed in 1 mL of Extract All reagent (Eurobio, Les Ulis, France) with ceramic beads (Bertin technologies, St Quentin en Yvelines, France). Total RNA was extracted according to the manufacturer's recommendations as already described. RNA concentration was determined by measuring optical density at 260 nm (OD260), and the RNA integrity was assessed by using both a NanoDrop spectrophotometric analysis (Nanodrop ND1000, Labtech International, Paris, France) and Agilent capillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies Inc., Santa‐Clara, CA).

treatment_protocol: The jejunal explants were treated for 4 hours at 39°C with 2 or 10μM of deoxynivalenol, nivalenol, fusarenon-x, 3-acetyldeoxynivalenol or 15-acetyl deoxynivalenol or vehicle (DMSO) in complete medium. After incubation, treated explants were stored at −80°C for RNA extraction.

tag: treatment

value: NIV

tag: dose

tag: animal

value: E


title: Jejunal explant_3-ADON_2µM_rep4


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (1M10)

value: Sprague-Dawley

value: Male


title: Jejunal explant_15-ADON_10µM_rep4


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (8M90)


title: Jejunal explant_3-ADON_10µM_rep3

value: D


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (7M73)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (7M82)


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M69)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M15)


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M71)


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M68)


title: Jejunal explant_DON_2µM_rep3

value: DON


title: Jejunal explant_NIV_2µM_rep3


title: Jejunal explant_NIV_10µM_rep4


title: Jejunal explant_15-ADON_2µM_rep3


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (1M5.N2)


title: Jejunal explant_15-ADON_10µM_rep3


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (6M65)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (7M78)


title: Jejunal explant_3-ADON_10µM_rep4


title: Jejunal explant_15-ADON_2µM_rep4


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (5M60)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M20)

value: 1 hr


title: Jejunal explant_3-ADON_2µM_rep3


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (5M51)


title: Jejunal explant_DON_2µM_rep4


title: Jejunal explant_NIV_10µM_rep3


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 1 hr(s) (1M1)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (2M16)


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 24 hr(s) (1M12)


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M70)

value: Liver


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (6M64)


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (5M57)

value: Sunitinib


title: Jejunal explant_DON_2µM_rep1

value: B


title: Jejunal explant_NIV_2µM_rep1


title: Jejunal explant_15-ADON_2µM_rep2

value: C


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M61)


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (5M53)


title: Jejunal explant_3-ADON_2µM_rep2


title: Jejunal explant_NIV_10µM_rep2


title: Jejunal explant_3-ADON_2µM_rep1


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (5M52)

value: 6 hr


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (5M56)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M48)

value: Heart

value: 24 hr


title: Jejunal explant_3-ADON_10µM_rep2


title: Jejunal explant_15-ADON_2µM_rep1


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (5M58)

value: 7-8 weeks


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 6 hr(s) (1M3)

value: sterile water


title: Jejunal explant_3-ADON_10µM_rep1


title: Jejunal explant_NIV_10µM_rep1


title: Jejunal explant_15-ADON_10µM_rep1


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (5M50)

value: Temsirolimus


title: Jejunal explant_15-ADON_10µM_rep2


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (4M44)

value: Bone Marrow


title: Cheese 4B

type: SRA

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

library_source: genomic

data_processing:
Library strategy: DNA-seq
Barcodes from the raw data were identified and counted with MultiCodes.pl. The barcodes were correlated with their insertion sites using CombineBarSeq.pl. Both scripts are from Wetmore et al. 2015.
The 20 bp-barcode sequence is located beginning at nucleotide 36.
Genome_build: GenBank accession CP001340
Supplementary_files_format_and_content: Processed data shows the genome position, barcode sequence and number of hits for each insertion across all 30 fitness experiments.

molecule: genomic DNA

organism: Caulobacter vibrioides

source_name: whole bacterial cells

growth_protocol: Barcoded transposon library caulo_47 (Hentchel et al. 2018) was passaged in 12-well plates containing 1.5mL PYE and a sterile plug of cheesecloth.

extract_protocol:
Whole cells were used directly in PCR reaction described below
Adaptors were added directly by PCR amplifying the barcode region from the transposons according to Wetmore et al. 2015.

treatment_protocol: After 24 hours the spend medium was used to innoculate a fresh culture with a fresh piece of cheesecloth. Passaging was continued for a total of 5 passaages.

tag: growth medium

value: PYE with cheesecloth plug

tag: passage


title: Cheese 4A


title: Cheese 4C


title: Cheese 5B


title: Cheese 5A


title: Cheese 3C


title: Cheese 3B


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (4M38)

value: Sprague-Dawley


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (1M7.N2)

value: Male


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (8M96)

value: Sorafenib


title: Cheese 3A


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 1 hr(s) (3M25)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M47)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M42)


title: Jejunal explant_DON_2µM_rep2

value: DON


title: Cheese 2C


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (8M92)

value: 1 hr


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 24 hr(s) (1M6)

value: Liver


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (1M1)


title: Cheese 2A


title: Cheese 2B


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 24 hr(s) (3M30)


title: Jejunal explant_NIV_2µM_rep2

value: NIV


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (8M91)


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (8M88)


title: Cheese 1B


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (4M43)


title: PYE 5B

value: PYE without cheesecloth


title: PYE 5C


title: Cheese1A


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 6 hr(s) (1M4)


title: PYE 4A


title: PYE 5A


title: PYE 4B


title: PYE 3C


title: PYE 4C


title: PYE 3B


title: PYE 3A


title: PYE 2C


title: PYE 2B


title: PYE 1C


title: PYE 1A


title: PYE 1B


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (7M83)

value: Sunitinib


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (3M26)


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (8M87)

value: 6 hr


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (2M13)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (2M18)


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 24 hr(s) (3M35)

value: Heart


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M22)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (7M77)

value: 24 hr


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M39)

value: 7-8 weeks


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (8M85)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (7M76)


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (6M71)


title: TQ324-SMAD3

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Quality control of ChIP-seq data was performed using Fastqc, and then low-quality bases and adaptor contamination were trimmed by cutadapt. After quality control and data filtering, data was mapped to hg19 using BWA mem algorithm. Duplicate reads were marked by Picard Markduplicate module and removed with unmapped reads by samtools view -f 2 -F 1804. MACS2.1.1 was used for peaks calling with default parameters and input as control. We utilized the Genomic Regions Enrichment of Annotations Tool (GREAT 3.0) to analyze the detected peaks, with the parameter “Basal plus extension”, which is proximal: 5 kb upstream, 1 kb downstream, plus Distal: up to 1000 kb. Gene ontology from GREAT output were analyzed by DAVID. KEGG pathways, biological processes, molecular functions, and GAD disease enrichment analysis was carried out using default settings. The HOMER findMotifsGenome.pl script was employed to search for known TRANSFAC motifs and to generate de novo motifs. The intersecBed was used to find overlapped peaks between SMAD3 and TCF21. The filter used to cut off SMAD3 peaks is: fold change> 5 and -logq_value>10. Pooled TCF21 peaks were cut off with three different thresholds, liberal: fold change>5, -logq_value>25; standard: fold change>10, -logq_value>60; stringent: fold change>15, -logq_value>200. The fastq files of SMAD3 ChIPseq in A549 cell lines was extracted from GSM1246721/SRR1014002 by fastq-dump. Similar methods were used in quality control, alignment, peak calling and intersection with SMAD3 peaks in HCASMC. NarrowPeaks is the peaks file call by macs2.1.1 callpeaks module using aligned bam files with default configuration.   Aligned reads in Bam file was converted to Bed format by bedtools bamToBed module and then generated .bedGraph file using bedItemOverlapCount. bedGraphToBigWig was used to create the.bigwig file from .bedGraph.
Genome_build: hg19
Supplementary_files_format_and_content: bed and bigwig

organism: Homo sapiens

source_name: HCASMC

growth_protocol: HCASMC were grown in the presence of serum and additives.

extract_protocol:
HCASMC were crosslinked in the dish, 2 million cells, and harvested.
ChIP was performed using the SMAD3 antibody Abcam, ab28379, and library was prepared using standard procedures. Briefly, DNA was prepared for end repair (Lucigen Endi-it, ER0720) and “A” tailing (NEB Klenow, M0212S), adaptor ligation (Promega, M180A), and library amplification (NEB, M0531S). ChIP-seq libraries were sequenced on HiSeq X10 for 150-bp paired-end sequencing.

tag: cell type

value: Human coronary artery smooth muscle cells (HCASMC)

tag: chip antibody


title: TQ325-IgG

value: IgG


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (8M93)


title: PYE 2A


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 24 hr(s) (3M36)

value: Temsirolimus

value: sterile water


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (7M82)

value: Sprague-Dawley


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 6 hr(s) (3M33)

value: Male


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M14)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (7M84)


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (8M86)

value: Sorafenib


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (2M23)

value: Bone Marrow


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 6 hr(s) (3M28)


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 1 hr(s) (1M1)

value: 1 hr


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M67)

value: Liver


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M65)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (7M78)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M19)


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (6M70)


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 24 hr(s) (1M11)


title: LUAD_patient50_metastasis

type: genomic

city: Basel

last: Lorber

address: Schönbeinstrasse 40

department: Institute for Pathology

country: Switzerland

institute: University Hospital Basel

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment on 180K SurePrint G3 Human CGH Microarrays (Agilent Technologies, CA, USA) for 24h at 67°C and 25 rpm; then washed according to array supplier's (Agilent) protocol.

scan_protocol: All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing: Images were analyzed with Agilent’s Feature Extraction v10.7 using default settings. Feature-extracted aCGH data were evaluated using Agilent’s CytoGenomics v3.0.1.1 software. Recentralization was performed by setting ploidy within +/- 0.5 of the prior ploidy estimate, as calculated from DNA-based flow cytometry. Aberrations were called with the aberration detection algorithm ADM2 set to a threshold of 12.0, with Fuzzy Zero and GC-content (window size: 2 kb) correction.

source_name: fresh frozen tissue

label_protocol: 1000 ng of Phi29 amplified sample and reference DNA was digested with DNase I in a thermo cycler for 15-18 min at 30°C, followed by DNase I inactivation at 75°C for 10 min. Degraded DNA with a molecular weight of 100-1000 bp was labeled with a fluorescent nucleotide (Cy3 for sample or Cy5 for reference, dye flip) using the BioPrime labeling kit (Invitrogen) according to manufacturer's protocol. DNA of FFPE tissues (n=2) was not amplified and not digested. In these cases, 600 ng of unamplified reference DNA was used and digested as described above. Labeling was performed according to the manufacturer's protocol.

growth_protocol: Not applicable

extract_protocol: For fresh frozen tissue, nuclei were isolated by mincing tissue in ice-cold NIM buffer [10 mM Tris-HCl (pH 7.4) containing 146 mM NaCl, 22 mM MgCl2, 2 mM CaCl2, 10% (v/v) DMSO, 0.05% (w/v) BSA and 0.1% (v/v) IGEPAL CA-630]. Nuclei were pelleted in a cooled centrifuge (300×g, 3 min, 4°C). The nuclei pellet was resuspended in ice-cold NIM buffer and stored on ice for subsequent flow cytometric analysis for up to 8 hours or at -20°C for longer storage up to 6 months. For FFPE tissues, nuclei isolation was performed as follows: Histological sections of 55 µm were deparaffinized in xylene and rehydrated in subsequent washings of 100%, 95%, 70%, 50% and 30% (v/v) ethanol. Antigen retrieval was performed in citrate buffer (pH 6.0) in a heat block at 95°C for 30 min. Nuclei were obtained after digestion with Collagenase III (final: 50 units/ml in 0.1 mM CaCl2/PBS) in a shaking heat block (16 hours, 37°C, 1000 rpm). After the nuclei were pelleted at 500×g for 5 min, they were resuspended in FACS buffer [PBS (pH 7.4) containing 1 mM EDTA, 1% (v/v) FCS and 0.1% (v/v) IGEPAL CA-630] to stop the digestion. After subsequent washings, isolated nuclei were stored in FACS buffer at 4°C for up to 1 week or at -20°C for up to 6 months. Nuclei were stained with 5 µg/ml DAPI at least 30 min before flow sorting was performed on a BD Influx™ cell sorter (Becton-Dickinson, San Jose, CA, USA). Genomic DNA (gDNA) was extracted by automation using Maxwell® 16 FFPE plus LEV DNA Purification Kit. DNA of sorted populations from fresh-frozen tissues was WGA with the illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare Life Sciences, PA, USA) following the manufacturer's instructions. DNA from FFPE tissues was not amplified.

treatment_protocol: Not applicable

tag: disease

value: lung adenocarcinoma

tag: tissue specimen

value: metastasis

tag: tumor site

value: brain, left (parietal)

tag: gender

value: male

source_name: reference pooled 46XX (Promega G1521)

tag: sample type

value: reference

value: female


title: LUAD_patient48_primary

value: primary tumor

value: lung, left upper lobe


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (5M57)

tag: strain

tag: Sex

tag: age

value: 7-8 weeks

tag: tissue

value: Heart

tag: compound given 1st

value: Sunitinib

value: 6 hr


title: LUAD_patient49_metastasis

value: pleura, left


title: LUAD_patient46_primary

value: lung, right upper lobe


title: LUAD_patient46_metastasis

value: pleura, right


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (5M59)

value: Sprague-Dawley

value: Male

value: Temsirolimus

tag: dose (mg/kg) compound given 1st

tag: compound given 2nd

tag: dose (mg/kg) compound 2nd

tag: time

value: 24 hr


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (7M74)

value: Liver

value: 1 hr


title: LUAD_patient49_primary

value: lung adenocarcinoma

value: male

value: reference


title: LUAD_patient50_primary

value: primary tumor

value: female


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M16)

value: 7-8 weeks

value: Heart


title: LUAD_patient44_metastasis

value: metastasis

value: adrenal gland, left


title: LUAD_patient42_metastasis


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M64)

value: Sorafenib

value: 6 hr


title: LUAD_patient42_primaryAN2

value: primary tumor AN2

value: lung, right lower lobe


title: LUAD_patient44_primary

value: lung, left upper lobe


title: LUAD_patient42_primaryAN1

value: primary tumor AN1


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (1M4)

value: Sprague-Dawley

value: Male

value: Bone Marrow

value: sterile water


title: LUAD_patient48_metastasis

value: lung adenocarcinoma

value: male

value: reference


title: LUAD_patient42_primary2N

value: primary tumor 2N

value: female


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (5M58)

value: 7-8 weeks

value: Temsirolimus

value: Sunitinib


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M66)

value: Liver

value: Sorafenib

value: 24 hr


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (4M45)

value: 6 hr


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (8M95)


title: Cheese 1C

tag: growth medium

value: PYE with cheesecloth plug

tag: passage


title: LUAD_patient41_primary

value: primary tumor

value: lung, left upper lobe


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (5M56)

value: Sprague-Dawley

value: Male

value: Heart

value: 1 hr


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M47)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M41)


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (5M49)


title: LUAD_patient41_metastasis

value: lung adenocarcinoma

value: metastasis

value: brain, left (parietal)

value: reference


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (5M52)

value: 7-8 weeks

value: Bone Marrow

value: Temsirolimus


title: LUAD_patient39_metastasis

value: lung, right upper lobe

value: male

value: female


title: LUAD_patient39_primary

value: lung, right lower lobe


title: LUAD_patient38_primary

value: primary tumor


title: LUAD_patient36_metastasis3

source_name: FFPE tissue

value: metastasis 3


title: LUAD_patient38_metastasis

value: adrenal gland, left


title: LUAD_patient36_primary

value: lung, left upper lobe


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (8M92)

value: Sprague-Dawley

value: Male

value: Heart

value: Sorafenib


title: LUAD_patient36_metastasis2

value: lung adenocarcinoma

value: metastasis 2

value: lung, left lower lobe


title: LUAD_patient36_metastasis1

value: metastasis 1

value: reference


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M43)

value: 7-8 weeks

value: Temsirolimus

value: 1 hr


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 6 hr(s) (1M4)

value: Liver

value: sterile water

value: 6 hr


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (3M33)

value: Bone Marrow


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (8M91)


title: LUAD_patient35_metastasis

value: metastasis

value: brain, left (frontal)

value: female


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M38)

value: Sprague-Dawley

value: Male

value: Heart


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 24 hr(s) (3M29)

value: 24 hr


title: LUAD_patient34_primary

value: lung adenocarcinoma

value: primary tumor

value: lung, right upper lobe

value: male


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 6 hr(s) (1M9)

value: 7-8 weeks


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M46)

value: Temsirolimus


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (8M87)

value: Sorafenib


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M13)

value: 1 hr


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 1 hr(s) (1M2)

value: sterile water


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (8M88)

value: Bone Marrow

value: 6 hr


title: LUAD_patient35_primary

value: lung, right lower lobe

value: reference


title: LUAD_patient31_primary

value: female


title: LUAD_patient34_metastasis

value: metastasis


title: LUAD_patient31_metastasis1

value: metastasis 1

value: lung, left lower lobe


title: LUAD_patient31_metastasis2

value: lung adenocarcinoma

value: metastasis 2


title: LUAD_patient20_metastasis2

value: kidney, right


title: LUAD_patient22_metastasis1

value: brain, right (parental)


title: LUAD_patient22_metastasis2


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M21)

value: Sprague-Dawley

value: Male

value: 7-8 weeks

value: Liver


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (4M39)

value: Temsirolimus


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (7M79)

value: Bone Marrow

value: Sunitinib

value: 1 hr


title: exoNOD1

city: Lausanne

first: Claudiane

last: Guay

state: Vaud

address: Du Bugnon 9

department: DNF

institute: University of Lausanne

description: Gene expression after 72h of incubation

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Mouse Genome Oligo Microarray (4 x 44K, Agilent Technologies) based on the manufacturer’s standard protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

organism: Mus musculus

source_name: Mouse dispersed islet cells, 50ug/ml exoNOD, repliate 1

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent Cyanine-3 (cy3) cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen), according to manufacturer guidelines.

treatment_protocol: 50ug/ml of exoNOD were added to the culture media of dispersed mouse islet cells (in RPMI 1640-GlutaMAX media supplemented with 10% heat-inactivated fetal calf serum, 10 mM Hepes pH 7.4, 1 mM sodium pyruvate, 100 μg/mL streptomycin and 100 IU/mL penicillin. Islet cells were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Pancreatic islet cells

value: male


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (7M84)

value: 24 hr


title: LUAD_patient22_primary

value: primary tumor

value: lung, left upper lobe

value: female

value: reference


title: LUAD_patient20_metastasis1

value: lung adenocarcinoma

value: metastasis 1

value: kidney, left


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (8M90)

value: Sprague-Dawley

value: Male

value: Heart

value: Sorafenib


title: exoNOD2

description: Gene expression after 72h of incubation

source_name: Mouse dispersed islet cells, 50ug/ml exoNOD, repliate 2


title: LUAD_patient12_metastasis

value: metastasis

value: thyroid gland


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M71)

value: 7-8 weeks

value: Temsirolimus


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M23)


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (3M31)

value: Bone Marrow

value: sterile water

value: 1 hr


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M18)

value: 24 hr


title: Ctl3

description: Gene expression after 72h of incubation

source_name: Mouse dispersed islet cells, no exoNOD, repliate 3

value: Pancreatic islet cells

value: male


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (5M53)

value: Sunitinib


title: Ctl2

description: Gene expression after 72h of incubation

source_name: Mouse dispersed islet cells, no exoNOD, repliate 2


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 6 hr(s) (1M10)

value: 6 hr


title: LUAD_patient12_primary

value: lung adenocarcinoma

value: primary tumor

value: lung, left lower lobe

value: reference

value: female


title: LUAD_patient20_primary

value: lung, left upper lobe


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (3M36)

value: Sprague-Dawley

value: Male


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (2M14)

value: 7-8 weeks


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (7M75)

value: Liver


title: MCD1_2_4_T15

city: MADRID

last: VALDECANTOS

state: MADRID

address: C/ARTURO DUPERIER, 4

country: Spain

institute: IIB ALBERTO SOLS

description: Biological replicate 4 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH

hyb_protocol: Preparation of probes and hybridization was performed as  described One-Color Microarray Based Gene Expression Analysis Manual  Ver. 6.5, Agilent Technologies. Briefly, for each hybridization 600 ng  of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul  of 25x Fragmentation Buffer and Nuclease free water in a 25 ul  reaction, incubated at 60ºC for 30 minutes to fragment RNA and  stopped with  25 ul of 2x Hybridization Buffer. The samples were  placed on ice and quickly loaded onto arrays, hybridized at 65ºC for  17 hours in a Hybridization oven rotator and then washed in GE wash  buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at  37ºC (1 minute)

scan_protocol: The slides were scanned with a GenePix 4000B scanner and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried-out using the LIMMA package (Smyth, 2003) of Bioconductor project. Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that we developed 70% partial hepatectomy and continuous with the same diet for other two weeks [MCD1_2_4_T15]

label_protocol: RNA was labeled with Cy3 by using the SuperScript indirect cDNA labeling system (invitrogen) as described in the instruction manual.

growth_protocol: Transcriptomic analyses were done with livers from diferent treated animals. Total RNA was extracted from livers at final treatment period. The CHD animals were fec on standard diet for during 3 weeks. MCD animals were fed on methionine and choline deficient (MCD) diet during 3 weeks. CG49  were fed on standard diet and treated during 2 weeks with 4,4 mg/kg/day of dual agonist of GLP1R/GCGR every two days. MG49 animals were fed on MCD diet during 3 weeks, after first week were treated with 4,4 mg/kg/day of dual agonist of GLP1R/GCGR every two days. T15 refeers to livers from animals sacrified 2 weeks after partial hepatectomy (70%) and treated before and after PH with the same diet and treatment were recipt the same diet and treatments

extract_protocol: Total RNA was isolated from livers frozen in liquid nitrogen with Trizol® reagent (Invitrogen, Madrid, Spain) and purified using the RNeasy midi Kit from Qiagen according to manufacturer’s instructions. Quality of the RNA samples was ensured in a Bioanalyzer 2100.


title: MGLP1-t15-4_2_4

description: Biological replicate 4 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment [MGLP1-t15-4_2_4]


title: MGLP1-t15-1_2_1

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment [MGLP1-t15-1_2_1]


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (7M73)

value: Heart


title: MGLP1-t15-3_2_3

description: Biological replicate 3 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment [MGLP1-t15-3_2_3]


title: MGLP1-t15-2_2_2

description: Biological replicate 2 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  dual agonist of GLP1R/GCGR  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment versus animals fed on MCD diet two weeks after PH

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks after that were hepatectomized (70%PH) and continuous with the same diet and treatment [MGLP1-t15-2_2_2]


title: MCD1_2_3_T15

description: Biological replicate 3 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that we developed 70% partial hepatectomy and continuous with the same diet for other two weeks [MCD1_2_3_T15]


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (1M2)

value: Bone Marrow

value: sterile water

value: 1 hr


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 6 hr(s) (3M27)

value: Temsirolimus


title: MCD1_2_2_T15

description: Biological replicate 2 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that we developed 70% partial hepatectomy and continuous with the same diet for other two weeks [MCD1_2_2_T15]


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (1M9)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (7M80)

value: Sunitinib


title: CGLP1-t15-1_1_4

description: Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks and two weeks after 70 % partial hepatectomy treated with dual agonist [CGLP1-t15-1_1_4]


title: MCD1_2_1_T15

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that were hepatectomized (70% PH) and continues with the same diet for other two weeks versus animals fed on standard diet after two weeks of 70% PH

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks after that we developed 70% partial hepatectomy and continuous with the same diet for other two weeks [MCD1_2_1_T15]


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (7M81)

value: 6 hr


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (7M78)

value: 24 hr


title: CHD1_1_3_T15

description: Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy

source_name: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy [CHD1_1_3_T15]


title: CGLP1-t15-1_1_1

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks and two weeks after 70 % partial hepatectomy treated with dual agonist [CGLP1-t15-1_1_1]


title: CHD1_1_4_T15

description: Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy

source_name: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy [CHD1_1_4_T15]


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (6M67)

value: Sorafenib


title: CGLP1-t15-1_1_3

description: Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks and two weeks after 70 % partial hepatectomy treated with dual agonist [CGLP1-t15-1_1_3]


title: CGLP1-t15-1_1_2

description: Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist two weeks before and after 70 % partial hepatectomy versus untreated animals

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks and two weeks after 70 % partial hepatectomy treated with dual agonist [CGLP1-t15-1_1_2]


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (2M19)


title: CHD1_1_2_T15

description: Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy

source_name: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy [CHD1_1_2_T15]


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 1 hr(s) (3M32)


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M72)


title: CHD1_1_1_T15

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet two weeks after 70 % partial hepatectomy

source_name: C57/BL6 fed with standard diet two weeks after 70 % partial hepatectomy [CHD1_1_1_T15]


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (5M59)

description: The rat was administered a single bolus intravenous (iv) dose of temsirolimus or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of temsirolimus or vehicle formulation, sorafenib, sunitinib, or respective vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent body weight taken.


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M63)


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (6M70)


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (1M11)


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (6M61)


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (5M55)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M15)


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (5M52)


title: MGLP1-1_2_2

description: Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks [MGLP1-1_2_2]


title: MGLP1-1_2_1

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks [MGLP1-1_2_1]


title: CGLP1-1_1_2

description: Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks [CGLP1-1_1_2]


title: MGLP1-1_2_4

description: Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks [MGLP1-1_2_4]


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (6M66)


title: CGLP1-1_1_4

description: Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks [CGLP1-1_1_4]


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (5M53)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M24)


title: MCD1_2_4

description: Biological replicate 4 of 4. Gene expression of livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks [MCD1_2_4]


title: MGLP1-1_2_3

description: Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet  and treated with dual agonist versus animals fed on MCD diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks and treated with  Fc-GLP-1  during two weeks [MGLP1-1_2_3]


title: CGLP1-1_1_3

description: Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks [CGLP1-1_1_3]


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M45)


title: MCD1_2_2

description: Biological replicate 2 of 4. Gene expression of livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks [MCD1_2_2]


title: Ctl1

description: Gene expression after 72h of incubation

source_name: Mouse dispersed islet cells, no exoNOD, repliate 1

value: Pancreatic islet cells

value: male


title: CGLP1-1_1_1

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet and treated with dual agonist versus  C57/BL6 un-treated

source_name: C57/BL6 fed with standard diet treated with Fc-GLP-1 during two weeks [CGLP1-1_1_1]


title: MCD1_2_1

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks [MCD1_2_1]


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (5M49)


title: exoNOD3

description: Gene expression after 72h of incubation

source_name: Mouse dispersed islet cells, 50ug/ml exoNOD, repliate 3


title: MCD1_2_3

description: Biological replicate 3 of 4. Gene expression of livers from C57/BL6 animals fed on MCD diet versus animals fed on standard diet

source_name: C57/BL6 fed with methyl and choline deficient diet during 3 weeks [MCD1_2_3]


title: CHD1_1_3

description: Biological replicate 3 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet

source_name: C57/BL6 fed with standard diet [CHD1_1_3]


title: CHD1_1_4

description: Biological replicate 4 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet

source_name: C57/BL6 fed with standard diet [CHD1_1_4]


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 24 hr(s) (1M12)


title: CHD1_1_2

description: Biological replicate 2 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet

source_name: C57/BL6 fed with standard diet [CHD1_1_2]


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M62)


title: CHD1_1_1

description: Biological replicate 1 of 4. Gene expression in livers from C57/BL6 animals fed on standard diet

source_name: C57/BL6 fed with standard diet [CHD1_1_1]


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 6 hr(s) (1M9)

description: The rat was administered a single bolus intravenous (iv) dose of temsirolimus or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of temsirolimus or vehicle formulation, sorafenib, sunitinib, or respective vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent body weight taken.


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (8M95)


title: Mouse small intestine mucosa

city: Seoul

first: Ki-Ho

last: Song

state: Korea

address: Yeouido St. Mary’s Hospital,10,63-ro,Youngdeungpo-gu

department: Department of Internal Medicine

country: South Korea

institute: Catholic University

description: Small intestine mucosa gene expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: mouse small intestine mucosa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were maintained in DMEM containing 25 mM glucose and 10% fetal bovine serum (FBS), and incubated in a humidified atmosphere containing 5% CO2 at 37°C. The medium was changed every 2-3 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: C2C12 cells (a mouse myoblast cell line), MIN6 cells (a mouse β-cell line), or isolated mouse islets were used as controls. K0 cells (a K cell line), which were obtained by transfection of a GIP promoter-expressing vector into STC-1 cells and selection of transfected cells, were also used.

value: Enteroendocrine cell


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 1 hr(s) (1M2)


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 6 hr(s) (3M33)


title: Mouse enteroendocrine L cell-23_2

description: Enteroendocrine cell gene expression

source_name: STC-1 cells (a heterogenous EEC line)


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (5M54)


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (8M86.N2)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (4M41)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (4M46)


title: Mouse enteroendocrine S cell-41_2

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine L cell-6_2

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine L cell-33_2

description: Enteroendocrine cell gene expression


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 1 hr(s) (1M7)


title: Mouse enteroendocrine K cell-36_2

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine S cell-35_2

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine K cell-34_2

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine K cell-50_2

description: Enteroendocrine cell gene expression


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M37)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M42)


title: Mouse enteroendocrine G cell-31_2

description: Enteroendocrine cell gene expression


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (8M91)


title: Mouse enteroendocrine G cell-12_2

description: Enteroendocrine cell gene expression


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 1 hr(s) (3M26)


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (5M60)


title: Mouse enteroendocrine S cell-30_2

description: Enteroendocrine cell gene expression


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (8M87)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (2M21)


title: Mouse enteroendocrine I cell-14_2

description: Enteroendocrine cell gene expression


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M39)


title: Mouse β-cell line_2

description: β-cell gene expression

source_name: β-cell line

value: beta-cell


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (8M93)

value: Sprague-Dawley


title: Mouse pancreas islet_2

description: Islet gene expression

source_name: mouse islet

value: Islet


title: Mouse enteroendocrine G cell-26_2

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine I cell-45_2

description: Enteroendocrine cell gene expression


title: Mouse myoblast cell line_2

description: Muscle gene expression

source_name: myoblast cell line

value: Muscle


title: Mouse enteroendocrine L cell-6_1

description: Enteroendocrine cell gene expression

source_name: STC-3 cells (a heterogenous EEC line)


title: Mouse enteroendocrine S cell-30_1

description: Enteroendocrine cell gene expression

source_name: STC-4 cells (a heterogenous EEC line)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (7M79)

value: Male

value: 7-8 weeks


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M17)

value: Liver


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (8M89)


title: Mouse enteroendocrine L cell-23_1

description: Enteroendocrine cell gene expression

source_name: STC-2 cells (a heterogenous EEC line)


title: Mouse enteroendocrine I cell-14_1

description: Enteroendocrine cell gene expression


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 1 hr(s) (3M31)

value: Heart

value: sterile water


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 24 hr(s) (3M36)

value: Temsirolimus


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (7M84)

value: Sunitinib


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M14)

value: 1 hr


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (7M75)

value: Bone Marrow

value: 6 hr


title: Mouse enteroendocrine K cell-0_2

description: Enteroendocrine cell gene expression


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 6 hr(s) (3M34)


title: Mouse enteroendocrine K cell-0_1

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine I cell-27_1

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine S cell-35_1

description: Enteroendocrine cell gene expression


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (8M86)

value: Sorafenib


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (3M27)


title: Mouse enteroendocrine I cell-27_2

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine G cell-31_1

description: Enteroendocrine cell gene expression


title: Mouse β-cell line_1

description: β-cell gene expression


title: Mouse enteroendocrine K cell-50_1

description: Enteroendocrine cell gene expression


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (7M81)


title: Mouse enteroendocrine K cell-36_1

description: Enteroendocrine cell gene expression


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M67)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M40)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (2M19)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (7M80)


title: Mouse pancreas islet_1

description: Islet gene expression


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (5M59)

value: 24 hr


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (8M94)


title: Mouse enteroendocrine G cell-12_1

description: Enteroendocrine cell gene expression

value: Enteroendocrine cell


title: Mouse enteroendocrine K cell-34_1

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine I cell-45_1

description: Enteroendocrine cell gene expression


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (3M32)


title: Mouse enteroendocrine S cell-41_1

description: Enteroendocrine cell gene expression


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (7M76)


title: Mouse myoblast cell line_1

description: Muscle gene expression


title: Mouse enteroendocrine L cell-33_1

description: Enteroendocrine cell gene expression


title: Mouse enteroendocrine G cell-26_1

description: Enteroendocrine cell gene expression


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 24 hr(s) (1M11)


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (6M72)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (2M24)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (7M77)


title: wt_rep2

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

country: Germany

institute: Universitätsklinikum Tübingen

hyb_protocol: Following fragmentation, 15 ug cRNA were hybridized for 16 h at 45°C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data was analyzed with Affymetrix Expression Console version 1.4.1 using default settings and RMA as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard GeneChip WT Kit protocol from 100ng total RNA.

extract_protocol: Total liver RNA was isolated from liver tissues using RNeasy Mini Kit (Qiagen, Germany) with MagNA Lyser Green Beads (Roche, Germany) according to the manufacturer description.

tag: strain background

tag: genotype/variation

value: wild type

value: male

value: liver


title: TALL_JS_64 (total RNA)

city: Ghent

first: Karen

last: Verboom

address: De Pintelaan 185

department: Pediatrics and Genetics

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
fastq files were aligned to GRCh38 primary annotation with STARv2.4.2a using a 2-pass strategy. In the first pass gencode.v25 was used as guide, in the second pass all sjdb files from the first pass were used as guide
Genes were quantified by STARv2.4.2a on Gencode.v25
Genome_build: GRCh38
Supplementary_files_format_and_content: reads per gene as generated by STAR2.4.2a

source_name: bone marrow

extract_protocol:
RNA was extracted using the miRNAeasy mini kit (Qiagen). TruSeq Stranded Total RNA (w/RiboZero Gold) sample prep kit (Illumina) was used for the preparation of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subgroup

value: TAL


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M69)

value: Sprague-Dawley

value: Male


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (6M68)

value: 7-8 weeks

value: Liver


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (5M51)


title: ko_rep3


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (5M55)


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M66)

value: Heart


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (5M60)

value: Temsirolimus


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (6M62)


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (5M54)

value: Sunitinib


title: wt_rep3


title: ko_rep1


title: TALL_JS_63 (total RNA)

value: IMM


title: ko_rep2


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (5M58)


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (5M49)

value: 1 hr


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M20)


title: wt_rep1


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (4M41)


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 24 hr(s) (1M5)

value: sterile water


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (8M95)

value: Sorafenib


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M61)


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (1M12)

value: Bone Marrow

value: 24 hr


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 6 hr(s) (3M28)

value: 6 hr


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (1M6.N2)


title: TALL_JS_61 (total RNA)

value: HOXA


title: TALL_JS_60 (total RNA)

value: TLX


title: TALL_JS_58 (total RNA)


title: TALL_JS_51 (total RNA)

value: TAL


title: TALL_JS_42 (total RNA)


title: TALL_JS_23 (total RNA)


title: TALL_JS_37 (total RNA)


title: TALL_JS_18 (total RNA)


title: TALL_JS_31 (total RNA)


title: TALL_JS_35 (total RNA)


title: TALL_JS_14 (total RNA)


title: TALL_JS_56 (total RNA)


title: TALL_JS_55 (total RNA)


title: TALL_JS_39 (total RNA)


title: TALL_JS_44 (total RNA)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (4M48)

value: Sprague-Dawley


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (4M37)

value: Male


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (4M42)

value: 7-8 weeks


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (5M50)

value: Liver


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (3M29)


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (3M34)


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (8M89)


title: TALL_JS_13 (total RNA)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M46)

value: Heart


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 1 hr(s) (1M7)


title: TALL_JS_26 (total RNA)


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (8M96)


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (1M8.N2)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M44)

value: Temsirolimus


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (8M93)


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 1 hr(s) (3M25)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (2M17)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (2M21)


title: TALL_JS_11 (total RNA)


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 24 hr(s) (3M30)


title: TALL_JS_10 (total RNA)


title: TALL_JS_5 (total RNA)


title: TALL_JS_4 (total RNA)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (7M75)

value: Sunitinib


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M22)


title: TALL_JS_2 (total RNA)

value: IMM


title: TALL_JS_3 (total RNA)


title: ALL-SIL scrambled siRNA 400nM 24h repl 1

source_name: ALL-SIL cell line

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol:
RNA was extracted using the miRNAeasy mini kit (Qiagen). TruSeq Stranded Total RNA (w/RiboZero Gold) sample prep kit (Illumina, RS-122-2301) was used for the preparation of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were electroporated with a NTC and TLX1 siRNA

tag: cell line

value: ALL-SIL


title: ALL-SIL siTLX1 s46 24h repl 1


title: ALL-SIL siTLX1 s47 24h repl 1


title: ALL-SIL scrambled siRNA 400nM 24h repl 2


title: ALL-SIL siTLX1 s46 24h repl 3


title: ALL-SIL siTLX1 s47 24h repl 3


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 6 hr(s) (3M27)

value: sterile water


title: ALL-SIL siTLX1 s47 24h repl 2


title: DMSO_rep3

extract_protocol:
RNA was extracted using the miRNAeasy mini kit (Qiagen). TruSeq Stranded Total RNA sample prep kit (Illumina) was used for the preparation of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were treated with 1 µM JQ1 for 24h


title: DMSO_rep2


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 24 hr(s) (7M83)


title: DMSO_rep1


title: ALL-SIL siTLX1 s46 24h repl 2


title: JQ1_rep3


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 6 hr(s) (7M81)


title: ALL-SIL scrambled siRNA 400nM 24h repl 3


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 1 hr(s) (3M32)

value: 1 hr


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (8M94)

value: Bone Marrow

value: Sorafenib


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (4M40)

value: 6 hr


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 24 hr(s) (3M35)

value: 24 hr


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (8M90)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (2M13)


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 1 hr(s) (1M8)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (7M80)


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (8M85)


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M24)


title: JQ1_rep1


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (6M72)


title: NHBE, 20%CO2, rep3

city: Chicago

first: Marina

last: Casalino-Matsuda

address: 240 E Huron M340

institute: Northwestern University

description: NHBE cells exposed to 20%CO2 for 24 hrs

hyb_protocol: GeneChip Hybridized in Affymetrix Hybridization Oven for 16 hrs at 45C at 60 RPM.

scan_protocol: GeneChips were scaned using Affymetrix GeneChip 3000 Scanner.

data_processing: The data were analyzed with RMA using Stratagene ArrayAssist

source_name: NHBE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Qiagen RNeasy kit

tag: cell type

value: Normal Bronchial Epithelial Cells

tag: stress

value: 20%CO2 for 24 hrs


title: TALL_JS_64 (polyA+ RNA)

molecule: polyA RNA

extract_protocol:
RNA was extracted using the miRNAeasy mini kit (Qiagen). Truseq stranded mRNA  sample preparation kit (Illumina) was used for the preparation of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TAL


title: NHBE, 20%CO2, rep2

description: NHBE cells exposed to 20%CO2 for 24 hrs


title: JQ1_rep2


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (6M69)

tag: strain

value: Sprague-Dawley

value: Male


title: TALL_JS_62 (polyA+ RNA)

value: TLX


title: NHBE, 5%CO2, rep3

description: NHBE cells exposed to 5%CO2 for 24 hrs

value: 5%CO2 for 24 hrs


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 6 hr(s) (6M63)

tag: Sex

value: 7-8 weeks

value: Temsirolimus


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (7M76)

tag: age

value: Sunitinib


title: TALL_JS_63 (polyA+ RNA)

value: IMM


title: TALL_JS_61 (polyA+ RNA)

value: HOXA


title: NHBE, 20%CO2, rep1

description: NHBE cells exposed to 20%CO2 for 24 hrs


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 6 hr(s) (1M10)

tag: tissue

value: Liver

value: sterile water


title: TALL_JS_60 (polyA+ RNA)


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (3M28)

value: Bone Marrow

tag: compound given 1st


title: NHBE, 5%CO2, rep2

description: NHBE cells exposed to 5%CO2 for 24 hrs


title: TEM_vehicle (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (7M74)

value: Heart

tag: dose (mg/kg) compound given 1st

value: 1 hr


title: TALL_JS_58 (polyA+ RNA)


title: NHBE, 5%CO2, rep1

description: NHBE cells exposed to 5%CO2 for 24 hrs

value: Normal Bronchial Epithelial Cells


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 1 hr(s) (5M55)

tag: compound given 2nd


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (2M15)

tag: dose (mg/kg) compound 2nd

value: 6 hr


title: subject S_34 [expression]

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

description:
S_34
Gene expression data from liver biopsy from subject S_34.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: The Affymetrix GeneChip Command Console Software (AGCC) was used to generate probe level data that were then converted to expression values using the Robust Multiarray Average (RMA) procedure.

source_name: subject S_34

label_protocol: Standard Affymetrix procedures.

extract_protocol: Total RNA (including miRNAs) was extracted using the mirVana miRNA Isolation Kit (Ambion), following manufacturer’s instructions.

tag: disease

value: normal

value: 90 years

value: Female


title: subject S_29 [expression]

description:
S_29
Gene expression data from liver biopsy from subject S_29.

source_name: subject S_29

value: 84 years

value: Male


title: subject S_33 [expression]

description:
S_33
Gene expression data from liver biopsy from subject S_33.

source_name: subject S_33

value: 82 years


title: TALL_JS_59 (polyA+ RNA)

value: TLX


title: subject S_19 [expression]

description:
S_19
Gene expression data from liver biopsy from subject S_19.

source_name: subject S_19

value: 87 years


title: TALL_JS_57 (polyA+ RNA)


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (7M82)

value: Sprague-Dawley

value: 7-8 weeks

value: Sunitinib

tag: time


title: subject S_42 [expression]

description:
S_42
Gene expression data from liver biopsy from subject S_42.

source_name: subject S_42

value: Liver

value: 77 years


title: Temsirolimus (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (6M68)

value: Bone Marrow

value: Temsirolimus

value: Sorafenib


title: subject S_42 [methylation]

description: DNA methylation data from liver biopsy from subject S_42.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: HiScan SQ scanner (Illumina).

data_processing: Signal intensities files were extracted using the methylumi Bioconductor package. Data preprocessing and normalization were performed using the wateRmelon Bioconductor package. Beta-values were normalized using the dasen function.

label: Cy5 and Cy3

label_protocol: DNA was bisulfite-converted using the EZDNA Methylation-Gold Kit (Zymo Research).

extract_protocol: Genomic DNA was extracted from liver biopsies using the Qiagen kit QiAmp mini Kit®, following manufacturer’s instructions.


title: subject S_33 [methylation]

description: DNA methylation data from liver biopsy from subject S_33.


title: TALL_JS_56 (polyA+ RNA)


title: subject S_45 [methylation]

description: DNA methylation data from liver biopsy from subject S_45.

source_name: subject S_45

value: 45 years


title: subject S_34 [methylation]

description: DNA methylation data from liver biopsy from subject S_34.

value: normal


title: subject S_36 [methylation]

description: DNA methylation data from liver biopsy from subject S_36.

source_name: subject S_36


title: subject S_32 [methylation]

description: DNA methylation data from liver biopsy from subject S_32.

source_name: subject S_32


title: TALL_JS_54 (polyA+ RNA)

value: TAL


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 1 hr(s) (2M20)

value: 1 hr


title: subject S_44 [methylation]

description: DNA methylation data from liver biopsy from subject S_44.

source_name: subject S_44

value: 43 years


title: subject S_31 [methylation]

description: DNA methylation data from liver biopsy from subject S_31.

source_name: subject S_31

value: 69 years

value: Female


title: subject S_32 [expression]

description:
S_32
Gene expression data from liver biopsy from subject S_32.


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 6 hr(s) (5M51)

value: Male

value: 6 hr


title: TALL_JS_53 (polyA+ RNA)


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 6 hr(s) (6M64)

value: Sprague-Dawley


title: TALL_JS_55 (polyA+ RNA)

value: TLX


title: TALL_JS_52 (polyA+ RNA)


title: Temsirolimus (iv) followed by Sorafenib (po) in Liver for 24 hr(s) (6M65)

value: 7-8 weeks

value: 24 hr


title: subject S_30 [expression]

description:
S_30
Gene expression data from liver biopsy from subject S_30.

source_name: subject S_30

value: Liver

value: 76 years


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 6 hr(s) (5M57)

value: Temsirolimus

value: Sunitinib


title: subject S_8 [expression]

description:
S_8
Gene expression data from liver biopsy from subject S_8.

source_name: subject S_8

value: 73 years


title: TALL_JS_51 (polyA+ RNA)


title: subject S_23 [methylation]

description: DNA methylation data from liver biopsy from subject S_23.

source_name: subject S_23

value: normal

value: 53 years


title: TALL_JS_50 (polyA+ RNA)

value: TAL


title: subject S_31 [expression]

description:
S_31
Gene expression data from liver biopsy from subject S_31.


title: subject S_22 [methylation]

description: DNA methylation data from liver biopsy from subject S_22.

source_name: subject S_22

value: 29 years


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (2M16)

description: The rat was administered a single bolus intravenous (iv) dose of temsirolimus or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of temsirolimus or vehicle formulation, sorafenib, sunitinib, or respective vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent body weight taken.


title: subject S_29 [methylation]

description: DNA methylation data from liver biopsy from subject S_29.

value: 84 years


title: subject S_36 [expression]

description:
S_36
Gene expression data from liver biopsy from subject S_36.

value: 82 years


title: subject S_12 [expression]

description:
S_12
Gene expression data from liver biopsy from subject S_12.

source_name: subject S_12

value: 67 years

value: Female


title: subject S_3 [expression]

description:
S_3
Gene expression data from liver biopsy from subject S_3.

source_name: subject S_3

value: 69 years


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 24 hr(s) (1M5)

value: Sprague-Dawley

value: Male

value: sterile water


title: subject S_26 [expression]

description:
S_26
Gene expression data from liver biopsy from subject S_26.

source_name: subject S_26

value: Liver

value: 66 years


title: subject S_20 [methylation]

description: DNA methylation data from liver biopsy from subject S_20.

source_name: subject S_20

value: 26 years


title: subject S_11 [expression]

description:
S_11
Gene expression data from liver biopsy from subject S_11.

source_name: subject S_11

value: 63 years