title: GRO-seq_LucKD_PJ34_MCF7

description: nascent RNA

data_processing:
Library strategy: GRO-Seq
Trimmed human GRO-seq reads were aligned to the human reference genome (hg19) using the bwa aligner {Li and Durbin, 2009} with default settings (uniquely aligned, 2 mismatches allowed, and 19 bp seed sequence).  The 5’-most base pair from each read was used in all analyses, with no more than 2 duplicates allowed at any genomic location. RNA-seq reads were mapped to the hg19 human genome using Tophat and converted to bed files.
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: GRO-seq in MCF7 cells with shRNA-mediated knockdown of Luciferase as a control with 1 hour 1 µM PJ34 Treatment

extract_protocol:
GRO-seq: MCF-7 cells were washed three times with ice-cold PBS and then resuspended for swelling in ice-cold Hypotonic Lysis Buffer [10 mM Tris•HCl, pH 7.4, 0.5% NP-40, 10% Glycerol, 3 mM CaCl2, 2 mM MgCl2, and 1 mM DTT containing 1x protease inhibitor cocktail (Sigma-Aldrich) and 4 units/mL SUPERase-In (Ambion)].   The swollen cells were collected by centrifugation at 1000 RCF for 10 min at 4°C and then resuspended in 1.5 ml of lysis buffer and pipetted up and down through a narrow opening tip 30 to 50 times to lyse the cells and release the nuclei.  The nuclei were collected by centrifugation and washed once with 1 mL of Hypotonic Lysis Buffer.  After a final collection by centrifugation, the resulting pellets of nuclei were resuspended in 500 μL of Freezing Buffer (50 mM Tris•HCl, pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 4 units/mL of SUPERase-In per mL), counted, frozen in liquid nitrogen in 100 μL aliquots containing 5 x 106 nuclei, and stored at -80°C until use. RNA-seq: Following 3 hours of treatment, RNA was harvested using QIAGEN RNeasy Kit.
GRO-seq: Nuclear run-on and GRO-seq library preparation were performed as previously described {Core, 2008;Hah, 2011}.  Briefly, nuclear run-on reactions were performed for ~100 bases in the presence of sarksoyl (to prevent reengagement of RNA polymerases), rNTPs, α32P-CTP, and 5-bromo-UTP.  The nascent RNAs were isolated, hydrolyzed to ~100 bases, and enriched using α-BrdUTP antibody-conjugated agarose beads (Santa Cruz).  The bound RNAs were washed several times and eluted.  The 5’ RNA cap was removed and the ends were repaired in preparation for adapter ligation.  Small RNA adapters were ligated to the 5’ end, followed by another bead binding enrichment using α-BrdUTP antibody-conjugated agarose beads.  These steps were repeated using a 3’ adapter.  The resulting RNAs were reverse transcribed, amplified using PCR, and analyzed by high throughput sequencing using an Illumina 1G Genome Analyzer. RNA-seq: RNA was prepared for sequencing as previously described (Sun, M. et al. Mol. Cell 2015).

treatment_protocol: GRO-seq: Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum. RNA-seq: Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum and 1 µg/mL Doxycycline for 4 days prior to treatment with DRB or vehicle (DMSO) treatment for 3 hours prior to RNA harvest.


title: 2011 TIV subject ID 1149 at D0 post-vaccination

status: Public on Dec 16 2015

type: RNA

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Hybridization was performed on Human U133 Plus 2.0 Arrays (using GeneTitan platform, Affymetrix, or individual cartridges) for 16 h at 45 oC, and 60 r.p.m. in a Hybridization Oven 640 (Affymetrix), slides were washed and stained with a Fluidics Station 450 (Affymetrix).

scan_protocol: Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix software was used to perform image analysis and generate raw intensity data.

data_processing: RMA normalization was performed using Expression Console software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination), and days 3 and 7 post-vaccination.

label_protocol: Total RNA sample quality was evaluated by spectrophotometer to determine quantity, protein contamination and organic solvent contamination, and an Agilent 2100 Bioanalyzer was used to check for RNA degradation. Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol.

extract_protocol: Following PMBC isolation from CPT, 2 x 10^6 cells were lysed in 1 ml of TRIzol and stored at -80C (Cat# 15596-026; Invitrogen Life Technologies). After all time points were collected for a subject, the samples were thawed, and the RNA isolation proceeded according to the manufacturer’s protocol.

tag: tissue

value: blood

tag: cell type

value: mononuclear cells

tag: time point

tag: subject id


title: 2011 TIV subject ID 1180 at D7 post-vaccination


title: 2011 TIV subject ID 1147 at D0 post-vaccination


title: 2011 TIV subject ID 1144 at D7 post-vaccination


title: 2011 TIV subject ID 1179 at D3 post-vaccination


title: 2011 TIV subject ID 1178 at D7 post-vaccination


title: 2011 TIV subject ID 1176 at D7 post-vaccination


title: 2011 TIV subject ID 1177 at D7 post-vaccination


title: 2011 TIV subject ID 1174 at D7 post-vaccination


title: 2011 TIV subject ID 1180 at D0 post-vaccination


title: 2011 TIV subject ID 1183 at D0 post-vaccination


title: 2011 TIV subject ID 1174 at D3 post-vaccination


title: 2011 TIV subject ID 1144 at D0 post-vaccination


title: 2011 TIV subject ID 1179 at D7 post-vaccination


title: 2011 TIV subject ID 1149 at D7 post-vaccination


title: 2011 TIV subject ID 1185 at D0 post-vaccination


title: 2011 TIV subject ID 1184 at D7 post-vaccination


title: 2011 TIV subject ID 1185 at D7 post-vaccination


title: 2011 TIV subject ID 1177 at D0 post-vaccination


title: 2011 TIV subject ID 1176 at D0 post-vaccination


title: 2011 TIV subject ID 1179 at D0 post-vaccination


title: 2011 TIV subject ID 1147 at D7 post-vaccination


title: 2011 TIV subject ID 1177 at D3 post-vaccination


title: 2011 TIV subject ID 1178 at D0 post-vaccination


title: 2011 TIV subject ID 1186 at D7 post-vaccination


title: 2011 TIV subject ID 1178 at D3 post-vaccination


title: 2011 TIV subject ID 1174 at D0 post-vaccination


title: 2011 TIV subject ID 1186 at D0 post-vaccination


title: 2011 TIV subject ID 1183 at D7 post-vaccination


title: 2011 TIV subject ID 1184 at D0 post-vaccination


title: 2011 TIV subject ID 1173 at D0 post-vaccination


title: 2011 TIV subject ID 1170 at D0 post-vaccination


title: 2011 TIV subject ID 1172 at D7 post-vaccination


title: 2011 TIV subject ID 1161 at D7 post-vaccination


title: 2011 TIV subject ID 1169 at D7 post-vaccination


title: 2011 TIV subject ID 1170 at D7 post-vaccination


title: 2011 TIV subject ID 1172 at D0 post-vaccination


title: 2011 TIV subject ID 1168 at D7 post-vaccination


title: 2011 TIV subject ID 1153 at D7 post-vaccination


title: 2011 TIV subject ID 1157 at D0 post-vaccination


title: 2011 TIV subject ID 1154 at D0 post-vaccination


title: 2011 TIV subject ID 1169 at D0 post-vaccination


title: 2011 TIV subject ID 1155 at D3 post-vaccination


title: 2011 TIV subject ID 1168 at D0 post-vaccination


title: 2011 TIV subject ID 1155 at D0 post-vaccination


title: 2011 TIV subject ID 1156 at D0 post-vaccination


title: 2011 TIV subject ID 1156 at D7 post-vaccination


title: 2011 TIV subject ID 1173 at D7 post-vaccination


title: 2011 TIV subject ID 1153 at D0 post-vaccination


title: 2011 TIV subject ID 1166 at D7 post-vaccination


title: 2011 TIV subject ID 1152 at D0 post-vaccination


title: 2011 TIV subject ID 1148 at D7 post-vaccination


title: 2011 TIV subject ID 1157 at D7 post-vaccination


title: 2011 TIV subject ID 1159 at D0 post-vaccination


title: 2011 TIV subject ID 1154 at D7 post-vaccination


title: 2011 TIV subject ID 1159 at D7 post-vaccination


title: 2011 TIV subject ID 1161 at D0 post-vaccination


title: 2011 TIV subject ID 1152 at D7 post-vaccination


title: 2011 TIV subject ID 1166 at D0 post-vaccination


title: 2011 TIV subject ID 1145 at D7 post-vaccination


title: 2011 TIV subject ID 1143 at D7 post-vaccination


title: 2011 TIV subject ID 1146 at D7 post-vaccination


title: 2011 TIV subject ID 1142 at D7 post-vaccination


title: 2011 TIV subject ID 1143 at D0 post-vaccination


title: 2011 TIV subject ID 1141 at D0 post-vaccination


title: 2011 TIV subject ID 1139 at D7 post-vaccination


title: 2011 TIV subject ID 1140 at D7 post-vaccination


title: 2011 TIV subject ID 1136 at D0 post-vaccination


title: 2011 TIV subject ID 1142 at D0 post-vaccination


title: 2011 TIV subject ID 1141 at D7 post-vaccination


title: 2011 TIV subject ID 1140 at D0 post-vaccination


title: 2011 TIV subject ID 1129 at D0 post-vaccination


title: 2011 TIV subject ID 1122 at D7 post-vaccination


title: 2011 TIV subject ID 1129 at D7 post-vaccination


title: 2011 TIV subject ID 1164 at D7 post-vaccination


title: 2011 TIV subject ID 1112 at D7 post-vaccination


title: 2011 TIV subject ID 1148 at D0 post-vaccination


title: 2011 TIV subject ID 1136 at D7 post-vaccination


title: 2011 TIV subject ID 1122 at D0 post-vaccination


title: 2011 TIV subject ID 1137 at D0 post-vaccination


title: 2011 TIV subject ID 1132 at D7 post-vaccination


title: 2011 TIV subject ID 1137 at D7 post-vaccination


title: 2011 TIV subject ID 1112 at D0 post-vaccination


title: 2011 TIV subject ID 1101 at D0 post-vaccination


title: 2011 TIV subject ID 1139 at D0 post-vaccination


title: 2011 TIV subject ID 1132 at D0 post-vaccination


title: 2011 TIV subject ID 1101 at D7 post-vaccination


title: 2011 TIV subject ID 1164 at D0 post-vaccination


title: 2011 TIV subject ID 1164 at D3 post-vaccination


title: 2011 TIV subject ID 1162 at D7 post-vaccination


title: 2011 TIV subject ID 1158 at D3 post-vaccination


title: 2011 TIV subject ID 1162 at D0 post-vaccination


title: 2011 TIV subject ID 1150 at D7 post-vaccination


title: 2011 TIV subject ID 1151 at D3 post-vaccination


title: 2011 TIV subject ID 1158 at D7 post-vaccination


title: 2011 TIV subject ID 1162 at D3 post-vaccination


title: 2011 TIV subject ID 1151 at D7 post-vaccination


title: 2011 TIV subject ID 1134 at D0 post-vaccination


title: 2011 TIV subject ID 1151 at D0 post-vaccination


title: 2011 TIV subject ID 1131 at D3 post-vaccination


title: 2011 TIV subject ID 1131 at D0 post-vaccination


title: 2011 TIV subject ID 1130 at D3 post-vaccination


title: 2011 TIV subject ID 1133 at D7 post-vaccination


title: 2011 TIV subject ID 1131 at D7 post-vaccination


title: 2011 TIV subject ID 1150 at D0 post-vaccination


title: 2011 TIV subject ID 1133 at D0 post-vaccination


title: 2011 TIV subject ID 1135 at D7 post-vaccination


title: 2011 TIV subject ID 1130 at D7 post-vaccination


title: 2011 TIV subject ID 1134 at D3 post-vaccination


title: 2011 TIV subject ID 1150 at D3 post-vaccination


title: 2011 TIV subject ID 1158 at D0 post-vaccination


title: 2011 TIV subject ID 1135 at D0 post-vaccination


title: 2011 TIV subject ID 1133 at D3 post-vaccination


title: 2011 TIV subject ID 1134 at D7 post-vaccination


title: 2011 TIV subject ID 1135 at D3 post-vaccination


title: 2011 TIV subject ID 1130 at D0 post-vaccination


title: 2011 TIV subject ID 1126 at D0 post-vaccination


title: 2011 TIV subject ID 1123 at D7 post-vaccination


title: 2011 TIV subject ID 1123 at D3 post-vaccination


title: 2011 TIV subject ID 1128 at D0 post-vaccination


title: 2011 TIV subject ID 1126 at D3 post-vaccination


title: 2011 TIV subject ID 1127 at D7 post-vaccination


title: 2011 TIV subject ID 1127 at D3 post-vaccination


title: 2011 TIV subject ID 1119 at D0 post-vaccination


title: 2011 TIV subject ID 1118 at D7 post-vaccination


title: 2011 TIV subject ID 1117 at D0 post-vaccination


title: 2011 TIV subject ID 1119 at D7 post-vaccination


title: 2011 TIV subject ID 1128 at D7 post-vaccination


title: 2011 TIV subject ID 1128 at D3 post-vaccination


title: 2011 TIV subject ID 1116 at D7 post-vaccination


title: 2011 TIV subject ID 1119 at D3 post-vaccination


title: 2011 TIV subject ID 1118 at D0 post-vaccination


title: 2011 TIV subject ID 1115 at D7 post-vaccination


title: 2011 TIV subject ID 1124 at D7 post-vaccination


title: 2011 TIV subject ID 1118 at D3 post-vaccination


title: 2011 TIV subject ID 1127 at D0 post-vaccination


title: 2011 TIV subject ID 1124 at D3 post-vaccination


title: 2011 TIV subject ID 1124 at D0 post-vaccination


title: 2011 TIV subject ID 1116 at D0 post-vaccination


title: 2011 TIV subject ID 1117 at D3 post-vaccination


title: 2011 TIV subject ID 1117 at D7 post-vaccination


title: 2011 TIV subject ID 1116 at D3 post-vaccination


title: 2011 TIV subject ID 1123 at D0 post-vaccination


title: 2011 TIV subject ID 1145 at D0 post-vaccination


title: 2011 TIV subject ID 1115 at D3 post-vaccination


title: 2011 TIV subject ID 1146 at D0 post-vaccination


title: 2011 TIV subject ID 1114 at D3 post-vaccination


title: 2011 TIV subject ID 1113 at D7 post-vaccination


title: 2011 TIV subject ID 1111 at D7 post-vaccination


title: 2011 TIV subject ID 1110 at D0 post-vaccination


title: 2011 TIV subject ID 1110 at D7 post-vaccination


title: 2011 TIV subject ID 1113 at D3 post-vaccination


title: 2011 TIV subject ID 1126 at D7 post-vaccination


title: 2011 TIV subject ID 1109 at D0 post-vaccination


title: 2011 TIV subject ID 1111 at D3 post-vaccination


title: 2011 TIV subject ID 1106 at D3 post-vaccination


title: 2011 TIV subject ID 1104 at D3 post-vaccination


title: 2011 TIV subject ID 1107 at D0 post-vaccination


title: 2011 TIV subject ID 1114 at D0 post-vaccination


title: 2011 TIV subject ID 1111 at D0 post-vaccination


title: 2011 TIV subject ID 1104 at D7 post-vaccination


title: 2011 TIV subject ID 1109 at D7 post-vaccination


title: 2011 TIV subject ID 1109 at D3 post-vaccination


title: 2011 TIV subject ID 1113 at D0 post-vaccination


title: 2011 TIV subject ID 1103 at D7 post-vaccination


title: 2011 TIV subject ID 1103 at D3 post-vaccination


title: 2011 TIV subject ID 1103 at D0 post-vaccination


title: 2011 TIV subject ID 1106 at D7 post-vaccination


title: 2011 TIV subject ID 1106 at D0 post-vaccination


title: 2011 TIV subject ID 1114 at D7 post-vaccination


title: 2011 TIV subject ID 1107 at D7 post-vaccination


title: 2011 TIV subject ID 1102 at D7 post-vaccination


title: 2011 TIV subject ID 1102 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 90 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 91 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 90 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 90 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 91 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 85 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 65 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 86 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 63 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 65 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 80 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 78 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 83 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 78 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 65 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 63 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 80 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 91 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 78 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 86 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 85 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 83 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 53 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 80 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 85 at D7 post-vaccination


title: 2011 TIV subject ID 1102 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 51 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 53 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 47 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 51 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 47 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 46 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 46 at D0 post-vaccination


title: 2011 TIV subject ID 1110 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 51 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 46 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 4 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 53 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 42 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 42 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 35 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 44 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 44 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 4 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 42 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 47 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 4 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 116 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 35 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 118 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 118 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 118 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 111 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 44 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 116 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 111 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 110 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 105 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 108 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 107 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 116 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 107 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 58 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 110 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 105 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 103 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 58 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 103 at D0 post-vaccination


title: 2011 TIV subject ID 1104 at D0 post-vaccination


title: 2011 TIV subject ID 1115 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 103 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 9 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 110 at D7 post-vaccination


title: 2010 FluCenter TIV subject ID 105 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 58 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 107 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 108 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 9 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 9 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 8 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 9 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 8 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 70 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 7 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 70 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 70 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 7 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 69 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 70 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 8 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 70 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 68 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 7 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 69 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 66 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 66 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 68 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 69 at D14 post-vaccination


title: 2010 FluCenter TIV subject ID 63 at D0 post-vaccination


title: 2010 FluCenter TIV subject ID 108 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 68 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 69 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 66 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 69 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 66 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 7 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 68 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 68 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 66 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 65 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 8 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 65 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 64 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 65 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 63 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 63 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 64 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 65 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 62 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 62 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 61 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 64 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 64 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 60 at D3 post-vaccination


title: 2010 FluCenter TIV subject ID 111 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 61 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 60 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 63 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 64 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 61 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 63 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 62 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 63 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 62 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 62 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 61 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 65 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 60 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 61 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 60 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 60 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 59 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 59 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 50 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 59 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 58 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 57 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 58 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 57 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 59 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 3 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 3 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 44 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 33 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 45 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 59 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 11 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 11 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 58 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 58 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 3 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 48 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 58 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 12 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 12 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 57 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 12 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 3 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 12 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 11 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 10 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 10 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 10 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 56 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 57 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 57 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 54 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 10 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 56 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 56 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 54 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 55 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 56 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 52 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 53 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 56 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 55 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 55 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 54 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 11 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 52 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 54 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 55 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 53 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 54 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 53 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 53 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 52 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 52 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 53 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 52 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 55 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 51 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 51 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 51 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 51 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 46 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 47 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 51 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 43 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 47 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 46 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 46 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 40 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 47 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 43 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 43 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 42 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 47 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 43 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 40 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 40 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 43 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 47 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 40 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 40 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 42 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 46 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 42 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 39 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 46 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 42 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 39 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 42 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 39 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 37 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 38 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 39 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 38 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 35 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 32 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 39 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 37 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 37 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 34 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 34 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 38 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 38 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 34 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 34 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 31 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 35 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 37 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 35 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 34 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 32 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 38 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 32 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 31 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 35 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 37 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 32 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 32 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 31 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 30 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 30 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 30 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 5 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 5 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 31 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 29 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 4 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 5 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 5 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 6 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 4 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 6 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 30 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 4 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 4 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 29 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 6 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 4 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 5 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 6 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 6 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 29 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 28 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 30 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 29 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 31 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 28 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 28 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 26 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 26 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 25 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 28 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 25 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 28 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 24 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 26 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 25 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 26 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 22 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 22 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 22 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 24 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 24 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 23 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 25 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 24 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 23 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 23 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 23 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 21 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 24 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 22 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 25 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 26 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 23 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 29 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 21 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 21 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 21 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 20 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 21 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 2 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 20 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 2 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 20 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 2 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 19 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 18 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 19 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 2 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 18 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 2 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 19 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 19 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 18 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 17 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 20 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 18 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 19 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 17 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 18 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 17 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 17 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 17 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 20 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 16 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 16 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 14 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 22 at D7 post-vaccination


title: 2010 HIPC TIV subject ID 16 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 16 at D14 post-vaccination


title: 2010 HIPC TIV subject ID 14 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 14 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 14 at D1 post-vaccination


title: 2010 HIPC TIV subject ID 14 at D14 post-vaccination


title: 2009 TIV subject ID 97 at D3 post-vaccination

scan_protocol: Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.


title: 2009 TIV subject ID 96 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 1 at D1 post-vaccination


title: 2009 TIV subject ID 91 at D3 post-vaccination


title: 2010 HIPC TIV subject ID 1 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 1 at D3 post-vaccination


title: 2009 TIV subject ID 86 at D7 post-vaccination


title: 2009 TIV subject ID 91 at D0 post-vaccination


title: 2009 TIV subject ID 97 at D7 post-vaccination


title: 2009 TIV subject ID 86 at D3 post-vaccination


title: 2009 TIV subject ID 83 at D7 post-vaccination


title: 2009 TIV subject ID 97 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 1 at D7 post-vaccination


title: 2009 TIV subject ID 83 at D3 post-vaccination


title: 2009 TIV subject ID 80 at D3 post-vaccination


title: 2009 TIV subject ID 83 at D0 post-vaccination


title: 2009 TIV subject ID 80 at D7 post-vaccination


title: 2009 TIV subject ID 67 at D7 post-vaccination


title: 2009 TIV subject ID 78 at D3 post-vaccination


title: 2009 TIV subject ID 78 at D0 post-vaccination


title: 2009 TIV subject ID 68 at D7 post-vaccination


title: 2009 TIV subject ID 78 at D7 post-vaccination


title: 2009 TIV subject ID 96 at D0 post-vaccination


title: 2010 HIPC TIV subject ID 1 at D14 post-vaccination


title: 2009 TIV subject ID 80 at D0 post-vaccination


title: 2009 TIV subject ID 68 at D3 post-vaccination


title: 2009 TIV subject ID 65 at D7 post-vaccination


title: 2009 TIV subject ID 96 at D7 post-vaccination


title: 2009 TIV subject ID 65 at D0 post-vaccination


title: 2009 TIV subject ID 67 at D0 post-vaccination


title: 2009 TIV subject ID 63 at D7 post-vaccination


title: 2009 TIV subject ID 63 at D0 post-vaccination


title: 2009 TIV subject ID 63 at D3 post-vaccination


title: 2009 TIV subject ID 58 at D7 post-vaccination


title: 2009 TIV subject ID 58 at D3 post-vaccination


title: 2009 TIV subject ID 68 at D0 post-vaccination


title: 2009 TIV subject ID 58 at D0 post-vaccination


title: 2009 TIV subject ID 67 at D3 post-vaccination


title: 2009 TIV subject ID 53 at D0 post-vaccination


title: 2009 TIV subject ID 53 at D7 post-vaccination


title: 2009 TIV subject ID 53 at D3 post-vaccination


title: 2009 TIV subject ID 51 at D3 post-vaccination


title: 2009 TIV subject ID 51 at D7 post-vaccination


title: 2009 TIV subject ID 51 at D0 post-vaccination


title: 2009 TIV subject ID 46 at D0 post-vaccination


title: 2009 TIV subject ID 44 at D3 post-vaccination


title: 2009 TIV subject ID 44 at D0 post-vaccination


title: 2009 TIV subject ID 46 at D7 post-vaccination


title: 2009 TIV subject ID 43 at D7 post-vaccination


title: 2009 TIV subject ID 44 at D7 post-vaccination


title: 2009 TIV subject ID 4 at D3 post-vaccination


title: 2009 TIV subject ID 35 at D3 post-vaccination


title: 2009 TIV subject ID 43 at D0 post-vaccination


title: 2009 TIV subject ID 35 at D0 post-vaccination


title: 2009 TIV subject ID 35 at D7 post-vaccination


title: 2009 TIV subject ID 29 at D7 post-vaccination


title: 2009 TIV subject ID 29 at D0 post-vaccination


title: 2009 TIV subject ID 32 at D0 post-vaccination


title: 2009 TIV subject ID 42 at D3 post-vaccination


title: 2009 TIV subject ID 39 at D0 post-vaccination


title: 2009 TIV subject ID 39 at D7 post-vaccination


title: 2009 TIV subject ID 42 at D0 post-vaccination


title: 2009 TIV subject ID 4 at D0 post-vaccination


title: 2009 TIV subject ID 32 at D7 post-vaccination


title: 2009 TIV subject ID 39 at D3 post-vaccination


title: 2009 TIV subject ID 42 at D7 post-vaccination


title: 2009 TIV subject ID 2 at D3 post-vaccination


title: 2009 TIV subject ID 43 at D3 post-vaccination


title: 2009 TIV subject ID 16 at D7 post-vaccination


title: 2009 TIV subject ID 2 at D0 post-vaccination


title: 2009 TIV subject ID 32 at D3 post-vaccination


title: 2009 TIV subject ID 2 at D7 post-vaccination


title: 2009 TIV subject ID 29 at D3 post-vaccination


title: 2009 TIV subject ID 4 at D7 post-vaccination


title: A632-root-1 (CAGE)

status: Public on Nov 04 2015

type: SRA

city: East Lansing

first: Erich

last: Grotewold

state: Michigan

address: 603 Wilson Rd

department: Department of Biochemistry and Molecular Biology

country: USA

institute: Michigan State University

library_source: transcriptomic

data_processing:
Sequences corresponding to specific samples were defined according to barcode presence. In summary, after barcode recognition and removal, reads were filtered according to PHRED values. Next, TagDust was used to identify chimeric sequences that were explained by mistaken combination of adapter sequences and only sequences ~27 bp were kept for further analyses.
34,666,735 trimmed CAGE tags were mapped using Bowtie2 v2.0.4, allowing for unique mapping and a maximum of two mismatches.
The alignment files were further used as input of the bioconductor package CAGEr v1.2.9 for the following tasks: (a) to correct for G-addition when a mismatching G was encountered at the first position; (b) to estimate CAGE transcriptional start sites; (c) to cluster CAGE TSSs into non-overlapping TSS Clusters and TCs in non-overlapping regions; (d) to determine dominant CTSSs for each TC; (e) applied a power-law based normalization to next calculate expression values in tags per million (TPM) for CTSSd and TCs; (f) to calculate the interquartile width, which is defined as the absolute distance in basepairs between the 10th and 90th percentile positions of the cumulative sum of CAGE tags for each TC; and (g) to determine differential usage of TSSs between tissues and between inbred lines .
The final set of obtained TC regions were evaluated to eliminate rRNA and organelle contamination. For rRNA contamination, all the reads from which TCs were derived were compared against a MIPS database of repetitive elements (Spannagl M et al., 2007) using BLAST (Camacho C et al., 2009). TCs for which reads were found to be hitting the databases were removed from further analyses (to consider a hit the following combined threshold was used: e-value 1e-15, 98% coverage and 98% similarity). For organelle contamination, TCs mapping to pseudomolecules different from nuclear chromosomes 1 to 10 were discarded to generate a final dataset of 75,681 TCs (Table 2.3).
Genome_build: Zea mays B73 genome assembly (Maize B73 RefGen v3) obtained from GRAMENE was used as the reference genome across all the steps
Supplementary_files_format_and_content: 130507_OSU_CAGE_CTSS_Clusters.bed, bed file: contains per each row information for a CTSS cluster. It is the chromosome, start, end, CTSS cluster identifier, score (tags per million for CTSS cluster)
Supplementary_files_format_and_content: 130507_OSU_CAGE_CTSS_dominant.bed, bed file: contains per each row information for a CTSS cluster. It is the chromosome, start, end, CTSS cluster identifier, score (tags per million for CTSS dominant)
Supplementary_files_format_and_content: 130507_OSU_CAGE_TC_iq10th-90th.bed, bed file: contains per each row information for a CTSS cluster. It is the chromosome, start, end, CTSS cluster identifier, score (interquartile width for interquartile ranges)
Supplementary_files_format_and_content: 130507_OSU_CAGE_CTSS_Clusters.csv, csv file: contains per each row information for a CTSS cluster. It is CTSS cluster identifier, chromosome, start, end, tpm (tags per million) TC, position of CTSS dominant, tpm CTSS dominant, interquartile range start, interquartile range end, interquartile range width, strand and shape index

organism: Zea mays subsp. mays

source_name: seedling

growth_protocol: B73 and A632 maize lines were grown under controlled environmental conditions 16 h light/27°C, 8 h dark/21°C.

extract_protocol: At 14 days shoots and roots from 5 different seedlings were harvested and pooled. Samples were ground in liquid nitrogen and used to isolate RNA by the Direct-zolTM RNA MiniPrep Kit following manufacturer's recommendations (Zymo Research, Irvine, CA). In brief, 5 μg of the total RNA from each replicate were used as templates for reverse transcription to cDNA using random primers that includes the recognition sequence for EcoP15I. Biotinylation of 5’ end (Cap) was followed by RNAse digestion to cleave ssRNA molecules and then capped RNAs hybridized with cDNAs were pulled down using streptavidin coated magnetic beads. RNA-cDNA hybrids were denatured, and next, 5’ end cDNA molecules were ligated to 5’ linkers, including barcodes (B73-root-1:GAT; B73-root-2: in order to pool all the samples in the same lane. Single strand 5’ linkers were used as primable sequences to allow for the synthesis of a 2nd strand cDNA. Next, ds-cDNAs were digested with EcoP15I to release 27 bp of the 5’ cDNA. Subsequently, digested cDNA were ligated to 3’ linkers containing Illumina primer sequences for further library sequencing. Whole CAGE libraries were PCR amplified (B73 roots 5’ end cDNAs for 16 cycles and all other tissues for 14 cycles) to reach the appropriate concentration for library sequencing. PCR products were treated with 20 units of exonuclease I (NEB, Ipswich, MA) at 37°C for 1 h and purified with MinElute PCR Purification Kit (Qiagen, Valencia, CA). Concentration and size distribution were evaluated by the high-sensitivity DNA Bioanalyzer (Agilent, Santa Clara, CA). Equal amounts of each replicate were pulled at a 5 pM concentration and sequenced using the Illumina HiSeq 2000 sequencer (Illumina, San Diego, CA).

treatment_protocol: no treatment

tag: line

value: root

tag: age

tag: genotype

value: wild type


title: 2009 TIV subject ID 46 at D3 post-vaccination


title: A632-root-2 (CAGE)


title: B73-root-2


title: A632-shoot-2 (CAGE)

value: shoot


title: A632-shoot-1 (CAGE)


title: B73-root-1


title: B73-shoot-2


title: B73-shoot-1


title: 2009 TIV subject ID 16 at D0 post-vaccination


title: 2009 TIV subject ID 103 at D7 post-vaccination


title: 2009 TIV subject ID 102 at D7 post-vaccination


title: 2009 TIV subject ID 102 at D0 post-vaccination


title: 2009 TIV subject ID 102 at D3 post-vaccination


title: 2009 TIV subject ID 100 at D0 post-vaccination


title: 2009 TIV subject ID 103 at D0 post-vaccination


title: 2009 TIV subject ID 100 at D7 post-vaccination


title: 2009 TIV subject ID 100 at D3 post-vaccination


title: 2009 TIV subject ID 103 at D3 post-vaccination


title: 2009 TIV subject ID 86 at D0 post-vaccination


title: RBFOX2 knockdown rep2

status: Public on Jul 15 2015

city: Sangareddy

first: Ashish

last: Misra

state: Telangana

address: Kandi

department: Biotechnology

country: India

institute: Indian Institute of Technology Hyderabad

data_processing:
Images were analyzed using OLB 1.9 and CASAVA_v1.8.2
TopHat v2.0.9 (bowtie2/2.1.0) was used to map the sequences to human genome hg19
Reads counts were processed by DEXSeq v 1.10.6
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include exon level count values for each Sample

source_name: Flip-In-293 cells

growth_protocol: Cells were grown in DMEM + 10% FBS media + 1% Pen/Strep

extract_protocol:
RNA was isolated for Flip-In-293 cells using RNeasy mini kit (qiagen) according to manufacturer's protocol
Library was prepared using Illumina TrueSeq kit

treatment_protocol: Knockdown was performed using lentivirus shRNA against NS, RBFOX2 and CPSF2.

tag: genotype/variation


title: non-silence rep1

value: WT


title: non-silence rep2


title: CPSF2 knockdown rep2


title: RBFOX2 knockdown rep1


title: CPSF2 knockdown rep1


title: WT_Ncrassa_BSseq

status: Public on Mar 22 2015

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

library_source: genomic

data_processing:
The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping.
BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged.
A python script (bidensity) was written to calculate the average 5mC level over a 500bp sliding window across the genome, producing a .wig file
.wig files were displayed on IGV (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011)
Genome_build: Ncrassa version12
Supplementary_files_format_and_content: .wig files show the ratio (0-1.0; 0 is DNA that is not cytosine methylated, 1.0 is DNA where all of the cytosines are methylated) of methylated cytosines to unmethylated cytosines as peaks of cytosine methylation enrichment

molecule: genomic DNA

organism: Neurospora crassa

source_name: N3752 WT Ncrassa (Selker)

growth_protocol: grown under standard dark cycle in 1xVogels medium + 1.5% sucrose (minimum medium) or minimum medium supplemented with histidine (0.5mg/mL [final]) for 48 hours on rocking shaker at 32oC

extract_protocol:
Genomic DNA was isolated using a protocol modified from (Oakley et al, 1987).  Genomic DNA (50ng) was treated with bisulfite using the EZ DNA Methylation LightningTM kit (ZYMO Research) per the manufacturer's protocol.
Libraries were prepared for sequencing with the EpiGnomeTM Methyl-Seq Kit (Epicentre cat #EGMK91324) and EpiGnomeTM Index PCR Primers (Epicentre cat#  EGIDX81312) per the manufacturer's protocol, purified with Agencourt AMPure XP beads (Beckman Coulter) per the manufacturer's protocol, Qubit HS Assay quantified (Life Technologies) per the manufacturer's protocol, visualized on the Fragment AnalyzerTM (Advanced Analytical) per the manufacturer's protocol, and sequenced on a Illumina HiSeq 2000

tag: strain

value: wildtype

tag: time point in light cycle

tag: growth medium

value: 1xVogels, 1.5% sucrose (minimum)

tag: bisulfite treated

value: bisulfite


title: Hi-C, Liver STL011, replicate one

status: Public on Feb 18 2015

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description: Sample 4

data_processing:
library strategy: HaploSeq
fastq:  Illumina's HiSeq Control Software
For Hi-C read alignment, we aligned Hi-C reads to the hg18 (human) genome. We masked any bases in the genome that were genotyped as SNPs in the individual genome. These bases were masked to “N” in order to reduce reference bias mapping artifacts. Hi-C reads were aligned as single end reads using Novoalign. After mapping was finished, read pairs were re-constructed from single reads using an in house pipeline.  Unmapped reads were filtered out and PCR duplicate reads were removed.
Haplotypes were generated from the final aligned bam file using the HapCUT algorithm.  The details of HapCUT are described previously (Bansal and Bafna, Bioinformatics 24, i153-159, 2008).
The final processed haplotypes were generateds after removing local biases through following three steps. First the alignment biases were removed by aligning simulated reads spanning surrounding variants location. If there is more than 5% difference between alleles those variant loci were considered to subject an inherent mapping bias. Second, we removed alleles located in copy number variable regions and allelic biased copy number variable regions by comparing the coverage between two alleles based on WGS data. Any variants that had more coverage than three standard deviation above the mean of each haplotype were excluded. Any variants showing biased WGS coverage between two alleles were also excluded (binomial test p-value 0.05 after Benjamini correction). Lastly, we remove erroneously called as heterozygous variant during genotyping. We calculated the probability of each heterozygous variants were actually homozygous from the likelihood of observing the coverage on each allele from whole genome sequencing. Only heterozygous SNPs that had a FDR of less than 0.5% were included in downstream analysis.
HaploSeq generates two haplotypes for each chromosome, one for the maternal allele and one for the paternal allele. One allele is named as P1 (parent1) and another allele is named as P2 (parent2) since we do not have information regarding the parent of origin in each donor genome. For the chr9 we can generate haplotypes in each chromosome arm. The haplotypes in chrX STL002 was independtly generated based on hg19 genome build.
Genome_build: hg18
Supplementary_files_format_and_content: The processed haplotypes for the individual genome ("*_haps.vcf") are available in VCF format.

source_name: Liver STL011

growth_protocol: Tissues samples were obtained from deceased donors at the time of organ procurement at the Barnes-Jewish Hospital (St. Louis, USA).  Samples were flash frozen and pulverized prior to formaldehyde cross-linking.  Research consent from family was obtained, and this study was approved by Mid-American Transplant Services.

extract_protocol:
Hi-C experiments were conducted using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).
Sequencing libraries were constructed according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

value: Liver


title: Hi-C, Aorta STL002, replicate one

description: Sample 2

source_name: Aorta STL002

value: Aorta


title: Hi-C, LeftVentricle STL003, replicate one

description: Sample 3

source_name: LeftVentricle STL003

value: LeftVentricle


title: CPSF2 rep1 and rep2

data_processing:
Images were analyzed using OLB 1.9 and CASAVA_v1.8.2
bowtie (v1.0.0) was used to map the sequences to human genome hg19
Genome_build: hg19
Supplementary_files_format_and_content: bed file were generated for the region with one or more hits by 5’end of iCLIP-seq

growth_protocol: Cells were grown in DMEM + 10% FBS media

extract_protocol:
Cells were lysed in buffer containng 50mM Tris-HCl pH 7.4, 100mM NaCl, 1mM MgCl2, 0.1mM CaCl2, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate and immunoprecipitation using antibodies was performed.
Library was constructed using standard iCLIP library preparation protocol.

treatment_protocol: RNA-protein crosslink was performed with 200mj/cm2 UV irradiation using UV stratalinker

tag: antibody


title: RBFOX2 rep1 and rep2


title: HepaRG control, rep3

city: Brussels

first: Robim

middle: M

last: Rodrigues

address: Laarbeeklaan 103

department: IVTD

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: 12.5 μg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 arrays along with a hybridization cocktail solution and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the quality control matrices were confirmed with the Affymetrix GCOS software following the manufacturer’s guidelines.

data_processing: Background correction, summarization (median polish) and normalization (quantile) were done with Robust Multi-array Analysis using RMAExpress v1.0.5

source_name: HepaRG not exposed

label_protocol: Total RNA (100 ng) was used for amplification and in vitro transcription using the Genechip 3’ IVT Express Kit following the manufacturer’s instructions (Affymetrix). The amplified RNA was purified with magnetic beads and 15 μg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: hSKP-HPC: hSKP cells were cultivated using growth medium composed of DMEM+GLUTAMAX/F12 Nutrient Mixture (3:1; Life Technologies) supplemented with 7.33 IU/mL benzyl penicillin (Continental Pharma), 50 mg/mL streptomycin sulfate (Sigma-Aldrich), 2.5 mg/mL fungizone, 2 % (v/v) B27 Supplement (Life Technologies), 40 ng/mL basic fibroblast growth factor (FGF) 2 (Promega)  and 20 ng/mL epidermal growth factor (EGF) (Promega). Approximately two weeks after isolation, hSKP spheroids were dissociated to single cells using Liberase DH (Roche). The cells were subsequently cultivated as a moolayer. Hepatic differentiation of hSKP was carried out using a 24-day protocol in which cells were exposed in a time-dependent manner to the following growth factors and cytokines: Activin A (Life Technologies), FGF4 (Biosource), bone morphogenetic protein 4 (BMP4), hepatocyte growth factor (HGF) (Life Technologies), insulin-transferin-sodium selenite solution (ITS) (Sigma-Aldrich), dexamethasone (Sigma-Aldrich) and oncostatin M (Life Technologies). The obtained differentiated hepatocyte-like cells are referred to as hepatic progenitor cells (hSKP-HPC).   HepG2: HepG2 cells (ATCC; clone HB-8065) were recovered from liquid nitrogen and were cultured in 75 cm2 tissue culture flasks (Falcon) in a humidified incubator (37oC, 5% (v/v) CO2). The cell culture medium was composed of DMEM (Lonza) containing 10% (v/v) bovine calf serum (Gibco). The cells were passaged at sub confluence at least three times before use in exposure experiments. A seeding density of approximately 13,000 cells / cm2 was employed each time.  HepaRG: cryo-preserved differentiated HepaRG cells were obtained from Biopredic International and cultivated as per the supplier's instructions. The cells were cultivated using basal hepatic medium supplemented with HepaRG Maintenance and Metabolism Supplement (Biopredic International). During the exposure experiments the basal hepatic medium was supplemented with HepaRG Induction Supplement (Biopredic International).

extract_protocol: The isolation was conducted using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich) following the manufacturer’s instructions.

treatment_protocol: Hepatic in vitro models, i.e. HepaRG, HepG2 and hSKP-HPC were exposed to acetaminophen for 24 hours at concentrations (IC10) of 13mM, 2mM and 18mM, respectively. Corresponding vehicle controls were incubated to the same medium without acetaminophen.

tag: cell line

value: HepaRG

value: hepatic cell line

tag: exposed to

value: none (vehicle control)


title: Hi-C, H1 embryonic stem cells, replicate two

city: La Jolla

first: Jesse

middle: R

last: Dixon

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

description:
H1_R2_T1_read1.fastq.gz
H1_R2_T1_read2.fastq.gz
H1_R2_T2_read1.fastq.gz
H1_R2_T2_read2.fastq.gz
H1_R2_T3_read1.fastq.gz
H1_R2_T3_read2.fastq.gz
H1_R2_T4_read1.fastq.gz
H1_R2_T4_read2.fastq.gz
H1_R2_T5_read1.fastq.gz
H1_R2_T5_read2.fastq.gz
H1_R2_T6_read1.fastq.gz
H1_R2_T6_read2.fastq.gz

data_processing:
Library strategy: Hi-C
fastq:  Illumina's HiSeq Control Software
For Hi-C read alignment, we aligned Hi-C reads to the hg18 (human) genome. We masked any bases in the genome that were genotyped as SNPs in the H1 genome. These bases were masked to “N” in order to reduce reference bias mapping artifacts. Hi-C reads were aligned iteratively as single end reads using Novoalign. Specifically, for iterative alignment, we first aligned the entire sequencing read to either the mouse or human genome. Unmapped reads are then trimmed by 5 base pairs and realigned. This process is repeated until the read successfully aligns to the genome or until the trimmed read is less than 25 base pairs long.  After iterative mapping was finished, read pairs were re-constructed from single reads using an in house pipeline.  Unmapped reads were filtered out and PCR duplicate reads were removed.  Final alignment files were then processed using the GATK pipeline, specifically using Indel Realignment and Variant Recalibration.  A similar pipeline was used for alignment of the other high-throughput sequencing datasets without the iterative alignment step.
Haplotypes were generated from the final aligned bam file after merging the two biological replicats using the HapCUT algorithm.  The details of HapCUT are described previously (Bansal and Bafna, Bioinformatics 24, i153-159, 2008).
Genome_build: hg18
Supplementary_files_format_and_content: Reads are listed in bed format with one line for each sequencing read.  The reads have been split by haplotype into the "A" and "B" (alternatively, "p1" and "p2") alleles according to which haplotype the bases within each sequencing read correspond.  For paired end Hi-C data, each line lists a single read, and paired infomration can be obtained from the read names.  The original fastq files for data other than the Hi-C and CTCF ChIP-seq are available in the GSE16256 dataset.
Supplementary_files_format_and_content: The processed haplotypes for the H1 genome ("H1_haps.vcf") are available in VCF format.

source_name: H1 embryonic stem cells

growth_protocol: Growth and differentiation of H1 hESCs was performed as previously described in Xie et al., 2013, Cell 153 (1134-1148)

extract_protocol: Sequencing libraries were constructed according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

value: H1 embryonic stem cells


title: AC individual Anti-DMC1

status: Public on Nov 17 2014

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the hg19 genome assembly. BWA was used to align genomic DNA and H3K4me3 ChIP-Seq data, while the pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome.
For SSDS DMC1 data, hotspots were called using MACS version 2.0.10 and matched control data. The following MACS arguments were used (--nomodel; --shiftsize: 400; --bw: 1000; -q: 0.1). For the H3K4me3 ChIP-Seq experiment, SICER v1.1 (Zang et al., 2009) was used for peak calling. The following arguments were used (species: hg19; redundancy threshold: 1; window size: 200; fragment size: 200; effective genome fraction: 0.8; gap size: 200; FDR: 0.1).
Genome_build: hg19
Supplementary_files_format_and_content: For each SSDS experiment, the associated BED file contains all ssDNA fragments identified for that sample. The bed file columns are as follows:  1. Chromosome  2. Fragment start  3. Fragment end  4. Read1Quality_Read2Quality  5. ITRLength_microhomologyLength  6. Fragment strand; Peak positions called by MACS or SICER are available on the series record.

source_name: Testis

extract_protocol:
For H3K4me3 CHiP-Seq and DMC1 SSDS protocols, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen).
DMC1 and H3K4Me3 ChIP were performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.  Sequencing libraries for anti-H3K4Me3 samples were prepared according to manufacturer’s protocol (Illumina) and anti-DMC1 libraries were prepared following the method described in (Khil et al., 2012).  For genomic DNA sequencing, DNA was sheared using a Covaris S series (Covaris, MS, USA) focused-ultrasonicator. Standard sequencing library construction was done using enzymes from New England Biolabs according to the protocol provided by Illumina. The PCR amplified library was size selected on a 2% agarose gel to extract the 300 to 500 bp band.

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

value: PRDM9A / PRDM9C

tag: sequencing technique

value: SSDS


title: AB1 individual Anti-DMC1

value: PRDM9A / PRDM9B


title: Hi-C, H1 embryonic stem cells, replicate one

description:
H1_R1_T1_read1.fastq.gz
H1_R1_T1_read2.fastq.gz
H1_R1_T2_read1.fastq.gz
H1_R1_T2_read2.fastq.gz
H1_R1_T3_read1.fastq.gz
H1_R1_T3_read2.fastq.gz
H1_R1_T4_read1.fastq.gz
H1_R1_T4_read2.fastq.gz


title: HIC035

status: Public on Dec 11 2014

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
library strategy: HiC-Seq
The paired end reads were aligned separately using BWA against the b37 human build or the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
Contact matrices were constructed at various resolutions and normalized using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
loops were annotated using HiCCUPS (see Rao, Huntley, et al), domains were annotated using Arrowhead (see Rao, Huntley, et al), subcompartments were annotated using a Gaussian HMM (see Rao, Huntley, et al)
Genome_build: b37 (human), mm9 (mouse)
Supplementary_files_format_and_content: HiCCUPS_looplist.txt files contain loop calls generated via HiCCUPS; first three fields represent the locus participating in the loop closer to the p-end of the chromosome; fields 4-6 represent the locus participating in the loop closer to the q-end of the chromosome; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 represents the observed number of counts at the loop; fields 9-12 represent the expected number of counts at the loop using four different expected models; fields 13-16 are the q-values over each of the expected values; field 17 is the number of enriched pixels that was clustered into a particular loop; field 18-19 are the centroid of the loop; field 20 is the radius of the loop
Supplementary_files_format_and_content: Arrowhead_domainlist.txt files contain domain calls generated via Arrowhead; first 6 fields represent the boundaries of the domain; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 is the corner score for the domain (see Rao, Huntley, et al); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al)
Supplementary_files_format_and_content: the subcompartment bed file contains the coordinates of the 6 nuclear subcompartments identified in Rao, Huntley, et al.
Supplementary_files_format_and_content: HIC*_merged_nodups.txt files specify each Hi-C read pair (i.e., the mapping locations of each individual read pair).

source_name: B-lymphoblastoids

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq/HiSeq2000/HiSeq2500 following the manufacturer's protocols

tag: protocol

value: dilution Hi-C


title: HepaRG control, rep1


title: HIC034


title: HepaRG control, rep2


title: AC individual Input DNA

value: none (input)


title: 2009 TIV subject ID 91 at D7 post-vaccination

tag: tissue

value: blood

value: mononuclear cells


title: AA2 individual Input DNA

value: PRDM9A / PRDM9A


title: AA1 individual Input DNA


title: AA1 individual Anti-DMC1


title: AA2 individual Anti-DMC1


title: AB1 individual Input DNA


title: HIC037


title: Hi-C IMR90 replicate 6

status: Public on Oct 20 2013

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

data_processing:
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
RNA-seq data were analyzed using TOPHAT and CUFFLINK packages.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped non-redundant reads for RNA-seq, GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.

source_name: fetal lung fibroblast

growth_protocol: IMR90 cells were grown as described in (Hawkins, R.D. et al. Cell Stem Cell 6, 479-91). MCF7 cells (ATCC), LNCaP cells (ATCC), and Human primary HUVEC cells (Lonza) were cultured following manufacturer’s instructions.

extract_protocol:
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).  ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).
Libraries were prepared according to Illumina's instruction or cited literatures.

treatment_protocol: TNF-a (R&D Systems, 10 ng/mL, 1 hr) treatment were performed in IMR90 or HUVEC cells.  Flavopiridol (Sigma, 1 μM for 1 hr) and IFN-γ (R&D, 50ng/mL for 2hrs) were performed in IMR90 cells. To find out primary TNF-α responsive genes, IMR90 cells were pre-treated with 5µg/mL of cycloheximide (sigma) for 30mins before TNF-α was added. Starvation and treatment of MCF7 cells with β-estradiol (Sigma, 100nM for 160min) were performed as described in previous literature (Hah, N. et al. Cell 145, 622-634, 2011); and LNCaP cells were starved and treated with 5α-dihydrotestosterone (DHT, 100nM, 4hr) as previously described(Wang, D. et al. Nature 474, 390-394, 2011)

tag: treatment

value: no treat

tag: experiment

value: Hi-C

value: no

tag: restriction enzyme

value: HindIII


title: Hi-C IMR90 replicate 5


title: Hi-C IMR90 replicate 4


title: Hi-C, F123 mouse ES cells, replicate one

status: Public on Nov 03 2013

description:
castx129_variants.vcf
F123.haps

data_processing:
fastq:  Illumina's HiSeq Control Software
For Hi-C read alignment, we aligned Hi-C reads to the mm9 (mouse) or the hg18 (human) genome. In each case, we masked any bases in the genome that were genotyped as SNPs in either Mus musculus castaneus or S129/SvJae (for mouse) or GM12878 (for humans). These bases were masked to “N” in order to reduce reference bias mapping artifacts. Hi-C reads were aligned iteratively as single end reads using Novoalign. Specifically, for iterative alignment, we first aligned the entire sequencing read to either the mouse or human genome. Unmapped reads are then trimmed by 5 base pairs and realigned. This process is repeated until the read successfully aligns to the genome or until the trimmed read is less than 25 base pairs long.  After iterative mapping was finished, read pairs were re-constructed from single reads using an in house pipeline.  Unmapped reads were filtered out and PCR duplicate reads were removed.  Final alignment files were then processed using the GATK pipeline, specifically using Indel Realignment and Variant Recalibration
Haplotypes were generated from the final aligned bam file after merging the two biological replicats using the HapCUT algorithm.  The details of HapCUT are described previously (Bansal and Bafna, Bioinformatics 24, i153-159, 2008).
Genome_build: mm9
Genome_build: hg18
Supplementary_files_format_and_content: The castx129_variants.vcf and GM12878_depristoeal.vcf are VCF format files of the variants used for input into the haplotyping algorithm.  Both of these files are derived from publicly available datasets. WIth regards to the "publicly available datasets", the castx129_variants.vcf file is derived from data downloaded from the ENA (ERP000042) and the SRA (SRX037820).  The GM12878_depristoeal.vcf is downloaded from the 1000 genomes project.
Supplementary_files_format_and_content: The F123.haps and GM12878_seed.haps are modified bed format files.  In this files, the first column is the chromosome, and the second column is the location of the variant.  The third and fourth column are the phased variants in the "A" and "B" haplotypes.  The choice of "A" and "B" is arbitrary, and it should be noted that the "A" haplotype from one chromosome is not necessarily derived from the same parent as the "A" haplotype from a different chromosome.
Supplementary_files_format_and_content: The GM12878_lcp.vcf file is a VCF format file from after local conditional phasing of variants in the seed haplotype

organism: Mus musculus

source_name: F123 mouse embyronic stem cells

growth_protocol:
F123 cells were grown in KnockOut Serum Replacement containing mouse ES cell media: DMEM 85%, 15% KnockOut Serum Replacement (Invitrogen), penicillin/streptomycin, 1X Non-essential amino acids (Gibco), 1X GlutaMax, 1000U/mL LIF (Millipore), 0.4mM b-mercaptoethanol. F123 mouse ES cells were initially cultured on 0.1% Gelatin-coated plates with mitomycin-C treated mouse embryonic fibroblasts (Millipore). Cells were passaged twice on 0.1% gelatin-coated feeder free plates before harvesting.
see samples section

value: F123 mouse ES cell line


title: Hi-C, GM12878 Lymphoblastoid cells, replicate one

description:
GM12878_lcp.vcf
GM12878_depristoeal.vcf
GM12878_seed.haps

source_name: GM12878 Lymphoblastoid cells

growth_protocol:
GM12878 cells (Coriell) were cultured in suspension in 85% RPMI media supplemental with 15% fetal bovine serum and 1X penicillin/streptomycin.
see samples section

value: GM12878 Lymphoblastoid cell line


title: Hi-C, GM12878 Lymphoblastoid cells, replicate two


title: Hi-C IMR90 replicate 3


title: Hi-C, F123 mouse ES cells, replicate two

description:
castx129_variants.vcf
F123.haps


title: Hi-C IMR90 replicate 1

description: Raw data for this sample has been previously published with accession code GSM862724

data_processing:
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
Genome_build: NCBI36
Supplementary_files_format_and_content: Mapped non-redundant reads for GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.

growth_protocol: IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91

treatment_protocol: Untreated or IMR90 cells treated with TNF-α (R&D Systems, 10 ng/mL, 1 hr) or flavopiridol (Sigma, 1 μM for 1 hr for ChIP-seq experiments, and 1 μM for 2 hr for Hi-C experiments) were used.


title: Hi-C IMR90 replicate 2

description: Part of raw data for this sample has been previously published with accession code GSM892307. The processed data file is generated from all raw data


title: patient 101, ccRCC tumour tissue

status: Public on Jun 03 2013

city: Lyon

first: Magdalena

middle: Barbara

last: Wozniak

address: 150 cours Albert Thomas

department: Genetics

country: France

institute: International Agency for Research on Cancer

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using vst transformation and quantile normalisation with lumi package (v2.6.0) in R (v.2.14.1) [Bioconductor v.2.10]

source_name: ccRCC tumour tissue

label_protocol: 500ng of mRNA was amplified into cRNA and biotinylated cRNA using Illumina® TotalPrep™-24 RNA Amplification Kit (Life Technologies) for the first batch, and two Illumina® TotalPrep™-96 RNA Amplification for the second and third batches (batches 2 and 3 included 2 technical replicate pairs from batch 1, and batch 3 included an additional technical replicate from batch 2).

extract_protocol: RNA was extracted withTotal RNA Isolation NucleoSpin® RNA II kit (Macherey Nagel) in accordance with the prescribed protocol provided with the kit. Quality control was performed withAgilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

tag: gender

value: male

tag: grade

value: III

value: kidney

tag: tissue type

value: clear cell renal cell carcinoma


title: patient 101, adjacent non-tumour renal tissue

source_name: adjacent non-tumour renal tissue

tag: age

value: adjacent non-tumour renal tissue


title: patient 98, ccRCC tumour tissue

value: I


title: patient 100, ccRCC tumour tissue


title: patient 97, ccRCC tumour tissue

value: female

value: II


title: patient 96, adjacent non-tumour renal tissue


title: patient 100, adjacent non-tumour renal tissue


title: patient 94, ccRCC tumour tissue


title: patient 95, adjacent non-tumour renal tissue


title: patient 95, ccRCC tumour tissue


title: patient 96, ccRCC tumour tissue


title: patient 94, adjacent non-tumour renal tissue


title: patient 92, adjacent non-tumour renal tissue


title: patient 98, adjacent non-tumour renal tissue


title: 2009 TIV subject ID 65 at D3 post-vaccination

value: blood

tag: cell type

tag: time point

tag: subject id


title: patient 99, ccRCC tumour tissue


title: control, biological rep3

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Massachusetts Medical School Genomics Core Facility.

scan_protocol: GeneChip Scanner 3000, with 7G upgrade

data_processing:
Data were processed using Affymetrix Power Tools software. RMA style background correction were applied to probe intensities, exon level expression were summarized from the corrected intensities, quantile normalized and then median polished.
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2/HuEx-1_0-st-v2.r2.dt1.hg18.comprehensive.mps

source_name: control, biological rep3

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Flip-In-293 cells were grown on DMEM suplemented with 10%FBS, penicilin and streptomycin.

extract_protocol: RNA was isolated for Flip-In-293 cells using RNeasy mini kit (qiagen) according to manufacturer's protocol

treatment_protocol: Flip-In-293 cells were infected with lentivirus expressing NS, RBFOX2 and CPSF shRNAs and were cultured for 10 days before RNA isolation.

tag: shRNA

value: Non silencing lentivirus infected


title: patient 92, ccRCC tumour tissue


title: patient 97, adjacent non-tumour renal tissue


title: patient 99, adjacent non-tumour renal tissue


title: fox2 knock down, biological rep2

source_name: fox2 knock down, biological rep2

value: RBFOX2 lentiviral shRNA infected


title: fox2 knock down, biological rep3

source_name: fox2 knock down, biological rep3


title: patient 89, adjacent non-tumour renal tissue


title: patient 87, adjacent non-tumour renal tissue


title: patient 91, ccRCC tumour tissue


title: cpsf3 knock down, biological rep1

source_name: cpsf3 knock down, biological rep1

value: CPSF3 lentiviral shRNA infected


title: patient 84, adjacent non-tumour renal tissue


title: patient 90, adjacent non-tumour renal tissue


title: patient 90, ccRCC tumour tissue


title: patient 85, adjacent non-tumour renal tissue


title: patient 86, ccRCC tumour tissue

value: IV


title: patient 85, ccRCC tumour tissue


title: patient 91, adjacent non-tumour renal tissue


title: patient 88, adjacent non-tumour renal tissue


title: patient 84, ccRCC tumour tissue


title: patient 83, adjacent non-tumour renal tissue


title: patient 89, ccRCC tumour tissue


title: patient 86, adjacent non-tumour renal tissue


title: patient 82, adjacent non-tumour renal tissue


title: patient 83, ccRCC tumour tissue


title: patient 93, ccRCC tumour tissue


title: patient 82, ccRCC tumour tissue


title: fox2 knock down, biological rep1

source_name: fox2 knock down, biological rep1


title: cpsf3 knock down, biological rep3

source_name: cpsf3 knock down, biological rep3


title: patient 81, adjacent non-tumour renal tissue


title: control, biological rep2

source_name: control, biological rep2


title: patient 81, ccRCC tumour tissue


title: patient 80, ccRCC tumour tissue


title: patient 78, adjacent non-tumour renal tissue


title: patient 79, ccRCC tumour tissue


title: patient 80, adjacent non-tumour renal tissue


title: cpsf3 knock down, biological rep2

source_name: cpsf3 knock down, biological rep2


title: patient 76, adjacent non-tumour renal tissue


title: patient 77, ccRCC tumour tissue


title: patient 79, adjacent non-tumour renal tissue


title: control, biological rep1

source_name: control, biological rep1


title: patient 77, adjacent non-tumour renal tissue


title: patient 78, ccRCC tumour tissue


title: patient 76, ccRCC tumour tissue


title: patient 75, adjacent non-tumour renal tissue


title: patient 75, ccRCC tumour tissue


title: patient 93, adjacent non-tumour renal tissue


title: patient 71, ccRCC tumour tissue


title: patient 71, adjacent non-tumour renal tissue


title: patient 73, ccRCC tumour tissue


title: patient 73, adjacent non-tumour renal tissue


title: patient 74, adjacent non-tumour renal tissue


title: patient 72, adjacent non-tumour renal tissue


title: patient 74, ccRCC tumour tissue


title: patient 72, ccRCC tumour tissue


title: patient 70, ccRCC tumour tissue


title: patient 70, adjacent non-tumour renal tissue


title: patient 67, ccRCC tumour tissue


title: patient 69, ccRCC tumour tissue


title: patient 66, adjacent non-tumour renal tissue


title: patient 64, ccRCC tumour tissue


title: patient 65, ccRCC tumour tissue


title: patient 68, adjacent non-tumour renal tissue


title: patient 66, ccRCC tumour tissue


title: patient 63, adjacent non-tumour renal tissue


title: patient 68, ccRCC tumour tissue


title: patient 58, ccRCC tumour tissue


title: patient 67, adjacent non-tumour renal tissue


title: patient 62, adjacent non-tumour renal tissue


title: patient 60, adjacent non-tumour renal tissue


title: patient 60, ccRCC tumour tissue


title: patient 87, ccRCC tumour tissue


title: patient 64, adjacent non-tumour renal tissue


title: patient 59, ccRCC tumour tissue


title: patient 65, adjacent non-tumour renal tissue


title: patient 57, adjacent non-tumour renal tissue


title: patient 61, adjacent non-tumour renal tissue


title: patient 58, adjacent non-tumour renal tissue


title: patient 63, ccRCC tumour tissue


title: patient 69, adjacent non-tumour renal tissue


title: patient 59, adjacent non-tumour renal tissue


title: patient 56, adjacent non-tumour renal tissue


title: patient 57, ccRCC tumour tissue


title: patient 56, ccRCC tumour tissue


title: patient 88, ccRCC tumour tissue


title: patient 61, ccRCC tumour tissue


title: patient 62, ccRCC tumour tissue


title: patient 55, adjacent non-tumour renal tissue


title: patient 54, adjacent non-tumour renal tissue


title: patient 53, adjacent non-tumour renal tissue


title: patient 54, ccRCC tumour tissue


title: patient 50, ccRCC tumour tissue


title: patient 52, ccRCC tumour tissue


title: patient 50, adjacent non-tumour renal tissue


title: patient 51, ccRCC tumour tissue


title: patient 49, adjacent non-tumour renal tissue


title: patient 55, ccRCC tumour tissue


title: patient 48, adjacent non-tumour renal tissue


title: patient 47, ccRCC tumour tissue


title: patient 48, ccRCC tumour tissue


title: patient 43, ccRCC tumour tissue


title: patient 49, ccRCC tumour tissue


title: patient 53, ccRCC tumour tissue


title: patient 46, ccRCC tumour tissue


title: patient 41, ccRCC tumour tissue


title: patient 51, adjacent non-tumour renal tissue


title: patient 47, adjacent non-tumour renal tissue


title: patient 46, adjacent non-tumour renal tissue


title: patient 45, adjacent non-tumour renal tissue


title: patient 44, adjacent non-tumour renal tissue


title: patient 45, ccRCC tumour tissue


title: patient 41, adjacent non-tumour renal tissue


title: patient 44, ccRCC tumour tissue


title: patient 52, adjacent non-tumour renal tissue


title: patient 42, adjacent non-tumour renal tissue


title: patient 42, ccRCC tumour tissue


title: patient 43, adjacent non-tumour renal tissue


title: patient 39, adjacent non-tumour renal tissue


title: patient 38, adjacent non-tumour renal tissue


title: patient 40, ccRCC tumour tissue


title: patient 40, adjacent non-tumour renal tissue


title: patient 38, ccRCC tumour tissue


title: patient 36, adjacent non-tumour renal tissue


title: patient 39, ccRCC tumour tissue


title: patient 37, adjacent non-tumour renal tissue


title: patient 35, ccRCC tumour tissue


title: patient 34, adjacent non-tumour renal tissue


title: patient 36, ccRCC tumour tissue


title: patient 35, adjacent non-tumour renal tissue


title: patient 37, ccRCC tumour tissue


title: patient 28, adjacent non-tumour renal tissue


title: patient 27, ccRCC tumour tissue


title: patient 28, ccRCC tumour tissue


title: patient 27, adjacent non-tumour renal tissue


title: patient 26, adjacent non-tumour renal tissue


title: patient 31, ccRCC tumour tissue


title: patient 32, ccRCC tumour tissue


title: patient 34, ccRCC tumour tissue


title: patient 30, adjacent non-tumour renal tissue


title: patient 29, ccRCC tumour tissue


title: patient 31, adjacent non-tumour renal tissue


title: patient 29, adjacent non-tumour renal tissue


title: patient 30, ccRCC tumour tissue


title: patient 32, adjacent non-tumour renal tissue


title: patient 33, adjacent non-tumour renal tissue


title: patient 33, ccRCC tumour tissue


title: patient 25, adjacent non-tumour renal tissue


title: patient 25, ccRCC tumour tissue


title: patient 24, ccRCC tumour tissue


title: patient 23, ccRCC tumour tissue


title: patient 26, ccRCC tumour tissue


title: patient 23, adjacent non-tumour renal tissue


title: patient 24, adjacent non-tumour renal tissue


title: patient 22, ccRCC tumour tissue


title: patient 21, adjacent non-tumour renal tissue


title: patient 15, adjacent non-tumour renal tissue


title: patient 18, ccRCC tumour tissue


title: patient 19, adjacent non-tumour renal tissue


title: patient 16, ccRCC tumour tissue


title: patient 20, ccRCC tumour tissue


title: patient 16, adjacent non-tumour renal tissue


title: patient 21, ccRCC tumour tissue


title: patient 22, adjacent non-tumour renal tissue


title: patient 17, adjacent non-tumour renal tissue


title: patient 18, adjacent non-tumour renal tissue


title: patient 19, ccRCC tumour tissue


title: patient 17, ccRCC tumour tissue


title: patient 15, ccRCC tumour tissue


title: patient 13, adjacent non-tumour renal tissue


title: patient 14, adjacent non-tumour renal tissue


title: patient 20, adjacent non-tumour renal tissue


title: patient 11, adjacent non-tumour renal tissue


title: patient 12, adjacent non-tumour renal tissue


title: patient 14, ccRCC tumour tissue


title: patient 12, ccRCC tumour tissue


title: patient 9, adjacent non-tumour renal tissue


title: patient 10, adjacent non-tumour renal tissue


title: RenLab-HiC-mESC-HindIII, replicate two

status: Public on Apr 10 2012

first: Feng

last: Yue

address: 9500 Gilman Dr.

institute: Ludwig Institue for Cancer Research

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
J1_mESC_HindIII_rep_HiC.nodup.summary.txt: mm9

source_name: Mouse ES

growth_protocol: mESC line J1 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments. H1 and IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91

extract_protocol: Hi-C experiment were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).

tag: strain

value: mESC line J1


title: RenLab-HiC-mESC-HindIII, replicate one

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 and human genome hg18 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
J1_mESC_HindIII_ori_HiC.nodup.summary.txt: mm9

tag: cell line

value: HindIII


title: patient 13, ccRCC tumour tissue


title: patient 8, ccRCC tumour tissue


title: patient 11, ccRCC tumour tissue


title: patient 7, ccRCC tumour tissue


title: patient 6, ccRCC tumour tissue


title: patient 4, adjacent non-tumour renal tissue


title: patient 8, adjacent non-tumour renal tissue


title: patient 10, ccRCC tumour tissue


title: patient 6, adjacent non-tumour renal tissue


title: patient 3, adjacent non-tumour renal tissue


title: patient 2, adjacent non-tumour renal tissue


title: patient 5, ccRCC tumour tissue


title: patient 9, ccRCC tumour tissue


title: patient 1, adjacent non-tumour renal tissue


title: patient 5, adjacent non-tumour renal tissue


title: patient 3, ccRCC tumour tissue


title: patient 1, ccRCC tumour tissue


title: patient 4, ccRCC tumour tissue


title: patient 7, adjacent non-tumour renal tissue


title: patient 2, ccRCC tumour tissue


title: healthy volunteers HV11

status: Public on Jan 01 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: PBMC from HV group

hyb_protocol: Standard Affymetrix protocol

scan_protocol: The labelled arrays were scanned with a Gene chip scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) 'affy' in R.2.9.1

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted from peripheral blood using the TRIzol method (Invitrogen, Cergy Pontoise, France). Genomic DNA was removed by DNase treatment (Roche, Indianapolis, IN, USA). RNA quality and quantity was determined using an Agilent 2100 BioAnalyzer (Palo Alto, CA, USA). RNA was reverse transcribed into cDNA using polydT oligonucleotide and Maloney leukemia virus reverse transcription (Invitrogen).

treatment_protocol: Ficoll PBMC isolation from peripheral blood

tag: immunotolerance group

value: HV

tag: outcome

value: healthy volunteers

value: Peripheral blood mononuclear cells


title: healthy volunteers HV07

description: PBMC from HV group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA03

description: PBMC from K-Sta group

value: K-Sta


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA01

description: PBMC from K-Sta group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA12

description: PBMC from K-Sta group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA04

description: PBMC from K-Sta group


title: healthy volunteers HV02

description: PBMC from HV group


title: healthy volunteers HV04

description: PBMC from HV group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL11

description: PBMC from K-Tol group

value: K-Tol

value: Kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy


title: healthy volunteers HV09

description: PBMC from HV group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA07

description: PBMC from K-Sta group


title: healthy volunteers HV06

description: PBMC from HV group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA09

description: PBMC from K-Sta group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA10

description: PBMC from K-Sta group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA11

description: PBMC from K-Sta group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL12

description: PBMC from K-Tol group


title: healthy volunteers HV12

description: PBMC from HV group


title: healthy volunteers HV08

description: PBMC from HV group


title: healthy volunteers HV05

description: PBMC from HV group


title: healthy volunteers HV01

description: PBMC from HV group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL10

description: PBMC from K-Tol group


title: healthy volunteers HV10

description: PBMC from HV group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA05

description: PBMC from K-Sta group


title: healthy volunteers HV03

description: PBMC from HV group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL08

description: PBMC from K-Tol group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA06

description: PBMC from K-Sta group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA08

description: PBMC from K-Sta group


title: kidney recipients with stable graft function under maintenance immunosuppression KSTA02

description: PBMC from K-Sta group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL09

description: PBMC from K-Tol group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL06

description: PBMC from K-Tol group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL07

description: PBMC from K-Tol group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL03

description: PBMC from K-Tol group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL05

description: PBMC from K-Tol group


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL01

description: PBMC from K-Tol group


title: 2008 TIV subject ID 80 at D3 post-vaccination

status: Public on Jul 10 2011

data_processing: RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).

source_name: Peripheral blood mononuclear cells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination), and days 3 and 7 post-vaccination.

value: PBMC

tag: vaccine

value: TIV (Fluarix, GlaxoSmithKline Biologicals)

tag: hai titer (day 0) - a/uruguay (h3n2)

tag: hai titer (day 28) - a/uruguay (h3n2)

tag: hai titer (day 0) - a/brisbane/59/2007 (h1n1)

tag: hai titer (day 28) - a/brisbane/59/2007 (h1n1)

tag: hai titer (day 0) - b/brisbane/3/2007

tag: hai titer (day 28) - b/brisbane/3/2007


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL02

description: PBMC from K-Tol group


title: 2008 TIV subject ID 73 at D3 post-vaccination


title: kidney recipients with stable long-term graft function in the absence of immunosuppressive therapy KTOL04

description: PBMC from K-Tol group


title: 2008 TIV subject ID 78 at D7 post-vaccination


title: 2008 TIV subject ID 72 at D3 post-vaccination


title: 2008 TIV subject ID 74 at D7 post-vaccination


title: 2008 TIV subject ID 85 at D3 post-vaccination


title: 2008 TIV subject ID 83 at D3 post-vaccination


title: 2008 TIV subject ID 78 at D3 post-vaccination


title: 2008 TIV subject ID 83 at D0 post-vaccination


title: 2008 TIV subject ID 85 at D0 post-vaccination


title: 2008 TIV subject ID 85 at D7 post-vaccination


title: 2008 TIV subject ID 80 at D7 post-vaccination


title: 2008 TIV subject ID 70 at D7 post-vaccination