Dataset Information

CHPP chr 1,8,20 proteome dataset using the HCC cell lines of Hep3B and MHCC97H, instrument is Q Exactive, part 2 of 3

ABSTRACT: The fresh cells as described above were harvested and lysed in buffer containing 8 M Urea, 50 mM NH4HCO3 and 5 mM IAA. The total cell lysates were centrifuged with 12,000 g for 10 min at 4 degrees Celsius to remove cell debris, and 1.5 mg proteins for each cell line were followed by sequential in-solution protein digestion by Lys-C and trypsin at 37 degrees Celsius, respectively. The tryptic peptides were cleaned by C18 Sep-Pak column (Waters UK Ltd, Manchester, UK). The mass spectrometer used in this dataset was Q-Exactive. The dataset was produced with two technical replicates and 24 fractions per repeat. The database searching procedure was achieved using Mascot v2.3. The database is Swiss-prot (release 2013 -6).

REANALYSED by: PAe005197

OTHER RELATED OMICS DATASETS IN: MSV000080255PRJNA215765MSV000080256MSV000080254PAe005194PAe005189PAe005197

INSTRUMENT(S): instrument model

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver, Permanent Cell Line Cell

SUBMITTER: Zhang Chengpu Zhang Chengpu

PROVIDER: PXD000533 | Pride | 2013-12-16

REPOSITORIES: Pride

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Publications

Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications.

Liu Yang Y Ying Wantao W Ren Zhe Z Gu Wei W Zhang Yang Y Yan Guoquan G Yang Pengyuan P Liu Yinkun Y Yin Xuefei X Chang Cheng C Jiang Jing J Fan Fengxu F Zhang Chengpu C Xu Ping P Wang Quanhui Q Wen Bo B Lin Liang L Wang Tingyou T Du Chaoqin C Zhong Jiayong J Wang Tong T He Qing-Yu QY Qian Xiaohong X Lou Xiaomin X Zhang Gong G Zhong Fan F

Journal of proteome research 20131211 1

We upgraded the preliminary CCPD 1.0 to CCPD 2.0 using the latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, and PXD000535). CCPD 2.0 totally covered 63.6% (438/689) of Chr. 8-coded proteins and 62.6% (439/701) of Chr. 8-coded protein-coding genes. Interestingly, we found that the missing proteins exhibited a tendency to form a cluster region in chromosomes, such as ...[more]

PMID: 24328083

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Project description:This study measured the differential expression of genes from a single clonal Daphnia pulex isolate obtained from an eutrophic flooded opencast mine near Gräfenhain (Saxony, Germany) and has been kept in the laboratory since 2002. The daphniids (50 adult animals per batch) were raised in 3-L glass beakers under a 16 h:8 h L:D photoperiod. Three-quarter of the culture medium (M4) was renewed once a week, and the animals were equally fed ad libitum with algae (Desmodesmus subspicatus; SAG 53.80, Göttingen, Germany). Long-term-acclimated animals were kept at three different temperatures (i.e., 10 ± 0.5°C, 20 ± 0.3°C, and 24 ± 0.3°C) under normoxia (Po2 ≥ 20 kPa) for at least twelve weeks. Time-resolved experiments (acute heat stress) were carried out with long-term 20°C acclimated animals, which were exposed for three different time intervals (2, 4, and 8 h) to either 30 ± 0.2°C (test conditions) or 20 ± 0.3°C (control conditions). For this, 50 animals each were rapidly transferred with a sieve (mesh size: 1.2 mm) from 20°C-medium to a set of beakers containing 30°C-medium. As control, 50 animals each were transferred from 20°C-medium to another set of beakers with 20°C-medium. Only adult female animals with a body length of 2−2.5 mm (between the base of the apical spine and the anterior part of the head) and carrying parthenogenetic eggs and embryos were used for experiments. Animals were not fed during short-term exposures. During experiments, all animals were in good physical condition. After thermal acclimation or heat exposure, animals were transferred into 1.5-ml microcentrifuge tubes and shock-frozen in liquid nitrogen after removing adhering water with a tissue paper. Samples were short-term stored at -80°C. For all experimental conditions, four independent replicates (50 animals each) were analyzed. This GEO record is for the contrasts between animals conditioned to 10 degrees Celsius (condition 1) versus 20 degrees Celsius (condition 2), 10 degrees Celsius (condition 1) versus 24 degrees Celsius (condition 3), and 20 degrees Celsius (condition 2) versus 24 degrees Celsius (condition 3)

Dataset Information

CHPP chr 1,8,20 proteome dataset using the HCC cell lines of Hep3B and MHCC97H, instrument is Q Exactive, part 2 of 3

Publications

Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications.

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