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Series GSE108716 Query DataSets for GSE108716
Status Public on Dec 30, 2020
Title Genome-wide mapping of RNAPII and its phosphoisoforms in Plasmodium falciparum
Organism Plasmodium falciparum
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary RNAPII ChIP seq was carried out with various phospho antibodies and compared and correlated with the RNA -seq expression data from the same stage sample
 
Overall design RNAPII ChIP -seq was carried out with anti-CTD, anti-Ser5-P, anti-Ser2/5-P and N20 antibodies at three different stages, ring, trophozoites and schizonts across the inter-erythrocytic developmental cycle (IDC) of Plasmodium falciparum. RNAPII binding was correlated with mRNA expression levels generated by RNA Seq. RNA- seq experiment includes three biological replicates.
 
Contributor(s) Khandelia RR, Mohan A, Lei Z, Balasubramaniam U, Zheng J, Bozdech Z, Featherstone M
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jan 03, 2018
Last update date Oct 08, 2021
Contact name Mark Stephen Featherstone
E-mail(s) msfeatherstone@gmail.com
Organization name Nanyang Technological University
Department School of Biological Sciences
Lab 03n-39
Street address 60, Nanyang Drive
City Singapore
State/province Singapore
ZIP/Postal code 637551
Country Singapore
 
Platforms (2)
GPL19269 Illumina MiSeq (Plasmodium falciparum)
GPL21078 Illumina HiSeq 2500 (Plasmodium falciparum)
Samples (30)
GSM2912439 RNA_Ring rep1
GSM2912440 RNA_Ring rep2
GSM2912441 RNA_Ring rep3
Relations
BioProject PRJNA428361
SRA SRP127979

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE108716_RAW.tar 245.2 Mb (http)(custom) TAR (of BEDGRAPH)
GSE108716_RingN20ab_CGATGT_L001_frag_1bp_log2ratio.bw 30.0 Mb (ftp)(http) BW
GSE108716_Ring_T2-CTD_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 28.4 Mb (ftp)(http) BEDGRAPH
GSE108716_Ring_T2-CTD_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 87.9 Kb (ftp)(http) NARROWPEAK
GSE108716_Ring_T2-CTD_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 102.1 Kb (ftp)(http) XLS
GSE108716_Ring_T2-CTD_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 49.2 Kb (ftp)(http) BED
GSE108716_Ring_T2-CTD_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 17.9 Mb (ftp)(http) BEDGRAPH
GSE108716_Ring_T2_N20_vs_input_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 28.4 Mb (ftp)(http) BEDGRAPH
GSE108716_Ring_T2_N20_vs_input_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 114.5 Kb (ftp)(http) NARROWPEAK
GSE108716_Ring_T2_N20_vs_input_narrow_p0.05_BSPMR_peaks.xls.gz 134.1 Kb (ftp)(http) XLS
GSE108716_Ring_T2_N20_vs_input_narrow_p0.05_BSPMR_summits.bed.gz 63.2 Kb (ftp)(http) BED
GSE108716_Ring_T2_N20_vs_input_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 19.5 Mb (ftp)(http) BEDGRAPH
GSE108716_Ring_T2_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 28.4 Mb (ftp)(http) BEDGRAPH
GSE108716_Ring_T2_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 76.7 Kb (ftp)(http) NARROWPEAK
GSE108716_Ring_T2_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 88.8 Kb (ftp)(http) XLS
GSE108716_Ring_T2_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 40.0 Kb (ftp)(http) BED
GSE108716_Ring_T2_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 13.1 Mb (ftp)(http) BEDGRAPH
GSE108716_Ring_T2_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 28.3 Mb (ftp)(http) BEDGRAPH
GSE108716_Ring_T2_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 70.3 Kb (ftp)(http) NARROWPEAK
GSE108716_Ring_T2_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 82.0 Kb (ftp)(http) XLS
GSE108716_Ring_T2_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 39.5 Kb (ftp)(http) BED
GSE108716_Ring_T2_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 20.0 Mb (ftp)(http) BEDGRAPH
GSE108716_SchN20ab_GATCAG_L001_frag_1bp_log2ratio.bw 45.8 Mb (ftp)(http) BW
GSE108716_Schizont_T5_CTD_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 43.6 Mb (ftp)(http) BEDGRAPH
GSE108716_Schizont_T5_CTD_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 79.4 Kb (ftp)(http) NARROWPEAK
GSE108716_Schizont_T5_CTD_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 92.6 Kb (ftp)(http) XLS
GSE108716_Schizont_T5_CTD_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 43.6 Kb (ftp)(http) BED
GSE108716_Schizont_T5_CTD_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 28.7 Mb (ftp)(http) BEDGRAPH
GSE108716_Schizont_T5_N20_vs_input_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 43.7 Mb (ftp)(http) BEDGRAPH
GSE108716_Schizont_T5_N20_vs_input_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 86.4 Kb (ftp)(http) NARROWPEAK
GSE108716_Schizont_T5_N20_vs_input_narrow_p0.05_BSPMR_peaks.xls.gz 101.1 Kb (ftp)(http) XLS
GSE108716_Schizont_T5_N20_vs_input_narrow_p0.05_BSPMR_summits.bed.gz 47.0 Kb (ftp)(http) BED
GSE108716_Schizont_T5_N20_vs_input_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 29.6 Mb (ftp)(http) BEDGRAPH
GSE108716_Schizont_T5_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 43.8 Mb (ftp)(http) BEDGRAPH
GSE108716_Schizont_T5_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 75.2 Kb (ftp)(http) NARROWPEAK
GSE108716_Schizont_T5_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 87.5 Kb (ftp)(http) XLS
GSE108716_Schizont_T5_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 40.3 Kb (ftp)(http) BED
GSE108716_Schizont_T5_Ser25_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 10.2 Mb (ftp)(http) BEDGRAPH
GSE108716_Schizont_T5_Ser5_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 43.8 Mb (ftp)(http) BEDGRAPH
GSE108716_Schizont_T5_Ser5_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 75.3 Kb (ftp)(http) NARROWPEAK
GSE108716_Schizont_T5_Ser5_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 88.4 Kb (ftp)(http) XLS
GSE108716_Schizont_T5_Ser5_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 41.0 Kb (ftp)(http) BED
GSE108716_Schizont_T5_Ser5_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 33.9 Mb (ftp)(http) BEDGRAPH
GSE108716_T2-CTD_GCCAAT_L001_frag_1bp_log2ratio.bw 29.1 Mb (ftp)(http) BW
GSE108716_T2_Ser25_L001_frag_1bp_log2ratio.bw 25.2 Mb (ftp)(http) BW
GSE108716_T2_Ser5_GCCAAT_L001_frag_1bp_log2ratio.bw 30.0 Mb (ftp)(http) BW
GSE108716_T5_CTD_CTTGTA_L001_frag_1bp_log2ratio.bw 45.9 Mb (ftp)(http) BW
GSE108716_T5_Ser25_L001_frag_1bp_log2ratio.bw 29.6 Mb (ftp)(http) BW
GSE108716_T5_Ser25_by_input_frag_1bp_log2ratio.bw 29.6 Mb (ftp)(http) BW
GSE108716_T5_Ser5_CTTGTA_L001_frag_1bp_log2ratio.bw 48.1 Mb (ftp)(http) BW
GSE108716_T996Eluate_ACAGTG_L001_frag_1bp_log2ratio.bw 47.0 Mb (ftp)(http) BW
GSE108716_TrophN20ab_TTAGGC_L001_frag_1bp_log2ratio.bw 47.2 Mb (ftp)(http) BW
GSE108716_Troph_CTD_TGACCA_L001_frag_1bp_log2ratio.bw 45.2 Mb (ftp)(http) BW
GSE108716_Troph_Ser25_CTTGTA_L001_frag_1bp_log2ratio.bw 38.3 Mb (ftp)(http) BW
GSE108716_Troph_Ser5_GCCAAT_L001_frag_1bp_log2ratio.bw 48.2 Mb (ftp)(http) BW
GSE108716_Trophs_Troph_CTD_TGACCA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 54.2 Mb (ftp)(http) BEDGRAPH
GSE108716_Trophs_Troph_CTD_TGACCA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 69.7 Kb (ftp)(http) NARROWPEAK
GSE108716_Trophs_Troph_CTD_TGACCA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 81.0 Kb (ftp)(http) XLS
GSE108716_Trophs_Troph_CTD_TGACCA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 38.6 Kb (ftp)(http) BED
GSE108716_Trophs_Troph_CTD_TGACCA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 17.0 Mb (ftp)(http) BEDGRAPH
GSE108716_Trophs_Troph_Ser25_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 54.3 Mb (ftp)(http) BEDGRAPH
GSE108716_Trophs_Troph_Ser25_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 79.4 Kb (ftp)(http) NARROWPEAK
GSE108716_Trophs_Troph_Ser25_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 92.0 Kb (ftp)(http) XLS
GSE108716_Trophs_Troph_Ser25_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 43.2 Kb (ftp)(http) BED
GSE108716_Trophs_Troph_Ser25_CTTGTA_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 11.0 Mb (ftp)(http) BEDGRAPH
GSE108716_Trophs_Troph_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 53.9 Mb (ftp)(http) BEDGRAPH
GSE108716_Trophs_Troph_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 108.5 Kb (ftp)(http) NARROWPEAK
GSE108716_Trophs_Troph_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_peaks.xls.gz 126.4 Kb (ftp)(http) XLS
GSE108716_Trophs_Troph_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_summits.bed.gz 58.4 Kb (ftp)(http) BED
GSE108716_Trophs_Troph_Ser5_GCCAAT_L001_trimmed_CP_UP_rname_sorted_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 25.1 Mb (ftp)(http) BEDGRAPH
GSE108716_Trophs_Trophs_N20_vs_input_narrow_p0.05_BSPMR_control_lambda.bedgraph.gz 54.1 Mb (ftp)(http) BEDGRAPH
GSE108716_Trophs_Trophs_N20_vs_input_narrow_p0.05_BSPMR_peaks.narrowPeak.gz 132.3 Kb (ftp)(http) NARROWPEAK
GSE108716_Trophs_Trophs_N20_vs_input_narrow_p0.05_BSPMR_peaks.xls.gz 154.5 Kb (ftp)(http) XLS
GSE108716_Trophs_Trophs_N20_vs_input_narrow_p0.05_BSPMR_summits.bed.gz 71.1 Kb (ftp)(http) BED
GSE108716_Trophs_Trophs_N20_vs_input_narrow_p0.05_BSPMR_treat_pileup.bedgraph.gz 21.4 Mb (ftp)(http) BEDGRAPH
GSE108716_allstage_triplicates_htseq_counts.txt.gz 131.4 Kb (ftp)(http) TXT
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