PCBP2 RNA-Seq in HepG2

General Information


RBP	PCBP2
Cell_Line	HepG2
Method	shRNA
Exp_Name	PCBP2-BGHLV14-HepG2
ENCODE_series_ID	ENCSR195CHH
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR028ITN
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	PCBP2_BGHLV14-29
Rep2	PCBP2_BGHLV14-30
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	56.1
Rep2_qPCR	58.0
Rep1_WB	75.5
Rep2_WB	63.5
Antibody Cat#	RN025P
Antibody Lot#	RN025P
Antibody DCC ID	ENCAB000BFY
Status	Released
Project	ENCODE3
ID	397

Experiment Information (Status: Released)

	BGHLV14-29	BGHLV14-30
idx	125	126
TRCN#_or_BGC#	TRCN0000074684	TRCN0000074684
shRNA_or_gRNA_sequence	CCCACTAATGCCATCTTCAAA	CCCACTAATGCCATCTTCAAA
PAM
Name	PCBP2	PCBP2
Sample_ID	BGHLV14-29	BGHLV14-30
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	PCBP2	PCBP2
qPCR_result	56.1	58.0
Ave_qPCR	57.1
RT-qPCR_primer-F	CATCACTGGATCTGCTGCC
RT-qPCR_primer-R	GCATTGTTCTAGCTGCTCCC
protein_conc	4094	4098
WB_result	75.5	63.5
Ave_WB	69.5
WB_DONE_date	7/20/2015
MW	39kDa
IP	1	1
antibody_Cat#	RN025P	RN025P
Antibody DCC ID	ENCAB000BFY	ENCAB000BFY
submitted_to_DCC_date	8/6/2015
Rep1_TPM	116.7	0
Rep2_TPM	137.4	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2184	2185

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PCBP2	Product_ID: RN025P Lot_ID: 1 Source: MBLI Target Name: PCBP2-human

Experiment Status

	BGHLV14-29	BGHLV14-30
Sample_ID	BGHLV14-29	BGHLV14-30
Sample Name	PCBP2_BGHLV14-29	PCBP2_BGHLV14-30
Sample Name	PCBP2_BGHLV14-29	PCBP2_BGHLV14-30
RBP	PCBP2	PCBP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	520	521

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-29	BGHLV14-30
Sample #
Sample Name	PCBP2-BGHLV14-29	PCBP2-BGHLV14-30
Sample_Name_Alias	PCBP2_BGHLV14-29	PCBP2_BGHLV14-30
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D11.png	DNA_Library_LV13-14/set1/E11.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E7.png	RNA_Library_LV13-14-16/set1/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-29	BGHLV14-30
RBP	PCBP2	PCBP2
Batch_ID	BGHLV14	BGHLV14
WB_result	75.500	63.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2202	2203

Sequencing Information

	BGHLV14-29	BGHLV14-30
Sample_ID	BGHLV14-29	BGHLV14-30
Sample Name	PCBP2_BGHLV14-29	PCBP2_BGHLV14-30
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	55,300,000	54,910,000
total_aligned_reads	50,452,446	49,976,398
unique_aligned_reads	47,612,650	47,184,908
percent_uniqueAligned	0.86099	0.85931
correlation_replicates	0.998780	0.998780
spikein_reads	380,304	383,644
percent_spikeins	0.00688	0.00699
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	844	845

Data Submission Information

	BGHLV14-29	BGHLV14-29
ENCODE_alias	brenton-graveley:PCBP2_BGHLV14	brenton-graveley:PCBP2-BGHLV14-HepG2
ENCODE_accession	ENCSR028ITN	ENCSR195CHH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-29	BGHLV14-29
Sample Name	PCBP2_BGHLV14-29	PCBP2_BGHLV14-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2809	6850

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
PCBP2_BGHLV14-29_GGCTAC_L004_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	844	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13812
PCBP2_BGHLV14-29_GGCTAC_L004_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	844	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13874
PCBP2_BGHLV14-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	844					GRCh38	V40	PCBP2_BGHLV14-29_GGCTAC_L004_R1_001.fastq.gz,PCBP2_BGHLV14-29_GGCTAC_L004_R2_001.fastq.gz		ENCORE2	13936
PCBP2_BGHLV14-29_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	844					GRCh38	V40	PCBP2_BGHLV14-29/Aligned.sortedByCoord.out.bam		ENCORE2	13998
PCBP2_BGHLV14-29_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	844					GRCh38	V40	PCBP2_BGHLV14-29/Aligned.sortedByCoord.out.bam		ENCORE2	14060
PCBP2_BGHLV14-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	844					GRCh38	V40	PCBP2_BGHLV14-29/Aligned.sortedByCoord.out.bam		ENCORE2	14122
PCBP2_BGHLV14-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	844					GRCh38	V40	PCBP2_BGHLV14-29/Aligned.sortedByCoord.out.bam		ENCORE2	14184
PCBP2_BGHLV14-29_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	844					GRCh38	V40	PCBP2_BGHLV14-29_GGCTAC_L004_R1_001.fastq.gz,PCBP2_BGHLV14-29_GGCTAC_L004_R2_001.fastq.gz		ENCORE2	14246
PCBP2_BGHLV14-30_CTTGTA_L004_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	845	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13813
PCBP2_BGHLV14-30_CTTGTA_L004_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	845	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13875
PCBP2_BGHLV14-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	845					GRCh38	V40	PCBP2_BGHLV14-30_CTTGTA_L004_R1_001.fastq.gz,PCBP2_BGHLV14-30_CTTGTA_L004_R2_001.fastq.gz		ENCORE2	13937
PCBP2_BGHLV14-30_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	845					GRCh38	V40	PCBP2_BGHLV14-30/Aligned.sortedByCoord.out.bam		ENCORE2	13999
PCBP2_BGHLV14-30_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	845					GRCh38	V40	PCBP2_BGHLV14-30/Aligned.sortedByCoord.out.bam		ENCORE2	14061
PCBP2_BGHLV14-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	845					GRCh38	V40	PCBP2_BGHLV14-30/Aligned.sortedByCoord.out.bam		ENCORE2	14123
PCBP2_BGHLV14-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	845					GRCh38	V40	PCBP2_BGHLV14-30/Aligned.sortedByCoord.out.bam		ENCORE2	14185
PCBP2_BGHLV14-30_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	845					GRCh38	V40	PCBP2_BGHLV14-30_CTTGTA_L004_R1_001.fastq.gz,PCBP2_BGHLV14-30_CTTGTA_L004_R2_001.fastq.gz		ENCORE2	14247