PCBP1 RNA-Seq in HepG2

General Information


RBP	PCBP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PCBP1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR496JBC
Batch_ID	BGHLV12
Pool ID	Pool-140801
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR635FRH
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	PCBP1-BGHLV12-55
Rep2	PCBP1-BGHLV12-56
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	67.7
Rep2_qPCR	75.2
Rep1_WB	94.2
Rep2_WB	93.6
Antibody Cat#	RN024P
Antibody Lot#	RN024P
Antibody DCC ID	ENCAB000BFX
Status	Released
Project	ENCODE3
ID	354

Experiment Information (Status: Released)

	BGHLV12-55	BGHLV12-56
idx	55	56
TRCN#_or_BGC#	TRCN0000074668	TRCN0000074668
shRNA_or_gRNA_sequence	CCCATGATCCAACTGTGTAAT	CCCATGATCCAACTGTGTAAT
PAM
Name	PCBP1	PCBP1
Sample_ID	BGHLV12-55	BGHLV12-56
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	PCBP1	PCBP1
qPCR_result	67.7	75.2
Ave_qPCR	71.5
RT-qPCR_primer-F	ACCACCCATGAACTCACCAT
RT-qPCR_primer-R	GACATCTGGCGGATCTCATT
protein_conc	2409	2161
WB_result	94.2	93.6
Ave_WB	93.9
WB_DONE_date
MW	37kDa
IP	1	1
antibody_Cat#	RN024P	RN024P
Antibody DCC ID	ENCAB000BFX	ENCAB000BFX
submitted_to_DCC_date	4/2/2015
Rep1_TPM	74.3	0
Rep2_TPM	76	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2102	2103

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PCBP1	Product_ID: RN024P Lot_ID: 1 Source: MBLI Target Name: PCBP1-human

Experiment Status

	BGHLV12-55	BGHLV12-56
Sample_ID	BGHLV12-55	BGHLV12-56
Sample Name	PCBP1-BGHLV12-55	PCBP1-BGHLV12-56
Sample Name	PCBP1-BGHLV12-55	PCBP1-BGHLV12-56
RBP	PCBP1	PCBP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	414	415

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-55	BGHLV12-56
Sample #
Sample Name	PCBP1-BGHLV12-55	PCBP1-BGHLV12-56
Sample_Name_Alias	PCBP1-BGHLV12-55	PCBP1-BGHLV12-56
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/C2.png	DNA_Library_LV12/set3/D2.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/C6.png	RNA_Library_LV12/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-55	BGHLV12-56
RBP	PCBP1	PCBP1
Batch_ID	BGHLV12	BGHLV12
WB_result	94.200	93.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2038	2039

Sequencing Information

	BGHLV12-55	BGHLV12-56
Sample_ID	BGHLV12-55	BGHLV12-56
Sample Name	PCBP1-BGHLV12-55	PCBP1-BGHLV12-56
Pool ID	Pool-140801	Pool-140801
LocalServer_folder	set12	set12
total_reads	62,190,000	65,530,000
total_aligned_reads	56,354,094	59,203,526
unique_aligned_reads	53,343,994	56,055,074
percent_uniqueAligned	0.85776	0.85541
correlation_replicates	0.999055	0.999055
spikein_reads	610,374	720,418
percent_spikeins	0.00981	0.01099
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	750	751

Data Submission Information

	BGHLV12-55	BGHLV12-55
ENCODE_alias	brenton-graveley:PCBP1-BGHLV12	brenton-graveley:PCBP1-BGHLV12-HepG2
ENCODE_accession	ENCSR635FRH	ENCSR496JBC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-55	BGHLV12-55
Sample Name	PCBP1-BGHLV12-55	PCBP1-BGHLV12-55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2756	6848

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
PCBP1-BGHLV12-55_GTGGCC_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	750	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12797
PCBP1-BGHLV12-55_GTGGCC_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	750	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12866
PCBP1-BGHLV12-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	750					GRCh38	V40	PCBP1-BGHLV12-55_GTGGCC_L006_R1_001.fastq.gz,PCBP1-BGHLV12-55_GTGGCC_L006_R2_001.fastq.gz		ENCORE2	12936
PCBP1-BGHLV12-55_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	750					GRCh38	V40	PCBP1-BGHLV12-55/Aligned.sortedByCoord.out.bam		ENCORE2	13006
PCBP1-BGHLV12-55_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	750					GRCh38	V40	PCBP1-BGHLV12-55/Aligned.sortedByCoord.out.bam		ENCORE2	13076
PCBP1-BGHLV12-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	750					GRCh38	V40	PCBP1-BGHLV12-55/Aligned.sortedByCoord.out.bam		ENCORE2	13146
PCBP1-BGHLV12-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	750					GRCh38	V40	PCBP1-BGHLV12-55/Aligned.sortedByCoord.out.bam		ENCORE2	13216
PCBP1-BGHLV12-55_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	750					GRCh38	V40	PCBP1-BGHLV12-55_GTGGCC_L006_R1_001.fastq.gz,PCBP1-BGHLV12-55_GTGGCC_L006_R2_001.fastq.gz		ENCORE2	13286
PCBP1-BGHLV12-56_GTTTCG_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	751	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12798
PCBP1-BGHLV12-56_GTTTCG_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	751	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12867
PCBP1-BGHLV12-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	751					GRCh38	V40	PCBP1-BGHLV12-56_GTTTCG_L006_R1_001.fastq.gz,PCBP1-BGHLV12-56_GTTTCG_L006_R2_001.fastq.gz		ENCORE2	12937
PCBP1-BGHLV12-56_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	751					GRCh38	V40	PCBP1-BGHLV12-56/Aligned.sortedByCoord.out.bam		ENCORE2	13007
PCBP1-BGHLV12-56_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	751					GRCh38	V40	PCBP1-BGHLV12-56/Aligned.sortedByCoord.out.bam		ENCORE2	13077
PCBP1-BGHLV12-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	751					GRCh38	V40	PCBP1-BGHLV12-56/Aligned.sortedByCoord.out.bam		ENCORE2	13147
PCBP1-BGHLV12-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	751					GRCh38	V40	PCBP1-BGHLV12-56/Aligned.sortedByCoord.out.bam		ENCORE2	13217
PCBP1-BGHLV12-56_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	751					GRCh38	V40	PCBP1-BGHLV12-56_GTTTCG_L006_R1_001.fastq.gz,PCBP1-BGHLV12-56_GTTTCG_L006_R2_001.fastq.gz		ENCORE2	13287