PCBP2 RNA-Seq in K562

General Information


RBP	PCBP2
Cell_Line	K562
Method	shRNA
Exp_Name	PCBP2-BGKLV11-K562
ENCODE_series_ID	ENCSR947MUV
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR648QFY
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	PCBP2-LV11-31
Rep2	PCBP2-LV11-32
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	58.5
Rep2_qPCR	54.1
Rep1_WB	46.5
Rep2_WB	41.7
Antibody Cat#	RN025P
Antibody Lot#	RN025P
Antibody DCC ID	ENCAB000BFY
Status	Released
Project	ENCODE3
ID	317

Experiment Information (Status: Released)

	BGKLV11-31	BGKLV11-32
idx	100	101
TRCN#_or_BGC#	TRCN0000074684	TRCN0000074684
shRNA_or_gRNA_sequence	CCCACTAATGCCATCTTCAAA	CCCACTAATGCCATCTTCAAA
PAM
Name	PCBP2	PCBP2
Sample_ID	BGKLV11-31	BGKLV11-32
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	PCBP2	PCBP2
qPCR_result	58.5	54.1
Ave_qPCR	56.3
RT-qPCR_primer-F	CATCACTGGATCTGCTGCC
RT-qPCR_primer-R	GCATTGTTCTAGCTGCTCCC
protein_conc	1907	1770
WB_result	46.5	41.7
Ave_WB	44.1
WB_DONE_date	6/10/2015
MW	39kDa
IP	1	1
antibody_Cat#	RN025P	RN025P
Antibody DCC ID	ENCAB000BFY	ENCAB000BFY
submitted_to_DCC_date	8/6/2015
Rep1_TPM	123.916964	0
Rep2_TPM	153.592433	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	113	114

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

	BGKLV11-31	BGKLV11-32
Sample_ID	BGKLV11-31	BGKLV11-32
Sample Name	PCBP2-LV11-31	PCBP2-LV11-32
Sample Name	PCBP2-LV11-31	PCBP2-LV11-32
RBP	PCBP2	PCBP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	348	349

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-31	BGKLV11-32
Sample #
Sample Name	PCBP2-BGKLV11-31	PCBP2-BGKLV11-32
Sample_Name_Alias	PCBP2-LV11-31	PCBP2-LV11-32
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set2/C2.png	DNA_Library_LV11/set2/D2.png
RIN	8.9	9.1
libSample_RNA_Well	RNA_Library_LV11/set1/A4.png	RNA_Library_LV11/set1/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-31	BGKLV11-32
RBP	PCBP2	PCBP2
Batch_ID	BGKLV11	BGKLV11
WB_result	46.500	41.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1970	1971

Sequencing Information

	BGKLV11-31	BGKLV11-32
Sample_ID	BGKLV11-31	BGKLV11-32
Sample Name	PCBP2-LV11-31	PCBP2-LV11-32
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	57,190,000	67,190,000
total_aligned_reads	45,672,466	52,568,274
unique_aligned_reads	41,928,236	48,252,312
percent_uniqueAligned	0.73314	0.71815
correlation_replicates	0.996397	0.996397
spikein_reads	352,492	357,440
percent_spikeins	0.00616	0.00532
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	670	671

Data Submission Information

	BGKLV11-31	BGKLV11-31
ENCODE_alias	brenton-graveley:PCBP2-LV11	brenton-graveley:PCBP2-BGKLV11-K562
ENCODE_accession	ENCSR648QFY	ENCSR947MUV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-31	BGKLV11-31
Sample Name	PCBP2-LV11-31	PCBP2-LV11-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2723	6851

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-LV11-31_ATCACG_L005_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	670	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12391
PCBP2-LV11-31_ATCACG_L005_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	670	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12439
PCBP2-LV11-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	670					GRCh38	V40	PCBP2-LV11-31_ATCACG_L005_R1_001.fastq.gz,PCBP2-LV11-31_ATCACG_L005_R2_001.fastq.gz		ENCORE2	12487
PCBP2-LV11-31_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	670					GRCh38	V40	PCBP2-LV11-31/Aligned.sortedByCoord.out.bam		ENCORE2	12535
PCBP2-LV11-31_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	670					GRCh38	V40	PCBP2-LV11-31/Aligned.sortedByCoord.out.bam		ENCORE2	12583
PCBP2-LV11-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	670					GRCh38	V40	PCBP2-LV11-31/Aligned.sortedByCoord.out.bam		ENCORE2	12631
PCBP2-LV11-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	670					GRCh38	V40	PCBP2-LV11-31/Aligned.sortedByCoord.out.bam		ENCORE2	12679
PCBP2-LV11-31_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	670					GRCh38	V40	PCBP2-LV11-31_ATCACG_L005_R1_001.fastq.gz,PCBP2-LV11-31_ATCACG_L005_R2_001.fastq.gz		ENCORE2	12727
PCBP2-LV11-32_CGATGT_L005_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	671	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12392
PCBP2-LV11-32_CGATGT_L005_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	671	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12440
PCBP2-LV11-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	671					GRCh38	V40	PCBP2-LV11-32_CGATGT_L005_R1_001.fastq.gz,PCBP2-LV11-32_CGATGT_L005_R2_001.fastq.gz		ENCORE2	12488
PCBP2-LV11-32_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	671					GRCh38	V40	PCBP2-LV11-32/Aligned.sortedByCoord.out.bam		ENCORE2	12536
PCBP2-LV11-32_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	671					GRCh38	V40	PCBP2-LV11-32/Aligned.sortedByCoord.out.bam		ENCORE2	12584
PCBP2-LV11-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	671					GRCh38	V40	PCBP2-LV11-32/Aligned.sortedByCoord.out.bam		ENCORE2	12632
PCBP2-LV11-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	671					GRCh38	V40	PCBP2-LV11-32/Aligned.sortedByCoord.out.bam		ENCORE2	12680
PCBP2-LV11-32_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	671					GRCh38	V40	PCBP2-LV11-32_CGATGT_L005_R1_001.fastq.gz,PCBP2-LV11-32_CGATGT_L005_R2_001.fastq.gz		ENCORE2	12728