PCBP1 RNA-Seq in K562

General Information


RBP	PCBP1
Cell_Line	K562
Method	shRNA
Exp_Name	PCBP1-BGKLV11-K562
ENCODE_series_ID	ENCSR542DWE
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR545AIK
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	PCBP1-LV11-29
Rep2	PCBP1-LV11-30
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	64.0
Rep2_qPCR	65.8
Rep1_WB	91.3
Rep2_WB	89.8
Antibody Cat#	RN024P
Antibody Lot#	RN024P
Antibody DCC ID	ENCAB000BFX
Status	Released
Project	ENCODE3
ID	316

Experiment Information (Status: Released)

	BGKLV11-29	BGKLV11-30
idx	98	99
TRCN#_or_BGC#	TRCN0000074668	TRCN0000074668
shRNA_or_gRNA_sequence	CCTCAACACCAAGGATTACAA	CCTCAACACCAAGGATTACAA
PAM
Name	PCBP1	PCBP1
Sample_ID	BGKLV11-29	BGKLV11-30
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	PCBP1	PCBP1
qPCR_result	64.0	65.8
Ave_qPCR	64.9
RT-qPCR_primer-F	ACCACCCATGAACTCACCAT
RT-qPCR_primer-R	GACATCTGGCGGATCTCATT
protein_conc	1995	1975
WB_result	91.3	89.8
Ave_WB	90.6
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	143.943664	0
Rep2_TPM	136.889736	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	111	112

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

	BGKLV11-29	BGKLV11-30
Sample_ID	BGKLV11-29	BGKLV11-30
Sample Name	PCBP1-LV11-29	PCBP1-LV11-30
Sample Name	PCBP1-LV11-29	PCBP1-LV11-30
RBP	PCBP1	PCBP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	346	347

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-29	BGKLV11-30
Sample #
Sample Name	PCBP1-BGKLV11-29	PCBP1-BGKLV11-30
Sample_Name_Alias	PCBP1-LV11-29	PCBP1-LV11-30
Index Well Position	S25	S27
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/A2.png	DNA_Library_LV11/set2/B2.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/G3.png	RNA_Library_LV11/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-29	BGKLV11-30
RBP	PCBP1	PCBP1
Batch_ID	BGKLV11	BGKLV11
WB_result	91.300	89.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1968	1969

Sequencing Information

	BGKLV11-29	BGKLV11-30
Sample_ID	BGKLV11-29	BGKLV11-30
Sample Name	PCBP1-LV11-29	PCBP1-LV11-30
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	66,310,000	65,970,000
total_aligned_reads	53,752,592	53,015,282
unique_aligned_reads	49,223,174	48,598,154
percent_uniqueAligned	0.74232	0.73667
correlation_replicates	0.997556	0.997556
spikein_reads	328,746	360,456
percent_spikeins	0.00496	0.00546
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	668	669

Data Submission Information

	BGKLV11-29	BGKLV11-29
ENCODE_alias	brenton-graveley:PCBP1-LV11	brenton-graveley:PCBP1-BGKLV11-K562
ENCODE_accession	ENCSR545AIK	ENCSR542DWE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-29	BGKLV11-29
Sample Name	PCBP1-LV11-29	PCBP1-LV11-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2722	6849

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-LV11-29_ACTGAT_L004_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	668	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12389
PCBP1-LV11-29_ACTGAT_L004_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	668	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12437
PCBP1-LV11-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	668					GRCh38	V40	PCBP1-LV11-29_ACTGAT_L004_R1_001.fastq.gz,PCBP1-LV11-29_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	12485
PCBP1-LV11-29_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	668					GRCh38	V40	PCBP1-LV11-29/Aligned.sortedByCoord.out.bam		ENCORE2	12533
PCBP1-LV11-29_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	668					GRCh38	V40	PCBP1-LV11-29/Aligned.sortedByCoord.out.bam		ENCORE2	12581
PCBP1-LV11-29_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	668					GRCh38	V40	PCBP1-LV11-29/Aligned.sortedByCoord.out.bam		ENCORE2	12629
PCBP1-LV11-29_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	668					GRCh38	V40	PCBP1-LV11-29/Aligned.sortedByCoord.out.bam		ENCORE2	12677
PCBP1-LV11-29_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	668					GRCh38	V40	PCBP1-LV11-29_ACTGAT_L004_R1_001.fastq.gz,PCBP1-LV11-29_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	12725
PCBP1-LV11-30_ATTCCT_L004_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	669	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12390
PCBP1-LV11-30_ATTCCT_L004_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	669	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12438
PCBP1-LV11-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	669					GRCh38	V40	PCBP1-LV11-30_ATTCCT_L004_R1_001.fastq.gz,PCBP1-LV11-30_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	12486
PCBP1-LV11-30_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	669					GRCh38	V40	PCBP1-LV11-30/Aligned.sortedByCoord.out.bam		ENCORE2	12534
PCBP1-LV11-30_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	669					GRCh38	V40	PCBP1-LV11-30/Aligned.sortedByCoord.out.bam		ENCORE2	12582
PCBP1-LV11-30_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	669					GRCh38	V40	PCBP1-LV11-30/Aligned.sortedByCoord.out.bam		ENCORE2	12630
PCBP1-LV11-30_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	669					GRCh38	V40	PCBP1-LV11-30/Aligned.sortedByCoord.out.bam		ENCORE2	12678
PCBP1-LV11-30_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	669					GRCh38	V40	PCBP1-LV11-30_ATTCCT_L004_R1_001.fastq.gz,PCBP1-LV11-30_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	12726