PABPC4 RNA-Seq in K562

General Information


RBP	PABPC4
Cell_Line	K562
Method	shRNA
Exp_Name	PABPC4-BGKLV08-K562
ENCODE_series_ID	ENCSR169IXL
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR047EEG
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	PABPC4-LV08-37
Rep2	PABPC4-LV08-38
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	84.1
Rep2_qPCR	72.0
Rep1_WB	72.4
Rep2_WB	61.7
Antibody Cat#	A301-466A
Antibody Lot#	A301-466A
Antibody DCC ID	ENCAB596MHX
Status	Released
Project	ENCODE3
ID	295

Experiment Information (Status: Released)

	BGKLV08-37	BGKLV08-38
idx	38	39
TRCN#_or_BGC#	TRCN0000074658	TRCN0000074658
shRNA_or_gRNA_sequence	CCTCAACACCAAGGATTACAA	CCTCAACACCAAGGATTACAA
PAM
Name	PABPC4	PABPC4
Sample_ID	BGKLV08-37	BGKLV08-38
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	PABPC4	PABPC4
qPCR_result	84.1	72.0
Ave_qPCR	78.0
RT-qPCR_primer-F	CAAATACGCCTCCAGTGTCC
RT-qPCR_primer-R	GCAGTCAGTGGCTCCTGC
protein_conc	2767	2804
WB_result	72.4	61.7
Ave_WB	67.1
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A301-466A	A301-466A
Antibody DCC ID	ENCAB596MHX	ENCAB596MHX
submitted_to_DCC_date	4/2/2015
Rep1_TPM	154.781415	0
Rep2_TPM	111.665185	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	39	40

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PABPC4	Product_ID: A301-466A Lot_ID: 1 Source: Bethyl Labs Target Name: PABPC4-human

Experiment Status

	BGKLV08-37	BGKLV08-38
Sample_ID	BGKLV08-37	BGKLV08-38
Sample Name	PABPC4-LV08-37	PABPC4-LV08-38
Sample Name	PABPC4-LV08-37	PABPC4-LV08-38
RBP	PABPC4	PABPC4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	302	303

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-37	BGKLV08-38
Sample #
Sample Name	PABPC4-BGKLV08-37	PABPC4-BGKLV08-38
Sample_Name_Alias	PABPC4-LV08-37	PABPC4-LV08-38
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set4/D1.png	DNA_Library_LV08/set4/E1.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_LV08/set3/E1.png	RNA_Library_LV08/set3/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-37	BGKLV08-38
RBP	PABPC4	PABPC4
Batch_ID	BGKLV08	BGKLV08
WB_result	72.400	61.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1922	1923

Sequencing Information

	BGKLV08-37	BGKLV08-38
Sample_ID	BGKLV08-37	BGKLV08-38
Sample Name	PABPC4-LV08-37	PABPC4-LV08-38
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	49,970,000	50,490,000
total_aligned_reads	45,583,336	45,130,618
unique_aligned_reads	41,729,486	41,196,998
percent_uniqueAligned	0.83509	0.81594
correlation_replicates	0.993367	0.993367
spikein_reads	451,152	411,218
percent_spikeins	0.00903	0.00814
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	622	623

Data Submission Information

	BGKLV08-37	BGKLV08-37
ENCODE_alias	brenton-graveley:PABPC4-LV08	brenton-graveley:PABPC4-BGKLV08-K562
ENCODE_accession	ENCSR047EEG	ENCSR169IXL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-37	BGKLV08-37
Sample Name	PABPC4-LV08-37	PABPC4-LV08-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2700	6844

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
PABPC4-LV08-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	622					GRCh38	V40	PABPC4-LV08-37_GGCTAC_L005_R1_001.fastq.gz,PABPC4-LV08-37_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	12009
PABPC4-LV08-37_GGCTAC_L005_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	622	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12065
PABPC4-LV08-37_GGCTAC_L005_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	622	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12121
PABPC4-LV08-37_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	622					GRCh38	V40	PABPC4-LV08-37/Aligned.sortedByCoord.out.bam		ENCORE2	12177
PABPC4-LV08-37_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	622					GRCh38	V40	PABPC4-LV08-37/Aligned.sortedByCoord.out.bam		ENCORE2	12233
PABPC4-LV08-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	622					GRCh38	V40	PABPC4-LV08-37/Aligned.sortedByCoord.out.bam		ENCORE2	12289
PABPC4-LV08-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	622					GRCh38	V40	PABPC4-LV08-37/Aligned.sortedByCoord.out.bam		ENCORE2	12345
PABPC4-LV08-37_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	622					GRCh38	V40	PABPC4-LV08-37_GGCTAC_L005_R1_001.fastq.gz,PABPC4-LV08-37_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	13344
PABPC4-LV08-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	623					GRCh38	V40	PABPC4-LV08-38_CTTGTA_L006_R1_001.fastq.gz,PABPC4-LV08-38_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	12010
PABPC4-LV08-38_CTTGTA_L006_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	623	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12066
PABPC4-LV08-38_CTTGTA_L006_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	623	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12122
PABPC4-LV08-38_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	623					GRCh38	V40	PABPC4-LV08-38/Aligned.sortedByCoord.out.bam		ENCORE2	12178
PABPC4-LV08-38_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	623					GRCh38	V40	PABPC4-LV08-38/Aligned.sortedByCoord.out.bam		ENCORE2	12234
PABPC4-LV08-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	623					GRCh38	V40	PABPC4-LV08-38/Aligned.sortedByCoord.out.bam		ENCORE2	12290
PABPC4-LV08-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	623					GRCh38	V40	PABPC4-LV08-38/Aligned.sortedByCoord.out.bam		ENCORE2	12346
PABPC4-LV08-38_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	623					GRCh38	V40	PABPC4-LV08-38_CTTGTA_L006_R1_001.fastq.gz,PABPC4-LV08-38_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	13345