PTBP1 RNA-Seq in K562

General Information


RBP	PTBP1
Cell_Line	K562
Method	shRNA
Exp_Name	PTBP1-BGKLV11-K562
ENCODE_series_ID	ENCSR445NMP
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR527IVX
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	PTBP1-LV11-35
Rep2	PTBP1-LV11-36
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	67.6
Rep2_qPCR	74.4
Rep1_WB	99.1
Rep2_WB	99.7
Antibody Cat#	RN011P
Antibody Lot#	RN011P
Antibody DCC ID	ENCAB553IRN
Status	Released
Project	ENCODE3
ID	318

Experiment Information (Status: Released)

	BGKLV11-35	BGKLV11-36
idx	104	105
TRCN#_or_BGC#	TRCN0000001062	TRCN0000001062
shRNA_or_gRNA_sequence	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT
PAM
Name	PTBP1	PTBP1
Sample_ID	BGKLV11-35	BGKLV11-36
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	PTBP1	PTBP1
qPCR_result	67.6	74.4
Ave_qPCR	71.0
RT-qPCR_primer-F	ACGGACCGTTTATCATGAGC
RT-qPCR_primer-R	CGGCTGTCACCTTTGAACTT
protein_conc	1350	1698
WB_result	99.1	99.7
Ave_WB	99.4	no more samples
WB_DONE_date	6/25/2014
MW	58kDa
IP	1	1
antibody_Cat#	RN011P	RN011P
Antibody DCC ID	ENCAB553IRN	ENCAB553IRN
submitted_to_DCC_date	4/2/2015
Rep1_TPM	93.2253184	0
Rep2_TPM	74.0774318	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	117	118

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PTBP1	Product_ID: RN011P Lot_ID: 1 Source: MBLI Target Name: PTBP1-human

Experiment Status

	BGKLV11-35	BGKLV11-36
Sample_ID	BGKLV11-35	BGKLV11-36
Sample Name	PTBP1-LV11-35	PTBP1-LV11-36
Sample Name	PTBP1-LV11-35	PTBP1-LV11-36
RBP	PTBP1	PTBP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	350	351

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-35	BGKLV11-36
Sample #
Sample Name	PTBP1-BGKLV11-35	PTBP1-BGKLV11-36
Sample_Name_Alias	PTBP1-LV11-35	PTBP1-LV11-36
Index Well Position	S03	S04
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/E2.png	DNA_Library_LV11/set2/F2.png
RIN	9.1	9.2
libSample_RNA_Well	RNA_Library_LV11/set1/C4.png	RNA_Library_LV11/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-35	BGKLV11-36
RBP	PTBP1	PTBP1
Batch_ID	BGKLV11	BGKLV11
WB_result	99.100	99.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1972	1973

Sequencing Information

	BGKLV11-35	BGKLV11-36
Sample_ID	BGKLV11-35	BGKLV11-36
Sample Name	PTBP1-LV11-35	PTBP1-LV11-36
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	64,600,000	61,020,000
total_aligned_reads	50,741,566	48,963,314
unique_aligned_reads	46,716,352	45,135,074
percent_uniqueAligned	0.72316	0.73968
correlation_replicates	0.999174	0.999174
spikein_reads	462,860	383,064
percent_spikeins	0.00717	0.00628
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	672	673

Data Submission Information

	BGKLV11-35	BGKLV11-35
ENCODE_alias	brenton-graveley:PTBP1-LV11	brenton-graveley:PTBP1-BGKLV11-K562
ENCODE_accession	ENCSR527IVX	ENCSR445NMP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-35	BGKLV11-35
Sample Name	PTBP1-LV11-35	PTBP1-LV11-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2724	6876

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
PTBP1-LV11-35_TTAGGC_L005_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	672	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12393
PTBP1-LV11-35_TTAGGC_L005_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	672	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12441
PTBP1-LV11-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	672					GRCh38	V40	PTBP1-LV11-35_TTAGGC_L005_R1_001.fastq.gz,PTBP1-LV11-35_TTAGGC_L005_R2_001.fastq.gz		ENCORE2	12489
PTBP1-LV11-35_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	672					GRCh38	V40	PTBP1-LV11-35/Aligned.sortedByCoord.out.bam		ENCORE2	12537
PTBP1-LV11-35_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	672					GRCh38	V40	PTBP1-LV11-35/Aligned.sortedByCoord.out.bam		ENCORE2	12585
PTBP1-LV11-35_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	672					GRCh38	V40	PTBP1-LV11-35/Aligned.sortedByCoord.out.bam		ENCORE2	12633
PTBP1-LV11-35_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	672					GRCh38	V40	PTBP1-LV11-35/Aligned.sortedByCoord.out.bam		ENCORE2	12681
PTBP1-LV11-35_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	672					GRCh38	V40	PTBP1-LV11-35_TTAGGC_L005_R1_001.fastq.gz,PTBP1-LV11-35_TTAGGC_L005_R2_001.fastq.gz		ENCORE2	12729
PTBP1-LV11-36_TGACCA_L005_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	673	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12394
PTBP1-LV11-36_TGACCA_L005_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	673	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12442
PTBP1-LV11-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	673					GRCh38	V40	PTBP1-LV11-36_TGACCA_L005_R1_001.fastq.gz,PTBP1-LV11-36_TGACCA_L005_R2_001.fastq.gz		ENCORE2	12490
PTBP1-LV11-36_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	673					GRCh38	V40	PTBP1-LV11-36/Aligned.sortedByCoord.out.bam		ENCORE2	12538
PTBP1-LV11-36_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	673					GRCh38	V40	PTBP1-LV11-36/Aligned.sortedByCoord.out.bam		ENCORE2	12586
PTBP1-LV11-36_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	673					GRCh38	V40	PTBP1-LV11-36/Aligned.sortedByCoord.out.bam		ENCORE2	12634
PTBP1-LV11-36_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	673					GRCh38	V40	PTBP1-LV11-36/Aligned.sortedByCoord.out.bam		ENCORE2	12682
PTBP1-LV11-36_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	673					GRCh38	V40	PTBP1-LV11-36_TGACCA_L005_R1_001.fastq.gz,PTBP1-LV11-36_TGACCA_L005_R2_001.fastq.gz		ENCORE2	12730