PTBP1 RNA-Seq in K562

General Information


RBP	PTBP1
Cell_Line	K562
Method	CRISPR
Exp_Name	PTBP1-BGKcLV02-K562
ENCODE_series_ID	ENCSR233BRU
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID	ENCSR415DJT
ENCODE_CN_Exp_ID	ENCSR163JUC
Rep1	PTBP1_BGKcLV02-7
Rep2	PTBP1_BGKcLV02-8
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	77.1
Rep2_qPCR	54.9
Rep1_WB	90.9
Rep2_WB	87.9
Antibody Cat#	RN011P
Antibody Lot#	RN011P
Antibody DCC ID	ENCAB553IRN
Status	Archived
Project	ENCODE3
ID	588

Experiment Information (Status: Released)

	BGKcLV02-7	BGKcLV02-7	BGKcLV02-8	BGKcLV02-8
idx	7	9	8	10
TRCN#_or_BGC#	BGC#0000006	BGC#0000006	BGC#0000006	BGC#0000006
shRNA_or_gRNA_sequence	CCTCTAGAGTGATCCACATC	CCTCTAGAGTGATCCACATC	CCTCTAGAGTGATCCACATC	CCTCTAGAGTGATCCACATC
PAM
Name	PTBP1-C2-A	PTBP1-C2-A	PTBP1-C2-A	PTBP1-C2-A
Sample_ID	BGKcLV02-7	BGKcLV02-7	BGKcLV02-8	BGKcLV02-8
transduction_Date	12/15/2015	12/15/2015	12/15/2015	12/15/2015
days	day 6	day 6	day 6	day 6
RBP_name	PTBP1	PTBP1	PTBP1	PTBP1
qPCR_result	77.1	77.1	54.9	54.9
Ave_qPCR	66.0	66.0
RT-qPCR_primer-F	ACGGACCGTTTATCATGAGC	ACGGACCGTTTATCATGAGC
RT-qPCR_primer-R	CGGCTGTCACCTTTGAACTT	CGGCTGTCACCTTTGAACTT
protein_conc	3507	3507	3552	3552
WB_result	90.9	67.1	87.9	66.2
Ave_WB	89.4	66.6	no more samples
WB_DONE_date	12/28/2015	10/23/2018
MW	58kDa			wes
IP	1
antibody_Cat#	RN011P	32-4800	RN011P	Lot ID TG268402
Antibody DCC ID	ENCAB553IRN	ENCAB609DDA	ENCAB553IRN
submitted_to_DCC_date	9/28/16	3/11/19
Rep1_TPM	93.2	93.2	0	0
Rep2_TPM	74.1	74.1	0	0
Action	Ready		Ready
Library_start_date	1/8/2016		1/8/2016
repeat_library
Note
ID	4101	4103	4102	4104

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PTBP1	Product_ID: 32-4800 Lot_ID: TG268402 Source: Thermo Fisher Target Name: PTBP1-human
PTBP1	Product_ID: RN011P Lot_ID: 1 Source: MBLI Target Name: PTBP1-human

Experiment Status

	BGKcLV02-7	BGKcLV02-8
Sample_ID	BGKcLV02-7	BGKcLV02-8
Sample Name	PTBP1_BGKcLV02-7	PTBP1_BGKcLV02-8
Sample Name	PTBP1_BGKcLV02-7	PTBP1_BGKcLV02-8
RBP	PTBP1	PTBP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1093	1094

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-7	BGKcLV02-8
Sample #
Sample Name	PTBP1-BGKcLV02-7	PTBP1-BGKcLV02-8
Sample_Name_Alias	PTBP1_BGKcLV02-7	PTBP1_BGKcLV02-8
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/A4.png	DNA_Library_cLV02/set1/B4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_cLV02/set1/C5.png	RNA_Library_cLV02/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-7	BGKcLV02-8
RBP	PTBP1	PTBP1
Batch_ID	BGKcLV02	BGKcLV02
WB_result	90.900	87.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2784	2785

Sequencing Information

	BGKcLV02-7	BGKcLV02-8
Sample_ID	BGKcLV02-7	BGKcLV02-8
Sample Name	PTBP1_BGKcLV02-7	PTBP1_BGKcLV02-8
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	60,914,954	64,935,048
total_aligned_reads	54,850,192	59,327,288
unique_aligned_reads	50,130,248	54,161,962
percent_uniqueAligned	0.82295	0.83409
correlation_replicates	0.998016	0.998016
spikein_reads	110,154	161,376
percent_spikeins	0.00181	0.00249
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1433	1434

Data Submission Information

	BGKcLV02-7	BGKcLV02-7
ENCODE_alias	brenton-graveley:PTBP1_BGKcLV02	brenton-graveley:PTBP1-BGKcLV02-K562
ENCODE_accession	ENCSR415DJT	ENCSR233BRU
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV02-7	BGKcLV02-7
Sample Name	PTBP1_BGKcLV02-7	PTBP1_BGKcLV02-7
Selected	Yes	No
Status	Released	Archived
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3108	6875

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_BGKcLV02-7_GTCCGC_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1433	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22766
PTBP1_BGKcLV02-7_GTCCGC_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1433	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22786
PTBP1_BGKcLV02-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1433					GRCh38	V40	PTBP1_BGKcLV02-7_GTCCGC_L007_001.R1.fastq.gz,PTBP1_BGKcLV02-7_GTCCGC_L007_001.R2.fastq.gz		ENCORE2	22806
PTBP1_BGKcLV02-7_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1433					GRCh38	V40	PTBP1_BGKcLV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	22826
PTBP1_BGKcLV02-7_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1433					GRCh38	V40	PTBP1_BGKcLV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	22846
PTBP1_BGKcLV02-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1433					GRCh38	V40	PTBP1_BGKcLV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	22866
PTBP1_BGKcLV02-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1433					GRCh38	V40	PTBP1_BGKcLV02-7/Aligned.sortedByCoord.out.bam		ENCORE2	22886
PTBP1_BGKcLV02-7_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1433					GRCh38	V40	PTBP1_BGKcLV02-7_GTCCGC_L007_001.R1.fastq.gz,PTBP1_BGKcLV02-7_GTCCGC_L007_001.R2.fastq.gz		ENCORE2	22906
PTBP1_BGKcLV02-8_GTGAAA_L007_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1434	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22767
PTBP1_BGKcLV02-8_GTGAAA_L007_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1434	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22787
PTBP1_BGKcLV02-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1434					GRCh38	V40	PTBP1_BGKcLV02-8_GTGAAA_L007_001.R1.fastq.gz,PTBP1_BGKcLV02-8_GTGAAA_L007_001.R2.fastq.gz		ENCORE2	22807
PTBP1_BGKcLV02-8_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1434					GRCh38	V40	PTBP1_BGKcLV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	22827
PTBP1_BGKcLV02-8_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1434					GRCh38	V40	PTBP1_BGKcLV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	22847
PTBP1_BGKcLV02-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1434					GRCh38	V40	PTBP1_BGKcLV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	22867
PTBP1_BGKcLV02-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1434					GRCh38	V40	PTBP1_BGKcLV02-8/Aligned.sortedByCoord.out.bam		ENCORE2	22887
PTBP1_BGKcLV02-8_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1434					GRCh38	V40	PTBP1_BGKcLV02-8_GTGAAA_L007_001.R1.fastq.gz,PTBP1_BGKcLV02-8_GTGAAA_L007_001.R2.fastq.gz		ENCORE2	22907