PTBP1 RNA-Seq in HepG2

General Information


RBP	PTBP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PTBP1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR526EYK
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR064DXG
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	PTBP1-BGHLV12-59
Rep2	PTBP1-BGHLV12-60
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	53.3
Rep2_qPCR	67.5
Rep1_WB	99.6
Rep2_WB	99.8
Antibody Cat#	RN011P
Antibody Lot#	RN011P
Antibody DCC ID	ENCAB553IRN
Status	Released
Project	ENCODE3
ID	348

Experiment Information (Status: Released)

	BGHLV12-59	BGHLV12-59	BGHLV12-59	BGHLV12-59	BGHLV12-60	BGHLV12-60	BGHLV12-60	BGHLV12-60
idx	59	59	59	59	60	60	60	60
TRCN#_or_BGC#	TRCN0000001062	TRCN0000001062	TRCN0000001062	TRCN0000001062	TRCN0000001062	TRCN0000001062	TRCN0000001062	TRCN0000001062
shRNA_or_gRNA_sequence	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT	CTCAACGTCAAGTACAACAAT
PAM
Name	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1
Sample_ID	BGHLV12-59	BGHLV12-59	BGHLV12-59	BGHLV12-59	BGHLV12-60	BGHLV12-60	BGHLV12-60	BGHLV12-60
transduction_Date	5/15/2014	5/15/2014	5/15/2014	5/15/2014	5/15/2014	5/15/2014	5/15/2014	5/15/2014
days
RBP_name	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1	PTBP1
qPCR_result	53.3	53.3	53.3	53.3	67.5	67.5	67.5	67.5
Ave_qPCR	60.4	60.4	60.4	60.4
RT-qPCR_primer-F	ACGGACCGTTTATCATGAGC	ACGGACCGTTTATCATGAGC	ACGGACCGTTTATCATGAGC	ACGGACCGTTTATCATGAGC
RT-qPCR_primer-R	CGGCTGTCACCTTTGAACTT	CGGCTGTCACCTTTGAACTT	CGGCTGTCACCTTTGAACTT	CGGCTGTCACCTTTGAACTT
protein_conc	2394	2394	2394	2394	2764	2764	2764	2764
WB_result	99.6	83.7	98.0	95.0	99.8	83.5	98.1	97.1
Ave_WB	99.7	83.6	98.0	96.1
WB_DONE_date	6/25/2014	10/23/2018	6/14/2023	6/26/2023
MW	58kDa	58kDa	58kDa	58kDa		wes
IP	1				1
antibody_Cat#	RN011P	32-4800	72669S	57246S	RN011P	Lot ID TG268402	lot# 1	LOT # 1
Antibody DCC ID	ENCAB553IRN	ENCAB609DDA	submitted	submitted	ENCAB553IRN		10/18/23	10/18/23
submitted_to_DCC_date	4/2/2015	3/11/2019
Rep1_TPM	39.1	0	0	0	0	0	0	0
Rep2_TPM	40.9	0	0	0	0	0	0	0
Action
Library_start_date	6/12/2014				6/12/2014
repeat_library
Note
ID	2106	2108	2110	2112	2107	2109	2111	2113

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
PTBP1	Product_ID: 57246S Lot_ID: 1 Source: Cell Signaling Technology Target Name: PTBP1-human
PTBP1	Product_ID: 72669S Lot_ID: 1 Source: Cell Signaling Technology Target Name: PTBP1-human

Experiment Status

	BGHLV12-59	BGHLV12-60
Sample_ID	BGHLV12-59	BGHLV12-60
Sample Name	PTBP1-BGHLV12-59	PTBP1-BGHLV12-60
Sample Name	PTBP1-BGHLV12-59	PTBP1-BGHLV12-60
RBP	PTBP1	PTBP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	416	417

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-59	BGHLV12-60
Sample #
Sample Name	PTBP1-BGHLV12-59	PTBP1-BGHLV12-60
Sample_Name_Alias	PTBP1-BGHLV12-59	PTBP1-BGHLV12-60
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/E2.png	DNA_Library_LV12/set3/F2.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV12/set1/E6.png	RNA_Library_LV12/set1/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-59	BGHLV12-60
RBP	PTBP1	PTBP1
Batch_ID	BGHLV12	BGHLV12
WB_result	99.600	99.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2040	2041

Sequencing Information

	BGHLV12-59	BGHLV12-60
Sample_ID	BGHLV12-59	BGHLV12-60
Sample Name	PTBP1-BGHLV12-59	PTBP1-BGHLV12-60
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	43,780,000	72,700,000
total_aligned_reads	40,041,190	66,411,466
unique_aligned_reads	37,965,322	62,958,068
percent_uniqueAligned	0.86718	0.86600
correlation_replicates	0.998983	0.998983
spikein_reads	389,518	423,356
percent_spikeins	0.00890	0.00582
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	738	739

Data Submission Information

	BGHLV12-59	BGHLV12-59
ENCODE_alias	brenton-graveley:PTBP1-BGHLV12	brenton-graveley:PTBP1-BGHLV12-HepG2
ENCODE_accession	ENCSR064DXG	ENCSR526EYK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-59	BGHLV12-59
Sample Name	PTBP1-BGHLV12-59	PTBP1-BGHLV12-59
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2757	6874

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-BGHLV12-59_CGTACG_L007_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	738	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12799
PTBP1-BGHLV12-59_CGTACG_L007_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	738	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12868
PTBP1-BGHLV12-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	738					GRCh38	V40	PTBP1-BGHLV12-59_CGTACG_L007_R1_001.fastq.gz,PTBP1-BGHLV12-59_CGTACG_L007_R2_001.fastq.gz		ENCORE2	12938
PTBP1-BGHLV12-59_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	738					GRCh38	V40	PTBP1-BGHLV12-59/Aligned.sortedByCoord.out.bam		ENCORE2	13008
PTBP1-BGHLV12-59_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	738					GRCh38	V40	PTBP1-BGHLV12-59/Aligned.sortedByCoord.out.bam		ENCORE2	13078
PTBP1-BGHLV12-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	738					GRCh38	V40	PTBP1-BGHLV12-59/Aligned.sortedByCoord.out.bam		ENCORE2	13148
PTBP1-BGHLV12-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	738					GRCh38	V40	PTBP1-BGHLV12-59/Aligned.sortedByCoord.out.bam		ENCORE2	13218
PTBP1-BGHLV12-59_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	738					GRCh38	V40	PTBP1-BGHLV12-59_CGTACG_L007_R1_001.fastq.gz,PTBP1-BGHLV12-59_CGTACG_L007_R2_001.fastq.gz		ENCORE2	13288
PTBP1-BGHLV12-60_GAGTGG_L007_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	739	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12800
PTBP1-BGHLV12-60_GAGTGG_L007_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	739	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12869
PTBP1-BGHLV12-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	739					GRCh38	V40	PTBP1-BGHLV12-60_GAGTGG_L007_R1_001.fastq.gz,PTBP1-BGHLV12-60_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	12939
PTBP1-BGHLV12-60_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	739					GRCh38	V40	PTBP1-BGHLV12-60/Aligned.sortedByCoord.out.bam		ENCORE2	13009
PTBP1-BGHLV12-60_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	739					GRCh38	V40	PTBP1-BGHLV12-60/Aligned.sortedByCoord.out.bam		ENCORE2	13079
PTBP1-BGHLV12-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	739					GRCh38	V40	PTBP1-BGHLV12-60/Aligned.sortedByCoord.out.bam		ENCORE2	13149
PTBP1-BGHLV12-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	739					GRCh38	V40	PTBP1-BGHLV12-60/Aligned.sortedByCoord.out.bam		ENCORE2	13219
PTBP1-BGHLV12-60_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	739					GRCh38	V40	PTBP1-BGHLV12-60_GAGTGG_L007_R1_001.fastq.gz,PTBP1-BGHLV12-60_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	13289