HNRNPAB RNA-Seq in HepG2

General Information


RBP	HNRNPAB
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPAB-BGHLV22-HepG2
ENCODE_series_ID	ENCSR418EER
Batch_ID	BGHLV22
Pool ID	Pool-150705
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR354XQY
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	HNRNPAB--BGHLV22-23_17758
Rep2	HNRNPAB--BGHLV22-24_17759
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	71.8
Rep2_qPCR	63.3
Rep1_WB	90.3
Rep2_WB	98.0
Antibody Cat#	PA5-27549
Antibody Lot#	TL2692997
Antibody DCC ID	ENCAB577EYI
Status	Released
Project	ENCODE3
ID	537

Experiment Information (Status: Released)

	BGHLV22-23	BGHLV22-24
idx	451	452
TRCN#_or_BGC#	TRCN0000074520	TRCN0000074520
shRNA_or_gRNA_sequence	TGGAAGCAAGTGTGAGATCAA	TGGAAGCAAGTGTGAGATCAA
PAM
Name	HNRNPAB	HNRNPAB
Sample_ID	BGHLV22-23	BGHLV22-24
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	HNRNPAB	HNRNPAB
qPCR_result	71.8	63.3
Ave_qPCR	67.5
RT-qPCR_primer-F	ATCCTGAAGCCACTGAGGAA
RT-qPCR_primer-R	TCAACTTTGGATCCATTGGC
protein_conc	6461	6527
WB_result	90.3	98.0
Ave_WB	94.2
WB_DONE_date	4/21/19
MW	36KD
IP
antibody_Cat#	PA5-27549
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	53.5	0
Rep2_TPM	48.3	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2520	2521

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPAB	Product_ID: PA5-27549 Lot_ID: TL2692997 Source: Thermo Fisher Target Name: HNRNPAB-human

Experiment Status

	BGHLV22-23	BGHLV22-24
Sample_ID	BGHLV22-23	BGHLV22-24
Sample Name	HNRNPAB--BGHLV22-23_17758	HNRNPAB--BGHLV22-24_17759
Sample Name	HNRNPAB--BGHLV22-23_17758	HNRNPAB--BGHLV22-24_17759
RBP	HNRNPAB	HNRNPAB
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	788	789

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-23	BGHLV22-24
Sample #
Sample Name	HNRNPAB-BGHLV22-23	HNRNPAB-BGHLV22-24
Sample_Name_Alias	HNRNPAB--BGHLV22-23_17758	HNRNPAB--BGHLV22-24_17759
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/E7.png	DNA_Library_LV20-22-23/set1/F7.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/H4.png	RNA_Library_LV22-23-25/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-23	BGHLV22-24
RBP	HNRNPAB	HNRNPAB
Batch_ID	BGHLV22	BGHLV22
WB_result	90.300	98.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2474	2475

Sequencing Information

	BGHLV22-23	BGHLV22-24
Sample_ID	BGHLV22-23	BGHLV22-24
Sample Name	HNRNPAB--BGHLV22-23_17758	HNRNPAB--BGHLV22-24_17759
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set22	set22
total_reads	42,990,000	41,520,000
total_aligned_reads	39,953,344	38,826,936
unique_aligned_reads	37,687,400	36,573,754
percent_uniqueAligned	0.87666	0.88087
correlation_replicates	0.996926	0.996926
spikein_reads	240,490	231,138
percent_spikeins	0.00559	0.00557
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1208	1209

Data Submission Information

	BGHLV22-23	BGHLV22-23
ENCODE_alias	brenton-graveley:HNRNPAB--BGHLV22	brenton-graveley:HNRNPAB-BGHLV22-HepG2
ENCODE_accession	ENCSR354XQY	ENCSR418EER
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-23	BGHLV22-23
Sample Name	HNRNPAB--BGHLV22-23_17758	HNRNPAB--BGHLV22-23_17758
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2926	6752

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
HNRNPAB--BGHLV22-23_17758_AGTCAA_L008_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1208	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16284
HNRNPAB--BGHLV22-23_17758_AGTCAA_L008_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1208	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16324
HNRNPAB--BGHLV22-23_17758_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1208					GRCh38	V40	HNRNPAB--BGHLV22-23_17758_AGTCAA_L008_R1_001.fastq.gz,HNRNPAB--BGHLV22-23_17758_AGTCAA_L008_R2_001.fastq.gz		ENCORE2	16422
HNRNPAB--BGHLV22-23_17758_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1208					GRCh38	V40	HNRNPAB--BGHLV22-23_17758/Aligned.sortedByCoord.out.bam		ENCORE2	16462
HNRNPAB--BGHLV22-23_17758_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1208					GRCh38	V40	HNRNPAB--BGHLV22-23_17758/Aligned.sortedByCoord.out.bam		ENCORE2	16502
HNRNPAB--BGHLV22-23_17758_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1208					GRCh38	V40	HNRNPAB--BGHLV22-23_17758/Aligned.sortedByCoord.out.bam		ENCORE2	16542
HNRNPAB--BGHLV22-23_17758_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1208					GRCh38	V40	HNRNPAB--BGHLV22-23_17758/Aligned.sortedByCoord.out.bam		ENCORE2	16582
HNRNPAB--BGHLV22-23_17758_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1208					GRCh38	V40	HNRNPAB--BGHLV22-23_17758_AGTCAA_L008_R1_001.fastq.gz,HNRNPAB--BGHLV22-23_17758_AGTCAA_L008_R2_001.fastq.gz		ENCORE2	16622
HNRNPAB--BGHLV22-24_17759_AGTTCC_L008_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1209	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16285
HNRNPAB--BGHLV22-24_17759_AGTTCC_L008_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1209	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16325
HNRNPAB--BGHLV22-24_17759_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1209					GRCh38	V40	HNRNPAB--BGHLV22-24_17759_AGTTCC_L008_R1_001.fastq.gz,HNRNPAB--BGHLV22-24_17759_AGTTCC_L008_R2_001.fastq.gz		ENCORE2	16423
HNRNPAB--BGHLV22-24_17759_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1209					GRCh38	V40	HNRNPAB--BGHLV22-24_17759/Aligned.sortedByCoord.out.bam		ENCORE2	16463
HNRNPAB--BGHLV22-24_17759_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1209					GRCh38	V40	HNRNPAB--BGHLV22-24_17759/Aligned.sortedByCoord.out.bam		ENCORE2	16503
HNRNPAB--BGHLV22-24_17759_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1209					GRCh38	V40	HNRNPAB--BGHLV22-24_17759/Aligned.sortedByCoord.out.bam		ENCORE2	16543
HNRNPAB--BGHLV22-24_17759_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1209					GRCh38	V40	HNRNPAB--BGHLV22-24_17759/Aligned.sortedByCoord.out.bam		ENCORE2	16583
HNRNPAB--BGHLV22-24_17759_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1209					GRCh38	V40	HNRNPAB--BGHLV22-24_17759_AGTTCC_L008_R1_001.fastq.gz,HNRNPAB--BGHLV22-24_17759_AGTTCC_L008_R2_001.fastq.gz		ENCORE2	16623