HNRNPAB RNA-Seq in K562

General Information


RBP	HNRNPAB
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPAB-BGKLV24-K562
ENCODE_series_ID	ENCSR248OUZ
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR552NBS
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	HNRNPAB_BGKLV24_31B
Rep2	HNRNPAB_BGKLV24_32B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	84.0
Rep2_qPCR	82.9
Rep1_WB	86.0
Rep2_WB	91.3
Antibody Cat#	PA5-27549
Antibody Lot#	LOT# TL2692997
Antibody DCC ID	ENCAB577EYI
Status	Released
Project	ENCODE3
ID	603

Experiment Information (Status: Released)

	BGKLV24-31	BGKLV24-32
idx	368	369
TRCN#_or_BGC#	TRCN0000074520	TRCN0000074520
shRNA_or_gRNA_sequence	TGGAAGCAAGTGTGAGATCAA	TGGAAGCAAGTGTGAGATCAA
PAM
Name	HNRNPAB	HNRNPAB
Sample_ID	BGKLV24-31	BGKLV24-32
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	HNRNPAB	HNRNPAB
qPCR_result	84.0	82.9
Ave_qPCR	83.5
RT-qPCR_primer-F	ATCCTGAAGCCACTGAGGAA
RT-qPCR_primer-R	TCAACTTTGGATCCATTGGC
protein_conc	3925	4605
WB_result	86.0	91.3
Ave_WB	88.6
WB_DONE_date	4/4/19
MW
IP
antibody_Cat#	PA5-27549	LOT# TL2692997
Antibody DCC ID	ENCAB577EYI
submitted_to_DCC_date	4/17/19
Rep1_TPM	181.925761	0
Rep2_TPM	100.183264	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	x	x
ID	425	426

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

	BGKLV24-31	BGKLV24-32
Sample_ID	BGKLV24-31	BGKLV24-32
Sample Name	HNRNPAB_BGKLV24_31B	HNRNPAB_BGKLV24_32B
Sample Name	HNRNPAB_BGKLV24_31B	HNRNPAB_BGKLV24_32B
RBP	HNRNPAB	HNRNPAB
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	886	887

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-31	BGKLV24-32
Sample #
Sample Name	HNRNPAB-BGKLV24-31B	HNRNPAB-BGKLV24-32B
Sample_Name_Alias	HNRNPAB_BGKLV24_31B	HNRNPAB_BGKLV24_32B
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/G5.png	DNA_Library_LV24-25-26/set1/H5.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G3.png	RNA_Library_LV20-22-24/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-31	BGKLV24-32
RBP	HNRNPAB	HNRNPAB
Batch_ID	BGKLV24	BGKLV24
WB_result	86.000	91.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2574	2575

Sequencing Information

	BGKLV24-31	BGKLV24-32
Sample_ID	BGKLV24-31	BGKLV24-32
Sample Name	HNRNPAB_BGKLV24_31B	HNRNPAB_BGKLV24_32B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	82,773,582	83,357,668
total_aligned_reads	79,254,148	80,460,090
unique_aligned_reads	72,258,746	72,919,658
percent_uniqueAligned	0.87297	0.87478
correlation_replicates	0.997958	0.997958
spikein_reads	293,064	241,730
percent_spikeins	0.00354	0.00290
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1216	1217

Data Submission Information

	BGKLV24-31	BGKLV24-31
ENCODE_alias	brenton-graveley:HNRNPA0_BGKLV24_B	brenton-graveley:HNRNPAB-BGKLV24-K562
ENCODE_accession	ENCSR552NBS	ENCSR248OUZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-31	BGKLV24-31
Sample Name	HNRNPAB_BGKLV24_31B	HNRNPAB_BGKLV24_31B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2992	6753

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_BGKLV24_31B_CAGATC_L001_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1216	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17474
HNRNPAB_BGKLV24_31B_CAGATC_L001_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1216	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17498
HNRNPAB_BGKLV24_31B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1216					GRCh38	V40	HNRNPAB_BGKLV24_31B_CAGATC_L001_001.R1.fastq.gz,HNRNPAB_BGKLV24_31B_CAGATC_L001_001.R2.fastq.gz		ENCORE2	17522
HNRNPAB_BGKLV24_31B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1216					GRCh38	V40	HNRNPAB_BGKLV24_31B/Aligned.sortedByCoord.out.bam		ENCORE2	17546
HNRNPAB_BGKLV24_31B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1216					GRCh38	V40	HNRNPAB_BGKLV24_31B/Aligned.sortedByCoord.out.bam		ENCORE2	17570
HNRNPAB_BGKLV24_31B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1216					GRCh38	V40	HNRNPAB_BGKLV24_31B/Aligned.sortedByCoord.out.bam		ENCORE2	17594
HNRNPAB_BGKLV24_31B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1216					GRCh38	V40	HNRNPAB_BGKLV24_31B/Aligned.sortedByCoord.out.bam		ENCORE2	17618
HNRNPAB_BGKLV24_31B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1216					GRCh38	V40	HNRNPAB_BGKLV24_31B_CAGATC_L001_001.R1.fastq.gz,HNRNPAB_BGKLV24_31B_CAGATC_L001_001.R2.fastq.gz		ENCORE2	17642
HNRNPAB_BGKLV24_32B_ACTTGA_L002_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1217	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17475
HNRNPAB_BGKLV24_32B_ACTTGA_L002_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1217	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17499
HNRNPAB_BGKLV24_32B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1217					GRCh38	V40	HNRNPAB_BGKLV24_32B_ACTTGA_L002_001.R1.fastq.gz,HNRNPAB_BGKLV24_32B_ACTTGA_L002_001.R2.fastq.gz		ENCORE2	17523
HNRNPAB_BGKLV24_32B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1217					GRCh38	V40	HNRNPAB_BGKLV24_32B/Aligned.sortedByCoord.out.bam		ENCORE2	17547
HNRNPAB_BGKLV24_32B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1217					GRCh38	V40	HNRNPAB_BGKLV24_32B/Aligned.sortedByCoord.out.bam		ENCORE2	17571
HNRNPAB_BGKLV24_32B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1217					GRCh38	V40	HNRNPAB_BGKLV24_32B/Aligned.sortedByCoord.out.bam		ENCORE2	17595
HNRNPAB_BGKLV24_32B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1217					GRCh38	V40	HNRNPAB_BGKLV24_32B/Aligned.sortedByCoord.out.bam		ENCORE2	17619
HNRNPAB_BGKLV24_32B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1217					GRCh38	V40	HNRNPAB_BGKLV24_32B_ACTTGA_L002_001.R1.fastq.gz,HNRNPAB_BGKLV24_32B_ACTTGA_L002_001.R2.fastq.gz		ENCORE2	17643