HNRNPA2B1 RNA-Seq in K562

General Information


RBP	HNRNPA2B1
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPA2B1-BGKLV28-K562
ENCODE_series_ID	ENCSR050NGU
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR794NUE
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	HNRNPA2B1_BGKLV28-19
Rep2	HNRNPA2B1_BGKLV28-20
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	46.0
Rep2_qPCR	50.9
Rep1_WB	59.5
Rep2_WB	71.1
Antibody Cat#	GTX127928
Antibody Lot#	GTX127928
Antibody DCC ID	ENCAB421UFR
Status	Released
Project	ENCODE3
ID	648

Experiment Information (Status: Released)

	BGKLV28-19	BGKLV28-20
idx	486	487
TRCN#_or_BGC#	TRCN0000001059	TRCN0000001059
shRNA_or_gRNA_sequence	CAGAAATACCATACCATCAAT	CAGAAATACCATACCATCAAT
PAM
Name	HNRNPA2B1_59	HNRNPA2B1_59
Sample_ID	BGKLV28-19	BGKLV28-20
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	HNRNPA2B1	HNRNPA2B1
qPCR_result	46.0	50.9
Ave_qPCR	48.4
RT-qPCR_primer-F	TGGTGGCTTAAGCTTTGAAAC
RT-qPCR_primer-R	GCTTGCAGGATCCCTCATTA
protein_conc	2976	2825
WB_result	59.5	71.1
Ave_WB	65.3
WB_DONE_date	6/30/2015
MW	37kDa
IP	0.5	0.5
antibody_Cat#	GTX127928	GTX127928
Antibody DCC ID	ENCAB421UFR	ENCAB421UFR
submitted_to_DCC_date	12/7/2015
Rep1_TPM	980.808302	0
Rep2_TPM	588.800327	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	561	562

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPA2B1	Product_ID: GTX127928 Lot_ID: 41094 Source: GeneTex Target Name: HNRNPA2B1-human

Experiment Status

	BGKLV28-19	BGKLV28-20
Sample_ID	BGKLV28-19	BGKLV28-20
Sample Name	HNRNPA2B1_BGKLV28-19	HNRNPA2B1_BGKLV28-20
Sample Name	HNRNPA2B1_BGKLV28-19	HNRNPA2B1_BGKLV28-20
RBP	HNRNPA2B1	HNRNPA2B1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	980	981

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-19	BGKLV28-20
Sample #
Sample Name	HNRNPA2B1-BGKLV28-19	HNRNPA2B1-BGKLV28-20
Sample_Name_Alias	HNRNPA2B1_BGKLV28-19	HNRNPA2B1_BGKLV28-20
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C1.png	DNA_Library_LV28-29-30/set1/D1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/F7.png	RNA_Library_LV19-21-24/set2/G7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-19	BGKLV28-20
RBP	HNRNPA2B1	HNRNPA2B1
Batch_ID	BGKLV28	BGKLV28
WB_result	59.500	71.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2672	2673

Sequencing Information

	BGKLV28-19	BGKLV28-20
Sample_ID	BGKLV28-19	BGKLV28-20
Sample Name	HNRNPA2B1_BGKLV28-19	HNRNPA2B1_BGKLV28-20
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	92,186,658	86,345,514
total_aligned_reads	74,624,068	71,253,780
unique_aligned_reads	68,184,716	65,057,750
percent_uniqueAligned	0.73964	0.75346
correlation_replicates	0.997495	0.997495
spikein_reads	294,528	262,486
percent_spikeins	0.00319	0.00304
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1314	1315

Data Submission Information

	BGKLV28-19	BGKLV28-19
ENCODE_alias	brenton-graveley:HNRNPA2B1_BGKLV28	brenton-graveley:HNRNPA2B1-BGKLV28-K562
ENCODE_accession	ENCSR794NUE	ENCSR050NGU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-19	BGKLV28-19
Sample Name	HNRNPA2B1_BGKLV28-19	HNRNPA2B1_BGKLV28-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3039	6751

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
HNRNPA2B1_BGKLV28-19_TTAGGC_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1314	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20158
HNRNPA2B1_BGKLV28-19_TTAGGC_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1314	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20190
HNRNPA2B1_BGKLV28-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1314					GRCh38	V40	HNRNPA2B1_BGKLV28-19_TTAGGC_L001_001.R1.fastq.gz,HNRNPA2B1_BGKLV28-19_TTAGGC_L001_001.R2.fastq.gz		ENCORE2	20222
HNRNPA2B1_BGKLV28-19_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1314					GRCh38	V40	HNRNPA2B1_BGKLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	20254
HNRNPA2B1_BGKLV28-19_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1314					GRCh38	V40	HNRNPA2B1_BGKLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	20286
HNRNPA2B1_BGKLV28-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1314					GRCh38	V40	HNRNPA2B1_BGKLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	20318
HNRNPA2B1_BGKLV28-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1314					GRCh38	V40	HNRNPA2B1_BGKLV28-19/Aligned.sortedByCoord.out.bam		ENCORE2	20350
HNRNPA2B1_BGKLV28-19_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1314					GRCh38	V40	HNRNPA2B1_BGKLV28-19_TTAGGC_L001_001.R1.fastq.gz,HNRNPA2B1_BGKLV28-19_TTAGGC_L001_001.R2.fastq.gz		ENCORE2	20382
HNRNPA2B1_BGKLV28-20_TGACCA_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1315	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20159
HNRNPA2B1_BGKLV28-20_TGACCA_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1315	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20191
HNRNPA2B1_BGKLV28-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1315					GRCh38	V40	HNRNPA2B1_BGKLV28-20_TGACCA_L001_001.R1.fastq.gz,HNRNPA2B1_BGKLV28-20_TGACCA_L001_001.R2.fastq.gz		ENCORE2	20223
HNRNPA2B1_BGKLV28-20_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1315					GRCh38	V40	HNRNPA2B1_BGKLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	20255
HNRNPA2B1_BGKLV28-20_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1315					GRCh38	V40	HNRNPA2B1_BGKLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	20287
HNRNPA2B1_BGKLV28-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1315					GRCh38	V40	HNRNPA2B1_BGKLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	20319
HNRNPA2B1_BGKLV28-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1315					GRCh38	V40	HNRNPA2B1_BGKLV28-20/Aligned.sortedByCoord.out.bam		ENCORE2	20351
HNRNPA2B1_BGKLV28-20_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1315					GRCh38	V40	HNRNPA2B1_BGKLV28-20_TGACCA_L001_001.R1.fastq.gz,HNRNPA2B1_BGKLV28-20_TGACCA_L001_001.R2.fastq.gz		ENCORE2	20383