HNRNPA2B1 RNA-Seq in HepG2

General Information


RBP	HNRNPA2B1
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPA2B1-BGHLV23-HepG2
ENCODE_series_ID	ENCSR281SSX
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR769GES
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	HNRNPA2B1-BGHLV23-19
Rep2	HNRNPA2B1-BGHLV23-20
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	47.8
Rep2_qPCR	58.3
Rep1_WB	41.3
Rep2_WB	51.1
Antibody Cat#	GTX127928
Antibody Lot#	GTX127928
Antibody DCC ID	ENCAB421UFR
Status	Released
Project	ENCODE3
ID	544

Experiment Information (Status: Released)

	BGHLV23-19	BGHLV23-20
idx	511	512
TRCN#_or_BGC#	TRCN0000001060	TRCN0000001060
shRNA_or_gRNA_sequence	AGACAAGAAATGCAGGAAGTT	AGACAAGAAATGCAGGAAGTT
PAM
Name	HNRNPA2B1_60	HNRNPA2B1_60
Sample_ID	BGHLV23-19	BGHLV23-20
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	HNRNPA2B1	HNRNPA2B1
qPCR_result	47.8	58.3
Ave_qPCR	53.0
RT-qPCR_primer-F	TGGTGGCTTAAGCTTTGAAAC
RT-qPCR_primer-R	GCTTGCAGGATCCCTCATTA
protein_conc	6809	6767
WB_result	41.3	51.1
Ave_WB	46.2
WB_DONE_date	4/7/2015
MW
IP	0.5	0.5
antibody_Cat#	GTX127928	GTX127928
Antibody DCC ID	ENCAB421UFR	ENCAB421UFR
submitted_to_DCC_date	5/6/2015
Rep1_TPM	524.3	0
Rep2_TPM	342.5	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2590	2591

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

	BGHLV23-19	BGHLV23-20
Sample_ID	BGHLV23-19	BGHLV23-20
Sample Name	HNRNPA2B1-BGHLV23-19	HNRNPA2B1-BGHLV23-20
Sample Name	HNRNPA2B1-BGHLV23-19	HNRNPA2B1-BGHLV23-20
RBP	HNRNPA2B1	HNRNPA2B1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	824	825

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-19	BGHLV23-20
Sample #
Sample Name	HNRNPA2B1-BGHLV23-19	HNRNPA2B1-BGHLV23-20
Sample_Name_Alias	HNRNPA2B1-BGHLV23-19	HNRNPA2B1-BGHLV23-20
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G12.png	DNA_Library_LV20-22-23/set1/H12.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/A6.png	RNA_Library_LV19-21-24/set2/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-19	BGHLV23-20
RBP	HNRNPA2B1	HNRNPA2B1
Batch_ID	BGHLV23	BGHLV23
WB_result	41.300	51.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2512	2513

Sequencing Information

	BGHLV23-19	BGHLV23-20
Sample_ID	BGHLV23-19	BGHLV23-20
Sample Name	HNRNPA2B1-BGHLV23-19	HNRNPA2B1-BGHLV23-20
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	51,280,000	60,260,000
total_aligned_reads	45,865,528	51,828,456
unique_aligned_reads	43,248,204	48,809,946
percent_uniqueAligned	0.84337	0.80999
correlation_replicates	0.996629	0.996629
spikein_reads	349,496	349,554
percent_spikeins	0.00682	0.00580
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1134	1135

Data Submission Information

	BGHLV23-19	BGHLV23-19
ENCODE_alias	brenton-graveley:HNRNPA2B1-BGHLV23	brenton-graveley:HNRNPA2B1-BGHLV23-HepG2
ENCODE_accession	ENCSR769GES	ENCSR281SSX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-19	BGHLV23-19
Sample Name	HNRNPA2B1-BGHLV23-19	HNRNPA2B1-BGHLV23-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2944	6750

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-BGHLV23-19_CAGATC_L005_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1134	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16662
HNRNPA2B1-BGHLV23-19_CAGATC_L005_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1134	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16700
HNRNPA2B1-BGHLV23-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1134					GRCh38	V40	HNRNPA2B1-BGHLV23-19_CAGATC_L005_R1_001.fastq.gz,HNRNPA2B1-BGHLV23-19_CAGATC_L005_R2_001.fastq.gz		ENCORE2	16738
HNRNPA2B1-BGHLV23-19_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1134					GRCh38	V40	HNRNPA2B1-BGHLV23-19/Aligned.sortedByCoord.out.bam		ENCORE2	16776
HNRNPA2B1-BGHLV23-19_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1134					GRCh38	V40	HNRNPA2B1-BGHLV23-19/Aligned.sortedByCoord.out.bam		ENCORE2	16814
HNRNPA2B1-BGHLV23-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1134					GRCh38	V40	HNRNPA2B1-BGHLV23-19/Aligned.sortedByCoord.out.bam		ENCORE2	16852
HNRNPA2B1-BGHLV23-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1134					GRCh38	V40	HNRNPA2B1-BGHLV23-19/Aligned.sortedByCoord.out.bam		ENCORE2	16890
HNRNPA2B1-BGHLV23-19_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1134					GRCh38	V40	HNRNPA2B1-BGHLV23-19_CAGATC_L005_R1_001.fastq.gz,HNRNPA2B1-BGHLV23-19_CAGATC_L005_R2_001.fastq.gz		ENCORE2	16928
HNRNPA2B1-BGHLV23-20_ACTTGA_L006_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1135	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16663
HNRNPA2B1-BGHLV23-20_ACTTGA_L006_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1135	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16701
HNRNPA2B1-BGHLV23-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1135					GRCh38	V40	HNRNPA2B1-BGHLV23-20_ACTTGA_L006_R1_001.fastq.gz,HNRNPA2B1-BGHLV23-20_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	16739
HNRNPA2B1-BGHLV23-20_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1135					GRCh38	V40	HNRNPA2B1-BGHLV23-20/Aligned.sortedByCoord.out.bam		ENCORE2	16777
HNRNPA2B1-BGHLV23-20_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1135					GRCh38	V40	HNRNPA2B1-BGHLV23-20/Aligned.sortedByCoord.out.bam		ENCORE2	16815
HNRNPA2B1-BGHLV23-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1135					GRCh38	V40	HNRNPA2B1-BGHLV23-20/Aligned.sortedByCoord.out.bam		ENCORE2	16853
HNRNPA2B1-BGHLV23-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1135					GRCh38	V40	HNRNPA2B1-BGHLV23-20/Aligned.sortedByCoord.out.bam		ENCORE2	16891
HNRNPA2B1-BGHLV23-20_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1135					GRCh38	V40	HNRNPA2B1-BGHLV23-20_ACTTGA_L006_R1_001.fastq.gz,HNRNPA2B1-BGHLV23-20_ACTTGA_L006_R2_001.fastq.gz		ENCORE2	16929