HNRNPA0 RNA-Seq in K562

General Information


RBP	HNRNPA0
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPA0-BGKLV24-K562
ENCODE_series_ID	ENCSR894MMO
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR778WPL
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	HNRNPA0_BGKLV24_29B
Rep2	HNRNPA0_BGKLV24_30B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	59.3
Rep2_qPCR	73.1
Rep1_WB	no clear band
Rep2_WB	no clear band
Antibody Cat#	RN061PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB119UHC
Status	Released
Project	ENCODE3
ID	604

Experiment Information (Status: Released)

	BGKLV24-29	BGKLV24-29	BGKLV24-30	BGKLV24-30
idx	366	0	367	0
TRCN#_or_BGC#	TRCN0000017235	TRCN0000017235	TRCN0000017235	TRCN0000017235
shRNA_or_gRNA_sequence	GCCAAGGTTAAGAAGCTCTTT	GCCAAGGTTAAGAAGCTCTTT	GCCAAGGTTAAGAAGCTCTTT	GCCAAGGTTAAGAAGCTCTTT
PAM
Name	HNRNPA0	HNRNPA0	HNRNPA0	HNRNPA0
Sample_ID	BGKLV24-29	BGKLV24-29	BGKLV24-30	BGKLV24-30
transduction_Date	2/27/2015	2/27/2015	2/27/2015	2/27/2015
days
RBP_name	HNRNPA0	HNRNPA0	HNRNPA0	HNRNPA0
qPCR_result	59.3	59.3	73.1	73.1
Ave_qPCR	66.2	66.2
RT-qPCR_primer-F	ATCGAGCACTTCTCGCAGTT	ATCGAGCACTTCTCGCAGTT
RT-qPCR_primer-R	ATACACGAAGCCGAATCCAC	ATACACGAAGCCGAATCCAC
protein_conc	4141	4141	4237	4237
WB_result	no clear band	79.3	no clear band	78.5
Ave_WB		78.9
WB_DONE_date	7/21/16	4/4/19	wes
MW	34/36kDa
IP			fu's
antibody_Cat#	RN061PW	PA5-57722	RN061PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	17.8234034	0	0	0
Rep2_TPM	19.7003077	0	0	0
Action
Library_start_date	9/2/2015		9/2/2015
repeat_library
Note	x		x
ID	421	423	422	424

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPA0	Product_ID: PA5-57722 Lot_ID: TK2671525A Source: Thermo Fisher Target Name: HNRNPA0-human

Experiment Status

	BGKLV24-29	BGKLV24-30
Sample_ID	BGKLV24-29	BGKLV24-30
Sample Name	HNRNPA0_BGKLV24_29B	HNRNPA0_BGKLV24_30B
Sample Name	HNRNPA0_BGKLV24_29B	HNRNPA0_BGKLV24_30B
RBP	HNRNPA0	HNRNPA0
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	888	889

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-29	BGKLV24-30
Sample #
Sample Name	HNRNPA0-BGKLV24-29B	HNRNPA0-BGKLV24-30B
Sample_Name_Alias	HNRNPA0_BGKLV24_29B	HNRNPA0_BGKLV24_30B
Index Well Position	S05	S06
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/E5.png	DNA_Library_LV24-25-26/set1/F5.png
RIN	9.6	9.9
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E3.png	RNA_Library_LV19-21-24/set2/C3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-29	BGKLV24-30
RBP	HNRNPA0	HNRNPA0
Batch_ID	BGKLV24	BGKLV24
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2576	2577

Sequencing Information

	BGKLV24-29	BGKLV24-30
Sample_ID	BGKLV24-29	BGKLV24-30
Sample Name	HNRNPA0_BGKLV24_29B	HNRNPA0_BGKLV24_30B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	77,777,144	84,007,948
total_aligned_reads	73,985,516	79,702,408
unique_aligned_reads	67,169,012	72,195,918
percent_uniqueAligned	0.86361	0.85939
correlation_replicates	0.994277	0.994277
spikein_reads	231,382	248,300
percent_spikeins	0.00297	0.00296
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1218	1219

Data Submission Information

	BGKLV24-29	BGKLV24-29
ENCODE_alias	brenton-graveley:HNRNPAB_BGKLV24_B	brenton-graveley:HNRNPA0-BGKLV24-K562
ENCODE_accession	ENCSR778WPL	ENCSR894MMO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-29	BGKLV24-29
Sample Name	HNRNPA0_BGKLV24_29B	HNRNPA0_BGKLV24_29B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2993	6747

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
HNRNPA0_BGKLV24_29B_ACAGTG_L001_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1218	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	17472
HNRNPA0_BGKLV24_29B_ACAGTG_L001_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1218	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	17496
HNRNPA0_BGKLV24_29B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1218					GRCh38	V40	HNRNPA0_BGKLV24_29B_ACAGTG_L001_001.R1.fastq.gz,HNRNPA0_BGKLV24_29B_ACAGTG_L001_001.R2.fastq.gz		ENCORE2	17520
HNRNPA0_BGKLV24_29B_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	1218					GRCh38	V40	HNRNPA0_BGKLV24_29B/Aligned.sortedByCoord.out.bam		ENCORE2	17544
HNRNPA0_BGKLV24_29B_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	1218					GRCh38	V40	HNRNPA0_BGKLV24_29B/Aligned.sortedByCoord.out.bam		ENCORE2	17568
HNRNPA0_BGKLV24_29B_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	1218					GRCh38	V40	HNRNPA0_BGKLV24_29B/Aligned.sortedByCoord.out.bam		ENCORE2	17592
HNRNPA0_BGKLV24_29B_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	1218					GRCh38	V40	HNRNPA0_BGKLV24_29B/Aligned.sortedByCoord.out.bam		ENCORE2	17616
HNRNPA0_BGKLV24_29B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1218					GRCh38	V40	HNRNPA0_BGKLV24_29B_ACAGTG_L001_001.R1.fastq.gz,HNRNPA0_BGKLV24_29B_ACAGTG_L001_001.R2.fastq.gz		ENCORE2	17640
HNRNPA0_BGKLV24_30B_GCCAAT_L001_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1219	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	17473
HNRNPA0_BGKLV24_30B_GCCAAT_L001_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1219	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	17497
HNRNPA0_BGKLV24_30B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1219					GRCh38	V40	HNRNPA0_BGKLV24_30B_GCCAAT_L001_001.R1.fastq.gz,HNRNPA0_BGKLV24_30B_GCCAAT_L001_001.R2.fastq.gz		ENCORE2	17521
HNRNPA0_BGKLV24_30B_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	1219					GRCh38	V40	HNRNPA0_BGKLV24_30B/Aligned.sortedByCoord.out.bam		ENCORE2	17545
HNRNPA0_BGKLV24_30B_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	1219					GRCh38	V40	HNRNPA0_BGKLV24_30B/Aligned.sortedByCoord.out.bam		ENCORE2	17569
HNRNPA0_BGKLV24_30B_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	1219					GRCh38	V40	HNRNPA0_BGKLV24_30B/Aligned.sortedByCoord.out.bam		ENCORE2	17593
HNRNPA0_BGKLV24_30B_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	1219					GRCh38	V40	HNRNPA0_BGKLV24_30B/Aligned.sortedByCoord.out.bam		ENCORE2	17617
HNRNPA0_BGKLV24_30B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1219					GRCh38	V40	HNRNPA0_BGKLV24_30B_GCCAAT_L001_001.R1.fastq.gz,HNRNPA0_BGKLV24_30B_GCCAAT_L001_001.R2.fastq.gz		ENCORE2	17641