HNRNPA1 RNA-Seq in K562

General Information


RBP	HNRNPA1
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPA1-BGKLV21-K562
ENCODE_series_ID	ENCSR596JUF
Batch_ID	BGKLV21
Pool ID	Pool-160229
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR048BWH
ENCODE_CN_Exp_ID	ENCSR438MDN
Rep1	HNRNPA1_BGKLV21-17B
Rep2	HNRNPA1_BGKLV21-18B
CN1	NT_BGKLV21-1B
CN2	NT_BGKLV21-2B
Rep1_qPCR	91.0
Rep2_qPCR	90.6
Rep1_WB	69.5
Rep2_WB	71.2
Antibody Cat#	sc-32301/LOT I2413
Antibody Lot#	sc-32301/LOT I2413
Antibody DCC ID	ENCAB603WLW
Status	Released
Project	ENCODE3
ID	595

Experiment Information (Status: Released)

	BGKLV21-17	BGKLV21-17	BGKLV21-17	BGKLV21-18	BGKLV21-18	BGKLV21-18
idx	288	288	288	289	289	289
TRCN#_or_BGC#	TRCN0000006583	TRCN0000006583	TRCN0000006583	TRCN0000006583	TRCN0000006583	TRCN0000006583
shRNA_or_gRNA_sequence	GCCACAACTGTGAAGTTAGAA	GCCACAACTGTGAAGTTAGAA	GCCACAACTGTGAAGTTAGAA	GCCACAACTGTGAAGTTAGAA	GCCACAACTGTGAAGTTAGAA	GCCACAACTGTGAAGTTAGAA
PAM
Name	HNRNPA1	HNRNPA1	HNRNPA1	HNRNPA1	HNRNPA1	HNRNPA1
Sample_ID	BGKLV21-17	BGKLV21-17	BGKLV21-17	BGKLV21-18	BGKLV21-18	BGKLV21-18
transduction_Date	10/9/2014	10/9/2014	10/9/2014	10/9/2014	10/9/2014	10/9/2014
days
RBP_name	HNRNPA1	HNRNPA1	HNRNPA1	HNRNPA1	HNRNPA1	HNRNPA1
qPCR_result	91.0	91.0	91.0	90.6	90.6	90.6
Ave_qPCR	90.8	90.8	90.8
RT-qPCR_primer-F	CCTTTGACGACCATGACTCC	CCTTTGACGACCATGACTCC	CCTTTGACGACCATGACTCC
RT-qPCR_primer-R	TCTTGCTTTGACAGGGCTTT	TCTTGCTTTGACAGGGCTTT	TCTTGCTTTGACAGGGCTTT
protein_conc	4120	4120	4120	3500	3500	3500
WB_result	69.5	64.6	98.0	71.2	64.7	95.5
Ave_WB	70.4	64.7	96.7
WB_DONE_date	7/16/2015	9/16/2019	6/27/2023
MW	39kDa	39kDa	39kDa
IP	1			1
antibody_Cat#	sc-32301/LOT I2413	MA1-26736	8443S	sc-32301/LOT I2413	Mouse / IgG2b	LOT#4
Antibody DCC ID	ENCAB603WLW			ENCAB603WLW
submitted_to_DCC_date	8/6/2015	1/8/2024
Rep1_TPM	1018.39683	0	0	0	0	0
Rep2_TPM	962.872414	0	0	0	0	0
Action
Library_start_date	2/4/2016			2/4/2016
repeat_library
Note	x			x
ID	313	315	317	314	316	318

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPA1	Product_ID: sc-32301 Lot_ID: I2413 Source: Santa Cruz Biotech Target Name: HNRNPA1-human
HNRNPA1	Product_ID: MA1-26736 Lot_ID: TL2692993B Source: Thermo Fisher Target Name: HNRNPA1-human
HNRNPA1	Product_ID: 8443S Lot_ID: 4 Source: Cell Signaling Technology Target Name: HNRNPA1-human

Experiment Status

	BGKLV21-17	BGKLV21-18
Sample_ID	BGKLV21-17	BGKLV21-18
Sample Name	HNRNPA1_BGKLV21-17B	HNRNPA1_BGKLV21-18B
Sample Name	HNRNPA1_BGKLV21-17B	HNRNPA1_BGKLV21-18B
RBP	HNRNPA1	HNRNPA1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1131	1132

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-17	BGKLV21-18
Sample #
Sample Name	HNRNPA1-BGKLV21-17B	HNRNPA1-BGKLV21-18B
Sample_Name_Alias	HNRNPA1_BGKLV21-17B	HNRNPA1_BGKLV21-18B
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/A8.png	DNA_Library_LV31-21B/set1/B8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E8.png	RNA_Library_LV19-21-24/set1/F8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-17	BGKLV21-18
RBP	HNRNPA1	HNRNPA1
Batch_ID	BGKLV21	BGKLV21
WB_result	69.500	71.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2828	2829

Sequencing Information

	BGKLV21-17	BGKLV21-18
Sample_ID	BGKLV21-17	BGKLV21-18
Sample Name	HNRNPA1_BGKLV21-17B	HNRNPA1_BGKLV21-18B
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set21	set21
total_reads	54,444,194	59,214,214
total_aligned_reads	50,479,074	54,304,032
unique_aligned_reads	45,821,568	49,439,418
percent_uniqueAligned	0.84162	0.83492
correlation_replicates	0.994124	0.994124
spikein_reads	354,228	348,452
percent_spikeins	0.00651	0.00588
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1477	1478

Data Submission Information

	BGKLV21-17	BGKLV21-17
ENCODE_alias	brenton-graveley:HNRNPA1_BGKLV21-B	brenton-graveley:HNRNPA1-BGKLV21-K562
ENCODE_accession	ENCSR048BWH	ENCSR596JUF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-17	BGKLV21-17
Sample Name	HNRNPA1_BGKLV21-17B	HNRNPA1_BGKLV21-17B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3098	6749

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
HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1477	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15928
HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1477	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	15972
HNRNPA1_BGKLV21-17B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1477					GRCh38	V40	HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R2.fastq.gz		ENCORE2	16016
HNRNPA1_BGKLV21-17B_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1477					GRCh38	V40	HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam		ENCORE2	16060
HNRNPA1_BGKLV21-17B_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1477					GRCh38	V40	HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam		ENCORE2	16104
HNRNPA1_BGKLV21-17B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1477					GRCh38	V40	HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam		ENCORE2	16148
HNRNPA1_BGKLV21-17B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1477					GRCh38	V40	HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam		ENCORE2	16192
HNRNPA1_BGKLV21-17B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1477					GRCh38	V40	HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R2.fastq.gz		ENCORE2	16236
HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1478	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15929
HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1478	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	15973
HNRNPA1_BGKLV21-18B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1478					GRCh38	V40	HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R2.fastq.gz		ENCORE2	16017
HNRNPA1_BGKLV21-18B_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1478					GRCh38	V40	HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam		ENCORE2	16061
HNRNPA1_BGKLV21-18B_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1478					GRCh38	V40	HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam		ENCORE2	16105
HNRNPA1_BGKLV21-18B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1478					GRCh38	V40	HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam		ENCORE2	16149
HNRNPA1_BGKLV21-18B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1478					GRCh38	V40	HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam		ENCORE2	16193
HNRNPA1_BGKLV21-18B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1478					GRCh38	V40	HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R2.fastq.gz		ENCORE2	16237