HNRNPU RNA-Seq in K562

General Information


RBP	HNRNPU
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPU-BGKLV21-K562
ENCODE_series_ID	ENCSR409NTU
Batch_ID	BGKLV21
Pool ID	Pool-160229
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR047IUS
ENCODE_CN_Exp_ID	ENCSR438MDN
Rep1	HNRNPU_BGKLV21-23B
Rep2	HNRNPU_BGKLV21-24B
CN1	NT_BGKLV21-1B
CN2	NT_BGKLV21-2B
Rep1_qPCR	67.7
Rep2_qPCR	50.3
Rep1_WB	67.3
Rep2_WB	73.5
Antibody Cat#	sc-32315/LOT C3012
Antibody Lot#	sc-32315/LOT C3012
Antibody DCC ID	ENCAB502MPG
Status	Released
Project	ENCODE3
ID	596

Experiment Information (Status: Released)

	BGKLV21-23	BGKLV21-24
idx	294	295
TRCN#_or_BGC#	TRCN0000001298	TRCN0000001298
shRNA_or_gRNA_sequence	CAGTGCTTCTTCCCTTACAAT	CAGTGCTTCTTCCCTTACAAT
PAM
Name	HNRNPU	HNRNPU
Sample_ID	BGKLV21-23	BGKLV21-24
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	HNRNPU	HNRNPU
qPCR_result	67.7	50.3
Ave_qPCR	59.0
RT-qPCR_primer-F	GGAGGATTCAATATGCGTGG
RT-qPCR_primer-R	GATAATGCTGACTCCATGGCT
protein_conc	3442	3585
WB_result	67.3	73.5
Ave_WB	70.4	LZ
WB_DONE_date	6/30/2015
MW	91kDa
IP	1MW	1MW
antibody_Cat#	sc-32315/LOT C3012	sc-32315/LOT C3012
Antibody DCC ID	ENCAB502MPG	ENCAB502MPG
submitted_to_DCC_date	8/6/2015
Rep1_TPM	213.700325	0
Rep2_TPM	115.22062	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note	x	x
ID	325	326

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPU	Product_ID: sc-32315 Lot_ID: C3012 Source: Santa Cruz Biotech Target Name: HNRNPU-human

Experiment Status

	BGKLV21-23	BGKLV21-24
Sample_ID	BGKLV21-23	BGKLV21-24
Sample Name	HNRNPU_BGKLV21-23B	HNRNPU_BGKLV21-24B
Sample Name	HNRNPU_BGKLV21-23B	HNRNPU_BGKLV21-24B
RBP	HNRNPU	HNRNPU
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1133	1134

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-23	BGKLV21-24
Sample #
Sample Name	HNRNPU-BGKLV21-23B	HNRNPU-BGKLV21-24B
Sample_Name_Alias	HNRNPU_BGKLV21-23B	HNRNPU_BGKLV21-24B
Index Well Position	S11	S12
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/C8.png	DNA_Library_LV31-21B/set1/D8.png
RIN	7.0	9.4
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C9.png	RNA_Library_LV19-21-24/set1/D9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-23	BGKLV21-24
RBP	HNRNPU	HNRNPU
Batch_ID	BGKLV21	BGKLV21
WB_result	67.300	73.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2830	2831

Sequencing Information

	BGKLV21-23	BGKLV21-24
Sample_ID	BGKLV21-23	BGKLV21-24
Sample Name	HNRNPU_BGKLV21-23B	HNRNPU_BGKLV21-24B
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set21	set21
total_reads	60,233,744	70,461,530
total_aligned_reads	55,978,404	65,079,282
unique_aligned_reads	51,248,420	59,515,562
percent_uniqueAligned	0.85083	0.84465
correlation_replicates	0.998718	0.998718
spikein_reads	285,422	344,820
percent_spikeins	0.00474	0.00489
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1479	1480

Data Submission Information

	BGKLV21-23	BGKLV21-23
ENCODE_alias	brenton-graveley:HNRNPU_BGKLV21-B	brenton-graveley:HNRNPU-BGKLV21-K562
ENCODE_accession	ENCSR047IUS	ENCSR409NTU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-23	BGKLV21-23
Sample Name	HNRNPU_BGKLV21-23B	HNRNPU_BGKLV21-23B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3099	6770

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
HNRNPU_BGKLV21-23B_GGCTAC_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1479	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15934
HNRNPU_BGKLV21-23B_GGCTAC_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1479	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	15978
HNRNPU_BGKLV21-23B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1479					GRCh38	V40	HNRNPU_BGKLV21-23B_GGCTAC_L008_001.R1.fastq.gz,HNRNPU_BGKLV21-23B_GGCTAC_L008_001.R2.fastq.gz		ENCORE2	16022
HNRNPU_BGKLV21-23B_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	1479					GRCh38	V40	HNRNPU_BGKLV21-23B/Aligned.sortedByCoord.out.bam		ENCORE2	16066
HNRNPU_BGKLV21-23B_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	1479					GRCh38	V40	HNRNPU_BGKLV21-23B/Aligned.sortedByCoord.out.bam		ENCORE2	16110
HNRNPU_BGKLV21-23B_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	1479					GRCh38	V40	HNRNPU_BGKLV21-23B/Aligned.sortedByCoord.out.bam		ENCORE2	16154
HNRNPU_BGKLV21-23B_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	1479					GRCh38	V40	HNRNPU_BGKLV21-23B/Aligned.sortedByCoord.out.bam		ENCORE2	16198
HNRNPU_BGKLV21-23B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1479					GRCh38	V40	HNRNPU_BGKLV21-23B_GGCTAC_L008_001.R1.fastq.gz,HNRNPU_BGKLV21-23B_GGCTAC_L008_001.R2.fastq.gz		ENCORE2	16242
HNRNPU_BGKLV21-24B_CTTGTA_L008_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1480	HiSeq2000	100	paired-ended	1				NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE3	15935
HNRNPU_BGKLV21-24B_CTTGTA_L008_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1480	HiSeq2000	100	paired-ended	2				NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE3	15979
HNRNPU_BGKLV21-24B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1480					GRCh38	V40	HNRNPU_BGKLV21-24B_CTTGTA_L008_001.R1.fastq.gz,HNRNPU_BGKLV21-24B_CTTGTA_L008_001.R2.fastq.gz		ENCORE2	16023
HNRNPU_BGKLV21-24B_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	1480					GRCh38	V40	HNRNPU_BGKLV21-24B/Aligned.sortedByCoord.out.bam		ENCORE2	16067
HNRNPU_BGKLV21-24B_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	1480					GRCh38	V40	HNRNPU_BGKLV21-24B/Aligned.sortedByCoord.out.bam		ENCORE2	16111
HNRNPU_BGKLV21-24B_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	1480					GRCh38	V40	HNRNPU_BGKLV21-24B/Aligned.sortedByCoord.out.bam		ENCORE2	16155
HNRNPU_BGKLV21-24B_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	1480					GRCh38	V40	HNRNPU_BGKLV21-24B/Aligned.sortedByCoord.out.bam		ENCORE2	16199
HNRNPU_BGKLV21-24B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1480					GRCh38	V40	HNRNPU_BGKLV21-24B_CTTGTA_L008_001.R1.fastq.gz,HNRNPU_BGKLV21-24B_CTTGTA_L008_001.R2.fastq.gz		ENCORE2	16243