U2AF1 RNA-Seq in K562

General Information


RBP	U2AF1
Cell_Line	K562
Method	shRNA
Exp_Name	U2AF1-BGKLV08-K562
ENCODE_series_ID	ENCSR171NIH
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR342EDG
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	U2AF1-LV08-61
Rep2	U2AF1-LV08-62
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	82.6
Rep2_qPCR	84.3
Rep1_WB	52.7
Rep2_WB	63.7
Antibody Cat#	A302-079A
Antibody Lot#	A302-079A
Antibody DCC ID	ENCAB298WVV
Status	Released
Project	ENCODE3
ID	304

Experiment Information (Status: Released)

	BGKLV08-61	BGKLV08-62
idx	66	67
TRCN#_or_BGC#	TRCN0000001155	TRCN0000001155
shRNA_or_gRNA_sequence	GAAAGTGTTGTAGTTGATTGA	GAAAGTGTTGTAGTTGATTGA
PAM
Name	U2AF1	U2AF1
Sample_ID	BGKLV08-61	BGKLV08-62
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	U2AF1	U2AF1
qPCR_result	82.6	84.3
Ave_qPCR	83.4
RT-qPCR_primer-F	GTGACAACCTGGGAGACCAC
RT-qPCR_primer-R	GGTTATTCAAGTCAATCACAGCC
protein_conc	2653	2962
WB_result	52.7	63.7
Ave_WB	58.2
WB_DONE_date	8/19/2015
MW	28kDa
IP	1	1
antibody_Cat#	A302-079A	A302-079A
Antibody DCC ID	ENCAB298WVV	ENCAB298WVV
submitted_to_DCC_date	12/7/2015
Rep1_TPM	33.6905192	0
Rep2_TPM	24.8050299	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note		5
ID	71	72

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
U2AF1	Product_ID: A302-079A Lot_ID: 1 Source: Bethyl Labs Target Name: U2AF1-human

Experiment Status

	BGKLV08-61	BGKLV08-62
Sample_ID	BGKLV08-61	BGKLV08-62
Sample Name	U2AF1-LV08-61	U2AF1-LV08-62
Sample Name	U2AF1-LV08-61	U2AF1-LV08-62
RBP	U2AF1	U2AF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	320	321

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-61	BGKLV08-62
Sample #
Sample Name	U2AF1-BGKLV08-61	U2AF1-BGKLV08-62
Sample_Name_Alias	U2AF1-LV08-61	U2AF1-LV08-62
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set5/G1.png	DNA_Library_LV08/set5/H1.png
RIN	9.3	9.0
libSample_RNA_Well	RNA_Library_LV08/set4/G1.png	RNA_Library_LV08/set4/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-61	BGKLV08-62
RBP	U2AF1	U2AF1
Batch_ID	BGKLV08	BGKLV08
WB_result	52.700	63.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1940	1941

Sequencing Information

	BGKLV08-61	BGKLV08-62
Sample_ID	BGKLV08-61	BGKLV08-62
Sample Name	U2AF1-LV08-61	U2AF1-LV08-62
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	47,770,000	48,370,000
total_aligned_reads	42,401,054	42,911,212
unique_aligned_reads	38,947,356	39,428,758
percent_uniqueAligned	0.81531	0.81515
correlation_replicates	0.998354	0.998354
spikein_reads	349,246	295,030
percent_spikeins	0.00731	0.00610
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	640	641

Data Submission Information

	BGKLV08-61	BGKLV08-61
ENCODE_alias	brenton-graveley:U2AF1-LV08	brenton-graveley:U2AF1-BGKLV08-K562
ENCODE_accession	ENCSR342EDG	ENCSR171NIH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-61	BGKLV08-61
Sample Name	U2AF1-LV08-61	U2AF1-LV08-61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2709	7022

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
U2AF1-LV08-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	640					GRCh38	V40	U2AF1-LV08-61_ACAGTG_L008_R1_001.fastq.gz,U2AF1-LV08-61_ACAGTG_L008_R2_001.fastq.gz		ENCORE2	12027
U2AF1-LV08-61_ACAGTG_L008_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	640	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12083
U2AF1-LV08-61_ACAGTG_L008_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	640	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12139
U2AF1-LV08-61_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	640					GRCh38	V40	U2AF1-LV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	12195
U2AF1-LV08-61_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	640					GRCh38	V40	U2AF1-LV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	12251
U2AF1-LV08-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	640					GRCh38	V40	U2AF1-LV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	12307
U2AF1-LV08-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	640					GRCh38	V40	U2AF1-LV08-61/Aligned.sortedByCoord.out.bam		ENCORE2	12363
U2AF1-LV08-61_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	640					GRCh38	V40	U2AF1-LV08-61_ACAGTG_L008_R1_001.fastq.gz,U2AF1-LV08-61_ACAGTG_L008_R2_001.fastq.gz		ENCORE2	13362
U2AF1-LV08-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	641					GRCh38	V40	U2AF1-LV08-62_GCCAAT_L008_R1_001.fastq.gz,U2AF1-LV08-62_GCCAAT_L008_R2_001.fastq.gz		ENCORE2	12028
U2AF1-LV08-62_GCCAAT_L008_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	641	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12084
U2AF1-LV08-62_GCCAAT_L008_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	641	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12140
U2AF1-LV08-62_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	641					GRCh38	V40	U2AF1-LV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	12196
U2AF1-LV08-62_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	641					GRCh38	V40	U2AF1-LV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	12252
U2AF1-LV08-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	641					GRCh38	V40	U2AF1-LV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	12308
U2AF1-LV08-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	641					GRCh38	V40	U2AF1-LV08-62/Aligned.sortedByCoord.out.bam		ENCORE2	12364
U2AF1-LV08-62_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	641					GRCh38	V40	U2AF1-LV08-62_GCCAAT_L008_R1_001.fastq.gz,U2AF1-LV08-62_GCCAAT_L008_R2_001.fastq.gz		ENCORE2	13363