U2AF1 RNA-Seq in HepG2

General Information


RBP	U2AF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	U2AF1-BGHLV30-HepG2
ENCODE_series_ID	ENCSR054NQG
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR372UWV
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	U2AF1_BGHLV30-55
Rep2	U2AF1_BGHLV30-56
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	63.3
Rep2_qPCR	54.9
Rep1_WB	72.5
Rep2_WB	76.1
Antibody Cat#	A302-079A
Antibody Lot#	A302-079A
Antibody DCC ID	ENCAB298WVV
Status	Released
Project	ENCODE3
ID	689

Experiment Information (Status: Released)

	BGHLV30-55	BGHLV30-56
idx	743	744
TRCN#_or_BGC#	TRCN0000001158	TRCN0000001158
shRNA_or_gRNA_sequence	GAGATGCAGGAACACTATGAT	GAGATGCAGGAACACTATGAT
PAM
Name	U2AF1	U2AF1
Sample_ID	BGHLV30-55	BGHLV30-56
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	U2AF1	U2AF1
qPCR_result	63.3	54.9
Ave_qPCR	59.1
RT-qPCR_primer-F	GTGACAACCTGGGAGACCAC
RT-qPCR_primer-R	GGTTATTCAAGTCAATCACAGCC
protein_conc	3705	3203
WB_result	72.5	76.1
Ave_WB	74.3
WB_DONE_date	9/16/2015
MW	28kDa
IP	1	1
antibody_Cat#	A302-079A	A302-079A
Antibody DCC ID	ENCAB298WVV	ENCAB298WVV
submitted_to_DCC_date	3/8/2016
Rep1_TPM	9.3	0
Rep2_TPM	8	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2832	2833

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

	BGHLV30-55	BGHLV30-56
Sample_ID	BGHLV30-55	BGHLV30-56
Sample Name	U2AF1_BGHLV30-55	U2AF1_BGHLV30-56
Sample Name	U2AF1_BGHLV30-55	U2AF1_BGHLV30-56
RBP	U2AF1	U2AF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1070	1071

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-55	BGHLV30-56
Sample #
Sample Name	U2AF1-BGHLV30-55	U2AF1-BGHLV30-56
Sample_Name_Alias	U2AF1_BGHLV30-55	U2AF1_BGHLV30-56
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E12.png	DNA_Library_LV28-29-30/set1/F12.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G7.png	RNA_Library_LV29-30-31-32/set1/H7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-55	BGHLV30-56
RBP	U2AF1	U2AF1
Batch_ID	BGHLV30	BGHLV30
WB_result	72.500	76.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2762	2763

Sequencing Information

	BGHLV30-55	BGHLV30-56
Sample_ID	BGHLV30-55	BGHLV30-56
Sample Name	U2AF1_BGHLV30-55	U2AF1_BGHLV30-56
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	113,272,002	68,958,884
total_aligned_reads	102,651,824	61,991,018
unique_aligned_reads	96,602,368	58,412,660
percent_uniqueAligned	0.85284	0.84707
correlation_replicates	0.998214	0.998214
spikein_reads	346,818	168,146
percent_spikeins	0.00306	0.00244
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1411	1412

Data Submission Information

	BGHLV30-55	BGHLV30-55
ENCODE_alias	brenton-graveley:U2AF1_BGHLV30	brenton-graveley:U2AF1-BGHLV30-HepG2
ENCODE_accession	ENCSR372UWV	ENCSR054NQG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-55	BGHLV30-55
Sample Name	U2AF1_BGHLV30-55	U2AF1_BGHLV30-55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3084	7021

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_BGHLV30-55_CGTACG_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1411	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20730
U2AF1_BGHLV30-55_CGTACG_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1411	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20764
U2AF1_BGHLV30-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1411					GRCh38	V40	U2AF1_BGHLV30-55_CGTACG_L004_001.R1.fastq.gz,U2AF1_BGHLV30-55_CGTACG_L004_001.R2.fastq.gz		ENCORE2	20798
U2AF1_BGHLV30-55_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1411					GRCh38	V40	U2AF1_BGHLV30-55/Aligned.sortedByCoord.out.bam		ENCORE2	20832
U2AF1_BGHLV30-55_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1411					GRCh38	V40	U2AF1_BGHLV30-55/Aligned.sortedByCoord.out.bam		ENCORE2	20866
U2AF1_BGHLV30-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1411					GRCh38	V40	U2AF1_BGHLV30-55/Aligned.sortedByCoord.out.bam		ENCORE2	20900
U2AF1_BGHLV30-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1411					GRCh38	V40	U2AF1_BGHLV30-55/Aligned.sortedByCoord.out.bam		ENCORE2	20934
U2AF1_BGHLV30-55_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1411					GRCh38	V40	U2AF1_BGHLV30-55_CGTACG_L004_001.R1.fastq.gz,U2AF1_BGHLV30-55_CGTACG_L004_001.R2.fastq.gz		ENCORE2	20968
U2AF1_BGHLV30-56_GAGTGG_L004_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1412	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20731
U2AF1_BGHLV30-56_GAGTGG_L004_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1412	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20765
U2AF1_BGHLV30-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1412					GRCh38	V40	U2AF1_BGHLV30-56_GAGTGG_L004_001.R1.fastq.gz,U2AF1_BGHLV30-56_GAGTGG_L004_001.R2.fastq.gz		ENCORE2	20799
U2AF1_BGHLV30-56_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1412					GRCh38	V40	U2AF1_BGHLV30-56/Aligned.sortedByCoord.out.bam		ENCORE2	20833
U2AF1_BGHLV30-56_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1412					GRCh38	V40	U2AF1_BGHLV30-56/Aligned.sortedByCoord.out.bam		ENCORE2	20867
U2AF1_BGHLV30-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1412					GRCh38	V40	U2AF1_BGHLV30-56/Aligned.sortedByCoord.out.bam		ENCORE2	20901
U2AF1_BGHLV30-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1412					GRCh38	V40	U2AF1_BGHLV30-56/Aligned.sortedByCoord.out.bam		ENCORE2	20935
U2AF1_BGHLV30-56_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1412					GRCh38	V40	U2AF1_BGHLV30-56_GAGTGG_L004_001.R1.fastq.gz,U2AF1_BGHLV30-56_GAGTGG_L004_001.R2.fastq.gz		ENCORE2	20969