U2AF2 RNA-Seq in HepG2

General Information


RBP	U2AF2
Cell_Line	HepG2
Method	shRNA
Exp_Name	U2AF2-BGHLV14-HepG2
ENCODE_series_ID	ENCSR892NHE
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR622MCX
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	U2AF2_BGHLV14-65
Rep2	U2AF2_BGHLV14-66
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	46.9
Rep2_qPCR	51.3
Rep1_WB	77.8
Rep2_WB	63.4
Antibody Cat#	A303-665A
Antibody Lot#	A303-665A
Antibody DCC ID	ENCAB511TCT
Status	Archived
Project	ENCODE3
ID	410

Experiment Information (Status: Released)

	BGHLV14-65	BGHLV14-66
idx	161	162
TRCN#_or_BGC#	TRCN0000001162	TRCN0000001162
shRNA_or_gRNA_sequence	CGACGAGGAGTATGAGGAGAT	CGACGAGGAGTATGAGGAGAT
PAM
Name	U2AF2	U2AF2
Sample_ID	BGHLV14-65	BGHLV14-66
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	U2AF2	U2AF2
qPCR_result	46.9	51.3
Ave_qPCR	49.1
RT-qPCR_primer-F	GGCTTGTCAAGTCCATCGAG
RT-qPCR_primer-R	TGGCAGTCAAACACAGAGGT
protein_conc	3423	3142
WB_result	77.8	63.4
Ave_WB	70.6
WB_DONE_date	7/20/2015
MW	54kDa
IP	1	1
antibody_Cat#	A303-665A	A303-665A
Antibody DCC ID	ENCAB511TCT	ENCAB511TCT
submitted_to_DCC_date	8/6/2015
Rep1_TPM	49.9	0
Rep2_TPM	60	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2224	2225

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
U2AF2	Product_ID: A303-665A Lot_ID: 1 Source: Bethyl Labs Target Name: U2AF2-human

Experiment Status

	BGHLV14-65	BGHLV14-66
Sample_ID	BGHLV14-65	BGHLV14-66
Sample Name	U2AF2_BGHLV14-65	U2AF2_BGHLV14-66
Sample Name	U2AF2_BGHLV14-65	U2AF2_BGHLV14-66
RBP	U2AF2	U2AF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	544	545

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-65	BGHLV14-66
Sample #
Sample Name	U2AF2-BGHLV14-65	U2AF2-BGHLV14-66
Sample_Name_Alias	U2AF2_BGHLV14-65	U2AF2_BGHLV14-66
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set2/G2.png	DNA_Library_LV13-14/set2/H2.png
RIN	9.5	9.3
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G10.png	RNA_Library_LV13-14-16/set1/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-65	BGHLV14-66
RBP	U2AF2	U2AF2
Batch_ID	BGHLV14	BGHLV14
WB_result	77.800	63.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2228	2229

Sequencing Information

	BGHLV14-65	BGHLV14-66
Sample_ID	BGHLV14-65	BGHLV14-66
Sample Name	U2AF2_BGHLV14-65	U2AF2_BGHLV14-66
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	51,460,000	48,700,000
total_aligned_reads	47,196,482	45,413,014
unique_aligned_reads	44,550,140	42,882,830
percent_uniqueAligned	0.86572	0.88055
correlation_replicates	0.996257	0.996257
spikein_reads	190,346	235,784
percent_spikeins	0.00370	0.00484
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	870	871

Data Submission Information

	BGHLV14-65	BGHLV14-65
ENCODE_alias	brenton-graveley:U2AF2_BGHLV14	brenton-graveley:U2AF2-BGHLV14-HepG2
ENCODE_accession	ENCSR622MCX	ENCSR892NHE
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-65	BGHLV14-65
Sample Name	U2AF2_BGHLV14-65	U2AF2_BGHLV14-65
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2821	7023

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
U2AF2_BGHLV14-65_AGTCAA_L007_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	870	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13836
U2AF2_BGHLV14-65_AGTCAA_L007_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	870	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13898
U2AF2_BGHLV14-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	870					GRCh38	V40	U2AF2_BGHLV14-65_AGTCAA_L007_R1_001.fastq.gz,U2AF2_BGHLV14-65_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	13960
U2AF2_BGHLV14-65_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	870					GRCh38	V40	U2AF2_BGHLV14-65/Aligned.sortedByCoord.out.bam		ENCORE2	14022
U2AF2_BGHLV14-65_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	870					GRCh38	V40	U2AF2_BGHLV14-65/Aligned.sortedByCoord.out.bam		ENCORE2	14084
U2AF2_BGHLV14-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	870					GRCh38	V40	U2AF2_BGHLV14-65/Aligned.sortedByCoord.out.bam		ENCORE2	14146
U2AF2_BGHLV14-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	870					GRCh38	V40	U2AF2_BGHLV14-65/Aligned.sortedByCoord.out.bam		ENCORE2	14208
U2AF2_BGHLV14-65_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	870					GRCh38	V40	U2AF2_BGHLV14-65_AGTCAA_L007_R1_001.fastq.gz,U2AF2_BGHLV14-65_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	14270
U2AF2_BGHLV14-66_AGTTCC_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	871	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13837
U2AF2_BGHLV14-66_AGTTCC_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	871	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13899
U2AF2_BGHLV14-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	871					GRCh38	V40	U2AF2_BGHLV14-66_AGTTCC_L008_R1_001.fastq.gz,U2AF2_BGHLV14-66_AGTTCC_L008_R2_001.fastq.gz		ENCORE2	13961
U2AF2_BGHLV14-66_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	871					GRCh38	V40	U2AF2_BGHLV14-66/Aligned.sortedByCoord.out.bam		ENCORE2	14023
U2AF2_BGHLV14-66_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	871					GRCh38	V40	U2AF2_BGHLV14-66/Aligned.sortedByCoord.out.bam		ENCORE2	14085
U2AF2_BGHLV14-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	871					GRCh38	V40	U2AF2_BGHLV14-66/Aligned.sortedByCoord.out.bam		ENCORE2	14147
U2AF2_BGHLV14-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	871					GRCh38	V40	U2AF2_BGHLV14-66/Aligned.sortedByCoord.out.bam		ENCORE2	14209
U2AF2_BGHLV14-66_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	871					GRCh38	V40	U2AF2_BGHLV14-66_AGTTCC_L008_R1_001.fastq.gz,U2AF2_BGHLV14-66_AGTTCC_L008_R2_001.fastq.gz		ENCORE2	14271