U2AF2 RNA-Seq in HepG2

General Information


RBP	U2AF2
Cell_Line	HepG2
Method	shRNA
Exp_Name	U2AF2-BGHLV26-HepG2
ENCODE_series_ID	ENCSR914FDC
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR426UUG
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	U2AF2_BGHLV26_63
Rep2	U2AF2_BGHLV26_64
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	52.4
Rep2_qPCR	53.2
Rep1_WB	90.7
Rep2_WB	93.5
Antibody Cat#	A303-665A
Antibody Lot#	A303-665A
Antibody DCC ID	ENCAB511TCT
Status	Released
Project	ENCODE3
ID	638

Experiment Information (Status: Released)

	BGHLV26-63	BGHLV26-64
idx	619	620
TRCN#_or_BGC#	TRCN0000001162	TRCN0000001162
shRNA_or_gRNA_sequence	CGACGAGGAGTATGAGGAGAT	CGACGAGGAGTATGAGGAGAT
PAM
Name	U2AF2	U2AF2
Sample_ID	BGHLV26-63	BGHLV26-64
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	U2AF2	U2AF2
qPCR_result	52.4	53.2
Ave_qPCR	52.8
RT-qPCR_primer-F	GGCTTGTCAAGTCCATCGAG
RT-qPCR_primer-R	TGGCAGTCAAACACAGAGGT
protein_conc	3540	4028
WB_result	90.7	93.5
Ave_WB	92.1
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	11/16/17
Rep1_TPM	49.9	0
Rep2_TPM	60	0
Action
Library_start_date	9/8/2015	9/8/2015
repeat_library
Note
ID	2706	2707

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

	BGHLV26-63	BGHLV26-64
Sample_ID	BGHLV26-63	BGHLV26-64
Sample Name	U2AF2_BGHLV26_63	U2AF2_BGHLV26_64
Sample Name	U2AF2_BGHLV26_63	U2AF2_BGHLV26_64
RBP	U2AF2	U2AF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	960	961

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-63	BGHLV26-64
Sample #
Sample Name	U2AF2-BGHLV26-63	U2AF2-BGHLV26-64
Sample_Name_Alias	U2AF2_BGHLV26_63	U2AF2_BGHLV26_64
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/E10.png	DNA_Library_LV24-25-26/set1/F10.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/G3.png	RNA_Library_LV26-27-28-29/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-63	BGHLV26-64
RBP	U2AF2	U2AF2
Batch_ID	BGHLV26	BGHLV26
WB_result	90.700	93.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2648	2649

Sequencing Information

	BGHLV26-63	BGHLV26-64
Sample_ID	BGHLV26-63	BGHLV26-64
Sample Name	U2AF2_BGHLV26_63	U2AF2_BGHLV26_64
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	111,285,404	92,117,488
total_aligned_reads	97,479,584	73,549,828
unique_aligned_reads	90,798,150	68,339,960
percent_uniqueAligned	0.81590	0.74188
correlation_replicates	0.998171	0.998171
spikein_reads	233,560	186,040
percent_spikeins	0.00210	0.00202
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1290	1291

Data Submission Information

	BGHLV26-63	BGHLV26-63
ENCODE_alias	brenton-graveley:U2AF2_BGHLV26	brenton-graveley:U2AF2-BGHLV26-HepG2
ENCODE_accession	ENCSR426UUG	ENCSR914FDC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-63	BGHLV26-63
Sample Name	U2AF2_BGHLV26_63	U2AF2_BGHLV26_63
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3027	7024

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_BGHLV26_63_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1290	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19834
U2AF2_BGHLV26_63_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1290	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19856
U2AF2_BGHLV26_63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1290					GRCh38	V40	U2AF2_BGHLV26_63_1.fastq.gz,U2AF2_BGHLV26_63_2.fastq.gz		ENCORE2	19878
U2AF2_BGHLV26_63_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1290					GRCh38	V40	U2AF2_BGHLV26_63/Aligned.sortedByCoord.out.bam		ENCORE2	19900
U2AF2_BGHLV26_63_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1290					GRCh38	V40	U2AF2_BGHLV26_63/Aligned.sortedByCoord.out.bam		ENCORE2	19922
U2AF2_BGHLV26_63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1290					GRCh38	V40	U2AF2_BGHLV26_63/Aligned.sortedByCoord.out.bam		ENCORE2	19944
U2AF2_BGHLV26_63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1290					GRCh38	V40	U2AF2_BGHLV26_63/Aligned.sortedByCoord.out.bam		ENCORE2	19966
U2AF2_BGHLV26_63_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1290					GRCh38	V40	U2AF2_BGHLV26_63_1.fastq.gz,U2AF2_BGHLV26_63_2.fastq.gz		ENCORE2	20674
U2AF2_BGHLV26_64_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1291	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19835
U2AF2_BGHLV26_64_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1291	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19857
U2AF2_BGHLV26_64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1291					GRCh38	V40	U2AF2_BGHLV26_64_1.fastq.gz,U2AF2_BGHLV26_64_2.fastq.gz		ENCORE2	19879
U2AF2_BGHLV26_64_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1291					GRCh38	V40	U2AF2_BGHLV26_64/Aligned.sortedByCoord.out.bam		ENCORE2	19901
U2AF2_BGHLV26_64_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1291					GRCh38	V40	U2AF2_BGHLV26_64/Aligned.sortedByCoord.out.bam		ENCORE2	19923
U2AF2_BGHLV26_64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1291					GRCh38	V40	U2AF2_BGHLV26_64/Aligned.sortedByCoord.out.bam		ENCORE2	19945
U2AF2_BGHLV26_64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1291					GRCh38	V40	U2AF2_BGHLV26_64/Aligned.sortedByCoord.out.bam		ENCORE2	19967
U2AF2_BGHLV26_64_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1291					GRCh38	V40	U2AF2_BGHLV26_64_1.fastq.gz,U2AF2_BGHLV26_64_2.fastq.gz		ENCORE2	20675