UBE2L3 RNA-Seq in HepG2

General Information


RBP	UBE2L3
Cell_Line	HepG2
Method	shRNA
Exp_Name	UBE2L3-BGHLV23-HepG2
ENCODE_series_ID	ENCSR561ONH
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR424JSU
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	UBE2L3-BGHLV23-57
Rep2	UBE2L3-BGHLV23-58
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	90.2
Rep2_qPCR	86.9
Rep1_WB	76.6
Rep2_WB	85.6
Antibody Cat#	A300-737A
Antibody Lot#	A300-737A
Antibody DCC ID	ENCAB492XKE
Status	Released
Project	ENCODE3
ID	554

Experiment Information (Status: Released)

	BGHLV23-57	BGHLV23-58
idx	549	550
TRCN#_or_BGC#	TRCN0000007209	TRCN0000007209
shRNA_or_gRNA_sequence	CCAGCAGAGTACCCATTCAAA	CCAGCAGAGTACCCATTCAAA
PAM
Name	UBE2L3_09	UBE2L3_09
Sample_ID	BGHLV23-57	BGHLV23-58
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	UBE2L3	UBE2L3
qPCR_result	90.2	86.9
Ave_qPCR	88.5
RT-qPCR_primer-F	ttagtgccgaaaactggaag
RT-qPCR_primer-R	ggggtcattcaccagtgcta
protein_conc	5387	6017
WB_result	76.6	85.6
Ave_WB	81.1
WB_DONE_date	5/14/2015
MW	18kDa
IP	1	1
antibody_Cat#	A300-737A	A300-737A
Antibody DCC ID	ENCAB492XKE	ENCAB492XKE
submitted_to_DCC_date	8/6/2015
Rep1_TPM	8.3	0
Rep2_TPM	8.4	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2630	2631

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UBE2L3	Product_ID: A300-737A Lot_ID: 1 Source: Bethyl Labs Target Name: UBE2L3-human

Experiment Status

	BGHLV23-57	BGHLV23-58
Sample_ID	BGHLV23-57	BGHLV23-58
Sample Name	UBE2L3-BGHLV23-57	UBE2L3-BGHLV23-58
Sample Name	UBE2L3-BGHLV23-57	UBE2L3-BGHLV23-58
RBP	UBE2L3	UBE2L3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	846	847

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-57	BGHLV23-58
Sample #
Sample Name	UBE2L3-BGHLV23-57	UBE2L3-BGHLV23-58
Sample_Name_Alias	UBE2L3-BGHLV23-57	UBE2L3-BGHLV23-58
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set2/E2.png	DNA_Library_LV20-22-23/set1/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G8.png	RNA_Library_LV22-23-25/set1/H8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-57	BGHLV23-58
RBP	UBE2L3	UBE2L3
Batch_ID	BGHLV23	BGHLV23
WB_result	76.600	85.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2534	2535

Sequencing Information

	BGHLV23-57	BGHLV23-58
Sample_ID	BGHLV23-57	BGHLV23-58
Sample Name	UBE2L3-BGHLV23-57	UBE2L3-BGHLV23-58
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	52,090,000	65,540,000
total_aligned_reads	47,233,136	59,653,772
unique_aligned_reads	44,729,476	56,345,118
percent_uniqueAligned	0.85870	0.85971
correlation_replicates	0.971170	0.971170
spikein_reads	177,460	86,462
percent_spikeins	0.00341	0.00132
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1156	1157

Data Submission Information

	BGHLV23-57	BGHLV23-57
ENCODE_alias	brenton-graveley:UBE2L3-BGHLV23	brenton-graveley:UBE2L3-BGHLV23-HepG2
ENCODE_accession	ENCSR424JSU	ENCSR561ONH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-57	BGHLV23-57
Sample Name	UBE2L3-BGHLV23-57	UBE2L3-BGHLV23-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2955	7026

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
UBE2L3-BGHLV23-57_ATGTCA_L008_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1156	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16686
UBE2L3-BGHLV23-57_ATGTCA_L008_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1156	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16724
UBE2L3-BGHLV23-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1156					GRCh38	V40	UBE2L3-BGHLV23-57_ATGTCA_L008_R1_001.fastq.gz,UBE2L3-BGHLV23-57_ATGTCA_L008_R2_001.fastq.gz		ENCORE2	16762
UBE2L3-BGHLV23-57_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1156					GRCh38	V40	UBE2L3-BGHLV23-57/Aligned.sortedByCoord.out.bam		ENCORE2	16800
UBE2L3-BGHLV23-57_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1156					GRCh38	V40	UBE2L3-BGHLV23-57/Aligned.sortedByCoord.out.bam		ENCORE2	16838
UBE2L3-BGHLV23-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1156					GRCh38	V40	UBE2L3-BGHLV23-57/Aligned.sortedByCoord.out.bam		ENCORE2	16876
UBE2L3-BGHLV23-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1156					GRCh38	V40	UBE2L3-BGHLV23-57/Aligned.sortedByCoord.out.bam		ENCORE2	16914
UBE2L3-BGHLV23-57_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1156					GRCh38	V40	UBE2L3-BGHLV23-57_ATGTCA_L008_R1_001.fastq.gz,UBE2L3-BGHLV23-57_ATGTCA_L008_R2_001.fastq.gz		ENCORE2	16952
UBE2L3-BGHLV23-58_CCGTCC_L008_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1157	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16687
UBE2L3-BGHLV23-58_CCGTCC_L008_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1157	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16725
UBE2L3-BGHLV23-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1157					GRCh38	V40	UBE2L3-BGHLV23-58_CCGTCC_L008_R1_001.fastq.gz,UBE2L3-BGHLV23-58_CCGTCC_L008_R2_001.fastq.gz		ENCORE2	16763
UBE2L3-BGHLV23-58_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1157					GRCh38	V40	UBE2L3-BGHLV23-58/Aligned.sortedByCoord.out.bam		ENCORE2	16801
UBE2L3-BGHLV23-58_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1157					GRCh38	V40	UBE2L3-BGHLV23-58/Aligned.sortedByCoord.out.bam		ENCORE2	16839
UBE2L3-BGHLV23-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1157					GRCh38	V40	UBE2L3-BGHLV23-58/Aligned.sortedByCoord.out.bam		ENCORE2	16877
UBE2L3-BGHLV23-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1157					GRCh38	V40	UBE2L3-BGHLV23-58/Aligned.sortedByCoord.out.bam		ENCORE2	16915
UBE2L3-BGHLV23-58_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1157					GRCh38	V40	UBE2L3-BGHLV23-58_CCGTCC_L008_R1_001.fastq.gz,UBE2L3-BGHLV23-58_CCGTCC_L008_R2_001.fastq.gz		ENCORE2	16953