UBE2L3 RNA-Seq in K562

General Information


RBP	UBE2L3
Cell_Line	K562
Method	shRNA
Exp_Name	UBE2L3-BGKLV25-K562
ENCODE_series_ID	ENCSR777OSI
Batch_ID	BGKLV25
Pool ID	Pool-151201
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR362XMY
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	UBE2L3-BGKLV25-61
Rep2	UBE2L3-BGKLV25-62
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	86.9
Rep2_qPCR	79.5
Rep1_WB	69.4
Rep2_WB	60.0
Antibody Cat#	A300-737A
Antibody Lot#	A300-737A
Antibody DCC ID	ENCAB492XKE
Status	Released
Project	ENCODE3
ID	627

Experiment Information (Status: Released)

	BGKLV25-61	BGKLV25-61	BGKLV25-62	BGKLV25-62
idx	464	464	465	465
TRCN#_or_BGC#	TRCN0000007209	TRCN0000007209	TRCN0000007209	TRCN0000007209
shRNA_or_gRNA_sequence	CCAGCAGAGTACCCATTCAAA	CCAGCAGAGTACCCATTCAAA	CCAGCAGAGTACCCATTCAAA	CCAGCAGAGTACCCATTCAAA
PAM
Name	UBE2L3_09	UBE2L3_09	UBE2L3_09	UBE2L3_09
Sample_ID	BGKLV25-61	BGKLV25-61	BGKLV25-62	BGKLV25-62
transduction_Date	3/17/2015	3/17/2015	3/17/2015	3/17/2015
days
RBP_name	UBE2L3	UBE2L3	UBE2L3	UBE2L3
qPCR_result	86.9	86.9	79.5	79.5
Ave_qPCR	83.2	83.2
RT-qPCR_primer-F	ttagtgccgaaaactggaag	ttagtgccgaaaactggaag
RT-qPCR_primer-R	ggggtcattcaccagtgcta	ggggtcattcaccagtgcta
protein_conc	3302	3302	3605	3605
WB_result	69.4	55.6	60.0	64.4
Ave_WB	64.7	60.0
WB_DONE_date	5/14/2015	6/27/23
MW	18kDa	18kDa
IP	1		1
antibody_Cat#	A300-737A	8721S	A300-737A	lot# 1
Antibody DCC ID	ENCAB492XKE		ENCAB492XKE
submitted_to_DCC_date	8/6/2015	1/8/24
Rep1_TPM	150.541573	0	0	0
Rep2_TPM	85.0670213	0	0	0
Action
Library_start_date	6/23/2015		6/23/2015
repeat_library
Note
ID	537	539	538	540

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
UBE2L3	Product_ID: 8721S Lot_ID: 1 Source: Cell Signaling Technology Target Name: UBE2L3-human

Experiment Status

	BGKLV25-61	BGKLV25-62
Sample_ID	BGKLV25-61	BGKLV25-62
Sample Name	UBE2L3-BGKLV25-61	UBE2L3-BGKLV25-62
Sample Name	UBE2L3-BGKLV25-61	UBE2L3-BGKLV25-62
RBP	UBE2L3	UBE2L3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	934	935

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-61	BGKLV25-62
Sample #
Sample Name	UBE2L3-BGKLV25-61	UBE2L3-BGKLV25-62
Sample_Name_Alias	UBE2L3-BGKLV25-61	UBE2L3-BGKLV25-62
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/G4.png	DNA_Library_LV24-25-26/set1/H4.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV25-26/set1/A1.png	RNA_Library_LV25-26/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-61	BGKLV25-62
RBP	UBE2L3	UBE2L3
Batch_ID	BGKLV25	BGKLV25
WB_result	69.400	60.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2626	2627

Sequencing Information

	BGKLV25-61	BGKLV25-62
Sample_ID	BGKLV25-61	BGKLV25-62
Sample Name	UBE2L3-BGKLV25-61	UBE2L3-BGKLV25-62
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set25	set25
total_reads	102,191,440	192,934,296
total_aligned_reads	97,938,808	184,525,288
unique_aligned_reads	89,740,578	168,754,242
percent_uniqueAligned	0.87816	0.87467
correlation_replicates	0.990047	0.990047
spikein_reads	487,004	976,342
percent_spikeins	0.00477	0.00506
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1268	1269

Data Submission Information

	BGKLV25-61	BGKLV25-61
ENCODE_alias	brenton-graveley:UBE2L3-BGKLV25	brenton-graveley:UBE2L3-BGKLV25-K562
ENCODE_accession	ENCSR362XMY	ENCSR777OSI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-61	BGKLV25-61
Sample Name	UBE2L3-BGKLV25-61	UBE2L3-BGKLV25-61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3016	7027

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-BGKLV25-61_1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1268	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19596
UBE2L3-BGKLV25-61_2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1268	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19632
UBE2L3-BGKLV25-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1268					GRCh38	V40	UBE2L3-BGKLV25-61_1.fastq.gz,UBE2L3-BGKLV25-61_2.fastq.gz		ENCORE2	19668
UBE2L3-BGKLV25-61_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1268					GRCh38	V40	UBE2L3-BGKLV25-61/Aligned.sortedByCoord.out.bam		ENCORE2	19704
UBE2L3-BGKLV25-61_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1268					GRCh38	V40	UBE2L3-BGKLV25-61/Aligned.sortedByCoord.out.bam		ENCORE2	19740
UBE2L3-BGKLV25-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1268					GRCh38	V40	UBE2L3-BGKLV25-61/Aligned.sortedByCoord.out.bam		ENCORE2	19776
UBE2L3-BGKLV25-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1268					GRCh38	V40	UBE2L3-BGKLV25-61/Aligned.sortedByCoord.out.bam		ENCORE2	19812
UBE2L3-BGKLV25-61_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1268					GRCh38	V40	UBE2L3-BGKLV25-61_1.fastq.gz,UBE2L3-BGKLV25-61_2.fastq.gz		ENCORE2	20002
UBE2L3-BGKLV25-62_1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1269	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19597
UBE2L3-BGKLV25-62_2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1269	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19633
UBE2L3-BGKLV25-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1269					GRCh38	V40	UBE2L3-BGKLV25-62_1.fastq.gz,UBE2L3-BGKLV25-62_2.fastq.gz		ENCORE2	19669
UBE2L3-BGKLV25-62_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1269					GRCh38	V40	UBE2L3-BGKLV25-62/Aligned.sortedByCoord.out.bam		ENCORE2	19705
UBE2L3-BGKLV25-62_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1269					GRCh38	V40	UBE2L3-BGKLV25-62/Aligned.sortedByCoord.out.bam		ENCORE2	19741
UBE2L3-BGKLV25-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1269					GRCh38	V40	UBE2L3-BGKLV25-62/Aligned.sortedByCoord.out.bam		ENCORE2	19777
UBE2L3-BGKLV25-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1269					GRCh38	V40	UBE2L3-BGKLV25-62/Aligned.sortedByCoord.out.bam		ENCORE2	19813
UBE2L3-BGKLV25-62_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1269					GRCh38	V40	UBE2L3-BGKLV25-62_1.fastq.gz,UBE2L3-BGKLV25-62_2.fastq.gz		ENCORE2	20003