UCHL5 RNA-Seq in K562

General Information


RBP	UCHL5
Cell_Line	K562
Method	shRNA
Exp_Name	UCHL5-BGKLV19-K562
ENCODE_series_ID	ENCSR759TWA
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR678MVE
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	UCHL5_BGKLV19_59B
Rep2	UCHL5_BGKLV19_60B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	75.7
Rep2_qPCR	82.1
Rep1_WB	57.2
Rep2_WB	49.4
Antibody Cat#	A304-099A
Antibody Lot#	A304-099A
Antibody DCC ID	ENCAB421XHI
Status	Released
Project	ENCODE3
ID	486

Experiment Information (Status: Released)

	BGKLV19-59	BGKLV19-60
idx	266	267
TRCN#_or_BGC#	TRCN0000004127	TRCN0000004127
shRNA_or_gRNA_sequence	CCTGTTAATGGGAGACTGTAT	CCTGTTAATGGGAGACTGTAT
PAM
Name	UCHL5	UCHL5
Sample_ID	BGKLV19-59	BGKLV19-60
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	UCHL5	UCHL5
qPCR_result	75.7	82.1
Ave_qPCR	78.9
RT-qPCR_primer-F	tgttcctgttaatgggagactg
RT-qPCR_primer-R	aggccttactgcactgatcc
protein_conc	2883	3099
WB_result	57.2	49.4
Ave_WB	53.3
WB_DONE_date	2/13/2015
MW	38kDa
IP	1	1
antibody_Cat#	A304-099A	A304-099A
Antibody DCC ID	ENCAB421XHI	ENCAB421XHI
submitted_to_DCC_date	4/2/2015
Rep1_TPM	73.1324851	0
Rep2_TPM	48.0733646	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	291	292

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UCHL5	Product_ID: A304-099A Lot_ID: 1 Source: Bethyl Labs Target Name: UCHL5-human

Experiment Status

	BGKLV19-59	BGKLV19-60
Sample_ID	BGKLV19-59	BGKLV19-60
Sample Name	UCHL5_BGKLV19_59B	UCHL5_BGKLV19_60B
Sample Name	UCHL5_BGKLV19_59B	UCHL5_BGKLV19_60B
RBP	UCHL5	UCHL5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	704	705

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-59	BGKLV19-60
Sample #
Sample Name	UCHL5-BGKLV19-59B	UCHL5-BGKLV19-60B
Sample_Name_Alias	UCHL5_BGKLV19_59B	UCHL5_BGKLV19_60B
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C12.png	DNA_Library_LV18-19/set1/D12.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G6.png	RNA_Library_LV19-21-24/set1/H6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-59	BGKLV19-60
RBP	UCHL5	UCHL5
Batch_ID	BGKLV19	BGKLV19
WB_result	57.200	49.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2390	2391

Sequencing Information

	BGKLV19-59	BGKLV19-60
Sample_ID	BGKLV19-59	BGKLV19-60
Sample Name	UCHL5_BGKLV19_59B	UCHL5_BGKLV19_60B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	45,240,000	50,000,000
total_aligned_reads	41,630,488	46,163,594
unique_aligned_reads	38,043,088	42,269,734
percent_uniqueAligned	0.84092	0.84539
correlation_replicates	0.996061	0.996061
spikein_reads	172,742	139,124
percent_spikeins	0.00382	0.00278
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1032	1033

Data Submission Information

	BGKLV19-59	BGKLV19-59
ENCODE_alias	brenton-graveley:UCHL5_BGKLV19	brenton-graveley:UCHL5-BGKLV19-K562
ENCODE_accession	ENCSR678MVE	ENCSR759TWA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-59	BGKLV19-59
Sample Name	UCHL5_BGKLV19_59B	UCHL5_BGKLV19_59B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2900	7029

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
UCHL5_BGKLV19_59B_GTGGCC_L007_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1032	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15148
UCHL5_BGKLV19_59B_GTGGCC_L007_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1032	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15206
UCHL5_BGKLV19_59B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1032					GRCh38	V40	UCHL5_BGKLV19_59B_GTGGCC_L007_R1_001.fastq.gz,UCHL5_BGKLV19_59B_GTGGCC_L007_R2_001.fastq.gz		ENCORE2	15264
UCHL5_BGKLV19_59B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1032					GRCh38	V40	UCHL5_BGKLV19_59B/Aligned.sortedByCoord.out.bam		ENCORE2	15335
UCHL5_BGKLV19_59B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1032					GRCh38	V40	UCHL5_BGKLV19_59B/Aligned.sortedByCoord.out.bam		ENCORE2	15393
UCHL5_BGKLV19_59B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1032					GRCh38	V40	UCHL5_BGKLV19_59B/Aligned.sortedByCoord.out.bam		ENCORE2	15451
UCHL5_BGKLV19_59B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1032					GRCh38	V40	UCHL5_BGKLV19_59B/Aligned.sortedByCoord.out.bam		ENCORE2	15509
UCHL5_BGKLV19_59B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1032					GRCh38	V40	UCHL5_BGKLV19_59B_GTGGCC_L007_R1_001.fastq.gz,UCHL5_BGKLV19_59B_GTGGCC_L007_R2_001.fastq.gz		ENCORE2	16406
UCHL5_BGKLV19_60B_GTTTCG_L007_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1033	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15149
UCHL5_BGKLV19_60B_GTTTCG_L007_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1033	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15207
UCHL5_BGKLV19_60B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1033					GRCh38	V40	UCHL5_BGKLV19_60B_GTTTCG_L007_R1_001.fastq.gz,UCHL5_BGKLV19_60B_GTTTCG_L007_R2_001.fastq.gz		ENCORE2	15265
UCHL5_BGKLV19_60B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1033					GRCh38	V40	UCHL5_BGKLV19_60B/Aligned.sortedByCoord.out.bam		ENCORE2	15336
UCHL5_BGKLV19_60B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1033					GRCh38	V40	UCHL5_BGKLV19_60B/Aligned.sortedByCoord.out.bam		ENCORE2	15394
UCHL5_BGKLV19_60B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1033					GRCh38	V40	UCHL5_BGKLV19_60B/Aligned.sortedByCoord.out.bam		ENCORE2	15452
UCHL5_BGKLV19_60B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1033					GRCh38	V40	UCHL5_BGKLV19_60B/Aligned.sortedByCoord.out.bam		ENCORE2	15510
UCHL5_BGKLV19_60B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1033					GRCh38	V40	UCHL5_BGKLV19_60B_GTTTCG_L007_R1_001.fastq.gz,UCHL5_BGKLV19_60B_GTTTCG_L007_R2_001.fastq.gz		ENCORE2	16407