UCHL5 RNA-Seq in HepG2

General Information


RBP	UCHL5
Cell_Line	HepG2
Method	shRNA
Exp_Name	UCHL5-BGHLV17-HepG2
ENCODE_series_ID	ENCSR009SJR
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR684HTV
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	UCHL5_BGHLV17_37
Rep2	UCHL5_BGHLV17_38
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	58.5
Rep2_qPCR	60.6
Rep1_WB	58.8
Rep2_WB	58.4
Antibody Cat#	A304-099A
Antibody Lot#	A304-099A
Antibody DCC ID	ENCAB421XHI
Status	Released
Project	ENCODE3
ID	441

Experiment Information (Status: Released)

	BGHLV17-37	BGHLV17-38
idx	273	274
TRCN#_or_BGC#	TRCN0000004127	TRCN0000004127
shRNA_or_gRNA_sequence	CCTGTTAATGGGAGACTGTAT	CCTGTTAATGGGAGACTGTAT
PAM
Name	UCHL5	UCHL5
Sample_ID	BGHLV17-37	BGHLV17-38
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	UCHL5	UCHL5
qPCR_result	58.5	60.6
Ave_qPCR	59.6
RT-qPCR_primer-F	tgttcctgttaatgggagactg
RT-qPCR_primer-R	aggccttactgcactgatcc
protein_conc	2396	2423
WB_result	58.8	58.4
Ave_WB	58.6
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	22.9	0
Rep2_TPM	17.9	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2338	2339

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

	BGHLV17-37	BGHLV17-38
Sample_ID	BGHLV17-37	BGHLV17-38
Sample Name	UCHL5_BGHLV17_37	UCHL5_BGHLV17_38
Sample Name	UCHL5_BGHLV17_37	UCHL5_BGHLV17_38
RBP	UCHL5	UCHL5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	610	611

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-37	BGHLV17-38
Sample #
Sample Name	UCHL5-BGHLV17-37	UCHL5-BGHLV17-38
Sample_Name_Alias	UCHL5_BGHLV17_37	UCHL5_BGHLV17_38
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/G3.png	DNA_Library_LV16-17/set1/H3.png
RIN	8.4	8.2
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G5.png	RNA_Library_LV16-17-18/set1/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-37	BGHLV17-38
RBP	UCHL5	UCHL5
Batch_ID	BGHLV17	BGHLV17
WB_result	58.800	58.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2294	2295

Sequencing Information

	BGHLV17-37	BGHLV17-38
Sample_ID	BGHLV17-37	BGHLV17-38
Sample Name	UCHL5_BGHLV17_37	UCHL5_BGHLV17_38
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	24,500,000	24,300,000
total_aligned_reads	22,037,848	21,944,260
unique_aligned_reads	20,668,184	20,597,616
percent_uniqueAligned	0.84360	0.84764
correlation_replicates	0.999199	0.999199
spikein_reads	56,824	76,762
percent_spikeins	0.00232	0.00316
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	936	937

Data Submission Information

	BGHLV17-37	BGHLV17-37
ENCODE_alias	brenton-graveley:UCHL5_BGHLV17	brenton-graveley:UCHL5-BGHLV17-HepG2
ENCODE_accession	ENCSR684HTV	ENCSR009SJR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-37	BGHLV17-37
Sample Name	UCHL5_BGHLV17_37	UCHL5_BGHLV17_37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2872	7028

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_BGHLV17_37_ACTGAT_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	936	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14518
UCHL5_BGHLV17_37_ACTGAT_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	936	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14556
UCHL5_BGHLV17_37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	936					GRCh38	V40	UCHL5_BGHLV17_37_ACTGAT_L003_R1_001.fastq.gz,UCHL5_BGHLV17_37_ACTGAT_L003_R2_001.fastq.gz		ENCORE2	14594
UCHL5_BGHLV17_37_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	936					GRCh38	V40	UCHL5_BGHLV17_37/Aligned.sortedByCoord.out.bam		ENCORE2	14632
UCHL5_BGHLV17_37_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	936					GRCh38	V40	UCHL5_BGHLV17_37/Aligned.sortedByCoord.out.bam		ENCORE2	14670
UCHL5_BGHLV17_37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	936					GRCh38	V40	UCHL5_BGHLV17_37/Aligned.sortedByCoord.out.bam		ENCORE2	14708
UCHL5_BGHLV17_37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	936					GRCh38	V40	UCHL5_BGHLV17_37/Aligned.sortedByCoord.out.bam		ENCORE2	14746
UCHL5_BGHLV17_37_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	936					GRCh38	V40	UCHL5_BGHLV17_37_ACTGAT_L003_R1_001.fastq.gz,UCHL5_BGHLV17_37_ACTGAT_L003_R2_001.fastq.gz		ENCORE2	14784
UCHL5_BGHLV17_38_ATTCCT_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	937	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14519
UCHL5_BGHLV17_38_ATTCCT_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	937	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14557
UCHL5_BGHLV17_38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	937					GRCh38	V40	UCHL5_BGHLV17_38_ATTCCT_L003_R1_001.fastq.gz,UCHL5_BGHLV17_38_ATTCCT_L003_R2_001.fastq.gz		ENCORE2	14595
UCHL5_BGHLV17_38_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	937					GRCh38	V40	UCHL5_BGHLV17_38/Aligned.sortedByCoord.out.bam		ENCORE2	14633
UCHL5_BGHLV17_38_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	937					GRCh38	V40	UCHL5_BGHLV17_38/Aligned.sortedByCoord.out.bam		ENCORE2	14671
UCHL5_BGHLV17_38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	937					GRCh38	V40	UCHL5_BGHLV17_38/Aligned.sortedByCoord.out.bam		ENCORE2	14709
UCHL5_BGHLV17_38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	937					GRCh38	V40	UCHL5_BGHLV17_38/Aligned.sortedByCoord.out.bam		ENCORE2	14747
UCHL5_BGHLV17_38_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	937					GRCh38	V40	UCHL5_BGHLV17_38_ATTCCT_L003_R1_001.fastq.gz,UCHL5_BGHLV17_38_ATTCCT_L003_R2_001.fastq.gz		ENCORE2	14785