USP15 RNA-Seq in HepG2

General Information


RBP	USP15
Cell_Line	HepG2
Method	CRISPR
Exp_Name	USP15-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	USP15-BGHcLV43-59
Rep2	USP15-BGHcLV43-60
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	84.3
Rep2_WB	88.4
Antibody Cat#	66310S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1592

Experiment Information (Status: Submitting)

	BGHcLV43-59	BGHcLV43-60
idx	1427	1428
TRCN#_or_BGC#	BGC#0001202	BGC#0001202
shRNA_or_gRNA_sequence	TGAACCAGCGACTATCGACT	TGAACCAGCGACTATCGACT
PAM	AGG	AGG
Name	USP15_96	USP15_96
Sample_ID	BGHcLV43-59	BGHcLV43-60
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	USP15	USP15
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	tgtgtatcctggacccattg
RT-qPCR_primer-R	aagtgactgggcatcaccat
protein_conc	4323	4163
WB_result	84.3	88.4
Ave_WB	86.3
WB_DONE_date	6/21/24
MW	120kd
IP
antibody_Cat#	66310S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9682	9683

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
USP15	Product_ID: 66310S Lot_ID: 1 Source: Cell Signaling Technology Target Name: USP15-human

Experiment Status

	BGHcLV43-59	BGHcLV43-60
Sample_ID	BGHcLV43-59	BGHcLV43-60
Sample Name
Sample Name	USP15-BGHcLV43-59	USP15-BGHcLV43-60
RBP	USP15	USP15
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13274	13275

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-59	BGHcLV43-60
Sample #	47	48
Sample Name	USP15-BGHcLV43-59	USP15-BGHcLV43-60
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	293	288
Peak_Molarity	65.50	69.40
libSampleQC_DNA_Well	DNA_Library_set74/set1/G6.png	DNA_Library_set74/set1/H6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/C12.png	RNA_Library_set74/set1/D12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-59	BGHcLV43-60
RBP	USP15	USP15
Batch_ID	BGHcLV43	BGHcLV43
WB_result	84.300	88.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4406	4407

Sequencing Information

	BGHcLV43-59	BGHcLV43-60
Sample_ID	BGHcLV43-59	BGHcLV43-60
Sample Name	USP15-BGHcLV43-59	USP15-BGHcLV43-60
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	51,476,360	58,717,015
total_aligned_reads	47,962,558	54,687,315
unique_aligned_reads	44,979,275	51,504,440
percent_uniqueAligned	0.87379	0.87716
correlation_replicates	0.991140	0.991140
spikein_reads	27,148	44,638
percent_spikeins	0.00053	0.00076
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3273	3274

Data Submission Information DCC submission information was not avaliable

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
USP15-BGHcLV43-59_S137_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3273	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30566
USP15-BGHcLV43-59_S137_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3273	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30618
USP15-BGHcLV43-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3273					GRCh38	V40	USP15-BGHcLV43-59_S137_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGHcLV43-59_S137_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30670
USP15-BGHcLV43-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3273					GRCh38	V40	USP15-BGHcLV43-59_Aligned.sortedByCoord.out.bam		ENCORE2	30722
USP15-BGHcLV43-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3273					GRCh38	V40	USP15-BGHcLV43-59_Aligned.sortedByCoord.out.bam		ENCORE2	30774
USP15-BGHcLV43-59_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3273					GRCh38	V40	USP15-BGHcLV43-59_Aligned.sortedByCoord.out.bam		ENCORE2	30826
USP15-BGHcLV43-59_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3273					GRCh38	V40	USP15-BGHcLV43-59_Aligned.sortedByCoord.out.bam		ENCORE2	30878
USP15-BGHcLV43-59_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3273					GRCh38	V40	USP15-BGHcLV43-59_S137_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGHcLV43-59_S137_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30930
USP15-BGHcLV43-60_S138_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3274	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30567
USP15-BGHcLV43-60_S138_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3274	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30619
USP15-BGHcLV43-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3274					GRCh38	V40	USP15-BGHcLV43-60_S138_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGHcLV43-60_S138_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30671
USP15-BGHcLV43-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3274					GRCh38	V40	USP15-BGHcLV43-60_Aligned.sortedByCoord.out.bam		ENCORE2	30723
USP15-BGHcLV43-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3274					GRCh38	V40	USP15-BGHcLV43-60_Aligned.sortedByCoord.out.bam		ENCORE2	30775
USP15-BGHcLV43-60_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3274					GRCh38	V40	USP15-BGHcLV43-60_Aligned.sortedByCoord.out.bam		ENCORE2	30827
USP15-BGHcLV43-60_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3274					GRCh38	V40	USP15-BGHcLV43-60_Aligned.sortedByCoord.out.bam		ENCORE2	30879
USP15-BGHcLV43-60_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3274					GRCh38	V40	USP15-BGHcLV43-60_S138_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGHcLV43-60_S138_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30931