USP10 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-85	BGHcLV47-86
idx	1691	1692
TRCN#_or_BGC#	BGC#0001070	BGC#0001070
shRNA_or_gRNA_sequence	GCCTGGGTACTGGCAGTCGA	GCCTGGGTACTGGCAGTCGA
PAM	TGG	TGG
Name	USP10_88	USP10_88
Sample_ID	BGHcLV47-85	BGHcLV47-86
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	USP10	USP10
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ggaaaaactccctcctgtcc
RT-qPCR_primer-R	aacccctggagaaagcagtt
protein_conc	4279	4615
WB_result	90.7	83.5
Ave_WB
WB_DONE_date	3/25/25
MW	87kd
IP
antibody_Cat#	A300-900A	lot # 2
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	9880	9881

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
USP10	Product_ID: A300-900A Lot_ID: 2 Source: Bethyl Labs Target Name: USP10-human

Experiment Status

	BGHcLV47-85	BGHcLV47-86
Sample_ID	BGHcLV47-85	BGHcLV47-86
Sample Name
Sample Name	USP10-BGHcLV47-85	USP10-BGHcLV47-86
RBP	USP10	USP10
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14178	14179

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-85	BGHcLV47-86
Sample #	31	32
Sample Name	USP10-BGHcLV47-85	USP10-BGHcLV47-86
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	263	264
Peak_Molarity	68.00	82.10
libSampleQC_DNA_Well	DNA_Library_set78/set1/G9.png	DNA_Library_set78/set1/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set78/set1/G4.png	RNA_Library_set78/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-85	BGHcLV47-86
RBP	USP10	USP10
Batch_ID	BGHcLV47	BGHcLV47
WB_result	90.700	83.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4742	4743

Sequencing Information

	BGHcLV47-85	BGHcLV47-86
Sample_ID	BGHcLV47-85	BGHcLV47-86
Sample Name	USP10-BGHcLV47-85	USP10-BGHcLV47-86
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	24,554,370	18,162,810
total_aligned_reads	22,338,178	16,126,927
unique_aligned_reads	21,058,502	15,150,545
percent_uniqueAligned	0.85763	0.83415
correlation_replicates	0.995025	0.995025
spikein_reads	17,230	19,666
percent_spikeins	0.00070	0.00108
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3445	3446

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
USP10-BGHcLV47-85_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3445	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32578
USP10-BGHcLV47-85_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3445	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32612
USP10-BGHcLV47-85_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3445					GRCh38	V40	USP10-BGHcLV47-85_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGHcLV47-85_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32646
USP10-BGHcLV47-85_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3445					GRCh38	V40	USP10-BGHcLV47-85_Aligned.sortedByCoord.out.bam		ENCORE2	32680
USP10-BGHcLV47-85_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3445					GRCh38	V40	USP10-BGHcLV47-85_Aligned.sortedByCoord.out.bam		ENCORE2	32714
USP10-BGHcLV47-85_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3445					GRCh38	V40	USP10-BGHcLV47-85_Aligned.sortedByCoord.out.bam		ENCORE2	32748
USP10-BGHcLV47-85_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3445					GRCh38	V40	USP10-BGHcLV47-85_Aligned.sortedByCoord.out.bam		ENCORE2	32782
USP10-BGHcLV47-85_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3445					GRCh38	V40	USP10-BGHcLV47-85_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGHcLV47-85_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32816
USP10-BGHcLV47-86_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3446	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32579
USP10-BGHcLV47-86_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3446	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32613
USP10-BGHcLV47-86_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3446					GRCh38	V40	USP10-BGHcLV47-86_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGHcLV47-86_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32647
USP10-BGHcLV47-86_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3446					GRCh38	V40	USP10-BGHcLV47-86_Aligned.sortedByCoord.out.bam		ENCORE2	32681
USP10-BGHcLV47-86_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3446					GRCh38	V40	USP10-BGHcLV47-86_Aligned.sortedByCoord.out.bam		ENCORE2	32715
USP10-BGHcLV47-86_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3446					GRCh38	V40	USP10-BGHcLV47-86_Aligned.sortedByCoord.out.bam		ENCORE2	32749
USP10-BGHcLV47-86_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3446					GRCh38	V40	USP10-BGHcLV47-86_Aligned.sortedByCoord.out.bam		ENCORE2	32783
USP10-BGHcLV47-86_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3446					GRCh38	V40	USP10-BGHcLV47-86_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,USP10-BGHcLV47-86_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32817