USP15 RNA-Seq in K562

General Information


RBP	USP15
Cell_Line	K562
Method	CRISPR
Exp_Name	USP15-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	USP15-BGKcLV42-99
Rep2	USP15-BGKcLV42-100
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	44.5
Rep2_qPCR	40.7
Rep1_WB	90.5
Rep2_WB	91.8
Antibody Cat#	66310S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1565

Experiment Information (Status: Submitting)

	BGKcLV42-99	BGKcLV42-100
idx	0	0
TRCN#_or_BGC#	BGC#0001200	BGC#0001200
shRNA_or_gRNA_sequence	TGAACCAGCGACTATCGACT	TGAACCAGCGACTATCGACT
PAM	AGG	AGG
Name	USP15_96	USP15_96
Sample_ID	BGKcLV42-99	BGKcLV42-100
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	USP15	USP15
qPCR_result	44.5	40.7
Ave_qPCR	42.6
RT-qPCR_primer-F	tgtgtatcctggacccattg
RT-qPCR_primer-R	aagtgactgggcatcaccat
protein_conc	2534	2730
WB_result	90.5	91.8
Ave_WB	91.2
WB_DONE_date	5/10/24
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	5867	5868

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

	BGKcLV42-99	BGKcLV42-100
Sample_ID	BGKcLV42-99	BGKcLV42-100
Sample Name
Sample Name	USP15-BGKcLV42-99	USP15-BGKcLV42-100
RBP	USP15	USP15
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13124	13125

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-99	BGKcLV42-100
Sample #	81	82
Sample Name	USP15-BGKcLV42-99	USP15-BGKcLV42-100
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	300	315
Peak_Molarity	90.20	90.10
libSampleQC_DNA_Well	DNA_Library_set73/set1/A11.png	DNA_Library_set73/set1/B11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A11.png	RNA_Library_set73/set1/B11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-99	BGKcLV42-100
RBP	USP15	USP15
Batch_ID	BGKcLV42	BGKcLV42
WB_result	90.500	91.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4350	4351

Sequencing Information

	BGKcLV42-99	BGKcLV42-100
Sample_ID	BGKcLV42-99	BGKcLV42-100
Sample Name	USP15-BGKcLV42-99	USP15-BGKcLV42-100
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	40,705,410	45,447,231
total_aligned_reads	34,500,525	42,879,019
unique_aligned_reads	31,871,610	39,754,872
percent_uniqueAligned	0.78298	0.87475
correlation_replicates	0.997131	0.997131
spikein_reads	5,296	1,130
percent_spikeins	0.00013	0.00002
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3217	3218

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-BGKcLV42-99_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3217	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30421
USP15-BGKcLV42-99_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3217	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30511
USP15-BGKcLV42-99_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3217					GRCh38	V40	USP15-BGKcLV42-99_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGKcLV42-99_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31353
USP15-BGKcLV42-99_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3217					GRCh38	V40	USP15-BGKcLV42-99_Aligned.sortedByCoord.out.bam		ENCORE2	31443
USP15-BGKcLV42-99_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3217					GRCh38	V40	USP15-BGKcLV42-99_Aligned.sortedByCoord.out.bam		ENCORE2	31533
USP15-BGKcLV42-99_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3217					GRCh38	V40	USP15-BGKcLV42-99_Aligned.sortedByCoord.out.bam		ENCORE2	31623
USP15-BGKcLV42-99_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3217					GRCh38	V40	USP15-BGKcLV42-99_Aligned.sortedByCoord.out.bam		ENCORE2	31713
USP15-BGKcLV42-99_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3217					GRCh38	V40	USP15-BGKcLV42-99_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGKcLV42-99_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31803
USP15-BGKcLV42-100_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3218	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30420
USP15-BGKcLV42-100_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3218	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30510
USP15-BGKcLV42-100_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3218					GRCh38	V40	USP15-BGKcLV42-100_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGKcLV42-100_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31352
USP15-BGKcLV42-100_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3218					GRCh38	V40	USP15-BGKcLV42-100_Aligned.sortedByCoord.out.bam		ENCORE2	31442
USP15-BGKcLV42-100_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3218					GRCh38	V40	USP15-BGKcLV42-100_Aligned.sortedByCoord.out.bam		ENCORE2	31532
USP15-BGKcLV42-100_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3218					GRCh38	V40	USP15-BGKcLV42-100_Aligned.sortedByCoord.out.bam		ENCORE2	31622
USP15-BGKcLV42-100_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3218					GRCh38	V40	USP15-BGKcLV42-100_Aligned.sortedByCoord.out.bam		ENCORE2	31712
USP15-BGKcLV42-100_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3218					GRCh38	V40	USP15-BGKcLV42-100_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP15-BGKcLV42-100_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31802