USP39 RNA-Seq in K562

General Information


RBP	USP39
Cell_Line	K562
Method	CRISPR
Exp_Name	USP39-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	USP39-BGKcLV42-101
Rep2	USP39-BGKcLV42-102
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	50.9
Rep2_qPCR	53.0
Rep1_WB	89.4
Rep2_WB	88.5
Antibody Cat#	23303S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1566

Experiment Information (Status: Submitting)

	BGKcLV42-101	BGKcLV42-102
idx	0	0
TRCN#_or_BGC#	BGC#0001202	BGC#0001202
shRNA_or_gRNA_sequence	CACCGTGATATCCTCCAATG	CACCGTGATATCCTCCAATG
PAM	AGG	AGG
Name	USP39_90	USP39_90
Sample_ID	BGKcLV42-101	BGKcLV42-102
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	USP39	USP39
qPCR_result	50.9	53.0
Ave_qPCR	51.9
RT-qPCR_primer-F	caacctccacaccctcaagt
RT-qPCR_primer-R	gcaatttgctgctttgtgaa
protein_conc	2502	2571
WB_result	89.4	88.5
Ave_WB	88.9
WB_DONE_date	5/10/24
MW	65kd
IP
antibody_Cat#	23303S	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	5869	5870

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
USP39	Product_ID: 23303S Lot_ID: 1 Source: Cell Signaling Technology Target Name: USP39-human

Experiment Status

	BGKcLV42-101	BGKcLV42-102
Sample_ID	BGKcLV42-101	BGKcLV42-102
Sample Name
Sample Name	USP39-BGKcLV42-101	USP39-BGKcLV42-102
RBP	USP39	USP39
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13126	13127

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-101	BGKcLV42-102
Sample #	83	84
Sample Name	USP39-BGKcLV42-101	USP39-BGKcLV42-102
Sample_Name_Alias
Index Well Position	C11	D11
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	309	309
Peak_Molarity	107.00	101.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/C11.png	DNA_Library_set73/set1/D11.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set73/set1/C11.png	RNA_Library_set73/set1/D11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-101	BGKcLV42-102
RBP	USP39	USP39
Batch_ID	BGKcLV42	BGKcLV42
WB_result	89.400	88.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4352	4353

Sequencing Information

	BGKcLV42-101	BGKcLV42-102
Sample_ID	BGKcLV42-101	BGKcLV42-102
Sample Name	USP39-BGKcLV42-101	USP39-BGKcLV42-102
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	31,311,620	50,717,531
total_aligned_reads	28,301,429	46,648,858
unique_aligned_reads	26,107,885	43,161,740
percent_uniqueAligned	0.83381	0.85102
correlation_replicates	0.999017	0.999017
spikein_reads	1,054	254
percent_spikeins	0.00003	0.00001
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3219	3220

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
USP39-BGKcLV42-101_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3219	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	30422
USP39-BGKcLV42-101_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3219	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	30512
USP39-BGKcLV42-101_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3219					GRCh38	V40	USP39-BGKcLV42-101_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGKcLV42-101_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31354
USP39-BGKcLV42-101_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	3219					GRCh38	V40	USP39-BGKcLV42-101_Aligned.sortedByCoord.out.bam		ENCORE2	31444
USP39-BGKcLV42-101_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	3219					GRCh38	V40	USP39-BGKcLV42-101_Aligned.sortedByCoord.out.bam		ENCORE2	31534
USP39-BGKcLV42-101_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	3219					GRCh38	V40	USP39-BGKcLV42-101_Aligned.sortedByCoord.out.bam		ENCORE2	31624
USP39-BGKcLV42-101_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	3219					GRCh38	V40	USP39-BGKcLV42-101_Aligned.sortedByCoord.out.bam		ENCORE2	31714
USP39-BGKcLV42-101_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3219					GRCh38	V40	USP39-BGKcLV42-101_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGKcLV42-101_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31804
USP39-BGKcLV42-102_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3220	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	30423
USP39-BGKcLV42-102_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3220	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	30513
USP39-BGKcLV42-102_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3220					GRCh38	V40	USP39-BGKcLV42-102_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGKcLV42-102_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31355
USP39-BGKcLV42-102_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	3220					GRCh38	V40	USP39-BGKcLV42-102_Aligned.sortedByCoord.out.bam		ENCORE2	31445
USP39-BGKcLV42-102_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	3220					GRCh38	V40	USP39-BGKcLV42-102_Aligned.sortedByCoord.out.bam		ENCORE2	31535
USP39-BGKcLV42-102_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	3220					GRCh38	V40	USP39-BGKcLV42-102_Aligned.sortedByCoord.out.bam		ENCORE2	31625
USP39-BGKcLV42-102_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	3220					GRCh38	V40	USP39-BGKcLV42-102_Aligned.sortedByCoord.out.bam		ENCORE2	31715
USP39-BGKcLV42-102_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3220					GRCh38	V40	USP39-BGKcLV42-102_L001_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGKcLV42-102_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31805