USP39 RNA-Seq in HepG2

General Information


RBP	USP39
Cell_Line	HepG2
Method	CRISPR
Exp_Name	USP39-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	USP39-BGHcLV43-61
Rep2	USP39-BGHcLV43-62
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	63.6
Rep2_WB	63.3
Antibody Cat#	23303S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1593

Experiment Information (Status: Submitting)

	BGHcLV43-61	BGHcLV43-62
idx	1429	1430
TRCN#_or_BGC#	BGC#0001203	BGC#0001203
shRNA_or_gRNA_sequence	GAGTGGATTCTGAGGACCGG	GAGTGGATTCTGAGGACCGG
PAM	AGG	AGG
Name	USP39_86	USP39_86
Sample_ID	BGHcLV43-61	BGHcLV43-62
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	USP39	USP39
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	agctcatcattccccaagtg
RT-qPCR_primer-R	aggcaacttggtaagctgga
protein_conc	0	4701
WB_result	63.6	63.3
Ave_WB	63.4
WB_DONE_date	6/21/24
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	9684	9685

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV43-61	BGHcLV43-62
Sample_ID	BGHcLV43-61	BGHcLV43-62
Sample Name
Sample Name	USP39-BGHcLV43-61	USP39-BGHcLV43-62
RBP	USP39	USP39
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13276	13277

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-61	BGHcLV43-62
Sample #	49	50
Sample Name	USP39-BGHcLV43-61	USP39-BGHcLV43-62
Sample_Name_Alias
Index Well Position	A12	B12
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	299	300
Peak_Molarity	101.00	84.70
libSampleQC_DNA_Well	DNA_Library_set74/set2/A7.png	DNA_Library_set74/set2/B7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/E12.png	RNA_Library_set74/set1/F12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-61	BGHcLV43-62
RBP	USP39	USP39
Batch_ID	BGHcLV43	BGHcLV43
WB_result	63.600	63.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4408	4409

Sequencing Information

	BGHcLV43-61	BGHcLV43-62
Sample_ID	BGHcLV43-61	BGHcLV43-62
Sample Name	USP39-BGHcLV43-61	USP39-BGHcLV43-62
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	40,243,498	49,666,147
total_aligned_reads	36,523,774	46,075,880
unique_aligned_reads	34,300,002	43,313,313
percent_uniqueAligned	0.85231	0.87209
correlation_replicates	0.998973	0.998973
spikein_reads	32,860	20,024
percent_spikeins	0.00082	0.00040
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3275	3276

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-BGHcLV43-61_S139_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3275	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	30568
USP39-BGHcLV43-61_S139_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3275	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	30620
USP39-BGHcLV43-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3275					GRCh38	V40	USP39-BGHcLV43-61_S139_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGHcLV43-61_S139_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30672
USP39-BGHcLV43-61_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	3275					GRCh38	V40	USP39-BGHcLV43-61_Aligned.sortedByCoord.out.bam		ENCORE2	30724
USP39-BGHcLV43-61_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	3275					GRCh38	V40	USP39-BGHcLV43-61_Aligned.sortedByCoord.out.bam		ENCORE2	30776
USP39-BGHcLV43-61_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	3275					GRCh38	V40	USP39-BGHcLV43-61_Aligned.sortedByCoord.out.bam		ENCORE2	30828
USP39-BGHcLV43-61_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	3275					GRCh38	V40	USP39-BGHcLV43-61_Aligned.sortedByCoord.out.bam		ENCORE2	30880
USP39-BGHcLV43-61_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3275					GRCh38	V40	USP39-BGHcLV43-61_S139_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGHcLV43-61_S139_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30932
USP39-BGHcLV43-62_S140_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3276	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	30569
USP39-BGHcLV43-62_S140_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3276	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	30621
USP39-BGHcLV43-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3276					GRCh38	V40	USP39-BGHcLV43-62_S140_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGHcLV43-62_S140_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30673
USP39-BGHcLV43-62_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	3276					GRCh38	V40	USP39-BGHcLV43-62_Aligned.sortedByCoord.out.bam		ENCORE2	30725
USP39-BGHcLV43-62_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	3276					GRCh38	V40	USP39-BGHcLV43-62_Aligned.sortedByCoord.out.bam		ENCORE2	30777
USP39-BGHcLV43-62_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	3276					GRCh38	V40	USP39-BGHcLV43-62_Aligned.sortedByCoord.out.bam		ENCORE2	30829
USP39-BGHcLV43-62_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	3276					GRCh38	V40	USP39-BGHcLV43-62_Aligned.sortedByCoord.out.bam		ENCORE2	30881
USP39-BGHcLV43-62_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3276					GRCh38	V40	USP39-BGHcLV43-62_S140_L003_R1_001.filtered.trimmed.paired.fastq.gz,USP39-BGHcLV43-62_S140_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30933