SENP3 RNA-Seq in HepG2

General Information


RBP	SENP3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SENP3-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SENP3-BGHcLV45-61
Rep2	SENP3-BGHcLV45-62
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	45.5
Rep2_qPCR	35.9
Rep1_WB	91.0
Rep2_WB	84.6
Antibody Cat#	5591S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1627

Experiment Information (Status: Submitting)

	BGHcLV45-61	BGHcLV45-62
idx	1217	1217
TRCN#_or_BGC#	BGC#0001187	BGC#0001187
shRNA_or_gRNA_sequence	CCCCGACTCAAGTCAGGTGG	CCCCGACTCAAGTCAGGTGG
PAM	AGG	AGG
Name	SENP3_85	SENP3_85
Sample_ID	BGHcLV45-61	BGHcLV45-62
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	SENP3	SENP3
qPCR_result	45.5	35.9
Ave_qPCR	40.7
RT-qPCR_primer-F	ggagacctggtcatggacac
RT-qPCR_primer-R	accccatcataacccttggt
protein_conc	3489	3183
WB_result	91.0	84.6
Ave_WB
WB_DONE_date	10/18/24
MW	75kd
IP
antibody_Cat#	5591S	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	9751	9752

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SENP3	Product_ID: 5591S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SENP3-human

Experiment Status

	BGHcLV45-61	BGHcLV45-62
Sample_ID	BGHcLV45-61	BGHcLV45-62
Sample Name
Sample Name	SENP3-BGHcLV45-61	SENP3-BGHcLV45-62
RBP	SENP3	SENP3
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13712	13713

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-61	BGHcLV45-62
Sample #	27	28
Sample Name	SENP3-BGHcLV45-61	SENP3-BGHcLV45-62
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	286	296
Peak_Molarity	76.10	77.60
libSampleQC_DNA_Well	DNA_Library_set76/set1/C10.png	DNA_Library_set76/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/C4.png	RNA_Library_set76/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-61	BGHcLV45-62
RBP	SENP3	SENP3
Batch_ID	BGHcLV45	BGHcLV45
WB_result	91.000	84.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4636	4637

Sequencing Information

	BGHcLV45-61	BGHcLV45-62
Sample_ID	BGHcLV45-61	BGHcLV45-62
Sample Name	SENP3-BGHcLV45-61	SENP3-BGHcLV45-62
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	26,249,721	46,255,857
total_aligned_reads	22,518,938	43,365,642
unique_aligned_reads	21,203,404	40,897,373
percent_uniqueAligned	0.80776	0.88416
correlation_replicates	0.998706	0.998706
spikein_reads	14,954	20,828
percent_spikeins	0.00057	0.00045
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3347	3348

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
SENP3-BGHcLV45-61_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3347	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31838
SENP3-BGHcLV45-61_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3347	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31880
SENP3-BGHcLV45-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3347					GRCh38	V40	SENP3-BGHcLV45-61_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGHcLV45-61_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31922
SENP3-BGHcLV45-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3347					GRCh38	V40	SENP3-BGHcLV45-61_Aligned.sortedByCoord.out.bam		ENCORE2	31964
SENP3-BGHcLV45-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3347					GRCh38	V40	SENP3-BGHcLV45-61_Aligned.sortedByCoord.out.bam		ENCORE2	32006
SENP3-BGHcLV45-61_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3347					GRCh38	V40	SENP3-BGHcLV45-61_Aligned.sortedByCoord.out.bam		ENCORE2	32048
SENP3-BGHcLV45-61_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3347					GRCh38	V40	SENP3-BGHcLV45-61_Aligned.sortedByCoord.out.bam		ENCORE2	32090
SENP3-BGHcLV45-61_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3347					GRCh38	V40	SENP3-BGHcLV45-61_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGHcLV45-61_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32132
SENP3-BGHcLV45-62_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3348	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31839
SENP3-BGHcLV45-62_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3348	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31881
SENP3-BGHcLV45-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3348					GRCh38	V40	SENP3-BGHcLV45-62_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGHcLV45-62_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31923
SENP3-BGHcLV45-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3348					GRCh38	V40	SENP3-BGHcLV45-62_Aligned.sortedByCoord.out.bam		ENCORE2	31965
SENP3-BGHcLV45-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3348					GRCh38	V40	SENP3-BGHcLV45-62_Aligned.sortedByCoord.out.bam		ENCORE2	32007
SENP3-BGHcLV45-62_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3348					GRCh38	V40	SENP3-BGHcLV45-62_Aligned.sortedByCoord.out.bam		ENCORE2	32049
SENP3-BGHcLV45-62_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3348					GRCh38	V40	SENP3-BGHcLV45-62_Aligned.sortedByCoord.out.bam		ENCORE2	32091
SENP3-BGHcLV45-62_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3348					GRCh38	V40	SENP3-BGHcLV45-62_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGHcLV45-62_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32133