SENP3 RNA-Seq in K562

General Information


RBP	SENP3
Cell_Line	K562
Method	CRISPR
Exp_Name	SENP3-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SENP3-BGKcLV44-61
Rep2	SENP3-BGKcLV44-62
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	60.1
Rep2_qPCR	63.5
Rep1_WB	70.9
Rep2_WB	63.6
Antibody Cat#	5591S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1608

Experiment Information (Status: Submitting)

	BGKcLV44-61	BGKcLV44-62
idx	0	0
TRCN#_or_BGC#	BGC#0001187	BGC#0001187
shRNA_or_gRNA_sequence	CCCCGACTCAAGTCAGGTGG	CCCCGACTCAAGTCAGGTGG
PAM	AGG	AGG
Name	SENP3_85	SENP3_85
Sample_ID	BGKcLV44-61	BGKcLV44-62
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	SENP3	SENP3
qPCR_result	60.1	63.5
Ave_qPCR	61.8
RT-qPCR_primer-F	ggagacctggtcatggacac
RT-qPCR_primer-R	accccatcataacccttggt
protein_conc	4177	4711
WB_result	70.9	63.6
Ave_WB	67.2
WB_DONE_date	8/14/24
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	5944	5945

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

	BGKcLV44-61	BGKcLV44-62
Sample_ID	BGKcLV44-61	BGKcLV44-62
Sample Name
Sample Name	SENP3-BGKcLV44-61	SENP3-BGKcLV44-62
RBP	SENP3	SENP3
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13608	13609

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-61	BGKcLV44-62
Sample #	37	38
Sample Name	SENP3-BGKcLV44-61	SENP3-BGKcLV44-62
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	297	291
Peak_Molarity	86.30	73.30
libSampleQC_DNA_Well	DNA_Library_set75/set1/E10.png	DNA_Library_set75/set1/F10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set75/set1/E4.png	RNA_Library_set75/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-61	BGKcLV44-62
RBP	SENP3	SENP3
Batch_ID	BGKcLV44	BGKcLV44
WB_result	70.900	63.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4596	4597

Sequencing Information

	BGKcLV44-61	BGKcLV44-62
Sample_ID	BGKcLV44-61	BGKcLV44-62
Sample Name	SENP3-BGKcLV44-61	SENP3-BGKcLV44-62
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	51,035,845	54,083,828
total_aligned_reads	48,900,405	51,489,872
unique_aligned_reads	45,346,607	47,879,070
percent_uniqueAligned	0.88852	0.88528
correlation_replicates	0.995319	0.995319
spikein_reads	65,858	62,568
percent_spikeins	0.00129	0.00116
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3307	3308

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-BGKcLV44-61_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3307	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30966
SENP3-BGKcLV44-61_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3307	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31008
SENP3-BGKcLV44-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3307					GRCh38	V40	SENP3-BGKcLV44-61_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGKcLV44-61_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31050
SENP3-BGKcLV44-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3307					GRCh38	V40	SENP3-BGKcLV44-61_Aligned.sortedByCoord.out.bam		ENCORE2	31092
SENP3-BGKcLV44-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3307					GRCh38	V40	SENP3-BGKcLV44-61_Aligned.sortedByCoord.out.bam		ENCORE2	31134
SENP3-BGKcLV44-61_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3307					GRCh38	V40	SENP3-BGKcLV44-61_Aligned.sortedByCoord.out.bam		ENCORE2	31176
SENP3-BGKcLV44-61_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3307					GRCh38	V40	SENP3-BGKcLV44-61_Aligned.sortedByCoord.out.bam		ENCORE2	31218
SENP3-BGKcLV44-61_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3307					GRCh38	V40	SENP3-BGKcLV44-61_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGKcLV44-61_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31260
SENP3-BGKcLV44-62_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3308	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30967
SENP3-BGKcLV44-62_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3308	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31009
SENP3-BGKcLV44-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3308					GRCh38	V40	SENP3-BGKcLV44-62_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGKcLV44-62_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31051
SENP3-BGKcLV44-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3308					GRCh38	V40	SENP3-BGKcLV44-62_Aligned.sortedByCoord.out.bam		ENCORE2	31093
SENP3-BGKcLV44-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3308					GRCh38	V40	SENP3-BGKcLV44-62_Aligned.sortedByCoord.out.bam		ENCORE2	31135
SENP3-BGKcLV44-62_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3308					GRCh38	V40	SENP3-BGKcLV44-62_Aligned.sortedByCoord.out.bam		ENCORE2	31177
SENP3-BGKcLV44-62_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3308					GRCh38	V40	SENP3-BGKcLV44-62_Aligned.sortedByCoord.out.bam		ENCORE2	31219
SENP3-BGKcLV44-62_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3308					GRCh38	V40	SENP3-BGKcLV44-62_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,SENP3-BGKcLV44-62_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31261