SNUPN RNA-Seq in K562

General Information


RBP	SNUPN
Cell_Line	K562
Method	CRISPR
Exp_Name	SNUPN-BGKcLV53-K562
ENCODE_series_ID
Batch_ID	BGKcLV53
Pool ID	Pool-260528
Local_Set_Name	set82
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SNUPN-BGKcLV53-131
Rep2	SNUPN-BGKcLV53-132
CN1	NT-BGKcLV53-1
CN2	NT-BGKcLV53-2
Rep1_qPCR	49.5
Rep2_qPCR	52.8
Rep1_WB	78.5
Rep2_WB	65.1
Antibody Cat#	A305-567A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1740

Experiment Information (Status: Sequenced)

	BGKcLV53-131	BGKcLV53-131	BGKcLV53-132	BGKcLV53-132
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001553	BGC#0001553	BGC#0001553	BGC#0001553
shRNA_or_gRNA_sequence	CTGGATGTGATGTGCTGGCG	CTGGATGTGATGTGCTGGCG	CTGGATGTGATGTGCTGGCG	CTGGATGTGATGTGCTGGCG
PAM	GGG	GGG	GGG	GGG
Name	SNUPN_77	SNUPN_77	SNUPN_77	SNUPN_77
Sample_ID	BGKcLV53-131	BGKcLV53-131	BGKcLV53-132	BGKcLV53-132
transduction_Date	2/24/26	2/24/26	2/24/26	2/24/26
days	D6	D6	D6	D6
RBP_name	SNUPN	SNUPN	SNUPN	SNUPN
qPCR_result	49.5		52.8
Ave_qPCR	51.2
RT-qPCR_primer-F	tgaagaaatggacattgacactg
RT-qPCR_primer-R	tccattcctgccccaaatct
protein_conc	4667	4667	4450	4450
WB_result	78.5	85.1	65.1	89.3575
Ave_WB
WB_DONE_date	4/17/26,4/6/26	5/7/26
MW	41kd	41kd
IP
antibody_Cat#	A305-567A	A305-568A	LOT #1	LOT #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	6493	6495	6494	6496

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SNUPN	Product_ID: A305-567A Lot_ID: 1 Source: Bethyl Labs Target Name: SNUPN-human
SNUPN	Product_ID: A305-568A Lot_ID: 1 Source: Bethyl Labs Target Name: SNUPN-human

Experiment Status

	BGKcLV53-131	BGKcLV53-131	BGKcLV53-132	BGKcLV53-132
Sample_ID	BGKcLV53-131	BGKcLV53-131	BGKcLV53-132	BGKcLV53-132
Sample Name
Sample Name	SNUPN-BGKcLV53-131		SNUPN-BGKcLV53-132
RBP	SNUPN	SNUPN	SNUPN	SNUPN
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Sequenced	NotSatisfied	Sequenced	NotSatisfied
Status_date	2026-09-16	2026-05-18	2026-09-16	2026-05-18
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14804	14922	14805	14923

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV53-131	BGKcLV53-132
Sample #	55	56
Sample Name	SNUPN-BGKcLV53-131	SNUPN-BGKcLV53-132
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-26	2026-05-26
Lib_ID	Lib-260526	Lib-260526
Tecan_Location
Tecan
Tecan_date
Size_bp	282	285
Peak_Molarity	71.20	63.30
libSampleQC_DNA_Well	DNA_Library_set82/set2/E11.png	DNA_Library_set82/set2/F11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set82/set2/E8.png	RNA_Library_set82/set2/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-27	2026-05-27
Sample_ID	BGKcLV53-131	BGKcLV53-132
RBP	SNUPN	SNUPN
Batch_ID	BGKcLV53	BGKcLV53
WB_result	78.500	65.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4894	4895

Sequencing Information

	BGKcLV53-131	BGKcLV53-132
Sample_ID	BGKcLV53-131	BGKcLV53-132
Sample Name	SNUPN-BGKcLV53-131	SNUPN-BGKcLV53-132
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	46,239,919	39,556,646
total_aligned_reads	41,831,916	35,615,441
unique_aligned_reads	38,802,164	33,054,659
percent_uniqueAligned	0.83915	0.83563
correlation_replicates	0.996481	0.996481
spikein_reads	38,386	47,058
percent_spikeins	0.00083	0.00119
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3595	3596

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
SNUPN-BGKcLV53-131_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3595	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33702
SNUPN-BGKcLV53-131_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3595	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33760
SNUPN-BGKcLV53-131_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3595					GRCh38	V40	SNUPN-BGKcLV53-131_R1.filtered.trimmed.paired.fastq.gz,SNUPN-BGKcLV53-131_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33820
SNUPN-BGKcLV53-131_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3595					GRCh38	V40	SNUPN-BGKcLV53-131_Aligned.sortedByCoord.out.bam		ENCORE2	33878
SNUPN-BGKcLV53-131_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3595					GRCh38	V40	SNUPN-BGKcLV53-131_Aligned.sortedByCoord.out.bam		ENCORE2	33936
SNUPN-BGKcLV53-131_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3595					GRCh38	V40	SNUPN-BGKcLV53-131_Aligned.sortedByCoord.out.bam		ENCORE2	33994
SNUPN-BGKcLV53-131_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3595					GRCh38	V40	SNUPN-BGKcLV53-131_Aligned.sortedByCoord.out.bam		ENCORE2	34052
SNUPN-BGKcLV53-131_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3595					GRCh38	V40	SNUPN-BGKcLV53-131_R1.filtered.trimmed.paired.fastq.gz,SNUPN-BGKcLV53-131_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34110
SNUPN-BGKcLV53-132_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3596	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33703
SNUPN-BGKcLV53-132_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3596	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33761
SNUPN-BGKcLV53-132_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3596					GRCh38	V40	SNUPN-BGKcLV53-132_R1.filtered.trimmed.paired.fastq.gz,SNUPN-BGKcLV53-132_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33821
SNUPN-BGKcLV53-132_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3596					GRCh38	V40	SNUPN-BGKcLV53-132_Aligned.sortedByCoord.out.bam		ENCORE2	33879
SNUPN-BGKcLV53-132_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3596					GRCh38	V40	SNUPN-BGKcLV53-132_Aligned.sortedByCoord.out.bam		ENCORE2	33937
SNUPN-BGKcLV53-132_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3596					GRCh38	V40	SNUPN-BGKcLV53-132_Aligned.sortedByCoord.out.bam		ENCORE2	33995
SNUPN-BGKcLV53-132_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3596					GRCh38	V40	SNUPN-BGKcLV53-132_Aligned.sortedByCoord.out.bam		ENCORE2	34053
SNUPN-BGKcLV53-132_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3596					GRCh38	V40	SNUPN-BGKcLV53-132_R1.filtered.trimmed.paired.fastq.gz,SNUPN-BGKcLV53-132_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34111