SEC23IP RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV51-95	BGKcLV51-96
idx	0	0
TRCN#_or_BGC#	BGC#0000847	BGC#0000847
shRNA_or_gRNA_sequence	AAGTAAGTTAGTGCCCGATG	AAGTAAGTTAGTGCCCGATG
PAM	AGG	AGG
Name	SEC23IP_94	SEC23IP_94
Sample_ID	BGKcLV51-95	BGKcLV51-96
transduction_Date	9/30/2025	9/30/2025
days	D6	D6
RBP_name	SEC23IP	SEC23IP
qPCR_result	56.9	58.2
Ave_qPCR	57.6
RT-qPCR_primer-F	tcctcagtgccagatgaatg
RT-qPCR_primer-R	ccacaaacaccaaatggtca
protein_conc	2027	2164
WB_result	70.4	84.0
Ave_WB
WB_DONE_date	10/30/25
MW
IP
antibody_Cat#	A300-592A	lot# 1
Antibody DCC ID	ENCAB911OUO
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	6336	6337

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SEC23IP	Product_ID: A300-592A Lot_ID: 1 Source: Bethyl Labs Target Name: SEC23IP-human

Experiment Status

	BGKcLV51-95	BGKcLV51-96
Sample_ID	BGKcLV51-95	BGKcLV51-96
Sample Name
Sample Name	SEC23IP-BGKcLV51-95	SEC23IP-BGKcLV51-96
RBP	SEC23IP	SEC23IP
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2026-09-16	2026-09-16
Project	ENCORE2	ENCORE2
Note
ID	14582	14583

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV51-95	BGKcLV51-96
Sample #	17	18
Sample Name	SEC23IP-BGKcLV51-95	SEC23IP-BGKcLV51-96
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-18	2026-05-18
Lib_ID	Lib-260518	Lib-260518
Tecan_Location
Tecan
Tecan_date
Size_bp	292	300
Peak_Molarity	39.10	41.10
libSampleQC_DNA_Well	DNA_Library_set82/set1/A10.png	DNA_Library_set82/set1/B10.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set82/set1/A3.png	RNA_Library_set82/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGKcLV51-95	BGKcLV51-96
RBP	SEC23IP	SEC23IP
Batch_ID	BGKcLV51	BGKcLV51
WB_result	70.400	84.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4856	4857

Sequencing Information

	BGKcLV51-95	BGKcLV51-96
Sample_ID	BGKcLV51-95	BGKcLV51-96
Sample Name	SEC23IP-BGKcLV51-95	SEC23IP-BGKcLV51-96
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	26,104,847	36,067,493
total_aligned_reads	21,830,672	29,925,488
unique_aligned_reads	20,401,573	27,995,421
percent_uniqueAligned	0.78152	0.77620
correlation_replicates	0.998464	0.998464
spikein_reads	105,730	104,520
percent_spikeins	0.00405	0.00290
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3557	3558

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
SEC23IP-BGKcLV51-95_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3557	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33696
SEC23IP-BGKcLV51-95_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3557	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33754
SEC23IP-BGKcLV51-95_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3557					GRCh38	V40	SEC23IP-BGKcLV51-95_R1.filtered.trimmed.paired.fastq.gz,SEC23IP-BGKcLV51-95_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33814
SEC23IP-BGKcLV51-95_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	3557					GRCh38	V40	SEC23IP-BGKcLV51-95_Aligned.sortedByCoord.out.bam		ENCORE2	33872
SEC23IP-BGKcLV51-95_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	3557					GRCh38	V40	SEC23IP-BGKcLV51-95_Aligned.sortedByCoord.out.bam		ENCORE2	33930
SEC23IP-BGKcLV51-95_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	3557					GRCh38	V40	SEC23IP-BGKcLV51-95_Aligned.sortedByCoord.out.bam		ENCORE2	33988
SEC23IP-BGKcLV51-95_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	3557					GRCh38	V40	SEC23IP-BGKcLV51-95_Aligned.sortedByCoord.out.bam		ENCORE2	34046
SEC23IP-BGKcLV51-95_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3557					GRCh38	V40	SEC23IP-BGKcLV51-95_R1.filtered.trimmed.paired.fastq.gz,SEC23IP-BGKcLV51-95_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34104
SEC23IP-BGKcLV51-96_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3558	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33697
SEC23IP-BGKcLV51-96_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3558	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33755
SEC23IP-BGKcLV51-96_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3558					GRCh38	V40	SEC23IP-BGKcLV51-96_R1.filtered.trimmed.paired.fastq.gz,SEC23IP-BGKcLV51-96_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33815
SEC23IP-BGKcLV51-96_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	3558					GRCh38	V40	SEC23IP-BGKcLV51-96_Aligned.sortedByCoord.out.bam		ENCORE2	33873
SEC23IP-BGKcLV51-96_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	3558					GRCh38	V40	SEC23IP-BGKcLV51-96_Aligned.sortedByCoord.out.bam		ENCORE2	33931
SEC23IP-BGKcLV51-96_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	3558					GRCh38	V40	SEC23IP-BGKcLV51-96_Aligned.sortedByCoord.out.bam		ENCORE2	33989
SEC23IP-BGKcLV51-96_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	3558					GRCh38	V40	SEC23IP-BGKcLV51-96_Aligned.sortedByCoord.out.bam		ENCORE2	34047
SEC23IP-BGKcLV51-96_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3558					GRCh38	V40	SEC23IP-BGKcLV51-96_R1.filtered.trimmed.paired.fastq.gz,SEC23IP-BGKcLV51-96_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34105