NUP153 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-75	BGHcLV49-76
idx	1776	1777
TRCN#_or_BGC#	BGC#0001039	BGC#0001039
shRNA_or_gRNA_sequence	GTGGCGGCAAGATCCGGACG	GTGGCGGCAAGATCCGGACG
PAM	CGG	CGG
Name	NUP153_96	NUP153_96
Sample_ID	BGHcLV49-75	BGHcLV49-76
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	NUP153	NUP153
qPCR_result	26.4	39.9
Ave_qPCR	33.2
RT-qPCR_primer-F	accaaatgtttggcatgtga
RT-qPCR_primer-R	aaggcccagaagaggatgat
protein_conc	4899	3617
WB_result	90.7	93.4
Ave_WB
WB_DONE_date	7/3/25	need discussion
MW	154kd
IP
antibody_Cat#	A301-788A	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	9965	9966

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV49-75	BGHcLV49-76
Sample_ID	BGHcLV49-75	BGHcLV49-76
Sample Name
Sample Name	NUP153-BGHcLV49-75	NUP153-BGHcLV49-76
RBP	NUP153	NUP153
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14358	14359

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-75	BGHcLV49-76
Sample #	55	56
Sample Name	NUP153-BGHcLV49-75	NUP153-BGHcLV49-76
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	273	276
Peak_Molarity	74.70	81.10
libSampleQC_DNA_Well	DNA_Library_set81/set1/A5.png	DNA_Library_set81/set1/B5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/A8.png	RNA_Library_set81/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-75	BGHcLV49-76
RBP	NUP153	NUP153
Batch_ID	BGHcLV49	BGHcLV49
WB_result	90.700	93.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4800	4801

Sequencing Information

	BGHcLV49-75	BGHcLV49-76
Sample_ID	BGHcLV49-75	BGHcLV49-76
Sample Name	NUP153-BGHcLV49-75	NUP153-BGHcLV49-76
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	28,901,871	33,189,143
total_aligned_reads	25,004,043	29,266,255
unique_aligned_reads	23,580,371	27,630,136
percent_uniqueAligned	0.81588	0.83251
correlation_replicates	0.997958	0.997958
spikein_reads	100,818	98,336
percent_spikeins	0.00349	0.00296
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3527	3528

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
NUP153-BGHcLV49-75_S156_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3527	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33200
NUP153-BGHcLV49-75_S156_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3527	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33246
NUP153-BGHcLV49-75_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3527					GRCh38	V40	NUP153-BGHcLV49-75_S156_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGHcLV49-75_S156_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33292
NUP153-BGHcLV49-75_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3527					GRCh38	V40	NUP153-BGHcLV49-75_Aligned.sortedByCoord.out.bam		ENCORE2	33338
NUP153-BGHcLV49-75_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3527					GRCh38	V40	NUP153-BGHcLV49-75_Aligned.sortedByCoord.out.bam		ENCORE2	33384
NUP153-BGHcLV49-75_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3527					GRCh38	V40	NUP153-BGHcLV49-75_Aligned.sortedByCoord.out.bam		ENCORE2	33430
NUP153-BGHcLV49-75_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3527					GRCh38	V40	NUP153-BGHcLV49-75_Aligned.sortedByCoord.out.bam		ENCORE2	33476
NUP153-BGHcLV49-75_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3527					GRCh38	V40	NUP153-BGHcLV49-75_S156_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGHcLV49-75_S156_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33522
NUP153-BGHcLV49-76_S124_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3528	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33201
NUP153-BGHcLV49-76_S124_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3528	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33247
NUP153-BGHcLV49-76_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3528					GRCh38	V40	NUP153-BGHcLV49-76_S124_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGHcLV49-76_S124_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33293
NUP153-BGHcLV49-76_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3528					GRCh38	V40	NUP153-BGHcLV49-76_Aligned.sortedByCoord.out.bam		ENCORE2	33339
NUP153-BGHcLV49-76_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3528					GRCh38	V40	NUP153-BGHcLV49-76_Aligned.sortedByCoord.out.bam		ENCORE2	33385
NUP153-BGHcLV49-76_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3528					GRCh38	V40	NUP153-BGHcLV49-76_Aligned.sortedByCoord.out.bam		ENCORE2	33431
NUP153-BGHcLV49-76_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3528					GRCh38	V40	NUP153-BGHcLV49-76_Aligned.sortedByCoord.out.bam		ENCORE2	33477
NUP153-BGHcLV49-76_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3528					GRCh38	V40	NUP153-BGHcLV49-76_S124_L008_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGHcLV49-76_S124_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33523