NUP153 RNA-Seq in K562

General Information


RBP	NUP153
Cell_Line	K562
Method	CRISPR
Exp_Name	NUP153-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	NUP153-BGKcLV37-23
Rep2	NUP153-BGKcLV37-24
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	3.5
Rep2_qPCR	5.7
Rep1_WB	87.3
Rep2_WB	81.8
Antibody Cat#	A301-788A
Antibody Lot#	lot # 1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	1054

Experiment Information (Status: Submitting)

	BGKcLV37-23	BGKcLV37-24
idx	1375	1376
TRCN#_or_BGC#	BGC#0001039	BGC#0001039
shRNA_or_gRNA_sequence	GTGGCGGCAAGATCCGGACG	GTGGCGGCAAGATCCGGACG
PAM	CGG	CGG
Name	NUP153_96	NUP153_96
Sample_ID	BGKcLV37-23	BGKcLV37-24
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	NUP153	NUP153
qPCR_result	3.5	5.7
Ave_qPCR	4.6
RT-qPCR_primer-F	accaaatgtttggcatgtga
RT-qPCR_primer-R	aaggcccagaagaggatgat
protein_conc	1995	1809
WB_result	87.3	81.8
Ave_WB	84.5
WB_DONE_date	9/27/22,12/12/22	JESS, Licor
MW	154kd
IP
antibody_Cat#	A301-788A	lot # 1
Antibody DCC ID	NO ID
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5525	5526

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NUP153	Product_ID: A301-788A Lot_ID: 1 Source: Bethyl Labs Target Name: NUP153-human

Experiment Status

	BGKcLV37-23	BGKcLV37-24
Sample_ID	BGKcLV37-23	BGKcLV37-24
Sample Name
Sample Name	NUP153-BGKcLV37-23	NUP153-BGKcLV37-24
RBP	NUP153	NUP153
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11092	11093

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-23	BGKcLV37-24
Sample #	31	32
Sample Name	NUP153-BGKcLV37-23	NUP153-BGKcLV37-24
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	297	283
Peak_Molarity	62.30	48.10
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/G4.png	DNA_Library_set54-56/set1/H4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/G4.png	RNA_Library_set54-56/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-23	BGKcLV37-24
RBP	NUP153	NUP153
Batch_ID	BGKcLV37	BGKcLV37
WB_result	87.300	81.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3402	3403

Sequencing Information

	BGKcLV37-23	BGKcLV37-24
Sample_ID	BGKcLV37-23	BGKcLV37-24
Sample Name	NUP153-BGKcLV37-23	NUP153-BGKcLV37-24
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	29,022,048	52,185,732
total_aligned_reads	27,532,374	48,910,272
unique_aligned_reads	25,271,942	45,499,051
percent_uniqueAligned	0.87078	0.87187
correlation_replicates	0.981450	0.981450
spikein_reads	2,162	9,790
percent_spikeins	0.00007	0.00019
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2275	2276

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-BGKcLV37-23_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2275	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8390
NUP153-BGKcLV37-23_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2275	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8440
NUP153-BGKcLV37-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2275					GRCh38	V40	NUP153-BGKcLV37-23_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGKcLV37-23_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25631
NUP153-BGKcLV37-23_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2275					GRCh38	V40	NUP153-BGKcLV37-23/Aligned.sortedByCoord.out.bam		ENCORE2	25681
NUP153-BGKcLV37-23_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2275					GRCh38	V40	NUP153-BGKcLV37-23/Aligned.sortedByCoord.out.bam		ENCORE2	25731
NUP153-BGKcLV37-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2275					GRCh38	V40	NUP153-BGKcLV37-23/Aligned.sortedByCoord.out.bam		ENCORE2	25781
NUP153-BGKcLV37-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2275					GRCh38	V40	NUP153-BGKcLV37-23/Aligned.sortedByCoord.out.bam		ENCORE2	25831
NUP153-BGKcLV37-23_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2275					GRCh38	V40	NUP153-BGKcLV37-23_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGKcLV37-23_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25881
NUP153-BGKcLV37-24_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2276	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8391
NUP153-BGKcLV37-24_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2276	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8441
NUP153-BGKcLV37-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2276					GRCh38	V40	NUP153-BGKcLV37-24_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGKcLV37-24_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25632
NUP153-BGKcLV37-24_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2276					GRCh38	V40	NUP153-BGKcLV37-24/Aligned.sortedByCoord.out.bam		ENCORE2	25682
NUP153-BGKcLV37-24_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2276					GRCh38	V40	NUP153-BGKcLV37-24/Aligned.sortedByCoord.out.bam		ENCORE2	25732
NUP153-BGKcLV37-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2276					GRCh38	V40	NUP153-BGKcLV37-24/Aligned.sortedByCoord.out.bam		ENCORE2	25782
NUP153-BGKcLV37-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2276					GRCh38	V40	NUP153-BGKcLV37-24/Aligned.sortedByCoord.out.bam		ENCORE2	25832
NUP153-BGKcLV37-24_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2276					GRCh38	V40	NUP153-BGKcLV37-24_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,NUP153-BGKcLV37-24_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25882