NEDD4 RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV51-71	BGKcLV51-72
idx	0	0
TRCN#_or_BGC#	BGC#0001475	BGC#0001475
shRNA_or_gRNA_sequence	GGAAATGGCAACTTGCGCGG	GGAAATGGCAACTTGCGCGG
PAM	TGG	TGG
Name	NEDD4_98	NEDD4_98
Sample_ID	BGKcLV51-71	BGKcLV51-72
transduction_Date	9/30/2025	9/30/2025
days	D6	D6
RBP_name	NEDD4	NEDD4
qPCR_result	8.7	0.8
Ave_qPCR	4.8
RT-qPCR_primer-F	gagctgaaaaatggtggatca
RT-qPCR_primer-R	cagccatttgcttctggatt
protein_conc	2452	2885
WB_result	68.8	69.8
Ave_WB
WB_DONE_date	10/28/25
MW	149kd
IP
antibody_Cat#	A303-254A	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	6312	6313

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NEDD4	Product_ID: A303-254 Lot_ID: 1 Source: Bethyl Labs Target Name: NEDD4-human

Experiment Status

	BGKcLV51-71	BGKcLV51-72
Sample_ID	BGKcLV51-71	BGKcLV51-72
Sample Name
Sample Name	NEDD4-BGKcLV51-71	NEDD4-BGKcLV51-72
RBP	NEDD4	NEDD4
Cell_Line	K562	K562
Exp UID
Status	Sequenced	Sequenced
Status_date	2026-09-16	2026-09-16
Project	ENCORE2	ENCORE2
Note
ID	14576	14577

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV51-71	BGKcLV51-72
Sample #	11	12
Sample Name	NEDD4-BGKcLV51-71	NEDD4-BGKcLV51-72
Sample_Name_Alias
Index Well Position	C02	D02
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	300	303
Peak_Molarity	54.50	87.50
libSampleQC_DNA_Well	DNA_Library_set82/set1/C9.png	DNA_Library_set82/set1/D9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set82/set1/C2.png	RNA_Library_set82/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGKcLV51-71	BGKcLV51-72
RBP	NEDD4	NEDD4
Batch_ID	BGKcLV51	BGKcLV51
WB_result	68.800	69.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4850	4851

Sequencing Information

	BGKcLV51-71	BGKcLV51-72
Sample_ID	BGKcLV51-71	BGKcLV51-72
Sample Name	NEDD4-BGKcLV51-71	NEDD4-BGKcLV51-72
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	30,884,503	31,736,943
total_aligned_reads	25,851,497	30,054,350
unique_aligned_reads	24,160,130	28,178,515
percent_uniqueAligned	0.78227	0.88788
correlation_replicates	0.992785	0.992785
spikein_reads	67,808	92,076
percent_spikeins	0.00220	0.00290
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3551	3552

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
NEDD4-BGKcLV51-71_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3551	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33676
NEDD4-BGKcLV51-71_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3551	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33734
NEDD4-BGKcLV51-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3551					GRCh38	V40	NEDD4-BGKcLV51-71_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGKcLV51-71_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33792
NEDD4-BGKcLV51-71_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	3551					GRCh38	V40	NEDD4-BGKcLV51-71_Aligned.sortedByCoord.out.bam		ENCORE2	33850
NEDD4-BGKcLV51-71_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	3551					GRCh38	V40	NEDD4-BGKcLV51-71_Aligned.sortedByCoord.out.bam		ENCORE2	33908
NEDD4-BGKcLV51-71_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	3551					GRCh38	V40	NEDD4-BGKcLV51-71_Aligned.sortedByCoord.out.bam		ENCORE2	33966
NEDD4-BGKcLV51-71_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	3551					GRCh38	V40	NEDD4-BGKcLV51-71_Aligned.sortedByCoord.out.bam		ENCORE2	34024
NEDD4-BGKcLV51-71_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3551					GRCh38	V40	NEDD4-BGKcLV51-71_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGKcLV51-71_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34082
NEDD4-BGKcLV51-72_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3552	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33677
NEDD4-BGKcLV51-72_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3552	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33735
NEDD4-BGKcLV51-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3552					GRCh38	V40	NEDD4-BGKcLV51-72_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGKcLV51-72_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33793
NEDD4-BGKcLV51-72_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	3552					GRCh38	V40	NEDD4-BGKcLV51-72_Aligned.sortedByCoord.out.bam		ENCORE2	33851
NEDD4-BGKcLV51-72_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	3552					GRCh38	V40	NEDD4-BGKcLV51-72_Aligned.sortedByCoord.out.bam		ENCORE2	33909
NEDD4-BGKcLV51-72_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	3552					GRCh38	V40	NEDD4-BGKcLV51-72_Aligned.sortedByCoord.out.bam		ENCORE2	33967
NEDD4-BGKcLV51-72_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	3552					GRCh38	V40	NEDD4-BGKcLV51-72_Aligned.sortedByCoord.out.bam		ENCORE2	34025
NEDD4-BGKcLV51-72_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3552					GRCh38	V40	NEDD4-BGKcLV51-72_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGKcLV51-72_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34083