NEDD4 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV52-21	BGHcLV52-22
idx	1965	1966
TRCN#_or_BGC#	BGC#0001475	BGC#0001475
shRNA_or_gRNA_sequence	GGAAATGGCAACTTGCGCGG	GGAAATGGCAACTTGCGCGG
PAM	TGG	TGG
Name	NEDD4_98	NEDD4_98
Sample_ID	BGHcLV52-21	BGHcLV52-22
transduction_Date	1/8/26	1/8/26
days	D6	D6
RBP_name	NEDD4	NEDD4
qPCR_result	9	0
Ave_qPCR	4.5
RT-qPCR_primer-F	gagctgaaaaatggtggatca
RT-qPCR_primer-R	cagccatttgcttctggatt
protein_conc	3188	2534
WB_result	76.5	78.4
Ave_WB
WB_DONE_date	1/21/26
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	10154	10155

Western Blot

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

Experiment Status

	BGHcLV52-21	BGHcLV52-22
Sample_ID	BGHcLV52-21	BGHcLV52-22
Sample Name
Sample Name	NEDD4-BGHcLV52-21	NEDD4-BGHcLV52-22
RBP	NEDD4	NEDD4
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2026-09-16	2026-09-16
Project	ENCORE2	ENCORE2
Note
ID	14692	14693

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV52-21	BGHcLV52-22
Sample #	25	26
Sample Name	NEDD4-BGHcLV52-21	NEDD4-BGHcLV52-22
Sample_Name_Alias
Index Well Position	A04	B04
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	317	302
Peak_Molarity	40.80	48.50
libSampleQC_DNA_Well	DNA_Library_set82/set1/A11.png	DNA_Library_set82/set1/B11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set82/set1/A4.png	RNA_Library_set82/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGHcLV52-21	BGHcLV52-22
RBP	NEDD4	NEDD4
Batch_ID	BGHcLV52	BGHcLV52
WB_result	76.500	78.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4864	4865

Sequencing Information

	BGHcLV52-21	BGHcLV52-22
Sample_ID	BGHcLV52-21	BGHcLV52-22
Sample Name	NEDD4-BGHcLV52-21	NEDD4-BGHcLV52-22
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	27,691,436	31,528,641
total_aligned_reads	23,528,727	27,970,290
unique_aligned_reads	22,408,280	26,647,934
percent_uniqueAligned	0.80921	0.84520
correlation_replicates	0.999677	0.999677
spikein_reads	70,036	75,118
percent_spikeins	0.00253	0.00238
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3565	3566

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-BGHcLV52-21_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3565	NovaSeq6000	100	paired-ended	1				NT-BGHcLV52-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33674
NEDD4-BGHcLV52-21_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3565	NovaSeq6000	100	paired-ended	2				NT-BGHcLV52-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33732
NEDD4-BGHcLV52-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3565					GRCh38	V40	NEDD4-BGHcLV52-21_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGHcLV52-21_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33790
NEDD4-BGHcLV52-21_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	3565					GRCh38	V40	NEDD4-BGHcLV52-21_Aligned.sortedByCoord.out.bam		ENCORE2	33848
NEDD4-BGHcLV52-21_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	3565					GRCh38	V40	NEDD4-BGHcLV52-21_Aligned.sortedByCoord.out.bam		ENCORE2	33906
NEDD4-BGHcLV52-21_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	3565					GRCh38	V40	NEDD4-BGHcLV52-21_Aligned.sortedByCoord.out.bam		ENCORE2	33964
NEDD4-BGHcLV52-21_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	3565					GRCh38	V40	NEDD4-BGHcLV52-21_Aligned.sortedByCoord.out.bam		ENCORE2	34022
NEDD4-BGHcLV52-21_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3565					GRCh38	V40	NEDD4-BGHcLV52-21_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGHcLV52-21_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34080
NEDD4-BGHcLV52-22_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3566	NovaSeq6000	100	paired-ended	1				NT-BGHcLV52-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33675
NEDD4-BGHcLV52-22_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3566	NovaSeq6000	100	paired-ended	2				NT-BGHcLV52-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33733
NEDD4-BGHcLV52-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3566					GRCh38	V40	NEDD4-BGHcLV52-22_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGHcLV52-22_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33791
NEDD4-BGHcLV52-22_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	3566					GRCh38	V40	NEDD4-BGHcLV52-22_Aligned.sortedByCoord.out.bam		ENCORE2	33849
NEDD4-BGHcLV52-22_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	3566					GRCh38	V40	NEDD4-BGHcLV52-22_Aligned.sortedByCoord.out.bam		ENCORE2	33907
NEDD4-BGHcLV52-22_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	3566					GRCh38	V40	NEDD4-BGHcLV52-22_Aligned.sortedByCoord.out.bam		ENCORE2	33965
NEDD4-BGHcLV52-22_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	3566					GRCh38	V40	NEDD4-BGHcLV52-22_Aligned.sortedByCoord.out.bam		ENCORE2	34023
NEDD4-BGHcLV52-22_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3566					GRCh38	V40	NEDD4-BGHcLV52-22_R1.filtered.trimmed.paired.fastq.gz,NEDD4-BGHcLV52-22_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34081