EDC4 RNA-Seq in K562

Experiment Information (Status: Sequenced)

	BGKcLV53-43	BGKcLV53-43	BGKcLV53-44	BGKcLV53-44
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001461	BGC#0001461	BGC#0001461	BGC#0001461
shRNA_or_gRNA_sequence	CTGCGCGAGCATCGACATCG	CTGCGCGAGCATCGACATCG	CTGCGCGAGCATCGACATCG	CTGCGCGAGCATCGACATCG
PAM	AGG	AGG	AGG	AGG
Name	EDC4_99B	EDC4_99B	EDC4_99B	EDC4_99B
Sample_ID	BGKcLV53-43	BGKcLV53-43	BGKcLV53-44	BGKcLV53-44
transduction_Date	2/24/26	2/24/26	2/24/26	2/24/26
days	D6	D6	D6	D6
RBP_name	EDC4	EDC4	EDC4	EDC4
qPCR_result	45.5		55.9
Ave_qPCR	50.7
RT-qPCR_primer-F	ggaggtggagattgtggcta
RT-qPCR_primer-R	ccagtcatacttggcgacag
protein_conc	3789	3789	3479	3479
WB_result	78.5		71.8
Ave_WB
WB_DONE_date	3/17/26	5/5/26
MW	152KD	152KD
IP
antibody_Cat#	A300-745A	A300-746A	lot# 2	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	6403	6405	6404	6406

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EDC4	Product_ID: A300-745A Lot_ID: 2 Source: Bethyl Labs Target Name: EDC4-human

Experiment Status

	BGKcLV53-43	BGKcLV53-43	BGKcLV53-44	BGKcLV53-44
Sample_ID	BGKcLV53-43	BGKcLV53-43	BGKcLV53-44	BGKcLV53-44
Sample Name
Sample Name	EDC4-BGKcLV53-43		EDC4-BGKcLV53-44
RBP	EDC4	EDC4	EDC4	EDC4
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Sequenced	NotSatisfied	Sequenced	NotSatisfied
Status_date	2026-09-16	2026-05-18	2026-09-16	2026-05-18
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14792	14844	14793	14845

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV53-43	BGKcLV53-44
Sample #	43	44
Sample Name	EDC4-BGKcLV53-43	EDC4-BGKcLV53-44
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-26	2026-05-26
Lib_ID	Lib-260526	Lib-260526
Tecan_Location
Tecan
Tecan_date
Size_bp	292	295
Peak_Molarity	63.00	70.50
libSampleQC_DNA_Well	DNA_Library_set82/set2/A10.png	DNA_Library_set82/set2/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set82/set2/A7.png	RNA_Library_set82/set2/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-27	2026-05-27
Sample_ID	BGKcLV53-43	BGKcLV53-44
RBP	EDC4	EDC4
Batch_ID	BGKcLV53	BGKcLV53
WB_result	78.500	71.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4882	4883

Sequencing Information

	BGKcLV53-43	BGKcLV53-44
Sample_ID	BGKcLV53-43	BGKcLV53-44
Sample Name	EDC4-BGKcLV53-43	EDC4-BGKcLV53-44
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	26,590,908	35,769,796
total_aligned_reads	22,800,312	33,615,755
unique_aligned_reads	21,088,279	31,255,059
percent_uniqueAligned	0.79306	0.87378
correlation_replicates	0.999807	0.999807
spikein_reads	62,308	56,922
percent_spikeins	0.00234	0.00159
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3583	3584

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
EDC4-BGKcLV53-43_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3583	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33666
EDC4-BGKcLV53-43_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3583	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33724
EDC4-BGKcLV53-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3583					GRCh38	V40	EDC4-BGKcLV53-43_R1.filtered.trimmed.paired.fastq.gz,EDC4-BGKcLV53-43_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33782
EDC4-BGKcLV53-43_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	3583					GRCh38	V40	EDC4-BGKcLV53-43_Aligned.sortedByCoord.out.bam		ENCORE2	33840
EDC4-BGKcLV53-43_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	3583					GRCh38	V40	EDC4-BGKcLV53-43_Aligned.sortedByCoord.out.bam		ENCORE2	33898
EDC4-BGKcLV53-43_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	3583					GRCh38	V40	EDC4-BGKcLV53-43_Aligned.sortedByCoord.out.bam		ENCORE2	33956
EDC4-BGKcLV53-43_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	3583					GRCh38	V40	EDC4-BGKcLV53-43_Aligned.sortedByCoord.out.bam		ENCORE2	34014
EDC4-BGKcLV53-43_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3583					GRCh38	V40	EDC4-BGKcLV53-43_R1.filtered.trimmed.paired.fastq.gz,EDC4-BGKcLV53-43_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34072
EDC4-BGKcLV53-44_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3584	NovaSeq6000	100	paired-ended	1				NT-BGKcLV53-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33667
EDC4-BGKcLV53-44_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3584	NovaSeq6000	100	paired-ended	2				NT-BGKcLV53-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV53-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33725
EDC4-BGKcLV53-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3584					GRCh38	V40	EDC4-BGKcLV53-44_R1.filtered.trimmed.paired.fastq.gz,EDC4-BGKcLV53-44_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33783
EDC4-BGKcLV53-44_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	3584					GRCh38	V40	EDC4-BGKcLV53-44_Aligned.sortedByCoord.out.bam		ENCORE2	33841
EDC4-BGKcLV53-44_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	3584					GRCh38	V40	EDC4-BGKcLV53-44_Aligned.sortedByCoord.out.bam		ENCORE2	33899
EDC4-BGKcLV53-44_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	3584					GRCh38	V40	EDC4-BGKcLV53-44_Aligned.sortedByCoord.out.bam		ENCORE2	33957
EDC4-BGKcLV53-44_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	3584					GRCh38	V40	EDC4-BGKcLV53-44_Aligned.sortedByCoord.out.bam		ENCORE2	34015
EDC4-BGKcLV53-44_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3584					GRCh38	V40	EDC4-BGKcLV53-44_R1.filtered.trimmed.paired.fastq.gz,EDC4-BGKcLV53-44_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34073