CDC5L RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-15	BGHcLV49-16
idx	1714	1715
TRCN#_or_BGC#	BGC#0000688	BGC#0000688
shRNA_or_gRNA_sequence	GCCCGCTTGGCTAATACTCA	GCCCGCTTGGCTAATACTCA
PAM	GGG	GGG
Name	CDC5L_93	CDC5L_93
Sample_ID	BGHcLV49-15	BGHcLV49-16
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	CDC5L	CDC5L
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	atgggaccaaattgaacagg
RT-qPCR_primer-R	tttcttgttgtcgctgaacg
protein_conc	3365	3669
WB_result	61.8	49.8
Ave_WB
WB_DONE_date	6/17/25
MW	92kd
IP
antibody_Cat#	A301-681A	LOT# 1
Antibody DCC ID	ENCAB386CPV
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9903	9904

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CDC5L	Product_ID: A301-681A Lot_ID: 1 Source: Bethyl Labs Target Name: CDC5L-human

Experiment Status

	BGHcLV49-15	BGHcLV49-16
Sample_ID	BGHcLV49-15	BGHcLV49-16
Sample Name
Sample Name	CDC5L-BGHcLV49-15	CDC5L-BGHcLV49-16
RBP	CDC5L	CDC5L
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14334	14335

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-15	BGHcLV49-16
Sample #	31	32
Sample Name	CDC5L-BGHcLV49-15	CDC5L-BGHcLV49-16
Sample_Name_Alias
Index Well Position	A05	B05
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	262	264
Peak_Molarity	99.80	73.20
libSampleQC_DNA_Well	DNA_Library_set81/set1/A2.png	DNA_Library_set81/set1/B2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set81/set1/A5.png	RNA_Library_set81/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-15	BGHcLV49-16
RBP	CDC5L	CDC5L
Batch_ID	BGHcLV49	BGHcLV49
WB_result	61.800	49.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4776	4777

Sequencing Information

	BGHcLV49-15	BGHcLV49-16
Sample_ID	BGHcLV49-15	BGHcLV49-16
Sample Name	CDC5L-BGHcLV49-15	CDC5L-BGHcLV49-16
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	31,500,032	24,357,514
total_aligned_reads	25,917,795	20,411,244
unique_aligned_reads	24,479,703	19,247,023
percent_uniqueAligned	0.77713	0.79019
correlation_replicates	0.998638	0.998638
spikein_reads	109,474	86,490
percent_spikeins	0.00348	0.00355
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3503	3504

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
CDC5L-BGHcLV49-15_S115_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3503	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	33172
CDC5L-BGHcLV49-15_S115_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3503	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	33218
CDC5L-BGHcLV49-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3503					GRCh38	V40	CDC5L-BGHcLV49-15_S115_L008_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGHcLV49-15_S115_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33264
CDC5L-BGHcLV49-15_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	3503					GRCh38	V40	CDC5L-BGHcLV49-15_Aligned.sortedByCoord.out.bam		ENCORE2	33310
CDC5L-BGHcLV49-15_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	3503					GRCh38	V40	CDC5L-BGHcLV49-15_Aligned.sortedByCoord.out.bam		ENCORE2	33356
CDC5L-BGHcLV49-15_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	3503					GRCh38	V40	CDC5L-BGHcLV49-15_Aligned.sortedByCoord.out.bam		ENCORE2	33402
CDC5L-BGHcLV49-15_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	3503					GRCh38	V40	CDC5L-BGHcLV49-15_Aligned.sortedByCoord.out.bam		ENCORE2	33448
CDC5L-BGHcLV49-15_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3503					GRCh38	V40	CDC5L-BGHcLV49-15_S115_L008_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGHcLV49-15_S115_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33494
CDC5L-BGHcLV49-16_S118_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3504	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	33173
CDC5L-BGHcLV49-16_S118_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3504	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	33219
CDC5L-BGHcLV49-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3504					GRCh38	V40	CDC5L-BGHcLV49-16_S118_L008_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGHcLV49-16_S118_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33265
CDC5L-BGHcLV49-16_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	3504					GRCh38	V40	CDC5L-BGHcLV49-16_Aligned.sortedByCoord.out.bam		ENCORE2	33311
CDC5L-BGHcLV49-16_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	3504					GRCh38	V40	CDC5L-BGHcLV49-16_Aligned.sortedByCoord.out.bam		ENCORE2	33357
CDC5L-BGHcLV49-16_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	3504					GRCh38	V40	CDC5L-BGHcLV49-16_Aligned.sortedByCoord.out.bam		ENCORE2	33403
CDC5L-BGHcLV49-16_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	3504					GRCh38	V40	CDC5L-BGHcLV49-16_Aligned.sortedByCoord.out.bam		ENCORE2	33449
CDC5L-BGHcLV49-16_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3504					GRCh38	V40	CDC5L-BGHcLV49-16_S118_L008_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGHcLV49-16_S118_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33495