CACYBP RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV50-11	BGHcLV50-11	BGHcLV50-12	BGHcLV50-12
idx	1828	1830	1829	1831
TRCN#_or_BGC#	BGC#0001401	BGC#0001401	BGC#0001401	BGC#0001401
shRNA_or_gRNA_sequence	ACGGATCTCGAACCTTCGCG	ACGGATCTCGAACCTTCGCG	ACGGATCTCGAACCTTCGCG	ACGGATCTCGAACCTTCGCG
PAM	AGG	AGG	AGG	AGG
Name	CACYBP_99U	CACYBP_99U	CACYBP_99U	CACYBP_99U
Sample_ID	BGHcLV50-11	BGHcLV50-11	BGHcLV50-12	BGHcLV50-12
transduction_Date	7/29/25	7/29/25	7/29/25	7/29/25
days	D6	D6	D6	D6
RBP_name	CACYBP	CACYBP	CACYBP	CACYBP
qPCR_result	45.3	45.3	62.8	62.8
Ave_qPCR	54.0	54.0
RT-qPCR_primer-F	ccatctctgtggaaggcagt	ccatctctgtggaaggcagt
RT-qPCR_primer-R	gggtcaggtaatcccacctt	gggtcaggtaatcccacctt
protein_conc	3206	3206	3076	3076
WB_result	51.1	57.6	52.8	57.3
Ave_WB
WB_DONE_date	8/11/25,8/19/25	10/10/25
MW	26kDa	26kDa
IP	Rabbit / I
antibody_Cat#	A302-904A	A302-905A	LOT# 1	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	10017	10019	10018	10020

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV50-11	BGHcLV50-12
Sample_ID	BGHcLV50-11	BGHcLV50-12
Sample Name
Sample Name	CACYBP-BGHcLV50-11	CACYBP-BGHcLV50-12
RBP	CACYBP	CACYBP
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14450	14451

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV50-11	BGHcLV50-12
Sample #	3	4
Sample Name	CACYBP-BGHcLV50-11	CACYBP-BGHcLV50-12
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-10-01	2025-10-01
Lib_ID	Lib-251001	Lib-251001
Tecan_Location
Tecan
Tecan_date
Size_bp	286	285
Peak_Molarity	58.90	58.30
libSampleQC_DNA_Well	DNA_Library_set80/set1/C10.png	DNA_Library_set80/set1/D10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set80/set1/C7.png	RNA_Library_set80/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-10-03	2025-10-03
Sample_ID	BGHcLV50-11	BGHcLV50-12
RBP	CACYBP	CACYBP
Batch_ID	BGHcLV50	BGHcLV50
WB_result	51.100	52.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4818	4819

Sequencing Information

	BGHcLV50-11	BGHcLV50-12
Sample_ID	BGHcLV50-11	BGHcLV50-12
Sample Name	CACYBP-BGHcLV50-11	CACYBP-BGHcLV50-12
Pool ID	Pool-251003	Pool-251003
LocalServer_folder	set80	set80
total_reads	17,560,017	16,238,378
total_aligned_reads	15,659,192	14,698,258
unique_aligned_reads	14,745,845	13,865,247
percent_uniqueAligned	0.83974	0.85386
correlation_replicates	0.991941	0.991941
spikein_reads	36,328	39,690
percent_spikeins	0.00207	0.00244
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3473	3474

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
CACYBP-BGHcLV50-11_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3473	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32974
CACYBP-BGHcLV50-11_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3473	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32998
CACYBP-BGHcLV50-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3473					GRCh38	V40	CACYBP-BGHcLV50-11_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACYBP-BGHcLV50-11_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33022
CACYBP-BGHcLV50-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3473					GRCh38	V40	CACYBP-BGHcLV50-11_Aligned.sortedByCoord.out.bam		ENCORE2	33046
CACYBP-BGHcLV50-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3473					GRCh38	V40	CACYBP-BGHcLV50-11_Aligned.sortedByCoord.out.bam		ENCORE2	33070
CACYBP-BGHcLV50-11_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3473					GRCh38	V40	CACYBP-BGHcLV50-11_Aligned.sortedByCoord.out.bam		ENCORE2	33094
CACYBP-BGHcLV50-11_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3473					GRCh38	V40	CACYBP-BGHcLV50-11_Aligned.sortedByCoord.out.bam		ENCORE2	33118
CACYBP-BGHcLV50-11_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3473					GRCh38	V40	CACYBP-BGHcLV50-11_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACYBP-BGHcLV50-11_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33142
CACYBP-BGHcLV50-12_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3474	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32975
CACYBP-BGHcLV50-12_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3474	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32999
CACYBP-BGHcLV50-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3474					GRCh38	V40	CACYBP-BGHcLV50-12_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACYBP-BGHcLV50-12_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33023
CACYBP-BGHcLV50-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3474					GRCh38	V40	CACYBP-BGHcLV50-12_Aligned.sortedByCoord.out.bam		ENCORE2	33047
CACYBP-BGHcLV50-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3474					GRCh38	V40	CACYBP-BGHcLV50-12_Aligned.sortedByCoord.out.bam		ENCORE2	33071
CACYBP-BGHcLV50-12_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3474					GRCh38	V40	CACYBP-BGHcLV50-12_Aligned.sortedByCoord.out.bam		ENCORE2	33095
CACYBP-BGHcLV50-12_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3474					GRCh38	V40	CACYBP-BGHcLV50-12_Aligned.sortedByCoord.out.bam		ENCORE2	33119
CACYBP-BGHcLV50-12_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3474					GRCh38	V40	CACYBP-BGHcLV50-12_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACYBP-BGHcLV50-12_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33143