CANX RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV52-9	BGHcLV52-9	BGHcLV52-9	BGHcLV52-10	BGHcLV52-10	BGHcLV52-10
idx	1949	1951	1953	1950	1952	1954
TRCN#_or_BGC#	BGC#0000462	BGC#0000462	BGC#0000462	BGC#0000462	BGC#0000462	BGC#0000462
shRNA_or_gRNA_sequence	TCGTATAAGGGGTCTTGTCA	TCGTATAAGGGGTCTTGTCA	TCGTATAAGGGGTCTTGTCA	TCGTATAAGGGGTCTTGTCA	TCGTATAAGGGGTCTTGTCA	TCGTATAAGGGGTCTTGTCA
PAM	TGG	TGG	TGG	TGG	TGG	TGG
Name	CANX_89	CANX_89	CANX_89	CANX_89	CANX_89	CANX_89
Sample_ID	BGHcLV52-9	BGHcLV52-9	BGHcLV52-9	BGHcLV52-10	BGHcLV52-10	BGHcLV52-10
transduction_Date	1/8/26	1/8/26	1/8/26	1/8/26	1/8/26	1/8/26
days	D6	D6	D6	D6	D6	D6
RBP_name	CANX	CANX	CANX	CANX	CANX	CANX
qPCR_result	78.3	78.3		79.3	79.3
Ave_qPCR	78.8	78.8
RT-qPCR_primer-F	atgtggtggtgcctatgtga	atgtggtggtgcctatgtga
RT-qPCR_primer-R	ggggtcttgtcatggaactg	ggggtcttgtcatggaactg
protein_conc	2845	2845	2845	2697	2697	2697
WB_result	52.7	75.7		56.2	73.4
Ave_WB
WB_DONE_date	1/23/26	1/30/26	2/17/26			no band
MW	68kd		68kd
IP
antibody_Cat#	A303-694A	A303-696A	MA3-027	lot# 1	lot# 1	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action		Ready			Ready
Library_start_date
repeat_library
Note
ID	10138	10140	10142	10139	10141	10143

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CANX	Product_ID: A303-694A Lot_ID: 1 Source: Bethyl Labs Target Name: CANX-human
CANX	Product_ID: A303-696A Lot_ID: 1 Source: Bethyl Labs Target Name: CANX-human

Experiment Status

	BGHcLV52-9	BGHcLV52-9	BGHcLV52-9	BGHcLV52-10	BGHcLV52-10	BGHcLV52-10
Sample_ID	BGHcLV52-9	BGHcLV52-9	BGHcLV52-9	BGHcLV52-10	BGHcLV52-10	BGHcLV52-10
Sample Name
Sample Name	CANX-BGHcLV52-9			CANX-BGHcLV52-10
RBP	CANX	CANX	CANX	CANX	CANX	CANX
Cell_Line	HepG2	HepG2	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Sequenced	NotSatisfied	NotSatisfied	Sequenced	NotSatisfied	NotSatisfied
Status_date	2026-09-16	2026-05-13	2026-05-13	2026-09-16	2026-05-13	2026-05-13
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14690	14710	14712	14691	14711	14713

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV52-9	BGHcLV52-10
Sample #	23	24
Sample Name	CANX-BGHcLV52-9	CANX-BGHcLV52-10
Sample_Name_Alias
Index Well Position	G03	H03
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	281	282
Peak_Molarity	38.20	37.40
libSampleQC_DNA_Well	DNA_Library_set82/set1/G10.png	DNA_Library_set82/set1/H10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set82/set1/G3.png	RNA_Library_set82/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGHcLV52-9	BGHcLV52-10
RBP	CANX	CANX
Batch_ID	BGHcLV52	BGHcLV52
WB_result	75.700	73.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4862	4863

Sequencing Information

	BGHcLV52-9	BGHcLV52-10
Sample_ID	BGHcLV52-9	BGHcLV52-10
Sample Name	CANX-BGHcLV52-9	CANX-BGHcLV52-10
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	45,825,487	38,273,581
total_aligned_reads	38,992,185	32,044,300
unique_aligned_reads	37,094,728	30,461,850
percent_uniqueAligned	0.80948	0.79590
correlation_replicates	0.997712	0.997712
spikein_reads	70,258	72,144
percent_spikeins	0.00153	0.00188
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3563	3564

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
CANX-BGHcLV52-9_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3563	NovaSeq6000	100	paired-ended	1				NT-BGHcLV52-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33661
CANX-BGHcLV52-9_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3563	NovaSeq6000	100	paired-ended	2				NT-BGHcLV52-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33719
CANX-BGHcLV52-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3563					GRCh38	V40	CANX-BGHcLV52-9_R1.filtered.trimmed.paired.fastq.gz,CANX-BGHcLV52-9_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33777
CANX-BGHcLV52-9_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	3563					GRCh38	V40	CANX-BGHcLV52-9_Aligned.sortedByCoord.out.bam		ENCORE2	33835
CANX-BGHcLV52-9_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	3563					GRCh38	V40	CANX-BGHcLV52-9_Aligned.sortedByCoord.out.bam		ENCORE2	33893
CANX-BGHcLV52-9_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	3563					GRCh38	V40	CANX-BGHcLV52-9_Aligned.sortedByCoord.out.bam		ENCORE2	33951
CANX-BGHcLV52-9_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	3563					GRCh38	V40	CANX-BGHcLV52-9_Aligned.sortedByCoord.out.bam		ENCORE2	34009
CANX-BGHcLV52-9_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3563					GRCh38	V40	CANX-BGHcLV52-9_R1.filtered.trimmed.paired.fastq.gz,CANX-BGHcLV52-9_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34067
CANX-BGHcLV52-10_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3564	NovaSeq6000	100	paired-ended	1				NT-BGHcLV52-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33660
CANX-BGHcLV52-10_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3564	NovaSeq6000	100	paired-ended	2				NT-BGHcLV52-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGHcLV52-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33718
CANX-BGHcLV52-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3564					GRCh38	V40	CANX-BGHcLV52-10_R1.filtered.trimmed.paired.fastq.gz,CANX-BGHcLV52-10_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33776
CANX-BGHcLV52-10_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	3564					GRCh38	V40	CANX-BGHcLV52-10_Aligned.sortedByCoord.out.bam		ENCORE2	33834
CANX-BGHcLV52-10_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	3564					GRCh38	V40	CANX-BGHcLV52-10_Aligned.sortedByCoord.out.bam		ENCORE2	33892
CANX-BGHcLV52-10_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	3564					GRCh38	V40	CANX-BGHcLV52-10_Aligned.sortedByCoord.out.bam		ENCORE2	33950
CANX-BGHcLV52-10_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	3564					GRCh38	V40	CANX-BGHcLV52-10_Aligned.sortedByCoord.out.bam		ENCORE2	34008
CANX-BGHcLV52-10_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3564					GRCh38	V40	CANX-BGHcLV52-10_R1.filtered.trimmed.paired.fastq.gz,CANX-BGHcLV52-10_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34066