DENR RNA-Seq in HepG2

General Information


RBP	DENR
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DENR-BGHcLV47-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV47
Pool ID	Pool-250422
Local_Set_Name	set78
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DENR-BGHcLV47-11
Rep2	DENR-BGHcLV47-12
CN1	NT-BGHcLV47-1
CN2	NT-BGHcLV47-2
Rep1_qPCR	31.2
Rep2_qPCR	14.4
Rep1_WB	63.6
Rep2_WB	58.2
Antibody Cat#	A303-010A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1661

Experiment Information (Status: Submitting)

	BGHcLV47-11	BGHcLV47-12
idx	1615	1616
TRCN#_or_BGC#	BGC#0001230	BGC#0001230
shRNA_or_gRNA_sequence	TGACATTTCTGAATCCAGCG	TGACATTTCTGAATCCAGCG
PAM	GGG	GGG
Name	DENR_79	DENR_79
Sample_ID	BGHcLV47-11	BGHcLV47-12
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	DENR	DENR
qPCR_result	31.2	14.4
Ave_qPCR	22.8
RT-qPCR_primer-F	atgcctgatgttgctaaatgt
RT-qPCR_primer-R	cagcttcttgtttgggtgaa
protein_conc	3709	3623
WB_result	63.6	58.2
Ave_WB
WB_DONE_date	2/5/25
MW	22KD
IP
antibody_Cat#	A303-010A	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	9804	9805

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DENR	Product_ID: A303-010A Lot_ID: 1 Source: Bethyl Labs Target Name: DENR-human

Experiment Status

	BGHcLV47-11	BGHcLV47-12
Sample_ID	BGHcLV47-11	BGHcLV47-12
Sample Name
Sample Name	DENR-BGHcLV47-11	DENR-BGHcLV47-12
RBP	DENR	DENR
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2026-10-30	2026-10-30
Project	ENCORE2	ENCORE2
Note
ID	14156	14157

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-11	BGHcLV47-12
Sample #	9	10
Sample Name	DENR-BGHcLV47-11	DENR-BGHcLV47-12
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	267	271
Peak_Molarity	55.10	40.70
libSampleQC_DNA_Well	DNA_Library_set78/set1/A7.png	DNA_Library_set78/set1/B7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set78/set1/A2.png	RNA_Library_set78/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-11	BGHcLV47-12
RBP	DENR	DENR
Batch_ID	BGHcLV47	BGHcLV47
WB_result	63.600	58.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4720	4721

Sequencing Information

	BGHcLV47-11	BGHcLV47-12
Sample_ID	BGHcLV47-11	BGHcLV47-12
Sample Name	DENR-BGHcLV47-11	DENR-BGHcLV47-12
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	15,767,048	15,344,599
total_aligned_reads	13,324,900	13,620,460
unique_aligned_reads	12,548,496	12,829,824
percent_uniqueAligned	0.79587	0.83611
correlation_replicates	0.996240	0.996240
spikein_reads	6,980	25,178
percent_spikeins	0.00044	0.00164
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3423	3424

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
DENR-BGHcLV47-11_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3423	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32554
DENR-BGHcLV47-11_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3423	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32588
DENR-BGHcLV47-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3423					GRCh38	V40	DENR-BGHcLV47-11_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGHcLV47-11_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32622
DENR-BGHcLV47-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3423					GRCh38	V40	DENR-BGHcLV47-11_Aligned.sortedByCoord.out.bam		ENCORE2	32656
DENR-BGHcLV47-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3423					GRCh38	V40	DENR-BGHcLV47-11_Aligned.sortedByCoord.out.bam		ENCORE2	32690
DENR-BGHcLV47-11_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3423					GRCh38	V40	DENR-BGHcLV47-11_Aligned.sortedByCoord.out.bam		ENCORE2	32724
DENR-BGHcLV47-11_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3423					GRCh38	V40	DENR-BGHcLV47-11_Aligned.sortedByCoord.out.bam		ENCORE2	32758
DENR-BGHcLV47-11_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3423					GRCh38	V40	DENR-BGHcLV47-11_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGHcLV47-11_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32792
DENR-BGHcLV47-12_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3424	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32555
DENR-BGHcLV47-12_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3424	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32589
DENR-BGHcLV47-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3424					GRCh38	V40	DENR-BGHcLV47-12_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGHcLV47-12_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32623
DENR-BGHcLV47-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3424					GRCh38	V40	DENR-BGHcLV47-12_Aligned.sortedByCoord.out.bam		ENCORE2	32657
DENR-BGHcLV47-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3424					GRCh38	V40	DENR-BGHcLV47-12_Aligned.sortedByCoord.out.bam		ENCORE2	32691
DENR-BGHcLV47-12_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3424					GRCh38	V40	DENR-BGHcLV47-12_Aligned.sortedByCoord.out.bam		ENCORE2	32725
DENR-BGHcLV47-12_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3424					GRCh38	V40	DENR-BGHcLV47-12_Aligned.sortedByCoord.out.bam		ENCORE2	32759
DENR-BGHcLV47-12_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3424					GRCh38	V40	DENR-BGHcLV47-12_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,DENR-BGHcLV47-12_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32793