ADD1 RNA-Seq in HepG2

General Information


RBP	ADD1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ADD1-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ADD1-BGHcLV45-3
Rep2	ADD1-BGHcLV45-4
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	71.5
Rep2_qPCR	66.0
Rep1_WB	70.5
Rep2_WB	60.3
Antibody Cat#	70174S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1615

Experiment Information (Status: Submitting)

	BGHcLV45-3	BGHcLV45-4
idx	1436	1437
TRCN#_or_BGC#	BGC#0001107	BGC#0001107
shRNA_or_gRNA_sequence	GATCCTCTAAGATCGTTCAC	GATCCTCTAAGATCGTTCAC
PAM	AGG	AGG
Name	ADD1_97	ADD1_97
Sample_ID	BGHcLV45-3	BGHcLV45-4
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	ADD1	ADD1
qPCR_result	71.5	66.0
Ave_qPCR	68.7
RT-qPCR_primer-F	tctttgggtggtctcagctt
RT-qPCR_primer-R	agaagcccaaaagggacaat
protein_conc	5063	4978
WB_result	70.5	60.3
Ave_WB
WB_DONE_date	10/9/24
MW	120KD
IP
antibody_Cat#	70174S	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	9691	9692

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ADD1	Product_ID: 70174S Lot_ID: 1 Source: Cell Signaling Technology Target Name: ADD1-human

Experiment Status

	BGHcLV45-3	BGHcLV45-4
Sample_ID	BGHcLV45-3	BGHcLV45-4
Sample Name
Sample Name	ADD1-BGHcLV45-3	ADD1-BGHcLV45-4
RBP	ADD1	ADD1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13688	13689

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-3	BGHcLV45-4
Sample #	3	4
Sample Name	ADD1-BGHcLV45-3	ADD1-BGHcLV45-4
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	280	283
Peak_Molarity	77.80	81.30
libSampleQC_DNA_Well	DNA_Library_set76/set1/C7.png	DNA_Library_set76/set1/D7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/C1.png	RNA_Library_set76/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-3	BGHcLV45-4
RBP	ADD1	ADD1
Batch_ID	BGHcLV45	BGHcLV45
WB_result	70.500	60.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4612	4613

Sequencing Information

	BGHcLV45-3	BGHcLV45-4
Sample_ID	BGHcLV45-3	BGHcLV45-4
Sample Name	ADD1-BGHcLV45-3	ADD1-BGHcLV45-4
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	45,004,949	32,894,585
total_aligned_reads	38,748,470	29,122,604
unique_aligned_reads	36,413,106	27,336,698
percent_uniqueAligned	0.80909	0.83104
correlation_replicates	0.997756	0.997756
spikein_reads	54,568	34,704
percent_spikeins	0.00121	0.00106
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3323	3324

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
ADD1-BGHcLV45-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3323	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31812
ADD1-BGHcLV45-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3323	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31854
ADD1-BGHcLV45-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3323					GRCh38	V40	ADD1-BGHcLV45-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADD1-BGHcLV45-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31896
ADD1-BGHcLV45-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3323					GRCh38	V40	ADD1-BGHcLV45-3_Aligned.sortedByCoord.out.bam		ENCORE2	31938
ADD1-BGHcLV45-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3323					GRCh38	V40	ADD1-BGHcLV45-3_Aligned.sortedByCoord.out.bam		ENCORE2	31980
ADD1-BGHcLV45-3_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3323					GRCh38	V40	ADD1-BGHcLV45-3_Aligned.sortedByCoord.out.bam		ENCORE2	32022
ADD1-BGHcLV45-3_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3323					GRCh38	V40	ADD1-BGHcLV45-3_Aligned.sortedByCoord.out.bam		ENCORE2	32064
ADD1-BGHcLV45-3_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3323					GRCh38	V40	ADD1-BGHcLV45-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADD1-BGHcLV45-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32106
ADD1-BGHcLV45-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3324	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31813
ADD1-BGHcLV45-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3324	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31855
ADD1-BGHcLV45-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3324					GRCh38	V40	ADD1-BGHcLV45-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADD1-BGHcLV45-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31897
ADD1-BGHcLV45-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3324					GRCh38	V40	ADD1-BGHcLV45-4_Aligned.sortedByCoord.out.bam		ENCORE2	31939
ADD1-BGHcLV45-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3324					GRCh38	V40	ADD1-BGHcLV45-4_Aligned.sortedByCoord.out.bam		ENCORE2	31981
ADD1-BGHcLV45-4_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3324					GRCh38	V40	ADD1-BGHcLV45-4_Aligned.sortedByCoord.out.bam		ENCORE2	32023
ADD1-BGHcLV45-4_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3324					GRCh38	V40	ADD1-BGHcLV45-4_Aligned.sortedByCoord.out.bam		ENCORE2	32065
ADD1-BGHcLV45-4_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3324					GRCh38	V40	ADD1-BGHcLV45-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,ADD1-BGHcLV45-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32107