SEC24D RNA-Seq in HepG2

General Information


RBP	SEC24D
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SEC24D-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SEC24D-BGHcLV43-49
Rep2	SEC24D-BGHcLV43-50
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	61.7
Rep2_qPCR	60.4
Rep1_WB	63.8
Rep2_WB	64.9
Antibody Cat#	14687S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1588

Experiment Information (Status: Submitting)

	BGHcLV43-49	BGHcLV43-50
idx	1417	1418
TRCN#_or_BGC#	BGC#0001185	BGC#0001185
shRNA_or_gRNA_sequence	TTGGGGGCCACCGCCACTAG	TTGGGGGCCACCGCCACTAG
PAM	GGG	GGG
Name	SEC24D_92	SEC24D_92
Sample_ID	BGHcLV43-49	BGHcLV43-50
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	SEC24D	SEC24D
qPCR_result	61.7	60.4
Ave_qPCR	61.1
RT-qPCR_primer-F	agaatggagctcatgccact
RT-qPCR_primer-R	gatgccacattgttgacagg
protein_conc	4147	4281
WB_result	63.8	64.9
Ave_WB	64.3
WB_DONE_date	6/17/24
MW	115kd
IP
antibody_Cat#	14687S	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	9672	9673

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SEC24D	Product_ID: 14687S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SEC24D-human

Experiment Status

	BGHcLV43-49	BGHcLV43-50
Sample_ID	BGHcLV43-49	BGHcLV43-50
Sample Name
Sample Name	SEC24D-BGHcLV43-49	SEC24D-BGHcLV43-50
RBP	SEC24D	SEC24D
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13266	13267

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-49	BGHcLV43-50
Sample #	39	40
Sample Name	SEC24D-BGHcLV43-49	SEC24D-BGHcLV43-50
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	289	290
Peak_Molarity	72.70	67.60
libSampleQC_DNA_Well	DNA_Library_set74/set1/G5.png	DNA_Library_set74/set1/H5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/C11.png	RNA_Library_set74/set1/D11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-49	BGHcLV43-50
RBP	SEC24D	SEC24D
Batch_ID	BGHcLV43	BGHcLV43
WB_result	63.800	64.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4398	4399

Sequencing Information

	BGHcLV43-49	BGHcLV43-50
Sample_ID	BGHcLV43-49	BGHcLV43-50
Sample Name	SEC24D-BGHcLV43-49	SEC24D-BGHcLV43-50
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	42,606,328	59,442,874
total_aligned_reads	39,912,020	56,129,392
unique_aligned_reads	37,488,594	52,701,315
percent_uniqueAligned	0.87988	0.88659
correlation_replicates	0.998513	0.998513
spikein_reads	35,544	42,844
percent_spikeins	0.00083	0.00072
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3265	3266

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
SEC24D-BGHcLV43-49_S129_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3265	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30558
SEC24D-BGHcLV43-49_S129_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3265	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30610
SEC24D-BGHcLV43-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3265					GRCh38	V40	SEC24D-BGHcLV43-49_S129_L003_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGHcLV43-49_S129_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30662
SEC24D-BGHcLV43-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3265					GRCh38	V40	SEC24D-BGHcLV43-49_Aligned.sortedByCoord.out.bam		ENCORE2	30714
SEC24D-BGHcLV43-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3265					GRCh38	V40	SEC24D-BGHcLV43-49_Aligned.sortedByCoord.out.bam		ENCORE2	30766
SEC24D-BGHcLV43-49_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3265					GRCh38	V40	SEC24D-BGHcLV43-49_Aligned.sortedByCoord.out.bam		ENCORE2	30818
SEC24D-BGHcLV43-49_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3265					GRCh38	V40	SEC24D-BGHcLV43-49_Aligned.sortedByCoord.out.bam		ENCORE2	30870
SEC24D-BGHcLV43-49_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3265					GRCh38	V40	SEC24D-BGHcLV43-49_S129_L003_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGHcLV43-49_S129_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30922
SEC24D-BGHcLV43-50_S130_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3266	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30559
SEC24D-BGHcLV43-50_S130_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3266	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30611
SEC24D-BGHcLV43-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3266					GRCh38	V40	SEC24D-BGHcLV43-50_S130_L003_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGHcLV43-50_S130_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30663
SEC24D-BGHcLV43-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3266					GRCh38	V40	SEC24D-BGHcLV43-50_Aligned.sortedByCoord.out.bam		ENCORE2	30715
SEC24D-BGHcLV43-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3266					GRCh38	V40	SEC24D-BGHcLV43-50_Aligned.sortedByCoord.out.bam		ENCORE2	30767
SEC24D-BGHcLV43-50_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3266					GRCh38	V40	SEC24D-BGHcLV43-50_Aligned.sortedByCoord.out.bam		ENCORE2	30819
SEC24D-BGHcLV43-50_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3266					GRCh38	V40	SEC24D-BGHcLV43-50_Aligned.sortedByCoord.out.bam		ENCORE2	30871
SEC24D-BGHcLV43-50_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3266					GRCh38	V40	SEC24D-BGHcLV43-50_S130_L003_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGHcLV43-50_S130_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30923