SEC24D RNA-Seq in K562

General Information


RBP	SEC24D
Cell_Line	K562
Method	CRISPR
Exp_Name	SEC24D-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SEC24D-BGKcLV42-83
Rep2	SEC24D-BGKcLV42-84
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	76.4
Rep2_qPCR	69.6
Rep1_WB	73.9
Rep2_WB	81.6
Antibody Cat#	14687S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1559

Experiment Information (Status: Submitting)

	BGKcLV42-83	BGKcLV42-84
idx	0	0
TRCN#_or_BGC#	BGC#0001183	BGC#0001183
shRNA_or_gRNA_sequence	TTGGGGGCCACCGCCACTAG	TTGGGGGCCACCGCCACTAG
PAM	GGG	GGG
Name	SEC24D_92	SEC24D_92
Sample_ID	BGKcLV42-83	BGKcLV42-84
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	SEC24D	SEC24D
qPCR_result	76.4	69.6
Ave_qPCR	73.0
RT-qPCR_primer-F	agaatggagctcatgccact
RT-qPCR_primer-R	gatgccacattgttgacagg
protein_conc	2195	2798
WB_result	73.9	81.6
Ave_WB	77.8
WB_DONE_date	5/10/24
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	5851	5852

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

	BGKcLV42-83	BGKcLV42-84
Sample_ID	BGKcLV42-83	BGKcLV42-84
Sample Name
Sample Name	SEC24D-BGKcLV42-83	SEC24D-BGKcLV42-84
RBP	SEC24D	SEC24D
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13112	13113

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-83	BGKcLV42-84
Sample #	69	70
Sample Name	SEC24D-BGKcLV42-83	SEC24D-BGKcLV42-84
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	301	305
Peak_Molarity	61.40	92.90
libSampleQC_DNA_Well	DNA_Library_set73/set1/E9.png	DNA_Library_set73/set1/F9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/E9.png	RNA_Library_set73/set1/F9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-83	BGKcLV42-84
RBP	SEC24D	SEC24D
Batch_ID	BGKcLV42	BGKcLV42
WB_result	73.900	81.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4338	4339

Sequencing Information

	BGKcLV42-83	BGKcLV42-84
Sample_ID	BGKcLV42-83	BGKcLV42-84
Sample Name	SEC24D-BGKcLV42-83	SEC24D-BGKcLV42-84
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	38,664,884	38,463,312
total_aligned_reads	32,787,990	32,117,348
unique_aligned_reads	30,205,088	29,662,175
percent_uniqueAligned	0.78120	0.77118
correlation_replicates	0.995296	0.995296
spikein_reads	3,218	514
percent_spikeins	0.00008	0.00001
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3205	3206

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-BGKcLV42-83_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3205	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30408
SEC24D-BGKcLV42-83_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3205	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30498
SEC24D-BGKcLV42-83_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3205					GRCh38	V40	SEC24D-BGKcLV42-83_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGKcLV42-83_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31340
SEC24D-BGKcLV42-83_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3205					GRCh38	V40	SEC24D-BGKcLV42-83_Aligned.sortedByCoord.out.bam		ENCORE2	31430
SEC24D-BGKcLV42-83_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3205					GRCh38	V40	SEC24D-BGKcLV42-83_Aligned.sortedByCoord.out.bam		ENCORE2	31520
SEC24D-BGKcLV42-83_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3205					GRCh38	V40	SEC24D-BGKcLV42-83_Aligned.sortedByCoord.out.bam		ENCORE2	31610
SEC24D-BGKcLV42-83_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3205					GRCh38	V40	SEC24D-BGKcLV42-83_Aligned.sortedByCoord.out.bam		ENCORE2	31700
SEC24D-BGKcLV42-83_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3205					GRCh38	V40	SEC24D-BGKcLV42-83_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGKcLV42-83_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31790
SEC24D-BGKcLV42-84_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3206	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30409
SEC24D-BGKcLV42-84_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3206	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30499
SEC24D-BGKcLV42-84_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3206					GRCh38	V40	SEC24D-BGKcLV42-84_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGKcLV42-84_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31341
SEC24D-BGKcLV42-84_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3206					GRCh38	V40	SEC24D-BGKcLV42-84_Aligned.sortedByCoord.out.bam		ENCORE2	31431
SEC24D-BGKcLV42-84_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3206					GRCh38	V40	SEC24D-BGKcLV42-84_Aligned.sortedByCoord.out.bam		ENCORE2	31521
SEC24D-BGKcLV42-84_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3206					GRCh38	V40	SEC24D-BGKcLV42-84_Aligned.sortedByCoord.out.bam		ENCORE2	31611
SEC24D-BGKcLV42-84_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3206					GRCh38	V40	SEC24D-BGKcLV42-84_Aligned.sortedByCoord.out.bam		ENCORE2	31701
SEC24D-BGKcLV42-84_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3206					GRCh38	V40	SEC24D-BGKcLV42-84_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC24D-BGKcLV42-84_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31791