EDC3 RNA-Seq in K562

General Information


RBP	EDC3
Cell_Line	K562
Method	CRISPR
Exp_Name	EDC3-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EDC3-BGKcLV40-11
Rep2	EDC3-BGKcLV40-12
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	50.6
Rep2_qPCR	44.3
Rep1_WB	76.6
Rep2_WB	66.0
Antibody Cat#	A303-986A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1358

Experiment Information (Status: Submitting)

	BGKcLV40-11	BGKcLV40-12
idx	1494	0
TRCN#_or_BGC#	BGC#0000941	BGC#0000941
shRNA_or_gRNA_sequence	AGTCCAAAAGTTTCCGTCGT	AGTCCAAAAGTTTCCGTCGT
PAM	CGG	CGG
Name	EDC3_98	EDC3_98
Sample_ID	BGKcLV40-11	BGKcLV40-12
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	EDC3	EDC3
qPCR_result	50.6	44.3
Ave_qPCR	47.5
RT-qPCR_primer-F	ggatcatagtgccccacaac
RT-qPCR_primer-R	atctccagtctccgctcaag
protein_conc	3005	3281
WB_result	76.6	66.0
Ave_WB	71.3
WB_DONE_date	11/15/23,11/17/23
MW	56kd
IP
antibody_Cat#	A303-986A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5680	5681

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EDC3	Product_ID: A303-986A Lot_ID: 1 Source: Bethyl Labs Target Name: EDC3-human

Experiment Status

	BGKcLV40-11	BGKcLV40-12
Sample_ID	BGKcLV40-11	BGKcLV40-12
Sample Name
Sample Name	EDC3-BGKcLV40-11	EDC3-BGKcLV40-12
RBP	EDC3	EDC3
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12760	12761

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-11	BGKcLV40-12
Sample #	7	8
Sample Name	EDC3-BGKcLV40-11	EDC3-BGKcLV40-12
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	291	282
Peak_Molarity	41.00	33.40
libSampleQC_DNA_Well	DNA_Library_set67/set1/G7.png	DNA_Library_set67/set1/H7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/G1.png	RNA_Library_set67/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-11	BGKcLV40-12
RBP	EDC3	EDC3
Batch_ID	BGKcLV40	BGKcLV40
WB_result	76.600	66.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4144	4145

Sequencing Information

	BGKcLV40-11	BGKcLV40-12
Sample_ID	BGKcLV40-11	BGKcLV40-12
Sample Name	EDC3-BGKcLV40-11	EDC3-BGKcLV40-12
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	33,766,555	32,383,273
total_aligned_reads	28,048,133	26,990,162
unique_aligned_reads	25,744,183	24,799,517
percent_uniqueAligned	0.76242	0.76581
correlation_replicates	0.999105	0.999105
spikein_reads	6,168	8,646
percent_spikeins	0.00018	0.00027
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2799	2800

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
EDC3-BGKcLV40-11_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2799	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28145
EDC3-BGKcLV40-11_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2799	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28189
EDC3-BGKcLV40-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2799					GRCh38	V40	EDC3-BGKcLV40-11_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDC3-BGKcLV40-11_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28233
EDC3-BGKcLV40-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2799					GRCh38	V40	EDC3-BGKcLV40-11/Aligned.sortedByCoord.out.bam		ENCORE2	28277
EDC3-BGKcLV40-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2799					GRCh38	V40	EDC3-BGKcLV40-11/Aligned.sortedByCoord.out.bam		ENCORE2	28321
EDC3-BGKcLV40-11_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2799					GRCh38	V40	EDC3-BGKcLV40-11/Aligned.sortedByCoord.out.bam		ENCORE2	28365
EDC3-BGKcLV40-11_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2799					GRCh38	V40	EDC3-BGKcLV40-11/Aligned.sortedByCoord.out.bam		ENCORE2	28409
EDC3-BGKcLV40-11_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2799					GRCh38	V40	EDC3-BGKcLV40-11_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDC3-BGKcLV40-11_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28453
EDC3-BGKcLV40-12_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2800	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28146
EDC3-BGKcLV40-12_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2800	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28190
EDC3-BGKcLV40-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2800					GRCh38	V40	EDC3-BGKcLV40-12_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDC3-BGKcLV40-12_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28234
EDC3-BGKcLV40-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2800					GRCh38	V40	EDC3-BGKcLV40-12/Aligned.sortedByCoord.out.bam		ENCORE2	28278
EDC3-BGKcLV40-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2800					GRCh38	V40	EDC3-BGKcLV40-12/Aligned.sortedByCoord.out.bam		ENCORE2	28322
EDC3-BGKcLV40-12_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2800					GRCh38	V40	EDC3-BGKcLV40-12/Aligned.sortedByCoord.out.bam		ENCORE2	28366
EDC3-BGKcLV40-12_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2800					GRCh38	V40	EDC3-BGKcLV40-12/Aligned.sortedByCoord.out.bam		ENCORE2	28410
EDC3-BGKcLV40-12_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2800					GRCh38	V40	EDC3-BGKcLV40-12_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,EDC3-BGKcLV40-12_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28454