EPRS RNA-Seq in K562

General Information


RBP	EPRS
Cell_Line	K562
Method	CRISPR
Exp_Name	EPRS-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	EPRS-BGKcLV40-25
Rep2	EPRS-BGKcLV40-26
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	58.9
Rep2_qPCR	55.1
Rep1_WB	60.8
Rep2_WB	61.6
Antibody Cat#	A303-958A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1362

Experiment Information (Status: Submitting)

	BGKcLV40-25	BGKcLV40-25	BGKcLV40-26	BGKcLV40-26
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0000990	BGC#0000990	BGC#0000990	BGC#0000990
shRNA_or_gRNA_sequence	TCAGCATTTCCGTTGAAGAA	TCAGCATTTCCGTTGAAGAA	TCAGCATTTCCGTTGAAGAA	TCAGCATTTCCGTTGAAGAA
PAM	GGG	GGG	GGG	GGG
Name	EPRS_81	EPRS_81	EPRS_81	EPRS_81
Sample_ID	BGKcLV40-25	BGKcLV40-25	BGKcLV40-26	BGKcLV40-26
transduction_Date	10/31/23	10/31/23	10/31/23	10/31/23
days	D6	D6	D6	D6
RBP_name	EPRS	EPRS	EPRS	EPRS
qPCR_result	58.9		55.1
Ave_qPCR	57.0
RT-qPCR_primer-F	tttgctggcagtagaacacg
RT-qPCR_primer-R	caactctagccaagtagcgaag
protein_conc	3220	3220	3099	3099
WB_result	60.8	50.9	61.6	50.0626
Ave_WB	61.2	50.5
WB_DONE_date	12/7/23	12/12/23
MW	171kd	171kd
IP
antibody_Cat#	A303-958A	A303-957A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24	1/4/24
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5698	5700	5699	5701

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EPRS	Product_ID: A303-958A Lot_ID: 1 Source: Bethyl Labs Target Name: EPRS-human
EPRS	Product_ID: A303-957A Lot_ID: 1 Source: Bethyl Labs Target Name: EPRS-human

Experiment Status

	BGKcLV40-25	BGKcLV40-25	BGKcLV40-26	BGKcLV40-26
Sample_ID	BGKcLV40-25	BGKcLV40-25	BGKcLV40-26	BGKcLV40-26
Sample Name
Sample Name	EPRS-BGKcLV40-25		EPRS-BGKcLV40-26
RBP	EPRS	EPRS	EPRS	EPRS
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2024-02-16	2023-12-15	2024-02-16	2023-12-15
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	12768	12814	12769	12815

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-25	BGKcLV40-26
Sample #	15	16
Sample Name	EPRS-BGKcLV40-25	EPRS-BGKcLV40-26
Sample_Name_Alias
Index Well Position	G02	H02
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	283	281
Peak_Molarity	87.00	83.40
libSampleQC_DNA_Well	DNA_Library_set67/set1/G8.png	DNA_Library_set67/set1/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/G2.png	RNA_Library_set67/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-25	BGKcLV40-26
RBP	EPRS	EPRS
Batch_ID	BGKcLV40	BGKcLV40
WB_result	60.800	61.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4152	4153

Sequencing Information

	BGKcLV40-25	BGKcLV40-26
Sample_ID	BGKcLV40-25	BGKcLV40-26
Sample Name	EPRS-BGKcLV40-25	EPRS-BGKcLV40-26
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	30,488,664	36,974,258
total_aligned_reads	26,618,401	31,943,051
unique_aligned_reads	24,586,949	29,334,882
percent_uniqueAligned	0.80643	0.79339
correlation_replicates	0.997763	0.997763
spikein_reads	5,334	11,884
percent_spikeins	0.00017	0.00032
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2807	2808

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
EPRS-BGKcLV40-25_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2807	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	28153
EPRS-BGKcLV40-25_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2807	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	28197
EPRS-BGKcLV40-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2807					GRCh38	V40	EPRS-BGKcLV40-25_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPRS-BGKcLV40-25_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28241
EPRS-BGKcLV40-25_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	2807					GRCh38	V40	EPRS-BGKcLV40-25/Aligned.sortedByCoord.out.bam		ENCORE2	28285
EPRS-BGKcLV40-25_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	2807					GRCh38	V40	EPRS-BGKcLV40-25/Aligned.sortedByCoord.out.bam		ENCORE2	28329
EPRS-BGKcLV40-25_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	2807					GRCh38	V40	EPRS-BGKcLV40-25/Aligned.sortedByCoord.out.bam		ENCORE2	28373
EPRS-BGKcLV40-25_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	2807					GRCh38	V40	EPRS-BGKcLV40-25/Aligned.sortedByCoord.out.bam		ENCORE2	28417
EPRS-BGKcLV40-25_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2807					GRCh38	V40	EPRS-BGKcLV40-25_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPRS-BGKcLV40-25_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28461
EPRS-BGKcLV40-26_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2808	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	28154
EPRS-BGKcLV40-26_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2808	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	28198
EPRS-BGKcLV40-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2808					GRCh38	V40	EPRS-BGKcLV40-26_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPRS-BGKcLV40-26_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28242
EPRS-BGKcLV40-26_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	2808					GRCh38	V40	EPRS-BGKcLV40-26/Aligned.sortedByCoord.out.bam		ENCORE2	28286
EPRS-BGKcLV40-26_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	2808					GRCh38	V40	EPRS-BGKcLV40-26/Aligned.sortedByCoord.out.bam		ENCORE2	28330
EPRS-BGKcLV40-26_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	2808					GRCh38	V40	EPRS-BGKcLV40-26/Aligned.sortedByCoord.out.bam		ENCORE2	28374
EPRS-BGKcLV40-26_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	2808					GRCh38	V40	EPRS-BGKcLV40-26/Aligned.sortedByCoord.out.bam		ENCORE2	28418
EPRS-BGKcLV40-26_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2808					GRCh38	V40	EPRS-BGKcLV40-26_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,EPRS-BGKcLV40-26_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28462