KARS RNA-Seq in K562

General Information


RBP	KARS
Cell_Line	K562
Method	CRISPR
Exp_Name	KARS-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	KARS-BGKcLV42-45
Rep2	KARS-BGKcLV42-46
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	90.5
Rep2_qPCR	90.6
Rep1_WB	96.4
Rep2_WB	98.1
Antibody Cat#	9990S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1544

Experiment Information (Status: Submitting)

	BGKcLV42-45	BGKcLV42-46
idx	0	0
TRCN#_or_BGC#	BGC#0001148	BGC#0001148
shRNA_or_gRNA_sequence	GACGCCAGTTCCGGAATGAG	GACGCCAGTTCCGGAATGAG
PAM	GGG	GGG
Name	KARS_91	KARS_91
Sample_ID	BGKcLV42-45	BGKcLV42-46
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	KARS	KARS
qPCR_result	90.5	90.6
Ave_qPCR	90.6
RT-qPCR_primer-F	tgtggcaaaagctgttgaat
RT-qPCR_primer-R	gccaaagggctcattatctg
protein_conc	2772	3131
WB_result	96.4	98.1
Ave_WB	97.3
WB_DONE_date	5/6/24
MW	75kd
IP
antibody_Cat#	9990S	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	5807	5808

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KARS	Product_ID: 9990S Lot_ID: 1 Source: Cell Signaling Technology Target Name: KARS-human

Experiment Status

	BGKcLV42-45	BGKcLV42-46
Sample_ID	BGKcLV42-45	BGKcLV42-46
Sample Name
Sample Name	KARS-BGKcLV42-45	KARS-BGKcLV42-46
RBP	KARS	KARS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13082	13083

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-45	BGKcLV42-46
Sample #	39	40
Sample Name	KARS-BGKcLV42-45	KARS-BGKcLV42-46
Sample_Name_Alias
Index Well Position	G05	H05
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	288	288
Peak_Molarity	84.30	87.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/G5.png	DNA_Library_set73/set1/H5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/G5.png	RNA_Library_set73/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-45	BGKcLV42-46
RBP	KARS	KARS
Batch_ID	BGKcLV42	BGKcLV42
WB_result	96.400	98.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4308	4309

Sequencing Information

	BGKcLV42-45	BGKcLV42-46
Sample_ID	BGKcLV42-45	BGKcLV42-46
Sample Name	KARS-BGKcLV42-45	KARS-BGKcLV42-46
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	43,401,163	38,540,417
total_aligned_reads	38,023,280	31,889,779
unique_aligned_reads	35,070,175	29,452,181
percent_uniqueAligned	0.80805	0.76419
correlation_replicates	0.998225	0.998225
spikein_reads	4,470	4,704
percent_spikeins	0.00010	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3175	3176

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
KARS-BGKcLV42-45_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3175	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	30376
KARS-BGKcLV42-45_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3175	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	30466
KARS-BGKcLV42-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3175					GRCh38	V40	KARS-BGKcLV42-45_L001_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGKcLV42-45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31308
KARS-BGKcLV42-45_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	3175					GRCh38	V40	KARS-BGKcLV42-45_Aligned.sortedByCoord.out.bam		ENCORE2	31398
KARS-BGKcLV42-45_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	3175					GRCh38	V40	KARS-BGKcLV42-45_Aligned.sortedByCoord.out.bam		ENCORE2	31488
KARS-BGKcLV42-45_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	3175					GRCh38	V40	KARS-BGKcLV42-45_Aligned.sortedByCoord.out.bam		ENCORE2	31578
KARS-BGKcLV42-45_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	3175					GRCh38	V40	KARS-BGKcLV42-45_Aligned.sortedByCoord.out.bam		ENCORE2	31668
KARS-BGKcLV42-45_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3175					GRCh38	V40	KARS-BGKcLV42-45_L001_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGKcLV42-45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31758
KARS-BGKcLV42-46_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3176	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	30377
KARS-BGKcLV42-46_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3176	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	30467
KARS-BGKcLV42-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3176					GRCh38	V40	KARS-BGKcLV42-46_L001_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGKcLV42-46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31309
KARS-BGKcLV42-46_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	3176					GRCh38	V40	KARS-BGKcLV42-46_Aligned.sortedByCoord.out.bam		ENCORE2	31399
KARS-BGKcLV42-46_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	3176					GRCh38	V40	KARS-BGKcLV42-46_Aligned.sortedByCoord.out.bam		ENCORE2	31489
KARS-BGKcLV42-46_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	3176					GRCh38	V40	KARS-BGKcLV42-46_Aligned.sortedByCoord.out.bam		ENCORE2	31579
KARS-BGKcLV42-46_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	3176					GRCh38	V40	KARS-BGKcLV42-46_Aligned.sortedByCoord.out.bam		ENCORE2	31669
KARS-BGKcLV42-46_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3176					GRCh38	V40	KARS-BGKcLV42-46_L001_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGKcLV42-46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31759