KARS RNA-Seq in HepG2

General Information


RBP	KARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	KARS-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	KARS-BGHcLV43-25
Rep2	KARS-BGHcLV43-26
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	83.4
Rep2_qPCR	83.8
Rep1_WB	77.9
Rep2_WB	87.0
Antibody Cat#	9990S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1578

Experiment Information (Status: Submitting)

	BGHcLV43-25	BGHcLV43-26
idx	1393	1394
TRCN#_or_BGC#	BGC#0001150	BGC#0001150
shRNA_or_gRNA_sequence	GACGCCAGTTCCGGAATGAG	GACGCCAGTTCCGGAATGAG
PAM	GGG	GGG
Name	KARS_91	KARS_91
Sample_ID	BGHcLV43-25	BGHcLV43-26
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	KARS	KARS
qPCR_result	83.4	83.8
Ave_qPCR	83.6
RT-qPCR_primer-F	tgtggcaaaagctgttgaat
RT-qPCR_primer-R	gccaaagggctcattatctg
protein_conc	3807	2975
WB_result	77.9	87.0
Ave_WB	82.4
WB_DONE_date	6/13/24
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	9646	9647

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

	BGHcLV43-25	BGHcLV43-26
Sample_ID	BGHcLV43-25	BGHcLV43-26
Sample Name
Sample Name	KARS-BGHcLV43-25	KARS-BGHcLV43-26
RBP	KARS	KARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13246	13247

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-25	BGHcLV43-26
Sample #	19	20
Sample Name	KARS-BGHcLV43-25	KARS-BGHcLV43-26
Sample_Name_Alias
Index Well Position	C08	D08
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	292	298
Peak_Molarity	97.00	93.40
libSampleQC_DNA_Well	DNA_Library_set74/set1/C3.png	DNA_Library_set74/set1/D3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/G8.png	RNA_Library_set74/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-25	BGHcLV43-26
RBP	KARS	KARS
Batch_ID	BGHcLV43	BGHcLV43
WB_result	77.900	87.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4378	4379

Sequencing Information

	BGHcLV43-25	BGHcLV43-26
Sample_ID	BGHcLV43-25	BGHcLV43-26
Sample Name	KARS-BGHcLV43-25	KARS-BGHcLV43-26
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	38,161,626	41,073,207
total_aligned_reads	33,339,971	37,473,577
unique_aligned_reads	31,352,813	35,298,308
percent_uniqueAligned	0.82158	0.85940
correlation_replicates	0.998516	0.998516
spikein_reads	29,206	22,008
percent_spikeins	0.00077	0.00054
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3245	3246

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-BGHcLV43-25_S109_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3245	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	30536
KARS-BGHcLV43-25_S109_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3245	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	30588
KARS-BGHcLV43-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3245					GRCh38	V40	KARS-BGHcLV43-25_S109_L003_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGHcLV43-25_S109_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30640
KARS-BGHcLV43-25_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	3245					GRCh38	V40	KARS-BGHcLV43-25_Aligned.sortedByCoord.out.bam		ENCORE2	30692
KARS-BGHcLV43-25_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	3245					GRCh38	V40	KARS-BGHcLV43-25_Aligned.sortedByCoord.out.bam		ENCORE2	30744
KARS-BGHcLV43-25_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	3245					GRCh38	V40	KARS-BGHcLV43-25_Aligned.sortedByCoord.out.bam		ENCORE2	30796
KARS-BGHcLV43-25_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	3245					GRCh38	V40	KARS-BGHcLV43-25_Aligned.sortedByCoord.out.bam		ENCORE2	30848
KARS-BGHcLV43-25_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3245					GRCh38	V40	KARS-BGHcLV43-25_S109_L003_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGHcLV43-25_S109_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30900
KARS-BGHcLV43-26_S110_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3246	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	30537
KARS-BGHcLV43-26_S110_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3246	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	30589
KARS-BGHcLV43-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3246					GRCh38	V40	KARS-BGHcLV43-26_S110_L003_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGHcLV43-26_S110_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30641
KARS-BGHcLV43-26_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	3246					GRCh38	V40	KARS-BGHcLV43-26_Aligned.sortedByCoord.out.bam		ENCORE2	30693
KARS-BGHcLV43-26_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	3246					GRCh38	V40	KARS-BGHcLV43-26_Aligned.sortedByCoord.out.bam		ENCORE2	30745
KARS-BGHcLV43-26_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	3246					GRCh38	V40	KARS-BGHcLV43-26_Aligned.sortedByCoord.out.bam		ENCORE2	30797
KARS-BGHcLV43-26_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	3246					GRCh38	V40	KARS-BGHcLV43-26_Aligned.sortedByCoord.out.bam		ENCORE2	30849
KARS-BGHcLV43-26_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3246					GRCh38	V40	KARS-BGHcLV43-26_S110_L003_R1_001.filtered.trimmed.paired.fastq.gz,KARS-BGHcLV43-26_S110_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30901