YARS RNA-Seq in K562

General Information


RBP	YARS
Cell_Line	K562
Method	CRISPR
Exp_Name	YARS-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	YARS-BGKcLV44-85
Rep2	YARS-BGKcLV44-86
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	62.5
Rep2_qPCR	62.4
Rep1_WB	63.4
Rep2_WB	60.5
Antibody Cat#	A305-064A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1613

Experiment Information (Status: Submitting)

	BGKcLV44-85	BGKcLV44-86
idx	0	0
TRCN#_or_BGC#	BGC#0001216	BGC#0001216
shRNA_or_gRNA_sequence	AGAAACTGCACCTTATCACC	AGAAACTGCACCTTATCACC
PAM	CGG	CGG
Name	YARS_82	YARS_82
Sample_ID	BGKcLV44-85	BGKcLV44-86
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	YARS	YARS
qPCR_result	62.5	62.4
Ave_qPCR	62.5
RT-qPCR_primer-F	ctccctgcacttggctattc
RT-qPCR_primer-R	ccttccgatcaaggagatca
protein_conc	3321	4670
WB_result	63.4	60.5
Ave_WB	61.9
WB_DONE_date	8/19/24,8/28/24
MW	59kd
IP
antibody_Cat#	A305-064A	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	5968	5969

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YARS	Product_ID: A305-064A Lot_ID: 1 Source: Bethyl Labs Target Name: YARS-human

Experiment Status

	BGKcLV44-85	BGKcLV44-86
Sample_ID	BGKcLV44-85	BGKcLV44-86
Sample Name
Sample Name	YARS-BGKcLV44-85	YARS-BGKcLV44-86
RBP	YARS	YARS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13618	13619

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-85	BGKcLV44-86
Sample #	47	48
Sample Name	YARS-BGKcLV44-85	YARS-BGKcLV44-86
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	286	288
Peak_Molarity	77.30	79.90
libSampleQC_DNA_Well	DNA_Library_set75/set1/G11.png	DNA_Library_set75/set1/H11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/G5.png	RNA_Library_set75/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-85	BGKcLV44-86
RBP	YARS	YARS
Batch_ID	BGKcLV44	BGKcLV44
WB_result	63.400	60.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4606	4607

Sequencing Information

	BGKcLV44-85	BGKcLV44-86
Sample_ID	BGKcLV44-85	BGKcLV44-86
Sample Name	YARS-BGKcLV44-85	YARS-BGKcLV44-86
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	49,706,851	58,686,921
total_aligned_reads	47,879,385	56,162,914
unique_aligned_reads	44,452,337	52,082,784
percent_uniqueAligned	0.89429	0.88747
correlation_replicates	0.999340	0.999340
spikein_reads	53,796	109,074
percent_spikeins	0.00108	0.00186
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3317	3318

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
YARS-BGKcLV44-85_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3317	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30976
YARS-BGKcLV44-85_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3317	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31018
YARS-BGKcLV44-85_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3317					GRCh38	V40	YARS-BGKcLV44-85_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGKcLV44-85_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31060
YARS-BGKcLV44-85_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3317					GRCh38	V40	YARS-BGKcLV44-85_Aligned.sortedByCoord.out.bam		ENCORE2	31102
YARS-BGKcLV44-85_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3317					GRCh38	V40	YARS-BGKcLV44-85_Aligned.sortedByCoord.out.bam		ENCORE2	31144
YARS-BGKcLV44-85_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3317					GRCh38	V40	YARS-BGKcLV44-85_Aligned.sortedByCoord.out.bam		ENCORE2	31186
YARS-BGKcLV44-85_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3317					GRCh38	V40	YARS-BGKcLV44-85_Aligned.sortedByCoord.out.bam		ENCORE2	31228
YARS-BGKcLV44-85_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3317					GRCh38	V40	YARS-BGKcLV44-85_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGKcLV44-85_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31270
YARS-BGKcLV44-86_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3318	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30977
YARS-BGKcLV44-86_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3318	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31019
YARS-BGKcLV44-86_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3318					GRCh38	V40	YARS-BGKcLV44-86_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGKcLV44-86_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31061
YARS-BGKcLV44-86_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3318					GRCh38	V40	YARS-BGKcLV44-86_Aligned.sortedByCoord.out.bam		ENCORE2	31103
YARS-BGKcLV44-86_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3318					GRCh38	V40	YARS-BGKcLV44-86_Aligned.sortedByCoord.out.bam		ENCORE2	31145
YARS-BGKcLV44-86_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3318					GRCh38	V40	YARS-BGKcLV44-86_Aligned.sortedByCoord.out.bam		ENCORE2	31187
YARS-BGKcLV44-86_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3318					GRCh38	V40	YARS-BGKcLV44-86_Aligned.sortedByCoord.out.bam		ENCORE2	31229
YARS-BGKcLV44-86_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3318					GRCh38	V40	YARS-BGKcLV44-86_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGKcLV44-86_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31271