YARS RNA-Seq in HepG2

General Information


RBP	YARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	YARS-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	YARS-BGHcLV45-81
Rep2	YARS-BGHcLV45-82
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	50.4
Rep2_qPCR	55.3
Rep1_WB	65.5
Rep2_WB	63.7
Antibody Cat#	A305-064A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1633

Experiment Information (Status: Submitting)

	BGHcLV45-81	BGHcLV45-82
idx	0	0
TRCN#_or_BGC#	BGC#0001217	BGC#0001217
shRNA_or_gRNA_sequence	AGCCACATGTGGTTTGCCCG	AGCCACATGTGGTTTGCCCG
PAM	TGG	TGG
Name	YARS_92	YARS_92
Sample_ID	BGHcLV45-81	BGHcLV45-82
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	YARS	YARS
qPCR_result	50.4	55.3
Ave_qPCR	52.9
RT-qPCR_primer-F	tgatcaaagcaatgctggag
RT-qPCR_primer-R	gtgtgaccacggaggagagt
protein_conc	3883	3694
WB_result	65.5	63.7
Ave_WB
WB_DONE_date	10/25/24
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	9773	9774

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

	BGHcLV45-81	BGHcLV45-82
Sample_ID	BGHcLV45-81	BGHcLV45-82
Sample Name
Sample Name	YARS-BGHcLV45-81	YARS-BGHcLV45-82
RBP	YARS	YARS
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13724	13725

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-81	BGHcLV45-82
Sample #	39	40
Sample Name	YARS-BGHcLV45-81	YARS-BGHcLV45-82
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	291	290
Peak_Molarity	71.90	58.80
libSampleQC_DNA_Well	DNA_Library_set76/set1/G11.png	DNA_Library_set76/set1/H11.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set76/set1/G5.png	RNA_Library_set76/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-81	BGHcLV45-82
RBP	YARS	YARS
Batch_ID	BGHcLV45	BGHcLV45
WB_result	65.500	63.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4648	4649

Sequencing Information

	BGHcLV45-81	BGHcLV45-82
Sample_ID	BGHcLV45-81	BGHcLV45-82
Sample Name	YARS-BGHcLV45-81	YARS-BGHcLV45-82
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	44,049,701	53,720,973
total_aligned_reads	41,223,255	50,277,919
unique_aligned_reads	38,769,956	47,343,089
percent_uniqueAligned	0.88014	0.88128
correlation_replicates	0.998118	0.998118
spikein_reads	21,380	62,830
percent_spikeins	0.00049	0.00117
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3359	3360

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-BGHcLV45-81_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3359	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31850
YARS-BGHcLV45-81_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3359	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31892
YARS-BGHcLV45-81_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3359					GRCh38	V40	YARS-BGHcLV45-81_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGHcLV45-81_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31934
YARS-BGHcLV45-81_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3359					GRCh38	V40	YARS-BGHcLV45-81_Aligned.sortedByCoord.out.bam		ENCORE2	31976
YARS-BGHcLV45-81_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3359					GRCh38	V40	YARS-BGHcLV45-81_Aligned.sortedByCoord.out.bam		ENCORE2	32018
YARS-BGHcLV45-81_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3359					GRCh38	V40	YARS-BGHcLV45-81_Aligned.sortedByCoord.out.bam		ENCORE2	32060
YARS-BGHcLV45-81_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3359					GRCh38	V40	YARS-BGHcLV45-81_Aligned.sortedByCoord.out.bam		ENCORE2	32102
YARS-BGHcLV45-81_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3359					GRCh38	V40	YARS-BGHcLV45-81_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGHcLV45-81_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32144
YARS-BGHcLV45-82_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3360	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31851
YARS-BGHcLV45-82_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3360	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31893
YARS-BGHcLV45-82_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3360					GRCh38	V40	YARS-BGHcLV45-82_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGHcLV45-82_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31935
YARS-BGHcLV45-82_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3360					GRCh38	V40	YARS-BGHcLV45-82_Aligned.sortedByCoord.out.bam		ENCORE2	31977
YARS-BGHcLV45-82_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3360					GRCh38	V40	YARS-BGHcLV45-82_Aligned.sortedByCoord.out.bam		ENCORE2	32019
YARS-BGHcLV45-82_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3360					GRCh38	V40	YARS-BGHcLV45-82_Aligned.sortedByCoord.out.bam		ENCORE2	32061
YARS-BGHcLV45-82_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3360					GRCh38	V40	YARS-BGHcLV45-82_Aligned.sortedByCoord.out.bam		ENCORE2	32103
YARS-BGHcLV45-82_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3360					GRCh38	V40	YARS-BGHcLV45-82_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,YARS-BGHcLV45-82_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32145