IARS RNA-Seq in K562

General Information


RBP	IARS
Cell_Line	K562
Method	CRISPR
Exp_Name	IARS-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	IARS-BGKcLV46-43
Rep2	IARS-BGKcLV46-44
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	53.6
Rep2_qPCR	40.2
Rep1_WB	50.2
Rep2_WB	58.6
Antibody Cat#	A304-748A
Antibody Lot#
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1642

Experiment Information (Status: Submitting)

	BGKcLV46-43	BGKcLV46-44
idx	0	0
TRCN#_or_BGC#	BGC#0001028	BGC#0001028
shRNA_or_gRNA_sequence	TGGATACTCAAACATACCAC	TGGATACTCAAACATACCAC
PAM	AGG	AGG
Name	IARS_84	IARS_84
Sample_ID	BGKcLV46-43	BGKcLV46-44
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	IARS	IARS
qPCR_result	53.6	40.2
Ave_qPCR	46.9
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3761	3575
WB_result	50.2	58.6
Ave_WB
WB_DONE_date	1/2/25
MW	145kd
IP
antibody_Cat#	A304-748A
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	6037	6038

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
IARS	Product_ID: A304-748A Lot_ID: 1 Source: Bethyl Labs Target Name: IARS-human

Experiment Status

	BGKcLV46-43	BGKcLV46-44
Sample_ID	BGKcLV46-43	BGKcLV46-44
Sample Name
Sample Name	IARS-BGKcLV46-43	IARS-BGKcLV46-44
RBP	IARS	IARS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14038	14039

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-43	BGKcLV46-44
Sample #	17	18
Sample Name	IARS-BGKcLV46-43	IARS-BGKcLV46-44
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	312	308
Peak_Molarity	67.60	58.40
libSampleQC_DNA_Well	DNA_Library_set77/set1/A9.png	DNA_Library_set77/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/A3.png	RNA_Library_set77/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-43	BGKcLV46-44
RBP	IARS	IARS
Batch_ID	BGKcLV46	BGKcLV46
WB_result	50.200	58.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4676	4677

Sequencing Information

	BGKcLV46-43	BGKcLV46-44
Sample_ID	BGKcLV46-43	BGKcLV46-44
Sample Name	IARS-BGKcLV46-43	IARS-BGKcLV46-44
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	55,796,830	60,644,910
total_aligned_reads	50,875,763	56,440,098
unique_aligned_reads	46,992,168	52,209,986
percent_uniqueAligned	0.84220	0.86091
correlation_replicates	0.991990	0.991990
spikein_reads	122,194	115,672
percent_spikeins	0.00219	0.00191
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3381	3382

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
IARS-BGKcLV46-43_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3381	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32162
IARS-BGKcLV46-43_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3381	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32212
IARS-BGKcLV46-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3381					GRCh38	V40	IARS-BGKcLV46-43_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,IARS-BGKcLV46-43_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32262
IARS-BGKcLV46-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3381					GRCh38	V40	IARS-BGKcLV46-43_Aligned.sortedByCoord.out.bam		ENCORE2	32312
IARS-BGKcLV46-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3381					GRCh38	V40	IARS-BGKcLV46-43_Aligned.sortedByCoord.out.bam		ENCORE2	32362
IARS-BGKcLV46-43_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3381					GRCh38	V40	IARS-BGKcLV46-43_Aligned.sortedByCoord.out.bam		ENCORE2	32412
IARS-BGKcLV46-43_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3381					GRCh38	V40	IARS-BGKcLV46-43_Aligned.sortedByCoord.out.bam		ENCORE2	32462
IARS-BGKcLV46-43_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3381					GRCh38	V40	IARS-BGKcLV46-43_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,IARS-BGKcLV46-43_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32512
IARS-BGKcLV46-44_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3382	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32163
IARS-BGKcLV46-44_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3382	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32213
IARS-BGKcLV46-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3382					GRCh38	V40	IARS-BGKcLV46-44_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,IARS-BGKcLV46-44_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32263
IARS-BGKcLV46-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3382					GRCh38	V40	IARS-BGKcLV46-44_Aligned.sortedByCoord.out.bam		ENCORE2	32313
IARS-BGKcLV46-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3382					GRCh38	V40	IARS-BGKcLV46-44_Aligned.sortedByCoord.out.bam		ENCORE2	32363
IARS-BGKcLV46-44_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3382					GRCh38	V40	IARS-BGKcLV46-44_Aligned.sortedByCoord.out.bam		ENCORE2	32413
IARS-BGKcLV46-44_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3382					GRCh38	V40	IARS-BGKcLV46-44_Aligned.sortedByCoord.out.bam		ENCORE2	32463
IARS-BGKcLV46-44_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3382					GRCh38	V40	IARS-BGKcLV46-44_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,IARS-BGKcLV46-44_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32513