WARS RNA-Seq in K562

General Information


RBP	WARS
Cell_Line	K562
Method	CRISPR
Exp_Name	WARS-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	WARS-BGKcLV44-83
Rep2	WARS-BGKcLV44-84
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	70.3
Rep2_qPCR	76.5
Rep1_WB	75.4
Rep2_WB	79.5
Antibody Cat#	A304-274A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1612

Experiment Information (Status: Submitting)

	BGKcLV44-83	BGKcLV44-84
idx	0	0
TRCN#_or_BGC#	BGC#0001075	BGC#0001075
shRNA_or_gRNA_sequence	GAGCTACAAAGCTGCCGCGG	GAGCTACAAAGCTGCCGCGG
PAM	GGG	GGG
Name	WARS_94B	WARS_94B
Sample_ID	BGKcLV44-83	BGKcLV44-84
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	WARS	WARS
qPCR_result	70.3	76.5
Ave_qPCR	73.4
RT-qPCR_primer-F	cgcagaggcatcttcttctc
RT-qPCR_primer-R	cggcccgtgtacagataaaa
protein_conc	4296	4956
WB_result	75.4	79.5
Ave_WB	77.5
WB_DONE_date	8/19/24
MW	53KD
IP
antibody_Cat#	A304-274A	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	5979	5980

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WARS	Product_ID: A304-274A Lot_ID: 1 Source: Bethyl Labs Target Name: WARS-human

Experiment Status

	BGKcLV44-83	BGKcLV44-84
Sample_ID	BGKcLV44-83	BGKcLV44-84
Sample Name
Sample Name	WARS-BGKcLV44-83	WARS-BGKcLV44-84
RBP	WARS	WARS
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13616	13617

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-83	BGKcLV44-84
Sample #	45	46
Sample Name	WARS-BGKcLV44-83	WARS-BGKcLV44-84
Sample_Name_Alias
Index Well Position	E11	F11
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	289	290
Peak_Molarity	70.00	65.00
libSampleQC_DNA_Well	DNA_Library_set75/set1/E11.png	DNA_Library_set75/set1/F11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/E5.png	RNA_Library_set75/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-83	BGKcLV44-84
RBP	WARS	WARS
Batch_ID	BGKcLV44	BGKcLV44
WB_result	75.400	79.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4604	4605

Sequencing Information

	BGKcLV44-83	BGKcLV44-84
Sample_ID	BGKcLV44-83	BGKcLV44-84
Sample Name	WARS-BGKcLV44-83	WARS-BGKcLV44-84
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	52,411,704	50,791,871
total_aligned_reads	50,106,571	48,922,765
unique_aligned_reads	46,547,329	45,038,981
percent_uniqueAligned	0.88811	0.88674
correlation_replicates	0.997166	0.997166
spikein_reads	65,730	64,418
percent_spikeins	0.00125	0.00127
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3315	3316

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
WARS-BGKcLV44-83_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3315	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	30974
WARS-BGKcLV44-83_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3315	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	31016
WARS-BGKcLV44-83_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3315					GRCh38	V40	WARS-BGKcLV44-83_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGKcLV44-83_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31058
WARS-BGKcLV44-83_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	3315					GRCh38	V40	WARS-BGKcLV44-83_Aligned.sortedByCoord.out.bam		ENCORE2	31100
WARS-BGKcLV44-83_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	3315					GRCh38	V40	WARS-BGKcLV44-83_Aligned.sortedByCoord.out.bam		ENCORE2	31142
WARS-BGKcLV44-83_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	3315					GRCh38	V40	WARS-BGKcLV44-83_Aligned.sortedByCoord.out.bam		ENCORE2	31184
WARS-BGKcLV44-83_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	3315					GRCh38	V40	WARS-BGKcLV44-83_Aligned.sortedByCoord.out.bam		ENCORE2	31226
WARS-BGKcLV44-83_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3315					GRCh38	V40	WARS-BGKcLV44-83_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGKcLV44-83_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31268
WARS-BGKcLV44-84_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3316	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	30975
WARS-BGKcLV44-84_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3316	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	31017
WARS-BGKcLV44-84_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3316					GRCh38	V40	WARS-BGKcLV44-84_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGKcLV44-84_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31059
WARS-BGKcLV44-84_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	3316					GRCh38	V40	WARS-BGKcLV44-84_Aligned.sortedByCoord.out.bam		ENCORE2	31101
WARS-BGKcLV44-84_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	3316					GRCh38	V40	WARS-BGKcLV44-84_Aligned.sortedByCoord.out.bam		ENCORE2	31143
WARS-BGKcLV44-84_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	3316					GRCh38	V40	WARS-BGKcLV44-84_Aligned.sortedByCoord.out.bam		ENCORE2	31185
WARS-BGKcLV44-84_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	3316					GRCh38	V40	WARS-BGKcLV44-84_Aligned.sortedByCoord.out.bam		ENCORE2	31227
WARS-BGKcLV44-84_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3316					GRCh38	V40	WARS-BGKcLV44-84_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGKcLV44-84_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31269