WARS RNA-Seq in HepG2

General Information


RBP	WARS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	WARS-BGHcLV36-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV36
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	WARS-BGHcLV36-57
Rep2	WARS-BGHcLV36-58
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	60.0
Rep2_qPCR	66.2
Rep1_WB	66.2
Rep2_WB	70.1
Antibody Cat#	A304-274A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1048

Experiment Information (Status: Submitting)

	BGHcLV36-57	BGHcLV36-57	BGHcLV36-58	BGHcLV36-58
idx	1188	1188	1189	1189
TRCN#_or_BGC#	BGC#0001074	BGC#0001074	BGC#0001074	BGC#0001074
shRNA_or_gRNA_sequence	AGCCTTGTAATCCTCCCCCG	AGCCTTGTAATCCTCCCCCG	AGCCTTGTAATCCTCCCCCG	AGCCTTGTAATCCTCCCCCG
PAM	CGG	CGG	CGG	CGG
Name	WARS_94	WARS_94	WARS_94	WARS_94
Sample_ID	BGHcLV36-57	BGHcLV36-57	BGHcLV36-58	BGHcLV36-58
transduction_Date	8/2/22	8/2/22	8/2/22	8/2/22
days	D6	D6	D6	D6
RBP_name	WARS	WARS	WARS	WARS
qPCR_result	60.0	60.0	66.2	66.2
Ave_qPCR	63.1	63.1
RT-qPCR_primer-F	cgcagaggcatcttcttctc	cgcagaggcatcttcttctc
RT-qPCR_primer-R	cggcccgtgtacagataaaa	cggcccgtgtacagataaaa
protein_conc	4018	0	3738	0
WB_result	66.2	62.0	70.1	59.2
Ave_WB	68.1	60.6
WB_DONE_date	8/10/22	9/14/22
MW	53kd	53kd
IP
antibody_Cat#	A304-274A	A304-275A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	7371	7373	7372	7374

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
WARS	Product_ID: A304-275A Lot_ID: 1 Source: Bethyl Labs Target Name: WARS-human

Experiment Status

	BGHcLV36-57	BGHcLV36-57	BGHcLV36-58	BGHcLV36-58
Sample_ID	BGHcLV36-57	BGHcLV36-57	BGHcLV36-58	BGHcLV36-58
Sample Name
Sample Name	WARS-BGHcLV36-57		WARS-BGHcLV36-58
RBP	WARS	WARS	WARS	WARS
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2023-04-14	2023-01-03	2023-04-14	2023-01-03
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	10958	11004	10959	11005

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-57	BGHcLV36-58
Sample #	17	18
Sample Name	WARS-BGHcLV36-57	WARS-BGHcLV36-58
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	294	316
Peak_Molarity	67.00	62.20
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/A3.png	DNA_Library_set54-56/set1/B3.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/A3.png	RNA_Library_set54-56/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-57	BGHcLV36-58
RBP	WARS	WARS
Batch_ID	BGHcLV36	BGHcLV36
WB_result	66.200	70.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3388	3389

Sequencing Information

	BGHcLV36-57	BGHcLV36-58
Sample_ID	BGHcLV36-57	BGHcLV36-58
Sample Name	WARS-BGHcLV36-57	WARS-BGHcLV36-58
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	61,385,935	67,565,746
total_aligned_reads	54,513,906	63,122,122
unique_aligned_reads	51,531,451	59,807,483
percent_uniqueAligned	0.83947	0.88517
correlation_replicates	0.998540	0.998540
spikein_reads	13,564	10,636
percent_spikeins	0.00022	0.00016
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2261	2262

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-BGHcLV36-57_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2261	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8426
WARS-BGHcLV36-57_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2261	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8476
WARS-BGHcLV36-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2261					GRCh38	V40	WARS-BGHcLV36-57_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGHcLV36-57_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25667
WARS-BGHcLV36-57_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2261					GRCh38	V40	WARS-BGHcLV36-57/Aligned.sortedByCoord.out.bam		ENCORE2	25717
WARS-BGHcLV36-57_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2261					GRCh38	V40	WARS-BGHcLV36-57/Aligned.sortedByCoord.out.bam		ENCORE2	25767
WARS-BGHcLV36-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2261					GRCh38	V40	WARS-BGHcLV36-57/Aligned.sortedByCoord.out.bam		ENCORE2	25817
WARS-BGHcLV36-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2261					GRCh38	V40	WARS-BGHcLV36-57/Aligned.sortedByCoord.out.bam		ENCORE2	25867
WARS-BGHcLV36-57_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2261					GRCh38	V40	WARS-BGHcLV36-57_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGHcLV36-57_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25917
WARS-BGHcLV36-58_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2262	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8427
WARS-BGHcLV36-58_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2262	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8477
WARS-BGHcLV36-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2262					GRCh38	V40	WARS-BGHcLV36-58_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGHcLV36-58_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25668
WARS-BGHcLV36-58_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2262					GRCh38	V40	WARS-BGHcLV36-58/Aligned.sortedByCoord.out.bam		ENCORE2	25718
WARS-BGHcLV36-58_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2262					GRCh38	V40	WARS-BGHcLV36-58/Aligned.sortedByCoord.out.bam		ENCORE2	25768
WARS-BGHcLV36-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2262					GRCh38	V40	WARS-BGHcLV36-58/Aligned.sortedByCoord.out.bam		ENCORE2	25818
WARS-BGHcLV36-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2262					GRCh38	V40	WARS-BGHcLV36-58/Aligned.sortedByCoord.out.bam		ENCORE2	25868
WARS-BGHcLV36-58_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2262					GRCh38	V40	WARS-BGHcLV36-58_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,WARS-BGHcLV36-58_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25918