FUS RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-17	BGRSDLV03-18
idx	0	0
TRCN#_or_BGC#	TRCN0000039824	TRCN0000039824
shRNA_or_gRNA_sequence	GCTGATTACTTCAAGCAGATTCTCGAGAATCTGCTTGAAGTAATCAGC	GCTGATTACTTCAAGCAGATTCTCGAGAATCTGCTTGAAGTAATCAGC
PAM
Name	FUS	FUS
Sample_ID	BGRSDLV03-17	BGRSDLV03-18
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	FUS	FUS
qPCR_result	70.7	73.3
Ave_qPCR	72.0
RT-qPCR_primer-F	GGCCAGAGCAGCTATTCTTC
RT-qPCR_primer-R	CAGTCGAGCCATATCCCTG
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
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	9331	9332

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-17	BGRSDLV03-18
Sample_ID	BGRSDLV03-17	BGRSDLV03-18
Sample Name
Sample Name	FUS-BGRSDLV03-17	FUS-BGRSDLV03-18
RBP	FUS	FUS
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12614	12615

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-17	BGRSDLV03-18
Sample #	17	18
Sample Name	FUS-BGRSDLV03-17	FUS-BGRSDLV03-18
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-17	2023-10-17
Lib_ID	Lib-231017	Lib-231017
Tecan_Location
Tecan
Tecan_date
Size_bp	272	272
Peak_Molarity	55.30	63.00
libSampleQC_DNA_Well	DNA_Library_set66/set1/A8.png	DNA_Library_set66/set1/B8.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set66/set1/A3.png	RNA_Library_set66/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-17	BGRSDLV03-18
RBP	FUS	FUS
Batch_ID	BGRSDLV03	BGRSDLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4050	4051

Sequencing Information

	BGRSDLV03-17	BGRSDLV03-18
Sample_ID	BGRSDLV03-17	BGRSDLV03-18
Sample Name	FUS-BGRSDLV03-17	FUS-BGRSDLV03-18
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,711,550	22,959,273
total_aligned_reads	11,770,647	20,542,374
unique_aligned_reads	10,917,524	18,979,585
percent_uniqueAligned	0.79623	0.82666
correlation_replicates	0.992617	0.992617
spikein_reads	3,362	376
percent_spikeins	0.00025	0.00002
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2769	2770

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
FUS-BGRSDLV03-17_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2769	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8918
FUS-BGRSDLV03-17_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2769	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8958
FUS-BGRSDLV03-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2769					GRCh38	V40	FUS-BGRSDLV03-17_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-17_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8998
FUS-BGRSDLV03-17_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2769					GRCh38	V40	FUS-BGRSDLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	9038
FUS-BGRSDLV03-17_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2769					GRCh38	V40	FUS-BGRSDLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	9078
FUS-BGRSDLV03-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2769					GRCh38	V40	FUS-BGRSDLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	9118
FUS-BGRSDLV03-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2769					GRCh38	V40	FUS-BGRSDLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	9158
FUS-BGRSDLV03-17_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2769					GRCh38	V40	FUS-BGRSDLV03-17_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-17_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9198
FUS-BGRSDLV03-18_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2770	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8919
FUS-BGRSDLV03-18_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2770	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8959
FUS-BGRSDLV03-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2770					GRCh38	V40	FUS-BGRSDLV03-18_merged_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-18_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8999
FUS-BGRSDLV03-18_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2770					GRCh38	V40	FUS-BGRSDLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	9039
FUS-BGRSDLV03-18_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2770					GRCh38	V40	FUS-BGRSDLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	9079
FUS-BGRSDLV03-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2770					GRCh38	V40	FUS-BGRSDLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	9119
FUS-BGRSDLV03-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2770					GRCh38	V40	FUS-BGRSDLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	9159
FUS-BGRSDLV03-18_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2770					GRCh38	V40	FUS-BGRSDLV03-18_merged_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-18_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9199