FUS RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-19dox	BGRSDLV03-20dox
idx	0	0
TRCN#_or_BGC#	TRCN0000039824	TRCN0000039824
shRNA_or_gRNA_sequence	GCTGATTACTTCAAGCAGATTCTCGAGAATCTGCTTGAAGTAATCAGC	GCTGATTACTTCAAGCAGATTCTCGAGAATCTGCTTGAAGTAATCAGC
PAM
Name	FUS	FUS
Sample_ID	BGRSDLV03-19dox	BGRSDLV03-20dox
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	FUS	FUS
qPCR_result	75.6	69.6
Ave_qPCR	72.6
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9333	9334

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-19dox	BGRSDLV03-20dox
Sample_ID	BGRSDLV03-19dox	BGRSDLV03-20dox
Sample Name
Sample Name	FUS-BGRSDLV03-19dox	FUS-BGRSDLV03-20dox
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	12616	12617

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-19dox	BGRSDLV03-20dox
Sample #	19	20
Sample Name	FUS-BGRSDLV03-19dox	FUS-BGRSDLV03-20dox
Sample_Name_Alias
Index Well Position	C07	D07
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	271	275
Peak_Molarity	67.40	62.00
libSampleQC_DNA_Well	DNA_Library_set66/set1/C8.png	DNA_Library_set66/set1/D8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set66/set1/C3.png	RNA_Library_set66/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-19dox	BGRSDLV03-20dox
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	4052	4053

Sequencing Information

	BGRSDLV03-19dox	BGRSDLV03-20dox
Sample_ID	BGRSDLV03-19dox	BGRSDLV03-20dox
Sample Name	FUS-BGRSDLV03-19dox	FUS-BGRSDLV03-20dox
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,719,987	26,930,859
total_aligned_reads	11,596,921	23,696,985
unique_aligned_reads	10,699,501	21,945,314
percent_uniqueAligned	0.77985	0.81488
correlation_replicates	0.996680	0.996680
spikein_reads	3,326	2,744
percent_spikeins	0.00024	0.00010
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2771	2772

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-BGRSDLV03-19dox_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2771	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8920
FUS-BGRSDLV03-19dox_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2771	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8960
FUS-BGRSDLV03-19dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2771					GRCh38	V40	FUS-BGRSDLV03-19dox_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-19dox_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9000
FUS-BGRSDLV03-19dox_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	2771					GRCh38	V40	FUS-BGRSDLV03-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9040
FUS-BGRSDLV03-19dox_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	2771					GRCh38	V40	FUS-BGRSDLV03-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9080
FUS-BGRSDLV03-19dox_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	2771					GRCh38	V40	FUS-BGRSDLV03-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9120
FUS-BGRSDLV03-19dox_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	2771					GRCh38	V40	FUS-BGRSDLV03-19dox/Aligned.sortedByCoord.out.bam		ENCORE2	9160
FUS-BGRSDLV03-19dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2771					GRCh38	V40	FUS-BGRSDLV03-19dox_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-19dox_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9200
FUS-BGRSDLV03-20dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2772	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8921
FUS-BGRSDLV03-20dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2772	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8961
FUS-BGRSDLV03-20dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2772					GRCh38	V40	FUS-BGRSDLV03-20dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-20dox_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9001
FUS-BGRSDLV03-20dox_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	2772					GRCh38	V40	FUS-BGRSDLV03-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9041
FUS-BGRSDLV03-20dox_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	2772					GRCh38	V40	FUS-BGRSDLV03-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9081
FUS-BGRSDLV03-20dox_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	2772					GRCh38	V40	FUS-BGRSDLV03-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9121
FUS-BGRSDLV03-20dox_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	2772					GRCh38	V40	FUS-BGRSDLV03-20dox/Aligned.sortedByCoord.out.bam		ENCORE2	9161
FUS-BGRSDLV03-20dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2772					GRCh38	V40	FUS-BGRSDLV03-20dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSDLV03-20dox_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9201