FUS RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-11	BGRSLV02-12
idx	0	0
TRCN#_or_BGC#	TRCN0000039824	TRCN0000039824
shRNA_or_gRNA_sequence	GCTGATTACTTCAAGCAGATTCTCGAGAATCTGCTTGAAGTAATCAGC	GCTGATTACTTCAAGCAGATTCTCGAGAATCTGCTTGAAGTAATCAGC
PAM
Name	FUS	FUS
Sample_ID	BGRSLV02-11	BGRSLV02-12
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	FUS	FUS
qPCR_result	59.4	52.8
Ave_qPCR	56.1
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	8248	8249

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-11	BGRSLV02-12
Sample_ID	BGRSLV02-11	BGRSLV02-12
Sample Name
Sample Name	FUS-BGRSLV02-11	FUS-BGRSLV02-12
RBP	FUS	FUS
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11302	11303

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-11	BGRSLV02-12
Sample #	5	6
Sample Name	FUS-BGRSLV02-11	FUS-BGRSLV02-12
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	283	284
Peak_Molarity	73.60	77.30
libSampleQC_DNA_Well	DNA_Library_set57/set1/E7.png	DNA_Library_set57/set1/F7.png
RIN	10.0	9.5
libSample_RNA_Well	RNA_Library_set57/set1/E1.png	RNA_Library_set57/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-11	BGRSLV02-12
RBP	FUS	FUS
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3466	3467

Sequencing Information

	BGRSLV02-11	BGRSLV02-12
Sample_ID	BGRSLV02-11	BGRSLV02-12
Sample Name	FUS-BGRSLV02-11	FUS-BGRSLV02-12
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	58,622,373	52,261,640
total_aligned_reads	53,103,338	47,035,926
unique_aligned_reads	49,014,656	43,808,823
percent_uniqueAligned	0.83611	0.83826
correlation_replicates	0.997375	0.997375
spikein_reads	23,206	49,016
percent_spikeins	0.00040	0.00094
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2337	2338

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-BGRSLV02-11_S93_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2337	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8218
FUS-BGRSLV02-11_S93_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2337	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8264
FUS-BGRSLV02-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2337					GRCh38	V40	FUS-BGRSLV02-11_S93_L003_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSLV02-11_S93_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11507
FUS-BGRSLV02-11_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2337					GRCh38	V40	FUS-BGRSLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	11553
FUS-BGRSLV02-11_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2337					GRCh38	V40	FUS-BGRSLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	11599
FUS-BGRSLV02-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2337					GRCh38	V40	FUS-BGRSLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	11645
FUS-BGRSLV02-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2337					GRCh38	V40	FUS-BGRSLV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	11691
FUS-BGRSLV02-11_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2337					GRCh38	V40	FUS-BGRSLV02-11_S93_L003_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSLV02-11_S93_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11737
FUS-BGRSLV02-12_S94_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2338	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8219
FUS-BGRSLV02-12_S94_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2338	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8265
FUS-BGRSLV02-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2338					GRCh38	V40	FUS-BGRSLV02-12_S94_L003_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSLV02-12_S94_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11508
FUS-BGRSLV02-12_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2338					GRCh38	V40	FUS-BGRSLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	11554
FUS-BGRSLV02-12_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2338					GRCh38	V40	FUS-BGRSLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	11600
FUS-BGRSLV02-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2338					GRCh38	V40	FUS-BGRSLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	11646
FUS-BGRSLV02-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2338					GRCh38	V40	FUS-BGRSLV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	11692
FUS-BGRSLV02-12_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2338					GRCh38	V40	FUS-BGRSLV02-12_S94_L003_R1_001.filtered.trimmed.paired.fastq.gz,FUS-BGRSLV02-12_S94_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11738