SNRNP48 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-33	BGRSDLV04-34
idx	0	0
TRCN#_or_BGC#	TRCN0000142131	TRCN0000142131
shRNA_or_gRNA_sequence	CCGGGCCACTTTCGAGTACAGCTAACTCGAGTTAGCTGTACTCGAAAGTGGCTTTTTTG	CCGGGCCACTTTCGAGTACAGCTAACTCGAGTTAGCTGTACTCGAAAGTGGCTTTTTTG
PAM
Name	SNRNP48	SNRNP48
Sample_ID	BGRSDLV04-33	BGRSDLV04-34
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	SNRNP48	SNRNP48
qPCR_result	69.31787	63.03327
Ave_qPCR	66.17557
RT-qPCR_primer-F	tgcagttgggaaagacagtg
RT-qPCR_primer-R	tagagggcaagacgatcagc
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	9397	9398

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-33	BGRSDLV04-34
Sample_ID	BGRSDLV04-33	BGRSDLV04-34
Sample Name
Sample Name	SNRNP48-BGRSDLV04-33	SNRNP48-BGRSDLV04-34
RBP	SNRNP48	SNRNP48
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12666	12667

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-33	BGRSDLV04-34
Sample #	21	22
Sample Name	SNRNP48-BGRSDLV04-33	SNRNP48-BGRSDLV04-34
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	293	285
Peak_Molarity	39.90	50.20
libSampleQC_DNA_Well	DNA_Library_set68/set1/E3.png	DNA_Library_set68/set1/F3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/E3.png	RNA_Library_set68/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-33	BGRSDLV04-34
RBP	SNRNP48	SNRNP48
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4094	4095

Sequencing Information

	BGRSDLV04-33	BGRSDLV04-34
Sample_ID	BGRSDLV04-33	BGRSDLV04-34
Sample Name	SNRNP48-BGRSDLV04-33	SNRNP48-BGRSDLV04-34
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	60,272,477	32,295,057
total_aligned_reads	52,472,734	28,346,306
unique_aligned_reads	49,202,715	26,597,969
percent_uniqueAligned	0.81634	0.82359
correlation_replicates	0.997609	0.997609
spikein_reads	4,468	5,838
percent_spikeins	0.00007	0.00018
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2857	2858

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
SNRNP48-BGRSDLV04-33_S21_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2857	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27649
SNRNP48-BGRSDLV04-33_S21_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2857	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27713
SNRNP48-BGRSDLV04-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2857					GRCh38	V40	SNRNP48-BGRSDLV04-33_S21_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-33_S21_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27777
SNRNP48-BGRSDLV04-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2857					GRCh38	V40	SNRNP48-BGRSDLV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	27841
SNRNP48-BGRSDLV04-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2857					GRCh38	V40	SNRNP48-BGRSDLV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	27905
SNRNP48-BGRSDLV04-33_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2857					GRCh38	V40	SNRNP48-BGRSDLV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	27969
SNRNP48-BGRSDLV04-33_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2857					GRCh38	V40	SNRNP48-BGRSDLV04-33/Aligned.sortedByCoord.out.bam		ENCORE2	28033
SNRNP48-BGRSDLV04-33_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2857					GRCh38	V40	SNRNP48-BGRSDLV04-33_S21_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-33_S21_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28097
SNRNP48-BGRSDLV04-34_S22_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2858	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27650
SNRNP48-BGRSDLV04-34_S22_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2858	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27714
SNRNP48-BGRSDLV04-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2858					GRCh38	V40	SNRNP48-BGRSDLV04-34_S22_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-34_S22_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27778
SNRNP48-BGRSDLV04-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2858					GRCh38	V40	SNRNP48-BGRSDLV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	27842
SNRNP48-BGRSDLV04-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2858					GRCh38	V40	SNRNP48-BGRSDLV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	27906
SNRNP48-BGRSDLV04-34_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2858					GRCh38	V40	SNRNP48-BGRSDLV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	27970
SNRNP48-BGRSDLV04-34_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2858					GRCh38	V40	SNRNP48-BGRSDLV04-34/Aligned.sortedByCoord.out.bam		ENCORE2	28034
SNRNP48-BGRSDLV04-34_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2858					GRCh38	V40	SNRNP48-BGRSDLV04-34_S22_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-34_S22_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28098