SNRNP48 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-45	BGRSLV03-46
idx	0	0
TRCN#_or_BGC#	TRCN0000142131	TRCN0000142131
shRNA_or_gRNA_sequence	CCGGGCCACTTTCGAGTACAGCTAACTCGAGTTAGCTGTACTCGAAAGTGGCTTTTTTG	CCGGGCCACTTTCGAGTACAGCTAACTCGAGTTAGCTGTACTCGAAAGTGGCTTTTTTG
PAM
Name	SNRNP48	SNRNP48
Sample_ID	BGRSLV03-45	BGRSLV03-46
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	SNRNP48	SNRNP48
qPCR_result	75.6	71.0
Ave_qPCR	73.3
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	8355	8356

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-45	BGRSLV03-46
Sample_ID	BGRSLV03-45	BGRSLV03-46
Sample Name
Sample Name	SNRNP48-BGRSLV03-45	SNRNP48-BGRSLV03-46
RBP	SNRNP48	SNRNP48
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	11394	11395

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-45	BGRSLV03-46
Sample #	25	26
Sample Name	SNRNP48-BGRSLV03-45	SNRNP48-BGRSLV03-46
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	293	295
Peak_Molarity	5.83	58.90
libSampleQC_DNA_Well	DNA_Library_set58/set1/A10.png	DNA_Library_set58/set1/B10.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set58/set1/A4.png	RNA_Library_set58/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-45	BGRSLV03-46
RBP	SNRNP48	SNRNP48
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3532	3533

Sequencing Information

	BGRSLV03-45	BGRSLV03-46
Sample_ID	BGRSLV03-45	BGRSLV03-46
Sample Name	SNRNP48-BGRSLV03-45	SNRNP48-BGRSLV03-46
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	167,996,861	59,642,638
total_aligned_reads	145,156,957	51,149,416
unique_aligned_reads	136,532,011	47,711,935
percent_uniqueAligned	0.81271	0.79996
correlation_replicates	0.991759	0.991759
spikein_reads	1,098,072	364,046
percent_spikeins	0.00654	0.00610
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2403	2404

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-BGRSLV03-45_S159_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2403	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8150
SNRNP48-BGRSLV03-45_S159_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2403	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8192
SNRNP48-BGRSLV03-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2403					GRCh38	V40	SNRNP48-BGRSLV03-45_S159_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSLV03-45_S159_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11271
SNRNP48-BGRSLV03-45_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2403					GRCh38	V40	SNRNP48-BGRSLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	11313
SNRNP48-BGRSLV03-45_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2403					GRCh38	V40	SNRNP48-BGRSLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	11355
SNRNP48-BGRSLV03-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2403					GRCh38	V40	SNRNP48-BGRSLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	11397
SNRNP48-BGRSLV03-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2403					GRCh38	V40	SNRNP48-BGRSLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	11439
SNRNP48-BGRSLV03-45_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2403					GRCh38	V40	SNRNP48-BGRSLV03-45_S159_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSLV03-45_S159_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11481
SNRNP48-BGRSLV03-46_S160_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2404	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8151
SNRNP48-BGRSLV03-46_S160_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2404	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8193
SNRNP48-BGRSLV03-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2404					GRCh38	V40	SNRNP48-BGRSLV03-46_S160_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSLV03-46_S160_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11272
SNRNP48-BGRSLV03-46_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2404					GRCh38	V40	SNRNP48-BGRSLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	11314
SNRNP48-BGRSLV03-46_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2404					GRCh38	V40	SNRNP48-BGRSLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	11356
SNRNP48-BGRSLV03-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2404					GRCh38	V40	SNRNP48-BGRSLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	11398
SNRNP48-BGRSLV03-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2404					GRCh38	V40	SNRNP48-BGRSLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	11440
SNRNP48-BGRSLV03-46_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2404					GRCh38	V40	SNRNP48-BGRSLV03-46_S160_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSLV03-46_S160_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11482