SNRNP48 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-35dox	BGRSDLV04-36dox
idx	0	0
TRCN#_or_BGC#	TRCN0000142131	TRCN0000142131
shRNA_or_gRNA_sequence	CCGGGCCACTTTCGAGTACAGCTAACTCGAGTTAGCTGTACTCGAAAGTGGCTTTTTTG	CCGGGCCACTTTCGAGTACAGCTAACTCGAGTTAGCTGTACTCGAAAGTGGCTTTTTTG
PAM
Name	SNRNP48	SNRNP48
Sample_ID	BGRSDLV04-35dox	BGRSDLV04-36dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	SNRNP48	SNRNP48
qPCR_result	49.11963	59.59224
Ave_qPCR	54.355935
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	9399	9400

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-35dox	BGRSDLV04-36dox
Sample_ID	BGRSDLV04-35dox	BGRSDLV04-36dox
Sample Name
Sample Name	SNRNP48-BGRSDLV04-35dox	SNRNP48-BGRSDLV04-36dox
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	12668	12669

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-35dox	BGRSDLV04-36dox
Sample #	23	24
Sample Name	SNRNP48-BGRSDLV04-35dox	SNRNP48-BGRSDLV04-36dox
Sample_Name_Alias
Index Well Position	G03	H03
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	277	284
Peak_Molarity	42.10	42.90
libSampleQC_DNA_Well	DNA_Library_set68/set1/G3.png	DNA_Library_set68/set1/H3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/G3.png	RNA_Library_set68/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-35dox	BGRSDLV04-36dox
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	4096	4097

Sequencing Information

	BGRSDLV04-35dox	BGRSDLV04-36dox
Sample_ID	BGRSDLV04-35dox	BGRSDLV04-36dox
Sample Name	SNRNP48-BGRSDLV04-35dox	SNRNP48-BGRSDLV04-36dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	26,038,158	24,200,067
total_aligned_reads	21,606,861	19,631,189
unique_aligned_reads	20,182,551	18,374,159
percent_uniqueAligned	0.77511	0.75926
correlation_replicates	0.993536	0.993536
spikein_reads	2,380	6,120
percent_spikeins	0.00009	0.00025
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2859	2860

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-BGRSDLV04-35dox_S23_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2859	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27651
SNRNP48-BGRSDLV04-35dox_S23_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2859	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27715
SNRNP48-BGRSDLV04-35dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2859					GRCh38	V40	SNRNP48-BGRSDLV04-35dox_S23_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-35dox_S23_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27779
SNRNP48-BGRSDLV04-35dox_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	2859					GRCh38	V40	SNRNP48-BGRSDLV04-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	27843
SNRNP48-BGRSDLV04-35dox_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	2859					GRCh38	V40	SNRNP48-BGRSDLV04-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	27907
SNRNP48-BGRSDLV04-35dox_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	2859					GRCh38	V40	SNRNP48-BGRSDLV04-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	27971
SNRNP48-BGRSDLV04-35dox_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	2859					GRCh38	V40	SNRNP48-BGRSDLV04-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	28035
SNRNP48-BGRSDLV04-35dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2859					GRCh38	V40	SNRNP48-BGRSDLV04-35dox_S23_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-35dox_S23_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28099
SNRNP48-BGRSDLV04-36dox_S24_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2860	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27652
SNRNP48-BGRSDLV04-36dox_S24_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2860	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27716
SNRNP48-BGRSDLV04-36dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2860					GRCh38	V40	SNRNP48-BGRSDLV04-36dox_S24_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-36dox_S24_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27780
SNRNP48-BGRSDLV04-36dox_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	2860					GRCh38	V40	SNRNP48-BGRSDLV04-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	27844
SNRNP48-BGRSDLV04-36dox_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	2860					GRCh38	V40	SNRNP48-BGRSDLV04-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	27908
SNRNP48-BGRSDLV04-36dox_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	2860					GRCh38	V40	SNRNP48-BGRSDLV04-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	27972
SNRNP48-BGRSDLV04-36dox_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	2860					GRCh38	V40	SNRNP48-BGRSDLV04-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	28036
SNRNP48-BGRSDLV04-36dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2860					GRCh38	V40	SNRNP48-BGRSDLV04-36dox_S24_L004_R1_001.filtered.trimmed.paired.fastq.gz,SNRNP48-BGRSDLV04-36dox_S24_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28100