RNPS1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-9	BG293LV06-10
idx	0	0
TRCN#_or_BGC#	TRCN0000000050	TRCN0000000050
shRNA_or_gRNA_sequence	CCGGTGATTGACATGCCCGTGGAAACTCGAGTTTCCACGGGCATGTCAATCATTTTT	CCGGTGATTGACATGCCCGTGGAAACTCGAGTTTCCACGGGCATGTCAATCATTTTT
PAM
Name	RNPS1	RNPS1
Sample_ID	BG293LV06-9	BG293LV06-10
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	RNPS1	RNPS1
qPCR_result	55.9	53.1
Ave_qPCR	54.5
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	12144	12145

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-9	BG293LV06-10
Sample_ID	BG293LV06-9	BG293LV06-10
Sample Name
Sample Name	RNPS1-BG293LV06-9	RNPS1-BG293LV06-10
RBP	RNPS1	RNPS1
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13446	13447

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-9	BG293LV06-10
Sample #	13	14
Sample Name	RNPS1-BG293LV06-9	RNPS1-BG293LV06-10
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	295	294
Peak_Molarity	87.80	84.20
libSampleQC_DNA_Well	DNA_Library_set71/set1/E2.png	DNA_Library_set71/set1/F2.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set71/set1/E2.png	RNA_Library_set71/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-9	BG293LV06-10
RBP	RNPS1	RNPS1
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4438	4439

Sequencing Information

	BG293LV06-9	BG293LV06-10
Sample_ID	BG293LV06-9	BG293LV06-10
Sample Name	RNPS1-BG293LV06-9	RNPS1-BG293LV06-10
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	40,907,514	35,986,302
total_aligned_reads	36,213,878	33,104,738
unique_aligned_reads	33,898,398	30,987,462
percent_uniqueAligned	0.82866	0.86109
correlation_replicates	0.992618	0.992618
spikein_reads	114,626	99,056
percent_spikeins	0.00280	0.00275
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3007	3008

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
RNPS1-BG293LV06-9_S13_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3007	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29370
RNPS1-BG293LV06-9_S13_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3007	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29434
RNPS1-BG293LV06-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3007					GRCh38	V40	RNPS1-BG293LV06-9_S13_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV06-9_S13_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29499
RNPS1-BG293LV06-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3007					GRCh38	V40	RNPS1-BG293LV06-9_Aligned.sortedByCoord.out.bam		ENCORE2	29563
RNPS1-BG293LV06-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3007					GRCh38	V40	RNPS1-BG293LV06-9_Aligned.sortedByCoord.out.bam		ENCORE2	29627
RNPS1-BG293LV06-9_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3007					GRCh38	V40	RNPS1-BG293LV06-9_Aligned.sortedByCoord.out.bam		ENCORE2	29691
RNPS1-BG293LV06-9_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3007					GRCh38	V40	RNPS1-BG293LV06-9_S13_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV06-9_S13_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29755
RNPS1-BG293LV06-10_S14_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3008	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29369
RNPS1-BG293LV06-10_S14_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3008	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29433
RNPS1-BG293LV06-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3008					GRCh38	V40	RNPS1-BG293LV06-10_S14_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV06-10_S14_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29498
RNPS1-BG293LV06-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3008					GRCh38	V40	RNPS1-BG293LV06-10_Aligned.sortedByCoord.out.bam		ENCORE2	29562
RNPS1-BG293LV06-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3008					GRCh38	V40	RNPS1-BG293LV06-10_Aligned.sortedByCoord.out.bam		ENCORE2	29626
RNPS1-BG293LV06-10_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3008					GRCh38	V40	RNPS1-BG293LV06-10_Aligned.sortedByCoord.out.bam		ENCORE2	29690
RNPS1-BG293LV06-10_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3008					GRCh38	V40	RNPS1-BG293LV06-10_S14_L002_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV06-10_S14_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29754