RNPS1 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV03-11	BG293LV03-12
idx	0	0
TRCN#_or_BGC#	TRCN0000000050	TRCN0000000050
shRNA_or_gRNA_sequence	CCGGTGATTGACATGCCCGTGGAAACTCGAGTTTCCACGGGCATGTCAATCATTTTT	CCGGTGATTGACATGCCCGTGGAAACTCGAGTTTCCACGGGCATGTCAATCATTTTT
PAM
Name	RNPS1	RNPS1
Sample_ID	BG293LV03-11	BG293LV03-12
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	RNPS1	RNPS1
qPCR_result	65	58
Ave_qPCR	61.5
RT-qPCR_primer-F	x
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	9861	9862

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV03-11	BG293LV03-12
Sample_ID	BG293LV03-11	BG293LV03-12
Sample Name
Sample Name	RNPS1-BG293LV03-11	RNPS1-BG293LV03-12
RBP	RNPS1	RNPS1
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11742	11743

Library-Prep
Sequencing

Library-Prep Information

	BG293LV03-11	BG293LV03-12
Sample #	7	8
Sample Name	RNPS1-BG293LV03-11	RNPS1-BG293LV03-12
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	287	287
Peak_Molarity	58.80	48.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/G1.png	DNA_Library_set60-62/set4/H1.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/G1.png	RNA_Library_set60-62/set2/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BG293LV03-11	BG293LV03-12
RBP	RNPS1	RNPS1
Batch_ID	BG293LV03	BG293LV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3690	3691

Sequencing Information

	BG293LV03-11	BG293LV03-12
Sample_ID	BG293LV03-11	BG293LV03-12
Sample Name	RNPS1-BG293LV03-11	RNPS1-BG293LV03-12
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_W	set62_W
total_reads	28,823,910	28,555,811
total_aligned_reads	22,505,291	22,048,946
unique_aligned_reads	21,012,197	20,550,725
percent_uniqueAligned	0.72898	0.71967
correlation_replicates	0.997570	0.997570
spikein_reads	71,184	80,346
percent_spikeins	0.00247	0.00281
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2561	2562

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-BG293LV03-11_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2561	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7848
RNPS1-BG293LV03-11_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2561	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7864
RNPS1-BG293LV03-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2561					GRCh38	V40	RNPS1-BG293LV03-11_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV03-11_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10089
RNPS1-BG293LV03-11_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2561					GRCh38	V40	RNPS1-BG293LV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	10105
RNPS1-BG293LV03-11_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2561					GRCh38	V40	RNPS1-BG293LV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	10121
RNPS1-BG293LV03-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2561					GRCh38	V40	RNPS1-BG293LV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	10137
RNPS1-BG293LV03-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2561					GRCh38	V40	RNPS1-BG293LV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	10153
RNPS1-BG293LV03-11_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2561					GRCh38	V40	RNPS1-BG293LV03-11_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV03-11_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10169
RNPS1-BG293LV03-12_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2562	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7849
RNPS1-BG293LV03-12_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2562	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7865
RNPS1-BG293LV03-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2562					GRCh38	V40	RNPS1-BG293LV03-12_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV03-12_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10090
RNPS1-BG293LV03-12_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2562					GRCh38	V40	RNPS1-BG293LV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	10106
RNPS1-BG293LV03-12_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2562					GRCh38	V40	RNPS1-BG293LV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	10122
RNPS1-BG293LV03-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2562					GRCh38	V40	RNPS1-BG293LV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	10138
RNPS1-BG293LV03-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2562					GRCh38	V40	RNPS1-BG293LV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	10154
RNPS1-BG293LV03-12_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2562					GRCh38	V40	RNPS1-BG293LV03-12_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNPS1-BG293LV03-12_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10170