PRR3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-39	BGRSLV04-40
idx	0	0
TRCN#_or_BGC#	TRCN0000152728	TRCN0000152728
shRNA_or_gRNA_sequence	CCGGCCATTCTTCTCCTGTTGGTTACTCGAGTAACCAACAGGAGAAGAATGGTTTTTTG	CCGGCCATTCTTCTCCTGTTGGTTACTCGAGTAACCAACAGGAGAAGAATGGTTTTTTG
PAM
Name	PRR3	PRR3
Sample_ID	BGRSLV04-39	BGRSLV04-40
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	PRR3	PRR3
qPCR_result	78.1	67.9
Ave_qPCR	73.0
RT-qPCR_primer-F	cgggaagagactggagatga
RT-qPCR_primer-R	ttgatcctggaggacctctg
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	8419	8420

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-39	BGRSLV04-40
Sample_ID	BGRSLV04-39	BGRSLV04-40
Sample Name
Sample Name	PRR3-BGRSLV04-39	PRR3-BGRSLV04-40
RBP	PRR3	PRR3
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	11458	11459

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-39	BGRSLV04-40
Sample #	23	24
Sample Name	PRR3-BGRSLV04-39	PRR3-BGRSLV04-40
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-03-02	2023-03-02
Lib_ID	Lib-230302	Lib-230302
Tecan_Location
Tecan
Tecan_date
Size_bp	294	284
Peak_Molarity	57.00	41.00
libSampleQC_DNA_Well	DNA_Library_set59/set1/G9.png	DNA_Library_set59/set1/H9.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set59/set1/G4.png	RNA_Library_set59/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-39	BGRSLV04-40
RBP	PRR3	PRR3
Batch_ID	BGRSLV04	BGRSLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3572	3573

Sequencing Information

	BGRSLV04-39	BGRSLV04-40
Sample_ID	BGRSLV04-39	BGRSLV04-40
Sample Name	PRR3-BGRSLV04-39	PRR3-BGRSLV04-40
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	68,488,397	49,349,048
total_aligned_reads	57,518,805	37,991,002
unique_aligned_reads	52,669,363	35,155,305
percent_uniqueAligned	0.76903	0.71238
correlation_replicates	0.963334	0.963334
spikein_reads	243,230	148,898
percent_spikeins	0.00355	0.00302
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2443	2444

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
PRR3-BGRSLV04-39_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2443	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8072
PRR3-BGRSLV04-39_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2443	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8110
PRR3-BGRSLV04-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2443					GRCh38	V40	PRR3-BGRSLV04-39_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRR3-BGRSLV04-39_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11041
PRR3-BGRSLV04-39_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2443					GRCh38	V40	PRR3-BGRSLV04-39/Aligned.sortedByCoord.out.bam		ENCORE2	11079
PRR3-BGRSLV04-39_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2443					GRCh38	V40	PRR3-BGRSLV04-39/Aligned.sortedByCoord.out.bam		ENCORE2	11117
PRR3-BGRSLV04-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2443					GRCh38	V40	PRR3-BGRSLV04-39/Aligned.sortedByCoord.out.bam		ENCORE2	11155
PRR3-BGRSLV04-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2443					GRCh38	V40	PRR3-BGRSLV04-39/Aligned.sortedByCoord.out.bam		ENCORE2	11193
PRR3-BGRSLV04-39_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2443					GRCh38	V40	PRR3-BGRSLV04-39_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRR3-BGRSLV04-39_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11231
PRR3-BGRSLV04-40_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2444	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8073
PRR3-BGRSLV04-40_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2444	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8111
PRR3-BGRSLV04-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2444					GRCh38	V40	PRR3-BGRSLV04-40_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRR3-BGRSLV04-40_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11042
PRR3-BGRSLV04-40_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2444					GRCh38	V40	PRR3-BGRSLV04-40/Aligned.sortedByCoord.out.bam		ENCORE2	11080
PRR3-BGRSLV04-40_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2444					GRCh38	V40	PRR3-BGRSLV04-40/Aligned.sortedByCoord.out.bam		ENCORE2	11118
PRR3-BGRSLV04-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2444					GRCh38	V40	PRR3-BGRSLV04-40/Aligned.sortedByCoord.out.bam		ENCORE2	11156
PRR3-BGRSLV04-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2444					GRCh38	V40	PRR3-BGRSLV04-40/Aligned.sortedByCoord.out.bam		ENCORE2	11194
PRR3-BGRSLV04-40_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2444					GRCh38	V40	PRR3-BGRSLV04-40_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRR3-BGRSLV04-40_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11232