REPIN1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-17	BGRSLV07-18
idx	0	0
TRCN#_or_BGC#	TRCN0000329976	TRCN0000329976
shRNA_or_gRNA_sequence	CCGGCTTGTCCCAAATGCGAGAGACCTCGAGGTCTCTCGCATTTGGGACAAGTTTTTG	CCGGCTTGTCCCAAATGCGAGAGACCTCGAGGTCTCTCGCATTTGGGACAAGTTTTTG
PAM
Name	REPIN1	REPIN1
Sample_ID	BGRSLV07-17	BGRSLV07-18
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	REPIN1	REPIN1
qPCR_result	78.4	84.3
Ave_qPCR	81.4
RT-qPCR_primer-F	cttccgccacaaaccctac
RT-qPCR_primer-R	cgacaccaggttggacttct
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	8599	8600

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-17	BGRSLV07-18
Sample_ID	BGRSLV07-17	BGRSLV07-18
Sample Name
Sample Name	REPIN1-BGRSLV07-17	REPIN1-BGRSLV07-18
RBP	REPIN1	REPIN1
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	11844	11845

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-17	BGRSLV07-18
Sample #	25	26
Sample Name	REPIN1-BGRSLV07-17	REPIN1-BGRSLV07-18
Sample_Name_Alias
Index Well Position	A04	B04
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	300	295
Peak_Molarity	33.60	72.30
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A4.png	DNA_Library_set60-62/set4/B4.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A4.png	RNA_Library_set60-62/set2/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-17	BGRSLV07-18
RBP	REPIN1	REPIN1
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3708	3709

Sequencing Information

	BGRSLV07-17	BGRSLV07-18
Sample_ID	BGRSLV07-17	BGRSLV07-18
Sample Name	REPIN1-BGRSLV07-17	REPIN1-BGRSLV07-18
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	23,084,752	24,123,359
total_aligned_reads	17,195,374	19,803,119
unique_aligned_reads	16,122,324	18,551,857
percent_uniqueAligned	0.69840	0.76904
correlation_replicates	0.991419	0.991419
spikein_reads	70,062	41,186
percent_spikeins	0.00303	0.00171
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2579	2580

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
REPIN1-BGRSLV07-17_S25_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2579	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7884
REPIN1-BGRSLV07-17_S25_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2579	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7928
REPIN1-BGRSLV07-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2579					GRCh38	V40	REPIN1-BGRSLV07-17_S25_L003_R1_001.filtered.trimmed.paired.fastq.gz,REPIN1-BGRSLV07-17_S25_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10189
REPIN1-BGRSLV07-17_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2579					GRCh38	V40	REPIN1-BGRSLV07-17/Aligned.sortedByCoord.out.bam		ENCORE2	10233
REPIN1-BGRSLV07-17_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2579					GRCh38	V40	REPIN1-BGRSLV07-17/Aligned.sortedByCoord.out.bam		ENCORE2	10277
REPIN1-BGRSLV07-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2579					GRCh38	V40	REPIN1-BGRSLV07-17/Aligned.sortedByCoord.out.bam		ENCORE2	10321
REPIN1-BGRSLV07-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2579					GRCh38	V40	REPIN1-BGRSLV07-17/Aligned.sortedByCoord.out.bam		ENCORE2	10365
REPIN1-BGRSLV07-17_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2579					GRCh38	V40	REPIN1-BGRSLV07-17_S25_L003_R1_001.filtered.trimmed.paired.fastq.gz,REPIN1-BGRSLV07-17_S25_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10409
REPIN1-BGRSLV07-18_S26_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2580	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7885
REPIN1-BGRSLV07-18_S26_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2580	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7929
REPIN1-BGRSLV07-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2580					GRCh38	V40	REPIN1-BGRSLV07-18_S26_L003_R1_001.filtered.trimmed.paired.fastq.gz,REPIN1-BGRSLV07-18_S26_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10190
REPIN1-BGRSLV07-18_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2580					GRCh38	V40	REPIN1-BGRSLV07-18/Aligned.sortedByCoord.out.bam		ENCORE2	10234
REPIN1-BGRSLV07-18_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2580					GRCh38	V40	REPIN1-BGRSLV07-18/Aligned.sortedByCoord.out.bam		ENCORE2	10278
REPIN1-BGRSLV07-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2580					GRCh38	V40	REPIN1-BGRSLV07-18/Aligned.sortedByCoord.out.bam		ENCORE2	10322
REPIN1-BGRSLV07-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2580					GRCh38	V40	REPIN1-BGRSLV07-18/Aligned.sortedByCoord.out.bam		ENCORE2	10366
REPIN1-BGRSLV07-18_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2580					GRCh38	V40	REPIN1-BGRSLV07-18_S26_L003_R1_001.filtered.trimmed.paired.fastq.gz,REPIN1-BGRSLV07-18_S26_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10410