MNAT1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSLV02-29	BGRSLV02-30
idx	0	0
TRCN#_or_BGC#	TRCN0000019944	TRCN0000019944
shRNA_or_gRNA_sequence	CCGGCCTAGTCTAAGAGAATACAATCTCGAGATTGTATTCTCTTAGACTAGGTTTTT	CCGGCCTAGTCTAAGAGAATACAATCTCGAGATTGTATTCTCTTAGACTAGGTTTTT
PAM
Name	MNAT1	MNAT1
Sample_ID	BGRSLV02-29	BGRSLV02-30
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	MNAT1	MNAT1
qPCR_result	85.7	89.0
Ave_qPCR	87.3
RT-qPCR_primer-F	GCTCTGTATGAATACCAGCCACT
RT-qPCR_primer-R	ATAGCCTCCAGCAAGGTCCTGT
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	10314	10315

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-29	BGRSLV02-30
Sample_ID	BGRSLV02-29	BGRSLV02-30
Sample Name
Sample Name	MNAT1-BGRSLV02-29	MNAT1-BGRSLV02-30
RBP	MNAT1	MNAT1
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Released	Released
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	11316	11317

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-29	BGRSLV02-30
Sample #	19	20
Sample Name	MNAT1-BGRSLV02-29	MNAT1-BGRSLV02-30
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	294	292
Peak_Molarity	54.10	48.40
libSampleQC_DNA_Well	DNA_Library_set57/set1/C9.png	DNA_Library_set57/set1/D9.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set57/set1/C3.png	RNA_Library_set57/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-29	BGRSLV02-30
RBP	MNAT1	MNAT1
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3480	3481

Sequencing Information

	BGRSLV02-29	BGRSLV02-30
Sample_ID	BGRSLV02-29	BGRSLV02-30
Sample Name	MNAT1-BGRSLV02-29	MNAT1-BGRSLV02-30
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	70,229,533	67,191,729
total_aligned_reads	65,669,062	62,429,745
unique_aligned_reads	61,179,039	58,311,162
percent_uniqueAligned	0.87113	0.86783
correlation_replicates	0.996726	0.996726
spikein_reads	37,770	39,572
percent_spikeins	0.00054	0.00059
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2351	2352

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
MNAT1-BGRSLV02-29_S107_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2351	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8220
MNAT1-BGRSLV02-29_S107_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2351	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8266
MNAT1-BGRSLV02-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2351					GRCh38	V40	MNAT1-BGRSLV02-29_S107_L003_R1_001.filtered.trimmed.paired.fastq.gz,MNAT1-BGRSLV02-29_S107_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11509
MNAT1-BGRSLV02-29_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2351					GRCh38	V40	MNAT1-BGRSLV02-29/Aligned.sortedByCoord.out.bam		ENCORE2	11555
MNAT1-BGRSLV02-29_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2351					GRCh38	V40	MNAT1-BGRSLV02-29/Aligned.sortedByCoord.out.bam		ENCORE2	11601
MNAT1-BGRSLV02-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2351					GRCh38	V40	MNAT1-BGRSLV02-29/Aligned.sortedByCoord.out.bam		ENCORE2	11647
MNAT1-BGRSLV02-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2351					GRCh38	V40	MNAT1-BGRSLV02-29/Aligned.sortedByCoord.out.bam		ENCORE2	11693
MNAT1-BGRSLV02-29_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2351					GRCh38	V40	MNAT1-BGRSLV02-29_S107_L003_R1_001.filtered.trimmed.paired.fastq.gz,MNAT1-BGRSLV02-29_S107_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11739
MNAT1-BGRSLV02-30_S108_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2352	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8221
MNAT1-BGRSLV02-30_S108_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2352	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8267
MNAT1-BGRSLV02-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2352					GRCh38	V40	MNAT1-BGRSLV02-30_S108_L003_R1_001.filtered.trimmed.paired.fastq.gz,MNAT1-BGRSLV02-30_S108_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11510
MNAT1-BGRSLV02-30_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2352					GRCh38	V40	MNAT1-BGRSLV02-30/Aligned.sortedByCoord.out.bam		ENCORE2	11556
MNAT1-BGRSLV02-30_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2352					GRCh38	V40	MNAT1-BGRSLV02-30/Aligned.sortedByCoord.out.bam		ENCORE2	11602
MNAT1-BGRSLV02-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2352					GRCh38	V40	MNAT1-BGRSLV02-30/Aligned.sortedByCoord.out.bam		ENCORE2	11648
MNAT1-BGRSLV02-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2352					GRCh38	V40	MNAT1-BGRSLV02-30/Aligned.sortedByCoord.out.bam		ENCORE2	11694
MNAT1-BGRSLV02-30_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2352					GRCh38	V40	MNAT1-BGRSLV02-30_S108_L003_R1_001.filtered.trimmed.paired.fastq.gz,MNAT1-BGRSLV02-30_S108_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11740