MCM10 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-15	BGRSLV07-16
idx	0	0
TRCN#_or_BGC#	TRCN0000245428	TRCN0000245428
shRNA_or_gRNA_sequence	CCGGGGGATAACTAGAGGTCAAATTCTCGAGAATTTGACCTCTAGTTATCCCTTTTTG	CCGGGGGATAACTAGAGGTCAAATTCTCGAGAATTTGACCTCTAGTTATCCCTTTTTG
PAM
Name	MCM10	MCM10
Sample_ID	BGRSLV07-15	BGRSLV07-16
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	MCM10	MCM10
qPCR_result	68.3	65.9
Ave_qPCR	67.1
RT-qPCR_primer-F	gcctgtcttgctctgaggag
RT-qPCR_primer-R	gatggacttgatggctggtt
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	8597	8598

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-15	BGRSLV07-16
Sample_ID	BGRSLV07-15	BGRSLV07-16
Sample Name
Sample Name	MCM10-BGRSLV07-15	MCM10-BGRSLV07-16
RBP	MCM10	MCM10
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	11842	11843

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-15	BGRSLV07-16
Sample #	23	24
Sample Name	MCM10-BGRSLV07-15	MCM10-BGRSLV07-16
Sample_Name_Alias
Index Well Position	G03	H03
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	284	291
Peak_Molarity	63.10	44.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/G3.png	DNA_Library_set60-62/set4/H3.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set60-62/set2/G3.png	RNA_Library_set60-62/set2/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-15	BGRSLV07-16
RBP	MCM10	MCM10
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	3706	3707

Sequencing Information

	BGRSLV07-15	BGRSLV07-16
Sample_ID	BGRSLV07-15	BGRSLV07-16
Sample Name	MCM10-BGRSLV07-15	MCM10-BGRSLV07-16
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	39,426,269	36,019,939
total_aligned_reads	32,103,324	27,993,274
unique_aligned_reads	30,088,619	26,256,406
percent_uniqueAligned	0.76316	0.72894
correlation_replicates	0.997247	0.997247
spikein_reads	32,772	42,684
percent_spikeins	0.00083	0.00119
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2577	2578

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
MCM10-BGRSLV07-15_S23_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2577	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	7878
MCM10-BGRSLV07-15_S23_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2577	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	7922
MCM10-BGRSLV07-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2577					GRCh38	V40	MCM10-BGRSLV07-15_S23_L003_R1_001.filtered.trimmed.paired.fastq.gz,MCM10-BGRSLV07-15_S23_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10183
MCM10-BGRSLV07-15_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	2577					GRCh38	V40	MCM10-BGRSLV07-15/Aligned.sortedByCoord.out.bam		ENCORE2	10227
MCM10-BGRSLV07-15_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	2577					GRCh38	V40	MCM10-BGRSLV07-15/Aligned.sortedByCoord.out.bam		ENCORE2	10271
MCM10-BGRSLV07-15_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	2577					GRCh38	V40	MCM10-BGRSLV07-15/Aligned.sortedByCoord.out.bam		ENCORE2	10315
MCM10-BGRSLV07-15_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	2577					GRCh38	V40	MCM10-BGRSLV07-15/Aligned.sortedByCoord.out.bam		ENCORE2	10359
MCM10-BGRSLV07-15_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2577					GRCh38	V40	MCM10-BGRSLV07-15_S23_L003_R1_001.filtered.trimmed.paired.fastq.gz,MCM10-BGRSLV07-15_S23_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10403
MCM10-BGRSLV07-16_S24_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2578	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	7879
MCM10-BGRSLV07-16_S24_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2578	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	7923
MCM10-BGRSLV07-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2578					GRCh38	V40	MCM10-BGRSLV07-16_S24_L003_R1_001.filtered.trimmed.paired.fastq.gz,MCM10-BGRSLV07-16_S24_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10184
MCM10-BGRSLV07-16_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	2578					GRCh38	V40	MCM10-BGRSLV07-16/Aligned.sortedByCoord.out.bam		ENCORE2	10228
MCM10-BGRSLV07-16_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	2578					GRCh38	V40	MCM10-BGRSLV07-16/Aligned.sortedByCoord.out.bam		ENCORE2	10272
MCM10-BGRSLV07-16_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	2578					GRCh38	V40	MCM10-BGRSLV07-16/Aligned.sortedByCoord.out.bam		ENCORE2	10316
MCM10-BGRSLV07-16_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	2578					GRCh38	V40	MCM10-BGRSLV07-16/Aligned.sortedByCoord.out.bam		ENCORE2	10360
MCM10-BGRSLV07-16_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2578					GRCh38	V40	MCM10-BGRSLV07-16_S24_L003_R1_001.filtered.trimmed.paired.fastq.gz,MCM10-BGRSLV07-16_S24_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10404