BMI1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-27	BGRSLV02-28
idx	0	0
TRCN#_or_BGC#	TRCN0000020155	TRCN0000020155
shRNA_or_gRNA_sequence	CCGGCCAGACCACTACTGAATATAACTCGAGTTATATTCAGTAGTGGTCTGGTTTTT	CCGGCCAGACCACTACTGAATATAACTCGAGTTATATTCAGTAGTGGTCTGGTTTTT
PAM
Name	BMI1	BMI1
Sample_ID	BGRSLV02-27	BGRSLV02-28
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	BMI1	BMI1
qPCR_result	65.2	67.8
Ave_qPCR	66.5
RT-qPCR_primer-F	gatacttacgatgcccagca
RT-qPCR_primer-R	aaggttcctcctcatacatgaca
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	8264	8265

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-27	BGRSLV02-28
Sample_ID	BGRSLV02-27	BGRSLV02-28
Sample Name
Sample Name	BMI1-BGRSLV02-27	BMI1-BGRSLV02-28
RBP	BMI1	BMI1
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	11314	11315

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-27	BGRSLV02-28
Sample #	17	18
Sample Name	BMI1-BGRSLV02-27	BMI1-BGRSLV02-28
Sample_Name_Alias
Index Well Position	A03	B03
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	296
Peak_Molarity	49.20	49.90
libSampleQC_DNA_Well	DNA_Library_set57/set1/A9.png	DNA_Library_set57/set1/B9.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set57/set1/A3.png	RNA_Library_set57/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-27	BGRSLV02-28
RBP	BMI1	BMI1
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	3478	3479

Sequencing Information

	BGRSLV02-27	BGRSLV02-28
Sample_ID	BGRSLV02-27	BGRSLV02-28
Sample Name	BMI1-BGRSLV02-27	BMI1-BGRSLV02-28
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	78,604,157	39,931,024
total_aligned_reads	72,088,188	37,264,412
unique_aligned_reads	66,942,976	34,698,731
percent_uniqueAligned	0.85165	0.86897
correlation_replicates	0.998371	0.998371
spikein_reads	58,614	19,424
percent_spikeins	0.00075	0.00049
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2349	2350

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
BMI1-BGRSLV02-27_S105_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2349	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	8210
BMI1-BGRSLV02-27_S105_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2349	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	8256
BMI1-BGRSLV02-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2349					GRCh38	V40	BMI1-BGRSLV02-27_S105_L003_R1_001.filtered.trimmed.paired.fastq.gz,BMI1-BGRSLV02-27_S105_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11499
BMI1-BGRSLV02-27_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	2349					GRCh38	V40	BMI1-BGRSLV02-27/Aligned.sortedByCoord.out.bam		ENCORE2	11545
BMI1-BGRSLV02-27_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	2349					GRCh38	V40	BMI1-BGRSLV02-27/Aligned.sortedByCoord.out.bam		ENCORE2	11591
BMI1-BGRSLV02-27_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	2349					GRCh38	V40	BMI1-BGRSLV02-27/Aligned.sortedByCoord.out.bam		ENCORE2	11637
BMI1-BGRSLV02-27_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	2349					GRCh38	V40	BMI1-BGRSLV02-27/Aligned.sortedByCoord.out.bam		ENCORE2	11683
BMI1-BGRSLV02-27_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2349					GRCh38	V40	BMI1-BGRSLV02-27_S105_L003_R1_001.filtered.trimmed.paired.fastq.gz,BMI1-BGRSLV02-27_S105_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11729
BMI1-BGRSLV02-28_S106_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2350	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	8211
BMI1-BGRSLV02-28_S106_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2350	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	8257
BMI1-BGRSLV02-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2350					GRCh38	V40	BMI1-BGRSLV02-28_S106_L003_R1_001.filtered.trimmed.paired.fastq.gz,BMI1-BGRSLV02-28_S106_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11500
BMI1-BGRSLV02-28_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	2350					GRCh38	V40	BMI1-BGRSLV02-28/Aligned.sortedByCoord.out.bam		ENCORE2	11546
BMI1-BGRSLV02-28_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	2350					GRCh38	V40	BMI1-BGRSLV02-28/Aligned.sortedByCoord.out.bam		ENCORE2	11592
BMI1-BGRSLV02-28_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	2350					GRCh38	V40	BMI1-BGRSLV02-28/Aligned.sortedByCoord.out.bam		ENCORE2	11638
BMI1-BGRSLV02-28_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	2350					GRCh38	V40	BMI1-BGRSLV02-28/Aligned.sortedByCoord.out.bam		ENCORE2	11684
BMI1-BGRSLV02-28_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2350					GRCh38	V40	BMI1-BGRSLV02-28_S106_L003_R1_001.filtered.trimmed.paired.fastq.gz,BMI1-BGRSLV02-28_S106_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11730