PML RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-37	BGRSLV04-38
idx	0	0
TRCN#_or_BGC#	TRCN0000003867	TRCN0000003867
shRNA_or_gRNA_sequence	CCGGGCCAGTGTACGCCTTCTCCATCTCGAGATGGAGAAGGCGTACACTGGCTTTTT	CCGGGCCAGTGTACGCCTTCTCCATCTCGAGATGGAGAAGGCGTACACTGGCTTTTT
PAM
Name	PML	PML
Sample_ID	BGRSLV04-37	BGRSLV04-38
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	PML	PML
qPCR_result	61.4	58.9
Ave_qPCR	60.1
RT-qPCR_primer-F	gcttcgacgagttcaaggtg
RT-qPCR_primer-R	tcaatagggtccctgggagt
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	8417	8418

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-37	BGRSLV04-38
Sample_ID	BGRSLV04-37	BGRSLV04-38
Sample Name
Sample Name	PML-BGRSLV04-37	PML-BGRSLV04-38
RBP	PML	PML
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	11456	11457

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-37	BGRSLV04-38
Sample #	21	22
Sample Name	PML-BGRSLV04-37	PML-BGRSLV04-38
Sample_Name_Alias
Index Well Position	E03	F03
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	291	297
Peak_Molarity	72.50	79.00
libSampleQC_DNA_Well	DNA_Library_set59/set1/E9.png	DNA_Library_set59/set1/F9.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set59/set1/E4.png	RNA_Library_set59/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-37	BGRSLV04-38
RBP	PML	PML
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	3570	3571

Sequencing Information

	BGRSLV04-37	BGRSLV04-38
Sample_ID	BGRSLV04-37	BGRSLV04-38
Sample Name	PML-BGRSLV04-37	PML-BGRSLV04-38
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	76,892,917	42,224,793
total_aligned_reads	65,262,127	34,283,074
unique_aligned_reads	60,298,639	31,843,552
percent_uniqueAligned	0.78419	0.75414
correlation_replicates	0.996978	0.996978
spikein_reads	365,250	135,438
percent_spikeins	0.00475	0.00321
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2441	2442

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
PML-BGRSLV04-37_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2441	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	8070
PML-BGRSLV04-37_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2441	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	8108
PML-BGRSLV04-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2441					GRCh38	V40	PML-BGRSLV04-37_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,PML-BGRSLV04-37_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11039
PML-BGRSLV04-37_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	2441					GRCh38	V40	PML-BGRSLV04-37/Aligned.sortedByCoord.out.bam		ENCORE2	11077
PML-BGRSLV04-37_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	2441					GRCh38	V40	PML-BGRSLV04-37/Aligned.sortedByCoord.out.bam		ENCORE2	11115
PML-BGRSLV04-37_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	2441					GRCh38	V40	PML-BGRSLV04-37/Aligned.sortedByCoord.out.bam		ENCORE2	11153
PML-BGRSLV04-37_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	2441					GRCh38	V40	PML-BGRSLV04-37/Aligned.sortedByCoord.out.bam		ENCORE2	11191
PML-BGRSLV04-37_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2441					GRCh38	V40	PML-BGRSLV04-37_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,PML-BGRSLV04-37_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11229
PML-BGRSLV04-38_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2442	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	8071
PML-BGRSLV04-38_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2442	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	8109
PML-BGRSLV04-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2442					GRCh38	V40	PML-BGRSLV04-38_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,PML-BGRSLV04-38_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11040
PML-BGRSLV04-38_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	2442					GRCh38	V40	PML-BGRSLV04-38/Aligned.sortedByCoord.out.bam		ENCORE2	11078
PML-BGRSLV04-38_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	2442					GRCh38	V40	PML-BGRSLV04-38/Aligned.sortedByCoord.out.bam		ENCORE2	11116
PML-BGRSLV04-38_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	2442					GRCh38	V40	PML-BGRSLV04-38/Aligned.sortedByCoord.out.bam		ENCORE2	11154
PML-BGRSLV04-38_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	2442					GRCh38	V40	PML-BGRSLV04-38/Aligned.sortedByCoord.out.bam		ENCORE2	11192
PML-BGRSLV04-38_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2442					GRCh38	V40	PML-BGRSLV04-38_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,PML-BGRSLV04-38_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11230