PAN3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-29	BGRSLV04-30
idx	0	0
TRCN#_or_BGC#	TRCN0000049803	TRCN0000049803
shRNA_or_gRNA_sequence	CCGGCCCTCTCTTGTGTTTGCATATCTCGAGATATGCAAACACAAGAGAGGGTTTTTG	CCGGCCCTCTCTTGTGTTTGCATATCTCGAGATATGCAAACACAAGAGAGGGTTTTTG
PAM
Name	PAN3	PAN3
Sample_ID	BGRSLV04-29	BGRSLV04-30
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	PAN3	PAN3
qPCR_result	52.1	56.9
Ave_qPCR	54.5
RT-qPCR_primer-F	gctcctagcaaaattgggaac
RT-qPCR_primer-R	aggtcaatccagggagcac
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	8409	8410

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-29	BGRSLV04-30
Sample_ID	BGRSLV04-29	BGRSLV04-30
Sample Name
Sample Name	PAN3-BGRSLV04-29	PAN3-BGRSLV04-30
RBP	PAN3	PAN3
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	11450	11451

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-29	BGRSLV04-30
Sample #	15	16
Sample Name	PAN3-BGRSLV04-29	PAN3-BGRSLV04-30
Sample_Name_Alias
Index Well Position	G02	H02
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	314	294
Peak_Molarity	26.50	28.70
libSampleQC_DNA_Well	DNA_Library_set59/set1/G8.png	DNA_Library_set59/set1/H8.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set59/set1/G3.png	RNA_Library_set59/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-29	BGRSLV04-30
RBP	PAN3	PAN3
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	3564	3565

Sequencing Information

	BGRSLV04-29	BGRSLV04-30
Sample_ID	BGRSLV04-29	BGRSLV04-30
Sample Name	PAN3-BGRSLV04-29	PAN3-BGRSLV04-30
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	47,252,129	39,687,261
total_aligned_reads	35,158,696	28,252,672
unique_aligned_reads	32,434,125	26,124,559
percent_uniqueAligned	0.68641	0.65826
correlation_replicates	0.973611	0.973611
spikein_reads	181,320	137,322
percent_spikeins	0.00384	0.00346
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2435	2436

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
PAN3-BGRSLV04-29_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2435	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	8064
PAN3-BGRSLV04-29_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2435	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	8102
PAN3-BGRSLV04-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2435					GRCh38	V40	PAN3-BGRSLV04-29_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN3-BGRSLV04-29_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11033
PAN3-BGRSLV04-29_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	2435					GRCh38	V40	PAN3-BGRSLV04-29/Aligned.sortedByCoord.out.bam		ENCORE2	11071
PAN3-BGRSLV04-29_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	2435					GRCh38	V40	PAN3-BGRSLV04-29/Aligned.sortedByCoord.out.bam		ENCORE2	11109
PAN3-BGRSLV04-29_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	2435					GRCh38	V40	PAN3-BGRSLV04-29/Aligned.sortedByCoord.out.bam		ENCORE2	11147
PAN3-BGRSLV04-29_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	2435					GRCh38	V40	PAN3-BGRSLV04-29/Aligned.sortedByCoord.out.bam		ENCORE2	11185
PAN3-BGRSLV04-29_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2435					GRCh38	V40	PAN3-BGRSLV04-29_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN3-BGRSLV04-29_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11223
PAN3-BGRSLV04-30_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2436	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	8065
PAN3-BGRSLV04-30_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2436	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	8103
PAN3-BGRSLV04-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2436					GRCh38	V40	PAN3-BGRSLV04-30_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN3-BGRSLV04-30_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11034
PAN3-BGRSLV04-30_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	2436					GRCh38	V40	PAN3-BGRSLV04-30/Aligned.sortedByCoord.out.bam		ENCORE2	11072
PAN3-BGRSLV04-30_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	2436					GRCh38	V40	PAN3-BGRSLV04-30/Aligned.sortedByCoord.out.bam		ENCORE2	11110
PAN3-BGRSLV04-30_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	2436					GRCh38	V40	PAN3-BGRSLV04-30/Aligned.sortedByCoord.out.bam		ENCORE2	11148
PAN3-BGRSLV04-30_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	2436					GRCh38	V40	PAN3-BGRSLV04-30/Aligned.sortedByCoord.out.bam		ENCORE2	11186
PAN3-BGRSLV04-30_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2436					GRCh38	V40	PAN3-BGRSLV04-30_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN3-BGRSLV04-30_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11224