G2E3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-25	BGRSDLV02-26
idx	0	0
TRCN#_or_BGC#	TRCN0000004223	TRCN0000004223
shRNA_or_gRNA_sequence	CCGGGTTCTCATTACATTGGACATTCTCGAGAATGTCCAATGTAATGAGAACTTTTT	CCGGGTTCTCATTACATTGGACATTCTCGAGAATGTCCAATGTAATGAGAACTTTTT
PAM
Name	G2E3	G2E3
Sample_ID	BGRSDLV02-25	BGRSDLV02-26
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	G2E3	G2E3
qPCR_result	75.5	79.5
Ave_qPCR	77.5
RT-qPCR_primer-F	tgcagcactatgagcgttgt
RT-qPCR_primer-R	gctaaatgtgtgccactgga
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	9236	9237

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-25	BGRSDLV02-26
Sample_ID	BGRSDLV02-25	BGRSDLV02-26
Sample Name
Sample Name	G2E3-BGRSDLV02-25	G2E3-BGRSDLV02-26
RBP	G2E3	G2E3
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12344	12345

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-25	BGRSDLV02-26
Sample #	25	26
Sample Name	G2E3-BGRSDLV02-25	G2E3-BGRSDLV02-26
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	299	297
Peak_Molarity	90.30	90.90
libSampleQC_DNA_Well	DNA_Library_set65/set1/A4.png	DNA_Library_set65/set1/B4.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set65/set1/A4.png	RNA_Library_set65/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-25	BGRSDLV02-26
RBP	G2E3	G2E3
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3946	3947

Sequencing Information

	BGRSDLV02-25	BGRSDLV02-26
Sample_ID	BGRSDLV02-25	BGRSDLV02-26
Sample Name	G2E3-BGRSDLV02-25	G2E3-BGRSDLV02-26
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	43,235,498	18,590,469
total_aligned_reads	40,163,058	16,714,973
unique_aligned_reads	37,335,184	15,537,530
percent_uniqueAligned	0.86353	0.83578
correlation_replicates	0.982179	0.982179
spikein_reads	14,908	3,352
percent_spikeins	0.00034	0.00018
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2693	2694

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
G2E3-BGRSDLV02-25_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2693	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8762
G2E3-BGRSDLV02-25_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2693	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8838
G2E3-BGRSDLV02-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2693					GRCh38	V40	G2E3-BGRSDLV02-25_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-25_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9327
G2E3-BGRSDLV02-25_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2693					GRCh38	V40	G2E3-BGRSDLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	9403
G2E3-BGRSDLV02-25_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2693					GRCh38	V40	G2E3-BGRSDLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	9479
G2E3-BGRSDLV02-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2693					GRCh38	V40	G2E3-BGRSDLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	9555
G2E3-BGRSDLV02-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2693					GRCh38	V40	G2E3-BGRSDLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	9631
G2E3-BGRSDLV02-25_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2693					GRCh38	V40	G2E3-BGRSDLV02-25_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-25_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9707
G2E3-BGRSDLV02-26_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2694	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8763
G2E3-BGRSDLV02-26_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2694	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8839
G2E3-BGRSDLV02-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2694					GRCh38	V40	G2E3-BGRSDLV02-26_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-26_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9328
G2E3-BGRSDLV02-26_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2694					GRCh38	V40	G2E3-BGRSDLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	9404
G2E3-BGRSDLV02-26_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2694					GRCh38	V40	G2E3-BGRSDLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	9480
G2E3-BGRSDLV02-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2694					GRCh38	V40	G2E3-BGRSDLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	9556
G2E3-BGRSDLV02-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2694					GRCh38	V40	G2E3-BGRSDLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	9632
G2E3-BGRSDLV02-26_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2694					GRCh38	V40	G2E3-BGRSDLV02-26_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-26_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9708