G2E3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-27dox	BGRSDLV02-28dox
idx	0	0
TRCN#_or_BGC#	TRCN0000004223	TRCN0000004223
shRNA_or_gRNA_sequence	CCGGGTTCTCATTACATTGGACATTCTCGAGAATGTCCAATGTAATGAGAACTTTTT	CCGGGTTCTCATTACATTGGACATTCTCGAGAATGTCCAATGTAATGAGAACTTTTT
PAM
Name	G2E3	G2E3
Sample_ID	BGRSDLV02-27dox	BGRSDLV02-28dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	G2E3	G2E3
qPCR_result	67.7	71.0
Ave_qPCR	69.4
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9238	9239

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-27dox	BGRSDLV02-28dox
Sample_ID	BGRSDLV02-27dox	BGRSDLV02-28dox
Sample Name
Sample Name	G2E3-BGRSDLV02-27dox	G2E3-BGRSDLV02-28dox
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	12346	12347

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-27dox	BGRSDLV02-28dox
Sample #	27	28
Sample Name	G2E3-BGRSDLV02-27dox	G2E3-BGRSDLV02-28dox
Sample_Name_Alias
Index Well Position	C04	D04
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	294	293
Peak_Molarity	98.30	87.40
libSampleQC_DNA_Well	DNA_Library_set65/set1/C4.png	DNA_Library_set65/set1/D4.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set65/set1/C4.png	RNA_Library_set65/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-27dox	BGRSDLV02-28dox
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	3948	3949

Sequencing Information

	BGRSDLV02-27dox	BGRSDLV02-28dox
Sample_ID	BGRSDLV02-27dox	BGRSDLV02-28dox
Sample Name	G2E3-BGRSDLV02-27dox	G2E3-BGRSDLV02-28dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	35,723,840	24,099,648
total_aligned_reads	32,841,338	21,925,637
unique_aligned_reads	30,598,464	20,409,797
percent_uniqueAligned	0.85653	0.84689
correlation_replicates	0.995220	0.995220
spikein_reads	4,454	2,904
percent_spikeins	0.00012	0.00012
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2695	2696

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-BGRSDLV02-27dox_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2695	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8764
G2E3-BGRSDLV02-27dox_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2695	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8840
G2E3-BGRSDLV02-27dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2695					GRCh38	V40	G2E3-BGRSDLV02-27dox_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-27dox_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9329
G2E3-BGRSDLV02-27dox_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	2695					GRCh38	V40	G2E3-BGRSDLV02-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9405
G2E3-BGRSDLV02-27dox_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	2695					GRCh38	V40	G2E3-BGRSDLV02-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9481
G2E3-BGRSDLV02-27dox_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	2695					GRCh38	V40	G2E3-BGRSDLV02-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9557
G2E3-BGRSDLV02-27dox_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	2695					GRCh38	V40	G2E3-BGRSDLV02-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9633
G2E3-BGRSDLV02-27dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2695					GRCh38	V40	G2E3-BGRSDLV02-27dox_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-27dox_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9709
G2E3-BGRSDLV02-28dox_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2696	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8765
G2E3-BGRSDLV02-28dox_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2696	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8841
G2E3-BGRSDLV02-28dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2696					GRCh38	V40	G2E3-BGRSDLV02-28dox_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-28dox_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9330
G2E3-BGRSDLV02-28dox_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	2696					GRCh38	V40	G2E3-BGRSDLV02-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9406
G2E3-BGRSDLV02-28dox_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	2696					GRCh38	V40	G2E3-BGRSDLV02-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9482
G2E3-BGRSDLV02-28dox_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	2696					GRCh38	V40	G2E3-BGRSDLV02-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9558
G2E3-BGRSDLV02-28dox_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	2696					GRCh38	V40	G2E3-BGRSDLV02-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9634
G2E3-BGRSDLV02-28dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2696					GRCh38	V40	G2E3-BGRSDLV02-28dox_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,G2E3-BGRSDLV02-28dox_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9710