ERI2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-13	BGRSDLV03-14
idx	0	0
TRCN#_or_BGC#	TRCN0000277654	TRCN0000277654
shRNA_or_gRNA_sequence	CCGGGTTGGACGATTCTCGGAATACCTCGAGGTATTCCGAGAATCGTCCAACTTTTTG	CCGGGTTGGACGATTCTCGGAATACCTCGAGGTATTCCGAGAATCGTCCAACTTTTTG
PAM
Name	ERI2	ERI2
Sample_ID	BGRSDLV03-13	BGRSDLV03-14
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	ERI2	ERI2
qPCR_result	92.6	92.8
Ave_qPCR	92.7
RT-qPCR_primer-F	ggatttcagagccttctgctt
RT-qPCR_primer-R	cactcatactccaggcaaacc
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	9327	9328

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-13	BGRSDLV03-14
Sample_ID	BGRSDLV03-13	BGRSDLV03-14
Sample Name
Sample Name	ERI2-BGRSDLV03-13	ERI2-BGRSDLV03-14
RBP	ERI2	ERI2
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12610	12611

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-13	BGRSDLV03-14
Sample #	13	14
Sample Name	ERI2-BGRSDLV03-13	ERI2-BGRSDLV03-14
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-17	2023-10-17
Lib_ID	Lib-231017	Lib-231017
Tecan_Location
Tecan
Tecan_date
Size_bp	276	279
Peak_Molarity	48.40	78.60
libSampleQC_DNA_Well	DNA_Library_set66/set1/E7.png	DNA_Library_set66/set1/F7.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set66/set1/E2.png	RNA_Library_set66/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-13	BGRSDLV03-14
RBP	ERI2	ERI2
Batch_ID	BGRSDLV03	BGRSDLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4046	4047

Sequencing Information

	BGRSDLV03-13	BGRSDLV03-14
Sample_ID	BGRSDLV03-13	BGRSDLV03-14
Sample Name	ERI2-BGRSDLV03-13	ERI2-BGRSDLV03-14
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	15,902,979	23,863,672
total_aligned_reads	13,147,338	21,018,345
unique_aligned_reads	12,198,354	19,470,272
percent_uniqueAligned	0.76705	0.81590
correlation_replicates	0.993244	0.993244
spikein_reads	3,950	7,986
percent_spikeins	0.00025	0.00033
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2765	2766

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
ERI2-BGRSDLV03-13_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2765	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8914
ERI2-BGRSDLV03-13_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2765	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8954
ERI2-BGRSDLV03-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2765					GRCh38	V40	ERI2-BGRSDLV03-13_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,ERI2-BGRSDLV03-13_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8994
ERI2-BGRSDLV03-13_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2765					GRCh38	V40	ERI2-BGRSDLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	9034
ERI2-BGRSDLV03-13_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2765					GRCh38	V40	ERI2-BGRSDLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	9074
ERI2-BGRSDLV03-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2765					GRCh38	V40	ERI2-BGRSDLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	9114
ERI2-BGRSDLV03-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2765					GRCh38	V40	ERI2-BGRSDLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	9154
ERI2-BGRSDLV03-13_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2765					GRCh38	V40	ERI2-BGRSDLV03-13_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,ERI2-BGRSDLV03-13_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9194
ERI2-BGRSDLV03-14_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2766	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8915
ERI2-BGRSDLV03-14_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2766	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8955
ERI2-BGRSDLV03-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2766					GRCh38	V40	ERI2-BGRSDLV03-14_merged_R1_001.filtered.trimmed.paired.fastq.gz,ERI2-BGRSDLV03-14_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	8995
ERI2-BGRSDLV03-14_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2766					GRCh38	V40	ERI2-BGRSDLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	9035
ERI2-BGRSDLV03-14_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2766					GRCh38	V40	ERI2-BGRSDLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	9075
ERI2-BGRSDLV03-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2766					GRCh38	V40	ERI2-BGRSDLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	9115
ERI2-BGRSDLV03-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2766					GRCh38	V40	ERI2-BGRSDLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	9155
ERI2-BGRSDLV03-14_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2766					GRCh38	V40	ERI2-BGRSDLV03-14_merged_R1_001.filtered.trimmed.paired.fastq.gz,ERI2-BGRSDLV03-14_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9195