EGLN1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-23	BGRSLV03-24
idx	0	0
TRCN#_or_BGC#	TRCN0000001043	TRCN0000001043
shRNA_or_gRNA_sequence	CCGGGACGACCTGATACGCCACTGTCTCGAGACAGTGGCGTATCAGGTCGTCTTTTT	CCGGGACGACCTGATACGCCACTGTCTCGAGACAGTGGCGTATCAGGTCGTCTTTTT
PAM
Name	EGLN1	EGLN1
Sample_ID	BGRSLV03-23	BGRSLV03-24
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	EGLN1	EGLN1
qPCR_result	61.5	66.4
Ave_qPCR	63.9
RT-qPCR_primer-F	caatggaacgggttatgtacg
RT-qPCR_primer-R	ttgggttcaatgtcagcaaa
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	8333	8334

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-23	BGRSLV03-24
Sample_ID	BGRSLV03-23	BGRSLV03-24
Sample Name
Sample Name	EGLN1-BGRSLV03-23	EGLN1-BGRSLV03-24
RBP	EGLN1	EGLN1
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	11388	11389

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-23	BGRSLV03-24
Sample #	19	20
Sample Name	EGLN1-BGRSLV03-23	EGLN1-BGRSLV03-24
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	284	279
Peak_Molarity	119.00	120.00
libSampleQC_DNA_Well	DNA_Library_set58/set1/C9.png	DNA_Library_set58/set1/D9.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set58/set1/C3.png	RNA_Library_set58/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-23	BGRSLV03-24
RBP	EGLN1	EGLN1
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3526	3527

Sequencing Information

	BGRSLV03-23	BGRSLV03-24
Sample_ID	BGRSLV03-23	BGRSLV03-24
Sample Name	EGLN1-BGRSLV03-23	EGLN1-BGRSLV03-24
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	37,996,322	36,683,247
total_aligned_reads	28,924,317	32,157,573
unique_aligned_reads	26,788,511	29,875,457
percent_uniqueAligned	0.70503	0.81442
correlation_replicates	0.983875	0.983875
spikein_reads	252,652	262,706
percent_spikeins	0.00665	0.00716
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2397	2398

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
EGLN1-BGRSLV03-23_S153_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2397	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8142
EGLN1-BGRSLV03-23_S153_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2397	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8184
EGLN1-BGRSLV03-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2397					GRCh38	V40	EGLN1-BGRSLV03-23_S153_L004_R1_001.filtered.trimmed.paired.fastq.gz,EGLN1-BGRSLV03-23_S153_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11263
EGLN1-BGRSLV03-23_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2397					GRCh38	V40	EGLN1-BGRSLV03-23/Aligned.sortedByCoord.out.bam		ENCORE2	11305
EGLN1-BGRSLV03-23_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2397					GRCh38	V40	EGLN1-BGRSLV03-23/Aligned.sortedByCoord.out.bam		ENCORE2	11347
EGLN1-BGRSLV03-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2397					GRCh38	V40	EGLN1-BGRSLV03-23/Aligned.sortedByCoord.out.bam		ENCORE2	11389
EGLN1-BGRSLV03-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2397					GRCh38	V40	EGLN1-BGRSLV03-23/Aligned.sortedByCoord.out.bam		ENCORE2	11431
EGLN1-BGRSLV03-23_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2397					GRCh38	V40	EGLN1-BGRSLV03-23_S153_L004_R1_001.filtered.trimmed.paired.fastq.gz,EGLN1-BGRSLV03-23_S153_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11473
EGLN1-BGRSLV03-24_S154_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2398	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8143
EGLN1-BGRSLV03-24_S154_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2398	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8185
EGLN1-BGRSLV03-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2398					GRCh38	V40	EGLN1-BGRSLV03-24_S154_L004_R1_001.filtered.trimmed.paired.fastq.gz,EGLN1-BGRSLV03-24_S154_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11264
EGLN1-BGRSLV03-24_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2398					GRCh38	V40	EGLN1-BGRSLV03-24/Aligned.sortedByCoord.out.bam		ENCORE2	11306
EGLN1-BGRSLV03-24_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2398					GRCh38	V40	EGLN1-BGRSLV03-24/Aligned.sortedByCoord.out.bam		ENCORE2	11348
EGLN1-BGRSLV03-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2398					GRCh38	V40	EGLN1-BGRSLV03-24/Aligned.sortedByCoord.out.bam		ENCORE2	11390
EGLN1-BGRSLV03-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2398					GRCh38	V40	EGLN1-BGRSLV03-24/Aligned.sortedByCoord.out.bam		ENCORE2	11432
EGLN1-BGRSLV03-24_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2398					GRCh38	V40	EGLN1-BGRSLV03-24_S154_L004_R1_001.filtered.trimmed.paired.fastq.gz,EGLN1-BGRSLV03-24_S154_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11474