IRF2BP1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSLV04-11	BGRSLV04-12
idx	0	0
TRCN#_or_BGC#	TRCN0000033809	TRCN0000033809
shRNA_or_gRNA_sequence	CCGGCCCGGACACAAGTTCTGCTTTCTCGAGAAAGCAGAACTTGTGTCCGGGTTTTTG	CCGGCCCGGACACAAGTTCTGCTTTCTCGAGAAAGCAGAACTTGTGTCCGGGTTTTTG
PAM
Name	IRF2BP1	IRF2BP1
Sample_ID	BGRSLV04-11	BGRSLV04-12
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	IRF2BP1	IRF2BP1
qPCR_result	82.9	89.4
Ave_qPCR	86.2
RT-qPCR_primer-F	gagaagcagcagaggaatgc
RT-qPCR_primer-R	tcttgaagcgcacattgaac
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	10439	10440

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-11	BGRSLV04-12
Sample_ID	BGRSLV04-11	BGRSLV04-12
Sample Name
Sample Name	IRF2BP1-BGRSLV04-11	IRF2BP1-BGRSLV04-12
RBP	IRF2BP1	IRF2BP1
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Released	Released
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	11440	11441

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-11	BGRSLV04-12
Sample #	5	6
Sample Name	IRF2BP1-BGRSLV04-11	IRF2BP1-BGRSLV04-12
Sample_Name_Alias
Index Well Position	E01	F01
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	289	282
Peak_Molarity	50.70	55.40
libSampleQC_DNA_Well	DNA_Library_set59/set1/E7.png	DNA_Library_set59/set1/F7.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set59/set1/E2.png	RNA_Library_set59/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-11	BGRSLV04-12
RBP	IRF2BP1	IRF2BP1
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	3554	3555

Sequencing Information

	BGRSLV04-11	BGRSLV04-12
Sample_ID	BGRSLV04-11	BGRSLV04-12
Sample Name	IRF2BP1-BGRSLV04-11	IRF2BP1-BGRSLV04-12
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	49,541,953	50,714,833
total_aligned_reads	37,679,675	39,915,566
unique_aligned_reads	34,757,436	36,572,685
percent_uniqueAligned	0.70158	0.72114
correlation_replicates	0.997459	0.997459
spikein_reads	218,914	229,170
percent_spikeins	0.00442	0.00452
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2425	2426

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
IRF2BP1-BGRSLV04-11_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2425	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	8052
IRF2BP1-BGRSLV04-11_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2425	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	8090
IRF2BP1-BGRSLV04-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2425					GRCh38	V40	IRF2BP1-BGRSLV04-11_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,IRF2BP1-BGRSLV04-11_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11021
IRF2BP1-BGRSLV04-11_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	2425					GRCh38	V40	IRF2BP1-BGRSLV04-11/Aligned.sortedByCoord.out.bam		ENCORE2	11059
IRF2BP1-BGRSLV04-11_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	2425					GRCh38	V40	IRF2BP1-BGRSLV04-11/Aligned.sortedByCoord.out.bam		ENCORE2	11097
IRF2BP1-BGRSLV04-11_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	2425					GRCh38	V40	IRF2BP1-BGRSLV04-11/Aligned.sortedByCoord.out.bam		ENCORE2	11135
IRF2BP1-BGRSLV04-11_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	2425					GRCh38	V40	IRF2BP1-BGRSLV04-11/Aligned.sortedByCoord.out.bam		ENCORE2	11173
IRF2BP1-BGRSLV04-11_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2425					GRCh38	V40	IRF2BP1-BGRSLV04-11_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,IRF2BP1-BGRSLV04-11_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11211
IRF2BP1-BGRSLV04-12_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2426	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	8053
IRF2BP1-BGRSLV04-12_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2426	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	8091
IRF2BP1-BGRSLV04-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2426					GRCh38	V40	IRF2BP1-BGRSLV04-12_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,IRF2BP1-BGRSLV04-12_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11022
IRF2BP1-BGRSLV04-12_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	2426					GRCh38	V40	IRF2BP1-BGRSLV04-12/Aligned.sortedByCoord.out.bam		ENCORE2	11060
IRF2BP1-BGRSLV04-12_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	2426					GRCh38	V40	IRF2BP1-BGRSLV04-12/Aligned.sortedByCoord.out.bam		ENCORE2	11098
IRF2BP1-BGRSLV04-12_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	2426					GRCh38	V40	IRF2BP1-BGRSLV04-12/Aligned.sortedByCoord.out.bam		ENCORE2	11136
IRF2BP1-BGRSLV04-12_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	2426					GRCh38	V40	IRF2BP1-BGRSLV04-12/Aligned.sortedByCoord.out.bam		ENCORE2	11174
IRF2BP1-BGRSLV04-12_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2426					GRCh38	V40	IRF2BP1-BGRSLV04-12_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,IRF2BP1-BGRSLV04-12_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11212