RBM4B RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-43	BGRSLV04-44
idx	0	0
TRCN#_or_BGC#	TRCN0000159895	TRCN0000159895
shRNA_or_gRNA_sequence	CCGGGCTTCATGTTTCAGTAAACAACTCGAGTTGTTTACTGAAACATGAAGCTTTTTTG	CCGGGCTTCATGTTTCAGTAAACAACTCGAGTTGTTTACTGAAACATGAAGCTTTTTTG
PAM
Name	RBM4B	RBM4B
Sample_ID	BGRSLV04-43	BGRSLV04-44
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	RBM4B	RBM4B
qPCR_result	75.8	66.1
Ave_qPCR	71.0
RT-qPCR_primer-F	gggccttgacaacacagagt
RT-qPCR_primer-R	ttctttcccacaccgatagc
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	8423	8424

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-43	BGRSLV04-44
Sample_ID	BGRSLV04-43	BGRSLV04-44
Sample Name
Sample Name	RBM4B-BGRSLV04-43	RBM4B-BGRSLV04-44
RBP	RBM4B	RBM4B
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	11460	11461

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-43	BGRSLV04-44
Sample #	25	26
Sample Name	RBM4B-BGRSLV04-43	RBM4B-BGRSLV04-44
Sample_Name_Alias
Index Well Position	A04	B04
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	287	291
Peak_Molarity	29.60	54.30
libSampleQC_DNA_Well	DNA_Library_set59/set1/A10.png	DNA_Library_set59/set1/B10.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_set59/set1/A5.png	RNA_Library_set59/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-43	BGRSLV04-44
RBP	RBM4B	RBM4B
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	3574	3575

Sequencing Information

	BGRSLV04-43	BGRSLV04-44
Sample_ID	BGRSLV04-43	BGRSLV04-44
Sample Name	RBM4B-BGRSLV04-43	RBM4B-BGRSLV04-44
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	52,276,860	55,296,845
total_aligned_reads	38,308,485	44,454,641
unique_aligned_reads	35,402,019	41,111,915
percent_uniqueAligned	0.67720	0.74348
correlation_replicates	0.997281	0.997281
spikein_reads	269,016	254,146
percent_spikeins	0.00515	0.00460
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2445	2446

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
RBM4B-BGRSLV04-43_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2445	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	8074
RBM4B-BGRSLV04-43_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2445	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	8112
RBM4B-BGRSLV04-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2445					GRCh38	V40	RBM4B-BGRSLV04-43_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM4B-BGRSLV04-43_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11043
RBM4B-BGRSLV04-43_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	2445					GRCh38	V40	RBM4B-BGRSLV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	11081
RBM4B-BGRSLV04-43_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	2445					GRCh38	V40	RBM4B-BGRSLV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	11119
RBM4B-BGRSLV04-43_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	2445					GRCh38	V40	RBM4B-BGRSLV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	11157
RBM4B-BGRSLV04-43_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	2445					GRCh38	V40	RBM4B-BGRSLV04-43/Aligned.sortedByCoord.out.bam		ENCORE2	11195
RBM4B-BGRSLV04-43_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2445					GRCh38	V40	RBM4B-BGRSLV04-43_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM4B-BGRSLV04-43_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11233
RBM4B-BGRSLV04-44_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2446	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	8075
RBM4B-BGRSLV04-44_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2446	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	8113
RBM4B-BGRSLV04-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2446					GRCh38	V40	RBM4B-BGRSLV04-44_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM4B-BGRSLV04-44_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11044
RBM4B-BGRSLV04-44_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	2446					GRCh38	V40	RBM4B-BGRSLV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	11082
RBM4B-BGRSLV04-44_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	2446					GRCh38	V40	RBM4B-BGRSLV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	11120
RBM4B-BGRSLV04-44_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	2446					GRCh38	V40	RBM4B-BGRSLV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	11158
RBM4B-BGRSLV04-44_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	2446					GRCh38	V40	RBM4B-BGRSLV04-44/Aligned.sortedByCoord.out.bam		ENCORE2	11196
RBM4B-BGRSLV04-44_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2446					GRCh38	V40	RBM4B-BGRSLV04-44_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM4B-BGRSLV04-44_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11234