RFFL RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-47	BGRSLV04-48
idx	0	0
TRCN#_or_BGC#	TRCN0000034074	TRCN0000034074
shRNA_or_gRNA_sequence	CCGGCCGGCTATACAAGGATCAGAACTCGAGTTCTGATCCTTGTATAGCCGGTTTTTG	CCGGCCGGCTATACAAGGATCAGAACTCGAGTTCTGATCCTTGTATAGCCGGTTTTTG
PAM
Name	RFFL	RFFL
Sample_ID	BGRSLV04-47	BGRSLV04-48
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	RFFL	RFFL
qPCR_result	67.0	54.0
Ave_qPCR	60.5
RT-qPCR_primer-F	aaccctgggtacagctcctt
RT-qPCR_primer-R	ctcgaacaggtcatgcaaaa
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	8427	8428

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-47	BGRSLV04-48
Sample_ID	BGRSLV04-47	BGRSLV04-48
Sample Name
Sample Name	RFFL-BGRSLV04-47	RFFL-BGRSLV04-48
RBP	RFFL	RFFL
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	11464	11465

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-47	BGRSLV04-48
Sample #	29	30
Sample Name	RFFL-BGRSLV04-47	RFFL-BGRSLV04-48
Sample_Name_Alias
Index Well Position	E04	F04
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	293	289
Peak_Molarity	62.20	66.20
libSampleQC_DNA_Well	DNA_Library_set59/set1/E10.png	DNA_Library_set59/set1/F10.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set59/set1/E5.png	RNA_Library_set59/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-47	BGRSLV04-48
RBP	RFFL	RFFL
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	3578	3579

Sequencing Information

	BGRSLV04-47	BGRSLV04-48
Sample_ID	BGRSLV04-47	BGRSLV04-48
Sample Name	RFFL-BGRSLV04-47	RFFL-BGRSLV04-48
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	67,771,818	72,128,672
total_aligned_reads	58,990,001	62,378,133
unique_aligned_reads	54,462,333	57,475,302
percent_uniqueAligned	0.80361	0.79684
correlation_replicates	0.988221	0.988221
spikein_reads	217,852	238,806
percent_spikeins	0.00321	0.00331
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2449	2450

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
RFFL-BGRSLV04-47_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2449	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	8078
RFFL-BGRSLV04-47_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2449	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	8116
RFFL-BGRSLV04-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2449					GRCh38	V40	RFFL-BGRSLV04-47_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,RFFL-BGRSLV04-47_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11047
RFFL-BGRSLV04-47_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	2449					GRCh38	V40	RFFL-BGRSLV04-47/Aligned.sortedByCoord.out.bam		ENCORE2	11085
RFFL-BGRSLV04-47_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	2449					GRCh38	V40	RFFL-BGRSLV04-47/Aligned.sortedByCoord.out.bam		ENCORE2	11123
RFFL-BGRSLV04-47_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	2449					GRCh38	V40	RFFL-BGRSLV04-47/Aligned.sortedByCoord.out.bam		ENCORE2	11161
RFFL-BGRSLV04-47_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	2449					GRCh38	V40	RFFL-BGRSLV04-47/Aligned.sortedByCoord.out.bam		ENCORE2	11199
RFFL-BGRSLV04-47_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2449					GRCh38	V40	RFFL-BGRSLV04-47_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,RFFL-BGRSLV04-47_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11237
RFFL-BGRSLV04-48_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2450	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	8079
RFFL-BGRSLV04-48_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2450	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	8117
RFFL-BGRSLV04-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2450					GRCh38	V40	RFFL-BGRSLV04-48_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,RFFL-BGRSLV04-48_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11048
RFFL-BGRSLV04-48_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	2450					GRCh38	V40	RFFL-BGRSLV04-48/Aligned.sortedByCoord.out.bam		ENCORE2	11086
RFFL-BGRSLV04-48_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	2450					GRCh38	V40	RFFL-BGRSLV04-48/Aligned.sortedByCoord.out.bam		ENCORE2	11124
RFFL-BGRSLV04-48_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	2450					GRCh38	V40	RFFL-BGRSLV04-48/Aligned.sortedByCoord.out.bam		ENCORE2	11162
RFFL-BGRSLV04-48_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	2450					GRCh38	V40	RFFL-BGRSLV04-48/Aligned.sortedByCoord.out.bam		ENCORE2	11200
RFFL-BGRSLV04-48_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2450					GRCh38	V40	RFFL-BGRSLV04-48_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,RFFL-BGRSLV04-48_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11238