RC3H2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-45	BGRSLV04-46
idx	0	0
TRCN#_or_BGC#	TRCN0000294352	TRCN0000294352
shRNA_or_gRNA_sequence	CCGGTCGCTTTGTGAGGTCCAATAACTCGAGTTATTGGACCTCACAAAGCGATTTTTG	CCGGTCGCTTTGTGAGGTCCAATAACTCGAGTTATTGGACCTCACAAAGCGATTTTTG
PAM
Name	RC3H2	RC3H2
Sample_ID	BGRSLV04-45	BGRSLV04-46
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	RC3H2	RC3H2
qPCR_result	68.8	67.9
Ave_qPCR	68.4
RT-qPCR_primer-F	agcccaaagatgtcattgct
RT-qPCR_primer-R	tttgtccttctctgggtttca
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	8425	8426

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-45	BGRSLV04-46
Sample_ID	BGRSLV04-45	BGRSLV04-46
Sample Name
Sample Name	RC3H2-BGRSLV04-45	RC3H2-BGRSLV04-46
RBP	RC3H2	RC3H2
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	11462	11463

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-45	BGRSLV04-46
Sample #	27	28
Sample Name	RC3H2-BGRSLV04-45	RC3H2-BGRSLV04-46
Sample_Name_Alias
Index Well Position	C04	D04
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	285	299
Peak_Molarity	66.20	68.10
libSampleQC_DNA_Well	DNA_Library_set59/set1/C10.png	DNA_Library_set59/set1/D10.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_set59/set1/C5.png	RNA_Library_set59/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-45	BGRSLV04-46
RBP	RC3H2	RC3H2
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	3576	3577

Sequencing Information

	BGRSLV04-45	BGRSLV04-46
Sample_ID	BGRSLV04-45	BGRSLV04-46
Sample Name	RC3H2-BGRSLV04-45	RC3H2-BGRSLV04-46
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	70,448,590	44,929,023
total_aligned_reads	61,327,578	38,497,360
unique_aligned_reads	55,917,437	35,788,153
percent_uniqueAligned	0.79373	0.79655
correlation_replicates	0.994162	0.994162
spikein_reads	334,276	142,530
percent_spikeins	0.00474	0.00317
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2447	2448

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
RC3H2-BGRSLV04-45_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2447	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	8076
RC3H2-BGRSLV04-45_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2447	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	8114
RC3H2-BGRSLV04-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2447					GRCh38	V40	RC3H2-BGRSLV04-45_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RC3H2-BGRSLV04-45_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11045
RC3H2-BGRSLV04-45_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	2447					GRCh38	V40	RC3H2-BGRSLV04-45/Aligned.sortedByCoord.out.bam		ENCORE2	11083
RC3H2-BGRSLV04-45_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	2447					GRCh38	V40	RC3H2-BGRSLV04-45/Aligned.sortedByCoord.out.bam		ENCORE2	11121
RC3H2-BGRSLV04-45_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	2447					GRCh38	V40	RC3H2-BGRSLV04-45/Aligned.sortedByCoord.out.bam		ENCORE2	11159
RC3H2-BGRSLV04-45_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	2447					GRCh38	V40	RC3H2-BGRSLV04-45/Aligned.sortedByCoord.out.bam		ENCORE2	11197
RC3H2-BGRSLV04-45_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2447					GRCh38	V40	RC3H2-BGRSLV04-45_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RC3H2-BGRSLV04-45_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11235
RC3H2-BGRSLV04-46_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2448	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	8077
RC3H2-BGRSLV04-46_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2448	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	8115
RC3H2-BGRSLV04-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2448					GRCh38	V40	RC3H2-BGRSLV04-46_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RC3H2-BGRSLV04-46_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11046
RC3H2-BGRSLV04-46_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	2448					GRCh38	V40	RC3H2-BGRSLV04-46/Aligned.sortedByCoord.out.bam		ENCORE2	11084
RC3H2-BGRSLV04-46_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	2448					GRCh38	V40	RC3H2-BGRSLV04-46/Aligned.sortedByCoord.out.bam		ENCORE2	11122
RC3H2-BGRSLV04-46_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	2448					GRCh38	V40	RC3H2-BGRSLV04-46/Aligned.sortedByCoord.out.bam		ENCORE2	11160
RC3H2-BGRSLV04-46_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	2448					GRCh38	V40	RC3H2-BGRSLV04-46/Aligned.sortedByCoord.out.bam		ENCORE2	11198
RC3H2-BGRSLV04-46_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2448					GRCh38	V40	RC3H2-BGRSLV04-46_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RC3H2-BGRSLV04-46_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11236