RNF214 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-19	BGRSLV07-20
idx	0	0
TRCN#_or_BGC#	TRCN0000121748	TRCN0000121748
shRNA_or_gRNA_sequence	CCGGCGTGACCAATTTAATAGTCATCTCGAGATGACTATTAAATTGGTCACGTTTTTTG	CCGGCGTGACCAATTTAATAGTCATCTCGAGATGACTATTAAATTGGTCACGTTTTTTG
PAM
Name	RNF214	RNF214
Sample_ID	BGRSLV07-19	BGRSLV07-20
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	RNF214	RNF214
qPCR_result	56.3	49.4
Ave_qPCR	52.9
RT-qPCR_primer-F	cactggcccaaatcagtacc
RT-qPCR_primer-R	ggacgagtttctggcacatt
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	8601	8602

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-19	BGRSLV07-20
Sample_ID	BGRSLV07-19	BGRSLV07-20
Sample Name
Sample Name	RNF214-BGRSLV07-19	RNF214-BGRSLV07-20
RBP	RNF214	RNF214
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	11846	11847

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-19	BGRSLV07-20
Sample #	27	28
Sample Name	RNF214-BGRSLV07-19	RNF214-BGRSLV07-20
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	297	299
Peak_Molarity	74.90	67.80
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/C4.png	DNA_Library_set60-62/set4/D4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/C4.png	RNA_Library_set60-62/set2/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-19	BGRSLV07-20
RBP	RNF214	RNF214
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3710	3711

Sequencing Information

	BGRSLV07-19	BGRSLV07-20
Sample_ID	BGRSLV07-19	BGRSLV07-20
Sample Name	RNF214-BGRSLV07-19	RNF214-BGRSLV07-20
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	37,115,804	45,858,489
total_aligned_reads	29,821,370	38,028,066
unique_aligned_reads	27,795,100	35,663,101
percent_uniqueAligned	0.74888	0.77768
correlation_replicates	0.994474	0.994474
spikein_reads	63,406	38,142
percent_spikeins	0.00171	0.00083
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2581	2582

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
RNF214-BGRSLV07-19_S27_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2581	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7886
RNF214-BGRSLV07-19_S27_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2581	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7930
RNF214-BGRSLV07-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2581					GRCh38	V40	RNF214-BGRSLV07-19_S27_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF214-BGRSLV07-19_S27_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10191
RNF214-BGRSLV07-19_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2581					GRCh38	V40	RNF214-BGRSLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	10235
RNF214-BGRSLV07-19_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2581					GRCh38	V40	RNF214-BGRSLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	10279
RNF214-BGRSLV07-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2581					GRCh38	V40	RNF214-BGRSLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	10323
RNF214-BGRSLV07-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2581					GRCh38	V40	RNF214-BGRSLV07-19/Aligned.sortedByCoord.out.bam		ENCORE2	10367
RNF214-BGRSLV07-19_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2581					GRCh38	V40	RNF214-BGRSLV07-19_S27_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF214-BGRSLV07-19_S27_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10411
RNF214-BGRSLV07-20_S28_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2582	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7887
RNF214-BGRSLV07-20_S28_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2582	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7931
RNF214-BGRSLV07-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2582					GRCh38	V40	RNF214-BGRSLV07-20_S28_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF214-BGRSLV07-20_S28_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10192
RNF214-BGRSLV07-20_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2582					GRCh38	V40	RNF214-BGRSLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	10236
RNF214-BGRSLV07-20_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2582					GRCh38	V40	RNF214-BGRSLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	10280
RNF214-BGRSLV07-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2582					GRCh38	V40	RNF214-BGRSLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	10324
RNF214-BGRSLV07-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2582					GRCh38	V40	RNF214-BGRSLV07-20/Aligned.sortedByCoord.out.bam		ENCORE2	10368
RNF214-BGRSLV07-20_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2582					GRCh38	V40	RNF214-BGRSLV07-20_S28_L003_R1_001.filtered.trimmed.paired.fastq.gz,RNF214-BGRSLV07-20_S28_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10412