CISD2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-81	BGRSDLV02-82
idx	0	0
TRCN#_or_BGC#	TRCN0000239664	TRCN0000239664
shRNA_or_gRNA_sequence	CCGGTACTACTGGTTGAACAATTATCTCGAGATAATTGTTCAACCAGTAGTATTTTTG	CCGGTACTACTGGTTGAACAATTATCTCGAGATAATTGTTCAACCAGTAGTATTTTTG
PAM
Name	CISD2	CISD2
Sample_ID	BGRSDLV02-81	BGRSDLV02-82
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	CISD2	CISD2
qPCR_result	97.3	96.4
Ave_qPCR	96.9
RT-qPCR_primer-F	cccagtccctgaaagcatta
RT-qPCR_primer-R	gcaaggtagccaagaagtgc
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	9292	9293

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-81	BGRSDLV02-82
Sample_ID	BGRSDLV02-81	BGRSDLV02-82
Sample Name
Sample Name	CISD2-BGRSDLV02-81	CISD2-BGRSDLV02-82
RBP	CISD2	CISD2
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12388	12389

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-81	BGRSDLV02-82
Sample #	69	70
Sample Name	CISD2-BGRSDLV02-81	CISD2-BGRSDLV02-82
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	293	291
Peak_Molarity	83.60	84.20
libSampleQC_DNA_Well	DNA_Library_set65/set1/E9.png	DNA_Library_set65/set1/F9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/E9.png	RNA_Library_set65/set1/F9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-81	BGRSDLV02-82
RBP	CISD2	CISD2
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3990	3991

Sequencing Information

	BGRSDLV02-81	BGRSDLV02-82
Sample_ID	BGRSDLV02-81	BGRSDLV02-82
Sample Name	CISD2-BGRSDLV02-81	CISD2-BGRSDLV02-82
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	24,024,796	33,264,944
total_aligned_reads	22,642,525	31,229,418
unique_aligned_reads	21,133,141	29,203,270
percent_uniqueAligned	0.87964	0.87790
correlation_replicates	0.995917	0.995917
spikein_reads	1,602	4,402
percent_spikeins	0.00007	0.00013
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2737	2738

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
CISD2-BGRSDLV02-81_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2737	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8750
CISD2-BGRSDLV02-81_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2737	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8826
CISD2-BGRSDLV02-81_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2737					GRCh38	V40	CISD2-BGRSDLV02-81_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-81_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9315
CISD2-BGRSDLV02-81_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2737					GRCh38	V40	CISD2-BGRSDLV02-81/Aligned.sortedByCoord.out.bam		ENCORE2	9391
CISD2-BGRSDLV02-81_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2737					GRCh38	V40	CISD2-BGRSDLV02-81/Aligned.sortedByCoord.out.bam		ENCORE2	9467
CISD2-BGRSDLV02-81_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2737					GRCh38	V40	CISD2-BGRSDLV02-81/Aligned.sortedByCoord.out.bam		ENCORE2	9543
CISD2-BGRSDLV02-81_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2737					GRCh38	V40	CISD2-BGRSDLV02-81/Aligned.sortedByCoord.out.bam		ENCORE2	9619
CISD2-BGRSDLV02-81_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2737					GRCh38	V40	CISD2-BGRSDLV02-81_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-81_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9695
CISD2-BGRSDLV02-82_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2738	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8751
CISD2-BGRSDLV02-82_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2738	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8827
CISD2-BGRSDLV02-82_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2738					GRCh38	V40	CISD2-BGRSDLV02-82_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-82_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9316
CISD2-BGRSDLV02-82_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2738					GRCh38	V40	CISD2-BGRSDLV02-82/Aligned.sortedByCoord.out.bam		ENCORE2	9392
CISD2-BGRSDLV02-82_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2738					GRCh38	V40	CISD2-BGRSDLV02-82/Aligned.sortedByCoord.out.bam		ENCORE2	9468
CISD2-BGRSDLV02-82_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2738					GRCh38	V40	CISD2-BGRSDLV02-82/Aligned.sortedByCoord.out.bam		ENCORE2	9544
CISD2-BGRSDLV02-82_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2738					GRCh38	V40	CISD2-BGRSDLV02-82/Aligned.sortedByCoord.out.bam		ENCORE2	9620
CISD2-BGRSDLV02-82_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2738					GRCh38	V40	CISD2-BGRSDLV02-82_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-82_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9696