CISD2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-83dox	BGRSDLV02-84dox
idx	0	0
TRCN#_or_BGC#	TRCN0000239664	TRCN0000239664
shRNA_or_gRNA_sequence	CCGGTACTACTGGTTGAACAATTATCTCGAGATAATTGTTCAACCAGTAGTATTTTTG	CCGGTACTACTGGTTGAACAATTATCTCGAGATAATTGTTCAACCAGTAGTATTTTTG
PAM
Name	CISD2	CISD2
Sample_ID	BGRSDLV02-83dox	BGRSDLV02-84dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	CISD2	CISD2
qPCR_result	97.3	96.5
Ave_qPCR	96.9
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9294	9295

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-83dox	BGRSDLV02-84dox
Sample_ID	BGRSDLV02-83dox	BGRSDLV02-84dox
Sample Name
Sample Name	CISD2-BGRSDLV02-83dox	CISD2-BGRSDLV02-84dox
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	12390	12391

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-83dox	BGRSDLV02-84dox
Sample #	71	72
Sample Name	CISD2-BGRSDLV02-83dox	CISD2-BGRSDLV02-84dox
Sample_Name_Alias
Index Well Position	G09	H09
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	298	296
Peak_Molarity	87.40	58.60
libSampleQC_DNA_Well	DNA_Library_set65/set1/G9.png	DNA_Library_set65/set1/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/G9.png	RNA_Library_set65/set1/H9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-83dox	BGRSDLV02-84dox
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	3992	3993

Sequencing Information

	BGRSDLV02-83dox	BGRSDLV02-84dox
Sample_ID	BGRSDLV02-83dox	BGRSDLV02-84dox
Sample Name	CISD2-BGRSDLV02-83dox	CISD2-BGRSDLV02-84dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	30,404,946	31,577,356
total_aligned_reads	28,622,030	29,657,325
unique_aligned_reads	26,776,984	27,760,958
percent_uniqueAligned	0.88068	0.87914
correlation_replicates	0.991060	0.991060
spikein_reads	2,854	10,908
percent_spikeins	0.00009	0.00035
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2739	2740

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-BGRSDLV02-83dox_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2739	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8752
CISD2-BGRSDLV02-83dox_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2739	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8828
CISD2-BGRSDLV02-83dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2739					GRCh38	V40	CISD2-BGRSDLV02-83dox_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-83dox_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9317
CISD2-BGRSDLV02-83dox_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	2739					GRCh38	V40	CISD2-BGRSDLV02-83dox/Aligned.sortedByCoord.out.bam		ENCORE2	9393
CISD2-BGRSDLV02-83dox_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	2739					GRCh38	V40	CISD2-BGRSDLV02-83dox/Aligned.sortedByCoord.out.bam		ENCORE2	9469
CISD2-BGRSDLV02-83dox_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	2739					GRCh38	V40	CISD2-BGRSDLV02-83dox/Aligned.sortedByCoord.out.bam		ENCORE2	9545
CISD2-BGRSDLV02-83dox_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	2739					GRCh38	V40	CISD2-BGRSDLV02-83dox/Aligned.sortedByCoord.out.bam		ENCORE2	9621
CISD2-BGRSDLV02-83dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2739					GRCh38	V40	CISD2-BGRSDLV02-83dox_S71_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-83dox_S71_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9697
CISD2-BGRSDLV02-84dox_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2740	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8753
CISD2-BGRSDLV02-84dox_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2740	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8829
CISD2-BGRSDLV02-84dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2740					GRCh38	V40	CISD2-BGRSDLV02-84dox_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-84dox_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9318
CISD2-BGRSDLV02-84dox_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	2740					GRCh38	V40	CISD2-BGRSDLV02-84dox/Aligned.sortedByCoord.out.bam		ENCORE2	9394
CISD2-BGRSDLV02-84dox_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	2740					GRCh38	V40	CISD2-BGRSDLV02-84dox/Aligned.sortedByCoord.out.bam		ENCORE2	9470
CISD2-BGRSDLV02-84dox_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	2740					GRCh38	V40	CISD2-BGRSDLV02-84dox/Aligned.sortedByCoord.out.bam		ENCORE2	9546
CISD2-BGRSDLV02-84dox_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	2740					GRCh38	V40	CISD2-BGRSDLV02-84dox/Aligned.sortedByCoord.out.bam		ENCORE2	9622
CISD2-BGRSDLV02-84dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2740					GRCh38	V40	CISD2-BGRSDLV02-84dox_S72_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSDLV02-84dox_S72_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9698