CISD1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-13	BGRSDLV02-14
idx	0	0
TRCN#_or_BGC#	TRCN0000153128	TRCN0000153128
shRNA_or_gRNA_sequence	CCGGGCTGCAATTGGTTATCTAGCTCTCGAGAGCTAGATAACCAATTGCAGCTTTTTTG	CCGGGCTGCAATTGGTTATCTAGCTCTCGAGAGCTAGATAACCAATTGCAGCTTTTTTG
PAM
Name	CISD1	CISD1
Sample_ID	BGRSDLV02-13	BGRSDLV02-14
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	CISD1	CISD1
qPCR_result	98.3	98.3
Ave_qPCR	98.3
RT-qPCR_primer-F	gtactgccgttgttggaggt
RT-qPCR_primer-R	gcccacattgtctccagtct
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	9224	9225

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-13	BGRSDLV02-14
Sample_ID	BGRSDLV02-13	BGRSDLV02-14
Sample Name
Sample Name	CISD1-BGRSDLV02-13	CISD1-BGRSDLV02-14
RBP	CISD1	CISD1
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12332	12333

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-13	BGRSDLV02-14
Sample #	13	14
Sample Name	CISD1-BGRSDLV02-13	CISD1-BGRSDLV02-14
Sample_Name_Alias
Index Well Position	E02	F02
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	286	292
Peak_Molarity	74.90	102.00
libSampleQC_DNA_Well	DNA_Library_set65/set1/E2.png	DNA_Library_set65/set1/F2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set65/set1/E2.png	RNA_Library_set65/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-13	BGRSDLV02-14
RBP	CISD1	CISD1
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	3934	3935

Sequencing Information

	BGRSDLV02-13	BGRSDLV02-14
Sample_ID	BGRSDLV02-13	BGRSDLV02-14
Sample Name	CISD1-BGRSDLV02-13	CISD1-BGRSDLV02-14
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	33,844,010	21,396,556
total_aligned_reads	29,820,760	19,195,378
unique_aligned_reads	27,735,307	17,819,534
percent_uniqueAligned	0.81950	0.83282
correlation_replicates	0.994138	0.994138
spikein_reads	4,808	4,586
percent_spikeins	0.00014	0.00021
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2681	2682

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
CISD1-BGRSDLV02-13_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2681	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	8746
CISD1-BGRSDLV02-13_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2681	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	8822
CISD1-BGRSDLV02-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2681					GRCh38	V40	CISD1-BGRSDLV02-13_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSDLV02-13_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9311
CISD1-BGRSDLV02-13_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	2681					GRCh38	V40	CISD1-BGRSDLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	9387
CISD1-BGRSDLV02-13_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	2681					GRCh38	V40	CISD1-BGRSDLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	9463
CISD1-BGRSDLV02-13_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	2681					GRCh38	V40	CISD1-BGRSDLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	9539
CISD1-BGRSDLV02-13_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	2681					GRCh38	V40	CISD1-BGRSDLV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	9615
CISD1-BGRSDLV02-13_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2681					GRCh38	V40	CISD1-BGRSDLV02-13_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSDLV02-13_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9691
CISD1-BGRSDLV02-14_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2682	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	8747
CISD1-BGRSDLV02-14_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2682	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	8823
CISD1-BGRSDLV02-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2682					GRCh38	V40	CISD1-BGRSDLV02-14_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSDLV02-14_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9312
CISD1-BGRSDLV02-14_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	2682					GRCh38	V40	CISD1-BGRSDLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	9388
CISD1-BGRSDLV02-14_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	2682					GRCh38	V40	CISD1-BGRSDLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	9464
CISD1-BGRSDLV02-14_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	2682					GRCh38	V40	CISD1-BGRSDLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	9540
CISD1-BGRSDLV02-14_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	2682					GRCh38	V40	CISD1-BGRSDLV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	9616
CISD1-BGRSDLV02-14_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2682					GRCh38	V40	CISD1-BGRSDLV02-14_S14_L001_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSDLV02-14_S14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9692