CISD1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-11	BGRSLV03-12
idx	0	0
TRCN#_or_BGC#	TRCN0000153128	TRCN0000153128
shRNA_or_gRNA_sequence	CCGGGCTGCAATTGGTTATCTAGCTCTCGAGAGCTAGATAACCAATTGCAGCTTTTTTG	CCGGGCTGCAATTGGTTATCTAGCTCTCGAGAGCTAGATAACCAATTGCAGCTTTTTTG
PAM
Name	CISD1	CISD1
Sample_ID	BGRSLV03-11	BGRSLV03-12
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	CISD1	CISD1
qPCR_result	97.8	97.0
Ave_qPCR	97.4
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	8321	8322

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-11	BGRSLV03-12
Sample_ID	BGRSLV03-11	BGRSLV03-12
Sample Name
Sample Name	CISD1-BGRSLV03-11	CISD1-BGRSLV03-12
RBP	CISD1	CISD1
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	11376	11377

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-11	BGRSLV03-12
Sample #	7	8
Sample Name	CISD1-BGRSLV03-11	CISD1-BGRSLV03-12
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	297	299
Peak_Molarity	43.30	31.40
libSampleQC_DNA_Well	DNA_Library_set58/set1/G7.png	DNA_Library_set58/set1/H7.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_set58/set1/G1.png	RNA_Library_set58/set1/H1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-11	BGRSLV03-12
RBP	CISD1	CISD1
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3514	3515

Sequencing Information

	BGRSLV03-11	BGRSLV03-12
Sample_ID	BGRSLV03-11	BGRSLV03-12
Sample Name	CISD1-BGRSLV03-11	CISD1-BGRSLV03-12
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	57,741,360	52,188,662
total_aligned_reads	51,498,671	46,618,964
unique_aligned_reads	47,924,979	43,506,813
percent_uniqueAligned	0.82999	0.83364
correlation_replicates	0.995928	0.995928
spikein_reads	414,800	344,110
percent_spikeins	0.00718	0.00659
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2385	2386

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-BGRSLV03-11_S141_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2385	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8130
CISD1-BGRSLV03-11_S141_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2385	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8172
CISD1-BGRSLV03-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2385					GRCh38	V40	CISD1-BGRSLV03-11_S141_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSLV03-11_S141_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11251
CISD1-BGRSLV03-11_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2385					GRCh38	V40	CISD1-BGRSLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	11293
CISD1-BGRSLV03-11_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2385					GRCh38	V40	CISD1-BGRSLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	11335
CISD1-BGRSLV03-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2385					GRCh38	V40	CISD1-BGRSLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	11377
CISD1-BGRSLV03-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2385					GRCh38	V40	CISD1-BGRSLV03-11/Aligned.sortedByCoord.out.bam		ENCORE2	11419
CISD1-BGRSLV03-11_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2385					GRCh38	V40	CISD1-BGRSLV03-11_S141_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSLV03-11_S141_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11461
CISD1-BGRSLV03-12_S142_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2386	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8131
CISD1-BGRSLV03-12_S142_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2386	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8173
CISD1-BGRSLV03-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2386					GRCh38	V40	CISD1-BGRSLV03-12_S142_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSLV03-12_S142_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11252
CISD1-BGRSLV03-12_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2386					GRCh38	V40	CISD1-BGRSLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	11294
CISD1-BGRSLV03-12_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2386					GRCh38	V40	CISD1-BGRSLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	11336
CISD1-BGRSLV03-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2386					GRCh38	V40	CISD1-BGRSLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	11378
CISD1-BGRSLV03-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2386					GRCh38	V40	CISD1-BGRSLV03-12/Aligned.sortedByCoord.out.bam		ENCORE2	11420
CISD1-BGRSLV03-12_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2386					GRCh38	V40	CISD1-BGRSLV03-12_S142_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD1-BGRSLV03-12_S142_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11462