CISD2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-13	BGRSLV03-14
idx	0	0
TRCN#_or_BGC#	TRCN0000239664	TRCN0000239664
shRNA_or_gRNA_sequence	CCGGTACTACTGGTTGAACAATTATCTCGAGATAATTGTTCAACCAGTAGTATTTTTG	CCGGTACTACTGGTTGAACAATTATCTCGAGATAATTGTTCAACCAGTAGTATTTTTG
PAM
Name	CISD2	CISD2
Sample_ID	BGRSLV03-13	BGRSLV03-14
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	CISD2	CISD2
qPCR_result	75.9	76.4
Ave_qPCR	76.2
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	8323	8324

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-13	BGRSLV03-14
Sample_ID	BGRSLV03-13	BGRSLV03-14
Sample Name
Sample Name	CISD2-BGRSLV03-13	CISD2-BGRSLV03-14
RBP	CISD2	CISD2
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	11378	11379

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-13	BGRSLV03-14
Sample #	9	10
Sample Name	CISD2-BGRSLV03-13	CISD2-BGRSLV03-14
Sample_Name_Alias
Index Well Position	A08	B08
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	296	289
Peak_Molarity	22.00	64.90
libSampleQC_DNA_Well	DNA_Library_set58/set1/A8.png	DNA_Library_set58/set1/B8.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_set58/set1/A2.png	RNA_Library_set58/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-13	BGRSLV03-14
RBP	CISD2	CISD2
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	3516	3517

Sequencing Information

	BGRSLV03-13	BGRSLV03-14
Sample_ID	BGRSLV03-13	BGRSLV03-14
Sample Name	CISD2-BGRSLV03-13	CISD2-BGRSLV03-14
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	59,860,566	47,769,830
total_aligned_reads	47,242,493	39,342,683
unique_aligned_reads	44,181,843	36,621,890
percent_uniqueAligned	0.73808	0.76663
correlation_replicates	0.982242	0.982242
spikein_reads	379,988	311,626
percent_spikeins	0.00635	0.00652
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2387	2388

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-BGRSLV03-13_S143_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2387	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	8132
CISD2-BGRSLV03-13_S143_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2387	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	8174
CISD2-BGRSLV03-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2387					GRCh38	V40	CISD2-BGRSLV03-13_S143_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSLV03-13_S143_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11253
CISD2-BGRSLV03-13_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	2387					GRCh38	V40	CISD2-BGRSLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	11295
CISD2-BGRSLV03-13_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	2387					GRCh38	V40	CISD2-BGRSLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	11337
CISD2-BGRSLV03-13_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	2387					GRCh38	V40	CISD2-BGRSLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	11379
CISD2-BGRSLV03-13_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	2387					GRCh38	V40	CISD2-BGRSLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	11421
CISD2-BGRSLV03-13_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2387					GRCh38	V40	CISD2-BGRSLV03-13_S143_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSLV03-13_S143_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11463
CISD2-BGRSLV03-14_S144_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2388	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	8133
CISD2-BGRSLV03-14_S144_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2388	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	8175
CISD2-BGRSLV03-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2388					GRCh38	V40	CISD2-BGRSLV03-14_S144_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSLV03-14_S144_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11254
CISD2-BGRSLV03-14_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	2388					GRCh38	V40	CISD2-BGRSLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	11296
CISD2-BGRSLV03-14_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	2388					GRCh38	V40	CISD2-BGRSLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	11338
CISD2-BGRSLV03-14_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	2388					GRCh38	V40	CISD2-BGRSLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	11380
CISD2-BGRSLV03-14_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	2388					GRCh38	V40	CISD2-BGRSLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	11422
CISD2-BGRSLV03-14_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2388					GRCh38	V40	CISD2-BGRSLV03-14_S144_L004_R1_001.filtered.trimmed.paired.fastq.gz,CISD2-BGRSLV03-14_S144_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11464