CDCA7 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-9	BGRSLV03-10
idx	0	0
TRCN#_or_BGC#	TRCN0000140725	TRCN0000140725
shRNA_or_gRNA_sequence	CCGGGCCTGCCTTCTACTTCTCAAACTCGAGTTTGAGAAGTAGAAGGCAGGCTTTTTTG	CCGGGCCTGCCTTCTACTTCTCAAACTCGAGTTTGAGAAGTAGAAGGCAGGCTTTTTTG
PAM
Name	CDCA7	CDCA7
Sample_ID	BGRSLV03-9	BGRSLV03-10
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	CDCA7	CDCA7
qPCR_result	83.0	84.7
Ave_qPCR	83.8
RT-qPCR_primer-F	ttccaactccgattcagaaga
RT-qPCR_primer-R	gagccagggaagctttctaa
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	8319	8320

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-9	BGRSLV03-10
Sample_ID	BGRSLV03-9	BGRSLV03-10
Sample Name
Sample Name	CDCA7-BGRSLV03-9	CDCA7-BGRSLV03-10
RBP	CDCA7	CDCA7
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	11374	11375

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-9	BGRSLV03-10
Sample #	5	6
Sample Name	CDCA7-BGRSLV03-9	CDCA7-BGRSLV03-10
Sample_Name_Alias
Index Well Position	E07	F07
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	291	300
Peak_Molarity	70.90	63.80
libSampleQC_DNA_Well	DNA_Library_set58/set1/E7.png	DNA_Library_set58/set1/F7.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set58/set1/E1.png	RNA_Library_set58/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-9	BGRSLV03-10
RBP	CDCA7	CDCA7
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	3512	3513

Sequencing Information

	BGRSLV03-9	BGRSLV03-10
Sample_ID	BGRSLV03-9	BGRSLV03-10
Sample Name	CDCA7-BGRSLV03-9	CDCA7-BGRSLV03-10
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	47,095,106	52,535,139
total_aligned_reads	40,681,465	46,336,691
unique_aligned_reads	37,781,527	43,055,386
percent_uniqueAligned	0.80224	0.81955
correlation_replicates	0.996612	0.996612
spikein_reads	315,556	376,600
percent_spikeins	0.00670	0.00717
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2383	2384

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
CDCA7-BGRSLV03-9_S139_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2383	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	8129
CDCA7-BGRSLV03-9_S139_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2383	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	8171
CDCA7-BGRSLV03-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2383					GRCh38	V40	CDCA7-BGRSLV03-9_S139_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDCA7-BGRSLV03-9_S139_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11250
CDCA7-BGRSLV03-9_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	2383					GRCh38	V40	CDCA7-BGRSLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	11292
CDCA7-BGRSLV03-9_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	2383					GRCh38	V40	CDCA7-BGRSLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	11334
CDCA7-BGRSLV03-9_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	2383					GRCh38	V40	CDCA7-BGRSLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	11376
CDCA7-BGRSLV03-9_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	2383					GRCh38	V40	CDCA7-BGRSLV03-9/Aligned.sortedByCoord.out.bam		ENCORE2	11418
CDCA7-BGRSLV03-9_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2383					GRCh38	V40	CDCA7-BGRSLV03-9_S139_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDCA7-BGRSLV03-9_S139_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11460
CDCA7-BGRSLV03-10_S140_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2384	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	8128
CDCA7-BGRSLV03-10_S140_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2384	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	8170
CDCA7-BGRSLV03-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2384					GRCh38	V40	CDCA7-BGRSLV03-10_S140_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDCA7-BGRSLV03-10_S140_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11249
CDCA7-BGRSLV03-10_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	2384					GRCh38	V40	CDCA7-BGRSLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	11291
CDCA7-BGRSLV03-10_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	2384					GRCh38	V40	CDCA7-BGRSLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	11333
CDCA7-BGRSLV03-10_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	2384					GRCh38	V40	CDCA7-BGRSLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	11375
CDCA7-BGRSLV03-10_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	2384					GRCh38	V40	CDCA7-BGRSLV03-10/Aligned.sortedByCoord.out.bam		ENCORE2	11417
CDCA7-BGRSLV03-10_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2384					GRCh38	V40	CDCA7-BGRSLV03-10_S140_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDCA7-BGRSLV03-10_S140_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11459