ZCCHC9 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-51	BGRSLV05-52
idx	0	0
TRCN#_or_BGC#	TRCN0000033994	TRCN0000033994
shRNA_or_gRNA_sequence	CCGGGCACGAAATAACCAAGTGTAACTCGAGTTACACTTGGTTATTTCGTGCTTTTTG	CCGGGCACGAAATAACCAAGTGTAACTCGAGTTACACTTGGTTATTTCGTGCTTTTTG
PAM
Name	ZCCHC9	ZCCHC9
Sample_ID	BGRSLV05-51	BGRSLV05-52
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	ZCCHC9	ZCCHC9
qPCR_result	71.7	69.1
Ave_qPCR	70.4
RT-qPCR_primer-F	acatgggcactgggatatgt
RT-qPCR_primer-R	tctagacaggtgccccattt
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	8504	8505

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-51	BGRSLV05-52
Sample_ID	BGRSLV05-51	BGRSLV05-52
Sample Name
Sample Name	ZCCHC9-BGRSLV05-51	ZCCHC9-BGRSLV05-52
RBP	ZCCHC9	ZCCHC9
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	11624	11625

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-51	BGRSLV05-52
Sample #	57	58
Sample Name	ZCCHC9-BGRSLV05-51	ZCCHC9-BGRSLV05-52
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	284	284
Peak_Molarity	43.00	85.70
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/E8.png	DNA_Library_set60-62/set1/F8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/A8.png	RNA_Library_set60-62/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-51	BGRSLV05-52
RBP	ZCCHC9	ZCCHC9
Batch_ID	BGRSLV05	BGRSLV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3644	3645

Sequencing Information

	BGRSLV05-51	BGRSLV05-52
Sample_ID	BGRSLV05-51	BGRSLV05-52
Sample Name	ZCCHC9-BGRSLV05-51	ZCCHC9-BGRSLV05-52
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	48,382,864	22,606,067
total_aligned_reads	32,529,868	19,235,371
unique_aligned_reads	30,465,119	18,044,699
percent_uniqueAligned	0.62967	0.79822
correlation_replicates	0.960548	0.960548
spikein_reads	66,632	33,538
percent_spikeins	0.00138	0.00148
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2515	2516

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
ZCCHC9-BGRSLV05-51_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2515	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8616
ZCCHC9-BGRSLV05-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2515					GRCh38	V40	ZCCHC9-BGRSLV05-51_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC9-BGRSLV05-51_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10481
ZCCHC9-BGRSLV05-51_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2515					GRCh38	V40	ZCCHC9-BGRSLV05-51/Aligned.sortedByCoord.out.bam		ENCORE2	10533
ZCCHC9-BGRSLV05-51_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2515					GRCh38	V40	ZCCHC9-BGRSLV05-51/Aligned.sortedByCoord.out.bam		ENCORE2	10585
ZCCHC9-BGRSLV05-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2515					GRCh38	V40	ZCCHC9-BGRSLV05-51/Aligned.sortedByCoord.out.bam		ENCORE2	10637
ZCCHC9-BGRSLV05-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2515					GRCh38	V40	ZCCHC9-BGRSLV05-51/Aligned.sortedByCoord.out.bam		ENCORE2	10689
ZCCHC9-BGRSLV05-51_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2515					GRCh38	V40	ZCCHC9-BGRSLV05-51_S57_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC9-BGRSLV05-51_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10741
ZCCHC9-BGRSLV05-51_S57_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2515	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28883
ZCCHC9-BGRSLV05-52_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2516	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8617
ZCCHC9-BGRSLV05-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2516					GRCh38	V40	ZCCHC9-BGRSLV05-52_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC9-BGRSLV05-52_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10482
ZCCHC9-BGRSLV05-52_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2516					GRCh38	V40	ZCCHC9-BGRSLV05-52/Aligned.sortedByCoord.out.bam		ENCORE2	10534
ZCCHC9-BGRSLV05-52_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2516					GRCh38	V40	ZCCHC9-BGRSLV05-52/Aligned.sortedByCoord.out.bam		ENCORE2	10586
ZCCHC9-BGRSLV05-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2516					GRCh38	V40	ZCCHC9-BGRSLV05-52/Aligned.sortedByCoord.out.bam		ENCORE2	10638
ZCCHC9-BGRSLV05-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2516					GRCh38	V40	ZCCHC9-BGRSLV05-52/Aligned.sortedByCoord.out.bam		ENCORE2	10690
ZCCHC9-BGRSLV05-52_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2516					GRCh38	V40	ZCCHC9-BGRSLV05-52_S58_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC9-BGRSLV05-52_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10742
ZCCHC9-BGRSLV05-52_S58_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2516	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28884