ZNF385C RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-31	BGRSLV08-32
idx	0	0
TRCN#_or_BGC#	TRCN0000180871	TRCN0000180871
shRNA_or_gRNA_sequence	CCGGGCTGTGAGTATCCTCAAGTCTCTCGAGAGACTTGAGGATACTCACAGCTTTTTTG	CCGGGAAGCAACTCACCAAGACGTTCTCGAGAACGTCTTGGTGAGTTGCTTCTTTTTTG
PAM
Name	ZNF385C	ZNF385C
Sample_ID	BGRSLV08-31	BGRSLV08-32
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZNF385C	ZNF385C
qPCR_result	65.6	69.0
Ave_qPCR	67.3
RT-qPCR_primer-F	agcaggaggcacaaagacc
RT-qPCR_primer-R	tggtgagttgcttctgcaag
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	8680	8681

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-31	BGRSLV08-32
Sample_ID	BGRSLV08-31	BGRSLV08-32
Sample Name
Sample Name	ZNF385C-BGRSLV08-31	ZNF385C-BGRSLV08-32
RBP	ZNF385C	ZNF385C
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	11788	11789

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-31	BGRSLV08-32
Sample #	53	54
Sample Name	ZNF385C-BGRSLV08-31	ZNF385C-BGRSLV08-32
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	300	298
Peak_Molarity	75.50	83.80
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/E7.png	DNA_Library_set60-62/set4/F7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/E7.png	RNA_Library_set60-62/set2/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-31	BGRSLV08-32
RBP	ZNF385C	ZNF385C
Batch_ID	BGRSLV08	BGRSLV08
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3736	3737

Sequencing Information

	BGRSLV08-31	BGRSLV08-32
Sample_ID	BGRSLV08-31	BGRSLV08-32
Sample Name	ZNF385C-BGRSLV08-31	ZNF385C-BGRSLV08-32
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	27,553,697	58,124,561
total_aligned_reads	23,890,150	51,351,575
unique_aligned_reads	22,434,320	48,271,986
percent_uniqueAligned	0.81420	0.83049
correlation_replicates	0.995444	0.995444
spikein_reads	21,480	31,250
percent_spikeins	0.00078	0.00054
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2607	2608

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
ZNF385C-BGRSLV08-31_S53_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2607	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7910
ZNF385C-BGRSLV08-31_S53_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2607	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7954
ZNF385C-BGRSLV08-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2607					GRCh38	V40	ZNF385C-BGRSLV08-31_S53_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF385C-BGRSLV08-31_S53_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10215
ZNF385C-BGRSLV08-31_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2607					GRCh38	V40	ZNF385C-BGRSLV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	10259
ZNF385C-BGRSLV08-31_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2607					GRCh38	V40	ZNF385C-BGRSLV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	10303
ZNF385C-BGRSLV08-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2607					GRCh38	V40	ZNF385C-BGRSLV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	10347
ZNF385C-BGRSLV08-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2607					GRCh38	V40	ZNF385C-BGRSLV08-31/Aligned.sortedByCoord.out.bam		ENCORE2	10391
ZNF385C-BGRSLV08-31_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2607					GRCh38	V40	ZNF385C-BGRSLV08-31_S53_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF385C-BGRSLV08-31_S53_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10435
ZNF385C-BGRSLV08-32_S54_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2608	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7911
ZNF385C-BGRSLV08-32_S54_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2608	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7955
ZNF385C-BGRSLV08-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2608					GRCh38	V40	ZNF385C-BGRSLV08-32_S54_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF385C-BGRSLV08-32_S54_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10216
ZNF385C-BGRSLV08-32_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2608					GRCh38	V40	ZNF385C-BGRSLV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	10260
ZNF385C-BGRSLV08-32_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2608					GRCh38	V40	ZNF385C-BGRSLV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	10304
ZNF385C-BGRSLV08-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2608					GRCh38	V40	ZNF385C-BGRSLV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	10348
ZNF385C-BGRSLV08-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2608					GRCh38	V40	ZNF385C-BGRSLV08-32/Aligned.sortedByCoord.out.bam		ENCORE2	10392
ZNF385C-BGRSLV08-32_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2608					GRCh38	V40	ZNF385C-BGRSLV08-32_S54_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF385C-BGRSLV08-32_S54_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10436