ZCCHC24 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-9	BGRSLV08-10
idx	0	0
TRCN#_or_BGC#	TRCN0000315354	TRCN0000315354
shRNA_or_gRNA_sequence	CCGGAGTGCCACATCAACGTGTATCCTCGAGGATACACGTTGATGTGGCACTTTTTTG	CCGGAGTGCCACATCAACGTGTATCCTCGAGGATACACGTTGATGTGGCACTTTTTTG
PAM
Name	ZCCHC24	ZCCHC24
Sample_ID	BGRSLV08-9	BGRSLV08-10
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZCCHC24	ZCCHC24
qPCR_result	76.9	82.5
Ave_qPCR	79.7
RT-qPCR_primer-F	CAGGAGTGCATCAAGTGCCACA
RT-qPCR_primer-R	AGGACCTTGCACTTCTCGCAGA
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	8658	8659

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-9	BGRSLV08-10
Sample_ID	BGRSLV08-9	BGRSLV08-10
Sample Name
Sample Name	ZCCHC24-BGRSLV08-9	ZCCHC24-BGRSLV08-10
RBP	ZCCHC24	ZCCHC24
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	11782	11783

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-9	BGRSLV08-10
Sample #	47	48
Sample Name	ZCCHC24-BGRSLV08-9	ZCCHC24-BGRSLV08-10
Sample_Name_Alias
Index Well Position	G06	H06
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	288	285
Peak_Molarity	60.10	28.80
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/G6.png	DNA_Library_set60-62/set4/H6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set60-62/set2/G6.png	RNA_Library_set60-62/set2/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-9	BGRSLV08-10
RBP	ZCCHC24	ZCCHC24
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	3730	3731

Sequencing Information

	BGRSLV08-9	BGRSLV08-10
Sample_ID	BGRSLV08-9	BGRSLV08-10
Sample Name	ZCCHC24-BGRSLV08-9	ZCCHC24-BGRSLV08-10
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	22,142,353	36,947,467
total_aligned_reads	17,673,544	29,524,843
unique_aligned_reads	16,653,421	27,864,744
percent_uniqueAligned	0.75211	0.75417
correlation_replicates	0.982155	0.982155
spikein_reads	20,136	37,572
percent_spikeins	0.00091	0.00102
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2601	2602

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
ZCCHC24-BGRSLV08-9_S47_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2601	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	7901
ZCCHC24-BGRSLV08-9_S47_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2601	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	7945
ZCCHC24-BGRSLV08-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2601					GRCh38	V40	ZCCHC24-BGRSLV08-9_S47_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC24-BGRSLV08-9_S47_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10206
ZCCHC24-BGRSLV08-9_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	2601					GRCh38	V40	ZCCHC24-BGRSLV08-9/Aligned.sortedByCoord.out.bam		ENCORE2	10250
ZCCHC24-BGRSLV08-9_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	2601					GRCh38	V40	ZCCHC24-BGRSLV08-9/Aligned.sortedByCoord.out.bam		ENCORE2	10294
ZCCHC24-BGRSLV08-9_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	2601					GRCh38	V40	ZCCHC24-BGRSLV08-9/Aligned.sortedByCoord.out.bam		ENCORE2	10338
ZCCHC24-BGRSLV08-9_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	2601					GRCh38	V40	ZCCHC24-BGRSLV08-9/Aligned.sortedByCoord.out.bam		ENCORE2	10382
ZCCHC24-BGRSLV08-9_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2601					GRCh38	V40	ZCCHC24-BGRSLV08-9_S47_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC24-BGRSLV08-9_S47_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10426
ZCCHC24-BGRSLV08-10_S48_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2602	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	7900
ZCCHC24-BGRSLV08-10_S48_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2602	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	7944
ZCCHC24-BGRSLV08-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2602					GRCh38	V40	ZCCHC24-BGRSLV08-10_S48_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC24-BGRSLV08-10_S48_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10205
ZCCHC24-BGRSLV08-10_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	2602					GRCh38	V40	ZCCHC24-BGRSLV08-10/Aligned.sortedByCoord.out.bam		ENCORE2	10249
ZCCHC24-BGRSLV08-10_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	2602					GRCh38	V40	ZCCHC24-BGRSLV08-10/Aligned.sortedByCoord.out.bam		ENCORE2	10293
ZCCHC24-BGRSLV08-10_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	2602					GRCh38	V40	ZCCHC24-BGRSLV08-10/Aligned.sortedByCoord.out.bam		ENCORE2	10337
ZCCHC24-BGRSLV08-10_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	2602					GRCh38	V40	ZCCHC24-BGRSLV08-10/Aligned.sortedByCoord.out.bam		ENCORE2	10381
ZCCHC24-BGRSLV08-10_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2602					GRCh38	V40	ZCCHC24-BGRSLV08-10_S48_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC24-BGRSLV08-10_S48_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10425