ZNF800 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-41	BGRSLV02-42
idx	0	0
TRCN#_or_BGC#	TRCN0000021155	TRCN0000021155
shRNA_or_gRNA_sequence	CCGGCGTGATGTGATACGACATATACTCGAGTATATGTCGTATCACATCACGTTTTT	CCGGCGTGATGTGATACGACATATACTCGAGTATATGTCGTATCACATCACGTTTTT
PAM
Name	ZNF800	ZNF800
Sample_ID	BGRSLV02-41	BGRSLV02-42
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	ZNF800	ZNF800
qPCR_result	61.7	56.6
Ave_qPCR	59.1
RT-qPCR_primer-F	gactgaccaccatcatcacg
RT-qPCR_primer-R	ggttgctgtaacaaaggagga
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	8278	8279

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-41	BGRSLV02-42
Sample_ID	BGRSLV02-41	BGRSLV02-42
Sample Name
Sample Name	ZNF800-BGRSLV02-41	ZNF800-BGRSLV02-42
RBP	ZNF800	ZNF800
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	11328	11329

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-41	BGRSLV02-42
Sample #	31	32
Sample Name	ZNF800-BGRSLV02-41	ZNF800-BGRSLV02-42
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	317	304
Peak_Molarity	49.30	57.70
libSampleQC_DNA_Well	DNA_Library_set57/set1/G10.png	DNA_Library_set57/set1/H10.png
RIN	10.0	9.6
libSample_RNA_Well	RNA_Library_set57/set1/G4.png	RNA_Library_set57/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-41	BGRSLV02-42
RBP	ZNF800	ZNF800
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3492	3493

Sequencing Information

	BGRSLV02-41	BGRSLV02-42
Sample_ID	BGRSLV02-41	BGRSLV02-42
Sample Name	ZNF800-BGRSLV02-41	ZNF800-BGRSLV02-42
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	60,796,432	57,572,600
total_aligned_reads	55,920,457	52,920,195
unique_aligned_reads	52,156,320	49,162,315
percent_uniqueAligned	0.85788	0.85392
correlation_replicates	0.982974	0.982974
spikein_reads	60,878	33,880
percent_spikeins	0.00100	0.00059
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2363	2364

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
ZNF800-BGRSLV02-41_S119_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2363	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8250
ZNF800-BGRSLV02-41_S119_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2363	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8296
ZNF800-BGRSLV02-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2363					GRCh38	V40	ZNF800-BGRSLV02-41_S119_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSLV02-41_S119_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11539
ZNF800-BGRSLV02-41_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2363					GRCh38	V40	ZNF800-BGRSLV02-41/Aligned.sortedByCoord.out.bam		ENCORE2	11585
ZNF800-BGRSLV02-41_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2363					GRCh38	V40	ZNF800-BGRSLV02-41/Aligned.sortedByCoord.out.bam		ENCORE2	11631
ZNF800-BGRSLV02-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2363					GRCh38	V40	ZNF800-BGRSLV02-41/Aligned.sortedByCoord.out.bam		ENCORE2	11677
ZNF800-BGRSLV02-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2363					GRCh38	V40	ZNF800-BGRSLV02-41/Aligned.sortedByCoord.out.bam		ENCORE2	11723
ZNF800-BGRSLV02-41_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2363					GRCh38	V40	ZNF800-BGRSLV02-41_S119_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSLV02-41_S119_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11769
ZNF800-BGRSLV02-42_S120_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2364	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8251
ZNF800-BGRSLV02-42_S120_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2364	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8297
ZNF800-BGRSLV02-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2364					GRCh38	V40	ZNF800-BGRSLV02-42_S120_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSLV02-42_S120_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11540
ZNF800-BGRSLV02-42_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2364					GRCh38	V40	ZNF800-BGRSLV02-42/Aligned.sortedByCoord.out.bam		ENCORE2	11586
ZNF800-BGRSLV02-42_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2364					GRCh38	V40	ZNF800-BGRSLV02-42/Aligned.sortedByCoord.out.bam		ENCORE2	11632
ZNF800-BGRSLV02-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2364					GRCh38	V40	ZNF800-BGRSLV02-42/Aligned.sortedByCoord.out.bam		ENCORE2	11678
ZNF800-BGRSLV02-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2364					GRCh38	V40	ZNF800-BGRSLV02-42/Aligned.sortedByCoord.out.bam		ENCORE2	11724
ZNF800-BGRSLV02-42_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2364					GRCh38	V40	ZNF800-BGRSLV02-42_S120_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSLV02-42_S120_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11770