ZNF800 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-87dox	BGRSDLV04-88dox
idx	0	0
TRCN#_or_BGC#	TRCN0000021155	TRCN0000021155
shRNA_or_gRNA_sequence	CCGGCGTGATGTGATACGACATATACTCGAGTATATGTCGTATCACATCACGTTTTT	CCGGCGTGATGTGATACGACATATACTCGAGTATATGTCGTATCACATCACGTTTTT
PAM
Name	ZNF800	ZNF800
Sample_ID	BGRSDLV04-87dox	BGRSDLV04-88dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	ZNF800	ZNF800
qPCR_result	53.636	60.48133
Ave_qPCR	57.058665
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9451	9452

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-87dox	BGRSDLV04-88dox
Sample_ID	BGRSDLV04-87dox	BGRSDLV04-88dox
Sample Name
Sample Name	ZNF800-BGRSDLV04-87dox	ZNF800-BGRSDLV04-88dox
RBP	ZNF800	ZNF800
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12688	12689

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-87dox	BGRSDLV04-88dox
Sample #	43	44
Sample Name	ZNF800-BGRSDLV04-87dox	ZNF800-BGRSDLV04-88dox
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	297	298
Peak_Molarity	54.80	26.40
libSampleQC_DNA_Well	DNA_Library_set68/set1/C6.png	DNA_Library_set68/set1/D6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/C6.png	RNA_Library_set68/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-87dox	BGRSDLV04-88dox
RBP	ZNF800	ZNF800
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4116	4117

Sequencing Information

	BGRSDLV04-87dox	BGRSDLV04-88dox
Sample_ID	BGRSDLV04-87dox	BGRSDLV04-88dox
Sample Name	ZNF800-BGRSDLV04-87dox	ZNF800-BGRSDLV04-88dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	53,954,169	62,404,207
total_aligned_reads	49,483,203	55,608,265
unique_aligned_reads	46,477,858	52,336,641
percent_uniqueAligned	0.86143	0.83867
correlation_replicates	0.997206	0.997206
spikein_reads	10,778	8,062
percent_spikeins	0.00020	0.00013
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2879	2880

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-BGRSDLV04-87dox_S43_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2879	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27691
ZNF800-BGRSDLV04-87dox_S43_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2879	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27755
ZNF800-BGRSDLV04-87dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2879					GRCh38	V40	ZNF800-BGRSDLV04-87dox_S43_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSDLV04-87dox_S43_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27819
ZNF800-BGRSDLV04-87dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2879					GRCh38	V40	ZNF800-BGRSDLV04-87dox/Aligned.sortedByCoord.out.bam		ENCORE2	27883
ZNF800-BGRSDLV04-87dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2879					GRCh38	V40	ZNF800-BGRSDLV04-87dox/Aligned.sortedByCoord.out.bam		ENCORE2	27947
ZNF800-BGRSDLV04-87dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2879					GRCh38	V40	ZNF800-BGRSDLV04-87dox/Aligned.sortedByCoord.out.bam		ENCORE2	28011
ZNF800-BGRSDLV04-87dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2879					GRCh38	V40	ZNF800-BGRSDLV04-87dox/Aligned.sortedByCoord.out.bam		ENCORE2	28075
ZNF800-BGRSDLV04-87dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2879					GRCh38	V40	ZNF800-BGRSDLV04-87dox_S43_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSDLV04-87dox_S43_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28139
ZNF800-BGRSDLV04-88dox_S44_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2880	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27692
ZNF800-BGRSDLV04-88dox_S44_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2880	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27756
ZNF800-BGRSDLV04-88dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2880					GRCh38	V40	ZNF800-BGRSDLV04-88dox_S44_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSDLV04-88dox_S44_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27820
ZNF800-BGRSDLV04-88dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2880					GRCh38	V40	ZNF800-BGRSDLV04-88dox/Aligned.sortedByCoord.out.bam		ENCORE2	27884
ZNF800-BGRSDLV04-88dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2880					GRCh38	V40	ZNF800-BGRSDLV04-88dox/Aligned.sortedByCoord.out.bam		ENCORE2	27948
ZNF800-BGRSDLV04-88dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2880					GRCh38	V40	ZNF800-BGRSDLV04-88dox/Aligned.sortedByCoord.out.bam		ENCORE2	28012
ZNF800-BGRSDLV04-88dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2880					GRCh38	V40	ZNF800-BGRSDLV04-88dox/Aligned.sortedByCoord.out.bam		ENCORE2	28076
ZNF800-BGRSDLV04-88dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2880					GRCh38	V40	ZNF800-BGRSDLV04-88dox_S44_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF800-BGRSDLV04-88dox_S44_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28140