ZNF770 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-49	BGRSLV08-50
idx	0	0
TRCN#_or_BGC#	TRCN0000128871	TRCN0000128871
shRNA_or_gRNA_sequence	CCGGGCACTTTGAAACACCATCAAACTCGAGTTTGATGGTGTTTCAAAGTGCTTTTTTG	CCGGGCTAGTGCTATCTTTCTCAAACTCGAGTTTGAGAAAGATAGCACTAGCTTTTTTG
PAM
Name	ZNF770	ZNF770
Sample_ID	BGRSLV08-49	BGRSLV08-50
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZNF770	ZNF770
qPCR_result	74.6	71.2
Ave_qPCR	72.9
RT-qPCR_primer-F	ggcttttcgggctcttttat
RT-qPCR_primer-R	aaccaccctgatttgcattt
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	8698	8699

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-49	BGRSLV08-50
Sample_ID	BGRSLV08-49	BGRSLV08-50
Sample Name
Sample Name	ZNF770-BGRSLV08-49	ZNF770-BGRSLV08-50
RBP	ZNF770	ZNF770
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	11792	11793

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-49	BGRSLV08-50
Sample #	57	58
Sample Name	ZNF770-BGRSLV08-49	ZNF770-BGRSLV08-50
Sample_Name_Alias
Index Well Position	A08	B08
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	283	288
Peak_Molarity	38.60	65.50
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A8.png	DNA_Library_set60-62/set4/B8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A8.png	RNA_Library_set60-62/set2/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-49	BGRSLV08-50
RBP	ZNF770	ZNF770
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	3740	3741

Sequencing Information

	BGRSLV08-49	BGRSLV08-50
Sample_ID	BGRSLV08-49	BGRSLV08-50
Sample Name	ZNF770-BGRSLV08-49	ZNF770-BGRSLV08-50
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	24,024,602	36,033,728
total_aligned_reads	20,568,173	31,060,745
unique_aligned_reads	19,251,781	29,099,200
percent_uniqueAligned	0.80134	0.80755
correlation_replicates	0.996153	0.996153
spikein_reads	56,212	44,058
percent_spikeins	0.00234	0.00122
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2611	2612

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
ZNF770-BGRSLV08-49_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2611	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	7914
ZNF770-BGRSLV08-49_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2611	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	7958
ZNF770-BGRSLV08-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2611					GRCh38	V40	ZNF770-BGRSLV08-49_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF770-BGRSLV08-49_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10219
ZNF770-BGRSLV08-49_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	2611					GRCh38	V40	ZNF770-BGRSLV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	10263
ZNF770-BGRSLV08-49_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	2611					GRCh38	V40	ZNF770-BGRSLV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	10307
ZNF770-BGRSLV08-49_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	2611					GRCh38	V40	ZNF770-BGRSLV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	10351
ZNF770-BGRSLV08-49_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	2611					GRCh38	V40	ZNF770-BGRSLV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	10395
ZNF770-BGRSLV08-49_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2611					GRCh38	V40	ZNF770-BGRSLV08-49_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF770-BGRSLV08-49_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10439
ZNF770-BGRSLV08-50_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2612	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	7915
ZNF770-BGRSLV08-50_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2612	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	7959
ZNF770-BGRSLV08-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2612					GRCh38	V40	ZNF770-BGRSLV08-50_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF770-BGRSLV08-50_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10220
ZNF770-BGRSLV08-50_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	2612					GRCh38	V40	ZNF770-BGRSLV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	10264
ZNF770-BGRSLV08-50_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	2612					GRCh38	V40	ZNF770-BGRSLV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	10308
ZNF770-BGRSLV08-50_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	2612					GRCh38	V40	ZNF770-BGRSLV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	10352
ZNF770-BGRSLV08-50_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	2612					GRCh38	V40	ZNF770-BGRSLV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	10396
ZNF770-BGRSLV08-50_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2612					GRCh38	V40	ZNF770-BGRSLV08-50_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF770-BGRSLV08-50_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10440