YTHDF1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-63	BG293LV06-64
idx	0	0
TRCN#_or_BGC#	TRCN0000062770	TRCN0000062770
shRNA_or_gRNA_sequence	CCGGCCCGAAAGAGTTTGAGTGGAACTCGAGTTCCACTCAAACTCTTTCGGGTTTTTG	CCGGCCCGAAAGAGTTTGAGTGGAACTCGAGTTCCACTCAAACTCTTTCGGGTTTTTG
PAM
Name	YTHDF1	YTHDF1
Sample_ID	BG293LV06-63	BG293LV06-64
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	YTHDF1	YTHDF1
qPCR_result	65.6	69.0
Ave_qPCR	67.3
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	12198	12199

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-63	BG293LV06-64
Sample_ID	BG293LV06-63	BG293LV06-64
Sample Name
Sample Name	YTHDF1-BG293LV06-63B	YTHDF1-BG293LV06-64B
RBP	YTHDF1	YTHDF1
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13500	13501

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-63	BG293LV06-64
Sample #	65	66
Sample Name	YTHDF1-BG293LV06-63B	YTHDF1-BG293LV06-64B
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	283	280
Peak_Molarity	75.90	82.00
libSampleQC_DNA_Well	DNA_Library_set72/set1/A2.png	DNA_Library_set72/set1/B2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set72/set1/A2.png	RNA_Library_set72/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-63	BG293LV06-64
RBP	YTHDF1	YTHDF1
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4490	4491

Sequencing Information

	BG293LV06-63	BG293LV06-64
Sample_ID	BG293LV06-63	BG293LV06-64
Sample Name	YTHDF1-BG293LV06-63B	YTHDF1-BG293LV06-64B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	21,649,674	26,446,422
total_aligned_reads	17,833,214	23,528,449
unique_aligned_reads	16,617,259	21,929,566
percent_uniqueAligned	0.76755	0.82921
correlation_replicates	0.989660	0.989660
spikein_reads	87,512	117,422
percent_spikeins	0.00404	0.00444
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3059	3060

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
YTHDF1-BG293LV06-63B_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3059	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29828
YTHDF1-BG293LV06-63B_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3059	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29900
YTHDF1-BG293LV06-63B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3059					GRCh38	V40	YTHDF1-BG293LV06-63B_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV06-63B_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29972
YTHDF1-BG293LV06-63B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3059					GRCh38	V40	YTHDF1-BG293LV06-63B_Aligned.sortedByCoord.out.bam		ENCORE2	30044
YTHDF1-BG293LV06-63B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3059					GRCh38	V40	YTHDF1-BG293LV06-63B_Aligned.sortedByCoord.out.bam		ENCORE2	30116
YTHDF1-BG293LV06-63B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3059					GRCh38	V40	YTHDF1-BG293LV06-63B_Aligned.sortedByCoord.out.bam		ENCORE2	30188
YTHDF1-BG293LV06-63B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3059					GRCh38	V40	YTHDF1-BG293LV06-63B_Aligned.sortedByCoord.out.bam		ENCORE2	30260
YTHDF1-BG293LV06-63B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3059					GRCh38	V40	YTHDF1-BG293LV06-63B_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV06-63B_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30332
YTHDF1-BG293LV06-64B_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3060	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29829
YTHDF1-BG293LV06-64B_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3060	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29901
YTHDF1-BG293LV06-64B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3060					GRCh38	V40	YTHDF1-BG293LV06-64B_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV06-64B_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29973
YTHDF1-BG293LV06-64B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3060					GRCh38	V40	YTHDF1-BG293LV06-64B_Aligned.sortedByCoord.out.bam		ENCORE2	30045
YTHDF1-BG293LV06-64B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3060					GRCh38	V40	YTHDF1-BG293LV06-64B_Aligned.sortedByCoord.out.bam		ENCORE2	30117
YTHDF1-BG293LV06-64B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3060					GRCh38	V40	YTHDF1-BG293LV06-64B_Aligned.sortedByCoord.out.bam		ENCORE2	30189
YTHDF1-BG293LV06-64B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3060					GRCh38	V40	YTHDF1-BG293LV06-64B_Aligned.sortedByCoord.out.bam		ENCORE2	30261
YTHDF1-BG293LV06-64B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3060					GRCh38	V40	YTHDF1-BG293LV06-64B_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV06-64B_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30333