METTL1 RNA-Seq in HepG2

General Information


RBP	METTL1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	METTL1-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR517QLP
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR925POR
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	METTL1-BGHcLV24-37
Rep2	METTL1-BGHcLV24-38
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	17.0
Rep2_qPCR	3.0
Rep1_WB	69.0
Rep2_WB	65.0
Antibody Cat#	PA5-80810
Antibody Lot#	LOT# UL2893376
Antibody DCC ID	ENCAB061GXO
Status	Released
Project	ENCODE4
ID	10

Experiment Information (Status: Released)

	BGHcLV24-37	BGHcLV24-38
idx	695	696
TRCN#_or_BGC#	BGC#0000578	BGC#0000578
shRNA_or_gRNA_sequence	CGGTAGTAGCGCTTCTGGGG	CGGTAGTAGCGCTTCTGGGG
PAM	CGG	CGG
Name	METTL1_91	METTL1_91
Sample_ID	BGHcLV24-37	BGHcLV24-38
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	METTL1	METTL1
qPCR_result	17.0	3.0
Ave_qPCR	10.0
RT-qPCR_primer-F	GTTTGCAGACATAGGCTGTGG
RT-qPCR_primer-R	ATGATTCGCCACTTGTGCTT
protein_conc	5294	5286
WB_result	69.0	65.0
Ave_WB	67.0
WB_DONE_date	11/9/20
MW	31.5KD
IP	Rabbit / I
antibody_Cat#	PA5-80810	LOT# UL2893376
Antibody DCC ID	ENCAB061GXO
submitted_to_DCC_date	12/9/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6850	6851

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
METTL1	Product_ID: PA5-80810 Lot_ID: UL2893376 Source: Thermo Fisher Target Name: METTL1-human

Experiment Status

	BGHcLV24-37	BGHcLV24-38
Sample_ID	BGHcLV24-37	BGHcLV24-38
Sample Name
Sample Name	METTL1-BGHcLV24-37	METTL1-BGHcLV24-38
RBP	METTL1	METTL1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7799	7800

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-37	BGHcLV24-38
Sample #	21	22
Sample Name	METTL1-BGHcLV24-37	METTL1-BGHcLV24-38
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	304	320
Peak_Molarity	80.10	85.40
libSampleQC_DNA_Well	DNA_Library_set47/set1/E6.png	DNA_Library_set47/set1/F6.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set47/set1/E3.png	RNA_Library_set47/set2/E6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-37	BGHcLV24-38
RBP	METTL1	METTL1
Batch_ID	BGHcLV24	BGHcLV24
WB_result	69.000	65.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1484	1485

Sequencing Information

	BGHcLV24-37	BGHcLV24-38
Sample_ID	BGHcLV24-37	BGHcLV24-38
Sample Name	METTL1-BGHcLV24-37	METTL1-BGHcLV24-38
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	136,937,376	119,284,510
total_aligned_reads	127,304,292	106,891,696
unique_aligned_reads	120,118,306	100,736,606
percent_uniqueAligned	0.87718	0.84451
correlation_replicates	0.993847	0.993847
spikein_reads	38,482	30,530
percent_spikeins	0.00028	0.00026
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	566	567

Data Submission Information

	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-38	BGHcLV24-38	BGHcLV24-38	BGHcLV24-38
ENCODE_alias	brenton-graveley:METTL1-BGHcLV24	brenton-graveley:METTL1-BGHcLV24-37	brenton-graveley:L-METTL1-BGHcLV24-37	brenton-graveley:METTL1-BGHcLV24-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL1-BGHcLV24-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL1-BGHcLV24-HepG2	brenton-graveley:METTL1-BGHcLV24-38	brenton-graveley:L-METTL1-BGHcLV24-38	brenton-graveley:METTL1-BGHcLV24-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL1-BGHcLV24-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR925POR	ENCBS203SVC	ENCLB087QKG	ENCFF214BCE	ENCFF780PGK	ENCSR517QLP	ENCBS805VQZ	ENCLB070RXY	ENCFF676NSO	ENCFF839KJR
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-37	BGHcLV24-38	BGHcLV24-38	BGHcLV24-38	BGHcLV24-38
Sample Name	METTL1-BGHcLV24-37	METTL1-BGHcLV24-37	METTL1-BGHcLV24-37	METTL1-BGHcLV24-37	METTL1-BGHcLV24-37	METTL1-BGHcLV24-37	METTL1-BGHcLV24-38	METTL1-BGHcLV24-38	METTL1-BGHcLV24-38	METTL1-BGHcLV24-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		METTL1-BGHcLV24-37.pdf	L-METTL1-BGHcLV24-37.pdf				METTL1-BGHcLV24-38.pdf	L-METTL1-BGHcLV24-38.pdf
ID	3245	3277	3321	3365	3409	7255	3278	3322	3366	3410

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
METTL1-BGHcLV24-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	566	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3724
METTL1-BGHcLV24-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	566	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3770
METTL1-BGHcLV24-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	566					GRCh38	V40	METTL1-BGHcLV24-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz,METTL1-BGHcLV24-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25413
METTL1-BGHcLV24-37_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	566					GRCh38	V40	METTL1-BGHcLV24-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz,METTL1-BGHcLV24-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25457
METTL1-BGHcLV24-37_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	566					GRCh38	V40	METTL1-BGHcLV24-37/Aligned.sortedByCoord.out.bam		ENCORE2	26289
METTL1-BGHcLV24-37_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	566					GRCh38	V40	METTL1-BGHcLV24-37/Aligned.sortedByCoord.out.bam		ENCORE2	26333
METTL1-BGHcLV24-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	566					GRCh38	V40	METTL1-BGHcLV24-37/Aligned.sortedByCoord.out.bam		ENCORE2	26377
METTL1-BGHcLV24-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	566					GRCh38	V40	METTL1-BGHcLV24-37/Aligned.sortedByCoord.out.bam		ENCORE2	26421
METTL1-BGHcLV24-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	567	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3725
METTL1-BGHcLV24-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	567	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3771
METTL1-BGHcLV24-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	567					GRCh38	V40	METTL1-BGHcLV24-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz,METTL1-BGHcLV24-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25414
METTL1-BGHcLV24-38_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	567					GRCh38	V40	METTL1-BGHcLV24-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz,METTL1-BGHcLV24-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25458
METTL1-BGHcLV24-38_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	567					GRCh38	V40	METTL1-BGHcLV24-38/Aligned.sortedByCoord.out.bam		ENCORE2	26290
METTL1-BGHcLV24-38_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	567					GRCh38	V40	METTL1-BGHcLV24-38/Aligned.sortedByCoord.out.bam		ENCORE2	26334
METTL1-BGHcLV24-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	567					GRCh38	V40	METTL1-BGHcLV24-38/Aligned.sortedByCoord.out.bam		ENCORE2	26378
METTL1-BGHcLV24-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	567					GRCh38	V40	METTL1-BGHcLV24-38/Aligned.sortedByCoord.out.bam		ENCORE2	26422