METTL3 RNA-Seq in HepG2

General Information


RBP	METTL3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	METTL3-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR153PIC
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR884REL
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	METTL3-BGHcLV22-31
Rep2	METTL3-BGHcLV22-32
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	71.3
Rep2_WB	87.0
Antibody Cat#	A301-568A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB373NTV
Status	Released
Project	ENCODE4
ID	44

Experiment Information (Status: Released)

	BGHcLV22-31	BGHcLV22-32
idx	624	625
TRCN#_or_BGC#	BGC#0000523	BGC#0000523
shRNA_or_gRNA_sequence	TCTGAACCAACAGTCCACTA	TCTGAACCAACAGTCCACTA
PAM	AGG	AGG
Name	METTL3_86	METTL3_86
Sample_ID	BGHcLV22-31	BGHcLV22-32
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	METTL3	METTL3
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TTGATCTGGAGATAGAGAGCCTTC
RT-qPCR_primer-R	TGGATTGTTCCTTGGCTGTT
protein_conc	900	1095
WB_result	71.3	87.0
Ave_WB	79.1
WB_DONE_date	8/31/20	JESS
MW	64.4kDa
IP	Rabbit / I
antibody_Cat#	A301-568A	LOT# 1
Antibody DCC ID	ENCAB373NTV
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	8827	8828

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
METTL3	Product_ID: A301-568A Lot_ID: 1 Source: Bethyl Labs Target Name: METTL3-human

Experiment Status

	BGHcLV22-31	BGHcLV22-32
Sample_ID	BGHcLV22-31	BGHcLV22-32
Sample Name
Sample Name	METTL3-BGHcLV22-31	METTL3-BGHcLV22-32
RBP	METTL3	METTL3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7381	7382

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-31	BGHcLV22-32
Sample #	17	18
Sample Name	METTL3-BGHcLV22-31	METTL3-BGHcLV22-32
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	290	305
Peak_Molarity	114.00	110.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/A3.png	DNA_Library_set46/set1/B3.png
RIN	9.0	9.4
libSample_RNA_Well	RNA_Library_set46/set1/A11.png	RNA_Library_set46/set3/D12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-31	BGHcLV22-32
RBP	METTL3	METTL3
Batch_ID	BGHcLV22	BGHcLV22
WB_result	71.300	87.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1392	1393

Sequencing Information

	BGHcLV22-31	BGHcLV22-32
Sample_ID	BGHcLV22-31	BGHcLV22-32
Sample Name	METTL3-BGHcLV22-31	METTL3-BGHcLV22-32
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	252,206,314	269,224,724
total_aligned_reads	201,752,922	234,051,470
unique_aligned_reads	188,318,740	218,528,680
percent_uniqueAligned	0.74669	0.81170
correlation_replicates	0.997557	0.997557
spikein_reads	158,602	188,866
percent_spikeins	0.00063	0.00070
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	498	499

Data Submission Information

	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-32	BGHcLV22-32	BGHcLV22-32	BGHcLV22-32
ENCODE_alias	brenton-graveley:METTL3-BGHcLV22	brenton-graveley:METTL3-BGHcLV22-31	brenton-graveley:L-METTL3-BGHcLV22-31	brenton-graveley:METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL3-BGHcLV22-HepG2	brenton-graveley:METTL3-BGHcLV22-32	brenton-graveley:L-METTL3-BGHcLV22-32	brenton-graveley:METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR884REL	ENCBS025VCL	ENCLB995GUI	ENCFF803ANX	ENCFF243SCW	ENCSR153PIC	ENCBS280DNN	ENCLB110DIL	ENCFF328MDS	ENCFF658MRD
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	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-31	BGHcLV22-32	BGHcLV22-32	BGHcLV22-32	BGHcLV22-32
Sample Name	METTL3-BGHcLV22-31	METTL3-BGHcLV22-31	METTL3-BGHcLV22-31	METTL3-BGHcLV22-31	METTL3-BGHcLV22-31	METTL3-BGHcLV22-31	METTL3-BGHcLV22-32	METTL3-BGHcLV22-32	METTL3-BGHcLV22-32	METTL3-BGHcLV22-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		METTL3-BGHcLV22-31.pdf	L-METTL3-BGHcLV22-31.pdf				METTL3-BGHcLV22-32.pdf	L-METTL3-BGHcLV22-32.pdf
ID	2403	2443	2507	2571	2601	7257	2444	2508	2572	2602

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
METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	498	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1362
METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	498	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1426
METTL3-BGHcLV22-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	498					GRCh38	V40	METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25265
METTL3-BGHcLV22-31_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	498					GRCh38	V40	METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGHcLV22-31_TAATACAG+GTGAATAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25363
METTL3-BGHcLV22-31_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	498					GRCh38	V40	METTL3-BGHcLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	26013
METTL3-BGHcLV22-31_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	498					GRCh38	V40	METTL3-BGHcLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	26043
METTL3-BGHcLV22-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	498					GRCh38	V40	METTL3-BGHcLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	26073
METTL3-BGHcLV22-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	498					GRCh38	V40	METTL3-BGHcLV22-31/Aligned.sortedByCoord.out.bam		ENCORE2	26103
METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	499	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1363
METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	499	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1427
METTL3-BGHcLV22-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	499					GRCh38	V40	METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25266
METTL3-BGHcLV22-32_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	499					GRCh38	V40	METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGHcLV22-32_CGGCGTGA+ACAGGCGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25364
METTL3-BGHcLV22-32_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	499					GRCh38	V40	METTL3-BGHcLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	26014
METTL3-BGHcLV22-32_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	499					GRCh38	V40	METTL3-BGHcLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	26044
METTL3-BGHcLV22-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	499					GRCh38	V40	METTL3-BGHcLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	26074
METTL3-BGHcLV22-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	499					GRCh38	V40	METTL3-BGHcLV22-32/Aligned.sortedByCoord.out.bam		ENCORE2	26104