DNMT3B RNA-Seq in HepG2

General Information


RBP	DNMT3B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DNMT3B-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR816QIL
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR290GUQ
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	DNMT3B-BGHcLV20-5
Rep2	DNMT3B-BGHcLV20-6
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	92.0
Rep2_qPCR	87.0
Rep1_WB	73.9
Rep2_WB	81.3
Antibody Cat#	49-1028
Antibody Lot#	A234200170712
Antibody DCC ID	ENCAB175PCI
Status	Released
Project	ENCODE4
ID	75

Experiment Information (Status: Released)

	BGHcLV20-5	BGHcLV20-6
idx	555	556
TRCN#_or_BGC#	BGC#0000466	BGC#0000466
shRNA_or_gRNA_sequence	AGAGTCGCGAGCTTGATCTT	AGAGTCGCGAGCTTGATCTT
PAM	CGG	CGG
Name	DNMT3B-96	DNMT3B-96
Sample_ID	BGHcLV20-5	BGHcLV20-6
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	DNMT3B	DNMT3B
qPCR_result	92.0	87.0
Ave_qPCR	89.5
RT-qPCR_primer-F	ACTCGATCCTCGTCAACGG
RT-qPCR_primer-R	GAGTCGCGAGCTTGATCTTC
protein_conc	3896	4923
WB_result	73.9	81.3
Ave_WB	77.6
WB_DONE_date	1/22/20
MW	96KD
IP	Rabbit / I
antibody_Cat#	49-1028	A234200170712
Antibody DCC ID	ENCAB175PCI
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	6710	6711

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DNMT3B	Product_ID: 49-1028 Lot_ID: A234200170712 Source: Thermo Fisher Target Name: DNMT3B-human

Experiment Status

	BGHcLV20-5	BGHcLV20-6
Sample_ID	BGHcLV20-5	BGHcLV20-6
Sample Name
Sample Name	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-6
RBP	DNMT3B	DNMT3B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5811	5812

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-5	BGHcLV20-6
Sample #	61	62
Sample Name	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-6
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	296	307
Peak_Molarity	207.00	84.10
libSampleQC_DNA_Well	DNA_Library_set45/set1/G7.png	DNA_Library_set45/set1/H7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set45/set1/G7.png	RNA_Library_set45/set1/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-5	BGHcLV20-6
RBP	DNMT3B	DNMT3B
Batch_ID	BGHcLV20	BGHcLV20
WB_result	73.900	81.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	835	836

Sequencing Information

	BGHcLV20-5	BGHcLV20-6
Sample_ID	BGHcLV20-5	BGHcLV20-6
Sample Name	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-6
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	143,157,858	115,383,494
total_aligned_reads	138,388,096	109,882,638
unique_aligned_reads	130,572,556	103,573,832
percent_uniqueAligned	0.91209	0.89765
correlation_replicates	0.994324	0.994324
spikein_reads	64,706	56,648
percent_spikeins	0.00045	0.00049
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	466	467

Data Submission Information

	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-6	BGHcLV20-6	BGHcLV20-6	BGHcLV20-6
ENCODE_alias	brenton-graveley:DNMT3B-BGHcLV20	brenton-graveley:DNMT3B-BGHcLV20-5	brenton-graveley:L-DNMT3B-BGHcLV20-5	brenton-graveley:DNMT3B-BGHcLV20-5_S55_R1_001.fastq.gz	brenton-graveley:DNMT3B-BGHcLV20-5_S55_R2_001.fastq.gz	brenton-graveley:DNMT3B-BGHcLV20-HepG2	brenton-graveley:DNMT3B-BGHcLV20-6	brenton-graveley:L-DNMT3B-BGHcLV20-6	brenton-graveley:DNMT3B-BGHcLV20-6_S56_R1_001.fastq.gz	brenton-graveley:DNMT3B-BGHcLV20-6_S56_R2_001.fastq.gz
ENCODE_accession	ENCSR290GUQ	ENCBS470NZT	ENCLB642NGH	ENCFF738OGJ	ENCFF200MXH	ENCSR816QIL	ENCBS350DLG	ENCLB868GAM	ENCFF621IJR	ENCFF805FZT
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	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-5	BGHcLV20-6	BGHcLV20-6	BGHcLV20-6	BGHcLV20-6
Sample Name	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-5	DNMT3B-BGHcLV20-6	DNMT3B-BGHcLV20-6	DNMT3B-BGHcLV20-6	DNMT3B-BGHcLV20-6
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45H_biosample_protocol	LV45H_library_protocol				LV45H_biosample_protocol	LV45H_library_protocol
protocol_URL		DNMT3B-BGHcLV20-5.pdf	L-DNMT3B-BGHcLV20-5.pdf				DNMT3B-BGHcLV20-6.pdf	L-DNMT3B-BGHcLV20-6.pdf
ID	2082	2119	2189	2259	2329	7191	2120	2190	2260	2330

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
DNMT3B-BGHcLV20-5_S55_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	466	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1310
DNMT3B-BGHcLV20-5_S55_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	466	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1330
DNMT3B-BGHcLV20-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	466					GRCh38	V40	DNMT3B-BGHcLV20-5_S55_R1_001.filtered.trimmed.paired.fastq.gz,DNMT3B-BGHcLV20-5_S55_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24851
DNMT3B-BGHcLV20-5_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	466					GRCh38	V40	DNMT3B-BGHcLV20-5_S55_R1_001.filtered.trimmed.paired.fastq.gz,DNMT3B-BGHcLV20-5_S55_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24871
DNMT3B-BGHcLV20-5_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	466					GRCh38	V40	DNMT3B-BGHcLV20-5/Aligned.sortedByCoord.out.bam		ENCORE2	25921
DNMT3B-BGHcLV20-5_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	466					GRCh38	V40	DNMT3B-BGHcLV20-5/Aligned.sortedByCoord.out.bam		ENCORE2	25941
DNMT3B-BGHcLV20-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	466					GRCh38	V40	DNMT3B-BGHcLV20-5/Aligned.sortedByCoord.out.bam		ENCORE2	25961
DNMT3B-BGHcLV20-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	466					GRCh38	V40	DNMT3B-BGHcLV20-5/Aligned.sortedByCoord.out.bam		ENCORE2	25981
DNMT3B-BGHcLV20-6_S56_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	467	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1311
DNMT3B-BGHcLV20-6_S56_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	467	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1331
DNMT3B-BGHcLV20-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	467					GRCh38	V40	DNMT3B-BGHcLV20-6_S56_R1_001.filtered.trimmed.paired.fastq.gz,DNMT3B-BGHcLV20-6_S56_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24852
DNMT3B-BGHcLV20-6_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	467					GRCh38	V40	DNMT3B-BGHcLV20-6_S56_R1_001.filtered.trimmed.paired.fastq.gz,DNMT3B-BGHcLV20-6_S56_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24872
DNMT3B-BGHcLV20-6_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	467					GRCh38	V40	DNMT3B-BGHcLV20-6/Aligned.sortedByCoord.out.bam		ENCORE2	25922
DNMT3B-BGHcLV20-6_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	467					GRCh38	V40	DNMT3B-BGHcLV20-6/Aligned.sortedByCoord.out.bam		ENCORE2	25942
DNMT3B-BGHcLV20-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	467					GRCh38	V40	DNMT3B-BGHcLV20-6/Aligned.sortedByCoord.out.bam		ENCORE2	25962
DNMT3B-BGHcLV20-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	467					GRCh38	V40	DNMT3B-BGHcLV20-6/Aligned.sortedByCoord.out.bam		ENCORE2	25982