SMYD3 RNA-Seq in HepG2

General Information


RBP	SMYD3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SMYD3-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR284LYJ
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR989GNV
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	SMYD3-BGHcLV20-35
Rep2	SMYD3-BGHcLV20-36
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	66.9
Rep2_qPCR	71.0
Rep1_WB	99.0
Rep2_WB	99.0
Antibody Cat#	PA5-31919
Antibody Lot#	Lot# UA2701668D
Antibody DCC ID	ENCAB101UYP
Status	Released
Project	ENCODE4
ID	81

Experiment Information (Status: Released)

	BGHcLV20-35	BGHcLV20-36
idx	585	586
TRCN#_or_BGC#	BGC#0000430	BGC#0000430
shRNA_or_gRNA_sequence	GCGAGCAGTCCGAGACATCG	GCGAGCAGTCCGAGACATCG
PAM	AGG	AGG
Name	SMYD3_95	SMYD3_95
Sample_ID	BGHcLV20-35	BGHcLV20-36
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	SMYD3	SMYD3
qPCR_result	66.9	71.0
Ave_qPCR	69.0
RT-qPCR_primer-F	AGACATCGAGGTGGGAGAGG
RT-qPCR_primer-R	GGCAACGGAAACAGTCACAT
protein_conc	4630	4951
WB_result	99.0	99.0
Ave_WB	99.0
WB_DONE_date	1/28/20
MW	49kd
IP	Rabbit / I
antibody_Cat#	PA5-31919	Lot# UA2701668D
Antibody DCC ID	ENCAB101UYP
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	8788	8789

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMYD3	Product_ID: PA5-31919 Lot_ID: UA2701668D Source: Thermo Fisher Target Name: SMYD3-human

Experiment Status

	BGHcLV20-35	BGHcLV20-36
Sample_ID	BGHcLV20-35	BGHcLV20-36
Sample Name
Sample Name	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-36
RBP	SMYD3	SMYD3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5823	5824

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-35	BGHcLV20-36
Sample #	73	74
Sample Name	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-36
Sample_Name_Alias
Index Well Position	C09	D09
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	332	309
Peak_Molarity	142.00	106.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/C9.png	DNA_Library_set45/set1/D9.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set45/set1/C9.png	RNA_Library_set45/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-35	BGHcLV20-36
RBP	SMYD3	SMYD3
Batch_ID	BGHcLV20	BGHcLV20
WB_result	99.000	99.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	847	848

Sequencing Information

	BGHcLV20-35	BGHcLV20-36
Sample_ID	BGHcLV20-35	BGHcLV20-36
Sample Name	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-36
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	84,207,090	77,719,238
total_aligned_reads	82,291,894	75,149,898
unique_aligned_reads	77,858,782	70,817,434
percent_uniqueAligned	0.92461	0.91120
correlation_replicates	0.993724	0.993724
spikein_reads	55,930	35,314
percent_spikeins	0.00066	0.00045
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	478	479

Data Submission Information

	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-36	BGHcLV20-36	BGHcLV20-36	BGHcLV20-36
ENCODE_alias	brenton-graveley:SMYD3-BGHcLV20	brenton-graveley:SMYD3-BGHcLV20-35	brenton-graveley:L-SMYD3-BGHcLV20-35	brenton-graveley:SMYD3-BGHcLV20-35_S67_R1_001.fastq.gz	brenton-graveley:SMYD3-BGHcLV20-35_S67_R2_001.fastq.gz	brenton-graveley:SMYD3-BGHcLV20-HepG2	brenton-graveley:SMYD3-BGHcLV20-36	brenton-graveley:L-SMYD3-BGHcLV20-36	brenton-graveley:SMYD3-BGHcLV20-36_S68_R1_001.fastq.gz	brenton-graveley:SMYD3-BGHcLV20-36_S68_R2_001.fastq.gz
ENCODE_accession	ENCSR989GNV	ENCBS310PBV	ENCLB062YJT	ENCFF666NLT	ENCFF612FHM	ENCSR284LYJ	ENCBS521JYS	ENCLB373KGK	ENCFF867UNS	ENCFF101QIC
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	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-35	BGHcLV20-36	BGHcLV20-36	BGHcLV20-36	BGHcLV20-36
Sample Name	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-35	SMYD3-BGHcLV20-36	SMYD3-BGHcLV20-36	SMYD3-BGHcLV20-36	SMYD3-BGHcLV20-36
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		SMYD3-BGHcLV20-35.pdf	L-SMYD3-BGHcLV20-35.pdf				SMYD3-BGHcLV20-36.pdf	L-SMYD3-BGHcLV20-36.pdf
ID	2088	2131	2201	2271	2341	7331	2132	2202	2272	2342

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
SMYD3-BGHcLV20-35_S67_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	478	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1324
SMYD3-BGHcLV20-35_S67_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	478	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1344
SMYD3-BGHcLV20-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	478					GRCh38	V40	SMYD3-BGHcLV20-35_S67_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGHcLV20-35_S67_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24865
SMYD3-BGHcLV20-35_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	478					GRCh38	V40	SMYD3-BGHcLV20-35_S67_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGHcLV20-35_S67_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24885
SMYD3-BGHcLV20-35_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	478					GRCh38	V40	SMYD3-BGHcLV20-35/Aligned.sortedByCoord.out.bam		ENCORE2	25935
SMYD3-BGHcLV20-35_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	478					GRCh38	V40	SMYD3-BGHcLV20-35/Aligned.sortedByCoord.out.bam		ENCORE2	25955
SMYD3-BGHcLV20-35_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	478					GRCh38	V40	SMYD3-BGHcLV20-35/Aligned.sortedByCoord.out.bam		ENCORE2	25975
SMYD3-BGHcLV20-35_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	478					GRCh38	V40	SMYD3-BGHcLV20-35/Aligned.sortedByCoord.out.bam		ENCORE2	25995
SMYD3-BGHcLV20-36_S68_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	479	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1325
SMYD3-BGHcLV20-36_S68_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	479	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1345
SMYD3-BGHcLV20-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	479					GRCh38	V40	SMYD3-BGHcLV20-36_S68_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGHcLV20-36_S68_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24866
SMYD3-BGHcLV20-36_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	479					GRCh38	V40	SMYD3-BGHcLV20-36_S68_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGHcLV20-36_S68_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24886
SMYD3-BGHcLV20-36_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	479					GRCh38	V40	SMYD3-BGHcLV20-36/Aligned.sortedByCoord.out.bam		ENCORE2	25936
SMYD3-BGHcLV20-36_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	479					GRCh38	V40	SMYD3-BGHcLV20-36/Aligned.sortedByCoord.out.bam		ENCORE2	25956
SMYD3-BGHcLV20-36_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	479					GRCh38	V40	SMYD3-BGHcLV20-36/Aligned.sortedByCoord.out.bam		ENCORE2	25976
SMYD3-BGHcLV20-36_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	479					GRCh38	V40	SMYD3-BGHcLV20-36/Aligned.sortedByCoord.out.bam		ENCORE2	25996