SMYD3 RNA-Seq in K562

General Information


RBP	SMYD3
Cell_Line	K562
Method	CRISPR
Exp_Name	SMYD3-BGKcLV19-K562
ENCODE_series_ID	ENCSR441UTQ
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR775USN
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	SMYD3-BGKcLV19-51
Rep2	SMYD3-BGKcLV19-52
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	31.23
Rep2_qPCR	45.08
Rep1_WB	91.4
Rep2_WB	90.6
Antibody Cat#	PA5-31919
Antibody Lot#	Lot# UA2701668D
Antibody DCC ID	ENCAB101UYP
Status	Released
Project	ENCODE4
ID	60

Experiment Information (Status: Released)

	BGKcLV19-51	BGKcLV19-52
idx	725	726
TRCN#_or_BGC#	BGC#0000430	BGC#0000430
shRNA_or_gRNA_sequence	GCGAGCAGTCCGAGACATCG	GCGAGCAGTCCGAGACATCG
PAM	AGG	AGG
Name	SMYD3_95	SMYD3_95
Sample_ID	BGKcLV19-51	BGKcLV19-52
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	SMYD3	SMYD3
qPCR_result	31.23	45.08
Ave_qPCR
RT-qPCR_primer-F	AGACATCGAGGTGGGAGAGG
RT-qPCR_primer-R	GGCAACGGAAACAGTCACAT
protein_conc	3813	3818
WB_result	91.4	90.6
Ave_WB	91.0
WB_DONE_date	11/20/19
MW	49kd
IP	Rabbit / I
antibody_Cat#	PA5-31919	Lot# UA2701668D
Antibody DCC ID	ENCAB101UYP
submitted_to_DCC_date	11/16/20
Rep1_TPM	101.8	0
Rep2_TPM	103.9	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4845	4846

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV19-51	BGKcLV19-52
Sample_ID	BGKcLV19-51	BGKcLV19-52
Sample Name
Sample Name	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-52
RBP	SMYD3	SMYD3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5713	5714

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-51	BGKcLV19-52
Sample #	27	28
Sample Name	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-52
Sample_Name_Alias
Index Well Position	E03	F03
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	310	306
Peak_Molarity	306.00	232.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E3.png	DNA_Library_set45/set1/F3.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set45/set1/E3.png	RNA_Library_set45/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-51	BGKcLV19-52
RBP	SMYD3	SMYD3
Batch_ID	BGKcLV19	BGKcLV19
WB_result	91.400	90.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	801	802

Sequencing Information

	BGKcLV19-51	BGKcLV19-52
Sample_ID	BGKcLV19-51	BGKcLV19-52
Sample Name	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-52
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	170,755,606	206,716,210
total_aligned_reads	160,495,296	193,442,428
unique_aligned_reads	146,460,924	176,504,242
percent_uniqueAligned	0.85772	0.85385
correlation_replicates	0.992167	0.992167
spikein_reads	91,094	99,740
percent_spikeins	0.00053	0.00048
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	432	433

Data Submission Information

	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-52	BGKcLV19-52	BGKcLV19-52	BGKcLV19-52
ENCODE_alias	brenton-graveley:SMYD3-BGKcLV19	brenton-graveley:SMYD3-BGKcLV19-51	brenton-graveley:L-SMYD3-BGKcLV19-51	brenton-graveley:SMYD3-BGKcLV19-51_S21_R1_001.fastq.gz	brenton-graveley:SMYD3-BGKcLV19-51_S21_R2_001.fastq.gz	brenton-graveley:SMYD3-BGKcLV19-K562	brenton-graveley:SMYD3-BGKcLV19-52	brenton-graveley:L-SMYD3-BGKcLV19-52	brenton-graveley:SMYD3-BGKcLV19-52_S22_R1_001.fastq.gz	brenton-graveley:SMYD3-BGKcLV19-52_S22_R2_001.fastq.gz
ENCODE_accession	ENCSR775USN	ENCBS689KXA	ENCLB028MCJ	ENCFF377AID	ENCFF106VYU	ENCSR441UTQ	ENCBS686RDU	ENCLB602PPG	ENCFF307GDU	ENCFF251QLL
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	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-51	BGKcLV19-52	BGKcLV19-52	BGKcLV19-52	BGKcLV19-52
Sample Name	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-51	SMYD3-BGKcLV19-52	SMYD3-BGKcLV19-52	SMYD3-BGKcLV19-52	SMYD3-BGKcLV19-52
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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
			LV45K_library_protocol					LV45K_library_protocol
protocol_URL			L-SMYD3-BGKcLV19-51.pdf					L-SMYD3-BGKcLV19-52.pdf
ID	2100	2155	2225	2295	2365	7332	2156	2226	2296	2366

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-BGKcLV19-51_S21_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	432	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1254
SMYD3-BGKcLV19-51_S21_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	432	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1304
SMYD3-BGKcLV19-51_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	432					GRCh38	V40	SMYD3-BGKcLV19-51_S21_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGKcLV19-51_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25247
SMYD3-BGKcLV19-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	432					GRCh38	V40	SMYD3-BGKcLV19-51_S21_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGKcLV19-51_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27201
SMYD3-BGKcLV19-51_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	432					GRCh38	V40	SMYD3-BGKcLV19-51/Aligned.sortedByCoord.out.bam		ENCORE2	27251
SMYD3-BGKcLV19-51_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	432					GRCh38	V40	SMYD3-BGKcLV19-51/Aligned.sortedByCoord.out.bam		ENCORE2	27301
SMYD3-BGKcLV19-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	432					GRCh38	V40	SMYD3-BGKcLV19-51/Aligned.sortedByCoord.out.bam		ENCORE2	27351
SMYD3-BGKcLV19-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	432					GRCh38	V40	SMYD3-BGKcLV19-51/Aligned.sortedByCoord.out.bam		ENCORE2	27401
SMYD3-BGKcLV19-52_S22_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	433	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1255
SMYD3-BGKcLV19-52_S22_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	433	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1305
SMYD3-BGKcLV19-52_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	433					GRCh38	V40	SMYD3-BGKcLV19-52_S22_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGKcLV19-52_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25248
SMYD3-BGKcLV19-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	433					GRCh38	V40	SMYD3-BGKcLV19-52_S22_R1_001.filtered.trimmed.paired.fastq.gz,SMYD3-BGKcLV19-52_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27202
SMYD3-BGKcLV19-52_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	433					GRCh38	V40	SMYD3-BGKcLV19-52/Aligned.sortedByCoord.out.bam		ENCORE2	27252
SMYD3-BGKcLV19-52_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	433					GRCh38	V40	SMYD3-BGKcLV19-52/Aligned.sortedByCoord.out.bam		ENCORE2	27302
SMYD3-BGKcLV19-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	433					GRCh38	V40	SMYD3-BGKcLV19-52/Aligned.sortedByCoord.out.bam		ENCORE2	27352
SMYD3-BGKcLV19-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	433					GRCh38	V40	SMYD3-BGKcLV19-52/Aligned.sortedByCoord.out.bam		ENCORE2	27402