SUZ12 RNA-Seq in K562

General Information


RBP	SUZ12
Cell_Line	K562
Method	CRISPR
Exp_Name	SUZ12-BGKcLV17-K562
ENCODE_series_ID	ENCSR993SAX
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR682DZY
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	SUZ12-BGKcLV17-49
Rep2	SUZ12-BGKcLV17-50
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	54.7
Rep2_qPCR	51.7
Rep1_WB	69.7
Rep2_WB	65.4
Antibody Cat#	702490
Antibody Lot#	LOT#SG255323
Antibody DCC ID	ENCAB078IGL
Status	Released
Project	ENCODE4
ID	95

Experiment Information (Status: Released)

	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-50	BGKcLV17-50	BGKcLV17-50
idx	656	658	658	657	659	659
TRCN#_or_BGC#	BGC#0000392	BGC#0000392	BGC#0000392	BGC#0000392	BGC#0000392	BGC#0000392
shRNA_or_gRNA_sequence	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG
PAM	CGG	CGG	CGG	CGG	CGG	CGG
Name	SUZ12_58	SUZ12_58	SUZ12_58	SUZ12_58	SUZ12_58	SUZ12_58
Sample_ID	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-50	BGKcLV17-50	BGKcLV17-50
transduction_Date	7/2/19	7/2/19	7/2/19	7/2/19	7/2/19	7/2/19
days	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6
RBP_name	SUZ12	SUZ12	SUZ12	SUZ12	SUZ12	SUZ12
qPCR_result	54.7	54.7	54.7	51.7	51.7	51.7
Ave_qPCR	53.2	53.2	53.2
RT-qPCR_primer-F	AGTAGCCATGCAGGAAATGG	AGTAGCCATGCAGGAAATGG	AGTAGCCATGCAGGAAATGG
RT-qPCR_primer-R	ACTGCAACGTAGGTCCCTGA	ACTGCAACGTAGGTCCCTGA	ACTGCAACGTAGGTCCCTGA
protein_conc	5626	5626	5626	4917	4917	4917
WB_result	69.7	53.7	63.2	65.4	59.5	69.9421
Ave_WB	67.5	56.6	66.6
WB_DONE_date	8/26/19	7/22/19	10/12/22	WES	wes
MW	83kd	83kd	83kd
IP	Rabbit / I	Rabbit / I		Monoclonal	Oligoclona
antibody_Cat#	702490	711520	3737	LOT#SG255323	lot# SH256087	LOT # 8
Antibody DCC ID	ENCAB078IGL	ENCAB023NWH
submitted_to_DCC_date			1/9/24
Rep1_TPM	36.8	36.8	0	0	0	0
Rep2_TPM	40.4	40.4	0	0	0	0
Action	Ready			Ready
Library_start_date	12/05/19			12/05/19
repeat_library
Note
ID	4774	4776	4778	4775	4777	4779

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUZ12	Product_ID: 702490 Lot_ID: SG255323 Source: Thermo Fisher Target Name: SUZ12-human
SUZ12	Product_ID: 711520 Lot_ID: SH256087 Source: Thermo Fisher Target Name: SUZ12-human
SUZ12	Product_ID: 3737S Lot_ID: 8 Source: Cell Signaling Technology Target Name: SUZ12-human

Experiment Status

	BGKcLV17-49	BGKcLV17-50
Sample_ID	BGKcLV17-49	BGKcLV17-50
Sample Name
Sample Name	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-50
RBP	SUZ12	SUZ12
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5523	5524

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-49	BGKcLV17-50
Sample #	113	114
Sample Name	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-50
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	2-E2	2-F2
Tecan	40.75	30.64
Tecan_date	2019-12-16	2019-12-16
Size_bp	273	279
Peak_Molarity	22.10	30.00
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E10.png	DNA_Library_set43-44/set1/F10.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set43-44/set4/E5.png	RNA_Library_set43-44/set4/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-49	BGKcLV17-50
RBP	SUZ12	SUZ12
Batch_ID	BGKcLV17	BGKcLV17
WB_result	69.700	65.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	689	690

Sequencing Information

	BGKcLV17-49	BGKcLV17-50
Sample_ID	BGKcLV17-49	BGKcLV17-50
Sample Name	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-50
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	138,305,446	118,889,076
total_aligned_reads	136,715,230	117,629,666
unique_aligned_reads	123,880,978	106,805,016
percent_uniqueAligned	0.89571	0.89836
correlation_replicates	0.997144	0.997144
spikein_reads	43,248	42,620
percent_spikeins	0.00031	0.00036
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	195	196

Data Submission Information

	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-50	BGKcLV17-50	BGKcLV17-50	BGKcLV17-50
ENCODE_alias	brenton-graveley:SUZ12-BGKcLV17	brenton-graveley:SUZ12-BGKcLV17-49	brenton-graveley:L-SUZ12-BGKcLV17-49	brenton-graveley:SUZ12-BGKcLV17-49_S23_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SUZ12-BGKcLV17-49_S23_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SUZ12-BGKcLV17-K562	brenton-graveley:SUZ12-BGKcLV17-50	brenton-graveley:L-SUZ12-BGKcLV17-50	brenton-graveley:SUZ12-BGKcLV17-50_S24_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SUZ12-BGKcLV17-50_S24_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR682DZY	ENCBS159DJP	ENCLB194UJD	ENCFF539TDD	ENCFF500XLE	ENCSR993SAX	ENCBS930MOC	ENCLB999PPX	ENCFF648BHR	ENCFF491IAL
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	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-49	BGKcLV17-50	BGKcLV17-50	BGKcLV17-50	BGKcLV17-50
Sample Name	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-49	SUZ12-BGKcLV17-50	SUZ12-BGKcLV17-50	SUZ12-BGKcLV17-50	SUZ12-BGKcLV17-50
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		SUZ12-BGKcLV17-49.pdf	L-SUZ12-BGKcLV17-49.pdf				SUZ12-BGKcLV17-50.pdf	L-SUZ12-BGKcLV17-50.pdf
ID	81	242	408	710	740	7342	243	409	711	741

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
SUZ12-BGKcLV17-49_S23_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	195	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	297
SUZ12-BGKcLV17-49_S23_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	195	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	327
SUZ12-BGKcLV17-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	195					GRCh38	V40	SUZ12-BGKcLV17-49_S23_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGKcLV17-49_S23_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24693
SUZ12-BGKcLV17-49_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	195					GRCh38	V40	SUZ12-BGKcLV17-49/Aligned.sortedByCoord.out.bam		ENCORE2	24723
SUZ12-BGKcLV17-49_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	195					GRCh38	V40	SUZ12-BGKcLV17-49/Aligned.sortedByCoord.out.bam		ENCORE2	24753
SUZ12-BGKcLV17-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	195					GRCh38	V40	SUZ12-BGKcLV17-49/Aligned.sortedByCoord.out.bam		ENCORE2	24783
SUZ12-BGKcLV17-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	195					GRCh38	V40	SUZ12-BGKcLV17-49/Aligned.sortedByCoord.out.bam		ENCORE2	24813
SUZ12-BGKcLV17-49_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	195					GRCh38	V40	SUZ12-BGKcLV17-49_S23_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGKcLV17-49_S23_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24843
SUZ12-BGKcLV17-50_S24_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	196	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	298
SUZ12-BGKcLV17-50_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	196	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	328
SUZ12-BGKcLV17-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	196					GRCh38	V40	SUZ12-BGKcLV17-50_S24_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGKcLV17-50_S24_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24694
SUZ12-BGKcLV17-50_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	196					GRCh38	V40	SUZ12-BGKcLV17-50/Aligned.sortedByCoord.out.bam		ENCORE2	24724
SUZ12-BGKcLV17-50_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	196					GRCh38	V40	SUZ12-BGKcLV17-50/Aligned.sortedByCoord.out.bam		ENCORE2	24754
SUZ12-BGKcLV17-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	196					GRCh38	V40	SUZ12-BGKcLV17-50/Aligned.sortedByCoord.out.bam		ENCORE2	24784
SUZ12-BGKcLV17-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	196					GRCh38	V40	SUZ12-BGKcLV17-50/Aligned.sortedByCoord.out.bam		ENCORE2	24814
SUZ12-BGKcLV17-50_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	196					GRCh38	V40	SUZ12-BGKcLV17-50_S24_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGKcLV17-50_S24_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24844