SUZ12 RNA-Seq in HepG2

General Information


RBP	SUZ12
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SUZ12-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR629NUQ
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR380LKB
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	SUZ12-BGHcLV18-49
Rep2	SUZ12-BGHcLV18-50
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	31.4
Rep2_qPCR	34.5
Rep1_WB	68.4
Rep2_WB	63.4
Antibody Cat#	702490
Antibody Lot#	LOT#SG255323
Antibody DCC ID	ENCAB078IGL
Status	Released
Project	ENCODE4
ID	120

Experiment Information (Status: Released)

	BGHcLV18-49	BGHcLV18-49	BGHcLV18-50	BGHcLV18-50
idx	542	544	543	545
TRCN#_or_BGC#	BGC#0000392	BGC#0000392	BGC#0000392	BGC#0000392
shRNA_or_gRNA_sequence	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG	GCTTCGGGCGGCAAATCCGG
PAM	CGG	CGG	CGG	CGG
Name	SUZ12_58	SUZ12_58	SUZ12_58	SUZ12_58
Sample_ID	BGHcLV18-49	BGHcLV18-49	BGHcLV18-50	BGHcLV18-50
transduction_Date	8/13/19	8/13/19	8/13/19	8/13/19
days	D6	D6	D6	D6
RBP_name	SUZ12	SUZ12	SUZ12	SUZ12
qPCR_result	31.4	31.4	34.5	34.5
Ave_qPCR	33.0	33.0
RT-qPCR_primer-F	AGTAGCCATGCAGGAAATGG	AGTAGCCATGCAGGAAATGG
RT-qPCR_primer-R	ACTGCAACGTAGGTCCCTGA	ACTGCAACGTAGGTCCCTGA
protein_conc	3896	3896	4215	4215
WB_result	68.4	64.1	63.4	58.2
Ave_WB	65.9	61.2
WB_DONE_date	8/22/19	8/22/19	wes	wes
MW	83kd	83kd
IP	Rabbit / I	Rabbit / I	Monoclonal	Oligoclona
antibody_Cat#	702490	711520	LOT#SG255323	lot# SH256087
Antibody DCC ID	ENCAB078IGL	ENCAB023NWH
submitted_to_DCC_date
Rep1_TPM	13	13	0	0
Rep2_TPM	25	25	0	0
Action	Ready		Ready
Library_start_date	12/11/19		12/11/19
repeat_library
Note
ID	6697	6699	6698	6700

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

Experiment Status

	BGHcLV18-49	BGHcLV18-50
Sample_ID	BGHcLV18-49	BGHcLV18-50
Sample Name
Sample Name	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-50
RBP	SUZ12	SUZ12
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5657	5658

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-49	BGHcLV18-50
Sample #	163	164
Sample Name	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-50
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	5-G2	5-H2
Tecan	19.81	38.64
Tecan_date	2019-12-16	2019-12-16
Size_bp	285	284
Peak_Molarity	33.00	29.30
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A10.png	DNA_Library_set43-44/set2/B10.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set43-44/set4/E11.png	RNA_Library_set43-44/set4/F11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-49	BGHcLV18-50
RBP	SUZ12	SUZ12
Batch_ID	BGHcLV18	BGHcLV18
WB_result	68.400	63.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	739	740

Sequencing Information

	BGHcLV18-49	BGHcLV18-50
Sample_ID	BGHcLV18-49	BGHcLV18-50
Sample Name	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-50
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	136,634,216	138,309,088
total_aligned_reads	132,997,482	135,152,484
unique_aligned_reads	124,574,582	126,610,878
percent_uniqueAligned	0.91174	0.91542
correlation_replicates	0.991987	0.991987
spikein_reads	284,788	296,246
percent_spikeins	0.00208	0.00214
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	245	246

Data Submission Information

	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-50	BGHcLV18-50	BGHcLV18-50	BGHcLV18-50
ENCODE_alias	brenton-graveley:SUZ12-BGHcLV18	brenton-graveley:SUZ12-BGHcLV18-49	brenton-graveley:L-SUZ12-BGHcLV18-49	brenton-graveley:SUZ12-BGHcLV18-49_S75_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SUZ12-BGHcLV18-49_S75_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SUZ12-BGHcLV18-HepG2	brenton-graveley:SUZ12-BGHcLV18-50	brenton-graveley:L-SUZ12-BGHcLV18-50	brenton-graveley:SUZ12-BGHcLV18-50_S76_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SUZ12-BGHcLV18-50_S76_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR380LKB	ENCBS180VCE	ENCLB914KCH	ENCFF562LRE	ENCFF307TWG	ENCSR629NUQ	ENCBS215AZA	ENCLB472CXH	ENCFF681PDS	ENCFF521MHV
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	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-49	BGHcLV18-50	BGHcLV18-50	BGHcLV18-50	BGHcLV18-50
Sample Name	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-49	SUZ12-BGHcLV18-50	SUZ12-BGHcLV18-50	SUZ12-BGHcLV18-50	SUZ12-BGHcLV18-50
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		SUZ12-BGHcLV18-49.pdf	L-SUZ12-BGHcLV18-49.pdf				SUZ12-BGHcLV18-50.pdf	L-SUZ12-BGHcLV18-50.pdf
ID	67	214	380	630	682	7341	215	381	631	683

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-BGHcLV18-49_S75_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	245	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	217
SUZ12-BGHcLV18-49_S75_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	245	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	269
SUZ12-BGHcLV18-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	245					GRCh38	V40	SUZ12-BGHcLV18-49_S75_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGHcLV18-49_S75_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24937
SUZ12-BGHcLV18-49_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	245					GRCh38	V40	SUZ12-BGHcLV18-49/Aligned.sortedByCoord.out.bam		ENCORE2	24989
SUZ12-BGHcLV18-49_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	245					GRCh38	V40	SUZ12-BGHcLV18-49/Aligned.sortedByCoord.out.bam		ENCORE2	25041
SUZ12-BGHcLV18-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	245					GRCh38	V40	SUZ12-BGHcLV18-49/Aligned.sortedByCoord.out.bam		ENCORE2	25093
SUZ12-BGHcLV18-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	245					GRCh38	V40	SUZ12-BGHcLV18-49/Aligned.sortedByCoord.out.bam		ENCORE2	25145
SUZ12-BGHcLV18-49_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	245					GRCh38	V40	SUZ12-BGHcLV18-49_S75_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGHcLV18-49_S75_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25197
SUZ12-BGHcLV18-50_S76_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	246	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	218
SUZ12-BGHcLV18-50_S76_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	246	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	270
SUZ12-BGHcLV18-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	246					GRCh38	V40	SUZ12-BGHcLV18-50_S76_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGHcLV18-50_S76_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24938
SUZ12-BGHcLV18-50_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	246					GRCh38	V40	SUZ12-BGHcLV18-50/Aligned.sortedByCoord.out.bam		ENCORE2	24990
SUZ12-BGHcLV18-50_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	246					GRCh38	V40	SUZ12-BGHcLV18-50/Aligned.sortedByCoord.out.bam		ENCORE2	25042
SUZ12-BGHcLV18-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	246					GRCh38	V40	SUZ12-BGHcLV18-50/Aligned.sortedByCoord.out.bam		ENCORE2	25094
SUZ12-BGHcLV18-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	246					GRCh38	V40	SUZ12-BGHcLV18-50/Aligned.sortedByCoord.out.bam		ENCORE2	25146
SUZ12-BGHcLV18-50_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	246					GRCh38	V40	SUZ12-BGHcLV18-50_S76_R1_001.filtered.trimmed.paired.fastq.gz,SUZ12-BGHcLV18-50_S76_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25198