SPAG9 RNA-Seq in HepG2

General Information


RBP	SPAG9
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SPAG9-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR210JCP
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR293VAR
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SPAG9-BGHcLV31-63
Rep2	SPAG9-BGHcLV31-64
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	48.9
Rep2_qPCR	58.0
Rep1_WB	83.7
Rep2_WB	72.2
Antibody Cat#	A300-336A
Antibody Lot#	LOT #4
Antibody DCC ID	ENCAB002WNS
Status	Submitted
Project	ENCODE4
ID	931

Experiment Information (Status: Released)

	BGHcLV31-63	BGHcLV31-64
idx	983	984
TRCN#_or_BGC#	BGC#0000881	BGC#0000881
shRNA_or_gRNA_sequence	TATCGGGCGCTATGACGAGG	TATCGGGCGCTATGACGAGG
PAM	AGG	AGG
Name	SPAG9_98	SPAG9_98
Sample_ID	BGHcLV31-63	BGHcLV31-64
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SPAG9	SPAG9
qPCR_result	48.9	58.0
Ave_qPCR	53.5
RT-qPCR_primer-F	cacccttgcaatctttcaca
RT-qPCR_primer-R	agtcatgcaacggatggaat
protein_conc	3583	3776
WB_result	83.7	72.2
Ave_WB	78.0
WB_DONE_date	10/18/21	JESS
MW	146kd
IP
antibody_Cat#	A300-336A	LOT #4
Antibody DCC ID	ENCAB002WNS
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7162	7163

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SPAG9	Product_ID: A300-336A Lot_ID: 4 Source: Bethyl Labs Target Name: SPAG9-human

Experiment Status

	BGHcLV31-63	BGHcLV31-64
Sample_ID	BGHcLV31-63	BGHcLV31-64
Sample Name
Sample Name	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-64
RBP	SPAG9	SPAG9
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10317	10318

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-63	BGHcLV31-64
Sample #	31	32
Sample Name	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-64
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	287	278
Peak_Molarity	75.00	64.50
libSampleQC_DNA_Well	DNA_Library_set52/set1/G11.png	DNA_Library_set52/set1/H11.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set52/set1/G4.png	RNA_Library_set52/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-63	BGHcLV31-64
RBP	SPAG9	SPAG9
Batch_ID	BGHcLV31	BGHcLV31
WB_result	83.700	72.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3208	3209

Sequencing Information

	BGHcLV31-63	BGHcLV31-64
Sample_ID	BGHcLV31-63	BGHcLV31-64
Sample Name	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-64
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	70,469,288	107,451,710
total_aligned_reads	63,310,766	96,124,946
unique_aligned_reads	59,622,176	90,431,838
percent_uniqueAligned	0.84607	0.84160
correlation_replicates	0.987883	0.987883
spikein_reads	2,572	5,216
percent_spikeins	0.00004	0.00005
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2005	2006

Data Submission Information

	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-64	BGHcLV31-64	BGHcLV31-64	BGHcLV31-64
ENCODE_alias	brenton-graveley:SPAG9-BGHcLV31	brenton-graveley:SPAG9-BGHcLV31-63	brenton-graveley:L-SPAG9-BGHcLV31-63	brenton-graveley:SPAG9-BGHcLV31-63_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPAG9-BGHcLV31-63_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPAG9-BGHcLV31-HepG2	brenton-graveley:SPAG9-BGHcLV31-64	brenton-graveley:L-SPAG9-BGHcLV31-64	brenton-graveley:SPAG9-BGHcLV31-64_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPAG9-BGHcLV31-64_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR293VAR	ENCBS657JNU	ENCLB100TVZ	ENCFF373LUX	ENCFF342WBP	ENCSR210JCP	ENCBS558TFT	ENCLB297GIP	ENCFF929XDN	ENCFF128XLV
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	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-63	BGHcLV31-64	BGHcLV31-64	BGHcLV31-64	BGHcLV31-64
Sample Name	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-63	SPAG9-BGHcLV31-64	SPAG9-BGHcLV31-64	SPAG9-BGHcLV31-64	SPAG9-BGHcLV31-64
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		SPAG9-BGHcLV31-63.pdf	L-SPAG9-BGHcLV31-63.pdf				SPAG9-BGHcLV31-64.pdf	L-SPAG9-BGHcLV31-64.pdf
ID	7459	7529	7637	7747	7857	7951	7530	7638	7748	7858

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
SPAG9-BGHcLV31-63_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2005	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6553
SPAG9-BGHcLV31-63_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2005	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6607
SPAG9-BGHcLV31-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2005					GRCh38	V40	SPAG9-BGHcLV31-63_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGHcLV31-63_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18474
SPAG9-BGHcLV31-63_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2005					GRCh38	V40	SPAG9-BGHcLV31-63/Aligned.sortedByCoord.out.bam		ENCORE2	18528
SPAG9-BGHcLV31-63_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2005					GRCh38	V40	SPAG9-BGHcLV31-63/Aligned.sortedByCoord.out.bam		ENCORE2	18582
SPAG9-BGHcLV31-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2005					GRCh38	V40	SPAG9-BGHcLV31-63/Aligned.sortedByCoord.out.bam		ENCORE2	18636
SPAG9-BGHcLV31-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2005					GRCh38	V40	SPAG9-BGHcLV31-63/Aligned.sortedByCoord.out.bam		ENCORE2	18690
SPAG9-BGHcLV31-63_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2005					GRCh38	V40	SPAG9-BGHcLV31-63_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGHcLV31-63_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18744
SPAG9-BGHcLV31-64_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2006	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6554
SPAG9-BGHcLV31-64_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2006	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6608
SPAG9-BGHcLV31-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2006					GRCh38	V40	SPAG9-BGHcLV31-64_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGHcLV31-64_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18475
SPAG9-BGHcLV31-64_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2006					GRCh38	V40	SPAG9-BGHcLV31-64/Aligned.sortedByCoord.out.bam		ENCORE2	18529
SPAG9-BGHcLV31-64_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2006					GRCh38	V40	SPAG9-BGHcLV31-64/Aligned.sortedByCoord.out.bam		ENCORE2	18583
SPAG9-BGHcLV31-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2006					GRCh38	V40	SPAG9-BGHcLV31-64/Aligned.sortedByCoord.out.bam		ENCORE2	18637
SPAG9-BGHcLV31-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2006					GRCh38	V40	SPAG9-BGHcLV31-64/Aligned.sortedByCoord.out.bam		ENCORE2	18691
SPAG9-BGHcLV31-64_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2006					GRCh38	V40	SPAG9-BGHcLV31-64_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGHcLV31-64_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18745