SCAF8 RNA-Seq in HepG2

General Information


RBP	SCAF8
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SCAF8-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR648NMQ
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR330VES
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SCAF8-BGHcLV31-29
Rep2	SCAF8-BGHcLV31-30
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	22.8
Rep2_qPCR	23.5
Rep1_WB	86.7
Rep2_WB	79.1
Antibody Cat#	A301-036A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB569CKW
Status	Submitted
Project	ENCODE4
ID	926

Experiment Information (Status: Released)

	BGHcLV31-29	BGHcLV31-30
idx	947	948
TRCN#_or_BGC#	BGC#0000846	BGC#0000846
shRNA_or_gRNA_sequence	ATGTCGGGATTGTCGCACAA	ATGTCGGGATTGTCGCACAA
PAM	TGG	TGG
Name	SCAF8_97	SCAF8_97
Sample_ID	BGHcLV31-29	BGHcLV31-30
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SCAF8	SCAF8
qPCR_result	22.8	23.5
Ave_qPCR	23.2
RT-qPCR_primer-F	gttttggccagcactaccac
RT-qPCR_primer-R	tacccacggatcaggtaagc
protein_conc	3936	3947
WB_result	86.7	79.1
Ave_WB	82.9
WB_DONE_date	11/12/21
MW	141kd
IP
antibody_Cat#	A301-036A	LOT #1
Antibody DCC ID	ENCAB569CKW
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	7126	7127

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SCAF8	Product_ID: A301-036A Lot_ID: 1 Source: Bethyl Labs Target Name: SCAF8-human

Experiment Status

	BGHcLV31-29	BGHcLV31-30
Sample_ID	BGHcLV31-29	BGHcLV31-30
Sample Name
Sample Name	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-30
RBP	SCAF8	SCAF8
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10307	10308

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-29	BGHcLV31-30
Sample #	21	22
Sample Name	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-30
Sample_Name_Alias
Index Well Position	E03	F03
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	281	286
Peak_Molarity	73.40	77.60
libSampleQC_DNA_Well	DNA_Library_set52/set1/E10.png	DNA_Library_set52/set1/F10.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set52/set1/E3.png	RNA_Library_set52/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-29	BGHcLV31-30
RBP	SCAF8	SCAF8
Batch_ID	BGHcLV31	BGHcLV31
WB_result	86.700	79.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3198	3199

Sequencing Information

	BGHcLV31-29	BGHcLV31-30
Sample_ID	BGHcLV31-29	BGHcLV31-30
Sample Name	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-30
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	136,431,822	134,247,464
total_aligned_reads	120,866,410	121,049,642
unique_aligned_reads	113,536,918	114,062,290
percent_uniqueAligned	0.83219	0.84964
correlation_replicates	0.999269	0.999269
spikein_reads	7,648	8,326
percent_spikeins	0.00006	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1995	1996

Data Submission Information

	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-30	BGHcLV31-30	BGHcLV31-30	BGHcLV31-30
ENCODE_alias	brenton-graveley:SCAF8-BGHcLV31	brenton-graveley:SCAF8-BGHcLV31-29	brenton-graveley:L-SCAF8-BGHcLV31-29	brenton-graveley:SCAF8-BGHcLV31-29_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SCAF8-BGHcLV31-29_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SCAF8-BGHcLV31-HepG2	brenton-graveley:SCAF8-BGHcLV31-30	brenton-graveley:L-SCAF8-BGHcLV31-30	brenton-graveley:SCAF8-BGHcLV31-30_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SCAF8-BGHcLV31-30_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR330VES	ENCBS320ZIE	ENCLB580AXP	ENCFF252HDU	ENCFF019JLK	ENCSR648NMQ	ENCBS320KXQ	ENCLB080DMV	ENCFF640XUZ	ENCFF111KIY
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	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-29	BGHcLV31-30	BGHcLV31-30	BGHcLV31-30	BGHcLV31-30
Sample Name	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-29	SCAF8-BGHcLV31-30	SCAF8-BGHcLV31-30	SCAF8-BGHcLV31-30	SCAF8-BGHcLV31-30
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		SCAF8-BGHcLV31-29.pdf	L-SCAF8-BGHcLV31-29.pdf				SCAF8-BGHcLV31-30.pdf	L-SCAF8-BGHcLV31-30.pdf
ID	7454	7519	7627	7737	7847	7946	7520	7628	7738	7848

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
SCAF8-BGHcLV31-29_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1995	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	6541
SCAF8-BGHcLV31-29_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1995	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	6595
SCAF8-BGHcLV31-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1995					GRCh38	V40	SCAF8-BGHcLV31-29_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGHcLV31-29_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18462
SCAF8-BGHcLV31-29_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	1995					GRCh38	V40	SCAF8-BGHcLV31-29/Aligned.sortedByCoord.out.bam		ENCORE2	18516
SCAF8-BGHcLV31-29_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	1995					GRCh38	V40	SCAF8-BGHcLV31-29/Aligned.sortedByCoord.out.bam		ENCORE2	18570
SCAF8-BGHcLV31-29_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	1995					GRCh38	V40	SCAF8-BGHcLV31-29/Aligned.sortedByCoord.out.bam		ENCORE2	18624
SCAF8-BGHcLV31-29_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	1995					GRCh38	V40	SCAF8-BGHcLV31-29/Aligned.sortedByCoord.out.bam		ENCORE2	18678
SCAF8-BGHcLV31-29_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1995					GRCh38	V40	SCAF8-BGHcLV31-29_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGHcLV31-29_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18732
SCAF8-BGHcLV31-30_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1996	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	6542
SCAF8-BGHcLV31-30_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1996	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	6596
SCAF8-BGHcLV31-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1996					GRCh38	V40	SCAF8-BGHcLV31-30_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGHcLV31-30_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18463
SCAF8-BGHcLV31-30_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	1996					GRCh38	V40	SCAF8-BGHcLV31-30/Aligned.sortedByCoord.out.bam		ENCORE2	18517
SCAF8-BGHcLV31-30_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	1996					GRCh38	V40	SCAF8-BGHcLV31-30/Aligned.sortedByCoord.out.bam		ENCORE2	18571
SCAF8-BGHcLV31-30_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	1996					GRCh38	V40	SCAF8-BGHcLV31-30/Aligned.sortedByCoord.out.bam		ENCORE2	18625
SCAF8-BGHcLV31-30_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	1996					GRCh38	V40	SCAF8-BGHcLV31-30/Aligned.sortedByCoord.out.bam		ENCORE2	18679
SCAF8-BGHcLV31-30_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1996					GRCh38	V40	SCAF8-BGHcLV31-30_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BGHcLV31-30_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18733