SCAF8 RNA-Seq in K562

General Information


RBP	SCAF8
Cell_Line	K562
Method	CRISPR
Exp_Name	SCAF8-BGKcLV33-K562
ENCODE_series_ID	ENCSR184MTJ
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR329UEC
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SCAF8-BGKcLV33-33
Rep2	SCAF8-BGKcLV33-34
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	95.7
Rep2_WB	98.3
Antibody Cat#	A303-981A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	901

Experiment Information (Status: Released)

	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-28	BGKcLV33-28	BGKcLV33-28
idx	1129	1208	1208	1130	1209	1209
TRCN#_or_BGC#	BGC#0000846	BGC#0000839	BGC#0000839	BGC#0000846	BGC#0000839	BGC#0000839
shRNA_or_gRNA_sequence	ATGTCGGGATTGTCGCACAA	CTCGGGCTGTCATCGCAACG	CTCGGGCTGTCATCGCAACG	ATGTCGGGATTGTCGCACAA	CTCGGGCTGTCATCGCAACG	CTCGGGCTGTCATCGCAACG
PAM	TGG	GGG	GGG	TGG	GGG	GGG
Name	SCAF8_97	SAMHD1_96	SAMHD1_96	SCAF8_97	SAMHD1_96	SAMHD1_96
Sample_ID	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-28	BGKcLV33-28	BGKcLV33-28
transduction_Date	12/7/21	2/22/22	2/22/22	12/7/21	2/22/22	2/22/22
days	D6	D6	D6	D6	D6	D6
RBP_name	SCAF8	SAMHD1	SAMHD1	SCAF8	SAMHD1	SAMHD1
qPCR_result		XX	XX		XX	XX
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	361	2034	2034	426	2124	2124
WB_result	69.0	86.7	62.0	73.3	76.4	72.0
Ave_WB	71.2	81.6	67.0
WB_DONE_date	2/4/22	3/2/22	2/3/22
MW	141kd	72kd	72kd
IP
antibody_Cat#	A301-036A	A303-690A	A303-691A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB434HZO	ENCAB065TLL		8/4/22	8/4/22
submitted_to_DCC_date		8/16/22	8/16/22
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action		Ready			Ready
Library_start_date		04/13/22			04/13/22
repeat_library
Note
ID	5269	5348	5350	5270	5349	5351

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAMHD1	Product_ID: A303-690A Lot_ID: 1 Source: Bethyl Labs Target Name: SAMHD1-human
SAMHD1	Product_ID: A303-691A Lot_ID: 1 Source: Bethyl Labs Target Name: SAMHD1-human

Experiment Status

	BGKcLV33-27	BGKcLV33-27	BGKcLV33-28	BGKcLV33-28
Sample_ID	BGKcLV33-27	BGKcLV33-27	BGKcLV33-28	BGKcLV33-28
Sample Name
Sample Name	SAMHD1-BGKcLV33-27		SAMHD1-BGKcLV33-28
RBP	SAMHD1	SCAF8	SAMHD1	SCAF8
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-10-28	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10649	10713	10650	10714

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-27	BGKcLV33-28
Sample #	19	20
Sample Name	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-28
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	285	289
Peak_Molarity	73.70	55.90
libSampleQC_DNA_Well	DNA_Library_set53/set1/C7.png	DNA_Library_set53/set1/D7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set53/set1/C3.png	RNA_Library_set53/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-27	BGKcLV33-28
RBP	SAMHD1	SAMHD1
Batch_ID	BGKcLV33	BGKcLV33
WB_result	86.700	76.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3280	3281

Sequencing Information

	BGKcLV33-27	BGKcLV33-28
Sample_ID	BGKcLV33-27	BGKcLV33-28
Sample Name	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-28
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	79,144,238	131,506,810
total_aligned_reads	69,992,622	120,041,934
unique_aligned_reads	63,983,290	109,660,882
percent_uniqueAligned	0.80844	0.83388
correlation_replicates	0.993447	0.993447
spikein_reads	5,680	9,780
percent_spikeins	0.00007	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2047	2048

Data Submission Information

	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-28	BGKcLV33-28	BGKcLV33-28	BGKcLV33-28
ENCODE_alias	brenton-graveley:SAMHD1-BGKcLV33	brenton-graveley:SAMHD1-BGKcLV33-27	brenton-graveley:L-SAMHD1-BGKcLV33-27	brenton-graveley:SAMHD1-BGKcLV33-27_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAMHD1-BGKcLV33-27_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAMHD1-BGKcLV33-K562	brenton-graveley:SAMHD1-BGKcLV33-28	brenton-graveley:L-SAMHD1-BGKcLV33-28	brenton-graveley:SAMHD1-BGKcLV33-28_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAMHD1-BGKcLV33-28_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR870EBU	ENCBS444BPA	ENCLB999WOD	ENCFF718NPB	ENCFF021LJS	ENCSR843GJZ	ENCBS617OXH	ENCLB478CAH	ENCFF215QBC	ENCFF858YRV
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	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-27	BGKcLV33-28	BGKcLV33-28	BGKcLV33-28	BGKcLV33-28
Sample Name	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-27	SAMHD1-BGKcLV33-28	SAMHD1-BGKcLV33-28	SAMHD1-BGKcLV33-28	SAMHD1-BGKcLV33-28
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
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		SAMHD1-BGKcLV33-27.pdf	L-SAMHD1-BGKcLV33-27.pdf				SAMHD1-BGKcLV33-28.pdf	L-SAMHD1-BGKcLV33-28.pdf
ID	7480	7569	7679	7789	7899	7969	7570	7680	7790	7900

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
SAMHD1-BGKcLV33-27_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2047	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6625
SAMHD1-BGKcLV33-27_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2047	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6681
SAMHD1-BGKcLV33-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2047					GRCh38	V40	SAMHD1-BGKcLV33-27_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGKcLV33-27_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18102
SAMHD1-BGKcLV33-27_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2047					GRCh38	V40	SAMHD1-BGKcLV33-27/Aligned.sortedByCoord.out.bam		ENCORE2	18158
SAMHD1-BGKcLV33-27_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2047					GRCh38	V40	SAMHD1-BGKcLV33-27/Aligned.sortedByCoord.out.bam		ENCORE2	18214
SAMHD1-BGKcLV33-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2047					GRCh38	V40	SAMHD1-BGKcLV33-27/Aligned.sortedByCoord.out.bam		ENCORE2	18270
SAMHD1-BGKcLV33-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2047					GRCh38	V40	SAMHD1-BGKcLV33-27/Aligned.sortedByCoord.out.bam		ENCORE2	18326
SAMHD1-BGKcLV33-27_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2047					GRCh38	V40	SAMHD1-BGKcLV33-27_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGKcLV33-27_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18382
SAMHD1-BGKcLV33-28_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2048	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6626
SAMHD1-BGKcLV33-28_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2048	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6682
SAMHD1-BGKcLV33-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2048					GRCh38	V40	SAMHD1-BGKcLV33-28_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGKcLV33-28_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18103
SAMHD1-BGKcLV33-28_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2048					GRCh38	V40	SAMHD1-BGKcLV33-28/Aligned.sortedByCoord.out.bam		ENCORE2	18159
SAMHD1-BGKcLV33-28_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2048					GRCh38	V40	SAMHD1-BGKcLV33-28/Aligned.sortedByCoord.out.bam		ENCORE2	18215
SAMHD1-BGKcLV33-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2048					GRCh38	V40	SAMHD1-BGKcLV33-28/Aligned.sortedByCoord.out.bam		ENCORE2	18271
SAMHD1-BGKcLV33-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2048					GRCh38	V40	SAMHD1-BGKcLV33-28/Aligned.sortedByCoord.out.bam		ENCORE2	18327
SAMHD1-BGKcLV33-28_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2048					GRCh38	V40	SAMHD1-BGKcLV33-28_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAMHD1-BGKcLV33-28_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18383