SF3A1 RNA-Seq in K562

General Information


RBP	SF3A1
Cell_Line	K562
Method	CRISPR
Exp_Name	SF3A1-BGKcLV17-K562
ENCODE_series_ID	ENCSR644JZK
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR547ICR
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	SF3A1-BGKcLV17-45
Rep2	SF3A1-BGKcLV17-46
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	34.0
Rep2_qPCR	37.9
Rep1_WB	76.8
Rep2_WB	77.378703
Antibody Cat#	A301-601A
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB549NKF
Status	Released
Project	ENCODE4
ID	93

Experiment Information (Status: Released)

	BGKcLV17-45	BGKcLV17-46
idx	652	653
TRCN#_or_BGC#	BGC#0000413	BGC#0000413
shRNA_or_gRNA_sequence	CATGCCGGCCGGACCCGTGC	CATGCCGGCCGGACCCGTGC
PAM	AGG	AGG
Name	SF3A1_94	SF3A1_94
Sample_ID	BGKcLV17-45	BGKcLV17-46
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	SF3A1	SF3A1
qPCR_result	34.0	37.9
Ave_qPCR	36.0
RT-qPCR_primer-F	ACCCTCCTCCAGAGGTCAGA
RT-qPCR_primer-R	TGGGGTTGTTGATCTCGTTC
protein_conc	5764	5491
WB_result	76.8	77.378703
Ave_WB	77.1
WB_DONE_date	8/29/19	WES
MW	89KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	A301-601A	lot #1
Antibody DCC ID	ENCAB549NKF
submitted_to_DCC_date	8/20/19
Rep1_TPM	80.4	0
Rep2_TPM	77.8	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4770	4771

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3A1	Product_ID: A301-601A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3A1-human

Experiment Status

	BGKcLV17-45	BGKcLV17-46
Sample_ID	BGKcLV17-45	BGKcLV17-46
Sample Name
Sample Name	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-46
RBP	SF3A1	SF3A1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5519	5520

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-45	BGKcLV17-46
Sample #	109	110
Sample Name	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-46
Sample_Name_Alias
Index Well Position	A02	B02
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-A2	2-B2
Tecan	21.29	37.88
Tecan_date	2019-12-16	2019-12-16
Size_bp	277	271
Peak_Molarity	29.80	27.90
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A10.png	DNA_Library_set43-44/set1/B10.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_set43-44/set4/A5.png	RNA_Library_set43-44/set4/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-45	BGKcLV17-46
RBP	SF3A1	SF3A1
Batch_ID	BGKcLV17	BGKcLV17
WB_result	76.800	77.379
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	685	686

Sequencing Information

	BGKcLV17-45	BGKcLV17-46
Sample_ID	BGKcLV17-45	BGKcLV17-46
Sample Name	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-46
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	122,123,632	362,556,486
total_aligned_reads	116,019,092	343,736,014
unique_aligned_reads	105,519,012	310,374,006
percent_uniqueAligned	0.86403	0.85607
correlation_replicates	0.998862	0.998862
spikein_reads	35,420	141,848
percent_spikeins	0.00029	0.00039
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	191	192

Data Submission Information

	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-46	BGKcLV17-46	BGKcLV17-46	BGKcLV17-46
ENCODE_alias	brenton-graveley:SF3A1-BGKcLV17	brenton-graveley:SF3A1-BGKcLV17-45	brenton-graveley:L-SF3A1-BGKcLV17-45	brenton-graveley:SF3A1-BGKcLV17-45_S19_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A1-BGKcLV17-45_S19_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A1-BGKcLV17-K562	brenton-graveley:SF3A1-BGKcLV17-46	brenton-graveley:L-SF3A1-BGKcLV17-46	brenton-graveley:SF3A1-BGKcLV17-46_S20_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A1-BGKcLV17-46_S20_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR547ICR	ENCBS534HNG	ENCLB451MES	ENCFF903QKH	ENCFF625DEE	ENCSR644JZK	ENCBS668GOX	ENCLB572DMW	ENCFF916IRV	ENCFF256EKE
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	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-45	BGKcLV17-46	BGKcLV17-46	BGKcLV17-46	BGKcLV17-46
Sample Name	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-45	SF3A1-BGKcLV17-46	SF3A1-BGKcLV17-46	SF3A1-BGKcLV17-46	SF3A1-BGKcLV17-46
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		SF3A1-BGKcLV17-45.pdf	L-SF3A1-BGKcLV17-45.pdf				SF3A1-BGKcLV17-46.pdf	L-SF3A1-BGKcLV17-46.pdf
ID	79	238	404	706	736	7321	239	405	707	737

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
SF3A1-BGKcLV17-45_S19_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	191	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	293
SF3A1-BGKcLV17-45_S19_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	191	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	323
SF3A1-BGKcLV17-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	191					GRCh38	V40	SF3A1-BGKcLV17-45_S19_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGKcLV17-45_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24689
SF3A1-BGKcLV17-45_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	191					GRCh38	V40	SF3A1-BGKcLV17-45/Aligned.sortedByCoord.out.bam		ENCORE2	24719
SF3A1-BGKcLV17-45_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	191					GRCh38	V40	SF3A1-BGKcLV17-45/Aligned.sortedByCoord.out.bam		ENCORE2	24749
SF3A1-BGKcLV17-45_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	191					GRCh38	V40	SF3A1-BGKcLV17-45/Aligned.sortedByCoord.out.bam		ENCORE2	24779
SF3A1-BGKcLV17-45_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	191					GRCh38	V40	SF3A1-BGKcLV17-45/Aligned.sortedByCoord.out.bam		ENCORE2	24809
SF3A1-BGKcLV17-45_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	191					GRCh38	V40	SF3A1-BGKcLV17-45_S19_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGKcLV17-45_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24839
SF3A1-BGKcLV17-46_S20_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	192	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	294
SF3A1-BGKcLV17-46_S20_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	192	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	324
SF3A1-BGKcLV17-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	192					GRCh38	V40	SF3A1-BGKcLV17-46_S20_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGKcLV17-46_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24690
SF3A1-BGKcLV17-46_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	192					GRCh38	V40	SF3A1-BGKcLV17-46/Aligned.sortedByCoord.out.bam		ENCORE2	24720
SF3A1-BGKcLV17-46_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	192					GRCh38	V40	SF3A1-BGKcLV17-46/Aligned.sortedByCoord.out.bam		ENCORE2	24750
SF3A1-BGKcLV17-46_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	192					GRCh38	V40	SF3A1-BGKcLV17-46/Aligned.sortedByCoord.out.bam		ENCORE2	24780
SF3A1-BGKcLV17-46_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	192					GRCh38	V40	SF3A1-BGKcLV17-46/Aligned.sortedByCoord.out.bam		ENCORE2	24810
SF3A1-BGKcLV17-46_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	192					GRCh38	V40	SF3A1-BGKcLV17-46_S20_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGKcLV17-46_S20_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24840