SF3A1 RNA-Seq in HepG2

General Information


RBP	SF3A1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SF3A1-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR326WWQ
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR556TJU
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	SF3A1-BGHcLV18-43
Rep2	SF3A1-BGHcLV18-44
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	96.2
Rep2_WB	93.3
Antibody Cat#	301-601A
Antibody Lot#	lot #1
Antibody DCC ID
Status	Released
Project	ENCODE4
ID	117

Experiment Information (Status: Released)

	BGHcLV18-43	BGHcLV18-44
idx	536	537
TRCN#_or_BGC#	BGC#0000412	BGC#0000412
shRNA_or_gRNA_sequence	GGTACCTGTTTGGGCTCCGT	GGTACCTGTTTGGGCTCCGT
PAM	GGG	GGG
Name	SF3A1_89	SF3A1_89
Sample_ID	BGHcLV18-43	BGHcLV18-44
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	SF3A1	SF3A1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ACCCTCCTCCAGAGGTCAGA
RT-qPCR_primer-R	TGGGGTTGTTGATCTCGTTC
protein_conc	3590	3439
WB_result	96.2	93.3
Ave_WB	94.7
WB_DONE_date	8/26/19	wes
MW	89KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	301-601A	lot #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	54	0
Rep2_TPM	27	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6691	6692

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

	BGHcLV18-43	BGHcLV18-44
Sample_ID	BGHcLV18-43	BGHcLV18-44
Sample Name
Sample Name	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-44
RBP	SF3A1	SF3A1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5651	5652

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-43	BGHcLV18-44
Sample #	157	158
Sample Name	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-44
Sample_Name_Alias
Index Well Position	E08	F08
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-A2	5-B2
Tecan	40.30	37.06
Tecan_date	2019-12-16	2019-12-16
Size_bp	274	277
Peak_Molarity	29.30	29.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C9.png	DNA_Library_set43-44/set2/D9.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/G10.png	RNA_Library_set43-44/set4/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-43	BGHcLV18-44
RBP	SF3A1	SF3A1
Batch_ID	BGHcLV18	BGHcLV18
WB_result	96.200	93.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	733	734

Sequencing Information

	BGHcLV18-43	BGHcLV18-44
Sample_ID	BGHcLV18-43	BGHcLV18-44
Sample Name	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-44
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	194,103,964	154,298,780
total_aligned_reads	187,791,486	148,092,450
unique_aligned_reads	175,545,042	138,587,410
percent_uniqueAligned	0.90439	0.89818
correlation_replicates	0.999428	0.999428
spikein_reads	307,934	199,952
percent_spikeins	0.00159	0.00130
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	239	240

Data Submission Information

	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-44	BGHcLV18-44	BGHcLV18-44	BGHcLV18-44
ENCODE_alias	brenton-graveley:SF3A1-BGHcLV18	brenton-graveley:SF3A1-BGHcLV18-43	brenton-graveley:L-SF3A1-BGHcLV18-43	brenton-graveley:SF3A1-BGHcLV18-43_S69_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A1-BGHcLV18-43_S69_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A1-BGHcLV18-HepG2	brenton-graveley:SF3A1-BGHcLV18-44	brenton-graveley:L-SF3A1-BGHcLV18-44	brenton-graveley:SF3A1-BGHcLV18-44_S70_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A1-BGHcLV18-44_S70_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR556TJU	ENCBS239SWM	ENCLB396EJD	ENCFF596AXH	ENCFF434IKM	ENCSR326WWQ	ENCBS684VDW	ENCLB138MZJ	ENCFF581ZLN	ENCFF170JEX
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	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-43	BGHcLV18-44	BGHcLV18-44	BGHcLV18-44	BGHcLV18-44
Sample Name	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-43	SF3A1-BGHcLV18-44	SF3A1-BGHcLV18-44	SF3A1-BGHcLV18-44	SF3A1-BGHcLV18-44
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		SF3A1-BGHcLV18-43.pdf	L-SF3A1-BGHcLV18-43.pdf				SF3A1-BGHcLV18-44.pdf	L-SF3A1-BGHcLV18-44.pdf
ID	64	208	374	624	676	7320	209	375	625	677

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-BGHcLV18-43_S69_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	239	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	211
SF3A1-BGHcLV18-43_S69_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	239	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	263
SF3A1-BGHcLV18-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	239					GRCh38	V40	SF3A1-BGHcLV18-43_S69_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGHcLV18-43_S69_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24931
SF3A1-BGHcLV18-43_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	239					GRCh38	V40	SF3A1-BGHcLV18-43/Aligned.sortedByCoord.out.bam		ENCORE2	24983
SF3A1-BGHcLV18-43_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	239					GRCh38	V40	SF3A1-BGHcLV18-43/Aligned.sortedByCoord.out.bam		ENCORE2	25035
SF3A1-BGHcLV18-43_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	239					GRCh38	V40	SF3A1-BGHcLV18-43/Aligned.sortedByCoord.out.bam		ENCORE2	25087
SF3A1-BGHcLV18-43_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	239					GRCh38	V40	SF3A1-BGHcLV18-43/Aligned.sortedByCoord.out.bam		ENCORE2	25139
SF3A1-BGHcLV18-43_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	239					GRCh38	V40	SF3A1-BGHcLV18-43_S69_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGHcLV18-43_S69_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25191
SF3A1-BGHcLV18-44_S70_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	240	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	212
SF3A1-BGHcLV18-44_S70_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	240	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	264
SF3A1-BGHcLV18-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	240					GRCh38	V40	SF3A1-BGHcLV18-44_S70_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGHcLV18-44_S70_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24932
SF3A1-BGHcLV18-44_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	240					GRCh38	V40	SF3A1-BGHcLV18-44/Aligned.sortedByCoord.out.bam		ENCORE2	24984
SF3A1-BGHcLV18-44_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	240					GRCh38	V40	SF3A1-BGHcLV18-44/Aligned.sortedByCoord.out.bam		ENCORE2	25036
SF3A1-BGHcLV18-44_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	240					GRCh38	V40	SF3A1-BGHcLV18-44/Aligned.sortedByCoord.out.bam		ENCORE2	25088
SF3A1-BGHcLV18-44_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	240					GRCh38	V40	SF3A1-BGHcLV18-44/Aligned.sortedByCoord.out.bam		ENCORE2	25140
SF3A1-BGHcLV18-44_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	240					GRCh38	V40	SF3A1-BGHcLV18-44_S70_R1_001.filtered.trimmed.paired.fastq.gz,SF3A1-BGHcLV18-44_S70_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25192