SF3A2 RNA-Seq in HepG2

General Information


RBP	SF3A2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SF3A2-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR915AOZ
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR402BZZ
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	SF3A2-BGHcLV24-47
Rep2	SF3A2-BGHcLV24-48
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	9.0
Rep2_qPCR	5.0
Rep1_WB	55.0
Rep2_WB	52.0
Antibody Cat#	A304-821A
Antibody Lot#
Antibody DCC ID	ENCAB309KDW
Status	Released
Project	ENCODE4
ID	11

Experiment Information (Status: Released)

	BGHcLV24-47	BGHcLV24-48
idx	705	706
TRCN#_or_BGC#	BGC#0000541	BGC#0000541
shRNA_or_gRNA_sequence	GACTTCCAGCATCGCCCCGG	GACTTCCAGCATCGCCCCGG
PAM	GGG	GGG
Name	SF3A2_90	SF3A2_90
Sample_ID	BGHcLV24-47	BGHcLV24-48
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	SF3A2	SF3A2
qPCR_result	9.0	5.0
Ave_qPCR	7.0
RT-qPCR_primer-F	GCAGAGAGACTCGGAGATGG
RT-qPCR_primer-R	GCTCGTACGCAGACATGAAG
protein_conc	6060	5710
WB_result	55.0	52.0
Ave_WB	53.5
WB_DONE_date	11/12/20	JESS
MW	49.3kDa
IP	Rabbit / I
antibody_Cat#	A304-821A
Antibody DCC ID	ENCAB309KDW
submitted_to_DCC_date	10/25/21
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6860	6861

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3A2	Product_ID: A304-821A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3A2-human

Experiment Status

	BGHcLV24-47	BGHcLV24-48
Sample_ID	BGHcLV24-47	BGHcLV24-48
Sample Name
Sample Name	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-48
RBP	SF3A2	SF3A2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7801	7802

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-47	BGHcLV24-48
Sample #	23	24
Sample Name	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-48
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	306	303
Peak_Molarity	83.30	68.10
libSampleQC_DNA_Well	DNA_Library_set47/set1/G6.png	DNA_Library_set47/set1/H6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set47/set1/G3.png	RNA_Library_set47/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-47	BGHcLV24-48
RBP	SF3A2	SF3A2
Batch_ID	BGHcLV24	BGHcLV24
WB_result	55.000	52.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1486	1487

Sequencing Information

	BGHcLV24-47	BGHcLV24-48
Sample_ID	BGHcLV24-47	BGHcLV24-48
Sample Name	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-48
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	123,176,654	108,003,076
total_aligned_reads	113,643,416	95,465,908
unique_aligned_reads	107,124,764	89,894,006
percent_uniqueAligned	0.86968	0.83233
correlation_replicates	0.996266	0.996266
spikein_reads	41,416	34,386
percent_spikeins	0.00034	0.00032
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	568	569

Data Submission Information

	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-48	BGHcLV24-48	BGHcLV24-48	BGHcLV24-48
ENCODE_alias	brenton-graveley:SF3A2-BGHcLV24	brenton-graveley:SF3A2-BGHcLV24-47	brenton-graveley:L-SF3A2-BGHcLV24-47	brenton-graveley:SF3A2-BGHcLV24-47_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A2-BGHcLV24-47_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A2-BGHcLV24-HepG2	brenton-graveley:SF3A2-BGHcLV24-48	brenton-graveley:L-SF3A2-BGHcLV24-48	brenton-graveley:SF3A2-BGHcLV24-48_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3A2-BGHcLV24-48_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR402BZZ	ENCBS946OYT	ENCLB847JIH	ENCFF781HFL	ENCFF308KDM	ENCSR915AOZ	ENCBS448YLZ	ENCLB087QPB	ENCFF425SWJ	ENCFF344JLE
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	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-47	BGHcLV24-48	BGHcLV24-48	BGHcLV24-48	BGHcLV24-48
Sample Name	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-47	SF3A2-BGHcLV24-48	SF3A2-BGHcLV24-48	SF3A2-BGHcLV24-48	SF3A2-BGHcLV24-48
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		SF3A2-BGHcLV24-47.pdf	L-SF3A2-BGHcLV24-47.pdf				SF3A2-BGHcLV24-48.pdf	L-SF3A2-BGHcLV24-48.pdf
ID	3246	3279	3323	3367	3411	7322	3280	3324	3368	3412

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
SF3A2-BGHcLV24-47_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	568	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3732
SF3A2-BGHcLV24-47_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	568	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3778
SF3A2-BGHcLV24-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	568					GRCh38	V40	SF3A2-BGHcLV24-47_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGHcLV24-47_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25421
SF3A2-BGHcLV24-47_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	568					GRCh38	V40	SF3A2-BGHcLV24-47_S83_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGHcLV24-47_S83_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25465
SF3A2-BGHcLV24-47_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	568					GRCh38	V40	SF3A2-BGHcLV24-47/Aligned.sortedByCoord.out.bam		ENCORE2	26297
SF3A2-BGHcLV24-47_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	568					GRCh38	V40	SF3A2-BGHcLV24-47/Aligned.sortedByCoord.out.bam		ENCORE2	26341
SF3A2-BGHcLV24-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	568					GRCh38	V40	SF3A2-BGHcLV24-47/Aligned.sortedByCoord.out.bam		ENCORE2	26385
SF3A2-BGHcLV24-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	568					GRCh38	V40	SF3A2-BGHcLV24-47/Aligned.sortedByCoord.out.bam		ENCORE2	26429
SF3A2-BGHcLV24-48_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	569	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3733
SF3A2-BGHcLV24-48_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	569	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3779
SF3A2-BGHcLV24-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	569					GRCh38	V40	SF3A2-BGHcLV24-48_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGHcLV24-48_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25422
SF3A2-BGHcLV24-48_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	569					GRCh38	V40	SF3A2-BGHcLV24-48_S84_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGHcLV24-48_S84_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25466
SF3A2-BGHcLV24-48_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	569					GRCh38	V40	SF3A2-BGHcLV24-48/Aligned.sortedByCoord.out.bam		ENCORE2	26298
SF3A2-BGHcLV24-48_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	569					GRCh38	V40	SF3A2-BGHcLV24-48/Aligned.sortedByCoord.out.bam		ENCORE2	26342
SF3A2-BGHcLV24-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	569					GRCh38	V40	SF3A2-BGHcLV24-48/Aligned.sortedByCoord.out.bam		ENCORE2	26386
SF3A2-BGHcLV24-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	569					GRCh38	V40	SF3A2-BGHcLV24-48/Aligned.sortedByCoord.out.bam		ENCORE2	26430