SF3A2 RNA-Seq in K562

General Information


RBP	SF3A2
Cell_Line	K562
Method	CRISPR
Exp_Name	SF3A2-BGKcLV21-K562
ENCODE_series_ID	ENCSR497NTM
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR095TFW
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	SF3A2-BGKcLV21-41
Rep2	SF3A2-BGKcLV21-42
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	31.0
Rep2_qPCR	32.3
Rep1_WB	55.6
Rep2_WB	66.3
Antibody Cat#	A304-821A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB309KDW
Status	Released
Project	ENCODE4
ID	73

Experiment Information (Status: Released)

	BGKcLV21-41	BGKcLV21-42
idx	774	775
TRCN#_or_BGC#	BGC#0000540	BGC#0000540
shRNA_or_gRNA_sequence	GCGGTCACGGTTGCTCTCGG	GCGGTCACGGTTGCTCTCGG
PAM	AGG	AGG
Name	SF3A2_89	SF3A2_89
Sample_ID	BGKcLV21-41	BGKcLV21-42
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	SF3A2	SF3A2
qPCR_result	31.0	32.3
Ave_qPCR	31.7
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5279	5623
WB_result	55.6	66.3
Ave_WB	60.9
WB_DONE_date	8/12/20	JESS
MW	49.3kDa
IP	Rabbit / I
antibody_Cat#	A304-821A	lot# 1
Antibody DCC ID	ENCAB309KDW
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4894	4895

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

	BGKcLV21-41	BGKcLV21-42
Sample_ID	BGKcLV21-41	BGKcLV21-42
Sample Name
Sample Name	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-42
RBP	SF3A2	SF3A2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6137	6138

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-41	BGKcLV21-42
Sample #	55	56
Sample Name	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-42
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	313	312
Peak_Molarity	93.00	226.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/A7.png	DNA_Library_set45/set1/B7.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set45/set1/A7.png	RNA_Library_set45/set2/G10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-41	BGKcLV21-42
RBP	SF3A2	SF3A2
Batch_ID	BGKcLV21	BGKcLV21
WB_result	55.600	66.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	829	830

Sequencing Information

	BGKcLV21-41	BGKcLV21-42
Sample_ID	BGKcLV21-41	BGKcLV21-42
Sample Name	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-42
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	116,389,858	205,220,084
total_aligned_reads	115,001,626	200,251,010
unique_aligned_reads	105,302,224	182,723,644
percent_uniqueAligned	0.90474	0.89038
correlation_replicates	0.995512	0.995512
spikein_reads	115,318	178,718
percent_spikeins	0.00099	0.00087
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	460	461

Data Submission Information

	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-42	BGKcLV21-42	BGKcLV21-42	BGKcLV21-42
ENCODE_alias	brenton-graveley:SF3A2-BGKcLV21	brenton-graveley:SF3A2-BGKcLV21-41	brenton-graveley:L-SF3A2-BGKcLV21-41	brenton-graveley:SF3A2-BGKcLV21-41_S49_R1_001.fastq.gz	brenton-graveley:SF3A2-BGKcLV21-41_S49_R2_001.fastq.gz	brenton-graveley:SF3A2-BGKcLV21-K562	brenton-graveley:SF3A2-BGKcLV21-42	brenton-graveley:L-SF3A2-BGKcLV21-42	brenton-graveley:SF3A2-BGKcLV21-42_S50_R1_001.fastq.gz	brenton-graveley:SF3A2-BGKcLV21-42_S50_R2_001.fastq.gz
ENCODE_accession	ENCSR095TFW	ENCBS060QUM	ENCLB761BSK	ENCFF213MCU	ENCFF657IGD	ENCSR497NTM	ENCBS437VMI	ENCLB066LMY	ENCFF424KKC	ENCFF442PBB
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	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-41	BGKcLV21-42	BGKcLV21-42	BGKcLV21-42	BGKcLV21-42
Sample Name	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-41	SF3A2-BGKcLV21-42	SF3A2-BGKcLV21-42	SF3A2-BGKcLV21-42	SF3A2-BGKcLV21-42
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		SF3A2-BGKcLV21-41.pdf	L-SF3A2-BGKcLV21-41.pdf				SF3A2-BGKcLV21-42.pdf	L-SF3A2-BGKcLV21-42.pdf
ID	2114	2183	2253	2323	2393	7323	2184	2254	2324	2394

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-BGKcLV21-41_S49_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	460	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1250
SF3A2-BGKcLV21-41_S49_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	460	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1300
SF3A2-BGKcLV21-41_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	460					GRCh38	V40	SF3A2-BGKcLV21-41_S49_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGKcLV21-41_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25243
SF3A2-BGKcLV21-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	460					GRCh38	V40	SF3A2-BGKcLV21-41_S49_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGKcLV21-41_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27197
SF3A2-BGKcLV21-41_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	460					GRCh38	V40	SF3A2-BGKcLV21-41/Aligned.sortedByCoord.out.bam		ENCORE2	27247
SF3A2-BGKcLV21-41_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	460					GRCh38	V40	SF3A2-BGKcLV21-41/Aligned.sortedByCoord.out.bam		ENCORE2	27297
SF3A2-BGKcLV21-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	460					GRCh38	V40	SF3A2-BGKcLV21-41/Aligned.sortedByCoord.out.bam		ENCORE2	27347
SF3A2-BGKcLV21-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	460					GRCh38	V40	SF3A2-BGKcLV21-41/Aligned.sortedByCoord.out.bam		ENCORE2	27397
SF3A2-BGKcLV21-42_S50_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	461	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1251
SF3A2-BGKcLV21-42_S50_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	461	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1301
SF3A2-BGKcLV21-42_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	461					GRCh38	V40	SF3A2-BGKcLV21-42_S50_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGKcLV21-42_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25244
SF3A2-BGKcLV21-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	461					GRCh38	V40	SF3A2-BGKcLV21-42_S50_R1_001.filtered.trimmed.paired.fastq.gz,SF3A2-BGKcLV21-42_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27198
SF3A2-BGKcLV21-42_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	461					GRCh38	V40	SF3A2-BGKcLV21-42/Aligned.sortedByCoord.out.bam		ENCORE2	27248
SF3A2-BGKcLV21-42_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	461					GRCh38	V40	SF3A2-BGKcLV21-42/Aligned.sortedByCoord.out.bam		ENCORE2	27298
SF3A2-BGKcLV21-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	461					GRCh38	V40	SF3A2-BGKcLV21-42/Aligned.sortedByCoord.out.bam		ENCORE2	27348
SF3A2-BGKcLV21-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	461					GRCh38	V40	SF3A2-BGKcLV21-42/Aligned.sortedByCoord.out.bam		ENCORE2	27398