SF3B2 RNA-Seq in HepG2

General Information


RBP	SF3B2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SF3B2-BGHcLV34-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV34
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SF3B2-BGHcLV34-47
Rep2	SF3B2-BGHcLV34-48
CN1	NT-BGHcLV34-1
CN2	NT-BGHcLV34-2
Rep1_qPCR	43.3
Rep2_qPCR	45.0
Rep1_WB	65.9
Rep2_WB	77.2
Antibody Cat#	A301-605A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB244MZF
Status	Submitted
Project	ENCORE2
ID	947

Experiment Information (Status: Submitting)

	BGHcLV34-47	BGHcLV34-48
idx	1117	1118
TRCN#_or_BGC#	BGC#0000863	BGC#0000863
shRNA_or_gRNA_sequence	TGGCATCGTGCTGAATCGGC	TGGCATCGTGCTGAATCGGC
PAM	CGG	CGG
Name	SF3B2_94	SF3B2_94
Sample_ID	BGHcLV34-47	BGHcLV34-48
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	SF3B2	SF3B2
qPCR_result	43.3	45.0
Ave_qPCR	44.2
RT-qPCR_primer-F	tgaaggagaagaagccagga
RT-qPCR_primer-R	ttcaggttgggatacgatgg
protein_conc	2311	2938
WB_result	65.9	77.2
Ave_WB	71.5
WB_DONE_date	4/18/22
MW	100kd
IP
antibody_Cat#	A301-605A	LOT #1
Antibody DCC ID	ENCAB244MZF
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	7298	7299

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV34-47	BGHcLV34-48
Sample_ID	BGHcLV34-47	BGHcLV34-48
Sample Name
Sample Name	SF3B2-BGHcLV34-47	SF3B2-BGHcLV34-48
RBP	SF3B2	SF3B2
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10815	10816

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-47	BGHcLV34-48
Sample #	19	20
Sample Name	SF3B2-BGHcLV34-47	SF3B2-BGHcLV34-48
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	286	284
Peak_Molarity	26.80	59.10
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/C7.png	DNA_Library_set54-56/set3/D7.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set54-56/set2/C3.png	RNA_Library_set54-56/set2/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-47	BGHcLV34-48
RBP	SF3B2	SF3B2
Batch_ID	BGHcLV34	BGHcLV34
WB_result	65.900	77.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3336	3337

Sequencing Information

	BGHcLV34-47	BGHcLV34-48
Sample_ID	BGHcLV34-47	BGHcLV34-48
Sample Name	SF3B2-BGHcLV34-47	SF3B2-BGHcLV34-48
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	48,727,362	38,012,168
total_aligned_reads	40,482,166	31,554,670
unique_aligned_reads	38,211,658	29,805,066
percent_uniqueAligned	0.78419	0.78409
correlation_replicates	0.994580	0.994580
spikein_reads	3,514	3,810
percent_spikeins	0.00007	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2209	2210

Data Submission Information DCC submission information was not avaliable

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
SF3B2-BGHcLV34-47_S15_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2209	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8524
SF3B2-BGHcLV34-47_S15_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2209	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8574
SF3B2-BGHcLV34-47_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2209					GRCh38	V40	SF3B2-BGHcLV34-47/Aligned.sortedByCoord.out.bam		ENCORE2	17770
SF3B2-BGHcLV34-47_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2209					GRCh38	V40	SF3B2-BGHcLV34-47/Aligned.sortedByCoord.out.bam		ENCORE2	17820
SF3B2-BGHcLV34-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2209					GRCh38	V40	SF3B2-BGHcLV34-47/Aligned.sortedByCoord.out.bam		ENCORE2	17870
SF3B2-BGHcLV34-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2209					GRCh38	V40	SF3B2-BGHcLV34-47/Aligned.sortedByCoord.out.bam		ENCORE2	17920
SF3B2-BGHcLV34-47_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2209					GRCh38	V40	SF3B2-BGHcLV34-47_S15_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGHcLV34-47_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17970
SF3B2-BGHcLV34-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2209					GRCh38	V40	SF3B2-BGHcLV34-47_S15_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGHcLV34-47_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29311
SF3B2-BGHcLV34-48_S16_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2210	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8525
SF3B2-BGHcLV34-48_S16_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2210	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8575
SF3B2-BGHcLV34-48_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2210					GRCh38	V40	SF3B2-BGHcLV34-48/Aligned.sortedByCoord.out.bam		ENCORE2	17771
SF3B2-BGHcLV34-48_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2210					GRCh38	V40	SF3B2-BGHcLV34-48/Aligned.sortedByCoord.out.bam		ENCORE2	17821
SF3B2-BGHcLV34-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2210					GRCh38	V40	SF3B2-BGHcLV34-48/Aligned.sortedByCoord.out.bam		ENCORE2	17871
SF3B2-BGHcLV34-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2210					GRCh38	V40	SF3B2-BGHcLV34-48/Aligned.sortedByCoord.out.bam		ENCORE2	17921
SF3B2-BGHcLV34-48_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2210					GRCh38	V40	SF3B2-BGHcLV34-48_S16_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGHcLV34-48_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17971
SF3B2-BGHcLV34-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2210					GRCh38	V40	SF3B2-BGHcLV34-48_S16_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGHcLV34-48_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29312