SAP30BP RNA-Seq in HepG2

General Information


RBP	SAP30BP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SAP30BP-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR441GUL
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR954VJD
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SAP30BP-BGHcLV31-25
Rep2	SAP30BP-BGHcLV31-26
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	80.8
Rep2_WB	82.2
Antibody Cat#	A302-832A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	924

Experiment Information (Status: Released)

	BGHcLV31-25	BGHcLV31-26
idx	943	944
TRCN#_or_BGC#	BGC#0000842	BGC#0000842
shRNA_or_gRNA_sequence	GTCGTCTCTCGCAGTTTACG	GTCGTCTCTCGCAGTTTACG
PAM	CGG	CGG
Name	SAP30BP_97	SAP30BP_97
Sample_ID	BGHcLV31-25	BGHcLV31-26
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SAP30BP	SAP30BP
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	cctggcagatgttcaaatca
RT-qPCR_primer-R	gggttccgaaattctttcttc
protein_conc	4054	4596
WB_result	80.8	82.2
Ave_WB	81.5
WB_DONE_date	12/3/21
MW	34kd
IP
antibody_Cat#	A302-832A	LOT #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7122	7123

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV31-25	BGHcLV31-26
Sample_ID	BGHcLV31-25	BGHcLV31-26
Sample Name
Sample Name	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-26
RBP	SAP30BP	SAP30BP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10303	10304

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-25	BGHcLV31-26
Sample #	17	18
Sample Name	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-26
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	288	299
Peak_Molarity	61.50	53.20
libSampleQC_DNA_Well	DNA_Library_set52/set1/A10.png	DNA_Library_set52/set1/B10.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set52/set1/A3.png	RNA_Library_set52/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-25	BGHcLV31-26
RBP	SAP30BP	SAP30BP
Batch_ID	BGHcLV31	BGHcLV31
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3194	3195

Sequencing Information

	BGHcLV31-25	BGHcLV31-26
Sample_ID	BGHcLV31-25	BGHcLV31-26
Sample Name	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-26
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	228,294,608	115,206,394
total_aligned_reads	202,815,934	107,238,628
unique_aligned_reads	190,296,308	100,883,126
percent_uniqueAligned	0.83356	0.87567
correlation_replicates	0.994738	0.994738
spikein_reads	31,432	10,140
percent_spikeins	0.00014	0.00009
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1991	1992

Data Submission Information

	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-26	BGHcLV31-26	BGHcLV31-26	BGHcLV31-26
ENCODE_alias	brenton-graveley:SAP30BP-BGHcLV31	brenton-graveley:SAP30BP-BGHcLV31-25	brenton-graveley:L-SAP30BP-BGHcLV31-25	brenton-graveley:SAP30BP-BGHcLV31-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAP30BP-BGHcLV31-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAP30BP-BGHcLV31-HepG2	brenton-graveley:SAP30BP-BGHcLV31-26	brenton-graveley:L-SAP30BP-BGHcLV31-26	brenton-graveley:SAP30BP-BGHcLV31-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAP30BP-BGHcLV31-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR954VJD	ENCBS627QRR	ENCLB429UYO	ENCFF735NFI	ENCFF578JJD	ENCSR441GUL	ENCBS652UVX	ENCLB699NCV	ENCFF747JAG	ENCFF058PDK
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	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-25	BGHcLV31-26	BGHcLV31-26	BGHcLV31-26	BGHcLV31-26
Sample Name	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-25	SAP30BP-BGHcLV31-26	SAP30BP-BGHcLV31-26	SAP30BP-BGHcLV31-26	SAP30BP-BGHcLV31-26
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV52_library_protocol					LV52_library_protocol
protocol_URL			L-SAP30BP-BGHcLV31-25.pdf					L-SAP30BP-BGHcLV31-26.pdf
ID	7452	7515	7623	7733	7843	7944	7516	7624	7734	7844

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
SAP30BP-BGHcLV31-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1991	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6537
SAP30BP-BGHcLV31-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1991	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6591
SAP30BP-BGHcLV31-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1991					GRCh38	V40	SAP30BP-BGHcLV31-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGHcLV31-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18458
SAP30BP-BGHcLV31-25_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1991					GRCh38	V40	SAP30BP-BGHcLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	18512
SAP30BP-BGHcLV31-25_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1991					GRCh38	V40	SAP30BP-BGHcLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	18566
SAP30BP-BGHcLV31-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1991					GRCh38	V40	SAP30BP-BGHcLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	18620
SAP30BP-BGHcLV31-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1991					GRCh38	V40	SAP30BP-BGHcLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	18674
SAP30BP-BGHcLV31-25_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1991					GRCh38	V40	SAP30BP-BGHcLV31-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGHcLV31-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18728
SAP30BP-BGHcLV31-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1992	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6538
SAP30BP-BGHcLV31-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1992	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6592
SAP30BP-BGHcLV31-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1992					GRCh38	V40	SAP30BP-BGHcLV31-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGHcLV31-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18459
SAP30BP-BGHcLV31-26_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1992					GRCh38	V40	SAP30BP-BGHcLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	18513
SAP30BP-BGHcLV31-26_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1992					GRCh38	V40	SAP30BP-BGHcLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	18567
SAP30BP-BGHcLV31-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1992					GRCh38	V40	SAP30BP-BGHcLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	18621
SAP30BP-BGHcLV31-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1992					GRCh38	V40	SAP30BP-BGHcLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	18675
SAP30BP-BGHcLV31-26_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1992					GRCh38	V40	SAP30BP-BGHcLV31-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGHcLV31-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18729