RBM25 RNA-Seq in HepG2

General Information


RBP	RBM25
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBM25-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR211XXF
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR739ZMF
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	RBM25-BGHcLV32-9
Rep2	RBM25-BGHcLV32-10
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	0.0
Rep2_qPCR	4.0
Rep1_WB	55.2
Rep2_WB	61.0
Antibody Cat#	A301-067A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB042ILI
Status	Submitted
Project	ENCODE4
ID	932

Experiment Information (Status: Released)

	BGHcLV32-9	BGHcLV32-10
idx	1004	1005
TRCN#_or_BGC#	BGC#0000759	BGC#0000759
shRNA_or_gRNA_sequence	CATTTGAATCGCCCTCCCAT	CATTTGAATCGCCCTCCCAT
PAM	GGG	GGG
Name	RBM25_89	RBM25_89
Sample_ID	BGHcLV32-9	BGHcLV32-10
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	RBM25	RBM25
qPCR_result	0.0	4.0
Ave_qPCR	2.0
RT-qPCR_primer-F	GAATTCTTAGAAGACTATGATGATGA
RT-qPCR_primer-R	TTTCTCTATCACGCAACCTTT
protein_conc	3656	3989
WB_result	55.2	61.0
Ave_WB	58.1
WB_DONE_date	11/4/21
MW	100KD
IP
antibody_Cat#	A301-067A	LOT #1
Antibody DCC ID	ENCAB042ILI
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library
Note
ID	7183	7184

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM25	Product_ID: A301-067A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM25-human

Experiment Status

	BGHcLV32-9	BGHcLV32-10
Sample_ID	BGHcLV32-9	BGHcLV32-10
Sample Name
Sample Name	RBM25-BGHcLV32-9	RBM25-BGHcLV32-10
RBP	RBM25	RBM25
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10361	10362

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-9	BGHcLV32-10
Sample #	35	36
Sample Name	RBM25-BGHcLV32-9	RBM25-BGHcLV32-10
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-01
Lib_ID	Lib-220201	Lib-220201
Tecan_Location
Tecan
Tecan_date
Size_bp	326	323
Peak_Molarity	82.80	82.70
libSampleQC_DNA_Well	DNA_Library_set52/set2/C5.png	DNA_Library_set52/set2/D5.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set52/set2/G7.png	RNA_Library_set52/set2/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-9	BGHcLV32-10
RBP	RBM25	RBM25
Batch_ID	BGHcLV32	BGHcLV32
WB_result	55.200	61.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3212	3213

Sequencing Information

	BGHcLV32-9	BGHcLV32-10
Sample_ID	BGHcLV32-9	BGHcLV32-10
Sample Name	RBM25-BGHcLV32-9	RBM25-BGHcLV32-10
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	159,550,726	101,733,448
total_aligned_reads	140,305,446	80,434,684
unique_aligned_reads	131,739,450	75,534,554
percent_uniqueAligned	0.82569	0.74248
correlation_replicates	0.997795	0.997795
spikein_reads	16,414	3,800
percent_spikeins	0.00010	0.00004
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2009	2010

Data Submission Information

	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-10	BGHcLV32-10	BGHcLV32-10	BGHcLV32-10
ENCODE_alias	brenton-graveley:RBM25-BGHcLV32	brenton-graveley:RBM25-BGHcLV32-9	brenton-graveley:L-RBM25-BGHcLV32-9	brenton-graveley:RBM25-BGHcLV32-9_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGHcLV32-9_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGHcLV32-HepG2	brenton-graveley:RBM25-BGHcLV32-10	brenton-graveley:L-RBM25-BGHcLV32-10	brenton-graveley:RBM25-BGHcLV32-10_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGHcLV32-10_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR739ZMF	ENCBS652ECV	ENCLB043NCV	ENCFF519CCL	ENCFF102RMV	ENCSR211XXF	ENCBS876WAS	ENCLB076UGB	ENCFF982SFG	ENCFF686VWO
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	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-9	BGHcLV32-10	BGHcLV32-10	BGHcLV32-10	BGHcLV32-10
Sample Name	RBM25-BGHcLV32-9	RBM25-BGHcLV32-9	RBM25-BGHcLV32-9	RBM25-BGHcLV32-9	RBM25-BGHcLV32-9	RBM25-BGHcLV32-9	RBM25-BGHcLV32-10	RBM25-BGHcLV32-10	RBM25-BGHcLV32-10	RBM25-BGHcLV32-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	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_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		RBM25-BGHcLV32-9.pdf	L-RBM25-BGHcLV32-10.pdf				RBM25-BGHcLV32-10.pdf	L-RBM25-BGHcLV32-9.pdf
ID	7462	7531	7643	7751	7861	7952	7532	7644	7752	7862

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
RBM25-BGHcLV32-9_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2009	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6508
RBM25-BGHcLV32-9_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2009	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6562
RBM25-BGHcLV32-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2009					GRCh38	V40	RBM25-BGHcLV32-9_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGHcLV32-9_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18429
RBM25-BGHcLV32-9_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	2009					GRCh38	V40	RBM25-BGHcLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	18483
RBM25-BGHcLV32-9_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	2009					GRCh38	V40	RBM25-BGHcLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	18537
RBM25-BGHcLV32-9_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	2009					GRCh38	V40	RBM25-BGHcLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	18591
RBM25-BGHcLV32-9_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	2009					GRCh38	V40	RBM25-BGHcLV32-9/Aligned.sortedByCoord.out.bam		ENCORE2	18645
RBM25-BGHcLV32-9_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2009					GRCh38	V40	RBM25-BGHcLV32-9_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGHcLV32-9_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18699
RBM25-BGHcLV32-10_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2010	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6507
RBM25-BGHcLV32-10_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2010	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6561
RBM25-BGHcLV32-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2010					GRCh38	V40	RBM25-BGHcLV32-10_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGHcLV32-10_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18428
RBM25-BGHcLV32-10_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	2010					GRCh38	V40	RBM25-BGHcLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	18482
RBM25-BGHcLV32-10_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	2010					GRCh38	V40	RBM25-BGHcLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	18536
RBM25-BGHcLV32-10_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	2010					GRCh38	V40	RBM25-BGHcLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	18590
RBM25-BGHcLV32-10_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	2010					GRCh38	V40	RBM25-BGHcLV32-10/Aligned.sortedByCoord.out.bam		ENCORE2	18644
RBM25-BGHcLV32-10_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2010					GRCh38	V40	RBM25-BGHcLV32-10_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGHcLV32-10_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18698