RBM8A RNA-Seq in HepG2

General Information


RBP	RBM8A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBM8A-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	RBM8A-BGHcLV34-31
Rep2	RBM8A-BGHcLV34-32
CN1	NT-BGHcLV34-1
CN2	NT-BGHcLV34-2
Rep1_qPCR	12.4
Rep2_qPCR	1.3
Rep1_WB	70.8
Rep2_WB	79.8
Antibody Cat#	A301-033A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB121MYB
Status	Submitted
Project	ENCORE2
ID	945

Experiment Information (Status: Submitting)

	BGHcLV34-31	BGHcLV34-32
idx	1101	1102
TRCN#_or_BGC#	BGC#0000771	BGC#0000771
shRNA_or_gRNA_sequence	GACAGCCCATCAGCGTTGAC	GACAGCCCATCAGCGTTGAC
PAM	TGG	TGG
Name	RBM8A_91B	RBM8A_91B
Sample_ID	BGHcLV34-31	BGHcLV34-32
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	RBM8A	RBM8A
qPCR_result	12.4	1.3
Ave_qPCR	6.8
RT-qPCR_primer-F	ttcgcagaatatggggaaat
RT-qPCR_primer-R	atcaaatcctggccattgag
protein_conc	2249	2660
WB_result	70.8	79.8
Ave_WB	75.3
WB_DONE_date	4/6/22
MW	20KD
IP
antibody_Cat#	A301-033A	LOT #1
Antibody DCC ID	ENCAB121MYB
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	7280	7281

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM8A	Product_ID: A301-033A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM8A-human

Experiment Status

	BGHcLV34-31	BGHcLV34-32
Sample_ID	BGHcLV34-31	BGHcLV34-32
Sample Name
Sample Name	RBM8A-BGHcLV34-31	RBM8A-BGHcLV34-32
RBP	RBM8A	RBM8A
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10807	10808

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-31	BGHcLV34-32
Sample #	11	12
Sample Name	RBM8A-BGHcLV34-31	RBM8A-BGHcLV34-32
Sample_Name_Alias
Index Well Position	C02	D02
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	280	279
Peak_Molarity	43.20	76.10
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/C6.png	DNA_Library_set54-56/set3/D6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set54-56/set2/C2.png	RNA_Library_set54-56/set2/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-31	BGHcLV34-32
RBP	RBM8A	RBM8A
Batch_ID	BGHcLV34	BGHcLV34
WB_result	70.800	79.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3328	3329

Sequencing Information

	BGHcLV34-31	BGHcLV34-32
Sample_ID	BGHcLV34-31	BGHcLV34-32
Sample Name	RBM8A-BGHcLV34-31	RBM8A-BGHcLV34-32
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	46,676,620	41,717,486
total_aligned_reads	40,297,836	36,664,658
unique_aligned_reads	38,054,174	34,613,432
percent_uniqueAligned	0.81527	0.82971
correlation_replicates	0.997763	0.997763
spikein_reads	2,820	2,490
percent_spikeins	0.00006	0.00006
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2205	2206

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
RBM8A-BGHcLV34-31_S11_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2205	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	8506
RBM8A-BGHcLV34-31_S11_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2205	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	8556
RBM8A-BGHcLV34-31_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	2205					GRCh38	V40	RBM8A-BGHcLV34-31/Aligned.sortedByCoord.out.bam		ENCORE2	17752
RBM8A-BGHcLV34-31_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	2205					GRCh38	V40	RBM8A-BGHcLV34-31/Aligned.sortedByCoord.out.bam		ENCORE2	17802
RBM8A-BGHcLV34-31_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	2205					GRCh38	V40	RBM8A-BGHcLV34-31/Aligned.sortedByCoord.out.bam		ENCORE2	17852
RBM8A-BGHcLV34-31_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	2205					GRCh38	V40	RBM8A-BGHcLV34-31/Aligned.sortedByCoord.out.bam		ENCORE2	17902
RBM8A-BGHcLV34-31_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2205					GRCh38	V40	RBM8A-BGHcLV34-31_S11_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGHcLV34-31_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17952
RBM8A-BGHcLV34-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2205					GRCh38	V40	RBM8A-BGHcLV34-31_S11_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGHcLV34-31_S11_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29293
RBM8A-BGHcLV34-32_S12_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2206	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	8507
RBM8A-BGHcLV34-32_S12_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2206	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	8557
RBM8A-BGHcLV34-32_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	2206					GRCh38	V40	RBM8A-BGHcLV34-32/Aligned.sortedByCoord.out.bam		ENCORE2	17753
RBM8A-BGHcLV34-32_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	2206					GRCh38	V40	RBM8A-BGHcLV34-32/Aligned.sortedByCoord.out.bam		ENCORE2	17803
RBM8A-BGHcLV34-32_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	2206					GRCh38	V40	RBM8A-BGHcLV34-32/Aligned.sortedByCoord.out.bam		ENCORE2	17853
RBM8A-BGHcLV34-32_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	2206					GRCh38	V40	RBM8A-BGHcLV34-32/Aligned.sortedByCoord.out.bam		ENCORE2	17903
RBM8A-BGHcLV34-32_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2206					GRCh38	V40	RBM8A-BGHcLV34-32_S12_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGHcLV34-32_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17953
RBM8A-BGHcLV34-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2206					GRCh38	V40	RBM8A-BGHcLV34-32_S12_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGHcLV34-32_S12_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29294