RBM28 RNA-Seq in HepG2

General Information


RBP	RBM28
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBM28-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	RBM28-BGHcLV34-29
Rep2	RBM28-BGHcLV34-30
CN1	NT-BGHcLV34-1
CN2	NT-BGHcLV34-2
Rep1_qPCR	41.3
Rep2_qPCR	33.0
Rep1_WB	90.6
Rep2_WB	80.4
Antibody Cat#	A303-925A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	944

Experiment Information (Status: Submitting)

	BGHcLV34-29	BGHcLV34-30
idx	1099	1100
TRCN#_or_BGC#	BGC#0000764	BGC#0000764
shRNA_or_gRNA_sequence	CTGCTTGACAGGCCGGACAG	CTGCTTGACAGGCCGGACAG
PAM	TGG	TGG
Name	RBM28_86	RBM28_86
Sample_ID	BGHcLV34-29	BGHcLV34-30
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	RBM28	RBM28
qPCR_result	41.3	33.0
Ave_qPCR	37.1
RT-qPCR_primer-F	agttccaagagcacgagcat
RT-qPCR_primer-R	ctgcgctggatccttaattc
protein_conc	2717	3223
WB_result	90.6	80.4
Ave_WB	85.5
WB_DONE_date	7/6/22
MW	86KD
IP
antibody_Cat#	A303-925A	LOT #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	7278	7279

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV34-29	BGHcLV34-30
Sample_ID	BGHcLV34-29	BGHcLV34-30
Sample Name
Sample Name	RBM28-BGHcLV34-29	RBM28-BGHcLV34-30
RBP	RBM28	RBM28
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10805	10806

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-29	BGHcLV34-30
Sample #	9	10
Sample Name	RBM28-BGHcLV34-29	RBM28-BGHcLV34-30
Sample_Name_Alias
Index Well Position	A02	B02
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	284	283
Peak_Molarity	49.30	61.60
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/A6.png	DNA_Library_set54-56/set3/B6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set54-56/set2/A2.png	RNA_Library_set54-56/set2/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGHcLV34-29	BGHcLV34-30
RBP	RBM28	RBM28
Batch_ID	BGHcLV34	BGHcLV34
WB_result	52.000	60.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3326	3327

Sequencing Information

	BGHcLV34-29	BGHcLV34-30
Sample_ID	BGHcLV34-29	BGHcLV34-30
Sample Name	RBM28-BGHcLV34-29	RBM28-BGHcLV34-30
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	44,044,824	67,264,154
total_aligned_reads	38,805,184	58,743,432
unique_aligned_reads	36,694,112	55,434,186
percent_uniqueAligned	0.83311	0.82413
correlation_replicates	0.994181	0.994181
spikein_reads	5,656	4,294
percent_spikeins	0.00013	0.00006
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2203	2204

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
RBM28-BGHcLV34-29_S9_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2203	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	8504
RBM28-BGHcLV34-29_S9_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2203	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	8554
RBM28-BGHcLV34-29_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	2203					GRCh38	V40	RBM28-BGHcLV34-29/Aligned.sortedByCoord.out.bam		ENCORE2	17750
RBM28-BGHcLV34-29_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	2203					GRCh38	V40	RBM28-BGHcLV34-29/Aligned.sortedByCoord.out.bam		ENCORE2	17800
RBM28-BGHcLV34-29_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	2203					GRCh38	V40	RBM28-BGHcLV34-29/Aligned.sortedByCoord.out.bam		ENCORE2	17850
RBM28-BGHcLV34-29_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	2203					GRCh38	V40	RBM28-BGHcLV34-29/Aligned.sortedByCoord.out.bam		ENCORE2	17900
RBM28-BGHcLV34-29_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2203					GRCh38	V40	RBM28-BGHcLV34-29_S9_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGHcLV34-29_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17950
RBM28-BGHcLV34-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2203					GRCh38	V40	RBM28-BGHcLV34-29_S9_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGHcLV34-29_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29291
RBM28-BGHcLV34-30_S10_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2204	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	8505
RBM28-BGHcLV34-30_S10_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2204	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	8555
RBM28-BGHcLV34-30_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	2204					GRCh38	V40	RBM28-BGHcLV34-30/Aligned.sortedByCoord.out.bam		ENCORE2	17751
RBM28-BGHcLV34-30_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	2204					GRCh38	V40	RBM28-BGHcLV34-30/Aligned.sortedByCoord.out.bam		ENCORE2	17801
RBM28-BGHcLV34-30_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	2204					GRCh38	V40	RBM28-BGHcLV34-30/Aligned.sortedByCoord.out.bam		ENCORE2	17851
RBM28-BGHcLV34-30_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	2204					GRCh38	V40	RBM28-BGHcLV34-30/Aligned.sortedByCoord.out.bam		ENCORE2	17901
RBM28-BGHcLV34-30_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2204					GRCh38	V40	RBM28-BGHcLV34-30_S10_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGHcLV34-30_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17951
RBM28-BGHcLV34-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2204					GRCh38	V40	RBM28-BGHcLV34-30_S10_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGHcLV34-30_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29292