RBM22 RNA-Seq in HepG2

General Information


RBP	RBM22
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM22-BGHLV37-HepG2
ENCODE_series_ID	ENCSR972BSZ
Batch_ID	BGHLV37
Pool ID	Pool-161129
Local_Set_Name	set37
ENCODE_KD_Exp_ID	ENCSR330KHN
ENCODE_CN_Exp_ID	ENCSR997HCQ
Rep1	RBM22_BGHLV37-49
Rep2	RBM22_BGHLV37-50
CN1	NT_BGHLV37-1
CN2	NT_BGHLV37-2
Rep1_qPCR	29.7
Rep2_qPCR	28.1
Rep1_WB	77.5
Rep2_WB	72.7
Antibody Cat#	A303-923A
Antibody Lot#	A303-923A
Antibody DCC ID	ENCAB476CFS
Status	Released
Project	ENCODE3
ID	752

Experiment Information (Status: Released)

	BGHLV37-49	BGHLV37-50
idx	961	962
TRCN#_or_BGC#	TRCN0000232010	TRCN0000232010
shRNA_or_gRNA_sequence	CCATTACTGAGACAGATTTAA	CCATTACTGAGACAGATTTAA
PAM
Name	RBM22	RBM22
Sample_ID	BGHLV37-49	BGHLV37-50
transduction_Date	9/1/16	9/1/16
days
RBP_name	RBM22	RBM22
qPCR_result	29.7	28.1
Ave_qPCR	28.9
RT-qPCR_primer-F	ttctaccagttcggagagatcc
RT-qPCR_primer-R	tgtggcaaactggatgaaag
protein_conc	2147	2927
WB_result	77.5	72.7
Ave_WB	75.1
WB_DONE_date	9/19/16
MW	47kDa
IP	1	1
antibody_Cat#	A303-923A	A303-923A
Antibody DCC ID	ENCAB476CFS	ENCAB476CFS
submitted_to_DCC_date	10/26/16
Rep1_TPM	6.6	6.6
Rep2_TPM	5	5
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	3054	3055

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM22	Product_ID: A303-923A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM22-human

Experiment Status

	BGHLV37-49	BGHLV37-50
Sample_ID	BGHLV37-49	BGHLV37-50
Sample Name	RBM22_BGHLV37-49	RBM22_BGHLV37-50
Sample Name	RBM22_BGHLV37-49	RBM22_BGHLV37-50
RBP	RBM22	RBM22
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1299	1300

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-49	BGHLV37-50
Sample #
Sample Name	RBM22-BGHLV37-49	RBM22-BGHLV37-50
Sample_Name_Alias	RBM22_BGHLV37-49	RBM22_BGHLV37-50
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2016-11-03
Lib_ID	Lib-161103	Lib-161103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/A4.png	DNA_Library_LV37-38/set1/B4.png
RIN	10.0	9.6
libSample_RNA_Well	RNA_Library_LV37_38/set1/A2.png	RNA_Library_LV37_38/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV37-49	BGHLV37-50
RBP	RBM22	RBM22
Batch_ID	BGHLV37	BGHLV37
WB_result	77.500	72.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2986	2987

Sequencing Information

	BGHLV37-49	BGHLV37-50
Sample_ID	BGHLV37-49	BGHLV37-50
Sample Name	RBM22_BGHLV37-49	RBM22_BGHLV37-50
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set37	set37
total_reads	77,851,018	56,383,264
total_aligned_reads	69,315,810	51,192,630
unique_aligned_reads	64,892,914	47,967,112
percent_uniqueAligned	0.83355	0.85073
correlation_replicates	0.994688	0.994688
spikein_reads	345,138	262,576
percent_spikeins	0.00443	0.00466
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1635	1636

Data Submission Information

	BGHLV37-49	BGHLV37-49
ENCODE_alias	brenton-graveley:RBM22_BGHLV37	brenton-graveley:RBM22-BGHLV37-HepG2
ENCODE_accession	ENCSR330KHN	ENCSR972BSZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-49	BGHLV37-49
Sample Name	RBM22_BGHLV37-49	RBM22_BGHLV37-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3189	6896

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
RBM22_BGHLV37-49_ATCACG_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1635	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22042
RBM22_BGHLV37-49_ATCACG_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1635	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22058
RBM22_BGHLV37-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1635					GRCh38	V40	RBM22_BGHLV37-49_ATCACG_L006_001.R1.fastq.gz,RBM22_BGHLV37-49_ATCACG_L006_001.R2.fastq.gz		ENCORE2	22074
RBM22_BGHLV37-49_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1635					GRCh38	V40	RBM22_BGHLV37-49/Aligned.sortedByCoord.out.bam		ENCORE2	22090
RBM22_BGHLV37-49_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1635					GRCh38	V40	RBM22_BGHLV37-49/Aligned.sortedByCoord.out.bam		ENCORE2	22106
RBM22_BGHLV37-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1635					GRCh38	V40	RBM22_BGHLV37-49/Aligned.sortedByCoord.out.bam		ENCORE2	22122
RBM22_BGHLV37-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1635					GRCh38	V40	RBM22_BGHLV37-49/Aligned.sortedByCoord.out.bam		ENCORE2	22138
RBM22_BGHLV37-49_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1635					GRCh38	V40	RBM22_BGHLV37-49_ATCACG_L006_001.R1.fastq.gz,RBM22_BGHLV37-49_ATCACG_L006_001.R2.fastq.gz		ENCORE2	22154
RBM22_BGHLV37-50_CGATGT_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1636	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22043
RBM22_BGHLV37-50_CGATGT_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1636	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22059
RBM22_BGHLV37-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1636					GRCh38	V40	RBM22_BGHLV37-50_CGATGT_L006_001.R1.fastq.gz,RBM22_BGHLV37-50_CGATGT_L006_001.R2.fastq.gz		ENCORE2	22075
RBM22_BGHLV37-50_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1636					GRCh38	V40	RBM22_BGHLV37-50/Aligned.sortedByCoord.out.bam		ENCORE2	22091
RBM22_BGHLV37-50_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1636					GRCh38	V40	RBM22_BGHLV37-50/Aligned.sortedByCoord.out.bam		ENCORE2	22107
RBM22_BGHLV37-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1636					GRCh38	V40	RBM22_BGHLV37-50/Aligned.sortedByCoord.out.bam		ENCORE2	22123
RBM22_BGHLV37-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1636					GRCh38	V40	RBM22_BGHLV37-50/Aligned.sortedByCoord.out.bam		ENCORE2	22139
RBM22_BGHLV37-50_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1636					GRCh38	V40	RBM22_BGHLV37-50_CGATGT_L006_001.R1.fastq.gz,RBM22_BGHLV37-50_CGATGT_L006_001.R2.fastq.gz		ENCORE2	22155