RBM27 RNA-Seq in HepG2

General Information


RBP	RBM27
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM27-BGHLV18-HepG2
ENCODE_series_ID	ENCSR603CKC
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR222SMI
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	RBM27_BGHLV18_47
Rep2	RBM27_BGHLV18_48
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	60.2
Rep2_qPCR	56.3
Rep1_WB
Rep2_WB	NO CLEAR BAND
Antibody Cat#	A301-233A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB173QUF
Status	Released
Project	ENCODE3
ID	456

Experiment Information (Status: Released)

	BGHLV18-47	BGHLV18-48
idx	347	348
TRCN#_or_BGC#	TRCN0000247707	TRCN0000247707
shRNA_or_gRNA_sequence	ACAACTGAGAGTTGGTCTAAT	ACAACTGAGAGTTGGTCTAAT
PAM
Name	RBM27	RBM27
Sample_ID	BGHLV18-47	BGHLV18-48
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	RBM27	RBM27
qPCR_result	60.2	56.3
Ave_qPCR	58.3
RT-qPCR_primer-F	gccttttgtgctgatcaactt
RT-qPCR_primer-R	ctggttccaaaagtggaagg
protein_conc	3666	3762
WB_result		NO CLEAR BAND
Ave_WB	NO CLEAR BAND
WB_DONE_date	2/5/2015	1/22/2016
MW		wes
IP	1	1
antibody_Cat#	A301-233A	A301-233A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	6.5	0
Rep2_TPM	5.9	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2412	2413

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV18-47	BGHLV18-48
Sample_ID	BGHLV18-47	BGHLV18-48
Sample Name	RBM27_BGHLV18_47	RBM27_BGHLV18_48
Sample Name	RBM27_BGHLV18_47	RBM27_BGHLV18_48
RBP	RBM27	RBM27
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	642	643

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-47	BGHLV18-48
Sample #
Sample Name	RBM27-BGHLV18-47	RBM27-BGHLV18-48
Sample_Name_Alias	RBM27_BGHLV18_47	RBM27_BGHLV18_48
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C4.png	DNA_Library_LV18-19/set1/D4.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV18-19/set1/A11.png	RNA_Library_LV18-19/set1/B11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-47	BGHLV18-48
RBP	RBM27	RBM27
Batch_ID	BGHLV18	BGHLV18
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2326	2327

Sequencing Information

	BGHLV18-47	BGHLV18-48
Sample_ID	BGHLV18-47	BGHLV18-48
Sample Name	RBM27_BGHLV18_47	RBM27_BGHLV18_48
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	54,970,000	80,960,000
total_aligned_reads	49,980,542	73,809,804
unique_aligned_reads	46,930,220	69,332,048
percent_uniqueAligned	0.85374	0.85637
correlation_replicates	0.999570	0.999570
spikein_reads	160,326	169,684
percent_spikeins	0.00292	0.00210
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	968	969

Data Submission Information

	BGHLV18-47	BGHLV18-47
ENCODE_alias	brenton-graveley:RBM27_BGHLV18	brenton-graveley:RBM27-BGHLV18-HepG2
ENCODE_accession	ENCSR222SMI	ENCSR603CKC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-47	BGHLV18-47
Sample Name	RBM27_BGHLV18_47	RBM27_BGHLV18_47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2838	6900

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
RBM27_BGHLV18_47_TTAGGC_L004_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	968	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14816
RBM27_BGHLV18_47_TTAGGC_L004_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	968	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14854
RBM27_BGHLV18_47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	968					GRCh38	V40	RBM27_BGHLV18_47_TTAGGC_L004_R1_001.fastq.gz,RBM27_BGHLV18_47_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	14892
RBM27_BGHLV18_47_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	968					GRCh38	V40	RBM27_BGHLV18_47/Aligned.sortedByCoord.out.bam		ENCORE2	14930
RBM27_BGHLV18_47_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	968					GRCh38	V40	RBM27_BGHLV18_47/Aligned.sortedByCoord.out.bam		ENCORE2	14968
RBM27_BGHLV18_47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	968					GRCh38	V40	RBM27_BGHLV18_47/Aligned.sortedByCoord.out.bam		ENCORE2	15006
RBM27_BGHLV18_47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	968					GRCh38	V40	RBM27_BGHLV18_47/Aligned.sortedByCoord.out.bam		ENCORE2	15044
RBM27_BGHLV18_47_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	968					GRCh38	V40	RBM27_BGHLV18_47_TTAGGC_L004_R1_001.fastq.gz,RBM27_BGHLV18_47_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	15082
RBM27_BGHLV18_48_TGACCA_L004_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	969	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14817
RBM27_BGHLV18_48_TGACCA_L004_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	969	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14855
RBM27_BGHLV18_48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	969					GRCh38	V40	RBM27_BGHLV18_48_TGACCA_L004_R1_001.fastq.gz,RBM27_BGHLV18_48_TGACCA_L004_R2_001.fastq.gz		ENCORE2	14893
RBM27_BGHLV18_48_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	969					GRCh38	V40	RBM27_BGHLV18_48/Aligned.sortedByCoord.out.bam		ENCORE2	14931
RBM27_BGHLV18_48_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	969					GRCh38	V40	RBM27_BGHLV18_48/Aligned.sortedByCoord.out.bam		ENCORE2	14969
RBM27_BGHLV18_48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	969					GRCh38	V40	RBM27_BGHLV18_48/Aligned.sortedByCoord.out.bam		ENCORE2	15007
RBM27_BGHLV18_48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	969					GRCh38	V40	RBM27_BGHLV18_48/Aligned.sortedByCoord.out.bam		ENCORE2	15045
RBM27_BGHLV18_48_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	969					GRCh38	V40	RBM27_BGHLV18_48_TGACCA_L004_R1_001.fastq.gz,RBM27_BGHLV18_48_TGACCA_L004_R2_001.fastq.gz		ENCORE2	15083