RBM39 RNA-Seq in HepG2

General Information


RBP	RBM39
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM39-BGHLV26-HepG2
ENCODE_series_ID	ENCSR730AEK
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR760EGM
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	RBM39_BGHLV26_39
Rep2	RBM39_BGHLV26_40
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	55.0
Rep2_qPCR	57.7
Rep1_WB	47.8
Rep2_WB	63.8
Antibody Cat#	A300-291A
Antibody Lot#	A300-291A
Antibody DCC ID	ENCAB975CWB
Status	Released
Project	ENCODE3
ID	634

Experiment Information (Status: Released)

	BGHLV26-39	BGHLV26-40
idx	595	596
TRCN#_or_BGC#	TRCN0000021770	TRCN0000021770
shRNA_or_gRNA_sequence	GCTGGACCTATGAGGCTTTAT	GCTGGACCTATGAGGCTTTAT
PAM
Name	RBM39	RBM39
Sample_ID	BGHLV26-39	BGHLV26-40
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	RBM39	RBM39
qPCR_result	55.0	57.7
Ave_qPCR	56.3
RT-qPCR_primer-F	TTTAGGCGTGCCAATCATA
RT-qPCR_primer-R	TCATAGGTCCAGCACTTCCC
protein_conc	3835	4150
WB_result	47.8	63.8
Ave_WB	55.8
WB_DONE_date	6/26/2015
MW	59kd
IP	1	1
antibody_Cat#	A300-291A	A300-291A
Antibody DCC ID	ENCAB975CWB	ENCAB975CWB
submitted_to_DCC_date	8/6/2015
Rep1_TPM	218.9	0
Rep2_TPM	208.8	0
Action
Library_start_date	9/8/2015	9/8/2015
repeat_library
Note	x	x
ID	2678	2679

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM39	Product_ID: A300-291A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM39-human

Experiment Status

	BGHLV26-39	BGHLV26-40
Sample_ID	BGHLV26-39	BGHLV26-40
Sample Name	RBM39_BGHLV26_39	RBM39_BGHLV26_40
Sample Name	RBM39_BGHLV26_39	RBM39_BGHLV26_40
RBP	RBM39	RBM39
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	952	953

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-39	BGHLV26-40
Sample #
Sample Name	RBM39-BGHLV26-39	RBM39-BGHLV26-40
Sample_Name_Alias	RBM39_BGHLV26_39	RBM39_BGHLV26_40
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/E9.png	DNA_Library_LV24-25-26/set1/F9.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV25-26/set1/G2.png	RNA_Library_LV25-26/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-39	BGHLV26-40
RBP	RBM39	RBM39
Batch_ID	BGHLV26	BGHLV26
WB_result	47.800	63.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2640	2641

Sequencing Information

	BGHLV26-39	BGHLV26-40
Sample_ID	BGHLV26-39	BGHLV26-40
Sample Name	RBM39_BGHLV26_39	RBM39_BGHLV26_40
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	77,407,846	76,993,244
total_aligned_reads	62,844,772	59,491,702
unique_aligned_reads	58,772,484	55,666,024
percent_uniqueAligned	0.75926	0.72300
correlation_replicates	0.997966	0.997966
spikein_reads	191,132	143,512
percent_spikeins	0.00247	0.00186
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1282	1283

Data Submission Information

	BGHLV26-39	BGHLV26-39
ENCODE_alias	brenton-graveley:RBM39_BGHLV26	brenton-graveley:RBM39-BGHLV26-HepG2
ENCODE_accession	ENCSR760EGM	ENCSR730AEK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-39	BGHLV26-39
Sample Name	RBM39_BGHLV26_39	RBM39_BGHLV26_39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3023	6903

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
RBM39_BGHLV26_39_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1282	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19826
RBM39_BGHLV26_39_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1282	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19848
RBM39_BGHLV26_39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1282					GRCh38	V40	RBM39_BGHLV26_39_1.fastq.gz,RBM39_BGHLV26_39_2.fastq.gz		ENCORE2	19870
RBM39_BGHLV26_39_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1282					GRCh38	V40	RBM39_BGHLV26_39/Aligned.sortedByCoord.out.bam		ENCORE2	19892
RBM39_BGHLV26_39_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1282					GRCh38	V40	RBM39_BGHLV26_39/Aligned.sortedByCoord.out.bam		ENCORE2	19914
RBM39_BGHLV26_39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1282					GRCh38	V40	RBM39_BGHLV26_39/Aligned.sortedByCoord.out.bam		ENCORE2	19936
RBM39_BGHLV26_39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1282					GRCh38	V40	RBM39_BGHLV26_39/Aligned.sortedByCoord.out.bam		ENCORE2	19958
RBM39_BGHLV26_39_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1282					GRCh38	V40	RBM39_BGHLV26_39_1.fastq.gz,RBM39_BGHLV26_39_2.fastq.gz		ENCORE2	20666
RBM39_BGHLV26_40_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1283	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19827
RBM39_BGHLV26_40_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1283	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19849
RBM39_BGHLV26_40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1283					GRCh38	V40	RBM39_BGHLV26_40_1.fastq.gz,RBM39_BGHLV26_40_2.fastq.gz		ENCORE2	19871
RBM39_BGHLV26_40_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1283					GRCh38	V40	RBM39_BGHLV26_40/Aligned.sortedByCoord.out.bam		ENCORE2	19893
RBM39_BGHLV26_40_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1283					GRCh38	V40	RBM39_BGHLV26_40/Aligned.sortedByCoord.out.bam		ENCORE2	19915
RBM39_BGHLV26_40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1283					GRCh38	V40	RBM39_BGHLV26_40/Aligned.sortedByCoord.out.bam		ENCORE2	19937
RBM39_BGHLV26_40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1283					GRCh38	V40	RBM39_BGHLV26_40/Aligned.sortedByCoord.out.bam		ENCORE2	19959
RBM39_BGHLV26_40_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1283					GRCh38	V40	RBM39_BGHLV26_40_1.fastq.gz,RBM39_BGHLV26_40_2.fastq.gz		ENCORE2	20667