RBM14 RNA-Seq in HepG2

General Information


RBP	RBM14
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBM14-BGHcLV07-HepG2
ENCODE_series_ID	ENCSR809JAD
Batch_ID	BGHcLV07
Pool ID	Pool-170911
Local_Set_Name	set39_H
ENCODE_KD_Exp_ID	ENCSR166MWM
ENCODE_CN_Exp_ID	ENCSR521WAI
Rep1	RBM14-BGHcLV07-27
Rep2	RBM14-BGHcLV07-28
CN1	NT-BGHcLV07-1
CN2	NT-BGHcLV07-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	89.0
Rep2_WB	87.2
Antibody Cat#	RN069PW
Antibody Lot#
Antibody DCC ID	ENCAB047USE
Status	Released
Project	ENCODE3
ID	766

Experiment Information (Status: Released)

	BGHcLV07-27	BGHcLV07-28
idx	139	140
TRCN#_or_BGC#	BGC#0000100	BGC#0000100
shRNA_or_gRNA_sequence	GCCGTTGAGCTGCGCGATTG	GCCGTTGAGCTGCGCGATTG
PAM
Name	RBM14_96-1	RBM14_96-1
Sample_ID	BGHcLV07-27	BGHcLV07-28
transduction_Date	6/13/17	6/13/17
days	D6	D6
RBP_name	RBM14	RBM14
qPCR_result	0.0	0.0
Ave_qPCR	0
RT-qPCR_primer-F	ACTTTGTTCCTTCGCCTCAG
RT-qPCR_primer-R	AAACCGCAGATCTAGAGCCA
protein_conc	3757	3616
WB_result	89.0	87.2
Ave_WB	88.1
WB_DONE_date	7/6/17
MW	69kD
IP	FU'S
antibody_Cat#	RN069PW
Antibody DCC ID	ENCAB047USE	ENCAB047USE
submitted_to_DCC_date	9/27/17
Rep1_TPM	40	0
Rep2_TPM	32	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	6282	6283

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM14	Product_ID: RN069PW Lot_ID: 1 Source: MBLI Target Name: RBM14-human

Experiment Status

	BGHcLV07-27	BGHcLV07-28
Sample_ID	BGHcLV07-27	BGHcLV07-28
Sample Name	RBM14-BGHcLV07-27	RBM14-BGHcLV07-28
Sample Name	RBM14-BGHcLV07-27	RBM14-BGHcLV07-28
RBP	RBM14	RBM14
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1387	1388

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV07-27	BGHcLV07-28
Sample #
Sample Name	RBM14-BGHcLV07-27	RBM14-BGHcLV07-28
Sample_Name_Alias	RBM14-BGHcLV07-27	RBM14-BGHcLV07-28
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/E4.png	DNA_Library_set39/set2/F4.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set39/set2/G1.png	RNA_Library_set39/set2/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV07-27	BGHcLV07-28
RBP	RBM14	RBM14
Batch_ID	BGHcLV07	BGHcLV07
WB_result	89.000	87.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3082	3083

Sequencing Information

	BGHcLV07-27	BGHcLV07-28
Sample_ID	BGHcLV07-27	BGHcLV07-28
Sample Name	RBM14-BGHcLV07-27	RBM14-BGHcLV07-28
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_H	set39_H
total_reads	54,901,388	52,362,746
total_aligned_reads	48,005,874	44,195,350
unique_aligned_reads	45,320,668	41,624,256
percent_uniqueAligned	0.82549	0.79492
correlation_replicates	0.995384	0.995384
spikein_reads	13,044	11,518
percent_spikeins	0.00024	0.00022
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1733	1734

Data Submission Information

	BGHcLV07-27	BGHcLV07-27
ENCODE_alias	brenton-graveley:RBM14-BGHcLV07	brenton-graveley:RBM14-BGHcLV07-HepG2
ENCODE_accession	ENCSR166MWM	ENCSR809JAD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV07-27	BGHcLV07-27
Sample Name	RBM14-BGHcLV07-27	RBM14-BGHcLV07-27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3233	6891

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
RBM14-BGHcLV07-27_AGTCAA_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1733	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22286
RBM14-BGHcLV07-27_AGTCAA_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1733	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22310
RBM14-BGHcLV07-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1733					GRCh38	V40	RBM14-BGHcLV07-27_AGTCAA_ACBE67ANXX_L008_001.R1.fastq.gz,RBM14-BGHcLV07-27_AGTCAA_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22334
RBM14-BGHcLV07-27_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1733					GRCh38	V40	RBM14-BGHcLV07-27/Aligned.sortedByCoord.out.bam		ENCORE2	22358
RBM14-BGHcLV07-27_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1733					GRCh38	V40	RBM14-BGHcLV07-27/Aligned.sortedByCoord.out.bam		ENCORE2	22382
RBM14-BGHcLV07-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1733					GRCh38	V40	RBM14-BGHcLV07-27/Aligned.sortedByCoord.out.bam		ENCORE2	22406
RBM14-BGHcLV07-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1733					GRCh38	V40	RBM14-BGHcLV07-27/Aligned.sortedByCoord.out.bam		ENCORE2	22430
RBM14-BGHcLV07-27_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1733					GRCh38	V40	RBM14-BGHcLV07-27_AGTCAA_ACBE67ANXX_L008_001.R1.fastq.gz,RBM14-BGHcLV07-27_AGTCAA_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22454
RBM14-BGHcLV07-28_AGTTCC_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1734	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22287
RBM14-BGHcLV07-28_AGTTCC_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1734	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22311
RBM14-BGHcLV07-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1734					GRCh38	V40	RBM14-BGHcLV07-28_AGTTCC_ACBE67ANXX_L008_001.R1.fastq.gz,RBM14-BGHcLV07-28_AGTTCC_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22335
RBM14-BGHcLV07-28_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1734					GRCh38	V40	RBM14-BGHcLV07-28/Aligned.sortedByCoord.out.bam		ENCORE2	22359
RBM14-BGHcLV07-28_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1734					GRCh38	V40	RBM14-BGHcLV07-28/Aligned.sortedByCoord.out.bam		ENCORE2	22383
RBM14-BGHcLV07-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1734					GRCh38	V40	RBM14-BGHcLV07-28/Aligned.sortedByCoord.out.bam		ENCORE2	22407
RBM14-BGHcLV07-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1734					GRCh38	V40	RBM14-BGHcLV07-28/Aligned.sortedByCoord.out.bam		ENCORE2	22431
RBM14-BGHcLV07-28_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1734					GRCh38	V40	RBM14-BGHcLV07-28_AGTTCC_ACBE67ANXX_L008_001.R1.fastq.gz,RBM14-BGHcLV07-28_AGTTCC_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22455