RBM17 RNA-Seq in HepG2

General Information


RBP	RBM17
Cell_Line	HepG2
Method	shRNA
Exp_Name	RBM17-BGHLV26-HepG2
ENCODE_series_ID	ENCSR701KIW
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR385TMY
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	RBM17_BGHLV26_37
Rep2	RBM17_BGHLV26_38
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	62.6
Rep2_qPCR	58.7
Rep1_WB	85.0
Rep2_WB	93.3
Antibody Cat#	A302-498A
Antibody Lot#	A302-498A
Antibody DCC ID	ENCAB959TNR
Status	Released
Project	ENCODE3
ID	633

Experiment Information (Status: Released)

	BGHLV26-37	BGHLV26-38
idx	593	594
TRCN#_or_BGC#	TRCN0000010600	TRCN0000010600
shRNA_or_gRNA_sequence	CCGGTGATCCTTAAATGAACT	CCGGTGATCCTTAAATGAACT
PAM
Name	RBM17	RBM17
Sample_ID	BGHLV26-37	BGHLV26-38
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	RBM17	RBM17
qPCR_result	62.6	58.7
Ave_qPCR	60.6
RT-qPCR_primer-F	TGGAAGTTGAAACCAAGGAAG
RT-qPCR_primer-R	ATCCGTACTGCTTCATCATC
protein_conc	4012	3601
WB_result	85.0	93.3
Ave_WB	89.1
WB_DONE_date	7/30/2015
MW	45kDa
IP	1	1
antibody_Cat#	A302-498A	A302-498A
Antibody DCC ID	ENCAB959TNR	ENCAB959TNR
submitted_to_DCC_date	8/6/2015
Rep1_TPM	15.4	0
Rep2_TPM	12.9	0
Action
Library_start_date	9/8/2015	9/8/2015
repeat_library
Note	x	x
ID	2676	2677

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM17	Product_ID: A302-498A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM17-human

Experiment Status

	BGHLV26-37	BGHLV26-38
Sample_ID	BGHLV26-37	BGHLV26-38
Sample Name	RBM17_BGHLV26_37	RBM17_BGHLV26_38
Sample Name	RBM17_BGHLV26_37	RBM17_BGHLV26_38
RBP	RBM17	RBM17
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	950	951

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-37	BGHLV26-38
Sample #
Sample Name	RBM17-BGHLV26-37	RBM17-BGHLV26-38
Sample_Name_Alias	RBM17_BGHLV26_37	RBM17_BGHLV26_38
Index Well Position	S11	S12
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/set2/H2.png	DNA_Library_LV24-25-26/set1/D9.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV25-26/set1/E2.png	RNA_Library_LV25-26/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-37	BGHLV26-38
RBP	RBM17	RBM17
Batch_ID	BGHLV26	BGHLV26
WB_result	85.000	93.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2638	2639

Sequencing Information

	BGHLV26-37	BGHLV26-38
Sample_ID	BGHLV26-37	BGHLV26-38
Sample Name	RBM17_BGHLV26_37	RBM17_BGHLV26_38
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	80,022,968	87,371,626
total_aligned_reads	67,185,032	74,628,600
unique_aligned_reads	62,540,590	69,743,866
percent_uniqueAligned	0.78153	0.79824
correlation_replicates	0.998788	0.998788
spikein_reads	140,380	171,084
percent_spikeins	0.00175	0.00196
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1280	1281

Data Submission Information

	BGHLV26-37	BGHLV26-37
ENCODE_alias	brenton-graveley:RBM17_BGHLV26	brenton-graveley:RBM17-BGHLV26-HepG2
ENCODE_accession	ENCSR385TMY	ENCSR701KIW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-37	BGHLV26-37
Sample Name	RBM17_BGHLV26_37	RBM17_BGHLV26_37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3022	6894

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
RBM17_BGHLV26_37_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1280	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19824
RBM17_BGHLV26_37_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1280	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19846
RBM17_BGHLV26_37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1280					GRCh38	V40	RBM17_BGHLV26_37_1.fastq.gz,RBM17_BGHLV26_37_2.fastq.gz		ENCORE2	19868
RBM17_BGHLV26_37_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	1280					GRCh38	V40	RBM17_BGHLV26_37/Aligned.sortedByCoord.out.bam		ENCORE2	19890
RBM17_BGHLV26_37_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	1280					GRCh38	V40	RBM17_BGHLV26_37/Aligned.sortedByCoord.out.bam		ENCORE2	19912
RBM17_BGHLV26_37_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	1280					GRCh38	V40	RBM17_BGHLV26_37/Aligned.sortedByCoord.out.bam		ENCORE2	19934
RBM17_BGHLV26_37_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	1280					GRCh38	V40	RBM17_BGHLV26_37/Aligned.sortedByCoord.out.bam		ENCORE2	19956
RBM17_BGHLV26_37_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1280					GRCh38	V40	RBM17_BGHLV26_37_1.fastq.gz,RBM17_BGHLV26_37_2.fastq.gz		ENCORE2	20664
RBM17_BGHLV26_38_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1281	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19825
RBM17_BGHLV26_38_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1281	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19847
RBM17_BGHLV26_38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1281					GRCh38	V40	RBM17_BGHLV26_38_1.fastq.gz,RBM17_BGHLV26_38_2.fastq.gz		ENCORE2	19869
RBM17_BGHLV26_38_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	1281					GRCh38	V40	RBM17_BGHLV26_38/Aligned.sortedByCoord.out.bam		ENCORE2	19891
RBM17_BGHLV26_38_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	1281					GRCh38	V40	RBM17_BGHLV26_38/Aligned.sortedByCoord.out.bam		ENCORE2	19913
RBM17_BGHLV26_38_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	1281					GRCh38	V40	RBM17_BGHLV26_38/Aligned.sortedByCoord.out.bam		ENCORE2	19935
RBM17_BGHLV26_38_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	1281					GRCh38	V40	RBM17_BGHLV26_38/Aligned.sortedByCoord.out.bam		ENCORE2	19957
RBM17_BGHLV26_38_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1281					GRCh38	V40	RBM17_BGHLV26_38_1.fastq.gz,RBM17_BGHLV26_38_2.fastq.gz		ENCORE2	20665