LSM11 RNA-Seq in HepG2

General Information


RBP	LSM11
Cell_Line	HepG2
Method	shRNA
Exp_Name	LSM11-BGHLV18-HepG2
ENCODE_series_ID	ENCSR795XHB
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR883BXR
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	LSM11_BGHLV18_23
Rep2	LSM11_BGHLV18_24
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	81.1
Rep2_qPCR	63.7
Rep1_WB	89.7
Rep2_WB	88.6
Antibody Cat#	A303-709A
Antibody Lot#	A303-709A
Antibody DCC ID	ENCAB344HWD
Status	Released
Project	ENCODE3
ID	450

Experiment Information (Status: Released)

	BGHLV18-23	BGHLV18-24
idx	323	324
TRCN#_or_BGC#	TRCN0000074440	TRCN0000074440
shRNA_or_gRNA_sequence	GCATTCGACAAGTTCTGGAAT	GCATTCGACAAGTTCTGGAAT
PAM
Name	LSM11	LSM11
Sample_ID	BGHLV18-23	BGHLV18-24
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	LSM11	LSM11
qPCR_result	81.1	63.7
Ave_qPCR	72.4
RT-qPCR_primer-F	gaatgcccttgcacgaag
RT-qPCR_primer-R	attcaccttcaccccctcac
protein_conc	4697	4292
WB_result	89.7	88.6
Ave_WB	89.1
WB_DONE_date	3/31/2015
MW	40kDa
IP	1	1
antibody_Cat#	A303-709A	A303-709A
Antibody DCC ID	ENCAB344HWD	ENCAB344HWD
submitted_to_DCC_date	5/6/2015
Rep1_TPM	1	0
Rep2_TPM	0.7	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2388	2389

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LSM11	Product_ID: A303-709A Lot_ID: 1 Source: Bethyl Labs Target Name: LSM11-human

Experiment Status

	BGHLV18-23	BGHLV18-24
Sample_ID	BGHLV18-23	BGHLV18-24
Sample Name	LSM11_BGHLV18_23	LSM11_BGHLV18_24
Sample Name	LSM11_BGHLV18_23	LSM11_BGHLV18_24
RBP	LSM11	LSM11
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	628	629

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-23	BGHLV18-24
Sample #
Sample Name	LSM11-BGHLV18-23	LSM11-BGHLV18-24
Sample_Name_Alias	LSM11_BGHLV18_23	LSM11_BGHLV18_24
Index Well Position	S15	S16
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/G2.png	DNA_Library_LV18-19/set1/H2.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_LV18-19/set1/E9.png	RNA_Library_LV18-19/set1/F9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-23	BGHLV18-24
RBP	LSM11	LSM11
Batch_ID	BGHLV18	BGHLV18
WB_result	89.700	88.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2312	2313

Sequencing Information

	BGHLV18-23	BGHLV18-24
Sample_ID	BGHLV18-23	BGHLV18-24
Sample Name	LSM11_BGHLV18_23	LSM11_BGHLV18_24
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	67,140,000	37,230,000
total_aligned_reads	60,969,342	34,172,240
unique_aligned_reads	57,669,754	32,354,964
percent_uniqueAligned	0.85895	0.86906
correlation_replicates	0.993095	0.993095
spikein_reads	298,442	250,014
percent_spikeins	0.00445	0.00672
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	954	955

Data Submission Information

	BGHLV18-23	BGHLV18-23
ENCODE_alias	brenton-graveley:LSM11_BGHLV18	brenton-graveley:LSM11-BGHLV18-HepG2
ENCODE_accession	ENCSR883BXR	ENCSR795XHB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-23	BGHLV18-23
Sample Name	LSM11_BGHLV18_23	LSM11_BGHLV18_23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2831	6801

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
LSM11_BGHLV18_23_ATGTCA_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	954	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14802
LSM11_BGHLV18_23_ATGTCA_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	954	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14840
LSM11_BGHLV18_23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	954					GRCh38	V40	LSM11_BGHLV18_23_ATGTCA_L002_R1_001.fastq.gz,LSM11_BGHLV18_23_ATGTCA_L002_R2_001.fastq.gz		ENCORE2	14878
LSM11_BGHLV18_23_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	954					GRCh38	V40	LSM11_BGHLV18_23/Aligned.sortedByCoord.out.bam		ENCORE2	14916
LSM11_BGHLV18_23_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	954					GRCh38	V40	LSM11_BGHLV18_23/Aligned.sortedByCoord.out.bam		ENCORE2	14954
LSM11_BGHLV18_23_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	954					GRCh38	V40	LSM11_BGHLV18_23/Aligned.sortedByCoord.out.bam		ENCORE2	14992
LSM11_BGHLV18_23_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	954					GRCh38	V40	LSM11_BGHLV18_23/Aligned.sortedByCoord.out.bam		ENCORE2	15030
LSM11_BGHLV18_23_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	954					GRCh38	V40	LSM11_BGHLV18_23_ATGTCA_L002_R1_001.fastq.gz,LSM11_BGHLV18_23_ATGTCA_L002_R2_001.fastq.gz		ENCORE2	15068
LSM11_BGHLV18_24_CCGTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	955	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14803
LSM11_BGHLV18_24_CCGTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	955	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14841
LSM11_BGHLV18_24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	955					GRCh38	V40	LSM11_BGHLV18_24_CCGTCC_L002_R1_001.fastq.gz,LSM11_BGHLV18_24_CCGTCC_L002_R2_001.fastq.gz		ENCORE2	14879
LSM11_BGHLV18_24_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	955					GRCh38	V40	LSM11_BGHLV18_24/Aligned.sortedByCoord.out.bam		ENCORE2	14917
LSM11_BGHLV18_24_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	955					GRCh38	V40	LSM11_BGHLV18_24/Aligned.sortedByCoord.out.bam		ENCORE2	14955
LSM11_BGHLV18_24_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	955					GRCh38	V40	LSM11_BGHLV18_24/Aligned.sortedByCoord.out.bam		ENCORE2	14993
LSM11_BGHLV18_24_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	955					GRCh38	V40	LSM11_BGHLV18_24/Aligned.sortedByCoord.out.bam		ENCORE2	15031
LSM11_BGHLV18_24_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	955					GRCh38	V40	LSM11_BGHLV18_24_CCGTCC_L002_R1_001.fastq.gz,LSM11_BGHLV18_24_CCGTCC_L002_R2_001.fastq.gz		ENCORE2	15069