HNRNPM RNA-Seq in HepG2

General Information


RBP	HNRNPM
Cell_Line	HepG2
Method	shRNA
Exp_Name	HNRNPM-BGHLV30-HepG2
ENCODE_series_ID	ENCSR223RYC
Batch_ID	BGHLV30
Pool ID	Pool-151215A
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR995JMS
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	HNRNPM_BGHLV30-41
Rep2	HNRNPM_BGHLV30-42
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	64.4
Rep2_qPCR	66.7
Rep1_WB	70.9
Rep2_WB	63.8
Antibody Cat#	SC-20001/LOT D1304
Antibody Lot#	SC-20001/LOT D1304
Antibody DCC ID	ENCAB792TQV
Status	Released
Project	ENCODE3
ID	680

Experiment Information (Status: Released)

	BGHLV30-41	BGHLV30-42
idx	729	730
TRCN#_or_BGC#	TRCN0000001243	TRCN0000001243
shRNA_or_gRNA_sequence	AGAGCCTTCATTACAAACATA	AGAGCCTTCATTACAAACATA
PAM
Name	HNRNPM	HNRNPM
Sample_ID	BGHLV30-41	BGHLV30-42
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	HNRNPM	HNRNPM
qPCR_result	64.4	66.7
Ave_qPCR	65.6
RT-qPCR_primer-F	atggccagctgctatttgat
RT-qPCR_primer-R	gaagttgttgtggacgctca
protein_conc	4197	4061
WB_result	70.9	63.8
Ave_WB	67.3
WB_DONE_date	9/9/2015
MW	78kDa
IP
antibody_Cat#	SC-20001/LOT D1304	SC-20001/LOT D1304
Antibody DCC ID	ENCAB792TQV	ENCAB792TQV
submitted_to_DCC_date	12/7/2015
Rep1_TPM	86.6	0
Rep2_TPM	70.1	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2816	2817

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
HNRNPM	Product_ID: sc-20001 Lot_ID: D1304 Source: Santa Cruz Biotech Target Name: HNRNPM-human

Experiment Status

	BGHLV30-41	BGHLV30-42
Sample_ID	BGHLV30-41	BGHLV30-42
Sample Name	HNRNPM_BGHLV30-41	HNRNPM_BGHLV30-42
Sample Name	HNRNPM_BGHLV30-41	HNRNPM_BGHLV30-42
RBP	HNRNPM	HNRNPM
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1058	1059

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-41	BGHLV30-42
Sample #
Sample Name	HNRNPM-BGHLV30-41	HNRNPM-BGHLV30-42
Sample_Name_Alias	HNRNPM_BGHLV30-41	HNRNPM_BGHLV30-42
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C11.png	DNA_Library_LV28-29-30/set1/D11.png
RIN	10.0	9.7
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E6.png	RNA_Library_LV29-30-31-32/set1/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-41	BGHLV30-42
RBP	HNRNPM	HNRNPM
Batch_ID	BGHLV30	BGHLV30
WB_result	70.900	63.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2750	2751

Sequencing Information

	BGHLV30-41	BGHLV30-42
Sample_ID	BGHLV30-41	BGHLV30-42
Sample Name	HNRNPM_BGHLV30-41	HNRNPM_BGHLV30-42
Pool ID	Pool-151215A	Pool-151215A
LocalServer_folder	set30	set30
total_reads	52,793,446	58,588,934
total_aligned_reads	42,000,320	47,385,200
unique_aligned_reads	39,352,936	44,431,348
percent_uniqueAligned	0.74541	0.75836
correlation_replicates	0.999499	0.999499
spikein_reads	150,356	163,650
percent_spikeins	0.00285	0.00279
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1370	1371

Data Submission Information

	BGHLV30-41	BGHLV30-41
ENCODE_alias	brenton-graveley:HNRNPM_BGHLV30	brenton-graveley:HNRNPM-BGHLV30-HepG2
ENCODE_accession	ENCSR995JMS	ENCSR223RYC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-41	BGHLV30-41
Sample Name	HNRNPM_BGHLV30-41	HNRNPM_BGHLV30-41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3078	6767

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
HNRNPM_BGHLV30-41_GGCTAC_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1370	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20716
HNRNPM_BGHLV30-41_GGCTAC_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1370	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20750
HNRNPM_BGHLV30-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1370					GRCh38	V40	HNRNPM_BGHLV30-41_GGCTAC_L002_001.R1.fastq.gz,HNRNPM_BGHLV30-41_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	20784
HNRNPM_BGHLV30-41_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1370					GRCh38	V40	HNRNPM_BGHLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	20818
HNRNPM_BGHLV30-41_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1370					GRCh38	V40	HNRNPM_BGHLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	20852
HNRNPM_BGHLV30-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1370					GRCh38	V40	HNRNPM_BGHLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	20886
HNRNPM_BGHLV30-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1370					GRCh38	V40	HNRNPM_BGHLV30-41/Aligned.sortedByCoord.out.bam		ENCORE2	20920
HNRNPM_BGHLV30-41_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1370					GRCh38	V40	HNRNPM_BGHLV30-41_GGCTAC_L002_001.R1.fastq.gz,HNRNPM_BGHLV30-41_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	20954
HNRNPM_BGHLV30-42_CTTGTA_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1371	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20717
HNRNPM_BGHLV30-42_CTTGTA_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1371	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20751
HNRNPM_BGHLV30-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1371					GRCh38	V40	HNRNPM_BGHLV30-42_CTTGTA_L002_001.R1.fastq.gz,HNRNPM_BGHLV30-42_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	20785
HNRNPM_BGHLV30-42_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1371					GRCh38	V40	HNRNPM_BGHLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	20819
HNRNPM_BGHLV30-42_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1371					GRCh38	V40	HNRNPM_BGHLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	20853
HNRNPM_BGHLV30-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1371					GRCh38	V40	HNRNPM_BGHLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	20887
HNRNPM_BGHLV30-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1371					GRCh38	V40	HNRNPM_BGHLV30-42/Aligned.sortedByCoord.out.bam		ENCORE2	20921
HNRNPM_BGHLV30-42_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1371					GRCh38	V40	HNRNPM_BGHLV30-42_CTTGTA_L002_001.R1.fastq.gz,HNRNPM_BGHLV30-42_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	20955