HNRNPM RNA-Seq in K562

General Information


RBP	HNRNPM
Cell_Line	K562
Method	shRNA
Exp_Name	HNRNPM-BGKLV29-K562
ENCODE_series_ID	ENCSR306PSB
Batch_ID	BGKLV29
Pool ID	Pool-151215B
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR746NIM
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	HNRNPM_BGKLV29-39
Rep2	HNRNPM_BGKLV29-40
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	78.6
Rep2_qPCR	85.3
Rep1_WB	49.9
Rep2_WB	63.2
Antibody Cat#	SC-20001/LOT D1304
Antibody Lot#	SC-20001/LOT D1304
Antibody DCC ID	ENCAB792TQV
Status	Released
Project	ENCODE3
ID	670

Experiment Information (Status: Released)

	BGKLV29-39	BGKLV29-40
idx	574	575
TRCN#_or_BGC#	TRCN0000001243	TRCN0000001243
shRNA_or_gRNA_sequence	AGAGCCTTCATTACAAACATA	AGAGCCTTCATTACAAACATA
PAM
Name	HNRNPM_43	HNRNPM_43
Sample_ID	BGKLV29-39	BGKLV29-40
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	HNRNPM	HNRNPM
qPCR_result	78.6	85.3
Ave_qPCR	82.0
RT-qPCR_primer-F	atggccagctgctatttgat
RT-qPCR_primer-R	gaagttgttgtggacgctca
protein_conc	2064	2201
WB_result	49.9	63.2
Ave_WB	56.5
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	204.250439	0
Rep2_TPM	109.284013	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	653	654

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

	BGKLV29-39	BGKLV29-40
Sample_ID	BGKLV29-39	BGKLV29-40
Sample Name	HNRNPM_BGKLV29-39	HNRNPM_BGKLV29-40
Sample Name	HNRNPM_BGKLV29-39	HNRNPM_BGKLV29-40
RBP	HNRNPM	HNRNPM
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1024	1025

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-39	BGKLV29-40
Sample #
Sample Name	HNRNPM-BGKLV29-39	HNRNPM-BGKLV29-40
Sample_Name_Alias	HNRNPM_BGKLV29-39	HNRNPM_BGKLV29-40
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G6.png	DNA_Library_LV28-29-30/set1/H6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C2.png	RNA_Library_LV29-30-31-32/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-39	BGKLV29-40
RBP	HNRNPM	HNRNPM
Batch_ID	BGKLV29	BGKLV29
WB_result	49.900	63.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2712	2713

Sequencing Information

	BGKLV29-39	BGKLV29-40
Sample_ID	BGKLV29-39	BGKLV29-40
Sample Name	HNRNPM_BGKLV29-39	HNRNPM_BGKLV29-40
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set29	set29
total_reads	42,095,252	43,845,976
total_aligned_reads	38,092,036	39,645,670
unique_aligned_reads	34,653,816	36,071,934
percent_uniqueAligned	0.82322	0.82270
correlation_replicates	0.994448	0.994448
spikein_reads	226,268	215,094
percent_spikeins	0.00538	0.00491
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1383	1384

Data Submission Information

	BGKLV29-39	BGKLV29-39
ENCODE_alias	brenton-graveley:HNRNPM_BGKLV29	brenton-graveley:HNRNPM-BGKLV29-K562
ENCODE_accession	ENCSR746NIM	ENCSR306PSB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-39	BGKLV29-39
Sample Name	HNRNPM_BGKLV29-39	HNRNPM_BGKLV29-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3061	6768

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_BGKLV29-39_ACTGAT_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1383	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20426
HNRNPM_BGKLV29-39_ACTGAT_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1383	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20456
HNRNPM_BGKLV29-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1383					GRCh38	V40	HNRNPM_BGKLV29-39_ACTGAT_L002_001.R1.fastq.gz,HNRNPM_BGKLV29-39_ACTGAT_L002_001.R2.fastq.gz		ENCORE2	20486
HNRNPM_BGKLV29-39_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1383					GRCh38	V40	HNRNPM_BGKLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	20516
HNRNPM_BGKLV29-39_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1383					GRCh38	V40	HNRNPM_BGKLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	20546
HNRNPM_BGKLV29-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1383					GRCh38	V40	HNRNPM_BGKLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	20576
HNRNPM_BGKLV29-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1383					GRCh38	V40	HNRNPM_BGKLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	20606
HNRNPM_BGKLV29-39_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1383					GRCh38	V40	HNRNPM_BGKLV29-39_ACTGAT_L002_001.R1.fastq.gz,HNRNPM_BGKLV29-39_ACTGAT_L002_001.R2.fastq.gz		ENCORE2	20636
HNRNPM_BGKLV29-40_ATTCCT_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1384	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20427
HNRNPM_BGKLV29-40_ATTCCT_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1384	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20457
HNRNPM_BGKLV29-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1384					GRCh38	V40	HNRNPM_BGKLV29-40_ATTCCT_L002_001.R1.fastq.gz,HNRNPM_BGKLV29-40_ATTCCT_L002_001.R2.fastq.gz		ENCORE2	20487
HNRNPM_BGKLV29-40_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1384					GRCh38	V40	HNRNPM_BGKLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	20517
HNRNPM_BGKLV29-40_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1384					GRCh38	V40	HNRNPM_BGKLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	20547
HNRNPM_BGKLV29-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1384					GRCh38	V40	HNRNPM_BGKLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	20577
HNRNPM_BGKLV29-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1384					GRCh38	V40	HNRNPM_BGKLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	20607
HNRNPM_BGKLV29-40_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1384					GRCh38	V40	HNRNPM_BGKLV29-40_ATTCCT_L002_001.R1.fastq.gz,HNRNPM_BGKLV29-40_ATTCCT_L002_001.R2.fastq.gz		ENCORE2	20637