Home
NEWS
Summary
Data Files
Search
FAQ
Admin Login
Top
PUM1
shRNA
in K562
Control:
NT_BGKLV25
General Information
Experiment Information
Sequencing Information
Data Submission
Files
General Information
RBP
PUM1
Cell_Line
K562
Method
shRNA
Exp_Name
PUM1-BGKLV25-K562
ENCODE_series_ID
ENCSR449VKZ
Batch_ID
BGKLV25
Pool ID
Pool-151101
Local_Set_Name
set25
ENCODE_KD_Exp_ID
ENCSR745WVZ
ENCODE_CN_Exp_ID
ENCSR620PUP
Rep1
PUM1-BGKLV25-45
Rep2
PUM1-BGKLV25-46
CN1
NT_BGKLV25-1
CN2
NT_BGKLV25-2
Rep1_qPCR
55.0
Rep2_qPCR
60.6
Rep1_WB
97.1
Rep2_WB
97.3
Antibody Cat#
A302-576A
Antibody Lot#
A302-576A
Antibody DCC ID
ENCAB744LEE
Status
Released
Project
ENCODE3
ID
623
Experiment Information
Western Blot
Experiment Status
Experiment Information (Status:
Released
)
BGKLV25-45
BGKLV25-46
idx
448
449
TRCN#_or_BGC#
TRCN0000275489
TRCN0000275489
shRNA_or_gRNA_sequence
GCGTTTAAGGGACAGGTATTT
GCGTTTAAGGGACAGGTATTT
PAM
Name
PUM1_89
PUM1_89
Sample_ID
BGKLV25-45
BGKLV25-46
transduction_Date
3/17/2015
3/17/2015
days
RBP_name
PUM1
PUM1
qPCR_result
55.0
60.6
Ave_qPCR
57.8
RT-qPCR_primer-F
GCCCCAGTCTTTGCAATTTA
RT-qPCR_primer-R
AATCACTCGGCAGCCATAAG
protein_conc
3129
3382
WB_result
97.1
97.3
Ave_WB
97.2
WB_DONE_date
5/11/2015
MW
126kDa
IP
1
1
antibody_Cat#
A302-576A
A302-576A
Antibody DCC ID
ENCAB744LEE
ENCAB744LEE
submitted_to_DCC_date
8/6/2015
Rep1_TPM
17.7485463
0
Rep2_TPM
18.5950205
0
Action
Library_start_date
6/23/2015
6/23/2015
repeat_library
Note
ID
519
520
Western Blot
RBP
Antibody Info
Primary-HepG2
Secondary-HepG2
Primary-K562
Secondary-K562
Primary-UBERON
Primary-Hela
PUM1
Product_ID:
A302-576A
Lot_ID: 1
Source: Bethyl Labs
Target Name: PUM1-human
Experiment Status
BGKLV25-45
BGKLV25-46
Sample_ID
BGKLV25-45
BGKLV25-46
Sample Name
PUM1-BGKLV25-45
PUM1-BGKLV25-46
Sample Name
PUM1-BGKLV25-45
PUM1-BGKLV25-46
RBP
PUM1
PUM1
Cell_Line
K562
K562
Exp UID
Status
Released
Released
Status_date
2015-12-08
2015-12-08
Project
ENCODE3
ENCODE3
Note
ID
926
927
Library-Prep
Sequencing
Library-Prep Information
BGKLV25-45
BGKLV25-46
Sample #
Sample Name
PUM1-BGKLV25-45
PUM1-BGKLV25-46
Sample_Name_Alias
PUM1-BGKLV25-45
PUM1-BGKLV25-46
Index Well Position
S07
S08
Index_table
IDT_TruSeqSingleIndex_24
IDT_TruSeqSingleIndex_24
LibPrep_date
2015-06-23
2015-06-23
Lib_ID
Lib-150623
Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well
DNA_Library_LV24-25-26/set1/G3.png
DNA_Library_LV24-25-26/set1/H3.png
RIN
9.6
9.8
libSample_RNA_Well
RNA_Library_LV22-23-25/set1/A12.png
RNA_Library_LV22-23-25/set1/B12.png
SampleQC_method
SampleQC_date
Sample_ID
BGKLV25-45
BGKLV25-46
RBP
PUM1
PUM1
Batch_ID
BGKLV25
BGKLV25
WB_result
97.100
97.300
Library Description
TruSeq mRNA
TruSeq mRNA
Repeat_Library_Suffix
Lib_Status
SendToSequence
SendToSequence
Project
ENCODE3
ENCODE3
ID
2618
2619
Sequencing Information
BGKLV25-45
BGKLV25-46
Sample_ID
BGKLV25-45
BGKLV25-46
Sample Name
PUM1-BGKLV25-45
PUM1-BGKLV25-46
Pool ID
Pool-151101
Pool-151101
LocalServer_folder
set25
set25
total_reads
97,136,820
129,518,846
total_aligned_reads
99,062,598
134,166,432
unique_aligned_reads
90,719,356
122,440,156
percent_uniqueAligned
0.93393
0.94535
correlation_replicates
0.999176
0.999176
spikein_reads
545,486
792,280
percent_spikeins
0.00562
0.00612
original_ReadLength
100
100
QC_Status
Submitted
Submitted
ID
1260
1261
Data Submission Information
BGKLV25-45
BGKLV25-45
ENCODE_alias
brenton-graveley:PUM1-BGKLV25
brenton-graveley:PUM1-BGKLV25-K562
ENCODE_accession
ENCSR745WVZ
ENCSR449VKZ
object_type
experiment
gene_silencing_series
assay_type
knockdown followed by RNA-seq
knockdown followed by RNA-seq
Sample_ID
BGKLV25-45
BGKLV25-45
Sample Name
PUM1-BGKLV25-45
PUM1-BGKLV25-45
Selected
Yes
Yes
Status
Released
Released
Status_Date
2015-12-02
2022-03-01
Project
ENCODE3
ENCODE3
protocol_URL
ID
3012
6880
File Information
Search:
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
Note
FILE_ID
PUM1-BGKLV25-45_Aligned.sortedByCoord.out.bam
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bam
alignments
knockdown followed by RNA-seq
Graveley Lab
1260
GRCh38
V40
PUM1-BGKLV25-45_CAGATC_L008_001.R1.fastq.gz,PUM1-BGKLV25-45_CAGATC_L008_001.R2.fastq.gz
ENCORE2
19660
PUM1-BGKLV25-45_CAGATC_L008_001.R1.fastq.gz
ENCODE_DATA/set25/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1260
HiSeq2000
100
paired-ended
1
NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz
ENCODE3
19588
PUM1-BGKLV25-45_CAGATC_L008_001.R2.fastq.gz
ENCODE_DATA/set25/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1260
HiSeq2000
100
paired-ended
2
NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz
ENCODE3
19624
PUM1-BGKLV25-45_quant.sf
ENCODE_DATA/set25/salmon_ENCORE2_file_links
transcript_quantification
transcript quantifications
knockdown followed by RNA-seq
Graveley Lab
1260
GRCh38
V40
PUM1-BGKLV25-45_CAGATC_L008_001.R1.fastq.gz,PUM1-BGKLV25-45_CAGATC_L008_001.R2.fastq.gz
ENCORE2
19994
PUM1-BGKLV25-45_Signal.Unique.strand+.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig+unique
plus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1260
GRCh38
V40
PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam
ENCORE2
19696
PUM1-BGKLV25-45_Signal.Unique.strand-.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig-unique
minus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1260
GRCh38
V40
PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam
ENCORE2
19732
PUM1-BGKLV25-45_Signal.UniqueMultiple.strand+.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig+all
plus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1260
GRCh38
V40
PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam
ENCORE2
19768
PUM1-BGKLV25-45_Signal.UniqueMultiple.strand-.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig-all
minus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1260
GRCh38
V40
PUM1-BGKLV25-45/Aligned.sortedByCoord.out.bam
ENCORE2
19804
PUM1-BGKLV25-46_ACTTGA_L008_001.R1.fastq.gz
ENCODE_DATA/set25/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1261
HiSeq2000
100
paired-ended
1
NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz
ENCODE3
19589
PUM1-BGKLV25-46_ACTTGA_L008_001.R2.fastq.gz
ENCODE_DATA/set25/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1261
HiSeq2000
100
paired-ended
2
NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz
ENCODE3
19625
PUM1-BGKLV25-46_Aligned.sortedByCoord.out.bam
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bam
alignments
knockdown followed by RNA-seq
Graveley Lab
1261
GRCh38
V40
PUM1-BGKLV25-46_ACTTGA_L008_001.R1.fastq.gz,PUM1-BGKLV25-46_ACTTGA_L008_001.R2.fastq.gz
ENCORE2
19661
PUM1-BGKLV25-46_quant.sf
ENCODE_DATA/set25/salmon_ENCORE2_file_links
transcript_quantification
transcript quantifications
knockdown followed by RNA-seq
Graveley Lab
1261
GRCh38
V40
PUM1-BGKLV25-46_ACTTGA_L008_001.R1.fastq.gz,PUM1-BGKLV25-46_ACTTGA_L008_001.R2.fastq.gz
ENCORE2
19995
PUM1-BGKLV25-46_Signal.Unique.strand+.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig+unique
plus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1261
GRCh38
V40
PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam
ENCORE2
19697
PUM1-BGKLV25-46_Signal.Unique.strand-.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig-unique
minus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1261
GRCh38
V40
PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam
ENCORE2
19733
PUM1-BGKLV25-46_Signal.UniqueMultiple.strand+.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig+all
plus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1261
GRCh38
V40
PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam
ENCORE2
19769
PUM1-BGKLV25-46_Signal.UniqueMultiple.strand-.bw
ENCODE_DATA/set25/STAR_ENCORE2_file_links
bigWig-all
minus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1261
GRCh38
V40
PUM1-BGKLV25-46/Aligned.sortedByCoord.out.bam
ENCORE2
19805
Showing 1 to 16 of 16 entries
Back