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HNRNPA1
shRNA
in K562
Control:
NT_BGKLV21-B
General Information
Experiment Information
Sequencing Information
Data Submission
Files
General Information
RBP
HNRNPA1
Cell_Line
K562
Method
shRNA
Exp_Name
HNRNPA1-BGKLV21-K562
ENCODE_series_ID
ENCSR596JUF
Batch_ID
BGKLV21
Pool ID
Pool-160229
Local_Set_Name
set21
ENCODE_KD_Exp_ID
ENCSR048BWH
ENCODE_CN_Exp_ID
ENCSR438MDN
Rep1
HNRNPA1_BGKLV21-17B
Rep2
HNRNPA1_BGKLV21-18B
CN1
NT_BGKLV21-1B
CN2
NT_BGKLV21-2B
Rep1_qPCR
91.0
Rep2_qPCR
90.6
Rep1_WB
69.5
Rep2_WB
71.2
Antibody Cat#
sc-32301/LOT I2413
Antibody Lot#
sc-32301/LOT I2413
Antibody DCC ID
ENCAB603WLW
Status
Released
Project
ENCODE3
ID
595
Experiment Information
Western Blot
Experiment Status
Experiment Information (Status:
Released
)
BGKLV21-17
BGKLV21-17
BGKLV21-17
BGKLV21-18
BGKLV21-18
BGKLV21-18
idx
288
288
288
289
289
289
TRCN#_or_BGC#
TRCN0000006583
TRCN0000006583
TRCN0000006583
TRCN0000006583
TRCN0000006583
TRCN0000006583
shRNA_or_gRNA_sequence
GCCACAACTGTGAAGTTAGAA
GCCACAACTGTGAAGTTAGAA
GCCACAACTGTGAAGTTAGAA
GCCACAACTGTGAAGTTAGAA
GCCACAACTGTGAAGTTAGAA
GCCACAACTGTGAAGTTAGAA
PAM
Name
HNRNPA1
HNRNPA1
HNRNPA1
HNRNPA1
HNRNPA1
HNRNPA1
Sample_ID
BGKLV21-17
BGKLV21-17
BGKLV21-17
BGKLV21-18
BGKLV21-18
BGKLV21-18
transduction_Date
10/9/2014
10/9/2014
10/9/2014
10/9/2014
10/9/2014
10/9/2014
days
RBP_name
HNRNPA1
HNRNPA1
HNRNPA1
HNRNPA1
HNRNPA1
HNRNPA1
qPCR_result
91.0
91.0
91.0
90.6
90.6
90.6
Ave_qPCR
90.8
90.8
90.8
RT-qPCR_primer-F
CCTTTGACGACCATGACTCC
CCTTTGACGACCATGACTCC
CCTTTGACGACCATGACTCC
RT-qPCR_primer-R
TCTTGCTTTGACAGGGCTTT
TCTTGCTTTGACAGGGCTTT
TCTTGCTTTGACAGGGCTTT
protein_conc
4120
4120
4120
3500
3500
3500
WB_result
69.5
64.6
98.0
71.2
64.7
95.5
Ave_WB
70.4
64.7
96.7
WB_DONE_date
7/16/2015
9/16/2019
6/27/2023
MW
39kDa
39kDa
39kDa
IP
1
1
antibody_Cat#
sc-32301/LOT I2413
MA1-26736
8443S
sc-32301/LOT I2413
Mouse / IgG2b
LOT#4
Antibody DCC ID
ENCAB603WLW
ENCAB603WLW
submitted_to_DCC_date
8/6/2015
1/8/2024
Rep1_TPM
1018.39683
0
0
0
0
0
Rep2_TPM
962.872414
0
0
0
0
0
Action
Library_start_date
2/4/2016
2/4/2016
repeat_library
Note
x
x
ID
313
315
317
314
316
318
Western Blot
RBP
Antibody Info
Primary-HepG2
Secondary-HepG2
Primary-K562
Secondary-K562
Primary-UBERON
Primary-Hela
HNRNPA1
Product_ID:
sc-32301
Lot_ID: I2413
Source: Santa Cruz Biotech
Target Name: HNRNPA1-human
HNRNPA1
Product_ID:
MA1-26736
Lot_ID: TL2692993B
Source: Thermo Fisher
Target Name: HNRNPA1-human
HNRNPA1
Product_ID:
8443S
Lot_ID: 4
Source: Cell Signaling Technology
Target Name: HNRNPA1-human
Experiment Status
BGKLV21-17
BGKLV21-18
Sample_ID
BGKLV21-17
BGKLV21-18
Sample Name
HNRNPA1_BGKLV21-17B
HNRNPA1_BGKLV21-18B
Sample Name
HNRNPA1_BGKLV21-17B
HNRNPA1_BGKLV21-18B
RBP
HNRNPA1
HNRNPA1
Cell_Line
K562
K562
Exp UID
Status
Released
Released
Status_date
2016-03-07
2016-03-07
Project
ENCODE3
ENCODE3
Note
ID
1131
1132
Library-Prep
Sequencing
Library-Prep Information
BGKLV21-17
BGKLV21-18
Sample #
Sample Name
HNRNPA1-BGKLV21-17B
HNRNPA1-BGKLV21-18B
Sample_Name_Alias
HNRNPA1_BGKLV21-17B
HNRNPA1_BGKLV21-18B
Index Well Position
S09
S10
Index_table
IDT_TruSeqSingleIndex_24
IDT_TruSeqSingleIndex_24
LibPrep_date
2016-02-04
2016-02-04
Lib_ID
Lib-160204
Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well
DNA_Library_LV31-21B/set1/A8.png
DNA_Library_LV31-21B/set1/B8.png
RIN
9.7
9.8
libSample_RNA_Well
RNA_Library_LV19-21-24/set1/E8.png
RNA_Library_LV19-21-24/set1/F8.png
SampleQC_method
SampleQC_date
Sample_ID
BGKLV21-17
BGKLV21-18
RBP
HNRNPA1
HNRNPA1
Batch_ID
BGKLV21
BGKLV21
WB_result
69.500
71.200
Library Description
TruSeq mRNA
TruSeq mRNA
Repeat_Library_Suffix
B
B
Lib_Status
SendToSequence
SendToSequence
Project
ENCODE3
ENCODE3
ID
2828
2829
Sequencing Information
BGKLV21-17
BGKLV21-18
Sample_ID
BGKLV21-17
BGKLV21-18
Sample Name
HNRNPA1_BGKLV21-17B
HNRNPA1_BGKLV21-18B
Pool ID
Pool-160229
Pool-160229
LocalServer_folder
set21
set21
total_reads
54,444,194
59,214,214
total_aligned_reads
50,479,074
54,304,032
unique_aligned_reads
45,821,568
49,439,418
percent_uniqueAligned
0.84162
0.83492
correlation_replicates
0.994124
0.994124
spikein_reads
354,228
348,452
percent_spikeins
0.00651
0.00588
original_ReadLength
100
100
QC_Status
Submitted
Submitted
ID
1477
1478
Data Submission Information
BGKLV21-17
BGKLV21-17
ENCODE_alias
brenton-graveley:HNRNPA1_BGKLV21-B
brenton-graveley:HNRNPA1-BGKLV21-K562
ENCODE_accession
ENCSR048BWH
ENCSR596JUF
object_type
experiment
gene_silencing_series
assay_type
knockdown followed by RNA-seq
knockdown followed by RNA-seq
Sample_ID
BGKLV21-17
BGKLV21-17
Sample Name
HNRNPA1_BGKLV21-17B
HNRNPA1_BGKLV21-17B
Selected
Yes
Yes
Status
Released
Released
Status_Date
2016-03-07
2022-03-01
Project
ENCODE3
ENCODE3
protocol_URL
ID
3098
6749
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
HNRNPA1_BGKLV21-17B_Aligned.sortedByCoord.out.bam
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bam
alignments
knockdown followed by RNA-seq
Graveley Lab
1477
GRCh38
V40
HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R2.fastq.gz
ENCORE2
16016
HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R1.fastq.gz
ENCODE_DATA/set21/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1477
HiSeq2000
100
paired-ended
1
NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz
ENCODE3
15928
HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R2.fastq.gz
ENCODE_DATA/set21/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1477
HiSeq2000
100
paired-ended
2
NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz
ENCODE3
15972
HNRNPA1_BGKLV21-17B_quant.sf
ENCODE_DATA/set21/salmon_ENCORE2_file_links
transcript_quantification
transcript quantifications
knockdown followed by RNA-seq
Graveley Lab
1477
GRCh38
V40
HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-17B_GATCAG_L008_001.R2.fastq.gz
ENCORE2
16236
HNRNPA1_BGKLV21-17B_Signal.Unique.strand+.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig+unique
plus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1477
GRCh38
V40
HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam
ENCORE2
16060
HNRNPA1_BGKLV21-17B_Signal.Unique.strand-.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig-unique
minus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1477
GRCh38
V40
HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam
ENCORE2
16104
HNRNPA1_BGKLV21-17B_Signal.UniqueMultiple.strand+.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig+all
plus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1477
GRCh38
V40
HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam
ENCORE2
16148
HNRNPA1_BGKLV21-17B_Signal.UniqueMultiple.strand-.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig-all
minus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1477
GRCh38
V40
HNRNPA1_BGKLV21-17B/Aligned.sortedByCoord.out.bam
ENCORE2
16192
HNRNPA1_BGKLV21-18B_Aligned.sortedByCoord.out.bam
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bam
alignments
knockdown followed by RNA-seq
Graveley Lab
1478
GRCh38
V40
HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R2.fastq.gz
ENCORE2
16017
HNRNPA1_BGKLV21-18B_quant.sf
ENCODE_DATA/set21/salmon_ENCORE2_file_links
transcript_quantification
transcript quantifications
knockdown followed by RNA-seq
Graveley Lab
1478
GRCh38
V40
HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R1.fastq.gz,HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R2.fastq.gz
ENCORE2
16237
HNRNPA1_BGKLV21-18B_Signal.Unique.strand+.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig+unique
plus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1478
GRCh38
V40
HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam
ENCORE2
16061
HNRNPA1_BGKLV21-18B_Signal.Unique.strand-.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig-unique
minus strand signal of unique reads
knockdown followed by RNA-seq
Graveley Lab
1478
GRCh38
V40
HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam
ENCORE2
16105
HNRNPA1_BGKLV21-18B_Signal.UniqueMultiple.strand+.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig+all
plus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1478
GRCh38
V40
HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam
ENCORE2
16149
HNRNPA1_BGKLV21-18B_Signal.UniqueMultiple.strand-.bw
ENCODE_DATA/set21/STAR_ENCORE2_file_links
bigWig-all
minus strand signal of all reads
knockdown followed by RNA-seq
Graveley Lab
1478
GRCh38
V40
HNRNPA1_BGKLV21-18B/Aligned.sortedByCoord.out.bam
ENCORE2
16193
HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R1.fastq.gz
ENCODE_DATA/set21/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1478
HiSeq2000
100
paired-ended
1
NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz
ENCODE3
15929
HNRNPA1_BGKLV21-18B_TAGCTT_L008_001.R2.fastq.gz
ENCODE_DATA/set21/fastq
fastq
reads
knockdown followed by RNA-seq
Graveley Lab
1478
HiSeq2000
100
paired-ended
2
NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz
ENCODE3
15973
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