AIMP1 RNA-Seq in HepG2

General Information


RBP	AIMP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	AIMP1-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR907BFG
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR512BIT
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	AIMP1-BGHcLV27-3
Rep2	AIMP1-BGHcLV27-4
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	47.8
Rep2_qPCR	40.3
Rep1_WB	68.7
Rep2_WB	75.5
Antibody Cat#	A304-895A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB938MRH
Status	Released
Project	ENCODE4
ID	806

Experiment Information (Status: Released)

	BGHcLV27-3	BGHcLV27-3	BGHcLV27-4	BGHcLV27-4
idx	769	769	770	770
TRCN#_or_BGC#	BGC#0000604	BGC#0000604	BGC#0000604	BGC#0000604
shRNA_or_gRNA_sequence	ACCATAGAATTAGCGTGCAG	ACCATAGAATTAGCGTGCAG	ACCATAGAATTAGCGTGCAG	ACCATAGAATTAGCGTGCAG
PAM	TGG	TGG	TGG	TGG
Name	AIMP1_92F	AIMP1_92F	AIMP1_92F	AIMP1_92F
Sample_ID	BGHcLV27-3	BGHcLV27-3	BGHcLV27-4	BGHcLV27-4
transduction_Date	5/18/21	5/18/21	5/18/21	5/18/21
days	D6	D6	D6	D6
RBP_name	AIMP1	AIMP1	AIMP1	AIMP1
qPCR_result	47.8	47.8	40.3	40.3
Ave_qPCR	44.1	44.1
RT-qPCR_primer-F	ggagaaatagccccaaggac	ggagaaatagccccaaggac
RT-qPCR_primer-R	aaatcaccatccgattttgc	aaatcaccatccgattttgc
protein_conc	2959	2959	2725	2725
WB_result	68.7	99.4	75.5	99.5
Ave_WB	72.1	99.4
WB_DONE_date	6/1/21	3/2/22
MW	34kDa	34kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A304-895A	A304-896A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB938MRH		10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/03/21		09/03/21
repeat_library
Note
ID	6928	6930	6929	6931

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AIMP1	Product_ID: A304-895A Lot_ID: 1 Source: Bethyl Labs Target Name: AIMP1-human

Experiment Status

	BGHcLV27-3	BGHcLV27-4
Sample_ID	BGHcLV27-3	BGHcLV27-4
Sample Name
Sample Name	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-4
RBP	AIMP1	AIMP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9675	9676

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-3	BGHcLV27-4
Sample #	79	80
Sample Name	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-4
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	289	296
Peak_Molarity	142.00	149.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/C7.png	DNA_Library_set48-49/set2/D7.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set48-49/set1/E7.png	RNA_Library_set48-49/set1/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-3	BGHcLV27-4
RBP	AIMP1	AIMP1
Batch_ID	BGHcLV27	BGHcLV27
WB_result	68.700	75.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1638	1639

Sequencing Information

	BGHcLV27-3	BGHcLV27-4
Sample_ID	BGHcLV27-3	BGHcLV27-4
Sample Name	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-4
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	77,969,002	70,760,966
total_aligned_reads	68,882,164	63,964,232
unique_aligned_reads	64,931,660	60,307,148
percent_uniqueAligned	0.83279	0.85227
correlation_replicates	0.987164	0.987164
spikein_reads	23,164	12,104
percent_spikeins	0.00030	0.00017
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1789	1790

Data Submission Information

	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-4	BGHcLV27-4	BGHcLV27-4	BGHcLV27-4
ENCODE_alias	brenton-graveley:AIMP1-BGHcLV27	brenton-graveley:AIMP1-BGHcLV27-3	brenton-graveley:L-AIMP1-BGHcLV27-3	brenton-graveley:AIMP1-BGHcLV27-3_S59_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AIMP1-BGHcLV27-3_S59_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AIMP1-BGHcLV27-HepG2	brenton-graveley:AIMP1-BGHcLV27-4	brenton-graveley:L-AIMP1-BGHcLV27-4	brenton-graveley:AIMP1-BGHcLV27-4_S60_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AIMP1-BGHcLV27-4_S60_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR512BIT	ENCBS854FIQ	ENCLB765QLM	ENCFF213DYI	ENCFF322RXD	ENCSR907BFG	ENCBS317HMK	ENCLB885KIA	ENCFF073GFE	ENCFF236QQU
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-3	BGHcLV27-4	BGHcLV27-4	BGHcLV27-4	BGHcLV27-4
Sample Name	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-3	AIMP1-BGHcLV27-4	AIMP1-BGHcLV27-4	AIMP1-BGHcLV27-4	AIMP1-BGHcLV27-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		AIMP1-BGHcLV27-3.pdf	L-AIMP1-BGHcLV27-3.pdf				AIMP1-BGHcLV27-4.pdf	L-AIMP1-BGHcLV27-4.pdf
ID	3434	3502	3636	3770	3904	7076	3503	3637	3771	3905

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
AIMP1-BGHcLV27-3_S59_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1789	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3780
AIMP1-BGHcLV27-3_S59_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1789	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3806
AIMP1-BGHcLV27-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1789					GRCh38	V40	AIMP1-BGHcLV27-3_S59_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGHcLV27-3_S59_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25467
AIMP1-BGHcLV27-3_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1789					GRCh38	V40	AIMP1-BGHcLV27-3_S59_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGHcLV27-3_S59_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25493
AIMP1-BGHcLV27-3_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1789					GRCh38	V40	AIMP1-BGHcLV27-3/Aligned.sortedByCoord.out.bam		ENCORE2	26431
AIMP1-BGHcLV27-3_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1789					GRCh38	V40	AIMP1-BGHcLV27-3/Aligned.sortedByCoord.out.bam		ENCORE2	26457
AIMP1-BGHcLV27-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1789					GRCh38	V40	AIMP1-BGHcLV27-3/Aligned.sortedByCoord.out.bam		ENCORE2	26483
AIMP1-BGHcLV27-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1789					GRCh38	V40	AIMP1-BGHcLV27-3/Aligned.sortedByCoord.out.bam		ENCORE2	26509
AIMP1-BGHcLV27-4_S60_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1790	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3781
AIMP1-BGHcLV27-4_S60_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1790	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3807
AIMP1-BGHcLV27-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1790					GRCh38	V40	AIMP1-BGHcLV27-4_S60_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGHcLV27-4_S60_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25468
AIMP1-BGHcLV27-4_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1790					GRCh38	V40	AIMP1-BGHcLV27-4_S60_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGHcLV27-4_S60_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25494
AIMP1-BGHcLV27-4_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1790					GRCh38	V40	AIMP1-BGHcLV27-4/Aligned.sortedByCoord.out.bam		ENCORE2	26432
AIMP1-BGHcLV27-4_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1790					GRCh38	V40	AIMP1-BGHcLV27-4/Aligned.sortedByCoord.out.bam		ENCORE2	26458
AIMP1-BGHcLV27-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1790					GRCh38	V40	AIMP1-BGHcLV27-4/Aligned.sortedByCoord.out.bam		ENCORE2	26484
AIMP1-BGHcLV27-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1790					GRCh38	V40	AIMP1-BGHcLV27-4/Aligned.sortedByCoord.out.bam		ENCORE2	26510