AIMP1 RNA-Seq in K562

General Information


RBP	AIMP1
Cell_Line	K562
Method	CRISPR
Exp_Name	AIMP1-BGKcLV26-K562
ENCODE_series_ID	ENCSR678PZO
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR929YET
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	AIMP1-BGKcLV26-19
Rep2	AIMP1-BGKcLV26-20
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	51.2
Rep2_qPCR	50.6
Rep1_WB	62.6
Rep2_WB	57.917303
Antibody Cat#	A304-895A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB938MRH
Status	Released
Project	ENCODE4
ID	788

Experiment Information (Status: Released)

	BGKcLV26-19	BGKcLV26-19	BGKcLV26-20	BGKcLV26-20
idx	872	874	873	875
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_92	AIMP1_92	AIMP1_92	AIMP1_92
Sample_ID	BGKcLV26-19	BGKcLV26-19	BGKcLV26-20	BGKcLV26-20
transduction_Date	3/30/21	3/30/21	3/30/21	3/30/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	AIMP1	AIMP1	AIMP1	AIMP1
qPCR_result	51.2	51.2	50.6	50.6
Ave_qPCR	50.9	50.9
RT-qPCR_primer-F	ggagaaatagccccaaggac	ggagaaatagccccaaggac
RT-qPCR_primer-R	aaatcaccatccgattttgc	aaatcaccatccgattttgc
protein_conc	4667	4667	3890	3890
WB_result	62.6	61.2	57.917303	62.9731706
Ave_WB	60.3	62.1
WB_DONE_date	6/2/21	7/13/21
MW	34kDa	34kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A304-895A	A304-896A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB938MRH	ENCAB034EJC	10/22/21	10/22/21
submitted_to_DCC_date
Rep1_TPM	54.1	0	0	0
Rep2_TPM	60.2	0	0	0
Action	Ready		Ready
Library_start_date	09/01/21		09/01/21
repeat_library
Note
ID	5004	5006	5005	5007

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
AIMP1	Product_ID: A304-896A Lot_ID: 1 Source: Bethyl Labs Target Name: AIMP1-human

Experiment Status

	BGKcLV26-19	BGKcLV26-19	BGKcLV26-20	BGKcLV26-20
Sample_ID	BGKcLV26-19	BGKcLV26-19	BGKcLV26-20	BGKcLV26-20
Sample Name
Sample Name	AIMP1-BGKcLV26-19		AIMP1-BGKcLV26-20
RBP	AIMP1	AIMP1	AIMP1	AIMP1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2021-11-19	2021-09-15	2021-11-19	2021-09-15
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	9757	9797	9758	9798

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-19	BGKcLV26-20
Sample #	15	16
Sample Name	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-20
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	283	271
Peak_Molarity	56.60	46.90
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/G2.png	DNA_Library_set48-49/set1/H2.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set48-49/set1/G2.png	RNA_Library_set48-49/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-19	BGKcLV26-20
RBP	AIMP1	AIMP1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	62.600	57.917
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1574	1575

Sequencing Information

	BGKcLV26-19	BGKcLV26-20
Sample_ID	BGKcLV26-19	BGKcLV26-20
Sample Name	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-20
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	42,079,826	84,720,174
total_aligned_reads	29,563,866	73,966,408
unique_aligned_reads	27,089,512	67,521,490
percent_uniqueAligned	0.64376	0.79699
correlation_replicates	0.997927	0.997927
spikein_reads	12,194	26,898
percent_spikeins	0.00029	0.00032
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1751	1752

Data Submission Information

	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-20	BGKcLV26-20	BGKcLV26-20	BGKcLV26-20
ENCODE_alias	brenton-graveley:AIMP1-BGKcLV26	brenton-graveley:AIMP1-BGKcLV26-19	brenton-graveley:L-AIMP1-BGKcLV26-19	brenton-graveley:AIMP1-BGKcLV26-19_S21_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AIMP1-BGKcLV26-19_S21_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AIMP1-BGKcLV26-K562	brenton-graveley:AIMP1-BGKcLV26-20	brenton-graveley:L-AIMP1-BGKcLV26-20	brenton-graveley:AIMP1-BGKcLV26-20_S22_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AIMP1-BGKcLV26-20_S22_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR929YET	ENCBS629JYA	ENCLB341XRJ	ENCFF155CBR	ENCFF692LIC	ENCSR678PZO	ENCBS867AQR	ENCLB462CRO	ENCFF363LKF	ENCFF264MDS
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	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-19	BGKcLV26-20	BGKcLV26-20	BGKcLV26-20	BGKcLV26-20
Sample Name	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-19	AIMP1-BGKcLV26-20	AIMP1-BGKcLV26-20	AIMP1-BGKcLV26-20	AIMP1-BGKcLV26-20
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
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		AIMP1-BGKcLV26-19.pdf	L-AIMP1-BGKcLV26-19.pdf				AIMP1-BGKcLV26-20.pdf	L-AIMP1-BGKcLV26-20.pdf
ID	3453	3540	3674	3808	3942	7077	3541	3675	3809	3943

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-BGKcLV26-19_S21_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1751	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3844
AIMP1-BGKcLV26-19_S21_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1751	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3894
AIMP1-BGKcLV26-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1751					GRCh38	V40	AIMP1-BGKcLV26-19_S21_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGKcLV26-19_S21_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25531
AIMP1-BGKcLV26-19_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1751					GRCh38	V40	AIMP1-BGKcLV26-19_S21_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGKcLV26-19_S21_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25581
AIMP1-BGKcLV26-19_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1751					GRCh38	V40	AIMP1-BGKcLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	26547
AIMP1-BGKcLV26-19_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1751					GRCh38	V40	AIMP1-BGKcLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	26597
AIMP1-BGKcLV26-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1751					GRCh38	V40	AIMP1-BGKcLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	26647
AIMP1-BGKcLV26-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1751					GRCh38	V40	AIMP1-BGKcLV26-19/Aligned.sortedByCoord.out.bam		ENCORE2	26697
AIMP1-BGKcLV26-20_S22_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1752	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3845
AIMP1-BGKcLV26-20_S22_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1752	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3895
AIMP1-BGKcLV26-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1752					GRCh38	V40	AIMP1-BGKcLV26-20_S22_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGKcLV26-20_S22_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25532
AIMP1-BGKcLV26-20_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1752					GRCh38	V40	AIMP1-BGKcLV26-20_S22_L003_R1_001.filtered.trimmed.paired.fastq.gz,AIMP1-BGKcLV26-20_S22_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25582
AIMP1-BGKcLV26-20_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1752					GRCh38	V40	AIMP1-BGKcLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	26548
AIMP1-BGKcLV26-20_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1752					GRCh38	V40	AIMP1-BGKcLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	26598
AIMP1-BGKcLV26-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1752					GRCh38	V40	AIMP1-BGKcLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	26648
AIMP1-BGKcLV26-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1752					GRCh38	V40	AIMP1-BGKcLV26-20/Aligned.sortedByCoord.out.bam		ENCORE2	26698