EIF6 RNA-Seq in K562

General Information


RBP	EIF6
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF6-BGKcLV23-K562
ENCODE_series_ID	ENCSR596QGD
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR975NHV
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	EIF6-BGKcLV23-37
Rep2	EIF6-BGKcLV23-38
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	47.0
Rep2_qPCR	40.0
Rep1_WB	60.0
Rep2_WB	59.4
Antibody Cat#	PA5-79197
Antibody Lot#	LOT# UK2881425
Antibody DCC ID	ENCAB404EIO
Status	Released
Project	ENCODE4
ID	29

Experiment Information (Status: Released)

	BGKcLV23-37	BGKcLV23-37	BGKcLV23-38	BGKcLV23-38
idx	823	823	824	824
TRCN#_or_BGC#	BGC#0000573	BGC#0000573	BGC#0000573	BGC#0000573
shRNA_or_gRNA_sequence	TCCGATCGCTACCAGACAGT	TCCGATCGCTACCAGACAGT	TCCGATCGCTACCAGACAGT	TCCGATCGCTACCAGACAGT
PAM	AGG	AGG	AGG	AGG
Name	EIF6_91	EIF6_91	EIF6_91	EIF6_91
Sample_ID	BGKcLV23-37	BGKcLV23-37	BGKcLV23-38	BGKcLV23-38
transduction_Date	9/17/20	9/17/20	9/17/20	9/17/20
days	Day 6	Day 6	Day 6	Day 6
RBP_name	EIF6	EIF6	EIF6	EIF6
qPCR_result	47.0	47.0	40.0	40.0
Ave_qPCR	43.5	43.5
RT-qPCR_primer-F	ccaggatgagctgtcctctc	ccaggatgagctgtcctctc
RT-qPCR_primer-R	gcacaccagtcattcaccac	gcacaccagtcattcaccac
protein_conc	2213	2213	2822	2822
WB_result	60.0	87.0	59.4	85.9947
Ave_WB	59.7	86.5
WB_DONE_date	10/2/20	4/5/24
MW	26.6KD	26.6KD
IP	Rabbit / I
antibody_Cat#	PA5-79197	3833S	LOT# UK2881425	lot# 2
Antibody DCC ID	ENCAB404EIO
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/24/20		11/24/20
repeat_library
Note
ID	4945	4947	4946	4948

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF6	Product_ID: PA5-79197 Lot_ID: UK2881425 Source: Thermo Fisher Target Name: EIF6-human
EIF6	Product_ID: 3833S Lot_ID: 2 Source: Cell Signaling Technology Target Name: EIF6-human

Experiment Status

	BGKcLV23-37	BGKcLV23-38
Sample_ID	BGKcLV23-37	BGKcLV23-38
Sample Name
Sample Name	EIF6-BGKcLV23-37	EIF6-BGKcLV23-38
RBP	EIF6	EIF6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7447	7448

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-37	BGKcLV23-38
Sample #	49	50
Sample Name	EIF6-BGKcLV23-37	EIF6-BGKcLV23-38
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	288	294
Peak_Molarity	83.70	96.90
libSampleQC_DNA_Well	DNA_Library_set46/set1/A7.png	DNA_Library_set46/set1/B7.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_set46/set2/A11.png	RNA_Library_set46/set2/B11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-37	BGKcLV23-38
RBP	EIF6	EIF6
Batch_ID	BGKcLV23	BGKcLV23
WB_result	60.000	59.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1424	1425

Sequencing Information

	BGKcLV23-37	BGKcLV23-38
Sample_ID	BGKcLV23-37	BGKcLV23-38
Sample Name	EIF6-BGKcLV23-37	EIF6-BGKcLV23-38
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	231,763,206	162,048,524
total_aligned_reads	216,707,808	151,850,044
unique_aligned_reads	196,220,786	137,781,080
percent_uniqueAligned	0.84664	0.85025
correlation_replicates	0.994321	0.994321
spikein_reads	119,766	64,052
percent_spikeins	0.00052	0.00040
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	530	531

Data Submission Information

	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-38	BGKcLV23-38	BGKcLV23-38	BGKcLV23-38
ENCODE_alias	brenton-graveley:EIF6-BGKcLV23	brenton-graveley:EIF6-BGKcLV23-37	brenton-graveley:L-EIF6-BGKcLV23-37	brenton-graveley:EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF6-BGKcLV23-K562	brenton-graveley:EIF6-BGKcLV23-38	brenton-graveley:L-EIF6-BGKcLV23-38	brenton-graveley:EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR975NHV	ENCBS547HAA	ENCLB177RXP	ENCFF669KOQ	ENCFF658PRA	ENCSR596QGD	ENCBS990ZZB	ENCLB123BXC	ENCFF319RPT	ENCFF098JEU
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	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-37	BGKcLV23-38	BGKcLV23-38	BGKcLV23-38	BGKcLV23-38
Sample Name	EIF6-BGKcLV23-37	EIF6-BGKcLV23-37	EIF6-BGKcLV23-37	EIF6-BGKcLV23-37	EIF6-BGKcLV23-37	EIF6-BGKcLV23-37	EIF6-BGKcLV23-38	EIF6-BGKcLV23-38	EIF6-BGKcLV23-38	EIF6-BGKcLV23-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		EIF6-BGKcLV23-37.pdf	L-EIF6-BGKcLV23-37.pdf				EIF6-BGKcLV23-38.pdf	L-EIF6-BGKcLV23-38.pdf
ID	2419	2475	2539	2633	2667	7206	2476	2540	2634	2668

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
EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	530	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1394
EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	530	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1458
EIF6-BGKcLV23-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	530					GRCh38	V40	EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25297
EIF6-BGKcLV23-37_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	530					GRCh38	V40	EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGKcLV23-37_ATATCTCG+ACTAAGAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25331
EIF6-BGKcLV23-37_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	530					GRCh38	V40	EIF6-BGKcLV23-37/Aligned.sortedByCoord.out.bam		ENCORE2	26135
EIF6-BGKcLV23-37_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	530					GRCh38	V40	EIF6-BGKcLV23-37/Aligned.sortedByCoord.out.bam		ENCORE2	26169
EIF6-BGKcLV23-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	530					GRCh38	V40	EIF6-BGKcLV23-37/Aligned.sortedByCoord.out.bam		ENCORE2	26203
EIF6-BGKcLV23-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	530					GRCh38	V40	EIF6-BGKcLV23-37/Aligned.sortedByCoord.out.bam		ENCORE2	26237
EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	531	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1395
EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	531	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1459
EIF6-BGKcLV23-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	531					GRCh38	V40	EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25298
EIF6-BGKcLV23-38_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	531					GRCh38	V40	EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGKcLV23-38_GCGCTCTA+GTCGGAGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25332
EIF6-BGKcLV23-38_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	531					GRCh38	V40	EIF6-BGKcLV23-38/Aligned.sortedByCoord.out.bam		ENCORE2	26136
EIF6-BGKcLV23-38_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	531					GRCh38	V40	EIF6-BGKcLV23-38/Aligned.sortedByCoord.out.bam		ENCORE2	26170
EIF6-BGKcLV23-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	531					GRCh38	V40	EIF6-BGKcLV23-38/Aligned.sortedByCoord.out.bam		ENCORE2	26204
EIF6-BGKcLV23-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	531					GRCh38	V40	EIF6-BGKcLV23-38/Aligned.sortedByCoord.out.bam		ENCORE2	26238