EIF6 RNA-Seq in HepG2

General Information


RBP	EIF6
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF6-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR800UVZ
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR608WXK
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	EIF6-BGHcLV24-29
Rep2	EIF6-BGHcLV24-30
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	68.8
Rep2_WB	68.4
Antibody Cat#	PA5-79197
Antibody Lot#	LOT# UK2881425
Antibody DCC ID	ENCAB404EIO
Status	Released
Project	ENCODE4
ID	7

Experiment Information (Status: Released)

	BGHcLV24-29	BGHcLV24-30
idx	687	688
TRCN#_or_BGC#	BGC#0000573	BGC#0000573
shRNA_or_gRNA_sequence	TCCGATCGCTACCAGACAGT	TCCGATCGCTACCAGACAGT
PAM	AGG	AGG
Name	EIF6_91	EIF6_91
Sample_ID	BGHcLV24-29	BGHcLV24-30
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	EIF6	EIF6
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ccaggatgagctgtcctctc
RT-qPCR_primer-R	gcacaccagtcattcaccac
protein_conc	4828	4297
WB_result	68.8	68.4
Ave_WB	68.6
WB_DONE_date	12/14/20
MW	26.6KD
IP	Rabbit / I
antibody_Cat#	PA5-79197	LOT# UK2881425
Antibody DCC ID	ENCAB404EIO
submitted_to_DCC_date	12/9/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6842	6843

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

Experiment Status

	BGHcLV24-29	BGHcLV24-30
Sample_ID	BGHcLV24-29	BGHcLV24-30
Sample Name
Sample Name	EIF6-BGHcLV24-29	EIF6-BGHcLV24-30
RBP	EIF6	EIF6
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7793	7794

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-29	BGHcLV24-30
Sample #	15	16
Sample Name	EIF6-BGHcLV24-29	EIF6-BGHcLV24-30
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	305	292
Peak_Molarity	84.10	78.60
libSampleQC_DNA_Well	DNA_Library_set47/set1/G5.png	DNA_Library_set47/set1/H5.png
RIN	10.0	9.7
libSample_RNA_Well	RNA_Library_set47/set1/G2.png	RNA_Library_set47/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-29	BGHcLV24-30
RBP	EIF6	EIF6
Batch_ID	BGHcLV24	BGHcLV24
WB_result	68.800	68.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1478	1479

Sequencing Information

	BGHcLV24-29	BGHcLV24-30
Sample_ID	BGHcLV24-29	BGHcLV24-30
Sample Name	EIF6-BGHcLV24-29	EIF6-BGHcLV24-30
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	126,892,824	101,911,284
total_aligned_reads	115,147,162	90,003,800
unique_aligned_reads	108,456,868	84,683,504
percent_uniqueAligned	0.85471	0.83095
correlation_replicates	0.997166	0.997166
spikein_reads	54,514	25,484
percent_spikeins	0.00043	0.00025
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	560	561

Data Submission Information

	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-30	BGHcLV24-30	BGHcLV24-30	BGHcLV24-30
ENCODE_alias	brenton-graveley:EIF6-BGHcLV24	brenton-graveley:EIF6-BGHcLV24-29	brenton-graveley:L-EIF6-BGHcLV24-29	brenton-graveley:EIF6-BGHcLV24-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF6-BGHcLV24-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF6-BGHcLV24-HepG2	brenton-graveley:EIF6-BGHcLV24-30	brenton-graveley:L-EIF6-BGHcLV24-30	brenton-graveley:EIF6-BGHcLV24-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF6-BGHcLV24-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR608WXK	ENCBS673YTO	ENCLB486TCX	ENCFF153HAE	ENCFF605KHI	ENCSR800UVZ	ENCBS044SUT	ENCLB346BQX	ENCFF885OFB	ENCFF631DOB
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	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-29	BGHcLV24-30	BGHcLV24-30	BGHcLV24-30	BGHcLV24-30
Sample Name	EIF6-BGHcLV24-29	EIF6-BGHcLV24-29	EIF6-BGHcLV24-29	EIF6-BGHcLV24-29	EIF6-BGHcLV24-29	EIF6-BGHcLV24-29	EIF6-BGHcLV24-30	EIF6-BGHcLV24-30	EIF6-BGHcLV24-30	EIF6-BGHcLV24-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		EIF6-BGHcLV24-29.pdf	L-EIF6-BGHcLV24-29.pdf				EIF6-BGHcLV24-30.pdf	L-EIF6-BGHcLV24-30.pdf
ID	3242	3271	3315	3359	3403	7205	3272	3316	3360	3404

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-BGHcLV24-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	560	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3718
EIF6-BGHcLV24-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	560	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3764
EIF6-BGHcLV24-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	560					GRCh38	V40	EIF6-BGHcLV24-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGHcLV24-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25407
EIF6-BGHcLV24-29_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	560					GRCh38	V40	EIF6-BGHcLV24-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGHcLV24-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25451
EIF6-BGHcLV24-29_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	560					GRCh38	V40	EIF6-BGHcLV24-29/Aligned.sortedByCoord.out.bam		ENCORE2	26283
EIF6-BGHcLV24-29_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	560					GRCh38	V40	EIF6-BGHcLV24-29/Aligned.sortedByCoord.out.bam		ENCORE2	26327
EIF6-BGHcLV24-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	560					GRCh38	V40	EIF6-BGHcLV24-29/Aligned.sortedByCoord.out.bam		ENCORE2	26371
EIF6-BGHcLV24-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	560					GRCh38	V40	EIF6-BGHcLV24-29/Aligned.sortedByCoord.out.bam		ENCORE2	26415
EIF6-BGHcLV24-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	561	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3719
EIF6-BGHcLV24-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	561	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3765
EIF6-BGHcLV24-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	561					GRCh38	V40	EIF6-BGHcLV24-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGHcLV24-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25408
EIF6-BGHcLV24-30_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	561					GRCh38	V40	EIF6-BGHcLV24-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF6-BGHcLV24-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25452
EIF6-BGHcLV24-30_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	561					GRCh38	V40	EIF6-BGHcLV24-30/Aligned.sortedByCoord.out.bam		ENCORE2	26284
EIF6-BGHcLV24-30_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	561					GRCh38	V40	EIF6-BGHcLV24-30/Aligned.sortedByCoord.out.bam		ENCORE2	26328
EIF6-BGHcLV24-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	561					GRCh38	V40	EIF6-BGHcLV24-30/Aligned.sortedByCoord.out.bam		ENCORE2	26372
EIF6-BGHcLV24-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	561					GRCh38	V40	EIF6-BGHcLV24-30/Aligned.sortedByCoord.out.bam		ENCORE2	26416