EIF3D RNA-Seq in HepG2

General Information


RBP	EIF3D
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF3D-BGHLV16-HepG2
ENCODE_series_ID	ENCSR186NTP
Batch_ID	BGHLV16
Pool ID	Pool-151215B
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR788HVK
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	EIF3D_BGHLV16_23
Rep2	EIF3D_BGHLV16_24
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	72.9
Rep2_qPCR	74.3
Rep1_WB	72.3
Rep2_WB	68.9
Antibody Cat#	A301-758A
Antibody Lot#	A301-758A
Antibody DCC ID	ENCAB626JLZ
Status	Released
Project	ENCODE3
ID	417

Experiment Information (Status: Released)

	BGHLV16-23	BGHLV16-24
idx	191	192
TRCN#_or_BGC#	TRCN0000154123	TRCN0000154123
shRNA_or_gRNA_sequence	CGTAGTGATTGGGAAGTGAAA	CGTAGTGATTGGGAAGTGAAA
PAM
Name	EIF3D	EIF3D
Sample_ID	BGHLV16-23	BGHLV16-24
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	EIF3D	EIF3D
qPCR_result	72.9	74.3
Ave_qPCR	73.6
RT-qPCR_primer-F	aacggggaagtgtccttcat
RT-qPCR_primer-R	tcgctgagagtccagcttct
protein_conc	3241	3057
WB_result	72.3	68.9
Ave_WB	70.6
WB_DONE_date	12/22/2014
MW	64kDa
IP	1	1
antibody_Cat#	A301-758A	A301-758A
Antibody DCC ID	ENCAB626JLZ	ENCAB626JLZ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	41.7	0
Rep2_TPM	46	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2256	2257

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3D	Product_ID: A301-758A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3D-human

Experiment Status

	BGHLV16-23	BGHLV16-24
Sample_ID	BGHLV16-23	BGHLV16-24
Sample Name	EIF3D_BGHLV16_23	EIF3D_BGHLV16_24
Sample Name	EIF3D_BGHLV16_23	EIF3D_BGHLV16_24
RBP	EIF3D	EIF3D
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	558	559

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-23	BGHLV16-24
Sample #
Sample Name	EIF3D-BGHLV16-23	EIF3D-BGHLV16-24
Sample_Name_Alias	EIF3D_BGHLV16_23	EIF3D_BGHLV16_24
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/A7.png	DNA_Library_LV16-17/set1/B7.png
RIN	9.8	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G12.png	RNA_Library_LV13-14-16/set1/H12.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-23	BGHLV16-24
RBP	EIF3D	EIF3D
Batch_ID	BGHLV16	BGHLV16
WB_result	72.300	68.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2242	2243

Sequencing Information

	BGHLV16-23	BGHLV16-23	BGHLV16-24
Sample_ID	BGHLV16-23	BGHLV16-23	BGHLV16-24
Sample Name	EIF3D_BGHLV16_23	EIF3D_BGHLV16_23	EIF3D_BGHLV16_24
Pool ID	Pool-141001	Pool-151215B	Pool-141001
LocalServer_folder	set16	set16	set16
total_reads	17,490,000	65,081,048	30,810,000
total_aligned_reads	15,688,150	60,223,234	27,216,588
unique_aligned_reads	14,807,682	56,763,458	25,668,288
percent_uniqueAligned	0.84664	0.87220	0.83312
correlation_replicates	0.999143		0.999143
spikein_reads	46,604	173,784	54,350
percent_spikeins	0.00266	0.00267	0.00176
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	884	1374	885

Data Submission Information

	BGHLV16-23	BGHLV16-23
ENCODE_alias	brenton-graveley:EIF3D_BGHLV16	brenton-graveley:EIF3D-BGHLV16-HepG2
ENCODE_accession	ENCSR788HVK	ENCSR186NTP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-23	BGHLV16-23
Sample Name	EIF3D_BGHLV16_23	EIF3D_BGHLV16_23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2847	6683

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
EIF3D_BGHLV16_23_GATCAG_L006_R1_001.merged.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	884	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14284
EIF3D_BGHLV16_23_GATCAG_L006_R2_001.merged.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	884	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14310
EIF3D_BGHLV16_23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	884					GRCh38	V40	EIF3D_BGHLV16_23_GATCAG_L006_R1_001.merged.fastq.gz,EIF3D_BGHLV16_23_GATCAG_L006_R2_001.merged.fastq.gz		ENCORE2	14336
EIF3D_BGHLV16_23_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	884					GRCh38	V40	EIF3D_BGHLV16_23/Aligned.sortedByCoord.out.bam		ENCORE2	14362
EIF3D_BGHLV16_23_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	884					GRCh38	V40	EIF3D_BGHLV16_23/Aligned.sortedByCoord.out.bam		ENCORE2	14388
EIF3D_BGHLV16_23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	884					GRCh38	V40	EIF3D_BGHLV16_23/Aligned.sortedByCoord.out.bam		ENCORE2	14414
EIF3D_BGHLV16_23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	884					GRCh38	V40	EIF3D_BGHLV16_23/Aligned.sortedByCoord.out.bam		ENCORE2	14440
EIF3D_BGHLV16_23_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	884					GRCh38	V40	EIF3D_BGHLV16_23_GATCAG_L006_R1_001.merged.fastq.gz,EIF3D_BGHLV16_23_GATCAG_L006_R2_001.merged.fastq.gz		ENCORE2	14466
EIF3D_BGHLV16_24_TAGCTT_L006_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	885	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14285
EIF3D_BGHLV16_24_TAGCTT_L006_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	885	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14311
EIF3D_BGHLV16_24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	885					GRCh38	V40	EIF3D_BGHLV16_24_TAGCTT_L006_R1_001.fastq.gz,EIF3D_BGHLV16_24_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	14337
EIF3D_BGHLV16_24_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	885					GRCh38	V40	EIF3D_BGHLV16_24/Aligned.sortedByCoord.out.bam		ENCORE2	14363
EIF3D_BGHLV16_24_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	885					GRCh38	V40	EIF3D_BGHLV16_24/Aligned.sortedByCoord.out.bam		ENCORE2	14389
EIF3D_BGHLV16_24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	885					GRCh38	V40	EIF3D_BGHLV16_24/Aligned.sortedByCoord.out.bam		ENCORE2	14415
EIF3D_BGHLV16_24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	885					GRCh38	V40	EIF3D_BGHLV16_24/Aligned.sortedByCoord.out.bam		ENCORE2	14441
EIF3D_BGHLV16_24_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	885					GRCh38	V40	EIF3D_BGHLV16_24_TAGCTT_L006_R1_001.fastq.gz,EIF3D_BGHLV16_24_TAGCTT_L006_R2_001.fastq.gz		ENCORE2	14467