FAM120A RNA-Seq in HepG2

General Information


RBP	FAM120A
Cell_Line	HepG2
Method	shRNA
Exp_Name	FAM120A-BGHLV16-HepG2
ENCODE_series_ID	ENCSR602MKX
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR047VPW
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	FAM120A_BGHLV16_25
Rep2	FAM120A_BGHLV16_26
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	74.3
Rep2_qPCR	63.2
Rep1_WB	67.8
Rep2_WB	71.5
Antibody Cat#	A303-889A
Antibody Lot#	A303-889A
Antibody DCC ID	ENCAB468JSB
Status	Released
Project	ENCODE3
ID	418

Experiment Information (Status: Released)

	BGHLV16-25	BGHLV16-26
idx	193	194
TRCN#_or_BGC#	TRCN0000074920	TRCN0000074920
shRNA_or_gRNA_sequence	GCTGACTATGTACGCAACATT	GCTGACTATGTACGCAACATT
PAM
Name	FAM120A	FAM120A
Sample_ID	BGHLV16-25	BGHLV16-26
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	FAM120A	FAM120A
qPCR_result	74.3	63.2
Ave_qPCR	68.8
RT-qPCR_primer-F	ctggcttcctttcactggag
RT-qPCR_primer-R	gatcactacgtcgcaaggtg
protein_conc	3453	3341
WB_result	67.8	71.5
Ave_WB	69.7
WB_DONE_date	7/21/2015
MW	122kDa
IP	1	1
antibody_Cat#	A303-889A	A303-889A
Antibody DCC ID	ENCAB468JSB	ENCAB468JSB
submitted_to_DCC_date	8/6/2015
Rep1_TPM	14.7	0
Rep2_TPM	16.8	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2258	2259

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FAM120A	Product_ID: A303-889A Lot_ID: 1 Source: Bethyl Labs Target Name: FAM120A-human

Experiment Status

	BGHLV16-25	BGHLV16-26
Sample_ID	BGHLV16-25	BGHLV16-26
Sample Name	FAM120A_BGHLV16_25	FAM120A_BGHLV16_26
Sample Name	FAM120A_BGHLV16_25	FAM120A_BGHLV16_26
RBP	FAM120A	FAM120A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	560	561

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-25	BGHLV16-26
Sample #
Sample Name	FAM120A-BGHLV16-25	FAM120A-BGHLV16-26
Sample_Name_Alias	FAM120A_BGHLV16_25	FAM120A_BGHLV16_26
Index Well Position	S11	S12
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/C7.png	DNA_Library_LV16-17/set1/D7.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A1.png	RNA_Library_LV16-17-18/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-25	BGHLV16-26
RBP	FAM120A	FAM120A
Batch_ID	BGHLV16	BGHLV16
WB_result	67.800	71.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2244	2245

Sequencing Information

	BGHLV16-25	BGHLV16-26
Sample_ID	BGHLV16-25	BGHLV16-26
Sample Name	FAM120A_BGHLV16_25	FAM120A_BGHLV16_26
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	43,420,000	38,800,000
total_aligned_reads	38,815,582	34,758,754
unique_aligned_reads	36,636,040	32,815,902
percent_uniqueAligned	0.84376	0.84577
correlation_replicates	0.999194	0.999194
spikein_reads	87,044	50,978
percent_spikeins	0.00200	0.00131
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	886	887

Data Submission Information

	BGHLV16-25	BGHLV16-25
ENCODE_alias	brenton-graveley:FAM120A_BGHLV16	brenton-graveley:FAM120A-BGHLV16-HepG2
ENCODE_accession	ENCSR047VPW	ENCSR602MKX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-25	BGHLV16-25
Sample Name	FAM120A_BGHLV16_25	FAM120A_BGHLV16_25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2848	6706

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
FAM120A_BGHLV16_25_GGCTAC_L007_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	886	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14286
FAM120A_BGHLV16_25_GGCTAC_L007_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	886	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14312
FAM120A_BGHLV16_25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	886					GRCh38	V40	FAM120A_BGHLV16_25_GGCTAC_L007_R1_001.fastq.gz,FAM120A_BGHLV16_25_GGCTAC_L007_R2_001.fastq.gz		ENCORE2	14338
FAM120A_BGHLV16_25_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	886					GRCh38	V40	FAM120A_BGHLV16_25/Aligned.sortedByCoord.out.bam		ENCORE2	14364
FAM120A_BGHLV16_25_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	886					GRCh38	V40	FAM120A_BGHLV16_25/Aligned.sortedByCoord.out.bam		ENCORE2	14390
FAM120A_BGHLV16_25_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	886					GRCh38	V40	FAM120A_BGHLV16_25/Aligned.sortedByCoord.out.bam		ENCORE2	14416
FAM120A_BGHLV16_25_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	886					GRCh38	V40	FAM120A_BGHLV16_25/Aligned.sortedByCoord.out.bam		ENCORE2	14442
FAM120A_BGHLV16_25_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	886					GRCh38	V40	FAM120A_BGHLV16_25_GGCTAC_L007_R1_001.fastq.gz,FAM120A_BGHLV16_25_GGCTAC_L007_R2_001.fastq.gz		ENCORE2	14468
FAM120A_BGHLV16_26_CTTGTA_L007_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	887	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14287
FAM120A_BGHLV16_26_CTTGTA_L007_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	887	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14313
FAM120A_BGHLV16_26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	887					GRCh38	V40	FAM120A_BGHLV16_26_CTTGTA_L007_R1_001.fastq.gz,FAM120A_BGHLV16_26_CTTGTA_L007_R2_001.fastq.gz		ENCORE2	14339
FAM120A_BGHLV16_26_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	887					GRCh38	V40	FAM120A_BGHLV16_26/Aligned.sortedByCoord.out.bam		ENCORE2	14365
FAM120A_BGHLV16_26_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	887					GRCh38	V40	FAM120A_BGHLV16_26/Aligned.sortedByCoord.out.bam		ENCORE2	14391
FAM120A_BGHLV16_26_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	887					GRCh38	V40	FAM120A_BGHLV16_26/Aligned.sortedByCoord.out.bam		ENCORE2	14417
FAM120A_BGHLV16_26_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	887					GRCh38	V40	FAM120A_BGHLV16_26/Aligned.sortedByCoord.out.bam		ENCORE2	14443
FAM120A_BGHLV16_26_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	887					GRCh38	V40	FAM120A_BGHLV16_26_CTTGTA_L007_R1_001.fastq.gz,FAM120A_BGHLV16_26_CTTGTA_L007_R2_001.fastq.gz		ENCORE2	14469