FAM120A RNA-Seq in K562

General Information


RBP	FAM120A
Cell_Line	K562
Method	shRNA
Exp_Name	FAM120A-BGKLV19-K562
ENCODE_series_ID	ENCSR712BXM
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR492BKM
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	FAM120A_BGKLV19_27B
Rep2	FAM120A_BGKLV19_28B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	52.9
Rep2_qPCR	57.0
Rep1_WB	59.0
Rep2_WB	47.8
Antibody Cat#	A303-889A
Antibody Lot#	A303-889A
Antibody DCC ID	ENCAB468JSB
Status	Released
Project	ENCODE3
ID	473

Experiment Information (Status: Released)

	BGKLV19-27	BGKLV19-28
idx	234	235
TRCN#_or_BGC#	TRCN0000074920	TRCN0000074920
shRNA_or_gRNA_sequence	GCTGACTATGTACGCAACATT	GCTGACTATGTACGCAACATT
PAM
Name	FAM120A	FAM120A
Sample_ID	BGKLV19-27	BGKLV19-28
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	FAM120A	FAM120A
qPCR_result	52.9	57.0
Ave_qPCR	55.0
RT-qPCR_primer-F	ctggcttcctttcactggag
RT-qPCR_primer-R	gatcactacgtcgcaaggtg
protein_conc	2847	3044
WB_result	59.0	47.8
Ave_WB	53.4
WB_DONE_date	7/20/2015
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	22.707324	0
Rep2_TPM	15.9482174	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note	5
ID	259	260

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

	BGKLV19-27	BGKLV19-28
Sample_ID	BGKLV19-27	BGKLV19-28
Sample Name	FAM120A_BGKLV19_27B	FAM120A_BGKLV19_28B
Sample Name	FAM120A_BGKLV19_27B	FAM120A_BGKLV19_28B
RBP	FAM120A	FAM120A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	676	677

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-27	BGKLV19-28
Sample #
Sample Name	FAM120A-BGKLV19-27B	FAM120A-BGKLV19-28B
Sample_Name_Alias	FAM120A_BGKLV19_27B	FAM120A_BGKLV19_28B
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A9.png	DNA_Library_LV18-19/set1/B9.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E3.png	RNA_Library_LV19-21-24/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-27	BGKLV19-28
RBP	FAM120A	FAM120A
Batch_ID	BGKLV19	BGKLV19
WB_result	59.000	47.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2362	2363

Sequencing Information

	BGKLV19-27	BGKLV19-28
Sample_ID	BGKLV19-27	BGKLV19-28
Sample Name	FAM120A_BGKLV19_27B	FAM120A_BGKLV19_28B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	41,920,000	35,120,000
total_aligned_reads	38,974,898	32,551,174
unique_aligned_reads	35,831,034	29,935,978
percent_uniqueAligned	0.85475	0.85239
correlation_replicates	0.991246	0.991246
spikein_reads	175,248	133,768
percent_spikeins	0.00418	0.00381
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1004	1005

Data Submission Information

	BGKLV19-27	BGKLV19-27
ENCODE_alias	brenton-graveley:FAM120A_BGKLV19	brenton-graveley:FAM120A-BGKLV19-K562
ENCODE_accession	ENCSR492BKM	ENCSR712BXM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-27	BGKLV19-27
Sample Name	FAM120A_BGKLV19_27B	FAM120A_BGKLV19_27B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2887	6707

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_BGKLV19_27B_GTCCGC_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1004	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15116
FAM120A_BGKLV19_27B_GTCCGC_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1004	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15174
FAM120A_BGKLV19_27B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1004					GRCh38	V40	FAM120A_BGKLV19_27B_GTCCGC_L004_R1_001.fastq.gz,FAM120A_BGKLV19_27B_GTCCGC_L004_R2_001.fastq.gz		ENCORE2	15232
FAM120A_BGKLV19_27B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1004					GRCh38	V40	FAM120A_BGKLV19_27B/Aligned.sortedByCoord.out.bam		ENCORE2	15303
FAM120A_BGKLV19_27B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1004					GRCh38	V40	FAM120A_BGKLV19_27B/Aligned.sortedByCoord.out.bam		ENCORE2	15361
FAM120A_BGKLV19_27B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1004					GRCh38	V40	FAM120A_BGKLV19_27B/Aligned.sortedByCoord.out.bam		ENCORE2	15419
FAM120A_BGKLV19_27B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1004					GRCh38	V40	FAM120A_BGKLV19_27B/Aligned.sortedByCoord.out.bam		ENCORE2	15477
FAM120A_BGKLV19_27B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1004					GRCh38	V40	FAM120A_BGKLV19_27B_GTCCGC_L004_R1_001.fastq.gz,FAM120A_BGKLV19_27B_GTCCGC_L004_R2_001.fastq.gz		ENCORE2	16374
FAM120A_BGKLV19_28B_GTGAAA_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1005	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15117
FAM120A_BGKLV19_28B_GTGAAA_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1005	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15175
FAM120A_BGKLV19_28B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1005					GRCh38	V40	FAM120A_BGKLV19_28B_GTGAAA_L004_R1_001.fastq.gz,FAM120A_BGKLV19_28B_GTGAAA_L004_R2_001.fastq.gz		ENCORE2	15233
FAM120A_BGKLV19_28B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1005					GRCh38	V40	FAM120A_BGKLV19_28B/Aligned.sortedByCoord.out.bam		ENCORE2	15304
FAM120A_BGKLV19_28B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1005					GRCh38	V40	FAM120A_BGKLV19_28B/Aligned.sortedByCoord.out.bam		ENCORE2	15362
FAM120A_BGKLV19_28B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1005					GRCh38	V40	FAM120A_BGKLV19_28B/Aligned.sortedByCoord.out.bam		ENCORE2	15420
FAM120A_BGKLV19_28B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1005					GRCh38	V40	FAM120A_BGKLV19_28B/Aligned.sortedByCoord.out.bam		ENCORE2	15478
FAM120A_BGKLV19_28B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1005					GRCh38	V40	FAM120A_BGKLV19_28B_GTGAAA_L004_R1_001.fastq.gz,FAM120A_BGKLV19_28B_GTGAAA_L004_R2_001.fastq.gz		ENCORE2	16375