SF1 RNA-Seq in HepG2

General Information


RBP	SF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	SF1-BGHLV26-HepG2
ENCODE_series_ID	ENCSR711FIY
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR644AIM
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	SF1_BGHLV26_51
Rep2	SF1_BGHLV26_52
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	52.6
Rep2_qPCR	54.5
Rep1_WB	52.9
Rep2_WB	56.8
Antibody Cat#	GTX104540
Antibody Lot#	GTX104540
Antibody DCC ID	ENCAB000AUN
Status	Released
Project	ENCODE3
ID	635

Experiment Information (Status: Released)

	BGHLV26-51	BGHLV26-51	BGHLV26-51	BGHLV26-52	BGHLV26-52	BGHLV26-52
idx	607	607	607	608	608	608
TRCN#_or_BGC#	TRCN0000001069	TRCN0000001069	TRCN0000001069	TRCN0000001069	TRCN0000001069	TRCN0000001069
shRNA_or_gRNA_sequence	GCGTTCTCTTCACTGGTTTAT	GCGTTCTCTTCACTGGTTTAT	GCGTTCTCTTCACTGGTTTAT	GCGTTCTCTTCACTGGTTTAT	GCGTTCTCTTCACTGGTTTAT	GCGTTCTCTTCACTGGTTTAT
PAM
Name	SF1	SF1	SF1	SF1	SF1	SF1
Sample_ID	BGHLV26-51	BGHLV26-51	BGHLV26-51	BGHLV26-52	BGHLV26-52	BGHLV26-52
transduction_Date	5/25/2015	5/25/2015	5/25/2015	5/25/2015	5/25/2015	5/25/2015
days
RBP_name	SF1	SF1	SF1	SF1	SF1	SF1
qPCR_result	52.6	52.6	52.6	54.5	54.5	54.5
Ave_qPCR	53.6	53.6	53.6
RT-qPCR_primer-F	TGTGTACCAAGTGTGGAGGG	TGTGTACCAAGTGTGGAGGG	TGTGTACCAAGTGTGGAGGG
RT-qPCR_primer-R	ATCCGTGCTTTATCCTGAGC	ATCCGTGCTTTATCCTGAGC	ATCCGTGCTTTATCCTGAGC
protein_conc	4860	4860	4860	4426	4426	4426
WB_result	52.9	64.9	77.9	56.8	75.5	74.9
Ave_WB	54.9	70.2	76.4	very light band
WB_DONE_date	7/6/2015	6/13/22	6/28/22
MW	68kDa	68kd	68kd
IP	1IP			1IP
antibody_Cat#	GTX104540	A303-213A	A303-214A	GTX104540	lot# 1	lot# 1
Antibody DCC ID	ENCAB000AUN			ENCAB000AUN
submitted_to_DCC_date	12/7/2015
Rep1_TPM	58.5	0	0	0	0	0
Rep2_TPM	56.2	0	0	0	0	0
Action
Library_start_date	9/8/2015			9/8/2015
repeat_library
Note	x			x
ID	2696	2698	2700	2697	2699	2701

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF1	Product_ID: GTX104540 Lot_ID: 40002 Source: GeneTex Target Name: SF1-human
SF1	Product_ID: A303-213A Lot_ID: 1 Source: Bethyl Labs Target Name: SF1-human
SF1	Product_ID: A303-214A Lot_ID: 1 Source: Bethyl Labs Target Name: SF1-human

Experiment Status

	BGHLV26-51	BGHLV26-52
Sample_ID	BGHLV26-51	BGHLV26-52
Sample Name	SF1_BGHLV26_51	SF1_BGHLV26_52
Sample Name	SF1_BGHLV26_51	SF1_BGHLV26_52
RBP	SF1	SF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	954	955

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-51	BGHLV26-52
Sample #
Sample Name	SF1-BGHLV26-51	SF1-BGHLV26-52
Sample_Name_Alias	SF1_BGHLV26_51	SF1_BGHLV26_52
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/G9.png	DNA_Library_LV24-25-26/set1/H9.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/A3.png	RNA_Library_LV26-27-28-29/set1/B3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-51	BGHLV26-52
RBP	SF1	SF1
Batch_ID	BGHLV26	BGHLV26
WB_result	52.900	56.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2642	2643

Sequencing Information

	BGHLV26-51	BGHLV26-52
Sample_ID	BGHLV26-51	BGHLV26-52
Sample Name	SF1_BGHLV26_51	SF1_BGHLV26_52
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	76,369,312	74,856,296
total_aligned_reads	63,671,026	64,081,398
unique_aligned_reads	59,603,616	60,086,490
percent_uniqueAligned	0.78047	0.80269
correlation_replicates	0.992582	0.992582
spikein_reads	147,856	132,848
percent_spikeins	0.00194	0.00177
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1284	1285

Data Submission Information

	BGHLV26-51	BGHLV26-51
ENCODE_alias	brenton-graveley:SF1_BGHLV26	brenton-graveley:SF1-BGHLV26-HepG2
ENCODE_accession	ENCSR644AIM	ENCSR711FIY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-51	BGHLV26-51
Sample Name	SF1_BGHLV26_51	SF1_BGHLV26_51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3024	6938

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
SF1_BGHLV26_51_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1284	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19828
SF1_BGHLV26_51_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1284	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19850
SF1_BGHLV26_51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1284					GRCh38	V40	SF1_BGHLV26_51_1.fastq.gz,SF1_BGHLV26_51_2.fastq.gz		ENCORE2	19872
SF1_BGHLV26_51_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1284					GRCh38	V40	SF1_BGHLV26_51/Aligned.sortedByCoord.out.bam		ENCORE2	19894
SF1_BGHLV26_51_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1284					GRCh38	V40	SF1_BGHLV26_51/Aligned.sortedByCoord.out.bam		ENCORE2	19916
SF1_BGHLV26_51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1284					GRCh38	V40	SF1_BGHLV26_51/Aligned.sortedByCoord.out.bam		ENCORE2	19938
SF1_BGHLV26_51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1284					GRCh38	V40	SF1_BGHLV26_51/Aligned.sortedByCoord.out.bam		ENCORE2	19960
SF1_BGHLV26_51_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1284					GRCh38	V40	SF1_BGHLV26_51_1.fastq.gz,SF1_BGHLV26_51_2.fastq.gz		ENCORE2	20668
SF1_BGHLV26_52_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1285	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19829
SF1_BGHLV26_52_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1285	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19851
SF1_BGHLV26_52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1285					GRCh38	V40	SF1_BGHLV26_52_1.fastq.gz,SF1_BGHLV26_52_2.fastq.gz		ENCORE2	19873
SF1_BGHLV26_52_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1285					GRCh38	V40	SF1_BGHLV26_52/Aligned.sortedByCoord.out.bam		ENCORE2	19895
SF1_BGHLV26_52_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1285					GRCh38	V40	SF1_BGHLV26_52/Aligned.sortedByCoord.out.bam		ENCORE2	19917
SF1_BGHLV26_52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1285					GRCh38	V40	SF1_BGHLV26_52/Aligned.sortedByCoord.out.bam		ENCORE2	19939
SF1_BGHLV26_52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1285					GRCh38	V40	SF1_BGHLV26_52/Aligned.sortedByCoord.out.bam		ENCORE2	19961
SF1_BGHLV26_52_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1285					GRCh38	V40	SF1_BGHLV26_52_1.fastq.gz,SF1_BGHLV26_52_2.fastq.gz		ENCORE2	20669