title: CALGB03-1040043-I-13

description:
Sample_PRE_RNA_140
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Oaf1_lactis_rpt1

status: Public on Jan 21 2022

type: SRA

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
Library strategy: Chec-Seq
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S2988C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Genome_build: GCA_000146045.2 (R64)
Supplementary_files_format_and_content: zip of *.out file contains gneome coverage for all 12,157,105  bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: genotype

value: BY4741 OAF1::K.lactis A03443-Mnase PIP2::kanMX

tag: expname

tag: strainid


title: Stp3_dSTP4_rpt1

value: BY4741 STP3::Stp3-Mnase STP4::kanMX


title: C03_Q-3-CALGB03-1057761-1

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description:
Sample_PRE_RNA_138
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

library_source: transcriptomic

data_processing:
Basecalls by Casava.
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a.
Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.030 in ‘-quant’ mode, based on the STAR alignments.
Fixed upper quartile normalization.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: CALGB40603.389PreTreat.JUNCTION.salmon_gene_normalized.matrix_FOR_GEO.v2.txt: Tab-delimited, normalized, transcript abundance estimates.

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast

extract_protocol: Fresh-frozen RNA was isolated with Qiagen RNeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002).

tag: tissue

value: Breast carcinoma

tag: treatment

value: None - Pretreatment Neoadjuvant Therapy


title: C03_Q-47-CALGB03-1069641-1

description:
Sample_PRE_RNA_135
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Stp4_dSTP3_rpt1

value: BY4741 STP4::Stp4-Mnase STP3::kanMX


title: C03-R-7-CALGB03-1057256-1

description:
Sample_PRE_RNA_131
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yrr1_dPDR8_rpt1

value: BY4741 YRR1::Yrr1-Mnase PDR8::kanMX


title: C03-Q-40-CALGB03-1047333

description:
Sample_PRE_RNA_142
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Upc2_dECM22_rpt1

value: BY4741 UPC2::Upc2-Mnase ECM22::kanMX


title: Ecm22_dUPC2_rpt1

value: BY4741 ECM22::Ecm22-Mnase UPC2::kanMX


title: CALGB03-1046611-L-25

description:
Sample_PRE_RNA_141
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Vhr1_dVHR2_rpt1

value: BY4741 VHR1::Vhr1-Mnase VHR2::kanMX


title: C03_R-47-CALGB03-1070751-1

description:
Sample_PRE_RNA_130
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-28-CALGB03-1052004-1

description:
Sample_PRE_RNA_127
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Vhr2_dVHR1_rpt1

value: BY4741 VHR2::Vhr2-Mnase VHR1::kanMX


title: CALGB03-1047392-L-29

description:
Sample_PRE_RNA_126
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-35-CALGB03-1052132-1

description:
Sample_PRE_RNA_129
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Dot6_dTOD6_rpt2

value: BY4741 DOT6::Dot6-Mnase TOD6::kanMX


title: Stp1_rpt2

value: BY4741 STP1::Stp1-Mnase


title: Stp2_rpt2

value: BY4741 STP2::Stp2-Mnase


title: C03_R-4-CALGB03-1069495-1

description:
Sample_PRE_RNA_145
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-25-CALGB03-1052532-1

description:
Sample_PRE_RNA_124
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-6-CALGB03-1050644-1

description:
Sample_PRE_RNA_122
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Pdr1_dPDR3_rpt2

value: BY4741 PDR1::Pdr1-Mnase PDR3::kanMX


title: Hal9_dTBS1_rpt2

value: BY4741 HAL9::Hal9-Mnase TBS1::kanMX


title: Pdr3_dPDR1_rpt2

value: BY4741 PDR3::Pdr3-Mnase PDR1::kanMX


title: C03-Q-30-CALGB03-1041018

description:
Sample_PRE_RNA_111
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1037699-I-4

description:
Sample_PRE_RNA_110
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Gzf3_dDAL80_rpt2

value: BY4741 GZF3::Gzf3-Mnase DAL80::kanMX


title: C03_S-2-CALGB03-1071235-1

description:
Sample_PRE_RNA_109
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Gis1_dRPH1_rpt2

value: BY4741 GIS1::Gis1-Mnase RPH1::kanMX


title: C03_Q-31-CALGB03-1066694-1

description:
Sample_PRE_RNA_099
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1048894-M-35

description:
Sample_PRE_RNA_104
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-3-CALGB03-1051358-1

description:
Sample_PRE_RNA_101
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Stp2_rpt1


title: Rph1_dGIS1_rpt1

value: BY4741 RPH1::Rph1-Mnase GIS1::kanMX


title: Oaf1_dPIP2_rpt1

value: BY4741 OAF1::Oaf1-Mnase PIP2::kanMX


title: C03_Q-45-CALGB03-1069817-1

description:
Sample_PRE_RNA_089
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: Stp1_rpt1


title: C03_Q-1-CALGB03-1057766-1

description:
Sample_PRE_RNA_087
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Pdr1_dPDR3_rpt1


title: CALGB03-1047391-L-39

description:
Sample_PRE_RNA_086
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Gzf3_dDAL80_rpt1


title: C03-Q-11-CALGB03-1042817

description:
Sample_PRE_RNA_088
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Hal9_dTBS1_rpt1


title: CALGB03-1050331-1-M-27

description:
Sample_PRE_RNA_082
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-38-CALGB03-1069537-1

description:
Sample_PRE_RNA_119
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Pdr3_dPDR1_rpt1


title: CALGB03-1042605-K-45

description:
Sample_PRE_RNA_081
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tbs1_dHAL9_rpt1

value: BY4741 TBS1::Tbs1-Mnase HAL9::kanMX


title: Dot6_dTOD6_rpt1


title: Met31_dMET32_rpt1

value: BY4741 MET31::Met31-Mnase MET32::kanMX


title: Gis1_dRPH1_rpt1


title: C03-Q-2-CALGB03-1032172

description:
Sample_PRE_RNA_078
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-33-CALGB03-1057258-1

description:
Sample_PRE_RNA_077
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-15-CALGB03-1050185-1

description:
Sample_PRE_RNA_076
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Sut1_rpt2

value: BY4741 SUT1::Sut1-Mnase


title: CALGB03-1042943-I-22

description:
Sample_PRE_RNA_074
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-15-CALGB03-1064506-1

description:
Sample_PRE_RNA_073
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Sut2_rpt2

value: BY4741 SUT2::Sut2-Mnase


title: Dal80_rpt4

value: BY4741 DAL80::Dal80-Mnase


title: CALGB03-1041227-I-18

description:
Sample_PRE_RNA_067
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Mga2_rpt1

value: BY4741 MGA2::Mnase-Mga2


title: Mga2_rpt2


title: C03_N-27-CALGB03-1051954-1

description:
Sample_PRE_RNA_068
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Spt23_rpt3

value: BY4741 SPT23::Mnase-Spt23


title: Spt23_rpt2


title: Cup9_rpt3

value: BY4741 CUP9::Cup9-Mnase


title: C03-Q-6-CALGB03-1039634

description:
Sample_PRE_RNA_065
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-39-CALGB03-1046317

description:
Sample_PRE_RNA_061
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-10-CALGB03-1050188-1

description:
Sample_PRE_RNA_060
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Pdr8_rpt2

value: BY4741 PDR8::Pdr8-Mnase


title: Spt23_rpt1


title: CALGB03-1049119-I-31

description:
Sample_PRE_RNA_063
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Sut1_rpt1


title: Sut2_rpt1


title: CALGB03-1039179-I-6

description:
Sample_PRE_RNA_056
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Dal80_rpt3


title: Usv1_rpt3

value: BY4741 USV1::Usv1-Mnase


title: CALGB03-1050296-1-M-34

description:
Sample_PRE_RNA_054
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rgm1_rpt2

value: BY4741 RGM1::Rgm1-Mnase


title: C03-Q-22-CALGB03-1035136

description:
Sample_PRE_RNA_051
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-11-CALGB03-1058435-1

description:
Sample_PRE_RNA_050
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Smp1_rpt3

value: BY4741 SMP1::Smp1-Mnase


title: C03-Q-18-CALGB03-1049047

description:
Sample_PRE_RNA_049
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049472-M-36

description:
Sample_PRE_RNA_072
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047187-L-32

description:
Sample_PRE_RNA_066
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yhp1_rpt2

value: BY4741 YHP1::Yhp1-Mnase


title: C03_Q-29-CALGB03-1064701-1

description:
Sample_PRE_RNA_043
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tos8_rpt2

value: BY4741 TOS8::Tos8-Mnase


title: CALGB03-1039165-I-5

description:
Sample_PRE_RNA_046
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03-Q-8-CALGB03-1040464

description:
Sample_PRE_RNA_039
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047603-M-5

description:
Sample_PRE_RNA_058
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rgm1_rpt1


title: CALGB03-1039212-I-7

description:
Sample_PRE_RNA_029
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-23-CALGB03-1065897-1

description:
Sample_PRE_RNA_037
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Phd1_rpt1

value: BY4741 PHD1::Phd1-Mnase


title: Tod6_rpt1

value: BY4741 TOD6::Tod6-Mnase


title: C03_R-40-CALGB03-1071022-1

description:
Sample_PRE_RNA_053
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: CALGB03-1036564-I-2

description:
Sample_PRE_RNA_027
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1046556-I-27

description:
Sample_PRE_RNA_026
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-32-CALGB03-1052347-1

description:
Sample_PRE_RNA_052
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yox1_rpt1

value: BY4741 YOX1::Yox1-Mnase


title: C03_Q-42-CALGB03-1069171-1

description:
Sample_PRE_RNA_038
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Yhp1_rpt1


title: Smp1_rpt2


title: Phd1_rpt2


title: C03-Q-16-CALGB03-1048004

description:
Sample_PRE_RNA_025
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1046241-L-24

description:
Sample_PRE_RNA_023
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Tos8_rpt1


title: Tod6_rpt2


title: Vhr2_rpt3

value: BY4741 VHR2::Vhr2-Mnase


title: CALGB03-1046369-I-24

description:
Sample_PRE_RNA_021
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Vhr1_rpt3

value: BY4741 VHR1::Vhr1-Mnase


title: Yox1_rpt2


title: C03_Q-37-CALGB03-1067839-1

description:
Sample_PRE_RNA_018
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1047586-I-30

description:
Sample_PRE_RNA_016
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Usv1_rpt2


title: Yap5_rpt2

value: BY4741 YAP5::Yap5-Mnase


title: Yap4_rpt2

value: BY4741 YAP4::Yap4-Mnase


title: C03-Q-9-CALGB03-1042130

description:
Sample_PRE_RNA_014
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1046365-L-40

description:
Sample_PRE_RNA_034
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Rsf2_rpt2

value: BY4741 RSF2::Rsf2-Mnase


title: Yap7_rpt2

value: BY4741 YAP7::Yap7-Mnase


title: Yap6_rpt2

value: BY4741 YAP6::Yap6-Mnase


title: C03_R-46-CALGB03-1070759-1

description:
Sample_PRE_RNA_015
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_N-5-CALGB03-1049990-1

description:
Sample_PRE_RNA_009
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1049079-M-18

description:
Sample_PRE_RNA_008
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-6-CALGB03-1057721-1

description:
Sample_PRE_RNA_007
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Hal9_rpt2

value: BY4741 HAL9::Hal9-Mnase


title: Tda9_rpt2

value: BY4741 TDA9::Tda9-Mnase


title: CALGB03-1049273-M-24

description:
Sample_PRE_RNA_013
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1042459-K-43

description:
Sample_PRE_RNA_005
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: Upc2_rpt2

value: BY4741 UPC2::Upc2-Mnase


title: C03_Q-46-CALGB03-1069427-1

description:
Sample_PRE_RNA_001
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: E9_H3K4me1_CnT_rep3

city: Austin

first: Steven

middle: A.

last: Vokes

state: Texas

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Library strategy: Cut&Tag
Base calling was done using Illumina bcl2fasq version 1.8.4 or version 2.17.1
Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.2.5).
Peak calling was done using MACS2 or SEACR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

organism: Mus musculus

source_name: mouse limb buds

extract_protocol:
limbs were dissociated using 100ug/mL Liberase (Roche 05401119001) in PBS at 37 degrees for 6 minutes.
Libraries were prepared with the following number of amplification cycles, for each given experiment: CUT&Tag/Run- 14 cycles, ChIP- 15 cycles, ATAC- 11 cycles. Excess primers were removed from PCR reactions using AmpureXP beads (A63880) at a ratio of 0.8x beads.
ChIP & CUT&RUN library- NEBNext Ultra II DNA Library Prep Kit; ATAC & CUT&Tag- NEBNext HF 2x PCR Master Mix; RNA-seq- NEBNext Ultra II RNA Library Prep Kit

tag: strain/background

value: Swiss Webster

value: 1 litter FLs (100k cells)

tag: Stage

value: forelimb bud


title: Yap7_rpt1


title: C2C12-Mm-MUNC-dCH4-CF-5NIA

city: Charlottesville

first: Roza

middle: Kamila

last: Przanowska

state: Virginia

department: Biomedical Engineering

institute: University of Virginia

description:
Input fasta file: Mn_MUNC_dCH4_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_dCH4_CellFree_SHAPE_profile.txt
C2C12_Mm_MUNC_dCH4_CellFree_SHAPE_MAP.map
C2C12_Mm_MUNC_dCH4_CellFree_SHAPE_pairing_prob.dp

data_processing:
library strategy: SHAPE-MaP
Adduct locations identified by Shapemapper2 software
RNA structure models were generated from SHAPE data using SuperFold software
Supplementary_files_format_and_content: Shapemapper2 MAP file for Superfold; Superfold output pairing probabilities; Cell-free In-cell difference file

molecule: total RNA

source_name: Murine myoblasts C2C12

growth_protocol: C2C12 PAX7 NEG cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles Medium (GE #SH30081.01) with 20% FBS.

extract_protocol:
Cells were grown to ~80% confluency and washed briefly twice with ice-cold PBS. Total RNA for in-cell treatments was extracted by Trizol reagent (Invitrogen #15596018) and purified with column-based Direct-zol RNA Miniprep kit (Zymo Research #R2051), while cell-free samples were prepared according to SHAPE-MaP protocol.
MUNC amplicons were generated by gene-specific MaP reverse transcription and PCR. cDNA products were converted to libraries using Illumina Nextera XT library prep kit and sequenced on an Illumina MiSeq instrument.

tag: cell line

tag: genotype/variation

value: MUNC spliced CH4 deletion overexpressing

tag: cell type

value: Myoblasts

tag: molecule subtype

value: reverse transcribed RNA

value: 25 mM 5NIA

tag: treatment type

value: Extracted RNA


title: Yap5_rpt1


title: Yap4_rpt1


title: C2C12-Mm-MUNC-genomic-IC-5NIA

description:
Input fasta file: Mn_MUNC_genomic_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_genomic_InCell_Amp1_SHAPE_profile.txt
C2C12_Mm_MUNC_genomic_InCell_Amp2_SHAPE_profile.txt
C2C12_Mm_MUNC_genomic_InCell_MergedAmps_SHAPE_profile.txt

value: MUNC genomic overexpressing

value: In cell


title: C2C12-Mm-MUNC-dCH1-CF-5NIA

description:
Input fasta file: Mn_MUNC_dCH1_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_dCH1_CellFree_SHAPE_profile.txt
C2C12_Mm_MUNC_dCH1_CellFree_SHAPE_MAP.map
C2C12_Mm_MUNC_dCH1_CellFree_SHAPE_pairing_prob.dp

value: MUNC spliced CH1 deletion overexpressing


title: C2C12-Mm-MUNC-genomic-CF-5NIA

description:
Input fasta file: Mn_MUNC_genomic_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_genomic_CellFree_Amp1_SHAPE_profile.txt
C2C12_Mm_MUNC_genomic_CellFree_Amp2_SHAPE_profile.txt
C2C12_Mm_MUNC_genomic_CellFree_MergedAmps_SHAPE_profile.txt
C2C12_Mm_MUNC_genomic_CellFree_MergedAmps_SHAPE_MAP.map
C2C12_Mm_MUNC_genomic_CellFree_MergedAmps_SHAPE_pairing_prob.dp


title: Rsf2_rpt1

value: BY4741 RSF2::Rsf2-Mnase


title: C2C12-Mm-MUNC-spliced-IC-Rep2-5NIA

description:
Input fasta file: Mn_MUNC_spliced_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_spliced_InCell_Rep2_SHAPE_profile.txt
C2C12_Mm_MUNC_spliced_Rep2_InCell_CellFree_diff.csv

value: MUNC spliced overexpressing


title: C2C12-Mm-MUNC-spliced-IC-Rep1-5NIA

description:
Input fasta file: Mn_MUNC_spliced_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_spliced_InCell_Rep1_SHAPE_profile.txt
C2C12_Mm_MUNC_spliced_Rep1_InCell_CellFree_diff.csv


title: C2C12-Mm-MUNC-spliced-CF-Rep2-5NIA

description:
Input fasta file: Mn_MUNC_spliced_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_spliced_CellFree_Rep2_SHAPE_profile.txt
C2C12_Mm_MUNC_spliced_CellFree_Rep2_SHAPE_MAP.map
C2C12_Mm_MUNC_spliced_CellFree_Rep2_SHAPE_pairing_prob.dp
C2C12_Mm_MUNC_spliced_CellFree_JoinedReps_SHAPE_MAP.map
C2C12_Mm_MUNC_spliced_CellFree_JoinedReps_SHAPE_pairing_prob.dp


title: C2C12-Mm-MUNC-spliced-CF-Rep1-5NIA

description:
Input fasta file: Mn_MUNC_spliced_ncRNA.fa
processed data file:
C2C12_Mm_MUNC_spliced_CellFree_Rep1_SHAPE_profile.txt
C2C12_Mm_MUNC_spliced_CellFree_Rep1_SHAPE_MAP.map
C2C12_Mm_MUNC_spliced_CellFree_Rep1_SHAPE_pairing_prob.dp
C2C12_Mm_MUNC_spliced_CellFree_JoinedReps_SHAPE_MAP.map
C2C12_Mm_MUNC_spliced_CellFree_JoinedReps_SHAPE_pairing_prob.dp


title: Tda9_rpt1


title: Yrr1_rpt1

value: BY4741 YRR1::Yrr1-Mnase


title: C2C12-Mm-MUNC-dCH4-CF-DMSO

value: DMSO


title: Tbs1_rpt1

value: BY4741 TBS1::Tbs1-Mnase


title: C2C12-Mm-MUNC-genomic-IC-DMSO


title: C2C12-Mm-MUNC-dCH1-CF-DMSO


title: Ecm22_rpt1

value: BY4741 ECM22::Ecm22-Mnase


title: Yrr1_rpt2


title: Hal9_rpt1

value: BY4741 HAL9::Hal9-Mnase


title: Upc2_rpt1

value: BY4741 UPC2::Upc2-Mnase


title: CALGB03-1049585-M-33

description:
Sample_PRE_RNA_006
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: Pdr8_rpt1

value: BY4741 PDR8::Pdr8-Mnase


title: C2C12-Mm-MUNC-genomic-CF-DMSO

value: Myoblasts

value: reverse transcribed RNA


title: Ixr1_rpt2

value: BY4741 IXR1::Ixr1-Mnase


title: C2C12-Mm-MUNC-spliced-IC-Rep2-DMSO


title: Oaf1_rpt3

value: BY4741 OAF1::Oaf1-Mnase


title: C2C12-Mm-MUNC-spliced-IC-Rep1-DMSO

value: In cell


title: Ecm22_rpt2


title: Oaf1_rpt2


title: Pip2_rpt3

value: BY4741 PIP2::Pip2-Mnase


title: C2C12-Mm-MUNC-spliced-CF-Rep2-DMSO

value: Extracted RNA


title: Pip2_rpt2


title: C2C12-Mm-MUNC-spliced-CF-Rep1-DMSO

value: MUNC spliced overexpressing


title: Yap6_rpt1

value: BY4741 YAP6::Yap6-Mnase


title: Vhr2_rpt2

value: BY4741 VHR2::Vhr2-Mnase


title: Vhr1_rpt2

value: BY4741 VHR1::Vhr1-Mnase


title: MUNC_R1_ChIRPseq

data_processing:
Library strategy: ChIRP-seq
bowtie2 version 2.3.4.1
MACS2 version 2.1.1.20160309
GREAT
Genome_build: mm10
Supplementary_files_format_and_content: .txt: table with chromosomal coordinates for MUNC peaks

growth_protocol: C2C12 PAX7 NEG cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles Medium (GE #SH30081.01) with 20% FBS. For differentiation to myotubes serum was exchanged to 2%HS.

extract_protocol:
Cells were grown to ~80% confluency for GM or differentiated for 3 days for DM3 and washed briefly twice with ice-cold PBS. Chromatin Isolation by RNA Purification (ChIRP) procedure was performed as described (Chu et al., 2012) using biotinylated antisense probes complementary to MUNC genomic sequence.
Sequencin was performed by Genome Analysis and Technology Core at University of Virginia School of Medicine using the Illumina MiSeq instrument.

value: Wild-type

value: Myotubes

value: MUNC


title: Pdr3_rpt2

value: BY4741 PDR3::Pdr3-Mnase


title: lacZ_R2_ChIRPseq

value: lacZ


title: Pdr1_rpt2

value: BY4741 PDR1::Pdr1-Mnase


title: lacZ_R1_ChIRPseq


title: Oaf1_rpt1


title: Vhr2_rpt1


title: Pip2_rpt1


title: Ixr1_rpt1


title: Vhr1_rpt1


title: 0309_Panc89_DMSO

city: Muenster

first: Michael

last: Meisterernst

address: Robert-Koch-Straße 43

department: Faculty of Medicine

country: Germany

institute: University of Muenster

description:
DESeq2_diffExpr_result_panc_annot_meisterernst_11217.xlsx
normalized_read_counts_meisterernst_141117.tab.xlsx

data_processing:
The sequences were demultiplexed (bcl2fastq2) to fastq data and quality controlled.
Trimmomatic (v. 0.38) was used for adapter trimming and read filtering.  (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
The resulted reads were aligned to the  hg38 using Hisat2 (v.2.1.0; Parameter: default) and sorted using SAM tools (v. 1.9)
The sorted and aligned reads were counted into genes using HTSeq (v.0.11.1;  Parameter: --minaqual 0,  --stranded reverse)
Testing for differential expression was performed using DESeq2 r-package (v. 1.24.0)
Genome_build: hg38
Supplementary_files_format_and_content: Ecxel files containing changes in gene expression after treatment with LDC4297 in comparison to DMSO treatment
Supplementary_files_format_and_content: Excel file containing table with normalized read counts for every gene and every sample

source_name: Panc89 cells

growth_protocol: Cells were cultured in RPMI medium containing antibiotics and glutamine.

extract_protocol:
Samples were extracted using standard TRIZOL procedure.
Libraries were prepared via NEBNext mRNA enrichment and the NEBNext Ultra RNA Prep Kit. Quality of the librabries was controlled via Agilent Bioanalyzer HighSens DNA Chip followed by NEBNext qPCR library quantification and equimolar pooling. Samples were sequenced using an Illumina NextSeq500 system (v2 chemistry).

treatment_protocol: Prior to sample generation cells were treated with 0.1 µM LDC4297 or DMSO for 3 days.

value: pancreatic ductal adenocarcinoma cells

value: lymphnode metastasis

value: DMSO

value: Panc89 cells


title: 0409_Panc89_297


title: 0109_Panc89_DMSO


title: 0309_Panc89_297


title: 0109_Panc89_297


title: Pdr3_rpt1


title: 0409_Panc89_DMSO


title: 0309_MP2_297

description:
DESeq2_diffExpr_result_mp2-297_annot_meisterernst_11217.xlsx
normalized_read_counts_meisterernst_141117.tab.xlsx

source_name: Mia-Paca2 cells

value: primary tumor

value: Mia-Paca2 cells


title: Sok2_rpt2

value: BY4741 SOK2::Sok2-Mnase


title: 0109_MP2_297


title: Rlm1_rpt1

value: BY4741 RLM1::Rlm1-Mnase


title: 0309_MP2_DMSO


title: MUNC_R2_ChIRPseq


title: Smp1_rpt1

value: BY4741 SMP1::Smp1-Mnase


title: Dot6_rpt2

value: BY4741 DOT6::Dot6-Mnase


title: 0409_MP2_DMSO


title: Sok2_rpt1


title: Dot6_rpt1


title: ATAC_tNGFR_stim_2

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
genomic DNA tagmented for ATACseq
processed data file: ATAC_counts.csv

data_processing:
For the screen, equal numbers of reads from all three donors were combined per bin before trimming and alignment. The barcodes were mapped to the reference library after adaptor trimming with cutadapt 1.13 (-m 24 -e 0.1 --discard-untrimmed) using bowtie 1.1.2 (-v 1 -m 1 --best --strata).
For single cell, gene expression unique molecular identifier (UMI) count matrices and TCR clonotypes were derived using 10X Genomics Cell Ranger 3.1.0. HTO and antibody UMI count matrices were generated using kallisto 0.46.0 and bustools 0.39.3. ORF reads were first aligned to plasmid references using bowtie2 2.2.8 and indexed to the associated ORF, after which kallisto and bustools were used to generate UMI count matrices. All modalities were normalised using a centred log ratio (CLR) transformation. Cell doublets and negatives were identified using the HTODemux function and then excluded from downstream analysis. The UMI cutoff quantile for HTODemux was optimised to maximize singlet recovery using grid search with values between 0 and 1. ORF singlets were identified using MULTIseqDemux. We then excluded cells with low quality gene expression metrics and removed cells with less than 200 unique RNA features or greater than 5% of reads mapping to the mitochondrial transcriptome.
For bulk RNAseq, paired-end reads were aligned to the transcriptome (human Ensembl v96 reference) using kallisto 0.46.0 and loaded into RStudio 1.1.419 with R 4.0.0.2 using tximport package.
For ATACseq, single-end reads were aligned to the Gencode hg38 primary assembly using Bowtie2 v2.4.4. We then used Samtools v1.9 to filter out alignments with low-mapping quality (MAPQ < 30) and subsequently to sort and index the filtered BAM files. Read duplicates were removed using Picard v4.1.8.1. Peaks were called using MACS3 v3.0.0 with default parameters (-g 2.7e9 -q 0.05). To construct the union feature space (“union peaks”) used for much of the downstream analyses, we began by performing intersections on pairs of biological replicate narrowPeak files using bedtools v2.29.0 (using bedtools intersect), keeping only those peaks found in both replicates. After marking the shared peaks between replicates, we used bedtools merge to consolidate the biological replicates at each shared peak (at least 1 bp overlap). In this new peak BED file, each shared peak includes all sequence found under the peak in either of the biological replicates. Next, we took the union of each of these peak files (LTBR resting, LTBR stimulated, tNGFR resting, tNGFR stimulation); we combined any peaks with at least 1 base pair of overlap. Using the “union peaks”, we generated a peak read count matrix (union peaks x ATAC samples) where each entry in the matrix corresponds to the number of reads overlapping that peak in the specified sample — we term this the per-peak ATAC matrix. The overlapping reads are taken directly from the BAM files (converted to BED) that provide an alignment for each sample. Thus, the matrix includes a column for each biological replicate. Although samples had minimal differences in aligned reads, we normalised each entry in the matrix by the number of reads that overlapped the TSS regions in each sample. In this manner, any difference in read/alignment depth between samples would be normalized appropriately. In addition to the per-peak ATAC matrix, we also constructed a per-gene ATAC matrix as follows: We assigned a gene’s total ATAC reads as the sum of normalized reads from the per-peak ATAC matrix for all peaks within 3 kb of a gene’s start or end coordinates.
Genome_build: hg38
Supplementary_files_format_and_content: For the screen, bulk RNAseq and bulk ATACseq, raw counts of features (barcodes, transcripts, peaks, respectively, are provided). For the single cell experiment, UMI counts of each respective feature corresponding to a given cell barcode are shown.

source_name: T cell - CD8

growth_protocol: HEK293FT cells were obtained from Thermo Fisher and cultured in DMEM supplemented with 10% Serum Plus-II (Thermo Fisher). We produced lentivirus by co-transfecting third-generation lentiviral transfer plasmids together with packaging plasmid psPAX2 (Addgene 12260) and envelope plasmid pMD2.G (Addgene 12259) into HEK293FT cells, using polyethyleneimine linear MW 25000 (Polysciences). After 72 hours, we harvested the supernatants, filtered them through a 0.45 um Steriflip-HV filter (Millipore), and concentrated the virus using Lentivirus Precipitation Solution (Alstem). Concentrated lentivirus was resuspended in T-cell Media containing IL-2 and stored at -80C. Regular buffy coats containing peripheral blood from de-identified healthy donors were obtained from the New York Blood Center. Peripheral blood mononuclear cells (PBMC) were isolated from buffy coats using Lymphoprep (Stemcell) gradient centrifugation. For most assays, CD8+ and CD4+ were isolated sequentially from the same donor. First, CD8+ T-cells were isolated by magnetic positive selection using EasySep Human CD8 Positive Selection Kit II (Stemcell). Then, CD4+ T-cells were isolated from the resulting flowthrough by negative magnetic selection using EasySep Human CD4+ T-cell Isolation Kit (Stemcell). Activation of T cells was performed with Immunocult Human CD3/CD28 T-cell Activator (Stemcell) and plated at 10^6 cells per mL. Typically, T-cells were transduced with concentrated lentivirus 24 h post isolation. 72 h post isolation, lentivirally transduced T-cells were selected with 2 ug mL-1 puromycin. Every 2-3 days T-cells were either split or had media replaced to maintain cell density of 1-2 × 10^6 cells per mL. Lentivirally transduced T-cells were maintained in media containing 2 ug mL-1 puromycin for the duration of culture.

extract_protocol:
For the screen, gDNA was extracted using GeneJET DNA Purification Kit (Thermo Fisher Scientific). For the single cell experiment, isolations were performed according to manufacturer’s protocol. For bulk RNAseq, total RNA was extracted using the Direct-zol RNA purification kit (Zymo). For ATAC-seq, cell membranes were lysed in the RSB buffer (10mM Tris-HCL pH 7.4, 3mM MgCl2, 10mM NaCl) with 0.1% IGEPAL freshly added. After pipetting up and down, nuclei were isolated by centrifugation at 500g for 5 minutes at 4°C. After discarding the supernatant, the nuclei were resuspended in the Tagmentation DNA (TD) Buffer with homemade transposase TnY protein and incubated at 37°C for 30 minutes, and purified on a MinElute column (Qiagen).
For the screen, two rounds of PCR to amplify ORF barcodes and add Illumina adaptors were performed on gDNA.   For the single cell experiment: cDNA amplification, additive primers for amplification of sample hashing and surface antigen barcodes were included, as well as a nested reverse primer binding to the puromycin resistance cassette downstream of the ORF. Following cDNA amplification, SPRI beads were used for size selection of resulting PCR products – small size (<300 bp) sample hashing and surface antigen barcodes were physically separated from larger cDNA and ORF amplicons for downstream processing. Sample hashing and surface antigen barcodes were also processed. Amplified cDNA was then separated into three conditions, for construction of the gene expression library, alpha beta TCR library and ORF library. The ORF library was processed similarly to alpha beta TCR library, using nested reverse primers binding downstream of the ORF. The quality of produced libraries was verified on BioAnalyzer using High Sensitivity DNA kit (Agilent). The libraries were sequenced on NextSeq 500. For the gene expression library, >25,000 reads per cell were generated. For other libraries, >5,000 reads per cell were generated.  For bulk RNAseq, RNA was reverse transcribed using SMARTScribe Reverse Transcriptase (Takara Bio) and a poly(dT) oligo containing a partial Nextera handle. Resulting cDNA was then PCR amplified for 3 cycles using OneTaq polymerase (NEB) and tagmented for 5 minutes at 55C using homemade transposase TnY. Immediately afterwards the tagmented DNA was purified on a MinElute column (Qiagen) and PCR amplified using OneTaq polymerase and barcoded primers for 12 cycles. The PCR product was purified using a dual (0.5X-0.8X) SPRI cleanup (Agencourt) and the size distribution was determined using Tapestation (Agilent). Samples were sequenced on a NextSeq 500 (Illumina) using a v2.5 75-cycle kit (paired end).  For ATAC-seq, the tagmented DNA was PCR amplified using a homemade Pfu X7 DNA polymerase and barcoded primers for 12 cycles. The PCR product was purified via a 1.5X SPRI cleanup (Agencourt) and checked for a characteristic nucleosome banding pattern using TapeStation (Agilent). Samples were sequenced on a NextSeq 500 (Illumina) using the v2.5 75-cycle kit (single end).

treatment_protocol: For pooled ORF library screening, CD4+ and CD8+ T-cells were isolated from a minimum of 500 x 10^6 PBMC from three healthy donors. The amount of lentivirus used for transduction was titrated to result in 20-30% transduction efficiency, to minimize the probability of multiple ORFs being introduced into a single cell. The cells were maintained in T-cell media containing 2 mg mL-1 puromycin and counted every 2-3 days to maintain cell density of 1-2 x 106 cells mL-1. On day 14 after isolation, T-cells were harvested, counted, labelled with 5 mM carboxyfluorescein succinimidyl ester (CFSE) (Biolegend) and stimulated with CD3/CD28 Activator (StemCell) at 1.56 mL per 1 x 10^6 cells. An aliquot of cells representing 1,000X coverage of the library was frozen down at this step to be used as a pre-stimulation control. After 4 days of stimulation, cells were harvested and an aliquot of cells representing 1,000X coverage of the library was frozen down to be used as a pre-sort control. The remaining cells were stained with LIVE/DEAD Violet cell viability dye (Thermo Fisher), and CFSElow cells (corresponding to the bottom 15% of the distribution) were sorted using Sony SH800S cell sorter.   For single cell sequencing, CD8+ T-cells were individually transduced with ORFs and kept, separately, under puromycin selection for 14 days. Then, transduced cells were combined and split into two conditions: one was cultured for 24 hours only in presence of IL-2, the other was further supplemented with 6.25 ul CD3/CD28 Activator per 10^6 cells. After stimulation, the cells were harvested, counted and resuspended in staining buffer (2% BSA + 0.01% Tween-20 in PBS) at 2 x 10^7 cells per mL. Then, 10% (v/v) Human TruStain FcX Fc Receptor Blocking Solution (Biolegend) was added and the cells were incubated at 4C for 10 min. After Fc receptor blocking, the cell concentration was adjusted to 5 x 10^6 cells per mL and the stimulated and unstimulated cells were split into 4 conditions each. Each condition received a different oligonucleotide-conjugated (barcoded) cell hashing antibody to allow for pooling of different conditions in the same 10x Genomics Chromium lane. After 20 min co-incubation on ice, the cells were washed 3X with staining buffer and counted using Trypan blue exclusion. Cell viability was typically ~95%. Then, cells stained with different hashing antibodies were pooled together at equal numbers and stained with the following oligonucleotide-conjugated (barcoded) antibodies for quantification of cell surface antigens: CD11c (0.1 ug), CD14 (0.2 ug),  CD16 (0.1 ug),  CD19 (0.1 ug),  CD56 (0.2 ug),  CD3 (0.2 ug),  CD45 (0.01 ug),  CD45RA (0.2 ug),  CD45RO (0.2 ug),  CD4 (0.1 ug),  CD8 (0.1 ug),  CD25 (0.25 ug),  CD69 (0.25 ug),  NGFR (0.25 ug) (TotalSeq-C, Biolegend). The cells were stained for 30 min on ice, washed 3X with staining buffer, resuspended in PBS and filtered through 40 um cell strainer. The cells were then counted and the concentration was adjusted to 1 x 10^6 mL-1. For loading into the 10x Genomics Chromium, 3 x 10^4 cells were combined with Chromium Next GEM Single Cell 5’ v2 Master Mix (10x Genomics) supplemented with a custom reverse primer binding to the puromycin resistance cassette for boosting ORF transcript capture at the reverse transcription stage. The custom reverse primer was added at 1:1 or 1:3 ratio to poly-dT primer included in the Master Mix.   For bulk RNAseq, CD4+ and CD8+ LTBR- or tNGFR-transduced T-cells were stimulated for 24 hours with CD3/CD28 Activator (25 ul per 10^6 cells) or left unstimulated (n = 3 biological replicates).  For ATAC-seq, CD8+ LTBR and tNGFR T-cells were stimulated for 24 hours with CD3/CD28 Activator (25 ul per 10^6 cells) or left unstimulated (n = 2 biological replicates).

value: T cell - CD8

value: CD3/CD28 stimulation for 24h


title: 0109_MP2_DMSO


title: Hms2_rpt3

value: BY4741 HMS2::Hms2-Mnase


title: ATAC_tNGFR_stim_1


title: Pdr1_rpt1


title: Skn7_rpt2

value: BY4741 SKN7::Skn7-Mnase


title: ATAC_tNGFR_rest_2

value: no stimulation


title: Rlm1_rpt2


title: 0409_MP2_297


title: Skn7_rpt1


title: Cup9_rpt2

value: BY4741 CUP9::Cup9-Mnase


title: Hms2_rpt2


title: ATAC_tNGFR_rest_1


title: ATAC_LTBR_rest_1


title: Hms2_rpt1


title: ATAC_LTBR_stim_1


title: ATAC_LTBR_stim_2


title: Dal80_rpt2

value: BY4741 DAL80::Dal80-Mnase


title: Cup9_rpt1


title: RNAseq_CD8_tNGFR_stim_3

description:
total transcriptome
processed data file: bulkRNAseq_counts.csv


title: Rph1_rpt3

value: BY4741 RPH1::Rph1-Mnase


title: RNAseq_CD8_tNGFR_stim_2


title: RNAseq_CD8_tNGFR_stim_1


title: Stp4_rpt3

value: BY4741 STP4::Stp4-Mnase


title: Stp4_rpt2


title: Stp3_rpt2

value: BY4741 STP3::Stp3-Mnase


title: RNAseq_CD8_tNGFR_rest_2


title: Met31_rpt2

value: BY4741 MET31::Met31-Mnase


title: RNAseq_CD8_tNGFR_rest_3


title: Rph1_rpt2


title: Gis1_rpt2

value: BY4741 GIS1::Gis1-Mnase


title: RNAseq_CD4_tNGFR_stim_2

source_name: T cell - CD4

value: T cell - CD4


title: Gzf3_rpt2

value: BY4741 GZF3::Gzf3-Mnase


title: Usv1_rpt1

value: BY4741 USV1::Usv1-Mnase


title: RNAseq_CD4_tNGFR_rest_3


title: Stp4_rpt1


title: RNAseq_CD4_tNGFR_stim_3


title: ATAC_LTBR_rest_2


title: RNAseq_CD4_tNGFR_rest_2


title: RNAseq_CD4_tNGFR_stim_1


title: Stp3_rpt1


title: RNAseq_CD8_LTBR_stim_1


title: RNAseq_CD8_LTBR_stim_3


title: Met31_rpt1


title: RNAseq_CD8_LTBR_stim_2


title: Met32_rpt1

value: BY4741 MET32::Met32-Mnase


title: RNAseq_CD8_LTBR_rest_3


title: Dal80_rpt1


title: Rph1_rpt1


title: RNAseq_CD8_LTBR_rest_1


title: RNAseq_CD4_LTBR_stim_3


title: RNAseq_CD8_tNGFR_rest_1


title: RNAseq_CD8_LTBR_rest_2


title: Gis1_rpt1


title: Met32_rpt2


title: Gzf3_rpt1


title: RNAseq_CD4_LTBR_stim_2


title: RNAseq_CD4_tNGFR_rest_1


title: RNAseq_CD4_LTBR_stim_1


title: RNAseq_CD4_LTBR_rest_3


title: RNAseq_CD4_LTBR_rest_1


title: RNAseq_CD4_LTBR_rest_2


title: sc_TCR

description: TCR enriched transcriptome

value: single cell - alpha and beta TCR


title: sc_ORF

description: direct capture of ORF transcript

value: T cell - CD8

value: single cell - ORF identity


title: Lico_6D_2

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

description: Cultured hADSC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg18 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: hg18
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: Human adipose-derived mesenchymal stem cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according   to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2   mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The   mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a   new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for   15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper   aqueous phase where RNA remained was transferred into a new tube with equal volume of   supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After   deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix   was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the   pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated   water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using   a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented   into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was   generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA   synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end   repair. The cDNA fragments obtained from previous step were amplified by PCR, and products   were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on   the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products   from previous step were heated denatured and circularized by the splint oligo sequence to get the   final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The   final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300   copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases   reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: strain

value: China

tag: age

value: adult

value: Licochalcone A  treatment 6 days


title: Lico_6D_1

description: Cultured hADSC

value: Human adipose-derived mesenchymal stem cells


title: sc_GEX

description: total transcriptome

value: single cell - 5' RNA


title: C_MLN [BCR]

city: Oxford

first: Jacqueline

middle: HY

last: Siu

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

description:
5' Gene RNA with CITE-seq, VDJ libraries
C_MLN.tar.gz

data_processing:
Processing of sequencing results to generate transcript matrices was performed using the 10X Genomics Cell Ranger count v3.1.0 pipeline with default settings, using GRCh38 reference for alignment and Ensembl 93 (GRCh38-3.0.0) for gene quantification.
Seurat v3 was used for QC, integration of samples into single dataset
Genome_build: GRCh38
Supplementary_files_format_and_content: gzip files contain the filtered_feature_bc_matrix folder for each sample output from cellranger, containing barcodes, features,  matrix files as well as VDJ filtered contig fasta and annotation file

source_name: Mesenteric lymph node

growth_protocol: Lymphocytes were isolated from tissues using Lymphoprep centrifugation.

extract_protocol:
Labelled cells were loaded into 10x Genomics platform.
5' gene expression libraries were constructed following the manusfacturers protocols.

treatment_protocol: CD19+ cells were sorted by FACS. Cells were also labelled using oligonucleotide tagged 'CITE-seq' antibodies and washed.

tag: donor

value: C

tag: disease state

value: healthy

tag: Sex

value: Male

value: B cells


title: C_APP [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
C_APP.tar.gz

source_name: Appendix


title: C_SPL [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
C_SPL.tar.gz

source_name: Spleen


title: Ctrl_6D_2

description: Cultured hADSC

value: Normal Culture


title: Ctrl_6D_1

description: Cultured hADSC


title: sc_ADT

description: barcoded antibody for surface antigen quantification

value: single cell - other antibodies

value: oligo DNA


title: B_MLN [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
B_MLN.tar.gz

value: B

value: Female


title: B_APP [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
B_APP.tar.gz


title: sc_HTO

description: hashtag antibody for sample demultiplexing

value: single cell - hashtag antibody


title: Mmp14 Knockout SSCs NO1

type: RNA

city: Ann Arbor

first: Stephen

middle: J

last: Weiss

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

institute: University of Michigan

description: Gene expression data from SSCs cultured in Collagen gel for 48 hours.

hyb_protocol: Following labeling procedure, 3.75µg of biotinylated cDNA were hybridized on Mouse Gene ST 2.1 Strip (4 arrays), and were washed and stained using the Affymetrix Gene Atlas system.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical enviroment version 3.3.0 .

label: biotin

source_name: SSCs cultured in Collagen gel

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA system V2 kit prococol from 10ng toal RNA. Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75µg of cDNA.

growth_protocol: SSCs were isolated from 4-6 week old Mmp14 wild type (WT) and Mmp14 knockout (KO) mice.

extract_protocol: RNA extracted and purified by a QIAGEN RNeasy Fibrous Tissue Mini kit.

treatment_protocol: SSCs isolated from  Mmp14 wild type (WT) and Mmp14 knockout (KO) mice, and cultured in 3D collagen gels for 48 hours.

value: Skeletal stem cells

tag: genotype

value: Cells from 4-6 week old mouse


title: Mmp14 wild type SSCs NO1


title: screen_plasmid

description:
plasmid library
processed data file: ORF_screen_counts.csv

organism: Escherichia coli

value: plasmid

value: plasmid DNA


title: A_SPL [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
A_SPL.tar.gz

value: A


title: Mmp14 Knockout SSCs NO2


title: screen_CD8_CFSElow

description:
stimulated sorted cells (bottom 15% CFSE, most proliferating)
processed data file: ORF_screen_counts.csv

value: T cell - CD8

value: sorted (CFSElow)


title: Mmp14 wild type SSCs NO2


title: screen_CD8_presort

description:
stimulated unsorted cells
processed data file: ORF_screen_counts.csv

value: unsorted


title: A_MLN [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
A_MLN.tar.gz

value: healthy


title: screen_CD8_prestim

description:
transduced cells pre-stimulation
processed data file: ORF_screen_counts.csv

value: no stimulation


title: B_SPL [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
B_SPL.tar.gz

value: B cells


title: screen_CD4_CFSElow

value: T cell - CD4


title: C_SPL

value: C

value: Male


title: IN-133-D180_RSV_Day 180_IN

city: Beerse

first: Kim

last: Thys

state: Antwerpen

address: Turnhoutseweg 30

department: Infectious Diseases

country: Belgium

institute: Janssen

hyb_protocol: Array Plate Hybridization on the GeneTitan® Instrument following the GeneTitan®Instrument User Guide for Expression Array Plates  (P/N 702933)

scan_protocol: The HT Array Plate was scanned with the GeneTitan Instrument as per instructions provided in the GeneTitan® Instrument User Guide for Expression Arrays Plates  (P/N 702933).

data_processing: Microarray data was pre-processed using R version 3.4.2 and Bioconductor. Raw data was pre-processed using Robust Multi-array Average (RMA) and summarized at the gene level using alternative CDF mappings (ENTREZG, version 20).

source_name: whole blood_RSV_Day 180_IN

label_protocol: The GeneChip® Pico Reagent Kit (Affymetrix) was used to prepare hybridization ready targets from total RNA samples for gene expression profiling analysis

extract_protocol: Whole blood RNA was extracted with the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (ThermoFisher) as per the manufacturer’s instructions.

tag: disease

value: RSV

tag: day

value: Day 180

tag: arm

value: IN


title: C_MLN


title: A_APP [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
A_APP.tar.gz


title: screen_CD4_presort

tag: treatment


title: screen_CD4_prestim


title: IN-138-D180_RSV_Day 180_IN


title: B_SPL

value: B

value: Female


title: IN-55_RSV_Day 180_IN


title: IN-111_RSV_Day 180_IN


title: OUT-306-D180_RSV_Day 180_OUT

source_name: whole blood_RSV_Day 180_OUT

value: OUT


title: IN-46_RSV_Day 180_IN


title: IN-149-D180_RSV_Day 180_IN


title: OUT-308-D180_RSV_Day 180_OUT


title: OUT-303-D180_RSV_Day 180_OUT


title: IN-121-D180_RSV_Day 180_IN


title: IN-146-D180_RSV_Day 180_IN


title: B_MLN


title: JH335_S52

city: Dallas

first: Jeremiah

last: Herbert

address: 5323 Harry Hines Blvd., MC 8511

department: Green Center for Reproductive Biology

institute: University of Texas Southwestern Medical Center

data_processing:
Raw sequencing fastq files were mapped to the human genome build hg38 using the bwa mem aligner (0.7.5), with the following options: (-M: samtools view -q10 -bS -o).
Genome browser tracks were generated using the bedtools (version 2.29.2) utilities: genomecov sort, then processed to bigwig files with bedGraphToBigWig.

source_name: HS3,4 KO 1B3 GFP+

growth_protocol: Cells were cultured in accordance with ATCC guidelines, in Iscove′s Modified Dulbecco′s Medium (Sigma-Aldrich I3390) supplemented with 10% FBS , 1% Pen/Strep (Sigma-Aldrich P4333), and 1% GlutaMAX (ThermoFisher 35050061).

extract_protocol: Viable cells were pelleted by centrifugation at 500g for 5 min at 4°C, then cell membranes were lysed in RSB with 0.1% Tween-20, 0.01% Digitonin, and 0.1% NP-40. Cell nuclei were pelleted by centrifugation at 500g for 10 min at 4°C, and digested with Tn5 for 30 minutes at 37°C. Transposition reaction was cleaned up with Qiagen PCR Clean-Up, and sequencing adapters added by PCR with KAPA HiFi enzyme mix . Final libraries were cleaned up with two 1.2x SPRI Select beads purifications and assayed by Qubit and TapeStation before submission for sequencing.

treatment_protocol: When seeking maximal GFP expression in tagged lines, enhancer knockout cell lines were treated with 2µg/mL of puromycin for 7 days, then assayed with FACS, analyzing mean fluorescence intensity with FlowJo.

value: K562 cell line

value: bgl HS3,4 KO

value: GFP+ Sort


title: JH334_S51


title: IN-123-D180_RSV_Day 180_IN


title: JH48_S2

source_name: K562 WT

value: K562 WT


title: B_APP


title: A_SPL

value: A


title: IN-59_RSV_Day 180_IN


title: OUT-304-D180_RSV_Day 180_OUT


title: IN-114_RSV_Day 180_IN


title: JH333_S50

source_name: HS3,4 KO 1B3 GFP-

value: GFP- Sort


title: C_APP

value: healthy


title: OUT-402-D180_RSV_Day 180_OUT


title: IN-71_RSV_Day 180_IN


title: JH332_S49


title: IN-75-D180_RSV_Day 180_IN


title: IN-124-D180_RSV_Day 180_OUT


title: JH331_S48

source_name: HS4 KO 3H4 GFP+

value: bgl HS4 KO


title: IN-62_RSV_Day 180_IN


title: A_MLN

value: B cells


title: A_APP


title: JH330_S47


title: SLE_3 [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
SLE_3.tar.gz

source_name: PBMC

growth_protocol: Lymphocytes were isolated from blood using Lymphoprep centrifugation.

value: lupus


title: IN-129-D180_RSV_Day 180_IN


title: SLE_2 [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
SLE_2.tar.gz


title: JH329_S46

source_name: HS4 KO 3H4 GFP-


title: IN-148-D180_RSV_Day 180_IN


title: SLE_1 [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
SLE_1.tar.gz


title: JH327_S44

source_name: HS3 KO 2B6 GFP+

value: bgl HS3 KO


title: IN-48_RSV_Day 180_IN

value: RSV


title: IN-141-D180_RSV_Day 180_IN

value: Day 180


title: IN-43_RSV_Day 180_IN

value: IN


title: OUT-56_RSV_Day 180_OUT


title: IN-47_RSV_Day 180_IN


title: HCD_3 [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
HCD_3.tar.gz


title: HCD_2 [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
HCD_2.tar.gz


title: IN-61_RSV_Day 180_IN


title: JH326_S43


title: JH325_S42

source_name: HS3 KO 2B6 GFP-


title: IN-39_RSV_Day 180_IN


title: OUT-305-D180_RSV_Day 180_OUT


title: HCD_1 [BCR]

description:
5' Gene RNA with CITE-seq, VDJ libraries
HCD_1.tar.gz


title: SLE_3


title: JH324_S41


title: IN-38_RSV_Day 180_IN


title: IN-150-D180_RSV_Day 180_IN


title: JH328_S45


title: JH323_S40

source_name: HS3 KO 1H3 GFP+


title: SLE_2


title: IN-106_RSV_Day 180_IN


title: IN-09_RSV_Day 180_IN


title: IN-102_RSV_Day 180_IN


title: JH322_S39


title: SLE_1


title: JH321_S38

source_name: HS3 KO 1H3 GFP-


title: IN-122-D180_RSV_Day 180_IN


title: HCD_3


title: JH320_S37


title: HCD_2


title: JH319_S36

source_name: HS3 KO 1B5 GFP+


title: HCD_1


title: OUT-52_RSV_Day 180_OUT


title: IN-60_RSV_Day 180_OUT


title: OUT-309-D180_RSV_Day 180_OUT


title: IN-70_RSV_Day 180_IN


title: JH318_S35


title: IN-128-D180_RSV_Day 180_IN


title: IN-119-D180_RSV_Day 180_IN


title: IN-20_RSV_Day 180_IN


title: IN-17_RSV_Day 180_IN


title: human left ventricular myocardial tissue doxorubicin 6

city: London

first: Angela

last: Yiu

address: Hammersmith Campus, Du Cane Road

department: Department of Surgery and Cancer

institute: Imperial College London

data_processing:
Genome alignment with TopHat2
Feature count with HTseq-count v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files raw counts for each sample

source_name: left ventricular myocardial tissue

extract_protocol:
Total RNA was purified using Rneasy columns (Qiagen) according to the manufacturer’s instructions.
Sequencing library for RNA-seq was prepared with TruSeq RNA Library Prep Kit v2 (Illumina), according to the manufacturer’s protocols.

treatment_protocol: Failing hearts were processed within minutes of the cross-clamp of the coronary arteries. Non-failing (donor) heart were perfused with cardioplegic solution and quickly transported to the Sydney Heart Bank for processing. Approximately 1 g-sized pieces of tissue was immediately frozen in liquid nitrogen and stored in nitrogen vapour.

tag: tissue

value: heart

value: Doxorubicin-induced cardiomyopathy


title: IN-112_RSV_Day 180_IN


title: JH317_S34

source_name: HS3 KO 1B5 GFP-


title: IN-120-D180_RSV_Day 180_IN


title: human left ventricular myocardial tissue doxorubicin 4


title: OUT-54_RSV_Day 180_OUT

value: OUT


title: JH316_S33

value: K562 cell line


title: IN-07_RSV_Day 180_IN


title: human left ventricular myocardial tissue doxorubicin 3


title: IN-132-D180_RSV_Day 180_IN


title: OUT-58_RSV_Day 180_OUT


title: JH315_S32

source_name: HS2 KO 4B5 GFP+

value: bgl HS2 KO


title: IN-104_RSV_Day 180_IN


title: OUT-13_RSV_Day 180_OUT


title: IN-136-D180_RSV_Day 180_IN


title: human left ventricular myocardial tissue doxorubicin 2


title: JH314_S31

value: GFP+ Sort


title: IN-44_RSV_Day 180_IN


title: human left ventricular myocardial tissue control 5

value: Non-failing


title: IN-127-D180_RSV_Day 180_IN


title: IN-06_RSV_Day 180_IN


title: human left ventricular myocardial tissue doxorubicin 1


title: IN-25_RSV_Day 180_IN


title: human left ventricular myocardial tissue control 4


title: JH312_S29

source_name: HS2 KO 4B5 GFP-


title: JH311_S28

source_name: HBG-GdTaP GFP+

value: Single bgl locus parental, GFP-tagged


title: JH310_S27


title: human left ventricular myocardial tissue control 3


title: JH313_S30

value: GFP- Sort


title: IN-64_RSV_Day 180_IN

source_name: whole blood_RSV_Day 180_IN


title: IN-117-D180_RSV_Day 180_IN


title: JH309_S26

source_name: HBG-GdTaP GFP-


title: OUT-06_RSV_Day 180_OUT

source_name: whole blood_RSV_Day 180_OUT


title: human left ventricular myocardial tissue control 2


title: IN-15_RSV_Day 180_IN


title: JH308_S25


title: IN-19_RSV_Day 180_IN


title: IN-143-D180_RSV_Day 180_IN


title: CALGB03-1041647-K-27

description:
Sample_PRE_RNA_442
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

source_name: Breast

value: Breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: JH301_S64

source_name: Random HS KO 4H7

value: Potential Random bgl HS KO


title: C03_R-29-CALGB03-1070493-1

description:
Sample_PRE_RNA_437
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH300_S63


title: JH299_S62

source_name: Random HS KO 3A6


title: human left ventricular myocardial tissue control 1


title: IN-73_RSV_Day 180_IN


title: IN-40_RSV_Day 180_IN


title: JH298_S61


title: IN-66_RSV_Day 180_IN


title: CALGB03-1039133-J-7

description:
Sample_PRE_RNA_430
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-144-D180_RSV_Day 180_IN


title: JH297_S60

source_name: Random HS KO 1B6


title: CALGB03-1042163-K-20

description:
Sample_PRE_RNA_428
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: OUT-12_RSV_Day 30_OUT

source_name: whole blood_RSV_Day 30_OUT

value: Day 30


title: IN-49_RSV_Day 180_IN


title: IN-43_RSV_Day 30_IN

source_name: whole blood_RSV_Day 30_IN


title: OUT-305-D30_RSV_Day 30_OUT


title: OUT-400-D180_RSV_Day 180_OUT


title: IN-60_RSV_Day 30_OUT


title: JH296_S59


title: OUT-56_RSV_Day 30_OUT


title: IN-71_RSV_Day 30_IN


title: CALGB03-1042478-K-32

description:
Sample_PRE_RNA_432
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-128-D30_RSV_Day 30_IN


title: IN-20_RSV_Day 30_IN


title: IN-32_RSV_Day 30_IN


title: IN-17_RSV_Day 30_IN


title: CALGB03-1034969-J-2

description:
Sample_PRE_RNA_431
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH295_S58

source_name: Random HS KO 4C8


title: C03_R-35-CALGB03-1070489-1

description:
Sample_PRE_RNA_424
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH294_S57


title: IN-54_RSV_Day 30_IN


title: C03_Q-34-CALGB03-1067490-1

description:
Sample_PRE_RNA_419
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH293_S56

source_name: Random HS KO 3E7


title: IN-104_RSV_Day 30_IN


title: IN-123-D30_RSV_Day 30_IN


title: IN-40_RSV_Day 30_IN


title: IN-38_RSV_Day 30_IN


title: CALGB03-1041253-K-26

description:
Sample_PRE_RNA_417
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH292_S55


title: C03_Q-25-CALGB03-1067152-1

description:
Sample_PRE_RNA_407
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH291_S54

source_name: Random HS KO 3E5


title: JH290_S53


title: CALGB03-1037610-J-35

description:
Sample_PRE_RNA_409
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_T-5-CALGB03-1069972-1

description:
Sample_PRE_RNA_404
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: OUT-13_RSV_Day 30_OUT


title: IN-114_RSV_Day 30_IN


title: IN-12_RSV_Day 30_IN


title: JH289_S52

source_name: Random HS KO 2E6


title: IN-144-D30_RSV_Day 30_IN


title: IN-39_RSV_Day 30_IN


title: CALGB03-1040587-K-8

description:
Sample_PRE_RNA_403
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH288_S51


title: OUT-54_RSV_Day 30_OUT


title: IN-150-D30_RSV_Day 30_IN


title: IN-76-D30_RSV_Day 30_IN


title: CALGB03-1040812-K-17

description:
Sample_PRE_RNA_401
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH287_S50

source_name: Random HS KO 2C8


title: IN-05_RSV_Day 30_IN


title: IN-59_RSV_Day 30_IN


title: CALGB03-1040202-K-5

description:
Sample_PRE_RNA_400
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1033262-L-1

description:
Sample_PRE_RNA_399
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH286_S49


title: IN-48_RSV_Day 30_IN


title: CALGB03-1045924-L-7

description:
Sample_PRE_RNA_394
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH285_S48

source_name: HS4 KO 4H7

value: Potential bgl HS4 KO


title: IN-07_RSV_Day 30_IN

value: RSV


title: IN-61_RSV_Day 30_IN


title: IN-11_RSV_Day 30_IN


title: IN-149-D30_RSV_Day 30_IN


title: OUT-304-D30_RSV_Day 30_OUT


title: IN-13_RSV_Day 30_IN


title: IN-46_RSV_Day 30_IN


title: JH284_S47


title: CALGB03-1039369-J-36

description:
Sample_PRE_RNA_393
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-111_RSV_Day 30_IN


title: JH283_S46

source_name: HS4 KO 4G11


title: JH282_S45


title: CALGB03-1035070-J-13

description:
Sample_PRE_RNA_392
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-70_RSV_Day 30_IN


title: OUT-11_RSV_Day 30_OUT


title: CALGB03-1037675-J-24

description:
Sample_PRE_RNA_391
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH281_S44

source_name: HS4 KO 4B4


title: IN-113_RSV_Day 30_IN


title: IN-03_RSV_Day 30_IN


title: CALGB03-1039521-J-8

description:
Sample_PRE_RNA_380
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-06_RSV_Day 30_IN


title: JH280_S43


title: CALGB03-1039640-J-46

description:
Sample_PRE_RNA_378
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-146-D30_RSV_Day 30_IN


title: CALGB03-1039520-K-4

description:
Sample_PRE_RNA_377
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: OUT-52_RSV_Day 30_OUT


title: JH278_S41

source_name: HS4 KO 3G12


title: IN-64_RSV_Day 30_IN


title: OUT-58_RSV_Day 30_OUT


title: CALGB03-1040384-J-40

description:
Sample_PRE_RNA_375
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-112_RSV_Day 30_IN


title: JH277_S40

source_name: HS4 KO 3C5


title: IN-124-D30_RSV_Day 30_OUT


title: CALGB03-1039675-J-47

description:
Sample_PRE_RNA_427
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1039531-J-43

description:
Sample_PRE_RNA_368
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH276_S39


title: IN-44_RSV_Day 30_IN


title: C03_R-17-CALGB03-1068481-1

description:
Sample_PRE_RNA_367
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-126-D30_RSV_Day 30_IN


title: IN-15_RSV_Day 30_IN


title: IN-66_RSV_Day 30_IN


title: IN-36_RSV_Day 30_IN


title: IN-105_RSV_Day 30_IN


title: JH275_S38

source_name: HS1 KO 3A6

value: Potential bgl HS1 KO


title: CALGB03-1041657-K-37

description:
Sample_PRE_RNA_363
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

source_name: Breast


title: JH274_S37


title: IN-52_RSV_Day 30_IN

value: IN


title: OUT-06_RSV_Day 30_OUT


title: CALGB03-1034965-L-4

description:
Sample_PRE_RNA_361
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-62_RSV_Day 30_IN


title: JH279_S42


title: JH273_S36

source_name: HS1 KO 1H2


title: OUT-62-D30_RSV_Day 30_OUT


title: IN-143-D30_RSV_Day 30_IN


title: IN-102_RSV_Day 30_IN


title: C03_Q-8-CALGB03-1057731-1

description:
Sample_PRE_RNA_360
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH272_S35


title: CALGB03-1040515-K-15

description:
Sample_PRE_RNA_359
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-33-CALGB03-1070491-1

description:
Sample_PRE_RNA_358
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH271_S34

source_name: HS1 KO 4E9


title: JH270_S33


title: CALGB03-1042718-L-15

description:
Sample_PRE_RNA_354
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-09_RSV_Day 30_IN


title: JH269_S32

source_name: HS1 KO 4A10


title: OUT-309-D30_RSV_Day 30_OUT

source_name: whole blood_RSV_Day 30_OUT


title: IN-21_RSV_Day 30_IN

source_name: whole blood_RSV_Day 30_IN


title: CALGB03-1039642-J-39

description:
Sample_PRE_RNA_347
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH268_S31


title: OUT-303-D30_RSV_Day 30_OUT


title: JH267_S30

source_name: HS1 KO 3F1


title: IN-106_RSV_Day 30_IN


title: IN-122-D30_RSV_Day 30_IN


title: IN-133-D30_RSV_Day 30_IN


title: OUT-01_RSV_Day 30_OUT


title: IN-49_RSV_Day 30_IN


title: IN-08_RSV_Day 30_IN


title: CALGB03-1039471-J-45

description:
Sample_PRE_RNA_346
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1042092-K-31

description:
Sample_PRE_RNA_340
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH266_S29


title: IN-75-D30_RSV_Day 30_IN


title: JH265_S28

source_name: HS1 KO 2F2


title: CALGB03-1042581-L-6

description:
Sample_PRE_RNA_339
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-47_RSV_Day 30_IN


title: OUT-402-D30_RSV_Day 30_OUT


title: JH264_S27


title: IN-139-D30_RSV_Day 30_IN


title: IN-117_RSV_Day 30_IN


title: CALGB03-1037477-J-37

description:
Sample_PRE_RNA_338
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1036723-J-4

description:
Sample_PRE_RNA_335
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: OUT-308-D30_RSV_Day 30_OUT


title: JH263_S26

source_name: HS1 KO 1C11


title: IN-148-D30_RSV_Day 30_IN


title: JH262_S25


title: CALGB03-1037625-J-29

description:
Sample_PRE_RNA_330
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH252_S23

source_name: HS4 KO 3H4 GFP+

value: bgl HS4 KO


title: JH253_S24


title: CALGB03-1039930-K-2

description:
Sample_PRE_RNA_329
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_T-2-CALGB03-1069819-1

description:
Sample_PRE_RNA_319
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-53_RSV_Day 30_IN


title: JH251_S22

source_name: HS4 KO 3H4 GFP-


title: IN-22_RSV_Day 30_IN


title: CALGB03-1039697-J-44

description:
Sample_PRE_RNA_314
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-115_RSV_Day 30_IN


title: IN-119-D30_RSV_Day 30_IN


title: OUT-400-D30_RSV_Day 30_OUT


title: IN-136-D30_RSV_Day 30_IN


title: IN-19_RSV_Day 30_IN


title: IN-73_RSV_Day 30_IN


title: JH250_S21


title: IN-129-D30_RSV_Day 30_IN


title: C03_Q-44-CALGB03-1069534-1

description:
Sample_PRE_RNA_304
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-41_RSV_Day 1_IN

source_name: whole blood_RSV_Day 1_IN

value: Day 1


title: IN-39_RSV_Day 1_IN


title: IN-29_RSV_Day 1_IN


title: JH249_S20

source_name: HS3 KO 2B6 GFP+

value: bgl HS3 KO


title: CALGB03-1032163-I-43

description:
Sample_PRE_RNA_296
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH248_S19

value: K562 cell line


title: OUT-400-D1_RSV_Day 1_OUT

source_name: whole blood_RSV_Day 1_OUT

value: OUT


title: IN-106_RSV_Day 1_IN


title: CALGB03-1041845-K-29

description:
Sample_PRE_RNA_352
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-49_RSV_Day 1_IN


title: IN-25_RSV_Day 30_IN


title: CALGB03-1042165-K-25

description:
Sample_PRE_RNA_289
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-24-CALGB03-1069339-1

description:
Sample_PRE_RNA_293
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH247_S18

source_name: HS3 KO 2B6 GFP-


title: C03_R-2-CALGB03-1070315-1

description:
Sample_PRE_RNA_285
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH246_S17


title: JH245_S16

source_name: HS3 KO 1B5 GFP+

value: GFP+ Sort


title: IN-50_RSV_Day 1_IN


title: IN-104_RSV_Day 1_IN


title: IN-20_RSV_Day 1_IN


title: IN-144-D1_RSV_Day 1_IN


title: JH244_S15


title: C03_R-34-CALGB03-1070368-1

description:
Sample_PRE_RNA_280
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-15-CALGB03-1068372-1

description:
Sample_PRE_RNA_281
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-52_RSV_Day 1_IN


title: OUT-304-D1_RSV_Day 1_OUT


title: CALGB03-1039678-J-10

description:
Sample_PRE_RNA_278
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH242_S13

source_name: HS3 KO 1B5 GFP-


title: IN-111_RSV_Day 1_IN


title: JH241_S12

source_name: HS2 KO 4B5 GFP+

value: bgl HS2 KO


title: OUT-60_RSV_Day 1_OUT


title: IN-01_RSV_Day 1_IN


title: OUT-12_RSV_Day 1_OUT


title: C03_R-7-CALGB03-1068093-1

description:
Sample_PRE_RNA_273
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

source_name: Breast


title: OUT-17_RSV_Day 1_OUT


title: CALGB03-1033145-J-1

description:
Sample_PRE_RNA_275
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-7-CALGB03-1058286-1

description:
Sample_PRE_RNA_267
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-121_RSV_Day 1_IN


title: JH239_S10

source_name: HS2 KO 4B5 GFP-


title: IN-117_RSV_Day 1_IN


title: IN-119_RSV_Day 1_IN


title: OUT-62_RSV_Day 1_OUT


title: IN-55_RSV_Day 30_IN


title: IN-112_RSV_Day 1_IN


title: OUT-64-D1_RSV_Day 1_OUT


title: IN-07_RSV_Day 1_IN


title: C03_R-12-CALGB03-1068300-1

description:
Sample_PRE_RNA_263
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH238_S9


title: JH243_S14


title: IN-53_RSV_Day 1_IN


title: C03_R-16-CALGB03-1068377-1

description:
Sample_PRE_RNA_265
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-14_RSV_Day 1_IN


title: JH253_S16


title: C03_U-1-CALGB03_1047558

description:
Sample_PRE_RNA_261
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH240_S11


title: IN-33_RSV_Day 1_IN


title: OUT-55_RSV_Day 1_OUT


title: JH252_S15


title: IN-37_RSV_Day 1_IN


title: C03_T-3-CALGB03-1069283-1

description:
Sample_PRE_RNA_253
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH250_S13


title: JH251_S14


title: IN-137-D1_RSV_Day 1_IN


title: CALGB03-1040552-K-10

description:
Sample_PRE_RNA_249
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-107_RSV_Day 1_IN


title: IN-108_RSV_Day 1_IN


title: OUT-303-D1_RSV_Day 1_OUT


title: OUT-305-D1_RSV_Day 1_OUT


title: JH249_S12


title: CALGB03-1042558-L-21

description:
Sample_PRE_RNA_248
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-60_RSV_Day 1_OUT


title: IN-48_RSV_Day 1_IN


title: CALGB03-1042471-K-40

description:
Sample_PRE_RNA_247
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH248_S11


title: JH247_S10


title: IN-66_RSV_Day 1_IN


title: CALGB03-1048109-M-7

description:
Sample_PRE_RNA_257
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1040662-K-16

description:
Sample_PRE_RNA_245
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-43_RSV_Day 1_IN


title: JH246_S9


title: OUT-61_RSV_Day 1_OUT


title: OUT-13_RSV_Day 1_OUT


title: C03_R-23-CALGB03-1069214-1

description:
Sample_PRE_RNA_239
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH245_S8


title: IN-120_RSV_Day 1_IN


title: C03_R-10-CALGB03-1068162-1

description:
Sample_PRE_RNA_237
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH244_S7


title: IN-115_RSV_Day 1_IN


title: JH243_S6


title: IN-38_RSV_Day 1_IN


title: IN-110_RSV_Day 1_IN


title: CALGB03-1046244-L-18

description:
Sample_PRE_RNA_234
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH242_S5


title: C03_R-31-CALGB03-1071200-1

description:
Sample_PRE_RNA_233
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-113_RSV_Day 1_IN


title: IN-12_RSV_Day 1_IN


title: IN-109_RSV_Day 1_IN


title: IN-146-D1_RSV_Day 1_IN


title: IN-143-D1_RSV_Day 1_IN


title: JH241_S4


title: IN-131-D1_RSV_Day 1_IN


title: IN-138-D30_RSV_Day 30_IN


title: CALGB03-1041868-K-38

description:
Sample_PRE_RNA_244
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-77-D1_RSV_Day 1_IN


title: IN-123_RSV_Day 1_IN


title: OUT-16_RSV_Day 1_OUT


title: CALGB03-1039674-J-9

description:
Sample_PRE_RNA_225
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1041091-K-22

description:
Sample_PRE_RNA_223
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH239_S2


title: JH217_S50

source_name: HS3 KO 1H3 GFP+ Sort

value: bgl HS3,4 KO


title: JH238_S1

value: GFP- Sort


title: C03_Q-48-CALGB03-1067574-1

description:
Sample_PRE_RNA_232
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: CALGB03-1042415-K-41

description:
Sample_PRE_RNA_220
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: JH216_S49


title: JH215_S48

source_name: HS3 KO 1H3 GFP- Sort


title: OUT-56_RSV_Day 1_OUT


title: IN-114_RSV_Day 1_IN


title: IN-11_RSV_Day 1_IN


title: IN-15_RSV_Day 1_IN


title: JH240_S3


title: C03_R-26-CALGB03-1070222-1

description:
Sample_PRE_RNA_219
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1042010-K-35

description:
Sample_PRE_RNA_231
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-55_RSV_Day 1_IN


title: IN-61_RSV_Day 1_IN


title: IN-76-D1_RSV_Day 1_IN


title: OUT-01_RSV_Day 1_OUT


title: OUT-59_RSV_Day 1_OUT


title: IN-24_RSV_Day 1_IN


title: IN-122_RSV_Day 1_IN


title: JH214_S47


title: IN-59_RSV_Day 1_IN


title: OUT-58_RSV_Day 1_OUT


title: CALGB03-1042166-K-33

description:
Sample_PRE_RNA_214
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-19-CALGB03-1068556-1

description:
Sample_PRE_RNA_211
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH213_S46

source_name: HS3 KO 1B3 GFP+ Sort


title: IN-105_RSV_Day 1_IN


title: IN-04_RSV_Day 1_IN


title: JH212_S45


title: OUT-15_RSV_Day 1_OUT


title: OUT-53_RSV_Day 1_OUT


title: C03_R-1-CALGB03-1069728-1

description:
Sample_PRE_RNA_201
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-134-D1_RSV_Day 1_IN


title: JH210_S43

source_name: HS3 KO 1B3 GFP- Sort


title: CALGB03-1037556-J-32

description:
Sample_PRE_RNA_200
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-45_RSV_Day 1_IN


title: JH217_S50_1


title: IN-126-D1_RSV_Day 1_IN


title: IN-58_RSV_Day 1_IN


title: JH216_S49_1


title: OUT-308-D1_RSV_Day 1_OUT


title: CALGB03-1039291-J-27

description:
Sample_PRE_RNA_199
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-36_RSV_Day 1_IN


title: JH211_S44


title: C03_R-28-CALGB03-1070312-1

description:
Sample_PRE_RNA_197
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1040130-K-3

description:
Sample_PRE_RNA_191
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-11-CALGB03-1068230-1

description:
Sample_PRE_RNA_209
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1033044-L-3

description:
Sample_PRE_RNA_193
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH215_S48_1


title: IN-42_RSV_Day 1_IN


title: OUT-06_RSV_Day 1_OUT


title: CALGB03-1041865-J-12

description:
Sample_PRE_RNA_204
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-30_RSV_Day 1_IN


title: IN-23_RSV_Day 1_IN


title: JH214_S47_1


title: JH213_S46_1


title: CALGB03-1036745-J-31

description:
Sample_PRE_RNA_182
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: OUT-402-D1_RSV_Day 1_OUT


title: IN-35_RSV_Day 1_IN


title: JH212_S45_1


title: IN-40_RSV_Day 1_IN


title: IN-139-D1_RSV_Day 1_IN


title: CALGB03-1036460-J-28

description:
Sample_PRE_RNA_179
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-44_RSV_Day 1_IN


title: IN-149-D1_RSV_Day 1_IN


title: CALGB03-1037375-J-25

description:
Sample_PRE_RNA_177
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1032409-I-46

description:
Sample_PRE_RNA_171
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH211_S44_1


title: JH210_S43_1


title: OUT-51_RSV_Day 1_OUT


title: JH217_S8


title: CALGB03-1042574-K-42

description:
Sample_PRE_RNA_168
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH216_S7


title: CALGB03-1029464-J-19

description:
Sample_PRE_RNA_158
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-28_RSV_Day 1_IN


title: IN-67_RSV_Day 1_OUT


title: JH215_S6


title: IN-78-D1_RSV_Day 1_IN


title: CALGB03-1037690-J-26

description:
Sample_PRE_RNA_156
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH214_S5


title: IN-133-D1_RSV_Day 1_IN


title: OUT-307-D1_RSV_Day 1_OUT


title: IN-54_RSV_Day 1_IN


title: JH213_S4


title: OUT-57_RSV_Day 1_OUT


title: IN-138-D1_RSV_Day 1_IN


title: OUT-11_RSV_Day 1_OUT


title: IN-56_RSV_Day 1_IN


title: OUT-66-D1_RSV_Day 1_OUT


title: C03_R-20-CALGB03-1068613-1

description:
Sample_PRE_RNA_153
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH212_S3


title: IN-47_RSV_Day 1_IN


title: IN-72_RSV_Day 1_IN


title: JH211_S2


title: IN-10_RSV_Day 1_IN


title: IN-142-D1_RSV_Day 1_IN


title: C03_R-36-CALGB03-1070693-1

description:
Sample_PRE_RNA_152
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1042557-K-46

description:
Sample_PRE_RNA_157
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1041806-K-19

description:
Sample_PRE_RNA_150
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH210_S1


title: IN-136-D1_RSV_Day 1_IN


title: IN-62_RSV_Day 1_IN


title: IN-147-D1_RSV_Day 1_IN


title: CALGB03-1036459-L-5

description:
Sample_PRE_RNA_155
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1040524-K-13

description:
Sample_PRE_RNA_147
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH209_S42

source_name: HS4 KO 3H4+Puro

value: Puromycin treated


title: CALGB03-1018962-K-21

description:
Sample_PRE_RNA_146
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH208_S41


title: OUT-300-D1_RSV_Day 1_OUT


title: JH207_S40

source_name: HS3 KO 2B6+Puro


title: IN-75-D1_RSV_Day 1_IN


title: CALGB03-1039812-J-42

description:
Sample_PRE_RNA_139
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-64_RSV_Day 1_IN


title: JH206_S39


title: CALGB03-1043103-L-17

description:
Sample_PRE_RNA_137
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-57_RSV_Day 1_IN


title: OUT-50_RSV_Day 1_OUT


title: IN-148-D1_RSV_Day 1_IN


title: IN-06_RSV_Day 1_IN


title: IN-145-D1_RSV_Day 1_IN


title: CALGB03-1042591-L-12

description:
Sample_PRE_RNA_134
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1048258-M-1

description:
Sample_PRE_RNA_136
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN 129-D1_RSV_Day 1_IN


title: IN-27_RSV_Day 1_IN


title: IN-13_RSV_Day 1_IN


title: CALGB03-1039987-J-41

description:
Sample_PRE_RNA_133
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_Q-40-CALGB03-1067492-1

description:
Sample_PRE_RNA_132
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-68_RSV_Day 1_IN


title: JH202_S35

source_name: HS3 KO 1B5+Puro


title: IN-32_RSV_Day 1_IN


title: JH203_S36


title: JH205_S38

source_name: HS3 KO 1H3+Puro


title: OUT-52_RSV_Day 1_OUT


title: IN-128-D1_RSV_Day 1_IN

source_name: whole blood_RSV_Day 1_IN


title: IN-127-D1_RSV_Day 1_IN


title: IN-79-D1_RSV_Day 1_IN


title: IN-21_RSV_Day 1_IN


title: OUT-65-D1_RSV_Day 1_OUT


title: IN-25_RSV_Day 1_IN


title: C03_R-3-CALGB03-1067720-1

description:
Sample_PRE_RNA_125
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH199_S32

source_name: HS4 KO 2A11 GFP-


title: IN-22_RSV_Day 1_IN


title: OUT-301_RSV_Day 1_OUT

source_name: whole blood_RSV_Day 1_OUT


title: C03_Q-30-CALGB03-1066122-1

description:
Sample_PRE_RNA_123
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-70_RSV_Day 1_IN


title: C03_Q-14-CALGB03-1058363-1

description:
Sample_PRE_RNA_120
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH198_S31


title: JH201_S34

source_name: HS3 KO 1B3+Puro


title: CALGB03-1035942-J-18

description:
Sample_PRE_RNA_128
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-19_RSV_Day 1_IN


title: JH197_S30

source_name: HS4 KO 3H4


title: CALGB03-1032170-I-44

description:
Sample_PRE_RNA_117
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-124-D1_RSV_Day 1_OUT


title: JH196_S29


title: IN-17_RSV_Day 1_IN


title: IN-51_RSV_Day 1_IN


title: JH200_S33


title: IN-46_RSV_Day 1_IN


title: JH195_S28

source_name: HS3 KO 2B6


title: CALGB03-1037509-J-6

description:
Sample_PRE_RNA_115
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1034916-J-14

description:
Sample_PRE_RNA_114
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH194_S27


title: C03_R-18-CALGB03-1068548-1

description:
Sample_PRE_RNA_113
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH193_S26

source_name: HS3 KO 1H3


title: JH192_S25


title: OUT-54_RSV_Day 1_OUT


title: C03_R-38-CALGB03-1070691-1

description:
Sample_PRE_RNA_112
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

source_name: Breast


title: CALGB03-1037478-J-23

description:
Sample_PRE_RNA_108
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1041847-K-34

description:
Sample_PRE_RNA_106
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-102_RSV_Day 1_IN


title: IN-63_RSV_Day 1_IN


title: OUT-309-D1_RSV_Day 1_OUT


title: IN-141-D1_RSV_Day 1_IN


title: IN-09_RSV_Day 1_IN


title: IN-71_RSV_Day 1_IN


title: IN-73_RSV_Day 1_IN


title: HC-28_Healthy person_Day 1_HC

source_name: whole blood_Healthy person_Day 1_HC

value: Healthy person

value: HC


title: IN-05_RSV_Day 1_IN

value: RSV


title: CALGB03-1042698-L-20

description:
Sample_PRE_RNA_103
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1039230-J-34

description:
Sample_PRE_RNA_116
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-03_RSV_Day 1_IN


title: CALGB03-1046311-L-19

description:
Sample_PRE_RNA_105
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: C03_R-14-CALGB03-1068293-1

description:
Sample_PRE_RNA_102
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: IN-132-D1_RSV_Day 1_IN


title: HC-53_Healthy person_Day 1_HC


title: JH190_S23

source_name: HS3 KO 1B5


title: JH187_S20

source_name: LCR KO 1H4 GFP+

value: Potential blg LCR KO


title: JH188_S21

source_name: HS3 KO 1B3


title: HC-25_Healthy person_Day 1_HC


title: JH191_S24


title: JH186_S19


title: JH189_S22


title: IN-69_RSV_Day 1_IN

value: IN


title: C03_T-1-CALGB03-1059211-1

description:
Sample_PRE_RNA_100
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH185_S18

source_name: LCR KO 3E9


title: C03_R-30-CALGB03-1071042-1

description:
Sample_PRE_RNA_096
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-05_Healthy person_Day 1_HC


title: JH184_S17


title: IN-150-D1_RSV_Day 1_IN


title: HC-08_Healthy person_Day 1_HC


title: JH183_S16

source_name: LCR KO 3B12


title: IN-34_RSV_Day 1_IN


title: HC-16_Healthy person_Day 1_HC


title: HC-38_Healthy person_Day 1_HC


title: C03_R-22-CALGB03-1069026-1

description:
Sample_PRE_RNA_094
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-49_Healthy person_Day 1_HC


title: HC-06_Healthy person_Day 1_HC


title: JH182_S15


title: CALGB03-1040582-J-11

description:
Sample_PRE_RNA_092
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH181_S14

source_name: LCR KO 2E11


title: CALGB03-1035570-J-20

description:
Sample_PRE_RNA_093
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-19_Healthy person_Day 1_HC


title: HC-44_Healthy person_Day 1_HC


title: HC-40_Healthy person_Day 1_HC


title: HC-48_Healthy person_Day 1_HC


title: HC-10_Healthy person_Day 1_HC


title: CALGB03-1046064-L-10

description:
Sample_PRE_RNA_095
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1041889-K-39

description:
Sample_PRE_RNA_091
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH180_S13


title: HC-11_Healthy person_Day 1_HC


title: HC-51_Healthy person_Day 1_HC


title: HC-45_Healthy person_Day 1_HC


title: HC-20_Healthy person_Day 1_HC


title: HC-13_Healthy person_Day 1_HC


title: CALGB03-1041807-K-23

description:
Sample_PRE_RNA_090
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-35_Healthy person_Day 1_HC


title: HC-32_Healthy person_Day 1_HC


title: HC-12_Healthy person_Day 1_HC


title: JH178_S11

source_name: LCR KO 1H6


title: CALGB03-1040180-J-48

description:
Sample_PRE_RNA_084
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1033045-J-16

description:
Sample_PRE_RNA_083
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH177_S10

source_name: LCR KO 1D5


title: C03_R-21-CALGB03-1068993-1

description:
Sample_PRE_RNA_080
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-09_Healthy person_Day 1_HC


title: HC-03_Healthy person_Day 1_HC


title: HC-21_Healthy person_Day 1_HC


title: HC-54_Healthy person_Day 1_HC


title: JH175_S8

source_name: HS2-4 KO 1F5 GFP+

value: Potential bgl HS2-4 KO


title: JH174_S7


title: C03_R-13-CALGB03-1068298-1

description:
Sample_PRE_RNA_079
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH179_S12


title: JH204_S37

source_name: HS3 KO 1H3+Puro


title: HC-27_Healthy person_Day 1_HC

value: Day 1


title: HC-07_Healthy person_Day 1_HC


title: HC-43_Healthy person_Day 1_HC


title: HC-47_Healthy person_Day 1_HC


title: JH172_S5

source_name: HS2-4 KO 4B5


title: HC-04_Healthy person_Day 1_HC


title: C03_Q-2-CALGB03-1057425-1

description:
Sample_PRE_RNA_069
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1040686-K-9

description:
Sample_PRE_RNA_075
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-02_Healthy person_Day 1_HC


title: JH173_S6


title: CALGB03-1040512-K-14

description:
Sample_PRE_RNA_070
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-01_Healthy person_Day 1_HC


title: JH176_S9


title: JH171_S4

source_name: HS2-4 KO 2H5


title: HC-31_Healthy person_Day 1_HC


title: CALGB03-1032265-I-45

description:
Sample_PRE_RNA_062
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-39_Healthy person_Day 1_HC


title: C03_Q-27-CALGB03-1066808-1

description:
Sample_PRE_RNA_059
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-42_Healthy person_Day 1_HC


title: 3p

city: Washington

first: Joseph

last: Spangler

state: DC

address: 4555 Overlook Ave SW

institute: US Naval Research Lab

data_processing:
raw MiSeq reads were trimmed with Trimmomatic 0.33 (HEADCROP:8, LEADING:20, SLIDINGWINDOW:5:20, MINLEN:50)
Trimmed reads were mapped to the closed L. plantarum WCFS1 genome (GenBank accession GCA_000203855.3) with Bowtie 2 (“-very-sensitive” parameter).
Statistically significant differentially expressed genes were determined by analyzing raw read counts with the R package DESeq2 version 1.8.1 (Love et al., 2014). Size factors to normalize for sequencing depth were generated by both R packages DESeq2 and cqn version 1.14 (Hansen et al., 2012).
Comparisons were made between controls and samples treated with 3OC12.  A statistical cutoff for differentially expressed genes of adjusted P value (Benjamin and Hockberg adjustment) was set at < 0.05, where genes satisfying this criteria were defined as differentially expressed.
Annotations for these genes were obtained from the NCBI website with protein accession numbers or determined manually using Gene Ontology (GO) terms generated by Pfam reference numbers.
Genome_build: WCFS1 genome (GenBank accession GCA_000203855.3)
Supplementary_files_format_and_content: Count tables

organism: Lactiplantibacillus plantarum

extract_protocol:
Frozen sample aliquots thawed at room temperature and pelleted to remove residual RNA Later before treating with 400 µL Lysozyme Solution (1 mg mL-1 lysozyme, 40 mM EDTA, pH 8) for 1 h at 37 °C. Lysozyme treated cells were pelleted and resuspended in RNAzol RT following the manufacturer’s protocol for large RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: CALGB03-1035332-L-2

description:
Sample_PRE_RNA_057
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-30_Healthy person_Day 1_HC


title: 2p


title: JH169_S2

source_name: HS2-4 KO 2H3


title: JH168_S1


title: JH170_S3


title: CALGB03-1032799-I-48

description:
Sample_PRE_RNA_055
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: HC-34_Healthy person_Day 1_HC


title: CALGB03-1046309-L-11

description:
Sample_PRE_RNA_047
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1028823-J-15

description:
Sample_PRE_RNA_048
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH209_S42_1

source_name: HS4 KO 3H4+Puro

value: bgl HS4 KO


title: 1p


title: 3m

source_name: control


title: HC-18_Healthy person_Day 1_HC


title: 2m


title: HC-33_Healthy person_Day 1_HC


title: HC-14_Healthy person_Day 1_HC


title: HC-23_Healthy person_Day 1_HC


title: C03_R-25-CALGB03-1069941-1

description:
Sample_PRE_RNA_045
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

source_name: Breast


title: HC-37_Healthy person_Day 1_HC

source_name: whole blood_Healthy person_Day 1_HC


title: JH207_S40_1

source_name: HS3 KO 2B6+Puro

value: K562 cell line

value: bgl HS3 KO


title: HC-24_Healthy person_Day 1_HC


title: HC-41_Healthy person_Day 1_HC


title: 1m


title: JH206_S39_1


title: CALGB03-1041129-K-18

description:
Sample_PRE_RNA_042
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1032697-I-47

description:
Sample_PRE_RNA_040
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: hakai_3_input [re-analysis]

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

institute: University of Nottingham

description:
B2-1-10_S3_ME
processed data file:
hakai_diffE.csv

data_processing:
reads trimmed with trimmomatic
alignment performed with Bowtie2 to TAIR10.48 genome
indexing with samtools
gene counting performed with htseq
differential expression analysis with DEseq2
Genome_build: TAIR10.48
Supplementary_files_format_and_content: .csv, differential expression analysis results

organism: Arabidopsis thaliana

source_name: hakai  input

growth_protocol: Arabidopsis seeds were cultured in plates. Seeds planted in plates were sterilized by soaking in 5% NaClO for 4 min and then washed with sterile water for 5 times before being planted onto 0.5 × MS medium plus 1% sucrose. Plates were placed in the cold room (4°C, dark) for 2 days and then kept in the tissue culture room (16 h light: 8 h dark, 22°C) until used.

extract_protocol:
Total RNA was isolated using hot phenol extration. Poly(A) RNA was prepared according to the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, NEB). m6A levels were measured by two-dimensional thin layer chromatography (TLC) analysis as described previously
The libraries from fragmented poly (A) RNA (100-150 nt) were prepared using ScriptSeq v2 RNA-Seq Library Preparation Kit (Illumina) followed by size selection  using E-Gel SizeSelect II (Invitrogen), and quality checked on Agilent High Sensitivity DNA Chips (Agilent).

tag: developmental stage/tissue

value: 2 weeks old, whole seedlings

tag: ecotype

value: Columbia

value: hakai


title: JH205_S38_1

tag: cell line


title: JH204_S37_1


title: JH208_S41_1


title: CALGB03-1042894-L-22

description:
Sample_PRE_RNA_035
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1035296-J-22

description:
Sample_PRE_RNA_032
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: hakai_2_input [re-analysis]

description:
B2-2-4_S2_ME
processed data file:
hakai_diffE.csv


title: hakai_1_input [re-analysis]

description:
B2-2-2_S11_ME
processed data file:
hakai_diffE.csv


title: JH203_S36_1

source_name: HS3 KO 1B5+Puro


title: vir_4_input

description:
B1-5-2_S10_ME
processed data file:
vir_diffE.csv

source_name: virilizer input

value: vir


title: HC-15_Healthy person_Day 1_HC


title: HC-36_Healthy person_Day 1_HC


title: HC-22_Healthy person_Day 1_HC


title: HC-17_Healthy person_Day 1_HC


title: CALGB03-1042087-K-24

description:
Sample_PRE_RNA_033
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: JH202_S35_1


title: vir_3_input [re-analysis]

description:
B1-4-4_S6_ME
processed data file:
vir_diffE.csv


title: JH201_S34_1

source_name: HS3 KO 1B3+Puro


title: JH200_S33_1


title: HC-29_Healthy person_Day 1_HC


title: VMH_F_Virgin_NonAgg_Rep3

city: Pasadena

first: Mengyu

state: California

address: 1200 E California Blvd

department: BBE

institute: Caltech

data_processing:
alignment using CellRanger v3.0
filtering out cells using CellRanger v3.0 "cell-calling algorithm"
Genome_build: mm10
Supplementary_files_format_and_content: Features table with every gene (.tsv)
Supplementary_files_format_and_content: Barcodes table with unique barcode for each cell (.tsv)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell (.mtx)

source_name: female ventral VMH

extract_protocol:
Method section in publication: 10.1016/j.neuron.2021.12.002
10x Chromium 3' v3 sequencing

tag: developmental stage

value: adult

value: female

tag: reproductive state

value: virgin

tag: social behavior

value: non aggressive

value: brain


title: VMH_F_Virgin_Mate_Rep2

tag: strain

value: mating


title: VMH_F_Post_Control_Rep2

value: post-lactating

value: control


title: HC-52_Healthy person_Day 1_HC

value: Healthy person

value: Day 1

value: HC


title: C03_R-32-CALGB03-1070310-1

description:
Sample_PRE_RNA_028
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: fip37_6_input

description:
B1-5-8_S14_ME
processed data file:
fip37_diffE.csv

source_name: fip37 input

value: 2 weeks old, whole seedlings


title: CALGB03-1042911-L-9

description:
Sample_PRE_RNA_012
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: fip37_5_input [re-analysis]

description:
B1-5-6_S15_ME
processed data file:
fip37_diffE.csv

value: Columbia


title: C03_T-4-CALGB03-1069281-1

description:
Sample_PRE_RNA_022
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: vir_1_input [re-analysis]

description:
B1-4-10_S7_ME
processed data file:
vir_diffE.csv


title: vir_2_input [re-analysis]

description:
B1-4-2_S3_ME
processed data file:
vir_diffE.csv


title: CALGB03-1033264-J-21

description:
Sample_PRE_RNA_011
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: CALGB03-1035276-J-17

description:
Sample_PRE_RNA_031
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH196_S29_1

source_name: HS4 KO 3H4

value: K562 cell line

value: bgl HS4 KO


title: JH197_S30_1


title: JH199_S32_1

source_name: HS4 KO 2A11 GFP-


title: fip37_4_input

description:
B1-5-4_S13_ME
processed data file:
fip37_diffE.csv


title: JH195_S28_1

source_name: HS3 KO 2B6

value: bgl HS3 KO


title: JH198_S31_1


title: CALGB03-1042598-L-8

description:
Sample_PRE_RNA_004
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: Breast carcinoma


title: VMH_F_Lac_Agg_Rep3

value: adult

value: female

value: lactating

value: aggressive


title: CALGB03-1046090-L-16

description:
Sample_PRE_RNA_030
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: fip37_2_input [re-analysis]

description:
B1-4-8_S2_ME
processed data file:
fip37_diffE.csv


title: 19-L-958-13bp-KO-LT-2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-seq was performed with three biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) with TopHat (v2.1.1) with default parameters. Uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation [University of California at Santa Cruz (UCSC) gene models] with Cufflinks (v2.2.1). The expression level of each gene was quantified as FPKM, and FPKM values of replicates were averaged.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

growth_protocol: All mice were bred in-house under specific-pathogen-free (SPF) conditions in individually ventilated cages (IVC).

extract_protocol:
Total RNA from 1500 FACS-sorted LT-HSCs was extracted using Quick-RNA Kits (ZYMO) and resuspended in nuclease-free water.
cDNA synthesized and amplified from the total RNA was used the Smart-seq2 method as described previously (Picelli et al., 2014). Sequencing libraries were generated from 500pg cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer’s protocols. All the samples were sequenced on the Illumina HiSeq X Ten sequencers with 150 bp paired-end reads.

treatment_protocol: Bone marrow cells stained with fluorochrome-labeled HSC antibodies were sorted on an Influx cell sorter (BD Biosciences).

tag: stain

tag: age

value: 2 months

tag: genotype/variation

value: Hmces knockout

value: bone marrow

tag: cell type

value: FACS-sorted LT-HSCs


title: fip37_1_input

description:
B1-3-10_S12_ME
processed data file:
fip37_diffE.csv

tag: genotype


title: 19-L-958-13bp-KO-LT-1


title: JH193_S26_1

source_name: HS3 KO 1H3


title: C03_R-27-CALGB03-1070267-1

description:
Sample_PRE_RNA_003
RNA-Seq of Homo sapiens; primary breast; breast carcinoma


title: JH194_S27_1


title: VMH_F_Virgin_Mate_Rep1

tag: Sex

value: virgin

value: mating

value: brain


title: VMH_F_Lac_NonAgg_Rep2

value: non aggressive


title: fip37_3_input [re-analysis]

description:
B1-5-10_S4_ME
processed data file:
fip37_diffE.csv

value: 2 weeks old, whole seedlings

value: Columbia


title: CALGB03-1039132-J-33

description:
Sample_PRE_RNA_002
RNA-Seq of Homo sapiens; primary breast; breast carcinoma

value: None - Pretreatment Neoadjuvant Therapy


title: JH192_S25_1

value: K562 cell line

value: bgl HS3 KO


title: wt_5_input [re-analysis]

description:
B2-2-6_S12_ME
processed data file:
fip37_diffE.csv
vir_diffE.csv
hakai_diffE.csv

source_name: wild type input

value: wt


title: 19-L-958-13bp-KO-LT-3